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IEEE Transactions on Nanobioscience

Hoon Seonwoo, Won-Gyu Bae, Sunho Park, Hong-Nam Kim, Kyoung Soon Choi, Ki Taek Lim, Hoon Hyun, Jin-Woo Kim, Jangho Kim, Jong Hoon Chung
Living cells receive biochemical and physical information from the surrounding microenvironment and respond to this information. Multiscale hierarchical substrates with micro- and nanogrooves have been shown to mimic the native extracellular matrix (ECM) better than conventional nanopatterned substrates; therefore, substrates with hierarchical topographical cues are considered suitable for investigating the role of physical factors in tissue functions. In this study, precisely controllable, multiscale hierarchical substrates that could mimic the micro- and nanotopography of complex ECMs were fabricated and used to culture various cell types, including fibroblasts, endothelial cells, osteoblasts, and human mesenchymal stem cells...
December 1, 2016: IEEE Transactions on Nanobioscience
Wei Peng, Wei Lan, Zeng Yu, Jianxin Wang, Yi Pan
MicroRNAs have close relationship with human diseases. Therefore, identifying disease related MicroRNAs plays an important role in disease diagnosis, prognosis and therapy. However, designing an effective computational method which can make good use of various biological resources and correctly predict the associations between MicroRNA and disease is still a big challenge. Previous researchers have pointed out that there are complex relationships among microRNAs, diseases and environment factors. There are inter-relationships between microRNAs, diseases or environment factors based on their functional similarity or phenotype similarity or chemical structure similarity and so on...
November 29, 2016: IEEE Transactions on Nanobioscience
Ka-Chun Wong, Chengbin Peng, Shankai Yan, Cheng Liang
Understanding genome-wide protein-DNA interactions forms the basis for further focused studies. In particular, the chromatin immunoprecipitation (ChIP) with sequencing (ChIPSeq) technology can enable us to measure the genome-wide occupancy of DNA-binding protein of interest in vivo. Multiple ChIP-Seq runs thus inherent the potential for us to decipher the combinatorial interactions among multiple DNA-binding proteins. To handle those multiple genome-wide runs, we propose to integrate regularized regression functions (i...
November 21, 2016: IEEE Transactions on Nanobioscience
Saizalmursidi Md Mustam, Sharifah Kamilah Syed-Yusof, Suleiman Zubair
In nanoscale communication, diffusion-based molecular communication (DBMC) in which information is encoded into molecule patterns by a transmitter nanomachine, has emerged as a promising communication system, particularly for biomedical and healthcare applications. Although, numerous studies have been conducted to evaluate and analyze DBMC systems, investigation on DBMC system through a multilayer channel has received less attention. The aims of this paper are to formulate channel characteristics and to evaluate the performance of multilayer DBMC channel in terms of delay spread and capacity...
November 21, 2016: IEEE Transactions on Nanobioscience
Rohit Chand, Dawoon Han, Yong-Sang Kim
In this study, we developed a capacitive sensor for the one-step and label-free detection of protein kinase A (PKA) enzyme. Metal-insulator-semiconductor (MIS) and electrolyte-insulator-semiconductor (EIS) are a simple electronic transducer, which allows efficient detection of the target analyte. For this reason, we performed a comparative sensing of PKA on the MIS and EIS capacitive sensor. The PKA-specific aptamer was used for the one-step detection. For the immobilization of thiolated aptamer, the MIS sensor contained a thin gold layer, whereas the EIS sensor had a self-aligned monolayer of gold nanoparticles...
November 18, 2016: IEEE Transactions on Nanobioscience
Nooshin Tavakkoli, Paeiz Azmi, Nader Mokari
In this paper, we consider a decode-and-forward (DF) relay-assisted diffusion-based molecular communication system inside one of the blood vessels of a human body with positive drift from transmitter to receiver. We use the normal approximation to the distribution of the number of received molecules and derive a closed-form expression for the end-toend bit error probability of the system. We then propose an optimization problem that aims at minimizing the bit error probability of the system and solve it at the receiver nanomachine by an algorithm based on the bisection method to determine the optimal detection threshold...
November 16, 2016: IEEE Transactions on Nanobioscience
Bige Deniz Unluturk, Ian Akyildiz
A new track in molecular communication is using pheromones which can scale up the range of diffusion-based communication from meters to meters and enable new applications requiring long range. Pheromone communication is the emission of molecules in the air which trigger behavioral or physiological responses in receiving organisms. The objective of this paper is to introduce a new end-to-end model which incorporates pheromone behavior with communication theory for plants. The proposed model includes both the transmission and reception processes as well as the propagation channel...
November 11, 2016: IEEE Transactions on Nanobioscience
Bige Deniz Unluturk, Sasitharan Balasubramaniam, Ian Akyildiz
Molecular communication (MC) is a new paradigm for developing communication systems that exchanges information through the transmission and reception of molecules. One proposed model for MC is using bacteria to carry information encoded into DNA plasmids, and this is termed bacterial nanonetworks. However, a limiting factor in the models that have been studied so far is the environment considered only in ideal conditions with a single population. This is far from realistic in natural environments, where bacteria co-exist in multiple populations of same and different species, resulting in a very complex social community...
November 11, 2016: IEEE Transactions on Nanobioscience
Ki-Taek Lim, Hexiu Jin, Hoon Seonwoo, Hye-Been Kim, Jangho Kim, Jin-Woo Kim, Chen Renji, Pill-Hoon Choung, Jong Hoon Chung
Human alveolar bone-derived mesenchymal stem cells (hABMSCs) are promising candidates for bone therapies, which have the capacity to differentiate into osteoblasts. Recently, secretion of inducible cytokines and growth factors from mesenchymal stem cells (MSCs) has been discovered, and we also have reported the osteogenic effects of cell physical stimulation. In this study, we investigated the effects of hABMSCs-conditioned secretion media (B-CSM) on osteogenic differentiation of hABMSCs in vitro. Furthermore, we analyzed the B-CSM by proteomics array to identify inducible factors which facilitate osteogenic differentiation...
November 11, 2016: IEEE Transactions on Nanobioscience
Wenqiong Su, Jiamei Xu, Xianting Ding
Conventional glass-based pH sensors are usually fragile and space consuming. Herein, a miniature electrochemical pH sensor based on amino-functionalized graphene fragments and polyaniline (NH2-G/PANI) composite film is developed via simply one-pot electrochemical polymerization on the ITO-coated glass substrates. Cyclic Voltammetry (CV), Scanning Electron Microscopy (SEM), Transmission electron microscopy (TEM), X-ray Photoelectron Spectroscopy (XPS) and Raman Spectra are involved to confirm the successful synthesis and to characterize the properties of the NH2-G/PANI composite film...
November 7, 2016: IEEE Transactions on Nanobioscience
Lin Zhu, Wei-Li Guo, Canyi Lu, De-Shuang Huang
Although the newly available ChIP-seq data provides immense opportunities for comparative study of regulatory activities across different biological conditions, due to cost, time or sample material availability, it is not always possible for researchers to obtain binding profiles for every protein in every sample of interest, which considerably limits the power of integrative studies. Recently, by leveraging related information from measured data, Ernst et al. proposed ChromImpute for predicting additional ChIP-seq and other types of datasets, it is demonstrated that the imputed signal tracks accurately approximate the experimentally measured signals, and thereby could potentially enhance the power of integrative analysis...
November 7, 2016: IEEE Transactions on Nanobioscience
Wei Zhang, Jia Xu, Xiong Li, Xiufen Zou
Identification of essential proteins is a fundamental task for understanding cellular life. With the increasing availability of high-throughput data, which enable the identification of essential proteins by computational methods from the network level. Various computational methods have been proposed based on topological properties of protein-protein interaction (PPI) network or combining additional biological information. However, the prediction precision is still unsatisfied especially when predicting a small amount of essential proteins...
November 4, 2016: IEEE Transactions on Nanobioscience
Mohammad Upal Mahfuz
In this paper, the expressions of achievable strength-based detection probabilities of concentration-encoded molecular communication (CEMC) system have been derived based on finite pulse-width (FP) pulse-amplitude modulated (PAM) on-off keying (OOK) modulation scheme and strength threshold. An FP-PAM system is characterized by its duty cycle [Formula: see text] that indicates the fraction of the entire symbol duration the transmitter remains on and transmits the signal. Results show that the detection performance of an FP-PAM OOK CEMC system significantly depends on the statistical distribution parameters of diffusion-based propagation noise and intersymbol interference (ISI)...
November 4, 2016: IEEE Transactions on Nanobioscience
Minkyung Sim, Kyunghwa Lee, Yeri Jeong, Jeonghee Shin, Jung Inn Sohn, Seung Nam Cha, Jae Eun Jang
Structural design factors of sensor units have been studied in order to enhance the sensitivity of pressure sensors based on utilizing a piezoelectric material for an artificial tactile sensor. In this study, we have primarily demonstrated the effect of a square pattern array design in a pressure sensor using ZnO nanowires. Nanowires grown on the edge of cells can be bent easily because of growth direction, density control, and buckling effect. Since smaller square pattern arrays induce a higher circumference to cell area ratio, if one sensor unit consists of many micro-level square pattern arrays, the design enhances the piezoelectric efficiency and the sensitivity...
October 27, 2016: IEEE Transactions on Nanobioscience
Yi Lu, Matthew D Higgins, Adam Noel, Mark S Leeson, Yunfei Chen
Molecular communication is a paradigm that utilizes molecules to exchange information between nano-machines. When considering such systems where multiple receivers are present, prior work has assumed for simplicity that they do not interfere with each other. This paper aims to address this issue and shows to what extent an interfering receiver, RI, will have an impact on the target receiver, RT, with respect to Bit Error Rate (BER) and capacity. Furthermore, approximations of the Binomial distribution are applied to reduce the complexity of calculations...
October 21, 2016: IEEE Transactions on Nanobioscience
Jessica M Andriolo, Richard J Rossi, Casey A McConnell, Baili I Connors, Kevin Trout, M K Hailer, Marisa L Pedulla, Jack L Skinner
The Centers for Disease Control and Prevention have estimated that each year, two million people in the United States become infected with antibiotic-resistant bacteria, of which, approximately 23 000 die as a direct result of these infections. Phage therapy, or the treatment of bacterial infection by specific, antagonistic viruses, provides one alternative to traditional antibiotics. Bacteriophages, or phages, are bacteriaspecific viruses that possess biological traits that allow for not only the removal of bacterial infection, but also the evasion of bacterial resistance which renders antibiotics ineffective...
October 19, 2016: IEEE Transactions on Nanobioscience
Puneet Manocha, Gitanjali Chandwani, Soumen Das
With current research focus to interconnect the molecular communication environment with external environment, it is imperative to design external devices working on molecular communication schemes to be interfaced with in-vivo molecular network. Recently, efforts have been made to integrate molecular communication with Lab-on-chip (LOC); one of the techniques used in LOC for manipulation and transportation of molecules is Dielectrophoresis (DEP). We propose the use of DEP in molecular communication to maintain in-sequence delivery of molecules...
October 19, 2016: IEEE Transactions on Nanobioscience
Jundi Hou, Tao Luo, Ka Lam Ng, Raymond Liang, Anskar Y H Leung, Dong Sun
One of the greatest challenges in acute myeloid leukemia (AML) treatment is preventing relapse. Leukemia cells can hide in bone marrow niche or vascular niche. Hence, many chemical drugs cannot kill these cells. To characterize migration and adhesion properties of leukemia cells in specific niches, CXCR4/SDF-1α signal pathway has been widely used for investigation. AMD3100 is treated as one of the most common chemical drugs that can inhibit this signal. In the current study, we particularly investigate the effect of AMD3100 on the adhesion property of leukemia cells on stromal cells by using engineering tools, namely, optical tweezers (OT) and dielectrophoresis (DEP), to probe single cell property...
October 19, 2016: IEEE Transactions on Nanobioscience
Eleonora Alfinito, Lino Reggiani
Current-voltage characteristics of metal-protein-metal structures made of proteorhodopsin and bacteriorhodopsin are modeled by using a percolation-like approach. Starting from the tertiary structure pertaining to the single protein, an analogous resistance network is created. Charge transfer inside the network is described as a sequential tunneling mechanism and the current is calculated for each value of the given voltage. The theory is validated with available experiments, in dark and light. The role of the tertiary structure of the single protein and of the mechanisms responsible for the photo-activity is discussed...
October 18, 2016: IEEE Transactions on Nanobioscience
Ethungshan Shitiri, Ho-Shin Cho
For nanonetworks to be able to achieve large-scale functionality, such as to respond collectively to a trigger, synchrony between nanomachines is essential. However, to facilitate synchronization, some sort of physical clocking mechanism is required, such as the oscillators driven by auto-inhibitory molecules or by auto-inducing molecules. In this study, taking inspiration from the widely studied biological oscillatory phenomena called Calcium (Ca2+) oscillations, we undertake a different approach to design an oscillator...
October 18, 2016: IEEE Transactions on Nanobioscience
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