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IEEE Transactions on Nanobioscience

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https://www.readbyqxmd.com/read/28541904/diffusion-based-model-for-synaptic-molecular-communication-channel
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
https://www.readbyqxmd.com/read/28534779/fpga-implementation-of-the-coupled-filtering-method-and-the-affine-warping-method
#8
Chen Zhang, Tianzhu Liang, Philip Mok, Weichuan Yu
In ultrasound image analysis, speckle tracking methods are widely applied to study the elasticity of body tissue. However, "feature-motion decorrelation" still remains as a challenge for speckle tracking methods. Recently, a coupled filtering method and an affine warping method were proposed to accurately estimate strain values when the tissue deformation is large. The major drawback of these methods is the high computational complexity. Even the GPU-based program requires a long time to finish the analysis...
May 17, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28504945/a-bio-inspired-hybrid-thermal-management-approach-for-three-dimensional-network-on-chip-systems
#9
Ranjita Dash, Jose Luis Risco-Martin, Ashok Kumar Turuk, Vinod Pangracious, Jose L Ayala, Amartya Majumdar
Three-dimensional network-on-chip systems are getting popular among the integrated circuit (IC) manufacturer because of reduced latency, heterogeneous integration of technologies on a single chip, high yield, and consumption of less interconnecting power. However, the addition of functional units in the Z-direction has resulted in higher on-chip temperature and appearance of local hotspots on the die. The increase in temperature degrades the performance, lifetime, reliability, and increases the maintenance cost of 3-D ICs...
May 15, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28504944/it-s-all-about-time
#10
Gaetano Valenza, Athanasios Vasilakos
New knowledge on multi-scale temporal dynamics linking nanobio-time series, seasonal changes, immune response, and gut mictobiota can milestone (neuro)science soon.
May 12, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28475065/catalytic-degradation-of-dichlorvos-using-biosynthesized-zero-valent-iron-nanoparticles
#11
Neha Mehrotra, Ravi M Tripathi, Fahmina Zafar, M P Singh
The removal of dichlorvos contamination from water is challenging task because of the presence of direct carbon to phosphorous covalent bond which make them resistant to chemical and thermal degradation. Although there have been reports in the literature for degradation of dichlorvos using nanomaterials but those are based on photocatalysis. In this study, we report a simple and rapid method for catalytic degradation of dichlorvos using protein capped zero valent iron nanoparticles (FeNPs). We have developed unprecedented reliable, clean, nontoxic, eco-friendly and cost effective biological method for the synthesis of uniformly distributed FeNPs...
May 2, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28459695/detection-of-glutathione-by-glutathione-s-transferase-nanoconjugate-ensemble-electrochemical-device
#12
Ujjwol Barman, Gargi Mukhopadhyay, Namami Goswami, Siddhartha S Ghosh, Roy P Palathinkal
This paper reports a novel electrochemical method for detection of Glutathione (GSH) using Glutathione-S-Transferase (GST) - ZnO composite nanoparticles to investigate the prospects of the method for detection of cancer at an early stage. The purified GST enzyme was bound with ZnO nanoparticles by electrostatic interactions and the nanocomposite was dropcast on a silicon dioxide wafer. The GST functionalized deposited layer was then used as a chemiresistive channel to detect conjugation reaction between GSH and 1-Chloro-2,4-Dinitrobenzene (CDNB)...
April 26, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28422687/theoretical-limits-on-multiuser-molecular-communication-in-internet-of-nano-bio-things
#13
Ergin Dinc, Ozgur B Akan
In nano-bio networks, multiple transmitter-receiver pairs will operate in the same medium. Both inter-symbol interference and multi-user interference can cause saturation at the receiver side, and this effect may cause an outage. Thus, we propose a tractable framework to calculate the theoretical operating points for fully absorbing receiver.
April 12, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28371780/pca-based-on-graph-laplacian-regularization-and-p-norm-for-gene-selection-and-clustering
#14
Chunmei Feng, Ying-Lian Gao, Jin-Xing Liu, Chun-Hou Zheng, Jiguo Yu
In modern molecular biology, the hotspots and difficulties of this field are identifying characteristic genes from gene expression data. Traditional reconstruction-error- minimization model Principal Component Analysis (PCA) as a matrix decomposition method uses quadratic error function´╝î which is known sensitive to outliers and noise. Hence it is necessary to learn a good PCA method when outliers and noise exist. In this paper, we develop a novel PCA method enforcing P-norm on error function and graph-Laplacian regularization term for matrix decomposition problem, which is called as PgLPCA...
March 31, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28368825/a-communication-theoretical-modeling-of-axonal-propagation-in-hippocampal-pyramidal-neurons
#15
Hamideh Ramezani, Ozgur B Akan
Understanding the fundamentals of communication among neurons, known as neuro-spike communication, leads to reach bio-inspired nanoscale communication paradigms. In this work, we focus on a part of neuro-spike communication, known as axonal transmission, and propose a realistic model for it. The shape of the spike during axonal transmission varies according to previously applied stimulations to the neuron and these variations affect the amount of information communicated between neurons. Hence, to reach an accurate model for neurospike communication, the memory of axon and its effect on the axonal transmission should be considered, which are not studied in the existing literature...
March 28, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28368824/monte-carlo-analysis-of-molecule-absorption-probabilities-in-diffusion-based-nanoscale-communication-systems-with-multiple-receivers
#16
Dogu Arifler, Dizem Arifler
For biomedical applications of nanonetworks, employing molecular communication for information transport is advantageous over nano-electromagnetic communication: molecular communication is potentially biocompatible and inherently energy-efficient. Recently, several studies have modeled receivers in diffusion-based molecular communication systems as "perfectly monitoring" or "perfectly absorbing" spheres based on idealized descriptions of chemoreception. In this work, we focus on perfectly absorbing receivers and present methods to improve the accuracy of simulation procedures that are used to analyze these receivers...
March 27, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28278478/abnormality-detection-in-correlated-gaussian-molecular-nano-networks-design-and-analysis
#17
Siavash Ghavami, Farshad Lahouti
A nano abnormality detection scheme (NADS) in molecular nano-networks is studied. This is motivated by the fact that early detection of diseases such as cancer play a crucial role in their successful treatment. The proposed NADS is in fact a two-tier network of sensor nano-machines (SNMs) in the first tier and a data-gathering node (DGN) at the sink. The SNMs detect the presence of competitor cells (abnormality) by variations in input and/or parameters of a nano-communications channel (NCC). The noise of SNMs as their nature suggest is considered correlated in time and space and herein assumed additive Gaussian...
March 2, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28362613/oscillatory-behaviors-in-genetic-regulatory-networks-mediated-by-microrna-with-time-delays-and-reaction-diffusion-terms
#18
Yuan Zhang, Haihong Liu, Fang Yan, Jin Zhou
In this paper, we investigate the oscillatory expression in Escherichia coli mediated by microRNA with time delays and reaction-diffusion terms. First of all, the integrated effects of delays and diffusions are first introduced into the genetic regulatory networks involving microRNAs, and a general model of genetic regulatory networks is then formulated. Secondly, two functional issues on gene regulatory networks, i.e. stability and oscillation of such model, are addressed in detail, and an explicit algorithm determining the properties of periodic oscillation is also presented...
March 1, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28328508/hapiso-an-accurate-method-for-the-haplotype-specific-isoforms-reconstruction-from-long-single-molecule-reads
#19
Serghei Mangul, Taegyun Harry Yang, Farhad Hormozdiari, Alexandra Marie Dainis, Elizabeth Tseng, Euan A Ashley, Alex Zelikovsky, Eleazar Eskin
Sequencing of RNA provides the possibility to study an individual's transcriptome landscape and determine allelic expression ratios. Single-molecule protocols generate multi-kilobase reads longer than most transcripts, allowing sequencing of complete haplotype isoforms. This allows partitioning the reads into two parental haplotypes. While the read length of the single-molecule protocols is long, the relatively high error rate limits the ability to accurately detect the genetic variants and assemble them into the haplotype-specific isoforms...
March 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28278480/mixture-modeling-of-2-d-gel-electrophoresis-spots-enhances-the-performance-of-spot-detection
#20
Michal Marczyk
2-D gel electrophoresis is the most commonly used method in biomedicine to separate even thousands of proteins in a complex sample on a single gel. Even though the technique is quite known, there is still a need to find an efficient and reliable method for detection of protein spots on gel image. In this paper, a three-step algorithm based on mixture of 2-D normal distribution functions is introduced to improve the efficiency of spot detection performed by the existing algorithms, namely Pinnacle software and watershed segmentation method...
March 2017: IEEE Transactions on Nanobioscience
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