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COTiR: Molecular Communication Model for Synthetic Exosome-Based Tissue Regeneration COTiR:基于合成外泌体的组织再生分子交流模型。
IF 3.9 4区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2023-08-07 DOI: 10.1109/TNB.2023.3302773
Saswati Pal;Sudip Misra;Ranjan K. Mallik
Mesenchymal stem cell (MSC)-derived exosomes are recognized as an unparalleled therapy for tissue damage rendered by COVID-19 infection and subsequent hyper-inflammatory immune response. However, the natural targeting mechanism of exosomes is challenging to detect the damaged tissue over long diffusion distances efficiently. The coordinated movement of exosomes is desired for successful identification of target sites. In this work, we propose a molecular communication model, CoTiR, with a bio-inspired directional migration strategy (DMS) for guided propagation of exosomes to target the damaged tissues. The model includes directional propagation, reception, and regeneration of tissue. The proposed model has the potential to be used in designing efficient communication systems in the nanodomain. We compare the proposed model to the basic random propagation model and show the efficacy of our model regarding the detection of multiple targets and the detection time required. Simulation results indicate that the proposed model requires a shorter period of time for a similar number of exosomes to detect the targets compared to the basic random propagation model. Furthermore, the results reveal a 99.96% decrease in the collagen concentration in the absence of inflammatory cytokine molecules compared to the collagen concentration in the presence of inflammatory cytokine molecules.
间充质干细胞(MSC)衍生的外泌体被认为是治疗COVID-19感染和随后的高炎症免疫反应造成的组织损伤的一种无与伦比的疗法。然而,外泌体的天然靶向机制很难有效地检测到长距离扩散的受损组织。为了成功识别目标部位,我们需要外泌体的协调运动。在这项工作中,我们提出了一种分子通信模型 CoTiR,该模型具有生物启发的定向迁移策略(DMS),用于引导外泌体传播,以靶向受损组织。该模型包括定向传播、接收和组织再生。所提出的模型有望用于设计纳米领域的高效通信系统。我们将提出的模型与基本随机传播模型进行了比较,并展示了我们的模型在检测多个目标和所需检测时间方面的功效。仿真结果表明,与基本随机传播模型相比,提议的模型需要更短的时间来检测相似数量的外泌体目标。此外,结果显示,与存在炎性细胞因子分子时的胶原蛋白浓度相比,不存在炎性细胞因子分子时的胶原蛋白浓度降低了 99.96%。
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引用次数: 0
Ratio Shift Keying Modulation for Time-Varying Molecular Communication Channels 时变分子通信信道的比移键控调制。
IF 3.9 4区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2023-07-25 DOI: 10.1109/TNB.2023.3298600
M. Okan Araz;Ahmet R. Emirdagi;M. Serkan Kopuzlu;Murat Kuscu
Molecular Communications (MC) is a bio-inspired communication technique that uses molecules to encode and transfer information. Many efforts have been devoted to developing novel modulation techniques for MC based on various distinguishable characteristics of molecules, such as their concentrations or types. In this paper, we investigate a particular modulation scheme called Ratio Shift Keying (RSK), where the information is encoded in the concentration ratio of two different types of molecules. RSK modulation is hypothesized to enable accurate information transfer in dynamic MC scenarios where the time-varying channel characteristics affect both types of molecules equally. To validate this hypothesis, we first conduct an information-theoretical analysis of RSK modulation and derive the capacity of the end-to-end MC channel where the receiver estimates concentration ratio based on ligand-receptor binding statistics in an optimal or suboptimal manner. We then analyze the error performance of RSK modulation in a practical time-varying MC scenario, that is mobile MC, in which both the transmitter and the receiver undergo diffusion-based propagation. Our numerical and analytical results, obtained for varying levels of similarity between the ligand types used for ratio-encoding, and varying number of receptors, show that RSK can significantly outperform the most commonly considered MC modulation technique, concentration shift keying (CSK), in dynamic MC scenarios.
分子通信(MC)是一种利用分子编码和传输信息的生物启发通信技术。许多人致力于根据分子的各种可区分特性(如浓度或类型)为 MC 开发新型调制技术。在本文中,我们研究了一种名为 "比移键控(RSK)"的特殊调制方案,在这种方案中,信息以两种不同类型分子的浓度比进行编码。根据假设,RSK 调制能在动态 MC 场景中实现准确的信息传输,在这种场景中,时变信道特性对两种分子的影响相同。为了验证这一假设,我们首先对 RSK 调制进行了信息理论分析,并得出了端到端 MC 信道的容量,在这种信道中,接收器根据配体-受体结合统计数据以最优或次优方式估计浓度比。然后,我们分析了 RSK 调制在实际时变 MC 场景(即移动 MC)中的误差性能,在这种场景中,发射器和接收器都经历了基于扩散的传播。我们对用于比率编码的配体类型之间不同程度的相似性和不同数量的受体进行的数值和分析结果表明,在动态 MC 场景中,RSK 的性能明显优于最常用的 MC 调制技术--浓度偏移键控(CSK)。
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引用次数: 0
Multi-Level Residual Dual Attention Network for Major Cerebral Arteries Segmentation in MRA Toward Diagnosis of Cerebrovascular Disorders 多层残差双注意网络在脑血管疾病诊断中的脑主动脉MRA分割。
IF 3.9 4区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2023-07-24 DOI: 10.1109/TNB.2023.3298444
Subhash Chandra Pal;Dimitrios Toumpanakis;Johan Wikström;Chirag Kamal Ahuja;Robin Strand;Ashis Kumar Dhara
Segmentation of major brain vessels is very important for the diagnosis of cerebrovascular disorders and subsequent surgical planning. Vessel segmentation is an important preprocessing step for a wide range of algorithms for the automatic diagnosis or treatment of several vascular pathologies and as such, it is valuable to have a well-performing vascular segmentation pipeline. In this article, we propose an end-to-end multiscale residual dual attention deep neural network for resilient major brain vessel segmentation. In the proposed network, the encoder and decoder blocks of the U-Net are replaced with the multi-level atrous residual blocks to enhance the learning capability by increasing the receptive field to extract the various semantic coarse- and fine-grained features. Dual attention block is incorporated in the bottleneck to perform effective multiscale information fusion to obtain detailed structure of blood vessels. The methods were evaluated on the publicly available TubeTK data set. The proposed method outperforms the state-of-the-art techniques with dice of 0.79 on the whole-brain prediction. The statistical and visual assessments indicate that proposed network is robust to outliers and maintains higher consistency in vessel continuity than the traditional U-Net and its variations.
脑主要血管的分割对于脑血管疾病的诊断和随后的手术计划非常重要。血管分割是用于几种血管病理的自动诊断或治疗的各种算法的重要预处理步骤,因此,拥有一个性能良好的血管分割管道是很有价值的。在本文中,我们提出了一种端到端的多尺度残差双注意深度神经网络,用于弹性主脑血管分割。在所提出的网络中,U-Net的编码器和解码器块被多级atrous残差块取代,以通过增加感受野来提取各种语义粗粒度和细粒度特征来增强学习能力。在瓶颈中加入双注意力块,进行有效的多尺度信息融合,获得血管的详细结构。这些方法在公开的TubeTK数据集上进行了评估。所提出的方法在全脑预测方面优于最先进的技术,骰子为0.79。统计和视觉评估表明,与传统的U-Net及其变体相比,所提出的网络对异常值具有鲁棒性,并在血管连续性方面保持更高的一致性。
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引用次数: 0
A Novel Plasmonic Sensor Based on Dual-Channel D-Shaped Photonic Crystal Fiber for Enhanced Sensitivity in Simultaneous Detection of Different Analytes 基于双通道 D 形光子晶体光纤的新型等离子传感器,用于提高同时检测不同分析物的灵敏度。
IF 3.9 4区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2023-07-11 DOI: 10.1109/TNB.2023.3294330
J. Divya;S. Selvendran;A. Sivanantha Raja;Vamsi Borra
A dual-channel D-shaped photonic crystal fiber (PCF) based plasmonic sensor is proposed in this paper for the simultaneous detection of two different analytes using the surface plasmon resonance (SPR) technique. The sensor employs a 50 nm-thick layer of chemically stable gold on both cleaved surfaces of the PCF to induce the SPR effect. This configuration offers superior sensitivity and rapid response, making it highly effective for sensing applications. Numerical investigations are conducted using the finite element method (FEM). After optimizing the structural parameters, the sensor exhibits a maximum wavelength sensitivity of 10000 nm/RIU and an amplitude sensitivity of −216 RIU $^{-{1}}$ between the two channels. Additionally, each channel of the sensor exhibits its unique maximal wavelength and amplitude sensitivities for different refractive index (RI) ranges. Both channels demonstrate a maximal wavelength sensitivity of 6000 nm/RIU. In the RI range of 1.31-1.41, Channel 1 (Ch1) and Channel 2 (Ch2) achieved their maximum amplitude sensitivities of −85.39RIU $^{-{1}}$ and -304.52 RIU $^{-{1}}$ , respectively, with a resolution of ${5}times {10} ^{-{5}}$ . This sensor structure is noteworthy for its ability to measure both amplitude and wavelength sensitivity, providing enhanced performance characteristics suitable for various sensing purposes in chemical, biomedical, and industrial fields.
本文提出了一种基于 D 型光子晶体光纤 (PCF) 的双通道质子传感器,利用表面等离子体共振 (SPR) 技术同时检测两种不同的分析物。该传感器在 PCF 的两个裂开表面上都使用了 50 nm 厚的化学性质稳定的金层来诱导 SPR 效应。这种配置具有卓越的灵敏度和快速响应能力,因此在传感应用中非常有效。我们使用有限元法(FEM)进行了数值研究。优化结构参数后,传感器的最大波长灵敏度为 10000 nm/RIU,两个通道之间的振幅灵敏度为 -216 RIU -1 。此外,对于不同的折射率(RI)范围,传感器的每个通道都具有独特的最大波长和振幅灵敏度。两个通道的最大波长灵敏度均为 6000 nm/RIU。在 1.31-1.41 折射率范围内,通道 1 (Ch1) 和通道 2 (Ch2) 的最大振幅灵敏度分别为 -85.39RIU -1 和 -304.52RIU -1 ,分辨率为 5×10 -5。值得注意的是,这种传感器结构能够同时测量振幅和波长灵敏度,从而增强了性能特征,适用于化学、生物医学和工业领域的各种传感用途。
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引用次数: 0
Green Synthesis of pH-Responsive Metal–Organic Frameworks for Delivery of Diclofenac Sodium 用于递送双氯芬酸钠的 pH 响应性金属有机框架的绿色合成。
IF 3.9 4区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2023-07-10 DOI: 10.1109/TNB.2023.3289787
Hafezeh Nabipour;Sohrab Rohani
The current study developed a drug delivery system through the green chemistry-based synthesis of a biologically friendly metal-organic framework (bio-MOF) called Asp-Cu, which included copper ions and the environmentally friendly molecule L(+)-aspartic acid (Asp). For the first time, diclofenac sodium (DS) was loaded onto the synthesized bio-MOF simultaneously. The system’s efficiency was then improved by encapsulating it with sodium alginate (SA). FT-IR, SEM, BET, TGA, and XRD analyses confirmed that DS@Cu-ASP was successfully synthesized. DS@Asp-Cu was found to release the total load within 2 h when used with simulated stomach media. This challenge was overcome by coating DS@Cu-ASP with SA (SA@DS@Cu-ASP). SA@DS@Cu-ASP displayed limited drug release at pH 1.2, and a higher percentage of the drug was released at pH 6.8 and 7.4 due to the pH-responsive nature of SA. $Itextit {n vitro}$ cytotoxicity screening showed that SA@DS@Cu-ASP could be an appropriate biocompatible carrier with >90% cell viability. The on-command drug carrier was observed to be more applicable biocompatible with lower toxicity, as well as adequate loading properties and responsiveness, indicating its applicability as a feasible drug carrier with controlled release.
本研究通过基于绿色化学的方法合成了一种名为 Asp-Cu 的生物友好型金属有机框架(bio-MOF),其中包括铜离子和环境友好型分子 L(+)- 天冬氨酸(Asp),从而开发出一种药物输送系统。首次将双氯芬酸钠(DS)同时负载到合成的生物有机框架上。然后,通过用海藻酸钠(SA)对其进行封装,提高了该系统的效率。FT-IR、SEM、BET、TGA 和 XRD 分析证实,DS@Cu-ASP 已成功合成。在使用模拟胃介质时,DS@Asp-Cu 在 2 小时内释放了总负荷。通过在 DS@Cu-ASP 上涂覆 SA(SA@DS@Cu-ASP),克服了这一难题。在 pH 值为 1.2 时,SA@DS@Cu-ASP 的药物释放量有限,而在 pH 值为 6.8 和 7.4 时,由于 SA 的 pH 响应特性,药物释放量的比例较高。体外细胞毒性筛选表明,SA@DS@Cu-ASP 是一种合适的生物相容性载体,细胞存活率大于 90%。据观察,该药物载体具有更高的生物相容性、更低的毒性、足够的负载特性和响应性,表明其可作为一种可行的控释药物载体。
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引用次数: 0
Game-Theoretic Analysis of Fusion Rules Over Molecular Reporting Channels 分子报告渠道融合规则的博弈论分析。
IF 3.9 4区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2023-07-06 DOI: 10.1109/TNB.2023.3290609
Sunil Kumar;Prabhat Kumar Sharma;Manav R. Bhatnagar
This work adopts a game theoretic approach to analyze the behavior of transmitter nanomachines (TNMs) in a diffusive 3-dimensional (3-D) channel. In order to communicate the local observations about the region of interest (RoI) to a common supervisor nanomachine (SNM), TNMs transmit information-carrying molecules to SNM. For the production of information-carrying molecules, all the TNMs share the common food molecular budget (CFMB). The TNMs apply cooperative and greedy strategic efforts to get their share from the CFMB. In the cooperative case, all the TNMs communicate to SNM as a group, therefore they cooperatively consume the CFMB to increase the group outcome, whereas, in the greedy scenario, all TNMs decide to perform alone and thus greedily consume the CFMB to increase their individual outcomes. The performance is evaluated in terms of the average rate of success, the average probability of error, and the receiver operating characteristic (ROC) of RoI detection. The derived results are verified through Monte-Carlo and particle-based simulations (PBS).
这项研究采用博弈论方法分析了发射纳米机械(TNMs)在扩散三维(3-D)通道中的行为。为了将对感兴趣区域(RoI)的局部观察结果传递给一个共同的主管纳米机器(SNM),TNM 向 SNM 传递携带信息的分子。为了生产携带信息的分子,所有 TNM 共享共同的食物分子预算(CFMB)。TNM 采用合作和贪婪两种策略努力从 CFMB 中获取各自的份额。在合作情况下,所有 TNM 作为一个群体与 SNM 通信,因此它们合作消耗 CFMB 以增加群体成果;而在贪婪情况下,所有 TNM 决定单独行动,因此贪婪地消耗 CFMB 以增加它们的个体成果。通过平均成功率、平均错误概率和 RoI 检测的接收器操作特性 (ROC) 对性能进行了评估。得出的结果通过蒙特卡洛和粒子模拟(PBS)进行了验证。
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引用次数: 0
Molecular Beamforming for Actuation in Molecular Communication Networks 分子通信网络中的分子波束成形。
IF 3.9 4区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2023-07-04 DOI: 10.1109/TNB.2023.3292131
Joana Angjo;Ali E. Pusane;H. Birkan Yilmaz;Ertugrul Basar;Tuna Tugcu
The actuation accuracy of sensing tasks performed by molecular communication (MC) schemes is a very important metric. Reducing the effect of sensors fallibility can be achieved by improvements and advancements in the sensor and communication networks design. Inspired by the technique of beamforming used extensively in radio frequency communication systems, a novel molecular beamforming design is proposed in this paper. This design can find application in tasks related to actuation of nano machines in MC networks. The main idea behind the proposed scheme is that the utilization of more sensing nano machines in a network can increase the overall accuracy of that network. In other words, the probability of an actuation error reduces as the number of sensors that collectively take the actuation decision increases. In order to achieve this, several design procedures are proposed. Three different scenarios for the observation of the actuation error are investigated. For each case, the analytical background is provided and compared with the results obtained by computer simulations. The improvement in the actuation accuracy by means of molecular beamforming is verified for a uniform linear array as well as for a random topology.
分子通信(MC)方案所执行的传感任务的执行精度是一个非常重要的指标。传感器和通信网络设计的改进和进步可以降低传感器易损性的影响。受射频通信系统中广泛使用的波束成形技术的启发,本文提出了一种新型分子波束成形设计。这种设计可应用于 MC 网络中与纳米机器驱动相关的任务。建议方案背后的主要理念是,在网络中利用更多的传感纳米机器可以提高该网络的整体精度。换句话说,随着共同做出执行决策的传感器数量增加,执行错误的概率也会降低。为此,我们提出了几种设计程序。本文研究了观察致动误差的三种不同情况。针对每种情况,都提供了分析背景,并与计算机模拟获得的结果进行了比较。对于均匀线性阵列和随机拓扑结构,通过分子波束成形技术提高致动精度的效果得到了验证。
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引用次数: 0
Microfluidic Point-of-Care Diagnostics for Multi-Disease Detection Using Optical Techniques: A Review 利用光学技术进行多种疾病检测的微流控医疗点诊断:综述。
IF 3.9 4区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2023-07-03 DOI: 10.1109/TNB.2023.3291544
Shaik Ahmadsaidulu;Oindrila Banik;Prasoon Kumar;Santosh Kumar;Earu Banoth
The lifestyle of modern society is a major contributing factor for the majority of patients suffering from more than one disease. To Screen and diagnose each of those diseases, there is a great need for portable, and economical diagnostic tools, which are highly stipulated to yield rapid and accurate results using a small volume of the samples such as blood, saliva, sweat, etc. Point-of-care Testing (POCT) is one of the approaches to harvest prompt diagnosis of numerous diseases. The Majority of Point-of-Care Devices (POCD) are developed to diagnose one disease within the specimen. On the other hand, multi-disease detection capabilities in the same point-of-care devices are considered to be an efficient candidate to execute the state-of-the-art platform for multi-disease detection. Most of the literature reviews in this field focus on Point-of-Care (POC) devices, their underlying principles of operation, and their potential applications. It is evident from a perusal of the scholarly works that no review articles have been written on multi-disease detection POC devices. A review study analyzing the current level and functionality of multi-disease detection POC devices would be of great use to future researchers and device manufacturers. This review paper is addressing the above gap by focusing on various optical techniques like fluorescence, Absorbance, and Surface Plasmon Resonance (SPR) for multi-disease detection by harnessing the microfluidic-based POC device.
现代社会的生活方式是导致大多数患者罹患一种以上疾病的主要因素。为了筛查和诊断每一种疾病,我们亟需便携、经济的诊断工具,这些工具只需少量样本,如血液、唾液、汗液等,就能快速、准确地得出结果。床旁检测(POCT)是迅速诊断多种疾病的方法之一。大多数护理点设备(POCD)是为诊断标本中的一种疾病而开发的。另一方面,同一护理点设备的多疾病检测功能被认为是执行多疾病检测先进平台的有效候选方案。该领域的大多数文献综述都侧重于护理点(POC)设备、其基本工作原理及其潜在应用。从学术著作中可以明显看出,还没有关于多疾病检测 POC 设备的综述文章。对多种疾病检测 POC 设备的现有水平和功能进行综述分析,对未来的研究人员和设备制造商大有裨益。本综述论文针对上述空白,重点介绍了利用微流体 POC 设备进行多种疾病检测的各种光学技术,如荧光、吸光和表面等离子体共振 (SPR)。
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引用次数: 0
IEEE Transactions on NanoBioscience Publication Information IEEE纳米生物科学学报
IF 3.9 4区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2023-06-29 DOI: 10.1109/TNB.2023.3283631
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引用次数: 0
IEEE Transactions on NanoBioscience Information for Authors IEEE纳米生物科学信息汇刊
IF 3.9 4区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2023-06-29 DOI: 10.1109/TNB.2023.3283635
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引用次数: 0
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