Pub Date : 2024-03-07DOI: 10.1109/TNB.2024.3373597
Jiayu Sun;Yang Jiao;Fei Pan;Shuk Han Cheng;Dong Sun
The efficient application of the newly developed gene-editing method CRISPR/Cas9 requires more accurate intracellular gene delivery. Traditional delivery approaches, such as lipotransfection and non-viral delivery methods, must contend with major problems to overcome the drawbacks of low efficiency, high toxicity, and cell-type dependency. The high-throughput microdroplet-based single-cell transfection method presented herein provides an alternative method for delivering genome-editing reagents into single living cells. By accurately controlling the number of exogenous plasmids in microdroplets, this method can achieve high-efficiency delivery of nucleic acids to different types of single cells. This paper presents a high-throughput quantitative DNA transfection method for single cells and explores the optimal DNA transfection conditions for specific cell lines. The transfection efficiency of cells at different concentrations of DNA in microdroplets is measured. Under the optimized transfection conditions, the method is used to construct gene-knockout cancer cell lines to determine specific gene functions through the CRISPR/Cas9 knockout system. In a case study, the migration ability of TRIM72 knockout cancer cells is inhibited, and the tumorigenicity of cells in a zebrafish tumor model is reduced. A single-cell microfluidic chip is designed to achieve CRISPR/Cas9 DNA transfection, dramatically improving the transfection efficiency of difficult-to-transfect cells. This research demonstrates that the microdroplet method developed herein has a unique advantage in CRISPR/Cas9 gene-editing applications.
新开发的基因编辑方法 CRISPR/Cas9 的高效应用需要更精确的细胞内基因递送。传统的递送方法，如脂质转染和非病毒递送方法，必须克服低效率、高毒性和细胞类型依赖性等主要问题。本文介绍的基于微滴的高通量单细胞转染方法为向单个活细胞递送基因组编辑试剂提供了另一种方法。通过精确控制微滴中外源质粒的数量，这种方法可以实现向不同类型的单细胞高效递送核酸。本文介绍了一种高通量定量 DNA 单细胞转染方法，并探讨了特定细胞系的最佳 DNA 转染条件。测量了微滴中不同浓度 DNA 对细胞的转染效率。在优化的转染条件下，该方法被用于构建基因敲除癌症细胞系，通过 CRISPR/Cas9 基因敲除系统确定特定基因的功能。在一项案例研究中，TRIM72基因敲除癌细胞的迁移能力受到抑制，斑马鱼肿瘤模型中细胞的致瘤性降低。设计了一种单细胞微流控芯片来实现 CRISPR/Cas9 DNA 转染，大大提高了难以转染细胞的转染效率。这项研究表明，本文开发的微滴方法在 CRISPR/Cas9 基因编辑应用中具有独特的优势。
{"title":"A High-Throughput Microdroplet-Based Single Cell Transfection Method for Gene Knockout Based on the CRISPR/Cas9 System","authors":"Jiayu Sun;Yang Jiao;Fei Pan;Shuk Han Cheng;Dong Sun","doi":"10.1109/TNB.2024.3373597","DOIUrl":"10.1109/TNB.2024.3373597","url":null,"abstract":"The efficient application of the newly developed gene-editing method CRISPR/Cas9 requires more accurate intracellular gene delivery. Traditional delivery approaches, such as lipotransfection and non-viral delivery methods, must contend with major problems to overcome the drawbacks of low efficiency, high toxicity, and cell-type dependency. The high-throughput microdroplet-based single-cell transfection method presented herein provides an alternative method for delivering genome-editing reagents into single living cells. By accurately controlling the number of exogenous plasmids in microdroplets, this method can achieve high-efficiency delivery of nucleic acids to different types of single cells. This paper presents a high-throughput quantitative DNA transfection method for single cells and explores the optimal DNA transfection conditions for specific cell lines. The transfection efficiency of cells at different concentrations of DNA in microdroplets is measured. Under the optimized transfection conditions, the method is used to construct gene-knockout cancer cell lines to determine specific gene functions through the CRISPR/Cas9 knockout system. In a case study, the migration ability of TRIM72 knockout cancer cells is inhibited, and the tumorigenicity of cells in a zebrafish tumor model is reduced. A single-cell microfluidic chip is designed to achieve CRISPR/Cas9 DNA transfection, dramatically improving the transfection efficiency of difficult-to-transfect cells. This research demonstrates that the microdroplet method developed herein has a unique advantage in CRISPR/Cas9 gene-editing applications.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"23 2","pages":"378-388"},"PeriodicalIF":3.9,"publicationDate":"2024-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140039243","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 : 2024-03-06DOI: 10.1109/TNB.2024.3396142
Zhao-Cai Wang;Xian Wu;Kun Liang;Tun-Hua Wu
The traveling car renter problem (TCRP) is a variant of the Traveling Salesman Problem (TSP) wherein the salesman utilizes rented cars for travel. The primary objective of this problem is to identify a solution that minimizes the cumulative operating costs. Given its classification as a non-deterministic polynomial (NP) problem, traditional computers are not proficient in effectively resolving it. Conversely, DNA computing exhibits unparalleled advantages when confronted with NP-hard problems. This paper presents a DNA algorithm, based on the Adleman-Lipton model, as a proposed approach to address TCRP. The solution for TCRP can be acquired by following a series of fundamental steps, including coding, interaction, and extraction. The time computing complexity of the proposed DNA algorithm is $boldsymbol {O}(boldsymbol {n}^{boldsymbol {2}}boldsymbol {m})$ for TCRP with n cities and m types of cars. By conducting simulation experiments, the solutions for certain instances of TCRP are computed and compared to those obtained by alternative algorithms. The proposed algorithm further illustrates the potential of DNA computing, as a form of parallel computing, to address more intricate large-scale problems.
旅行汽车租赁问题（TCRP）是旅行推销员问题（TSP）的一种变体，其中推销员利用租赁的汽车进行旅行。该问题的主要目标是找出一个能使累计运营成本最小化的解决方案。鉴于该问题被归类为非确定性多项式 (NP) 问题，传统计算机无法有效解决该问题。相反，DNA 计算在面对 NP 难问题时却表现出无与伦比的优势。本文提出了一种基于 Adleman-Lipton 模型的 DNA 算法，作为解决 TCRP 的建议方法。通过一系列基本步骤，包括编码、交互和提取，可以获得 TCRP 的解决方案。对于有 n 个城市和 m 种汽车的 TCRP，所提出的 DNA 算法的时间计算复杂度为 O(n2m)。通过模拟实验，计算出了 TCRP 某些实例的解决方案，并与其他算法的解决方案进行了比较。所提出的算法进一步说明了 DNA 计算作为并行计算的一种形式，在解决更复杂的大规模问题方面的潜力。
{"title":"Exploring the Potential of DNA Computing for Complex Big Data Problems: A Case Study on the Traveling Car Renter Problem","authors":"Zhao-Cai Wang;Xian Wu;Kun Liang;Tun-Hua Wu","doi":"10.1109/TNB.2024.3396142","DOIUrl":"10.1109/TNB.2024.3396142","url":null,"abstract":"The traveling car renter problem (TCRP) is a variant of the Traveling Salesman Problem (TSP) wherein the salesman utilizes rented cars for travel. The primary objective of this problem is to identify a solution that minimizes the cumulative operating costs. Given its classification as a non-deterministic polynomial (NP) problem, traditional computers are not proficient in effectively resolving it. Conversely, DNA computing exhibits unparalleled advantages when confronted with NP-hard problems. This paper presents a DNA algorithm, based on the Adleman-Lipton model, as a proposed approach to address TCRP. The solution for TCRP can be acquired by following a series of fundamental steps, including coding, interaction, and extraction. The time computing complexity of the proposed DNA algorithm is \u0000<inline-formula> <tex-math>$boldsymbol {O}(boldsymbol {n}^{boldsymbol {2}}boldsymbol {m})$ </tex-math></inline-formula>\u0000 for TCRP with n cities and m types of cars. By conducting simulation experiments, the solutions for certain instances of TCRP are computed and compared to those obtained by alternative algorithms. The proposed algorithm further illustrates the potential of DNA computing, as a form of parallel computing, to address more intricate large-scale problems.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"23 3","pages":"391-402"},"PeriodicalIF":3.7,"publicationDate":"2024-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140854996","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 : 2024-03-01DOI: 10.1109/TNB.2024.3371224
Thi Phuong Anh Tran;Anh Hue Luong;Wei-Chih Lin
Known for its water solubility, flexibility, strong adhesion, and eco-friendly nature, polyvinyl alcohol (PVA) is widely used in various industries. In the medical field, it is used for applications such as creating bandages and orthopaedic devices. Incorporating sodium alginate (SA) into PVA membranes enhances their structural integrity, breathability, and permeability, thereby minimising the risk of cellular damage in the wound zone. Moreover, the addition of tamanu oil (C alophyllum inophyllum L.) and silver nanoparticles, both of which are known for their antibacterial properties and benefits in traditional wound healing, further enhances the membranes’ wound-healing effectiveness. Following production, the membranes undergo a series of tests designed to evaluate their physical properties as well as their antioxidant and antibacterial capabilities. Subsequently, in vitro testing is conducted using human skin cells; experiments on Wistar rats are then performed. Numerous experiments have consistently demonstrated that the performance of polyvinyl alcohol/sodium alginate/tamanu oil (PVA/SA/Oil) membrane is superior to that of polyvinyl alcohol/sodium alginate/tamanu oil/silver nanoparticles (PVA/SA/Oil/Ag NP) membrane. Specifically, the polyvinyl alcohol/sodium alginate (PVA/SA) combination exhibits an impressive wound-healing rate of 98.82% after 15 days, with cells maintaining a high viability of 92% in a nourishing environment. Moreover, these membranes exhibit exceptional resistance to the oxidation of free radicals, surpassing the 70% threshold, and they possess antibacterial activity against Staphylococcus aureus subsp. aureus in vitro. Based on the obtained results, the nanofiber membranes composed of polyvinyl alcohol/ alginate/ tamanu oil, with or without silver nanoparticles, have shown potential as wound dressings in the wound care discipline.
{"title":"Characterizations of Centrifugal Electrospun Polyvinyl Alcohol/Sodium Alginate/Tamanu Oil/Silver Nanoparticles Wound Dressing","authors":"Thi Phuong Anh Tran;Anh Hue Luong;Wei-Chih Lin","doi":"10.1109/TNB.2024.3371224","DOIUrl":"10.1109/TNB.2024.3371224","url":null,"abstract":"Known for its water solubility, flexibility, strong adhesion, and eco-friendly nature, polyvinyl alcohol (PVA) is widely used in various industries. In the medical field, it is used for applications such as creating bandages and orthopaedic devices. Incorporating sodium alginate (SA) into PVA membranes enhances their structural integrity, breathability, and permeability, thereby minimising the risk of cellular damage in the wound zone. Moreover, the addition of tamanu oil (C alophyllum inophyllum L.) and silver nanoparticles, both of which are known for their antibacterial properties and benefits in traditional wound healing, further enhances the membranes’ wound-healing effectiveness. Following production, the membranes undergo a series of tests designed to evaluate their physical properties as well as their antioxidant and antibacterial capabilities. Subsequently, in vitro testing is conducted using human skin cells; experiments on Wistar rats are then performed. Numerous experiments have consistently demonstrated that the performance of polyvinyl alcohol/sodium alginate/tamanu oil (PVA/SA/Oil) membrane is superior to that of polyvinyl alcohol/sodium alginate/tamanu oil/silver nanoparticles (PVA/SA/Oil/Ag NP) membrane. Specifically, the polyvinyl alcohol/sodium alginate (PVA/SA) combination exhibits an impressive wound-healing rate of 98.82% after 15 days, with cells maintaining a high viability of 92% in a nourishing environment. Moreover, these membranes exhibit exceptional resistance to the oxidation of free radicals, surpassing the 70% threshold, and they possess antibacterial activity against Staphylococcus aureus subsp. aureus in vitro. Based on the obtained results, the nanofiber membranes composed of polyvinyl alcohol/ alginate/ tamanu oil, with or without silver nanoparticles, have shown potential as wound dressings in the wound care discipline.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"23 2","pages":"368-377"},"PeriodicalIF":3.9,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=10457035","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140012540","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 : 2024-02-13DOI: 10.1109/TNB.2024.3365737
Ghazaleh Kianfar;Mehdi Azadi;Jamshid Abouei;Arash Mohammadi;Konstantinos N. Plataniotis
Advancements in biotechnology and molecular communication have enabled the utilization of nanomachines in Wireless Body Area Networks (WBAN2) for applications such as drug delivery, cancer detection, and emergency rescue services. To study these networks effectively, it is essential to develop an ideal propagation model that includes the channel response between each pair of in-range nanomachines and accounts for the interference received at each receiver node. In this paper, we employ an advection-diffusion equation to obtain a deterministic channel matrix through a vascular WBAN2. Additionally, the closed forms of inter-symbol interference (ISI) and co-channel interference (CCI) are derived for both full duplex (FDX) and half duplex transmission (HDX) modes. By applying these deterministic formulations, we then present the stochastic equivalents of the ideal channel model and interference to provide an innovative communication model by simultaneously incorporating CCI, ISI, and background noise. Finally, we evaluate the results with numerous experiments and use signal-to-interference-plus-noise ratio (SINR) and capacity as metrics.
{"title":"Wireless Body Area Nanonetworks via Vascular Molecular Communication","authors":"Ghazaleh Kianfar;Mehdi Azadi;Jamshid Abouei;Arash Mohammadi;Konstantinos N. Plataniotis","doi":"10.1109/TNB.2024.3365737","DOIUrl":"10.1109/TNB.2024.3365737","url":null,"abstract":"Advancements in biotechnology and molecular communication have enabled the utilization of nanomachines in Wireless Body Area Networks (WBAN2) for applications such as drug delivery, cancer detection, and emergency rescue services. To study these networks effectively, it is essential to develop an ideal propagation model that includes the channel response between each pair of in-range nanomachines and accounts for the interference received at each receiver node. In this paper, we employ an advection-diffusion equation to obtain a deterministic channel matrix through a vascular WBAN2. Additionally, the closed forms of inter-symbol interference (ISI) and co-channel interference (CCI) are derived for both full duplex (FDX) and half duplex transmission (HDX) modes. By applying these deterministic formulations, we then present the stochastic equivalents of the ideal channel model and interference to provide an innovative communication model by simultaneously incorporating CCI, ISI, and background noise. Finally, we evaluate the results with numerous experiments and use signal-to-interference-plus-noise ratio (SINR) and capacity as metrics.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"23 2","pages":"355-367"},"PeriodicalIF":3.9,"publicationDate":"2024-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139729535","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 : 2024-01-25DOI: 10.1109/TNB.2024.3354810
Shobhit K. Patel;Jaymit Surve;Abdullah Baz;Yagnesh Parmar
Biosensors are needed for today’s health monitoring system for detecting different biomolecules. Graphene is a monolayer material that can be utilized to sense biomolecules and design biosensors. We have proposed a Graphene-Gold-Silver hybrid structure design based on Zinc Oxide which gives sensitive performance to detect hemoglobin biomolecules. The advanced biosensor designed based on this hybrid structure shows the highest sensitivity of 1000 nm/RIU which is far better concerning similar structure previously analyzed. The graphene-gold-silver hybrid structure is presented for its possible reflectance results and electric field results. The E-field results match well with the reflectance results given by the sensitive hybrid structure. The sensing biomolecules are presented above the structure where a combination of graphene-gold-silver hybrid structure improves the sensitivity to a great extent. The optimized parameters are obtained by applying variations in the physical parameters of the design. The machine learning algorithm employed for reflectance prediction shows a high prediction accuracy and can be utilized for simulation resource reduction. The proposed biosensor can be used in real-time hemoglobin monitoring.
{"title":"Optimization of Novel 2D Material Based SPR Biosensor Using Machine Learning","authors":"Shobhit K. Patel;Jaymit Surve;Abdullah Baz;Yagnesh Parmar","doi":"10.1109/TNB.2024.3354810","DOIUrl":"10.1109/TNB.2024.3354810","url":null,"abstract":"Biosensors are needed for today’s health monitoring system for detecting different biomolecules. Graphene is a monolayer material that can be utilized to sense biomolecules and design biosensors. We have proposed a Graphene-Gold-Silver hybrid structure design based on Zinc Oxide which gives sensitive performance to detect hemoglobin biomolecules. The advanced biosensor designed based on this hybrid structure shows the highest sensitivity of 1000 nm/RIU which is far better concerning similar structure previously analyzed. The graphene-gold-silver hybrid structure is presented for its possible reflectance results and electric field results. The E-field results match well with the reflectance results given by the sensitive hybrid structure. The sensing biomolecules are presented above the structure where a combination of graphene-gold-silver hybrid structure improves the sensitivity to a great extent. The optimized parameters are obtained by applying variations in the physical parameters of the design. The machine learning algorithm employed for reflectance prediction shows a high prediction accuracy and can be utilized for simulation resource reduction. The proposed biosensor can be used in real-time hemoglobin monitoring.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"23 2","pages":"328-335"},"PeriodicalIF":3.9,"publicationDate":"2024-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139563924","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 : 2024-01-22DOI: 10.1109/TNB.2024.3356522
Xuncai Zhang;Fuzhen Zhou
DNA storage stands out from other storage media due to its high capacity, eco-friendliness, long lifespan, high stability, low energy consumption, and low data maintenance costs. To standardize the DNA encoding system, maintain consistency in character representation and transmission, and link binary, base, and character together, this paper combines the encoding method with ASCII code to construct an ASCII-DNA encoding table. The encoding method can encode not only pure text information but also audio and video information and satisfies the GC content constraint and the homopolymer constraint, with the encoding density reaching 1.4 bits/nt. In particular, when encoding textual information, it directly skips the binary conversion process, which reduces the complexity of encoding, and increasing the encoding density to 1.6 bits/nt. In order to solve the problem of errors in sequences, under the influence of heuristic algorithms, this paper proposes a new error correction method (HMSA) by combining minimum Hamming distance, multiple sequence alignment, and encoding scheme. It can correct not only substitution, insertion, and deletion errors in Reads but also consecutive errors in Reads. It greatly improves the utilization of the Reads and avoids the waste of resources. Simulation results show that the recovery rate of Reads increases with the increasing number of sequencing times. When the number of erroneous bases in a 150nt sequence reaches 5nt, the error correction rate can exceed 96% by sequencing the base sequence only 10 times regardless of whether the errors are consecutive or not. Additionally, the HMSA error correction method is applicable to all coding schemes for lookup code table types.
{"title":"An Encoding Table Corresponding to ASCII Codes for DNA Data Storage and a New Error Correction Method HMSA","authors":"Xuncai Zhang;Fuzhen Zhou","doi":"10.1109/TNB.2024.3356522","DOIUrl":"10.1109/TNB.2024.3356522","url":null,"abstract":"DNA storage stands out from other storage media due to its high capacity, eco-friendliness, long lifespan, high stability, low energy consumption, and low data maintenance costs. To standardize the DNA encoding system, maintain consistency in character representation and transmission, and link binary, base, and character together, this paper combines the encoding method with ASCII code to construct an ASCII-DNA encoding table. The encoding method can encode not only pure text information but also audio and video information and satisfies the GC content constraint and the homopolymer constraint, with the encoding density reaching 1.4 bits/nt. In particular, when encoding textual information, it directly skips the binary conversion process, which reduces the complexity of encoding, and increasing the encoding density to 1.6 bits/nt. In order to solve the problem of errors in sequences, under the influence of heuristic algorithms, this paper proposes a new error correction method (HMSA) by combining minimum Hamming distance, multiple sequence alignment, and encoding scheme. It can correct not only substitution, insertion, and deletion errors in Reads but also consecutive errors in Reads. It greatly improves the utilization of the Reads and avoids the waste of resources. Simulation results show that the recovery rate of Reads increases with the increasing number of sequencing times. When the number of erroneous bases in a 150nt sequence reaches 5nt, the error correction rate can exceed 96% by sequencing the base sequence only 10 times regardless of whether the errors are consecutive or not. Additionally, the HMSA error correction method is applicable to all coding schemes for lookup code table types.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"23 2","pages":"344-354"},"PeriodicalIF":3.9,"publicationDate":"2024-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139520221","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 : 2024-01-15DOI: 10.1109/TNB.2024.3354571
Shatrughna Kumar;Archana Yadav;Boris A. Malomed
This work introduces a systematic approach for the development of Kretschmann configuration-based biosensors designed for non-invasive urine glucose detection. The methodology encompasses the utilization of various semiconductors, including Silicon (Si), Germanium (Ge), Gallium Nitride (GaN), Aluminum Nitride (AlN), and Indium Nitride (InN), in combination with a bimetallic layer (comprising Au and Ag films of equal thickness) to enhance the biosensor sensitivity. Additionally, 2D nanomaterials, such as Black Phosphorus and Graphene, are integrated into the semiconductor layers to enhance performance further. These configurations are meticulously optimized through the application of the transfer matrix method (TMM), and the sensing parameters are assessed using the angular modulation method. Among the semiconductors, AlN and GaN exhibit superior results. On these substrates, Graphene and Black phosphorous (BP) layers are applied, resulting in four final structures (thicknesses in nm): BK7/Au(26)/Ag(26)/Si(6)/BP(0.53)/Biosample, BK7/Au(26)/Ag(26)/AlN(14)/BP(0.53)/Biosample, BK7/Au(26)/Ag(26)/GaN(12)/BP(0.53)/Biosample, and BK7/Au(26)/Ag(26)/GaN(12)/Graphene(0.34)/Biosample. These biosensors achieve Sensitivity(° /RIU) and Figure of Merit (FoM) (1/RIU) of 380, 360, 440, 400, and 58.5, 90, 90.65, and 82.4, respectively. Subsequently, these high-performing sensors undergo testing with actual urine glucose samples. Among them, two biosensors, BK7/Au(26)/Ag(26)/AlN(14)/BP (0.53)/Biosample and BK7/Au(26)/Ag(26)/GaN(14)/Graphene(0.34)/Biosample, exhibit outstanding performance, with sensitivities (° /RIU) and FoM (1/RIU) of 394.44 & 294.44, and 112.6 & 92.01 respectively. A comparison is also made with relevant previously published work, revealing improved performance in glucose detection.
{"title":"Bimetal Thin Film, Semiconductors, and 2D Nanomaterials in SPR Biosensors: An Approach to Enhanced Urine Glucose Sensing","authors":"Shatrughna Kumar;Archana Yadav;Boris A. Malomed","doi":"10.1109/TNB.2024.3354571","DOIUrl":"10.1109/TNB.2024.3354571","url":null,"abstract":"This work introduces a systematic approach for the development of Kretschmann configuration-based biosensors designed for non-invasive urine glucose detection. The methodology encompasses the utilization of various semiconductors, including Silicon (Si), Germanium (Ge), Gallium Nitride (GaN), Aluminum Nitride (AlN), and Indium Nitride (InN), in combination with a bimetallic layer (comprising Au and Ag films of equal thickness) to enhance the biosensor sensitivity. Additionally, 2D nanomaterials, such as Black Phosphorus and Graphene, are integrated into the semiconductor layers to enhance performance further. These configurations are meticulously optimized through the application of the transfer matrix method (TMM), and the sensing parameters are assessed using the angular modulation method. Among the semiconductors, AlN and GaN exhibit superior results. On these substrates, Graphene and Black phosphorous (BP) layers are applied, resulting in four final structures (thicknesses in nm): BK7/Au(26)/Ag(26)/Si(6)/BP(0.53)/Biosample, BK7/Au(26)/Ag(26)/AlN(14)/BP(0.53)/Biosample, BK7/Au(26)/Ag(26)/GaN(12)/BP(0.53)/Biosample, and BK7/Au(26)/Ag(26)/GaN(12)/Graphene(0.34)/Biosample. These biosensors achieve Sensitivity(° /RIU) and Figure of Merit (FoM) (1/RIU) of 380, 360, 440, 400, and 58.5, 90, 90.65, and 82.4, respectively. Subsequently, these high-performing sensors undergo testing with actual urine glucose samples. Among them, two biosensors, BK7/Au(26)/Ag(26)/AlN(14)/BP (0.53)/Biosample and BK7/Au(26)/Ag(26)/GaN(14)/Graphene(0.34)/Biosample, exhibit outstanding performance, with sensitivities (° /RIU) and FoM (1/RIU) of 394.44 & 294.44, and 112.6 & 92.01 respectively. A comparison is also made with relevant previously published work, revealing improved performance in glucose detection.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"23 2","pages":"336-343"},"PeriodicalIF":3.9,"publicationDate":"2024-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139472336","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 : 2024-01-09DOI: 10.1109/TNB.2024.3351480
A A Siller-Ceniceros, J C Martinez-Loyola, A Leon-Buitimea, D C Almonte-Flores, M E Sanchez-Castro, J R Morones-Ramirez
In the field of coordination and bioorganometallic chemistry, a notable shift is occurring. This mini-review explores a new generation of carefully 3D-crafted coordination and organometallic complexes that differ from conventional structures. Emphasizing disease intervention and microbial control, these compounds, incorporate noble and transition metals, and aim to enhance therapeutic efficacy while minimizing potential health risks. The mini-review covers diverse applications, showcasing their effectiveness against bacteria, viruses, fungi, and as potential tools in cancer treatment. Additionally, it sheds light on the inventive aspects of these complexes within biological systems. By highlighting advancements in bioorganometallic chemistry, the review offers insights and guidance for future developments in safer and more effective therapeutics.
{"title":"Coordination and Bioorganometallic Chemistry: Exploring the Potential Applications of Metal Coordination and Organometallic Complexes in Medical and Microbiological Advancements.","authors":"A A Siller-Ceniceros, J C Martinez-Loyola, A Leon-Buitimea, D C Almonte-Flores, M E Sanchez-Castro, J R Morones-Ramirez","doi":"10.1109/TNB.2024.3351480","DOIUrl":"10.1109/TNB.2024.3351480","url":null,"abstract":"<p><p>In the field of coordination and bioorganometallic chemistry, a notable shift is occurring. This mini-review explores a new generation of carefully 3D-crafted coordination and organometallic complexes that differ from conventional structures. Emphasizing disease intervention and microbial control, these compounds, incorporate noble and transition metals, and aim to enhance therapeutic efficacy while minimizing potential health risks. The mini-review covers diverse applications, showcasing their effectiveness against bacteria, viruses, fungi, and as potential tools in cancer treatment. Additionally, it sheds light on the inventive aspects of these complexes within biological systems. By highlighting advancements in bioorganometallic chemistry, the review offers insights and guidance for future developments in safer and more effective therapeutics.</p>","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"PP ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139402648","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 : 2024-01-09DOI: 10.1109/TNB.2024.3351768
Na Liu;Tianyuan Zhang;Ziheng Chen;Yue Wang;Tao Yue;Jialin Shi;Gongxin Li;Chen Yang;Haowen Jiang;Yu Sun
Viscoelasticity is a crucial property of cells, which plays an important role in label-free cell characterization. This paper reports a model-fitting-free viscoelasticity calculation method, correcting the effects of frequency, surface adhesion and liquid resistance on AFM force-distance (FD) curves. As demonstrated by quantifying the viscosity and elastic modulus of PC-3 cells, this method shows high self-consistency and little dependence on experimental parameters such as loading frequency, and loading mode (Force-volume vs. PeakForce Tapping). The rapid calculating speed of less than 1ms per curve without the need for a model fitting process is another advantage. Furthermore, this method was utilized to characterize the viscoelastic properties of primary clinical prostate cells from 38 patients. The results demonstrate that the reported characterization method a comparable performance with the Gleason Score system in grading prostate cancer cells, This method achieves a high average accuracy of 97.6% in distinguishing low-risk prostate tumors (BPH and GS6) from higher-risk (GS7-GS10) prostate tumors and a high average accuracy of 93.3% in distinguishing BPH from prostate cancer.
{"title":"An AFM-Based Model-Fitting-Free Viscoelasticity Characterization Method for Accurate Grading of Primary Prostate Tumor","authors":"Na Liu;Tianyuan Zhang;Ziheng Chen;Yue Wang;Tao Yue;Jialin Shi;Gongxin Li;Chen Yang;Haowen Jiang;Yu Sun","doi":"10.1109/TNB.2024.3351768","DOIUrl":"10.1109/TNB.2024.3351768","url":null,"abstract":"Viscoelasticity is a crucial property of cells, which plays an important role in label-free cell characterization. This paper reports a model-fitting-free viscoelasticity calculation method, correcting the effects of frequency, surface adhesion and liquid resistance on AFM force-distance (FD) curves. As demonstrated by quantifying the viscosity and elastic modulus of PC-3 cells, this method shows high self-consistency and little dependence on experimental parameters such as loading frequency, and loading mode (Force-volume vs. PeakForce Tapping). The rapid calculating speed of less than 1ms per curve without the need for a model fitting process is another advantage. Furthermore, this method was utilized to characterize the viscoelastic properties of primary clinical prostate cells from 38 patients. The results demonstrate that the reported characterization method a comparable performance with the Gleason Score system in grading prostate cancer cells, This method achieves a high average accuracy of 97.6% in distinguishing low-risk prostate tumors (BPH and GS6) from higher-risk (GS7-GS10) prostate tumors and a high average accuracy of 93.3% in distinguishing BPH from prostate cancer.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"23 2","pages":"319-327"},"PeriodicalIF":3.9,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139402647","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 : 2024-01-04DOI: 10.1109/TNB.2024.3350001
Adrian Vidal;V. B. Wijekoon;Emanuele Viterbo
In nanopore sequencers, single-stranded DNA molecules (or k-mers) enter a small opening in a membrane called a nanopore and modulate the ionic current through the pore, producing a channel output in the form of a noisy piecewise constant signal. An important problem in DNA-based data storage is finding a set of k-mers, i.e. a DNA code, that is robust against noisy sample duplication introduced by nanopore sequencers. Good DNA codes should contain as many k-mers as possible that produce distinguishable current signals (squiggles) as measured by the sequencer. The dissimilarity between squiggles can be estimated using a bound on their pairwise error probability, which is used as a metric for code design. Unfortunately, code construction using the union bound is limited to small k’s due to the difficulty of finding maximum cliques in large graphs. In this paper, we construct large codes by concatenating codewords from a base code, thereby packing more information in a single strand while retaining the storage efficiency of the base code. To facilitate decoding, we include a circumfix in the base code to reduce the effect of the nanopore channel memory. We show that the decoding complexity scales as $text {O}{(}text {m}^{{2}} text { k}^{{3}}{)}$ , where m is the number of concatenated k-mers. Simulations show that the base code error rate is stable as m increases.
在纳米孔测序仪中，单链 DNA 分子（或 k-mer）进入被称为纳米孔的膜上的一个小开口，并调节通过孔道的离子电流，产生噪声片断常数信号形式的通道输出。基于 DNA 的数据存储中的一个重要问题是找到一组 k-mers，即 DNA 代码，该代码能够抵御纳米孔测序仪带来的噪声样本复制。好的 DNA 代码应包含尽可能多的 k-分子，这些 k-分子能产生测序仪测量到的可区分的电流信号（斜线）。方格之间的不相似性可以用它们的成对误差概率约束来估算，这被用作代码设计的衡量标准。遗憾的是，由于难以在大型图中找到最大小块，使用联合边界构建代码仅限于小 k。在本文中，我们通过串联基础代码中的编码词来构建大型代码，从而在单链中包含更多信息，同时保留基础代码的存储效率。为了便于解码，我们在基码中加入了一个圆周后缀，以减少纳米孔通道存储器的影响。我们的研究表明，解码复杂度为 $text {O}{(}text {m}^{{2}} text { k}^{{3}}{)}$ ，其中 m 是连接 k-mers 的数量。仿真结果表明，随着 m 的增加，基本编码错误率是稳定的。
{"title":"Concatenated Nanopore DNA Codes","authors":"Adrian Vidal;V. B. Wijekoon;Emanuele Viterbo","doi":"10.1109/TNB.2024.3350001","DOIUrl":"10.1109/TNB.2024.3350001","url":null,"abstract":"In nanopore sequencers, single-stranded DNA molecules (or k-mers) enter a small opening in a membrane called a nanopore and modulate the ionic current through the pore, producing a channel output in the form of a noisy piecewise constant signal. An important problem in DNA-based data storage is finding a set of k-mers, i.e. a DNA code, that is robust against noisy sample duplication introduced by nanopore sequencers. Good DNA codes should contain as many k-mers as possible that produce distinguishable current signals (squiggles) as measured by the sequencer. The dissimilarity between squiggles can be estimated using a bound on their pairwise error probability, which is used as a metric for code design. Unfortunately, code construction using the union bound is limited to small k’s due to the difficulty of finding maximum cliques in large graphs. In this paper, we construct large codes by concatenating codewords from a base code, thereby packing more information in a single strand while retaining the storage efficiency of the base code. To facilitate decoding, we include a circumfix in the base code to reduce the effect of the nanopore channel memory. We show that the decoding complexity scales as \u0000<inline-formula> <tex-math>$text {O}{(}text {m}^{{2}} text { k}^{{3}}{)}$ </tex-math></inline-formula>\u0000, where m is the number of concatenated k-mers. Simulations show that the base code error rate is stable as m increases.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"23 2","pages":"310-318"},"PeriodicalIF":3.9,"publicationDate":"2024-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139953450","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}
京公网安备 11010802042870号
京ICP备2023020795号-1
扫码关注我们
求助内容：
应助结果提醒方式：