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Endothelial Cell Adhesion Molecules- (un)Attainable Targets for Nanomedicines 内皮细胞粘附分子-纳米药物(无法)达到的目标
Q3 ENGINEERING, BIOMEDICAL Pub Date : 2022-04-07 DOI: 10.3389/fmedt.2022.846065
N. Milosevic, M. Rütter, A. David
Endothelial cell adhesion molecules have long been proposed as promising targets in many pathologies. Despite promising preclinical data, several efforts to develop small molecule inhibitors or monoclonal antibodies (mAbs) against cell adhesion molecules (CAMs) ended in clinical-stage failure. In parallel, many well-validated approaches for targeting CAMs with nanomedicine (NM) were reported over the years. A wide range of potential applications has been demonstrated in various preclinical studies, from drug delivery to the tumor vasculature, imaging of the inflamed endothelium, or blocking immune cells infiltration. However, no NM drug candidate emerged further into clinical development. In this review, we will summarize the most advanced examples of CAM-targeted NMs and juxtapose them with known traditional drugs against CAMs, in an attempt to identify important translational hurdles. Most importantly, we will summarize the proposed strategies to enhance endothelial CAM targeting by NMs, in an attempt to offer a catalog of tools for further development.
内皮细胞粘附分子长期以来被认为是许多病理的有希望的靶点。尽管有很好的临床前数据,但开发抗细胞粘附分子(CAMs)的小分子抑制剂或单克隆抗体(mab)的一些努力以临床阶段失败告终。与此同时,近年来也报道了许多经过验证的纳米药物靶向cam的方法。广泛的潜在应用已经在各种临床前研究中得到证明,从药物输送到肿瘤血管,炎症内皮的成像,或阻断免疫细胞浸润。然而,没有任何NM候选药物进一步进入临床开发。在这篇综述中,我们将总结针对cam的最先进的NMs的例子,并将它们与已知的针对cam的传统药物并列,试图找出重要的转化障碍。最重要的是,我们将总结提出的策略,以增强内皮CAM靶向NMs,试图提供一个工具目录,以进一步发展。
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引用次数: 4
In silico Effects of Synaptic Connections in the Visual Thalamocortical Pathway 视觉丘脑皮质通路突触连接的计算机效应
Q3 ENGINEERING, BIOMEDICAL Pub Date : 2022-04-05 DOI: 10.3389/fmedt.2022.856412
Swapna Sasi, Basabdatta Sen Bhattacharya
We have studied brain connectivity using a biologically inspired in silico model of the visual pathway consisting of the lateral geniculate nucleus (LGN) of the thalamus, and layers 4 and 6 of the primary visual cortex. The connectivity parameters in the model are informed by the existing anatomical parameters from mammals and rodents. In the base state, the LGN and layer 6 populations in the model oscillate with dominant alpha frequency, while the layer 4 oscillates in the theta band. By changing intra-cortical hyperparameters, specifically inhibition from layer 6 to layer 4, we demonstrate a transition to alpha mode for all the populations. Furthermore, by increasing the feedforward connectivities in the thalamo-cortico-thalamic loop, we could transition into the beta band for all the populations. On looking closely, we observed that the origin of this beta band is in the layer 6 (infragranular layers); lesioning the thalamic feedback from layer 6 removed the beta from the LGN and the layer 4. This agrees with existing physiological studies where it is shown that beta rhythm is generated in the infragranular layers. Lastly, we present a case study to demonstrate a neurological condition in the model. By changing connectivities in the network, we could simulate the condition of significant (P < 0.001) decrease in beta band power and a simultaneous increase in the theta band power, similar to that observed in Schizophrenia patients. Overall, we have shown that the connectivity changes in a simple visual thalamocortical in silico model can simulate state changes in the brain corresponding to both health and disease conditions.
我们已经研究了大脑连接使用一个生物学启发的视觉通路的计算机模型,该模型由丘脑的外侧膝状核(LGN)和初级视觉皮层的第4层和第6层组成。模型中的连通性参数由哺乳动物和啮齿动物的现有解剖参数提供。在基本状态下,模型中的LGN和第6层种群以α频带为主振荡,而第4层在θ频带振荡。通过改变皮质内高参数,特别是从第6层到第4层的抑制,我们证明了所有种群都向α模式过渡。此外,通过增加丘脑-皮质-丘脑回路的前馈连接,我们可以在所有人群中过渡到β波段。通过仔细观察,我们观察到这个β带的起源在第6层(小颗粒层);从第6层的丘脑反馈中删除了LGN和第4层的β。这与现有的生理学研究一致,研究表明β节律是在小颗粒层中产生的。最后,我们提出了一个案例研究,以证明在模型神经条件。通过改变网络中的连接,我们可以模拟出β波段功率显著(P < 0.001)下降而θ波段功率同时增加的情况,类似于在精神分裂症患者中观察到的情况。总的来说,我们已经证明,在一个简单的视觉丘脑皮质计算机模型中,连接的变化可以模拟大脑中与健康和疾病状况相对应的状态变化。
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引用次数: 0
Preliminary Analysis of Burn Degree Using Non-invasive Microwave Spiral Resonator Sensor for Clinical Applications 无创微波螺旋谐振器传感器在烧伤程度检测中的临床应用初步分析
Q3 ENGINEERING, BIOMEDICAL Pub Date : 2022-04-05 DOI: 10.3389/fmedt.2022.859498
P. Rangaiah, Bappaditya Mandal, E. Avetisyan, A. Chezhian, B. Augustine, M. Pérez, Robin Augustine
The European “Senseburn” project aims to develop a smart, portable, non-invasive microwave early effective diagnostic tool to assess the depth(d) and degree of burn. The objective of the work is to design and develop a convenient non-invasive microwave sensor for the analysis of the burn degree on burnt human skin. The flexible and biocompatible microwave sensor is developed using a magnetically coupled loop probe with a spiral resonator (SR). The sensor is realized with precise knowledge of the lumped element characteristics (resistor (R), an inductor (L), and a capacitor (C) RLC parameters). The estimated electrical equivalent circuit technique relies on a rigorous method enabling a comprehensive characterization of the sensor (loop probe and SR). The microwave resonator sensor with high quality factor (Q) is simulated using a CST studio suite, AWR microwave office, and fabricated on the RO 3003 substrate with a standard thickness of 0.13 mm. The sensor is prepared based on the change in dielectric property variation in the burnt skin. The sensor can detect a range of permittivity variations (εr 3–38). The sensor is showing a good response in changing resonance frequency between 1.5 and 1.71 GHz for (εr 3 to 38). The sensor is encapsulated with PDMS for the biocompatible property. The dimension of the sensor element is length (L) = 39 mm, width (W) = 34 mm, and thickness (T) = 1.4 mm. The software algorithm is prepared to automate the process of burn analysis. The proposed electromagnetic (EM) resonator based sensor provides a non-invasive technique to assess burn degree by monitoring the changes in resonance frequency. Most of the results are based on numerical simulation. We propose the unique circuit set up and the sensor device based on the information generated from the simulation in this article. The clinical validation of the sensor will be in our future work, where we will understand closely the practical functioning of the sensor based on burn degrees. The senseburn system is designed to support doctors to gather vital info of the injuries wirelessly and hence provide efficient treatment for burn victims, thus saving lives.
欧洲“Senseburn”项目旨在开发一种智能、便携、无创的微波早期有效诊断工具,以评估烧伤的深度和程度。本工作的目的是设计和开发一种方便的无创微波传感器,用于分析烧伤人体皮肤的烧伤程度。采用带螺旋谐振器(SR)的磁耦合环探头,研制了柔性的生物相容性微波传感器。该传感器是通过精确了解集总元件特性(电阻(R),电感(L)和电容(C) RLC参数)来实现的。估计等效电路技术依赖于一种严格的方法,能够全面表征传感器(环路探头和SR)。采用CST studio suite, AWR microwave office对具有高品质因子(Q)的微波谐振器传感器进行了仿真,并在标准厚度为0.13 mm的RO 3003衬底上制作。该传感器是根据烧伤皮肤的介电特性变化来制备的。该传感器可检测介电常数变化范围(εr 3-38)。在(εr 3 ~ 38)的1.5 ~ 1.71 GHz范围内,传感器的响应良好。该传感器采用PDMS封装,具有生物相容性。传感器元件的尺寸为长(L) = 39mm,宽(W) = 34mm,厚(T) = 1.4 mm。软件算法是准备自动化过程烧伤分析。所提出的基于电磁谐振器的传感器提供了一种非侵入性技术,通过监测谐振频率的变化来评估烧伤程度。大多数结果是基于数值模拟的。本文根据仿真产生的信息,提出了独特的电路设置和传感器装置。传感器的临床验证将在我们未来的工作中进行,在那里我们将密切了解基于烧伤程度的传感器的实际功能。senseburn系统旨在支持医生无线收集受伤的重要信息,从而为烧伤患者提供有效的治疗,从而挽救生命。
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引用次数: 3
Effect of Patent Expiry on the Performance of Innovator Multinational Pharmaceutical Companies in a Low Middle Income Country 中低收入国家专利到期对创新型跨国制药公司绩效的影响
Q3 ENGINEERING, BIOMEDICAL Pub Date : 2022-04-04 DOI: 10.3389/fmedt.2022.783460
Farrukh Khalil, J. Onyango
Patent expiry or loss of exclusivity exposes innovator pharmaceutical companies to changes in the market dynamics brought about by increased production of generics by rival companies after patent expiration. This current study focused on the effect of generic products manufacturing and competitive market pressures, price changes, and changes in sales volumes and profitability of innovator multinational pharmaceutical companies after patent expiry. The methodology of this study involved a descriptive survey design and utilized both qualitative and quantitative techniques for data collection, analysis, and presentation. Primary data were collected using the key informants' in-depth interviews and survey questionnaires. The top management, including regional managers, general managers, and directors of each of the eight companies participating in this study, were interviewed to gather the qualitative data. Thirty-six respondents comprising of Product Development Managers and Business Supervising Managers responded to a survey questionnaire through purposive sampling. Findings depicted a significant effect of patent expiry on the generic production and subsequent decline in the performance of multinational innovator companies in the pharmaceutical industry. This study recommends that multinational innovator companies operating in low-income countries, such as Kenya, develop strategic policies to tap into the market by leveraging generic production through collaborative manufacturing with generic companies to share revenues.
专利到期或排他性的丧失使创新制药公司面临竞争对手在专利到期后增加仿制药生产所带来的市场动态变化。本研究主要关注仿制药生产和竞争市场压力、价格变化以及创新跨国制药公司在专利到期后销量和盈利能力的变化的影响。本研究的方法包括描述性调查设计,并利用定性和定量技术进行数据收集、分析和呈现。主要数据的收集采用了对关键信息者的深度访谈和调查问卷。对参与本研究的八家公司的高层管理人员,包括区域经理、总经理和董事进行了访谈,以收集定性数据。由产品开发经理和业务监督经理组成的36名受访者通过有目的抽样的方式回答了一份调查问卷。研究结果表明,专利到期对制药行业跨国创新公司的仿制药生产和随后的业绩下降有显著影响。本研究建议,在肯尼亚等低收入国家运营的跨国创新公司制定战略政策,通过与仿制药公司合作制造来利用仿制药生产来分享收入,从而进入市场。
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引用次数: 1
Crossing Total Occlusions Using a Hydraulic Pressure Wave: Development of the Wave Catheter 用液压波穿越全闭塞:波导管的发展
Q3 ENGINEERING, BIOMEDICAL Pub Date : 2022-04-01 DOI: 10.3389/fmedt.2022.851927
A. Sakes, Menno Lageweg, R. van Starkenburg, Saurabh Sontakke, J. Spronck
With the ongoing miniaturization of surgical instruments, the ability to apply large forces on tissues for resection becomes challenging and the risk of buckling becomes more real. In an effort to allow for high force application in slender instruments, in this study, we have investigated using a hydraulic pressure wave (COMSOL model) and developed an innovative 5F cardiac catheter (L = 1,000 mm) that allows for applying high forces up to 9.0 ± 0.2 N on target tissues without buckling. The catheter uses high-speed pressure waves to transfer high-force impulses through a slender flexible shaft consisted of a flat wire coil, a double braid, and a nylon outer coating. The handle allows for single-handed operation of the catheter with easy adjusting of the input impulse characteristic, including frequency (1–10 Hz), time and number of strokes using a solenoid actuator, and easy connection of an off-the-shelf inflator for catheter filling. In a proof-of-principle experiment, we illustrated that the Wave catheter was able to penetrate a phantom model of a coronary Chronic Total Occlusion (CTO) manufactured out of hydroxyapatite and gelatin. It was found that the time until puncture decreased from 80 ± 5.4 s to 7.8 ± 0.4 s, for a stroke frequency of 1–10 Hz, respectively. The number of strikes until puncture was approximately constant at 80 ± 5.4, 76.7 ± 2.6, and 77.7 ± 3.9 for the different stroke frequencies. With the development of the Wave catheter, first steps have been made toward high force application through slender shafts.
随着手术器械的不断小型化,在组织上施加大的力进行切除的能力变得具有挑战性,屈曲的风险变得更加真实。为了在细长的器械上施加大的力,在这项研究中,我们研究了使用液压波(COMSOL模型)并开发了一种创新的5F心导管(L = 1,000 mm),它允许在目标组织上施加高达9.0±0.2 N的大力而不会弯曲。导管使用高速压力波通过一个细长的柔性轴传递高强度脉冲,该轴由一个扁平的线圈、一个双编织带和一个尼龙外层组成。手柄允许单手操作导管,易于调整输入脉冲特性,包括频率(1-10 Hz),使用电磁致动器的时间和笔划次数,以及易于连接用于导管填充的现成充气机。在一个原理验证实验中,我们证明了Wave导管能够穿透由羟基磷灰石和明胶制成的冠状动脉慢性完全闭塞(CTO)的幻影模型。结果表明,在1 ~ 10 Hz行程频率下,穿刺时间由80±5.4 s缩短至7.8±0.4 s。在不同的冲程频率下,直到穿刺的撞击次数大致恒定在80±5.4,76.7±2.6和77.7±3.9。随着波导管的发展,通过细长轴向高力应用迈出了第一步。
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引用次数: 0
A Novel Laser Energy Ablation Catheter for Endocardial Cavo-Tricuspid Isthmus Ablation and Epicardial Ventricular Lesion Formation: An in vivo Proof-of-Concept Study 一种用于心内膜腔-三尖瓣峡部消融和心外膜心室病变形成的新型激光能量消融导管:一项体内概念验证研究
Q3 ENGINEERING, BIOMEDICAL Pub Date : 2022-03-21 DOI: 10.3389/fmedt.2022.834856
D. Krist, D. Linz, U. Schotten, S. Zeemering, Dwayne Leenen
Aim This proof-of-concept study aimed to investigate atrial and ventricular lesion formation by a 20-mm linear laser ablation catheter, regarding lesion depth and tissue damage. Methods In total, 6 female swines underwent standard femoral vein access to introduce a novel 20-mm linear laser ablation catheter in the right atrium to perform endocardial cavotricuspid isthmus (CTI) ablations. The navigation took place under fluoroscopy with additional visualization by intracardiac echocardiograph. Via a sternotomy, epicardial ablations were performed on the surface of the left ventricle (LV), right ventricle (RV), and right atrial appendage (RAA). Procedural safety was assessed by registration of intraprocedural adverse events and by macroscopic examination of the excised hearts for the presence of charring or tissue disruption at the lesion site. Results Altogether 39 lesions were created, including 8 endocardial CTI (mean lesion length 20.6 ± 1.65 mm), 26 epicardial ventricle (mean lesion length LV: 25.3 ± 1.35 mm, RV: 24.9 ± 2.40 mm), and 5 epicardial appendage ablations (mean lesion length RAA: 26.0 ± 3.16 mm). Transmurality was achieved in all CTI and atrial appendage ablations, in 62% of the RV ablations and in none of the LV ablations. No perforation or steam pop occurred, and no animal died during the procedure. Conclusion In this porcine study, the 20-mm linear laser ablation catheter has shown excellent results for endocardial cavotricuspid isthmus ablation, and it resulted in acceptable lesion depth during atrial and ventricular epicardial ablation. The absence of tissue charring, steam pops, or microbubbles under the experimental conditions suggests a high degree of procedural safety.
目的:本概念验证研究旨在探讨20毫米线性激光消融导管对心房和心室病变形成的影响,包括病变深度和组织损伤。方法6头母猪经标准股静脉入路,在右心房置入新型20mm线性激光消融导管,行心内膜腔尖峡部(CTI)消融。导航在x线透视下进行,并通过心内超声心动图进行额外的可视化。经胸骨切开,在左心室(LV)、右心室(RV)和右心房附件(RAA)表面进行心外膜消融。通过登记术中不良事件和对切除的心脏进行宏观检查以确定病变部位是否存在炭化或组织破坏来评估手术安全性。结果共形成39个病灶,其中心内膜CTI 8个(平均病灶长度20.6±1.65 mm),心外膜室26个(平均病灶长度LV: 25.3±1.35 mm, RV: 24.9±2.40 mm),心外膜附件消融5个(平均病灶长度RAA: 26.0±3.16 mm)。所有CTI和心房附件消融均实现了透性,62%的右心室消融和左心室消融均未实现。没有穿孔或蒸汽爆裂发生,也没有动物在手术过程中死亡。结论在猪的研究中,20mm线性激光消融导管对心内膜腔三尖瓣峡部的消融有很好的效果,在心房和心室心外膜消融时病灶深度可接受。在实验条件下,没有组织炭化,蒸汽爆裂或微气泡表明高度的程序安全性。
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引用次数: 0
Improvement of Mesenchymal Stromal Cell Proliferation and Differentiation via Decellularized Extracellular Matrix on Substrates With a Range of Surface Chemistries 在一系列表面化学的基质上通过脱细胞细胞外基质改善间充质间质细胞增殖和分化
Q3 ENGINEERING, BIOMEDICAL Pub Date : 2022-03-17 DOI: 10.3389/fmedt.2022.834123
Michael C. Yang, A. O’Connor, B. Kalionis, D. Heath
Decellularized extracellular matrix (dECM) deposited by mesenchymal stromal cells (MSCs) has emerged as a promising substrate for improved expansion of MSCs. To date, essentially all studies that have produced dECM for MSC expansion have done so on tissue culture plastic or glass. However, substrate surface chemistry has a profound impact on the adsorption of proteins that mediate cell-material interactions, and different surface chemistries can cause changes in cell behavior, ECM deposition, and the in vivo response to a material. This study tested the hypothesis that substrate surface chemistry impacts the deposition of ECM and its subsequent bioactivity. This hypothesis was tested by producing glass surfaces with various surface chemistries (amine, carboxylic acid, propyl, and octyl groups) using silane chemistry. ECM was deposited by an immortalized MSC line, decellularized, and characterized through SDS-PAGE and immunofluorescence microscopy. No significant difference was observed in dECM composition or microarchitecture on the different surfaces. The decellularized surfaces were seeded with primary MSCs and their proliferation and differentiation were assessed. The presence of dECM improved the proliferation of primary MSCs by ~100% in comparison to surface chemistry controls. Additionally, the adipogenesis increased by 50–90% on all dECM surfaces in comparison to surface chemistry controls, and the osteogenesis increased by ~50% on the octyl-modified surfaces when dECM was present. However, no statistically significant differences were observed within the set of dECM surfaces or control surfaces. These results support the null hypothesis, meaning surface chemistry (over the range tested in this work) is not a key regulator of the composition or bioactivity of MSC-derived dECM. These results are significant because they provide an important insight into regenerative engineering technologies. Specifically, the utilization of dECM in stem cell manufacturing and tissue engineering applications would require the dECM to be produced on a wide variety of substrates. This work indicates that it can be produced on materials with a range of surface chemistries without undesired changes in the bioactivity of the dECM.
间充质间质细胞(MSCs)沉积的脱细胞外基质(dECM)已成为一种有希望改善MSCs扩增的底物。到目前为止,基本上所有的研究都是在组织培养塑料或玻璃上进行的。然而,底物表面化学对介导细胞-物质相互作用的蛋白质的吸附有深远的影响,不同的表面化学可以引起细胞行为、ECM沉积和对物质的体内反应的变化。本研究验证了底物表面化学影响ECM沉积及其随后生物活性的假设。通过使用硅烷化学生产具有不同表面化学成分(胺、羧酸、丙基和辛基)的玻璃表面,验证了这一假设。ECM通过永生化间充质细胞系沉积,脱细胞,并通过SDS-PAGE和免疫荧光显微镜进行表征。不同表面的dECM组成和微结构无显著差异。在脱细胞表面播种原代MSCs,观察其增殖和分化情况。与表面化学对照相比,dECM的存在使原代MSCs的增殖提高了~100%。此外,与表面化学对照相比,所有dECM表面的脂肪生成增加了50-90%,当dECM存在时,辛基修饰表面的成骨增加了~50%。然而,在一组dECM表面或对照表面内,没有观察到统计学上的显著差异。这些结果支持零假设,这意味着表面化学(在本工作测试的范围内)不是msc衍生的dECM的组成或生物活性的关键调节因子。这些结果意义重大,因为它们为再生工程技术提供了重要的见解。具体来说,在干细胞制造和组织工程应用中使用dECM将需要在各种各样的基质上生产dECM。这项工作表明,它可以在具有一系列表面化学物质的材料上生产,而不会改变dECM的生物活性。
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引用次数: 1
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
期刊
Frontiers in medical technology
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