IEEE Transactions on NanoBioscience最新文献

Effective IDS Error Correction Algorithms for DNA Storage Channels with Multiple Output Sequences. 多输出序列DNA存储通道的有效IDS纠错算法。

IF 3.7 4区生物学

IEEE Transactions on NanoBioscience Pub Date : 2025-04-08 DOI: 10.1109/TNB.2025.3558853

Caiyun Deng, Guojun Han, Pengchao Han, Yi Fang

{"title":"Effective IDS Error Correction Algorithms for DNA Storage Channels with Multiple Output Sequences.","authors":"Caiyun Deng, Guojun Han, Pengchao Han, Yi Fang","doi":"10.1109/TNB.2025.3558853","DOIUrl":"https://doi.org/10.1109/TNB.2025.3558853","url":null,"abstract":"DNA data storage is a cutting-edge storage technique due to its high density, replicability, and long-term capability. It involves encoding, insertion, deletion, and substitution (IDS) channels for data synthesis and sequencing, and decoding processes. The IDS channels that feature multiple output sequences are prone to IDS errors, complicating the decoding process and degrading the performance of DNA data storage. To address this issue, we investigate effective IDS error correction algorithms considering two encoding schemes in DNA data storage. Specifically in the encoding process, we use marker codes (MC) and embedded marker codes (EMC) as inner codes, respectively, both connected to low-density parity-check (LDPC) codes as outer codes. First, we propose the segmented progressive matching (SPM) algorithm to infer the consensus sequence from multiple output sequences, thereby facilitating the decoding processes. Moreover, when using MC as the inner code, we propose a synchronous decoding algorithm based on the Hidden Markov Model (SDH) to infer the a posteriori probability (APP) of base symbols, which supports the external decoding algorithm. Furthermore, when the inner code is EMC, we propose the iterative external decoding (IED) algorithm. IED integrates synchronous decoding with embedded normalized min-sum decoding (ENMS) to achieve an enhanced APP for external decoding, enabling lower bit-error rate (BER) transmission. Meanwhile, we reduce the complexity of the external decoder by minimizing checksum node computations. Comparing the two schemes reveals that the SDH algorithm with MC as the inner code offers a lightweight solution for DNA data storage. In contrast, the IED with EMC demonstrates superior decoding performance with a linear complexity scale by the number of iterations. Compared with existing studies, simulation results show that our proposed decoding algorithm reduces the BER by 21.72% ~ 99.75%.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"PP ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2025-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143811400","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}

引用次数: 0

IEEE Transactions on NanoBioscience Publication Information IEEE纳米生物科学学报

IF 3.7 4区生物学

IEEE Transactions on NanoBioscience Pub Date : 2025-03-26 DOI: 10.1109/TNB.2025.3551707

引用次数: 0

IEEE Transactions on NanoBioscience Information for Authors IEEE纳米生物科学信息汇刊

IF 3.7 4区生物学

IEEE Transactions on NanoBioscience Pub Date : 2025-03-26 DOI: 10.1109/TNB.2025.3551711

引用次数: 0

Carbon Nitride-Supported Copper Oxide for Non-Enzymatic Glucose Sensor: A Multi-Platform Approach Utilizing Electrochemical, Field Effect Transistor and Microcontroller-based IoT Systems. 用于非酶葡萄糖传感器的碳氮负载氧化铜：利用电化学，场效应晶体管和基于微控制器的物联网系统的多平台方法。

IF 3.7 4区生物学

IEEE Transactions on NanoBioscience Pub Date : 2025-03-21 DOI: 10.1109/TNB.2025.3553622

Chandan Saha, Pooja Kumari, Lungelo Mgenge, Sarit Ghosh, Venkata Perla, Harishchandra Singh, Kaushik Mallick

{"title":"Carbon Nitride-Supported Copper Oxide for Non-Enzymatic Glucose Sensor: A Multi-Platform Approach Utilizing Electrochemical, Field Effect Transistor and Microcontroller-based IoT Systems.","authors":"Chandan Saha, Pooja Kumari, Lungelo Mgenge, Sarit Ghosh, Venkata Perla, Harishchandra Singh, Kaushik Mallick","doi":"10.1109/TNB.2025.3553622","DOIUrl":"10.1109/TNB.2025.3553622","url":null,"abstract":"The new generation of glucose biosensors has attracted significant research interest due to its fast response, high stability, reproducibility, portability and low detection limit. In this work, various types of high-performance non-enzymatic glucose sensors are proposed, based on carbon nitride supported copper oxide nanoparticles (CNCO). The hybrid system was synthesized using a modified deposition-precipitation route where the copper oxide nanoparticles were dispersed on the carbon nitride matrix. The X-ray diffraction pattern revealed that the copper oxide nanoparticles exhibit a high degree of crystallinity with a monoclinic structure. The synthesized hybrid material was used as a catalyst for the electrochemical detection of glucose in the range of 0 to 15.6 mM, demonstrating a detection limit of 0.59 mM and a sensitivity of 0.53 mA.mM-1.cm-2. The CNCO based extended gate field effect transistor, at different glucose concentrations (1-9 mM), showed limit of detection and sensitivity values of 0.59 mM and 0.065 mA.mM-1.cm-2, respectively. A microcontroller-based glucose sensor was also implemented in this study that exhibited the sensitivity value of 1.46 mV/mM within the concentration range of 2-8 mM. The carbon nitride-supported copper oxide-based glucose sensors exhibit excellent reproducibility, sufficient stability and high selectivity, making them a promising candidate for real-life sensing applications.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"PP ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143673712","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}

引用次数: 0

Enhanced Redundant Residue Number System Codes for Reliable Diffusive Molecular Communication. 可靠扩散分子通信的增强型冗余数系统码。

IF 3.7 4区生物学

IEEE Transactions on NanoBioscience Pub Date : 2025-03-20 DOI: 10.1109/TNB.2025.3553183

Liwei Mu

{"title":"Enhanced Redundant Residue Number System Codes for Reliable Diffusive Molecular Communication.","authors":"Liwei Mu","doi":"10.1109/TNB.2025.3553183","DOIUrl":"10.1109/TNB.2025.3553183","url":null,"abstract":"This paper introduces an improved redundant residue number system (RRNS) encoding method to enhance the reliability of information transmission in diffusive molecular communication (DMC). In addressing the 2-1 mapping issue in RRNS encoding, we propose a simplified low-mapping solution that effectively avoids the 2-1 mapping problem, thereby simplifying the decoding process. Leveraging the superior performance of the low-mapping algorithm, we further developed a direct decision algorithm that further simplifies the decoding algorithm by omitting the traditional minimum distance decision-making steps. Furthermore, this study delves into the impact of modulus selection on RRNS decoding performance and provides guidelines for optimizing code construction. Through simulation experiments on DMC channels, we have validated the effectiveness of the proposed RRNS encoding method, especially when employing binary concentration shift keying (BCSK) modulation and considering intersymbol interference (ISI). The simulation results show that the proposed encoding method not only significantly reduces the bit error rate (BER) but also fully meets the requirements of DMC systems, offering a promising new direction for the development of molecular communication technology. With these improvements, our method not only enhances the reliability of information transmission in DMC systems but also lays a solid foundation for future research and applications in molecular communication technology.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"PP ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143669794","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}

引用次数: 0

A High Sensitive Nanomaterial Coated Side Polished Fiber Sensor for Detection of Cardiac Troponin I Antibody. 一种用于检测心肌肌钙蛋白I抗体的高灵敏度纳米材料涂层侧抛光纤维传感器。

IF 3.7 4区生物学

IEEE Transactions on NanoBioscience Pub Date : 2025-03-06 DOI: 10.1109/TNB.2025.3548823

M Valliammai, J Mohanraj, Balasubramanian Esakki, Lung-Jieh Yang, Chua-Chin Wang, A Bakiya

{"title":"A High Sensitive Nanomaterial Coated Side Polished Fiber Sensor for Detection of Cardiac Troponin I Antibody.","authors":"M Valliammai, J Mohanraj, Balasubramanian Esakki, Lung-Jieh Yang, Chua-Chin Wang, A Bakiya","doi":"10.1109/TNB.2025.3548823","DOIUrl":"https://doi.org/10.1109/TNB.2025.3548823","url":null,"abstract":"The advent of evanescent field based fiber optic biosensor and advancements in nanotechnology has create an excellent opportunity in label-free detection of biomarkers which plays vital role in the early, rapid and accurate diagnosis of acute diseases. In this work, we demonstrate a high sensitive Molybdenum Tungsten Disulfide (MoWS2) coated side polished fiber (SPF) biosensor for accurate and early diagnosis of cardio vascular disease (CVD). The Cardiac Troponins I (cTnI) is identified as a biomarker of interest for early and rapid diagnonis of CVD. The proposed SPF biosensor exhibits surface plasmonic resonance (SPR) detection due to the evanescent field interaction between MoWS2 nano coated side polished region and anti-CTnI. The proposed SPF biosensor possess the high sensitivity of 82% to detect the cTnI antibody with a limit of detection (LOD) about 17.5 pg/mL. The peak SPR shift have been calculated as 61 nm for analyte concentrations of 500 pg/mL Moreover, the proposed SPF biosensor possess the high degree of selectivity and environmental stability to CTnI among three analytes such as CTnI, Estrogen and Glucose. The hydrophobic interactions of MoWS2 and cTnI antibody leads to chemical free biofunctionalization of antibody in the sensing region. Hence, the simulation results shows the surface interaction strength calculated as 1.29 KJ mol-1/nm2 in order to evaluate the hydrophobic interactions. Thus, the proposed optical biosensor is a promising candidate for \"point-of-care\" testing of CVD disorders and preclinical assessments.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"PP ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143572947","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}

引用次数: 0

Synthesis of heteroatom doped polymer coated nanomaterials for slow and controlled drug release in the physiological microenvironment. 杂原子掺杂聚合物包被纳米材料在生理微环境下缓释药物的合成。

IF 3.7 4区生物学

IEEE Transactions on NanoBioscience Pub Date : 2025-03-06 DOI: 10.1109/TNB.2025.3548916

Nargish Parvin, Tapas Kumar Mandal, Sang Woo Joo

{"title":"Synthesis of heteroatom doped polymer coated nanomaterials for slow and controlled drug release in the physiological microenvironment.","authors":"Nargish Parvin, Tapas Kumar Mandal, Sang Woo Joo","doi":"10.1109/TNB.2025.3548916","DOIUrl":"https://doi.org/10.1109/TNB.2025.3548916","url":null,"abstract":"Objective: This study aimed to develop doped carbon dots and coat them with carboxyl-polymer to explore their applications in imaging living tissue cells and achieving targeted drug release, particularly for tumor therapy.Methods: The synthesis of NP-CDs involved a one-pot hydrothermal reaction of seaweed powder, ethylene diamine, and phosphoric acid at atmospheric pressure. Subsequently, the NP-CDs were coated with carboxyl-mounted PEG to create PEG@NP-CDs, serving as a nano carrier for delivering the anti-cancer drug Doxorubicin (DOX). The drug delivery capabilities of PEG@NP-CDs were assessed, and their sensitivity to variations in pH value was studied.Results: The hydrothermal reaction successfully yielded NP-CDs with distinctive fluorescence properties, exhibiting green fluorescence at 430 nm and varying emission peaks depending on the excitation wavelength used. The subsequent coating of NP-CDs with carboxyl-mounted PEG resulted in PEG@NP-CDs, which demonstrated biocompatibility and potential for drug delivery applications. The MTT assay confirmed the high biocompatibility of PEG@NP-CDs, rendering them suitable for biomedical applications.Conclusions: The study successfully developed a straightforward method to synthesize CDs doped with nitrogen and phosphorus, which exhibited green fluorescence and sensitivity to excitation wavelengths. These nanomaterials have potential for imaging living tissue cells and achieving slow drug release. Their drug delivery capabilities, especially pH sensitivity, make them promising for targeted therapy, particularly in tumors. The biocompatibility of PEG@NP-CDs further supports their safe biomedical use. Overall, PEG@NP-CDs offer a valuable tool for simultaneous imaging and drug delivery, with promising applications in tumor detection and therapy.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"PP ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143572949","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}

引用次数: 0

Spatial Pattern Switching Strategy: a Successful Application in the Bimolecular Model. 空间模式转换策略：在双分子模型中的成功应用。

IF 3.7 4区生物学

IEEE Transactions on NanoBioscience Pub Date : 2025-02-28 DOI: 10.1109/TNB.2025.3546665

Yifeng Luan, Min Xiao, Jinling Liang, Wenwu Yu, Wei Xing Zheng

{"title":"Spatial Pattern Switching Strategy: a Successful Application in the Bimolecular Model.","authors":"Yifeng Luan, Min Xiao, Jinling Liang, Wenwu Yu, Wei Xing Zheng","doi":"10.1109/TNB.2025.3546665","DOIUrl":"https://doi.org/10.1109/TNB.2025.3546665","url":null,"abstract":"The formation of spatial patterns plays a crucial role in the study of system spatiotemporal dynamics. Previous research has demonstrated that spatial patterns can effectively characterize the macro-scopic spatial structure of the reaction-diffusion system. While specific pattern structures, such as the hexagonal, mixed, and stripe pattern, have been identified, the interconnection between these patterns appears to be isolated and invariant. To facilitate the selection and switching between individual spatial patterns, the hybrid control strategy is applied to the bimolecular model for the first time. For the classical bimolecular model of the chemical reaction-diffusion system, the incorporation of two-dimensional diffusion extends its reaction space to the two-dimensional plane. The Turing instability conditions are obtained for the controlled bimolecular system. Through the weakly nonlinear analysis, the amplitude equations are derived near the Turing bifurcation threshold. Furthermore, we investigate the impact of each control parameter on the Turing bifurcation threshold and determine the distribution of spatial patterns and their stability through the amplitude equations. Simulation results indicate that by selecting appropriate control parameters, we can suppress the occurrence of Turing instability and facilitate transitions between the spatial patterns. The findings of the analysis offer valuable insights into the dynamics and control of pattern formation in reaction-diffusion systems.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"PP ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143541780","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}

引用次数: 0

High fault-tolerant DNA image storage system based on VAE. 基于 VAE 的高容错 DNA 图像存储系统。

IF 3.7 4区生物学

IEEE Transactions on NanoBioscience Pub Date : 2025-02-21 DOI: 10.1109/TNB.2025.3544401

Yuyang Lu, Zhihao Zhang, Jing Yang, Cheng Zhang

{"title":"High fault-tolerant DNA image storage system based on VAE.","authors":"Yuyang Lu, Zhihao Zhang, Jing Yang, Cheng Zhang","doi":"10.1109/TNB.2025.3544401","DOIUrl":"10.1109/TNB.2025.3544401","url":null,"abstract":"DNA-based storage has emerged as a promising storage paradigm due to its immense storage potential. However, the error-prone nature of DNA sequencing and synthesis processes limits this potential. Image data is typically compressed before storage, and even a single mismatch can lead to catastrophic error propagation during decompression, rendering the image unrecoverable. To reduce the error rate of DNA storage-based image compression, we have designed a high fault-tolerant DNA image storage system and applied it to image compression for DNA storage. This system achieves significant improvements in both image data compression ratio and resilience through three key innovations: 1) Using a Variational Autoencoder (VAE) to compress the image into uniformly sized latent variable blocks, followed by further compression via Singular Value Decomposition (SVD); 2) Quantizing the floating-point numbers in the latent variable blocks and applying rotational coding to the resulting ternary sequences, effectively ensuring positive constraints on homopolymer run lengths and GC content; 3) Optimizing the error-correction scheme to best recover each type of error by quantizing it back to its original value. Through image scaling, we adjust the compression ratio, and the comparative results of image compression simulations demonstrate the performance of the proposed model, highlighting its superiority in fault tolerance and storage density.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"PP ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143541767","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}

引用次数: 0

DNA-CBIR: DNA Translation Inspired Codon Pattern-based Deep Image Feature Extraction for Content-based Image Retrieval. DNA- cbir：基于DNA翻译启发密码子模式的深度图像特征提取，用于基于内容的图像检索。

IF 3.7 4区生物学

IEEE Transactions on NanoBioscience Pub Date : 2025-02-10 DOI: 10.1109/TNB.2025.3540102

Jitesh Pradhan, Hathiram Nenavath

{"title":"DNA-CBIR: DNA Translation Inspired Codon Pattern-based Deep Image Feature Extraction for Content-based Image Retrieval.","authors":"Jitesh Pradhan, Hathiram Nenavath","doi":"10.1109/TNB.2025.3540102","DOIUrl":"10.1109/TNB.2025.3540102","url":null,"abstract":"DNA is emerging as a promising medium for storing huge volumes of data in a confined space that remains intact for thousands of years. Although this technique is very efficient, especially for multimedia data like images, there is a lack of efficient searching and retrieval technique. This paper addresses this issue and proposes a novel Content Based Image Retrieval (CBIR) technique to retrieve similar images from the generated DNA-based image feature vectors. The features are obtained by a novel encoding scheme that uses the three Most-Significant Bits from the images and converts them into a string of nucleotides that follow run length and GC constraints to form DNA planes stored in a DNA medium. The nucleotides in these planes are interpreted through three consecutive sequences forming codons. The codon-based features are then utilized to perform instance-based image retrieval. The DNA planes are further adapted and implemented on diverse deep learning architectures, including ResNet-50, VGG-16, VGG-19, and Inception V3, to facilitate classification-based image retrieval tasks. The system's performance has been assessed using a range of datasets, encompassing coral, medical, and multi-label images. Experimental results demonstrate that the proposed approach achieves notable improvements when compared to existing state-of-the-art methods.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"PP ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143541757","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}

引用次数: 0