MedWorm.com provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest items from the 'IEE Transactions on NanoBioscience' source. Sat, 28 Jan 2012 15:30:10 +0100 http://www.medworm.com/index.php?rid=5626489&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D6133477%26arnumber%3D6133479 (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=5626489 Thu, 01 Dec 2011 05:00:00 +0100 5626489 http://www.medworm.com/index.php?rid=5626488&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D6133477%26arnumber%3D6133480 (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=5626488 Thu, 01 Dec 2011 05:00:00 +0100 5626488 http://www.medworm.com/index.php?rid=5626487&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D6133477%26arnumber%3D6133482 (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=5626487 Thu, 01 Dec 2011 05:00:00 +0100 5626487 http://www.medworm.com/index.php?rid=5626486&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D6133477%26arnumber%3D6133483 (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=5626486 Thu, 01 Dec 2011 05:00:00 +0100 5626486 http://www.medworm.com/index.php?rid=5626485&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D6133477%26arnumber%3D6133485 In this study, we present a new, fast, and biologically reliable scoring method, hierarchical expected matching probability (HEP), to use in protein multiple sequence alignment. The new scoring method eliminates the burden of gap cost selection process. And it has consistently proven to be more biologically reliable than all other tested scoring methods through all tests on four different theoretical and experimental benchmarks, Valdar's theoretical conservation benchmark, RT-OSM, BAliBASE3.0, and PREFAB4.0. An implementation of our new scoring method into progressive multiple sequence alignment, resembling the alignment algorithm in PIMA, ClustalW, and T-COFFEE, has shown an accuracy improvement up to 7% on BAliBASE3.0 and up to 5% on PREFAB4.0 benchmarks. (Source: IEE Transactions on Nan... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=5626485 Thu, 01 Dec 2011 05:00:00 +0100 5626485 http://www.medworm.com/index.php?rid=5626484&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D6133477%26arnumber%3D6096421 Undesired biofilm development is a major concern in many areas, especially in the medical field. The purpose of the present study was to comparatively investigate the antibiofilm efficacy of usnic acid, in soluble versus nanofluid formulation, in order to highlight the potential use of ${rm Fe}_{3} {rm O}_{4}/{rm oleic}$ acid (FeOA) nanofluid as potential controlled release vehicle of this antibiofilm agent. The $(+)$ -UA loaded into nanofluid exhibited an improved antibiofilm effect on S. aureus biofilm formation, revealed by the drastic decrease of the viable cell counts as well as by confocal laser scanning microscopy images. Our results demonstrate that FeOA nanoparticles could be used as successful coating agents for obtaining antibiofilm pellicles on different medical devices, openin... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=5626484 Thu, 01 Dec 2011 05:00:00 +0100 5626484 http://www.medworm.com/index.php?rid=5626483&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D6133477%26arnumber%3D6133484 This work applies a three-dimensional lattice Boltzmann method (LBM), to solve the Pennes bio-heat equation (BHE), in order to predict the temperature distribution in a spherical tissue, with blood perfusion, metabolism and magnetic nanoparticles (MNPs) heat sources, during magnetic fluid hyperthermia (MFH). So, heat dissipation of MNPs under an alternating magnetic field has been studied and effect of different factors such as induction and frequency of magnetic field and volume fraction of MNPs has been investigated. Then, effect of MNPs dispersion on temperature distribution inside tumor and its surrounding healthy tissue has been shown. Also, effect of blood perfusion, thermal conductivity of tumor, frequency and amplitude of magnetic field on temperature distribution has been explaine... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=5626483 Thu, 01 Dec 2011 05:00:00 +0100 5626483 http://www.medworm.com/index.php?rid=5626482&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D6133477%26arnumber%3D6086628 Nanoparticles (NP) have drawn increasing interest from many fields in medicine and are a relatively new class of biomedical products. Because there are concerns about the health effects of nanoparticles, it is important to understand how nanoparticles interact specifically with red blood cells (RBC), a central object in the blood circulation. As numerous studies that have examined NP/RBC interaction concentrated on the hemolytic potential of nanoparticles, we describe an investigation of hemolytic activity of polystyrene nanoparticles (PS-NP) in protein free medium and its modulation by albumin. We found that treatment of RBCs with PS-NP induces hemolysis (dose and particle size dependent) in plasma free medium but not in full plasma or in buffer, which contain albumin. Critical albumin co... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=5626482 Thu, 01 Dec 2011 05:00:00 +0100 5626482 http://www.medworm.com/index.php?rid=5626481&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D6133477%26arnumber%3D6086629 A coral-like macroporous Au electrode with electroplated Pt nanoparticles (hybrid macroporous Au-/nPts) coated with Nafion has been fabricated for the first time and used for highly selective and sensitive determination of dopamine (DA). The physically characterized results indicated that the electroplated Pt nanoparticles were dispersed uniformly on the macroporous Au electrode. The porosity and window pore size of the fabricated macroporous Au electrode were 50% and 100–300 nm, respectively. Also the electroplated Pt nanoparticles size was approximately 10–20 nm. The cyclic voltammograms results showed that the hybrid macroporous Au-/nPts exhibited a much larger surface activation area, a roughness factor (RF) of 2024.7, much higher than that of the macroporous Au electrode... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=5626481 Thu, 01 Dec 2011 05:00:00 +0100 5626481 http://www.medworm.com/index.php?rid=5626480&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D6133477%26arnumber%3D6026252 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. (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=5626480 Thu, 01 Dec 2011 05:00:00 +0100 5626480 http://www.medworm.com/index.php?rid=5626479&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D6133477%26arnumber%3D6096430 Notch-Delta signaling is indispensable for somitogenesis, which controls the vertebrate segmentation during embryonic development. Several theoretical models have been proposed to explain this interesting process. In zebrafish somitogenesis, genes her1, her7, delta, and their proteins plays the important roles. However, an auto-repression model with time delay involved only by her1/her7 is able to explain zebrafish somitogenesis. This paper will systematically study the dynamics of this model. Specifically we investigate its stability, bifurcation (oscillation), and stability of oscillation. First, the conditions for both stability and bifurcation are presented based on the linearized model. Then three indices for bifurcation of this nonlinear model are derived by using linear functional o... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=5626479 Thu, 01 Dec 2011 05:00:00 +0100 5626479 http://www.medworm.com/index.php?rid=5626478&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D6133477%26arnumber%3D6096429 Genomic signal processing is a new area of research that combines advanced digital signal processing methodologies for enhanced genetic data analysis. It has many promising applications in bioinformatics and next generation of healthcare systems, in particular, in the field of microarray data clustering. In this paper we present a comparative performance analysis of enhanced digital spectral analysis methods for robust clustering of gene expression across multiple microarray data samples. Three digital signal processing methods: linear predictive coding, wavelet decomposition, and fractal dimension are studied to provide a comparative evaluation of the clustering performance of these methods on several microarray datasets. The results of this study show that the fractal approach provides t... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=5626478 Thu, 01 Dec 2011 05:00:00 +0100 5626478 http://www.medworm.com/index.php?rid=5626477&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D6133477%26arnumber%3D6126046 Cell-surface adhesion force is important for cell activities and the development of bio materials. In this paper, a method for in situ single cell $(W303)$ adhesion force measurement was proposed based on nanorobotic manipulation system inside an environment scanning electron microscope (ESEM). An end effector was fabricated from a commercial atomic force microscope (AFM) cantilever by focused ion beam (FIB) etching. The spring constant of it was calibrated by nanomanipulation approach. Three kinds of hydrophilic and hydrophobic ITO plates were prepared by using VUV-irradiation and OTS coating techniques. The shear adhesion strength of the single yeast cell to each substrate was measured based on the deflection of the end effector. The results demonstrated that the cell adhesion force was ... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=5626477 Thu, 01 Dec 2011 05:00:00 +0100 5626477 http://www.medworm.com/index.php?rid=5626476&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D6133477%26arnumber%3D6133481 (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=5626476 Thu, 01 Dec 2011 05:00:00 +0100 5626476 http://www.medworm.com/index.php?rid=5626475&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D6133477%26arnumber%3D6133478 (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=5626475 Thu, 01 Dec 2011 05:00:00 +0100 5626475 http://www.medworm.com/index.php?rid=5345174&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D6048006%26arnumber%3D6048008 This page or pages intentionally left blank. (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=5345174 Thu, 01 Sep 2011 04:00:00 +0100 5345174 http://www.medworm.com/index.php?rid=5345173&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D6048006%26arnumber%3D6048009 (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=5345173 Thu, 01 Sep 2011 04:00:00 +0100 5345173 http://www.medworm.com/index.php?rid=5345172&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D6048006%26arnumber%3D6048011 (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=5345172 Thu, 01 Sep 2011 04:00:00 +0100 5345172 http://www.medworm.com/index.php?rid=5345171&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D6048006%26arnumber%3D6015559 Immunofluorescence techniques on formalin fixed paraffin-embedded sections allow for the evaluation of the expression and spatial distribution of specific markers in patient tissue specimens or for monitoring the fate of labeled cells after in vivo injection. This technique suffers however from the auto-fluorescence background signal of the embedded tissue that eventually confounds the analysis. Here we show that rod-like semiconductor nanocrystals (QRs), intramuscularly injected in living mice, could be clearly detected by confocal microscopy in formalin fixed paraffin-embedded tissue sections. Despite the low amount of QRs amount injected (25 picomoles), these were clearly visible after 24 h in the muscle sections and their fluorescence signal was stronger than that of CdSe/ZnS quantum d... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=5345171 Thu, 01 Sep 2011 04:00:00 +0100 5345171 http://www.medworm.com/index.php?rid=5345170&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D6048006%26arnumber%3D6018311 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 $({sim}{6}~hbox{nm})$ 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 cu... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=5345170 Thu, 01 Sep 2011 04:00:00 +0100 5345170 http://www.medworm.com/index.php?rid=5345169&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D6048006%26arnumber%3D6048013 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 res... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=5345169 Thu, 01 Sep 2011 04:00:00 +0100 5345169 http://www.medworm.com/index.php?rid=5345168&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D6048006%26arnumber%3D6018313 Supported lipid bilayers (SLBs) at surfaces provide a route to quantitatively study molecular interactions with and at lipid membranes via different surface-based analytical techniques. Here, a method to fabricate SLBs with controlled curvatures, in the nanometer regime over large areas, is presented, utilizing lipid vesicle rupture onto nanostructured sensor substrates. Heat treated colloidal particle masks were used as templates to produce silicon dioxide films with systematically varied radius of curvature (ROC, 70 to 170 nm are demonstrated) and quartz crystal microbalance with dissipation monitoring (QCM-D) was used to confirm vesicle rupture onto such structured surfaces. Fluorescence microscopy was used to show fluidity of the supported membranes. The formation of confluent SLBs is ... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=5345168 Thu, 01 Sep 2011 04:00:00 +0100 5345168 http://www.medworm.com/index.php?rid=5345167&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D6048006%26arnumber%3D6018310 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 cali... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=5345167 Thu, 01 Sep 2011 04:00:00 +0100 5345167 http://www.medworm.com/index.php?rid=5345166&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D6048006%26arnumber%3D6018309 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. (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=5345166 Thu, 01 Sep 2011 04:00:00 +0100 5345166 http://www.medworm.com/index.php?rid=5345165&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D6048006%26arnumber%3D6018312 We present a theoretical design of an all-optical reconfigurable logic unit based on optically controlled microcavity switches, for realization of all-optical computing circuits. It can execute different logic and arithmetic operations such as half and full adder or subtractor, by only changing the control inputs on the same circuit. Theoretical designs considering bacteriorhodopsin (BR) protein coated microcavities in tree architecture have been presented. The combined advantages of high $ {rm Q}$-factor, tunability, compactness, switching of near-IR signals at telecom wavelengths (1310/1550 nm) with low-power control signals, and flexibility of cascading switches to form circuits, makes the designs promising for practical applications. They combine the ultrahigh sensitivity of both BR an... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=5345165 Thu, 01 Sep 2011 04:00:00 +0100 5345165 http://www.medworm.com/index.php?rid=5345164&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D6048006%26arnumber%3D6015560 A new method to analyze single ionic channel current conduction is presented. It is based on an automatic classification by K-means algorithm and on the concept of information entropy. This method is used to study the conductance of multistate ion current jumps induced by tetanus toxin in planar lipid bilayers. A comparison is presented with the widely used Gaussian best fit approach, whose main drawback is the fact that it is based on the manual choice of the base line and of meaningful fragments of current signal. On the contrary, the proposed method is able to automatically process a great amount of information and to remove spurious transitions and multichannels. The number of levels and their amplitudes do not have to be known a priori. In this way the presented method is able to prod... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=5345164 Thu, 01 Sep 2011 04:00:00 +0100 5345164 http://www.medworm.com/index.php?rid=5345163&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D6048006%26arnumber%3D6048012 Rough sets are often exploited for data reduction and classification. While they are conceptually appealing, the techniques used with rough sets can be computationally demanding. To address this obstacle, the objective of this study is to investigate the use of DNA molecules and associated techniques as an optimization vehicle to support algorithms of rough sets. In particular, we develop a DNA-based algorithm to derive decision rules of minimal length. This new approach can be of value when dealing with a large number of objects and their attributes, in which case the complexity of rough-sets-based methods is NP-hard. The proposed algorithm shows how the essential components involved in the minimization of decision rules in data processing can be realized. (Source: IEE Transactions on Nan... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=5345163 Thu, 01 Sep 2011 04:00:00 +0100 5345163 http://www.medworm.com/index.php?rid=5345162&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D6048006%26arnumber%3D6017202 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 $mu hbox{S/cm}$ and have been treated with the applicat... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=5345162 Thu, 01 Sep 2011 04:00:00 +0100 5345162 http://www.medworm.com/index.php?rid=5345161&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D6048006%26arnumber%3D6048010 (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=5345161 Thu, 01 Sep 2011 04:00:00 +0100 5345161 http://www.medworm.com/index.php?rid=5345160&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D6048006%26arnumber%3D6048007 (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=5345160 Thu, 01 Sep 2011 04:00:00 +0100 5345160 http://www.medworm.com/index.php?rid=5181584&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5978269%26arnumber%3D5978275 (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=5181584 Tue, 31 May 2011 23:00:00 +0100 5181584 http://www.medworm.com/index.php?rid=5181583&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5978269%26arnumber%3D5978270 (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=5181583 Tue, 31 May 2011 23:00:00 +0100 5181583 http://www.medworm.com/index.php?rid=5181582&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5978269%26arnumber%3D5978272 (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=5181582 Tue, 31 May 2011 23:00:00 +0100 5181582 http://www.medworm.com/index.php?rid=5181581&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5978269%26arnumber%3D5978273 (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=5181581 Tue, 31 May 2011 23:00:00 +0100 5181581 http://www.medworm.com/index.php?rid=5181580&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5978269%26arnumber%3D5978835 (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=5181580 Tue, 31 May 2011 23:00:00 +0100 5181580 http://www.medworm.com/index.php?rid=5181579&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5978269%26arnumber%3D5942175 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... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=5181579 Tue, 31 May 2011 23:00:00 +0100 5181579 http://www.medworm.com/index.php?rid=5181578&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5978269%26arnumber%3D5934419 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 $beta$ - dispersion type, are widely investigated with special stress on physical mechanisms. However, no publication in the literature deals with the presence of $alpha$ - dispersion in human blood. In the present study, a mechanism associated with $alpha$-, $beta$-, and $gamma$- 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, $(1-alpha)$. A Gaussian distribu... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=5181578 Tue, 31 May 2011 23:00:00 +0100 5181578 http://www.medworm.com/index.php?rid=5181577&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5978269%26arnumber%3D5753943 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, w... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=5181577 Tue, 31 May 2011 23:00:00 +0100 5181577 http://www.medworm.com/index.php?rid=5181576&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5978269%26arnumber%3D5934420 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. (Source: IEE Transactions on NanoBioscie... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=5181576 Tue, 31 May 2011 23:00:00 +0100 5181576 http://www.medworm.com/index.php?rid=5181575&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5978269%26arnumber%3D5942174 The solution space exponential explosion caused by the enumeration of the candidate solutions maybe is the biggest obstacle in DNA computing. In the paper, a new unenumerative DNA computing model for graph vertex coloring problem is presented based on two techniques: 1) ordering the vertex sequence for a given graph in such a way that any two consecutive labeled vertices i and i+1 should be adjacent in the graph as much as possible; 2) reducing the number of encodings representing colors according to the construture of the given graph. A graph with 12 vertices without triangles is solved and its initial solution space includes only 283 DNA strands, which is 0.0532 of 312 (the worst complexity). (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=5181575 Tue, 31 May 2011 23:00:00 +0100 5181575 http://www.medworm.com/index.php?rid=5181574&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5978269%26arnumber%3D5942177 This paper presents a new method for tumor classification using gene expression data. In the proposed method, we first select genes using nonnegative matrix factorization (NMF) or sparse NMF (SNMF), and then we extract features from the selected genes by virtue of NMF or SNMF. At last, we apply support vector machines (SVM) to classify the tumor samples using the extracted features. In order for a better classification, a modified SNMF algorithm is also proposed. The experimental results on benchmark three microarray data sets validate that the proposed method is efficient. Moreover, the biological meaning of the selected genes are also analyzed. (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=5181574 Tue, 31 May 2011 23:00:00 +0100 5181574 http://www.medworm.com/index.php?rid=5181573&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5978269%26arnumber%3D5942176 The adoption of microarray techniques in biological and medical research provides a new way for cancer diagnosis and treatment. In order to perform successful diagnosis and treatment of cancer, discovering and classifying cancer types correctly is essential. Class discovery is one of the most important tasks in cancer classification using biomolecular data. Most of the existing works adopt single clustering algorithms to perform class discovery from biomolecular data. However, single clustering algorithms have limitations, which include a lack of robustness, stability, and accuracy. In this paper, we propose a new cluster ensemble approach called knowledge based cluster ensemble (KCE) which incorporates the prior knowledge of the data sets into the cluster ensemble framework. Specifically,... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=5181573 Tue, 31 May 2011 23:00:00 +0100 5181573 http://www.medworm.com/index.php?rid=5181572&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5978269%26arnumber%3D5942173 The protein folding problem is a fundamental problem in computational molecular biology and biochemical physics. The previously best known branch and bound method for the protein folding problem may find optimal or near-optimal energy structure from the benchmark sequences, but the total computation time is rather lengthy because it usually needs to run a great deal of simulating tests or else lack of accuracy. In this paper, we develop a new branch and bound method for the the protein folding problem under the two-dimensional HP model to overcome the mentioned drawbacks. By using benchmark sequences for evaluation, we demonstrate that the performance of our method is superior than previously known methods. Moreover, our method is a simple, flexible and easily implemented one for the prote... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=5181572 Tue, 31 May 2011 23:00:00 +0100 5181572 http://www.medworm.com/index.php?rid=5181571&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5978269%26arnumber%3D5978271 (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=5181571 Tue, 31 May 2011 23:00:00 +0100 5181571 http://www.medworm.com/index.php?rid=5181570&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5978269%26arnumber%3D5978274 (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=5181570 Tue, 31 May 2011 23:00:00 +0100 5181570 http://www.medworm.com/index.php?rid=4767843&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5756256%26arnumber%3D5756260 (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=4767843 Tue, 01 Mar 2011 00:00:00 +0100 4767843 http://www.medworm.com/index.php?rid=4767842&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5756256%26arnumber%3D5756259 (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=4767842 Tue, 01 Mar 2011 00:00:00 +0100 4767842 http://www.medworm.com/index.php?rid=4767841&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5756256%26arnumber%3D5756257 (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=4767841 Tue, 01 Mar 2011 00:00:00 +0100 4767841 http://www.medworm.com/index.php?rid=4767839&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5756256%26arnumber%3D5753942 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, $hbox{pO}_{2}$, 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. S... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=4767839 Tue, 01 Mar 2011 00:00:00 +0100 4767839 http://www.medworm.com/index.php?rid=4767838&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5756256%26arnumber%3D5752247 The invention of microfluidic lab-on-a-chip alleviates the burden of traditional biochemical laboratory procedures which are often very expensive. Device miniaturization and increasing design complexity have mandated a shift in digital microfluidic lab-on-a-chip design from traditional manual design to computer-aided design (CAD) methodologies. As an important procedure in the lab-on-a-chip layout CAD, the lab-on-a-chip component placement determines the physical location and the starting time of each operation such that the overall completion time is minimized while satisfying nonoverlapping constraint, resource constraint, and scheduling constraint. In this paper, a multiscale variation-aware optimization technique based on integer linear programming is proposed for the lab-on-a-chip com... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=4767838 Tue, 01 Mar 2011 00:00:00 +0100 4767838 http://www.medworm.com/index.php?rid=4767837&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5756256%26arnumber%3D5754600 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 (${hbox{CeO}} _{2}$). In particular, ${hbox{CeO}} _{2}$ based NPs are widely used in automotive industry, healthcare, and cosmetics. In this paper, we propose a method for the production of radioactive ${hbox{CeO}} _{2}$ 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 mo... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=4767837 Tue, 01 Mar 2011 00:00:00 +0100 4767837 http://www.medworm.com/index.php?rid=4767836&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5756256%26arnumber%3D5752248 We describe the development, fabrication and testing of a microfluidic chamber for dielectrophoretic field-flow separation of biological cells based on their electrical properties. The chamber was constructed from a single Pyrex wafer with interdigitated Au electrodes, a spacer, and a top cover glass, making the events in the chamber observable under most optical microscopes. The dimensions were optimized based on numerical computations of the electric field, its gradient and the fluid-flow velocity profile. The electrodes were fabricated using photolithography. A double-sided self-adhesive tape of 100 $ mu hbox{m}$ thickness was used as a spacer, with an opening of 80 mm length and 20 mm width cut in its middle to form a channel of 100 $mu hbox{m}$ height, and with water-resistant acrylic... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=4767836 Tue, 01 Mar 2011 00:00:00 +0100 4767836 http://www.medworm.com/index.php?rid=4767835&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5756256%26arnumber%3D5756262 Among the immunoglobulins, IgM class-antibodies are now considered to be potent immunological reagents for anticancer remedies. However, only a few reports are available about the effective labeling of IgM with enzymes, fluorescence, or other bioreactive reagents. Here, we report an effective application of luminescent semiconductive nanoparticles, quantum dots (QDs), as a labeling material of the IgM antibody. The CdSe carboxyl QDs were reacted with 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride and N-hydroxysulfo- succinimide in 2-(morpholino) ethanesulfonic acid. The reacted QDs were then coupled to JT95 IgM antibody, which recognizes thyroid carcinoma associated antigen. The specificity and activity of the conjugates were tested by immunoblot, immunoquantitive assay and i... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=4767835 Tue, 01 Mar 2011 00:00:00 +0100 4767835 http://www.medworm.com/index.php?rid=4767834&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5756256%26arnumber%3D5716677 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... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=4767834 Tue, 01 Mar 2011 00:00:00 +0100 4767834 http://www.medworm.com/index.php?rid=4767833&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5756256%26arnumber%3D5720318 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... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=4767833 Tue, 01 Mar 2011 00:00:00 +0100 4767833 http://www.medworm.com/index.php?rid=4767832&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5756256%26arnumber%3D5719553 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 regulatio... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=4767832 Tue, 01 Mar 2011 00:00:00 +0100 4767832 http://www.medworm.com/index.php?rid=4767831&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5756256%26arnumber%3D5756258 (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=4767831 Tue, 01 Mar 2011 00:00:00 +0100 4767831 http://www.medworm.com/index.php?rid=4767830&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5756256%26arnumber%3D5756261 (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=4767830 Tue, 01 Mar 2011 00:00:00 +0100 4767830 http://www.medworm.com/index.php?rid=4445700&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5701726%26arnumber%3D5704890 (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=4445700 Wed, 01 Dec 2010 00:00:00 +0100 4445700 http://www.medworm.com/index.php?rid=4394274&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5701726%26arnumber%3D5701730 (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=4394274 Wed, 01 Dec 2010 00:00:00 +0100 4394274 http://www.medworm.com/index.php?rid=4394273&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5701726%26arnumber%3D5701728 (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=4394273 Wed, 01 Dec 2010 00:00:00 +0100 4394273 http://www.medworm.com/index.php?rid=4394272&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5701726%26arnumber%3D5586656 In conclusion, the NBC is a competitive taxonomic classifier, and language models can improve performance when only partial training data is available. (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=4394272 Wed, 01 Dec 2010 00:00:00 +0100 4394272 http://www.medworm.com/index.php?rid=4394271&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5701726%26arnumber%3D5585772 We show that a single-crystal quartz substrate provides a working platform for ion channel research. Single-crystal quartz is piezoelectric, so it can be nanomechanically actuated to perform precise membrane deformations. This, along with its superior noise properties, makes single-crystal quartz ideal for analyzing mechanosensitive ion channels. (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=4394271 Wed, 01 Dec 2010 00:00:00 +0100 4394271 http://www.medworm.com/index.php?rid=4394270&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5701726%26arnumber%3D5570977 Molecular dynamics simulations are performed to study the physical mechanism of cobra cardiotoxin (CTX) proteins adsorption on alkanethiol self-assembled monolayers (SAMs) composed of $ hbox{S}{( hbox{CH}_{2})}_{5} hbox{CH}_{3}$ and $ hbox{S}{( hbox{CH}_{2})}_{9} hbox{CH}_{3}$. The binding energy of the CTX protein to the SAM surface of different mixing ratios of alkanethiol chains is calculated. The results show that the affinity of CTX to SAM reaches a maximum value when the ratio $ hbox{S}{( hbox{CH}_{2})}_{5} hbox{CH}_{3}: hbox{S}{( hbox{CH}_{2})}_{9} hbox{CH}_{3}$ is 1:1, which agrees with the measurements of atomic force microscope obtained in Part I of our dual paper. Moreover, the binding energy is found to be linearly proportional to the CTX-SAM contact area. The hydrophobicity on... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=4394270 Wed, 01 Dec 2010 00:00:00 +0100 4394270 http://www.medworm.com/index.php?rid=4394269&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5701726%26arnumber%3D5570976 Fast and efficient detection of Cobra cardiotoxin (CTX) protein molecules on biochip surfaces is an example of application in biotechnology. One potential application of mixed self assembled monolayers (SAMs) as chip surfaces yield different binding affinities of the CTX proteins, a series of studies on the interaction force between CTX proteins and the mixed SAMs surfaces formed from mixtures of two thiols with the same/different chain lengths and/or with the same/different terminal groups will be investigated. In these dual papers, the mixed SAMs of n-alkinethiol SAMs of different chain lengths are chosen as the first examples of this series due to the simple functions of the mixed SAMs surface structure. Thus, the adhesion force measurements of CTX protein molecules on mixed SAMs of n-a... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=4394269 Wed, 01 Dec 2010 00:00:00 +0100 4394269 http://www.medworm.com/index.php?rid=4394268&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5701726%26arnumber%3D5701731 In this paper we propose an algorithm named Incremental Structural Mountain Clustering Method (ISMCM) with a view to finding a library of building blocks for reconstruction of 3-D structures of proteins/peptides. The building blocks are short structural motifs that are identified based on an estimate of local “density” of 3-D fragments computed using a measure of structural similarity. The structural similarity is computed after the best-molecular-fit alignment of pairs of fragments. The algorithm is tested on two well known benchmark data sets. Following the protocols used by other researchers, for the first data set we reconstruct a set of 71 test peptides (up to first 60 residues) whereas for the second data set we reconstruct all 143 test peptides. The ISMCM algorithm is ... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=4394268 Wed, 01 Dec 2010 00:00:00 +0100 4394268 http://www.medworm.com/index.php?rid=4394267&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5701726%26arnumber%3D5571047 The problem of data and information encoding on DNA bears an increasing interest for both biological and nonbiological applications of biomolecular computing. Recent experimental and theoretical advances have produced and tested to obtain large code sets of oligonucleotides to support virtually any kind of application. In this paper, we have developed an algorithm to design DNA short-word sets based on minimum free energy (MFE) criteria. The MFE constraint is the minimum value among free energies of all the possible structures and the effective approach to control the generation of unexpected secondary structure of DNA sequences may cause error. The algorithm is constructive and directly produces the actual DNA words of the sets, unlike other academic and statistical numbers. According to ... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=4394267 Wed, 01 Dec 2010 00:00:00 +0100 4394267 http://www.medworm.com/index.php?rid=4394266&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5701726%26arnumber%3D5613189 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 propos... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=4394266 Wed, 01 Dec 2010 00:00:00 +0100 4394266 http://www.medworm.com/index.php?rid=4394265&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5701726%26arnumber%3D5701733 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... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=4394265 Wed, 01 Dec 2010 00:00:00 +0100 4394265 http://www.medworm.com/index.php?rid=4394264&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5701726%26arnumber%3D5701732 The prediction of functional sites in proteins is an important issue in protein function studies and drug design. To apply the kernel based pattern recognition algorithms such as support vector machines for protein functional sites prediction, a new string kernel function, termed as the modified bio-basis function, is proposed recently. The bio-basis strings for the new kernel function are selected by an efficient method that integrates the Fisher ratio and the concept of degree of resemblance. In this regard, this paper introduces some quantitative indices for evaluating the quality of selected bio-basis strings. Moreover, the effectiveness of the new string kernel function and bio-basis string selection method, along with a comparison with existing bio-basis function and related bio-basi... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=4394264 Wed, 01 Dec 2010 00:00:00 +0100 4394264 http://www.medworm.com/index.php?rid=4394263&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5701726%26arnumber%3D5587898 In order to apply the powerful kernel-based pattern recognition algorithms such as support vector machines to predict functional sites in proteins, amino acids need encoding prior to input. In this regard, a new string kernel function, termed as the modified bio-basis function, is proposed that maps a nonnumerical sequence space to a numerical feature space. The proposed string kernel function is developed based on the conventional bio-basis function and needs a bio-basis string as a support like conventional kernel function. The concept of zone of influence of a bio-basis string is introduced in the proposed kernel function to take into account the influence of each bio-basis string in nonnumerical sequence space. An efficient method is described to select a set of bio-basis strings for t... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=4394263 Wed, 01 Dec 2010 00:00:00 +0100 4394263 http://www.medworm.com/index.php?rid=4394262&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5701726%26arnumber%3D5571046 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... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=4394262 Wed, 01 Dec 2010 00:00:00 +0100 4394262 http://www.medworm.com/index.php?rid=4394261&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5701726%26arnumber%3D5551211 All cells receive and respond to signals from their environment, whether they live freely or are part of a tissue. Feedback loops are one among the interactions in signal-transduction cascades, in which the information from the downstream components is sent back to the upstream components of the system. Crosstalks between signal-transduction cascades are able to combine the information's received and processed to trigger the appropriate response. To understand how signaling networks make decisions, the dynamic interactions of proteins in the signal-transduction cascades are important rather than just creating static maps of pathways. Based on reaction kinetics, we have developed mathematical models to predict and analyze the impacts of the feedback loops in JNK cascades and the crosstalks ... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=4394261 Wed, 01 Dec 2010 00:00:00 +0100 4394261 http://www.medworm.com/index.php?rid=4394260&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5701726%26arnumber%3D5701729 (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=4394260 Wed, 01 Dec 2010 00:00:00 +0100 4394260 http://www.medworm.com/index.php?rid=4394259&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5701726%26arnumber%3D5701727 (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=4394259 Wed, 01 Dec 2010 00:00:00 +0100 4394259 http://www.medworm.com/index.php?rid=3914838&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5559624%26arnumber%3D5559628 (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3914838 Tue, 31 Aug 2010 05:28:38 +0100 3914838 http://www.medworm.com/index.php?rid=3914837&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5559624%26arnumber%3D5559626 (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3914837 Tue, 31 Aug 2010 05:28:38 +0100 3914837 http://www.medworm.com/index.php?rid=3914836&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5559624%26arnumber%3D5559630 (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3914836 Tue, 31 Aug 2010 05:28:38 +0100 3914836 http://www.medworm.com/index.php?rid=3914835&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5559624%26arnumber%3D5559629 (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3914835 Tue, 31 Aug 2010 05:28:38 +0100 3914835 http://www.medworm.com/index.php?rid=3914834&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5559624%26arnumber%3D5477172 In this paper, we consider a molecular relay channel in which signal molecules are transmitted by a sender of communication, propagated, amplified, removed in the channel, and sensed by the receiver of communication that decodes the signal molecules. To understand and characterize the communication capacity of the molecular relay channel, we develop an information communication model that consists of the transmitter, channel, and receiver. Mutual information is used to quantify the amount of information that is transfered from the transmitter through the channel to the receiver. The method employed and results presented in this paper may help elucidate design principles of biological systems as well as help in the design and engineering of synthetic biological systems from the perspective ... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3914834 Tue, 31 Aug 2010 05:28:38 +0100 3914834 http://www.medworm.com/index.php?rid=3914833&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5559624%26arnumber%3D5559632 A detailed numerical investigation concerning the influence on the electrical response of an eukaryotic cell model due to the variations of the conductivity and permittivity of the plasma and nuclear membranes is carried out by means of a vertex analysis. The dynamics of three cell performances, the voltages across the external and the nuclear membrane, and the pores density are analyzed by adopting a novel FEM-based model coupled with the nonlinear equation describing the electroporation (EP) phenomenon. The variations of the electrical and morphological performances, when the cell is stressed by a nonideal step input, are studied in three interesting regimes, i.e., at the nominal threshold for the onset of EP, and when the applied stress is over or under the EP threshold. The performed n... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3914833 Tue, 31 Aug 2010 05:28:38 +0100 3914833 http://www.medworm.com/index.php?rid=3914832&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5559624%26arnumber%3D5559631 This paper proposes a novel model for gross damage as occurring in tile-based nanomanufacturing by DNA self-assembly. Gross damage occurs due to exogenous agents (such as radiation and tip-sample interactions) and is modeled as a hole (with a large number of empty tile sites) in the aggregate of the self-assembly. A stochastic analysis based on Markov chains for the tile binding process is pursued for regrowth of the tiles. This analysis establishes resilience as the probability to regrow the target pattern in the area affected by the gross damage. The conditions by which regrowth of a hole is favorable (i.e., at high resilience) compared with normal growth are established by considering temperature of aggregation and bond energy. As examples, two patterns for nano interconnects are analyz... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3914832 Tue, 31 Aug 2010 05:28:37 +0100 3914832 http://www.medworm.com/index.php?rid=3914831&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5559624%26arnumber%3D5475215 Spot segmentation—the second essential stage of cDNA microarray image analysis—constitutes a challenging process. At present, several up-to-date spot-segmentation techniques or software programs—proposed in the literature—are often characterized as “automatic.” On the contrary, they are in effect not fully automatic since they require human intervention in order to specify mandatory input parameters or to correct their results. Human intervention, however, can inevitably modify the actual results of the cDNA microarray experiment and lead to erroneous biological conclusions. Therefore, the development of an automated spot-segmentation process becomes of exceptional interest. In this paper, an original and fully automatic approach to accurately segm... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3914831 Tue, 31 Aug 2010 05:28:37 +0100 3914831 http://www.medworm.com/index.php?rid=3914830&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5559624%26arnumber%3D5477175 Microinjection has been demonstrated to be an effective technique to introduce foreign materials into biological cells. Despite the advance, whether cell injection can be used to characterize the mechanical properties of cells remains elusive. In this paper, extending the previously developed mechanical model, various constitutive materials are adopted to present the membrane characteristics of cells. To demonstrate the modeling approach and identify the most appropriate constitutive material for a specific biomembrane, finite element analysis (FEA) and experimental tests are carried out. It is shown that the modeling results agree well with those from both FEA and experiments, which demonstrates the validity of the developed approach. Moreover, Yeoh and Cheng materials are found to be the... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3914830 Tue, 31 Aug 2010 05:28:36 +0100 3914830 http://www.medworm.com/index.php?rid=3914829&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5559624%26arnumber%3D5504242 A new procedure for preparing iron oxide–silica nanocomposite particles using SBA-15 mesoporous silica as a template is described. These composite materials retained the 2-D hexagonal structure of the SBA-15 template. Transmission electron micrograms of the particles depicted the formation of iron oxide nanocrystals inside the mesochannels of SBA-15 silica framework. Powder x-ray diffraction showed that the iron oxide core of the composite particles consists of a mixture of maghemite ( $gamma$-Fe $_{2}$O $_{3}$) and heamatite ( $alpha$-Fe $_{2}$O $_{3}$), which is the predominant component. Superconducting quantum interference device (SQUID) magnetometry studies showed that these iron oxide–silica composite materials exhibit superparamagnetic properties. On increasing the iro... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3914829 Tue, 31 Aug 2010 05:28:36 +0100 3914829 http://www.medworm.com/index.php?rid=3914828&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5559624%26arnumber%3D5559627 (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3914828 Tue, 31 Aug 2010 05:28:36 +0100 3914828 http://www.medworm.com/index.php?rid=3914827&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5559624%26arnumber%3D5559625 (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3914827 Tue, 31 Aug 2010 05:28:36 +0100 3914827 http://www.medworm.com/index.php?rid=3640862&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5477190%26arnumber%3D5477198 (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3640862 Mon, 31 May 2010 23:00:00 +0100 3640862 http://www.medworm.com/index.php?rid=3640861&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5477190%26arnumber%3D5477195 (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3640861 Mon, 31 May 2010 23:00:00 +0100 3640861 http://www.medworm.com/index.php?rid=3640860&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5477190%26arnumber%3D5477197 (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3640860 Mon, 31 May 2010 23:00:00 +0100 3640860 http://www.medworm.com/index.php?rid=3640859&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5477190%26arnumber%3D5454342 Conclusions: The morphology, particle size, aggregation, and crystal phase of nanocrystallites in the urine of lithogenic patients are pronouncedly different from those of healthy persons. The results suggest, in ascending order of importance, that making nanocrystallites rounded, diminishing their size differentiation, and decreasing their aggregation in urine by physical and chemical methods maybe the means to prevent urinary stone formation. The most crucial among the four differences is the crystal phase differentia of calcium oxalate (CaOxa). That is, the formation of COD nanocrystallites in urine can be considered as being relatively more favorable in preventing stone formation than the formation of COM nanocrystallites, which are in accord with those found for larger crystallites. (... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3640859 Mon, 31 May 2010 23:00:00 +0100 3640859 http://www.medworm.com/index.php?rid=3640858&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5477190%26arnumber%3D5477191 Protein-structure comparison (PSC) is an essential component of biomedical research as it impacts on, e.g., drug design, molecular docking, protein folding and structure prediction algorithms as well as being essential to the assessment of these predictions. Each of these applications, as well as many others where molecular comparison plays an important role, requires a different notion of similarity that naturally lead to the multicriteria PSC (MC-PSC) problem. Protein (Structure) Comparison, Knowledge, Similarity, and Information (ProCKSI) (www.procksi.org) provides algorithmic solutions for the MC-PSC problem by means of an enhanced structural comparison that relies on the principled application of information fusion to similarity assessments derived from multiple comparison methods. Cu... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3640858 Mon, 31 May 2010 23:00:00 +0100 3640858 http://www.medworm.com/index.php?rid=3640857&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5477190%26arnumber%3D5427103 Protein phosphorylation is an important step in many biological processes, such as cell cycles, membrane transport, apoptosis, etc. In order to obtain more useful information about protein phosphorylation, it is necessary to develop a robust, stable, and accurate approach to predict phosphorylation sites. Although there exist a number of approaches to predict phosphorylation sites, such as those based on neural network and the support vector machine, they only use a single classifier. In general, the prediction results obtained by these approaches are not very stable and robust. In this paper, we design a new classifier ensemble approach called Bagging–AdaBoost ensemble (BAE) for the prediction of eukaryotic protein phosphorylation sites, which incorporates the bagging technique and... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3640857 Mon, 31 May 2010 23:00:00 +0100 3640857 http://www.medworm.com/index.php?rid=3640856&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5477190%26arnumber%3D5477192 In this paper, we propose a gene regulatory network (GRN) estimation method, which assumes that such networks are typically sparse, using time-series microarray datasets. We represent the regulatory relationships between the genes using weights, with the “net” regulation influence on a gene’s expression being the summation of the independent regulatory inputs. We estimate the weights using a Bayesian linear regression method for sparse parameter vectors. We apply our proposed method to the extraction of differential gene expression software selected genes of a human buffy-coat microarray expression profile dataset of ventilator-associated pneumonia (VAP), and compare the estimation result with the GRNs estimated using both a correlation coefficient method and a databas... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3640856 Mon, 31 May 2010 23:00:00 +0100 3640856 http://www.medworm.com/index.php?rid=3640855&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5477190%26arnumber%3D5427121 In conclusion, functionalized nanotube–collagen composites, particularly CFNT–collagen composites, could be promising materials, which provide structural support showing bundled fibril structure, biocompatibility, multifunctionality, and mechanical stability, but rigorous control over chemical modification, loading concentration, and nanotube dispersion are needed. (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3640855 Mon, 31 May 2010 23:00:00 +0100 3640855 http://www.medworm.com/index.php?rid=3640854&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5477190%26arnumber%3D5427138 The quantum mechanics/molecular mechanics ONIOM calculations have been performed to study the structure and metal-ion binding properties of all-trans $hbox{cyclo[1R-3S-}gammahbox{-Acc-}breakhbox{Gly]}_{3}$ hexapeptide nanotube $hbox{(TAG)}_{3}hbox{PNT}$. The intersubunit distances and tube angle of $hbox{(TAG)}_{3}hbox{PNT}$ exhibited the sturdy nature of $hbox{(TAG)}_{3}$ stacks upon $hbox{Li}^{+}, hbox{K}^{+}, hbox{Mg}^{2+}$, and $hbox{Zn}^{2+}$ enclosure. The calculated dimer binding energies of $hbox{(TAG)}_{3}hbox{PNT}$ and its ionic complexes confirm that the building blocks are bound by C=O…H-N hydrogen bond interactions. The binding energy of $hbox{(TAG)}_{3}hbox{PNT}$ with ions interacting at the surface cavity exhibit the affinity of ions at the entrance of the chan... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3640854 Mon, 31 May 2010 23:00:00 +0100 3640854 http://www.medworm.com/index.php?rid=3640853&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5477190%26arnumber%3D5427088 We propose a system to characterize the 3-D diffusion properties of the probing bead trapped by a photonic-force microscope. We follow a model-based approach, where the model of the dynamics of the bead is given by the Langevin equation. Our procedure combines software and analog hardware to measure the corresponding stiffness matrix. We are able to estimate all its elements in real time, including off-diagonal terms. To achieve our goal, we have built a simple analog computer that performs a continuous preprocessing of the data, which can be subsequently digitized at a much lower rate than is otherwise required. We also provide an effective numerical algorithm for compensating the correlation bias introduced by a quadrant photodiode detector in the microscope. We validate our approach usi... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3640853 Mon, 31 May 2010 23:00:00 +0100 3640853 http://www.medworm.com/index.php?rid=3640852&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5477190%26arnumber%3D5477194 Given a set of molecular structure data preclassified into a number of classes, the molecular classification problem is concerned with the discovering of interesting structural patterns in the data so that “unseen” molecules not originally in the dataset can be accurately classified. To tackle the problem, interesting molecular substructures have to be discovered and this is done typically by first representing molecular structures in molecular graphs, and then, using graph-mining algorithms to discover frequently occurring subgraphs in them. These subgraphs are then used to characterize different classes for molecular classification. While such an approach can be very effective, it should be noted that a substructure that occurs frequently in one class may also does occur in... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3640852 Mon, 31 May 2010 23:00:00 +0100 3640852 http://www.medworm.com/index.php?rid=3640851&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5477190%26arnumber%3D5477193 (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3640851 Mon, 31 May 2010 23:00:00 +0100 3640851 http://www.medworm.com/index.php?rid=3640850&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5477190%26arnumber%3D5477196 (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3640850 Mon, 31 May 2010 23:00:00 +0100 3640850 http://www.medworm.com/index.php?rid=3432801&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5440010%26arnumber%3D5440012 (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3432801 Mon, 01 Mar 2010 00:00:00 +0100 3432801 http://www.medworm.com/index.php?rid=3432800&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5440010%26arnumber%3D5440011 (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3432800 Mon, 01 Mar 2010 00:00:00 +0100 3432800 http://www.medworm.com/index.php?rid=3432799&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5440010%26arnumber%3D5440013 (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3432799 Mon, 01 Mar 2010 00:00:00 +0100 3432799 http://www.medworm.com/index.php?rid=3432798&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5440010%26arnumber%3D5440016 Magnetic particle tagging techniques are currently being applied to tissue engineering applications such as controlled differentiation of mesenchymal stem cells (MSC). In order to define key mechanotransducers underpinning these applications, the electrophysiological responses of human MSCs (hMSC) have been investigated. Ferromagnetic microparticles were coated with ${rm L}$-arginyl-glycyl- ${rm L}$-aspartic acid in order to target the application of dynamic force (6 pN) directly to cell surface integrins. Human MSCs demonstrated cell membrane hyperpolarization responses after the application of force, mediated by BK channels and intracellular calcium release. (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3432798 Mon, 01 Mar 2010 00:00:00 +0100 3432798 http://www.medworm.com/index.php?rid=3432797&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5440010%26arnumber%3D5401093 This paper extends our early study on a mathematical formulation of the central dogma of molecular biology, and focuses discussions on recent insights obtained by employing advanced systems theoretic analysis. The goal of this paper is to mathematically represent and interpret the genetic information flow at the molecular level, and explore the fundamental principle of molecular biology at the system level. Specifically, group theory was employed to interpret concepts and properties of gene mutation, and predict backbone torsion angle along the peptide chain. Finite state machine theory was extensively applied to interpret key concepts and analyze the processes related to DNA hybridization. Using the proposed model, we have transferred the character-based model in molecular biology to a so... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3432797 Mon, 01 Mar 2010 00:00:00 +0100 3432797 http://www.medworm.com/index.php?rid=3432796&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5440010%26arnumber%3D5401059 Bioanalytical chip-based assays have been enormously improved in sensitivity in the recent years; detection of trace amounts of substances down to the level of individual fluorescent molecules has become state-of-the-art technology. The impact of such detection methods, however, has yet not fully been exploited, mainly due to a lack of appropriate mathematical tools for robust data analysis. One particular example relates to the analysis of microarray data. While classical microarray analysis works at resolutions of 2–20 $,mu {}$m and quantifies the abundance of target molecules by determining average pixel intensities, a novel high-resolution approach directly visualizes individual bound molecules as diffraction-limited peaks. The now possible quantification via counting is less s... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3432796 Mon, 01 Mar 2010 00:00:00 +0100 3432796 http://www.medworm.com/index.php?rid=3432795&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5440010%26arnumber%3D5393033 Clustering is the grouping of similar objects into a class. Local clustering feature refers to the phenomenon whereby one group of data is separated from another, and the data from these different groups are clustered locally. A compact class is defined as one cluster in which all similar elements cluster tightly within the cluster. Herein, the essence of the local clustering feature, revealed by mathematical manipulation, results in a novel clustering algorithm termed as the special local clustering (SLC) algorithm that was used to process gene microarray data related to Alzheimer's disease (AD). SLC algorithm was able to group together genes with similar expression patterns and identify significantly varied gene expression values as isolated points. If a gene belongs to a compact ... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3432795 Mon, 01 Mar 2010 00:00:00 +0100 3432795 http://www.medworm.com/index.php?rid=3432794&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5440010%26arnumber%3D5325721 Independent sets of DNA oligonucleotides, which only bind with their Watson–Crick complements, have potential use in self-assembly of nanostructures, since they minimize errors and inefficiency from unwanted binding. A software tool implemented a thermodynamic model for DNA duplex formation and was used to generate large independent sets of DNA oligonucleotides. The principle of the approach was experimentally verified on a sample set of oligonucleotides. (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3432794 Mon, 01 Mar 2010 00:00:00 +0100 3432794 http://www.medworm.com/index.php?rid=3432793&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5440010%26arnumber%3D5299061 We enhance the support vector machine recursive feature elimination (SVM-RFE) method for gene selection by incorporating a minimum-redundancy maximum-relevancy (MRMR) filter. The relevancy of a set of genes are measured by the mutual information among genes and class labels, and the redundancy is given by the mutual information among the genes. The method improved identification of cancer tissues from benign tissues on several benchmark datasets, as it takes into account the redundancy among the genes during their selection. The method selected a less number of genes compared to MRMR or SVM-RFE on most datasets. Gene ontology analyses revealed that the method selected genes that are relevant for distinguishing cancerous samples and have similar functional properties. The method provides a ... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3432793 Mon, 01 Mar 2010 00:00:00 +0100 3432793 http://www.medworm.com/index.php?rid=3432792&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5440010%26arnumber%3D5308210 We present a theoretical approach based on physical principles to accurately simulate biomolecular networks using the Monte Carlo method. Incorporating this theory, a computational tool named Monte Carlo biomolecular simulator (MBS) was developed, enabling studies of biomolecular kinetics with both spatial and temporal resolutions. The accuracy of MBS was verified by comparison against the classical deterministic approaches. Furthermore, the effects of localization, spatial heterogeneity, and molecular fluctuations were studied in three simulated model systems, showing their impact on the overall reaction kinetics. This work demonstrates the unique insights that can be discovered by considering the subtle effects that can be created by the spatial and temporal kinetics of biomolecular reac... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3432792 Mon, 01 Mar 2010 00:00:00 +0100 3432792 http://www.medworm.com/index.php?rid=3432791&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5440010%26arnumber%3D5308235 In this paper, methods to measure viscoelastic properties of time-dependent materials are proposed using sharp, flat, and buckling tips inside an environmental SEM. Single W303 yeast cells were employed in this study. Each of the tips was used to indent single cells in a nanoindentation test. Three loading histories were used: 1) a ramp loading history, in which a sharp indenter was used; 2) a step loading history, in which a flat indenter was implemented; and 3) a fast unloading history, in which a buckling nanoneedle was applied. Analysis of the viscoelastic properties of single cells was performed for each of the loading histories by choosing an appropriate theory between the correspondence principle and the functional equation. Results from each of the tests show good agreement, from w... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3432791 Mon, 01 Mar 2010 00:00:00 +0100 3432791 http://www.medworm.com/index.php?rid=3432790&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5440010%26arnumber%3D5299055 In this paper, hydroxyapatite (HA) sol composed of nanosized HA particles was incorporated into collagen gel to regulate cell-mediated collagen contraction. Human bone marrow derived stromal cells (hMSCs) were cultured for 37 days in gels with HA to collagen ratios of 0:1, 0.5:1, 1:1, 1.5:1, and 2:1, respectively. The contraction of gels was evaluated by measuring diameter change with incubation time, and the microstructure of gels at the end of culture was visualized by SEM. The cytotoxicity of HA sol was evaluated according to the percentage of maximum lactate dehydrogenase (LDH) release from hMSCs. A combination of Hoechst 33342, propidium iodide, and calcein esters was used for imaging the live/dead cells and the distribution of loaded cells within the constructs. By incorporating HA s... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3432790 Mon, 01 Mar 2010 00:00:00 +0100 3432790 http://www.medworm.com/index.php?rid=3432789&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5440010%26arnumber%3D5440014 (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3432789 Mon, 01 Mar 2010 00:00:00 +0100 3432789 http://www.medworm.com/index.php?rid=3432788&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5440010%26arnumber%3D5440015 (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3432788 Mon, 01 Mar 2010 00:00:00 +0100 3432788 http://www.medworm.com/index.php?rid=3335226&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5401109%26arnumber%3D5308323 Single cell analysis has attracted much attention to reveal the detailed and localized biological information. Local environmental control technique is desired to analyze the detailed and localized properties of single cells. In this paper, we propose the local environmental control system with nano/micro dual pipettes to control the local reagent concentration dynamically and arbitrarily. Local environmental control by dual pipettes is applied to the rotational speed control of bacterial flagellar motor, which is a rotary molecular machine. We demonstrate quick response and iterative rotational speed control of Na+-driven flagellar motor in both accelerating and relaxing directions by switching the local spout between Na+-containing and Na+-free solutions with dual pipettes. It is shown t... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3335226 Tue, 01 Dec 2009 00:00:00 +0100 3335226 http://www.medworm.com/index.php?rid=3243662&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5401109%26arnumber%3D5406308 (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3243662 Tue, 01 Dec 2009 00:00:00 +0100 3243662 http://www.medworm.com/index.php?rid=3243661&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5401109%26arnumber%3D5406311 (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3243661 Tue, 01 Dec 2009 00:00:00 +0100 3243661 http://www.medworm.com/index.php?rid=3243660&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5401109%26arnumber%3D5406306 (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3243660 Tue, 01 Dec 2009 00:00:00 +0100 3243660 http://www.medworm.com/index.php?rid=3243659&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5401109%26arnumber%3D5406307 (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3243659 Tue, 01 Dec 2009 00:00:00 +0100 3243659 http://www.medworm.com/index.php?rid=3243658&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5401109%26arnumber%3D5401113 In this paper, we proposed to utilize a reconstructed cardiac tissue as microactuator with easy assembly. In a glucose solution, cardiomyocytes can contract autonomously using only chemical energy. However, a single cardiomyocyte is not enough to actuate a microrobot or a mechanical system. Though the output power will increase by using multiple cardiomyocyte, it is difficult to assemble those cardiomyocyte to predefined positions one-by-one using a micromanipulator. Reconstructed cardiac tissue not only will enable researchers to assemble the cells easily and but also has a potential to improve the contractile ability. To realize a bio-actuator in this paper, we reconstructed a microcardiac tissue using an extracellular matrix, and their displacements, displacement frequency, contractile ... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3243658 Tue, 01 Dec 2009 00:00:00 +0100 3243658 http://www.medworm.com/index.php?rid=3243657&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5401109%26arnumber%3D5308323 Single cell analysis has attracted much attention to reveal the detailed and localized biological information. Local environmental control technique is desired to analyze the detailed and localized properties of single cells. In this paper, we propose the local environmental control system with nano/micro dual pipettes to control the local reagent concentration dynamically and arbitrarily. Local environmental control by dual pipettes is applied to the rotational speed control of bacterial flagellar motor, which is a rotary molecular machine. We demonstrate quick response and iterative rotational speed control of Na$^{+}$-driven flagellar motor in both accelerating and relaxing directions by switching the local spout between Na $^{+}$-containing and Na$^{+}$ -free solutions with dual pipett... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3243657 Tue, 01 Dec 2009 00:00:00 +0100 3243657 http://www.medworm.com/index.php?rid=3243656&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5401109%26arnumber%3D5299060 Automated continuous individual cell transfer is a critical step in single-cell applications using microfluidic devices. Cells must be aspirated gently from a buffer before transferring to operation zone so as not to artificially perturb their biostructures. Vision-based manipulation is a key technique for allowing nondestructive cell transportation. In this paper, we presented a design for an automated single-cell loading and supply system that can be integrated with complex microfluidic applications for examining or processing one cell at a time such as the current nuclear transplantation method. The aim of the system is to automatically transfer mammalian donor ( $sim$15 $mu$m) or oocyte ($sim$100 $mu$ m) cells one by one from a container to a polydimethylsiloxane (PDMS) microchannel an... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3243656 Tue, 01 Dec 2009 00:00:00 +0100 3243656 http://www.medworm.com/index.php?rid=3243655&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5401109%26arnumber%3D5299058 An in vitro translation system, based on cell components of the hyperthermophilic archaeon, Thermococcus kodakaraensis, has previously been developed. The system has been optimized and applied for protein production at high temperatures (60–65  $^{circ}$C). In this paper, we have examined the possibilities to utilize this system at a lower temperature range using green fluorescence protein (GFP) as the reporter protein. By optimizing the composition of the reaction mixture, and adding chaperonins from the mesophilic Escherichia coli, the yield of protein production at 40  $^{circ}$C was increased by fivefold. For liposome encapsulation of the optimized system, water-in-oil cell-sized emulsions were prepared by adding the translation system/GFP mRNA mixture to mineral o... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3243655 Tue, 01 Dec 2009 00:00:00 +0100 3243655 http://www.medworm.com/index.php?rid=3243654&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5401109%26arnumber%3D5401111 In this study, we proposed and developed the first single embryo coculture device, which allows making an array of a single embryo coculture with endometrial cells by controlling the culture environment in a microfluidic device. To realize this concept, we investigated three key issues: selection of a culture medium for the embryo coculture with endometrial cells using a mouse embryo and endometrial cells, evaluation of an on-microporous-membrane coculture of endometrial cells and an embryo to control the polarization of endometrial cells on the membrane, and evaluation of the coculture of endometrial cells and the embryo in the microfluidic device. We successfully obtained an array of a single coculture of embryo with endometrial cells in a microfluidic device. This concept will open and ... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3243654 Tue, 01 Dec 2009 00:00:00 +0100 3243654 http://www.medworm.com/index.php?rid=3243653&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5401109%26arnumber%3D5299057 In this paper, we describe the fabrication of a temperature-controlled microfluidic chip for cell immobilization using a thermosensitive hydrogel of poly (N-isopropylacrylamide) (PNIPAAm). A mixture of PNIPAAm solution, yeast cells, and Calcein-AM fluorescent dye is flowed in the microchannel, and the indium-tin-oxide (ITO) microheaters that were fabricated by micromachining technology heat a PNIPAAm gel. However, if the gel is very thick, it blocks the observation of the culturing cells and reduces the SNR. To address this problem, we fabricate a suspended microbridge above the microheater that limits the height of the gel, ensuring that it forms a thin and transparent layer above the heater. Microheaters and suspended biocompatible microbridge are integrated on a chip in which yeast-cell... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3243653 Tue, 01 Dec 2009 00:00:00 +0100 3243653 http://www.medworm.com/index.php?rid=3243652&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5401109%26arnumber%3D5401110 Analysis of cellular responses to chemicals at high spatiotemporal resolution is required for precise understanding of intracellular signal transduction. Here, we demonstrated a novel method for applying different solutions to a part of or all of a cell at high spatiotemporal resolution. We fabricated a microfluidic device using polydimethylsiloxane, and the sharp interface between the two solution streams flowing in the channel was used for the application of different solutions. We constructed a computer-controlled system to control the interface movement precisely, rapidly, and reproducibly during positioning, and spatial and temporal resolutions attained were 1.6 $mu$m and 189 ms, respectively. We then applied the present system to the analysis of intracellular responses to chemicals. ... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3243652 Tue, 01 Dec 2009 00:00:00 +0100 3243652 http://www.medworm.com/index.php?rid=3243651&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5401109%26arnumber%3D5401115 Microorifice-based fusion makes use of electric field constriction to assure high-yield one-to-one fusion of selected cell pairs. The aim of this paper is to verify feasibility of high-yield cell fusion on a microfluidic chip. This paper also examines viability of the fusant created on the chip. We fabricated a microfluidic chip to fuse selected cell pairs and to study postfusion behavior. We used a self-forming meniscus-based fabrication process to create microorifice with a diameter of 2–10 $mu$m on the vertical walls in a microfluidic channel. When 1 MHz was applied to electrodes located on both sides of the microorifice, dielectrophoretic force attracted the cells toward microorifice to form a cell pair. Once the cells get into contact, fusion pulse was applied. Real time imagin... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3243651 Tue, 01 Dec 2009 00:00:00 +0100 3243651 http://www.medworm.com/index.php?rid=3243650&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5401109%26arnumber%3D5401114 Hyaluronan is a major component of extracellular matrix and involved in a variety of important biological processes such as cell motility, proliferation, differentiation, and survival. However, the structure of hyaluronan and the mode of interaction between hyaluronan and its receptor remain to be fully elucidated. Here, we visualized directly the structure of hyaluronan by nanoscale imaging using atomic force microscopy (AFM), and analyzed the pattern of interaction with its cell surface receptor CD44. We observed by AFM that hyaluronan formed honeycomb-like network structures, to which the recombinant protein of CD44 extracellular domain intensively adhered. The pattern of the meshwork varied with the concentration of hyaluronan and also with its molecular weight. These observations sugg... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3243650 Tue, 01 Dec 2009 00:00:00 +0100 3243650 http://www.medworm.com/index.php?rid=3243649&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5401109%26arnumber%3D5401112 The nine papers in this special issue review and discuss the latest major advances of analysis, design, and synthesis of biological systems based on good use of advanced manipulation. (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3243649 Tue, 01 Dec 2009 00:00:00 +0100 3243649 http://www.medworm.com/index.php?rid=3243648&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5401109%26arnumber%3D5406310 (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3243648 Tue, 01 Dec 2009 00:00:00 +0100 3243648 http://www.medworm.com/index.php?rid=3243647&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5401109%26arnumber%3D5406309 (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3243647 Tue, 01 Dec 2009 00:00:00 +0100 3243647 http://www.medworm.com/index.php?rid=3153278&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5371771%26arnumber%3D5371774 (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3153278 Tue, 01 Sep 2009 00:00:00 +0100 3153278 http://www.medworm.com/index.php?rid=3153277&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5371771%26arnumber%3D5371773 (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3153277 Tue, 01 Sep 2009 00:00:00 +0100 3153277 http://www.medworm.com/index.php?rid=3153276&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5371771%26arnumber%3D5371775 (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3153276 Tue, 01 Sep 2009 00:00:00 +0100 3153276 http://www.medworm.com/index.php?rid=3153275&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5371771%26arnumber%3D5371772 (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3153275 Tue, 01 Sep 2009 00:00:00 +0100 3153275 http://www.medworm.com/index.php?rid=3153274&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5371771%26arnumber%3D5371779 In this paper, we provide an in silico input–output characterization of a three-terminal transcriptional device employing polymerase per second (PoPS) as input and output. The device is assembled from well-characterized parts of the bacteriophage $lambda$ switch transcriptional circuit. We draw the analogy between voltage and protein concentration and between current and PoPS to demonstrate that the characteristics of the three-terminal transcriptional device are qualitatively similar to those of a bipolar junction transistor (BJT). In particular, as it occurs in a BJT, the device can be tuned to operate either as a linear amplifier or as a switch. When the device operates as a linear amplifier, gains of twofolds can be obtained, which are considerably smaller than those obtained in... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3153274 Tue, 01 Sep 2009 00:00:00 +0100 3153274 http://www.medworm.com/index.php?rid=3153273&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5371771%26arnumber%3D5371781 Gold-nanoparticle-based hyperthermia has attracted considerable attention in the recent ten years in cancer treatment. In hyperthermia-based cancer treatment, in order to produce efficient thermal therapy yet without excessive heat damage to human body, besides the steady-state thermal condition, the transient thermal response is of vital importance. As part of theoretical research associated with nanoparticle-mediated hyperthermia therapy for cancer treatment, the transient heat transfer process of laser interacting with gold nanoparticle in tissue-like medium is investigated. Within the framework of dual-phase-lag (DPL) model, this paper focuses on the microscopic heat transfer performance of a gold nanoparticle in a surrounding medium. A semianalytical solution of 1-D nonhomogenous DPL ... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3153273 Tue, 01 Sep 2009 00:00:00 +0100 3153273 http://www.medworm.com/index.php?rid=3153272&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5371771%26arnumber%3D5161324 Using DNA to store digital signals, or data in general, offers significant advantages when compared to other media. The DNA molecule, especially in its double-stranded form, is very stable, compact, and inexpensive. In the past, we have shown that DNA can be used to store and retrieve digital signals encoded and stored in DNA. We have also shown that DNA hybridization can be used as a similarity criterion for retrieving digital signals encoded and stored in a DNA database. Retrieval is achieved through hybridization of “query” and “data” DNA molecules. In this paper, we present a mathematical framework to simulate single-query and parallel-query scenarios, and to estimate hybridization efficiency. Our framework allows for exact numerical solutions as well as clo... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3153272 Tue, 01 Sep 2009 00:00:00 +0100 3153272 http://www.medworm.com/index.php?rid=3153271&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5371771%26arnumber%3D5164936 Clustering is concerned with the discovery of groupings of records in a database. Many clustering problems are defined as partitioning problems in the sense that the similar records are grouped into nonoverlapping partitions. However, the clustering of gene expression data to discover coexpressed genes may not always be meaningful if this problem is reduced into a partitioning problem. Due to the complexity of the underlying biological processes, a protein can interact with one or more other proteins belonging to different functional classes in order to perform a particular biological role. For this reason, when responding to different external stimulants, a gene that produces a particular protein can coexpress with more than one group of other genes. The gene can therefore belong to more ... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3153271 Tue, 01 Sep 2009 00:00:00 +0100 3153271 http://www.medworm.com/index.php?rid=3153270&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5371771%26arnumber%3D5089446 Nonlinear cooperative behavior appears naturally in many systems, such as cardiac cell oscillations; cellular calcium oscillations; oscillatory chemical reactions, and fireflies. Such systems have been studied in detail due to their inherent properties of robustness, adaptability, scalability, and emergence. In this paper, such nonlinear cooperative behaviors are considered within the domain of electronic system design. We investigate these desirable properties in a system composed of electronic oscillators. The paper presents a series of circuit simulation results showing that self-organizing principles, which can be emulated in an electronic circuit, enable the systems to show a phase transition to synchronization, in a manner similar to those of natural systems. Circuit simulation resul... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3153270 Tue, 01 Sep 2009 00:00:00 +0100 3153270 http://www.medworm.com/index.php?rid=3153269&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5371771%26arnumber%3D5371777 This study is expected to add to the knowledge of nanowire-based cell manipulation and contribute to a full spectrum of control strategies for efficient use of nanowires for micro-total-analysis. It may also facilitate mechanobiological studies at cellular level, and provide useful insights for development of 3-D in vivo-like multicellular models for various applications in tissue engineering. (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3153269 Tue, 01 Sep 2009 00:00:00 +0100 3153269 http://www.medworm.com/index.php?rid=3153268&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5371771%26arnumber%3D4799189 In this paper, we report on the influence of shallow micro- and nanopatterned substrata on the attachment and behavior of a human fibroblast [human telomerase transfected immortalized (hTERT)] cells. We identify a hierarchy of textural guidance cues with respect to cell alignment on these substrates. Cells were seeded and cultured for 48 h on silicon substrates patterned with two linear textures overlaid at 90 $^{circ}$, both with 24 $mu$m pitch: a micrograting and a nanopattern of rows of 140- nm-diameter pits arranged in a rectangular array with 300 nm centre-to-centre spacing. The cell response to these textures was shown to be highly dependent on textural feature dimensions. We show that cells align to the stripes of nanopits. Stripes of 30-nm deep nanopits were also shown to elicit a ... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3153268 Tue, 01 Sep 2009 00:00:00 +0100 3153268 http://www.medworm.com/index.php?rid=3153267&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5371771%26arnumber%3D5276846 Microarray technology for measuring gene expression values has created significant opportunities for advances in disease diagnosis and individualized treatment planning. However, the random noise introduced by the sample preparation, hybridization, and scanning stages of microarray processing creates significant inaccuracies in the gene expression levels, and hence presents a major barrier in realizing the anticipated advances. Literature presents several methodologies for noise reduction, which can be broadly categorized as: 1) model based approaches for estimation and removal of hybridization noise; 2) approaches using commonly available image denoising tools; and 3) approaches involving the need for control sample(s). In this paper, we present a novel methodology for identifying and rem... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3153267 Tue, 01 Sep 2009 00:00:00 +0100 3153267 http://www.medworm.com/index.php?rid=3153266&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5371771%26arnumber%3D5371780 In this paper, we show how to form partial-order multiple-sequence alignment graphs on two types of reconfigurable mesh architectures. The first reconfigurable mesh is a standard microscale that uses electrical interconnects, while the second type of reconfigurable mesh can be implemented at a nanoscale level and employs spin waves for interconnectivity. We consider graph formations for two cases. In one case, the number of distinct variables in the data sequences is constant. In the other case, it can be as much as $O(N)$ . We show that given $O(N)$ aligned sequences of length $L$, we can combine the sequences to form a graph in $O(1)$ time, using either architecture if there is a constant number of distinct variables in the sequence. Otherwise, it will take $O(1)$ time if we use the spin... IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3153266 Tue, 01 Sep 2009 00:00:00 +0100 3153266 http://www.medworm.com/index.php?rid=3153265&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5371771%26arnumber%3D5371776 (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3153265 Tue, 01 Sep 2009 00:00:00 +0100 3153265 http://www.medworm.com/index.php?rid=3153264&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5371771%26arnumber%3D5371778 (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=3153264 Tue, 01 Sep 2009 00:00:00 +0100 3153264 http://www.medworm.com/index.php?rid=2657546&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5185450%26arnumber%3D5185454 (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=2657546 Sun, 31 May 2009 23:00:00 +0100 2657546 http://www.medworm.com/index.php?rid=2657545&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5185450%26arnumber%3D5185453 (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=2657545 Sun, 31 May 2009 23:00:00 +0100 2657545 http://www.medworm.com/index.php?rid=2657544&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5185450%26arnumber%3D5185452 (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=2657544 Sun, 31 May 2009 23:00:00 +0100 2657544 http://www.medworm.com/index.php?rid=2657543&cid=s_37227_174_f&fid=37227&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Fisnumber%3D5185450%26arnumber%3D5185451 (Source: IEE Transactions on NanoBioscience) IEE Transactions on NanoBioscience journals http://www.medworm.com/rss/comments.php?id=2657543 Sun, 31 May 2009 23:00:00 +0100 2657543