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NanoBioscience, IEEE Transactions on

Issue 2 • Date June 2013

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Displaying Results 1 - 18 of 18
  • Table of Contents

    Page(s): C1
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  • IEEE Transactions on NanoBioscience publication information

    Page(s): C2
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  • Experimental Study on Low-Detection Limit for Immunomagnetic Reduction Assays by Manipulating Reagent Entities

    Page(s): 65 - 68
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (458 KB) |  | HTML iconHTML  

    The low limit of detection (LLD) plays an important role in biomolecular assays, especially for early-stage assays. Biomolecular detections usually involve the use of two main elements: a reagent and an analyzer, which both greatly contribute to the LLD. In this work, the relationships among the LLD and reagent-related factors are investigated. The to-be-detected biomolecule is c-reactive protein (CRP) as an example. The assay method is immunomagnetic reduction (IMR). The components of reagent are Fe3O4 magnetic nanoparticles bio-functionalized with antibodies against CRP, dispersed in pH-7.4 phosphate buffered saline solution. Several key factors of the reagent, such as particle concentration, volume ratio of reagent to sample, and particle size, are manipulated to optimize the LLD of detecting CRP. View full abstract»

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  • {\rm MS2DB}+ : A Software for Determination of Disulfide Bonds Using Multi-Ion Analysis

    Page(s): 69 - 71
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (383 KB) |  | HTML iconHTML  

    MS2DB+ is an open-source platform-independent web application for determining, in polynomial time, the disulfide linkages in proteins using tandem mass spectrometry (MS/MS) data. It utilizes an efficient approximation algorithm which allows the consideration of multiple ion-types ( a, ao, a*, b, bo, b*, c, x, y, yo, y*, and z ) in the analysis. Once putative disulfide bonds are identified, a graph optimization approach is used to obtain the most likely global disulfide connectivity pattern. Availability-http://haddock2.sfsu.edu/~ms2db/disulfidebond/. View full abstract»

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  • Characterization and Cytotoxicity of Nanostructured Lipid Carriers Formulated With Olive Oil, Hydrogenated Palm Oil, and Polysorbate 80

    Page(s): 72 - 78
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (697 KB) |  | HTML iconHTML  

    Nanostructured lipid carriers (NLC) composed of solid and liquid lipids, and surfactants are potentially good colloidal drug carriers. Before NLC can be used as drug carriers, the cytotoxicity of their components must be ascertained. The cytotoxicity of solid lipids (trilaurin, palmitin, docosanoid acid, and hydrogenated palm oil [HPO]) and surfactants (Polysorbate 20, 80, and 85) were determined on BALB/c 3T3 cells. The HPO and Polysorbate 80 were least cytotoxic and used with olive oil in the formulation of NLC. The particle size, polydispersity index, zeta potential, specific surface area, and crystallinity index of the NLC were 61.14 nm, 0.461, -25.4 mV, and 49.07 m2 and 27.12% respectively, while the melting point was 4.3°C lower than of HPO. Unlike in serum-free, NLC incubated in fetal bovine serum-supplemented medium did not show particle growth, suggesting that serum proteins in medium inhibit nanoparticles aggregation. The study also showed that NLC was less toxic to BALB/c 3T3 cells than Polysorbate 80. Thus, NLC with olive oil, HPO, and Polysorbate 80 as components are potentially good drug carriers with minimal cytotoxicity on normal cells. View full abstract»

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  • Extended Master Equation Models for Molecular Communication Networks

    Page(s): 79 - 92
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (2761 KB) |  | HTML iconHTML  

    We consider molecular communication networks consisting of transmitters and receivers distributed in a fluidic medium. In such networks, a transmitter sends one or more signaling molecules, which are diffused over the medium, to the receiver to realize the communication. In order to be able to engineer synthetic molecular communication networks, mathematical models for these networks are required. This paper proposes a new stochastic model for molecular communication networks called reaction-diffusion master equation with exogenous input (RDMEX). The key idea behind RDMEX is to model the transmitters as time series of signaling molecule counts, while diffusion in the medium and chemical reactions at the receivers are modeled as Markov processes using master equation. An advantage of RDMEX is that it can readily be used to model molecular communication networks with multiple transmitters and receivers. For the case where the reaction kinetics at the receivers is linear, we show how RDMEX can be used to determine the mean and covariance of the receiver output signals, and derive closed-form expressions for the mean receiver output signal of the RDMEX model. These closed-form expressions reveal that the output signal of a receiver can be affected by the presence of other receivers. Numerical examples are provided to demonstrate the properties of the model. View full abstract»

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  • Raman and Surface-Enhanced Raman Scattering (SERS) Studies of the Thrombin-Binding Aptamer

    Page(s): 93 - 97
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (530 KB) |  | HTML iconHTML  

    Surface-enhanced Raman scattering is used to study the Raman spectra and peak shifts the thrombin-binding aptamer (TBA) on substrates having two different geometries; one with a single stranded sequence and one with double stranded sequence. The Raman signals of the deoxyribonucleic acids on both substrates are enhanced and specific peaks of bases are identified. These results are highly reproducible and have promising applications in low cost nucleic acid detection. View full abstract»

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  • Effective Identification of Negative Regulation Patterns of Protein Kinases

    Page(s): 98 - 105
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (1586 KB) |  | HTML iconHTML  

    Recent studies point to the fact that protein kinases play an important role in the regulation of cellular pathways and show great potential in disease treatment. Thus, it is critical to discover characterized regulatory patterns of protein kinases in signaling pathway. There have been considerable efforts to explore the activities of protein kinases. However, the study of negative regulation patterns has been largely overlooked and undeveloped. This paper aims to identify inhibitory regulatory correlations of protein kinase according to negative association rule mining. Especially, mutual information is applied to sort out the items with strong dependency and the minimum support threshold is computed by support constraints to control rule generation. The obtained rules not only reveal the relationships between subunits of protein kinases and between subunits and stimuli, but also provide novel pharmacological insight into drug design for diseases. View full abstract»

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  • Adhesion and Proliferation of Osteoblast-Like Cells on Anodic Porous Alumina Substrates With Different Morphology

    Page(s): 106 - 111
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (1000 KB) |  | HTML iconHTML  

    We have fabricated nanoporous alumina surfaces by means of anodization in oxalic acid in different conditions and used them as the substrates for the growth of cells from a human osteoblast-like cell line. The rough nanoporous alumina substrates have been compared both with smooth standard Petri dishes used as the control and with commercial substrates of similar material. The viability of the cells has been assessed at different culture times of 4, 11, 18, and 25 days in vitro. It turned out that the porous side of the galvanostatically fabricated alumina performed similar to the control and better than the commercial porous alumina, whereas the potentiostatically fabricated porous alumina performed better than all the other substrates at all times, and in particular at the two shortest time periods of 4 and 11 days in vitro. The best performance of the substrates is associated with intermediate surface roughness and feature spacing. View full abstract»

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  • Nanoparticle Mediated Thermal Ablation of Breast Cancer Cells Using a Nanosecond Pulsed Electric Field

    Page(s): 112 - 118
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    In the past, ablation of cancer cells using radiofrequency heating techniques has been demonstrated, but the current methodology has many flaws, including inconsistent tumor ablation and significant ablation of normal cells. Other researchers have begun to develop a treatment that is more selective for cancer cells using metallic nanoparticles and constant electric field exposure. In these studies, cell necrosis is induced by heating antibody functionalized metallic nanoparticles attached to cancer cells. Our approach to studying this phenomenon is to use similarly functionalized metallic nanoparticles that are specific for the T47D breast cancer cell line, exposing these nanoparticle cell conjugates to a nanosecond pulsed electric field. Using fluorescent, polystyrene-coated, iron-oxide nanoparticles, the results of our pilot study indicated that we were able to ablate up to approximately 80% of the cells using 60 ns pulses in increasing numbers of pulses and up to approximately 90% of the cells using 300 ns pulses in increasing numbers of pulses. These quantities of ablated cells were achieved using a cumulative exposure time 6 orders of magnitude less than most in vitro constant electric field studies. View full abstract»

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  • Associate PCR-RFLP Assay Design With SNPs Based on Genetic Algorithm in Appropriate Parameters Estimation

    Page(s): 119 - 127
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    Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) is a commonly used laboratory technique and useful in small-scale basic research studies of complex genetic diseases that are associated with single nucleotide polymorphisms (SNPs). Before PCR-RFLP assay for SNP genotyping can be performed, a feasible primer pair observes numerous constraints and an available restriction enzyme for discriminating a target SNP, are required. The computation of feasible PCR-RFLP primers and find available restriction enzymes simultaneously aim at a target SNP is a challenging problem. Here, we propose an available method which combines the updated core of SNP-RFLPing with a genetic algorithm to reliably mine available restriction enzymes and search for feasible PCR-RFLP primers. We have in silico simulated the method in the SLC6A4 gene under different parameter settings and provided an appropriate parameter setting. The wet laboratory validation showed that it indeed usable in providing the available restriction enzymes and designing feasible primers that fit the common primer constraints. We have provided an easy and kindly interface to assist the researchers designing their PCR-RFLP assay for SNP genotyping. The program is implemented in JAVA and is freely available at http://bio.kuas.edu.tw/ganpd/. View full abstract»

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  • Robustness of TCA Cycle at Steady-State: An LMI-Based Analysis and Synthesis Framework

    Page(s): 128 - 134
    Save to Project icon | Request Permissions | Click to expandQuick Abstract | PDF file iconPDF (1983 KB) |  | HTML iconHTML  

    A novel analysis and synthesis framework is devised for synergism and saturation system, commonly known as S-system, for improving the robustness of the TCA cycle. In order to minimize the perturbation sensitivity, a measure of robustness of the network, a new design framework is proposed. The design constraints are formulated in computationally attractive convex optimization framework. The proposed multi-objective optimization problem, framed as Linear Matrix Inequality (LMI), makes a trade-off between the robustness and the control effort of the synthesized TCA cycle. View full abstract»

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  • 2013 International Conference on Bioinformatics and Biomedicine

    Page(s): 135 - 137
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  • 2013 IEEE International Conference on Bioinformatics and Biomedicine

    Page(s): 138
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  • Molecular Communications and Betworking IEEE Transactions on Nanobioscience Special Theme Issue

    Page(s): 139
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  • Open Access

    Page(s): 140
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  • IEEE Transactions on NanoBioscience information for authors

    Page(s): C3
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  • [Blank page - back cover]

    Page(s): C4
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Aims & Scope

The IEEE Transactions on NanoBioscience publishes basic and applied papers dealing both with engineering, physics, chemistry, modeling and computer science and with biology and medicine with respect to molecules, cells, tissues. The content of acceptable papers ranges from practical/clinical/environmental applications to formalized mathematical theory.

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Meet Our Editors

Editor-in-Chief
Henry Hess
Department of Biomedical Engineering
Columbia University