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IEEE Transactions on Nanobioscience

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https://www.readbyqxmd.com/read/28715334/exploring-the-feasibility-of-a-dna-computer-design-of-an-alu-using-sticker-based-dna-model
#1
Mayukh Sarkar, Prasun Ghosal, Saraju P Mohanty
Since its inception, DNA computing has advanced to offer an extremely powerful, energy-efficient emerging technology for solving hard computational problems with its inherent massive parallelism and extremely high data density. This would be much more powerful and general purpose when combined with other existing well known algorithmic solutions that exist for conventional computing architectures using a suitable ALU. Thus, a specifically designed DNA ALU that can address operations suitable for both domains can mitigate the gap between these two...
July 13, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28708564/improved-statistical-fault-detection-technique-and-application-to-biological-phenomena-modeled-by-s-systems
#2
Majdi Mansouri, Mohamed Nounou, Hazem Nounou
In our previous work [1], we have demonstrated the effectiveness of the linear multiscale PCA-based moving window (MW)- generalized likelihood ratio test (GLRT) technique over the classical PCA and MSPCA-based GLRT methods. The developed fault detection algorithm provided optimal properties by maximizing the detection probability for a particular false alarm rate with different values of windows, however, most real systems are nonlinear, which make the linear PCA method not able to tackle the issue of nonlinearity to a great extent...
July 12, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28708563/evolving-spatial-clusters-of-genomic-regions-from-high-throughput-chromatin-conformation-capture-data
#3
Xiangtao Li, Shijing Ma, Ka-Chun Wong
High-throughput chromosome-conformation-capture (Hi-C) methods have revealed a multitude of structural insights into interphase chromosomes. In this paper, we elucidate the spatial clusters of genomic regions from Hi-C contact maps by formulating the underlying problem as a global optimization problem. Given its nonconvex objective and nonnegativity constraints, we implement several evolutionary algorithms and compare their performance with non-negative matrix factorization, revealing novel insights into the problem...
July 11, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28692983/robust-principal-component-analysis-regularized-by-truncated-nuclear-norm-for-identifying-differentially-expressed-genes
#4
Ya-Xuan Wang, Ying-Lian Gao, Jin-Xing Liu, Xiang-Zhen Kong, Hai-Jun Li
Identifying differentially expressed genes from thousands of genes is a challenging task. Robust Principal Component Analysis (RPCA) is an efficient method in the identification of differentially expressed genes. RPCA method uses nuclear norm to approximate the rank function. However, theoretical studies showed that the nuclear norm minimizes all singular values, so it may not be the best solution to approximate the rank function. The truncated nuclear norm is defined as the sum of some smaller singular values, which may achieve a better approximation of the rank function than nuclear norm...
July 4, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28692982/multi-dielectric-brownian-dynamics-and-design-space-exploration-studies-of-permeation-in-ion-channels
#5
May Siksik, Vikram Krishnamurthy
This paper proposes a multi-dielectric Brownian Dynamics (BD) simulation framework for Design-Space-Exploration (DSE) studies of ion-channel permeation. The goal of such DSE studies is to estimate the channel modeling-parameters that minimize the mean-squared-error between the simulated and expected "permeation characteristics". To address this computational challenge, we use a methodology based on statistical inference that utilizes knowledge of channel structure to prune the design space. We demonstrate the proposed framework and DSE methodology using a case study based on the KcsA ion channel in which the design space is successfully reduced from a 6-dimensional space to a 2-dimensional space...
July 4, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28682262/cell-like-spiking-neural-p-systems-with-request-rules
#6
Linqiang Pan, Tingfang Wu, Yansen Su, Athanasios V Vasilakos
Cell-like spiking neural P systems (in short, cSN P systems) are a class of distributed and parallel computation models inspired by both the way in which neurons process information and communicate to each other by means of spikes and the compartmentalized structures of living cells. cSNP systems have been proved to be Turing universal if more spikes can be produced by consuming some spikes or spikes can be replicated. In this work, in order to answer the open problem whether this functioning of producing more spikes and replicating spikes can be avoided by using some strategy without the loss of computation power, we introduce cSN P systems with request rules, which have classical spiking rules and forgetting rules, and also request rules in the skin membrane...
July 3, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28650820/terahertz-channel-model-and-link-budget-analysis-for-intrabody-nanoscale-communication
#7
Hadeel Elayan, Raed M Shubair, Josep M Jornet, Pedram Johari
Nanosized devices operating inside the human body open up new prospects in the healthcare domain. In vivo wireless nanosensor networks (iWNSNs) will result in a plethora of applications ranging from intrabody health-monitoring to drug- delivery systems. With the development of miniature plasmonic signal sources, antennas and detectors, wireless communications among intrabody nanodevices will expectedly be enabled at both the Terahertz Band (0.1-10 THz) as well as optical frequencies (400-750 THz). This result motivates the analysis of the phenomena affecting the propagation of electromagnetic signals inside the human body...
June 22, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28644811/applying-pattern-recognition-to-high-resolution-images-to-determine-cellular-signaling-status
#8
Michael F Lohrer, Darrin M Hanna, Yang Liu, Kang-Hsin Wang, Fu-Tong Liu, Ted A Laurence, Gang-Yu Liu
Two frequently used tools to acquire high-resolution images of cells are scanning electron microscopy (SEM) and atomic force microscopy (AFM). The former provides a nanometer resolution view of cellular features rapidly and with high throughput, while the latter enables visualizing hydrated and living cells. In current practice, these images are viewed by eye to determine cellular status, e.g. activated versus resting. Automatic and quantitative data analysis is lacking. This work develops an algorithm of pattern recognition that works very effectively for AFM and SEM images...
June 21, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28641266/an-approach-to-identifying-phenomena-accompanying-micro-and-nanoparticles-in-contact-with-irregular-vessel-walls
#9
K Talaska, A Ferreira
OBJECTIVE: The objective of this manuscript is to present the method for determining the nature and values of the forces needed to set micro and nanoparticles sitting immobile at the blood vessel wall in motion. METHODS: The problem was tackled in two ways. Microparticles were examined as objects coming into contact with the wall with the actual large arteriole-type vessel structure. The forces acting on microparticles 10 μm, 30 μm and 50 μm in diameter were determined: drag force FD, lift force FL, electrostatic force FE and gravity force FG...
June 19, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28622672/physiological-effects-of-single-and-multi-walled-carbon-nanotubes-on-rice-seedlings
#10
Hao Zhang, Mengxia Yue, Xueke Zheng, Chengshen Xie, Hong Zhou, Lijia Li
In this paper, single-walled carbon nanotubes (SWCNTs) and multi-walled carbon nanotubes (MWCNTs) were found to accelerate leaf growth and development of rice seedlings at a low concentration (20 mg/L), accompanied with the increased chlorophyll content and net photosynthetic rate (PN). Quantitative real-time polymerase chain reaction (RT-PCR) results indicated that both SWCNTs and MWCNTs significantly increased expression of genes associated with chloroplast development and cell sizes. Further analysis revealed that the abscisic acid (ABA) content decreased and the gibberellin (GA) content increased while the content of O2 and H2O2 was slightly elevated and the activities of antioxidative enzymes (SOD, EC 1...
June 14, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28613180/atomic-force-microscopy-in-characterizing-cell-mechanics-for-biomedical-applications-a-review
#11
Mi Li, Dan Dang, Lianqing Liu, Ning Xi, Yuechao Wang
Cell mechanics is a novel label-free biomarker for indicating cell states and pathological changes. The advent of atomic force microscopy (AFM) provides a powerful tool for quantifying the mechanical properties of single living cells in aqueous conditions. The wide use of AFM in characterizing cell mechanics in the past two decades have yielded remarkable novel insights in understanding the development and progression of certain diseases such as cancer, showing the huge potential of cell mechanics for practical applications in the field of biomedicine...
June 9, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28613179/unsupervised-learning-of-spike-pattern-for-seizure-detection-and-wavefront-estimation-of-high-resolution-micro-electrocorticographic-%C3%AE-ecog-data
#12
Yilin Song, Yao Wang, Jonathan Viventi
For the past few years, we have developed flexible, active, multiplexed recording devices for high resolution recording over large, clinically relevant areas in the brain. While this technology has enabled a much higher-resolution view of the electrical activity of the brain, the analytical methods to process, categorize and respond to the huge volumes of seizure data produced by these devices have not yet been developed. In this work we proposed an unsupervised learning framework for spike analysis, which by itself reveals spike pattern...
June 9, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28600257/search-for-more-effective-microsatellite-markers-for-forensics-with-next-generation-sequencing
#13
Bowen Tan, Zicheng Zhao, Zhe Zhang, Shengbin Li, Shuai Cheng Li
Published by the Combined DNA Index System (CODIS) program of the Federal Bureau of Investigation (FBI) in 1997, the 13 core short tandem repeat (STR) loci are widely adopted as genetic markers in forensic applications, e.g., identity testing and paternity testing. However, these loci may be biased and suffer from reduced sensitivities towards specific population groups. In addition, the rapid growth of entries in forensic databases raises the chance of random hits, which can cause false recognitions of criminal suspects...
June 7, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28541904/diffusion-based-model-for-synaptic-molecular-communication-channel
#14
Tooba Khan, Bilgesu A Bilgin, Ozgur B Akan
Computational methods have been extensively used to understand underlying dynamics of molecular communication methods employed by nature. One very effective and popular approach is to utilize a Monte Carlo simulation. Although it is very reliable, this method can have a very high computational cost, which in some cases renders the simulation impractical. Therefore, in this paper, for the special case of an excitatory synaptic molecular communication channel, we present a novel mathematical model for the diffusion and binding of neurotransmitters that takes into account the effects of synaptic geometry in three-dimensional space and re-absorption of neurotransmitters by the transmitting neuron...
May 23, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28541903/alzheimer-s-disease-classification-based-on-individual-hierarchical-networks-constructed-with-3d-texture-features
#15
Jin Liu, Jianxin Wang, Bin Hu, Fang-Xiang Wu, Yi Pan
Brain network plays an important role in representing abnormalities in Alzheimers disease (AD) and mild cognitive impairment (MCI), which includes MCIc (MCI converted to AD) and MCInc (MCI not converted to AD). In our previous study, we proposed an AD classification approach based on individual hierarchical networks constructed with 3D texture features of brain images. However, we only used edge features of the networks without node features of the networks. In this study, we propose a framework of the combination of multiple kernels to combine edge features and node features for AD classification...
May 23, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28541219/inferring-social-influence-of-anti-tobacco-mass-media-campaign
#16
Qianyi Zhan, Jiawei Zhang, Philip Yu, Sherry Emery, Junyuan Xie
Anti-tobacco mass media campaigns are designed to influence tobacco users. It has been proved that campaigns will produce users' changes in awareness, knowledge, and attitudes, and also produce meaningful behavior change of audience. Antismoking television advertising is the most important part in the campaign. Meanwhile nowadays successful online social networks are creating new media environment, however little is known about the relation between social conversations and anti-tobacco campaigns. This paper aims to infer social influence of these campaigns, and the problem is formally referred to as the Social Influence inference of anti-Tobacco mass mEdia campaigns (SITE) problem...
May 23, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28541218/fast-post-processing-pipeline-for-optical-projection-tomography
#17
Xiaoqin Tang, Dennis V D Zwaan, Alan Zammit, Kristian F D Rietveld, Fons J Verbeek
To improve the effectiveness and efficiency of the optical projection tomography (OPT) 3D reconstruction, we presented a fast post-processing pipeline including cropping, background subtraction, center of rotation (COR) correction and 3D reconstruction. Regarding to the COR correction, a novel algorithm based on interest point detection of sinogram is proposed by considering the principle of OPT imaging. Instead of locating the COR on single sinogram, we intermittently and evenly select sinograms in the detected full range of specimen to make the located COR more convincing...
May 23, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28541217/towards-concurrent-data-transmission-exploiting-plasmid-diversity-by-bacterial-conjugation
#18
Bige D Unluturk, M Siblee Islam, Sasitharan Balasubramaniam, Stepan Ivanov
The progress of molecular communication is tightly connected to the progress of nanomachine design. State-of-the-art states that nanomachines can be built either from novel nanomaterials by the help of nanotechnology or they can be built from living cells which are modified to function as intended by synthetic biology. With the growing need of biomedical applications of MC, we focus on developing bio-compatible communication systems by engineering the cells to become MC nanomachines. Since this approach relies on modifying cellular functions, the improvements in the performance can only be achieved by integrating new biological properties...
May 23, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28541216/robust-and-efficient-biomolecular-clustering-of-tumor-based-on-p-norm-sigular-value-decomposition
#19
Xiang-Zhen Kong, Jin-Xing Liu, Chun-Hou Zheng, Mi-Xiao Hou, Juan Wang
High dimensionality has become a typical feature of biomolecular data. In this paper, a novel dimension reduction method named p-norm singular value decomposition (PSVD) is proposed to seek the low-rank approximation matrix to the biomolecular data. To enhance the robustness to outliers, the Lp-norm is taken as the error function and the Schatten p-norm is used as the regularization function in the optimization model. To evaluate the performance of PSVD, the Kmeans clustering method is then employed for tumor clustering based on the low-rank approximation matrix...
May 18, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28541215/balanceali-multiple-ppi-network-alignment-with-balanced-high-coverage-and-consistency
#20
Jianliang Gao, Bo Song, Weimao Ke, Xiaohua Hu
Coverage and consistency are two most considered metrics to evaluate the effectiveness of network alignment. But they are a pair of contradictory evaluation metrics in PPI network alignment. It is difficult, if not impossible, to achieve high coverage and consistency simultaneously. Furthermore, existing methods of multiple PPI network alignment mostly ignore k-coverage or k-consistency, where k indicates the number of aligned species. In this paper, we propose BalanceAli, a novel approach for global alignment of multiple PPI networks that achieves high k-coverage and k-consistency simultaneously...
May 18, 2017: IEEE Transactions on Nanobioscience
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