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A new mathematical modelling and parameter estimation of COVID-19: a case study in Iraq 新冠肺炎数学模型与参数估计:以伊拉克为例
IF 2.3 Q4 ENGINEERING, BIOMEDICAL Pub Date : 2022-01-01 DOI: 10.3934/bioeng.2022030
M. Yavuz, Waled Yavız Ahmed Haydar
Mathematical modelling has been widely used in many fields, especially in recent years. The applications of mathematical modelling in infectious diseases have shown that situations such as isolation, quarantine, vaccination and treatment are often necessary to eliminate most infectious diseases. In this study, a mathematical model of COVID-19 disease involving susceptible (S), exposed (E), infected (I), quarantined (Q), vaccinated (V) and recovered (R) populations is considered. In order to show the biological significance of the system, the non-negative solution region and the boundedness of the relevant biological compartments are shown. The endemic and disease-free equilibrium points of the model are calculated, and local stability analyses of these equilibrium points are performed. The basic reproduction number is also calculated for the relevant model. Sensitivity analysis of this number is studied, and it has been pointed out which parameters affect this number and how they affect it. Moreover, using real data from Iraq, the model parameters are estimated using the least squares curve fitting method, and numerical simulations are performed by using these estimated values. For the solution of the model, the Adams-Bashforth type predictive-corrective numerical method is used, and with the help of numerical simulations, several predictions are achieved about the future course of COVID-19.
数学建模在许多领域得到了广泛的应用,特别是近年来。数学模型在传染病中的应用表明,隔离、检疫、接种疫苗和治疗等情况往往是消除大多数传染病所必需的。在本研究中,考虑了涉及易感人群(S)、暴露人群(E)、感染人群(I)、隔离人群(Q)、接种人群(V)和恢复人群(R)的COVID-19疾病数学模型。为了显示系统的生物学意义,给出了系统的非负解域和相关生物区室的有界性。计算了模型的地方病平衡点和无病平衡点,并对平衡点进行了局部稳定性分析。并计算了相关型号的基本复制数。研究了该数值的敏感性分析,指出了影响该数值的参数及其影响方式。利用伊拉克实际资料,采用最小二乘曲线拟合方法对模型参数进行了估计,并进行了数值模拟。对于模型的求解,采用Adams-Bashforth型预测校正数值方法,并借助数值模拟对COVID-19的未来进程进行了几种预测。
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引用次数: 5
Epidemic dynamics on social interaction networks 社会互动网络中的流行病动态
IF 2.3 Q4 ENGINEERING, BIOMEDICAL Pub Date : 2022-01-01 DOI: 10.3934/bioeng.2022025
M. Jelassi, K. Oshinubi, Mustapha Rachdi, J. Demongeot
The present paper aims to apply the mathematical ideas of the contagion networks in a discrete dynamic context to the modeling of two current pandemics, i.e., COVID-19 and obesity, that are identified as major risks by the World Health Organization. After providing a reminder of the main tools necessary to model epidemic propagation in a Boolean framework (Hopfield-type propagation equation, notion of centrality, existence of stationary states), we present two applications derived from the observation of real data and involving mathematical models for their interpretation. After a discussion of the obtained results of model simulations, multidisciplinary work perspectives (both on mathematical and biomedical sides) are proposed in order to increase the efficiency of the models currently used and improve both the comprehension of the contagion mechanism and the prediction of the dynamic behaviors of the pandemics' present and future states.
本文旨在将离散动态背景下传染网络的数学思想应用于当前两种流行病的建模,即COVID-19和肥胖,这两种流行病被世界卫生组织确定为主要风险。在提供了在布尔框架中建模流行病传播所需的主要工具(hopfield型传播方程,中心性概念,稳态存在性)的提醒之后,我们提出了两个应用,这些应用来自于对真实数据的观察,并涉及数学模型来解释它们。在讨论了模型模拟所获得的结果之后,提出了多学科的工作前景(包括数学和生物医学方面),以提高目前使用的模型的效率,并改进对传染机制的理解以及对流行病当前和未来状态的动态行为的预测。
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引用次数: 2
Biotechnology – current achievements and future challenges 生物技术--当前的成就和未来的挑战
IF 2.3 Q4 ENGINEERING, BIOMEDICAL Pub Date : 2022-01-01 DOI: 10.3934/bioeng.2022005
J. Zdarta, K. Jankowska
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引用次数: 1
Current and future perspectives of atomic force microscopy to elicit the intrinsic properties of soft matter at the single molecule level 原子力显微镜在单分子水平上揭示软物质内在性质的当前和未来前景
IF 2.3 Q4 ENGINEERING, BIOMEDICAL Pub Date : 2022-01-01 DOI: 10.3934/bioeng.2022020
C. Marcuello
Soft matter encompasses multitude of systems like biomolecules, living cells, polymers, composites or blends. The increasing interest to better understand their physico-chemical properties has significantly favored the development of new techniques with unprecedented resolution. In this framework, atomic force microscopy (AFM) can act as one main actor to address multitude of intrinsic sample characteristics at the nanoscale level. AFM presents many advantages in comparison to other bulk techniques as the assessment of individual entities discharging thus, ensemble averaging phenomena. Moreover, AFM enables the visualization of singular events that eventually can provide response of some open questions that still remain unclear. The present manuscript aims to make the reader aware of the potential applications in the employment of this tool by providing recent examples of scientific studies where AFM has been employed with success. Several operational modes like AFM imaging, AFM based force spectroscopy (AFM-FS), nanoindentation, AFM-nanoscale infrared spectroscopy (AFM-nanoIR) or magnetic force microscopy (MFM) will be fully explained to detail the type of information that AFM is capable to gather. Finally, future prospects will be delivered to discern the following steps to be conducted in this field.
软物质包括许多系统,如生物分子、活细胞、聚合物、复合材料或混合物。对更好地了解其物理化学性质的兴趣日益增加,极大地促进了新技术的发展,其分辨率前所未有。在这个框架下,原子力显微镜(AFM)可以作为一个主要的参与者,在纳米尺度上解决大量的内在样品特征。与其他散装技术相比,AFM在评估单个实体放电时具有许多优势,因此,总体平均现象。此外,AFM使单个事件可视化,最终可以提供一些仍然不清楚的开放性问题的答案。目前的手稿旨在通过提供最近的科学研究的例子,其中AFM已被成功采用,使读者意识到在使用这个工具的潜在应用。几个操作模式,如AFM成像,AFM力谱(AFM- fs),纳米压痕,AFM纳米级红外光谱(AFM- nanoir)或磁力显微镜(MFM)将被充分解释,详细说明AFM能够收集的信息类型。最后,将提出未来展望,以确定在这一领域应采取的下列步骤。
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引用次数: 3
Finite state machine and Markovian equivalents of the lac Operon in E. coli bacterium 大肠杆菌中lac操纵子的有限状态机和马尔可夫等价
IF 2.3 Q4 ENGINEERING, BIOMEDICAL Pub Date : 2022-01-01 DOI: 10.3934/bioeng.2022029
Urooj Ainuddin, Maria Waqas

The lac operon in E. coli has been extensively studied by computational biologists. The bacterium uses it to survive in the absence of glucose, utilizing lactose for growth. This paper presents a novel modeling mechanism for the lac operon, transferring the process of lactose metabolism from the cell to a finite state machine (FSM). This FSM is implemented in field-programmable gate array (FPGA) and simulations are run in random conditions. A Markov chain is also proposed for the lac operon, which helps study its behavior in terms of probabilistic variables, validating the finite state machine at the same time. This work is focused towards conversion of biological processes into computing machines.

计算生物学家对大肠杆菌中的lac操纵子进行了广泛的研究。细菌利用它在没有葡萄糖的情况下生存,利用乳糖生长。本文提出了一种新的乳糖操纵子建模机制,将乳糖代谢过程从细胞转移到有限状态机(FSM)。该FSM在现场可编程门阵列(FPGA)中实现,并在随机条件下进行了仿真。对于lac操纵子,本文还提出了一个马尔可夫链,这有助于从概率变量的角度研究其行为,同时验证有限状态机。这项工作的重点是将生物过程转化为计算机器。
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引用次数: 0
A systematic review on the incidence and risk factors of surgical site infections following hepatopancreatobiliary (HPB) surgery 肝胆胰(HPB)手术后手术部位感染的发生率和危险因素的系统综述
IF 2.3 Q4 ENGINEERING, BIOMEDICAL Pub Date : 2022-01-01 DOI: 10.3934/bioeng.2022010
Lucy Chambers, A. Sheen, K. Whitehead
Background

Surgical site infections (SSI) are one of the most common hospital acquired infections and result in increased morbidity, mortality and financial burden on health services. The incidence of SSIs are not clearly defined and infection rates as varied as 20%–40% have been reported. The aim of this study was to systematically review the incidence and risk factors of SSI following HPB surgery.

Methods

The database of Medline (via PubMed) was systematically searched from 2013–2022. Articles were screened using the PRISMA statement and those that met the inclusion criteria were included in the study.

Results

Sixteen studies were eligible for inclusion in this systematic review. The average incidence of SSI was 29.8%. Key risk factors identified included male gender, open surgery, preoperative biliary stenting and obesity.

Conclusions

The incidence of SSI following HPB surgery varied, but it is generally high. A variety of pre-disposing patient factors can affect infection rates following HPB surgery. The results from this study suggest that perhaps laparoscopic surgery should be used where possible, and that there should be an awareness that gender, obesity and the use of stents may increase the incidence of SSIs following these operations.

背景手术部位感染(SSI)是最常见的医院获得性感染之一,导致发病率、死亡率增加和卫生服务的经济负担。ssi的发生率没有明确的定义,感染率高达20%-40%。本研究的目的是系统回顾HPB手术后SSI的发生率和危险因素。方法系统检索2013-2022年Medline数据库(通过PubMed)。使用PRISMA声明对文章进行筛选,符合纳入标准的文章被纳入研究。结果16项研究符合纳入本系统评价的条件。SSI的平均发生率为29.8%。确定的主要危险因素包括男性、开放手术、术前胆道支架置入术和肥胖。结论HPB术后SSI的发生率各不相同,但普遍较高。多种诱发因素可影响HPB手术后的感染率。这项研究的结果表明,也许腹腔镜手术应该在可能的情况下使用,并且应该意识到性别,肥胖和支架的使用可能会增加这些手术后ssi的发生率。
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引用次数: 0
Multicellular model of angiogenesis 血管生成的多细胞模型
IF 2.3 Q4 ENGINEERING, BIOMEDICAL Pub Date : 2022-01-01 DOI: 10.3934/bioeng.2022004
T. Nakazawa, Sohei Tasaki, Kiyohiko Nakai, Takashi Suzuki
This paper presents a mathematical model governing the dynamics of a morphogenetic vascular endothelial cell (EC) during angiogenesis, and vascular growth formed by EC. Especially, we adopt a multiparticle system for modeling these cells. This model does not distinguish a tip cell from a stalk cell. A formed vessel is modeled using phase-field equation to prevent capillary expansion with time stepping in particular. Numerical simulation reveals that all cells are moving in the direction of high concentration of vascular endothelial growth factor (VEGF), and that they are mutually repellent in cases in which they are closer than some threshold.
本文提出了一个控制血管内皮细胞(EC)在血管生成过程中形态发生动力学的数学模型,以及EC形成的血管生长。特别地,我们采用了多粒子系统来模拟这些细胞。这个模型不区分尖端细胞和柄细胞。采用相场方程对成形容器进行建模,以防止毛细管在时间步进过程中膨胀。数值模拟结果表明,所有细胞都向着血管内皮生长因子(VEGF)浓度较高的方向运动,并且当它们比某个阈值更接近时,它们是相互排斥的。
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引用次数: 1
Computational approach using machine learning modelling for optimization of transesterification process for linseed biodiesel production 利用机器学习建模优化亚麻籽生物柴油酯交换过程的计算方法
IF 2.3 Q4 ENGINEERING, BIOMEDICAL Pub Date : 2022-01-01 DOI: 10.3934/bioeng.2022023
Sunil Gautam, Sangeeta Kanakraj, Azriel Henry
In this research work, various machine learning models such as linear regression (LR), KNN and MLP were created to predict the optimized synthesis of biodiesel from pre-treated and non-treated Linseed oil in base transesterification reaction mode. Three input parameters were included for modelling, reaction time, catalyst concentrated ion, and methanol/oil-molar ratio. In biodiesel transesterification reaction 180 samples run with non-Pre-treated Linseed Methyl Ester (NPLME), Water Pre-treated Linseed Methyl Ester (WPLME) and Enzymatic Pre-treated Linseed Methyl Ester (EPLME) oil as feed stocks and optimized parameters are find out for maximum biodiesel yield to be 8:1 molar ratio, 0.4% weight catalyst, 60 °C reaction temperature.To test the technique, R2 and MAPE parameters were used. The average R2 values for linear regression, KNN, and MLP are 0.7030, 0.8554 and 0.7864 respectively. Moreover, the average MAPE values for these models are 11.1886, 6.0873 and 8.0669 respectively. Hence, it is observed that the KNN model outperforms other models with higher accuracy and low MAPE score.
在本研究中,建立了线性回归(LR)、KNN和MLP等多种机器学习模型来预测预处理和未处理亚麻籽油在碱酯交换反应模式下合成生物柴油的优化过程。三个输入参数包括建模,反应时间,催化剂浓度离子和甲醇/油摩尔比。以未预处理亚麻仁甲酯(NPLME)、水预处理亚麻仁甲酯(WPLME)和酶预处理亚麻仁甲酯(EPLME)油为原料,进行180个样品的生物柴油酯交换反应,优化了生物柴油收率为8:1摩尔比、催化剂重量0.4%、反应温度60℃的最佳参数。为了验证该技术,采用R2和MAPE参数。线性回归、KNN和MLP的平均R2值分别为0.7030、0.8554和0.7864。平均MAPE值分别为11.1886、6.0873和8.0669。因此,观察到KNN模型优于其他具有更高精度和低MAPE分数的模型。
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引用次数: 2
Model predictions and data fitting can effectively work in spreading COVID-19 pandemic 模型预测和数据拟合可以有效地用于COVID-19大流行的传播
IF 2.3 Q4 ENGINEERING, BIOMEDICAL Pub Date : 2022-01-01 DOI: 10.3934/bioeng.2022014
Bashdar A. Salam, S. Khoshnaw, A. M. Adabar, Hedayat M. Sharifi, A. S. Mohammed
Spreading COVID-19 pandemic has been considered as a global issue. Many international efforts including mathematical approaches have been recently discussed to control this disease more effectively. In this study, we have developed our previous SIUWR model and some transmission parameters are added. Accordingly, the basic reproduction number and elasticity coefficients are calculated at the equilibrium points. Then, some key critical model parameters are identified based on local sensitivities. In addition, the validation of the suggested model is checked by comparing some collected real data in Iraq and France from January 1st, 2021 to December 25th, 2021. Interestingly, there are good agreements between the model results and the real confirmed data using computational simulations in MATLAB. Results provide some biological interpretations and they can be used to control this pandemic more effectively. The model results will be used for both countries in minimizing the impact of this virus on their communities.
新冠肺炎疫情的蔓延被认为是一个全球性问题。最近讨论了包括数学方法在内的许多国际努力,以便更有效地控制这种疾病。在本研究中,我们发展了以前的小水波模型,并增加了一些传输参数。据此,计算了平衡点处的基本再生数和弹性系数。然后,基于局部灵敏度识别关键模型参数。此外,通过比较2021年1月1日至2021年12月25日在伊拉克和法国收集的一些实际数据,验证了所建议模型的有效性。有趣的是,在MATLAB中进行计算仿真,模型结果与实际确认数据吻合较好。研究结果提供了一些生物学解释,可用于更有效地控制这种大流行。模型结果将用于两国最大限度地减少这种病毒对其社区的影响。
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引用次数: 0
A micro-CT evaluation of bone density around two different types of surfaces on one-piece fixo implants with early loading-an experimental study in dogs at 3 months micro-CT评估早期负荷的一体式固定植入体两种不同表面周围的骨密度-一项3个月大的狗的实验研究
IF 2.3 Q4 ENGINEERING, BIOMEDICAL Pub Date : 2022-01-01 DOI: 10.3934/bioeng.2022028
J. Calvo-Guirado, Nuria García Carrillo, Félix de Carlos-Villafranca, M. Garcés-Villalá, L. Mahesh, J. Ibáñez, F. Martínez-Martínez
The study's main objective was to evaluate the bone density and osseointegration around dental implants with two different implant surfaces with early loading, using a micro-CT device. Twenty-four Fixo® implants (Oxyimplant, Biomec Italy) 3.5 × 8.5 mm with Laser (test group) and acid-etched surface (control group) were placed in six young beagle dog's mandibles. MicroCT (Albira, Germay) evaluation with seven regions of interest was defined in each implant on two different surfaces. A total of 168 sites were studied, and four isocountours were also done in each implant at coronal, transversal, and sagittal scanned areas to evaluate bone density location. The effect on the bone evaluation of two different surfaces variables was evaluated at the mesial and distal positions, showing crestal, medial, and apical types of bone density. Implant positions (P2, P3, P4, and M1) were also analyzed to determine bone density areas. The results of hard tissue density indicated a statistical significance for laser surface at crestal ROIs level (p < 0.001) and position of implants (p = 0.032) related to P3 areas compared to the acid-etched surface in Fixo® implants. Density D4 was the most common type of bone surrounding Fixo® standard implants at three different positions and density D3 was the most found on Fixo® laser surfaces. Micro-CT evaluation was a powerful tool for measuring the type of bone quality and location surrounding dental implants. Micro-CT study revealed that the most common density type found around Fixo® laser surface (test) implants was density D3 at the mesial and distal coronal part and density D4 at the middle and apical part. Fixo® implant with acid-etched surface showed the type of density D4 bone in hole implant at 3 months follow-up. It is a complementary histologic and histomorphometric analysis method for implant surrounding bone density.
该研究的主要目的是利用微型ct设备评估两种不同种植体表面早期加载牙种植体周围的骨密度和骨整合。将24颗Fixo®种植体(Oxyimplant, Biomec Italy) 3.5 × 8.5 mm,激光(试验组)和酸蚀表面(对照组)放置在6只幼年beagle犬的下颌骨上。MicroCT (Albira, germany)在每个种植体的两个不同表面上定义了七个感兴趣的区域。共研究了168个位置,并在每个种植体的冠状、横向和矢状扫描区域进行了4次等面扫描,以评估骨密度位置。在中、远端位置评估两种不同表面变量对骨评估的影响,显示骨密度的嵴、内侧和根尖类型。还分析种植体位置(P2、P3、P4和M1)以确定骨密度面积。硬组织密度结果显示,与Fixo®种植体的酸蚀表面相比,牙冠roi水平激光表面(p < 0.001)和种植体位置与P3区相关(p = 0.032)具有统计学意义。密度D4是Fixo®标准种植体周围三个不同位置最常见的骨类型,密度D3在Fixo®激光表面最常见。显微ct评价是测量种植体周围骨质量和位置的有力工具。Micro-CT研究显示,Fixo®激光表面(测试)种植体周围最常见的密度类型是冠状中、远端D3密度和中、根尖D4密度。Fixo®酸蚀面种植体在随访3个月时显示密度为D4型骨孔种植体。它是种植体周围骨密度的一种补充组织学和组织形态学分析方法。
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引用次数: 1
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AIMS Bioengineering
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