IEEE Transactions on NanoBioscience最新文献

{"title":"Guest Editorial Biomedical and Health Informatics Special Section","authors":"Xiaohua Hu","doi":"10.1109/TNB.2023.3316486","DOIUrl":"https://doi.org/10.1109/TNB.2023.3316486","url":null,"abstract":"Integrating nanotechnology with biomedical and health informatics could advance the understanding of human disease and help medical and healthcare professionals to make better diagnosis decisions and design better treatments. In this Biomedical and Health Informatics Special Section, we have selected six articles to report some of the latest developments in this area.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"22 4","pages":"780-780"},"PeriodicalIF":3.9,"publicationDate":"2023-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ieeexplore.ieee.org/iel7/7728/10269102/10269159.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49918401","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Guest Editorial Bioinformatics and Computational Biology Special Section","authors":"Xiaohua Hu","doi":"10.1109/TNB.2023.3316485","DOIUrl":"https://doi.org/10.1109/TNB.2023.3316485","url":null,"abstract":"In recent years, we have witnessed many successful applications of bioinformatics and computational biology methods in the field of Bionano to help us understand the biological system in the nanoscale, such as the BioNano nextgeneration mapping system to enhance the performance of physical map construction. Bioinformatics and computational tools and methods are essential to assemble, process, and analyze vast amounts of high-throughput datasets. In this Bioinformatics and Computational Biology Special Section, we have eight papers to reflect the latest developments and research in this exciting area.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"22 4","pages":"704-704"},"PeriodicalIF":3.9,"publicationDate":"2023-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ieeexplore.ieee.org/iel7/7728/10269102/10269158.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49919550","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"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":"23 2","pages":"262-271"},"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}

{"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":"23 2","pages":"252-261"},"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}

{"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":"23 2","pages":"242-251"},"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}

{"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":"23 2","pages":"233-241"},"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}

{"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":"23 2","pages":"220-232"},"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}

{"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":"23 2","pages":"212-219"},"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}

{"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":"23 1","pages":"190-201"},"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}

{"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":"23 1","pages":"157-166"},"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}