IEEE Transactions on NanoBioscience (IEEE T NANOBIOSCI)

Publications in this journal

• Article: Quantitative Analysis of the Combined Effect of Substrate Rigidity and Topographic Guidance on Cell Morphology

  J. Park, H.-N. Kim, D.-H. Kim, A. Levchenko, K.-Y. Suh
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  ABSTRACT: Live cells are exquisitely sensitive to both the substratum rigidity and texture. To explore cell responses to both these types of inputs in a precisely controlled fashion, we analyzed the responses of Chinese hamster ovary (CHO) cells to nanotopographically defined substrata of different rigidities, ranging from 1.8 MPa to 1.1 GPa. Parallel arrays of nanogrooves (800-nm width, 800-nm space, and 800-nm depth) on polyurethane (PU)-based material surfaces were fabricated by UV-assisted capillary force lithography (CFL) over an area of $5~{rm mm}times 3~{rm mm}$ . We observed dramatic morphological responses of CHO cells, evident in their elongation and polarization along the nanogrooves direction. The cells were progressively more spread and elongated as the substratum rigidity increased, in an integrin $beta 1$ dependent manner. However, the degree of orientation was independent of substratum rigidity, suggesting that the cell shape is primarily determined by the topographical cues.
  IEEE Transactions on NanoBioscience 04/2012;
• Source

  Available from: elte.hu

  Article: 3-D Brownian Motion Simulator for High-Sensitivity Nanobiotechnological Applications

  A. Toth, D. Banky, V. Grolmusz
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  ABSTRACT: A wide variety of nanobiotechnologic applications are being developed for nanoparticle based in vitro diagnostic and imaging systems. Some of these systems make possible highly sensitive detection of molecular biomarkers. Frequently, the very low concentration of the biomarkers makes impossible the classical, partial differential equation-based mathematical simulation of the motion of the nanoparticles involved. We present a three-dimensional Brownian motion simulation tool for the prediction of the movement of nanoparticles in various thermal, viscosity, and geometric settings in a rectangular cuvette. For nonprofit users the server is freely available at the site http://brownian.pitgroup.org.
  IEEE Transactions on NanoBioscience 01/2012;
• Article: The Influence of Size and Shape of Microorganism on Pulsed Electric Field Inactivation

  A.H. El-Hag, S.H. Jayaram, O.R. Gonzalez, M.W. Griffiths
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  ABSTRACT: In this paper the effect of microorganism size and shape on the killing efficiency of pulsed electric field (PEF) is investigated both experimentally and using a transient finite element program. The effect of cell size, membrane thickness, cell shape (spherical, elliptical, and cylindrical) on the calculated transmembrane voltage is studied. It has been found that both the cell size and cell membrane thickness have significant effect on the induced field across the cell membrane. The findings of the simulation results have been evaluated by comparing the trends with some experimental results. Five different types of microorganisms that have different shapes and dimensions have been inoculated with water at a conductivity level of 100 μS/cm and have been treated with the application of a pulsed electric field of 70 kV/cm. Significant difference in bacteria reduction was noticed between the treated cells which could be attributed to the cell size and shape.
  IEEE Transactions on NanoBioscience 10/2011;
• Article: Pulsed Laser Coating of Hydroxyapatite/Titanium Nanoparticles on Ti-6Al-4V Substrates: Multiphysics Simulation and Experiments

  M.Y. Zhang, G.J. Cheng
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  ABSTRACT: Pulsed laser coating (PLC) of bioceramics/metal nanomaterials on metal substrates was investigated in this research. It is found that due to the nature of the nanosized particles and pulse laser beam, PLC processed hydroxyapatite (HAp) coatings possess strong coating/substrate interfacial bonding strength, and minimum thermal decomposition. Feasibility analysis of PLC is conducted using both simulation and experiments. In the multiphysics simulation, laser interacting with metal nanoparticles and heat conduction is simulated by coupling the electromagnetic (EM) module and heat transfer (HT) module. In experiments, HAp and titanium nanoparticle mixture are coated on Ti-6Al-4V substrate using nanosecond pulsed Nd:YAG laser with wavelength of 1064 nm. Resulting temperature is measured by calibrated infrared (IR) camera and compared with simulation results. Experimental results agree well with simulation which serves as a guidance to find appropriate processing parameters. It is found that resulting temperature increases with increasing of pulse energy linearly and decreasing of pulse duration following the power law. It is recommended that shorter pulses to be used in PLC due to its better sinterability. Microstructure and chemical characterizations confirmed that HAp was physically and chemically maintained due to pulse laser caused rapid heating and cooling processes.
  IEEE Transactions on NanoBioscience 10/2011;
• Article: Negative Feedback Through mRNA Provides the Best Control of Gene-Expression Noise

  A. Singh
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  ABSTRACT: Genetically identical cell populations exposed to the same environment can exhibit considerable cell-to-cell variation in the levels of specific proteins. This variation or expression noise arises from the inherent stochastic nature of biochemical reactions that constitute gene expression. Negative feedback loops are common motifs in gene networks that reduce expression noise and intercellular variability in protein levels. Using stochastic models of gene expression we here compare different feedback architectures in their ability to reduce stochasticity in protein levels. A mathematically controlled comparison shows that in physiologically relevant parameter regimes, feedback regulation through the mRNA provides the best suppression of expression noise. Consistent with our theoretical results we find negative feedback loops though the mRNA in essential eukaryotic genes, where feedback is mediated via intron-derived microRNAs. Finally, we find that contrary to previous results, protein-mediated translational regulation may not always provide significantly better noise suppression than protein-mediated transcriptional regulation.
  IEEE Transactions on NanoBioscience 10/2011;
• Article: Isolated Photosystem I Reaction Centers on a Functionalized Gated High Electron Mobility Transistor

  S.A. Eliza, I. Lee, F.S. Tulip, S. Mostafa, E. Greenbaum, M.N. Ericson, S.K. Islam
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  ABSTRACT: In oxygenic plants, photons are captured with high quantum efficiency by two specialized reaction centers (RC) called Photosystem I (PS I) and Photosystem II (PS II). The captured photon triggers rapid charge separation and the photon energy is converted into an electrostatic potential across the nanometer-scale ( ~ 6 nm) reaction centers. The exogenous photovoltages from a single PS I RC have been previously measured using the technique of Kelvin force probe microscopy (KFM). However, biomolecular photovoltaic applications require two-terminal devices. This paper presents for the first time, a micro-device for detection and characterization of isolated PS I RCs. The device is based on an AlGaN/GaN high electron mobility transistor (HEMT) structure. AlGaN/GaN HEMTs show high current throughputs and greater sensitivity to surface charges compared to other field-effect devices. PS I complexes immobilized on the floating gate of AlGaN/GaN HEMTs resulted in significant changes in the device characteristics under illumination. An analytical model has been developed to estimate the RCs of a major orientation on the functionalized gate surface of the HEMTs.
  IEEE Transactions on NanoBioscience 10/2011;
• Article: Power Law Behavior in IF Model With Random Excitatory and Inhibitory Rates

  S.K. Sharma, Karmeshu
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  ABSTRACT: A new mechanism is proposed to generate power law behavior in interspike interval (ISI) distribution when a collection of neurons group together and fire together. Employing superstatistical framework, the mechanism requires a population of neurons which is characterized by randomly distributed excitatory and inhibitory rates. The distribution of these rates is characterized by independent gamma variates. The effect of randomness in the rates exhibits power law behavior in first passage time of the integrate and fire (IF) model. Extensive Monte Carlo simulation studies of the underlying stochastic differential equation (SDE) are carried out which also depict asymptotically power law behavior for ISI distribution for an ensemble of IF neurons.
  IEEE Transactions on NanoBioscience 10/2011;
• Source

  Available from: nustbio.org

  Article: SOMRuler: A Novel Interpretable Transmembrane Helices Predictor

  Dongjun Yu, Hongbin Shen, Jingyu Yang
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  ABSTRACT: Transmembrane helices (TMH) identification is one of the most important steps in membrane protein structure prediction. Existing TMH predictors tend to pursue accurate computational models without carefully considering the interpretability of these models and thus act as a black box. In this paper, a novel TMH predictor called SOMRuler with excellent interpretability while possessing high prediction accuracy is presented. The SOMRuler uses a self-organizing map (SOM) to learn helices distribution knowledge, which is encoded in the codebook vectors of the trained SOM, from the training samples. Human interpretable fuzzy rules are then extracted from the codebook vectors of the trained SOM. By extracting fuzzy rules from the learned knowledge rather than the original training samples, on the one hand, the computational burden of extracting fuzzy rules can be greatly reduced; on the other hand, the reliability of the extracted rules can also be enhanced since noise contained in the original samples can be smoothened by the learning procedure of SOM. The validity of the fuzzy rules extracted by SOMRuler is qualitatively and quantitatively analyzed. Experimental results on the benchmark dataset show that the SOMRuler outperforms most existing popular TMH predictors and is flexible to suite for a wide variety of problems in bioinformatics. The SOMRuler software is implemented by Java and Matlab and is available for academic use at: http://www.csbio.sjtu.edu.cn/bioinf/SOMRuler/.
  IEEE Transactions on NanoBioscience 07/2011;
• Article: Small Universal Spiking Neural P Systems Working in Exhaustive Mode

  Linqiang Pan, Xiangxiang Zeng
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  ABSTRACT: Spiking neural P systems are a class of distributed parallel computing devices inspired from the way neurons communicate by means of spikes. In this paper, the problem of looking for small universal computing devices is investigated in the framework of spiking neural P systems. A new approach is introduced to simulate register machines by spiking neural P systems, where only one neuron is used for all instructions of the simulated register machine; in this way, less neurons are used to construct universal spiking neural P systems working in exhaustive mode. Specifically, a universal spiking neural P system with 36 neurons is constructed, which works in exhaustive mode. This significantly improves the already known result, where 125 neurons are used.
  IEEE Transactions on NanoBioscience 07/2011;
• Article: Low Frequency Dielectric Properties of Human Blood

  S. Abdalla
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  ABSTRACT: Nano- and microparticles in human blood affect drastically the charge transfer CT through the viable fluid. Low-frequency dielectric properties of the blood, characterized by CT of β-dispersion type, are widely investigated with special stress on physical mechanisms. However, no publication in the literature deals with the presence of α-dispersion in human blood. In the present study, a mechanism associated with α-, β-, and γ-dispersions is presented. The dielectric losses (electrical conduction) phenomenon is also discussed with special emphasis on the distribution of relaxation times. These losses cause problems with low-frequency dielectric measurements, thus, they are correlated with the famous empirical Col-Cole factor, (1-α). A Gaussian distribution of relaxation times is suggested and found to be exponentially related with (1-α). The results suggest new diagnostic and therapeutic methods for blood disorders.
  IEEE Transactions on NanoBioscience 07/2011;
• Article: Nanoscopic Volume Trapping and Transportation Using a PANDA Ring Resonator for Drug Delivery

  M.A. Jalil, M. Tasakorn, N. Suwanpayak, J. Ali, P.P. Yupapin
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  ABSTRACT: A novel design of nanoscopic volume transmitter and receiver for drug delivery system using a PANDA ring resonator is proposed. By controlling some suitable parameters, the optical vortices (gradient optical fields/wells) can be generated and used to form the trapping tools in the same way as the optical tweezers. By using the intense optical vortices generated within the PANDA ring resonator, the nanoscopic volumes (drug) can be trapped and moved (transport) dynamically within the wavelength router or network. In principle, the trapping force is formed by the combination between the gradient field and scattering photons, which is reviewed. The advantage of the proposed system is that a transmitter and receiver can be formed within the same system (device), which is called a transceiver, which is available for nanoscopic volume (drug volume) trapping and transportation (delivery).
  IEEE Transactions on NanoBioscience 07/2011;
• Article: Quantitative Analysis of Human Keratinocyte Cell Elasticity Using Atomic Force Microscopy (AFM)

  C.K.M. Fung, Ning Xi, Ruiguo Yang, K. Seiffert-Sinha, King Wai Chiu Lai, A.A. Sinha
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  ABSTRACT: We present the use of atomic force microscopy (AFM) to visualize and quantify the dynamics of epithelial cell junction interactions under physiological and pathophysiological conditions at the nanoscale. Desmosomal junctions are critical cellular adhesion components within epithelial tissues and blistering skin diseases such as Pemphigus are the result in the disruption of these components. However, these structures are complex and mechanically inhomogeneous, making them difficult to study. The mechanisms of autoantibody mediated keratinocyte disassembly remain largely unknown. Here, we have used AFM technology to image and measure the mechanical properties of living skin epithelial cells in culture. We demonstrate that force measurement data can distinguish cells cultured with and without autoantibody treatment. Our demonstration of the use of AFM for in situ imaging and elasticity measurements at the local, or tissue level opens potential new avenues for the investigation of disease mechanisms and monitoring of therapeutic strategies in blistering skin diseases.
  IEEE Transactions on NanoBioscience 04/2011;
• Article: Highly Sensitive Carbon Nanotube-Based Sensing for Lactate and Glucose Monitoring in Cell Culture

  C. Boero, S. Carrara, G. Del Vecchio, L. Calzà, G. De Micheli
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  ABSTRACT: Monitoring of metabolic compounds in cell cultures can provide real-time information of cell line status. This is particularly important in those lines not fully known, as the case of embryonic and mesenchymal cells. On the other hand, such approach can pave the way to fully automated systems for growing cell cultures, when integrated in Petri dishes. To date, the main efforts emphasize the monitoring of few process variables, like pH, pO₂, electronic impedance, and temperature in bioreactors. Among different presented strategies to develop biosensors, carbon nanotubes exhibit great properties, particularly suitable for high-sensitive detection. In this work, nanostructured electrodes by using multiwalled carbon nanotubes are presented for the detection of lactate and glucose. Some results from simulations are illustrated in order to foresee the behavior of carbon nanotubes depending on their orientation, when they are randomly dispersed onto the electrode surface. A comparison between nonnanostructured and nanostructured electrodes is considered, showing that direct electron-transfer between the protein and the electrode is not possible without nanostructuration. Such developed biosensors are characterized in terms of sensitivity and detection limit, and are compared to previously published results. Lactate production is monitored in a cell culture by using the developed biosensor, and glucose detection is also performed to validate lactate behavior.
  IEEE Transactions on NanoBioscience 04/2011;
• Article: Statistical Design of Position-Encoded Microsphere Arrays

  P. Sarder, A. Nehorai
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  ABSTRACT: We propose a microsphere array device with microspheres having controllable positions for error-free target identification. We conduct a statistical design analysis to select the optimal distance between the microspheres as well as the optimal temperature. Our design simplifies the imaging and ensures a desired statistical performance for a given sensor cost. Specifically, we compute the posterior Cramér-Rao bound on the errors in estimating the unknown target concentrations. We use this performance bound to compute the optimal design variables. We discuss both uniform and sparse concentration levels of targets, and replace the unknown imaging parameters with their maximum likelihood estimates. We illustrate our design concept using numerical examples. The proposed microarray has high sensitivity, efficient packing, and guaranteed imaging performance. It simplifies the imaging analysis significantly by identifying targets based on the known positions of the microspheres. Potential applications include molecular recognition, specificity of targeting molecules, protein-protein dimerization, high throughput screening assays for enzyme inhibitors, drug discovery, and gene sequencing.
  IEEE Transactions on NanoBioscience 04/2011;
• Article: Mining Protein Kinases Regulation Using Graphical Models

  Qingfeng Chen, Y.-P.P. Chen
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  ABSTRACT: Abnormal kinase activity is a frequent cause of diseases, which makes kinases a promising pharmacological target. Thus, it is critical to identify the characteristics of protein kinases regulation by studying the activation and inhibition of kinase subunits in response to varied stimuli. Bayesian network (BN) is a formalism for probabilistic reasoning that has been widely used for learning dependency models. However, for high-dimensional discrete random vectors the set of plausible models becomes large and a full comparison of all the posterior probabilities related to the competing models becomes infeasible. A solution to this problem is based on the Markov Chain Monte Carlo (MCMC) method. This paper proposes a BN-based framework to discover the dependency correlations of kinase regulation. Our approach is to apply the MCMC method to generate a sequence of samples from a probability distribution, by which to approximate the distribution. The frequent connections (edges) are identified from the obtained sampling graphical models. Our results point to a number of novel candidate regulation patterns that are interesting in biology and include inferred associations that were unknown.
  IEEE Transactions on NanoBioscience 04/2011;
• Article: Cyclotron Production of Radioactive Nanoparticles and Their Application for In Vitro Uptake Studies

  F. Simonelli, P. Marmorato, K. Abbas, J. Ponti, J. Kozempel, U. Holzwarth, F. Franchini, F. Rossi
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  ABSTRACT: Nowadays, a wide variety of nanoparticles (NPs) are applied in different fields such as medical science and industry. Due to their large commercial volume, the OECD Working Party on Manufactured Nanomaterials (NMs) has proposed to study a set of 14 nanomaterials, one of which being cerium oxide (CeO₂). In particular, CeO₂ based NPs are widely used in automotive industry, healthcare, and cosmetics. In this paper, we propose a method for the production of radioactive CeO₂ NPs. We demonstrate that they maintain the same physicochemical characteristics as the “cold” ones in terms of size distribution and Zeta potential; we develop a new protocol to assess their cellular interaction in immortalized mouse fibroblast cell line Balb/3T3, a model for the study of basal cytotoxicity and carcinogenic potential induced by chemicals and in the present case by NPs. Experimental result of this work, which shows a quasi-linear concentration-uptake response of cells, can be useful as a reference dose-uptake curve for explaining effects following biological uptake after exposure to CeO₂ NPs.
  IEEE Transactions on NanoBioscience 04/2011;
• Article: Probability Theory-Based SNP Association Study Method for Identifying Susceptibility Loci and Genetic Disease Models in Human Case-Control Data

  Xiguo Yuan, Junying Zhang, Yue Wang
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  ABSTRACT: One of the most challenging points in studying human common complex diseases is to search for both strong and weak susceptibility single-nucleotide polymorphisms (SNPs) and identify forms of genetic disease models. Currently, a number of methods have been proposed for this purpose. Many of them have not been validated through applications into various genome datasets, so their abilities are not clear in real practice. In this paper, we present a novel SNP association study method based on probability theory, called ProbSNP. The method firstly detects SNPs by evaluating their joint probabilities in combining with disease status and selects those with the lowest joint probabilities as susceptibility ones, and then identifies some forms of genetic disease models through testing multiple-locus interactions among the selected SNPs. The joint probabilities of combined SNPs are estimated by establishing Gaussian distribution probability density functions, in which the related parameters (i.e., mean value and standard deviation) are evaluated based on allele and haplotype frequencies. Finally, we test and validate the method using various genome datasets. We find that ProbSNP has shown remarkable success in the applications to both simulated genome data and real genome-wide data.
  IEEE Transactions on NanoBioscience 01/2011;
• Article: Comparison of Statistical Methods to Classify Environmental Genomic Fragments

  G.L. Rosen, S.D. Essinger
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  ABSTRACT: “Binning” (or taxonomic classification) of DNA sequence reads is an initial step to analyzing an environmental biological sample. Currently, a homology-based tool, BLAST, is one of the most commonly used tools to label DNA reads, but it is argued that BLAST will quickly lose its classification ability as the genome databases grow. In this paper, we compare the accuracies of a naïve Bayes classifier (NBC) and statistical language model to BLAST for binning reads and demonstrate that NBC obtains good performance for the low cost of computational complexity. On the other hand, the back-off n-gram language model can improve accuracy when only partial training data is available (such as in-progress sequencing projects). NBC demonstrates comparable performance to BLAST and can also be optimized on partial training datasets by adjusting the word feature size. A fivefold cross validation is conducted to compare each method's accuracy for determining novel genomes at different taxonomic levels, with NBC outperforming BLAST for species-level classification but BLAST outperforming NBC for genus-level and phyla-level classification. In conclusion, the NBC is a competitive taxonomic classifier, and language models can improve performance when only partial training data is available.
  IEEE Transactions on NanoBioscience 01/2011;
• Article: Novel Tunable Dynamic Tweezers Using Dark-Bright Soliton Collision Control in an Optical Add/Drop Filter

  C. Teeka, M.A. Jalil, P.P. Yupapin, J. Ali
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  ABSTRACT: We propose a novel system of the dynamic optical tweezers generated by a dark soliton in the fiber optic loop. A dark soliton known as an optical tweezer is amplified and tuned within the microring resonator system. The required tunable tweezers with different widths and powers can be controlled. The analysis of dark-bright soliton conversion using a dark soliton pulse propagating within a microring resonator system is analyzed. The dynamic behaviors of soliton conversion in add/drop filter is also analyzed. The control dark soliton is input into the system via the add port of the add/drop filter. The dynamic behavior of the dark-bright soliton conversion is observed. The required stable signal is obtained via a drop and throughput ports of the add/drop filter with some suitable parameters. In application, the trapped light/atom and transportation can be realized by using the proposed system.
  IEEE Transactions on NanoBioscience 01/2011;
• Article: A New Approach to Dynamic Fuzzy Modeling of Genetic Regulatory Networks

  Yonghui Sun, Gang Feng, Jinde Cao
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  ABSTRACT: In this paper, the dynamic fuzzy modeling approach is applied for modeling genetic regulatory networks from gene expression data. The parameters of the dynamic fuzzy model and the optimal number of fuzzy rules for the fuzzy gene network can be obtained via the proposed modeling approach from the measured gene expression data. One of the main features of the proposed approach is that the prior qualitative knowledge on the network structure can be easily incorporated in the proposed identification algorithm, so that the faster learning convergence of the algorithm can be achieved. Two sets of data, one the synthetic data, and the other the experimental SOS DNA repair network data with structural knowledge, have been used to validate the proposed modeling approach. It is shown that the proposed approach is effective in modeling genetic regulatory networks.
  IEEE Transactions on NanoBioscience 01/2011;