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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 Engineering Pub Date : 2023-06-29 DOI: 10.1109/TNB.2023.3283635
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引用次数: 0
Biosynthesis of Gold Nanoparticles Using Quince Seed Water Extract and Investigation of Their Anticancer Effect Against Cancer Cell Lines 利用榅桲籽水提取物生物合成金纳米粒子并研究其对癌症细胞株的抗癌效果
IF 3.9 4区 生物学 Q1 Engineering Pub Date : 2023-06-28 DOI: 10.1109/TNB.2023.3287805
Mohammad Reza Ahmadpour;Mahdi Yousefi;Hassan Rakhshandeh;Majid Darroudi;Seyed Hadi Mousavi;Mohammad Soukhtanloo;Zahra Sabouri;Vahid Reza Askari;Alireza Hashemzadeh;Mohammad Azad Manjiri;Malihe Motavasselian
In this study, gold nanoparticles (Au-NPs) were synthesized using HAuCl4 and quince seed mucilage (QSM) extract, which was characterized by conventional methods including Fourier transforms electron microscopy (FTIR), UV-Visible spectroscopy (UV-Vis), Field emission electron microscopy (FESEM), Transmission electron microscopy (TEM), Dynamic light spectroscopy (DLS), and Zeta-potential. The QSM acted as reductant and stabilizing agents simultaneously. The NP’s anticancer activity was also investigated against osteosarcoma cell lines (MG-63), which showed an IC50 of $317 mu text{g}$ /mL.
本研究使用 HAuCl4 和榅桲籽粘液(QSM)提取物合成了金纳米粒子(Au-NPs),并通过傅立叶变换电子显微镜(FTIR)、紫外可见光谱(UV-Vis)、场发射电子显微镜(FESEM)、透射电子显微镜(TEM)、动态光光谱(DLS)和 Zeta 电位等传统方法对其进行了表征。QSM 同时起到还原剂和稳定剂的作用。还研究了 NP 对骨肉瘤细胞株 (MG-63) 的抗癌活性,结果显示其 IC50 为 [式中:见正文]/mL。
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引用次数: 0
Optimization of Extracellular Vesicle Release for Targeted Drug Delivery 优化细胞外囊泡释放,实现靶向给药。
IF 3.9 4区 生物学 Q1 Engineering Pub Date : 2023-06-19 DOI: 10.1109/TNB.2023.3287637
Martin Damrath;Mladen Veletić;Hamid Khoshfekr Rudsari;Ilangko Balasingham
Targeted drug delivery is a promising approach for many serious diseases, such as glioblastoma multiforme, one of the most common and devastating brain tumor. In this context, this work addresses the optimization of the controlled release of drugs which are carried by extracellular vesicles. Towards this goal, we derive and numerically verify an analytical solution for the end-to-end system model. We then apply the analytical solution either to reduce the disease treatment time or to reduce the amount of required drugs. The latter is formulated as a bilevel optimization problem, whose quasiconvex/quasiconcave property is proved here. For solving the optimization problem, we propose and utilize a combination of bisection method and golden-section search. The numerical results demonstrate that the optimization can significantly reduce the treatment time and/or the required drugs carried by extracellular vesicles for a therapy compared to the steady state solution.
靶向给药是治疗许多严重疾病(如多形性胶质母细胞瘤,一种最常见、最具破坏性的脑肿瘤)的一种前景广阔的方法。在此背景下,本研究致力于优化由细胞外囊泡携带的药物的控制释放。为此,我们推导出端到端系统模型的解析解,并进行了数值验证。然后,我们应用分析解来缩短疾病治疗时间或减少所需药物量。后者被表述为一个双层优化问题,其准凸/准凹特性在此得到了证明。为解决该优化问题,我们提出并使用了分段法和黄金分割搜索相结合的方法。数值结果表明,与稳态方案相比,优化方案能显著缩短治疗时间和/或减少治疗所需的细胞外囊泡携带的药物。
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引用次数: 0
Review of Physical Layer Security in Molecular Internet of Nano-Things 纳米物联网中的物理层安全回顾。
IF 3.9 4区 生物学 Q1 Engineering Pub Date : 2023-06-14 DOI: 10.1109/TNB.2023.3285973
Song Qiu;Zhuangkun Wei;Yu Huang;Mahmoud Abbaszadeh;Jerome Charmet;Bin Li;Weisi Guo
Molecular networking has been identified as a key enabling technology for Internet-of-Nano-Things (IoNT): microscopic devices that can monitor, process information, and take action in a wide range of medical applications. As the research matures into prototypes, the cybersecurity challenges of molecular networking are now being researched on at both the cryptographic and physical layer level. Due to the limited computation capabilities of IoNT devices, physical layer security (PLS) is of particular interest. As PLS leverages on channel physics and physical signal attributes, the fact that molecular signals differ significantly from radio frequency signals and propagation means new signal processing methods and hardware is needed. Here, we review new vectors of attack and new methods of PLS, focusing on 3 areas: (1) information theoretical secrecy bounds for molecular communications, (2) key-less steering and decentralized key-based PLS methods, and (3) new methods of achieving encoding and encryption through bio-molecular compounds. The review will also include prototype demonstrations from our own lab that will inform future research and related standardization efforts.
分子网络已被确定为纳米物联网(IoNT)的一项关键使能技术:可在广泛的医疗应用中监测、处理信息并采取行动的微型设备。随着原型研究的成熟,目前正在密码层和物理层研究分子网络的网络安全挑战。由于物联网设备的计算能力有限,物理层安全(PLS)尤其引人关注。由于物理层安全利用信道物理和物理信号属性,分子信号与射频信号和传播有很大不同,这意味着需要新的信号处理方法和硬件。在此,我们将回顾新的攻击载体和新的 PLS 方法,重点关注 3 个领域:(1) 分子通信的信息理论保密边界;(2) 无密钥转向和基于分散密钥的 PLS 方法;(3) 通过生物分子化合物实现编码和加密的新方法。综述还将包括我们自己实验室的原型演示,这些演示将为未来的研究和相关标准化工作提供参考。
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引用次数: 1
Multi-Disease Detection Using a Prism-Based Surface Plasmon Resonance Sensor: A TMM and FEM Approach 使用棱镜式表面等离子体共振传感器检测多种疾病:TMM 和有限元方法
IF 3.9 4区 生物学 Q1 Engineering Pub Date : 2023-06-14 DOI: 10.1109/TNB.2023.3286269
Rabeya Bosrin Rumi;Alok Kumar Paul;Salem A. Alyami;Mohammad Ali Moni
This research introduces a surface plasmon resonance (SPR)-based biosensor with multilayered structures for telecommunication wavelength in order to detect multiple diseases. The malaria and the chikungunya viruses are taken into account and the presence of these viruses are determined by examining several blood components in healthy and affected phases. Here, two distinct configurations (Al-BTO-Al-MoS2 and Cu-BTO-Cu-MoS2) are proposed and contrasted for the detection of numerous viruses. The performance characteristics of this work have been analyzed using Transfer Matrix Method (TMM) method and Finite Element Method (FEM) method under angle interrogation technique. From the TMM and FEM solutions, it is evident that the Al-BTO-Al-MoS2 structure provides the highest sensitivities of ~270 deg./RIU for malaria and ~262 deg./RIU for chikungunya viruses, with satisfactory detection accuracy of ~1.10 for malaria, ~1.64 for chikungunya, and quality factor of ~204.40 for malaria, ~208.20 for chikungunya. In addition, the Cu-BTO-Cu MoS2 structure offers the highest sensitivities of ~310 deg./RIU for malaria and ~298 deg./RIU for chikungunya, with satisfactory detection accuracy of ~0.40 for malaria, ~0.58 for chikungunya, and quality factor of ~89.85 for malaria, ~86.38 for chikungunya viruses. Therefore, the performance of the proposed sensors is analyzed using two distinct methods and gives around similar results. In a sum, this research could be utilized as a theoretical foundation and first step in the development of a real sensor.
本研究介绍了一种基于表面等离子体共振(SPR)的生物传感器,该传感器具有多层结构,可用于电信波长,以检测多种疾病。研究考虑了疟疾和基孔肯雅病毒,并通过检测健康和患病阶段的几种血液成分来确定这些病毒的存在。这里提出了两种不同的配置(Al-BTO-Al-MoS2 和 Cu-BTO-Cu-MoS2),并进行了对比,以检测多种病毒。在角度检测技术下,采用传递矩阵法(TMM)和有限元法(FEM)分析了这项工作的性能特征。从 TMM 法和有限元法的求解结果可以看出,Al-BTO-Al-MoS2 结构对疟疾病毒和基孔肯雅病毒的灵敏度最高,分别为 ~270 deg./RIU 和 ~262 deg./RIU ;对疟疾病毒和基孔肯雅病毒的检测精度分别为 ~1.10 和 ~1.64 ;对疟疾病毒和基孔肯雅病毒的品质因数分别为 ~204.40 和 ~208.20 。此外,Cu-BTO-Cu MoS2 结构对疟疾和基孔肯雅病毒的灵敏度最高,分别为 ~310 deg./RIU 和 ~298 deg./RIU ;检测精度令人满意,对疟疾为 ~0.40 ,对基孔肯雅病毒为 ~0.58 ;质量因子对疟疾为 ~89.85 ,对基孔肯雅病毒为 ~86.38 。因此,使用两种不同的方法分析了拟议传感器的性能,结果大致相似。总之,这项研究可作为开发实际传感器的理论基础和第一步。
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引用次数: 0
Modeling Extracellular Vesicles-Mediated Interactions of Cells in the Tumor Microenvironment 模拟细胞外囊泡介导的肿瘤微环境中细胞的相互作用
IF 3.9 4区 生物学 Q1 Engineering Pub Date : 2023-06-12 DOI: 10.1109/TNB.2023.3284090
Mohammad Zoofaghari;Fabrizio Pappalardo;Martin Damrath;Ilangko Balasingham
Interactions of cells via extracellular vesicles (EVs) manipulate various actions, including cancer initiation and progression, inflammation, anti-tumor signaling and cell migration, proliferation and apoptosis in the tumor microenvironment. EVs as the external stimulus can activate or inhibit some receptor pathways in a way that amplify or attenuate a kind of particle release at target cells. This can also be carried out in a biological feedback-loop where the transmitter is affected by the induced release initiated by the target cell due to the EVs received from the donor cell, to create a bilateral process. In this paper, at first we derive the frequency response of internalization function in the framework of a unilateral communication link. This solution is adapted to a closed-loop system to find the frequency response of a bilateral system. The overall releases of the cells, given by the combination of the natural release and the induced release, are reported at the end of this paper and the results are compared in terms of distance between the cells and reaction rates of EVs at the cell membranes.
细胞通过胞外囊泡(EVs)的相互作用操纵着各种行为,包括癌症的诱发和发展、炎症、抗肿瘤信号传导以及肿瘤微环境中的细胞迁移、增殖和凋亡。作为外部刺激物,EVs 可以激活或抑制某些受体通路,从而放大或减弱靶细胞中某种粒子的释放。这也可以在一个生物反馈环路中进行,在这个环路中,发射器受到靶细胞从供体细胞接收到的 EVs 引发的诱导释放的影响,从而形成一个双边过程。在本文中,我们首先推导了单边通信链路框架下内化函数的频率响应。我们将这一解决方案应用于闭环系统,以求得双边系统的频率响应。本文最后报告了由自然释放和诱导释放相结合得出的细胞整体释放量,并从细胞间距和细胞膜上的 EV 反应速率方面对结果进行了比较。
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引用次数: 0
Timed Tissue P Systems With Channel States 具有通道状态的定时组织 P 系统
IF 3.9 4区 生物学 Q1 Engineering Pub Date : 2023-06-12 DOI: 10.1109/TNB.2023.3278653
Yueguo Luo;Yuzhen Zhao;Yi Liu
Tissue P systems with channel states are a variant of tissue P systems that can be employed as highly parallel computing devices, where the channel states can control the movements of objects. In a sense, the time-free approach can improve the robustness of P systems; hence, in this work, we introduce the time-free property into such P systems and explore their computational performances. Specifically, in a time-free manner, it is proved that this type of P systems have Turing universality by using two cells and four channel states with a maximum rule length of 2, or by using two cells and noncooperative symport rules with a maximum rule length of 1. Moreover, in terms of computational efficiency, it is proved that a uniform solution of the satisfiability ( $mathcal {SAT}$ ) problem can be obtained in a time-free manner by applying noncooperative symport rules with a maximum rule length of 1. The research results of this paper show that a highly robust dynamic membrane computing system is constructed. Theoretically, relative to the existing system, our constructed system can enhance robustness and expand its application scope.
具有通道状态的组织 P 系统是组织 P 系统的一种变体,可用作高度并行计算设备,其中通道状态可控制物体的运动。从某种意义上说,无时间方法可以提高 P 系统的鲁棒性;因此,在这项工作中,我们将无时间特性引入此类 P 系统,并探索其计算性能。具体来说,在无时间方式下,通过使用最大规则长度为 2 的两个单元和四个通道状态,或使用最大规则长度为 1 的两个单元和非合作交配规则,证明了这类 P 系统具有图灵普遍性。此外,在计算效率方面,本文证明了通过应用最大规则长度为 1 的非合作交配规则,可以在无时间限制的情况下获得可满足性(SAT)问题的统一解。从理论上讲,相对于现有系统,我们构建的系统可以增强鲁棒性并扩大其应用范围。
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引用次数: 0
Iterative Soft Decoding Algorithm for DNA Storage Using Quality Score and Redecoding 利用质量分数和重编码的 DNA 存储迭代软解码算法
IF 3.9 4区 生物学 Q1 Engineering Pub Date : 2023-06-09 DOI: 10.1109/TNB.2023.3284406
Jaeho Jeong;Hosung Park;Hee-Youl Kwak;Jong-Seon No;Hahyeon Jeon;Jeong Wook Lee;Jae-Won Kim
Ever since deoxyribonucleic acid (DNA) was considered as a next-generation data-storage medium, lots of research efforts have been made to correct errors occurred during the synthesis, storage, and sequencing processes using error correcting codes (ECCs). Previous works on recovering the data from the sequenced DNA pool with errors have utilized hard decoding algorithms based on a majority decision rule. To improve the correction capability of ECCs and robustness of the DNA storage system, we propose a new iterative soft decoding algorithm, where soft information is obtained from FASTQ files and channel statistics. In particular, we propose a new formula for log-likelihood ratio (LLR) calculation using quality scores (Q-scores) and a redecoding method which may be suitable for the error correction and detection in the DNA sequencing area. Based on the widely adopted encoding scheme of the fountain code structure proposed by Erlich et al., we use three different sets of sequenced data to show consistency for the performance evaluation. The proposed soft decoding algorithm gives 2.3% $sim $ 7.0% improvement of the reading number reduction compared to the state-of-the-art decoding method and it is shown that it can deal with erroneous sequenced oligo reads with insertion and deletion errors.
自从脱氧核糖核酸(DNA)被视为下一代数据存储介质以来,人们一直在努力研究如何利用纠错码(ECC)纠正在合成、存储和测序过程中出现的错误。以前从有错误的 DNA 测序池中恢复数据的工作采用的是基于多数决定规则的硬解码算法。为了提高 ECC 的纠错能力和 DNA 存储系统的鲁棒性,我们提出了一种新的迭代软解码算法,其中软信息来自 FASTQ 文件和信道统计数据。特别是,我们提出了一种使用质量分数(Q-scores)计算对数似然比(LLR)的新公式和一种适合 DNA 测序领域纠错和检测的重解码方法。基于 Erlich 等人提出的被广泛采用的喷泉代码结构编码方案,我们使用了三组不同的测序数据来显示性能评估的一致性。与最先进的解码方法相比,所提出的软解码算法的读数减少率提高了 2.3% ∼ 7.0%,并证明它能处理带有插入和删除错误的错误寡核苷酸测序读数。
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引用次数: 0
PanDa Game: Optimized Privacy-Preserving Publishing of Individual-Level Pandemic Data Based on a Game Theoretic Model PanDa Game:基于博弈论模型的个人级流行病数据的优化隐私保护发布。
IF 3.9 4区 生物学 Q1 Engineering Pub Date : 2023-06-08 DOI: 10.1109/TNB.2023.3284092
Abinitha Gourabathina;Zhiyu Wan;J. Thomas Brown;Chao Yan;Bradley A. Malin
Sharing individual-level pandemic data is essential for accelerating the understanding of a disease. For example, COVID-19 data have been widely collected to support public health surveillance and research. In the United States, these data are typically de-identified before publication to protect the privacy of the corresponding individuals. However, current data publishing approaches for this type of data, such as those adopted by the U.S. Centers for Disease Control and Prevention (CDC), have not flexed over time to account for the dynamic nature of infection rates. Thus, the policies generated by these strategies have the potential to both raise privacy risks or overprotect the data and impair the data utility (or usability). To optimize the tradeoff between privacy risk and data utility, we introduce a game theoretic model that adaptively generates policies for the publication of individual-level COVID-19 data according to infection dynamics. We model the data publishing process as a two-player Stackelberg game between a data publisher and a data recipient and then search for the best strategy for the publisher. In this game, we consider 1) average performance of predicting future case counts; and 2) mutual information between the original data and the released data. We use COVID-19 case data from Vanderbilt University Medical Center from March 2020 to December 2021 to demonstrate the effectiveness of the new model. The results indicate that the game theoretic model outperforms all state-of-the-art baseline approaches, including those adopted by CDC, while maintaining low privacy risk. We further perform an extensive sensitivity analyses to show that our findings are robust to order-of-magnitude parameter fluctuations.
共享个人层面的流行病数据对于加快对疾病的理解至关重要。例如,新冠肺炎数据已被广泛收集,以支持公共卫生监测和研究。在美国,为了保护相应个人的隐私,这些数据通常在发布前被取消标识。然而,目前这类数据的数据发布方法,如美国疾病控制与预防中心(CDC)采用的方法,并没有随着时间的推移而改变,以考虑感染率的动态性质。因此,这些策略产生的策略有可能增加隐私风险或过度保护数据,并损害数据的实用性(或可用性)。为了优化隐私风险和数据效用之间的权衡,我们引入了一个博弈论模型,该模型根据感染动态自适应地生成用于发布个人级别新冠肺炎数据的策略。我们将数据发布过程建模为数据发布者和数据接收者之间的两人Stackelberg游戏,然后搜索发布者的最佳策略。在这个游戏中,我们考虑1)预测未来病例数的平均性能;以及2)原始数据和发布数据之间的相互信息。我们使用范德比尔特大学医学中心2020年3月至2021年12月的新冠肺炎病例数据来证明新模型的有效性。结果表明,博弈论模型在保持低隐私风险的同时,优于所有最先进的基线方法,包括美国疾病控制与预防中心采用的方法。我们进一步进行了广泛的敏感性分析,以表明我们的发现对数量级参数波动是稳健的。
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引用次数: 0
Developing a New Phylogeny-Driven Random Forest Model for Functional Metagenomics 为功能宏基因组学开发一个新的系统发育驱动的随机森林模型。
IF 3.9 4区 生物学 Q1 Engineering Pub Date : 2023-06-06 DOI: 10.1109/TNB.2023.3283462
Jyotsna Talreja Wassan;Haiying Wang;Huiru Zheng
Metagenomics is an unobtrusive science linking microbial genes to biological functions or environmental states. Classifying microbial genes into their functional repertoire is an important task in the downstream analysis of Metagenomic studies. The task involves Machine Learning (ML) based supervised methods to achieve good classification performance. Random Forest (RF) has been applied rigorously to microbial gene abundance profiles, mapping them to functional phenotypes. The current research targets tuning RF by the evolutionary ancestry of microbial phylogeny, developing a Phylogeny-RF model for functional classification of metagenomes. This method facilitates capturing the effects of phylogenetic relatedness in an ML classifier itself rather than just applying a supervised classifier over the raw abundances of microbial genes. The idea is rooted in the fact that closely related microbes by phylogeny are highly correlated and tend to have similar genetic and phenotypic traits. Such microbes behave similarly; and hence tend to be selected together, or one of these could be dropped from the analysis, to improve the ML process. The proposed Phylogeny-RF algorithm has been compared with state-of-the-art classification methods including RF and the phylogeny-aware methods of MetaPhyl and PhILR, using three real-world 16S rRNA metagenomic datasets. It has been observed that the proposed method not only achieved significantly better performance than the traditional RF model but also performed better than the other phylogeny-driven benchmarks (p < 0.05). For example, Phylogeny-RF attained a highest AUC of 0.949 and Kappa of 0.891 over soil microbiomes in comparison to other benchmarks.
宏基因组学是一门将微生物基因与生物功能或环境状态联系起来的不引人注目的科学。将微生物基因分类为其功能库是宏基因组研究下游分析的一项重要任务。该任务涉及基于机器学习(ML)的监督方法,以实现良好的分类性能。随机森林(RF)已被严格应用于微生物基因丰度谱,将其映射到功能表型。目前的研究目标是通过微生物系统发育的进化祖先来调整RF,开发用于宏基因组功能分类的系统发育RF模型。这种方法有助于在ML分类器本身中捕捉系统发育相关性的影响,而不仅仅是在微生物基因的原始丰度上应用监督分类器。这种想法植根于这样一个事实,即通过系统发育密切相关的微生物具有高度相关性,并且往往具有相似的遗传和表型特征。这些微生物的行为相似;因此倾向于一起选择,或者可以从分析中删除其中一个,以改进ML过程。使用三个真实世界的16S rRNA宏基因组数据集,将所提出的系统发育RF算法与最先进的分类方法进行了比较,包括RF以及MetaPhyl和PhILR的系统发育感知方法。已经观察到,所提出的方法不仅比传统的RF模型取得了显著更好的性能,而且比其他系统发育驱动的基准也取得了更好的性能(p<0.05)。例如,与其他基准相比,系统发育RF在土壤微生物组上获得了0.949的最高AUC和0.891的Kappa。
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引用次数: 0
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