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IEEE Transactions on Nanobioscience

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https://www.readbyqxmd.com/read/30640621/molecular-communications-with-molecular-circuit-based-transmitters-and-receivers
#1
Hamdan Awan, Chun Tung Chou
The performance of a communication link can be improved by maximising the mutual information between the input and output signals. This paper considers this maximisation problem in a molecular communication link where both the transmitter and receiver are molecular circuit. This general optimisation is hard to solve. We simplify the problem by limiting to reactions with linear reaction rates and molecular circuits with a limited number of species. We derive an expression of mutual information and use it for numerical maximisation...
January 11, 2019: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/30624223/dcde-an-efficient-deep-convolutional-divergence-encoding-method-for-human-promoter-recognition
#2
Wenxuan Xu, Lin Zhu, De-Shuang Huang
Efficient human promoter feature extraction is still a major challenge in genome analysis as it can better understand human gene regulation and will be useful for experimental guidance. Although many machine learning algorithms have been developed for eukaryotic gene recognition, performance on promoters is unsatisfactory due to the diverse nature. To extract discriminative features from human promoters, an efficient deep convolutional divergence encoding method (DCDE) is proposed based on statistical divergence (SD) and convolutional neural network (CNN)...
January 7, 2019: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/30624222/diffusion-based-molecular-communication-channel-in-presence-of-a-probabilistic-absorber-single-receptor-model-and-congestion-analysis
#3
Shirin Salehi, Naghmeh S Moayedian, Eduard Alarcon
In this paper, a diffusion-based molecular communication channel is modeled in presence of a probabilistic absorber. The probabilistic absorber is an absorber which absorbs molecules upon collision with probability q. With random walk analysis, the discrete probability function of particle location in presence of a probabilistic absorber can be found. Then a continuous probability function is fitted to this Markovbased results with introducing several fitting parameters to the known probability function of particle location in an unbounded environment without an absorbing barrier...
January 7, 2019: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/30575542/stability-analysis-of-genetic-regulatory-networks-with-general-random-disturbances
#4
Ticao Jiao, Guangdeng Zong, Sing Kiong Nguang, Cunshan Zhang
This paper establishes stability criteria for genetic regulatory networks with random disturbances. We assume the nonlinear feedback regulation function to satisfy the sector-like condition and the random perturbation to have a finite secondorder moment. Firstly, under the globally Lipschitz condition, the existence and uniqueness of solution to random genetic regulatory networks is considered by exploiting iterative approximation method. Then, by feat of the random analysis method and matrix technique, sufficient conditions are given to guarantee the noise-to-state stability in mean and globally asymptotic stability in probability, respectively...
December 19, 2018: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/30571644/joint-optimization-of-input-spike-rate-and-receiver-decision-threshold-to-maximize-achievable-bit-rate-of-neuro-spike-communication-channel
#5
Keyvan Aghababaiyan, Vahid Shah-Mansouri, Behrouz Maham
Nano-networks employ novel nano-scale communication techniques. These techniques are inspired by biological systems. Neuro-spike communication is an example of this communication paradigm. A new example of nanonetworks is the artificial neural system where nano-machines are linked to neurons to treat the neurodegenerative diseases. In these networks, nano-machines are used to replace the damaged segments of the nervous system and they behave exactly like biological entities. In this paper, by considering a point-to-point model for the neuro-spike communication which contains several sources of randomness such as the axonal noise, random amplitude and the synaptic noise; we analyze the achievable bit rate of the neuro-spike communication channel...
December 17, 2018: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/30561348/an-information-theoretical-approach-for-calcium-signaling-specificity
#6
Teresa Vaz Martins, Jennifer Hammelman, Sylvia Marinova, Clara O Ding, Richard J Morris
Calcium is a key signaling agent in animals and plants. Its involvement in the regulation of a wide range of processes has led to the question of how calcium signals can activate stimulus-specific responses. We introduce a computational framework for studying intracellular calcium signaling using elements of information theory. We use mutual information to quantify the differential activation of proteins in response to different calcium signals to provide an operational definition of specificity. Using optimisation procedures this framework allows us to explore the biochemical determinants of calcium decoding...
December 12, 2018: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/30530333/early-cancer-detection-in-blood-vessels-using-mobile-nanosensors
#7
Reza Mosayeb, Arman Ahmadzadeh, Wayan Wicke, Vahid Jamali, Robert Schober, Masoumeh Nasiri-Kenari
In this paper, we propose using mobile nanosensors (MNSs) for early stage anomaly detection. For concreteness, we focus on the detection of cancer cells located in a particular region of a blood vessel. These cancer cells produce and emit special molecules, so-called biomarkers, which are symptomatic for the presence of anomaly, into the cardiovascular system. Detection of cancer biomarkers with conventional blood tests is difficult in the early stages of a cancer due to the very low concentration of the biomarkers in the samples taken...
December 7, 2018: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/30530368/diffusive-molecular-communication-in-biological-cylindrical-environment
#8
Mohammad Zoofaghari, Hamidreza Arjmandi
Diffusive molecular communication (DMC) is one of the most promising approaches for realizing nano-scale communications in biological environments for healthcare applications. In this paper, a DMC system in biological cylindrical environment is considered, inspired by blood vessel structures in the body. The internal surface of the cylinder boundary is assumed to be covered by the biological receptors which may irreversibly react with hitting molecules. Also, information molecules diffusing in the fluid medium are subject to a degradation reaction and flow...
December 5, 2018: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/30530367/strategies-for-coexistence-in-molecular-communication
#9
Malcolm Egan, Valeria Loscri, Trung Q Duong, Marco Di Renzo
Some of the most ambitious applications of molecular communications are expected to lie in nanomedicine and advanced manufacturing. In these domains, the molecular communication system is surrounded by a range of biochemical processes, some of which may be sensitive to chemical species used for communication. Under these conditions, the biological system and the molecular communication system impact each other. As such, the problem of coexistence arises, where both the reliability of the molecular communication system and the function of the biological system must be ensured...
December 4, 2018: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/30507537/development-and-evaluation-of-multistructured-and-hierarchical-epidermal-growth-factor-poly-%C3%AE%C2%B5-caprolactone-scaffolds
#10
Wei-Chih Lin, I-Ting Yeh, Hsuan-Yi Hsiao
In this study, we separately fabricated the poly (ε-caprolactone) (PCL) scaffolds containing epidermal growth factor (EGF) by using our-self fabricated electrospinning machine for tissue regeneration application. Several fundamental properties, including the dimensions, wettability and EGF release profiles, of the fabricated EGF-PCL the bead, fibrous and multistructured scaffolds were characterised by using the Scanning Electron Microscopy (SEM), contact angle goniometer and vertical diffusion system. The EGF release profiles of three scaffolds were measured for 200 hours and the multistructured scaffold performed stable and long EGF release properties...
November 30, 2018: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/30475724/molecular-communications-in-the-context-of-synthetic-cells-research
#11
Giordano Rampioni, Livia Leoni, Pasquale Stano
The recent progresses in bottom-up synthetic biology allow the construction of cell-like systems (shortly called "synthetic cells") based on the encapsulation of chemicals and biological macromolecules inside lipid vesicles. Synthetic cells are far from being alive, but can be designed in order to imitate biological cells with respect to specific functions. The exchange of chemical signals is one of the most fascinating ones. Experimental papers have shown that synthetic cells can be designed to send and receive molecular signals, inaugurating a new research avenue that can be highly relevant not only for nano-medicine and nano-biotechnology, but also for basic understanding of minimal cognitive systems...
November 21, 2018: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/30452375/modulation-mode-detection-classification-for-in-vivo-nano-scale-communication-systems-operating-in-terahertz-band
#12
M Ozair Iqbal, M Mahboob Ur Rahman, Muhammad A Imran, Akram Alomainy, Qammer H Abbasi
This work initiates the efforts to design an intelligent/ cognitive nano receiver operating in Terahertz (THz) band. Specifically, we investigate two essential ingredients of an intelligent nano receiver-modulation mode detection (to differentiate between pulse based modulation and carrier based modulation), and modulation classification (to identify the exact modulation scheme in use). To implement modulation mode detection, we construct a binary hypothesis test in nano-receiver's passband, and provide closed-form expressions for the two error probabilities...
November 19, 2018: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/30442613/communication-and-information-theory-of-single-action-potential-signals-in-plants
#13
Hamdan Awan, Raviraj S Adve, Nigel Wallbridge, Carrol Plummer, Andrew W Eckford
Many plants, such as Mimosa pudica (the "sensitive plant"), employ electrochemical signals known as action potentials (APs) for rapid intercellular communication. In this paper, we consider a reaction-diffusion model of individual AP signals to analyze APs from a communication- and information-theoretic perspective. We use concepts from molecular communication to explain the underlying process of information transfer in a plant for a single AP pulse that is shared with one or more receiver cells. We also use the chemical Langevin equation to accommodate the deterministic as well as stochastic component of the system...
November 13, 2018: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/30442614/calcium-spike-patterns-reveal-linkage-of-electrical-stimulus-and-msc-osteogenic-differentiation
#14
Jundi Hou, Tao Luo, Shuxun Chen, Sien Lin, Michael M Yang, Gang Li, Dong Sun
Mesenchymal stromal/stem cells (MSCs) are easily obtained multipotent cells, which are widely applied in regenerative medicine. Electrical stimulation (ES) has a promoting effect on bone healing and osteogenic differentiation of MSCs. Direct and alternating currents (AC) are extensively used to promote the osteogenic differentiation of MSCs in vivo and in vitro. However, information on conducting effective differentiation remains scarce. In this study, we propose a method to optimize ES parameters based on calcium spike patterns of MSCs...
November 12, 2018: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/30334803/bond-graph-representation-of-chemical-reaction-networks
#15
Peter Gawthrop, Edmund J Crampin
The Bond Graph approach and the Chemical Reaction Network approach to modelling biomolecular systems developed independently. This paper brings together the two approaches by providing a bond graph interpretation of the chemical reaction network concept of complexes. Both closed and open systems are discussed. The method is illustrated using a simple enzyme-catalysed reaction and a trans-membrane transporter.
October 16, 2018: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/30307873/cryopreserved-cells-regeneration-monitored-by-atomic-force-microscopy-and-correlated-with-state-of-cytoskeleton-and-nuclear-membrane
#16
Martin Golan, Jan Pribyl, Martin Pesl, Sarka Jelinkova, Ivana Acimovic, Josef Jaros, Vladimir Rotrekl, Martin Falk, Ludek Sefc, Petr Skladal, Irena Kratochvilova
Atomic force microscopy (AFM) helps to describe and explain the mechanobiological properties of living cells on the nanoscale level under physiological conditions. The stiffness of cells is an important parameter reflecting cell physiology. Here, we have provided the first study of the stiffness of cryopreserved cells during post-thawing regeneration using atomic force microscopy combined with confocal fluorescence microscopy. We demonstrated that the non frozen cell stiffness decreased proportionally to the cryoprotectant concentration in the medium...
October 11, 2018: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/30296237/kernel-generalized-likelihood-ratio-test-for-fault-detection-of-biological-systems
#17
Majdi Mansouri, Raoudha Baklouti, Mohamed Faouzi Harkat, Mohamed Nounou, Hazem Nounou, Ahmed Ben Hamida
In this paper, we develop an improved fault detection (FD) technique in order to enhance monitoring abilities of nonlinear biological processes. Generalized likelihood ratio test (GLRT) based kernel principal component analysis (KPCA) (called also kernel GLRT) is an effective data driven technique for monitoring nonlinear processes. However, it is well known that data collected from complex and multivariate processes are multiscale due to the variety of changes that could occur in process with different localization in time and frequency...
October 5, 2018: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/30403634/on-string-languages-generated-by-spiking-neural-p-systems-with-structural-plasticity
#18
Francis George C Cabarle, Ren Tristan A de la Cruz, Xingyi Zhang, Min Jiang, Xiangrong Liu, Xiangxiang Zeng
Spiking neural P systems (SNP systems) are parallel and non-deterministic models of computation, inspired by the neural system of the brain. A variant of SNP systems known as SNP systems with structural plasticity (SNPSP systems) includes the feature of adding or removing synapses among neurons. This feature is inspired by plasticity from neuroscience during cognition and learning. Despite the reductionist framework of SNP and SNPSP systems, such as brain-like systems are capable of computational universality...
October 2018: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/30371384/magnetotactic-bacteria-magnetism-beyond-magnetosomes
#19
Carlos Marcuello, Lelia Chambel, Mario S Rodrigues, Liliana P Ferreira, Maria Margarida Cruz
Magnetotactic bacteria are a group of organisms deeply studied in the last years due to their interesting magnetic behavior and potential applications in nanometrology, hyperthermia, and biosensor devices. One intrinsic common characteristic is the presence, inside the bacteria, of magnetic nanoparticles called magnetosomes. The role of magnetosomes as bacterial tools to orient the bacteria and find new habitats is universally accepted, but the way they develop still is not fully understood. A strain of Magnetospirillum magnetotacticum was grown and investigated at the nanoscale using transmission electron microscopy and atomic/magnetic force microscopy techniques...
October 2018: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/30371383/algorithm-for-mesoscopic-advection-diffusion
#20
Adam Noel, Dimitrios Makrakis
In this paper, an algorithm is presented to calculate the transition rates between adjacent mesoscopic subvolumes in the presence of flow and diffusion. These rates can be integrated in stochastic simulations of reaction-diffusion systems that follow a mesoscopic approach, i.e., that partition the environment into homogeneous subvolumes and apply the spatial stochastic simulation algorithm (spatial SSA). The rates are derived by integrating Fick's second law over a single subvolume in 1D and are also shown to apply in 3D...
October 2018: IEEE Transactions on Nanobioscience
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