Pub Date : 2023-09-25DOI: 10.1109/TNB.2023.3319084
Sharique Ali Asghar;Manjunatha Mahadevappa
The main objective of the present study is to use graphene as electrode neural interface material to design novel microelectrodes topology for retinal prosthesis and investigate device operation safety based on the computational framework. The study’s first part establishes the electrode material selection based on electrochemical impedance and the equivalent circuit model. The second part of the study is modeling at the microelectrode-tissue level to investigate the potential distribution, generated resistive heat dissipation, and thermally induced stress in the tissue due to electrical stimulation. The formulation of Joule heating and thermal expansion between microelectrode-tissue-interface employing finite element method modeling is based on the three coupled equations, specifically Ohm’s law, Navier’s equation, and Fourier equation. Electrochemical simulation results of electrode material reveal that single-layer and few-layer graphene-based microelectrode has a specific impedance in the range of 0.02- $0.05 Omega text{m}^{{{2}}}$ , comparable to platinum counterparts. The microelectrode of $10 mu text{m}$ size can stimulate retinal tissue with a threshold current in the range of 8.7- $45 mu text{A}$ . Such stimulation with the observed microelectrode size indicates that both microelectrodes and retinal tissue stay structurally intact, and the device is thermally and mechanically stable, functioning within the safety limit. The results reveal the viability of high-density graphene-based microelectrodes for improved interface as stimulating electrodes to acquire higher visual acuity. Furthermore, the novel microelectrodes design configuration in the honeycomb pattern gives the retinal tissue non-invasive heating and minimal stress upon electrical stimulation. Thus, it paves the path to designing a graphene-based microelectrode array for retinal prosthesis for further in vitro or in vivo studies.
{"title":"Honeycomb-Patterned Graphene Microelectrodes: A Promising Approach for Safe and Effective Retinal Stimulation Based on Electro–Thermo–Mechanical Modeling and Simulation","authors":"Sharique Ali Asghar;Manjunatha Mahadevappa","doi":"10.1109/TNB.2023.3319084","DOIUrl":"10.1109/TNB.2023.3319084","url":null,"abstract":"The main objective of the present study is to use graphene as electrode neural interface material to design novel microelectrodes topology for retinal prosthesis and investigate device operation safety based on the computational framework. The study’s first part establishes the electrode material selection based on electrochemical impedance and the equivalent circuit model. The second part of the study is modeling at the microelectrode-tissue level to investigate the potential distribution, generated resistive heat dissipation, and thermally induced stress in the tissue due to electrical stimulation. The formulation of Joule heating and thermal expansion between microelectrode-tissue-interface employing finite element method modeling is based on the three coupled equations, specifically Ohm’s law, Navier’s equation, and Fourier equation. Electrochemical simulation results of electrode material reveal that single-layer and few-layer graphene-based microelectrode has a specific impedance in the range of 0.02-\u0000<inline-formula> <tex-math>$0.05 Omega text{m}^{{{2}}}$ </tex-math></inline-formula>\u0000, comparable to platinum counterparts. The microelectrode of \u0000<inline-formula> <tex-math>$10 mu text{m}$ </tex-math></inline-formula>\u0000 size can stimulate retinal tissue with a threshold current in the range of 8.7-\u0000<inline-formula> <tex-math>$45 mu text{A}$ </tex-math></inline-formula>\u0000. Such stimulation with the observed microelectrode size indicates that both microelectrodes and retinal tissue stay structurally intact, and the device is thermally and mechanically stable, functioning within the safety limit. The results reveal the viability of high-density graphene-based microelectrodes for improved interface as stimulating electrodes to acquire higher visual acuity. Furthermore, the novel microelectrodes design configuration in the honeycomb pattern gives the retinal tissue non-invasive heating and minimal stress upon electrical stimulation. Thus, it paves the path to designing a graphene-based microelectrode array for retinal prosthesis for further in vitro or in vivo studies.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2023-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41095879","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-09-18DOI: 10.1109/TNB.2023.3316431
Xuwei Yang;Changjun Zhou
DNA computing is a new computing method that has high efficiency in solving large-scale nonlinear and Non-deterministic Polynomial complete problems. The design of DNA sequences is an important step in DNA computing, and the quality of the DNA sequences directly affects the accuracy of DNA computing results. Efficiently designing high-quality DNA sequences is currently a significant challenge. In order to improve the efficiency of DNA sequence design, a sparrow evolutionary search algorithm (SESA) is proposed by us. It inherits the fast convergence of the sparrow search algorithm and avoids the situation that the sparrow search algorithm is prone to fall into a local optimum, which greatly improves the search performance of the algorithm on discrete numerical problems. In order to improve the quality of DNA sequence, a new constraint, multiple GC constraint, has been proposed in this paper. Simulated experiments in NUPACK show that this constraint can greatly improve the quality of the DNA sequences designed by us. Compared with previous results, our DNA sequences have better stability.
{"title":"DNA Sequences Under Multiple Guanine–Cytosine (GC) Base Pairs Constraint","authors":"Xuwei Yang;Changjun Zhou","doi":"10.1109/TNB.2023.3316431","DOIUrl":"10.1109/TNB.2023.3316431","url":null,"abstract":"DNA computing is a new computing method that has high efficiency in solving large-scale nonlinear and Non-deterministic Polynomial complete problems. The design of DNA sequences is an important step in DNA computing, and the quality of the DNA sequences directly affects the accuracy of DNA computing results. Efficiently designing high-quality DNA sequences is currently a significant challenge. In order to improve the efficiency of DNA sequence design, a sparrow evolutionary search algorithm (SESA) is proposed by us. It inherits the fast convergence of the sparrow search algorithm and avoids the situation that the sparrow search algorithm is prone to fall into a local optimum, which greatly improves the search performance of the algorithm on discrete numerical problems. In order to improve the quality of DNA sequence, a new constraint, multiple GC constraint, has been proposed in this paper. Simulated experiments in NUPACK show that this constraint can greatly improve the quality of the DNA sequences designed by us. Compared with previous results, our DNA sequences have better stability.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2023-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10360966","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-09-07DOI: 10.1109/TNB.2023.3312754
Yuxuan Xue;Ye Ma;Zhiyong Sun;Xinyu Liu;Mukun Zhang;Jiawei Zhang;Ning Xi
Since the COVID-19 disease has been further aggravated, the prevention of pathogen transmission becomes a vital issue to restrain casualties. Recent research outcomes have shown the possibilities of the viruses existing on inanimate surfaces up to few days, which carry the risk of touch propagation of the disease. Deep ultraviolet germicide irradiation (UVGI) with the wavelength of 255–280nm has been verified to efficiently disinfect various types of bacteria and virus, which could prevent the aggravation of pandemic spread. Even though considerable experiments and approaches have been applied to evaluate the disinfection effects, there are only few reports about how the individual bio-organism behaves after ultraviolet C (UVC) irradiation, especially in the aspect of mechanical changes. Furthermore, since the standard pathway of virus transmission and reproduction requires the host cell to assemble and transport newly generated virus, the dynamic response of infectious cell is always the vital aspect of virology study. In this work, high power LEDs array has been established with 270nm UVC irradiation to evaluate disinfection capability on various types of bio-organism, and incubator embedded atomic force microscopy (AFM) is used to investigate the single bacterium and virus under UVGI. The real-time tracking of the living Vero cells infected with adenovirus has also been presented in this study. The results show that after sufficient UVGI, the outer shell of bacteria and viruses remain intact in structure, however the bio-organisms lost the capability of reproduction and normal metabolism. The experiment results also indicate that once the host cell is infected with adenovirus, the rapid production of newborn virus capsid will gradually destroy the cellular normal metabolism and lose mechanical integrity.
由于 COVID-19 病情进一步恶化，预防病原体传播成为减少人员伤亡的关键问题。最近的研究结果表明，病毒有可能在无生命的物体表面存在长达数天的时间，这就带来了接触传播疾病的风险。波长为 255-280 纳米的深紫外线杀菌照射（UVGI）已被证实能有效消毒各种细菌和病毒，从而防止大流行病传播的加剧。尽管已有大量实验和方法用于评估消毒效果，但关于紫外线 C（UVC）照射后生物个体的表现，尤其是机械变化方面的报告却寥寥无几。此外，由于病毒传播和繁殖的标准途径需要宿主细胞组装和运输新产生的病毒，因此感染细胞的动态反应一直是病毒学研究的重要方面。在这项工作中，利用 270nm 紫外光照射建立了高功率 LED 阵列，以评估对各类生物的消毒能力，并使用培养箱嵌入式原子力显微镜（AFM）来研究紫外光照射下的单个细菌和病毒。本研究还对感染腺病毒的活体 Vero 细胞进行了实时跟踪。结果表明，经过充分紫外光照射后，细菌和病毒的外壳结构保持完好，但生物体失去了繁殖和正常新陈代谢的能力。实验结果还表明，宿主细胞一旦感染腺病毒，新生病毒壳的快速生成会逐渐破坏细胞的正常新陈代谢，并失去机械完整性。
{"title":"Identification and Measurement of Biomarkers at Single Microorganism Level for In Situ Monitoring Deep Ultraviolet Disinfection Process","authors":"Yuxuan Xue;Ye Ma;Zhiyong Sun;Xinyu Liu;Mukun Zhang;Jiawei Zhang;Ning Xi","doi":"10.1109/TNB.2023.3312754","DOIUrl":"10.1109/TNB.2023.3312754","url":null,"abstract":"Since the COVID-19 disease has been further aggravated, the prevention of pathogen transmission becomes a vital issue to restrain casualties. Recent research outcomes have shown the possibilities of the viruses existing on inanimate surfaces up to few days, which carry the risk of touch propagation of the disease. Deep ultraviolet germicide irradiation (UVGI) with the wavelength of 255–280nm has been verified to efficiently disinfect various types of bacteria and virus, which could prevent the aggravation of pandemic spread. Even though considerable experiments and approaches have been applied to evaluate the disinfection effects, there are only few reports about how the individual bio-organism behaves after ultraviolet C (UVC) irradiation, especially in the aspect of mechanical changes. Furthermore, since the standard pathway of virus transmission and reproduction requires the host cell to assemble and transport newly generated virus, the dynamic response of infectious cell is always the vital aspect of virology study. In this work, high power LEDs array has been established with 270nm UVC irradiation to evaluate disinfection capability on various types of bio-organism, and incubator embedded atomic force microscopy (AFM) is used to investigate the single bacterium and virus under UVGI. The real-time tracking of the living Vero cells infected with adenovirus has also been presented in this study. The results show that after sufficient UVGI, the outer shell of bacteria and viruses remain intact in structure, however the bio-organisms lost the capability of reproduction and normal metabolism. The experiment results also indicate that once the host cell is infected with adenovirus, the rapid production of newborn virus capsid will gradually destroy the cellular normal metabolism and lose mechanical integrity.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2023-09-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10182195","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-09-04DOI: 10.1109/TNB.2023.3311611
Md. Shahedul Hasan;Md. Anas Ebna Kalam;Mohammad Faisal
In this article, we have demonstrated a highly sensitive four-channel photonic crystal fiber (PCF) based surface plasmon resonance (SPR) biosensor which can detect four different analytes simultaneously. To ease practical implementation, four analyte sensing layers and plasmonic materials such as gold (Au) and gold (Au) with Tantalum Pentoxide (Ta2O5) are placed on the exterior of the four arms of the square shaped structure. The sensor’s structure consists of only nine circular air holes, making it simple and easy to fabricate using currently available technologies. Finite element method (FEM) based numerical analysis is used to evaluate the sensing performance of the proposed sensor. With optimum structure parameters, the sensor achieves maximum wavelength sensitivity of 11000, 25000, 11000 and 25000 nm/RIU for Channel-1, Channel-2, Channel-3, and Channel-4 respectively. It shows maximum amplitude sensitivity of 803.732, 709.171, 803.827, 709.146 RIU $^{-{1}}$ for Channel 1, 2, 3, and 4 respectively. It also shows maximum FOM of 232.55, 352.36, 231.57, 352.36 RIU $^{-{1}}$ in Ch-1, Ch-2, Ch-3 and Ch-4 respectively. Moreover, the proposed sensor shows a wide range of refractive index sensing capability from 1.30 to 1.41. Due to multi-analyte detection capability, large sensing range, and excellent sensitivity the proposed sensor unfolds unrivalled capacity of detecting chemicals, carcinogenic agents, biomolecules, and other analytes.
{"title":"PCF Based Four-Channel SPR Biosensor With Wide Sensing Range","authors":"Md. Shahedul Hasan;Md. Anas Ebna Kalam;Mohammad Faisal","doi":"10.1109/TNB.2023.3311611","DOIUrl":"10.1109/TNB.2023.3311611","url":null,"abstract":"In this article, we have demonstrated a highly sensitive four-channel photonic crystal fiber (PCF) based surface plasmon resonance (SPR) biosensor which can detect four different analytes simultaneously. To ease practical implementation, four analyte sensing layers and plasmonic materials such as gold (Au) and gold (Au) with Tantalum Pentoxide (Ta2O5) are placed on the exterior of the four arms of the square shaped structure. The sensor’s structure consists of only nine circular air holes, making it simple and easy to fabricate using currently available technologies. Finite element method (FEM) based numerical analysis is used to evaluate the sensing performance of the proposed sensor. With optimum structure parameters, the sensor achieves maximum wavelength sensitivity of 11000, 25000, 11000 and 25000 nm/RIU for Channel-1, Channel-2, Channel-3, and Channel-4 respectively. It shows maximum amplitude sensitivity of 803.732, 709.171, 803.827, 709.146 RIU\u0000<inline-formula> <tex-math>$^{-{1}}$ </tex-math></inline-formula>\u0000 for Channel 1, 2, 3, and 4 respectively. It also shows maximum FOM of 232.55, 352.36, 231.57, 352.36 RIU\u0000<inline-formula> <tex-math>$^{-{1}}$ </tex-math></inline-formula>\u0000 in Ch-1, Ch-2, Ch-3 and Ch-4 respectively. Moreover, the proposed sensor shows a wide range of refractive index sensing capability from 1.30 to 1.41. Due to multi-analyte detection capability, large sensing range, and excellent sensitivity the proposed sensor unfolds unrivalled capacity of detecting chemicals, carcinogenic agents, biomolecules, and other analytes.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2023-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10209867","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-08-22DOI: 10.1109/TNB.2023.3307458
Zhao-Cai Wang;Kun Liang;Xiao-Guang Bao;Tun-Hua Wu
DNA computing is a new pattern of computing that combines biotechnology and information technology. As a new technology born in less than three decades, it has developed at an extremely rapid rate, which can be attributed to its advantages, including high parallelism, powerful data storage capacity, and low power consumption. Nowadays, DNA computing has become one of the most popular research fields worldwide and has been effective in solving certain combinatorial optimization problems. In this study, we use the Adleman-Lipton model based on DNA computing for solving the Prize Collecting Traveling Salesman Problem (PCTSP) and demonstrate the feasibility of this model. Then, we design a simulation experiment of the model to solve some open instances of PCTSP. The results illustrate that the model can satisfactorily solve these instances. Finally, the comparison with the results of the Clustering Search algorithm and the Greedy Stochastic Adaptive Search Procedure/Variable Neighborhood Search method reveals that the optimal solutions obtained by this simulation experiment are significantly superior to those of the other two algorithms in all instances. This research also provides a method for proficiently solving additional combinatorial optimization problems.
DNA 计算是生物技术与信息技术相结合的一种新型计算模式。作为一项诞生不到三十年的新技术，它的发展速度极为迅猛，这得益于它具有高并行性、强大的数据存储能力和低功耗等优势。如今，DNA 计算已成为全球最热门的研究领域之一，并在解决某些组合优化问题方面卓有成效。在本研究中，我们使用基于 DNA 计算的 Adleman-Lipton 模型来解决有奖旅行推销员问题（PCTSP），并证明了该模型的可行性。然后，我们设计了该模型的仿真实验，以解决 PCTSP 的一些开放实例。结果表明，该模型能令人满意地解决这些实例。最后，通过与聚类搜索算法和贪婪随机自适应搜索程序/可变邻域搜索法的结果进行比较，发现该仿真实验所获得的最优解在所有实例中都明显优于其他两种算法。这项研究还为熟练解决其他组合优化问题提供了一种方法。
{"title":"A Novel Algorithm for Solving the Prize Collecting Traveling Salesman Problem Based on DNA Computing","authors":"Zhao-Cai Wang;Kun Liang;Xiao-Guang Bao;Tun-Hua Wu","doi":"10.1109/TNB.2023.3307458","DOIUrl":"10.1109/TNB.2023.3307458","url":null,"abstract":"DNA computing is a new pattern of computing that combines biotechnology and information technology. As a new technology born in less than three decades, it has developed at an extremely rapid rate, which can be attributed to its advantages, including high parallelism, powerful data storage capacity, and low power consumption. Nowadays, DNA computing has become one of the most popular research fields worldwide and has been effective in solving certain combinatorial optimization problems. In this study, we use the Adleman-Lipton model based on DNA computing for solving the Prize Collecting Traveling Salesman Problem (PCTSP) and demonstrate the feasibility of this model. Then, we design a simulation experiment of the model to solve some open instances of PCTSP. The results illustrate that the model can satisfactorily solve these instances. Finally, the comparison with the results of the Clustering Search algorithm and the Greedy Stochastic Adaptive Search Procedure/Variable Neighborhood Search method reveals that the optimal solutions obtained by this simulation experiment are significantly superior to those of the other two algorithms in all instances. This research also provides a method for proficiently solving additional combinatorial optimization problems.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2023-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10050844","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-08-16DOI: 10.1109/TNB.2023.3304601
Hamed Pezeshki
This paper introduces an ultracompact lab-on-a-chip device with a size of $8times 0.8~mu text{m}^{mathrm{ 2}}$ for surface-enhanced coherent anti-Stokes Raman scattering. This device comprises of a unique hybrid plasmonic-photonic vertical coupler, for light-coupling between the device and a light source, and a heptamer plasmonic nanotweezer for trapping and manipulation of nanoparticles. The coupler with its nanoscale size of $0.73times 0.8~mu text{m}^{mathrm{ 2}}$ offers maximum coupling efficiency and directivity of −4.2 dB and 17.8 dB with a 3 dB bandwidth across the wavelength range of $sim {1} - {1}.{13} , mu text{m}$ . Based on a finite element method, it is theoretically shown that the tear-drop based nanotweezer can empower the device to yield a very high Raman gain of $geq {10}^{{17}}$ , making the detection at the single-molecule level possible. The proposed device can exhibit low damage to bioparticles through the use of near infrared wavelengths range with lower energy photons. Due to its short optical path, this device is expected to improve the Raman signal to noise ratio by reducing the level of background in-coherent Raman signals. Finally, thanks to its configuration, this device can enable the creation of parallel measurement channels, paving the way toward the development of high-throughput and mass-produced biosensors.
{"title":"Ultracompact Lab-on-a-Chip Device for Surface-Enhanced Coherent Anti-Stokes Raman Scattering","authors":"Hamed Pezeshki","doi":"10.1109/TNB.2023.3304601","DOIUrl":"10.1109/TNB.2023.3304601","url":null,"abstract":"This paper introduces an ultracompact lab-on-a-chip device with a size of \u0000<inline-formula> <tex-math>$8times 0.8~mu text{m}^{mathrm{ 2}}$ </tex-math></inline-formula>\u0000 for surface-enhanced coherent anti-Stokes Raman scattering. This device comprises of a unique hybrid plasmonic-photonic vertical coupler, for light-coupling between the device and a light source, and a heptamer plasmonic nanotweezer for trapping and manipulation of nanoparticles. The coupler with its nanoscale size of \u0000<inline-formula> <tex-math>$0.73times 0.8~mu text{m}^{mathrm{ 2}}$ </tex-math></inline-formula>\u0000 offers maximum coupling efficiency and directivity of −4.2 dB and 17.8 dB with a 3 dB bandwidth across the wavelength range of \u0000<inline-formula> <tex-math>$sim {1} - {1}.{13} , mu text{m}$ </tex-math></inline-formula>\u0000. Based on a finite element method, it is theoretically shown that the tear-drop based nanotweezer can empower the device to yield a very high Raman gain of \u0000<inline-formula> <tex-math>$geq {10}^{{17}}$ </tex-math></inline-formula>\u0000, making the detection at the single-molecule level possible. The proposed device can exhibit low damage to bioparticles through the use of near infrared wavelengths range with lower energy photons. Due to its short optical path, this device is expected to improve the Raman signal to noise ratio by reducing the level of background in-coherent Raman signals. Finally, thanks to its configuration, this device can enable the creation of parallel measurement channels, paving the way toward the development of high-throughput and mass-produced biosensors.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2023-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10010744","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Recently, DNA encoding has shown its potential to store the vital information of the image in the form of nucleotides, namely ${A}, {C}, {T}$ , and ${G}$ , with the entire sequence following run-length and GC-constraint. As a result, the encoded DNA planes contain unique nucleotide strings, giving more salient image information using less storage. In this paper, the advantages of DNA encoding have been inherited to uplift the retrieval accuracy of the content-based image retrieval (CBIR) system. Initially, the most significant bit-plane-based DNA encoding scheme has been suggested to generate DNA planes from a given image. The generated DNA planes of the image efficiently capture the salient visual information in a compact form. Subsequently, the encoded DNA planes have been utilized for nucleotide patterns-based feature extraction and image retrieval. Simultaneously, the translated and amplified encoded DNA planes have also been deployed on different deep learning architectures like ResNet-50, VGG-16, VGG-19, and Inception V3 to perform classification-based image retrieval. The performance of the proposed system has been evaluated using two corals, an object, and a medical image dataset. All these datasets contain 28,200 images belonging to 134 different classes. The experimental results confirm that the proposed scheme achieves perceptible improvements compared with other state-of-the-art methods.
最近，DNA 编码显示了其潜力，它能以核苷酸（即 A、C、T 和 G）的形式存储图像的重要信息，整个序列遵循运行长度和 GC 限制。因此，编码后的 DNA 平面包含独特的核苷酸字符串，用更少的存储空间提供更多突出的图像信息。本文继承了 DNA 编码的优点，以提高基于内容的图像检索（CBIR）系统的检索精度。最初，我们提出了一种最重要的基于位平面的 DNA 编码方案，用于从给定图像生成 DNA 平面。生成的图像 DNA 平面能以紧凑的形式有效捕捉到突出的视觉信息。随后，编码后的 DNA 平面被用于基于核苷酸模式的特征提取和图像检索。同时，经过翻译和放大的编码 DNA 平面还被部署在不同的深度学习架构上，如 ResNet-50、VGG-16、VGG-19 和 Inception V3，以执行基于分类的图像检索。我们使用两个珊瑚、一个物体和一个医学图像数据集对所提议系统的性能进行了评估。所有这些数据集包含属于 134 个不同类别的 28 200 张图像。实验结果证实，与其他最先进的方法相比，所提出的方案实现了可感知的改进。
{"title":"DNA Encoding-Based Nucleotide Pattern and Deep Features for Instance and Class-Based Image Retrieval","authors":"Jitesh Pradhan;Arup Kumar Pal;Sk Hafizul Islam;Chiranjeev Bhaya","doi":"10.1109/TNB.2023.3303512","DOIUrl":"10.1109/TNB.2023.3303512","url":null,"abstract":"Recently, DNA encoding has shown its potential to store the vital information of the image in the form of nucleotides, namely \u0000<inline-formula> <tex-math>${A}, {C}, {T}$ </tex-math></inline-formula>\u0000, and \u0000<inline-formula> <tex-math>${G}$ </tex-math></inline-formula>\u0000, with the entire sequence following run-length and GC-constraint. As a result, the encoded DNA planes contain unique nucleotide strings, giving more salient image information using less storage. In this paper, the advantages of DNA encoding have been inherited to uplift the retrieval accuracy of the content-based image retrieval (CBIR) system. Initially, the most significant bit-plane-based DNA encoding scheme has been suggested to generate DNA planes from a given image. The generated DNA planes of the image efficiently capture the salient visual information in a compact form. Subsequently, the encoded DNA planes have been utilized for nucleotide patterns-based feature extraction and image retrieval. Simultaneously, the translated and amplified encoded DNA planes have also been deployed on different deep learning architectures like ResNet-50, VGG-16, VGG-19, and Inception V3 to perform classification-based image retrieval. The performance of the proposed system has been evaluated using two corals, an object, and a medical image dataset. All these datasets contain 28,200 images belonging to 134 different classes. The experimental results confirm that the proposed scheme achieves perceptible improvements compared with other state-of-the-art methods.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2023-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10358423","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-08-07DOI: 10.1109/TNB.2023.3303345
Souvik Kundu;Shawana Tabassum;Ritwesh A. Kumar;E. Dale Abel;Ratnesh Kumar
This paper reports a sensor architecture for continuous monitoring of biomarkers directly in the blood, especially for ICU/CCU patients requiring critical care and rapid biomarker measurement. The sensor is based on a simple optical fiber that can be inserted through a catheter into the bloodstream, wherein gold nanoparticles are attached at its far distal end as a plasmonic material for highly sensitive opto-chemical sensing of target biomolecules (glucose in our application) via the excitation of surface plasmon polaritons. For specificity, the nanoparticles are functionalized with a specific receptor enzyme that enables the localized surface plasmon resonance (LSPR)-based targeted bio-sensing. Further, a micro dialysis probe is introduced in the proposed architecture, which facilitates continuous monitoring for an extended period without fouling the sensor surface with cells and blood debris present in whole blood, leading to prolonged enhanced sensitivity and limit of detection, relative to existing state-of-the-art continuous monitoring devices that can conduct direct measurements in blood. To establish this proof-of-concept, we tested the sensor device to monitor glucose in-vivo involving an animal model, where continuous monitoring was done directly in the circulation of living rats. The sensor’s sensitivity to glucose was found to be 0.0354 a.u./mg.dl−1 with a detection limit of 50.89 mg/dl.
{"title":"Plasmonic Optical Fiber Based Continuous in-Vivo Glucose Monitoring for ICU/CCU Setup","authors":"Souvik Kundu;Shawana Tabassum;Ritwesh A. Kumar;E. Dale Abel;Ratnesh Kumar","doi":"10.1109/TNB.2023.3303345","DOIUrl":"10.1109/TNB.2023.3303345","url":null,"abstract":"This paper reports a sensor architecture for continuous monitoring of biomarkers directly in the blood, especially for ICU/CCU patients requiring critical care and rapid biomarker measurement. The sensor is based on a simple optical fiber that can be inserted through a catheter into the bloodstream, wherein gold nanoparticles are attached at its far distal end as a plasmonic material for highly sensitive opto-chemical sensing of target biomolecules (glucose in our application) via the excitation of surface plasmon polaritons. For specificity, the nanoparticles are functionalized with a specific receptor enzyme that enables the localized surface plasmon resonance (LSPR)-based targeted bio-sensing. Further, a micro dialysis probe is introduced in the proposed architecture, which facilitates continuous monitoring for an extended period without fouling the sensor surface with cells and blood debris present in whole blood, leading to prolonged enhanced sensitivity and limit of detection, relative to existing state-of-the-art continuous monitoring devices that can conduct direct measurements in blood. To establish this proof-of-concept, we tested the sensor device to monitor glucose in-vivo involving an animal model, where continuous monitoring was done directly in the circulation of living rats. The sensor’s sensitivity to glucose was found to be 0.0354 a.u./mg.dl−1 with a detection limit of 50.89 mg/dl.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2023-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9953605","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-08-07DOI: 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.
{"title":"COTiR: Molecular Communication Model for Synthetic Exosome-Based Tissue Regeneration","authors":"Saswati Pal;Sudip Misra;Ranjan K. Mallik","doi":"10.1109/TNB.2023.3302773","DOIUrl":"10.1109/TNB.2023.3302773","url":null,"abstract":"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.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2023-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9972527","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-07-25DOI: 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）。
{"title":"Ratio Shift Keying Modulation for Time-Varying Molecular Communication Channels","authors":"M. Okan Araz;Ahmet R. Emirdagi;M. Serkan Kopuzlu;Murat Kuscu","doi":"10.1109/TNB.2023.3298600","DOIUrl":"10.1109/TNB.2023.3298600","url":null,"abstract":"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.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":null,"pages":null},"PeriodicalIF":3.9,"publicationDate":"2023-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9924621","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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