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IET Systems Biology

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https://www.readbyqxmd.com/read/28518060/analysis-of-healthy-and-tumour-dna-methylation-distributions-in-kidney-renal-clear-cell-carcinoma-using-kullback-leibler-and-jensen-shannon-distance-measures
#1
Nithya Ramakrishnan, Ranjan Bose
DNA methylation is an epigenetic phenomenon in which methyl groups get bonded to the cytosines of the DNA molecule altering the expression of the associated genes. Cancer is linked with hypo or hyper-methylation of specific genes as well as global changes in DNA methylation. In this study, the authors study the probability density function distribution of DNA methylation in various significant genes and across the genome in healthy and tumour samples. They propose a unique 'average healthy methylation distribution' based on the methylation values of several healthy samples...
June 2017: IET Systems Biology
https://www.readbyqxmd.com/read/28518059/recent-omics-technologies-and-their-emerging-applications-for-personalised-medicine
#2
REVIEW
Dong-Hyuk Kim, Young-Sook Kim, Nam-Il Son, Chan-Koo Kang, Ah-Ram Kim
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 personalised medicine...
June 2017: IET Systems Biology
https://www.readbyqxmd.com/read/28518058/prediction-of-nsclc-recurrence-from-microarray-data-with-gep
#3
Russul Al-Anni, Jingyu Hou, Rana Dhia'a Abdu-Aljabar, Yong Xiang
Lung cancer is one of the deadliest diseases in the world. Non-small cell lung cancer (NSCLC) is the most common and dangerous type of lung cancer. Despite the fact that NSCLC is preventable and curable for some cases if diagnosed at early stages, the vast majority of patients are diagnosed very late. Furthermore, NSCLC usually recurs sometime after treatment. Therefore, it is of paramount importance to predict NSCLC recurrence, so that specific and suitable treatments can be sought. Nonetheless, conventional methods of predicting cancer recurrence rely solely on histopathology data and predictions are not reliable in many cases...
June 2017: IET Systems Biology
https://www.readbyqxmd.com/read/28476975/peripheral-arterial-disease-screening-for-hemodialysis-patients-using-a-fractional-order-integrator-and-transition-probability-decision-making-model
#4
Jian-Xing Wu, Chien-Ming Li, Guan-Chun Chen, Yueh-Ren Ho, Chia-Hung Lin
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)...
April 2017: IET Systems Biology
https://www.readbyqxmd.com/read/28476974/use-of-processed-data-to-design-an-orderly-logic-gate-to-construct-plasmids-in-genocad
#5
Pei Shi, Tao Wu, Panpan Li, Bingjie Guo, Gang Fang, Yafei Dong
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 comprehensive information for a complete data set without redundancy...
April 2017: IET Systems Biology
https://www.readbyqxmd.com/read/28476973/excluded-volume-effects-in-on-and-off-lattice-reaction-diffusion-models
#6
Lina Meinecke, Markus Eriksson
Mathematical models are important tools to study the excluded volume effects on reaction-diffusion systems, which are known to play an important role inside living cells. Detailed microscopic simulations with off-lattice Brownian dynamics become computationally expensive in crowded environments. 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...
April 2017: IET Systems Biology
https://www.readbyqxmd.com/read/28303793/prediction-of-the-containment-of-hiv-infection-by-antiretroviral-therapy-a-variable-structure-control-approach
#7
Anet J N Anelone, Sarah K Spurgeon
It is demonstrated that the reachability paradigm from variable structure control theory is a suitable framework to monitor and predict the progression of the human immunodeficiency virus (HIV) infection following initiation of antiretroviral therapy (ART). A manifold is selected which characterises the infection-free steady-state. A model of HIV infection together with an associated reachability analysis is used to formulate a dynamical condition for the containment of HIV infection on the manifold. This condition is tested using data from two different HIV clinical trials which contain measurements of the CD4+ T cell count and HIV load in the peripheral blood collected from HIV infected individuals for the six month period following initiation of ART...
February 2017: IET Systems Biology
https://www.readbyqxmd.com/read/28303792/toward-theoretical-synthesis-of-biocomputer
#8
Ting-Yu Kuo, Chun-Liang Lin, Natdanai Charoenkit, Yang-Yi Chen, Chakkrit Preuksakarn
Increasing applications of fundamental biological gates have been successfully built during this decade. Proceeding to the current development, this study presents a genetic arithmetic and logical unit (ALU) design based on a series of genetic logic gates. The system level's architecture consists of three parts: temp register, ALU and accumulator register. Using the concept of the ALU on the digital computer, the authors present the fundamental function of the genetic ALU via full adder register and also build the bio-storage devices to store data generated from the genetic ALU...
February 2017: IET Systems Biology
https://www.readbyqxmd.com/read/28303791/integer-programming-based-method-for-observability-of-singleton-attractors-in-boolean-networks
#9
Xiaoqing Cheng, Yushan Qiu, Wenpin Hou, Wai-Ki Ching
Boolean network (BN) is a popular mathematical model for revealing the behaviour of a genetic regulatory network. Furthermore, observability, an important network feature, plays a significant role in understanding the underlying network. Several studies have been done on analysis of observability of BNs and complex networks. However, the observability of attractor cycles, which can serve as biomarker detection, has not yet been addressed in the literature. This is an important, interesting and challenging problem that deserves a detailed study...
February 2017: IET Systems Biology
https://www.readbyqxmd.com/read/28303790/design-of-robust-adaptive-controller-and-feedback-error-learning-for-rehabilitation-in-parkinson-s-disease-a-simulation-study
#10
Korosh Rouhollahi, Mehran Emadi Andani, Seyed Mahdi Karbassi, Iman Izadi
Deep brain stimulation (DBS) is an efficient therapy to control movement disorders of Parkinson's tremor. Stimulation of one area of basal ganglia (BG) by DBS with no feedback is the prevalent opinion. Reduction of additional stimulatory signal delivered to the brain is the advantage of using feedback. This results in reduction of side effects caused by the excessive stimulation intensity. In fact, the stimulatory intensity of controllers is decreased proportional to reduction of hand tremor. The objective of this study is to design a new controller structure to decrease three indicators: (i) the hand tremor; (ii) the level of delivered stimulation in disease condition; and (iii) the ratio of the level of delivered stimulation in health condition to disease condition...
February 2017: IET Systems Biology
https://www.readbyqxmd.com/read/28303789/flatness-based-control-approach-to-drug-infusion-for-cardiac-function-regulation
#11
Gerasimos Rigatos, Nikolaos Zervos, Alexey Melkikh
A new control method based on differential flatness theory is developed in this study, aiming at solving the problem of regulation of haemodynamic parameters. Actually control of the cardiac output (volume of blood pumped out by heart per unit of time) and of the arterial blood pressure is achieved through the administered infusion of cardiovascular drugs such as dopamine and sodium nitroprusside. Time delays between the control inputs and the system's outputs are taken into account. Using the principle of dynamic extension, which means that by considering certain control inputs and their derivatives as additional state variables, a state-space description for the heart's function is obtained...
February 2017: IET Systems Biology
https://www.readbyqxmd.com/read/28303788/dynamics-and-robustness-of-the-cardiac-progenitor-cell-induced-pluripotent-stem-cell-network-during-cell-phenotypes-transition
#12
Yuangen Yao, Chengzhang Ma, Haiyou Deng, Quan Liu, Wei Cao, Rong Gui, Tianquan Feng, Ming Yi
Robustness is a fundamental characteristic of biological systems since all living systems need to adapt to internal or external perturbations, unpredictable environments, stochastic events and unreliable components, and so on. A long-term challenge in systems biology is to reveal the origin of robustness underlying molecular regulator network. In this study, a simple Boolean model is used to investigate the global dynamic properties and robustness of cardiac progenitor cell (CPC) induced pluripotent stem cell network that governs reprogramming and directed differentiation process...
February 2017: IET Systems Biology
https://www.readbyqxmd.com/read/27879480/adaptive-modelling-of-gene-regulatory-network-using-bayesian-information-criterion-guided-sparse-regression-approach
#13
Ming Shi, Weiming Shen, Hong-Qiang Wang, Yanwen Chong
Inferring gene regulatory networks (GRNs) from microarray expression data are an important but challenging issue in systems biology. In this study, the authors propose a Bayesian information criterion (BIC)-guided sparse regression approach for GRN reconstruction. This approach can adaptively model GRNs by optimising the l1-norm regularisation of sparse regression based on a modified version of BIC. The use of the regularisation strategy ensures the inferred GRNs to be as sparse as natural, while the modified BIC allows incorporating prior knowledge on expression regulation and thus avoids the overestimation of expression regulators as usual...
December 2016: IET Systems Biology
https://www.readbyqxmd.com/read/27879479/identify-signature-regulatory-network-for-glioblastoma-prognosis-by-integrative-mrna-and-mirna-co-expression-analysis
#14
Zhi-Tong Bing, Guang-Hui Yang, Jie Xiong, Ling Guo, Lei Yang
Glioblastoma multiforme (GBM) is the most common and aggressive type of primary brain tumor in adults. Patients with this disease have a poor prognosis. The objective of this study is to identify survival-related individual genes (or miRNAs) and miRNA -mRNA pairs in GBM using a multi-step approach. First, the weighted gene co-expression network analysis and survival analysis are applied to identify survival-related modules from mRNA and miRNA expression profiles, respectively. Subsequently, the role of individual genes (or miRNAs) within these modules in GBM prognosis are highlighted using survival analysis...
December 2016: IET Systems Biology
https://www.readbyqxmd.com/read/27879478/occurrence-of-hiv-eradication-for-preexposure-prophylaxis-treatment-with-a-deterministic-hiv-model
#15
Hyeygjeon Chang, Claude Moog, Alessandro Astolfi
The authors examine the human immunodeficiency virus (HIV) eradication in this study using a mathematical model and analyse the occurrence of virus eradication during the early stage of infection. To this end they use a deterministic HIV-infection model, modify it to describe the pharmacological dynamics of antiretroviral HIV drugs, and consider the clinical experimental results of preexposure prophylaxis HIV treatment. They also use numerical simulation to model the experimental scenario, thereby supporting the clinical results with a model-based explanation...
December 2016: IET Systems Biology
https://www.readbyqxmd.com/read/27879477/robust-group-fused-lasso-for-multisample-copy-number-variation-detection-under-uncertainty
#16
Hossein Sharifi Noghabi, Majid Mohammadi, Yao-Hua Tan
One of the most important needs in the post-genome era is providing the researchers with reliable and efficient computational tools to extract and analyse this huge amount of biological data, in which DNA copy number variation (CNV) is a vitally important one. Array-based comparative genomic hybridisation (aCGH) is a common approach in order to detect CNVs. Most of methods for this purpose were proposed for one-dimensional profiles. However, slightly this focus has moved from one- to multi-dimensional signals...
December 2016: IET Systems Biology
https://www.readbyqxmd.com/read/27879476/interactive-cooperation-and-hierarchical-operation-of-microrna-and-transcription-factor-crosstalk-in-human-transcriptional-regulatory-network
#17
Esra Gov, Kazim Yalcin Arga
Transcriptional regulation of gene expression is an essential cellular process that is arranged by transcription factors (TFs), microRNAs (miRNA) and their target genes through a variety of mechanisms. Here, we set out to reconstruct a comprehensive transcriptional regulatory network of Homo sapiens consisting of experimentally verified regulatory information on miRNAs, TFs and their target genes. We have performed topological analyses to elucidate the transcriptional regulatory roles of miRNAs and TFs. When we thoroughly investigated the network motifs, different gene regulatory scenarios were observed; whereas, mutual TF-miRNA regulation (interactive cooperation) and hierarchical operation where miRNAs were the upstream regulators of TFs came into prominence...
December 2016: IET Systems Biology
https://www.readbyqxmd.com/read/27879475/inferring-catalysis-in-biological-systems
#18
Ivan Kondofersky, Fabian J Theis, Christiane Fuchs
In systems biology, one is often interested in the communication patterns between several species, such as genes, enzymes or proteins. These patterns become more recognisable when temporal experiments are performed. This temporal communication can be structured by reaction networks such as gene regulatory networks or signalling pathways. Mathematical modelling of data arising from such networks can reveal important details, thus helping to understand the studied system. In many cases, however, corresponding models still deviate from the observed data...
December 2016: IET Systems Biology
https://www.readbyqxmd.com/read/27879474/oscillatory-expression-in-escherichia-coli-mediated-by-micrornas-with-transcriptional-and-translational-time-delays
#19
Yuan Zhang, Haihong Liu, Jin Zhou
The primary objective of this study is to study oscillatory expression of gene regulatory network in Escherichia coli mediated by microRNAs (sRNAs) with transcriptional and translational time delays. Motivated by the regulation of gene expression proposed by Shimoni et al. (Molecular Systems Biology, 2007), a general model of delayed gene regulatory network by sRNAs is formulated. This model can well describe many practical architectures of gene regulatory network by sRNAs, particularly when both transcriptional and translational time delays are introduced...
December 2016: IET Systems Biology
https://www.readbyqxmd.com/read/27762233/modular-bond-graph-modelling-and-analysis-of-biomolecular-systems
#20
Peter J Gawthrop, Edmund J Crampin
Bond graphs can be used to build thermodynamically-compliant hierarchical models of biomolecular systems. As bond graphs have been widely used to model, analyse and synthesise engineering systems, this study suggests that they can play the same rĂ´le in the modelling, analysis and synthesis of biomolecular systems. The particular structure of bond graphs arising from biomolecular systems is established and used to elucidate the relation between thermodynamically closed and open systems. Block diagram representations of the dynamics implied by these bond graphs are used to reveal implicit feedback structures and are linearised to allow the application of control-theoretical methods...
October 2016: IET Systems Biology
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