Mathematical Biosciences and Engineering最新文献_第4页

Mutation prediction in the SARS-CoV-2 genome using attention-based neural machine translation. 利用基于注意力的神经机器翻译预测 SARS-CoV-2 基因组中的突变。

IF 2.6 4区工程技术

Mathematical Biosciences and Engineering Pub Date : 2024-05-20 DOI: 10.3934/mbe.2024264

Darrak Moin Quddusi, Sandesh Athni Hiremath, Naim Bajcinca

{"title":"Mutation prediction in the SARS-CoV-2 genome using attention-based neural machine translation.","authors":"Darrak Moin Quddusi, Sandesh Athni Hiremath, Naim Bajcinca","doi":"10.3934/mbe.2024264","DOIUrl":"https://doi.org/10.3934/mbe.2024264","url":null,"abstract":"Severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) has been evolving rapidly after causing havoc worldwide in 2020. Since then, it has been very hard to contain the virus owing to its frequently mutating nature. Changes in its genome lead to viral evolution, rendering it more resistant to existing vaccines and drugs. Predicting viral mutations beforehand will help in gearing up against more infectious and virulent versions of the virus in turn decreasing the damage caused by them. In this paper, we have proposed different NMT (neural machine translation) architectures based on RNNs (recurrent neural networks) to predict mutations in the SARS-CoV-2-selected non-structural proteins (NSP), i.e., NSP1, NSP3, NSP5, NSP8, NSP9, NSP13, and NSP15. First, we created and pre-processed the pairs of sequences from two languages using k-means clustering and nearest neighbors for training a neural translation machine. We also provided insights for training NMTs on long biological sequences. In addition, we evaluated and benchmarked our models to demonstrate their efficiency and reliability.","PeriodicalId":49870,"journal":{"name":"Mathematical Biosciences and Engineering","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141318838","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Quantifying Geobacter sulfurreducens growth: A mathematical model based on acetate concentration as an oxidizing substrate. 量化硫化琥珀酸地质细菌的生长：基于醋酸盐浓度作为氧化底物的数学模型。

IF 2.6 4区工程技术

Mathematical Biosciences and Engineering Pub Date : 2024-05-17 DOI: 10.3934/mbe.2024263

Virgínia Villa-Cruz, Sumaya Jaimes-Reátegui, Juana E Alba-Cuevas, Lily Xochilt Zelaya-Molina, Rider Jaimes-Reátegui, Alexander N Pisarchik

{"title":"Quantifying Geobacter sulfurreducens growth: A mathematical model based on acetate concentration as an oxidizing substrate.","authors":"Virgínia Villa-Cruz, Sumaya Jaimes-Reátegui, Juana E Alba-Cuevas, Lily Xochilt Zelaya-Molina, Rider Jaimes-Reátegui, Alexander N Pisarchik","doi":"10.3934/mbe.2024263","DOIUrl":"https://doi.org/10.3934/mbe.2024263","url":null,"abstract":"We developed a mathematical model to simulate dynamics associated with the proliferation of Geobacter and ultimately optimize cellular operation by analyzing the interaction of its components. The model comprises two segments: an initial part comprising a logistic form and a subsequent segment that incorporates acetate oxidation as a saturation term for the microbial nutrient medium. Given that four parameters can be obtained by minimizing the square root of the mean square error between experimental Geobacter growth and the mathematical model, the model underscores the importance of incorporating nonlinear terms. The determined parameter values closely align with experimental data, providing insights into the mechanisms that govern Geobacter proliferation. Furthermore, the model has been transformed into a scaleless equation with only two parameters to simplify the exploration of qualitative properties. This allowed us to conduct stability analysis of the fixed point and construct a co-dimension two bifurcation diagram.","PeriodicalId":49870,"journal":{"name":"Mathematical Biosciences and Engineering","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141318841","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A prostate seed implantation robot system based on human-computer interactions: Augmented reality and voice control. 基于人机交互的前列腺种子植入机器人系统：增强现实和语音控制

IF 2.6 4区工程技术

Mathematical Biosciences and Engineering Pub Date : 2024-05-15 DOI: 10.3934/mbe.2024262

Xinran Zhang, Yongde Zhang, Jianzhi Yang, Haiyan Du

{"title":"A prostate seed implantation robot system based on human-computer interactions: Augmented reality and voice control.","authors":"Xinran Zhang, Yongde Zhang, Jianzhi Yang, Haiyan Du","doi":"10.3934/mbe.2024262","DOIUrl":"https://doi.org/10.3934/mbe.2024262","url":null,"abstract":"The technology of robot-assisted prostate seed implantation has developed rapidly. However, during the process, there are some problems to be solved, such as non-intuitive visualization effects and complicated robot control. To improve the intelligence and visualization of the operation process, a voice control technology of prostate seed implantation robot in augmented reality environment was proposed. Initially, the MRI image of the prostate was denoised and segmented. The three-dimensional model of prostate and its surrounding tissues was reconstructed by surface rendering technology. Combined with holographic application program, the augmented reality system of prostate seed implantation was built. An improved singular value decomposition three-dimensional registration algorithm based on iterative closest point was proposed, and the results of three-dimensional registration experiments verified that the algorithm could effectively improve the three-dimensional registration accuracy. A fusion algorithm based on spectral subtraction and BP neural network was proposed. The experimental results showed that the average delay of the fusion algorithm was 1.314 s, and the overall response time of the integrated system was 1.5 s. The fusion algorithm could effectively improve the reliability of the voice control system, and the integrated system could meet the responsiveness requirements of prostate seed implantation.","PeriodicalId":49870,"journal":{"name":"Mathematical Biosciences and Engineering","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141318834","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The role of immune cells in resistance to oncolytic viral therapy. 免疫细胞在抗溶瘤病毒疗法中的作用。

IF 2.6 4区工程技术

Mathematical Biosciences and Engineering Pub Date : 2024-05-15 DOI: 10.3934/mbe.2024261

Prathibha Ambegoda, Hsiu-Chuan Wei, Sophia R-J Jang

{"title":"The role of immune cells in resistance to oncolytic viral therapy.","authors":"Prathibha Ambegoda, Hsiu-Chuan Wei, Sophia R-J Jang","doi":"10.3934/mbe.2024261","DOIUrl":"https://doi.org/10.3934/mbe.2024261","url":null,"abstract":"Resistance to treatment poses a major challenge for cancer therapy, and oncoviral treatment encounters the issue of viral resistance as well. In this investigation, we introduce deterministic differential equation models to explore the effect of resistance on oncolytic viral therapy. Specifically, we classify tumor cells into resistant, sensitive, or infected with respect to oncolytic viruses for our analysis. Immune cells can eliminate both tumor cells and viruses. Our research shows that the introduction of immune cells into the tumor-virus interaction prevents all tumor cells from becoming resistant in the absence of conversion from resistance to sensitivity, given that the proliferation rate of immune cells exceeds their death rate. The inclusion of immune cells leads to an additional virus-free equilibrium when the immune cell recruitment rate is sufficiently high. The total tumor burden at this virus-free equilibrium is smaller than that at the virus-free and immune-free equilibrium. Therefore, immune cells are capable of reducing the tumor load under the condition of sufficient immune strength. Numerical investigations reveal that the virus transmission rate and parameters related to the immune response significantly impact treatment outcomes. However, monotherapy alone is insufficient for eradicating tumor cells, necessitating the implementation of additional therapies. Further numerical simulation shows that combination therapy with chimeric antigen receptor (CAR T-cell) therapy can enhance the success of treatment.","PeriodicalId":49870,"journal":{"name":"Mathematical Biosciences and Engineering","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141318842","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Threshold dynamics of a switching diffusion SIR model with logistic growth and healthcare resources. 具有逻辑增长和医疗资源的切换扩散 SIR 模型的阈值动态。

IF 2.6 4区工程技术

Mathematical Biosciences and Engineering Pub Date : 2024-05-14 DOI: 10.3934/mbe.2024260

Shuying Wu, Sanling Yuan

引用次数: 0

AttBiLFNet: A novel hybrid network for accurate and efficient arrhythmia detection in imbalanced ECG signals. AttBiLFNet：用于在不平衡心电图信号中准确、高效地检测心律失常的新型混合网络。

IF 2.6 4区工程技术

Mathematical Biosciences and Engineering Pub Date : 2024-05-10 DOI: 10.3934/mbe.2024259

Enes Efe, Emrehan Yavsan

{"title":"AttBiLFNet: A novel hybrid network for accurate and efficient arrhythmia detection in imbalanced ECG signals.","authors":"Enes Efe, Emrehan Yavsan","doi":"10.3934/mbe.2024259","DOIUrl":"https://doi.org/10.3934/mbe.2024259","url":null,"abstract":"Within the domain of cardiovascular diseases, arrhythmia is one of the leading anomalies causing sudden deaths. These anomalies, including arrhythmia, are detectable through the electrocardiogram, a pivotal component in the analysis of heart diseases. However, conventional methods like electrocardiography encounter challenges such as subjective analysis and limited monitoring duration. In this work, a novel hybrid model, AttBiLFNet, was proposed for precise arrhythmia detection in ECG signals, including imbalanced class distributions. AttBiLFNet integrates a Bidirectional Long Short-Term Memory (BiLSTM) network with a convolutional neural network (CNN) and incorporates an attention mechanism using the focal loss function. This architecture is capable of autonomously extracting features by harnessing BiLSTM's bidirectional information flow, which proves advantageous in capturing long-range dependencies. The attention mechanism enhances the model's focus on pertinent segments of the input sequence, which is particularly beneficial in class imbalance classification scenarios where minority class samples tend to be overshadowed. The focal loss function effectively addresses the impact of class imbalance, thereby improving overall classification performance. The proposed AttBiLFNet model achieved 99.55% accuracy and 98.52% precision. Moreover, performance metrics such as MF1, K score, and sensitivity were calculated, and the model was compared with various methods in the literature. Empirical evidence showed that AttBiLFNet outperformed other methods in terms of both accuracy and computational efficiency. The introduced model serves as a reliable tool for the timely identification of arrhythmias.","PeriodicalId":49870,"journal":{"name":"Mathematical Biosciences and Engineering","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141318764","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A lumped parameter model for evaluating coronary artery blood supply capacity. 用于评估冠状动脉供血能力的集合参数模型。

IF 2.6 4区工程技术

Mathematical Biosciences and Engineering Pub Date : 2024-05-07 DOI: 10.3934/mbe.2024258

Li Cai, Qian Zhong, Juan Xu, Yuan Huang, Hao Gao

{"title":"A lumped parameter model for evaluating coronary artery blood supply capacity.","authors":"Li Cai, Qian Zhong, Juan Xu, Yuan Huang, Hao Gao","doi":"10.3934/mbe.2024258","DOIUrl":"https://doi.org/10.3934/mbe.2024258","url":null,"abstract":"The coronary artery constitutes a vital vascular system that sustains cardiac function, with its primary role being the conveyance of indispensable nutrients to the myocardial tissue. When coronary artery disease occurs, it will affect the blood supply of the heart and induce myocardial ischemia. Therefore, it is of great significance to numerically simulate the coronary artery and evaluate its blood supply capacity. In this article, the coronary artery lumped parameter model was derived based on the relationship between circuit system parameters and cardiovascular system parameters, and the blood supply capacity of the coronary artery in healthy and stenosis states was studied. The aortic root pressure calculated by the aortic valve fluid-structure interaction (AV FSI) simulator was employed as the inlet boundary condition. To emulate the physiological phenomenon of sudden pressure drops resulting from an abrupt reduction in blood vessel radius, a head loss model was connected at the coronary artery's entrance. For each coronary artery outlet, the symmetric structured tree model was appended to simulate the terminal impedance of the missing downstream coronary arteries. The particle swarm optimization (PSO) algorithm was used to optimize the blood flow viscous resistance, blood flow inertia, and vascular compliance of the coronary artery model. In the stenosis states, the relative flow and fractional flow reserve (FFR) calculated by numerical simulation corresponded to the published literature data. It was anticipated that the proposed model can be readily adapted for clinical application, serving as a valuable reference for diagnosing and treating patients.","PeriodicalId":49870,"journal":{"name":"Mathematical Biosciences and Engineering","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141318754","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Unveiling critical ADHD biomarkers in limbic system and cerebellum using a binary hypothesis testing approach. 利用二元假设检验方法揭示边缘系统和小脑中关键的多动症生物标志物。

IF 2.6 4区工程技术

Mathematical Biosciences and Engineering Pub Date : 2024-04-28 DOI: 10.3934/mbe.2024256

Ying Chen, Lele Wang, Zhixin Li, Yibin Tang, Zhan Huan

{"title":"Unveiling critical ADHD biomarkers in limbic system and cerebellum using a binary hypothesis testing approach.","authors":"Ying Chen, Lele Wang, Zhixin Li, Yibin Tang, Zhan Huan","doi":"10.3934/mbe.2024256","DOIUrl":"https://doi.org/10.3934/mbe.2024256","url":null,"abstract":"Attention deficit hyperactivity disorder (ADHD) is a common childhood developmental disorder. In recent years, pattern recognition methods have been increasingly applied to neuroimaging studies of ADHD. However, these methods often suffer from limited accuracy and interpretability, impeding their contribution to the identification of ADHD-related biomarkers. To address these limitations, we applied the amplitude of low-frequency fluctuation (ALFF) results for the limbic system and cerebellar network as input data and conducted a binary hypothesis testing framework for ADHD biomarker detection. Our study on the ADHD-200 dataset at multiple sites resulted in an average classification accuracy of 93%, indicating strong discriminative power of the input brain regions between the ADHD and control groups. Moreover, our approach identified critical brain regions, including the thalamus, hippocampal gyrus, and cerebellum Crus 2, as biomarkers. Overall, this investigation uncovered potential ADHD biomarkers in the limbic system and cerebellar network through the use of ALFF realizing highly credible results, which can provide new insights for ADHD diagnosis and treatment.","PeriodicalId":49870,"journal":{"name":"Mathematical Biosciences and Engineering","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141318833","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Bayesian inverse problem for a fractional diffusion model of cell migration. 细胞迁移分数扩散模型的贝叶斯逆问题。

IF 2.6 4区工程技术

Mathematical Biosciences and Engineering Pub Date : 2024-04-28 DOI: 10.3934/mbe.2024257

Francisco Julian Ariza-Hernandez, Juan Carlos Najera-Tinoco, Martin Patricio Arciga-Alejandre, Eduardo Castañeda-Saucedo, Jorge Sanchez-Ortiz

引用次数: 0

Research on a vehicle and pedestrian detection algorithm based on improved attention and feature fusion. 基于改进的注意力和特征融合的车辆和行人检测算法研究。

IF 2.6 4区工程技术

Mathematical Biosciences and Engineering Pub Date : 2024-04-26 DOI: 10.3934/mbe.2024255

Wenjie Liang

{"title":"Research on a vehicle and pedestrian detection algorithm based on improved attention and feature fusion.","authors":"Wenjie Liang","doi":"10.3934/mbe.2024255","DOIUrl":"https://doi.org/10.3934/mbe.2024255","url":null,"abstract":"With the widespread integration of deep learning in intelligent transportation and various industrial sectors, target detection technology is gradually becoming one of the key research areas. Accurately detecting road vehicles and pedestrians is of great significance for the development of autonomous driving technology. Road object detection faces problems such as complex backgrounds, significant scale changes, and occlusion. To accurately identify traffic targets in complex environments, this paper proposes a road target detection algorithm based on the enhanced YOLOv5s. This algorithm introduces the weighted enhanced polarization self attention (WEPSA) self-attention mechanism, which uses spatial attention and channel attention to strengthen the important features extracted by the feature extraction network and suppress insignificant background information. In the neck network, we designed a weighted feature fusion network (CBiFPN) to enhance neck feature representation and enrich semantic information. This strategic feature fusion not only boosts the algorithm's adaptability to intricate scenes, but also contributes to its robust performance. Then, the bounding box regression loss function uses EIoU to accelerate model convergence and reduce losses. Finally, a large number of experiments have shown that the improved YOLOv5s algorithm achieves mAP@0.5 scores of 92.8% and 53.5% on the open-source datasets KITTI and Cityscapes. On the self-built dataset, the mAP@0.5 reaches 88.7%, which is 1.7%, 3.8%, and 3.3% higher than YOLOv5s, respectively, ensuring real-time performance while improving detection accuracy. In addition, compared to the latest YOLOv7 and YOLOv8, the improved YOLOv5 shows good overall performance on the open-source datasets.","PeriodicalId":49870,"journal":{"name":"Mathematical Biosciences and Engineering","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141318799","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0