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Hybrid computational modeling methods for systems biology 系统生物学的混合计算建模方法
Q1 ENGINEERING, BIOMEDICAL Pub Date : 2021-10-05 DOI: 10.1088/2516-1091/ac2cdf
Daniel A Cruz, Melissa L. Kemp
Systems biology models are typically considered across a spectrum from mechanistic to abstracted description; however, the lines between these forms of modeling are increasingly blurred. Ever-increasing computational power is providing novel opportunities for bridging time and length scales. Furthermore, despite biological mechanisms or network topology often ill-defined, the acquisition of high-throughput data leaves modelers with the desire to leverage available measurements. This review surveys modeling tools in which two or more mathematical forms are blended to describe time-dependent processes in a multivariate system. While most commonly manifested as continuous/discrete description, other forms such as mechanistic/inference or deterministic/stochastic hybrid models can be generated. Recent innovations in hybrid modeling methodologies and new applications illustrate advantages for combining model formats to gaining biological systems level insight.
系统生物学模型通常被认为是从机械描述到抽象描述的一个范围;然而,这些建模形式之间的界限越来越模糊。不断增长的计算能力为桥接时间和长度尺度提供了新的机会。此外,尽管生物学机制或网络拓扑结构往往定义不清,但高通量数据的获取使建模人员希望利用可用的测量结果。这篇综述综述了建模工具,其中两种或两种以上的数学形式被混合来描述多元系统中的时间依赖过程。虽然最常见的表现为连续/离散描述,但也可以生成其他形式,如机械/推理或确定性/随机混合模型。混合建模方法和新应用的最新创新说明了将模型格式结合起来以获得生物系统级洞察力的优势。
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引用次数: 6
Synthetic hydrogels as blood clot mimicking wound healing materials. 合成水凝胶作为模拟血凝块的伤口愈合材料。
IF 5 Q1 ENGINEERING, BIOMEDICAL Pub Date : 2021-10-01 Epub Date: 2021-09-30 DOI: 10.1088/2516-1091/ac23a4
Manuel K Rausch, Sapun H Parekh, Berkin Dortdivanlioglu, Adrianne M Rosales

Excessive bleeding-or hemorrhage-causes millions of civilian and non-civilian casualties every year. Additionally, wound sequelae, such as infections, are a significant source of chronic morbidity, even if the initial bleeding is successfully stopped. To treat acute and chronic wounds, numerous wound healing materials have been identified, tested, and adopted. Among them are topical dressings, such as gauzes, as well as natural and biomimetic materials. However, none of these materials successfully mimic the complex and dynamic properties of the body's own wound healing material: the blood clot. Specifically, blood clots exhibit complex mechanical and biochemical properties that vary across spatial and temporal scales to guide the wound healing response, which make them the ideal wound healing material. In this manuscript, we review blood clots' complex mechanical and biochemical properties, review current wound healing materials, and identify opportunities where new materials can provide additional functionality, with a specific focus on hydrogels. We highlight recent developments in synthetic hydrogels that make them capable of mimicking a larger subset of blood clot features: as plugs and as stimuli for tissue repair. We conclude that future hydrogel materials designed to mimic blood clot biochemistry, mechanics, and architecture can be combined with exciting platelet-like particles to serve as hemostats that also promote the biological wound healing response. Thus, we believe synthetic hydrogels are ideal candidates to address the clear need for better wound healing materials.

过度出血或大出血每年造成数百万平民和非平民伤亡。此外,即使最初的出血被成功止住,伤口后遗症(如感染)也是慢性发病率的一个重要来源。为了治疗急性和慢性伤口,人们发现、测试并采用了许多伤口愈合材料。其中包括纱布等局部敷料,以及天然材料和仿生物材料。然而,这些材料都无法成功模拟人体自身伤口愈合材料--血凝块--的复杂动态特性。具体来说,血凝块具有复杂的机械和生化特性,这些特性在空间和时间尺度上各不相同,可引导伤口愈合反应,因此是理想的伤口愈合材料。在本手稿中,我们回顾了血凝块复杂的机械和生化特性,评述了当前的伤口愈合材料,并确定了新材料可提供额外功能的机会,特别关注水凝胶。我们重点介绍了合成水凝胶的最新发展,这些水凝胶能够模拟血凝块的更多特性:作为血栓和组织修复的刺激物。我们的结论是,未来模仿血凝块生物化学、力学和结构设计的水凝胶材料可与令人兴奋的血小板样颗粒相结合,用作止血剂,同时促进生物伤口愈合反应。因此,我们相信合成水凝胶是满足对更好的伤口愈合材料的明确需求的理想候选材料。
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引用次数: 0
Human augmentation by wearable supernumerary robotic limbs: review and perspectives 可穿戴多功能机器人肢体的人体增重:回顾与展望
Q1 ENGINEERING, BIOMEDICAL Pub Date : 2021-09-17 DOI: 10.1088/2516-1091/ac2294
D. Prattichizzo, Maria Pozzi, Tommaso Lisini Baldi, M. Malvezzi, I. Hussain, S. Rossi, G. Salvietti
Supernumerary robotic limbs (SRLs) are wearable robots designed to enhance the sensorimotor abilities of humans. SRLs can be used to compensate for lost functions in patients with motor deficits and, more in general, to augment the sensorimotor capabilities of humans to interact with the environment. The design and control of SRLs present several challenges. SRLs must have high levels of ergonomics and wearability and, depending on the application, they might also require enhanced robustness and strength. Supernumerary robotics differs from collaborative robotics, since SRLs are not collaborative external agents but rather act under the direct command of the operator who, thanks to the use of suitable interfaces, gains the control of some actions of the SRLs. From the control point of view, it is fundamental to find the right trade-off between the degrees of freedom that are under the direct control of the user and the level of robot autonomy. The adoption of feedback interfaces can help the human to better command and use the SRL. In this review, we discuss all these aspects, relating them to the current literature on SRLs. We also present the main applications and the potential of these relatively recent devices, as well as the main neuroscientific questions they rise on the implications of their use on the users’ body schema.
超级机械臂(SRL)是一种可穿戴机器人,旨在增强人类的感觉运动能力。SRL可用于补偿运动缺陷患者的功能损失,更广泛地说,可用于增强人类与环境相互作用的感觉运动能力。SRL的设计和控制带来了一些挑战。SRL必须具有高水平的人体工程学和耐磨性,根据应用情况,它们可能还需要增强的坚固性和强度。超级机器人与协作机器人不同,因为SRL不是协作的外部代理,而是在操作员的直接指挥下行动,由于使用了合适的接口,操作员可以控制SRL的一些动作。从控制的角度来看,在用户直接控制的自由度和机器人自主性水平之间找到正确的权衡是至关重要的。反馈接口的采用可以帮助人类更好地指挥和使用SRL。在这篇综述中,我们讨论了所有这些方面,并将它们与当前关于SRL的文献联系起来。我们还介绍了这些相对较新设备的主要应用和潜力,以及它们在使用对用户身体模式的影响方面提出的主要神经科学问题。
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引用次数: 27
Known operator learning and hybrid machine learning in medical imaging—a review of the past, the present, and the future 医学成像中的已知算子学习和混合机器学习——回顾过去、现在和未来
Q1 ENGINEERING, BIOMEDICAL Pub Date : 2021-08-10 DOI: 10.1088/2516-1091/ac5b13
Andreas Maier, H. Köstler, M. Heisig, P. Krauss, S. Yang
In this article, we perform a review of the state-of-the-art of hybrid machine learning in medical imaging. We start with a short summary of the general developments of the past in machine learning and how general and specialized approaches have been in competition in the past decades. A particular focus will be the theoretical and experimental evidence pro and contra hybrid modelling. Next, we inspect several new developments regarding hybrid machine learning with a particular focus on so-called known operator learning and how hybrid approaches gain more and more momentum across essentially all applications in medical imaging and medical image analysis. As we will point out by numerous examples, hybrid models are taking over in image reconstruction and analysis. Even domains such as physical simulation and scanner and acquisition design are being addressed using machine learning grey box modelling approaches. Towards the end of the article, we will investigate a few future directions and point out relevant areas in which hybrid modelling, meta learning, and other domains will likely be able to drive the state-of-the-art ahead.
在本文中,我们对医学成像中混合机器学习的最新进展进行了回顾。我们首先简要总结一下过去机器学习的一般发展,以及过去几十年来通用和专业方法的竞争情况。一个特别的焦点将是理论和实验证据支持和反对混合建模。接下来,我们考察了关于混合机器学习的几个新发展,特别关注所谓的已知算子学习,以及混合方法如何在医学成像和医学图像分析的所有应用中获得越来越多的动力。正如我们将通过许多例子指出的那样,混合模型正在接管图像重建和分析。甚至在物理仿真、扫描仪和采集设计等领域,也在使用机器学习灰盒建模方法进行解决。在文章的最后,我们将研究几个未来的方向,并指出混合建模、元学习和其他领域可能推动最先进技术发展的相关领域。
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引用次数: 19
A review of low-cost and portable optical coherence tomography. 低成本便携式光学相干断层成像技术综述。
Q1 ENGINEERING, BIOMEDICAL Pub Date : 2021-07-01 DOI: 10.1088/2516-1091/abfeb7
Ge Song, Evan T Jelly, Kengyeh K Chu, Wesley Y Kendall, Adam Wax

Optical coherence tomography (OCT) is a powerful optical imaging technique capable of visualizing the internal structure of biological tissues at near cellular resolution. For years, OCT has been regarded as the standard of care in ophthalmology, acting as an invaluable tool for the assessment of retinal pathology. However, the costly nature of most current commercial OCT systems has limited its general accessibility, especially in low-resource environments. It is therefore timely to review the development of low-cost OCT systems as a route for applying this technology to population-scale disease screening. Low-cost, portable and easy to use OCT systems will be essential to facilitate widespread use at point of care settings while ensuring that they offer the necessary imaging performances needed for clinical detection of retinal pathology. The development of low-cost OCT also offers the potential to enable application in fields outside ophthalmology by lowering the barrier to entry. In this paper, we review the current development and applications of low-cost, portable and handheld OCT in both translational and research settings. Design and cost-reduction techniques are described for general low-cost OCT systems, including considerations regarding spectrometer-based detection, scanning optics, system control, signal processing, and the role of 3D printing technology. Lastly, a review of clinical applications enabled by low-cost OCT is presented, along with a detailed discussion of current limitations and outlook.

光学相干断层扫描(OCT)是一种强大的光学成像技术,能够以接近细胞的分辨率显示生物组织的内部结构。多年来,OCT一直被视为眼科护理的标准,作为评估视网膜病理的宝贵工具。然而,目前大多数商用OCT系统的昂贵性质限制了其一般可及性,特别是在低资源环境中。因此,回顾低成本OCT系统的发展作为将该技术应用于人群规模疾病筛查的途径是及时的。低成本,便携和易于使用的OCT系统对于促进在护理场所的广泛使用至关重要,同时确保它们提供临床检测视网膜病理所需的必要成像性能。低成本OCT的发展通过降低进入门槛,也为眼科以外的领域提供了应用潜力。在本文中,我们回顾了低成本、便携式和手持式OCT在翻译和研究方面的发展现状和应用。介绍了一般低成本OCT系统的设计和成本降低技术,包括基于光谱仪的检测、扫描光学、系统控制、信号处理和3D打印技术的作用。最后,回顾了低成本OCT的临床应用,并详细讨论了目前的局限性和前景。
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引用次数: 14
Scaffold-free and scaffold-based cellular strategies and opportunities for cornea tissue engineering 无支架和基于支架的细胞策略和角膜组织工程的机遇
Q1 ENGINEERING, BIOMEDICAL Pub Date : 2021-07-01 DOI: 10.1088/2516-1091/AC12D7
Z. Hussain, R. Pei
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引用次数: 6
Advances on gradient scaffolds for osteochondral tissue engineering 骨软骨组织工程梯度支架的研究进展
Q1 ENGINEERING, BIOMEDICAL Pub Date : 2021-04-27 DOI: 10.1088/2516-1091/abfc2c
J. Oliveira, V. Ribeiro, R. Reis
The osteochondral (OC) tissue is one of the most hierarchical and complex structures known and it is composed by two main compartments of hyaline articular cartilage and subchondral bone. It exhibits unique cellular and molecular transitions from the cartilage to the bone layers. OC diseases such as osteoarthritis and traumatic lesions may affect the articular cartilage, calcified cartilage (interface region) and subchondral bone, thus posing great regenerative challenges. Tissue engineering (TE) principles can offer novel technologies and combinatorial approaches that can better recapitulate the biological OC challenges and complexity in terms of biochemical, mechanical, structural and metabolic gradients, and ultimately can provide biofunctional 3D scaffolds with high reproducibility, versatility and adaptability to each patient’s needs, as it occurs in OC tissue defects. The recent reports and future directions dealing with gradient scaffolds for OCTE strategies are overviewed herein. A special focus on clinical translation/regulatory approval is given.
骨软骨(OC)组织是已知的最具层次性和复杂性的结构之一,它由透明关节软骨和软骨下骨两个主要部分组成。它表现出从软骨层到骨层的独特的细胞和分子转变。骨关节炎和创伤性病变等OC疾病可能会影响关节软骨、钙化软骨(界面区)和软骨下骨,从而对再生提出巨大挑战。组织工程(TE)原理可以提供新的技术和组合方法,更好地概括生物OC在生物化学、机械、结构和代谢梯度方面的挑战和复杂性,并最终提供具有高再现性、多功能性和适应性的生物功能3D支架,以满足每个患者的需求,因为它发生在OC组织缺陷中。本文综述了OCTE策略梯度支架的最新报道和未来发展方向。特别关注临床翻译/监管审批。
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引用次数: 8
Hybrid nanomaterials-based biomedical phototheranostic platforms 基于混合纳米材料的生物医学光电治疗平台
Q1 ENGINEERING, BIOMEDICAL Pub Date : 2021-04-14 DOI: 10.1088/2516-1091/abf821
Jing Ye, Xiawei Dong, Hui Jiang, Yunzhu Chen, Chunhui Wu, Xuemei Wang
The new hybrid nanomaterials have unique nanoparticle surface modification or core characteristics, with two or more chemical, physical, and optical properties. They have shown more personalized application prospects in disease management and treatment, and can significantly improve the diagnosis and treatment of various diseases. This article reviews the synthesis methods and structural characteristics of a series of new hybrid nanomaterials recently produced, including metallic oxide-containing hybrid nanomaterials, biopolymers-containing hybrid nanomaterials and in situ biosynthesis of hybrid nanomaterials. We focus on applying various types of hybrid nanomaterials in magnetic resonance imaging, photoacoustic, fluorescence imaging, and computed tomography imaging technology. At the same time, it summarizes the therapeutic effects of theranostics, cancer immunotherapy, photomedicine, and photothermal therapy under the guidance of imaging diagnosis. Finally, we briefly analyze the challenges in biomedical applications by hybrid materials as a nano-platform for imaging diagnosis and treatment and provides suggestions for future research in this field.
新型杂化纳米材料具有独特的纳米颗粒表面修饰或核心特性,具有两种或两种以上的化学、物理和光学性质。它们在疾病管理和治疗中显示出更个性化的应用前景,可以显著提高各种疾病的诊断和治疗水平。本文综述了近年来新型杂化纳米材料的合成方法和结构特点,包括含金属氧化物的杂化纳米材料、含生物聚合物的杂化纳米材料和原位生物合成的杂化纳米材料。我们专注于各种类型的混合纳米材料在磁共振成像、光声成像、荧光成像和计算机断层成像技术中的应用。同时总结了影像学诊断指导下的肿瘤学、肿瘤免疫疗法、光电医学、光热疗法的治疗效果。最后,我们简要分析了混合材料作为纳米成像诊断和治疗平台在生物医学应用中的挑战,并对该领域的未来研究提出了建议。
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引用次数: 0
Machine learning in patient flow: a review. 病人流中的机器学习:综述。
Q1 ENGINEERING, BIOMEDICAL Pub Date : 2021-04-01 Epub Date: 2021-02-22 DOI: 10.1088/2516-1091/abddc5
Rasheed El-Bouri, Thomas Taylor, Alexey Youssef, Tingting Zhu, David A Clifton

This work is a review of the ways in which machine learning has been used in order to plan, improve or aid the problem of moving patients through healthcare services. We decompose the patient flow problem into four subcategories: prediction of demand on a healthcare institution, prediction of the demand and resource required to transfer patients from the emergency department to the hospital, prediction of potential resource required for the treatment and movement of inpatients and prediction of length-of-stay and discharge timing. We argue that there are benefits to both approaches of considering the healthcare institution as a whole as well as the patient by patient case and that ideally a combination of these would be best for improving patient flow through hospitals. We also argue that it is essential for there to be a shared dataset that will allow researchers to benchmark their algorithms on and thereby allow future researchers to build on that which has already been done. We conclude that machine learning for the improvement of patient flow is still a young field with very few papers tailor-making machine learning methods for the problem being considered. Future works should consider the need to transfer algorithms trained on a dataset to multiple hospitals and allowing for dynamic algorithms which will allow real-time decision-making to help clinical staff on the shop floor.

本研究综述了机器学习用于规划、改善或帮助解决病人在医疗服务中流动问题的方法。我们将患者流动问题分解为四个子类别:预测医疗机构的需求、预测将患者从急诊科转至医院所需的需求和资源、预测住院患者治疗和流动所需的潜在资源以及预测住院时间和出院时间。我们认为,将医疗机构作为一个整体来考虑以及根据病人的具体情况来考虑这两种方法都有好处,理想的情况是将这两种方法结合起来,以改善医院的病人流量。我们还认为,有必要建立一个共享数据集,让研究人员能够以其算法为基准,从而让未来的研究人员在已有的基础上更上一层楼。我们的结论是,用于改善患者流量的机器学习仍是一个年轻的领域,很少有论文针对所考虑的问题量身定制机器学习方法。未来的工作应考虑将在数据集上训练的算法转移到多家医院的需要,并允许采用动态算法,从而实现实时决策,为车间的临床人员提供帮助。
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引用次数: 0
Optical sensors for continuous glucose monitoring 用于连续血糖监测的光学传感器
Q1 ENGINEERING, BIOMEDICAL Pub Date : 2021-04-01 DOI: 10.1088/2516-1091/abe6f8
Ziyi Yu, N. Jiang, S. Kazarian, S. Tasoglu, A. Yetisen
For decades, diabetes mellitus has been of wide concern with its high global prevalence, resulting in increasing social and financial burdens for individuals, clinical systems and governments. Continuous glucose monitoring (CGM) has become a popular alternative to the portable finger-prick glucometers available in the market for the convenience of diabetic patients. Hence, it has attracted much interest in various glucose sensing technologies to develop novel glucose sensors with better performance and longer lifetime, especially non-invasive or minimally invasive glucose sensing. Effort has also been put into finding biocompatible materials for implantable applications to achieve effective in vivo CGM. Here, we review the state-of-the-art researches in the field of CGM. The currently commercially available CGM technologies have been analyzed and a summary is provided of the potential types of recently researched non-invasive glucose monitors. Furthermore, the challenges and advances towards implantable applications have also been introduced and discussed, especially the novel biocompatible hydrogel aimed at minimizing the adverse impact from foreign-body response. In addition, a large variety of promising glucose-sensing technologies under research have been reviewed, from traditional electrochemical-based glucose sensors to novel optical and other electrical glucose sensors. The recent development and achievement of the reviewed glucose sensing technologies are discussed, together with the market analysis in terms of the statistical data for the newly published patents in the related field. Thus, the promising direction for future work in this field could be concluded.
几十年来,糖尿病因其全球高患病率而受到广泛关注,给个人、临床系统和政府带来越来越大的社会和经济负担。连续血糖监测(CGM)已成为一种流行的替代便携式手指点刺血糖仪在市场上,为方便糖尿病患者。因此,开发性能更好、寿命更长的新型葡萄糖传感器,特别是无创或微创葡萄糖传感技术已引起人们对各种葡萄糖传感技术的关注。人们还努力寻找生物相容性材料用于植入式应用,以实现有效的体内CGM。本文对CGM领域的最新研究进展进行了综述。分析了目前市面上可用的CGM技术,并总结了最近研究的无创血糖监测仪的潜在类型。此外,还介绍和讨论了植入式应用的挑战和进展,特别是旨在减少异物反应不利影响的新型生物相容性水凝胶。此外,从传统的基于电化学的葡萄糖传感器到新型的光学和其他电葡萄糖传感器,各种有前途的葡萄糖传感技术正在研究中。综述了葡萄糖传感技术的最新进展和取得的成果,并对相关领域新发表专利的统计数据进行了市场分析。从而总结出该领域今后工作的有希望的方向。
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引用次数: 21
期刊
Progress in biomedical engineering (Bristol, England)
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