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Exploring Unsupervised Machine Learning Classification Methods for Physiological Stress Detection 探索生理应激检测的无监督机器学习分类方法
Q3 ENGINEERING, BIOMEDICAL Pub Date : 2022-03-11 DOI: 10.3389/fmedt.2022.782756
Talha Iqbal, A. Elahi, W. Wijns, A. Shahzad
Over the past decade, there has been a significant development in wearable health technologies for diagnosis and monitoring, including application to stress monitoring. Most of the wearable stress monitoring systems are built on a supervised learning classification algorithm. These systems rely on the collection of sensor and reference data during the development phase. One of the most challenging tasks in physiological or pathological stress monitoring is the labeling of the physiological signals collected during an experiment. Commonly, different types of self-reporting questionnaires are used to label the perceived stress instances. These questionnaires only capture stress levels at a specific point in time. Moreover, self-reporting is subjective and prone to inaccuracies. This paper explores the potential feasibility of unsupervised learning clustering classifiers such as Affinity Propagation, Balanced Iterative Reducing and Clustering using Hierarchies (BIRCH), K-mean, Mini-Batch K-mean, Mean Shift, Density-Based Spatial Clustering of Applications with Noise (DBSCAN) and Ordering Points To Identify the Clustering Structure (OPTICS) for implementation in stress monitoring wearable devices. Traditional supervised machine learning (linear, ensembles, trees, and neighboring models) classifiers require hand-crafted features and labels while on the other hand, the unsupervised classifier does not require any labels of perceived stress levels and performs classification based on clustering algorithms. The classification results of unsupervised machine learning classifiers are found comparable to supervised machine learning classifiers on two publicly available datasets. The analysis and results of this comparative study demonstrate the potential of unsupervised learning for the development of non-invasive, continuous, and robust detection and monitoring of physiological and pathological stress.
在过去十年中,用于诊断和监测的可穿戴健康技术有了重大发展,包括应用于压力监测。大多数可穿戴应力监测系统都是建立在监督学习分类算法上的。这些系统在开发阶段依赖于传感器和参考数据的收集。生理或病理应激监测中最具挑战性的任务之一是对实验中收集的生理信号进行标记。通常,不同类型的自我报告问卷被用来标记感知到的压力实例。这些问卷只记录了特定时间点的压力水平。此外,自我报告是主观的,容易出现不准确的情况。本文探讨了无监督学习聚类分类器的潜在可行性,如亲和力传播、平衡迭代约简和分层聚类(BIRCH)、K-mean、Mini-Batch K-mean、Mean Shift、基于密度的带噪声应用空间聚类(DBSCAN)和排序点识别聚类结构(OPTICS),用于应力监测可穿戴设备的实现。传统的监督机器学习(线性、集成、树和邻近模型)分类器需要手工制作特征和标签,而另一方面,无监督分类器不需要感知压力水平的任何标签,并基于聚类算法执行分类。在两个公开可用的数据集上,发现无监督机器学习分类器的分类结果与监督机器学习分类器相当。这项比较研究的分析和结果表明,无监督学习在无创、连续和稳健的生理和病理应激检测和监测方面的发展潜力。
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引用次数: 8
Editorial: Verification and Validation of in silico Models for Biomedical Implantable Devices 社论:生物医学植入装置的计算机模型验证与验证
Q3 ENGINEERING, BIOMEDICAL Pub Date : 2022-03-10 DOI: 10.3389/fmedt.2022.856067
L. Petrini, G. Pennati, D. Fotiadis
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引用次数: 0
Application of Transcriptomics for Predicting Protein Interaction Networks, Drug Targets and Drug Candidates 转录组学在预测蛋白质相互作用网络、药物靶点和候选药物中的应用
Q3 ENGINEERING, BIOMEDICAL Pub Date : 2022-03-09 DOI: 10.3389/fmedt.2022.693148
Dulshani Kankanige, L. Liyanage, M. O’Connor
Protein interaction pathways and networks are critically-required for a vast range of biological processes. Improved discovery of candidate druggable proteins within specific cell, tissue and disease contexts will aid development of new treatments. Predicting protein interaction networks from gene expression data can provide valuable insights into normal and disease biology. For example, the resulting protein networks can be used to identify potentially druggable targets and drug candidates for testing in cell and animal disease models. The advent of whole-transcriptome expression profiling techniques—that catalogue protein-coding genes expressed within cells and tissues—has enabled development of individual algorithms for particular tasks. For example,: (i) gene ontology algorithms that predict gene/protein subsets involved in related cell processes; (ii) algorithms that predict intracellular protein interaction pathways; and (iii) algorithms that correlate druggable protein targets with known drugs and/or drug candidates. This review examines approaches, advantages and disadvantages of existing gene expression, gene ontology, and protein network prediction algorithms. Using this framework, we examine current efforts to combine these algorithms into pipelines to enable identification of druggable targets, and associated known drugs, using gene expression datasets. In doing so, new opportunities are identified for development of powerful algorithm pipelines, suitable for wide use by non-bioinformaticians, that can predict protein interaction networks, druggable proteins, and related drugs from user gene expression datasets.
蛋白质相互作用途径和网络对于广泛的生物过程是至关重要的。在特定的细胞、组织和疾病环境中改进候选药物蛋白的发现将有助于开发新的治疗方法。从基因表达数据预测蛋白质相互作用网络可以为正常和疾病生物学提供有价值的见解。例如,由此产生的蛋白质网络可用于识别潜在的可药物靶点和候选药物,以便在细胞和动物疾病模型中进行测试。全转录组表达谱技术的出现——对细胞和组织内表达的蛋白质编码基因进行编目——使得针对特定任务的个人算法得以发展。例如:(i)预测参与相关细胞过程的基因/蛋白质子集的基因本体算法;(ii)预测细胞内蛋白质相互作用途径的算法;以及(iii)将可药物蛋白靶点与已知药物和/或候选药物相关联的算法。本文综述了现有的基因表达、基因本体和蛋白质网络预测算法的方法、优缺点。利用这一框架,我们研究了目前将这些算法结合到管道中的努力,以便使用基因表达数据集识别可药物靶标和相关已知药物。在此过程中,为开发强大的算法管道确定了新的机会,适合非生物信息学家广泛使用,可以从用户基因表达数据集预测蛋白质相互作用网络,可药物蛋白质和相关药物。
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引用次数: 1
Corrigendum: A Psychometric Platform to Collect Somatosensory Sensations for Neuroprosthetic Use 更正:收集用于神经假肢的体感感觉的心理测量平台
Q3 ENGINEERING, BIOMEDICAL Pub Date : 2022-02-24 DOI: 10.3389/fmedt.2022.866538
G. Valle, F. Iberite, I. Strauss, E. D’Anna, G. Granata, R. Di Iorio, T. Stieglitz, S. Raspopovic, F. Petrini, P. Rossini, S. Micera
[This corrects the article DOI: 10.3389/fmedt.2021.619280.].
[这更正了文章DOI: 10.3389/fmedt.2021.619280.]。
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引用次数: 1
Where National Medicines Policies Have Taken Us With Patient Involvement and Health Technology Assessment in Africa 非洲国家药品政策对患者参与和卫生技术评估的影响
Q3 ENGINEERING, BIOMEDICAL Pub Date : 2022-02-24 DOI: 10.3389/fmedt.2022.810456
K. Sehmi, J. Wale
The Covid-19 pandemic has highlighted global knowledge about, but lack of equitable access to, life-changing medicines, and other innovative medical products by populations in African low and middle income countries. The World Health Organization (WHO) and other international non-profit foundations and organizations are constantly striving to address inequity. In the 1970s, WHO initiated a regularly updated essential medicines list, together with the concept of national medicines policies (NMPs) to ensure access and availability, affordability, rational, and effective use of medicines which are considered essential in addressing predominant population health issues and disease burden. We studied the NMPs of Ghana, South Africa, Uganda and Zimbabwe to highlight some of the important issues that these countries experience in the safe and effective use of medical products. Thailand is an example of how health technology assessment (HTA) can provide a country with an internationally supported, clearly defined and transparent process to broaden access to medicines and services. These medical services can add considerable value in accordance with local values and priorities. Involvement of civil society adds democratic legitimacy to such processes. Community health workers and patient advocacy groups are important in raising awareness and knowledge of safety issues and the effective use of quality medicines. They can apply pressure for increased funding to improve access to healthcare. Medicines and services that contribute to supported self-care are of benefit in any setting. Joint efforts across African countries such as with the African Medicines Agency are important in addressing some of the major health issues.
2019冠状病毒病大流行凸显了非洲低收入和中等收入国家人口对改变生活的药物和其他创新医疗产品的了解,但缺乏公平获取。世界卫生组织(卫生组织)和其他国际非营利基金会和组织正在不断努力解决不平等问题。20世纪70年代,世卫组织启动了定期更新的基本药物清单,并提出了国家药物政策概念,以确保被认为对解决主要人口健康问题和疾病负担至关重要的药物的可及性、可负担性、合理和有效使用。我们研究了加纳、南非、乌干达和津巴布韦的nmp,以突出这些国家在安全有效使用医疗产品方面遇到的一些重要问题。泰国是一个例子,说明卫生技术评估如何能够为一个国家提供国际支持、明确界定和透明的进程,以扩大获得药品和服务的机会。根据当地的价值观和优先事项,这些医疗服务可以增加相当大的价值。民间社会的参与增加了这些进程的民主合法性。社区卫生工作者和患者倡导团体在提高对安全问题和有效使用优质药物的认识和知识方面很重要。他们可以施加压力,要求增加资金,以改善获得医疗保健的机会。有助于支持自我保健的药物和服务在任何情况下都是有益的。非洲各国的共同努力,例如与非洲药品管理局的共同努力,对于解决一些重大卫生问题非常重要。
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引用次数: 3
Additive Manufacturing of a Miniature Functional Trocar for Eye Surgery 眼部手术用微型功能性套管针的增材制造
Q3 ENGINEERING, BIOMEDICAL Pub Date : 2022-02-17 DOI: 10.3389/fmedt.2022.842958
K. Lussenburg, M. Scali, A. Sakes, P. Breedveld
Stereolithography is emerging as a promising additive manufacturing technology for a range of applications in the medical domain. However, for miniature, medical devices such as those used in ophthalmic surgery, a number of production challenges arise due to the small size of the components. In this work, we investigate the challenges of creating sub-millimeter features for a miniature, functional trocar using Stereolithography. The trocar cannula system is used in eye surgery to facilitate a passage for other instruments. A standard trocar consists of a hollow cannula and a flexible check valve. The research was performed in two stages: in the first stage we investigated the effect of different materials and print settings on the current design of the cannula and the valve separately, and in the second stage we used these findings to optimize the design and production process. After the first investigation, it became apparent that even though the dimensions of the trocar are within the feature size range of Stereolithography, all hollow features tended to fuse shut during printing. This effect appeared regardless of the materials or print settings, and can be attributed to refraction of the laser source. In order to circumvent this, we identified two potential strategies: (1) increasing the negative space surrounding features; and (2) decreasing the surface area per layer. By applying these strategies, we tested a new design for the cannula and valve and managed to 3D print a functional trocar, which was tested in an artificial eye. The design of the 3D printed trocar allows for further personalization depending on the specific requirements of both patient and surgeon. The proposed strategies can be applied to different applications to create miniature features using Stereolithography. Graphical Abstract
立体光刻技术正在成为一种有前途的增材制造技术,在医疗领域有广泛的应用。然而,对于微型医疗设备,如用于眼科手术的设备,由于部件尺寸小,产生了许多生产挑战。在这项工作中,我们研究了使用立体光刻技术为微型功能性套管针创建亚毫米特征的挑战。套管针套管系统用于眼科手术,以方便其他器械的通过。标准套管针由一个空心套管和一个灵活的止回阀组成。研究分两个阶段进行:第一阶段,我们分别研究了不同材料和打印设置对导管和瓣膜当前设计的影响,第二阶段,我们利用这些发现来优化设计和生产过程。在第一次调查之后,很明显,即使套管针的尺寸在立体光刻的特征尺寸范围内,所有空心特征在印刷过程中都倾向于融合关闭。无论材料或打印设置如何,这种效果都会出现,并且可以归因于激光源的折射。为了避免这种情况,我们确定了两种潜在的策略:(1)增加特征周围的负空间;(2)减小每层的表面积。通过应用这些策略,我们测试了一种新的套管和瓣膜设计,并成功3D打印出了一个功能性套管针,并在人工眼睛中进行了测试。3D打印套管针的设计允许根据患者和外科医生的具体要求进一步个性化。所提出的策略可以应用于不同的应用程序,以创建使用立体光刻的微型特征。图形抽象
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引用次数: 1
Mechanism-Driven Modeling to Aid Non-invasive Monitoring of Cardiac Function via Ballistocardiography 机制驱动的建模,以帮助无创监测心功能通过弹道心动图
Q3 ENGINEERING, BIOMEDICAL Pub Date : 2022-02-16 DOI: 10.3389/fmedt.2022.788264
M. Zaid, Lorenzo Sala, Jan R. Ivey, D. Tharp, C. Mueller, P. Thorne, Shannon C. Kelly, K. Silva, Amira Rabee Mohamed Amin, P. Ruiz‐Lozano, M. Kapiloff, Laurel A. Despins, M. Popescu, James Keller, M. Skubic, Salman Ahmad, C. Emter, G. Guidoboni
Left ventricular (LV) catheterization provides LV pressure-volume (P-V) loops and it represents the gold standard for cardiac function monitoring. This technique, however, is invasive and this limits its applicability in clinical and in-home settings. Ballistocardiography (BCG) is a good candidate for non-invasive cardiac monitoring, as it is based on capturing non-invasively the body motion that results from the blood flowing through the cardiovascular system. This work aims at building a mechanistic connection between changes in the BCG signal, changes in the P-V loops and changes in cardiac function. A mechanism-driven model based on cardiovascular physiology has been used as a virtual laboratory to predict how changes in cardiac function will manifest in the BCG waveform. Specifically, model simulations indicate that a decline in LV contractility results in an increase of the relative timing between the ECG and BCG signal and a decrease in BCG amplitude. The predicted changes have subsequently been observed in measurements on three swine serving as pre-clinical models for pre- and post-myocardial infarction conditions. The reproducibility of BCG measurements has been assessed on repeated, consecutive sessions of data acquisitions on three additional swine. Overall, this study provides experimental evidence supporting the utilization of mechanism-driven mathematical modeling as a guide to interpret changes in the BCG signal on the basis of cardiovascular physiology, thereby advancing the BCG technique as an effective method for non-invasive monitoring of cardiac function.
左室(LV)导管术提供了左室压力-容积(P-V)循环,它代表了心功能监测的金标准。然而,这项技术是侵入性的,这限制了它在临床和家庭环境中的适用性。BCG是一种很好的无创心脏监测方法,因为它基于非侵入性地捕捉血液流经心血管系统所产生的身体运动。本工作旨在建立BCG信号变化、P-V回路变化和心功能变化之间的机制联系。基于心血管生理学的机制驱动模型已被用作虚拟实验室来预测心功能的变化将如何在BCG波形中表现出来。具体而言,模型模拟表明,左室收缩力的下降导致ECG与BCG信号的相对时序增加,BCG振幅下降。预测的变化随后在三头猪的测量中被观察到,作为心肌梗死前和后的临床前模型。通过对另外3头猪进行重复、连续的数据采集,评估了BCG测量结果的可重复性。总的来说,本研究提供了实验证据,支持利用机制驱动的数学模型作为指导,在心血管生理学的基础上解释BCG信号的变化,从而推进BCG技术作为一种无创心功能监测的有效方法。
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引用次数: 4
Identification of 1, 2, 4-Triazine and Its Derivatives Against Lanosterol 14-Demethylase (CYP51) Property of Candida albicans: Influence on the Development of New Antifungal Therapeutic Strategies 1,2,4 -三嗪及其衍生物抗白色念珠菌羊毛甾醇14-去甲基酶(CYP51)特性的鉴定及其对新抗真菌治疗策略的影响
Q3 ENGINEERING, BIOMEDICAL Pub Date : 2021-08-17 DOI: 10.3389/fmedt.2022.845322
A. Verma, Aarfah Majid, M. Hossain, Sk. Faisal Ahmed, Mohammad Ashid, A. A. Bhojiya, S. Ameta, S. K. Upadhyay, A. Srivastava, Naveen Kumar Vishwakarma, V. Yadav, Pankaj Teli, Harina Harina, Mudassir Alam
This research aims to find out whether the 1, 2, 4-triazine and its derivatives have antifungal effects and can protect humans from infection with Candida albicans. Molecular docking and molecular dynamic simulation are widely used in modern drug design to target a particular protein with a ligand. We are interested in using molecular docking and molecular dynamics modeling to investigate the interaction between the derivatives of 1, 2, 4-triazine with enzyme Lanosterol 14-demethylase (CYP51) of Candida albicans. The inhibition of Candida albicans CYP51 is the main goal of our research. The 1, 2, 4-triazine and its derivatives have been docked to the CYP51 enzyme, which is involved in Candida albicans Multidrug Drug Resistance (MDR). Autodock tools were used to identify the binding affinities of molecules against the target proteins. Compared to conventional fluconazole, the molecular docking results indicated that each drug has a high binding affinity for CYP51 proteins and forms unbound interactions and hydrogen bonds with their active residues and surrounding allosteric residues. The docking contacts were made using a 10 ns MD simulation with nine molecules. RMSD, RMSF, hydrogen bonds, and the Rg all confirm these conclusions. In addition, these compounds were expected to have a favorable pharmacological profile and low toxicity. The compounds are being offered as scaffolds for the development of new antifungal drugs and as candidates for future in vitro testing.
本研究旨在了解1,2,4 -三嗪及其衍生物是否具有抗真菌作用,并能保护人类免受白色念珠菌感染。分子对接和分子动力学模拟在现代药物设计中广泛应用于配体靶向特定蛋白质。我们有兴趣利用分子对接和分子动力学建模来研究1,2,4 -三嗪衍生物与白色念珠菌羊毛甾醇14-去甲基酶(CYP51)之间的相互作用。抑制白色念珠菌CYP51是我们研究的主要目标。1,2,4 -三嗪及其衍生物已与CYP51酶对接,该酶参与白色念珠菌多药耐药(MDR)。Autodock工具用于鉴定分子与靶蛋白的结合亲和力。与常规氟康唑相比,分子对接结果表明,每种药物与CYP51蛋白具有较高的结合亲和力,并与其活性残基和周围变构残基形成非结合相互作用和氢键。对接接触是用10毫微秒的九个分子模拟完成的。RMSD, RMSF,氢键和Rg都证实了这些结论。此外,这些化合物预计具有良好的药理学特征和低毒性。这些化合物被用作开发新的抗真菌药物的支架,并作为未来体外测试的候选物。
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引用次数: 10
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Frontiers in medical technology
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