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A review of molecular biology detection methods for human adenovirus 人腺病毒分子生物学检测方法综述
IF 1.5 Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2023-01-01 DOI: 10.3934/biophy.2023008
N. Datta
In humans particularly in children, adenovirus is one of the most common viruses that cause respiratory illnesses. Knowing how to detect adenovirus proficiently and rapidly will help reinforce surveillance of adenovirus infections, detect epidemic situations in real-time, and understand the trend of virus epidemics, which will allow effective actions to be taken quickly. The rapid detection of antiviral antibodies or viral antigens in clinical samples can be achieved by molecular diagnostic techniques like PCR, Real-Time PCR, LAMP, mPCR-RLB, PCR-ELISA, Tem-PCR, Gene Chip, and so on. Some of the molecular diagnostic methods are relatively economical, exceedingly sensitive and explicit. There are several commercially accessible molecular diagnostic techniques that enable their use in clinical laboratories all over the world. In this review, the principles, characteristics, and applications of molecular biology surveillance methods commonly used in labs and clinics for the detection of human adenoviruses are examined and highlighted.
在人类,特别是儿童中,腺病毒是引起呼吸道疾病的最常见病毒之一。掌握如何熟练、快速地检测腺病毒,有助于加强对腺病毒感染的监测,实时发现疫情,了解病毒流行趋势,从而迅速采取有效措施。PCR、Real-Time PCR、LAMP、mPCR-RLB、PCR- elisa、Tem-PCR、Gene Chip等分子诊断技术可实现临床样品中抗病毒抗体或病毒抗原的快速检测。一些分子诊断方法相对经济,非常敏感和明确。有几种商业上可获得的分子诊断技术,使它们能够在世界各地的临床实验室中使用。本文综述了实验室和临床常用的分子生物学监测方法的原理、特点和应用。
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引用次数: 0
Similarity of epidemic spreading and information network connectivity mechanisms demonstrated by analysis of two probabilistic models 通过对两种概率模型的分析,证明了疫情传播和信息网络连接机制的相似性
IF 1.5 Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2023-01-01 DOI: 10.3934/biophy.2023011
Into Almiala, Vesa Kuikka
The modelling of epidemic spreading is essential in understanding the mechanisms of outbreaks and pandemics. Many models for different kinds of spreading have been proposed throughout the history of modelling, each suited for a specific scenario and parameters. On the other hand, models of information networks provide important tools for the analysis of the performance and reliability of such networks. We have previously presented a model for simulating the spreading of infectious disease throughout a social network and another one for simulating the connectivity of data traffic in an information network. We argue that these models are similar in that they produce equivalent results with appropriate parameters when run on the same network. We explain this by reasoning that the manners in which the models carry out their calculations, although devised from different assumptions, turn out to be equivalent. We also show empirical results of applying the models to calculate the spread of contagion and information connectivity on two complex networks suitable for the models. Based on the results, we calculate centrality metrics reflecting the outcome of the application, highlighting its important properties. We note that the centrality values obtained by running the epidemic model and the connectivity model turn out to be mutually equivalent, as predicted by their similar fashions of calculation. As the models were independently developed for their own applications, the equivalence in their calculation can not be explained by the models purposefully built similarly. Thus, not only are the two apparently completely separate areas of interest analysable with a single model but there appear to be inherent similarities in the mechanisms of epidemic spreading and determining network connectivity.
建立流行病传播模型对于理解疾病爆发和大流行的机制至关重要。在整个建模历史中,已经提出了许多不同类型的扩散模型,每个模型都适合于特定的情景和参数。另一方面,信息网络模型为分析信息网络的性能和可靠性提供了重要的工具。我们之前已经提出了一个模拟传染病在整个社会网络中传播的模型,以及另一个模拟信息网络中数据流量连通性的模型。我们认为这些模型是相似的,因为它们在相同的网络上运行时,在适当的参数下产生等效的结果。我们通过推理来解释这一点,即模型进行计算的方式,尽管是从不同的假设中设计出来的,但结果是等效的。我们还展示了应用该模型在两个适合该模型的复杂网络上计算传染传播和信息连通性的实证结果。基于结果,我们计算反映应用程序结果的中心性度量,突出其重要属性。我们注意到,通过运行流行病模型和连通性模型得到的中心性值是相互等效的,正如它们相似的计算方式所预测的那样。由于这些模型是为各自的应用而独立开发的,它们计算中的等效性不能用有目的地建立相似的模型来解释。因此,不仅可以用单一模型分析这两个显然完全独立的领域,而且在流行病传播和决定网络连通性的机制方面似乎也存在固有的相似性。
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引用次数: 3
Analysis of a fractional pollution model in a system of three interconnecting lakes 三个相连湖泊系统的分级污染模型分析
IF 1.5 Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2023-01-01 DOI: 10.3934/biophy.2023014
Y. N. Anjam, Mehmet Yavuz, Mati ur Rahman, Amna Batool
Water pollution is a critical global concern that demands ongoing scrutiny and revision of water resource policies at all levels to safeguard a healthy living environment. In this study, we focus on examining the dynamics of a fractional-order model involving three interconnected lakes, utilizing the Caputo differential operator. The aim is to investigate the issue of lake pollution by analyzing a system of linear equations that represent the interconnecting waterways. To numerically solve the model, we employ two methods: The Laplace transform with the Adomian decomposition method (LADM) and the Homotopy perturbation method (HPM). We compare the obtained numerical solutions from both methods and present the results. The study encompasses three variations of the model: the periodic input model, the exponentially decaying input model, and the linear input model. MATLAB is employed to conduct numerical simulations for the proposed scheme, considering various fractional orders. The numerical results are further supported by informative graphical illustrations. Through simulation, we validate the suitability of the proposed model for addressing the issue at hand. The outcomes of this research contribute to the understanding and management of water pollution, aiding policymakers and researchers in formulating effective strategies for maintaining water quality and protecting our environment.
水污染是全球关注的一个重大问题,要求各级不断审查和修订水资源政策,以保障健康的生活环境。在这项研究中,我们重点研究了涉及三个相互关联的湖泊的分数阶模型的动力学,利用卡普托微分算子。目的是通过分析代表相互连接的水道的线性方程组来调查湖泊污染问题。本文采用拉普拉斯变换与Adomian分解法(LADM)和同伦摄动法(HPM)两种方法对模型进行数值求解。我们比较了两种方法得到的数值解,并给出了结果。该研究包含了模型的三种变体:周期输入模型、指数衰减输入模型和线性输入模型。利用MATLAB对所提出的方案进行了数值模拟,考虑了不同分数阶的情况。数值结果进一步得到了信息丰富的图形插图的支持。通过仿真,我们验证了所提出的模型对解决手头问题的适用性。本研究结果有助于了解和管理水污染,帮助决策者和研究人员制定有效的策略来维持水质和保护我们的环境。
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引用次数: 2
Mathematical modeling for solving fractional model cancer bosom malignant growth 求解分数型乳腺癌胸部恶性生长的数学模型
Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2023-01-01 DOI: 10.3934/biophy.2023018
Shaimaa A. M. Abdelmohsen, D. Sh. Mohamed, Haifa A. Alyousef, M. R. Gorji, Amr M. S. Mahdy

In this essay, we have presented a fractional numerical model of breast cancer stages with cardiac outcomes. Five compartments were used to build the model, each of which represented a subpopulation of breast cancer patients. Variables A, B, C, D, and E each represent a certain subpopulation. They are levels 1 and 2 (A), level 3 (B), level 4 (C), disease-free (D) and cardiotoxic (E). We have demonstrated that the fractional model has a stable solution. We also discuss how to optimally control this model and numerically simulate the control problem. Using numerical simulations, we computed the results of the dissection. The model's compartment diagram has been completed. A predictor-corrector method has been used to manage the fractional derivatives and produce numerical solutions. The Caputo sense has been used to describe fractional derivatives. The results have been illustrated through numerical simulations. Furthermore, the numerical simulations show that the cancer breast malignant growth fractional order model is easier to model than the traditional integer-order model. To compute the results, we have used mathematical programming. We have made it clear that the numerical method that was applied in this publication to solve this model was not utilized by any other author before that, nor has this method been investigated in the past. Our investigation established this approach.

& lt; abstract>在这篇文章中,我们提出了乳腺癌分期与心脏预后的分数数值模型。五个隔间被用来建立模型,每个隔间代表乳腺癌患者的一个亚群。变量A、B、C、D和E分别代表一个特定的子群体。它们分别是1级和2级(A), 3级(B), 4级(C),无病(D)和心脏毒性(E)。我们已经证明分数模型有一个稳定的解。讨论了如何对该模型进行最优控制,并对控制问题进行了数值模拟。通过数值模拟,我们计算了解剖的结果。模型的隔室图已经完成。一种预测校正方法被用来处理分数阶导数并产生数值解。卡普托意义已被用来描述分数阶导数。结果通过数值模拟得到了验证。此外,数值模拟表明,乳腺癌恶性生长分数阶模型比传统的整数阶模型更容易建模。为了计算结果,我们使用了数学规划。我们已经明确表示,在此之前,没有任何其他作者使用过本文中用于求解该模型的数值方法,也没有研究过该方法。我们的调查确立了这种方法。</p>& lt; / abstract>
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引用次数: 1
Quantum mechanical aspects of cardiac arrhythmias: A mathematical model and pathophysiological implications 心律失常的量子力学方面:数学模型和病理生理意义
Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2023-01-01 DOI: 10.3934/biophy.2023024
Mohammed I. A. Ismail, Abdallah Barjas Qaswal, Mo'ath Bani Ali, Anas Hamdan, Ahmad Alghrabli, Mohamad Harb, Dina Ibrahim, Mohammad Nayel Al-Jbour, Ibrahim Almobaiden, Khadija Alrowwad, Esra'a Jaibat, Mira Alrousan, Mohammad Banifawaz, Mohammed A. M. Aldrini, Aya Daikh, Nour Aldarawish, Ahmad Alabedallat, Ismail M. I. Ismail, Lou'i Al-Husinat

Cardiac arrhythmias are serious myocardial electrical disturbances that affect the rate and rhythm of heartbeats. Despite the rapidly accumulating data about the pathophysiology and the treatment, new insights are required to improve the overall clinical outcome of patients with cardiac arrhythmias. Three major arrhythmogenic processes can contribute to the pathogenesis of cardiac arrhythmias; 1) enhanced automaticity, 2) afterdepolarization-triggered activity and 3) reentry circuits. The mathematical model of the quantum tunneling of ions is used to investigate these mechanisms from a quantum mechanical perspective. The mathematical model focuses on applying the principle of quantum tunneling to sodium and potassium ions. This implies that these ions have a non-zero probability of passing through the gate, which has an energy that is higher than the kinetic energy of ions. Our mathematical findings indicate that, under pathological conditions, which affect ion channels, the quantum tunneling of sodium and potassium ions is augmented. This augmentation creates a state of hyperexcitability that can explain the enhanced automaticity, after depolarizations that are associated with triggered activity and a reentry circuit. Our mathematical findings stipulate that the augmented and thermally assisted quantum tunneling of sodium and potassium ions can depolarize the membrane potential and trigger spontaneous action potentials, which may explain the automaticity and afterdepolarization. Furthermore, the quantum tunneling of potassium ions during an action potential can provide a new insight regarding the formation of a reentry circuit. Introducing these quantum mechanical aspects may improve our understanding of the pathophysiological mechanisms of cardiac arrhythmias and, thus, contribute to finding more effective anti-arrhythmic drugs.

& lt; abstract>心律失常是严重的心肌电干扰,影响心跳的速率和节奏。尽管关于病理生理和治疗的数据迅速积累,但需要新的见解来改善心律失常患者的整体临床结果。三种主要的致心律失常过程可能导致心律失常的发病;1)增强的自动性,2)后去极化触发的活动,3)再入电路。利用离子量子隧穿的数学模型,从量子力学的角度研究了这些机制。该数学模型着重于将量子隧穿原理应用于钠离子和钾离子。这意味着这些离子通过栅极的概率非为零,栅极的能量高于离子的动能。我们的数学结果表明,在影响离子通道的病理条件下,钠离子和钾离子的量子隧穿增强。这种增强产生了一种超兴奋状态,这可以解释与触发活动和再入回路相关的去极化后自动性的增强。我们的数学结果表明,钠离子和钾离子的增强和热辅助量子隧穿可以使膜电位去极化并触发自发动作电位,这可能解释了膜电位的自动性和后去极化。此外,钾离子在动作电位期间的量子隧穿可以为再入电路的形成提供新的见解。引入这些量子力学方面可以提高我们对心律失常病理生理机制的理解,从而有助于发现更有效的抗心律失常药物。& lt; / abstract>
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引用次数: 0
Characterizing pulsatile blood flow in a specific carotid bifurcation: insights into hemodynamics and rheology models 表征特定颈动脉分支的脉动血流:对血流动力学和流变学模型的见解
Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2023-01-01 DOI: 10.3934/biophy.2023019
Boukedjane Mouloud, Bahi Lakhdar

This study uses laminar and turbulent flow models to investigate the blood flow dynamics in a specific carotid bifurcation. Pulsatile boundary conditions and the rigid carotid artery wall are considered. Three viscosity models describe the non-Newtonian blood behavior. The Fluent solver and the finite volume method solve the equations. Results show a Poiseuille-like flow in the common carotid artery (CCA), unaffected by the flow regime, viscosity model, or boundary conditions. The branching zone exhibits a C-shaped stagnation zone with low velocity and wall shear stress due to the CCA widening and ICA/ECA curvature. Strong secondary flow is observed in the carotid sinus; the flow is directed towards the inner wall with higher velocity in the internal carotid artery. Discrepancies between viscosity models are pronounced in laminar flow, particularly with the natural boundary conditions. The non-Newtonian blood behavior is more apparent in the laminar flow of the external carotid artery, especially with the second set of boundary conditions.

& lt; abstract>本研究采用层流和湍流模型来研究特定颈动脉分支的血流动力学。考虑了脉动边界条件和颈动脉壁刚性。三种粘度模型描述了非牛顿血液的行为。采用Fluent求解器和有限体积法求解。结果显示颈总动脉(CCA)有泊泽维尔样流动,不受流动状态、粘度模型或边界条件的影响。由于CCA变宽和ICA/ECA曲率,分支区表现为低速和低壁剪应力的c型停滞区。颈动脉窦内可见强烈的二次血流;血流以较快的速度在颈内动脉流向内壁。在层流中,粘度模型之间的差异是明显的,特别是在自然边界条件下。非牛顿血液行为在颈外动脉层流中更为明显,特别是在第二组边界条件下。& lt; / abstract>
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引用次数: 0
Scientific advances in complex systems of biophysical interest 生物物理领域复杂系统的科学进展
IF 1.5 Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2023-01-01 DOI: 10.3934/biophy.2023015
Salvatore Magazù, M. T. Caccamo
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引用次数: 0
Relationship between the major parameters of warm-blooded organisms' life activity and the properties of aqueous salt solutions 温血生物生命活动的主要参数与盐水溶液性质的关系
Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2023-01-01 DOI: 10.3934/biophy.2023022
Anatoliy I. Fisenko, Oleksii V. Khorolskyi, Nikolay P. Malomuzh, Artur A. Guslisty

We are devoted to the physical analysis of the habitat area of warm-blooded organisms – humans and many mammals. For this purpose, the establishment of equilibrium distribution of carbon dioxide in aqueous solutions of salts in contact with atmospheric air starting from some time is investigated. More precisely, the relaxation time of carbon dioxide, as a function of temperature and pH, is investigated. It is found that the pH-relaxation time τS is a very nontrivial function of temperature, pH values, and NaCl salt concentration. It was assumed that the minimum value of pH relaxation time corresponds to the optimal rate of physical processes in living matter. Using this selection principle and our experimental data, we have shown that the optimal temperature for human and mammalian life activity is close to To ≈ 37 °C. The lower and upper temperature limits for their possible activity are close to Tl ≈ 30 °C and Tu ≈ 42 °C, respectively. The optimal value of pHo, determined by the same selection principle, also becomes true if supplemented by the influence of albumin and other proteins.

& lt; abstract>我们致力于温血生物(人类和许多哺乳动物)栖息地的物理分析。为此,研究了从一段时间开始与大气空气接触的盐水溶液中二氧化碳平衡分布的建立。更准确地说,研究了二氧化碳的弛豫时间作为温度和pH值的函数。发现ph -弛豫时间<斜体>τ<sub>S</sub></斜体>是温度、pH值和NaCl盐浓度的重要函数。假设pH弛豫时间的最小值对应于生物体内物理过程的最优速率。利用这一选择原则和我们的实验数据,我们已经表明,人类和哺乳动物生命活动的最佳温度接近于<斜体>T<sub>o</sub></斜体>≈37℃。它们可能活动的温度下限和上限接近于<斜体>T<sub>l</sub></斜体>≈30°C和<斜体>T<sub>u</sub></斜体>≈42℃。由相同的选择原理决定的<italic>pH</italic><sub>o</sub>如果补充了白蛋白和其他蛋白质的影响,则最佳值也为真。</p>& lt; / abstract>
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引用次数: 0
Predicting factors and top gene identification for survival data of breast cancer 乳腺癌生存数据的预测因素及顶级基因鉴定
IF 1.5 Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2023-01-01 DOI: 10.3934/biophy.2023006
Sarada Ghosh, Guruprasad Samanta, Manuel De la Sen
For high-throughput research with biological data-sets generated sequentially or by transcriptional micro-arrays, proteomics or other means, analytic techniques that address their high dimensional aspects remain desirable. The computation part basically predicts the tendency towards mortality due to breast cancer (BC) by using several classification methods, i.e., Logistic Regression (LR), Random Forest (RF), Support Vector Machine (SVM), Linear Discriminant Analysis (LDA) and Decision Tree (DT), and compared the models' performances. We proceed with the RF method since it provides better results than any other underlying models based on accuracy. We have also demonstrated some traditional and competing risk models, illustrated the models with real data analysis, depicted their curves' natures and also compared their fits using prediction error curves and the concordance index. Furthermore, two different survival splitting rules are used by using separate Random Survival Forest (RSF) methods and also constructing the ranking of risk factors due to breast cancer. The results show that high-level grade and diameter are the most important predictors for mortality progression in the presence of competing events of death, and lymph nodes, age and angiography are other vital criteria for this purpose. We have also implemented RSF backward selection criteria, which enables top gene selection related to mortality progression due to breast cancer. This method identifies c-MYB, CDCA7, NUSAP1, BIRC5, ANGPTL4, JAG1, IL6ST, and remaining genes that are mainly responsible for mortality progression due to breast cancer. In this work, R software is used to obtain and evaluate the results.
对于使用顺序生成或通过转录微阵列、蛋白质组学或其他手段生成的生物数据集进行高通量研究,解决其高维方面的分析技术仍然是可取的。计算部分采用Logistic回归(LR)、随机森林(RF)、支持向量机(SVM)、线性判别分析(LDA)和决策树(DT)等几种分类方法,对乳腺癌(BC)死亡率趋势进行基本预测,并对模型性能进行比较。我们继续使用RF方法,因为它提供了比任何其他基于准确性的底层模型更好的结果。我们还展示了一些传统的和竞争的风险模型,用实际数据分析说明了这些模型,描述了它们的曲线性质,并使用预测误差曲线和一致性指数比较了它们的拟合。此外,通过使用不同的随机生存森林(RSF)方法,并构建乳腺癌危险因素排序,采用了两种不同的生存分裂规则。结果表明,在存在竞争性死亡事件的情况下,高级别和直径是死亡率进展的最重要预测因素,淋巴结、年龄和血管造影是其他重要标准。我们还实施了RSF向后选择标准,使与乳腺癌死亡率进展相关的顶级基因选择成为可能。该方法鉴定了c-MYB、CDCA7、NUSAP1、BIRC5、ANGPTL4、JAG1、IL6ST以及其他主要负责乳腺癌死亡率进展的基因。在这项工作中,使用R软件来获取和评估结果。
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引用次数: 0
On the dimensionless model of the transcription bubble dynamics 转录泡动力学的无量纲模型
IF 1.5 Q3 Biochemistry, Genetics and Molecular Biology Pub Date : 2023-01-01 DOI: 10.3934/biophy.2023013
L. Krasnobaeva, L. Yakushevich
The dynamics of transcription bubbles is modeled using a system of nonlinear differential equations, the one-soliton solutions of which (kinks), are interpreted as a mathematical images of transcription bubbles. These equations contain a lot of DNA dynamic parameters, including the moments of inertia of nitrous bases, distances between base pairs, distances from the centers of mass of bases to sugar-phosphate chains, rigidity of the sugar-phosphate backbone, and interactions between bases within pairs. However, estimates of the parameter values are often difficult, and it is not convenient or simple to operate with such multi-parameter systems. One of the ways to reduce the number of the DNA dynamic parameters is to transform the model equations to a dimensionless form. In this work, we construct a dimensionless DNA model and apply it to study transcription bubbles dynamics. We show that transformation to a dimensionless form really leads to a decrease in the number of the model parameters and really simplifies the analysis of model equations and their solutions.
转录泡的动力学是用非线性微分方程系统建模的,其单孤子解(扭结)被解释为转录泡的数学图像。这些方程包含了大量的DNA动力学参数,包括亚氮碱基的转动惯量、碱基对之间的距离、碱基质心到糖-磷酸链的距离、糖-磷酸主链的刚性以及碱基对之间的相互作用。然而,参数值的估计往往是困难的,并且在这种多参数系统中操作并不方便或简单。将模型方程转化为无量纲形式是减少DNA动态参数数目的方法之一。在这项工作中,我们构建了一个无量纲DNA模型,并将其应用于转录泡动力学研究。我们证明,转换为无量纲形式确实导致模型参数数量的减少,并且确实简化了模型方程及其解的分析。
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引用次数: 0
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AIMS Biophysics
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