IET Systems Biology最新文献_第8页

Long non-coding RNAs and their targets as potential biomarkers in breast cancer 长链非编码rna及其作为乳腺癌潜在生物标志物的靶点

IF 2.3 4区生物学

IET Systems Biology Pub Date : 2021-05-15 DOI: 10.1049/syb2.12020

Maryam Khalid, Rehan Zafar Paracha, Maryum Nisar, Sumaira Malik, Salma Tariq, Iqra Arshad, Amnah Siddiqa, Zamir Hussain, Jamil Ahmad, Amjad Ali

{"title":"Long non-coding RNAs and their targets as potential biomarkers in breast cancer","authors":"Maryam Khalid, Rehan Zafar Paracha, Maryum Nisar, Sumaira Malik, Salma Tariq, Iqra Arshad, Amnah Siddiqa, Zamir Hussain, Jamil Ahmad, Amjad Ali","doi":"10.1049/syb2.12020","DOIUrl":"10.1049/syb2.12020","url":null,"abstract":"Abstract Breast cancer is among the lethal types of cancer with a high mortality rate, globally. Its high prevalence can be controlled through improved analysis and identification of disease‐specific biomarkers. Recently, long non‐coding RNAs (lncRNAs) have been reported as key contributors of carcinogenesis and regulate various cellular pathways through post‐transcriptional regulatory mechanisms. The specific aim of this study was to identify the novel interactions of aberrantly expressed genetic components in breast cancer by applying integrative analysis of publicly available expression profiles of both lncRNAs and mRNAs. Differential expression patterns were identified by comparing the breast cancer expression profiles of samples with controls. Significant co‐expression networks were identified through WGCNA analysis. WGCNA is a systems biology approach used to elucidate the pattern of correlation between genes across microarray samples. It is also used to identify the highly correlated modules. The results obtained from this study revealed significantly differentially expressed and co‐expressed lncRNAs and their cis‐ and trans‐regulating mRNA targets which include RP11‐108F13.2 targeting TAF5L, RPL23AP2 targeting CYP4F3, CYP4F8 and AL022324.2 targeting LRP5L, AL022324.3, and Z99916.3, respectively. Moreover, pathway analysis revealed the involvement of identified mRNAs and lncRNAs in major cell signalling pathways, and target mRNAs expression is also validated through cohort data. Thus, the identified lncRNAs and their target mRNAs represent novel biomarkers that could serve as potential therapeutics for breast cancer and their roles could also be further validated through wet labs to employ them as potential therapeutic targets in future.","PeriodicalId":50379,"journal":{"name":"IET Systems Biology","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2021-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8675856/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38982766","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Bifurcation analyses and potential landscapes of a cortex-basal ganglia-thalamus model. 皮层-基底神经节-丘脑模型的分岔分析和潜在景观。

IF 2.3 4区生物学

IET Systems Biology Pub Date : 2021-05-01 Epub Date: 2021-04-16 DOI: 10.1049/syb2.12018

Chenri Yan, Quansheng Liu, Yuanhong Bi

{"title":"Bifurcation analyses and potential landscapes of a cortex-basal ganglia-thalamus model.","authors":"Chenri Yan, Quansheng Liu, Yuanhong Bi","doi":"10.1049/syb2.12018","DOIUrl":"https://doi.org/10.1049/syb2.12018","url":null,"abstract":"The dynamics of cortical neuronal activity plays important roles in controlling body movement and is regulated by connection weights between neurons in a cortex-basal ganglia-thalamus (BGCT) loop. Beta-band oscillation of cortical activity is closely associated with the movement disorder of Parkinson's disease, which is caused by an imbalance in the connection weights of direct and indirect pathways in the BGCT loop. In this study, the authors investigate how the dynamics of cortical activity are modulated by connection weights of direct and indirect pathways in the BGCT loop under low dopamine levels through bifurcation analyses and potential landscapes. The results reveal that cortical activity displays rich dynamics under different connection weights, including one, two, or three stable steady states, one or two stable limit cycles, and the coexistence of one stable limit cycle with one stable steady state or two stable ones. For a low dopamine level, cortical activity exhibits oscillation for larger connection weights of direct and indirect pathways. The stability of these stable dynamics is explored by the potential landscapes.","PeriodicalId":50379,"journal":{"name":"IET Systems Biology","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2021-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8675854/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38880590","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 6

State Feedback and Synergetic controllers for tuberculosis in infected population. 感染人群结核病的状态反馈和协同控制。

IF 2.3 4区生物学

IET Systems Biology Pub Date : 2021-05-01 Epub Date: 2021-03-30 DOI: 10.1049/syb2.12013

Muhammad Bilal, Iftikhar Ahmad, Sheraz Ahmad Babar, Khurram Shahzad

引用次数: 2

Pathway-based protein–protein association network to explore mechanism of α-glucosidase inhibitors from Scutellaria baicalensis Georgi against type 2 diabetes 通路蛋白结合网络探讨黄芩α-葡萄糖苷酶抑制剂抗2型糖尿病的作用机制

IF 2.3 4区生物学

IET Systems Biology Pub Date : 2021-04-26 DOI: 10.1049/syb2.12019

Le Wang, Wenbo Diwu, Nana Tan, Huan Wang, Jingbo Hu, Bailu Xu, Xiaoling Wang

{"title":"Pathway-based protein–protein association network to explore mechanism of α-glucosidase inhibitors from Scutellaria baicalensis Georgi against type 2 diabetes","authors":"Le Wang, Wenbo Diwu, Nana Tan, Huan Wang, Jingbo Hu, Bailu Xu, Xiaoling Wang","doi":"10.1049/syb2.12019","DOIUrl":"10.1049/syb2.12019","url":null,"abstract":"Natural products have been widely used in the treatment of type 2 diabetes (T2D). However, their mechanisms are often obscured due to multi-components and multi-targets. The authors constructed a pathway-based protein–protein association (PPA) network for target proteins of 13 α-glucosidase inhibitors (AGIs) identified from Scutellaria baicalensis Georgi (SBG), designed to explore the underlying mechanisms. This network contained 118 nodes and 1167 connections. An uneven degree distribution and small-world property were observed, characterised by high clustering coefficient and short average path length. The PPA network had an inherent hierarchy as C(k)∼k−0.71. It also exhibited potential weak disassortative mixing pattern, coupled with a decreased function Knn (k) and negative value of assortativity coefficient. These properties indicated that a few nodes were crucial to the network. PGH2, GNAS, MAPK1, MAPK3, PRKCA, and MAOA were then identified as key targets with the highest degree values and centrality indices. Additionally, a core subnetwork showed that chrysin, 5,8,2′-trihydroxy-7-methoxyflavone, and wogonin were the main active constituents of these AGIs, and that the serotonergic synapse pathway was the critical pathway for SBG against T2D. The application of a pathway-based protein–protein association network provides a novel strategy to explore the mechanisms of natural products on complex diseases.","PeriodicalId":50379,"journal":{"name":"IET Systems Biology","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2021-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8675860/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38909022","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Effects of noise and time delay on E2F's expression level in a bistable Rb-E2F gene’s regulatory network 噪声和时间延迟对双稳态Rb-E2F基因调控网络中E2F表达水平的影响

IF 2.3 4区生物学

IET Systems Biology Pub Date : 2021-04-21 DOI: 10.1049/syb2.12017

John Billy Kirunda, Lijian Yang, Lulu Lu, Ya Jia

{"title":"Effects of noise and time delay on E2F's expression level in a bistable Rb-E2F gene’s regulatory network","authors":"John Billy Kirunda, Lijian Yang, Lulu Lu, Ya Jia","doi":"10.1049/syb2.12017","DOIUrl":"10.1049/syb2.12017","url":null,"abstract":"The bistable Rb-E2F gene regulatory network plays a central role in regulating cellular proliferation-quiescence transition. Based on Gillespie's chemical Langevin method, the stochastic bistable Rb-E2F gene’s regulatory network with time delays is proposed. It is found that under the moderate intensity of internal noise, delay in the Cyclin E synthesis rate can greatly increase the average concentration value of E2F. When the delay is considered in both E2F-related positive feedback loops, within a specific range of delay (3-13)<math>\u0000 <mrow>\u0000 <mtext>hr</mtext>\u0000 </mrow></math>, the average expression of E2F is significantly increased. Also, this range is in the scope with that experimentally given by Dong et al. [65]. By analysing the quasi-potential curves at different delay times, simulation results show that delay regulates the dynamic behaviour of the system in the following way: small delay stabilises the bistable system; the medium delay is conducive to a high steady-state, making the system fluctuate near the high steady-state; large delay induces approximately periodic transitions between high and low steady-state. Therefore, by regulating noise and time delay, the cell itself can control the expression level of E2F to respond to different situations. These findings may provide an explanation of some experimental result intricacies related to the cell cycle.","PeriodicalId":50379,"journal":{"name":"IET Systems Biology","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2021-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/14/dc/SYB2-15-111.PMC8675803.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38894037","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Weighted gene co expression network analysis (WGCNA) with key pathways and hub-genes related to micro RNAs in ischemic stroke 加权基因共表达网络分析(WGCNA)在缺血性卒中中与微rna相关的关键途径和中心基因

IF 2.3 4区生物学

IET Systems Biology Pub Date : 2021-04-20 DOI: 10.1049/syb2.12016

Xiang Qu, Shuang Wu, Jinggui Gao, Zhenxiu Qin, Zhenhua Zhou, Jingli Liu

{"title":"Weighted gene co expression network analysis (WGCNA) with key pathways and hub-genes related to micro RNAs in ischemic stroke","authors":"Xiang Qu, Shuang Wu, Jinggui Gao, Zhenxiu Qin, Zhenhua Zhou, Jingli Liu","doi":"10.1049/syb2.12016","DOIUrl":"10.1049/syb2.12016","url":null,"abstract":"Ischemic stroke (IS) is one of the major causes of death and disability worldwide. However, the specific mechanism of gene interplay and the biological function in IS are not clear. Therefore, more research into IS is necessary. Dataset GSE110993 including 20 ischemic stroke (IS) and 20 control specimens are used to establish both groups and the raw RNA-seq data were analysed. Weighted gene co-expression network analysis (WGCNA) was used to screen the key micro-RNA modules. The centrality of key genes were determined by module membership (mm) and gene significance (GS). The key pathways were identified by enrichment analysis with Kyoto Protocol Gene and Genome Encyclopedia (KEGG), and the key genes were validated by protein-protein interactions network. Result: Upon investigation, 1185 up- and down-regulated genes were gathered and distributed into three modules in response to their degree of correlation to clinical traits of IS, among which the turquoise module show a trait-correlation of 0.77. The top 140 genes were further identified by GS and MM. KEGG analysis showed two pathways may evolve in the progress of IS. Discussion: CXCL12 and EIF2a may be important biomarkers for the accurate diagnosis and treatment in IS.","PeriodicalId":50379,"journal":{"name":"IET Systems Biology","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2021-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8675812/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38827692","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

Fuzzy logic and Lyapunov-based non-linear controllers for HCV infection. HCV感染的模糊逻辑和基于lyapunov的非线性控制器。

IF 2.3 4区生物学

IET Systems Biology Pub Date : 2021-04-01 DOI: 10.1049/syb2.12014

Ali Hamza, Iftikhar Ahmad, Muhammad Uneeb

{"title":"Fuzzy logic and Lyapunov-based non-linear controllers for HCV infection.","authors":"Ali Hamza, Iftikhar Ahmad, Muhammad Uneeb","doi":"10.1049/syb2.12014","DOIUrl":"https://doi.org/10.1049/syb2.12014","url":null,"abstract":"Hepatitis C is the liver disease caused by the Hepatitis C virus (HCV) which can lead to serious health problems such as liver cancer. In this research work, the non-linear model of HCV having three state variables (uninfected hepatocytes, infected hepatocytes and virions) and two control inputs has been taken into account, and four non-linear controllers namely non-linear PID controller, Lyapunov Redesign controller, Synergetic controller and Fuzzy Logic-Based controller have been proposed to control HCV infection inside the human body. The controllers have been designed for the anti-viral therapy in order to control the amount of uninfected hepatocytes to the desired safe limit and to track the amount of infected hepatocytes and virions to their reference value which is zero. One control input is the Pegylated interferon (peg-IFN-α) which acts in reducing the infected hepatocytes and the other input is ribavirin which blocks the production of virions. By doing so, the uninfected hepatocytes increase and achieve the required safe limit. Lyapunov stability analysis has been used to prove the stability of the whole system. The comparative analysis of the proposed nonlinear controllers using MATLAB/Simulink have been done with each other and with linear PID. These results depict that the infected hepatocytes and virions are reduced to the desired level, enhancing the rate of sustained virologic response (SVR) and reducing the treatment period as compared with previous strategies introduced in the literature.","PeriodicalId":50379,"journal":{"name":"IET Systems Biology","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2021-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8675797/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25528516","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

Model predictive control optimisation using the metaheuristic optimisation for blood pressure control. 使用血压控制的元启发式优化模型预测控制优化。

IF 2.3 4区生物学

IET Systems Biology Pub Date : 2021-04-01 Epub Date: 2021-02-14 DOI: 10.1049/syb2.12012

Mohammad Reza Ahmadpour, Hamid Ghadiri, Saeed Reza Hajian

{"title":"Model predictive control optimisation using the metaheuristic optimisation for blood pressure control.","authors":"Mohammad Reza Ahmadpour, Hamid Ghadiri, Saeed Reza Hajian","doi":"10.1049/syb2.12012","DOIUrl":"https://doi.org/10.1049/syb2.12012","url":null,"abstract":"Given the importance of high blood pressure, it is important to control and maintain a constant blood pressure level in the normal state. The main aim of this article is to design a model predictive controller with a genetic algorithm (GA) for the regulation of arterial blood pressure. The present study is an applied cross-sectional study. In order to do this research, studies related to designing mathematical models for blood pressure regulation and mechanical models for heart muscle and pressure sensors are investigated. Then, a model predictive controller with GA is designed for blood pressure control. All control and design operations are performed in the MATLAB software. According to the viscoelasticity of blood, transducer, and injection set, we can assume the mechanical model as Mass, Spring, and Damper. Initially, the patient's blood pressure is lower than normal, and after controlling, the patient's blood pressure returned to normal. By using a GA-based model predictive control (MPC), mathematical validation, and mechanical model, the patient's blood pressure can be adjusted and maintained. The simulation result shows that the GA-based MPC offers acceptable response and speed of operation and the proposed controller can achieve good tracking and disturbance rejection.","PeriodicalId":50379,"journal":{"name":"IET Systems Biology","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2021-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8675817/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25373382","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

Sliding-mode-based controllers for automation of blood glucose concentration for type 1 diabetes. 基于滑动模式的控制器，用于 1 型糖尿病患者血糖浓度的自动控制。

IF 2.3 4区生物学

IET Systems Biology Pub Date : 2021-04-01 DOI: 10.1049/syb2.12015

Sheraz Ahmad Babar, Iftikhar Ahmad, Iqra Shafeeq Mughal

{"title":"Sliding-mode-based controllers for automation of blood glucose concentration for type 1 diabetes.","authors":"Sheraz Ahmad Babar, Iftikhar Ahmad, Iqra Shafeeq Mughal","doi":"10.1049/syb2.12015","DOIUrl":"10.1049/syb2.12015","url":null,"abstract":"Destruction of β-cells in pancreas causes deficiency in insulin production that leads to diabetes in the human body. To cope with this problem, insulin is either taken orally during the day or injected into the patient's body using artificial pancreas (AP) during sleeping hours. Some mathematical models indicate that AP uses control algorithms to regulate blood glucose concentration (BGC). The extended Bergman minimal model (EBMM) incorporates, as a state variable, the disturbance in insulin level during medication due to either meal intake or burning sugar by engaging in physical exercise. In this research work, EBMM and proposed finite time robust controllers are used, including the sliding mode controller (SMC), backstepping SMC (BSMC) and supertwisting SMC (second-order SMC or SOSMC) for automatic stabilisation of BGC in type 1 diabetic patients. The proposed SOSMC diminishes the chattering phenomenon which appears in the conventional SMC. The proposed BSMC is a recursive technique which becomes robust by the addition of the SMC. Lyapunov theory has been used to prove the asymptotic stability of the proposed controllers. Simulations have been carried out in MATLAB/Simulink for the comparative study of the proposed controllers under varying data of six different type 1 diabetic patients available in the literature.","PeriodicalId":50379,"journal":{"name":"IET Systems Biology","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2021-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8675841/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25528517","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Optimal control methods for drug delivery in cancerous tumour by anti-angiogenic therapy and chemotherapy. 抗血管生成治疗和化疗在肿瘤中给药的最优控制方法。

IF 2.3 4区生物学

IET Systems Biology Pub Date : 2021-02-01 Epub Date: 2021-01-25 DOI: 10.1049/syb2.12010

Pariya Khalili, Sareh Zolatash, Ramin Vatankhah, Sajjad Taghvaei

{"title":"Optimal control methods for drug delivery in cancerous tumour by anti-angiogenic therapy and chemotherapy.","authors":"Pariya Khalili, Sareh Zolatash, Ramin Vatankhah, Sajjad Taghvaei","doi":"10.1049/syb2.12010","DOIUrl":"https://doi.org/10.1049/syb2.12010","url":null,"abstract":"There are numerous mathematical models simulating the behaviour of cancer by considering variety of states in different treatment strategies, such as chemotherapy. Among the models, one is developed which is able to consider the blood vessel-production (angiogenesis) in the vicinity of the tumour and the effect of anti-angiogenic therapy. In the mentioned-model, normal cells, cancer cells, endothelial cells, chemotherapy and anti-angiogenic agents are taking into account as state variables, and the rate of injection of the last two are considered as control inputs. Since controlling the cancerous tumour growth is a challenging matter for patient's life, the time schedule design of drug injection is very significant. Two optimal control strategies, an open-loop (calculus of variations) and a closed-loop (state-dependent Riccati equation), are applied on the system in order to find an optimal time scheduling for each drug injection. By defining a proper cost function, an optimal control signal is designed for each one. Both obtained control inputs have reasonable answers, and the system is controlled eventually, but by comparing them, it is concluded that both methods have their own benefits which will be discussed in details in the conclusion section.","PeriodicalId":50379,"journal":{"name":"IET Systems Biology","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2021-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8675840/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38856695","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 5