Skin health monitoring focuses on identifying diseases through the assessment of the mechanical properties of the skin. These properties may degrade with time, which can alter the skin's natural frequencies and the form of the modes associated with those frequencies. Exploring the skin's mechanical properties can enhance our understanding of its dynamics, improving clinical trials and diagnostics. In this work, the dynamics of the skin were measured using a laser-based non-invasive optical sensor experiment. We measured the skin's mechanical properties over time by analyzing its resonant frequencies and mode shapes. A nanocarrier gel and ketoconazole cream were topically applied to keep the skin hydrated and facilitate deeper penetration of the additives in the skin. Time-based research was used to assess the effect of different formulations on skin elasticity. Experimental results for the modulus of elasticity were compared with those obtained using Finite Element Analysis (FEA) simulations. We observed a reduction in frequencies of cream and gel-treated skin by 29.98% and 44.029% respectively compared to normal skin (frequency: 263.3 ± 1.18 Hz and Modulus of elasticity: 7.56 ± 2.60 MPa). A decrease in stiffness (function of frequency) attributed to increased water content, was observed in cream- and nanocarrier gel-treated skin compared to normal skin. Experimental and numerical results are found to be consistent with one another. This optical sensor-based approach has the potential for studying diseased skin mechanics and its response to gel and cream treatments, aiming to reduce skin disorder morbidity and severity.
{"title":"Influence of nanocarrier additives on biomechanical response of a rat skin.","authors":"Diplesh Gautam, Yashika Tomar, Pradeep Shukla, Vamshi Krishna Rapalli, Venkatesh Kp Rao, Gautam Singhvi","doi":"10.1109/TNB.2024.3471588","DOIUrl":"10.1109/TNB.2024.3471588","url":null,"abstract":"<p><p>Skin health monitoring focuses on identifying diseases through the assessment of the mechanical properties of the skin. These properties may degrade with time, which can alter the skin's natural frequencies and the form of the modes associated with those frequencies. Exploring the skin's mechanical properties can enhance our understanding of its dynamics, improving clinical trials and diagnostics. In this work, the dynamics of the skin were measured using a laser-based non-invasive optical sensor experiment. We measured the skin's mechanical properties over time by analyzing its resonant frequencies and mode shapes. A nanocarrier gel and ketoconazole cream were topically applied to keep the skin hydrated and facilitate deeper penetration of the additives in the skin. Time-based research was used to assess the effect of different formulations on skin elasticity. Experimental results for the modulus of elasticity were compared with those obtained using Finite Element Analysis (FEA) simulations. We observed a reduction in frequencies of cream and gel-treated skin by 29.98% and 44.029% respectively compared to normal skin (frequency: 263.3 ± 1.18 Hz and Modulus of elasticity: 7.56 ± 2.60 MPa). A decrease in stiffness (function of frequency) attributed to increased water content, was observed in cream- and nanocarrier gel-treated skin compared to normal skin. Experimental and numerical results are found to be consistent with one another. This optical sensor-based approach has the potential for studying diseased skin mechanics and its response to gel and cream treatments, aiming to reduce skin disorder morbidity and severity.</p>","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"PP ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2024-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142375388","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 : 2024-10-03DOI: 10.1109/TNB.2024.3471813
Hassan A Almarshad, Abozer Elderdery, Fawaz O Alenazy, Shawgi A Elissidig
The purpose of this study was to investigate the effects of two different types of gold nanoparticles (AuNPs) delivered by intraperitoneal (IP) injection on blood and kidney tissue changes in a mouse model. Three groups of fifteen adult male BALB/c healthy mice, weighing approximately 25-30 g, were used for the experiment and designated G1, G2, and G3, respectively. G1 mice received vehicle, whereas G2 and G3 received an IP injection of 10 mg/kg body weight of methoxy poly ethylene glycol gold nanoparticles (PEG-AuNPs) and fluorescently dye labeled gold nanoparticles (Dye-AuNPs), respectively. Hematological parameters were measured based on the standard complete blood cell count (CBC) technique. The two nanoparticles, i.e., PEG-AuNPs and Dye-AuNPs, significantly reduced most red blood cell (RBC) parameters in the groups with the exception of a nonsignificant effect on hemoglobin (HBG) levels. Both gold nanoparticles, i.e., PEG-AuNPs and Dye-AuNPs, led to a reduced RBC count, mean corpuscular volume (MCV), and mean corpuscular hemoglobin (MCH) level when compared with the control. Notably, Dye-AuNPs and PEG-AuNPs resulted in a considerably higher RBC distribution RDW-(CV % and SD fL). Glomerular injury was suggested based on the development of hydropic degeneration and the presence of a protein-rich fluid inside the tubules. Renal tissue and blood indices changed significantly in response to the two nanoparticles, suggesting possible organ injury.
{"title":"Impact of Gold Nanoparticles Intraperitoneal Injection on Mice's Erythrocytes and Renal Tissue.","authors":"Hassan A Almarshad, Abozer Elderdery, Fawaz O Alenazy, Shawgi A Elissidig","doi":"10.1109/TNB.2024.3471813","DOIUrl":"https://doi.org/10.1109/TNB.2024.3471813","url":null,"abstract":"<p><p>The purpose of this study was to investigate the effects of two different types of gold nanoparticles (AuNPs) delivered by intraperitoneal (IP) injection on blood and kidney tissue changes in a mouse model. Three groups of fifteen adult male BALB/c healthy mice, weighing approximately 25-30 g, were used for the experiment and designated G1, G2, and G3, respectively. G1 mice received vehicle, whereas G2 and G3 received an IP injection of 10 mg/kg body weight of methoxy poly ethylene glycol gold nanoparticles (PEG-AuNPs) and fluorescently dye labeled gold nanoparticles (Dye-AuNPs), respectively. Hematological parameters were measured based on the standard complete blood cell count (CBC) technique. The two nanoparticles, i.e., PEG-AuNPs and Dye-AuNPs, significantly reduced most red blood cell (RBC) parameters in the groups with the exception of a nonsignificant effect on hemoglobin (HBG) levels. Both gold nanoparticles, i.e., PEG-AuNPs and Dye-AuNPs, led to a reduced RBC count, mean corpuscular volume (MCV), and mean corpuscular hemoglobin (MCH) level when compared with the control. Notably, Dye-AuNPs and PEG-AuNPs resulted in a considerably higher RBC distribution RDW-(CV % and SD fL). Glomerular injury was suggested based on the development of hydropic degeneration and the presence of a protein-rich fluid inside the tubules. Renal tissue and blood indices changed significantly in response to the two nanoparticles, suggesting possible organ injury.</p>","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"PP ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2024-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142371713","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 : 2024-09-25DOI: 10.1109/TNB.2024.3467695
Lokendra Chouhan
Through this paper, a three-dimensional molecular communication (MC) inside a cuboid container is considered. Instead of normal diffusion phenomenon, the anomalous diffusion phenomenon is incorporated which enhances the practicability of the model. The Fick's law is re-defined for the considering rectangular coordinate system in which information carrying molecules (ICMs) diffuse anomalously in the environment. The impact of flow of the fluid along the +x direction in the environment is also considered. Moreover, considering free propagator phenomenon, the expressions of spatio-temporal probability density function (PDF) of the ICMs is derived for the considered model. Further, the novel closed-form expressions for first arrival time density (FATD) of the ICM, survival probability (SP) at any time, and its corresponding first arrival probability (FAP) are also derived. Furthermore, the considered MC model is also analyzed in terms of minimum bit-error-rate (BER) using log-likelihood ratio test (LLRT) optimal detector. The derived expressions are verified using MATLAB based particle-based and Monte-Carlo simulations.
{"title":"Impact of Anomalous Diffusion Phenomenon on Molecular Information Delivery in Bounded Environment.","authors":"Lokendra Chouhan","doi":"10.1109/TNB.2024.3467695","DOIUrl":"https://doi.org/10.1109/TNB.2024.3467695","url":null,"abstract":"<p><p>Through this paper, a three-dimensional molecular communication (MC) inside a cuboid container is considered. Instead of normal diffusion phenomenon, the anomalous diffusion phenomenon is incorporated which enhances the practicability of the model. The Fick's law is re-defined for the considering rectangular coordinate system in which information carrying molecules (ICMs) diffuse anomalously in the environment. The impact of flow of the fluid along the +x direction in the environment is also considered. Moreover, considering free propagator phenomenon, the expressions of spatio-temporal probability density function (PDF) of the ICMs is derived for the considered model. Further, the novel closed-form expressions for first arrival time density (FATD) of the ICM, survival probability (SP) at any time, and its corresponding first arrival probability (FAP) are also derived. Furthermore, the considered MC model is also analyzed in terms of minimum bit-error-rate (BER) using log-likelihood ratio test (LLRT) optimal detector. The derived expressions are verified using MATLAB based particle-based and Monte-Carlo simulations.</p>","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"PP ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2024-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142345830","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 : 2024-09-17DOI: 10.1109/tnb.2024.3462461
Xiaohua Wan, Yulong Hu, Dehui Qiu, Juan Zhang, Xiaotong Wang, Fa Zhang, Bin Hu
{"title":"A novel framework for tongue feature extraction framework based on sublingual vein segmentation","authors":"Xiaohua Wan, Yulong Hu, Dehui Qiu, Juan Zhang, Xiaotong Wang, Fa Zhang, Bin Hu","doi":"10.1109/tnb.2024.3462461","DOIUrl":"https://doi.org/10.1109/tnb.2024.3462461","url":null,"abstract":"","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"16 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142250067","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 : 2024-09-11DOI: 10.1109/tnb.2024.3457755
Zicheng Wang, Haojie Wang, Yanfeng Wang, Junwei Sun
{"title":"State Observer Synchronization of Three-dimensional Chaotic Oscillatory Systems Based on DNA Strand Displacement","authors":"Zicheng Wang, Haojie Wang, Yanfeng Wang, Junwei Sun","doi":"10.1109/tnb.2024.3457755","DOIUrl":"https://doi.org/10.1109/tnb.2024.3457755","url":null,"abstract":"","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"17 1","pages":""},"PeriodicalIF":3.9,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142213695","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}
The analysis and comprehension of multi-omics data has emerged as a prominent topic in the field of bioinformatics and data science. However, the sparsity characteristics and high dimensionality of omics data pose difficulties in terms of extracting meaningful information. Moreover, the heterogeneity inherent in multiple omics sources makes the effective integration of multi-omics data challenging To tackle these challenges, we propose MFCC-SAtt, a multi-level feature contrast clustering model based on self-attention to extract informative features from multi-omics data. MFCC-SAtt treats each omics type as a distinct modality and employs autoencoders with self-attention for each modality to integrate and compress their respective features into a shared feature space. By utilizing a multi-level feature extraction framework along with incorporating a semantic information extractor, we mitigate optimization conflicts arising from different learning objectives. Additionally, MFCC-SAtt guides deep clustering based on multi-level features which further enhances the quality of output labels. By conducting extensive experiments on multi-omics data, we have validated the exceptional performance of MFCC-SAtt. For instance, in a pan-cancer clustering task, MFCC-SAtt achieved an accuracy of over 80.38%.
{"title":"Strategic Multi-Omics Data Integration via Multi-Level Feature Contrasting and Matching","authors":"Jinli Zhang;Hongwei Ren;Zongli Jiang;Zheng Chen;Ziwei Yang;Yasuko Matsubara;Yasushi Sakurai","doi":"10.1109/TNB.2024.3456797","DOIUrl":"10.1109/TNB.2024.3456797","url":null,"abstract":"The analysis and comprehension of multi-omics data has emerged as a prominent topic in the field of bioinformatics and data science. However, the sparsity characteristics and high dimensionality of omics data pose difficulties in terms of extracting meaningful information. Moreover, the heterogeneity inherent in multiple omics sources makes the effective integration of multi-omics data challenging To tackle these challenges, we propose MFCC-SAtt, a multi-level feature contrast clustering model based on self-attention to extract informative features from multi-omics data. MFCC-SAtt treats each omics type as a distinct modality and employs autoencoders with self-attention for each modality to integrate and compress their respective features into a shared feature space. By utilizing a multi-level feature extraction framework along with incorporating a semantic information extractor, we mitigate optimization conflicts arising from different learning objectives. Additionally, MFCC-SAtt guides deep clustering based on multi-level features which further enhances the quality of output labels. By conducting extensive experiments on multi-omics data, we have validated the exceptional performance of MFCC-SAtt. For instance, in a pan-cancer clustering task, MFCC-SAtt achieved an accuracy of over 80.38%.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"23 4","pages":"579-590"},"PeriodicalIF":3.7,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142213696","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 : 2024-09-03DOI: 10.1109/TNB.2024.3453372
Abdullah Baz, Jacob Wekalao, Ngaira Mandela, Shobhit K Patel
This paper presents a terahertz metasurface based sensor design incorporating graphene and other plasmonic materials for highly sensitive detection of different chemicals. The proposed sensor employs the combination of multiple resonator designs - including circular and square ring resonators - to attain enhanced sensitivity among other performance parameters. Machine learning techniques like Random Forest regression, are employed to enhance the sensor design and predict its performance. The optimized sensor demonstrates excellent sensitivity of 417 GHzRIU-1 and a low detection limit of 0.264 RIU for ethanol and benzene detection. Furthermore, the integration of machine learning cuts down the simulation time and computational requirements by approximately 90% without compromising accuracy. The sensor's unique design and performance characteristics, including its high-quality factor of 14.476, position it as a promising candidate for environmental monitoring and chemical sensing applications. Moreover, it also demonstrates potential for 2-bit encoding applications through strategic modulation of graphene chemical potential values. On the other hand, it also shows prospects of 2-bit encoding applications via the modulation of graphene chemical. This work provides a major advancement to the terahertz sensing application by proposing new materials, structures, and methods in computation in order to develop a high-performance chemical sensor.
{"title":"Design and Performance Evaluation of Machine Learning-based Terahertz Metasurface Chemical Sensor.","authors":"Abdullah Baz, Jacob Wekalao, Ngaira Mandela, Shobhit K Patel","doi":"10.1109/TNB.2024.3453372","DOIUrl":"10.1109/TNB.2024.3453372","url":null,"abstract":"<p><p>This paper presents a terahertz metasurface based sensor design incorporating graphene and other plasmonic materials for highly sensitive detection of different chemicals. The proposed sensor employs the combination of multiple resonator designs - including circular and square ring resonators - to attain enhanced sensitivity among other performance parameters. Machine learning techniques like Random Forest regression, are employed to enhance the sensor design and predict its performance. The optimized sensor demonstrates excellent sensitivity of 417 GHzRIU<sup>-1</sup> and a low detection limit of 0.264 RIU for ethanol and benzene detection. Furthermore, the integration of machine learning cuts down the simulation time and computational requirements by approximately 90% without compromising accuracy. The sensor's unique design and performance characteristics, including its high-quality factor of 14.476, position it as a promising candidate for environmental monitoring and chemical sensing applications. Moreover, it also demonstrates potential for 2-bit encoding applications through strategic modulation of graphene chemical potential values. On the other hand, it also shows prospects of 2-bit encoding applications via the modulation of graphene chemical. This work provides a major advancement to the terahertz sensing application by proposing new materials, structures, and methods in computation in order to develop a high-performance chemical sensor.</p>","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"PP ","pages":""},"PeriodicalIF":3.7,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142125606","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}
Circular RNAs (circRNAs) play a crucial role in gene regulation and association with diseases because of their unique closed continuous loop structure, which is more stable and conserved than ordinary linear RNAs. As fundamental work to clarify their functions, a large number of computational approaches for identifying circRNA formation have been proposed. However, these methods fail to fully utilize the important characteristics of back-splicing events, i.e., the positional information of the splice sites and the interaction features of its flanking sequences, for predicting circRNAs. To this end, we hereby propose a novel approach called SIDE for predicting circRNA back-splicing events using only raw RNA sequences. Technically, SIDE employs a dual encoder to capture global and interactive features of the RNA sequence, and then a decoder designed by the contrastive learning to fuse out discriminative features improving the prediction of circRNAs formation. Empirical results on three real-world datasets show the effectiveness of SIDE. Further analysis also reveals that the effectiveness of SIDE.
环状 RNA(circRNA)因其独特的闭合连续环状结构而在基因调控和疾病相关方面发挥着至关重要的作用,这种结构比普通线性 RNA 更稳定、更保守。作为阐明其功能的基础性工作,人们提出了大量识别 circRNA 形成的计算方法。然而,这些方法未能充分利用反向剪接事件的重要特征,即剪接位点的位置信息及其侧翼序列的相互作用特征来预测 circRNA。为此,我们提出了一种名为 SIDE 的新方法,仅利用原始 RNA 序列预测 circRNA 的反向剪接事件。在技术上,SIDE 采用双重编码器捕捉 RNA 序列的全局和交互特征,然后通过对比学习设计解码器,融合出辨别特征,从而提高 circRNA 形成的预测能力。在三个真实世界数据集上的实证结果表明了 SIDE 的有效性。进一步的分析还显示了 SIDE 的有效性。
{"title":"A Representation Learning Approach for Predicting circRNA Back-Splicing Event via Sequence-Interaction-Aware Dual Encoder","authors":"Chengxin He;Lei Duan;Huiru Zheng;Xinye Wang;Lili Guan;Jiaxuan Xu","doi":"10.1109/TNB.2024.3454079","DOIUrl":"10.1109/TNB.2024.3454079","url":null,"abstract":"Circular RNAs (circRNAs) play a crucial role in gene regulation and association with diseases because of their unique closed continuous loop structure, which is more stable and conserved than ordinary linear RNAs. As fundamental work to clarify their functions, a large number of computational approaches for identifying circRNA formation have been proposed. However, these methods fail to fully utilize the important characteristics of back-splicing events, i.e., the positional information of the splice sites and the interaction features of its flanking sequences, for predicting circRNAs. To this end, we hereby propose a novel approach called SIDE for predicting circRNA back-splicing events using only raw RNA sequences. Technically, SIDE employs a dual encoder to capture global and interactive features of the RNA sequence, and then a decoder designed by the contrastive learning to fuse out discriminative features improving the prediction of circRNAs formation. Empirical results on three real-world datasets show the effectiveness of SIDE. Further analysis also reveals that the effectiveness of SIDE.","PeriodicalId":13264,"journal":{"name":"IEEE Transactions on NanoBioscience","volume":"23 4","pages":"603-611"},"PeriodicalIF":3.7,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142125605","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}