Pub Date : 2024-12-23DOI: 10.1109/TNB.2024.3520137
Zhongyi Guo;Nana Ai;Wei Ge;Qingsong Xu
Zebrafish have emerged as a powerful model organism in cardiovascular disease research. Accurately identifying zebrafish blood vessels and evaluating blood flow velocity without injury has a wide range of biological applications. This paper presents the design and development of a non-invasive microvision system for vascular recognition and blood flow monitoring of zebrafish larvae. For the first time, a visual algorithm based on color thresholding and discrete Fourier transform filtering is proposed to determine the position of zebrafish dorsal cardinal vein vessels. Next, the blood flow velocity is determined based on the change rate of pixel values near the centroid point of the blood vessel recognition results. Then, an independent software system is developed based on the producer-consumer underlying framework. A user-friendly interface is specifically designed for biomedical workers, and a complete prototype system is built in combination with hardware devices. In addition, relevant experiments were conducted, and the results indicated that the system can effectively recognize the position of vessels and monitor blood flow velocity in zebrafish larvae under different anesthesia concentrations and developmental days. The heart rate information obtained based on blood flow velocity is consistent with the heart beating frequency. Moreover, the system has also been successfully applied to blood flow velocity monitoring under fluorescence conditions. In future work, this system will be applied in drug screening research for cardiovascular-related diseases of zebrafish larvae.
{"title":"ZebraVas: A Non-Invasive Microvision System for Vascular Recognition and Blood Flow Monitoring of Zebrafish Larvae","authors":"Zhongyi Guo;Nana Ai;Wei Ge;Qingsong Xu","doi":"10.1109/TNB.2024.3520137","DOIUrl":"10.1109/TNB.2024.3520137","url":null,"abstract":"Zebrafish have emerged as a powerful model organism in cardiovascular disease research. Accurately identifying zebrafish blood vessels and evaluating blood flow velocity without injury has a wide range of biological applications. This paper presents the design and development of a non-invasive microvision system for vascular recognition and blood flow monitoring of zebrafish larvae. For the first time, a visual algorithm based on color thresholding and discrete Fourier transform filtering is proposed to determine the position of zebrafish dorsal cardinal vein vessels. Next, the blood flow velocity is determined based on the change rate of pixel values near the centroid point of the blood vessel recognition results. Then, an independent software system is developed based on the producer-consumer underlying framework. A user-friendly interface is specifically designed for biomedical workers, and a complete prototype system is built in combination with hardware devices. In addition, relevant experiments were conducted, and the results indicated that the system can effectively recognize the position of vessels and monitor blood flow velocity in zebrafish larvae under different anesthesia concentrations and developmental days. The heart rate information obtained based on blood flow velocity is consistent with the heart beating frequency. Moreover, the system has also been successfully applied to blood flow velocity monitoring under fluorescence conditions. In future work, this system will be applied in drug screening research for cardiovascular-related diseases of zebrafish larvae.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"24 2","pages":"225-233"},"PeriodicalIF":3.7,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143541726","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}
Mechanical stress on cells is transmitted through many biological processes, for example, cell shape control, tissue patterning, and axonal homeostasis. Microtubules, a cytoskeletal component, presumably play a significant role in the mechanoregulation of cellular processes. We investigate motor protein-driven transport of quantum dots along mechanically deformed microtubules. We found that microtubule deformation significantly slowed kinesin-driven transport, whereas we previously reported dynein-driven transport was rather robust. Such dualistic modulation of transportation dynamics of the motor proteins by microtubule deformation can be attributed to the altered affinity of the motor proteins for buckled microtubules. Our results may form the basis for understanding microtubules’ role in regulating cellular processes in a mechanically adverse environment through its detection ability and response to mechanical stress.
{"title":"Microtubule Deformation Modulates Intracellular Transport by Kinesin Differently Than Dynein","authors":"Syeda Rubaiya Nasrin;Tanjina Afrin;Arif Md. Rashedul Kabir;Daisuke Inoue;Takefumi Yamashita;Makoto Oura;Johtaro Yamamoto;Masataka Kinjo;Kazuki Sada;Akira Kakugo","doi":"10.1109/TNB.2024.3507021","DOIUrl":"10.1109/TNB.2024.3507021","url":null,"abstract":"Mechanical stress on cells is transmitted through many biological processes, for example, cell shape control, tissue patterning, and axonal homeostasis. Microtubules, a cytoskeletal component, presumably play a significant role in the mechanoregulation of cellular processes. We investigate motor protein-driven transport of quantum dots along mechanically deformed microtubules. We found that microtubule deformation significantly slowed kinesin-driven transport, whereas we previously reported dynein-driven transport was rather robust. Such dualistic modulation of transportation dynamics of the motor proteins by microtubule deformation can be attributed to the altered affinity of the motor proteins for buckled microtubules. Our results may form the basis for understanding microtubules’ role in regulating cellular processes in a mechanically adverse environment through its detection ability and response to mechanical stress.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"24 2","pages":"218-224"},"PeriodicalIF":3.7,"publicationDate":"2024-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143604646","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 : 2024-11-22DOI: 10.1109/TNB.2024.3504540
Fatemeh Sadat Saeidi;Naghmeh Sadat Moayedian
In molecular communication networks, understanding the security level allows us to assess the quality of information transmitted accurately. The presence of unintended nodes in these networks is one of the factors compromising the security of information. This paper considers the simultaneous presence of a jammer and an eavesdropper as unintended nodes. This existence of unintended nodes prompts us to explore methods for assessing the security of a proposed system. Physical layer approaches can be regarded as one of the most efficient methods for assessing security in molecular communication networks. In this paper, we have utilized these approaches instead of the conventional cryptographic methods. At this layer, we have used several metrics to evaluate the security of our system; secrecy capacity (SC), the average probability of error (APOE), and comprehensive secure distance (CSD). By using SC, we also employed other approaches to improve security, such as changing the time interval, jamming molecules, and varying the distance between the transmitter and the receiver. As the last step, Monte Carlo simulation is used to verify the results obtained through analytical analysis.
{"title":"Investigating Physical Layer Security in Molecular Communication Networks","authors":"Fatemeh Sadat Saeidi;Naghmeh Sadat Moayedian","doi":"10.1109/TNB.2024.3504540","DOIUrl":"10.1109/TNB.2024.3504540","url":null,"abstract":"In molecular communication networks, understanding the security level allows us to assess the quality of information transmitted accurately. The presence of unintended nodes in these networks is one of the factors compromising the security of information. This paper considers the simultaneous presence of a jammer and an eavesdropper as unintended nodes. This existence of unintended nodes prompts us to explore methods for assessing the security of a proposed system. Physical layer approaches can be regarded as one of the most efficient methods for assessing security in molecular communication networks. In this paper, we have utilized these approaches instead of the conventional cryptographic methods. At this layer, we have used several metrics to evaluate the security of our system; secrecy capacity (SC), the average probability of error (APOE), and comprehensive secure distance (CSD). By using SC, we also employed other approaches to improve security, such as changing the time interval, jamming molecules, and varying the distance between the transmitter and the receiver. As the last step, Monte Carlo simulation is used to verify the results obtained through analytical analysis.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"24 2","pages":"208-217"},"PeriodicalIF":3.7,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143604644","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}
This study presents a biosensor utilizing electrospun SnO2 nanofiber films for real-time monitoring of C2C12 cells. The biosensor demonstrates sensitivity towards cellular behaviors, including adhesion, proliferation, and detachment. Alterations in semi-circle and dielectric properties are validated through Nyquist plot and an EEC model, highlighting the biosensor’s potential for analyzing cellular dynamics.
{"title":"Electrospun Stannic Oxide Nanofiber Thin-Film Based Sensing Device for Monitoring Functional Behaviors of Adherent Mammalian Cells","authors":"Uvanesh Kasiviswanathan;Chandan Kumar;Ajay Kumar Sahi;Amit Kumar;Satyabrata Jit;Neeraj Sharma;Sanjeev Kumar Mahto","doi":"10.1109/TNB.2024.3489353","DOIUrl":"10.1109/TNB.2024.3489353","url":null,"abstract":"This study presents a biosensor utilizing electrospun SnO2 nanofiber films for real-time monitoring of C2C12 cells. The biosensor demonstrates sensitivity towards cellular behaviors, including adhesion, proliferation, and detachment. Alterations in semi-circle and dielectric properties are validated through Nyquist plot and an EEC model, highlighting the biosensor’s potential for analyzing cellular dynamics.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"24 1","pages":"120-126"},"PeriodicalIF":3.7,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142576049","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 : 2024-10-28DOI: 10.1109/TNB.2024.3481504
Xuncai Zhang;Yunfei Lu
DNA is considered one of the most attractive storage media because of its excellent reliability and durability. Early encoding schemes lacked flexibility and scalability. To address these limitations, we propose a combination of static mapping and dynamic encoding, named “Galaxy” encoding. This scheme uses both the “dual-rule interleaving” algorithm and the “twelve-element Huffman rotational encoding” algorithm. We tested it with “Shakespeare Sonnets” and other files, achieving an encoding information density of approximately 2.563 bits/nt. Additionally, the inclusion of Reed–Solomon error-correcting codes can correct nearly 5% of the errors. Our simulations show that it supports various file types (.gz, .tar, .exe, etc.). We also analyzed the cost and fault tolerance of “Galaxy” encoding, demonstrating its high coding efficiency and ability to fully recover original information while effectively reducing the costs of DNA synthesis and sequencing.
DNA 因其出色的可靠性和耐用性而被认为是最具吸引力的存储介质之一。早期的编码方案缺乏灵活性和可扩展性。为了解决这些局限性，我们提出了一种静态映射和动态编码相结合的方案，命名为 "银河 "编码。该方案同时使用了 "双规则交错 "算法和 "十二元素哈夫曼旋转编码 "算法。我们用 "莎士比亚十四行诗 "和其他文件对其进行了测试，编码信息密度约为 2.563 bits/nt。此外，加入里德-所罗门纠错码可纠正近 5%的错误。我们的模拟显示，它支持各种文件类型（.gz、.tar、.exe 等）。我们还分析了 "银河 "编码的成本和容错性，证明其编码效率高，能够完全恢复原始信息，同时有效降低 DNA 合成和测序的成本。
{"title":"“Galaxy” Encoding: Toward High Storage Density and Low Cost","authors":"Xuncai Zhang;Yunfei Lu","doi":"10.1109/TNB.2024.3481504","DOIUrl":"10.1109/TNB.2024.3481504","url":null,"abstract":"DNA is considered one of the most attractive storage media because of its excellent reliability and durability. Early encoding schemes lacked flexibility and scalability. To address these limitations, we propose a combination of static mapping and dynamic encoding, named “Galaxy” encoding. This scheme uses both the “dual-rule interleaving” algorithm and the “twelve-element Huffman rotational encoding” algorithm. We tested it with “Shakespeare Sonnets” and other files, achieving an encoding information density of approximately 2.563 bits/nt. Additionally, the inclusion of Reed–Solomon error-correcting codes can correct nearly 5% of the errors. Our simulations show that it supports various file types (.gz, .tar, .exe, etc.). We also analyzed the cost and fault tolerance of “Galaxy” encoding, demonstrating its high coding efficiency and ability to fully recover original information while effectively reducing the costs of DNA synthesis and sequencing.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"24 2","pages":"200-207"},"PeriodicalIF":3.7,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142521805","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 : 2024-10-23DOI: 10.1109/TNB.2024.3483609
{"title":"2024 Index IEEE Transactions on NanoBioscience Vol. 23","authors":"","doi":"10.1109/TNB.2024.3483609","DOIUrl":"https://doi.org/10.1109/TNB.2024.3483609","url":null,"abstract":"","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"23 4","pages":"1-14"},"PeriodicalIF":3.7,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=10731932","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142518145","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}
Pub Date : 2024-10-15DOI: 10.1109/TNB.2024.3460448
Xiaohua Hu
{"title":"Guest Editorial Special Section on Biomedical and Health Informatics","authors":"Xiaohua Hu","doi":"10.1109/TNB.2024.3460448","DOIUrl":"https://doi.org/10.1109/TNB.2024.3460448","url":null,"abstract":"","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"23 4","pages":"538-539"},"PeriodicalIF":3.7,"publicationDate":"2024-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=10718701","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142438497","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}
Pub Date : 2024-10-15DOI: 10.1109/TNB.2024.3443498
Yuvraj Maphrio Mao;Khairunnisa Amreen;Sanket Goel
Presents corrections to the paper, Benchmarking Power Generation From 2 Multiple Wastewater Electrolytes in Microbial 3 Fuel Cells With 3D Printed Disk-Electrodes.
对论文 "利用 3D 打印磁盘电极的微生物 3 燃料电池中 2 多种废水电解质的发电基准 "进行更正。
{"title":"Errata to “Benchmarking Power Generation From Multiple Wastewater Electrolytes in Microbial Fuel Cells With 3D Printed Disk-Electrodes”","authors":"Yuvraj Maphrio Mao;Khairunnisa Amreen;Sanket Goel","doi":"10.1109/TNB.2024.3443498","DOIUrl":"https://doi.org/10.1109/TNB.2024.3443498","url":null,"abstract":"Presents corrections to the paper, Benchmarking Power Generation From 2 Multiple Wastewater Electrolytes in Microbial 3 Fuel Cells With 3D Printed Disk-Electrodes.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"23 4","pages":"612-613"},"PeriodicalIF":3.7,"publicationDate":"2024-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=10718702","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142438541","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}
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