A Nuclease from Streptococcus mutans Facilitates Biofilm Dispersal and Escape from Killing by Neutrophil Extracellular Traps.

PubMed

Liu, Jia; Sun, Luping; Liu, Wei; Guo, Lihong; Liu, Zhaohui; Wei, Xi; Ling, Junqi

2017-01-01

Streptococcus mutans is the primary etiologic agent of dental caries and occasionally infective endocarditis, with the ability to form biofilms and disperse cells into distal sites to exacerbate and spread infection. In this study, we identified a nuclease (DeoC) as a S. mutans biofilm dispersal modulating factor through microarray analysis. In vitro assays revealed a dispersal defect of a deoC deletion mutant, and functional studies with purified protein were indicative of the biofilm dispersal activity of DeoC. Neutrophils are a key host response factor restraining bacterial spreading through the formation of neutrophil extracellular traps (NETs), which consist of a nuclear DNA backbone associated with antimicrobial peptides. Therefore, we hypothesized that the dispersed S. mutans might utilize DeoC to degrade NETs and escape killing by the immune system. It was found that S. mutans induced NET formation upon contact with neutrophils, while the presence of NETs in turn enhanced the deoC expression of S. mutans . Fluorescence microscopy inspection showed that deoC deletion resulted in a decreased NET degradation ability of S. mutans and enhanced susceptibility to neutrophil killing. Data obtained from this study assigned two important roles for DeoC in S. mutans : contributing to the spread of infection through mediating biofilm dispersal, and facilitating the escape of S. mutans from neutrophil killing through NET degradation.

The Genome-Wide Expression Profile of Saussurea lappa Extract on House Dust Mite-Induced Atopic Dermatitis in Nc/Nga Mice.

PubMed

Lim, Hye-Sun; Ha, Hyekyung; Shin, Hyeun-Kyoo; Jeong, Soo-Jin

2015-09-01

Saussurea lappa has been reported to possess anti-atopic properties. In this study, we have confirmed the S. lappa's anti-atopic properties in Nc/Nga mice and investigated the candidate gene related with its properties using microarray. We determined the target gene using real time PCR in in vitro experiment. S. lappa showed the significant reduction in atopic dermatitis (AD) score and immunoglobulin E compared with the AD induced Nc/Nga mice. In the results of microarray using back skin obtained from animals, we found that S. lappa's properties are closely associated with cytokine-cytokine receptor interaction and the JAK-STAT signaling pathway. Consistent with the microarray data, real-time RT-PCR confirmed these modulation at the mRNA level in skin tissues from S. lappa-treated mice. Among these genes, PI3Kca and IL20Rβ were significantly downregulated by S. lappa treatment in Nc/Nga mouse model. In in vitro experiment using HaCaT cells, we found that the S. lappa components, including alantolactone, caryophyllene, costic acid, costunolide and dehydrocostus lactone significantly decreased the expression of PI3Kca but not IL20Rβ in vitro. Therefore, our study suggests that PI3Kca-related signaling is closely related with the protective effects of S. lappa against the development of atopic-dermatitis.

A network model for biofilm development in Escherichia coli K-12.

PubMed

Shalá, Andrew A; Restrepo, Silvia; González Barrios, Andrés F

2011-09-22

In nature, bacteria often exist as biofilms. Biofilms are communities of microorganisms attached to a surface. It is clear that biofilm-grown cells harbor properties remarkably distinct from planktonic cells. Biofilms frequently complicate treatments of infections by protecting bacteria from the immune system, decreasing antibiotic efficacy and dispersing planktonic cells to distant body sites. In this work, we employed enhanced Boolean algebra to model biofilm formation. The network obtained describes biofilm formation successfully, assuming - in accordance with the literature - that when the negative regulators (RscCD and EnvZ/OmpR) are off, the positive regulator (FlhDC) is on. The network was modeled under three different conditions through time with satisfactory outcomes. Each cluster was constructed using the K-means/medians Clustering Support algorithm on the basis of published Affymetrix microarray gene expression data from biofilm-forming bacteria and the planktonic state over four time points for Escherichia coli K-12. The different phenotypes obtained demonstrate that the network model of biofilm formation can simulate the formation or repression of biofilm efficiently in E. coli K-12.

Data-adaptive test statistics for microarray data.

PubMed

Mukherjee, Sach; Roberts, Stephen J; van der Laan, Mark J

2005-09-01

An important task in microarray data analysis is the selection of genes that are differentially expressed between different tissue samples, such as healthy and diseased. However, microarray data contain an enormous number of dimensions (genes) and very few samples (arrays), a mismatch which poses fundamental statistical problems for the selection process that have defied easy resolution. In this paper, we present a novel approach to the selection of differentially expressed genes in which test statistics are learned from data using a simple notion of reproducibility in selection results as the learning criterion. Reproducibility, as we define it, can be computed without any knowledge of the 'ground-truth', but takes advantage of certain properties of microarray data to provide an asymptotically valid guide to expected loss under the true data-generating distribution. We are therefore able to indirectly minimize expected loss, and obtain results substantially more robust than conventional methods. We apply our method to simulated and oligonucleotide array data. By request to the corresponding author.

Quantifying protein-protein interactions in high throughput using protein domain microarrays.

PubMed

Kaushansky, Alexis; Allen, John E; Gordus, Andrew; Stiffler, Michael A; Karp, Ethan S; Chang, Bryan H; MacBeath, Gavin

2010-04-01

Protein microarrays provide an efficient way to identify and quantify protein-protein interactions in high throughput. One drawback of this technique is that proteins show a broad range of physicochemical properties and are often difficult to produce recombinantly. To circumvent these problems, we have focused on families of protein interaction domains. Here we provide protocols for constructing microarrays of protein interaction domains in individual wells of 96-well microtiter plates, and for quantifying domain-peptide interactions in high throughput using fluorescently labeled synthetic peptides. As specific examples, we will describe the construction of microarrays of virtually every human Src homology 2 (SH2) and phosphotyrosine binding (PTB) domain, as well as microarrays of mouse PDZ domains, all produced recombinantly in Escherichia coli. For domains that mediate high-affinity interactions, such as SH2 and PTB domains, equilibrium dissociation constants (K(D)s) for their peptide ligands can be measured directly on arrays by obtaining saturation binding curves. For weaker binding domains, such as PDZ domains, arrays are best used to identify candidate interactions, which are then retested and quantified by fluorescence polarization. Overall, protein domain microarrays provide the ability to rapidly identify and quantify protein-ligand interactions with minimal sample consumption. Because entire domain families can be interrogated simultaneously, they provide a powerful way to assess binding selectivity on a proteome-wide scale and provide an unbiased perspective on the connectivity of protein-protein interaction networks.

Transient thermal effect, nonlinear refraction and nonlinear absorption properties of graphene oxide sheets in dispersion.

PubMed

Zhang, Xiao-Liang; Liu, Zhi-Bo; Li, Xiao-Chun; Ma, Qiang; Chen, Xu-Dong; Tian, Jian-Guo; Xu, Yan-Fei; Chen, Yong-Sheng

2013-03-25

The nonlinear refraction (NLR) properties of graphene oxide (GO) in N, N-Dimethylformamide (DMF) was studied in nanosecond, picosecond and femtosecond time regimes by Z-scan technique. Results show that the dispersion of GO in DMF exhibits negative NLR properties in nanosecond time regime, which is mainly attributed to transient thermal effect in the dispersion. The dispersion also exhibits negative NLR in picosecond and femtosecond time regimes, which are arising from sp(2)- hybridized carbon domains and sp(3)- hybridized matrix in GO sheets. To illustrate the relations between NLR and nonlinear absorption (NLA), NLA properties of the dispersion were also studied in nanosecond, picosecond and femtosecond time regimes.

The AIDS and Cancer Specimen Resource: Role in HIV/AIDS scientific discovery

PubMed Central

Ayers, Leona W; Silver, Sylvia; McGrath, Michael S; Orenstein, Jan M

2007-01-01

The AIDS Cancer and Specimen Resource (ACSR) supports scientific discovery in the area of HIV/AIDS-associated malignancies. The ACSR was established as a cooperative agreement between the NCI (Office of the Director, Division of Cancer Treatment and Diagnosis) and regional consortia, University of California, San Francisco (West Coast), George Washington University (East Coast) and Ohio State University (Mid-Region) to collect, preserve and disperse HIV-related tissues and biologic fluids and controls along with clinical data to qualified investigators. The available biological samples with clinical data and the application process are described on the ACSR web site. The ACSR tissue bank has more than 100,000 human HIV positive specimens that represent different processing (43), specimen (15), and anatomical site (50) types. The ACSR provides special biospecimen collections and prepares speciality items, e.g., tissue microarrays (TMA), DNA libraries. Requests have been greatest for Kaposi's sarcoma (32%) and non-Hodgkin's lymphoma (26%). Dispersed requests include 83% tissue (frozen and paraffin embedded), 18% plasma/serum and 9% other. ACSR also provides tissue microarrays of, e.g., Kaposi's sarcoma and non-Hodgkin's lymphoma, for biomarker assays and has developed collaborations with other groups that provide access to additional AIDS-related malignancy specimens. ACSR members and associates have completed 63 podium and poster presentations. Investigators have submitted 125 letters of intent requests. Discoveries using ACSR have been reported in 61 scientific publications in notable journals with an average impact factor of 7. The ACSR promotes the scientific exploration of the relationship between HIV/AIDS and malignancy by participation at national and international scientific meetings, contact with investigators who have productive research in this area and identifying, collecting, preserving, enhancing, and dispersing HIV/AIDS-related malignancy specimens to funded, approved researchers at no fee. Scientific discovery has been advanced by this unique biorepository. Investigators are encouraged to browse the ACSR Internet site for materials to enhance their own scientific initiatives. PMID:17335575

Polymer microarray technology for stem cell engineering

PubMed Central

Coyle, Robert; Jia, Jia; Mei, Ying

2015-01-01

Stem cells hold remarkable promise for applications in tissue engineering and disease modeling. During the past decade, significant progress has been made in developing soluble factors (e.g., small molecules and growth factors) to direct stem cells into a desired phenotype. However, the current lack of suitable synthetic materials to regulate stem cell activity has limited the realization of the enormous potential of stem cells. This can be attributed to a large number of materials properties (e.g., chemical structures and physical properties of materials) that can affect stem cell fate. This makes it challenging to design biomaterials to direct stem cell behavior. To address this, polymer microarray technology has been developed to rapidly identify materials for a variety of stem cell applications. In this article, we summarize recent developments in polymer array technology and their applications in stem cell engineering. Statement of significance Stem cells hold remarkable promise for applications in tissue engineering and disease modeling. In the last decade, significant progress has been made in developing chemically defined media to direct stem cells into a desired phenotype. However, the current lack of the suitable synthetic materials to regulate stem cell activities has been limiting the realization of the potential of stem cells. This can be attributed to the number of variables in material properties (e.g., chemical structures and physical properties) that can affect stem cells. Polymer microarray technology has shown to be a powerful tool to rapidly identify materials for a variety of stem cell applications. Here we summarize recent developments in polymer array technology and their applications in stem cell engineering. PMID:26497624

Novel calibration tools and validation concepts for microarray-based platforms used in molecular diagnostics and food safety control.

PubMed

Brunner, C; Hoffmann, K; Thiele, T; Schedler, U; Jehle, H; Resch-Genger, U

2015-04-01

Commercial platforms consisting of ready-to-use microarrays printed with target-specific DNA probes, a microarray scanner, and software for data analysis are available for different applications in medical diagnostics and food analysis, detecting, e.g., viral and bacteriological DNA sequences. The transfer of these tools from basic research to routine analysis, their broad acceptance in regulated areas, and their use in medical practice requires suitable calibration tools for regular control of instrument performance in addition to internal assay controls. Here, we present the development of a novel assay-adapted calibration slide for a commercialized DNA-based assay platform, consisting of precisely arranged fluorescent areas of various intensities obtained by incorporating different concentrations of a "green" dye and a "red" dye in a polymer matrix. These dyes present "Cy3" and "Cy5" analogues with improved photostability, chosen based upon their spectroscopic properties closely matching those of common labels for the green and red channel of microarray scanners. This simple tool allows to efficiently and regularly assess and control the performance of the microarray scanner provided with the biochip platform and to compare different scanners. It will be eventually used as fluorescence intensity scale for referencing of assays results and to enhance the overall comparability of diagnostic tests.

Numerical calculation of phase-matching properties in photonic crystal fibers with three and four zero-dispersion wavelengths.

PubMed

Zhao, Xingtao; Liu, Xiaoxu; Wang, Shutao; Wang, Wei; Han, Ying; Liu, Zhaolun; Li, Shuguang; Hou, Lantian

2015-10-19

Photonic crystal fibers with three and four zero-dispersion wavelengths are presented through special design of the structural parameters, in which the closing to zero and ultra-flattened dispersion can be obtained. The unique phase-matching properties of the fibers with three and four zero-dispersion wavelengths are analyzed. Variation of the phase-matching wavelengths with the pump wavelengths, pump powers, dispersion properties, and fiber structural parameters is analyzed. The presence of three and four zero-dispersion wavelengths can realize wavelength conversion of optical soliton between two anomalous dispersion regions, generate six phase-matching sidebands through four-wave mixing and create more new photon pairs, which can be used for the study of supercontinuum generation, optical switches and quantum optics.

Implementation of plaid model biclustering method on microarray of carcinoma and adenoma tumor gene expression data

NASA Astrophysics Data System (ADS)

Ardaneswari, Gianinna; Bustamam, Alhadi; Sarwinda, Devvi

2017-10-01

A Tumor is an abnormal growth of cells that serves no purpose. Carcinoma is a tumor that grows from the top of the cell membrane and the organ adenoma is a benign tumor of the gland-like cells or epithelial tissue. In the field of molecular biology, the development of microarray technology is used in the data store of disease genetic expression. For each of microarray gene, an amount of information is stored for each trait or condition. In gene expression data clustering can be done with a bicluster algorithm, thats clustering method which not only the objects to be clustered, but also the properties or condition of the object. This research proposed Plaid Model Biclustering as one of biclustering method. In this study, we discuss the implementation of Plaid Model Biclustering Method on microarray of Carcinoma and Adenoma tumor gene expression data. From the experimental results, we found three biclusters are formed by Carcinoma gene expression data and four biclusters are formed by Adenoma gene expression data.

Carbohydrate Cluster Microarrays Fabricated on 3-Dimensional Dendrimeric Platforms for Functional Glycomics Exploration

PubMed Central

Zhou, Xichun; Turchi, Craig; Wang, Denong

2009-01-01

We reported here a novel, ready-to-use bioarray platform and methodology for construction of sensitive carbohydrate cluster microarrays. This technology utilizes a 3-dimensional (3-D) poly(amidoamine) starburst dendrimer monolayer assembled on glass surface, which is functionalized with terminal aminooxy and hydrazide groups for site-specific coupling of carbohydrates. A wide range of saccharides, including monosaccharides, oligosaccharides and polysaccharides of diverse structures, are applicable for the 3-D bioarray platform without prior chemical derivatization. The process of carbohydrate coupling is effectively accelerated by microwave radiation energy. The carbohydrate concentration required for microarray fabrication is substantially reduced using this technology. Importantly, this bioarray platform presents sugar chains in defined orientation and cluster configurations. It is, thus, uniquely useful for exploration of the structural and conformational diversities of glyco-epitope and their functional properties. PMID:19791771

Industrial and Commercial Property and the Dispersion of Assessed Valuation per Pupil

ERIC Educational Resources Information Center

Boltz, Paul W.

1973-01-01

Examines the dispersion of assessed valuation per pupil in Illinois and evaluates some proposals that might reduce this dispersion. The major proposal considered by the author is removal of industrial and commercial property (I & C) from local rolls. The conclusion is drawn that removing I & C from the property tax base has little or no…

Characterization of Nanoreinforcement Dispersion in Inorganic Nanocomposites: A Review

PubMed Central

Saheb, Nouari; Qadir, Najam Ul; Siddiqui, Muhammad Usama; Arif, Abul Fazl Muhammad; Akhtar, Syed Sohail; Al-Aqeeli, Nasser

2014-01-01

Metal and ceramic matrix composites have been developed to enhance the stiffness and strength of metals and alloys, and improve the toughness of monolithic ceramics, respectively. It is possible to further improve their properties by using nanoreinforcement, which led to the development of metal and ceramic matrix nanocomposites, in which case, the dimension of the reinforcement is on the order of nanometer, typically less than 100 nm. However, in many cases, the properties measured experimentally remain far from those estimated theoretically. This is mainly due to the fact that the properties of nanocomposites depend not only on the properties of the individual constituents, i.e., the matrix and reinforcement as well as the interface between them, but also on the extent of nanoreinforcement dispersion. Therefore, obtaining a uniform dispersion of the nanoreinforcement in the matrix remains a key issue in the development of nanocomposites with the desired properties. The issue of nanoreinforcement dispersion was not fully addressed in review papers dedicated to processing, characterization, and properties of inorganic nanocomposites. In addition, characterization of nanoparticles dispersion, reported in literature, remains largely qualitative. The objective of this review is to provide a comprehensive description of characterization techniques used to evaluate the extent of nanoreinforcement dispersion in inorganic nanocomposites and critically review published work. Moreover, methodologies and techniques used to characterize reinforcement dispersion in conventional composites, which may be used for quantitative characterization of nanoreinforcement dispersion in nanocomposites, is also presented. PMID:28788670

Uniformly Dispersed and Re-Agglomerated Graphene Oxide-Based Cement Pastes: A Comparison of Rheological Properties, Mechanical Properties and Microstructure.

PubMed

Long, Wu-Jian; Li, Hao-Dao; Fang, Chang-Le; Xing, Feng

2018-01-09

The properties of graphene oxide (GO)-based cement paste can be significantly affected by the state of GO dispersion. In this study, the effects of uniformly dispersed and re-agglomerated GO on the rheological, mechanical properties and microstructure of cement paste were systematically investigated. Two distinct dispersion states can be achieved by altering the mixing sequence: Polycarboxylate-ether (PCE) mixed with GO-cement or cement mixed with GO-PCE. The experimental results showed that the yield stress and plastic viscosity increased with the uniformly dispersed GO when compared to those of re-agglomerated GO cement paste. Moreover, the 3-day compressive and flexural strengths of uniformly dispersed GO paste were 8% and 27%, respectively, higher than those of re-agglomerated GO pastes. The results of X-ray diffraction, Fourier transform infrared spectroscopy and scanning electron microscopy analyses demonstrated that uniformly dispersed GO more effectively promotes the formation of hydration products in hardened cement paste. Furthermore, a porosity analysis using mercury intrusion porosimetry revealed that the homogeneous dispersion of GO can better inhibit the formation of large-size pores and optimize the pore size distribution at 3 and 7 days than the re-agglomerated GO.

The influence of the dispersion method on the electrical properties of vapor-grown carbon nanofiber/epoxy composites

PubMed Central

2011-01-01

The influence of the dispersion of vapor-grown carbon nanofibers (VGCNF) on the electrical properties of VGCNF/Epoxy composites has been studied. A homogenous dispersion of the VGCNF does not imply better electrical properties. In fact, it is demonstrated that the most simple of the tested dispersion methods results in higher conductivity, since the presence of well-distributed nanofiber clusters appears to be a key factor for increasing composite conductivity. PACS: 72.80.Tm; 73.63.Fg; 81.05.Qk PMID:21711873

Effect of nanoparticles dispersion on viscoelastic properties of epoxy–zirconia polymer nanocomposites

NASA Astrophysics Data System (ADS)

Singh, Sushil Kumar; Kumar, Abhishek; Jain, Anuj

2018-03-01

In the present work zirconia-nanoparticles were dispersed in epoxy matrix to form epoxy-zirconia polymer nanocomposites using ultrasonication and viscoelastic properties of nanocomposites were investigated. For the same spherical zirconia-nanoparticles (45 nm) were dispersed in weight fraction of 2, 4, 6 and 8 % to reinforce the epoxy. DMA results show the significant enhancement in viscoelastic properties with the dispersion of zirconia nanoparticles in the epoxy matrix. The value of storage modulus and glass transition temperature increases from 179 MPa (pristine) to 225 MPa (6 wt.% ZrO2) and 61 °C (pristine) to 70 °C (6 wt.% ZrO2) respectively with the dispersion of zirconia nanoparticles in the epoxy.

Effect of nanoparticles dispersion on viscoelastic properties of epoxy-zirconia polymer nanocomposites

NASA Astrophysics Data System (ADS)

Singh, Sushil Kumar; Kumar, Abhishek; Jain, Anuj

2018-03-01

In the present work zirconia-nanoparticles were dispersed in epoxy matrix to form epoxy-zirconia polymer nanocomposites using ultrasonication and viscoelastic properties of nanocomposites were investigated. For the same spherical zirconia-nanoparticles (45 nm) were dispersed in weight fraction of 2, 4, 6 and 8 % to reinforce the epoxy. DMA results show the significant enhancement in viscoelastic properties with the dispersion of zirconia nanoparticles in the epoxy matrix. The value of storage modulus and glass transition temperature increases from 179 MPa (pristine) to 225 MPa (6 wt.% ZrO2) and 61 °C (pristine) to 70 °C (6 wt.% ZrO2) respectively with the dispersion of zirconia nanoparticles in the epoxy.

Graded Interface Models for more accurate Determination of van der Waals-London Dispersion Interactions across Grain Boundaries

DOE Office of Scientific and Technical Information (OSTI.GOV)

van Benthem, Klaus; Tan, Guolong; French, Roger H

2006-01-01

Attractive van der Waals V London dispersion interactions between two half crystals arise from local physical property gradients within the interface layer separating the crystals. Hamaker coefficients and London dispersion energies were quantitatively determined for 5 and near- 13 grain boundaries in SrTiO3 by analysis of spatially resolved valence electron energy-loss spectroscopy (VEELS) data. From the experimental data, local complex dielectric functions were determined, from which optical properties can be locally analysed. Both local electronic structures and optical properties revealed gradients within the grain boundary cores of both investigated interfaces. The obtained results show that even in the presence ofmore » atomically structured grain boundary cores with widths of less than 1 nm, optical properties have to be represented with gradual changes across the grain boundary structures to quantitatively reproduce accurate van der Waals V London dispersion interactions. London dispersion energies of the order of 10% of the apparent interface energies of SrTiO3 were observed, demonstrating their significance in the grain boundary formation process. The application of different models to represent optical property gradients shows that long-range van der Waals V London dispersion interactions scale significantly with local, i.e atomic length scale property variations.« less

Attenuation and velocity dispersion in the exploration seismic frequency band

NASA Astrophysics Data System (ADS)

Sun, Langqiu

In an anelastic medium, seismic waves are distorted by attenuation and velocity dispersion, which depend on petrophysical properties of reservoir rocks. The effective attenuation and velocity dispersion is a combination of intrinsic attenuation and apparent attenuation due to scattering, transmission response, and data acquisition system. Velocity dispersion is usually neglected in seismic data processing partly because of insufficient observations in the exploration seismic frequency band. This thesis investigates the methods of measuring velocity dispersion in the exploration seismic frequency band and interprets the velocity dispersion data in terms of petrophysical properties. Broadband, uncorrelated vibrator data are suitable for measuring velocity dispersion in the exploration seismic frequency band, and a broad bandwidth optimizes the observability of velocity dispersion. Four methods of measuring velocity dispersion in uncorrelated vibrator VSP data are investigated, which are the sliding window crosscorrelation (SWCC) method, the instantaneous phase method, the spectral decomposition method, and the cross spectrum method. Among them, the SWCC method is a new method and has satisfactory robustness, accuracy, and efficiency. Using the SWCC method, velocity dispersion is measured in the uncorrelated vibrator VSP data from three areas with different geological settings, i.e., Mallik gas hydrate zone, McArthur River uranium mines, and Outokumpu crystalline rocks. The observed velocity dispersion is fitted to a straight line with respect to log frequency for a constant (frequency-independent) Q value. This provides an alternative method for calculating Q. A constant Q value does not directly link to petrophysical properties. A modeling study is implemented for the Mallik and McArthur River data to interpret the velocity dispersion observations in terms of petrophysical properties. The detailed multi-parameter petrophysical reservoir models are built according to the well logs; the models' parameters are adjusted by fitting the synthetic data to the observed data. In this way, seismic attenuation and velocity dispersion provide new insight into petrophysics properties at the Mallik and McArthur River sites. Potentially, observations of attenuation and velocity dispersion in the exploration seismic frequency band can improve the deconvolution process for vibrator data, Q-compensation, near-surface analysis, and first break picking for seismic data.

Mapping of Epitopes Occurring in Bovine α(s1)-Casein Variants by Peptide Microarray Immunoassay.

PubMed

Lisson, Maria; Erhardt, Georg

2016-01-01

Immunoglobulin E epitope mapping of milk proteins reveals important information about their immunologic properties. Genetic variants of αS1-casein, one of the major allergens in bovine milk, are until now not considered when discussing the allergenic potential. Here we describe the complete procedure to assess the allergenicity of αS1-casein variants B and C, which are frequent in most breeds, starting from milk with identification and purification of casein variants by isoelectric focusing (IEF) and anion-exchange chromatography, followed by in vitro gastrointestinal digestion of the casein variants, identification of the resulting peptides by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS), in silico analysis of the variant-specific peptides as allergenic epitopes, and determination of their IgE-binding properties by microarray immunoassay with cow's milk allergic human sera.

Chemical and rheological properties of an extracellular polysaccharide produced by the cyanobacterium Anabaena sp. ATCC 33047.

PubMed

Moreno, J; Vargas, M A; Madiedo, J M; Muñoz, J; Rivas, J; Guerrero, M G

2000-02-05

The cyanobacterium (blue-green alga) Anabaena sp. ATCC 33047 produces an exopolysaccharide (EPS) during the stationary growth phase in batch culture. Chemical analysis of EPS revealed a heteropolysaccharidic nature, with xylose, glucose, galactose, and mannose the main neutral sugars found. The infrared (IR) spectrum of EPS showed absorption bands of carboxylate groups. The average molecular mass of the polymer was 1.35 MDa. Aqueous dispersions at EPS concentrations ranging from 0.2% to 0.6% (w/w) showed marked shear-thinning properties (power-law behavior). Linear dynamic viscoelastic properties showed that the elastic component was always higher than the viscous component. Viscous and viscoelastic properties demonstrated the absence of conformational changes within the concentration range studied. Stress-growth experiments revealed that 0.4% and 0.6% (w/w) EPS dispersions showed thixotropic properties. A detailed comparison of the linear dynamic viscoelasticity, transient flow, and decreasing shear rate flow curve properties was made for 0.4% (w/w) dispersions of xanthan gum (XG), Alkemir 110 (AG), and EPS. Viscoelastic spectra demonstrated that the EPS dispersion turned out to be more "fluidlike" than the AG and XG dispersions. The flow indexes indicated that the EPS dispersion was less shear-sensitive than that of XG, showing essentially the same viscosity, that is, >50 s(-1). The fact that viscosities of EPS and AG dispersions were not substantially different within the shear-rate range covered must be emphasized, in relation to EPS potential applications. The rheological behavior of EPS dispersions indicates the formation of an intermediate structure between a random-coil polysaccharide and a weak gel. Copyright 2000 John Wiley & Sons, Inc.

Polymerization Behavior and Polymer Properties of Eosin-Mediated Surface Modification Reactions.

PubMed

Avens, Heather J; Randle, Thomas James; Bowman, Christopher N

2008-10-17

Surface modification by surface-mediated polymerization necessitates control of the grafted polymer film thicknesses to achieve the desired property changes. Here, a microarray format is used to assess a range of reaction conditions and formulations rapidly in regards to the film thicknesses achieved and the polymerization behavior. Monomer formulations initiated by eosin conjugates with varying concentrations of poly(ethylene glycol) diacrylate (PEGDA), N-methyldiethanolamine (MDEA), and 1-vinyl-2-pyrrolidone (VP) were evaluated. Acrylamide with MDEA or ascorbic acid as a coinitiator was also investigated. The best formulation was found to be 40 wt% acrylamide with MDEA which yielded four to eight fold thicker films (maximum polymer thickness increased from 180 nm to 1420 nm) and generated visible films from 5-fold lower eosin surface densities (2.8 vs. 14 eosins/µm(2)) compared to a corresponding PEGDA formulation. Using a microarray format to assess multiple initiator surface densities enabled facile identification of a monomer formulation that yields the desired polymer properties and polymerization behavior across the requisite range of initiator surface densities.

Polymerization Behavior and Polymer Properties of Eosin-Mediated Surface Modification Reactions

PubMed Central

Avens, Heather J.; Randle, Thomas James; Bowman, Christopher N.

2008-01-01

Surface modification by surface-mediated polymerization necessitates control of the grafted polymer film thicknesses to achieve the desired property changes. Here, a microarray format is used to assess a range of reaction conditions and formulations rapidly in regards to the film thicknesses achieved and the polymerization behavior. Monomer formulations initiated by eosin conjugates with varying concentrations of poly(ethylene glycol) diacrylate (PEGDA), N-methyldiethanolamine (MDEA), and 1-vinyl-2-pyrrolidone (VP) were evaluated. Acrylamide with MDEA or ascorbic acid as a coinitiator was also investigated. The best formulation was found to be 40 wt% acrylamide with MDEA which yielded four to eight fold thicker films (maximum polymer thickness increased from 180 nm to 1420 nm) and generated visible films from 5-fold lower eosin surface densities (2.8 vs. 14 eosins/µm2) compared to a corresponding PEGDA formulation. Using a microarray format to assess multiple initiator surface densities enabled facile identification of a monomer formulation that yields the desired polymer properties and polymerization behavior across the requisite range of initiator surface densities. PMID:19838291

The MGED ontology: a framework for describing functional genomics experiments.

PubMed

Stoeckert, Christian J; Parkinson, Helen

2003-01-01

The Microarray Gene Expression Data (MGED) society was formed with an initial focus on experiments involving microarray technology. Despite the diversity of applications, there are common concepts used and a common need to capture experimental information in a standardized manner. In building the MGED ontology, it was recognized that it would be impractical to cover all the different types of experiments on all the different types of organisms by listing and defining all the types of organisms and their properties. Our solution was to create a framework for describing microarray experiments with an initial focus on the biological sample and its manipulation. For concepts that are common for many species, we could provide a manageable listing of controlled terms. For concepts that are species-specific or whose values cannot be readily listed, we created an 'OntologyEntry' concept that referenced an external resource. The MGED ontology is a work in progress that needs additional instances and particularly needs constraints to be added. The ontology currently covers the experimental sample and design, and we have begun capturing aspects of the microarrays themselves as well. The primary application of the ontology will be to develop forms for entering information into databases, and consequently allowing queries, taking advantage of the structure provided by the ontology. The application of an ontology of experimental conditions extends beyond microarray experiments and, as the scope of MGED includes other aspects of functional genomics, so too will the MGED ontology.

A comprehensive simulation study on classification of RNA-Seq data.

PubMed

Zararsız, Gökmen; Goksuluk, Dincer; Korkmaz, Selcuk; Eldem, Vahap; Zararsiz, Gozde Erturk; Duru, Izzet Parug; Ozturk, Ahmet

2017-01-01

RNA sequencing (RNA-Seq) is a powerful technique for the gene-expression profiling of organisms that uses the capabilities of next-generation sequencing technologies. Developing gene-expression-based classification algorithms is an emerging powerful method for diagnosis, disease classification and monitoring at molecular level, as well as providing potential markers of diseases. Most of the statistical methods proposed for the classification of gene-expression data are either based on a continuous scale (eg. microarray data) or require a normal distribution assumption. Hence, these methods cannot be directly applied to RNA-Seq data since they violate both data structure and distributional assumptions. However, it is possible to apply these algorithms with appropriate modifications to RNA-Seq data. One way is to develop count-based classifiers, such as Poisson linear discriminant analysis and negative binomial linear discriminant analysis. Another way is to bring the data closer to microarrays and apply microarray-based classifiers. In this study, we compared several classifiers including PLDA with and without power transformation, NBLDA, single SVM, bagging SVM (bagSVM), classification and regression trees (CART), and random forests (RF). We also examined the effect of several parameters such as overdispersion, sample size, number of genes, number of classes, differential-expression rate, and the transformation method on model performances. A comprehensive simulation study is conducted and the results are compared with the results of two miRNA and two mRNA experimental datasets. The results revealed that increasing the sample size, differential-expression rate and decreasing the dispersion parameter and number of groups lead to an increase in classification accuracy. Similar with differential-expression studies, the classification of RNA-Seq data requires careful attention when handling data overdispersion. We conclude that, as a count-based classifier, the power transformed PLDA and, as a microarray-based classifier, vst or rlog transformed RF and SVM classifiers may be a good choice for classification. An R/BIOCONDUCTOR package, MLSeq, is freely available at https://www.bioconductor.org/packages/release/bioc/html/MLSeq.html.

Effect of hydroxypropylcellulose and Tween 80 on physicochemical properties and bioavailability of ezetimibe-loaded solid dispersion.

PubMed

Rashid, Rehmana; Kim, Dong Wuk; Din, Fakhar Ud; Mustapha, Omer; Yousaf, Abid Mehmood; Park, Jong Hyuck; Kim, Jong Oh; Yong, Chul Soon; Choi, Han-Gon

2015-10-05

The purpose of this research was to evaluate the effect of the HPC (hydroxypropylcellulose) and Tween 80 on the physicochemical properties and oral bioavailability of ezetimibe-loaded solid dispersions. The binary solid dispersions were prepared with drug and various amounts of HPC. Likewise, ternary solid dispersions were prepared with different ratios of drug, HPC and Tween 80. Both types of solid dispersions were prepared using the solvent evaporation method. Their aqueous solubility, physicochemical properties, dissolution and oral bioavailability were investigated in comparison with the drug powder. All the solid dispersions significantly improved the drug solubility and dissolution. As the amount of HPC increased in the binary solid dispersions to 10-fold, the drug solubility and dissolution were increased accordingly. However, further increase in HPC did not result in significant differences among them. Similarly, up to 0.1-fold, Tween 80 increased the drug solubility in the ternary solid dispersions followed by no significant change. However, Tween 80 hardly affected the drug dissolution. The physicochemical analysis proved that the drug in binary and ternary solid dispersion was existed in the amorphous form. The particle-size measurements of these formulations were also not significantly different from each other, which showed that Tween 80 had no impact on physicochemical properties. The ezetimibe-loaded binary and ternary solid dispersions gave 1.6- and 1.8-fold increased oral bioavailability in rats, respectively, as compared to the drug powder; however, these values were not significantly different from each other. Thus, HPC greatly affected the solubility, dissolution and oral bioavailability of drug, but Tween 80 hardly did. Furthermore, this ezetimibe-loaded binary solid dispersion prepared only with HPC would be suggested as a potential formulation for oral administration of ezetimibe. Copyright © 2015 Elsevier Ltd. All rights reserved.

Dissection of the cis-2-decenoic acid signaling network in Pseudomonas aeruginosa using microarray technique

PubMed Central

Rahmani-Badi, Azadeh; Sepehr, Shayesteh; Fallahi, Hossein; Heidari-Keshel, Saeed

2015-01-01

Many bacterial pathogens use quorum-sensing (QS) signaling to regulate the expression of factors contributing to virulence and persistence. Bacteria produce signals of different chemical classes. The signal molecule, known as diffusible signal factor (DSF), is a cis-unsaturated fatty acid that was first described in the plant pathogen Xanthomonas campestris. Previous works have shown that human pathogen, Pseudomonas aeruginosa, also synthesizes a structurally related molecule, characterized as cis-2-decenoic acid (C10: Δ2, CDA) that induces biofilm dispersal by multiple types of bacteria. Furthermore, CDA has been shown to be involved in inter-kingdom signaling that modulates fungal behavior. Therefore, an understanding of its signaling mechanism could suggest strategies for interference, with consequences for disease control. To identify the components of CDA signaling pathway in this pathogen, a comparative transcritpome analysis was conducted, in the presence and absence of CDA. A protein-protein interaction (PPI) network for differentially expressed (DE) genes with known function was then constructed by STRING and Cytoscape. In addition, the effects of CDA in combination with antimicrobial agents on the biofilm surface area and bacteria viability were evaluated using fluorescence microscopy and digital image analysis. Microarray analysis identified 666 differentially expressed genes in the presence of CDA and gene ontology (GO) analysis revealed that in P. aeruginosa, CDA mediates dispersion of biofilms through signaling pathways, including enhanced motility, metabolic activity, virulence as well as persistence at different temperatures. PPI data suggested that a cluster of five genes (PA4978, PA4979, PA4980, PA4982, PA4983) is involved in the CDA synthesis and perception. Combined treatments using both CDA and antimicrobial agents showed that following exposure of the biofilms to CDA, remaining cells on the surface were easily removed and killed by antimicrobials. PMID:25972860

Multi-instrumental characterization of carbon nanotubes dispersed in aqueous solutions

EPA Science Inventory

Previous studies showed that the dispersion extent and physicochemical properties of carbon nanotubes are highly dependent upon the preparation methods (e.g., dispersion methods and dispersants). In the present work, multiwalled carbon nanotubes (MWNTs) are dispersed in aqueous s...

Experimental analysis of oligonucleotide microarray design criteria to detect deletions by comparative genomic hybridization.

PubMed

Flibotte, Stephane; Moerman, Donald G

2008-10-21

Microarray comparative genomic hybridization (CGH) is currently one of the most powerful techniques to measure DNA copy number in large genomes. In humans, microarray CGH is widely used to assess copy number variants in healthy individuals and copy number aberrations associated with various diseases, syndromes and disease susceptibility. In model organisms such as Caenorhabditis elegans (C. elegans) the technique has been applied to detect mutations, primarily deletions, in strains of interest. Although various constraints on oligonucleotide properties have been suggested to minimize non-specific hybridization and improve the data quality, there have been few experimental validations for CGH experiments. For genomic regions where strict design filters would limit the coverage it would also be useful to quantify the expected loss in data quality associated with relaxed design criteria. We have quantified the effects of filtering various oligonucleotide properties by measuring the resolving power for detecting deletions in the human and C. elegans genomes using NimbleGen microarrays. Approximately twice as many oligonucleotides are typically required to be affected by a deletion in human DNA samples in order to achieve the same statistical confidence as one would observe for a deletion in C. elegans. Surprisingly, the ability to detect deletions strongly depends on the oligonucleotide 15-mer count, which is defined as the sum of the genomic frequency of all the constituent 15-mers within the oligonucleotide. A similarity level above 80% to non-target sequences over the length of the probe produces significant cross-hybridization. We recommend the use of a fairly large melting temperature window of up to 10 degrees C, the elimination of repeat sequences, the elimination of homopolymers longer than 5 nucleotides, and a threshold of -1 kcal/mol on the oligonucleotide self-folding energy. We observed very little difference in data quality when varying the oligonucleotide length between 50 and 70, and even when using an isothermal design strategy. We have determined experimentally the effects of varying several key oligonucleotide microarray design criteria for detection of deletions in C. elegans and humans with NimbleGen's CGH technology. Our oligonucleotide design recommendations should be applicable for CGH analysis in most species.

Investigating effects of nano cerium oxide reinforcement on mechanical properties of composite based on natural rubber

NASA Astrophysics Data System (ADS)

Bao, Le Quoc; Phan, Vu Hoang Giang; Khuyen, Nguyen Quang

2018-04-01

Polymer nanocomposites that based on combination of nanomaterials (such as nanoparticles, nanotubes, nanorods, nanofibers, and nanosheets) and polymeric matrices are receiving great attention in research and application. However, separate and homogenous dispersion rather than aggregates of nanoparticles into matrices meet big difficulty due to large interaction between nanoparticles. The poor dispersion leads to low properties of nanocomposites. In this study, we find out the appropriate method to separately disperse cerium oxides (CeO2) nanoparticles into natural rubber, aiming to increase mechanical properties of natural rubber. The SEM images were used to evaluate the dispersion of nano CeO2 in natural rubber matrix. The mechanical properties of nanocomposites were measured after vulcanization to investigate effects of nano CeO2 amount on prepared composite. The findings exhibited that the addition of CeO2 by dispersion of nano CeO2 in water via ultrasonication before mixing with rubber latex, significantly increase modulus, tear and wear resistance of natural rubber.

Plasma and cold sprayed aluminum carbon nanotube composites: Quantification of nanotube distribution and multi-scale mechanical properties

NASA Astrophysics Data System (ADS)

Bakshi, Srinivasa Rao

Carbon nanotubes (CNT) could serve as potential reinforcement for metal matrix composites for improved mechanical properties. However dispersion of carbon nanotubes (CNT) in the matrix has been a longstanding problem, since they tend to form clusters to minimize their surface area. The aim of this study was to use plasma and cold spraying techniques to synthesize CNT reinforced aluminum composite with improved dispersion and to quantify the degree of CNT dispersion as it influences the mechanical properties. Novel method of spray drying was used to disperse CNTs in Al-12 wt.% Si prealloyed powder, which was used as feedstock for plasma and cold spraying. A new method for quantification of CNT distribution was developed. Two parameters for CNT dispersion quantification, namely Dispersion parameter (DP) and Clustering Parameter (CP) have been proposed based on the image analysis and distance between the centers of CNTs. Nanomechanical properties were correlated with the dispersion of CNTs in the microstructure. Coating microstructure evolution has been discussed in terms of splat formation, deformation and damage of CNTs and CNT/matrix interface. Effect of Si and CNT content on the reaction at CNT/matrix interface was thermodynamically and kinetically studied. A pseudo phase diagram was computed which predicts the interfacial carbide for reaction between CNT and Al-Si alloy at processing temperature. Kinetic aspects showed that Al4C3 forms with Al-12 wt.% Si alloy while SiC forms with Al-23wt.% Si alloy. Mechanical properties at nano, micro and macro-scale were evaluated using nanoindentation and nanoscratch, microindentation and bulk tensile testing respectively. Nano and micro-scale mechanical properties (elastic modulus, hardness and yield strength) displayed improvement whereas macro-scale mechanical properties were poor. The inversion of the mechanical properties at different scale length was attributed to the porosity, CNT clustering, CNT-splat adhesion and Al 4C3 formation at the CNT/matrix interface. The Dispersion parameter (DP) was more sensitive than Clustering parameter (CP) in measuring degree of CNT distribution in the matrix.

Controlling dispersion characteristics of terahertz metasurface.

PubMed

Qu, Shi-Wei; Wu, Wei-Wei; Chen, Bao-Jie; Yi, Huan; Bai, Xue; Ng, Kung Bo; Chan, Chi Hou

2015-03-23

Terahertz (THz) metasurfaces have been explored recently due to their properties such as low material loss and ease of fabrication compared to three-dimensional (3D) metamaterials. Although the dispersion properties of the reflection/transmission-type THz metasurface were observed in some published literature, the method to control them at will has been scarcely reported to the best of our knowledge. In this context, flexible dispersion control of the THz metasurface will lead to great opportunities toward unprecedented THz devices. As an example, a THz metasurface with controllable dispersion characteristics has been successfully demonstrated in this article, and the incident waves at different frequencies from a source in front of the metasurface can be projected into different desired anomalous angular positions. Furthermore, this work provides a potential approach to other kinds of novel THz devices that need controllable metasurface dispersion properties.

Controlling Dispersion Characteristics of Terahertz Metasurface

PubMed Central

Qu, Shi-Wei; Wu, Wei-Wei; Chen, Bao-Jie; Yi, Huan; Bai, Xue; Ng, Kung Bo; Chan, Chi Hou

2015-01-01

Terahertz (THz) metasurfaces have been explored recently due to their properties such as low material loss and ease of fabrication compared to three-dimensional (3D) metamaterials. Although the dispersion properties of the reflection/transmission-type THz metasurface were observed in some published literature, the method to control them at will has been scarcely reported to the best of our knowledge. In this context, flexible dispersion control of the THz metasurface will lead to great opportunities toward unprecedented THz devices. As an example, a THz metasurface with controllable dispersion characteristics has been successfully demonstrated in this article, and the incident waves at different frequencies from a source in front of the metasurface can be projected into different desired anomalous angular positions. Furthermore, this work provides a potential approach to other kinds of novel THz devices that need controllable metasurface dispersion properties. PMID:25797336

Golden spiral photonic crystal fiber: polarization and dispersion properties.

PubMed

Agrawal, Arti; Kejalakshmy, N; Chen, J; Rahman, B M A; Grattan, K T V

2008-11-15

A golden spiral photonic crystal fiber (GS-PCF) design is presented in which air holes are arranged in a spiral pattern governed by the golden ratio, where the design has been inspired by the optimal arrangement of seeds found in nature. The birefringence and polarization properties of this fiber are analyzed using a vectorial finite-element method. The fiber that is investigated shows a large modal birefringence peak value of 0.016 at an operating wavelength of 1.55 microm and exhibits highly tuneable dispersion with multiple zero dispersion wavelengths and also large normal dispersion. The GS-PCF design has identical circular air holes that potentially simplify fabrication. In light of its properties, the GS-PCF could have application as a highly birefringent fiber and in nonlinear optics, and moreover the 2D chiral nature of the pattern could yield exotic properties.

Searching for links in the biotic characteristics and abiotic parameters of nine different biogas plants

PubMed Central

Walter, Andreas; Knapp, Brigitte A.; Farbmacher, Theresa; Ebner, Christian; Insam, Heribert; Franke‐Whittle, Ingrid H.

2012-01-01

Summary To find links between the biotic characteristics and abiotic process parameters in anaerobic digestion systems, the microbial communities of nine full‐scale biogas plants in South Tyrol (Italy) and Vorarlberg (Austria) were investigated using molecular techniques and the physical and chemical properties were monitored. DNA from sludge samples was subjected to microarray hybridization with the ANAEROCHIP microarray and results indicated that sludge samples grouped into two main clusters, dominated either by Methanosarcina or by Methanosaeta, both aceticlastic methanogens. Hydrogenotrophic methanogens were hardly detected or if detected, gave low hybridization signals. Results obtained using denaturing gradient gel electrophoresis (DGGE) supported the findings of microarray hybridization. Real‐time PCR targeting Methanosarcina and Methanosaeta was conducted to provide quantitative data on the dominating methanogens. Correlation analysis to determine any links between the microbial communities found by microarray analysis, and the physicochemical parameters investigated was conducted. It was shown that the sludge samples dominated by the genus Methanosarcina were positively correlated with higher concentrations of acetate, whereas sludge samples dominated by representatives of the genus Methanosaeta had lower acetate concentrations. No other correlations between biotic characteristics and abiotic parameters were found. Methanogenic communities in each reactor were highly stable and resilient over the whole year. PMID:22950603

Superhydrophilic-Superhydrophobic Patterned Surfaces as High-Density Cell Microarrays: Optimization of Reverse Transfection.

PubMed

Ueda, Erica; Feng, Wenqian; Levkin, Pavel A

2016-10-01

High-density microarrays can screen thousands of genetic and chemical probes at once in a miniaturized and parallelized manner, and thus are a cost-effective alternative to microwell plates. Here, high-density cell microarrays are fabricated by creating superhydrophilic-superhydrophobic micropatterns in thin, nanoporous polymer substrates such that the superhydrophobic barriers confine both aqueous solutions and adherent cells within each superhydrophilic microspot. The superhydrophobic barriers confine and prevent the mixing of larger droplet volumes, and also control the spreading of droplets independent of the volume, minimizing the variability that arises due to different liquid and surface properties. Using a novel liposomal transfection reagent, ScreenFect A, the method of reverse cell transfection is optimized on the patterned substrates and several factors that affect transfection efficiency and cytotoxicity are identified. Higher levels of transfection are achieved on HOOC- versus NH 2 -functionalized superhydrophilic spots, as well as when gelatin and fibronectin are added to the transfection mixture, while minimizing the amount of transfection reagent improves cell viability. Almost no diffusion of the printed transfection mixtures to the neighboring microspots is detected. Thus, superhydrophilic-superhydrophobic patterned surfaces can be used as cell microarrays and for optimizing reverse cell transfection conditions before performing further cell screenings. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Application of nanostructured biochips for efficient cell transfection microarrays

NASA Astrophysics Data System (ADS)

Akkamsetty, Yamini; Hook, Andrew L.; Thissen, Helmut; Hayes, Jason P.; Voelcker, Nicolas H.

2007-01-01

Microarrays, high-throughput devices for genomic analysis, can be further improved by developing materials that are able to manipulate the interfacial behaviour of biomolecules. This is achieved both spatially and temporally by smart materials possessing both switchable and patterned surface properties. A system had been developed to spatially manipulate both DNA and cell growth based upon the surface modification of highly doped silicon by plasma polymerisation and polyethylene grafting followed by masked laser ablation for formation of a pattered surface with both bioactive and non-fouling regions. This platform has been successfully applied to transfected cell microarray applications with the parallel expression of genes by utilising its ability to direct and limit both DNA and cell attachment to specific sites. One of the greatest advantages of this system is its application to reverse transfection, whereupon by utilising the switchable adsorption and desorption of DNA using a voltage bias, the efficiency of cell transfection can be enhanced. However, it was shown that application of a voltage also reduces the viability of neuroblastoma cells grown on a plasma polymer surface, but not human embryonic kidney cells. This suggests that the application of a voltage may not only result in the desorption of bound DNA but may also affect attached cells. The characterisation of a DNA microarray by contact printing has also been investigated.

Direct Assembly of Modified Proteins on Carbon Nanotubes in an Aqueous Solution

NASA Technical Reports Server (NTRS)

Kim, Jae-Woo; Lillehei, Peter T.; Park, Cheol; Harrison, Joycelyn S.

2007-01-01

Carbon nanotubes (CNTs) have superior mechanical and electrical properties that have opened up many potential applications. However, poor dispersibility and solubility, due to the substantial van der Waals attraction between tubes, have prevented the use of CNTs in practical applications, especially biotechnology applications. Effective dispersion of CNTs into small bundles or individual tubes in solvents is crucial to ensure homogeneous properties and enable practical applications. In addition to dispersion of CNTs into a solvent, the selection of appropriate solvent, which is compatible with a desired matrix, is an important factor to improve the mechanical, thermal, optical, and electrical properties of CNT-based fibers and composites. In particular, dispersion of CNTs into an aqueous system has been a challenge due to the hydrophobic nature of CNTs. Here we show an effective method for dispersion of both single wall CNTs (SWCNTs) and few wall CNTs (FWCNTs) in an aqueous buffer solution. We also show an assembly of cationized Pt-cored ferritins on the well dispersed CNTs in an aqueous buffer solution.

Dispersion of carbon nanotubes in vinyl ester polymer composites

NASA Astrophysics Data System (ADS)

Pena-Paras, Laura

This work focused on a parametric study of dispersions of different types of carbon nanotubes in a polymer resin. Single-walled (SWNTs), double-walled (DWNTs), multi-walled (MWNTs) and XD-grade carbon nanotubes (XD-CNTs) were dispersed in vinyl ester (VE) using an ultra-sonic probe at a fixed frequency. The power, amplitude, and mixing time parameters of sonication were correlated to the electrical and mechanical properties of the composite materials in order to optimize dispersion. The quality of dispersion was quantified by Raman spectroscopy and verified through optical and scanning electron microscopy. By Raman, the CNT distribution, unroping, and damage was monitored and correlated with the composite properties for dispersion optimization. Increasing the ultrasonication energy was found to improve the distribution of all CNT materials and to decrease the size of nanotube ropes, enhancing the electrical conductivity and storage modulus. However, excessive amounts of energy were found to damage CNTs, which negatively affected the properties of the composite. Based on these results the optimum dispersion energy inputs were determined for the different composite materials. The electrical resistivity was lowered by as much as 14, 13, 13, and 11 orders of magnitude for SWNT/VE, DWNT/VE, MWNT/VE, and XD-CNT/VE respectively, compared to the neat resin. The storage modulus was also increased compared to the neat resin by 77%, 82%, 45%, 40% and 85% in SWNT, SAP-f-SWNT, DWNT, MWNT and XD-CNT/VE composites, respectively. This study provides a detailed understanding of how the properties of, nanocomposites are determined by the composite mixing parameters and the distribution, concentration, shape and size of the CNTs. Importantly, it indicates the importance of the need for dispersion metrics to correlate and understand these properties.

Production, characterization, and mechanical behavior of cementitious materials incorporating carbon nanofibers

NASA Astrophysics Data System (ADS)

Yazdanbakhsh, Ardavan

Carbon nanotubes (CNTs) and carbon nanofirbers (CNFs) have excellent properties (mechanical, electrical, magnetic, etc.), which can make them effective nanoreinforcements for improving the properties of materials. The incorporation of CNT/Fs in a wide variety of materials has been researched extensively in the past decade. However, the past study on the reinforcement of cementitious materials with these nanofilaments has been limited. The findings from those studies indicate that CNT/Fs did not significantly improve the mechanical properties of cementitious materials. Two major parameters influence the effectiveness of any discrete inclusion in composite material: The dispersion quality of the inclusions and the interfacial bond between the inclusions and matrix. The main focus of this dissertation is on the dispersion factor, and consists of three main tasks: First a novel thermodynamic-based method for dispersion quantification was developed. Second, a new method, incorporating the utilization of silica fume, was devised to improve and stabilize the dispersion of CNFs in cement paste. And third, the dispersion quantification method and mechanical testing were employed to measure, compare, and correlate the dispersion and mechanical properties of CNF-incorporated cement paste produced with the conventional and new methods. Finally, the main benefits, including the increase in strength and resistance to shrinkage cracking, obtained from the utilization of CNFs in cement paste will be presented. The investigations and the corresponding results show that the novel dispersion quantification method can be implemented easily to perform a wide variety of tasks ranging from measuring dispersion of nanofilaments in composites using their optical/SEM micrographs as input, to measuring the effect of cement particle/clump size on the dispersion of nano inclusions in cement paste. It was found that cement particles do not affect the dispersion of nano inclusions in cement paste significantly while the dispersion of nano inclusions can notably degenerates if the cement particles are agglomerated. The novel dispersion quantification method shows that, the dispersion of CNFs in cement paste significantly improves by utilizing silica fume. However, it was found that the dispersion of silica fume particles is an important parameter and poorly dispersed silica fume cannot enhance the overall dispersion of nano inclusions in cementitious materials. Finally, the mechanical testing and experimentations showed that CNFs, in absence of moist curing, even if poorly dispersed, can provide important benefits in terms of strength and crack resistance.

Effect of exchange correlation potential on dispersion properties of lower hybrid wave in degenerate plasma

NASA Astrophysics Data System (ADS)

Rimza, Tripti; Sharma, Prerana

2017-05-01

The dispersion properties of lower hybrid wave are studied in electron-iondegenerate plasma with exchange effect in non-relativistic regime. It is found that the combined effect of Bohm potential and exchange correlation potential significantly modifies the dispersion properties of lower hybrid wave. The graphical results explicitly show the influence of degeneracy pressure, Bohm force and exchange correlation potential on the frequency of the lower hybrid mode. Present work should be of relevance for the dense astrophysical environments like white dwarfs and for laboratory experiments.

Dodecylamine functionalization of carbon nanotubes to improve dispersion, thermal and mechanical properties of polyethylene based nanocomposites

NASA Astrophysics Data System (ADS)

Ferreira, F. V.; Franceschi, W.; Menezes, B. R. C.; Brito, F. S.; Lozano, K.; Coutinho, A. R.; Cividanes, L. S.; Thim, G. P.

2017-07-01

This study presents the effect of dodecylamine (DDA) functionalization of carbon nanotubes (CNTs) on the thermo-physical and mechanical properties of high-density polyethylene (HDPE) based composites. Here, we showed that the functionalization with DDA improved the dispersion of the CNTs as well as the interfacial adhesion with the HDPE matrix via non-covalent interactions. The better dispersion and interaction of CNT in the HDPE matrix as a function of the surface chemistry was correlated with the improved thermo-physical and mechanical properties.

Dispersibility and biotransformation of oils with different properties in seawater.

PubMed

Brakstad, Odd G; Farooq, Umer; Ribicic, Deni; Netzer, Roman

2018-01-01

Dispersants are used to remove oils slicks from sea surfaces and to generate small oil-droplet dispersions, which may result in enhanced biodegradation of the oil. In this study, dispersibility and biodegradation of chemically dispersed oils with different physical-chemical properties (paraffinic, naphthenic and asphaltenic oils) were compared in natural temperate SW at 13 °C. All selected oils were chemically dispersible when well-known commercial dispersants were used. However, interfacial tension (IFT) studies of the dispersed oils showed different IFT properties of the oils at 13 °C, and also different leaching of the dispersants from oil droplet surfaces. Biodegradation studies of the chemically dispersed oils were performed in a carousel system, with initial median droplet sizes <30 μm and oil concentrations of 2.5-2.8 mg/L. During biodegradation, oil droplet concentrations were rapidly reduced, in association with the emergence of macroscopic 'flocs'. Biotransformation results showed that half-lives of semivolatile total extractable organic carbon (TEOC), single target 2- to 4-ring PAH, and 22 oil compound groups used as input data in the oil spill contingency model OSCAR, did not differ significantly between the oils (P > 0.05), while n-alkanes half-lives differed significantly (P < 0.05). Biotransformation was associated with rapid microbial growth in all oil dispersions, in association with n-alkane and PAH biotransformation. These results have implications for the predictions of biodegradation of oil slicks treated with dispersants in temperate SW. Copyright © 2017 Elsevier Ltd. All rights reserved.

Gene set analysis approaches for RNA-seq data: performance evaluation and application guideline

PubMed Central

Rahmatallah, Yasir; Emmert-Streib, Frank

2016-01-01

Transcriptome sequencing (RNA-seq) is gradually replacing microarrays for high-throughput studies of gene expression. The main challenge of analyzing microarray data is not in finding differentially expressed genes, but in gaining insights into the biological processes underlying phenotypic differences. To interpret experimental results from microarrays, gene set analysis (GSA) has become the method of choice, in particular because it incorporates pre-existing biological knowledge (in a form of functionally related gene sets) into the analysis. Here we provide a brief review of several statistically different GSA approaches (competitive and self-contained) that can be adapted from microarrays practice as well as those specifically designed for RNA-seq. We evaluate their performance (in terms of Type I error rate, power, robustness to the sample size and heterogeneity, as well as the sensitivity to different types of selection biases) on simulated and real RNA-seq data. Not surprisingly, the performance of various GSA approaches depends only on the statistical hypothesis they test and does not depend on whether the test was developed for microarrays or RNA-seq data. Interestingly, we found that competitive methods have lower power as well as robustness to the samples heterogeneity than self-contained methods, leading to poor results reproducibility. We also found that the power of unsupervised competitive methods depends on the balance between up- and down-regulated genes in tested gene sets. These properties of competitive methods have been overlooked before. Our evaluation provides a concise guideline for selecting GSA approaches, best performing under particular experimental settings in the context of RNA-seq. PMID:26342128

Influence of the refractive index and dispersion of spectacle lens on its imaging properties

NASA Astrophysics Data System (ADS)

Miks, Antonin; Novak, Jiri; Novak, Pavel

2007-12-01

The paper shows an influence of the refractive index and dispersion of the spectacle lens on its imaging properties. Relations are presented for calculation of radii of curvature of anastigmatic spectacle lenses and their chromatic aberration. Moreover, the formulas are derived for calculation of the change of astigmatism of spectacle lens due to dispersion of spectacle lens material.

Synthesis and properties of amphiphilic hyperbranched polyethers as pigment dispersant

NASA Astrophysics Data System (ADS)

Xu, Q.; Zhou, Y. J.; Long, S. J.; Liu, Y. G.; Li, J. H.

2018-01-01

Hyperbranched polymers possess prominent properties such as low viscosity, good solubility, high rheological property, environmental non-toxic, and so on, which have potential applications in coatings. In this study, the amphiphilic hyperbranched polyethers (AHPs) consisting of hydrophobic hyperbranched polyethers core and hydrophilic poly (ethylene glycol) arms with different degree of branching (DB) under various reaction temperatures was prepared by the cation ring-opening polymerization. Their structures were characterized by IR, 13CNMR and GPC. Their dispersion properties for pigment particles were investigated. The AHP47 with 0.47 DB was found to have good dispersion properties for Yellow HGR. This work would provide experimental data and theoretical foundation for the application of hyperbranched polyethers in environmental protection coating.

[Study on solid dispersion of precipitated calcium carbonate-based oleanolic acid].

PubMed

Yan, Hong-mei; Zhang, Zhen-hai; Jia, Xiao-bin; Jiang, Yan-rong; Sun, E

2015-05-01

Oleanolic acid-precipitated calcium carbonate solid dispersion was prepared by using solvent evaporation method. The microscopic structure and physicochemical properties of solid dispersion were analyzed using differential scanning calorimetry and scanning electron microscopy (SEM). And its in vitro release also was investigated. The properties of the precipitated calcium carbonate was studied which was as a carrier of oleanolic acid solid dispersion. Differential scanning calorimetry analysis suggested that oleanolic acid may be present in solid dispersion as amorphous substance. The in vitro release determination results of oleanolic acid-precipitated calcium carbonate (1: 5) solid dispersion showed accumulated dissolution rate of.oleanolic acid was up to 90% at 45 min. Accelerating experiment showed that content and in vitro dissolution of oleanolic acid solid dispersion did not change after storing over 6 months. The results indicated that in vitro dissolution of oleanolic acid was improved greatly by the solid dispersion with precipitated calcium carbonate as a carrier. The solid dispersion is a stabilizing system which has actual applied value.

Water repellent properties of dispersed metals containing low-dimensional forms of ammonium compounds on the surface

NASA Astrophysics Data System (ADS)

Syrkov, A. G.; Kabirov, V. R.; Silivanov, M. O.

2017-07-01

For the first time the change of the water repellent properties of dispersed copper, modified using quaternary ammonium compounds on 24 h time scale in saturated water vapours was studied. Exponential time dependences of the water repellent properties of dispersed copper with adsopted QAC were derived and characterized. It was established that the samples modified in mixed and consistent modes by both modifiers reach the saturation state faster than others, due to the small number of hydrophilic centers on the surface of metals. The last conclusion was confirmed by the distribution spectra of centers of adsorption, which were obtained by the adsorption of acid-base indicators for more dispersed samples based on aluminum powder.

The Effects of Polymer Carrier, Hot Melt Extrusion Process and Downstream Processing Parameters on the Moisture Sorption Properties of Amorphous Solid Dispersions

PubMed Central

Feng, Xin; Vo, Anh; Patil, Hemlata; Tiwari, Roshan V.; Alshetaili, Abdullah S.; Pimparade, Manjeet B.; Repka, Michael A.

2017-01-01

Objective The aim of this study was to evaluate the effect of polymer carrier, hot melt extrusion (HME) and downstream processing parameters on the water uptake properties of amorphous solid dispersions. Methods Three polymers and a model drug were used to prepare amorphous solid dispersions utilizing HME technology. The sorption-desorption isotherms of solid dispersions and their physical mixtures were measured by the Dynamic Vapor Sorption system, and the effect of polymer hydrophobicity, hygroscopicity, molecular weight and the HME process were investigated. FTIR imaging was performed to understand the phase separation driven by the moisture. Key findings Solid dispersions with polymeric carriers with lower hydrophilicity, hygroscopicity, and higher molecular weight could sorb less moisture under the high RH conditions. The water uptake ability of polymer-drug solid dispersion systems were decreased compared to the physical mixture after HME, which might be due to the decreased surface area and porosity. The FTIR imaging indicated the homogeneity of the drug molecularly dispersed within the polymer matrix was changed after exposure to high RH. Conclusion Understanding the effect of formulation and processing on the moisture sorption properties of solid dispersions is essential for the development of drug products with desired physical and chemical stability. PMID:26589107

Atypical effects of incorporated surfactants on stability and dissolution properties of amorphous polymeric dispersions.

PubMed

Al-Obaidi, Hisham; Lawrence, M Jayne; Buckton, Graham

2016-11-01

To understand the impact of ionic and non-ionic surfactants on the dissolution and stability properties of amorphous polymeric dispersions using griseofulvin (GF) as a model for poorly soluble drugs. Solid dispersions of the poorly water-soluble drug, griseofulvin (GF) and the polymers, poly(vinylpyrrolidone) (PVP) and poly(2-hydroxypropyl methacrylate) (PHPMA), have been prepared by spray drying and bead milling and the effect of the ionic and non-ionic surfactants, namely sodium dodecyl sulphate (SDS) and Tween-80, on the physico-chemical properties of the solid dispersions studied. The X-ray powder diffraction data and hot-stage microscopy showed a fast re-crystallisation of GF. While dynamic vapour sorption (DVS) measurements indicated an increased water uptake, slow dissolution rates were observed for the solid dispersions incorporating surfactants. The order by which surfactants free dispersions were prepared seemed critical as indicated by DVS and thermal analysis. Dispersions prepared by milling with SDS showed significantly better stability than spray-dried dispersions (drug remained amorphous for more than 6 months) as well as improved dissolution profile. We suggest that surfactants can hinder the dissolution by promoting aggregation of polymeric chains, however that effect depends mainly on how the particles were prepared. © 2016 Royal Pharmaceutical Society.

Marine fouling release silicone/carbon nanotube nanocomposite coatings: on the importance of the nanotube dispersion state.

PubMed

Beigbeder, Alexandre; Mincheva, Rosica; Pettitt, Michala E; Callow, Maureen E; Callow, James A; Claes, Michael; Dubois, Philippe

2010-05-01

The present work reports on the influence of the dispersion quality of multiwall carbon nanotubes (MWCNTs) in a silicone matrix on the marine fouling-release performance of the resulting nanocomposite coatings. A first set of coatings filled with different nanofiller contents was prepared by the dilution of a silicone/MWCNTs masterbatch within a hydrosilylation-curing polydimethylsiloxane resin. The fouling-release properties of the nanocomposite coatings were studied through laboratory assays with the marine alga (seaweed) Ulva, a common fouling species. As reported previously (see Ref. [19]), the addition of a small (0.05%) amount of carbon nanotubes substantially improves the fouling-release properties of the silicone matrix. This paper shows that this improvement is dependent on the amount of filler, with a maximum obtained with 0.1 wt% of multiwall carbon nanotubes (MWCNTs). The method of dispersion of carbon nanotubes in the silicone matrix is also shown to significantly (p = 0.05) influence the fouling-release properties of the coatings. Dispersing 0.1% MWCNTs using the masterbatch approach yielded coatings with circa 40% improved fouling-release properties over those where MWCNTs were dispersed directly in the polymeric matrix. This improvement is directly related to the state of nanofiller dispersion within the cross-linked silicone coating.

Cellulose nanocrystal/polyolefin biocomposites prepared by solid-state shear pulverization: Superior dispersion leading to synergistic property enhancements

Treesearch

Krishnan A. Iyer; Gregory T. Schueneman; John M. Torkelson

2015-01-01

Cellulose nanocrystals (CNCs), a class of renewable bionanomaterials with excellent mechanical properties, have gained major interest as filler for polymers. However, challenges associated with effective CNC dispersion have hindered the production of composites with desired property enhancements. Here, composites of polypropylene (PP) and low density polyethylene (LDPE...

Automated Dispersion and Orientation Analysis for Carbon Nanotube Reinforced Polymer Composites

PubMed Central

Gao, Yi; Li, Zhuo; Lin, Ziyin; Zhu, Liangjia; Tannenbaum, Allen; Bouix, Sylvain; Wong, C.P.

2012-01-01

The properties of carbon nanotube (CNT)/polymer composites are strongly dependent on the dispersion and orientation of CNTs in the host matrix. Quantification of the dispersion and orientation of CNTs by microstructure observation and image analysis has been demonstrated as a useful way to understand the structure-property relationship of CNT/polymer composites. However, due to the various morphologies and large amount of CNTs in one image, automatic and accurate identification of CNTs has become the bottleneck for dispersion/orientation analysis. To solve this problem, shape identification is performed for each pixel in the filler identification step, so that individual CNT can be exacted from images automatically. The improved filler identification enables more accurate analysis of CNT dispersion and orientation. The obtained dispersion index and orientation index of both synthetic and real images from model compounds correspond well with the observations. Moreover, these indices help to explain the electrical properties of CNT/Silicone composite, which is used as a model compound. This method can also be extended to other polymer composites with high aspect ratio fillers. PMID:23060008

Carbon Nanotube Composites from Modified Plant Oils

NASA Astrophysics Data System (ADS)

McAninch, Ian; Wool, Richard

2006-03-01

Carbon nanotubes (CNTs) with their impressive mechanical properties are ideal reinforcement material. Acrylated epoxidized soy oil (AESO) has been previously shown to have favorable interactions with carbon nanotubes. CNTs mixed into AESO, both with and without styrene as a co-monomer, using mechanical shear mixing showed dispersion only on the micron level, resulting in modest mechanical property improvements. Greater improvements were seen, especially in the rubbery modulus, when the resin's viscosity was kept high, either through a reduction of the styrene content, or by curing at a lower temperature. CNTs were also dispersed via sonication in methyl methacrylate. The resulting dispersion was then mixed with AESO. The resulting composites showed better CNT dispersion, with no micron-sized aggregates, as verified using SEM and optical microscopy. The mechanical properties also showed greater improvement.

A study of the electrical properties of carbon nanofiber polymer composites

NASA Astrophysics Data System (ADS)

Cardoso, Paulo Jorge Magalhaes

The interest of industry on using carbon nanofibers (CNF) as a possible alternative to carbon nanotubes (CNT) to produce polymer based composites is due to their lower price, the ability to be produced in large amounts and the their usefulness as a reinforcement filler in order to improve the matrix properties such as mechanical, thermal and electrical. Polymers like epoxy resins already have good-to-excellent properties and an extensive range of applications, but the reinforcement with fillers like CNF, which has high aspect ratio (AR) and surface energy, has the potential to extend the range of applications. The Van der Waals interactions between nanofillers, such as CNF, promote the clustering effect which affects their dispersion in the polymer and may interfere with some properties of the nanocomposites. In this sense, it is very important to use appropriate dispersion methods which are able to disentangle the nanofillers to a certain degree, but avoiding the reduction of the nanofibers AR as much as possible. In fact, the methods and conditions of nanocomposites processing have also influence on the filler orientation, dispersion, distribution and aspect ratio. To the present day, there is a lack of complete information in the literature about the relation between structure and properties, in particular electrical properties, for polymer nanocomposites. The main objective of this work is to study the electrical properties of composites based on CNF and epoxy resin using production methods which can be easily implemented in industrial environments and that provide different dispersion levels, investigating therefore the relationship between dispersion level and electrical response. Some of the requirements for such methods are the adaptability to the industrial processes and facilities which allow large scale productions and provide a good relation between quality and cost of the composite materials. In this work, morphological, electrical and electromechanical studies were performed in epoxy resin composites with vapor-grown carbon nanofibers (VGCNF). First, the electrical properties of VGCNF/epoxy resin composites produced with a simple method were studied. Then, it was investigated the relation between the electrical properties and the dispersion level of VGCNF/epoxy composites produced with different methods, which were selected to provide different levels of dispersion.The level of nanofiber dispersion of the composites produced with the different methods and filler contents was analyzed by transmission optical microscopy (TOM) and greyscale analysis (GSA) and then compared to the electrical conductivity measurements. After this study, the influence of different methods of VGCNF dispersion on the electrical conduction mechanism of the composites was investigated. Then, these composites were submitted to electromechanical tests in order to apply them as piezoresistive sensors. The last study of this work was dedicated to an initial comparison between the epoxy composites with VGCNG and multi-walled carbon nanotubes (MWCNT), in terms of electrical and morphological properties. As the main outcomes of the present work, it can be concluded that a better cluster dispersion seems to be more suitable than good filler dispersion for achieving larger electrical conductivities and lower percolation thresholds. It is also concluded that hopping conductivity is a relevant mechanism for determining the overall conductivity of the composites and that the CNF/epoxy composites are appropriate materials for piezoresistive sensors in particular at concentrations close to the percolation threshold.

Network-based de-noising improves prediction from microarray data.

PubMed

Kato, Tsuyoshi; Murata, Yukio; Miura, Koh; Asai, Kiyoshi; Horton, Paul B; Koji, Tsuda; Fujibuchi, Wataru

2006-03-20

Prediction of human cell response to anti-cancer drugs (compounds) from microarray data is a challenging problem, due to the noise properties of microarrays as well as the high variance of living cell responses to drugs. Hence there is a strong need for more practical and robust methods than standard methods for real-value prediction. We devised an extended version of the off-subspace noise-reduction (de-noising) method to incorporate heterogeneous network data such as sequence similarity or protein-protein interactions into a single framework. Using that method, we first de-noise the gene expression data for training and test data and also the drug-response data for training data. Then we predict the unknown responses of each drug from the de-noised input data. For ascertaining whether de-noising improves prediction or not, we carry out 12-fold cross-validation for assessment of the prediction performance. We use the Pearson's correlation coefficient between the true and predicted response values as the prediction performance. De-noising improves the prediction performance for 65% of drugs. Furthermore, we found that this noise reduction method is robust and effective even when a large amount of artificial noise is added to the input data. We found that our extended off-subspace noise-reduction method combining heterogeneous biological data is successful and quite useful to improve prediction of human cell cancer drug responses from microarray data.

Systematic validation and atomic force microscopy of non-covalent short oligonucleotide barcode microarrays.

PubMed

Cook, Michael A; Chan, Chi-Kin; Jorgensen, Paul; Ketela, Troy; So, Daniel; Tyers, Mike; Ho, Chi-Yip

2008-02-06

Molecular barcode arrays provide a powerful means to analyze cellular phenotypes in parallel through detection of short (20-60 base) unique sequence tags, or "barcodes", associated with each strain or clone in a collection. However, costs of current methods for microarray construction, whether by in situ oligonucleotide synthesis or ex situ coupling of modified oligonucleotides to the slide surface are often prohibitive to large-scale analyses. Here we demonstrate that unmodified 20mer oligonucleotide probes printed on conventional surfaces show comparable hybridization signals to covalently linked 5'-amino-modified probes. As a test case, we undertook systematic cell size analysis of the budding yeast Saccharomyces cerevisiae genome-wide deletion collection by size separation of the deletion pool followed by determination of strain abundance in size fractions by barcode arrays. We demonstrate that the properties of a 13K unique feature spotted 20 mer oligonucleotide barcode microarray compare favorably with an analogous covalently-linked oligonucleotide array. Further, cell size profiles obtained with the size selection/barcode array approach recapitulate previous cell size measurements of individual deletion strains. Finally, through atomic force microscopy (AFM), we characterize the mechanism of hybridization to unmodified barcode probes on the slide surface. These studies push the lower limit of probe size in genome-scale unmodified oligonucleotide microarray construction and demonstrate a versatile, cost-effective and reliable method for molecular barcode analysis.

Characterization of Bovine Serum Albumin Blocking Efficiency on Epoxy-Functionalized Substrates for Microarray Applications.

PubMed

Sun, Yung-Shin; Zhu, Xiangdong

2016-10-01

Microarrays provide a platform for high-throughput characterization of biomolecular interactions. To increase the sensitivity and specificity of microarrays, surface blocking is required to minimize the nonspecific interactions between analytes and unprinted yet functionalized surfaces. To block amine- or epoxy-functionalized substrates, bovine serum albumin (BSA) is one of the most commonly used blocking reagents because it is cheap and easy to use. Based on standard protocols from microarray manufactories, a BSA concentration of 1% (10 mg/mL or 200 μM) and reaction time of at least 30 min are required to efficiently block epoxy-coated slides. In this paper, we used both fluorescent and label-free methods to characterize the BSA blocking efficiency on epoxy-functionalized substrates. The blocking efficiency of BSA was characterized using a fluorescent scanner and a label-free oblique-incidence reflectivity difference (OI-RD) microscope. We found that (1) a BSA concentration of 0.05% (0.5 mg/mL or 10 μM) could give a blocking efficiency of 98%, and (2) the BSA blocking step took only about 5 min to be complete. Also, from real-time and in situ measurements, we were able to calculate the conformational properties (thickness, mass density, and number density) of BSA molecules deposited on the epoxy surface. © 2015 Society for Laboratory Automation and Screening.

Evaluation of the organization of the homoionic smectite layers (Na(+) or Ca(2+)) in diluted dispersions using granulometry, microscopy and rheometry.

PubMed

Paumier, S; Pantet, A; Monnet, P

2008-09-01

Smectites are swelling clay materials with pronounced colloidal properties that are widely used in industry. These properties originate in the electrokinetic properties of the smectite layers and their linkage capacities. Thin layers may be dispersed or aggregated according to many parameters, such as concentration, particle size and morphology, exchangeable cation nature and chemical environment (pH, ionic strength). The literature usually provides general rules, like the sodium dispersion contains a lot of small units whereas the calcium dispersion contains a few large units. A volume of water molecules bound to the clay surface is considered as the immobile water phase that behaves like the solid phase obstructing the flow. The water immobilized around layers and trapped inside aggregates cannot participate to the flow. In this study, we evaluated the volume occupied by calcium and sodium units inside the dispersion containing the immobile water phase. First, the smectite was cautiously extracted from a raw bentonite and its physicochemical properties were determined. A large quantity of extracted and saturated smectite (Na-smectite and Ca-smectite) was obtained. Second, the unit size and a shape factor for each sample were evaluated using granulometry and scanning transmission electron microscopy on wet samples (Wet STEM) and some flow curves. Na-smectite dispersions contain 0.13 microm(2) surface units with a shape factor of 50. Ca-smectite dispersions contain 0.32 microm(2) surface units with a shape factor of 3.3. Finally, rheometry allowed us to evaluate the unit occupancy using an adaptation of the Krieger-Dougherty law. We used shape factors and evaluated the concentration from which the entire immobile volume was connected (6.4% for Na-smectite and 11.9% for Ca-smectite). This study explains the evolution of flow properties with increasing concentrations by the evolution of layer interactions at the microscopic scale for homoionic smectite particles in diluted dispersions.

Quantification of the activity of biomolecules in microarrays obtained by direct laser transfer.

PubMed

Dinca, V; Ranella, A; Farsari, M; Kafetzopoulos, D; Dinescu, M; Popescu, A; Fotakis, C

2008-10-01

The direct-writing technique laser-induced forward transfer has been employed for the micro-array printing of liquid solutions of the enzyme horseradish peroxidase and the protein Titin on nitrocellulose solid surfaces. The effect of two UV laser pulse lengths, femtosecond and nanosecond has been studied in relation with maintaining the activity of the transferred biomolecules. The quantification of the active biomolecules after transfer has been carried out using Bradford assay, quantitative colorimetric enzymatic assay and fluorescence techniques. Spectrophotometric measurements of the HRP and the Titin activity as well as chromatogenic and fluorescence assay studies have revealed a connection between the properties of the deposited, biologically active biomolecules, the experimental conditions and the target composition. The bioassays have shown that up to 78% of the biomolecules remained active after femtosecond laser transfer, while this value reduced to 54% after nanosecond laser transfer. The addition of glycerol in a percentage up to 70% in the solution to be transferred has contributed to the stabilization of the micro-array patterns and the increase of their resolution.

Development of a Schistosoma mansoni shotgun O-glycan microarray and application to the discovery of new antigenic schistosome glycan motifs.

PubMed

van Diepen, Angela; van der Plas, Arend-Jan; Kozak, Radoslaw P; Royle, Louise; Dunne, David W; Hokke, Cornelis H

2015-06-01

Upon infection with Schistosoma, antibody responses are mounted that are largely directed against glycans. Over the last few years significant progress has been made in characterising the antigenic properties of N-glycans of Schistosoma mansoni. Despite also being abundantly expressed by schistosomes, much less is understood about O-glycans and antibody responses to these have not yet been systematically analysed. Antibody binding to schistosome glycans can be analysed efficiently and quantitatively using glycan microarrays, but O-glycan array construction and exploration is lagging behind because no universal O-glycanase is available, and release of O-glycans has been dependent on chemical methods. Recently, a modified hydrazinolysis method has been developed that allows the release of O-glycans with free reducing termini and limited degradation, and we applied this method to obtain O-glycans from different S. mansoni life stages. Two-dimensional HPLC separation of 2-aminobenzoic acid-labelled O-glycans generated 362 O-glycan-containing fractions that were printed on an epoxide-modified glass slide, thereby generating the first shotgun O-glycan microarray containing naturally occurring schistosome O-glycans. Monoclonal antibodies and mass spectrometry showed that the O-glycan microarray contains well-known antigenic glycan motifs as well as numerous other, potentially novel, antibody targets. Incubations of the microarrays with sera from Schistosoma-infected humans showed substantial antibody responses to O-glycans in addition to those observed to the previously investigated N- and glycosphingolipid glycans. This underlines the importance of the inclusion of these often schistosome-specific O-glycans in glycan antigen studies and indicates that O-glycans contain novel antigenic motifs that have potential for use in diagnostic methods and studies aiming at the discovery of vaccine targets. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

The effects of polymer carrier, hot melt extrusion process and downstream processing parameters on the moisture sorption properties of amorphous solid dispersions.

PubMed

Feng, Xin; Vo, Anh; Patil, Hemlata; Tiwari, Roshan V; Alshetaili, Abdullah S; Pimparade, Manjeet B; Repka, Michael A

2016-05-01

The aim of this study was to evaluate the effect of polymer carrier, hot melt extrusion and downstream processing parameters on the water uptake properties of amorphous solid dispersions. Three polymers and a model drug were used to prepare amorphous solid dispersions utilizing the hot melt extrusion technology. The sorption-desorption isotherms of solid dispersions and their physical mixtures were measured by the dynamic vapour sorption system, and the effects of polymer hydrophobicity, hygroscopicity, molecular weight and the hot melt extrusion process were investigated. Fourier transform infrared (FTIR) imaging was performed to understand the phase separation driven by the moisture. Solid dispersions with polymeric carriers with lower hydrophilicity, hygroscopicity and higher molecular weight could sorb less moisture under the high relative humidity (RH) conditions. The water uptake ability of polymer-drug solid dispersion systems were decreased compared with the physical mixture after hot melt extrusion, which might be due to the decreased surface area and porosity. The FTIR imaging indicated that the homogeneity of the drug molecularly dispersed within the polymer matrix was changed after exposure to high RH. Understanding the effect of formulation and processing on the moisture sorption properties of solid dispersions is essential for the development of drug products with desired physical and chemical stability. © 2015 Royal Pharmaceutical Society.

Highly birefringent large negative dispersion-flattened photonic crystal fibre for broadband residual dispersion compensation

NASA Astrophysics Data System (ADS)

Faisal, Mohammad; Bala, Animesh; Roy Chowdhury, Kanan; Mia, Md. Borhan

2018-07-01

A triangular lattice photonic crystal fibre is presented in this paper for residual dispersion compensation. The fibre exhibits a flattened negative dispersion of -992.01 ± 6.93 ps/(nm-km) over S+C+L wavelength bands and -995.83 ± 0.42 ps/(nm-km) over C-band. The birefringence is about 4.4 × 10-2 at the excitation wavelength of 1550 nm which is also very high. Full vector finite element method (FEM) with a perfectly matched absorbing layer (PML) boundary condition is applied to numerically investigate the guiding properties of this PCF. The fibre operates at fundamental mode only. All these properties endorse this fibre as a suitable candidate for compensating residual dispersion and polarization maintaining applications.

Relationship between microstructure and mechanical properties of Alloy 690 tubes for steam generators

NASA Astrophysics Data System (ADS)

Diano, P.; Muggeo, A.; Van Duysen, J. C.; Guttmann, M.

1989-12-01

Alloy 690 is used to replace Alloy 600 for the fabrication of tubes for steam generators of french pressurized water nuclear reactors. In order to reduce the dispersion in tensile properties observed for the first Alloy 690 industrial tubes, and which had already been noticed for Alloy 600, a joint research programme has been carried out by Electricité de France (Département Etude des Matériaux) and Valinox Montbard. The dispersion in the tensile properties of the first industrial Alloy 690 tubes for PWR steam generators arises from two main factors: - a grain size dispersion which is in particular controlled by the carbon content and by the final heat treatment, - differences in the degree of strain hardening induced by the straightening process with rollers. An improvement of the fabrication processes which have an influence on these two factors has allowed to reduce considerably the dispersion of the tensile properties of the more recent series of tubes.

Sintering Process and Mechanical Property of MWCNTs/HDPE Bulk Composite.

PubMed

Ming-Wen, Wang; Tze-Chi, Hsu; Jie-Ren, Zheng

2009-08-01

Studies have proved that increasing polymer matrices by carbon nanotubes to form structural reinforcement and electrical conductivity have significantly improved mechanical and electrical properties at very low carbon nanotubes loading. In other words, increasing polymer matrices by carbon nanotubes to form structural reinforcement can reduce friction coefficient and enhance anti-wear property. However, producing traditional MWCNTs in polymeric materix is an extremely complicated process. Using melt-mixing process or in situ polymerization leads to better dispersion effect on composite materials. In this study, therefore, to simplify MWCNTs /HDPE composite process and increase dispersion, powder was used directly to replace pellet to mix and sinter with MWCNTs. The composite bulks with 0, 0.5, 1, 2 and 4% nanotube content by weight was analyzed under SEM to observe nanotubes dispersion. At this rate, a MWCNTs/HDPE composite bulk with uniformly dispersed MWCNTs was achieved, and through the wear bench (Pin-on-Disk), the wear experiment has accomplished. Accordingly, the result suggests the sintered MWCNTs/HDPE composites amplify the hardness and wear-resist property.

Aqueous Polymer Dispersion Coating Used for Osmotic Pump Tablets: Membrane Property Investigation and IVIVC Evaluation.

PubMed

Cheng, Lizhen; Gai, Xiumei; Wen, Haoyang; Liu, Dandan; Tang, Xin; Wang, Yanyan; Wang, Tuanjie; Pan, Weisan; Yang, Xinggang

2018-01-01

The objective of this study was to investigate the fundamental properties of propranolol hydrochloride osmotic pump tablets coated by aqueous polymer dispersion, simultaneously exploring the in vitro and in vivo correlation of the tablet. The physicochemical properties and parameters of aqueous polymer dispersion membranes (SEM, water uptake, and water vapor transmission coefficient) were investigated. In addition, the release behavior and the in vitro release and in vivo absorption profiles of the tablets coated by aqueous polymer dispersion were investigated by comparing with propranolol hydrochloride osmotic pump tablets coated by an organic solvent. Results showed that the similarity factor (f 2 ) between cellulose acetate-coated tablet and Eudragit-coated tablet was 78.1, and f 2 between cellulose acetate-coated tablet and Kollicoat-coated tablet was 77.6. The linear IVIVC of Eudragit-coated and Kollicoat-coated osmotic pump tablets was determined, which confirmed excellent correlation between the absorption in vivo and the drug release in vitro. Consequently, the membrane coated by aqueous polymer dispersion or organic solvent has similar in vitro release rates of controlled release. Also, compared with organic solvent coating, aqueous polymer dispersion has numerous advantages, such as reduced toxicity and no environmental damage. Therefore, the aqueous polymer dispersion technology has enormous potential as a replacement of organic solvent coating.

Ink Wash Painting Style Rendering With Physically-based Ink Dispersion Model

NASA Astrophysics Data System (ADS)

Wang, Yifan; Li, Weiran; Zhu, Qing

2018-04-01

This paper presents a real-time rendering method based on the GPU programmable pipeline for rendering the 3D scene in ink wash painting style. The method is divided into main three parts: First, render the ink properties of 3D model by calculating its vertex curvature. Then, cached the ink properties to a paper structure and using an ink dispersion model which is defined by referencing the theory of porous media to simulate the dispersion of ink. Finally, convert the ink properties to the pixel color information and render it to the screen. This method has a better performance than previous methods in visual quality.

Dispersion controlled by permeable surfaces: surface properties and scaling

DOE PAGES

Ling, Bowen; Tartakovsky, Alexandre M.; Battiato, Ilenia

2016-08-25

Permeable and porous surfaces are common in natural and engineered systems. Flow and transport above such surfaces are significantly affected by the surface properties, e.g. matrix porosity and permeability. However, the relationship between such properties and macroscopic solute transport is largely unknown. In this work, we focus on mass transport in a two-dimensional channel with permeable porous walls under fully developed laminar flow conditions. By means of perturbation theory and asymptotic analysis, we derive the set of upscaled equations describing mass transport in the coupled channel–porous-matrix system and an analytical expression relating the dispersion coefficient with the properties of themore » surface, namely porosity and permeability. Our analysis shows that their impact on the dispersion coefficient strongly depends on the magnitude of the Péclet number, i.e. on the interplay between diffusive and advective mass transport. Additionally, we demonstrate different scaling behaviours of the dispersion coefficient for thin or thick porous matrices. Our analysis shows the possibility of controlling the dispersion coefficient, i.e. transverse mixing, by either active (i.e. changing the operating conditions) or passive mechanisms (i.e. controlling matrix effective properties) for a given Péclet number. By elucidating the impact of matrix porosity and permeability on solute transport, our upscaled model lays the foundation for the improved understanding, control and design of microporous coatings with targeted macroscopic transport features.« less

Co-dispersion of plasmonic nanorods in thermotropic nematic liquid crystals

NASA Astrophysics Data System (ADS)

Sheetah, Ghadah; Liu, Qinkun; Smalukh, Ivan

Colloidal dispersions of plasmonic metal nanoparticles in liquid crystals promise the capability of pre-engineering tunable optical properties of mesostructured metal-dielectric composites. Recently, concentrated dispersions of anisotropic gold, silver, and metal alloy nanoparticles in nematic hosts have been achieved and successfully controlled by low-voltage fields. However, to enable versatile designs of material behavior of the composites, simultaneous co-dispersion of anisotropic particles with different shapes, alignment properties, and compositions are often needed. We achieve such co-dispersions and explore their switching characteristics in response to external stimuli like light and electric fields. We demonstrated that spectral characteristics of co-dispersions of multiple types of anisotropic nanoparticles in a common nematic host provides unprecedented variety of electrically- and optically-tunable material behavior, with a host of potential practical applications in electro-optic devices and displays Ghadah acknowledges support from the King Faisal University (KFU) graduate fellowship.

Dope dyeing of lyocell fiber with NMMO-based carbon black dispersion.

PubMed

Zhang, Liping; Sun, Weize; Xu, Dan; Li, Min; Agbo, Christiana; Fu, Shaohai

2017-10-15

NMMO-based carbon black (CB) dispersion was prepared and its properties as well as its compatibility with lyocell spinning solution were further investigated. Modified lignosulfonate (SP) was verified to be the preeminent dispersant for the preparation of NMMO-based CB dispersion with mass ratio of SP to CB 20% and water to NMMO 13%. The compatibility of NMMO-based CB dispersion with lyocell spinning solution had close relation with dispersant structure and CB content. Mass ratio of CB to cellulose affects the mechanical properties, color strength and crystallinity of lyocell fiber. 0.5% CB increased the breaking strength and elongation of lyocell fiber, whiles breaking strength and elongation of the lyocell fiber were reduced slightly when 2.0% CB was used. The dope dyed fiber showed excellent rubbing and washing fastness as well as migration resistance to water, ethanol and acetone. Copyright © 2017 Elsevier Ltd. All rights reserved.

Dispersion and thermal properties of lithium aluminum silicate glasses doped with Cr3+ ions

NASA Astrophysics Data System (ADS)

El-Diasty, Fouad; Abdel-Baki, Manal; Abdel Wahab, Fathy A.; Darwish, Hussein

2006-10-01

A series of new lithium aluminum silicate (LAS) glass systems doped with chromium ion is prepared. The reflectance and transmittance of the glass slabs are recorded. By means of an iteration procedure, the glass refractive index n and the extinction coefficient k and their dispersions are obtained. Across a wide spectral range of 0.2-1.6 μm, the dispersion curves are used to determine the atomic and quantum constants of the prepared glasses. These findings provide the average oscillator wavelength, the average oscillator strength, oscillator energy, dispersion energy, lattice energy, and material dispersion of the glass materials to be calculated. For optical waveguide applications, the wavelength for zero material dispersion is obtained. Dilatometric measurements are performed and the thermal expansion coefficient is calculated to throw some light on the thermo-optical properties of the present glasses correlating them with their structure and the presence of nonbridging oxygen ions.

Valence holes observed in nanodiamonds dispersed in water

NASA Astrophysics Data System (ADS)

Petit, Tristan; Pflüger, Mika; Tolksdorf, Daniel; Xiao, Jie; Aziz, Emad F.

2015-02-01

Colloidal dispersion is essential for most nanodiamond applications, but its influence on nanodiamond electronic properties remains unknown. Here we have probed the electronic structure of oxidized detonation nanodiamonds dispersed in water by using soft X-ray absorption and emission spectroscopies at the carbon and oxygen K edges. Upon dispersion in water, the π* transitions from sp2-hybridized carbon disappear, and holes in the valence band are observed.Colloidal dispersion is essential for most nanodiamond applications, but its influence on nanodiamond electronic properties remains unknown. Here we have probed the electronic structure of oxidized detonation nanodiamonds dispersed in water by using soft X-ray absorption and emission spectroscopies at the carbon and oxygen K edges. Upon dispersion in water, the π* transitions from sp2-hybridized carbon disappear, and holes in the valence band are observed. Electronic supplementary information (ESI) available: Experimental methods, details on XAS/XES normalization and background correction procedures. See DOI: 10.1039/c4nr06639a

Dispersion of nanosized ceramic powders in aqueous suspensions

NASA Astrophysics Data System (ADS)

Chera, L.; Palcevskis, E.; Berzins, M.; Lipe, A.; Jansone, I.

2007-12-01

Seven commercially available dispersants have been applied to produce high concentrated aqueous suspensions of the nanosized alumina and partially stabilized zirconia powders processed by the plasma technique. Simultaneously, the electrokinetic behaviour of powders has been investigated in diluted suspensions by microelectrophoresis method. Zeta potential measurements are used to estimate the influence of selected dispersants on the electrokinetic properties of the powder surface. On the basis of obtained data the correlation between the surface electrokinetic properties in dilute suspensions and reached maximal suspension concentration is discussed.

Plasma influence on the dispersion properties of finite-length, corrugated waveguides

NASA Astrophysics Data System (ADS)

Shkvarunets, A.; Kobayashi, S.; Weaver, J.; Carmel, Y.; Rodgers, J.; Antonsen, T. M., Jr.; Granatstein, V. L.; Destler, W. W.; Ogura, K.; Minami, K.

1996-03-01

We present an experimental study of the electromagnetic properties of transverse magnetic modes in a corrugated-wall cavity filled with a radially inhomogeneous plasma. The shifts of the resonant frequencies of a finite-length, corrugated cavity were measured as a function of the background plasma density and the dispersion diagram was reconstructed up to a peak plasma density of 1012 cm-3. Good agreement with a calculated dispersion diagram is obtained for plasma densities below 5×1011 cm-3.

Measured backscatter and attenuation properties, including polarization effects, of various dispersions at 0.9 micron

NASA Technical Reports Server (NTRS)

Kohl, R. H.; Flaherty, M. I.; Partin, R. L.

1977-01-01

The optical properties of a wide variety of atmospheric dispersions were studied using a 0.9-micron lidar system which included a GaAs laser stack transmitter emitting a horizontally polarized beam of 4 milliradians vertical divergence and 1.5 milliradians horizontal divergence. A principal means for assessing optical properties was the polarization ratio, that is, the backscattered radiation power perpendicular to the transmitter beam divided by the backscattered radiation power parallel to the beam polarization. The ratio of the backscattered fraction to the attenuation coefficient was also determined. Data on the dispersion properties of black carbon smoke, road dust, fog, fair-weather cumulus clouds, snow and rain were obtained; the adverse effects of sunlight-induced background noise on the readings is also discussed.

Preparation and Properties of Nanocomposites Prepared From Shortened, Functionalized Single-Walled Carbon Nanotubes

NASA Technical Reports Server (NTRS)

Smith, J. G., Jr.; Delozier, D. M.; Watson, K. A.; Connell, J. W.; Yu, Aiping; Haddon, R. C.; Bekyarova, E.

2006-01-01

As part of a continuing materials development activity, low color space environmentally stable polymeric materials that possess sufficient electrical conductivity for electrostatic charge dissipation (ESD) have been investigated. One method of incorporating sufficient electrical conductivity for ESD without detrimental effects on other polymer properties of interest (i.e., optical and thermo-optical) is through the incorporation of single-walled carbon nanotubes (SWNTs). However, SWNTs are difficult to fully disperse in the polymer matrix. One means of improving dispersion is by shortening and functionalizing SWNTs. While this improves dispersion, other properties (i.e., electrical) of the SWNTs can be affected which can in turn alter the final nanocomposite properties. Additionally, functionalization of the polymer matrix can also influence nanocomposite properties obtained from shortened, functionalized SWNTs. The preparation and characterization of nanocomposites fabricated from a polyimide, both functionalized and unfunctionalized, and shortened, functionalized SWNTs will be presented.

Easily Dispersible NiFe2O4/RGO Composite for Microwave Absorption Properties in the X-Band

NASA Astrophysics Data System (ADS)

Bateer, Buhe; Zhang, Jianjao; Zhang, Hongchen; Zhang, Xiaochen; Wang, Chunyan; Qi, Haiqun

2018-01-01

Composites with good dispersion and excellent microwave absorption properties have important applications. Therefore, an easily dispersible NiFe2O4/reduced graphene oxide (RGO) composite has been prepared conveniently through a simple hydrothermal method. Highly crystalline, small size (about 7 nm) monodispersed NiFe2O4 nanoparticles (NPs) are evenly distributed on the surface of RGO. The microwave absorbability revealed that the NiFe2O4/RGO composite exhibits excellent microwave absorption properties in the X-band (8-12 GHz), and the minimum reflection loss of the NiFe2O4/RGO composite is -27.7 dB at 9.2 GHz. The NiFe2O4/RGO composite has good dispersibility in nonpolar solvent, which facilitates the preparation of stable commercial microwave absorbing coatings. It can be a promising candidate for lightweight microwave absorption materials in many application fields.

Targeted ENO schemes with tailored resolution property for hyperbolic conservation laws

NASA Astrophysics Data System (ADS)

Fu, Lin; Hu, Xiangyu Y.; Adams, Nikolaus A.

2017-11-01

In this paper, we extend the range of targeted ENO (TENO) schemes (Fu et al. (2016) [18]) by proposing an eighth-order TENO8 scheme. A general formulation to construct the high-order undivided difference τK within the weighting strategy is proposed. With the underlying scale-separation strategy, sixth-order accuracy for τK in the smooth solution regions is designed for good performance and robustness. Furthermore, a unified framework to optimize independently the dispersion and dissipation properties of high-order finite-difference schemes is proposed. The new framework enables tailoring of dispersion and dissipation as function of wavenumber. The optimal linear scheme has minimum dispersion error and a dissipation error that satisfies a dispersion-dissipation relation. Employing the optimal linear scheme, a sixth-order TENO8-opt scheme is constructed. A set of benchmark cases involving strong discontinuities and broadband fluctuations is computed to demonstrate the high-resolution properties of the new schemes.

At what scale should microarray data be analyzed?

PubMed

Huang, Shuguang; Yeo, Adeline A; Gelbert, Lawrence; Lin, Xi; Nisenbaum, Laura; Bemis, Kerry G

2004-01-01

The hybridization intensities derived from microarray experiments, for example Affymetrix's MAS5 signals, are very often transformed in one way or another before statistical models are fitted. The motivation for performing transformation is usually to satisfy the model assumptions such as normality and homogeneity in variance. Generally speaking, two types of strategies are often applied to microarray data depending on the analysis need: correlation analysis where all the gene intensities on the array are considered simultaneously, and gene-by-gene ANOVA where each gene is analyzed individually. We investigate the distributional properties of the Affymetrix GeneChip signal data under the two scenarios, focusing on the impact of analyzing the data at an inappropriate scale. The Box-Cox type of transformation is first investigated for the strategy of pooling genes. The commonly used log-transformation is particularly applied for comparison purposes. For the scenario where analysis is on a gene-by-gene basis, the model assumptions such as normality are explored. The impact of using a wrong scale is illustrated by log-transformation and quartic-root transformation. When all the genes on the array are considered together, the dependent relationship between the expression and its variation level can be satisfactorily removed by Box-Cox transformation. When genes are analyzed individually, the distributional properties of the intensities are shown to be gene dependent. Derivation and simulation show that some loss of power is incurred when a wrong scale is used, but due to the robustness of the t-test, the loss is acceptable when the fold-change is not very large.

Viscoelastic Properties of Core-Shell-Structured, Hemicellulose-Rich Nanofibrillated Cellulose in Dispersion and Wet-Film States.

PubMed

Tanaka, Reina; Saito, Tsuguyuki; Hänninen, Tuomas; Ono, Yuko; Hakalahti, Minna; Tammelin, Tekla; Isogai, Akira

2016-06-13

We report the viscoelastic properties of core-shell-structured, hemicellulose-rich nanofibrillated cellulose (NFC) in dispersion and wet-film states. The hemicellulose-rich NFC (hemicellulose neutral sugars 23%, carboxylate 0.2 mmol g(-1)), prepared from Japanese persimmons, had a core crystallite thickness of 2.3 nm and unit fibril thickness of 4.2 nm. A carboxylate-rich NFC (hemicellulose neutral sugars 7%, carboxylate 0.9 mmol g(-1)) with crystallite and fibril widths of 2.5 and 3.3 nm, respectively, was used as a reference. The solid-concentration dependencies of the storage moduli of gel-like water dispersions of the hemicellulose-rich NFC were weaker than those of carboxylate-rich NFC, and the dispersions were loosely flocculated even at high salt concentrations and low pH values. The viscoelastic properties of wet NFC films were similar to those of their dispersions; the hemicellulose-rich NFC films were significantly less sensitive to salt concentration and pH and were soft and swollen at high salt concentrations and low pH values.

Carbon nanotube modification using gum arabic and its effect on the dispersion and tensile properties of carbon nanotubes/epoxy nanocomposites.

PubMed

Kim, Man Tae; Park, Ho Seok; Hui, David; Rhee, Kyong Yop

2011-08-01

In this study, the effects of a MWCNT treatment on the dispersion of MWCNTs in aqueous solution and the tensile properties of MWCNT/epoxy nanocomposites were investigated. MWCNTs were treated using acid and gum arabic, and MWCNT/epoxy nanocomposites were fabricated with 0.3 wt.% unmodified, oxidized and gum-treated MWCNTs. The dispersion states of the unmodified, oxidized, and Gum-treated MWCNTs were characterized in distilled water. The tensile strengths and elastic modulus of the three nanocomposites were determined and compared. The results indicated that the gum treatment produced better dispersion of the MWCNTs in distilled water and that gum-treated MWCNT/epoxy nanocomposites had a better tensile strength and elastic modulus than did the unmodified and acid-treated MWCNT/epoxy nanocomposites. Scanning electron microscope examination of the fracture surface showed that the improved tensile properties of the gum-treated MWCNT/epoxy nanocomposites were attributed to the improved dispersion of MWCNTs in the epoxy and to interfacial bonding between nanotubes and the epoxy matrix.

Modeling ultrasonic transient scattering from biological tissues including their dispersive properties directly in the time domain.

PubMed

Norton, G V; Novarini, J C

2007-06-01

Ultrasonic imaging in medical applications involves propagation and scattering of acoustic waves within and by biological tissues that are intrinsically dispersive. Analytical approaches for modeling propagation and scattering in inhomogeneous media are difficult and often require extremely simplifying approximations in order to achieve a solution. To avoid such approximations, the direct numerical solution of the wave equation via the method of finite differences offers the most direct tool, which takes into account diffraction and refraction. It also allows for detailed modeling of the real anatomic structure and combination/layering of tissues. In all cases the correct inclusion of the dispersive properties of the tissues can make the difference in the interpretation of the results. However, the inclusion of dispersion directly in the time domain proved until recently to be an elusive problem. In order to model the transient signal a convolution operator that takes into account the dispersive characteristics of the medium is introduced to the linear wave equation. To test the ability of this operator to handle scattering from localized scatterers, in this work, two-dimensional numerical modeling of scattering from an infinite cylinder with physical properties associated with biological tissue is calculated. The numerical solutions are compared with the exact solution synthesized from the frequency domain for a variety of tissues having distinct dispersive properties. It is shown that in all cases, the use of the convolutional propagation operator leads to the correct solution for the scattered field.

Optimization of Processing Condition of Nanocomposites According to the Structural Changes of Halloysite Nanotubes Under Impact Behavior

NASA Astrophysics Data System (ADS)

Kim, Yun-Hae; Park, Soo-Jeong; Nakagaito, Antonio Norio

2017-08-01

In the present study, optimal dispersion conditions were developed to disperse nanocomposites containing halloysite nanotubes (HNTs) and unsaturated polyester (UP) resin using ultrasonic dispersion method. Due to the presence of a substantial amount of water in HNTs, their properties depend on the operating temperature when dispersing. It is, therefore, important to understand the structural changes of HNTs that occur when changing the operating temperature. HNTs heat-treated at various temperatures have different structures and mechanical/chemical properties. Therefore, in this research, HNTs were treated at two temperatures, 773.15 K and 973.15 K (500 °C and 700 °C), and the correlation between UP resin and heat-treated HNTs was studied in detail. The quantities of HNTs were 0.5 and 1 wt pct, for the 773.15 K and 973.15 K (500 °C and 700 °C) heat treatment temperatures, respectively. The contents of HNTs were restricted in order to demonstrate the aggregation phenomenon. The dispersion was carried out by ultrasonication. All structural changes including dispersion behavior were examined by TEM. The mechanical properties were assessed by impact tests. The results showed that the high impact strength of the nanocomposite containing 1 wt pct of 973.15 K (700 °C) heat-treated HNT was superior. In other words, it can be said that the rheological property of the matrix resin depended on the quantities of HNTs and the heat treatment temperature.

Systematic Validation and Atomic Force Microscopy of Non-Covalent Short Oligonucleotide Barcode Microarrays

PubMed Central

Cook, Michael A.; Chan, Chi-Kin; Jorgensen, Paul; Ketela, Troy; So, Daniel; Tyers, Mike; Ho, Chi-Yip

2008-01-01

Background Molecular barcode arrays provide a powerful means to analyze cellular phenotypes in parallel through detection of short (20–60 base) unique sequence tags, or “barcodes”, associated with each strain or clone in a collection. However, costs of current methods for microarray construction, whether by in situ oligonucleotide synthesis or ex situ coupling of modified oligonucleotides to the slide surface are often prohibitive to large-scale analyses. Methodology/Principal Findings Here we demonstrate that unmodified 20mer oligonucleotide probes printed on conventional surfaces show comparable hybridization signals to covalently linked 5′-amino-modified probes. As a test case, we undertook systematic cell size analysis of the budding yeast Saccharomyces cerevisiae genome-wide deletion collection by size separation of the deletion pool followed by determination of strain abundance in size fractions by barcode arrays. We demonstrate that the properties of a 13K unique feature spotted 20 mer oligonucleotide barcode microarray compare favorably with an analogous covalently-linked oligonucleotide array. Further, cell size profiles obtained with the size selection/barcode array approach recapitulate previous cell size measurements of individual deletion strains. Finally, through atomic force microscopy (AFM), we characterize the mechanism of hybridization to unmodified barcode probes on the slide surface. Conclusions/Significance These studies push the lower limit of probe size in genome-scale unmodified oligonucleotide microarray construction and demonstrate a versatile, cost-effective and reliable method for molecular barcode analysis. PMID:18253494

Waveguide-excited fluorescence microarray

NASA Astrophysics Data System (ADS)

Sagarzazu, Gabriel; Bedu, Mélanie; Martinelli, Lucio; Ha, Khoi-Nguyen; Pelletier, Nicolas; Safarov, Viatcheslav I.; Weisbuch, Claude; Gacoin, Thierry; Benisty, Henri

2008-04-01

Signal-to-noise ratio is a crucial issue in microarray fluorescence read-out. Several strategies are proposed for its improvement. First, light collection in conventional microarrays scanners is quite limited. It was recently shown that almost full collection can be achieved in an integrated lens-free biosensor, with labelled species hybridizing practically on the surface of a sensitive silicon detector [L. Martinelli et al. Appl. Phys. Lett. 91, 083901 (2007)]. However, even with such an improvement, the ultimate goal of real-time measurements during hybridization is challenging: the detector is dazzled by the large fluorescence of labelled species in the solution. In the present paper we show that this unwanted signal can effectively be reduced if the excitation light is confined in a waveguide. Moreover, the concentration of excitation light in a waveguide results in a huge signal gain. In our experiment we realized a structure consisting of a high index sol-gel waveguide deposited on a low-index substrate. The fluorescent molecules deposited on the surface of the waveguide were excited by the evanescent part of a wave travelling in the guide. The comparison with free-space excitation schemes confirms a huge gain (by several orders of magnitude) in favour of waveguide-based excitation. An optical guide deposited onto an integrated biosensor thus combines both advantages of ideal light collection and enhanced surface localized excitation without compromising the imaging properties. Modelling predicts a negligible penalty from spatial cross-talk in practical applications. We believe that such a system would bring microarrays to hitherto unattained sensitivities.

Transcriptome profiling of Pinus radiata juvenile wood with contrasting stiffness identifies putative candidate genes involved in microfibril orientation and cell wall mechanics

PubMed Central

2011-01-01

Background The mechanical properties of wood are largely determined by the orientation of cellulose microfibrils in secondary cell walls. Several genes and their allelic variants have previously been found to affect microfibril angle (MFA) and wood stiffness; however, the molecular mechanisms controlling microfibril orientation and mechanical strength are largely uncharacterised. In the present study, cDNA microarrays were used to compare gene expression in developing xylem with contrasting stiffness and MFA in juvenile Pinus radiata trees in order to gain further insights into the molecular mechanisms underlying microfibril orientation and cell wall mechanics. Results Juvenile radiata pine trees with higher stiffness (HS) had lower MFA in the earlywood and latewood of each ring compared to low stiffness (LS) trees. Approximately 3.4 to 14.5% out of 3, 320 xylem unigenes on cDNA microarrays were differentially regulated in juvenile wood with contrasting stiffness and MFA. Greater variation in MFA and stiffness was observed in earlywood compared to latewood, suggesting earlywood contributes most to differences in stiffness; however, 3-4 times more genes were differentially regulated in latewood than in earlywood. A total of 108 xylem unigenes were differentially regulated in juvenile wood with HS and LS in at least two seasons, including 43 unigenes with unknown functions. Many genes involved in cytoskeleton development and secondary wall formation (cellulose and lignin biosynthesis) were preferentially transcribed in wood with HS and low MFA. In contrast, several genes involved in cell division and primary wall synthesis were more abundantly transcribed in LS wood with high MFA. Conclusions Microarray expression profiles in Pinus radiata juvenile wood with contrasting stiffness has shed more light on the transcriptional control of microfibril orientation and the mechanical properties of wood. The identified candidate genes provide an invaluable resource for further gene function and association genetics studies aimed at deepening our understanding of cell wall biomechanics with a view to improving the mechanical properties of wood. PMID:21962175

Phonon Dispersion in Amorphous Ni-Alloys

NASA Astrophysics Data System (ADS)

Vora, A. M.

2007-06-01

The well-known model potential is used to investigate the longitudinal and transverse phonon dispersion curves for six Ni-based binary amorphous alloys, viz. Ni31Dy69, Ni33Y67, Ni36Zr64, Ni50Zr50, Ni60 Nb40, and Ni81B19. The thermodynamic and elastic properties are also computed from the elastic limits of the phonon dispersion curves. The theoretical approach given by Hubbard-Beeby is used in the present study to compute the phonon dispersion curves. Five local field correction functions proposed by Hartree, Taylor, Ichimaru-Utsumi, Farid et al. and Sarkar et al. are employed to see the effect of exchange and correlation in the aforesaid properties.

Manipulating dispersion and distribution of graphene in PLA through Novel Interface Engineering for improved conductive properties

USDA-ARS?s Scientific Manuscript database

This study aimed to enhance the conductive properties of PLA nanocomposite by controlling the dispersion and distribution of graphene within the minor phase of the polymer blend. Functionalized graphene (f-GO) was achieved by reacting graphene oxide (GO) with various silanes under the aid of an ioni...

Manipulating dispersion and distribution of graphene in PLA through novel interface engineering for improved conductive properties

USDA-ARS?s Scientific Manuscript database

This study aimed to enhance the conductive properties of PLA nanocomposite by controlling the dispersion and distribution of graphene within the minor phase of the polymer blend. Functionalized graphene (f-GO) was achieved by reacting graphene oxide (GO) with various silanes under the aid of an ioni...

Practical colloidal processing of multication ceramics

DOE PAGES

Bell, Nelson S.; Monson, Todd C.; Diantonio, Christopher; ...

2015-09-07

The use of colloidal processing principles in the formation of ceramic materials is well appreciated for developing homogeneous material properties in sintered products, enabling novel forming techniques for porous ceramics or 3D printing, and controlling microstructure to enable optimized material properties. The solution processing of electronic ceramic materials often involves multiple cationic elements or dopants to affect microstructure and properties. Material stability must be considered through the steps of colloidal processing to optimize desired component properties. This review provides strategies for preventing material degradation in particle synthesis, milling processes, and dispersion, with case studies of consolidation using spark plasma sinteringmore » of these systems. The prevention of multication corrosion in colloidal dispersions can be achieved by utilizing conditions similar to the synthesis environment or by the development of surface passivation layers. The choice of dispersing surfactants can be related to these surface states, which are of special importance for nanoparticle systems. A survey of dispersant chemistries related to some common synthesis conditions is provided for perovskite systems as an example. Furthermore, these principles can be applied to many colloidal systems related to electronic and optical applications.« less

Effect of the dispersing agent on the structural and magnetic properties of CoFe2O4 /SiO2 nanocomposites

NASA Astrophysics Data System (ADS)

Daboin, Viviana; Briceño, Sarah; Suárez, Jorge; Gonzalez, Gema

2018-04-01

Cobalt ferrite nanoparticles CoFe2O4 were synthesized using the thermal decomposition method; subsequently the NPs were functionalized using poli vinyl pyrrolidone (PVP) cetyl trimethyl ammonium bromide (CTAB) and polyethylene glycol (PEG) as dispersing agent. Surface modification with silica SiO2 was made using the Stöber method and tetraethyl orthosilicate (TEOS) as precursor. The purpose of this study is to investigate the influence of the different dispersing agents on the structure and therefore on the magnetic properties of the CoFe2O4 /SiO2 nanocomposites. Structural characterization was carried out using: X-ray diffraction (XRD), infrared spectroscopy (FTIR), transmission electron microscopy (TEM) and scanning electron microscopy (SEM). Magnetic properties were evaluated using a vibrating sample magnetometer (VSM) at room temperature. Our results revealed that the structural and magnetic properties of the CoFe2O4 /SiO2 nanocomposites were significantly different depending of the type of dispersing agents used before the surface modification with silica SiO2 .

GO/PEDOT:PSS nanocomposites: effect of different dispersing agents on rheological, thermal, wettability and electrochemical properties

NASA Astrophysics Data System (ADS)

Giuri, Antonella; Masi, Sofia; Colella, Silvia; Listorti, Andrea; Rizzo, Aurora; Liscio, Andrea; Treossi, Emanuele; Palermo, Vincenzo; Gigli, Giuseppe; Mele, Claudio; Esposito Corcione, Carola

2017-04-01

In this work glucose (G), α-cyclodextrin (α-CD) and sodium salt of carboxymethyl cellulose (CMCNa) are used as dispersing agents for graphene oxide (GO), exploring the influence of both saccharide units and geometric/steric hindrance on the rheological, thermal, wettability and electrochemical properties of a GO/poly(3,4-ethylenedioxythiophene) polystyrene sulfonate (PEDOT:PSS) nanocomposite. By acting on the saccharide-based additives, we can modulate the rheological, thermal, and wettability properties of the GO/PEDOT:PSS nanocomposite. Firstly, the influence of all the additives on the rheological behaviour of GO and PEDOT:PSS was investigated separately in order to understand the effect of the dispersing agent on both the components of the ternary nanocomposite, individually. Subsequently, steady shear and dynamic frequency tests were conducted on all the nanocomposite solutions, characterized by thermal, wettability and morphological analysis. Finally, the electrochemical properties of the GO/PEDOT composites with different dispersing agents for supercapacitors were investigated using cyclic voltammetry (CV). The CV results revealed that GO/PEDOT with glucose exhibited the highest specific capacitance among the systems investigated.

Sintering Process and Mechanical Property of MWCNTs/HDPE Bulk Composite

PubMed Central

Tze-Chi, Hsu; Jie-Ren, Zheng

2009-01-01

Studies have proved that increasing polymer matrices by carbon nanotubes to form structural reinforcement and electrical conductivity have significantly improved mechanical and electrical properties at very low carbon nanotubes loading. In other words, increasing polymer matrices by carbon nanotubes to form structural reinforcement can reduce friction coefficient and enhance anti-wear property. However, producing traditional MWCNTs in polymeric materix is an extremely complicated process. Using melt-mixing process or in situ polymerization leads to better dispersion effect on composite materials. In this study, therefore, to simplify MWCNTs /HDPE composite process and increase dispersion, powder was used directly to replace pellet to mix and sinter with MWCNTs. The composite bulks with 0, 0.5, 1, 2 and 4% nanotube content by weight was analyzed under SEM to observe nanotubes dispersion. At this rate, a MWCNTs/HDPE composite bulk with uniformly dispersed MWCNTs was achieved, and through the wear bench (Pin-on-Disk), the wear experiment has accomplished. Accordingly, the result suggests the sintered MWCNTs/HDPE composites amplify the hardness and wear-resist property. PMID:19730688

Spin-coating: A new approach for improving dispersion of cellulose nanocrystals and mechanical properties of poly (lactic acid) composites.

PubMed

Shojaeiarani, Jamileh; Bajwa, Dilpreet S; Stark, Nicole M

2018-06-15

This study systematically evaluated the influence of masterbatch preparation techniques, solvent casting and spin-coating methods, on composite properties. Composites were manufactured by combining CNCs masterbatches and PLA resin using twin screw extruder followed by injection molding. Different microscopy techniques were used to investigate the dispersion of CNCs in masterbatches and composites. Thermal, thermomechanical, and mechanical properties of composites were evaluated. Scanning electron microscopy (SEM) images showed superior dispersion of CNCs in spin-coated masterbatches compared to solvent cast masterbatches. At lower CNCs concentrations, both SEM and optical microscope images confirmed more uniform CNCs dispersion in spin-coated composites than solvent cast samples. Degree of crystallinity of PLA exhibited a major enhancement by 147% and 380% in solvent cast and spin-coated composites, respectively. Spin-coated composites with lower CNCs concentration exhibited a noticeable improvement in mechanical properties. However, lower thermal characteristics in spin-coated composites were observed, which could be attributed to the residual solvents in masterbatches. Copyright © 2018 Elsevier Ltd. All rights reserved.

A critical evaluation of the enhancement of mechanical properties of epoxy modified using CNTs

NASA Astrophysics Data System (ADS)

Bedsole, Robert W.; Park, Cheol; Bogert, Philip B.; Tippur, Hareesh V.

2015-09-01

Carbon nanotubes (CNTs) have been widely shown in the literature to improve mechanical properties of epoxy, such as tensile strength, elastic modulus, strain to failure, and fracture toughness. These improvements in nanocomposite properties have been attributed to the extraordinary properties of the nanotubes, as well as the quality of their dispersion within and adhesion to the epoxy matrix. However, many authors have also struggled to show significant mechanical improvements using similar methodologies and despite, in some cases, showing qualitative improvements in dispersion with optical microscopy. These authors have frequently resorted to other methods for improving the mechanical properties of CNT/epoxy, such as electrically aligning CNTs, using different types of CNTs, or modifying the stoichiometry. The current work examines many different dispersion techniques, types of CNTs, types of epoxies, curing cycles, and other variables in an attempt to improve the mechanical properties of neat epoxy with CNTs. Despite seeing significant changes in the microscopy, no significant improvements in tensile or fracture properties have been attributed to CNTs in this work.

Facile approach to fabricate waterborne polyaniline nanocomposites with environmental benignity and high physical properties

NASA Astrophysics Data System (ADS)

Wang, Haihua; Wen, Huan; Hu, Bin; Fei, Guiqiang; Shen, Yiding; Sun, Liyu; Yang, Dong

2017-03-01

Waterborne polyaniline (PANI) dispersion has got extensive attention due to its environmental friendliness and good processability, whereas the storage stability and mechanical property have been the challenge for the waterborne PANI composites. Here we prepare for waterborne PANI dispersion through the chemical graft polymerisation of PANI into epichlorohydrin modified poly (vinyl alcohol) (EPVA). In comparison with waterborne PANI dispersion prepared through physical blend and in situ polymerisation, the storage stability of PANI-g-EPVA dispersion is greatly improved and the dispersion keeps stable for one year. In addition, the as-prepared PANI-g-EPVA film displays more uniform and smooth morphology, as well as enhanced phase compatibility. PANI is homogeneously distributed in the EPVA matrix on the nanoscale. PANI-g-EPVA displays different morphology at different aniline content. The electrical conductivity corresponds to 7.3 S/cm when only 30% PANI is incorporated into the composites, and then increases up to 20.83 S/cm with further increase in the aniline content. Simultaneously, the tensile strength increases from 35 MPa to 64 MPa. The as-prepared PANI-g-EPVA dispersion can be directly used as the conductive ink or coatings for cellulose fibre paper to prepare flexible conductive paper with high conductivity and mechanical property, which is also suitable for large scalable production.

DOE Office of Scientific and Technical Information (OSTI.GOV)

SacconePhD, Scott F; Chesler, Elissa J; Bierut, Laura J

Commercial SNP microarrays now provide comprehensive and affordable coverage of the human genome. However, some diseases have biologically relevant genomic regions that may require additional coverage. Addiction, for example, is thought to be influenced by complex interactions among many relevant genes and pathways. We have assembled a list of 486 biologically relevant genes nominated by a panel of experts on addiction. We then added 424 genes that showed evidence of association with addiction phenotypes through mouse QTL mappings and gene co-expression analysis. We demonstrate that there are a substantial number of SNPs in these genes that are not well representedmore » by commercial SNP platforms. We address this problem by introducing a publicly available SNP database for addiction. The database is annotated using numeric prioritization scores indicating the extent of biological relevance. The scores incorporate a number of factors such as SNP/gene functional properties (including synonymy and promoter regions), data from mouse systems genetics and measures of human/mouse evolutionary conservation. We then used HapMap genotyping data to determine if a SNP is tagged by a commercial microarray through linkage disequilibrium. This combination of biological prioritization scores and LD tagging annotation will enable addiction researchers to supplement commercial SNP microarrays to ensure comprehensive coverage of biologically relevant regions.« less

Dependence of the clustering properties of galaxies on stellar velocity dispersion in the Main galaxy sample of SDSS DR10

NASA Astrophysics Data System (ADS)

Deng, Xin-Fa; Song, Jun; Chen, Yi-Qing; Jiang, Peng; Ding, Ying-Ping

2014-08-01

Using two volume-limited Main galaxy samples of the Sloan Digital Sky Survey Data Release 10 (SDSS DR10), we investigate the dependence of the clustering properties of galaxies on stellar velocity dispersion by cluster analysis. It is found that in the luminous volume-limited Main galaxy sample, except at r=1.2, richer and larger systems can be more easily formed in the large stellar velocity dispersion subsample, while in the faint volume-limited Main galaxy sample, at r≥0.9, an opposite trend is observed. According to statistical analyses of the multiplicity functions, we conclude in two volume-limited Main galaxy samples: small stellar velocity dispersion galaxies preferentially form isolated galaxies, close pairs and small group, while large stellar velocity dispersion galaxies preferentially inhabit the dense groups and clusters. However, we note the difference between two volume-limited Main galaxy samples: in the faint volume-limited Main galaxy sample, at r≥0.9, the small stellar velocity dispersion subsample has a higher proportion of galaxies in superclusters ( n≥200) than the large stellar velocity dispersion subsample.

Wave dispersion and propagation in state-based peridynamics

NASA Astrophysics Data System (ADS)

Butt, Sahir N.; Timothy, Jithender J.; Meschke, Günther

2017-11-01

Peridynamics is a nonlocal continuum model which offers benefits over classical continuum models in cases, where discontinuities, such as cracks, are present in the deformation field. However, the nonlocal characteristics of peridynamics leads to a dispersive dynamic response of the medium. In this study we focus on the dispersion properties of a state-based linear peridynamic solid model and specifically investigate the role of the peridynamic horizon. We derive the dispersion relation for one, two and three dimensional cases and investigate the effect of horizon size, mesh size (lattice spacing) and the influence function on the dispersion properties. We show how the influence function can be used to minimize wave dispersion at a fixed lattice spacing and demonstrate it qualitatively by wave propagation analysis in one- and two-dimensional models of elastic solids. As a main contribution of this paper, we propose to associate peridynamic non-locality expressed by the horizon with a characteristic length scale related to the material microstructure. To this end, the dispersion curves obtained from peridynamics are compared with experimental data for two kinds of sandstone.

Eulerian-Lagrangian solution of the convection-dispersion equation in natural coordinates

USGS Publications Warehouse

Cheng, Ralph T.; Casulli, Vincenzo; Milford, S. Nevil

1984-01-01

The vast majority of numerical investigations of transport phenomena use an Eulerian formulation for the convenience that the computational grids are fixed in space. An Eulerian-Lagrangian method (ELM) of solution for the convection-dispersion equation is discussed and analyzed. The ELM uses the Lagrangian concept in an Eulerian computational grid system. The values of the dependent variable off the grid are calculated by interpolation. When a linear interpolation is used, the method is a slight improvement over the upwind difference method. At this level of approximation both the ELM and the upwind difference method suffer from large numerical dispersion. However, if second-order Lagrangian polynomials are used in the interpolation, the ELM is proven to be free of artificial numerical dispersion for the convection-dispersion equation. The concept of the ELM is extended for treatment of anisotropic dispersion in natural coordinates. In this approach the anisotropic properties of dispersion can be conveniently related to the properties of the flow field. Several numerical examples are given to further substantiate the results of the present analysis.

Formation of nano/micro-dispersions with improved dissolution properties upon dispersion of ritonavir melt extrudate in aqueous media.

PubMed

Tho, Ingunn; Liepold, Bernd; Rosenberg, Joerg; Maegerlein, Markus; Brandl, Martin; Fricker, Gert

2010-04-16

The objective of the study was to characterise the aqueous dispersions of ritonavir melt extrudates. More specifically to look into the particular system formed when melt extrudate of a poorly soluble drug dissolved in a hydrophilic polymer matrix containing a surfactant is dispersed in an aqueous medium. Melt extrudates with and without ritonavir were studied. The drug containing extrudate was confirmed to be molecular dispersions of drug in a polymer/surfactant matrix. Particulate dispersions were formed in water from both drug and placebo extrudates. The dispersions were investigated with respect to mean particle size and particle size distribution (photon correlation spectroscopy and optical particle counting), surface charge (zeta potential), particle composition (ultracentrifugation), tendency to form aggregates and precipitate (turbidity), in vitro dissolution rate and drug release. It was concluded that dispersion of melt extrudates in aqueous medium give rise to nano/micro-dispersions. The stability of the nano/micro-dispersion is sensitive to anions and may be subjected to association/aggregation/flocculation as time proceeds after preparation of dispersion. Melt extrudate showed improved dissolution rate and drug release properties compared to crystalline raw material. From studies of single components and physical mixtures of the formulation composition it can be concluded that the drug delivery system itself, namely solid dispersion prepared by melt extrusion technology, plays a key role for the formation of the observed particles. 2010 Elsevier B.V. All rights reserved.

Thermodynamic Approach to Boron Nitride Nanotube Solubility and Dispersion

NASA Technical Reports Server (NTRS)

Tiano, A. L.; Gibbons, L.; Tsui, M.; Applin, S. I.; Silva, R.; Park, C.; Fay, C. C.

2016-01-01

Inadequate dispersion of nanomaterials is a critical issue that significantly limits the potential properties of nanocomposites and when overcome, will enable further enhancement of material properties. The most common methods used to improve dispersion include surface functionalization, surfactants, polymer wrapping, and sonication. Although these approaches have proven effective, they often achieve dispersion by altering the surface or structure of the nanomaterial and ultimately, their intrinsic properties. Co-solvents are commonly utilized in the polymer, paint, and art conservation industries to selectively dissolve materials. These co-solvents are utilized based on thermodynamic interaction parameters and are chosen so that the original materials are not affected. The same concept was applied to enhance the dispersion of boron nitride nanotubes (BNNTs) to facilitate the fabrication of BNNT nanocomposites. Of the solvents tested, dimethylacetamide (DMAc) exhibited the most stable, uniform dispersion of BNNTs, followed by N,N-dimethylformamide (DMF), acetone, and N-methyl-2-pyrrolidone (NMP). Utilizing the known Hansen solubility parameters of these solvents in comparison to the BNNT dispersion state, a region of good solubility was proposed. This solubility region was used to identify co-solvent systems that led to improved BNNT dispersion in poor solvents such as toluene, hexane, and ethanol. Incorporating the data from the co-solvent studies further refined the proposed solubility region. From this region, the Hansen solubility parameters for BNNTs are thought to lie at the midpoint of the solubility sphere: 16.8, 10.7, and 9.0 MPa(exp 1/2) for delta d, delta p, and delta h, respectively, with a calculated Hildebrand parameter of 21.8 MPa)exp 1/2).

Thermodynamic approach to boron nitride nanotube solubility and dispersion.

PubMed

Tiano, A L; Gibbons, L; Tsui, M; Applin, S I; Silva, R; Park, C; Fay, C C

2016-02-21

Inadequate dispersion of nanomaterials is a critical issue that significantly limits the potential properties of nanocomposites and when overcome, will enable further enhancement of material properties. The most common methods used to improve dispersion include surface functionalization, surfactants, polymer wrapping, and sonication. Although these approaches have proven effective, they often achieve dispersion by altering the surface or structure of the nanomaterial and ultimately, their intrinsic properties. Co-solvents are commonly utilized in the polymer, paint, and art conservation industries to selectively dissolve materials. These co-solvents are utilized based on thermodynamic interaction parameters and are chosen so that the original materials are not affected. The same concept was applied to enhance the dispersion of boron nitride nanotubes (BNNTs) to facilitate the fabrication of BNNT nanocomposites. Of the solvents tested, dimethylacetamide (DMAc) exhibited the most stable, uniform dispersion of BNNTs, followed by N,N-dimethylformamide (DMF), acetone, and N-methyl-2-pyrrolidone (NMP). Utilizing the known Hansen solubility parameters of these solvents in comparison to the BNNT dispersion state, a region of good solubility was proposed. This solubility region was used to identify co-solvent systems that led to improved BNNT dispersion in poor solvents such as toluene, hexane, and ethanol. Incorporating the data from the co-solvent studies further refined the proposed solubility region. From this region, the Hansen solubility parameters for BNNTs are thought to lie at the midpoint of the solubility sphere: 16.8, 10.7, and 9.0 MPa(1/2) for δd, δp, and δh, respectively, with a calculated Hildebrand parameter of 21.8 MPa(1/2).

DISPERSANT EFFECTIVENESS ON OIL SPILLS - EMPIRICAL CORRELATIONS

EPA Science Inventory

When a dispersant is applied to an oil slick, its effectiveness in dispersing the spilled oil depends on various factors such as oil properties, wave mixing energy, temperature of both oil and water, and salinity of the water. Estuaries represent water with varying salinities. In...

Vanishing characteristic speeds and critical dispersive points in nonlinear interfacial wave problems

NASA Astrophysics Data System (ADS)

Ratliff, Daniel J.

2017-11-01

Criticality plays a central role in the study of reductions and stability of hydrodynamical systems. At critical points, it is often the case that nonlinear reductions with dispersion arise to govern solution behavior. By considering when such models become bidirectional and lose their initial dispersive properties, it will be shown that higher order dispersive models may be supported in hydrodynamical systems. Precisely, this equation is a two-way Boussinesq equation with sixth order dispersion. The case of two layered shallow water is considered to illustrate this, and it is reasoned why such an environment is natural for such a system to emerge. Further, it is demonstrated that the regions in the parameter space for nontrivial flow, which admit this reduction, are vast and in fact form a continuum. The reduced model is then numerically simulated to illustrate how the two-way and higher dispersive properties suggest more exotic families of solitary wave solutions can emerge in stratified flows.

All-optical observation and reconstruction of spin wave dispersion

PubMed Central

Hashimoto, Yusuke; Daimon, Shunsuke; Iguchi, Ryo; Oikawa, Yasuyuki; Shen, Ka; Sato, Koji; Bossini, Davide; Tabuchi, Yutaka; Satoh, Takuya; Hillebrands, Burkard; Bauer, Gerrit E. W.; Johansen, Tom H.; Kirilyuk, Andrei; Rasing, Theo; Saitoh, Eiji

2017-01-01

To know the properties of a particle or a wave, one should measure how its energy changes with its momentum. The relation between them is called the dispersion relation, which encodes essential information of the kinetics. In a magnet, the wave motion of atomic spins serves as an elementary excitation, called a spin wave, and behaves like a fictitious particle. Although the dispersion relation of spin waves governs many of the magnetic properties, observation of their entire dispersion is one of the challenges today. Spin waves whose dispersion is dominated by magnetostatic interaction are called pure-magnetostatic waves, which are still missing despite of their practical importance. Here, we report observation of the band dispersion relation of pure-magnetostatic waves by developing a table-top all-optical spectroscopy named spin-wave tomography. The result unmasks characteristics of pure-magnetostatic waves. We also demonstrate time-resolved measurements, which reveal coherent energy transfer between spin waves and lattice vibrations. PMID:28604690

Importing MAGE-ML format microarray data into BioConductor.

PubMed

Durinck, Steffen; Allemeersch, Joke; Carey, Vincent J; Moreau, Yves; De Moor, Bart

2004-12-12

The microarray gene expression markup language (MAGE-ML) is a widely used XML (eXtensible Markup Language) standard for describing and exchanging information about microarray experiments. It can describe microarray designs, microarray experiment designs, gene expression data and data analysis results. We describe RMAGEML, a new Bioconductor package that provides a link between cDNA microarray data stored in MAGE-ML format and the Bioconductor framework for preprocessing, visualization and analysis of microarray experiments. http://www.bioconductor.org. Open Source.

Forging Oxide-Dispersion-Strengthened Superalloys

NASA Technical Reports Server (NTRS)

Harf, F. H.; Glasgow, T. K.; Moracz, D. J.; Austin, C. M.

1986-01-01

Cladding of mild steel prevents surface cracking when alloy contacts die. Continual need for improvements in properties of alloys capable of withstanding elevated temperatures. Accomplished by using oxide-dispersion-strengthed superalloys such as Inconel Alloy MA 6000. Elevated tensile properties of forged alloy equal those of hot-rolled MA 6000 bar. Stress-rupture properties somewhat lower than those of bar stock but, at 1,100 degrees C, exceed those of strongest commercial single crystal, directionally solidified and conventionally cast superalloys.

Structure-property relationships in thermomechanically treated beryllia dispersed nickel alloys

NASA Technical Reports Server (NTRS)

Grewal, M. S.; Sastri, S. A.; Grant, N. J.

1975-01-01

BeO dispersed nickel alloys, produced by powder metallurgy techniques, were studied extensively in stress rupture at 815, 982, and 1093 C (1088, 1255, and 1366 K) and by transmission electron microscopy. The alloys were subjected to a variety of thermomechanical treatments (TMT) to determine the benefits of TMT on properties. It is shown that the use of intermediate annealing treatments after 10 pct reduction steps is highly beneficial on both low and high temperature properties. It is indicated that the high temperature strength is not primarily dependent on the grain aspect ratio or texture but depends strongly on the dislocation density and distribution of dislocations in a stable substructure which is pinned by the fine oxide dispersion.

Detergent-dispersant additives based on high-molecular-weight alkylphenols

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kulieva, K.N.; Namazova, I.I.; Ismailova, N.D.

1988-09-01

This article describes the synthesis and investigation of Mannich bases produced for alkylphenols, obtained in turn from ethylene oligomers. These oligomers are the still bottoms from distillation products of high-temperature oligomerization of ethylene in the presence of triethylaluminum. Two narrow cuts obtained from the distillation of oligomer fraction were used to study the influence of ethylene oligomer molecular weight on the properties of the additives. The additives were blended in DS-11 oil to evaluate their detergency-dispersancy and other properties. Comparison blends were made with succinimide additives based on the same ethylene oligomers. The Mannich bases give improvements in the oxidationmore » resistance, anticorrosion properties, and detergency-dispersancy of the DS-11 diesel oil.« less

Dual-peak long-period fiber gratings with enhanced refractive index sensitivity by finely tailored mode dispersion that uses the light cladding etching technique.

PubMed

Chen, Xianfeng; Zhou, Kaiming; Zhang, Lin; Bennion, Ian

2007-02-01

We have experimentally investigated the mode dispersion property and refractive index sensitivity of dual-peak long-period fiber gratings (LPGs) that were sensitized by hydrofluoric acid (HF) etching. The nature of the coupled cladding modes close to the dispersion turning point makes the dual-peak LPGs ultrasensitive to cladding property, permitting a fine tailoring of the mode dispersion and index sensitivity by the light cladding etching method using HF acid of only 1% concentration. As an implementation of an optical biosensor, the etched device was used to detect the concentration of hemoglobin protein in a sugar solution, showing a sensitivity as high as 20 nm/1%.

Crystallization Kinetics of Indomethacin/Polyethylene Glycol Dispersions Containing High Drug Loadings.

PubMed

Duong, Tu Van; Van Humbeeck, Jan; Van den Mooter, Guy

2015-07-06

The reproducibility and consistency of physicochemical properties and pharmaceutical performance are major concerns during preparation of solid dispersions. The crystallization kinetics of drug/polyethylene glycol solid dispersions, an important factor that is governed by the properties of both drug and polymer has not been adequately explored, especially in systems containing high drug loadings. In this paper, by using standard and modulated differential scanning calorimetry and X-ray powder diffraction, we describe the influence of drug loading on crystallization behavior of dispersions made up of indomethacin and polyethylene glycol 6000. Higher drug loading increases the amorphicity of the polymer and inhibits the crystallization of PEG. At 52% drug loading, polyethylene glycol was completely transformed to the amorphous state. To the best of our knowledge, this is the first detailed investigation of the solubilization effect of a low molecular weight drug on a semicrystalline polymer in their dispersions. In mixtures containing up to 55% indomethacin, the dispersions exhibited distinct glass transition events resulting from amorphous-amorphous phase separation which generates polymer-rich and drug-rich domains upon the solidification of supercooled polyethylene glycol, whereas samples containing at least 60% drug showed a single amorphous phase during the period in which crystallization normally occurs. The current study demonstrates a wide range in physicochemical properties of drug/polyethylene glycol solid dispersions as a result of the complex nature in crystallization of this system, which should be taken into account during preparation and storage.

Polymer-Particle Nanocomposites: Size and Dispersion Effects

NASA Astrophysics Data System (ADS)

Moll, Joseph

Polymer-particle nanocomposites are used in industrial processes to enhance a broad range of material properties (e.g. mechanical, optical, electrical and gas permeability properties). This dissertation will focus on explanation and quantification of mechanical property improvements upon the addition of nanoparticles to polymeric materials. Nanoparticles, as enhancers of mechanical properties, are ubiquitous in synthetic and natural materials (e.g. automobile tires, packaging, bone), however, to date, there is no thorough understanding of the mechanism of their action. In this dissertation, silica (SiO2) nanoparticles, both bare and grafted with polystyrene (PS), are studied in polymeric matrices. Several variables of interest are considered, including particle dispersion state, particle size, length and density of grafted polymer chains, and volume fraction of SiO2. Polymer grafted nanoparticles behave akin to block copolymers, and this is critically leveraged to systematically vary nanoparticle dispersion and examine its role on the mechanical reinforcement in polymer based nanocomposites in the melt state. Rheology unequivocally shows that reinforcement is maximized by the formation of a transient, but long-lived, percolating polymer-particle network with the particles serving as the network junctions. The effects of dispersion and weight fraction of filler on nanocomposite mechanical properties are also studied in a bare particle system. Due to the interest in directional properties for many different materials, different means of inducing directional ordering of particle structures are also studied. Using a combination of electron microscopy and x-ray scattering, it is shown that shearing anisotropic NP assemblies (sheets or strings) causes them to orient, one in front of the other, into macroscopic two-dimensional structures along the flow direction. In contrast, no such flow-induced ordering occurs for well dispersed NPs or spherical NP aggregates! This work also addresses the interfacial, rigid polymer layer, or 'bound layer' which has long been of interest in polymer nanocomposites and polymer thin films. The divergent properties of the 'bound layer' as compared to the bulk material can have very important effects on properties, including mechanical properties. This is especially true in polymer nanocomposites, where at high weight fractions, 'bound layer' polymer can easily make up 20% or more of total material! Here we quantify this layer of bound polymer as a function of particle size, polymer molecular weight and other variables, primarily using thermogravimetric analysis but also dynamic light scattering and differential scanning calorimetry. We find that as nanoparticles become smaller, the 'bound layer' systematically decreases in thickness. This result is quite relevant to explanations of many polymer nanocomposite properties that depend on size, including mechanical and barrier properties. Many additional important and new results are reported herein. These include the importance of dispersion state in the resulting mechanical properties of polymer-particle nanocomposites, where a systematic study showed an optimal dispersion state of a connected particle network. An additional and unexpected finding in this system was the critical dependence of composite properties on grafted chain length of particles. As the grafted chain length is increased, the strain which leads to yielding in a steady shear experiment is increased in a linear relationship. At very high rates, this yielding process completely switches mechanisms, from yielding of the particle network to yielding of the entangled polymer network! A surprising correlation between the amount of bound polymer in solution and in the bulk was also found and is interpreted herein. Self-assembly was further explored in a range of different systems and it was found that grafted particles and there mimics have vast potential in the creation of a wide array of particle superstructures. In concert, these experiments provide a comprehensive picture of mechanical reinforcement in polymer-particle nanocomposites. Not only is the dispersion state of the particles crucial, but the presence of grafted chains is also so for proper reinforcement. Here many routes to ideal dispersion are detailed and the important role of grafted chains is also resolved.

Logistics of Oil Spill Dispersant Application. Volume I. Logistics-Related Properties of Oil Spill Dispersants.

DOT National Transportation Integrated Search

1982-11-01

The use of chemicals for oil spill dispersal, while not presently widespread in the U.S., would have implications for the U.S. Coast Guard's Marine Environmental Protection program. This report explores the logistics of oil disperant application by t...

DISPERSANT EFFECTIVENESS ON OIL SPILLS - IMPACT OF ENVIRONMENTAL FACTORS

EPA Science Inventory

When a dispersant is applied to an oil slick, its effectiveness in dispersing the spilled oil depends on various factors such as oil properties, wave mixing energy, temperature of both oil and water, and salinity of the water. Estuaries represent water with varying salinities. In...

Microarray Я US: a user-friendly graphical interface to Bioconductor tools that enables accurate microarray data analysis and expedites comprehensive functional analysis of microarray results.

PubMed

Dai, Yilin; Guo, Ling; Li, Meng; Chen, Yi-Bu

2012-06-08

Microarray data analysis presents a significant challenge to researchers who are unable to use the powerful Bioconductor and its numerous tools due to their lack of knowledge of R language. Among the few existing software programs that offer a graphic user interface to Bioconductor packages, none have implemented a comprehensive strategy to address the accuracy and reliability issue of microarray data analysis due to the well known probe design problems associated with many widely used microarray chips. There is also a lack of tools that would expedite the functional analysis of microarray results. We present Microarray Я US, an R-based graphical user interface that implements over a dozen popular Bioconductor packages to offer researchers a streamlined workflow for routine differential microarray expression data analysis without the need to learn R language. In order to enable a more accurate analysis and interpretation of microarray data, we incorporated the latest custom probe re-definition and re-annotation for Affymetrix and Illumina chips. A versatile microarray results output utility tool was also implemented for easy and fast generation of input files for over 20 of the most widely used functional analysis software programs. Coupled with a well-designed user interface, Microarray Я US leverages cutting edge Bioconductor packages for researchers with no knowledge in R language. It also enables a more reliable and accurate microarray data analysis and expedites downstream functional analysis of microarray results.

A dielectrophoresis-impedance method for protein detection and analysis

NASA Astrophysics Data System (ADS)

Mohamad, Ahmad Sabry; Hamzah, Roszymah; Hoettges, Kai F.; Hughes, Michael Pycraft

2017-01-01

Dielectrophoresis (DEP) has increasingly been used for the assessment of the electrical properties of molecular scale objects including proteins, DNA, nanotubes and nanowires. However, whilst techniques have been developed for the electrical characterisation of frequency-dependent DEP response, biomolecular study is usually limited to observation using fluorescent markers, limiting its applicability as a characterisation tool. In this paper we present a label-free, impedance-based method of characterisation applied to the determination of the electrical properties of colloidal protein molecules, specifically Bovine Serum Albumin (BSA). By monitoring the impedance between electrodes as proteins collect, it is shown to be possible to observe multi-dispersion behaviour. A DEP dispersion exhibited at 400 kHz is attributable to the orientational dispersion of the molecule, whilst a second, higher-frequency dispersion is attributed to a Maxwell-Wagner type dispersion; changes in behaviour with medium conductivity suggest that this is strongly influenced by the electrical double layer surrounding the molecule.

Dispersion analysis and measurement of potassium tantalate niobate crystals by broadband optical interferometers.

PubMed

Ren, Jian

2017-01-10

Electro-optic crystals, such as potassium tantalate niobate [KTa_1-xNb_xO₃(KTN)], are enabling materials for many optical devices. Their utility in broadband applications heavily depends on their dispersion property. To this end, an analysis of dispersion mismatch in broadband optical interferometers is first presented. Then a method utilizing polynomial phase fitting to measure the dispersion property of materials composing the arms of an interferometer is introduced. As a demonstration, an interferometry system based on optical coherence tomography (OCT) was built, where, for the first time, the group velocity dispersion of a KTN crystal around 1310 nm was measured and numerically compensated for OCT imaging. Several advantages over a widely used method in OCT, which is based on metric functions, are discussed. The results show the fitting method can provide a more reliable measurement with reduced computation complexity.

Optical properties of fly ash. Volume 1, Final report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Self, S.A.

1994-12-01

Research performed under this contract was divided into four tasks under the following headings: Task 1, Characterization of fly ash; Task 2, Measurements of the optical constants of slags; Task 3, Calculations of the radiant properties of fly ash dispersions; and Task 4, Measurements of the radiant properties of fly ash dispersions. Tasks 1 and 4 constituted the Ph.D. research topic of Sarbajit Ghosal, while Tasks 2 and 3 constituted the Ph.D. research topic of Jon Ebert. Together their doctoral dissertations give a complete account of the work performed. This final report, issued in two volumes consists of an executivemore » summary of the whole program followed by the dissertation of Ghosal. Volume 1 contains the dissertation of Ghosal which covers the characterization of fly ash and the measurements of the radiant properties of fly ash dispersions. A list of publications and conference presentations resulting from the work is also included.« less

Effect of TiO2 dispersion on mechanical properties of epoxy polymer

NASA Astrophysics Data System (ADS)

Singh, Sushil Kumar; Singh, Samarjit; Kohli, Raunak; Jain, Anuj; Kumar, Abhishek

2016-05-01

This study is focused to assess reinforcing effects of TiO2 particles on the mechanical properties of epoxy resins, particularly with regards to fracture and toughening mechanisms. An experimental study has been carried out on series of composites containing varying amount of micro size titanium dioxide (TiO2) up to 8 wt.%. The particles were dispersed via mixing with mechanical stirrer at 1000 rpm for 2 hours to ensure a well-dispersed phase of the particles. The epoxy resin with the dispersed particle has been cured with hardener at 40 °C for 16 hours. Test reveals improvement in up to 4 wt.% of the particles and decrease in the mechanical properties beyond 4 wt. %. This may be attributed to the significant increase in clustering and settlement of the particles during long curing time. The tensile strength increases by 32 % and fracture toughness (K1C) by 44.95 % and the fracture energy (G1C) by 150.29 % with particle loading of 4 wt. % TiO2.

Dynamic properties of molecular motors in burnt-bridge models

NASA Astrophysics Data System (ADS)

Artyomov, Maxim N.; Morozov, Alexander Yu; Pronina, Ekaterina; Kolomeisky, Anatoly B.

2007-08-01

Dynamic properties of molecular motors that fuel their motion by actively interacting with underlying molecular tracks are studied theoretically via discrete-state stochastic 'burnt-bridge' models. The transport of the particles is viewed as an effective diffusion along one-dimensional lattices with periodically distributed weak links. When an unbiased random walker passes the weak link it can be destroyed ('burned') with probability p, providing a bias in the motion of the molecular motor. We present a theoretical approach that allows one to calculate exactly all dynamic properties of motor proteins, such as velocity and dispersion, under general conditions. It is found that dispersion is a decreasing function of the concentration of bridges, while the dependence of dispersion on the burning probability is more complex. Our calculations also show a gap in dispersion for very low concentrations of weak links or for very low burning probabilities which indicates a dynamic phase transition between unbiased and biased diffusion regimes. Theoretical findings are supported by Monte Carlo computer simulations.

Structure, Nanomechanics and Dynamics of Dispersed Surfactant-Free Clay Nanocomposite Films

NASA Astrophysics Data System (ADS)

Zhang, Xiao; Zhao, Jing; Snyder, Chad; Karim, Alamgir; National Institute of Standards; Technology Collaboration

Natural Montmorillonite particles were dispersed as tactoids in thin films of polycaprolactone (PCL) through a flow coating technique assisted by ultra-sonication. Wide angle X-ray scattering (WAXS), Grazing-incidence wide angle X-ray scattering (GI-WAXS), and transmission electron microscopy (TEM) were used to confirm the level of dispersion. These characterization techniques are in conjunction with its nanomechanical properties via strain-induced buckling instability for modulus measurements (SIEBIMM), a high throughput technique to characterize thin film mechanical properties. The linear strengthening trend of the elastic modulus enhancements was fitted with Halpin-Tsai (HT) model, correlating the nanoparticle geometric effects and mechanical behaviors based on continuum theories. The overall aspect ratio of dispersed tactoids obtained through HT model fitting is in reasonable agreement with digital electron microscope image analysis. Moreover, glass transition behaviors of the composites were characterized using broadband dielectric relaxation spectroscopy. The segmental relaxation behaviors indicate that the associated mechanical property changes are due to the continuum filler effect rather than the interfacial confinement effect.

General relationships between ultrasonic attenuation and dispersion

NASA Technical Reports Server (NTRS)

Odonnell, M.; Jaynes, E. T.; Miller, J. G.

1978-01-01

General relationships between the ultrasonic attenuation and dispersion are presented. The validity of these nonlocal relationships hinges only on the properties of causality and linearity, and does not depend upon details of the mechanism responsible for the attenuation and dispersion. Approximate, nearly local relationships are presented and are demonstrated to predict accurately the ultrasonic dispersion in solutions of hemoglobin from the results of attenuation measurements.

An efficient pseudomedian filter for tiling microrrays.

PubMed

Royce, Thomas E; Carriero, Nicholas J; Gerstein, Mark B

2007-06-07

Tiling microarrays are becoming an essential technology in the functional genomics toolbox. They have been applied to the tasks of novel transcript identification, elucidation of transcription factor binding sites, detection of methylated DNA and several other applications in several model organisms. These experiments are being conducted at increasingly finer resolutions as the microarray technology enjoys increasingly greater feature densities. The increased densities naturally lead to increased data analysis requirements. Specifically, the most widely employed algorithm for tiling array analysis involves smoothing observed signals by computing pseudomedians within sliding windows, a O(n2logn) calculation in each window. This poor time complexity is an issue for tiling array analysis and could prove to be a real bottleneck as tiling microarray experiments become grander in scope and finer in resolution. We therefore implemented Monahan's HLQEST algorithm that reduces the runtime complexity for computing the pseudomedian of n numbers to O(nlogn) from O(n2logn). For a representative tiling microarray dataset, this modification reduced the smoothing procedure's runtime by nearly 90%. We then leveraged the fact that elements within sliding windows remain largely unchanged in overlapping windows (as one slides across genomic space) to further reduce computation by an additional 43%. This was achieved by the application of skip lists to maintaining a sorted list of values from window to window. This sorted list could be maintained with simple O(log n) inserts and deletes. We illustrate the favorable scaling properties of our algorithms with both time complexity analysis and benchmarking on synthetic datasets. Tiling microarray analyses that rely upon a sliding window pseudomedian calculation can require many hours of computation. We have eased this requirement significantly by implementing efficient algorithms that scale well with genomic feature density. This result not only speeds the current standard analyses, but also makes possible ones where many iterations of the filter may be required, such as might be required in a bootstrap or parameter estimation setting. Source code and executables are available at http://tiling.gersteinlab.org/pseudomedian/.

An efficient pseudomedian filter for tiling microrrays

PubMed Central

Royce, Thomas E; Carriero, Nicholas J; Gerstein, Mark B

2007-01-01

Background Tiling microarrays are becoming an essential technology in the functional genomics toolbox. They have been applied to the tasks of novel transcript identification, elucidation of transcription factor binding sites, detection of methylated DNA and several other applications in several model organisms. These experiments are being conducted at increasingly finer resolutions as the microarray technology enjoys increasingly greater feature densities. The increased densities naturally lead to increased data analysis requirements. Specifically, the most widely employed algorithm for tiling array analysis involves smoothing observed signals by computing pseudomedians within sliding windows, a O(n2logn) calculation in each window. This poor time complexity is an issue for tiling array analysis and could prove to be a real bottleneck as tiling microarray experiments become grander in scope and finer in resolution. Results We therefore implemented Monahan's HLQEST algorithm that reduces the runtime complexity for computing the pseudomedian of n numbers to O(nlogn) from O(n2logn). For a representative tiling microarray dataset, this modification reduced the smoothing procedure's runtime by nearly 90%. We then leveraged the fact that elements within sliding windows remain largely unchanged in overlapping windows (as one slides across genomic space) to further reduce computation by an additional 43%. This was achieved by the application of skip lists to maintaining a sorted list of values from window to window. This sorted list could be maintained with simple O(log n) inserts and deletes. We illustrate the favorable scaling properties of our algorithms with both time complexity analysis and benchmarking on synthetic datasets. Conclusion Tiling microarray analyses that rely upon a sliding window pseudomedian calculation can require many hours of computation. We have eased this requirement significantly by implementing efficient algorithms that scale well with genomic feature density. This result not only speeds the current standard analyses, but also makes possible ones where many iterations of the filter may be required, such as might be required in a bootstrap or parameter estimation setting. Source code and executables are available at . PMID:17555595

Optical Properties of Nanocellulose Dispersions in Water, Dimethylformamide and Poly(Methyl Methacrylate)

DTIC Science & Technology

2013-10-01

measurements for cellulose and PMMA thin- films . ..13  v List of Tables Table 1. Recorded optical data for nanocellulose in water...applications beyond thin films . In particular, the effects of nanocellulose fibers in higher concentrations, processed in different solvents, and...Optical Properties of Nanocellulose Dispersions in Water, Dimethylformamide and Poly(Methyl Methacrylate) by James F. Snyder, Joshua Steele

MGDB: crossing the marker genes of a user microarray with a database of public-microarrays marker genes.

PubMed

Huerta, Mario; Munyi, Marc; Expósito, David; Querol, Enric; Cedano, Juan

2014-06-15

The microarrays performed by scientific teams grow exponentially. These microarray data could be useful for researchers around the world, but unfortunately they are underused. To fully exploit these data, it is necessary (i) to extract these data from a repository of the high-throughput gene expression data like Gene Expression Omnibus (GEO) and (ii) to make the data from different microarrays comparable with tools easy to use for scientists. We have developed these two solutions in our server, implementing a database of microarray marker genes (Marker Genes Data Base). This database contains the marker genes of all GEO microarray datasets and it is updated monthly with the new microarrays from GEO. Thus, researchers can see whether the marker genes of their microarray are marker genes in other microarrays in the database, expanding the analysis of their microarray to the rest of the public microarrays. This solution helps not only to corroborate the conclusions regarding a researcher's microarray but also to identify the phenotype of different subsets of individuals under investigation, to frame the results with microarray experiments from other species, pathologies or tissues, to search for drugs that promote the transition between the studied phenotypes, to detect undesirable side effects of the treatment applied, etc. Thus, the researcher can quickly add relevant information to his/her studies from all of the previous analyses performed in other studies as long as they have been deposited in public repositories. Marker-gene database tool: http://ibb.uab.es/mgdb © The Author 2014. Published by Oxford University Press.

Geometrical optimization of the transmission and dispersion properties of arrayed waveguide gratings using two stigmatic point mountings.

PubMed

Muñoz, P; Pastor, D; Capmany, J; Martínez, A

2003-09-22

In this paper, the procedure to optimize flat-top Arrayed Waveguide Grating (AWG) devices in terms of transmission and dispersion properties is presented. The systematic procedure consists on the stigmatization and minimization of the Light Path Function (LPF) used in classic planar spectrograph theory. The resulting geometry arrangement for the Arrayed Waveguides (AW) and the Output Waveguides (OW) is not the classical Rowland mounting, but an arbitrary geometry arrangement. Simulation using previous published enhanced modeling show how this geometry reduces the passband ripple, asymmetry and dispersion, in a design example.

Detecting novel genes with sparse arrays

PubMed Central

Haiminen, Niina; Smit, Bart; Rautio, Jari; Vitikainen, Marika; Wiebe, Marilyn; Martinez, Diego; Chee, Christine; Kunkel, Joe; Sanchez, Charles; Nelson, Mary Anne; Pakula, Tiina; Saloheimo, Markku; Penttilä, Merja; Kivioja, Teemu

2014-01-01

Species-specific genes play an important role in defining the phenotype of an organism. However, current gene prediction methods can only efficiently find genes that share features such as sequence similarity or general sequence characteristics with previously known genes. Novel sequencing methods and tiling arrays can be used to find genes without prior information and they have demonstrated that novel genes can still be found from extensively studied model organisms. Unfortunately, these methods are expensive and thus are not easily applicable, e.g., to finding genes that are expressed only in very specific conditions. We demonstrate a method for finding novel genes with sparse arrays, applying it on the 33.9 Mb genome of the filamentous fungus Trichoderma reesei. Our computational method does not require normalisations between arrays and it takes into account the multiple-testing problem typical for analysis of microarray data. In contrast to tiling arrays, that use overlapping probes, only one 25mer microarray oligonucleotide probe was used for every 100 b. Thus, only relatively little space on a microarray slide was required to cover the intergenic regions of a genome. The analysis was done as a by-product of a conventional microarray experiment with no additional costs. We found at least 23 good candidates for novel transcripts that could code for proteins and all of which were expressed at high levels. Candidate genes were found to neighbour ire1 and cre1 and many other regulatory genes. Our simple, low-cost method can easily be applied to finding novel species-specific genes without prior knowledge of their sequence properties. PMID:20691772

2008 Microarray Research Group (MARG Survey): Sensing the State of Microarray Technology

EPA Science Inventory

Over the past several years, the field of microarrays has grown and evolved drastically. In its continued efforts to track this evolution and transformation, the ABRF-MARG has once again conducted a survey of international microarray facilities and individual microarray users. Th...

Effects of La2O3 content and particle size on the long-term stability and thermal cycling property of La2O3-dispersed SUS430 alloys for SOFC interconnect materials

NASA Astrophysics Data System (ADS)

Lee, Jung-Won; Mehran, Muhammad Taqi; Song, Rak-Hyun; Lee, Seung-Bok; Lee, Jong-Won; Lim, Tak-Hyoung; Park, Seok-Joo; Hong, Jong-Eun; Shim, Joon-Hyung

2017-11-01

We developed oxide-dispersed alloys as interconnect materials for a solid oxide fuel cell by adding La2O3 to SUS430 ferritic steels. For this purpose, we prepared two types of La2O3 with different particle sizes and added different amounts of La2O3 to SUS430 powder. Then, we mixed the powders using a high energy ball mill, so that nano-sized as well as micro-sized oxide particles were able to mix uniformly with the SUS430 powders. After preparing hexahedral green samples using uni-axial and cold isostatic presses, we were finally able to obtain oxide-dispersed alloys having high relative densities after firing at 1,400 °C under hydrogen atmosphere. The nano-sized La2O3 dispersed alloys showed properties superior to those of micro-sized dispersed alloys in terms of long-term stability and thermal cycling. Moreover, we determined the optimum amounts of added La2O3. Finally we were able to develop a new oxide-dispersed alloy showing excellent properties of low area specific resistance (16.23 mΩ cm2) after 1000 h at 800 °C, and no degradation after 10 iterations of thermal cycling under oxidizing atmosphere.

Nanomechanics of cellulose crystals and cellulose-based polymer composites

NASA Astrophysics Data System (ADS)

Pakzad, Anahita

Cellulose-polymer composites have potential applications in aerospace and transportation areas where lightweight materials with high mechanical properties are needed. In addition, these economical and biodegradable composites have been shown to be useful as polymer electrolytes, packaging structures, optoelectronic devices, and medical implants such as wound dressing and bone scaffolds. In spite of the above mentioned advantages and potential applications, due to the difficulties associated with synthesis and processing techniques, application of cellulose crystals (micro and nano sized) for preparation of new composite systems is limited. Cellulose is hydrophilic and polar as opposed to most of common thermoplastics, which are non-polar. This results in complications in addition of cellulose crystals to polymer matrices, and as a result in achieving sufficient dispersion levels, which directly affects the mechanical properties of the composites. As in other composite materials, the properties of cellulose-polymer composites depend on the volume fraction and the properties of individual phases (the reinforcement and the polymer matrix), the dispersion quality of the reinforcement through the matrix and the interaction between CNCs themselves and CNC and the matrix (interphase). In order to develop economical cellulose-polymer composites with superior qualities, the properties of individual cellulose crystals, as well as the effect of dispersion of reinforcements and the interphase on the properties of the final composites should be understood. In this research, the mechanical properties of CNC polymer composites were characterized at the macro and nano scales. A direct correlation was made between: - Dispersion quality and macro-mechanical properties - Nanomechanical properties at the surface and tensile properties - CNC diameter and interphase thickness. Lastly, individual CNCs from different sources were characterized and for the first time size-scale effect on their nanomechanical properties were reported. Then the effect of CNC surface modification on the mechanical properties was studied and correlated to the crystalline structure of these materials.

THE ABRF-MARG MICROARRAY SURVEY 2004: TAKING THE PULSE OF THE MICROARRAY FIELD

EPA Science Inventory

Over the past several years, the field of microarrays has grown and evolved drastically. In its continued efforts to track this evolution, the ABRF-MARG has once again conducted a survey of international microarray facilities and individual microarray users. The goal of the surve...

Contributions to Statistical Problems Related to Microarray Data

ERIC Educational Resources Information Center

Hong, Feng

2009-01-01

Microarray is a high throughput technology to measure the gene expression. Analysis of microarray data brings many interesting and challenging problems. This thesis consists three studies related to microarray data. First, we propose a Bayesian model for microarray data and use Bayes Factors to identify differentially expressed genes. Second, we…

Parallel, confocal, and complete spectrum imager for fluorescent detection of high-density microarray

NASA Astrophysics Data System (ADS)

Bogdanov, Valery L.; Boyce-Jacino, Michael

1999-05-01

Confined arrays of biochemical probes deposited on a solid support surface (analytical microarray or 'chip') provide an opportunity to analysis multiple reactions simultaneously. Microarrays are increasingly used in genetics, medicine and environment scanning as research and analytical instruments. A power of microarray technology comes from its parallelism which grows with array miniaturization, minimization of reagent volume per reaction site and reaction multiplexing. An optical detector of microarray signals should combine high sensitivity, spatial and spectral resolution. Additionally, low-cost and a high processing rate are needed to transfer microarray technology into biomedical practice. We designed an imager that provides confocal and complete spectrum detection of entire fluorescently-labeled microarray in parallel. Imager uses microlens array, non-slit spectral decomposer, and high- sensitive detector (cooled CCD). Two imaging channels provide a simultaneous detection of localization, integrated and spectral intensities for each reaction site in microarray. A dimensional matching between microarray and imager's optics eliminates all in moving parts in instrumentation, enabling highly informative, fast and low-cost microarray detection. We report theory of confocal hyperspectral imaging with microlenses array and experimental data for implementation of developed imager to detect fluorescently labeled microarray with a density approximately 103 sites per cm2.

Interference between wave modes may contribute to the apparent negative dispersion observed in cancellous bone

PubMed Central

Anderson, Christian C.; Marutyan, Karen R.; Holland, Mark R.; Wear, Keith A.; Miller, James G.

2008-01-01

Previous work has shown that ultrasonic waves propagating through cancellous bone often exhibit a linear-with-frequency attenuation coefficient, but a decrease in phase velocity with frequency (negative dispersion) that is inconsistent with the causality-imposed Kramers–Kronig relations. In the current study, interfering wave modes similar to those observed in bone are shown to potentially contribute to the observed negative dispersion. Biot theory, the modified Biot–Attenborogh model, and experimental results are used to aid in simulating multiple-mode wave propagation through cancellous bone. Simulations entail constructing individual wave modes exhibiting a positive dispersion using plausible velocities and amplitudes, and then summing the individual modes to create mixed-mode output wave forms. Results of the simulations indicate that mixed-mode wave forms can exhibit negative dispersion when analyzed conventionally under the assumption that only one wave is present, even when the individual interfering waves exhibit positive dispersions in accordance with the Kramers–Kronig relations. Furthermore, negative dispersion is observed when little or no visual evidence of interference exists in the time-domain data. Understanding the mechanisms responsible for the observed negative dispersion could aid in determining the true material properties of cancellous bone, as opposed to the apparent properties measured using conventional data analysis techniques. PMID:19045668

Dispersive shock waves and modulation theory

NASA Astrophysics Data System (ADS)

El, G. A.; Hoefer, M. A.

2016-10-01

There is growing physical and mathematical interest in the hydrodynamics of dissipationless/dispersive media. Since G.B. Whitham's seminal publication fifty years ago that ushered in the mathematical study of dispersive hydrodynamics, there has been a significant body of work in this area. However, there has been no comprehensive survey of the field of dispersive hydrodynamics. Utilizing Whitham's averaging theory as the primary mathematical tool, we review the rich mathematical developments over the past fifty years with an emphasis on physical applications. The fundamental, large scale, coherent excitation in dispersive hydrodynamic systems is an expanding, oscillatory dispersive shock wave or DSW. Both the macroscopic and microscopic properties of DSWs are analyzed in detail within the context of the universal, integrable, and foundational models for uni-directional (Korteweg-de Vries equation) and bi-directional (Nonlinear Schrödinger equation) dispersive hydrodynamics. A DSW fitting procedure that does not rely upon integrable structure yet reveals important macroscopic DSW properties is described. DSW theory is then applied to a number of physical applications: superfluids, nonlinear optics, geophysics, and fluid dynamics. Finally, we survey some of the more recent developments including non-classical DSWs, DSW interactions, DSWs in perturbed and inhomogeneous environments, and two-dimensional, oblique DSWs.

Physiochemical Characterization and Release Rate Studies of SolidDispersions of Ketoconazole with Pluronic F127 and PVP K-30

PubMed Central

Kumar, Pankaj; Mohan, Chander; KanamSrinivasan Uma Shankar, Mara; Gulati, Monica

2011-01-01

In the present study solid dispersions of the antifungal drug Ketoconazole were prepared with Pluronic F-127 and PVP K-30 with an intention to improve its dissolution properties. Investigations of the properties of the dispersions were performed using release studies, Differential scanning calorimetery (DSC), X-ray powder diffraction (XRD) and Fourier transform infrared (FTIR). The results obtained showed that the rate of dissolution of Ketoconazole was considerably improved when formulated in solid dispersions with PVP K-30 and Pluronic F-127 as compared with pure drug and physical mixtures. The results from DSC and XRD studies showed the transition of crystalline nature of drug to amorphous form, while FTIR studies demonstrated the absence of drug-carriers interaction. PMID:24250403

1300 K compressive properties of several dispersion strengthened NiAl materials

NASA Technical Reports Server (NTRS)

Whittenberger, J. Daniel; Gaydosh, D. J.; Kumar, K. S.

1990-01-01

To examine the potential of rapid solidification technology (RST) as a means to fabricate dispersion-strengthened aluminides, cylindrical compression samples were machined from the gauge section of their tensile specimens and tested in air at 1300 K. While microscopy indicates that RST can produce fine dispersions of TiB2, TiC and HfC in a NiAl matrix, the mechanical property data reveal that only HfC successfully strengthens the intermetallic matrix. The high stress exponents (above 10) and/or independence of strain rate on stress for NiAl-HfC materials suggest elevated temperature mechanical behavior similar to that found in oxide dispersion-strengthened alloys. Furthermore, an apparent example of departure side pinning has been observed, and as such, it is indicative of a threshold stress for creep.

Impact of ultrasonic assisted triangular lattice like arranged dispersion of nanoparticles on physical and mechanical properties of epoxy-TiO2 nanocomposites.

PubMed

Goyat, M S; Ghosh, P K

2018-04-01

Emerging ex-situ technique, ultrasonic dual mixing (UDM) offers unique and hitherto unapproachable opportunities to alter the physical and mechanical properties of polymer nanocomposites. In this study, triangular lattice-like arranged dispersion of TiO 2 nanoparticles (average size ∼ 48 nm) in the epoxy polymer has been attained via concurrent use of a probe ultra-sonicator and 4 blades pitched impeller which collectively named as UDM technique. The UDM processing of neat epoxy reveals the generation of triangular lattice-like arranged nanocavities with nanoscale inter-cavity spacing. The UDM processing of epoxy-TiO 2 nanocomposites reveals two unique features such as partial and complete entrapping of the nanoparticles by the nanocavities leading the arranged dispersion of particles in the epoxy matrix. Pristine TiO 2 nanoparticles were dispersed in the epoxy polymer at loading fractions of up to 20% by weight. The results display that the arranged dispersion of nanoparticles is very effective at enhancing the glass transition temperature (T g ) and tensile properties of the epoxy at loading fractions of 10 wt%. We quantify a direct relationship among three important parameters such as nanoparticle content, cluster size, and inter-particle spacing. Our results offer a novel understanding of these parameters on the T g and tensile properties of the epoxy nanocomposites. The tensile fracture surfaces revealed several toughening mechanisms such as particle pull-out, plastic void growth, crack deflection, crack bridging and plastic deformation. We show that a strong nanoparticle-matrix interface led to the enhanced mechanical properties due to leading toughening mechanisms such as crack deflection, plastic deformation and particle pull-out. We showed that the UDM has an inordinate prospective to alter the dispersion state of nanoparticles in viscous polymer matrices. Copyright © 2017 Elsevier B.V. All rights reserved.

Rheological and interfacial properties at the equilibrium of almond gum tree exudate (Prunus dulcis) in comparison with gum arabic.

PubMed

Mahfoudhi, Nesrine; Sessa, Mariarenata; Ferrari, Giovanna; Hamdi, Salem; Donsi, Francesco

2016-06-01

Almond gum contains an arabinogalactan-type polysaccharide, which plays an important role in defining its interfacial and rheological properties. In this study, rheological and interfacial properties of almond gum and gum arabic aqueous dispersions were comparatively investigated. The interfacial tension of almond gum and gum arabic aqueous dispersions was measured using the pendant drop method in hexadecane. The asymptotic interfacial tension values for almond gum were significantly lower than the corresponding values measured for gum arabic, especially at high concentration. Rheological properties were characterized by steady and oscillatory tests using a coaxial geometry. Almond gum flow curves exhibited a shear thinning non-Newtonian behavior with a tendency to a Newtonian plateau at low shear rate, while gum arabic flow curves exhibited such behavior only at high shear rate. The influence of temperature (5-50  ℃) on the flow curves was studied at 4% (m/m) gum concentration and the Newtonian viscosities at infinite and at zero shear rate, for gum arabic and almond gum, respectively, were accurately fitted by an Arrhenius-type equation. The dynamic properties of the two gum dispersions were also studied. Both gum dispersions exhibited viscoelastic properties, with the viscous component being predominant in a wider range of concentrations for almond gum, while for gum arabic the elastic component being higher than the elastic one especially at higher concentrations.The rheological and interfacial tension properties of almond gum suggest that it may represent a possible substitute of gum arabic in different food applications. © The Author(s) 2015.

Chemiluminescence microarrays in analytical chemistry: a critical review.

PubMed

Seidel, Michael; Niessner, Reinhard

2014-09-01

Multi-analyte immunoassays on microarrays and on multiplex DNA microarrays have been described for quantitative analysis of small organic molecules (e.g., antibiotics, drugs of abuse, small molecule toxins), proteins (e.g., antibodies or protein toxins), and microorganisms, viruses, and eukaryotic cells. In analytical chemistry, multi-analyte detection by use of analytical microarrays has become an innovative research topic because of the possibility of generating several sets of quantitative data for different analyte classes in a short time. Chemiluminescence (CL) microarrays are powerful tools for rapid multiplex analysis of complex matrices. A wide range of applications for CL microarrays is described in the literature dealing with analytical microarrays. The motivation for this review is to summarize the current state of CL-based analytical microarrays. Combining analysis of different compound classes on CL microarrays reduces analysis time, cost of reagents, and use of laboratory space. Applications are discussed, with examples from food safety, water safety, environmental monitoring, diagnostics, forensics, toxicology, and biosecurity. The potential and limitations of research on multiplex analysis by use of CL microarrays are discussed in this review.

Foray search: an effective systematic dispersal strategy in fragmented landscapes

Treesearch

L. Conradt; P.A. Zollner; T.J. Roper; C.D. Thomas

2003-01-01

In the absence of evidence to the contrary, population models generally assume that the dispersal trajectories of animals are random, but systematic dispersal could be more efficient at detecting new habitat and may therefore constitute a more realistic assumption. Here, we investigate, by means of simulations, the properties of a potentially widespread systematic...

Silicone-containing aqueous polymer dispersions with hybrid particle structure.

PubMed

Kozakiewicz, Janusz; Ofat, Izabela; Trzaskowska, Joanna

2015-09-01

In this paper the synthesis, characterization and application of silicone-containing aqueous polymer dispersions (APD) with hybrid particle structure are reviewed based on available literature data. Advantages of synthesis of dispersions with hybrid particle structure over blending of individual dispersions are pointed out. Three main processes leading to silicone-containing hybrid APD are identified and described in detail: (1) emulsion polymerization of organic unsaturated monomers in aqueous dispersions of silicone polymers or copolymers, (2) emulsion copolymerization of unsaturated organic monomers with alkoxysilanes or polysiloxanes with unsaturated functionality and (3) emulsion polymerization of alkoxysilanes (in particular with unsaturated functionality) and/or cyclic siloxanes in organic polymer dispersions. The effect of various factors on the properties of such hybrid APD and films as well as on hybrid particles composition and morphology is presented. It is shown that core-shell morphology where silicones constitute either the core or the shell is predominant in hybrid particles. Main applications of silicone-containing hybrid APD and related hybrid particles are reviewed including (1) coatings which show specific surface properties such as enhanced water repellency or antisoiling or antigraffiti properties due to migration of silicone to the surface, and (2) impact modifiers for thermoplastics and thermosets. Other processes in which silicone-containing particles with hybrid structure can be obtained (miniemulsion polymerization, polymerization in non-aqueous media, hybridization of organic polymer and polysiloxane, emulsion polymerization of silicone monomers in silicone polymer dispersions and physical methods) are also discussed. Prospects for further developments in the area of silicone-containing hybrid APD and related hybrid particles are presented. Copyright © 2015. Published by Elsevier B.V.

High-efficiency surfactant prepared from phenolic resin for multi-walled carbon nanotube aqueous suspension

NASA Astrophysics Data System (ADS)

Li, Yutong; Wei, Haixu; Li, Lizhi; Wang, Jie; Qian, Xin; He, Liu; Wang, Xuefei; Ouyang, Qin; Chen, Yousi; Zhang, Yonggang; Li, Yong

2018-06-01

Carbon nanotubes (CNTs) have been widely exploited to be used in many fields due to its perfect mechanical properties, but CNT agglomerates severely prevent CNTs' excellent properties from performing. Many dispersants were synthesized to resolve the difficulty reported in recent years. In this paper, a healthier and cheaper dispersant with phenolic resin as original reagent was synthesized (denoted as AEP-4). Fourier transform infrared spectroscopy, nuclear magnetic resonance, and mass spectra were carried out to characterize chemical structure of reagent and products. Ultraviolet-visible spectroscopy and transmission electron microscopy were employed to evaluate the dispersibility of multi-walled carbon nanotubes (MWCNTs) in aqueous solution. The results showed that AEP-4 containing tertiary ammonium cations exhibited strong ability to disperse MWCNTs in aqueous solution, which showed better dispersion ability than sodium dodecyl benzene sulfonate. The scanning electron microscope results of MWCNT/carbon fiber reinforcements showed that many single MWCNTs showed up and uniformly covered carbon fiber surface in the case of carbon fiber treated by MWCNT/AEP-4 suspension, which reflected that MWCNT suspension with AEP-4 had good dispersion.

Thermal properties for the thermal-hydraulics analyses of the BR2 maximum nominal heat flux.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dionne, B.; Kim, Y. S.; Hofman, G. L.

2011-05-23

This memo describes the assumptions and references used in determining the thermal properties for the various materials used in the BR2 HEU (93% enriched in {sup 235}U) to LEU (19.75% enriched in {sup 235}U) conversion feasibility analysis. More specifically, this memo focuses on the materials contained within the pressure vessel (PV), i.e., the materials that are most relevant to the study of impact of the change of fuel from HEU to LEU. This section is regrouping all of the thermal property tables. Section 2 provides a summary of the thermal properties in form of tables while the following sections presentmore » the justification of these values. Section 3 presents a brief background on the approach used to evaluate the thermal properties of the dispersion fuel meat and specific heat capacity. Sections 4 to 7 discuss the material properties for the following materials: (i) aluminum, (ii) dispersion fuel meat (UAlx-Al and U-7Mo-Al), (iii) beryllium, and (iv) stainless steel. Section 8 discusses the impact of irradiation on material properties. Section 9 summarizes the material properties for typical operating temperatures. Appendix A elaborates on how to calculate dispersed phase's volume fraction. Appendix B shows the evolution of the BR2 maximum heat flux with burnup.« less

Analysis of High-Throughput ELISA Microarray Data

DOE Office of Scientific and Technical Information (OSTI.GOV)

White, Amanda M.; Daly, Don S.; Zangar, Richard C.

Our research group develops analytical methods and software for the high-throughput analysis of quantitative enzyme-linked immunosorbent assay (ELISA) microarrays. ELISA microarrays differ from DNA microarrays in several fundamental aspects and most algorithms for analysis of DNA microarray data are not applicable to ELISA microarrays. In this review, we provide an overview of the steps involved in ELISA microarray data analysis and how the statistically sound algorithms we have developed provide an integrated software suite to address the needs of each data-processing step. The algorithms discussed are available in a set of open-source software tools (http://www.pnl.gov/statistics/ProMAT).

Thermophysical and tribological properties of nanolubricants: A review

NASA Astrophysics Data System (ADS)

Kotia, Ankit; Rajkhowa, Pranami; Rao, Gogineni Satyanarayana; Ghosh, Subrata Kumar

2018-05-01

Recent studies in heat transfer evident that the nanofluid shows better heat transfer results as compared to base fluid. This influences the research community for the dispersion of nanoparticles in lubricants to enhance its thermophysical and tribological properties and these suspensions are termed as Nanolubricants. This review focuses on the effect of nanoparticle additives on thermophysical and tribological properties of base lubricant. Initial section briefly summarizes the variation in thermophysical properties namely viscosity, thermal conductivity, density and specific heat of nanolubricants. In later section, the coefficient of friction and anti-wear properties of nanolubricants are summarized. This review along with the replenishment of current knowledge, also discusses the fundamental mechanisms that evolve with the dispersion of nanoparticles.

Effect of combination ultrasonic and ball milling techniques of commercial fillers dispersion on mechanical properties of natural rubber (NR) latex films

NASA Astrophysics Data System (ADS)

Hamran, Noramirah; Rashid, Azura A.

2017-07-01

Commercial fillers such as silica and carbon black generally impart the reinforcing effects in dry rubber compound, but have an adverse effect on Natural rubber (NR) latex compounds. The addition of commercial fillers in NR latex has reduced the mechanical properties of NR latex films due to the destabilization effect in the NR latex compounds which govern by the dispersion quality, particle size and also the pH of the dispersion itself. The ball milling process is the conventional meth od of preparation of dispersions and ultrasonic has successfully used in preparation of nano fillers such as carbon nanotube (CNT). In this study the combination between the conventional methods; ball milling together the ultrasonic method were used to prepare the silica and carbon black dispersions. The different duration of ball milling (24, 48 and 72 hours) was compared with the ultrasonic method (30, 60, 90 and 120 minutes). The combination of ball milling and ultrasonic from the optimum individual technique was used to investigate the reduction of particle size of the fillers. The particle size analyzer, transmission electron microscopy (TEM) and scanning electron microscopy (SEM) test were carried out to investigate the obtained particle size and the tensile and tear test were carried out to investigate the mechanical properties of the NR latex films. The reduction of filler particle size is expected to impart the properties of NR latex films.

Effects of carbon nanotube (CNT) dispersion and interface condition on thermo-mechanical behavior of CNT-reinforced vinyl ester

NASA Astrophysics Data System (ADS)

Sabet, Seyed Morteza

In fabrication of nanoparticle-reinforced polymers, two critical factors need to be taken into account to control properties of the final product; nanoparticle dispersion/distribution in the matrix; and interfacial interactions between nanoparticles and their surrounding matrix. The focus of this thesis was to examine the role of these two factors through experimental methodologies and molecular-level simulations. Carbon nanotubes (CNTs) and vinyl ester (VE) resin were used as nanoparticles and matrix, respectively. In a parametric study, a series of CNT/VE nanocomposites with different CNT dispersion conditions were fabricated using the ultrasonication mixing method. Thermomechanical properties of nanocomposites and quality of CNT dispersion were evaluated. By correlation between nanocomposite behavior and CNT dispersion, a thermomechanical model was suggested; at a certain threshold level of sonication energy, CNT dispersion would be optimal and result in maximum enhancement in properties. This threshold energy level is also related to particle concentration. Sonication above this threshold level, leads to destruction of nanotubes and renders a negative effect on the properties of nanocomposites. In an attempt to examine the interface condition, a novel process was developed to modify CNT surface with polyhedral oligomeric silsesquioxane (POSS). In this process, a chemical reaction was allowed to occur between CNTs and POSS in the presence of an effective catalyst. The functionalized CNTs were characterized using TEM, SEM-EDS, AFM, TGA, FTIR and Raman spectroscopy techniques. Formation of amide bonds between POSS and nanotubes was established and verified. Surface modification of CNTs with POSS resulted in significant improvement in nanotube dispersion. In-depth SEM analysis revealed formation of a 3D network of well-dispersed CNTs with POSS connections to the polymer. In parallel, molecular dynamics simulation of CNT-POSS/VE system showed an effective load transfer from polymer chains to the CNT due to POSS linkages at the interface. The rigid and flexible network of CNTs is found to be responsible for enhancement in elastic modulus, strength, fracture toughness and glass transition temperature (Tg) of the final nanocomposites.

Microbial community analysis of an Alabama coastal salt marsh impacted by the Deepwater Horizon Oil Spill

NASA Astrophysics Data System (ADS)

Beazley, M. J.; Martinez, R.; Rajan, S.; Powell, J.; Piceno, Y.; Tom, L.; Andersen, G. L.; Hazen, T. C.; Van Nostrand, J. D.; Zhou, J.; Mortazavi, B.; Sobecky, P. A.

2011-12-01

Microbial community responses of an Alabama coastal salt marsh environment to the Deepwater Horizon oil spill were studied by 16S rRNA (PhyloChip) and functional gene (GeoChip) microarray-based analysis. Oil and tar balls associated with the oil spill arrived along the Alabama coast in June 2010. Marsh and inlet sediment samples collected in June, July, and September 2010 from a salt marsh ecosystem at Point Aux Pines Alabama were analyzed to determine if bacterial community structure changed as a result of oil perturbation. Sediment total petroleum hydrocarbon (TPH) concentrations ranged from below detection to 189 mg kg-1 and were randomly dispersed throughout the salt marsh sediments. Total DNA extracted from sediment and particulates were used for PhyloChip and GeoChip hybridization. A total of 4000 to 8000 operational taxonomic units (OTUs) were detected in marsh and inlet samples. Distinctive changes in the number of detectable OTUs were observed between June, July, and September 2010. Surficial inlet sediments demonstrated a significant increase in the total number of OTUs between June and September that correlated with TPH concentrations. The most significant increases in bacterial abundance were observed in the phyla Actinobacteria, Firmicutes, Gemmatimonadetes, Proteobacteria, and Verrucomicrobia. Bacterial richness in marsh sediments also correlated with TPH concentrations with significant changes primarily in Acidobacteria, Actinobacteria, Firmicutes, Fusobacteria, Nitrospirae, and Proteobacteria. GeoChip microarray analysis detected 5000 to 8300 functional genes in marsh and inlet samples. Surficial inlet sediments demonstrated distinctive increases in the number of detectable genes and gene signal intensities in July samples compared to June. Signal intensities increased (> 1.5-fold) in genes associated with petroleum degradation. Genes related to metal resistance, stress, and carbon cycling also demonstrated increases in oiled sediments. This study demonstrates the value of applying phylogenetic and functional gene microarray technology to characterize the extensive microbial diversity of marsh environments. Moreover, this technology provides significant insight into bacterial community responses to anthropogenic oil events.

A novel surface modification approach for protein and cell microarrays

NASA Astrophysics Data System (ADS)

Kurkuri, Mahaveer D.; Driever, Chantelle; Thissen, Helmut W.; Voelcker, Nicholas H.

2007-01-01

Tissue engineering and stem cell technologies have led to a rapidly increasing interest in the control of the behavior of mammalian cells growing on tissue culture substrates. Multifunctional polymer coatings can assist research in this area in many ways, for example, by providing low non-specific protein adsorption properties and reactive functional groups at the surface. The latter can be used for immobilization of specific biological factors that influence cell behavior. In this study, glass slides were coated with copolymers of glycidyl methacrylate (GMA) and poly(ethylene glycol) methacrylate (PEGMA). The coatings were prepared by three different methods based on dip and spin coating as well as polymer grafting procedures. Coatings were characterized by X-ray photoelectron spectroscopy, surface sensitive infrared spectroscopy, ellipsometry and contact angle measurements. A fluorescently labelled protein was deposited onto reactive coatings using a contact microarrayer. Printing of a model protein (fluorescein labeled bovine serum albumin) was performed at different protein concentrations, pH, temperature, humidity and using different micropins. The arraying of proteins was studied with a microarray scanner. Arrays printed at a protein concentration above 50 μg/mL prepared in pH 5 phosphate buffer at 10°C and 65% relative humidity gave the most favourable results in terms of the homogeneity of the printed spots and the fluorescence intensity.

DNA microarray-based experimental strategy for trustworthy expression profiling of the hippocampal genes by astaxanthin supplementation in adult mouse

PubMed Central

Yook, Jang Soo; Shibato, Junko; Rakwal, Randeep; Soya, Hideaki

2015-01-01

Naturally occurring astaxantin (ASX) is one of the noticeable carotenoid and dietary supplement, which has strong antioxidant and anti-inflammatory properties, and neuroprotective effects in the brain through crossing the blood–brain barrier. Specially, we are interested in the role of ASX as a brain food. Although ASX has been suggested to have potential benefit to the brain function, the underlying molecular mechanisms and events mediating such effect remain unknown. Here we examined molecular factors in the hippocampus of adult mouse fed ASX diets (0.1% and 0.5% doses) using DNA microarray (Agilent 4 × 44 K whole mouse genome chip) analysis. In this study, we described in detail our experimental workflow and protocol, and validated quality controls with the housekeeping gene expression (Gapdh and Beta-actin) on the dye-swap based approach to advocate our microarray data, which have been uploaded to Gene Expression Omnibus (accession number GSE62197) as a gene resource for the scientific community. This data will also form an important basis for further detailed experiments and bioinformatics analysis with an aim to unravel the potential molecular pathways or mechanisms underlying the positive effects of ASX supplementation on the brain, in particular the hippocampus. PMID:26981356

Wave propagation in composite media and material characterization

NASA Technical Reports Server (NTRS)

Datta, Subhendu K.; Shah, A. H.; Karunasena, W.

1990-01-01

Characteristics of wave propagation in an undamaged composite medium are influenced by many factors, the most important of which are: microstructure, constituent properties, interfaces, residual stress fields, and ply lay-ups. Measurements of wave velocities, attenuation, and dispersion provide a powerful tool for nondestructive evaluation of these properties. Recent developments are reviewed for modeling ultrasonic wave propagation in fiber and particle-reinforced composite media. Additionally, some modeling studies are reviewed for the effects of interfaces and layering on attenuation and dispersion. These studies indicate possible ways of characterizing material properties by ultrasonic means.

Effect of carbon nanotube dispersion on glass transition in cross-linked epoxy-carbon nanotube nanocomposites: role of interfacial interactions.

PubMed

Khare, Ketan S; Khare, Rajesh

2013-06-20

We have used atomistic molecular simulations to study the effect of nanofiller dispersion on the glass transition behavior of cross-linked epoxy-carbon nanotube (CNT) nanocomposites. Specific chemical interactions at the interface of CNTs and cross-linked epoxy create an interphase region, whose impact on the properties of their nanocomposites increases with an increasing extent of dispersion. To investigate this aspect, we have compared the volumetric, structural, and dynamical properties of three systems: neat cross-linked epoxy, cross-linked epoxy nanocomposite containing dispersed CNTs, and cross-linked epoxy nanocomposite containing aggregated CNTs. We find that the nanocomposite containing dispersed CNTs shows a depression in the glass transition temperature (Tg) by ~66 K as compared to the neat cross-linked epoxy, whereas such a large depression is absent in the nanocomposite containing aggregated CNTs. Our results suggest that the poor interfacial interactions between the CNTs and the cross-linked epoxy matrix lead to a more compressible interphase region between the CNTs and the bulk matrix. An analysis of the resulting dynamic heterogeneity shows that the probability of percolation of immobile domains becomes unity near the Tg calculated from volumetric properties. Our observations also lend support to the conceptual analogy between polymer nanocomposites and the nanoconfinement of polymer thin films.

Uncovering dispersion properties in semiconductor waveguides to study photon-pair generation

NASA Astrophysics Data System (ADS)

Laiho, K.; Pressl, B.; Schlager, A.; Suchomel, H.; Kamp, M.; Höfling, S.; Schneider, C.; Weihs, G.

2016-10-01

We investigate the dispersion properties of ridge Bragg-reflection waveguides to deduce their phasematching characteristics. These are crucial for exploiting them as sources of parametric down-conversion (PDC). In order to estimate the phasematching bandwidth we first determine the group refractive indices of the interacting modes via Fabry-Perot experiments in two distant wavelength regions. Second, by measuring the spectra of the emitted PDC photons, we gain access to their group index dispersion. Our results offer a simple approach for determining the PDC process parameters in the spectral domain, and provide important feedback for designing such sources, especially in the broadband case.

Plasmon modes supported by left-handed material slab waveguide with conducting interfaces

NASA Astrophysics Data System (ADS)

Taya, Sofyan A.

2018-07-01

Theoretical analysis of left-handed material core layer waveguide in the presence of interface free charge layers is presented. The thickness of the interface charge layer can be neglected compared with the incident wavelength. The tangential component of the magnetic field is no longer continuous due to the conducting interfaces. The non-homogeneous boundary conditions are solved and the corresponding dispersion relation is found. The dispersion properties are studied. The proposed structure is found to support even as well as odd plasmon modes. Moreover, the structure shows abnormal dispersion property of decreasing the effective index with the increase of the frequency which means negative group velocity.

Study of pH-responsive microgels containing methacrylic acid: effects of particle composition and added calcium.

PubMed

Dalmont, Helene; Pinprayoon, Orawan; Saunders, Brian R

2008-03-18

pH-responsive microgel dispersions contain cross-linked polymer particles that swell when the pH approaches the pKa of the ionic monomer incorporated within the particles. In recent work from our group, it was demonstrated that the mechanical properties of degenerated intervertebral discs (IVDs) could be restored to normal values by injection of pH-responsive microgel dispersions (Saunders, J. M.; Tong, T.; LeMaitre, C.; Freemont, A. J.; Saunders, B. R. Soft Matter 2007, 3, 486). These dispersions change from a fluid to a gel with increasing pH. The present work investigates the pH-dependent properties of dispersions of microgel particles containing MAA (methacrylic acid) and also the effects of added Ca2+. Two microgels are discussed: microgel A is poly(EA/MAA/AM) (EA and AM are ethyl acrylate and allyl methacrylate), and microgel B is poly(EA/MAA/BDDA) (butanediol diacrylate). The pH-dependent particle properties investigated include hydrodynamic diameters and electrophoretic mobilities. The critical coagulation concentrations (CCC) of dilute dispersions and the elastic modulus (G') of concentrated, gelled microgel dispersions were also investigated. In the absence of added Ca2+, the particle swelling and G' were smallest and largest, respectively, for microgel A. The changes in hydrodynamic diameter and mobility with pH were explained in terms of a core-shell swelling mechanism. Added Ca2+ was found to significantly decrease the CCCs, extents of particle swelling, and magnitude of the electrophoretic mobility. This was attributed to the ionic cross-linking of neighboring RCOO- groups by Ca2+. It is suggested that the formation of ionic cross-links is inefficient within the microgel particles because of the presence of covalent cross-links that oppose the large-scale conformational rearrangement of neighboring RCOO- groups. The effect of Ca2+ on the properties of the gelled dispersions is important from the viewpoint of potential application in vivo. Rheological studies of the gelled microgel dispersions showed that added Ca2+ did not have a specific influence on G'. The differences observed in the presence of Ca2+ were attributed to ionic strength effects (screening). The key parameter that controls G' of the gelled microgel dispersions is pH. The results from this work suggest that the elasticity of the gels would be slightly reduced in vivo as a consequence of the high ionic strength present.

Intra-Platform Repeatability and Inter-Platform Comparability of MicroRNA Microarray Technology

PubMed Central

Sato, Fumiaki; Tsuchiya, Soken; Terasawa, Kazuya; Tsujimoto, Gozoh

2009-01-01

Over the last decade, DNA microarray technology has provided a great contribution to the life sciences. The MicroArray Quality Control (MAQC) project demonstrated the way to analyze the expression microarray. Recently, microarray technology has been utilized to analyze a comprehensive microRNA expression profiling. Currently, several platforms of microRNA microarray chips are commercially available. Thus, we compared repeatability and comparability of five different microRNA microarray platforms (Agilent, Ambion, Exiqon, Invitrogen and Toray) using 309 microRNAs probes, and the Taqman microRNA system using 142 microRNA probes. This study demonstrated that microRNA microarray has high intra-platform repeatability and comparability to quantitative RT-PCR of microRNA. Among the five platforms, Agilent and Toray array showed relatively better performances than the others. However, the current lineup of commercially available microRNA microarray systems fails to show good inter-platform concordance, probably because of lack of an adequate normalization method and severe divergence in stringency of detection call criteria between different platforms. This study provided the basic information about the performance and the problems specific to the current microRNA microarray systems. PMID:19436744

Living Cell Microarrays: An Overview of Concepts

PubMed Central

Jonczyk, Rebecca; Kurth, Tracy; Lavrentieva, Antonina; Walter, Johanna-Gabriela; Scheper, Thomas; Stahl, Frank

2016-01-01

Living cell microarrays are a highly efficient cellular screening system. Due to the low number of cells required per spot, cell microarrays enable the use of primary and stem cells and provide resolution close to the single-cell level. Apart from a variety of conventional static designs, microfluidic microarray systems have also been established. An alternative format is a microarray consisting of three-dimensional cell constructs ranging from cell spheroids to cells encapsulated in hydrogel. These systems provide an in vivo-like microenvironment and are preferably used for the investigation of cellular physiology, cytotoxicity, and drug screening. Thus, many different high-tech microarray platforms are currently available. Disadvantages of many systems include their high cost, the requirement of specialized equipment for their manufacture, and the poor comparability of results between different platforms. In this article, we provide an overview of static, microfluidic, and 3D cell microarrays. In addition, we describe a simple method for the printing of living cell microarrays on modified microscope glass slides using standard DNA microarray equipment available in most laboratories. Applications in research and diagnostics are discussed, e.g., the selective and sensitive detection of biomarkers. Finally, we highlight current limitations and the future prospects of living cell microarrays. PMID:27600077

A Study on the Rheological and Mechanical Properties of Photo-Curable Ceramic/Polymer Composites with Different Silane Coupling Agents for SLA 3D Printing Technology.

PubMed

Song, Se Yeon; Park, Min Soo; Lee, Jung Woo; Yun, Ji Sun

2018-02-07

Silane coupling agents (SCAs) with different organofunctional groups were coated on the surfaces of Al₂O₃ ceramic particles through hydrolysis and condensation reactions, and the SCA-coated Al₂O₃ ceramic particles were dispersed in a commercial photopolymer based on interpenetrating networks (IPNs). The organofunctional groups that have high radical reactivity and are more effective in UV curing systems are usually functional groups based on acryl, such as acryloxy groups, methacrloxy groups, and acrylamide groups, and these silane coupling agents seem to improve interfacial adhesion and dispersion stability. The coating morphology and the coating thickness distribution of SCA-coated Al₂O₃ ceramic particles according to the different organofunctional groups were observed by FE-TEM. The initial dispersibility and dispersion stability of the SCA-coated Al₂O₃/High-temp composite solutions were investigated by relaxation NMR and Turbiscan. The rheological properties of the composite solutions were investigated by viscoelastic analysis and the mechanical properties of 3D-printed objects were observed with a nanoindenter.

A Study on the Rheological and Mechanical Properties of Photo-Curable Ceramic/Polymer Composites with Different Silane Coupling Agents for SLA 3D Printing Technology

PubMed Central

Song, Se Yeon; Park, Min Soo; Lee, Jung Woo; Yun, Ji Sun

2018-01-01

Silane coupling agents (SCAs) with different organofunctional groups were coated on the surfaces of Al2O3 ceramic particles through hydrolysis and condensation reactions, and the SCA-coated Al2O3 ceramic particles were dispersed in a commercial photopolymer based on interpenetrating networks (IPNs). The organofunctional groups that have high radical reactivity and are more effective in UV curing systems are usually functional groups based on acryl, such as acryloxy groups, methacrloxy groups, and acrylamide groups, and these silane coupling agents seem to improve interfacial adhesion and dispersion stability. The coating morphology and the coating thickness distribution of SCA-coated Al2O3 ceramic particles according to the different organofunctional groups were observed by FE-TEM. The initial dispersibility and dispersion stability of the SCA-coated Al2O3/High-temp composite solutions were investigated by relaxation NMR and Turbiscan. The rheological properties of the composite solutions were investigated by viscoelastic analysis and the mechanical properties of 3D-printed objects were observed with a nanoindenter. PMID:29414912

Properties of Filamentary Sublimation Residues from Dispersions of Clay in Ice

NASA Technical Reports Server (NTRS)

Stephens, J. B.; Parker, T. J.; Saunders, R. S.; Laue, E. G.; Fanale, F. P.

1985-01-01

The properties of sublimate residues are of considerable interest in studies of the thermal modeling of Martian and cometary ice surfaces. The study of the formation of sand grains from this mantle on Martian polar ice is also supported by these experiments. To understand these properties, a series of low temperature vacuum experiments were run during which dirty ices that might be expected to be found in Martian polar caps and in comet nuclei were made and then freeze dried. In addition to using particulate material of appropriate grain size and minerology, particle nucleated ices were simulated by dispersing the particulates in the ice so that they did not contact one another. This noncontact dispersion was the most difficult requirement to achieve but the most rewarding in that it produced a new filamentary sublimate residue that was not a relic of the frozen dispersion. If the siliceous particles are allowed to touch one another in the ice the structure of the contacting particles in the ice will remain as a relic after the ice is sublimed away.

Optical properties of fly ash. Volume 2, Final report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Self, S.A.

1994-12-01

Research performed under this contract was divided into four tasks under the following headings: Task 1, Characterization of fly ash; Task 2, Measurements of the optical constants of slags; Task 3, Calculations of the radiant properties of fly ash dispersions; and Task 4, Measurements of the radiant properties of fly ash dispersions. Tasks 1 and 4 constituted the Ph.D. research topic of Sarbajit Ghosal, while Tasks 2 and 3 constituted the Ph.D. research topic of Jon Ebert. Together their doctoral dissertations give a complete account of the work performed. This final report, issued in two volumes consists of an executivemore » summary of the whole program followed by the dissertation of Ghosal and Ebert. Volume 2 contains the dissertation of Ebert which covers the measurements of the optical constants of slags, and calculations of the radiant properties of fly ash dispersions. A list of publications and conference presentations resulting from the work is also included.« less

Surface and protective properties of dispersions of film-formers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Turishcheva, R.A.; Bakaleinikov, M.B.; Minkina, E.N.

1983-03-01

This article reports on studies of the surface and protective properties of 20% dispersions of film-formers most typically used in film-forming inhibited petroleum-base compositions (FIPC): solid hydrocarbons, fatty acid soaps, asphalt, polymers, natural resins, modified vegetable oils, and an inorganic thickening agent. Investigates the dispersions of Butosil and lithium stearate at respective concentrations of 10% and 8%, in view of the high thickening power of these film-formers. Classifies all of the studied FIPC film-forming components into 2 groups: those wth little thickening effect, a low level of adhesion-cohesion interaction, and a high level of surface and protective properties (the oxidizedmore » solid hydrocarbons and the polymers); and the film-formers that have a large thickening effect, a high level of adhesion-cohesion interaction, and a low level of surface and protective properties (the fatty acid soaps, the solid hydrocarbons, and Butosil). Recommends combining film-formers of both groups in developing new grades of FIPCs.« less

ELISA-BASE: An Integrated Bioinformatics Tool for Analyzing and Tracking ELISA Microarray Data

DOE Office of Scientific and Technical Information (OSTI.GOV)

White, Amanda M.; Collett, James L.; Seurynck-Servoss, Shannon L.

ELISA-BASE is an open-source database for capturing, organizing and analyzing protein enzyme-linked immunosorbent assay (ELISA) microarray data. ELISA-BASE is an extension of the BioArray Soft-ware Environment (BASE) database system, which was developed for DNA microarrays. In order to make BASE suitable for protein microarray experiments, we developed several plugins for importing and analyzing quantitative ELISA microarray data. Most notably, our Protein Microarray Analysis Tool (ProMAT) for processing quantita-tive ELISA data is now available as a plugin to the database.

Functionalized Carbon Nanotubes in Modified Plant Oil Composites.

NASA Astrophysics Data System (ADS)

McAninch, Ian M.; Wool, Richard P.

2007-03-01

Carbon nanotubes (CNTs) with their impressive mechanical properties are ideal reinforcement material. Acrylated epoxidized soy oil (AESO) has been previously shown to have favorable interactions with carbon nanotubes; however a mixture of aggregates and dispersed tubes were found even at low CNT concentrations. In order to prevent re-aggregation, the CNTs were functionalized with a 10 carbon long aliphatic chain. These aliphatic chains are similar to the fatty acids that make up soy oil. Functionalization was verified using XPS and IR spectroscopy. These functionalized CNTs were dispersed by mechanical shear mixing into AESO both with and without styrene as a comonomer. No large aggregates were observed in the liquid, uncured, samples or in the final cured composites. Dispersion in the solid composites was verified using optical and electron microscopy. Better dispersion also resulted in improved mechanical properties.

Guiding properties and dispersion control of kagome lattice hollow-core photonic crystal fibers.

PubMed

Im, Song-Jin; Husakou, Anton; Herrmann, Joachim

2009-07-20

Dispersion properties, loss and optimum design of kagome lattice hollow-core photonic crystal fibers filled with argon are studied for the purpose of possible applications in ultrafast nonlinear optics. As will be shown numerically and by using an approximate analytical formula these fibers exhibit anomalous dispersion for visible or UV wavelengths both for a 1-cell-core as well for a 3-ring-core which can be controlled by the gas pressure and do not suffer from high loss. It is shown that while the loss is mainly influenced by the strut thickness of the kagome lattice the group velocity dispersion is almost independently controlled by the core size. These results demonstrate that kagome lattice hollow fibers have a promising potential in ultrashort pulse delivering of high-energy pulses and in several interesting applications in ultrafast nonlinear optics.

A dynamic gain equalizer based on holographic polymer dispersed liquid crystal gratings

NASA Astrophysics Data System (ADS)

Xin, Zhaohui; Cai, Jiguang; Shen, Guotu; Yang, Baocheng; Zheng, Jihong; Gu, Lingjuan; Zhuang, Songlin

2006-12-01

The dynamic gain equalizer consisting of gratings made of holographic polymer dispersed liquid crystal is explored and the structure and principle presented. The properties of the holographic polymer dispersed liquid crystal grating are analyzed in light of the rigorous coupled-wave theory. Experimental study is also conducted in which a beam of infrared laser was incident to the grating sample and an alternating current electric field applied. The electro-optical properties of the grating and the influence of the applied field were observed. The results of the experiment agree with that of the theory quite well. The design method of the dynamic gain equalizer with the help of numerical simulation is presented too. The study shows that holographic polymer dispersed liquid crystal gratings have great potential to play a role in fiber optics communication.

Effect of deposition temperature on the structural and optical properties of CdSe QDs thin films deposited by CBD method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Laatar, F., E-mail: fakher8laatar@gmail.com; Harizi, A.; Smida, A.

2016-06-15

Highlights: • Synthesis of CdSe QDs with L-Cysteine capping agent for applications in nanodevices. • The films of CdSe QDs present uniform and good dispersive particles at the surface. • Effect of bath temperature on the structural and optical properties of CdSe QDs thin films. • Investigation of the optical constants and dispersion parameters of CdSe QDs thin films. - Abstract: Cadmium selenide quantum dots (CdSe QDs) thin films were deposited onto glass substrates by a chemical bath deposition (CBD) method at different temperatures from an aqueous solution containing L-Cysteine (L-Cys) as capping agent. The evolution of the surface morphologymore » and elemental composition of the CdSe films were studied by AFM, SEM, and EDX analyses. Structural and optical properties of CdSe thin films were investigated by XRD, UV–vis and PL spectroscopy. The dispersion behavior of the refractive index is described using the single oscillator Wemple-DiDomenico (W-D) model, and the physical dispersion parameters are calculated as a function of deposition temperature. The dispersive optical parameters such as average oscillator energy (E{sub o}), dispersion energy (E{sub d}), and static refractive index (n{sub o}) were found to vary with the deposition temperature. Besides, the electrical free carrier susceptibility (χ{sub e}) and the carrier concentration of the effective mass ratio (N/m*) were evaluated according to the Spitzer-Fan model.« less

Sugar microarray via click chemistry: molecular recognition with lectins and amyloid β (1-42)

NASA Astrophysics Data System (ADS)

Matsumoto, Erino; Yamauchi, Takahiro; Fukuda, Tomohiro; Miura, Yoshiko

2009-06-01

Sugar microarrays were fabricated on various substrates via click chemistry. Acetylene-terminated substrates were prepared by forming self-assembled monolayers (SAMs) on a gold substrate with alkyl-disulfide and on silicon, quartz and glass substrates with a silane-coupling reagent. The gold substrates were subjected to surface plasmon resonance measurements, and the quartz and glass substrates were subjected to spectroscopy measurements and optical microscopy observation. The saccharide-immobilized substrate on the gold substrate showed specific interaction with the corresponding lectin, and the saccharides showed inert surface properties to other proteins with a high signal-to-noise ratio. We also focused on the saccharide-protein interaction on protein amyloidosis of Alzheimer amyloid β. Amyloid β peptide showed conformation transition on the saccharide-immobilization substrate into a β-sheet, and fibril formation and amyloid aggregates were found on the specific saccharides.

Ordered mesoporous ferrosilicate materials with highly dispersed iron oxide nanoparticles and investigation of their unique magnetic properties.

PubMed

Srinivasu, Pavuluri; Suresh, Koppoju; Datt, Gopal; Abhayankar, Ashutosh C; Rao, Pothuraju Nageswara; Lakshmi Kantam, Mannepalli; Bhargava, Suresh K; Tang, Jing; Yamauchi, Yusuke

2014-11-07

Ordered mesoporous ferrosilicate materials with highly dispersed iron oxide nanoparticles are directly synthesized through a hydrothermal approach under acidic conditions. The obtained samples possess a high surface area (up to 1236 m(2) g(-1)) and a large pore volume (up to 1.1 cm(3) g(-1)). By changing the amount of iron content, the magnetic properties can be tuned.

Measurement of viscoelastic properties of in vivo swine myocardium using Lamb Wave Dispersion Ultrasound Vibrometry (LDUV)

PubMed Central

Urban, Matthew W.; Pislaru, Cristina; Nenadic, Ivan Z.; Kinnick, Randall R.; Greenleaf, James F.

2012-01-01

Viscoelastic properties of the myocardium are important for normal cardiac function and may be altered by disease. Thus, quantification of these properties may aid with evaluation of the health of the heart. Lamb Wave Dispersion Ultrasound Vibrometry (LDUV) is a shear wave-based method that uses wave velocity dispersion to measure the underlying viscoelastic material properties of soft tissue with plate-like geometries. We tested this method in eight pigs in an open-chest preparation. A mechanical actuator was used to create harmonic, propagating mechanical waves in the myocardial wall. The motion was tracked using a high frame rate acquisition sequence, typically 2500 Hz. The velocities of wave propagation were measured over the 50–400 Hz frequency range in 50 Hz increments. Data were acquired over several cardiac cycles. Dispersion curves were fit with a viscoelastic, anti-symmetric Lamb wave model to obtain estimates of the shear elasticity, μ1, and viscosity, μ2 as defined by the Kelvin-Voigt rheological model. The sensitivity of the Lamb wave model was also studied using simulated data. We demonstrated that wave velocity measurements and Lamb wave theory allow one to estimate the variation of viscoelastic moduli of the myocardial walls in vivo throughout the course of the cardiac cycle. PMID:23060325

Thermodynamically optimal whole-genome tiling microarray design and validation.

PubMed

Cho, Hyejin; Chou, Hui-Hsien

2016-06-13

Microarray is an efficient apparatus to interrogate the whole transcriptome of species. Microarray can be designed according to annotated gene sets, but the resulted microarrays cannot be used to identify novel transcripts and this design method is not applicable to unannotated species. Alternatively, a whole-genome tiling microarray can be designed using only genomic sequences without gene annotations, and it can be used to detect novel RNA transcripts as well as known genes. The difficulty with tiling microarray design lies in the tradeoff between probe-specificity and coverage of the genome. Sequence comparison methods based on BLAST or similar software are commonly employed in microarray design, but they cannot precisely determine the subtle thermodynamic competition between probe targets and partially matched probe nontargets during hybridizations. Using the whole-genome thermodynamic analysis software PICKY to design tiling microarrays, we can achieve maximum whole-genome coverage allowable under the thermodynamic constraints of each target genome. The resulted tiling microarrays are thermodynamically optimal in the sense that all selected probes share the same melting temperature separation range between their targets and closest nontargets, and no additional probes can be added without violating the specificity of the microarray to the target genome. This new design method was used to create two whole-genome tiling microarrays for Escherichia coli MG1655 and Agrobacterium tumefaciens C58 and the experiment results validated the design.

Nanoroughened plasmonic films for enhanced biosensing detection

NASA Astrophysics Data System (ADS)

LeMoal, Eric; Lévêque-Fort, Sandrine; Potier, Marie-Claude; Fort, Emmanuel

2009-06-01

Although fluorescence is the prevailing labeling technique in biosensing applications, sensitivity improvement is still a striving challenge. We show that coating standard microscope slides with nanoroughened silver films provides a high fluorescence signal enhancement due to plasmonic interactions. As a proof of concept, we applied these films with tailored plasmonic properties to DNA microarrays. Using common optical scanning devices, we achieved signal amplifications of more than 40-fold.

Thermal Properties for the Thermal-Hydraulics Analyses of the BR2 Maximum Nominal Heat Flux

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dionne, B.; Bergeron, A.; Licht, J. R.

2015-02-01

This memo describes the assumptions and references used in determining the thermal properties for the various materials used in the BR2 HEU (93% enriched in 235U) to LEU (19.75% enriched in 235U) conversion feasibility analysis. More specifically, this memo focuses on the materials contained within the pressure vessel (PV), i.e., the materials that are most relevant to the study of impact of the change of fuel from HEU to LEU. Section 2 provides a summary of the thermal properties in the form of tables while the following sections and appendices present the justification of these values. Section 3 presents amore » brief background on the approach used to evaluate the thermal properties of the dispersion fuel meat and specific heat capacity. Sections 4 to 7 discuss the material properties for the following materials: i) aluminum, ii) dispersion fuel meat (UAlx-Al and U-7Mo-Al), iii) beryllium, and iv) stainless steel. Section 8 discusses the impact of irradiation on material properties. Section 9 summarizes the material properties for typical operating temperatures. Appendix A elaborates on how to calculate dispersed phase’s volume fraction. Appendix B provides a revised methodology for determining the thermal conductivity as a function of burnup for HEU and LEU.« less

Acoustic Rectification in Dispersive Media

NASA Technical Reports Server (NTRS)

Cantrell, John H.

2008-01-01

It is shown that the shapes of acoustic radiation-induced static strain and displacement pulses (rectified acoustic pulses) are defined locally by the energy density of the generating waveform. Dispersive properties are introduced analytically by assuming that the rectified pulses are functionally dependent on a phase factor that includes both dispersive and nonlinear terms. The dispersion causes an evolutionary change in the shape of the energy density profile that leads to the generation of solitons experimentally observed in fused silica.

Are There Optical Solitary Wave Solutions in Linear Media with Group Velocity Dispersion?

NASA Technical Reports Server (NTRS)

Li, Zhonghao; Zhou, Guosheng

1996-01-01

A generalized exact optical bright solitary wave solution in a three dimensional dispersive linear medium is presented. The most interesting property of the solution is that it can exist in the normal group-velocity-dispersion (GVD) region. In addition, another peculiar feature is that it may achieve a condition of 'zero-dispersion' to the media so that a solitary wave of arbitrarily small amplitude may be propagated with no dependence on is pulse width.

Preparation and characterization of azithromycin--Aerosil 200 solid dispersions with enhanced physical stability.

PubMed

Li, Xuechao; Peng, Huanhuan; Tian, Bin; Gou, Jingxin; Yao, Qing; Tao, Xiaoguang; He, Haibing; Zhang, Yu; Tang, Xing; Cai, Cuifang

2015-01-01

The main purpose of this study was to investigate the feasibility of azithromycin (AZI)--Aerosil 200 solid dispersions specifically with high stability under accelerated condition (40 °C/75% RH). Ball milling (BM) and hot-melt extrusion (HME) were used to prepare AZI solid dispersions. The physical properties of solid dispersions were evaluated by differential scanning calorimetry (DSC), scanning electron microscopy (SEM), powder X-ray diffraction (PXRD), Fourier transform infrared spectroscopy (FT-IR) and thermogravimetric analysis (TGA). For solid dispersions prepared with both methods, no crystalline of AZI was detected (except for AZI: Aerosil 200=75:25) by DSC or PXRD, indicating the amorphous state of AZI in solid dispersions. The FT-IR results demonstrated the loss of crystallization water and the formation of hydrogen bonds between Aerosil 200 and AZI during the preparation of solid dispersions. After 4 weeks storage under accelerated condition, the degree of crystallinity of AZI increased in solid dispersions prepared by BM, whereas for solid dispersions containing AZI, Aerosil 200 and glyceryl behenate (GB) prepared by HME, no crystalline of AZI was identified. This high stability can be attributed to the hydrophobic properties of GB and the presence of hydrogen bonds. Based on the above results, it is inferred the protection of hydrogen bonds between AZI and Aerosil 200 formed during preparation process effectively inhibited the recrystallization of AZI and improved the physical stability of amorphous AZI in the presence of Aerosil 200. Copyright © 2015 Elsevier B.V. All rights reserved.

Well-dispersed cellulose nanocrystals in hydrophobic polymers by in situ polymerization for synthesizing highly reinforced bio-nanocomposites.

PubMed

Geng, Shiyu; Wei, Jiayuan; Aitomäki, Yvonne; Noël, Maxime; Oksman, Kristiina

2018-04-20

In nanocomposites, dispersing hydrophilic nanomaterials in a hydrophobic matrix using simple and environmentally friendly methods remains challenging. Herein, we report a method based on in situ polymerization to synthesize nanocomposites of well-dispersed cellulose nanocrystals (CNCs) and poly(vinyl acetate) (PVAc). We have also shown that by blending this PVAc/CNC nanocomposite with poly(lactic acid) (PLA), a good dispersion of the CNCs can be reached in PLA. The outstanding dispersion of CNCs in both PVAc and PLA/PVAc matrices was shown by different microscopy techniques and was further supported by the mechanical and rheological properties of the composites. The in situ PVAc/CNC nanocomposites exhibit enhanced mechanical properties compared to the materials produced by mechanical mixing, and a theoretical model based on the interphase effect and dispersion that reflects this behavior was developed. Comparison of the rheological and thermal behaviors of the mixed and in situ PVAc/CNC also confirmed the great improvement in the dispersion of nanocellulose in the latter. Furthermore, a synergistic effect was observed with only 0.1 wt% CNCs when the in situ PVAc/CNC was blended with PLA, as demonstrated by significant increases in elastic modulus, yield strength, elongation to break and glass transition temperature compared to the PLA/PVAc only material.

Development of megestrol acetate solid dispersion nanoparticles for enhanced oral delivery by using a supercritical antisolvent process.

PubMed

Ha, Eun-Sol; Kim, Jeong-Soo; Baek, In-Hwan; Yoo, Jin-Wook; Jung, Yunjin; Moon, Hyung Ryong; Kim, Min-Soo

2015-01-01

In the present study, solid dispersion nanoparticles with a hydrophilic polymer and surfactant were developed using the supercritical antisolvent (SAS) process to improve the dissolution and oral absorption of megestrol acetate. The physicochemical properties of the megestrol acetate solid dispersion nanoparticles were characterized using scanning electron microscopy, differential scanning calorimetry, powder X-ray diffraction, and a particle-size analyzer. The dissolution and oral bioavailability of the nanoparticles were also evaluated in rats. The mean particle size of all solid dispersion nanoparticles that were prepared was <500 nm. Powder X-ray diffraction and differential scanning calorimetry measurements showed that megestrol acetate was present in an amorphous or molecular dispersion state within the solid dispersion nanoparticles. Hydroxypropylmethyl cellulose (HPMC) solid dispersion nanoparticles significantly increased the maximum dissolution when compared with polyvinylpyrrolidone K30 solid dispersion nanoparticles. The extent and rate of dissolution of megestrol acetate increased after the addition of a surfactant into the HPMC solid dispersion nanoparticles. The most effective surfactant was Ryoto sugar ester L1695, followed by D-α-tocopheryl polyethylene glycol 1000 succinate. In this study, the solid dispersion nanoparticles with a drug:HPMC:Ryoto sugar ester L1695 ratio of 1:2:1 showed >95% rapid dissolution within 30 minutes, in addition to good oral bioavailability, with approximately 4.0- and 5.5-fold higher area under the curve (0-24 hours) and maximum concentration, respectively, than raw megestrol acetate powder. These results suggest that the preparation of megestrol acetate solid dispersion nanoparticles using the supercritical antisolvent process is a promising approach to improve the dissolution and absorption properties of megestrol acetate.

cDNA microarray analysis of esophageal cancer: discoveries and prospects.

PubMed

Shimada, Yutaka; Sato, Fumiaki; Shimizu, Kazuharu; Tsujimoto, Gozoh; Tsukada, Kazuhiro

2009-07-01

Recent progress in molecular biology has revealed many genetic and epigenetic alterations that are involved in the development and progression of esophageal cancer. Microarray analysis has also revealed several genetic networks that are involved in esophageal cancer. However, clinical application of microarray techniques and use of microarray data have not yet occurred. In this review, we focus on the recent developments and problems with microarray analysis of esophageal cancer.

Manufacturing of microarrays.

PubMed

Petersen, David W; Kawasaki, Ernest S

2007-01-01

DNA microarray technology has become a powerful tool in the arsenal of the molecular biologist. Capitalizing on high precision robotics and the wealth of DNA sequences annotated from the genomes of a large number of organisms, the manufacture of microarrays is now possible for the average academic laboratory with the funds and motivation. Microarray production requires attention to both biological and physical resources, including DNA libraries, robotics, and qualified personnel. While the fabrication of microarrays is a very labor-intensive process, production of quality microarrays individually tailored on a project-by-project basis will help researchers shed light on future scientific questions.

The Longhorn Array Database (LAD): An Open-Source, MIAME compliant implementation of the Stanford Microarray Database (SMD)

PubMed Central

Killion, Patrick J; Sherlock, Gavin; Iyer, Vishwanath R

2003-01-01

Background The power of microarray analysis can be realized only if data is systematically archived and linked to biological annotations as well as analysis algorithms. Description The Longhorn Array Database (LAD) is a MIAME compliant microarray database that operates on PostgreSQL and Linux. It is a fully open source version of the Stanford Microarray Database (SMD), one of the largest microarray databases. LAD is available at Conclusions Our development of LAD provides a simple, free, open, reliable and proven solution for storage and analysis of two-color microarray data. PMID:12930545

Effect of preparation methods on dispersion stability and electrochemical performance of graphene sheets

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Li, E-mail: chenli1981@lut.cn; Li, Na; Zhang, Mingxia

Chemical exfoliation is one of the most important strategies for preparing graphene. The aggregation of graphene sheets severely prevents graphene from exhibiting excellent properties. However, there are no attempts to investigate the effect of preparation methods on the dispersity of graphene sheets. In this study, three chemical exfoliation methods, including Hummers method, modified Hummers method, and improved method, were used to prepare graphene sheets. The influence of preparation methods on the structure, dispersion stability in organic solvents, and electrochemical properties of graphene sheets were investigated. Fourier transform infrared microscopy, Raman spectra, transmission electron microscopy, and UV–vis spectrophotometry were employed tomore » analyze the structure of the as-prepared graphene sheets. The results showed that graphene prepared by improved method exhibits excellent dispersity and stability in organic solvents without any additional stabilizer or modifier, which is attributed to the completely exfoliation and regular structure. Moreover, cyclic voltammetric and electrochemical impedance spectroscopy measurements showed that graphene prepared by improved method exhibits superior electrochemical properties than that prepared by the other two methods. - Graphical abstract: Graphene oxides with different oxidation degree were obtained via three methods, and then graphene with different crystal structures were created by chemical reduction of exfoliated graphene oxides. - Highlights: • Graphene oxides with different oxidation degree were obtained via three oxidation methods. • The influence of oxidation methods on microstructure of graphene was investigated. • The effect of oxidation methods on dispersion stability of graphene was investigated. • The effect of oxidation methods on electrochemical properties of graphene was discussed.« less

Beyond local effective material properties for metamaterials

NASA Astrophysics Data System (ADS)

Mnasri, K.; Khrabustovskyi, A.; Stohrer, C.; Plum, M.; Rockstuhl, C.

2018-02-01

To discuss the properties of metamaterials on physical grounds and to consider them in applications, effective material parameters are usually introduced and assigned to a given metamaterial. In most cases, only weak spatial dispersion is considered. It allows to assign local material properties, e.g., a permittivity and a permeability. However, this turned out to be insufficient. To solve this problem, we study here the effective properties of metamaterials with constitutive relations beyond a local response and take strong spatial dispersion into account. This research requires two contributions. First, bulk properties in terms of eigenmodes need to be studied. We particularly investigate the isofrequency surfaces of their dispersion relation are investigated and compared to those of an actual metamaterial. The significant improvement to effectively describe it provides evidence for the necessity to use nonlocal material laws in the effective description of metamaterials. Second, to be able to capitalize on such constitutive relations, also interface conditions need to be known. They are derived in this contribution for our form of the nonlocality using a generalized (weak) formulation of Maxwell's equations. Based on such interface conditions, Fresnel expressions are obtained that predict the amplitude of the reflected and transmitted plane wave upon illuminating a slab of such a nonlocal metamaterial. This all together offers the necessary means for the in-depth analysis of metamaterials characterized by strong spatial dispersion. The general formulation we choose here renders our approach applicable to a wide class of metamaterials.

Polyfunctional dispersants for controlling viscosity of phyllosilicates

DOEpatents

Chaiko, David J.

2006-07-25

This invention provides phyllosilicates and polyfunctional dispersants which can be manipulated to selectively control the viscosity of phyllosilicate slurries. The polyfunctional dispersants used in the present invention, which include at least three functional groups, increase the dispersion and exfoliation of phyllosilicates in polymers and, when used in conjunction with phyllosilicate slurries, significantly reduce the viscosity of slurries having high concentrations of phyllosilicates. The functional groups of the polyfunctional dispersants are capable of associating with multivalent metal cations and low molecular weight organic polymers, which can be manipulated to substantially increase or decrease the viscosity of the slurry in a concentration dependent manner. The polyfunctional dispersants of the present invention can also impart desirable properties on the phyllosilicate dispersions including corrosion inhibition and enhanced exfoliation of the phyllosilicate platelets.

Dispersion and Mechanical Properties of Carbon Nanotube/Polymer Composites via Melt Compounding

NASA Astrophysics Data System (ADS)

Gorga, Russell; Cohen, Robert

2003-03-01

This work is focused on the fabrication of carbon nanotube/ polymer composites via melt compounding. The main objective of this work is to realize the outstanding properties of carbon nanotubes (high modulus, high thermal and electrical conductivity, elastic buckling) at the macroscopic level by blending carbon nanotubes into a polymer matrix. The challenge lies in dispersing these one dimensional nanoparticles in the polymer matrix. Dispersion of the nanotubes in the composites is analyzed via transmission and scanning electron microscopy. Mechanical properties as well as electrical and thermal conductivity are measured as a function of nanotube loading, orientation, and extrusion conditions. Multi-wall nanotube loadings in the range of 1 and 10 wtconcave-downward departures from the linear stress-strain behavior of the unmodified polymer below 5observations are discussed in the context of possible deformation mechanisms for the nanotube composites.

Characterization of Thermo-Elastic Properties and Microcracking Behaviors of CFRP Laminates Using Cup-Stacked Carbon Nanotubes (CSCNT) Dispersed Resin

NASA Astrophysics Data System (ADS)

Yokozeki, Tomohiro; Iwahori, Yutaka; Ishiwata, Shin

This study investigated the thermo-elastic properties and microscopic ply cracking behaviors in carbon fiber reinforced nanotube-dispersed epoxy laminates. The nanocomposite laminates used in this study consisted of traditional carbon fibers and epoxy resin filled with cup-stacked carbon nanotubes (CSCNTs). Thermo-mechanical properties of unidirectional nanocomposite laminates were evaluated, and quasi-static and fatigue tension tests of cross-ply laminates were carried out in order to observe the damage accumulation behaviors of matrix cracks. Clear retardation of matrix crack onset and accumulation was found in composite laminates with CSCNT compared to those without CSCNT. Fracture toughness associated with matrix cracking was evaluated based on the analytical model using the experimental results. It was concluded that the dispersion of CSCNT resulted in fracture toughness improvement and residual thermal strain decrease, and specifically, the former was the main contribution to the retardation of matrix crack formation.

Properties of alginate fiber spun-dyed with fluorescent pigment dispersion.

PubMed

Wang, Ping; Tawiah, Benjamin; Tian, Anli; Wang, Chunxia; Zhang, Liping; Fu, Shaohai

2015-03-15

Spun-dyed alginate fiber was prepared by the spun-dyeing method with the mixture of fluorescent pigment dispersion and sodium alginate fiber spinning solution, and its properties were characterized by SEM, TGA, DSC, and XRD. The results indicate that fluorescent pigment dispersion prepared with esterified poly (styrene-alt maleic acid) had excellent compatibility with sodium alginate fiber spinning solution, and small amount of fluorescent pigment could reduce the viscosity of spun-dyed spinning solutions. SEM photo of spun-dyed alginate fiber indicated that fewer pigment particles deposited on its surface. TGA, DSC, and XRD results suggested that thermal properties and crystal phase of spun-dyed alginate fibers had slight changes compared to the original alginate fibers. The fluorescence intensity of spun-dyed alginate fiber reached its maximum when the content of fluorescent pigment was 4%. The spun-dyed alginate fiber showed excellent rubbing and washing fastness. Copyright © 2014 Elsevier Ltd. All rights reserved.

Transcriptional and electrophysiological maturation of neocortical fastspiking GABAergic interneurons

PubMed Central

Okaty, Benjamin W; Miller, Mark N; Sugino, Ken; Hempel, Chris M; Nelson, Sacha B

2009-01-01

Fast-spiking (FS) interneurons are important elements of neocortical circuitry that constitute the primary source of synaptic inhibition in adult cortex and impart temporal organization on ongoing cortical activity. The highly specialized intrinsic membrane and firing properties that allow cortical FS interneurons to perform these functions are due to equally specialized gene expression, which is ultimately coordinated by cell-type-specific transcriptional regulation. While embryonic transcriptional events govern the initial steps of cell-type specification in most cortical interneurons, including FS cells, the electrophysiological properties that distinguish adult cortical cell types emerge relatively late in postnatal development, and the transcriptional events that drive this maturational process are not known. To address this, we used mouse whole-genome microarrays and whole-cell patch clamp to characterize the transcriptional and electrophysiological maturation of cortical FS interneurons between postnatal day 7 (P7) and P40. We found that the intrinsic and synaptic physiology of FS cells undergoes profound regulation over the first four postnatal weeks, and that these changes are correlated with largely monotonic but bidirectional transcriptional regulation of thousands of genes belonging to multiple functional classes. Using our microarray screen as a guide, we discovered that upregulation of 2-pore K+ leak channels between P10 and P25 contributes to one of the major differences between the intrinsic membrane properties of immature and adult FS cells, and found a number of other candidate genes that likely confer cell-type specificity on mature FS cells. PMID:19474331

EzArray: A web-based highly automated Affymetrix expression array data management and analysis system

PubMed Central

Zhu, Yuerong; Zhu, Yuelin; Xu, Wei

2008-01-01

Background Though microarray experiments are very popular in life science research, managing and analyzing microarray data are still challenging tasks for many biologists. Most microarray programs require users to have sophisticated knowledge of mathematics, statistics and computer skills for usage. With accumulating microarray data deposited in public databases, easy-to-use programs to re-analyze previously published microarray data are in high demand. Results EzArray is a web-based Affymetrix expression array data management and analysis system for researchers who need to organize microarray data efficiently and get data analyzed instantly. EzArray organizes microarray data into projects that can be analyzed online with predefined or custom procedures. EzArray performs data preprocessing and detection of differentially expressed genes with statistical methods. All analysis procedures are optimized and highly automated so that even novice users with limited pre-knowledge of microarray data analysis can complete initial analysis quickly. Since all input files, analysis parameters, and executed scripts can be downloaded, EzArray provides maximum reproducibility for each analysis. In addition, EzArray integrates with Gene Expression Omnibus (GEO) and allows instantaneous re-analysis of published array data. Conclusion EzArray is a novel Affymetrix expression array data analysis and sharing system. EzArray provides easy-to-use tools for re-analyzing published microarray data and will help both novice and experienced users perform initial analysis of their microarray data from the location of data storage. We believe EzArray will be a useful system for facilities with microarray services and laboratories with multiple members involved in microarray data analysis. EzArray is freely available from . PMID:18218103

Plasma Dispersion Function for the Kappa Distribution

NASA Technical Reports Server (NTRS)

Podesta, John J.

2004-01-01

The plasma dispersion function is computed for a homogeneous isotropic plasma in which the particle velocities are distributed according to a Kappa distribution. An ordinary differential equation is derived for the plasma dispersion function and it is shown that the solution can be written in terms of Gauss' hypergeometric function. Using the extensive theory of the hypergeometric function, various mathematical properties of the plasma dispersion function are derived including symmetry relations, series expansions, integral representations, and closed form expressions for integer and half-integer values of K.

Experimental observation of strong coupling effects on the dispersion of dust acoustic waves in a plasma

NASA Astrophysics Data System (ADS)

Bandyopadhyay, P.; Prasad, G.; Sen, A.; Kaw, P. K.

2007-09-01

The dispersion properties of low frequency dust acoustic waves in the strong coupling regime are investigated experimentally in an argon plasma embedded with a mixture of kaolin and MnO2 dust particles. The neutral pressure is varied over a wide range to change the collisional properties of the dusty plasma. In the low collisional regime the turnover of the dispersion curve at higher wave numbers and the resultant region of ∂ω/∂k<0 are identified as signatures of dust dust correlations. In the high collisional regime dust neutral collisions produce a similar effect and prevent an unambiguous identification of strong coupling effects.

Thermal expansion in dispersion-bound molecular crystals

DOE PAGES

Ko, Hsin -Yu; DiStasio, Robert A.; Santra, Biswajit; ...

2018-05-18

In this paper, we explore how anharmonicity, nuclear quantum effects (NQE), many-body dispersion interactions, and Pauli repulsion influence thermal properties of dispersion-bound molecular crystals. Accounting for anharmonicity with ab initio molecular dynamics yields cell parameters accurate to within 2% of experiment for a set of pyridinelike molecular crystals at finite temperatures and pressures. From the experimental thermal expansion curve, we find that pyridine-I has a Debye temperature just above its melting point, indicating sizable NQE across the entire crystalline range of stability. We find that NQE lead to a substantial volume increase in pyridine-I (≈ 40% more than classical thermalmore » expansion at 153 K) and attribute this to intermolecular Pauli repulsion promoted by intramolecular quantum fluctuations. Finally, when predicting delicate properties such as the thermal expansivity, we show that many-body dispersion interactions and more sophisticated density functional approximations improve the accuracy of the theoretical model.« less

Both solubility and chemical stability of curcumin are enhanced by solid dispersion in cellulose derivative matrices.

PubMed

Li, Bin; Konecke, Stephanie; Wegiel, Lindsay A; Taylor, Lynne S; Edgar, Kevin J

2013-10-15

Amorphous solid dispersions (ASD) of curcumin (Cur) in cellulose derivative matrices, hydroxypropylmethylcellulose acetate succinate (HPMCAS), carboxymethylcellulose acetate butyrate (CMCAB), and cellulose acetate adipate propionate (CAAdP) were prepared in order to investigate the structure-property relationship and identify polymer properties necessary to effectively increase Cur aqueous solution concentration. XRD results indicated that all investigated solid dispersions were amorphous, even at a 9:1 Cur:polymer ratio. Both stability against crystallization and Cur solution concentration from these ASDs were significantly higher than those from physical mixtures and crystalline Cur. Remarkably, curcumin was also stabilized against chemical degradation in solution. Chemical stabilization was polymer-dependent, with stabilization in CAAdP>CMCAB>HPMCAS>PVP, while matrices enhanced solution concentration as PVP>HPMCAS>CMCAB≈CAAdP. HPMCAS/Cur dispersions have useful combinations of pH-triggered release profile, chemical stabilization, and strong enhancement of Cur solution concentration. Copyright © 2013 Elsevier Ltd. All rights reserved.

Thermal expansion in dispersion-bound molecular crystals

NASA Astrophysics Data System (ADS)

Ko, Hsin-Yu; DiStasio, Robert A.; Santra, Biswajit; Car, Roberto

2018-05-01

We explore how anharmonicity, nuclear quantum effects (NQE), many-body dispersion interactions, and Pauli repulsion influence thermal properties of dispersion-bound molecular crystals. Accounting for anharmonicity with ab initio molecular dynamics yields cell parameters accurate to within 2 % of experiment for a set of pyridinelike molecular crystals at finite temperatures and pressures. From the experimental thermal expansion curve, we find that pyridine-I has a Debye temperature just above its melting point, indicating sizable NQE across the entire crystalline range of stability. We find that NQE lead to a substantial volume increase in pyridine-I (≈40 % more than classical thermal expansion at 153 K) and attribute this to intermolecular Pauli repulsion promoted by intramolecular quantum fluctuations. When predicting delicate properties such as the thermal expansivity, we show that many-body dispersion interactions and more sophisticated density functional approximations improve the accuracy of the theoretical model.

Thermal expansion in dispersion-bound molecular crystals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ko, Hsin -Yu; DiStasio, Robert A.; Santra, Biswajit

In this paper, we explore how anharmonicity, nuclear quantum effects (NQE), many-body dispersion interactions, and Pauli repulsion influence thermal properties of dispersion-bound molecular crystals. Accounting for anharmonicity with ab initio molecular dynamics yields cell parameters accurate to within 2% of experiment for a set of pyridinelike molecular crystals at finite temperatures and pressures. From the experimental thermal expansion curve, we find that pyridine-I has a Debye temperature just above its melting point, indicating sizable NQE across the entire crystalline range of stability. We find that NQE lead to a substantial volume increase in pyridine-I (≈ 40% more than classical thermalmore » expansion at 153 K) and attribute this to intermolecular Pauli repulsion promoted by intramolecular quantum fluctuations. Finally, when predicting delicate properties such as the thermal expansivity, we show that many-body dispersion interactions and more sophisticated density functional approximations improve the accuracy of the theoretical model.« less

A Java-based tool for the design of classification microarrays.

PubMed

Meng, Da; Broschat, Shira L; Call, Douglas R

2008-08-04

Classification microarrays are used for purposes such as identifying strains of bacteria and determining genetic relationships to understand the epidemiology of an infectious disease. For these cases, mixed microarrays, which are composed of DNA from more than one organism, are more effective than conventional microarrays composed of DNA from a single organism. Selection of probes is a key factor in designing successful mixed microarrays because redundant sequences are inefficient and limited representation of diversity can restrict application of the microarray. We have developed a Java-based software tool, called PLASMID, for use in selecting the minimum set of probe sequences needed to classify different groups of plasmids or bacteria. The software program was successfully applied to several different sets of data. The utility of PLASMID was illustrated using existing mixed-plasmid microarray data as well as data from a virtual mixed-genome microarray constructed from different strains of Streptococcus. Moreover, use of data from expression microarray experiments demonstrated the generality of PLASMID. In this paper we describe a new software tool for selecting a set of probes for a classification microarray. While the tool was developed for the design of mixed microarrays-and mixed-plasmid microarrays in particular-it can also be used to design expression arrays. The user can choose from several clustering methods (including hierarchical, non-hierarchical, and a model-based genetic algorithm), several probe ranking methods, and several different display methods. A novel approach is used for probe redundancy reduction, and probe selection is accomplished via stepwise discriminant analysis. Data can be entered in different formats (including Excel and comma-delimited text), and dendrogram, heat map, and scatter plot images can be saved in several different formats (including jpeg and tiff). Weights generated using stepwise discriminant analysis can be stored for analysis of subsequent experimental data. Additionally, PLASMID can be used to construct virtual microarrays with genomes from public databases, which can then be used to identify an optimal set of probes.

Accounting for the dispersion in the x ray properties of early-type galaxies

NASA Technical Reports Server (NTRS)

White, Raymond E., III; Sarazin, Craig L.

1990-01-01

The x ray luminosities of early-type galaxies are correlated with their optical (e.g., blue) luminosities (L sub X approx. L sub B exp 1.6), but the x ray luminosities exhibit considerable scatter for a given optical luminosity L sub B. This dispersion in x ray luminosity is much greater than the dispersion of other properties of early-type galaxies (for a given L sub B), such as luminosity scale-length, velocity dispersion, color, and metallicity. Here, researchers consider several possible sources for the dispersion in x ray luminosity. Some of the scatter in x ray luminosity may result from stellar population variations between galaxies with similar L sub B. Since the x ray emitting gas is from accumulated stellar mass loss, the L sub X dispersion may be due to variations in integrated stellar mass loss rates. Another possible cause of the L sub X dispersion may be variations in the amount of cool material in the galaxies; cool gas may act as an energy sink for the hot gas. Infrared emission may be used to trace such cool material, so researchers look for a correlation between the infrared emission and the x ray emission of early-type galaxies at fixed L sub B. Velocity dispersion variations between galaxies of similar L sub B may also contribute to the L sub X dispersion. The most likely a priori source of the dispersion in L sub X is probably the varying amount of ram-pressure stripping in a range of galaxy environments. The hot gaseous halos of early-type galaxies can be stripped in encounters with other galaxies or with ambient cluster gas if the intracluster gas is sufficiently dense. Researchers find that the most likely cause of dispersion in the x ray properties of early type galaxies is probably the ram-pressure stripping of gaseous halos from galaxies. For a sample of 81 early-type galaxies with x ray luminosities or upper limits derived from Einstein Observatory observations (CFT) researchers calculated the cumulative distribution of angular distances between the x ray sample members and bright galaxies from the Revised Shapley - Ames catalog. Collectively, galaxies with low x ray luminosities (for a given L sub B) tend to be in denser environments than galaxies with higher x ray luminosities.

THE ABRF MARG MICROARRAY SURVEY 2005: TAKING THE PULSE ON THE MICROARRAY FIELD

EPA Science Inventory

Over the past several years microarray technology has evolved into a critical component of any discovery based program. Since 1999, the Association of Biomolecular Resource Facilities (ABRF) Microarray Research Group (MARG) has conducted biennial surveys designed to generate a pr...

Development of a Digital Microarray with Interferometric Reflectance Imaging

NASA Astrophysics Data System (ADS)

Sevenler, Derin

This dissertation describes a new type of molecular assay for nucleic acids and proteins. We call this technique a digital microarray since it is conceptually similar to conventional fluorescence microarrays, yet it performs enumerative ('digital') counting of the number captured molecules. Digital microarrays are approximately 10,000-fold more sensitive than fluorescence microarrays, yet maintain all of the strengths of the platform including low cost and high multiplexing (i.e., many different tests on the same sample simultaneously). Digital microarrays use gold nanorods to label the captured target molecules. Each gold nanorod on the array is individually detected based on its light scattering, with an interferometric microscopy technique called SP-IRIS. Our optimized high-throughput version of SP-IRIS is able to scan a typical array of 500 spots in less than 10 minutes. Digital DNA microarrays may have utility in applications where sequencing is prohibitively expensive or slow. As an example, we describe a digital microarray assay for gene expression markers of bacterial drug resistance.

Implementation of mutual information and bayes theorem for classification microarray data

NASA Astrophysics Data System (ADS)

Dwifebri Purbolaksono, Mahendra; Widiastuti, Kurnia C.; Syahrul Mubarok, Mohamad; Adiwijaya; Aminy Ma’ruf, Firda

2018-03-01

Microarray Technology is one of technology which able to read the structure of gen. The analysis is important for this technology. It is for deciding which attribute is more important than the others. Microarray technology is able to get cancer information to diagnose a person’s gen. Preparation of microarray data is a huge problem and takes a long time. That is because microarray data contains high number of insignificant and irrelevant attributes. So, it needs a method to reduce the dimension of microarray data without eliminating important information in every attribute. This research uses Mutual Information to reduce dimension. System is built with Machine Learning approach specifically Bayes Theorem. This theorem uses a statistical and probability approach. By combining both methods, it will be powerful for Microarray Data Classification. The experiment results show that system is good to classify Microarray data with highest F1-score using Bayesian Network by 91.06%, and Naïve Bayes by 88.85%.

Protein microarray with horseradish peroxidase chemiluminescence for quantification of serum α-fetoprotein.

PubMed

Zhao, Yuanshun; Zhang, Yonghong; Lin, Dongdong; Li, Kang; Yin, Chengzeng; Liu, Xiuhong; Jin, Boxun; Sun, Libo; Liu, Jinhua; Zhang, Aiying; Li, Ning

2015-10-01

To develop and evaluate a protein microarray assay with horseradish peroxidase (HRP) chemiluminescence for quantification of α-fetoprotein (AFP) in serum from patients with hepatocellular carcinoma (HCC). A protein microarray assay for AFP was developed. Serum was collected from patients with HCC and healthy control subjects. AFP was quantified using protein microarray and enzyme-linked immunosorbent assay (ELISA). Serum AFP concentrations determined via protein microarray were positively correlated (r = 0.973) with those determined via ELISA in patients with HCC (n = 60) and healthy control subjects (n = 30). Protein microarray showed 80% sensitivity and 100% specificity for HCC diagnosis. ELISA had 83.3% sensitivity and 100% specificity. Protein microarray effectively distinguished between patients with HCC and healthy control subjects (area under ROC curve 0.974; 95% CI 0.000, 1.000). Protein microarray is a rapid, simple and low-cost alternative to ELISA for detecting AFP in human serum. © The Author(s) 2015.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Kyung Eun; Oh, Jung Jae; Yun, Taeyeong

Graphene is an emerging graphitic carbon materials, consisting of sp{sup 2} hybridized two dimensinal honeycomb structure. It has been widely studied to incorporate graphene with polymer to utilize unique property of graphene and reinforce electrical, mechanical and thermal property of polymer. In composite materials, orientation control of graphene significantly influences the property of composite. Until now, a few method has been developed for orientation control of graphene within polymer matrix. Here, we demonstrate facile fabrication of high aligned large graphene oxide (LGO) composites in polydimethylsiloxane (PDMS) matrix exploiting liquid crystallinity. Liquid crystalline aqueous dispersion of LGO is parallel oriented withinmore » flat confinement geometry. Freeze-drying of the aligned LGO dispersion and subsequent infiltration with PDMS produce highly aligned LGO/PDMS composites. Owing to the large shape anisotropy of LGO, liquid crystalline alignment occurred at low concentration of 2 mg/ml in aqueous dispersion, which leads to the 0.2 wt% LGO loaded composites. - Graphical abstract: Liquid crystalline LGO aqueous dispersions are spontaneous parallel aligned between geometric confinement for highly aligned LGO/polymer composite fabrication. - Highlights: • A simple fabrication method for highly aligned LGO/PDMS composites is proposed. • LGO aqueous dispersion shows nematic liquid crystalline phase at 0.8 mg/ml. • In nematic phase, LGO flakes are highly aligned by geometric confinement. • Infiltration of PDMS into freeze-dried LGO allows highly aligned LGO/PDMS composites.« less

Comparative study of classification algorithms for immunosignaturing data

PubMed Central

2012-01-01

Background High-throughput technologies such as DNA, RNA, protein, antibody and peptide microarrays are often used to examine differences across drug treatments, diseases, transgenic animals, and others. Typically one trains a classification system by gathering large amounts of probe-level data, selecting informative features, and classifies test samples using a small number of features. As new microarrays are invented, classification systems that worked well for other array types may not be ideal. Expression microarrays, arguably one of the most prevalent array types, have been used for years to help develop classification algorithms. Many biological assumptions are built into classifiers that were designed for these types of data. One of the more problematic is the assumption of independence, both at the probe level and again at the biological level. Probes for RNA transcripts are designed to bind single transcripts. At the biological level, many genes have dependencies across transcriptional pathways where co-regulation of transcriptional units may make many genes appear as being completely dependent. Thus, algorithms that perform well for gene expression data may not be suitable when other technologies with different binding characteristics exist. The immunosignaturing microarray is based on complex mixtures of antibodies binding to arrays of random sequence peptides. It relies on many-to-many binding of antibodies to the random sequence peptides. Each peptide can bind multiple antibodies and each antibody can bind multiple peptides. This technology has been shown to be highly reproducible and appears promising for diagnosing a variety of disease states. However, it is not clear what is the optimal classification algorithm for analyzing this new type of data. Results We characterized several classification algorithms to analyze immunosignaturing data. We selected several datasets that range from easy to difficult to classify, from simple monoclonal binding to complex binding patterns in asthma patients. We then classified the biological samples using 17 different classification algorithms. Using a wide variety of assessment criteria, we found ‘Naïve Bayes’ far more useful than other widely used methods due to its simplicity, robustness, speed and accuracy. Conclusions ‘Naïve Bayes’ algorithm appears to accommodate the complex patterns hidden within multilayered immunosignaturing microarray data due to its fundamental mathematical properties. PMID:22720696

Interpretation of magnetotelluric measurements over an electrically dispersive one-dimensional earth

DOE Office of Scientific and Technical Information (OSTI.GOV)

Patella, D.

1987-01-01

Frequency dispersion of electromagnetic parameters of earth materials has been widely documented in recent years. It is claimed that magnetotellurics (MT)may be significantly affected by dispersion. This paper studies the MT plane-wave interpretative problem for a one-dimensional earth characterized by the presence of dispersive layers. The theoretical properties of the MT field under the dispersion hypothesis, and the main features of the dispersion phenomenon are synthetically reviewed. The examination of previously published MT curve responses over some models of dispersive earth section shows that ambiguity can arise when interpreting MT data with no other source of information. Thus it maybemore » almost impossible to distinguish between the response of a dispersive section and an equally probable dispersion-free section. The dispersion magnetotelluric (DMT) method is proposed as a means to resolve the ambiguity. The DMT method is based on the execution, at the same site, of an MT sounding and of an always dispersion-free dc geoelectric deep sounding.« less

Polymer-Single Wall Carbon Nanotube Composites for Potential Spacecraft Applications

NASA Technical Reports Server (NTRS)

Park, C.; Ounaies, Z.; Watson, K. A.; Pawlowski, K.; Lowther, S. E.; Connell, J. W.; Siochi, E. J.; Harrison, J. S.; St.Clair, T. L.; Bushnell, Dennis M. (Technical Monitor)

2002-01-01

Polymer-single wall carbon nanotube (SWNT) composite films were prepared and characterized as part of an effort to develop polymeric materials with improved combinations of properties for potential use on future spacecraft. Next generation spacecraft will require ultra-lightweight materials that possess specific and unique combinations of properties such as radiation and atomic oxygen resistance, low solar absorptivity, high thermal emissitivity, electrical conductivity, tear resistance, ability to be folded and seamed, and good mechanical properties. The objective of this work is to incorporate sufficient electrical conductivity into space durable polyimides to mitigate static charge build-up. The challenge is to obtain this level of conductivity (10(exp -8) S/cm) without degrading other properties of importance, particularly optical transparency. Several different approaches were attempted to fully disperse the SWNTs into the polymer matrix. These included high shear mixing, sonication, and synthesizing the polymers in the presence of pre-dispersed SWNTs. Acceptable levels of conductivity were obtained at loading levels less than one tenth weight percent SWNT without significantly sacrificing optical properties. Characterization of the nanocomposite films and the effect of SWNT concentration and dispersion on the conductivity, solar absorptivity, thermal emissivity, mechanical and thermal properties were discussed. Fibers and non-woven porous mats of SWNT reinforced polymer nanocomposite were produced using electrospinning.

The Microarray Revolution: Perspectives from Educators

ERIC Educational Resources Information Center

Brewster, Jay L.; Beason, K. Beth; Eckdahl, Todd T.; Evans, Irene M.

2004-01-01

In recent years, microarray analysis has become a key experimental tool, enabling the analysis of genome-wide patterns of gene expression. This review approaches the microarray revolution with a focus upon four topics: 1) the early development of this technology and its application to cancer diagnostics; 2) a primer of microarray research,…

Individual dispersal, landscape connectivity and ecological networks.

PubMed

Baguette, Michel; Blanchet, Simon; Legrand, Delphine; Stevens, Virginie M; Turlure, Camille

2013-05-01

Connectivity is classically considered an emergent property of landscapes encapsulating individuals' flows across space. However, its operational use requires a precise understanding of why and how organisms disperse. Such movements, and hence landscape connectivity, will obviously vary according to both organism properties and landscape features. We review whether landscape connectivity estimates could gain in both precision and generality by incorporating three fundamental outcomes of dispersal theory. Firstly, dispersal is a multi-causal process; its restriction to an 'escape reaction' to environmental unsuitability is an oversimplification, as dispersing individuals can leave excellent quality habitat patches or stay in poor-quality habitats according to the relative costs and benefits of dispersal and philopatry. Secondly, species, populations and individuals do not always react similarly to those cues that trigger dispersal, which sometimes results in contrasting dispersal strategies. Finally, dispersal is a major component of fitness and is thus under strong selective pressures, which could generate rapid adaptations of dispersal strategies. Such evolutionary responses will entail spatiotemporal variation in landscape connectivity. We thus strongly recommend the use of genetic tools to: (i) assess gene flow intensity and direction among populations in a given landscape; and (ii) accurately estimate landscape features impacting gene flow, and hence landscape connectivity. Such approaches will provide the basic data for planning corridors or stepping stones aiming at (re)connecting local populations of a given species in a given landscape. This strategy is clearly species- and landscape-specific. But we suggest that the ecological network in a given landscape could be designed by stacking up such linkages designed for several species living in different ecosystems. This procedure relies on the use of umbrella species that are representative of other species living in the same ecosystem. © 2012 The Authors. Biological Reviews © 2012 Cambridge Philosophical Society.

Effect of secondary flows on dispersion in finite-length channels at high Peclet numbers

NASA Astrophysics Data System (ADS)

Adrover, Alessandra

2013-09-01

We investigate the effects of secondary (transverse) flows on convection-dominated dispersion of pressure driven, open column laminar flow in a conduit with rectangular cross-section. We show that secondary flows significantly reduce dispersion (enhancing transverse diffusion) in Taylor-Aris regime [H. Zhao and H. H. Bau, "Effect of secondary flows on Taylor-Aris dispersion," Anal. Chem. 79, 7792-7798 (2007)], as well as in convection-controlled regime. In the convection-controlled dispersion regime (i.e., laminar dispersion in finite-length channel with axial flow at high Peclet numbers) the properties of the dispersion boundary layer and the values of the scaling exponents controlling the dependence of the moment hierarchy on the Peclet number m^{(n)}_out ˜ Pe_eff^{θ _n} are determined by the local near-wall behaviour of the axial velocity. The presence of transverse flows strongly modify the localization properties of the dispersion boundary layer and consequently the moment scaling exponents. Different secondary flows, electrokinetically induced and independent of the primary axial flow are considered. A complete scaling theory is presented for the nth order moment of the outlet chromatogram as a function of the axial Peclet number, the secondary flow's pattern and intensity. We show that some secondary flows (the corotating and the counter-rotating cavity flows) significantly reduce dispersion and m^{(n)}_out ˜ Pe_eff^{(n-1)/3}. No significant dispersion reduction is obtained with the cavity cross-flow m^{(n)}_out ˜ Pe_eff^{(n-1)/2}. The best result is obtained with the two full-motion counter-rotating cross-flows because m^{(n)}_out saturates towards a constant value. Theoretical results from scaling theory are strongly supported by numerical results obtained by Finite Element Method.

Binary-corrected velocity dispersions from single- and multi-epoch radial velocities: massive stars in R136 as a test case

NASA Astrophysics Data System (ADS)

Cottaar, M.; Hénault-Brunet, V.

2014-02-01

Orbital motions from binary stars can broaden the observed line-of-sight velocity distribution of a stellar system and artificially inflate the measured line-of-sight velocity dispersion, which can in turn lead to erroneous conclusions about the dynamical state of the system. Recently, a maximum-likelihood procedure was proposed to recover the intrinsic velocity dispersion of a resolved star cluster from a single epoch of radial velocity data of individual stars, which was achieved by simultaneously fitting the intrinsic velocity distribution of the single stars and the centers of mass of the binaries along with the velocity shifts caused by binary orbital motions. Assuming well-characterized binary properties, this procedure can accurately reproduce intrinsic velocity dispersions below 1 km s-1 for solar-type stars. Here we investigate the systematic offsets induced when the binary properties are uncertain and we show that two epochs of radial velocity data with an appropriate baseline can help to mitigate these systematic effects. We first test the method described above using Monte Carlo simulations, taking into account the large uncertainties in the binary properties of OB stars. We then apply it to radial velocity data in the young massive cluster R136 for which the intrinsic velocity dispersion of O-type stars is known from an intensive multi-epoch approach. For typical velocity dispersions of young massive clusters (≳4 km s-1) and with a single epoch of data, we demonstrate that the method can just about distinguish between a cluster in virial equilibrium and an unbound cluster. This is due to the higher spectroscopic binary fraction and more loosely constrained distributions of orbital parameters of OB stars compared to solar-type stars. By extending the maximum-likelihood method to multi-epoch data, we show that the accuracy on the fitted velocity dispersion can be improved by only a few percent by using only two epochs of radial velocities. This procedure offers a promising method of accurately measuring the intrinsic stellar velocity dispersion in other systems for which the binary properties are poorly constrained, for example, young clusters and associations whose luminosity is dominated by OB stars. Appendix A is available in electronic form at http://www.aanda.org

Effect of purification method of β-chitin from squid pen on the properties of β-chitin nanofibers.

PubMed

Suenaga, Shin; Nikaido, Nozomi; Totani, Kazuhide; Kawasaki, Kazunori; Ito, Yoshihito; Yamashita, Kazuhiko; Osada, Mitsumasa

2016-10-01

The relationship between purification methods of β-chitin from squid pen and the physicochemical properties of β-chitin nanofibers (NFs) were investigated. Two types of β-chitin were prepared, with β-chitin (a→b) subjected to acid treatment for decalcification and then base treatment for deproteinization, while β-chitin (b→a) was treated in the opposite order. These β-chitins were disintegrated into NFs using wet pulverization. The β-chitin (b→a) NF dispersion has higher transmittance and viscosity than the β-chitin (a→b) NF dispersion. For the first time, we succeeded in obtaining 3D images of the β-chitin NF dispersion in water by using quick-freeze deep-etch replication with high-angle annular dark field scanning transmission electron microscopy. The β-chitin (b→a) NF dispersion has a denser and more uniform 3D network structure than the β-chitin (a→b) NF dispersion. Widths of the β-chitin (a→b) and (b→a) NFs were approximately 8-25 and 3-10nm, respectively. Copyright © 2016 Elsevier B.V. All rights reserved.

Influence of MWCNT/surfactant dispersions on the mechanical properties of Portland cement pastes

NASA Astrophysics Data System (ADS)

Rodríguez, B.; Quintero, J. H.; Arias, Y. P.; Mendoza-Reales, O. A.; Ochoa-Botero, J. C.; Toledo-Filho, R. D.

2017-12-01

This work studies the reinforcing effect of Multi Walled Carbon Nanotubes (MWCNT) on cement pastes. A 0.35% solid concentration of MWCNT in powder was dispersed in deionized water with sodium dodecyl sulfate (cationic surfactant), cetylpyridinium chloride (anionic surfactant) and triton X-100 (amphoteric surfactant) using an ultrasonic tip processor. Three concentrations of each surfactant (1mM, 10mM and 100mM) were tested, and all samples were sonicated until an adequate dispersion degree was obtained. Cement pastes with additions of carbon nanotubes of 0.15% by mass of cement were produced in two steps; first the dispersions of MWCNT were combined with the mixing water using an ultrasonic tip processor to guarantee homogeneity, and then cement was added and mixed until a homogeneous paste was obtained. Direct tensile strength, apparent density and open porosity of the pastes were measured after 7 days of curing. It was found that the MWCNT/surfactants dispersions decrease the mechanical properties of the cement based matrix due to an increased porosity caused by the presence of surfactants.

Electrical properties of dispersions of graphene in mineral oil

DOE Office of Scientific and Technical Information (OSTI.GOV)

Monteiro, O. R., E-mail: othon.monteiro@bakerhughes.com

2014-02-03

Dispersions of graphene in mineral oil have been prepared and electrical conductivity and permittivity have been measured. The direct current (DC) conductivity of the dispersions depends on the surface characteristics of the graphene platelets and followed a percolation model with a percolation threshold ranging from 0.05 to 0.1 wt. %. The difference in DC conductivities can be attributed to different states of aggregation of the graphene platelets and to the inter-particle electron transfer, which is affected by the surface radicals. The frequency-dependent conductivity (σ(ω)) and permittivity (ε(ω)) were also measured. The conductivity of dispersions with particle contents much greater than themore » percolation threshold remains constant and equal to the DC conductivity at low frequencies ω with and followed a power-law σ(ω)∝ ω{sup s} dependence at very high frequencies with s≈0.9. For dispersions with graphene concentration near the percolation threshold, a third regime was displayed at intermediate frequencies indicative of interfacial polarization consistent with Maxwell-Wagner effect typically observed in mixtures of two (or more) phases with very distinct electrical and dielectric properties.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mills, G.J.; Brown, G.G.; Waterman, D.D.

The feasibility of prestressing commercial boron/epoxy and graphite/epoxy prepreg material to higher strengths and lower property dispersions is demonstrated. Its practical application as an on-line process for improving quality levels is possible with minor modifications to current experimental practice. The mechanics of the bendstressing method affects a controlled alteration in the fiber defect content to the extent that composite improvements can be achieved approaching the inherent fiber quality with dispersions in properties reduced to the 1 to 2% range. (Author, modified-PL)

Improving the reliability of road materials based on micronized sulfur composites

NASA Astrophysics Data System (ADS)

Abdrakhmanova, K. K.

2015-01-01

The work contains the results of a nano-structural modification of sulfur that prevents polymorphic transformations from influencing the properties of sulfur composites where sulfur is present in a thermodynamic stable condition that precludes destruction when operated. It has been established that the properties of sulfur-based composite materials can be significantly improved by modifying sulfur and structuring sulfur binder by nano-dispersed fiber particles and ultra-dispersed state filler. The paper shows the possibility of modifying Tengiz sulfur by its fragmenting which ensures that the structured sulfur is structurally changed and stabilized through reinforcement by ultra-dispersed fiber particles allowing the phase contact area to be multiplied. Interaction between nano-dispersed fibers of chrysotile asbestos and sulfur ensures the implementation of the mechanical properties of chrysotile asbestos tubes in reinforced composite and its integrity provided that the surface of chrysotile asbestos tubes are highly moistened with molten sulfur and there is high adhesion between the tubes and the matrix that, in addition to sulfur, contains limestone microparticles. Ability to apply materials in severe operation conditions and possibility of exposure in both aggressive medium and mechanical loads makes produced sulfur composites required by the road construction industry.

Epoxy and Silicone Optical Nanocomposites Filled with Grafted Nanoparticles

NASA Astrophysics Data System (ADS)

Tao, Peng

Polymer nanocomposites, as a technologically important class of materials, exhibit diverse functional properties, and are used for applications ranging from structural and biomedical to electronic and optical. The properties of polymer nanocomposites are determined, in part, by the chemical composition of the polymer matrix and the nanofillers. Their properties are also sensitive to the geometry and size of the nanofillers, and to spatial distribution of the fillers. Control of the nanoparticle size and dispersion within a given polymer provides opportunities to tailor and optimize the properties of nanocomposites for specific application. For optical applications such as encapsulation of light emitting diodes (LEDs), polymer nanocomposites filled with homogeneously dispersed nanoparticles would endow the polymer encapsulant with new functionality without sacrificing optical transparency. To this end, this thesis focuses on developing a simple and versatile approach towards the fabrication of epoxy and silicone transparent nanocomposites using matrix compatible chain-grafted nanoparticles as fillers, and studying the optical properties of the nanocomposites. The surface chemistry and grafted polymer chain design have been shown to play an important role in determining the dispersion state of the grafted nanoparticles and hence the final optical properties of the nanocomposites. To prepare transparent epoxy nanocomposites, poly (glycidyl methacrylate) (PGMA) chains were grafted onto the optical nanoparticle surfaces via a combined phosphate ligand exchange process and azide-alkyne "click" chemistry. The dispersion behavior of PGMA-grafted nanoparticles within the epoxy matrix was investigated by systematically varying the grafting density and grafted chain length. It was found that within the small molecular weight epoxy resins, the dispersion states are more sensitive to the grafting density than the molecular weight of grafted chains. With high grafting densities, the grafted PGMA brushes effectively screen the van der Waals attraction between the particles, and homogenous nanoparticle dispersions of grafted nanoparticles were obtained. Transparent high refractive index TiO2/epoxy thin film and bulk nancomposites were obtained by dispersing PGMA brushes-grafted TiO2 nanoparticles into a commercial epoxy matrix. The refractive index of the nanocomposites showed a linear dependence on the volume fraction of TiO2 nanoparticles and the optical transparency could be generally described by the Rayleigh scattering model. This powerful dispersing technique was further employed to make visibly transparent, UV/IR blocking ITO/epoxy nanocomposites which can be easily applied onto glass and plastic substrates as energy saving optical coating materials. To produce transparent silicone nanocomposites, we directly coupled phosphate-terminated PDMS chains onto the optical nanoparticle surface. It was observed that the mono-modal PDMS-grafted particles usually formed agglomerates within silicone matrices, whereas the bimodal PDMS-grafted particles were able to be individually dispersed even within high molecular weight matrices. Transparent high refractive index bulk TiO2/silicone nanocomposites were successfully prepared by filling with bimodal PDMS-grafted TiO2 nanoparticles. Furthermore, we used the PDMS-grafted TiO2/silicone nanocomposite as a model system to create a methodology to predict and control the dispersion behavior of grafted nanoparticles. The good agreement between experimental observation of dispersion of mono-modal and bimodal grafted particles and theoretical prediction would better guide future experiments and lead to predictability in polymer composite design. Finally, the bimodal grafted chain design was implemented in the preparation of transparent and luminescent CdSe/silicone nanocomposites with potential application as non-scattering light conversion materials for LEDs. The homogeneous dispersion of bimodal PDMS-grafted CdSe quantum dots not only minimizes the transparency loss due to scattering, but also benefits the uniformity and long-term stability of photoluminescence of the nanocomposites.

Recent progress in making protein microarray through BioLP

NASA Astrophysics Data System (ADS)

Yang, Rusong; Wei, Lian; Feng, Ying; Li, Xiujian; Zhou, Quan

2017-02-01

Biological laser printing (BioLP) is a promising biomaterial printing technique. It has the advantage of high resolution, high bioactivity, high printing frequency and small transported liquid amount. In this paper, a set of BioLP device is design and made, and protein microarrays are printed by this device. It's found that both laser intensity and fluid layer thickness have an influence on the microarrays acquired. Besides, two kinds of the fluid layer coating methods are compared, and the results show that blade coating method is better than well-coating method in BioLP. A microarray of 0.76pL protein microarray and a "NUDT" patterned microarray are printed to testify the printing ability of BioLP.

The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models

EPA Science Inventory

The second phase of the MicroArray Quality Control (MAQC-II) project evaluated common practices for developing and validating microarray-based models aimed at predicting toxicological and clinical endpoints. Thirty-six teams developed classifiers for 13 endpoints - some easy, som...

Reconstructing the temporal ordering of biological samples using microarray data.

PubMed

Magwene, Paul M; Lizardi, Paul; Kim, Junhyong

2003-05-01

Accurate time series for biological processes are difficult to estimate due to problems of synchronization, temporal sampling and rate heterogeneity. Methods are needed that can utilize multi-dimensional data, such as those resulting from DNA microarray experiments, in order to reconstruct time series from unordered or poorly ordered sets of observations. We present a set of algorithms for estimating temporal orderings from unordered sets of sample elements. The techniques we describe are based on modifications of a minimum-spanning tree calculated from a weighted, undirected graph. We demonstrate the efficacy of our approach by applying these techniques to an artificial data set as well as several gene expression data sets derived from DNA microarray experiments. In addition to estimating orderings, the techniques we describe also provide useful heuristics for assessing relevant properties of sample datasets such as noise and sampling intensity, and we show how a data structure called a PQ-tree can be used to represent uncertainty in a reconstructed ordering. Academic implementations of the ordering algorithms are available as source code (in the programming language Python) on our web site, along with documentation on their use. The artificial 'jelly roll' data set upon which the algorithm was tested is also available from this web site. The publicly available gene expression data may be found at http://genome-www.stanford.edu/cellcycle/ and http://caulobacter.stanford.edu/CellCycle/.

Emission color-tuned light-emitting diode microarrays of nonpolar In xGa 1–xN/GaN multishell nanotube heterostructures

DOE PAGES

Hong, Young Joon; Lee, Chul -Ho; Yoo, Jinkyoung; ...

2015-12-09

Integration of nanostructure lighting source arrays with well-defined emission wavelengths is of great importance for optoelectronic integrated monolithic circuitry. We report on the fabrication and optical properties of GaN-based p–n junction multishell nanotube microarrays with composition-modulated nonpolar m-plane In xGa 1–xN/GaN multiple quantum wells (MQWs) integrated on c-sapphire or Si substrates. The emission wavelengths were controlled in the visible spectral range of green to violet by varying the indium mole fraction of the In xGa 1–xN MQWs in the range 0.13 ≤ x ≤ 0.36. Homogeneous emission from the entire area of the nanotube LED arrays was achieved via themore » formation of MQWs with uniform QW widths and composition by heteroepitaxy on the well-ordered nanotube arrays. Importantly, the wavelength-invariant electroluminescence emission was observed above a turn-on of 3.0 V because both the quantum-confinement Stark effect and band filling were suppressed due to the lack of spontaneous inherent electric field in the m-plane nanotube nonpolar MQWs. Lastly, the method of fabricating the multishell nanotube LED microarrays with controlled emission colors has potential applications in monolithic nonpolar photonic and optoelectronic devices on commonly used c-sapphire and Si substrates.« less

High-throughput screening of Erwinia chrysanthemi pectin methylesterase variants using carbohydrate microarrays.

PubMed

Øbro, Jens; Sørensen, Iben; Derkx, Patrick; Madsen, Christian T; Drews, Martin; Willer, Martin; Mikkelsen, Jørn D; Willats, William G T

2009-04-01

Pectin methylesterases (PMEs) catalyse the removal of methyl esters from the homogalacturonan (HG) backbone domain of pectin, a ubiquitous polysaccharide in plant cell walls. The degree of methyl esterification (DE) impacts upon the functional properties of HG within cell walls and plants produce numerous PMEs that act upon HG in muro. Many microbial plant pathogens also produce PMEs, the activity of which renders HG more susceptible to cleavage by pectin lyase and polygalacturonase enzymes and hence aids cell wall degradation. We have developed a novel microarray-based approach to investigate the activity of a series of variant enzymes based on the PME from the important pathogen Erwinia chrysanthemi. A library of 99 E. chrysanthemi PME mutants was created in which seven amino acids were altered by various different substitutions. Each mutant PME was incubated with a highly methyl esterified lime pectin substrate and, after digestion the enzyme/substrate mixtures were printed as microarrays. The loss of activity that resulted from certain mutations was detected by probing arrays with a mAb (JIM7) that preferentially binds to HG with a relatively high DE. Active PMEs therefore resulted in diminished JIM7 binding to the lime pectin substrate, whereas inactive PMEs did not. Our findings demonstrate the feasibility of our approach for rapidly testing the effects on PME activity of substituting a wide variety of amino acids at different positions.

Flow-pattern Guided Fabrication of High-density Barcode Antibody Microarray

PubMed Central

Ramirez, Lisa S.; Wang, Jun

2016-01-01

Antibody microarray as a well-developed technology is currently challenged by a few other established or emerging high-throughput technologies. In this report, we renovate the antibody microarray technology by using a novel approach for manufacturing and by introducing new features. The fabrication of our high-density antibody microarray is accomplished through perpendicularly oriented flow-patterning of single stranded DNAs and subsequent conversion mediated by DNA-antibody conjugates. This protocol outlines the critical steps in flow-patterning DNA, producing and purifying DNA-antibody conjugates, and assessing the quality of the fabricated microarray. The uniformity and sensitivity are comparable with conventional microarrays, while our microarray fabrication does not require the assistance of an array printer and can be performed in most research laboratories. The other major advantage is that the size of our microarray units is 10 times smaller than that of printed arrays, offering the unique capability of analyzing functional proteins from single cells when interfacing with generic microchip designs. This barcode technology can be widely employed in biomarker detection, cell signaling studies, tissue engineering, and a variety of clinical applications. PMID:26780370

Microarray platform for omics analysis

NASA Astrophysics Data System (ADS)

Mecklenburg, Michael; Xie, Bin

2001-09-01

Microarray technology has revolutionized genetic analysis. However, limitations in genome analysis has lead to renewed interest in establishing 'omic' strategies. As we enter the post-genomic era, new microarray technologies are needed to address these new classes of 'omic' targets, such as proteins, as well as lipids and carbohydrates. We have developed a microarray platform that combines self- assembling monolayers with the biotin-streptavidin system to provide a robust, versatile immobilization scheme. A hydrophobic film is patterned on the surface creating an array of tension wells that eliminates evaporation effects thereby reducing the shear stress to which biomolecules are exposed to during immobilization. The streptavidin linker layer makes it possible to adapt and/or develop microarray based assays using virtually any class of biomolecules including: carbohydrates, peptides, antibodies, receptors, as well as them ore traditional DNA based arrays. Our microarray technology is designed to furnish seamless compatibility across the various 'omic' platforms by providing a common blueprint for fabricating and analyzing arrays. The prototype microarray uses a microscope slide footprint patterned with 2 by 96 flat wells. Data on the microarray platform will be presented.

MAPPING SUNKEN POLLUTANT POOLS WITH DEPTH FINDERS

EPA Science Inventory

Many hazardous substances and mixtures are immiscible with and more dense than water. When spillages or releases into waterbodies occur, the hazardous materials will disperse in a pattern controlled by physical properties of the material, flow and dispersion effects, and topograp...

Pulse Transmission Over Dispersive Waveguides in Railroad Communications : Software for Computer Simulation

DOT National Transportation Integrated Search

1973-07-01

Waveguides and transmission lines employed in train communications exhibit dispersion, which is caused by (a) their inherent properties and (b) the cumulative effect of discontinuities at joints. To provide the means to evaluate such waveguides, seve...

On-Chip Synthesis of Protein Microarrays from DNA Microarrays Via Coupled In Vitro Transcription and Translation for Surface Plasmon Resonance Imaging Biosensor Applications

PubMed Central

Seefeld, Ting H.; Halpern, Aaron R.; Corn, Robert M.

2012-01-01

Protein microarrays are fabricated from double-stranded DNA (dsDNA) microarrays by a one-step, multiplexed enzymatic synthesis in an on-chip microfluidic format and then employed for antibody biosensing measurements with surface plasmon resonance imaging (SPRI). A microarray of dsDNA elements (denoted as generator elements) that encode either a His-tagged green fluorescent protein (GFP) or a His-tagged luciferase protein is utilized to create multiple copies of messenger RNA (mRNA) in a surface RNA polymerase reaction; the mRNA transcripts are then translated into proteins by cell-free protein synthesis in a microfluidic format. The His-tagged proteins diffuse to adjacent Cu(II)-NTA microarray elements (denoted as detector elements) and are specifically adsorbed. The net result is the on-chip, cell-free synthesis of a protein microarray that can be used immediately for SPRI protein biosensing. The dual element format greatly reduces any interference from the nonspecific adsorption of enzyme or proteins. SPRI measurements for the detection of the antibodies anti-GFP and anti-luciferase were used to verify the formation of the protein microarray. This convenient on-chip protein microarray fabrication method can be implemented for multiplexed SPRI biosensing measurements in both clinical and research applications. PMID:22793370

Fully Automated Complementary DNA Microarray Segmentation using a Novel Fuzzy-based Algorithm.

PubMed

Saberkari, Hamidreza; Bahrami, Sheyda; Shamsi, Mousa; Amoshahy, Mohammad Javad; Ghavifekr, Habib Badri; Sedaaghi, Mohammad Hossein

2015-01-01

DNA microarray is a powerful approach to study simultaneously, the expression of 1000 of genes in a single experiment. The average value of the fluorescent intensity could be calculated in a microarray experiment. The calculated intensity values are very close in amount to the levels of expression of a particular gene. However, determining the appropriate position of every spot in microarray images is a main challenge, which leads to the accurate classification of normal and abnormal (cancer) cells. In this paper, first a preprocessing approach is performed to eliminate the noise and artifacts available in microarray cells using the nonlinear anisotropic diffusion filtering method. Then, the coordinate center of each spot is positioned utilizing the mathematical morphology operations. Finally, the position of each spot is exactly determined through applying a novel hybrid model based on the principle component analysis and the spatial fuzzy c-means clustering (SFCM) algorithm. Using a Gaussian kernel in SFCM algorithm will lead to improving the quality in complementary DNA microarray segmentation. The performance of the proposed algorithm has been evaluated on the real microarray images, which is available in Stanford Microarray Databases. Results illustrate that the accuracy of microarray cells segmentation in the proposed algorithm reaches to 100% and 98% for noiseless/noisy cells, respectively.

Development and application of a fluorescence protein microarray for detecting serum alpha-fetoprotein in patients with hepatocellular carcinoma.

PubMed

Zhang, Aiying; Yin, Chengzeng; Wang, Zhenshun; Zhang, Yonghong; Zhao, Yuanshun; Li, Ang; Sun, Huanqin; Lin, Dongdong; Li, Ning

2016-12-01

Objective To develop a simple, effective, time-saving and low-cost fluorescence protein microarray method for detecting serum alpha-fetoprotein (AFP) in patients with hepatocellular carcinoma (HCC). Method Non-contact piezoelectric print techniques were applied to fluorescence protein microarray to reduce the cost of prey antibody. Serum samples from patients with HCC and healthy control subjects were collected and evaluated for the presence of AFP using a novel fluorescence protein microarray. To validate the fluorescence protein microarray, serum samples were tested for AFP using an enzyme-linked immunosorbent assay (ELISA). Results A total of 110 serum samples from patients with HCC ( n = 65) and healthy control subjects ( n = 45) were analysed. When the AFP cut-off value was set at 20 ng/ml, the fluorescence protein microarray had a sensitivity of 91.67% and a specificity of 93.24% for detecting serum AFP. Serum AFP quantified via fluorescence protein microarray had a similar diagnostic performance compared with ELISA in distinguishing patients with HCC from healthy control subjects (area under receiver operating characteristic curve: 0.906 for fluorescence protein microarray; 0.880 for ELISA). Conclusion A fluorescence protein microarray method was developed for detecting serum AFP in patients with HCC.

Development and application of a fluorescence protein microarray for detecting serum alpha-fetoprotein in patients with hepatocellular carcinoma

PubMed Central

Zhang, Aiying; Yin, Chengzeng; Wang, Zhenshun; Zhang, Yonghong; Zhao, Yuanshun; Li, Ang; Sun, Huanqin; Lin, Dongdong

2016-01-01

Objective To develop a simple, effective, time-saving and low-cost fluorescence protein microarray method for detecting serum alpha-fetoprotein (AFP) in patients with hepatocellular carcinoma (HCC). Method Non-contact piezoelectric print techniques were applied to fluorescence protein microarray to reduce the cost of prey antibody. Serum samples from patients with HCC and healthy control subjects were collected and evaluated for the presence of AFP using a novel fluorescence protein microarray. To validate the fluorescence protein microarray, serum samples were tested for AFP using an enzyme-linked immunosorbent assay (ELISA). Results A total of 110 serum samples from patients with HCC (n = 65) and healthy control subjects (n = 45) were analysed. When the AFP cut-off value was set at 20 ng/ml, the fluorescence protein microarray had a sensitivity of 91.67% and a specificity of 93.24% for detecting serum AFP. Serum AFP quantified via fluorescence protein microarray had a similar diagnostic performance compared with ELISA in distinguishing patients with HCC from healthy control subjects (area under receiver operating characteristic curve: 0.906 for fluorescence protein microarray; 0.880 for ELISA). Conclusion A fluorescence protein microarray method was developed for detecting serum AFP in patients with HCC. PMID:27885040

Genotyping microarray: Mutation screening in Spanish families with autosomal dominant retinitis pigmentosa

PubMed Central

García-Hoyos, María; Cortón, Marta; Ávila-Fernández, Almudena; Riveiro-Álvarez, Rosa; Giménez, Ascensión; Hernan, Inma; Carballo, Miguel; Ayuso, Carmen

2012-01-01

Purpose Presently, 22 genes have been described in association with autosomal dominant retinitis pigmentosa (adRP); however, they explain only 50% of all cases, making genetic diagnosis of this disease difficult and costly. The aim of this study was to evaluate a specific genotyping microarray for its application to the molecular diagnosis of adRP in Spanish patients. Methods We analyzed 139 unrelated Spanish families with adRP. Samples were studied by using a genotyping microarray (adRP). All mutations found were further confirmed with automatic sequencing. Rhodopsin (RHO) sequencing was performed in all negative samples for the genotyping microarray. Results The adRP genotyping microarray detected the mutation associated with the disease in 20 of the 139 families with adRP. As in other populations, RHO was found to be the most frequently mutated gene in these families (7.9% of the microarray genotyped families). The rate of false positives (microarray results not confirmed with sequencing) and false negatives (mutations in RHO detected with sequencing but not with the genotyping microarray) were established, and high levels of analytical sensitivity (95%) and specificity (100%) were found. Diagnostic accuracy was 15.1%. Conclusions The adRP genotyping microarray is a quick, cost-efficient first step in the molecular diagnosis of Spanish patients with adRP. PMID:22736939

Electrostatic stabilization of multi-walled carbon nanotubes dispersed in nonaqueous media.

PubMed

Damasceno, João Paulo V; Zarbin, Aldo J G

2018-06-04

Dispersing carbon nanotubes is an easy and low-cost way to manipulate these solids and allows the preparation of more complex materials or devices, so it is fundamental for further uses that these dispersions have controlled properties and high colloidal stability. In this work we report the spontaneous electrical charge build-up in pristine multi-walled carbon nanotubes dispersed in common organic solvents such as chloroform and tetrahydrofuran and the achievement of dispersions stable for long periods without adding passivant agents or functional groups on nanotubes surface. Results from electrokinetics, homo- and heterocoagulation provided macroscopic evidences that carbon nanotubes acquire electric charges after dispersion in some organic liquids and we confirmed this process by measuring in situ Raman spectra of the nanotubes dispersions with higher surface electric potentials. We also show that the signal of electric potential of the dispersions can be predicted by the acid-base behaviour of the dispersing medium, corroborating previously reports for other dispersions of carbon nanomaterials. Copyright © 2018 Elsevier Inc. All rights reserved.

The General Fishbone Like Dispersion Relation

NASA Astrophysics Data System (ADS)

Zonca, Fulvio

2015-12-01

The following sections are included: * Introduction * Motivation and outline * Fundamental equations * The collisionless gyrokinetic equation * Vorticity equation * Quasi-neutrality condition * Perpendicular Ampère's law * Studying collective modes in burning plasmas * Ideal plasma equilibrium in the low-β limit * Approximations for the energetic population * Characteristic frequencies of particle motions * Alfvén wave frequency and wavelength orderings * Applications of the general theoretical framework * The general fishbone like dispersion relation * Properties of the fishbone like dispersion relation * Derivation of the fishbone like dispersion relation * Special cases of the fishbone like dispersion relation * Toroidal Alfvén Eigenmodes (TAE) * Alfvén Cascades * Summary and discussions * Acknowledgments * References

Tailoring the dispersion behavior of silicon nanophotonic slot waveguides.

PubMed

Mas, Sara; Caraquitena, José; Galán, José V; Sanchis, Pablo; Martí, Javier

2010-09-27

We investigate the chromatic dispersion properties of silicon channel slot waveguides in a broad spectral region centered at ~1.5 μm. The variation of the dispersion profile as a function of the slot fill factor, i.e., the ratio between the slot and waveguide widths, is analyzed. Symmetric as well as asymmetric geometries are considered. In general, two different dispersion regimes are identified. Furthermore, our analysis shows that the zero and/or the peak dispersion wavelengths can be tailored by a careful control of the geometrical waveguide parameters including the cross-sectional area, the slot fill factor, and the slot asymmetry degree.

MicroArray Facility: a laboratory information management system with extended support for Nylon based technologies.

PubMed

Honoré, Paul; Granjeaud, Samuel; Tagett, Rebecca; Deraco, Stéphane; Beaudoing, Emmanuel; Rougemont, Jacques; Debono, Stéphane; Hingamp, Pascal

2006-09-20

High throughput gene expression profiling (GEP) is becoming a routine technique in life science laboratories. With experimental designs that repeatedly span thousands of genes and hundreds of samples, relying on a dedicated database infrastructure is no longer an option.GEP technology is a fast moving target, with new approaches constantly broadening the field diversity. This technology heterogeneity, compounded by the informatics complexity of GEP databases, means that software developments have so far focused on mainstream techniques, leaving less typical yet established techniques such as Nylon microarrays at best partially supported. MAF (MicroArray Facility) is the laboratory database system we have developed for managing the design, production and hybridization of spotted microarrays. Although it can support the widely used glass microarrays and oligo-chips, MAF was designed with the specific idiosyncrasies of Nylon based microarrays in mind. Notably single channel radioactive probes, microarray stripping and reuse, vector control hybridizations and spike-in controls are all natively supported by the software suite. MicroArray Facility is MIAME supportive and dynamically provides feedback on missing annotations to help users estimate effective MIAME compliance. Genomic data such as clone identifiers and gene symbols are also directly annotated by MAF software using standard public resources. The MAGE-ML data format is implemented for full data export. Journalized database operations (audit tracking), data anonymization, material traceability and user/project level confidentiality policies are also managed by MAF. MicroArray Facility is a complete data management system for microarray producers and end-users. Particular care has been devoted to adequately model Nylon based microarrays. The MAF system, developed and implemented in both private and academic environments, has proved a robust solution for shared facilities and industry service providers alike.

MicroArray Facility: a laboratory information management system with extended support for Nylon based technologies

PubMed Central

Honoré, Paul; Granjeaud, Samuel; Tagett, Rebecca; Deraco, Stéphane; Beaudoing, Emmanuel; Rougemont, Jacques; Debono, Stéphane; Hingamp, Pascal

2006-01-01

Background High throughput gene expression profiling (GEP) is becoming a routine technique in life science laboratories. With experimental designs that repeatedly span thousands of genes and hundreds of samples, relying on a dedicated database infrastructure is no longer an option. GEP technology is a fast moving target, with new approaches constantly broadening the field diversity. This technology heterogeneity, compounded by the informatics complexity of GEP databases, means that software developments have so far focused on mainstream techniques, leaving less typical yet established techniques such as Nylon microarrays at best partially supported. Results MAF (MicroArray Facility) is the laboratory database system we have developed for managing the design, production and hybridization of spotted microarrays. Although it can support the widely used glass microarrays and oligo-chips, MAF was designed with the specific idiosyncrasies of Nylon based microarrays in mind. Notably single channel radioactive probes, microarray stripping and reuse, vector control hybridizations and spike-in controls are all natively supported by the software suite. MicroArray Facility is MIAME supportive and dynamically provides feedback on missing annotations to help users estimate effective MIAME compliance. Genomic data such as clone identifiers and gene symbols are also directly annotated by MAF software using standard public resources. The MAGE-ML data format is implemented for full data export. Journalized database operations (audit tracking), data anonymization, material traceability and user/project level confidentiality policies are also managed by MAF. Conclusion MicroArray Facility is a complete data management system for microarray producers and end-users. Particular care has been devoted to adequately model Nylon based microarrays. The MAF system, developed and implemented in both private and academic environments, has proved a robust solution for shared facilities and industry service providers alike. PMID:16987406

Optical properties of Sulfur doped InP single crystals

NASA Astrophysics Data System (ADS)

El-Nahass, M. M.; Youssef, S. B.; Ali, H. A. M.

2014-05-01

Optical properties of InP:S single crystals were investigated using spectrophotometric measurements in the spectral range of 200-2500 nm. The absorption coefficient and refractive index were calculated. It was found that InP:S crystals exhibit allowed and forbidden direct transitions with energy gaps of 1.578 and 1.528 eV, respectively. Analysis of the refractive index in the normal dispersion region was discussed in terms of the single oscillator model. Some optical dispersion parameters namely: the dispersion energy (Ed), single oscillator energy (Eo), high frequency dielectric constant (ɛ∞), and lattice dielectric constant (ɛL) were determined. The volume and the surface energy loss functions (VELF & SELF) were estimated. Also, the real and imaginary parts of the complex conductivity were calculated.

Highly coherent tunable mid-infrared frequency comb pumped by supercontinuum at 1 µm

NASA Astrophysics Data System (ADS)

Jin, Lei; Yamanaka, Masahito; Sonnenschein, Volker; Tomita, Hideki; Iguchi, Tetsuo; Sato, Atsushi; Oh-hara, Toshinari; Nishizawa, Norihiko

2017-01-01

We report a tunable mid-infrared frequency comb working at 184 MHz, which is based on difference frequency generation in a periodically poled Mg-doped stoichiometric lithium tantalate (PPMgSLT) crystal pumped by high-power supercontinuum pulses. Supercontinuum pulses from two fibers with different dispersion properties were examined. With a photonic crystal fiber (PCF) having normal dispersion properties, a tunable wavelength range of 2.9-4.7 µm was achieved. With another PCF having zero dispersion at 1040 nm, a maximum power of 1.34 mW was observed at 3.9 µm. The high coherence of the pulses generated with this scheme was verified experimentally, and a fringe visibility of 0.90 was observed.

Electro-Optic Effects in Colloidal Dispersion of Metal Nano-Rods in Dielectric Fluid

PubMed Central

Golovin, Andrii B.; Xiang, Jie; Park, Heung-Shik; Tortora, Luana; Nastishin, Yuriy A.; Shiyanovskii, Sergij V.; Lavrentovich, Oleg D.

2011-01-01

In modern transformation optics, one explores metamaterials with properties that vary from point to point in space and time, suitable for application in devices such as an “optical invisibility cloak” and an “optical black hole”. We propose an approach to construct spatially varying and switchable metamaterials that are based on colloidal dispersions of metal nano-rods (NRs) in dielectric fluids, in which dielectrophoretic forces, originating in the electric field gradients, create spatially varying configurations of aligned NRs. The electric field controls orientation and concentration of NRs and thus modulates the optical properties of the medium. Using gold (Au) NRs dispersed in toluene, we demonstrate electrically induced change in refractive index on the order of 0.1. PMID:28879997

Tensile and creep properties of the experimental oxide dispersion strengthened iron-base sheet alloy MA-956E at 1365 K

NASA Technical Reports Server (NTRS)

Whittenberger, J. D.

1978-01-01

A study of the 1365 K tensile properties, creep characteristics and residual room temperature properties after creep testing of the experimental oxide dispersion strengthened iron-base alloy MA-956E (Fe-20Cr-4.5Al-0.5Ti-0.5Y2O3) was conducted. The 1365 K tensile properties, particularly ductility, are strongly dependent on strain rate. It appears that MA-956E does not easily undergo slow plastic deformation. Rather than deform under creep loading conditions, the alloy apparently fails by a crack nucleation and growth mechanism. Fortunately, there appears to be a threshold stress below which crack nucleation and/or growth does not occur.

Intercontinental dispersal of bacteria and archaea by transpacific winds

USGS Publications Warehouse

D. Smith,; H. Timonen,; D. Jaffe,; Griffin, Dale W.; M. Birmele,; Perry, K.D.; Ward, P.D.; M. Roberts,

2013-01-01

Microorganisms are abundant in the upper atmosphere, particularly downwind of arid regions, where winds can mobilize large amounts of topsoil and dust. However, the challenge of collecting samples from the upper atmosphere and reliance upon culture-based characterization methods have prevented a comprehensive understanding of globally dispersed airborne microbes. In spring 2011 at the Mt. Bachelor Observatory in North America (2.8 km above sea level), we captured enough microbial biomass in two transpacific air plumes to permit a microarray analysis using 16S rRNA genes. Thousands of distinct bacterial taxa spanning a wide range of phyla and surface environments were detected before, during, and after each Asian long-range transport event. Interestingly, the transpacific plumes delivered higher concentrations of taxa already in the background air (particularly Proteobacteria, Actinobacteria, and Firmicutes). While some bacterial families and a few marine archaea appeared for the first and only time during the plumes, the microbial community compositions were similar, despite the unique transport histories of the air masses. It seems plausible, when coupled with atmospheric modeling and chemical analysis, that microbial biogeography can be used to pinpoint the source of intercontinental dust plumes. Given the degree of richness measured in our study, the overall contribution of Asian aerosols to microbial species in North American air warrants additional investigation.

Intercontinental Dispersal of Bacteria and Archaea by Transpacific Winds

PubMed Central

Timonen, Hilkka J.; Jaffe, Daniel A.; Griffin, Dale W.; Birmele, Michele N.; Perry, Kevin D.; Ward, Peter D.; Roberts, Michael S.

2013-01-01

Microorganisms are abundant in the upper atmosphere, particularly downwind of arid regions, where winds can mobilize large amounts of topsoil and dust. However, the challenge of collecting samples from the upper atmosphere and reliance upon culture-based characterization methods have prevented a comprehensive understanding of globally dispersed airborne microbes. In spring 2011 at the Mt. Bachelor Observatory in North America (2.8 km above sea level), we captured enough microbial biomass in two transpacific air plumes to permit a microarray analysis using 16S rRNA genes. Thousands of distinct bacterial taxa spanning a wide range of phyla and surface environments were detected before, during, and after each Asian long-range transport event. Interestingly, the transpacific plumes delivered higher concentrations of taxa already in the background air (particularly Proteobacteria, Actinobacteria, and Firmicutes). While some bacterial families and a few marine archaea appeared for the first and only time during the plumes, the microbial community compositions were similar, despite the unique transport histories of the air masses. It seems plausible, when coupled with atmospheric modeling and chemical analysis, that microbial biogeography can be used to pinpoint the source of intercontinental dust plumes. Given the degree of richness measured in our study, the overall contribution of Asian aerosols to microbial species in North American air warrants additional investigation. PMID:23220959

Microwave Semiconductor Research - Materials, Devices, Circuits.

DTIC Science & Technology

1982-04-30

34, C.L. Tang and J-M. Halbout, invited talk, SPIE Technical Symposium, Los Angeles, CA (January, 1982). 3. "Observation of light induced refractive index ... index slab its desirable dispersive properties. The relatively poor dispersion characteristics of the uniform dielectric slab can be attributed to the...34, January 1982. 2. H. Zmuda completed his M.S. program. Thesis: "Simplified Dispersion Analysis of the Multistep and Graded Index Dielectric Slab Waveguide

iVPIC: A low-­dispersion, energy-­conserving relativistic PIC solver for LPI simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chacon, Luis

We have developed a novel low-­dispersion, exactly energy-­conserving PIC algorithm for the relativistic Vlasov-­Maxwell system. The approach features an exact energy conservation theorem while preserving the favorable performance and numerical dispersion properties of explicit PIC. The new algorithm has the potential to enable much longer laser-­plasma-­interaction (LPI) simulations than are currently possible.

Nanocrystal dispersed amorphous alloys

NASA Technical Reports Server (NTRS)

Perepezko, John H. (Inventor); Allen, Donald R. (Inventor); Foley, James C. (Inventor)

2001-01-01

Compositions and methods for obtaining nanocrystal dispersed amorphous alloys are described. A composition includes an amorphous matrix forming element (e.g., Al or Fe); at least one transition metal element; and at least one crystallizing agent that is insoluble in the resulting amorphous matrix. During devitrification, the crystallizing agent causes the formation of a high density nanocrystal dispersion. The compositions and methods provide advantages in that materials with superior properties are provided.

The role of process history, phase morphology and interface strength upon the mechanical properties of dispersion strengthened alloys

NASA Technical Reports Server (NTRS)

Ansell, G. S.

1972-01-01

An analytical rationale for the sensitivity-insensitivity of dispersion-strengthened systems to process history is provided. In particular, the research was focussed upon the influence of the particle-matrix interface bond in TD-Nickel and TD-Nichrome, and the manner in which the differences in both elastic constants and thermal expansion coefficients between these phases stress this interface when these alloys are subjected to mechanical and thermal loads upon the mechanical properties of these alloys.

Synthesis and antibacterial properties of water-dispersible silver nanoparticles stabilized by metal-carbon σ-bonds

NASA Astrophysics Data System (ADS)

Kawai, Koji; Narushima, Takashi; Kaneko, Kotaro; Kawakami, Hayato; Matsumoto, Miyuki; Hyono, Atsushi; Nishihara, Hiroshi; Yonezawa, Tetsu

2012-12-01

The synthesis of 4-diazoniumcarboxylbenzene fluoroborate, a new water-soluble stabilizer for metal nanoparticles (NPs), is described. A stable dispersion of Ag NPs in water was successfully produced by a simultaneous aqueous reduction of this diazonium salt and silver nitrate by NaBH4. UV-vis spectra, TEM images, XRD patterns, and XPS spectra of the obtained Ag NPs revealed that they were stabilized by Ag-C σ-bonds. These NPs showed excellent antimicrobial properties against Staphylococcus aureus.

Preparation, thermal property and morphology analysis of waterborne polyurethane-acrylate

NASA Astrophysics Data System (ADS)

Zhao, Zhenyu; Jing, Zefeng; Qiu, Fengxian; Dai, Yuting; Xu, Jicheng; Yu, Zongping; Yang, Pengfei

2017-01-01

A series of waterborne polyurethane-acrylate (WPUA) dispersions were prepared with isophorone diisocyanate (IPDI), polyether polyol (NJ-210), dimethylol propionic acid (DMPA), hydroxyethyl methyl acrylate (HEMA), different proportions of methyl methacrylate (MMA) and ethyl acrylate (MMA and EA) and initiating agent by the emulsion co-polymerization. The structures, thermal properties and morphology of WPUA films were characterized with FT-IR, DSC, SEM and AFM. Performances of the dispersions and films were studied by means of apparent viscidity, particle size and polydispersity, surface tension and mechanical properties. The obtained WPUA have great potential application such as coatings, leather finishing, adhesives, sealants, plastic coatings and wood finishes.

The electrical properties of zero-gravity processed immiscibles

NASA Technical Reports Server (NTRS)

Lacy, L. L.; Otto, G. H.

1974-01-01

When dispersed or mixed immiscibles are solidified on earth, a large amount of separation of the constituents takes place due to differences in densities. However, when the immiscibles are dispersed and solidified in zero-gravity, density separation does not occur, and unique composite solids can be formed with many new and promising electrical properties. By measuring the electrical resistivity and superconducting critical temperature, Tc, of zero-g processed Ga-Bi samples, it has been found that the electrical properties of such materials are entirely different from the basic constituents and the ground control samples. Our results indicate that space processed immiscible materials may form an entirely new class of electronic materials.

Investigation of process temperature and screw speed on properties of a pharmaceutical solid dispersion using corotating and counter-rotating twin-screw extruders.

PubMed

Keen, Justin M; Martin, Charlie; Machado, Augie; Sandhu, Harpreet; McGinity, James W; DiNunzio, James C

2014-02-01

The use of corotating twin screw hot-melt extruders to prepare amorphous drug/polymer systems has become commonplace. As small molecule drug candidates exiting discovery pipelines trend towards higher MW and become more structurally complicated, the acceptable operating space shifts below the drug melting point. The objective of this research is to investigate the extrusion process space, which should be selected to ensure that the drug is solubilized in the polymer with minimal thermal exposure, is critical in ensuring the performance, stability and purity of the solid dispersion. The properties of a model solid dispersion were investigated using both corotating and counter-rotating hot-melt twin-screw extruders operated at various temperatures and screw speeds. The solid state and dissolution performance of the resulting solid dispersions was investigated and evaluated in context of thermodynamic predictions from Flory-Huggins Theory. In addition, the residence time distributions were measured using a tracer, modelled and characterized. The amorphous content in the resulting solid dispersions was dependent on the combination of screw speed, temperature and operating mode. The counter-rotating extruder was observed to form amorphous solid dispersions at a slightly lower temperature and with a narrower residence time distribution, which also exhibited a more desirable shape. © 2013 Royal Pharmaceutical Society.

Microarrays in brain research: the good, the bad and the ugly.

PubMed

Mirnics, K

2001-06-01

Making sense of microarray data is a complex process, in which the interpretation of findings will depend on the overall experimental design and judgement of the investigator performing the analysis. As a result, differences in tissue harvesting, microarray types, sample labelling and data analysis procedures make post hoc sharing of microarray data a great challenge. To ensure rapid and meaningful data exchange, we need to create some order out of the existing chaos. In these ground-breaking microarray standardization and data sharing efforts, NIH agencies should take a leading role

Rheology Guided Rational Selection of Processing Temperature To Prepare Copovidone-Nifedipine Amorphous Solid Dispersions via Hot Melt Extrusion (HME).

PubMed

Yang, Fengyuan; Su, Yongchao; Zhang, Jingtao; DiNunzio, James; Leone, Anthony; Huang, Chengbin; Brown, Chad D

2016-10-03

The production of amorphous solid dispersions via hot melt extrusion (HME) relies on elevated temperature and prolonged residence time, which can result in potential degradation and decomposition of thermally sensitive components. Herein, the rheological properties of a physical mixture of polymer and an active pharmaceutical ingredient (API) were utilized to guide the selection of appropriate HME processing temperature. In the currently studied copovidone-nifedipine system, a critical temperature, which is substantially lower (∼13 °C) than the melting point of crystalline API, was captured during a temperature ramp examination and regarded as the critical point at which the API could molecularly dissolve into the polymer. Based on the identification of this critical point, various solid dispersions were prepared by HME processing below, at, and above the critical temperature (both below and above the melting temperature (T m ) of crystalline API). In addition, the resultant extrudates along with two control solid dispersions prepared by physical mixing and cryogenic milling were assessed by X-ray diffraction, differential scanning calorimetry, hot stage microscopy, rheology, and solid-state NMR. Physicochemical properties of resultant solid dispersions indicated that the identified critical temperature is sufficient for the polymer-API system to reach a molecular-level mixing, manifested by the transparent and smooth appearance of extrudates, the absence of API crystalline diffraction and melting peaks, dramatically decreased rheological properties, and significantly improved polymer-API miscibility. Once the critical temperature has been achieved, further raising the processing temperature only results in limited improvement of API dispersion, reflected by slightly reduced storage modulus and complex viscosity and limited improvement in miscibility.

Dispersion flattened single etch-step waveguide based on subwavelength grating

NASA Astrophysics Data System (ADS)

Jafari, Zeinab; Zarifkar, Abbas

2017-06-01

A novel subwavelength-grating-assisted (SWG-assisted) waveguide is proposed for dispersion flattening. Tuning the refractive index, which is a powerful tool in dispersion engineering, can be carried out through adjusting the properties of the SWG regions. It is particularly beneficial for controlling the flattened dispersion bandwidth. This will also eliminate the need for integration of other less compatible materials with silicon. Moreover, the SWG-assisted waveguide can be easily fabricated through a single etch-step process. By engineering the structural parameters of the waveguide, an ultra-flat dispersion profile with a total dispersion variation of 10 (ps/nm/km) over a wide bandwidth of 1615 nm is obtained. The possibility of bandwidth expansion, the fabrication friendly design, and the flattened dispersion profile of the proposed waveguide make it promising for wideband nonlinear applications.

Identification and Optimization of Classifier Genes from Multi-Class Earthworm Microarray Dataset

DTIC Science & Technology

2010-10-28

rapid and accurate diagnostic assays. A variety of toxicological effects have been associated with explosive compounds TNT and RDX. One important goal of...analyze toxicological mechanisms for two military- unique explosive compounds 2,4,6-trinitrotolune (TNT) and 1,3,5- trinitro-1,3,5-triazacyclohexane...also known as Royal Demolition eXplosive or RDX) [7,8]. These two compounds exhibit distinctive toxicological properties that are accompanied by

DNA Microarray for Rapid Detection and Identification of Food and Water Borne Bacteria: From Dry to Wet Lab.

PubMed

Ranjbar, Reza; Behzadi, Payam; Najafi, Ali; Roudi, Raheleh

2017-01-01

A rapid, accurate, flexible and reliable diagnostic method may significantly decrease the costs of diagnosis and treatment. Designing an appropriate microarray chip reduces noises and probable biases in the final result. The aim of this study was to design and construct a DNA Microarray Chip for a rapid detection and identification of 10 important bacterial agents. In the present survey, 10 unique genomic regions relating to 10 pathogenic bacterial agents including Escherichia coli (E.coli), Shigella boydii, Sh.dysenteriae, Sh.flexneri, Sh.sonnei, Salmonella typhi, S.typhimurium, Brucella sp., Legionella pneumophila, and Vibrio cholera were selected for designing specific long oligo microarray probes. For this reason, the in-silico operations including utilization of the NCBI RefSeq database, Servers of PanSeq and Gview, AlleleID 7.7 and Oligo Analyzer 3.1 was done. On the other hand, the in-vitro part of the study comprised stages of robotic microarray chip probe spotting, bacterial DNAs extraction and DNA labeling, hybridization and microarray chip scanning. In wet lab section, different tools and apparatus such as Nexterion® Slide E, Qarray mini spotter, NimbleGen kit, TrayMix TM S4, and Innoscan 710 were used. A DNA microarray chip including 10 long oligo microarray probes was designed and constructed for detection and identification of 10 pathogenic bacteria. The DNA microarray chip was capable to identify all 10 bacterial agents tested simultaneously. The presence of a professional bioinformatician as a probe designer is needed to design appropriate multifunctional microarray probes to increase the accuracy of the outcomes.

The Development of Protein Microarrays and Their Applications in DNA-Protein and Protein-Protein Interaction Analyses of Arabidopsis Transcription Factors

PubMed Central

Gong, Wei; He, Kun; Covington, Mike; Dinesh-Kumar, S. P.; Snyder, Michael; Harmer, Stacey L.; Zhu, Yu-Xian; Deng, Xing Wang

2009-01-01

We used our collection of Arabidopsis transcription factor (TF) ORFeome clones to construct protein microarrays containing as many as 802 TF proteins. These protein microarrays were used for both protein-DNA and protein-protein interaction analyses. For protein-DNA interaction studies, we examined AP2/ERF family TFs and their cognate cis-elements. By careful comparison of the DNA-binding specificity of 13 TFs on the protein microarray with previous non-microarray data, we showed that protein microarrays provide an efficient and high throughput tool for genome-wide analysis of TF-DNA interactions. This microarray protein-DNA interaction analysis allowed us to derive a comprehensive view of DNA-binding profiles of AP2/ERF family proteins in Arabidopsis. It also revealed four TFs that bound the EE (evening element) and had the expected phased gene expression under clock-regulation, thus providing a basis for further functional analysis of their roles in clock regulation of gene expression. We also developed procedures for detecting protein interactions using this TF protein microarray and discovered four novel partners that interact with HY5, which can be validated by yeast two-hybrid assays. Thus, plant TF protein microarrays offer an attractive high-throughput alternative to traditional techniques for TF functional characterization on a global scale. PMID:19802365

Plastic Polymers for Efficient DNA Microarray Hybridization: Application to Microbiological Diagnostics▿

PubMed Central

Zhao, Zhengshan; Peytavi, Régis; Diaz-Quijada, Gerardo A.; Picard, Francois J.; Huletsky, Ann; Leblanc, Éric; Frenette, Johanne; Boivin, Guy; Veres, Teodor; Dumoulin, Michel M.; Bergeron, Michel G.

2008-01-01

Fabrication of microarray devices using traditional glass slides is not easily adaptable to integration into microfluidic systems. There is thus a need for the development of polymeric materials showing a high hybridization signal-to-background ratio, enabling sensitive detection of microbial pathogens. We have developed such plastic supports suitable for highly sensitive DNA microarray hybridizations. The proof of concept of this microarray technology was done through the detection of four human respiratory viruses that were amplified and labeled with a fluorescent dye via a sensitive reverse transcriptase PCR (RT-PCR) assay. The performance of the microarray hybridization with plastic supports made of PMMA [poly(methylmethacrylate)]-VSUVT or Zeonor 1060R was compared to that with high-quality glass slide microarrays by using both passive and microfluidic hybridization systems. Specific hybridization signal-to-background ratios comparable to that obtained with high-quality commercial glass slides were achieved with both polymeric substrates. Microarray hybridizations demonstrated an analytical sensitivity equivalent to approximately 100 viral genome copies per RT-PCR, which is at least 100-fold higher than the sensitivities of previously reported DNA hybridizations on plastic supports. Testing of these plastic polymers using a microfluidic microarray hybridization platform also showed results that were comparable to those with glass supports. In conclusion, PMMA-VSUVT and Zeonor 1060R are both suitable for highly sensitive microarray hybridizations. PMID:18784318

Development and application of a microarray meter tool to optimize microarray experiments

PubMed Central

Rouse, Richard JD; Field, Katrine; Lapira, Jennifer; Lee, Allen; Wick, Ivan; Eckhardt, Colleen; Bhasker, C Ramana; Soverchia, Laura; Hardiman, Gary

2008-01-01

Background Successful microarray experimentation requires a complex interplay between the slide chemistry, the printing pins, the nucleic acid probes and targets, and the hybridization milieu. Optimization of these parameters and a careful evaluation of emerging slide chemistries are a prerequisite to any large scale array fabrication effort. We have developed a 'microarray meter' tool which assesses the inherent variations associated with microarray measurement prior to embarking on large scale projects. Findings The microarray meter consists of nucleic acid targets (reference and dynamic range control) and probe components. Different plate designs containing identical probe material were formulated to accommodate different robotic and pin designs. We examined the variability in probe quality and quantity (as judged by the amount of DNA printed and remaining post-hybridization) using three robots equipped with capillary printing pins. Discussion The generation of microarray data with minimal variation requires consistent quality control of the (DNA microarray) manufacturing and experimental processes. Spot reproducibility is a measure primarily of the variations associated with printing. The microarray meter assesses array quality by measuring the DNA content for every feature. It provides a post-hybridization analysis of array quality by scoring probe performance using three metrics, a) a measure of variability in the signal intensities, b) a measure of the signal dynamic range and c) a measure of variability of the spot morphologies. PMID:18710498

A Web-Based Multi-Database System Supporting Distributed Collaborative Management and Sharing of Microarray Experiment Information

PubMed Central

Burgarella, Sarah; Cattaneo, Dario; Masseroli, Marco

2006-01-01

We developed MicroGen, a multi-database Web based system for managing all the information characterizing spotted microarray experiments. It supports information gathering and storing according to the Minimum Information About Microarray Experiments (MIAME) standard. It also allows easy sharing of information and data among all multidisciplinary actors involved in spotted microarray experiments. PMID:17238488

Polysaccharide Microarray Technology for the Detection of Burkholderia Pseudomallei and Burkholderia Mallei Antibodies

DTIC Science & Technology

2006-04-27

polysaccharide microarray platform was prepared by immobilizing Burkholderia pseudomallei and Burkholderia mallei polysaccharides . This... polysaccharide array was tested with success for detecting B. pseudomallei and B. mallei serum (human and animal) antibodies. The advantages of this microarray... Polysaccharide microarrays; Burkholderia pseudomallei; Burkholderia mallei; Glanders; Melioidosis1. Introduction There has been a great deal of emphasis on the

Microarray-integrated optoelectrofluidic immunoassay system

PubMed Central

Han, Dongsik

2016-01-01

A microarray-based analytical platform has been utilized as a powerful tool in biological assay fields. However, an analyte depletion problem due to the slow mass transport based on molecular diffusion causes low reaction efficiency, resulting in a limitation for practical applications. This paper presents a novel method to improve the efficiency of microarray-based immunoassay via an optically induced electrokinetic phenomenon by integrating an optoelectrofluidic device with a conventional glass slide-based microarray format. A sample droplet was loaded between the microarray slide and the optoelectrofluidic device on which a photoconductive layer was deposited. Under the application of an AC voltage, optically induced AC electroosmotic flows caused by a microarray-patterned light actively enhanced the mass transport of target molecules at the multiple assay spots of the microarray simultaneously, which reduced tedious reaction time from more than 30 min to 10 min. Based on this enhancing effect, a heterogeneous immunoassay with a tiny volume of sample (5 μl) was successfully performed in the microarray-integrated optoelectrofluidic system using immunoglobulin G (IgG) and anti-IgG, resulting in improved efficiency compared to the static environment. Furthermore, the application of multiplex assays was also demonstrated by multiple protein detection. PMID:27190571

Microarray-integrated optoelectrofluidic immunoassay system.

PubMed

Han, Dongsik; Park, Je-Kyun

2016-05-01

A microarray-based analytical platform has been utilized as a powerful tool in biological assay fields. However, an analyte depletion problem due to the slow mass transport based on molecular diffusion causes low reaction efficiency, resulting in a limitation for practical applications. This paper presents a novel method to improve the efficiency of microarray-based immunoassay via an optically induced electrokinetic phenomenon by integrating an optoelectrofluidic device with a conventional glass slide-based microarray format. A sample droplet was loaded between the microarray slide and the optoelectrofluidic device on which a photoconductive layer was deposited. Under the application of an AC voltage, optically induced AC electroosmotic flows caused by a microarray-patterned light actively enhanced the mass transport of target molecules at the multiple assay spots of the microarray simultaneously, which reduced tedious reaction time from more than 30 min to 10 min. Based on this enhancing effect, a heterogeneous immunoassay with a tiny volume of sample (5 μl) was successfully performed in the microarray-integrated optoelectrofluidic system using immunoglobulin G (IgG) and anti-IgG, resulting in improved efficiency compared to the static environment. Furthermore, the application of multiplex assays was also demonstrated by multiple protein detection.

Advances in cell-free protein array methods.

PubMed

Yu, Xiaobo; Petritis, Brianne; Duan, Hu; Xu, Danke; LaBaer, Joshua

2018-01-01

Cell-free protein microarrays represent a special form of protein microarray which display proteins made fresh at the time of the experiment, avoiding storage and denaturation. They have been used increasingly in basic and translational research over the past decade to study protein-protein interactions, the pathogen-host relationship, post-translational modifications, and antibody biomarkers of different human diseases. Their role in the first blood-based diagnostic test for early stage breast cancer highlights their value in managing human health. Cell-free protein microarrays will continue to evolve to become widespread tools for research and clinical management. Areas covered: We review the advantages and disadvantages of different cell-free protein arrays, with an emphasis on the methods that have been studied in the last five years. We also discuss the applications of each microarray method. Expert commentary: Given the growing roles and impact of cell-free protein microarrays in research and medicine, we discuss: 1) the current technical and practical limitations of cell-free protein microarrays; 2) the biomarker discovery and verification pipeline using protein microarrays; and 3) how cell-free protein microarrays will advance over the next five years, both in their technology and applications.

Reactive solute transport in an asymmetric aquifer-aquitard system with scale-dependent dispersion

NASA Astrophysics Data System (ADS)

Zhou, R.; Zhan, H.

2017-12-01

Abstract: The understanding of reactive solute transport in an aquifer-aquitard system is important to study transport behavior in the more complex porous media. When transport properties are asymmetric in the upper and lower aquitards, reactive solute transport in such an aquifer-aquitard system becomes a coupled three domain problem that is more complex than the symmetric case in which the upper and lower aquitards have identical transport properties. Meanwhile, the dispersivity of transport in the aquifer is considered as a linear or exponential function of travel distance due to the heterogeneity of aquifer. This study proposed new transport models to describe reactive solute transport in such an asymmetric aquifer-aquitard system with scale-dependent dispersion. Mathematical models were developed for such problems under the first-type and third-type boundary conditions to analyze the spatial-temporal concentration and mass distribution in the aquifer and aquitards with the help of Laplace transform technique and the de Hoog numerical Laplace inversion method. Breakthrough curves (BTCs) and residence time distribution curves (RTDs) obtained from the models with scale-dependent dispersion, constant dispersion and constant effective dispersivity were compared to reflect the lumped scale-dispersion effect in the aquifer-aquitard system. The newly acquired solutions were then tested extensively against previous analytical and numerical solutions and were proven to be robust and accurate. Furthermore, to study the back diffusion of contaminant mass in aquitards, a zero-contaminant mass concentration boundary condition was imposed on the inlet boundary of the system after a certain time, which is also called the process of water flushing. The diffusion loss alone the aquifer/aquitard interfaces and mass stored ratio change in each of three domains (upper aquitard, aquifer, and lower aquitard) after water flushing provided an insightful and comprehensive analysis of transport behavior with asymmetric distribution of transport properties.

Reinvestigating the surface and bulk electronic properties of Cd3As2

NASA Astrophysics Data System (ADS)

Roth, S.; Lee, H.; Sterzi, A.; Zacchigna, M.; Politano, A.; Sankar, R.; Chou, F. C.; Di Santo, G.; Petaccia, L.; Yazyev, O. V.; Crepaldi, A.

2018-04-01

Cd3As2 is widely considered among the few materials realizing the three-dimensional (3D) Dirac semimetal phase. Linearly dispersing states, responsible for the ultrahigh charge mobility, have been reported by several angle-resolved photoelectron spectroscopy (ARPES) investigations. However, in spite of the general agreement between these studies, some details are at odds. From scanning tunneling microscopy and optical experiments under magnetic field, a puzzling scenario emerges in which multiple states show linear dispersion at different energy scales. Here, we solve this apparent controversy by reinvestigating the electronic properties of the (112) surface of Cd3As2 by combining ARPES and theoretical calculations. We disentangle the presence of massive and massless metallic bulk and surface states, characterized by different symmetries. Our systematic experimental and theoretical study clarifies the complex band dispersion of Cd3As2 by extending the simplistic 3D Dirac semimetal model to account for multiple bulk and surface states crossing the Fermi level, and thus contributing to the unique material transport properties.

Electrokinetic and hydrodynamic properties of charged-particles systems. From small electrolyte ions to large colloids

NASA Astrophysics Data System (ADS)

Nägele, G.; Heinen, M.; Banchio, A. J.; Contreras-Aburto, C.

2013-11-01

Dynamic processes in dispersions of charged spherical particles are of importance both in fundamental science, and in technical and bio-medical applications. There exists a large variety of charged-particles systems, ranging from nanometer-sized electrolyte ions to micron-sized charge-stabilized colloids. We review recent advances in theoretical methods for the calculation of linear transport coefficients in concentrated particulate systems, with the focus on hydrodynamic interactions and electrokinetic effects. Considered transport properties are the dispersion viscosity, self- and collective diffusion coefficients, sedimentation coefficients, and electrophoretic mobilities and conductivities of ionic particle species in an external electric field. Advances by our group are also discussed, including a novel mode-coupling-theory method for conduction-diffusion and viscoelastic properties of strong electrolyte solutions. Furthermore, results are presented for dispersions of solvent-permeable particles, and particles with non-zero hydrodynamic surface slip. The concentration-dependent swelling of ionic microgels is discussed, as well as a far-reaching dynamic scaling behavior relating colloidal long- to short-time dynamics.

Improved Mechanical and Tribological Properties of Metal-Matrix Composites Dispersion-Strengthened by Nanoparticles 

PubMed Central

Levashov, Evgenii; Kurbatkina, Victoria; Alexandr, Zaytsev

2009-01-01

Co- and Fe-based alloys produced by powder technology are being widely used as a matrix for diamond-containing composites in cutting, drilling, grinding pplications, etc. The severe service conditions demand that the mechanical and tribological properties of these alloys be improved. Development of metal-matrix composites (MMCs) and alloys reinforced with nanoparticles is a promising way to resolve this problem. In this work, we have investigated the effect of nano-sized WC, ZrO2, Al2O3, and Si3N4 additives on the properties of sintered dispersion-strengthened Co- and Fe-based MMCs. The results show an increase in the hardness (up to 10 HRB), bending strength (up to 50%), wear resistance (by a factor of 2–10) and a decrease in the friction coefficient (up to 4-fold) of the dispersion-strengthened materials. The use of designed alloys as a binder of cutting diamond tools gave a 4-fold increment in the service life, without reduction in their cutting speed.

Multifunctional PLA-PHB/cellulose nanocrystal films: processing, structural and thermal properties.

PubMed

Arrieta, M P; Fortunati, E; Dominici, F; Rayón, E; López, J; Kenny, J M

2014-07-17

Cellulose nanocrystals (CNCs) synthesized from microcrystalline cellulose by acid hydrolysis were added into poly(lactic acid)-poly(hydroxybutyrate) (PLA-PHB) blends to improve the final properties of the multifunctional systems. CNC were also modified with a surfactant (CNCs) to increase the interfacial adhesion in the systems maintaining the thermal stability. Firstly, masterbatch pellets were obtained for each formulation to improve the dispersion of the cellulose structures in the PLA-PHB and then nanocomposite films were processed. The thermal stability as well as the morphological and structural properties of nanocomposites was investigated. While PHB increased the PLA crystallinity due to its nucleation effect, well dispersed CNC and CNCs not only increased the crystallinity but also improved the processability, the thermal stability and the interaction between both polymers especially in the case of the modified CNCs based PLA-PHB formulation. Likewise, CNCs were better dispersed in PLA-CNCs and PLA-PHB-CNCs, than CNC. Copyright © 2014 Elsevier Ltd. All rights reserved.

Carbohydrate Microarray Technology Applied to High-Throughput Mapping of Plant Cell Wall Glycans Using Comprehensive Microarray Polymer Profiling (CoMPP).

PubMed

Kračun, Stjepan Krešimir; Fangel, Jonatan Ulrik; Rydahl, Maja Gro; Pedersen, Henriette Lodberg; Vidal-Melgosa, Silvia; Willats, William George Tycho

2017-01-01

Cell walls are an important feature of plant cells and a major component of the plant glycome. They have both structural and physiological functions and are critical for plant growth and development. The diversity and complexity of these structures demand advanced high-throughput techniques to answer questions about their structure, functions and roles in both fundamental and applied scientific fields. Microarray technology provides both the high-throughput and the feasibility aspects required to meet that demand. In this chapter, some of the most recent microarray-based techniques relating to plant cell walls are described together with an overview of related contemporary techniques applied to carbohydrate microarrays and their general potential in glycoscience. A detailed experimental procedure for high-throughput mapping of plant cell wall glycans using the comprehensive microarray polymer profiling (CoMPP) technique is included in the chapter and provides a good example of both the robust and high-throughput nature of microarrays as well as their applicability to plant glycomics.

Interim report on updated microarray probes for the LLNL Burkholderia pseudomallei SNP array

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gardner, S; Jaing, C

2012-03-27

The overall goal of this project is to forensically characterize 100 unknown Burkholderia isolates in the US-Australia collaboration. We will identify genome-wide single nucleotide polymorphisms (SNPs) from B. pseudomallei and near neighbor species including B. mallei, B. thailandensis and B. oklahomensis. We will design microarray probes to detect these SNP markers and analyze 100 Burkholderia genomic DNAs extracted from environmental, clinical and near neighbor isolates from Australian collaborators on the Burkholderia SNP microarray. We will analyze the microarray genotyping results to characterize the genetic diversity of these new isolates and triage the samples for whole genome sequencing. In this interimmore » report, we described the SNP analysis and the microarray probe design for the Burkholderia SNP microarray.« less

Magneto-optical characterization of colloidal dispersions. Application to nickel nanoparticles.

PubMed

Pascu, Oana; Caicedo, José Manuel; Fontcuberta, Josep; Herranz, Gervasi; Roig, Anna

2010-08-03

We report here on a fast magneto-optical characterization method for colloidal liquid dispersions of magnetic nanoparticles. We have applied our methodology to Ni nanoparticles with size equal or below 15 nm synthesized by a ligand stabilized solution-phase synthesis. We have measured the magnetic circular dichroism (MCD) of colloidal dispersions and found that we can probe the intrinsic magnetic properties within a wide concentration range, from 10(-5) up to 10(-2) M, with sensitivity to concentrations below 1 microg/mL of magnetic Ni particles. We found that the measured MCD signal scales up with the concentration thus providing a means of determining the concentration values of highly diluted dispersions. The methodology presented here exhibits large flexibility and versatility and might be suitable to study either fundamental problems related to properties of nanosize particles including surface related effects which are highly relevant for magnetic colloids in biomedical applications or to be applied to in situ testing and integration in production lines.

Performance Comparison with Different Antenna Properties in Time Reversal Ultra-Wideband Communications for Sensor System Applications

PubMed Central

Ding, Shuai

2017-01-01

The complexity reduction of receivers in ultrawideband (UWB) communication when time reversal (TR) technique is applied makes it suitable for low-cost and low-power sensor systems. Larger antenna dispersion can generally lead to a less stable phase center and will increase the interference in UWB communications based on pulse radio, whereas a higher antenna gain will result in higher channel gain and further larger channel capacity. To find out the trade-off between antenna gain and dispersion, we performed the channel measurements using different antennas in a dense multipath environment and established the distribution of channel capacities based on the measured channel responses. The results show that the capacity loss caused by antenna dispersion cannot be compensated by antenna gain with line-of-sight transmission to some extent, the effect of phase center on the communication system is negligible, and antennas with smaller time dispersion will have a better energy focusing property and anti-interference performance in TR systems. PMID:29301195

Performance Comparison with Different Antenna Properties in Time Reversal Ultra-Wideband Communications for Sensor System Applications.

PubMed

Yang, Yu; Wang, Bing-Zhong; Ding, Shuai

2017-12-30

The complexity reduction of receivers in ultrawideband (UWB) communication when time reversal (TR) technique is applied makes it suitable for low-cost and low-power sensor systems. Larger antenna dispersion can generally lead to a less stable phase center and will increase the interference in UWB communications based on pulse radio, whereas a higher antenna gain will result in higher channel gain and further larger channel capacity. To find out the trade-off between antenna gain and dispersion, we performed the channel measurements using different antennas in a dense multipath environment and established the distribution of channel capacities based on the measured channel responses. The results show that the capacity loss caused by antenna dispersion cannot be compensated by antenna gain with line-of-sight transmission to some extent, the effect of phase center on the communication system is negligible, and antennas with smaller time dispersion will have a better energy focusing property and anti-interference performance in TR systems.

Isolation of Aramid Nanofibers for High Strength and Toughness Polymer Nanocomposites.

PubMed

Lin, Jiajun; Bang, Sun Hwi; Malakooti, Mohammad H; Sodano, Henry A

2017-03-29

The development of nanoscale reinforcements that can be used to improve the mechanical properties of a polymer remains a challenge due to the long-standing difficulties with exfoliation and dispersion of existing materials. The dissimilar chemical nature of common nanofillers (e.g., carbon nanotubes, graphene) and polymeric matrix materials is the main reason for imperfect filler dispersion and, consequently, low mechanical performance of their composites relative to theoretical predictions. Here, aramid nanofibers that are intrinsically dispersible in many polymers are prepared from commercial aramid fibers (Kevlar) and isolated through a simple, scalable, and low-cost controlled dissolution method. Integration of the aramid nanofibers in an epoxy resin results in nanocomposites with simultaneously improved elastic modulus, strength, and fracture toughness. The improvement of these two mutually exclusive properties of nanocomposites is comparable to the enhancement of widely reported carbon nanotube reinforced nanocomposites but with a cost-effective and more feasible method to achieve uniform and stable dispersion. The results indicate the potential for aramid nanofibers as a new class of reinforcements for polymers.

Importance of intrinsic properties of dense caseinate dispersions for structure formation.

PubMed

Manski, Julita M; van Riemsdijk, Lieke E; van der Goot, Atze J; Boom, Remko M

2007-11-01

Rheological measurements of dense calcium caseinate and sodium caseinate dispersions (> or =15%) provided insight into the factors determining shear-induced structure formation in caseinates. Calcium caseinate at a sufficiently high concentration (30%) was shown to form highly anisotropic structures during shearing and concurrent enzymatic cross-linking. In contrast, sodium caseinate formed isotropic structures using similar processing conditions. The main difference between the two types of caseinates is the counterion present, and as a consequence, the size of structural elements and their interactions. The rheological behavior of calcium caseinate and sodium caseinate reflected these differences, yielding non-monotonic and shear thinning flow behavior for calcium caseinate whereas sodium caseinate behaved only slightly shear thinning. It appears that the intrinsic properties of the dense caseinate dispersions, which are reflected in their rheological behavior, affect the structure formation that was found after applying shear. Therefore, rheological measurements are useful to obtain an indication of the structure formation potential of caseinate dispersions.

“Sticky invasion” – the physical properties of Plantago lanceolata L. seed mucilage

PubMed Central

Kovalev, Alexander; Gorb, Stanislav N

2016-01-01

The mucilage envelope of seeds has various functions including the provision of different ways for the dispersal of diaspores. Chemical composition and water content of the mucilage yield particular adhesive and frictional properties in the envelope that also influence the dispersal of seeds. To determine the physical properties of Plantago lanceolata seed mucilage we studied (1) composition, (2) desiccation, (3) adhesion, and (4) friction properties of the mucilage under different hydration conditions. We revealed the presence of cellulose fibrils in the mucilage, which are responsible for a continuous and even distribution of the mucilaginous layer on the seed surface. The measured values of adhesive and frictional properties differed significantly in comparison to the previously studied pectic mucilage of Linum usitatissimum. Also, the water loss from the cellulose mucilage was more rapid. The obtained different values can result from the presence of cellulose fibrils and their interaction with pectins in the mucilage. Because of this feature the mucilage of P. lanceolata may represent a more regularly ordered and stabile system than the pectic mucilage of flax, which lacks cellulose. In spite of the fact that P. lanceolata mucilage revealed different adhesive and frictional properties than the pectic mucilage, it still demonstrates an effective system promoting zoochoric seed dispersal. Cellulose may additionally prevent the mucilage against loss from the seed surface. PMID:28144540

Inkjet-assisted layer-by-layer printing of quantum dot/enzyme microarrays for highly sensitive detection of organophosphorous pesticides.

PubMed

Luan, Enxiao; Zheng, Zhaozhu; Li, Xinyu; Gu, Hongxi; Liu, Shaoqin

2016-04-15

We present a facile fabrication of layer-by-layer (LbL) microarrays of quantum dots (QDs) and acetylcholinesterase enzyme (AChE). The resulting arrays had several unique properties, such as low cost, high integration and excellent flexibility and time-saving. The presence of organophosphorous pesticides (OPs) can inhibit the AChE activity and thus changes the fluorescent intensity of QDs/AChE microscopic dot arrays. Therefore, the QDs/AChE microscopic dot arrays were used for the sensitive visual detection of OPs. Linear calibration for parathion and paraoxon was obtained in the range of 5-100 μg L(-1) under the optimized conditions with the limit of detection (LOD) of 10 μg L(-1). The arrays have been successfully used for detection of OPs in fruits and water real samples. The new array was validated by comparison with conventional high performance liquid chromatography-mass spectrometry (HPLC-MS). Copyright © 2016 Elsevier B.V. All rights reserved.

Ionic liquids as lubricants of metal-polymer contacts. Preparation and properties of the first dispersions of ionic liquids and nanoparticles in polymers

NASA Astrophysics Data System (ADS)

Sanes Molina, Jose

Room-temperature ionic liquids (ILs) are high performance fluids that stand out because of a wide range of functional properties and exhibit a great potential for engineering applications. Although they have been employed as lubricants in metal-metal, metal-ceramic and ceramic-ceramic contacts, in this thesis we present the first study about the use of ILs as pure lubricants in polymer/steel contacts. The tests have established the efficacy of the ILs to reduce friction coefficient and wear rates in a variety of kinds of contacts, and criogenic to high temperature performance. Novel dispersions of ILs in polymers have been obtained with epoxy resin and thermoplastics as matrix. Therefore, the thermal, mechanical and tribological properties of the materials have studied and are discussed in the present thesis. Furthermore, the contents of ILs in the polymer matrix have been studied in relation to the tribological properties using Scanning Electron Microscopy (SEM) and Energy Dispersive X-Ray Spectrometry (EDS), the wear mechanisms that operated in the contacts were established. The novel dispersions showed a reduction in the friction coefficient and wear in comparison with neat polymers, reaching in some cases a decrease of 79%. In the case of thermoplastics such as polystyrene and polyamide 6, the new dispersions showed a reduction in friction coefficient and wear in the same range as that of the ILs when used as external lubricants in the steel/polymer contact. In addition nanoparticles of zinc oxide were used to obtain polycarbonate based nanohybrids with the purpose of improving the tribological properties. Novel nanohybrids of zinc oxide and modified zinc oxide were obtained. The mechanical, thermal and tribological properties were studied. The results of experiments clearly demonstrated that the use of ILs modifies the shape and size of the ZnO nanoparticles, increasing the tribological properties of the novel nanohybrids. Different techniques such as EDS, Transmission Electron Microscopy (TEM), X-Ray Diffraction (XRD) and X-Ray Photoelectron Spectrometry (XPS) were used to examine and establish the surface interactions and mechanism that operated between ILs and ZnO. In summary, the results reveal the importance of the processing parameters on the stability of the nature of the anion in the ILs.

The Process of Nanostructuring of Metal (Iron) Matrix in Composite Materials for Directional Control of the Mechanical Properties

PubMed Central

Zemtsova, Elena

2014-01-01

We justified theoretical and experimental bases of synthesis of new class of highly nanostructured composite nanomaterials based on metal matrix with titanium carbide nanowires as dispersed phase. A new combined method for obtaining of metal iron-based composite materials comprising the powder metallurgy processes and the surface design of the dispersed phase is considered. The following stages of material synthesis are investigated: (1) preparation of porous metal matrix; (2) surface structuring of the porous metal matrix by TiC nanowires; (3) pressing and sintering to give solid metal composite nanostructured materials based on iron with TiC nanostructures with size 1–50 nm. This material can be represented as the material type “frame in the frame” that represents iron metal frame reinforcing the frame of different chemical compositions based on TiC. Study of material functional properties showed that the mechanical properties of composite materials based on iron with TiC dispersed phase despite the presence of residual porosity are comparable to the properties of the best grades of steel containing expensive dopants and obtained by molding. This will solve the problem of developing a new generation of nanostructured metal (iron-based) materials with improved mechanical properties for the different areas of technology. PMID:24695459

The process of nanostructuring of metal (iron) matrix in composite materials for directional control of the mechanical properties.

PubMed

Zemtsova, Elena; Yurchuk, Denis; Smirnov, Vladimir

2014-01-01

We justified theoretical and experimental bases of synthesis of new class of highly nanostructured composite nanomaterials based on metal matrix with titanium carbide nanowires as dispersed phase. A new combined method for obtaining of metal iron-based composite materials comprising the powder metallurgy processes and the surface design of the dispersed phase is considered. The following stages of material synthesis are investigated: (1) preparation of porous metal matrix; (2) surface structuring of the porous metal matrix by TiC nanowires; (3) pressing and sintering to give solid metal composite nanostructured materials based on iron with TiC nanostructures with size 1-50 nm. This material can be represented as the material type "frame in the frame" that represents iron metal frame reinforcing the frame of different chemical compositions based on TiC. Study of material functional properties showed that the mechanical properties of composite materials based on iron with TiC dispersed phase despite the presence of residual porosity are comparable to the properties of the best grades of steel containing expensive dopants and obtained by molding. This will solve the problem of developing a new generation of nanostructured metal (iron-based) materials with improved mechanical properties for the different areas of technology.

An Investigation of the Effects of Deposit Feeding Invertebrates on the Structural Properties of Clay Minerals.

DTIC Science & Technology

1981-07-01

Dennis M. Lavoie of NORDA for chemical analysis of clay minerals with the x-ray energy dispersive spectrometer. We thank Fred Bowles, Peter Fleischer...diffractograi of Nuculana acuta fecal pellet 11 residue (illite experiment). TABLES TABLE 1. X-ray energy dispersive spectrometer chemical 8 analysis for...inontmorillonite experiments. Counts for elements after background counts removed. TABLE 2. X-ray energy dispersive spectroneter chemical analysis 12 for

The Logistics of Oil Spill Dispersant Application. Volume I. Logistics-Related Properties of Oil Spill Dispersants.

DTIC Science & Technology

1982-11-01

time of application. Such designs were probably influenced by the ready availabilit " 51 of fire-fighting hoses on ships and tugs; the water stream not...8217 I I1 ---- i . . .. . IIII . . . I I PREFACE The use of chemicals for the dispersal of oil spilled on water has been the subject of discussion (and of...20 Oil Type, Weathering and Emulsification.. 20 Slick Thickness .......................... 28 Water Temperature

The Theory of Thermodynamics for Chemical Reactions in Dispersed Heterogeneous Systems

PubMed

Yongqiang; Baojiao; Jianfeng

1997-07-01

In this paper, the expressions of Gibbs energy change, enthalpy change, entropy change, and equilibrium constant for chemical reactions in dispersed heterogeneous systems are derived using classical thermodynamics theory. The thermodynamical relations for the same reaction system between the dispersed and the block state are also derived. The effects of degree of dispersion on thermodynamical properties, reaction directions, and chemical equilibria are discussed. The results show that the present equation of thermodynamics for chemical reactions is only a special case of the above-mentioned formulas and that the effect of the dispersity of a heterogeneous system on the chemical reaction obeys the Le Chatelier principle of movement of equilibria.

Chromatic dispersion effects in ultra-low coherence interferometry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lychagov, V V; Ryabukho, V P

2015-06-30

We consider the properties of an interference signal shift from zero-path-difference position in the presence of an uncompensated dispersive layer in one of the interferometer arms. It is experimentally shown that in using an ultra-low coherence light source, the formation of the interference signal is also determined by the group velocity dispersion, which results in a nonlinear dependence of the position of the interference signal on the geometrical thickness of the dispersive layer. The discrepancy in the dispersive layer and compensator refractive indices in the third decimal place is experimentally shown to lead to an interference signal shift that ismore » an order of magnitude greater than the pulse width. (interferometry)« less

Rheology and phase behavior of dense casein micelle dispersions

NASA Astrophysics Data System (ADS)

Bouchoux, A.; Debbou, B.; Gésan-Guiziou, G.; Famelart, M.-H.; Doublier, J.-L.; Cabane, B.

2009-10-01

Casein micelle dispersions have been concentrated through osmotic stress and examined through rheological experiments. In conditions where the casein micelles are separated from each other, i.e., below random-close packing, the dispersions have exactly the flow and dynamic properties of the polydisperse hard-sphere fluid, demonstrating that the micelles interact only through excluded volume effects in this regime. These interactions cause the viscosity and the elastic modulus to increase by three orders of magnitude approaching the concentration of random-close packing estimated at Cmax≈178 g/l. Above Cmax, the dispersions progressively turn into "gels" (i.e., soft solids) as C increases, with elastic moduli G' that are nearly frequency independent. In this second regime, the micelles deform and/or deswell as C increases, and the resistance to deformation results from the formation of bonds between micelles combined with the intrinsic mechanical resistance of the micelles. The variation in G' with C is then very similar to that observed with concentrated emulsions where the resistance to deformation originates from a set of membranes that separate the droplets. As in the case of emulsions, the G' values at high frequency are also nearly identical to the osmotic pressures required to compress the casein dispersions. The rheology of sodium caseinate dispersions in which the caseins are not structured into micelles is also reported. Such dispersions have the behavior of associative polymer solutions at all the concentrations investigated, further confirming the importance of structure in determining the rheological properties of casein micelle systems.

Effects of ultrasound treatment on physico-chemical, functional properties and antioxidant activity of whey protein isolate in the presence of calcium lactate.

PubMed

Jiang, Zhanmei; Yao, Kun; Yuan, Xiangying; Mu, Zhishen; Gao, Zengli; Hou, Juncai; Jiang, Lianzhou

2018-03-01

The aim of this study was to investigate the effects of ultrasound applied at various powers (0, 200, 400, 600 or 800 W) and for different times (20 or 40 min) on the physico-chemical, functional properties and antioxidant activities of whey protein isolate (WPI) dispersions in the presence of 1.20 mmol L -1 calcium lactate. Surface hydrophobicity and free sulfhydryl group of the WPI dispersions containing 1.2 mmol L -1 calcium lactate were significantly enhanced after sonication. Furthermore, particle size of WPI dispersions containing 1.20 mmol L -1 calcium lactate was minimised after sonication. Scanning electron microscopy of sonicated WPI suspensions containing 1.20 mmol L -1 calcium lactate showed that WPI microstructure had significantly changed. After WPI dispersions were treated by sonication assisted with calcium lactate, its gel strength enhanced and solubility decreased. Gel strength of sonicated WPI dispersions (600 W, 40 min) was the maximum among all the WPI treatments. Emulsification activity of sonicated WPI dispersions reduced while its emulsion stability increased. The DPPH radical scavenging activity and ferrous reducing power of sonicated WPI dispersions mostly increased. Ultrasound treatments induced structural changes in WPI molecules, leading to different microstructure and improved gel strength of WPI in the presence of calcium lactate. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Rheology and phase behavior of dense casein micelle dispersions.

PubMed

Bouchoux, A; Debbou, B; Gésan-Guiziou, G; Famelart, M-H; Doublier, J-L; Cabane, B

2009-10-28

Casein micelle dispersions have been concentrated through osmotic stress and examined through rheological experiments. In conditions where the casein micelles are separated from each other, i.e., below random-close packing, the dispersions have exactly the flow and dynamic properties of the polydisperse hard-sphere fluid, demonstrating that the micelles interact only through excluded volume effects in this regime. These interactions cause the viscosity and the elastic modulus to increase by three orders of magnitude approaching the concentration of random-close packing estimated at C(max) approximately 178 g/l. Above C(max), the dispersions progressively turn into "gels" (i.e., soft solids) as C increases, with elastic moduli G(') that are nearly frequency independent. In this second regime, the micelles deform and/or deswell as C increases, and the resistance to deformation results from the formation of bonds between micelles combined with the intrinsic mechanical resistance of the micelles. The variation in G(') with C is then very similar to that observed with concentrated emulsions where the resistance to deformation originates from a set of membranes that separate the droplets. As in the case of emulsions, the G(') values at high frequency are also nearly identical to the osmotic pressures required to compress the casein dispersions. The rheology of sodium caseinate dispersions in which the caseins are not structured into micelles is also reported. Such dispersions have the behavior of associative polymer solutions at all the concentrations investigated, further confirming the importance of structure in determining the rheological properties of casein micelle systems.

BABAR: an R package to simplify the normalisation of common reference design microarray-based transcriptomic datasets

PubMed Central

2010-01-01

Background The development of DNA microarrays has facilitated the generation of hundreds of thousands of transcriptomic datasets. The use of a common reference microarray design allows existing transcriptomic data to be readily compared and re-analysed in the light of new data, and the combination of this design with large datasets is ideal for 'systems'-level analyses. One issue is that these datasets are typically collected over many years and may be heterogeneous in nature, containing different microarray file formats and gene array layouts, dye-swaps, and showing varying scales of log2- ratios of expression between microarrays. Excellent software exists for the normalisation and analysis of microarray data but many data have yet to be analysed as existing methods struggle with heterogeneous datasets; options include normalising microarrays on an individual or experimental group basis. Our solution was to develop the Batch Anti-Banana Algorithm in R (BABAR) algorithm and software package which uses cyclic loess to normalise across the complete dataset. We have already used BABAR to analyse the function of Salmonella genes involved in the process of infection of mammalian cells. Results The only input required by BABAR is unprocessed GenePix or BlueFuse microarray data files. BABAR provides a combination of 'within' and 'between' microarray normalisation steps and diagnostic boxplots. When applied to a real heterogeneous dataset, BABAR normalised the dataset to produce a comparable scaling between the microarrays, with the microarray data in excellent agreement with RT-PCR analysis. When applied to a real non-heterogeneous dataset and a simulated dataset, BABAR's performance in identifying differentially expressed genes showed some benefits over standard techniques. Conclusions BABAR is an easy-to-use software tool, simplifying the simultaneous normalisation of heterogeneous two-colour common reference design cDNA microarray-based transcriptomic datasets. We show BABAR transforms real and simulated datasets to allow for the correct interpretation of these data, and is the ideal tool to facilitate the identification of differentially expressed genes or network inference analysis from transcriptomic datasets. PMID:20128918

Quantitative dispersion microscopy

PubMed Central

Fu, Dan; Choi, Wonshik; Sung, Yongjin; Yaqoob, Zahid; Dasari, Ramachandra R.; Feld, Michael

2010-01-01

Refractive index dispersion is an intrinsic optical property and a useful source of contrast in biological imaging studies. In this report, we present the first dispersion phase imaging of living eukaryotic cells. We have developed quantitative dispersion microscopy based on the principle of quantitative phase microscopy. The dual-wavelength quantitative phase microscope makes phase measurements at 310 nm and 400 nm wavelengths to quantify dispersion (refractive index increment ratio) of live cells. The measured dispersion of living HeLa cells is found to be around 1.088, which agrees well with that measured directly for protein solutions using total internal reflection. This technique, together with the dry mass and morphology measurements provided by quantitative phase microscopy, could prove to be a useful tool for distinguishing different types of biomaterials and studying spatial inhomogeneities of biological samples. PMID:21113234

Molecular surface area based predictive models for the adsorption and diffusion of disperse dyes in polylactic acid matrix.

PubMed

Xu, Suxin; Chen, Jiangang; Wang, Bijia; Yang, Yiqi

2015-11-15

Two predictive models were presented for the adsorption affinities and diffusion coefficients of disperse dyes in polylactic acid matrix. Quantitative structure-sorption behavior relationship would not only provide insights into sorption process, but also enable rational engineering for desired properties. The thermodynamic and kinetic parameters for three disperse dyes were measured. The predictive model for adsorption affinity was based on two linear relationships derived by interpreting the experimental measurements with molecular structural parameters and compensation effect: ΔH° vs. dye size and ΔS° vs. ΔH°. Similarly, the predictive model for diffusion coefficient was based on two derived linear relationships: activation energy of diffusion vs. dye size and logarithm of pre-exponential factor vs. activation energy of diffusion. The only required parameters for both models are temperature and solvent accessible surface area of the dye molecule. These two predictive models were validated by testing the adsorption and diffusion properties of new disperse dyes. The models offer fairly good predictive ability. The linkage between structural parameter of disperse dyes and sorption behaviors might be generalized and extended to other similar polymer-penetrant systems. Copyright © 2015 Elsevier Inc. All rights reserved.

Observation of trapped light induced by Dwarf Dirac-cone in out-of-plane condition for photonic crystals

NASA Astrophysics Data System (ADS)

Majumder, Subir; Biswas, Tushar; Bhadra, Shaymal K.

2016-10-01

Existence of out-of-plane conical dispersion for a triangular photonic crystal lattice is reported. It is observed that conical dispersion is maintained for a number of out-of-plane wave vectors (k z ). We study a case where Dirac like linear dispersion exists but the photonic density of states is not vanishing, called Dwarf Dirac cone (DDC) which does not support localized modes. We demonstrate the trapping of such modes by introducing defects in the crystal. Interestingly, we find by k-point sampling as well as by tuning trapped frequency that such a conical dispersion has an inherent light confining property and it is governed by neither of the known wave confining mechanisms like total internal reflection, band gap guidance. Our study reveals that such a conical dispersion in a non-vanishing photonic density of states induces unexpected intense trapping of light compared with those at other points in the continuum. Such studies provoke fabrication of new devices with exciting properties and new functionalities. Project supported by Director, CSIR-CGCRI, the DST, Government of India, and the CSIR 12th Plan Project (GLASSFIB), India.

Modal expansions in periodic photonic systems with material loss and dispersion

NASA Astrophysics Data System (ADS)

Wolff, Christian; Busch, Kurt; Mortensen, N. Asger

2018-03-01

We study band-structure properties of periodic optical systems composed of lossy and intrinsically dispersive materials. To this end, we develop an analytical framework based on adjoint modes of a lossy periodic electromagnetic system and show how the problem of linearly dependent eigenmodes in the presence of material dispersion can be overcome. We then formulate expressions for the band-structure derivative (∂ ω )/(∂ k ) (complex group velocity) and the local and total density of transverse optical states. Our exact expressions hold for 3D periodic arrays of materials with arbitrary dispersion properties and in general need to be evaluated numerically. They can be generalized to systems with two, one, or no directions of periodicity provided the fields are localized along nonperiodic directions. Possible applications are photonic crystals, metamaterials, metasurfaces composed of highly dispersive materials such as metals or lossless photonic crystals, and metamaterials or metasurfaces strongly coupled to resonant perturbations such as quantum dots or excitons in 2D materials. For illustration purposes, we analytically evaluate our expressions for some simple systems consisting of lossless dielectrics with one sharp Lorentzian material resonance added. By combining several Lorentz poles, this provides an avenue to perturbatively treat quite general material loss bands in photonic crystals.

Electroactive Shape Memory Property of a Cu-decorated CNT Dispersed PLA/ESO Nanocomposite

PubMed Central

Alam, Javed; Khan, Aslam; Alam, Manawwer; Mohan, Raja

2015-01-01

Shape memory polymer (SMP) nanocomposites with a fast electro-actuation speed were prepared by dispersing Cu-decorated carbon nanotubes (CNTs) (Cu-CNTs, 1 wt %, 2 wt %, and 3 wt %) in a polylactic acid (PLA)/epoxidized soybean oil (ESO) blend matrix. The shape memory effect (SME) induced by an electrical current was investigated by a fold-deploy “U”-shape bending test. In addition, the Cu-CNT dispersed PLA/ESO nanocomposite was characterized by atomic force microscopy (AFM), dynamic mechanical analysis (DMA) and tensile and electrical measurements. The results demonstrated that the SME was dependent on the Cu-CNT content in the nanocomposites. When comparing the SMEs of the nanocomposite specimens with different Cu-CNT contents, the 2 wt % Cu-CNT dispersed system exhibited a shape recovery as high as 98% within 35 s due to its higher electrical conductivity that results from uniform Cu-CNT dispersion. However, the nanocomposites that contained 1 wt % and 3 wt % Cu-CNTs required 75 s and 63 s, respectively, to reach a maximum recovery level. In addition, the specimens exhibited better mechanical properties after the addition of Cu-CNTs. PMID:28793570

Computational sensitivity study of spray dispersion and mixing on the fuel properties in a gas turbine combustor

NASA Astrophysics Data System (ADS)

Grosshans, Holger; Cao, Le; Fuchs, Laszlo; Szász, Robert-Zoltán

2017-04-01

A swirl stabilized gas turbine burner has been simulated in order to assess the effects of the fuel properties on spray dispersion and fuel-air mixing. The properties under consideration include fuel surface tension, viscosity and density. The turbulence of the gas phase is modeled applying the methodology of large eddy simulation whereas the dispersed liquid phase is described by Lagrangian particle tracking. The exchange of mass, momentum and energy between the two phases is accounted for by two-way coupling. Bag and stripping breakup regimes are considered for secondary droplet breakup, using the Reitz-Diwakar and the Taylor analogy breakup models. Moreover, a model for droplet evaporation is included. The results reveal a high sensitivity of the spray structure to variations of all investigated parameters. In particular, a decrease in the surface tension or the fuel viscosity, or an increase in the fuel density, lead to less stable liquid structures. As a consequence, smaller droplets are generated and the overall spray surface area increases, leading to faster evaporation and mixing. Furthermore, with the trajectories of the small droplets being strongly influenced by aerodynamic forces (and less by their own inertia), the spray is more affected by the turbulent structures of the gaseous phase and the spray dispersion is enhanced.

Mechanical properties of glass fiber-reinforced endodontic posts.

PubMed

Cheleux, Nicolas; Sharrock, Patrick J

2009-10-01

Five types of posts from three different manufacturers (RTD, France, Carbotech, France and Ivoclar-Vivadent, Liechenstein) were subjected to three-point bending tests in order to obtain fatigue results, flexural strength and modulus. Transverse and longitudinal polished sections were examined by scanning electron microscopy and evaluated by computer-assisted image analysis. Physical parameters, including volume % of fibers, their dispersion index and coordination number, were calculated and correlated with mechanical properties. The weaker posts showed more fiber dispersion, higher resin contents, larger numbers of visible defects and reduced fatigue resistance. The flexural strength was inversely correlated with fiber diameter and the flexural modulus was weakly related to coordination number, volume % of fibers and dispersion index. The interfacial adhesion between the silica fibers and the resin matrix was observed to be of paramount importance.

Kubo formulas for dispersion in heterogeneous periodic nonequilibrium systems.

PubMed

Guérin, T; Dean, D S

2015-12-01

We consider the dispersion properties of tracer particles moving in nonequilibrium heterogeneous periodic media. The tracer motion is described by a Fokker-Planck equation with arbitrary spatially periodic (but constant in time) local diffusion tensors and drifts, eventually with the presence of obstacles. We derive a Kubo-like formula for the time-dependent effective diffusion tensor valid in any dimension. From this general formula, we derive expressions for the late time effective diffusion tensor and drift in these systems. In addition, we find an explicit formula for the late finite-time corrections to these transport coefficients. In one dimension, we give a closed analytical formula for the transport coefficients. The formulas derived here are very general and provide a straightforward method to compute the dispersion properties in arbitrary nonequilibrium periodic advection-diffusion systems.

Polarization and switching properties of holographic polymer-dispersed liquid-crystal gratings. I. Theoretical model

NASA Astrophysics Data System (ADS)

Sutherland, Richard L.

2002-12-01

Polarization properties and electro-optical switching behavior of holographic polymer-dispersed liquid-crystal (HPDLC) reflection and transmission gratings are studied. A theoretical model is developed that combines anisotropic coupled-wave theory with an elongated liquid-crystal-droplet switching model and includes the effects of a statistical orientational distribution of droplet-symmetry axes. Angle- and polarization-dependent switching behaviors of HPDLC gratings are elucidated, and the effects on dynamic range are described. A new type of electro-optical switching not seen in ordinary polymer-dispersed liquid crystals, to the best of the author's knowledge, is presented and given a physical interpretation. The model provides valuable insight to the physics of these gratings and can be applied to the design of HPDLC holographic optical elements.

Analysis of dispersion relation in three-dimensional single gyroid

NASA Astrophysics Data System (ADS)

Jheng, Pei-Lun; Hung, Yu-Chueh

2016-03-01

Gyroid is a type of three-dimensional chiral structures and has been found in many insect species. Besides the photonic crystal properties exhibited by gyroid structures, the chirality and gyroid network morphology also provide unique opportunities for manipulating propagation of light. In this work, we present studies based on finite-difference time domain (FDTD) method for analyzing the dispersion relation characteristics of dielectric single gyroid (SG) metamaterials. The band structures, transmission spectrum, dispersion surfaces, equifrequency contours (EFCs) of SG metamaterials are examined. Some interesting wave guiding characteristics, such as negative refraction and collimation, are presented and discussed. We also show how these optical properties are predicted by analyzing the EFCs at different frequencies. These results are crucial for the design of functional devices at optical frequencies based on dielectric single gyroid metamaterials.

EXPERIMENTAL DETERMINATION OF WHISTLER WAVE DISPERSION RELATION IN THE SOLAR WIND

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stansby, D.; Horbury, T. S.; Chen, C. H. K.

2016-09-20

The origins and properties of large-amplitude whistler wavepackets in the solar wind are still unclear. In this Letter, we utilize single spacecraft electric and magnetic field waveform measurements from the ARTEMIS mission to calculate the plasma frame frequency and wavevector of individual wavepackets over multiple intervals. This allows direct comparison of experimental measurements with theoretical dispersion relations to identify the observed waves as whistler waves. The whistlers are right-hand circularly polarized, travel anti-sunward, and are aligned with the background magnetic field. Their dispersion is strongly affected by the local electron parallel beta in agreement with linear theory. The properties measuredmore » are consistent with the electron heat flux instability acting in the solar wind to generate these waves.« less

UV response on dielectric properties of nano nematic liquid crystal

NASA Astrophysics Data System (ADS)

Pandey, Kamal Kumar; Tripathi, Pankaj Kumar; Misra, Abhishek Kumar; Manohar, Rajiv

2018-03-01

In this work, we investigate the effect of UV light irradiation on the dielectric parameters of nematic liquid crystal (5CB) and ZnO nanoparticles dispersed liquid crystal. With addition of nanoparticles in nematic LC are promising new materials for a variety of application in energy harvesting, displays and photonics including the liquid crystal laser. To realize many applications, however we optimize the properties of liquid crystal and understand how the UV light irradiation interact the nanoparticles and LC molecules in dispersed/doped LC. The dielectric permittivity and loss factor have discussed the pure nematic LC and dispersed/doped system after, during and before UV light exposure. The dielectric relaxation spectroscopy was carried out in the frequency range 100 Hz-10 MHz in the nematic mesophase range.

A genome-wide 20 K citrus microarray for gene expression analysis

PubMed Central

Martinez-Godoy, M Angeles; Mauri, Nuria; Juarez, Jose; Marques, M Carmen; Santiago, Julia; Forment, Javier; Gadea, Jose

2008-01-01

Background Understanding of genetic elements that contribute to key aspects of citrus biology will impact future improvements in this economically important crop. Global gene expression analysis demands microarray platforms with a high genome coverage. In the last years, genome-wide EST collections have been generated in citrus, opening the possibility to create new tools for functional genomics in this crop plant. Results We have designed and constructed a publicly available genome-wide cDNA microarray that include 21,081 putative unigenes of citrus. As a functional companion to the microarray, a web-browsable database [1] was created and populated with information about the unigenes represented in the microarray, including cDNA libraries, isolated clones, raw and processed nucleotide and protein sequences, and results of all the structural and functional annotation of the unigenes, like general description, BLAST hits, putative Arabidopsis orthologs, microsatellites, putative SNPs, GO classification and PFAM domains. We have performed a Gene Ontology comparison with the full set of Arabidopsis proteins to estimate the genome coverage of the microarray. We have also performed microarray hybridizations to check its usability. Conclusion This new cDNA microarray replaces the first 7K microarray generated two years ago and allows gene expression analysis at a more global scale. We have followed a rational design to minimize cross-hybridization while maintaining its utility for different citrus species. Furthermore, we also provide access to a website with full structural and functional annotation of the unigenes represented in the microarray, along with the ability to use this site to directly perform gene expression analysis using standard tools at different publicly available servers. Furthermore, we show how this microarray offers a good representation of the citrus genome and present the usefulness of this genomic tool for global studies in citrus by using it to catalogue genes expressed in citrus globular embryos. PMID:18598343

An evaluation of two-channel ChIP-on-chip and DNA methylation microarray normalization strategies

PubMed Central

2012-01-01

Background The combination of chromatin immunoprecipitation with two-channel microarray technology enables genome-wide mapping of binding sites of DNA-interacting proteins (ChIP-on-chip) or sites with methylated CpG di-nucleotides (DNA methylation microarray). These powerful tools are the gateway to understanding gene transcription regulation. Since the goals of such studies, the sample preparation procedures, the microarray content and study design are all different from transcriptomics microarrays, the data pre-processing strategies traditionally applied to transcriptomics microarrays may not be appropriate. Particularly, the main challenge of the normalization of "regulation microarrays" is (i) to make the data of individual microarrays quantitatively comparable and (ii) to keep the signals of the enriched probes, representing DNA sequences from the precipitate, as distinguishable as possible from the signals of the un-enriched probes, representing DNA sequences largely absent from the precipitate. Results We compare several widely used normalization approaches (VSN, LOWESS, quantile, T-quantile, Tukey's biweight scaling, Peng's method) applied to a selection of regulation microarray datasets, ranging from DNA methylation to transcription factor binding and histone modification studies. Through comparison of the data distributions of control probes and gene promoter probes before and after normalization, and assessment of the power to identify known enriched genomic regions after normalization, we demonstrate that there are clear differences in performance between normalization procedures. Conclusion T-quantile normalization applied separately on the channels and Tukey's biweight scaling outperform other methods in terms of the conservation of enriched and un-enriched signal separation, as well as in identification of genomic regions known to be enriched. T-quantile normalization is preferable as it additionally improves comparability between microarrays. In contrast, popular normalization approaches like quantile, LOWESS, Peng's method and VSN normalization alter the data distributions of regulation microarrays to such an extent that using these approaches will impact the reliability of the downstream analysis substantially. PMID:22276688

Advantages of RNA-seq compared to RNA microarrays for transcriptome profiling of anterior cruciate ligament tears.

PubMed

Rai, Muhammad Farooq; Tycksen, Eric D; Sandell, Linda J; Brophy, Robert H

2018-01-01

Microarrays and RNA-seq are at the forefront of high throughput transcriptome analyses. Since these methodologies are based on different principles, there are concerns about the concordance of data between the two techniques. The concordance of RNA-seq and microarrays for genome-wide analysis of differential gene expression has not been rigorously assessed in clinically derived ligament tissues. To demonstrate the concordance between RNA-seq and microarrays and to assess potential benefits of RNA-seq over microarrays, we assessed differences in transcript expression in anterior cruciate ligament (ACL) tissues based on time-from-injury. ACL remnants were collected from patients with an ACL tear at the time of ACL reconstruction. RNA prepared from torn ACL remnants was subjected to Agilent microarrays (N = 24) and RNA-seq (N = 8). The correlation of biological replicates in RNA-seq and microarrays data was similar (0.98 vs. 0.97), demonstrating that each platform has high internal reproducibility. Correlations between the RNA-seq data and the individual microarrays were low, but correlations between the RNA-seq values and the geometric mean of the microarrays values were moderate. The cross-platform concordance for differentially expressed transcripts or enriched pathways was linearly correlated (r = 0.64). RNA-Seq was superior in detecting low abundance transcripts and differentiating biologically critical isoforms. Additional independent validation of transcript expression was undertaken using microfluidic PCR for selected genes. PCR data showed 100% concordance (in expression pattern) with RNA-seq and microarrays data. These findings demonstrate that RNA-seq has advantages over microarrays for transcriptome profiling of ligament tissues when available and affordable. Furthermore, these findings are likely transferable to other musculoskeletal tissues where tissue collection is challenging and cells are in low abundance. © 2017 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 36:484-497, 2018. © 2017 Orthopaedic Research Society. Published by Wiley Periodicals, Inc.

The effect of column purification on cDNA indirect labelling for microarrays

PubMed Central

Molas, M Lia; Kiss, John Z

2007-01-01

Background The success of the microarray reproducibility is dependent upon the performance of standardized procedures. Since the introduction of microarray technology for the analysis of global gene expression, reproducibility of results among different laboratories has been a major problem. Two of the main contributors to this variability are the use of different microarray platforms and different laboratory practices. In this paper, we address the latter question in terms of how variation in one of the steps of a labelling procedure affects the cDNA product prior to microarray hybridization. Results We used a standard procedure to label cDNA for microarray hybridization and employed different types of column chromatography for cDNA purification. After purifying labelled cDNA, we used the Agilent 2100 Bioanalyzer and agarose gel electrophoresis to assess the quality of the labelled cDNA before its hybridization onto a microarray platform. There were major differences in the cDNA profile (i.e. cDNA fragment lengths and abundance) as a result of using four different columns for purification. In addition, different columns have different efficiencies to remove rRNA contamination. This study indicates that the appropriate column to use in this type of protocol has to be experimentally determined. Finally, we present new evidence establishing the importance of testing the method of purification used during an indirect labelling procedure. Our results confirm the importance of assessing the quality of the sample in the labelling procedure prior to hybridization onto a microarray platform. Conclusion Standardization of column purification systems to be used in labelling procedures will improve the reproducibility of microarray results among different laboratories. In addition, implementation of a quality control check point of the labelled samples prior to microarray hybridization will prevent hybridizing a poor quality sample to expensive micorarrays. PMID:17597522

The effect of column purification on cDNA indirect labelling for microarrays.

PubMed

Molas, M Lia; Kiss, John Z

2007-06-27

The success of the microarray reproducibility is dependent upon the performance of standardized procedures. Since the introduction of microarray technology for the analysis of global gene expression, reproducibility of results among different laboratories has been a major problem. Two of the main contributors to this variability are the use of different microarray platforms and different laboratory practices. In this paper, we address the latter question in terms of how variation in one of the steps of a labelling procedure affects the cDNA product prior to microarray hybridization. We used a standard procedure to label cDNA for microarray hybridization and employed different types of column chromatography for cDNA purification. After purifying labelled cDNA, we used the Agilent 2100 Bioanalyzer and agarose gel electrophoresis to assess the quality of the labelled cDNA before its hybridization onto a microarray platform. There were major differences in the cDNA profile (i.e. cDNA fragment lengths and abundance) as a result of using four different columns for purification. In addition, different columns have different efficiencies to remove rRNA contamination. This study indicates that the appropriate column to use in this type of protocol has to be experimentally determined. Finally, we present new evidence establishing the importance of testing the method of purification used during an indirect labelling procedure. Our results confirm the importance of assessing the quality of the sample in the labelling procedure prior to hybridization onto a microarray platform. Standardization of column purification systems to be used in labelling procedures will improve the reproducibility of microarray results among different laboratories. In addition, implementation of a quality control check point of the labelled samples prior to microarray hybridization will prevent hybridizing a poor quality sample to expensive micorarrays.

Evolution of the MIDTAL microarray: the adaption and testing of oligonucleotide 18S and 28S rDNA probes and evaluation of subsequent microarray generations with Prymnesium spp. cultures and field samples.

PubMed

McCoy, Gary R; Touzet, Nicolas; Fleming, Gerard T A; Raine, Robin

2015-07-01

The toxic microalgal species Prymnesium parvum and Prymnesium polylepis are responsible for numerous fish kills causing economic stress on the aquaculture industry and, through the consumption of contaminated shellfish, can potentially impact on human health. Monitoring of toxic phytoplankton is traditionally carried out by light microscopy. However, molecular methods of identification and quantification are becoming more common place. This study documents the optimisation of the novel Microarrays for the Detection of Toxic Algae (MIDTAL) microarray from its initial stages to the final commercial version now available from Microbia Environnement (France). Existing oligonucleotide probes used in whole-cell fluorescent in situ hybridisation (FISH) for Prymnesium species from higher group probes to species-level probes were adapted and tested on the first-generation microarray. The combination and interaction of numerous other probes specific for a whole range of phytoplankton taxa also spotted on the chip surface caused high cross reactivity, resulting in false-positive results on the microarray. The probe sequences were extended for the subsequent second-generation microarray, and further adaptations of the hybridisation protocol and incubation temperatures significantly reduced false-positive readings from the first to the second-generation chip, thereby increasing the specificity of the MIDTAL microarray. Additional refinement of the subsequent third-generation microarray protocols with the addition of a poly-T amino linker to the 5' end of each probe further enhanced the microarray performance but also highlighted the importance of optimising RNA labelling efficiency when testing with natural seawater samples from Killary Harbour, Ireland.

Simple display system of mechanical properties of cells and their dispersion.

PubMed

Shimizu, Yuji; Kihara, Takanori; Haghparast, Seyed Mohammad Ali; Yuba, Shunsuke; Miyake, Jun

2012-01-01

The mechanical properties of cells are unique indicators of their states and functions. Though, it is difficult to recognize the degrees of mechanical properties, due to small size of the cell and broad distribution of the mechanical properties. Here, we developed a simple virtual reality system for presenting the mechanical properties of cells and their dispersion using a haptic device and a PC. This system simulates atomic force microscopy (AFM) nanoindentation experiments for floating cells in virtual environments. An operator can virtually position the AFM spherical probe over a round cell with the haptic handle on the PC monitor and feel the force interaction. The Young's modulus of mesenchymal stem cells and HEK293 cells in the floating state was measured by AFM. The distribution of the Young's modulus of these cells was broad, and the distribution complied with a log-normal pattern. To represent the mechanical properties together with the cell variance, we used log-normal distribution-dependent random number determined by the mode and variance values of the Young's modulus of these cells. The represented Young's modulus was determined for each touching event of the probe surface and the cell object, and the haptic device-generating force was calculated using a Hertz model corresponding to the indentation depth and the fixed Young's modulus value. Using this system, we can feel the mechanical properties and their dispersion in each cell type in real time. This system will help us not only recognize the degrees of mechanical properties of diverse cells but also share them with others.

Simple Display System of Mechanical Properties of Cells and Their Dispersion

PubMed Central

Shimizu, Yuji; Kihara, Takanori; Haghparast, Seyed Mohammad Ali; Yuba, Shunsuke; Miyake, Jun

2012-01-01

The mechanical properties of cells are unique indicators of their states and functions. Though, it is difficult to recognize the degrees of mechanical properties, due to small size of the cell and broad distribution of the mechanical properties. Here, we developed a simple virtual reality system for presenting the mechanical properties of cells and their dispersion using a haptic device and a PC. This system simulates atomic force microscopy (AFM) nanoindentation experiments for floating cells in virtual environments. An operator can virtually position the AFM spherical probe over a round cell with the haptic handle on the PC monitor and feel the force interaction. The Young's modulus of mesenchymal stem cells and HEK293 cells in the floating state was measured by AFM. The distribution of the Young's modulus of these cells was broad, and the distribution complied with a log-normal pattern. To represent the mechanical properties together with the cell variance, we used log-normal distribution-dependent random number determined by the mode and variance values of the Young's modulus of these cells. The represented Young's modulus was determined for each touching event of the probe surface and the cell object, and the haptic device-generating force was calculated using a Hertz model corresponding to the indentation depth and the fixed Young's modulus value. Using this system, we can feel the mechanical properties and their dispersion in each cell type in real time. This system will help us not only recognize the degrees of mechanical properties of diverse cells but also share them with others. PMID:22479595

Two-Dimensional VO2 Mesoporous Microarrays for High-Performance Supercapacitor

NASA Astrophysics Data System (ADS)

Fan, Yuqi; Ouyang, Delong; Li, Bao-Wen; Dang, Feng; Ren, Zongming

2018-05-01

Two-dimensional (2D) mesoporous VO2 microarrays have been prepared using an organic-inorganic liquid interface. The units of microarrays consist of needle-like VO2 particles with a mesoporous structure, in which crack-like pores with a pore size of about 2 nm and depth of 20-100 nm are distributed on the particle surface. The liquid interface acts as a template for the formation of the 2D microarrays, as identified from the kinetic observation. Due to the mesoporous structure of the units and high conductivity of the microarray, such 2D VO2 microarrays exhibit a high specific capacitance of 265 F/g at 1 A/g and excellent rate capability (182 F/g at 10 A/g) and cycling stability, suggesting the effect of unique microstructure for improving the electrochemical performance.

Plant-pathogen interactions: what microarray tells about it?

PubMed

Lodha, T D; Basak, J

2012-01-01

Plant defense responses are mediated by elementary regulatory proteins that affect expression of thousands of genes. Over the last decade, microarray technology has played a key role in deciphering the underlying networks of gene regulation in plants that lead to a wide variety of defence responses. Microarray is an important tool to quantify and profile the expression of thousands of genes simultaneously, with two main aims: (1) gene discovery and (2) global expression profiling. Several microarray technologies are currently in use; most include a glass slide platform with spotted cDNA or oligonucleotides. Till date, microarray technology has been used in the identification of regulatory genes, end-point defence genes, to understand the signal transduction processes underlying disease resistance and its intimate links to other physiological pathways. Microarray technology can be used for in-depth, simultaneous profiling of host/pathogen genes as the disease progresses from infection to resistance/susceptibility at different developmental stages of the host, which can be done in different environments, for clearer understanding of the processes involved. A thorough knowledge of plant disease resistance using successful combination of microarray and other high throughput techniques, as well as biochemical, genetic, and cell biological experiments is needed for practical application to secure and stabilize yield of many crop plants. This review starts with a brief introduction to microarray technology, followed by the basics of plant-pathogen interaction, the use of DNA microarrays over the last decade to unravel the mysteries of plant-pathogen interaction, and ends with the future prospects of this technology.

Single-particle dispersion in compressible turbulence

NASA Astrophysics Data System (ADS)

Zhang, Qingqing; Xiao, Zuoli

2018-04-01

Single-particle dispersion statistics in compressible box turbulence are studied using direct numerical simulation. Focus is placed on the detailed discussion of effects of the particle Stokes number and turbulent Mach number, as well as the forcing type. When solenoidal forcing is adopted, it is found that the single-particle dispersion undergoes a transition from the ballistic regime at short times to the diffusive regime at long times, in agreement with Taylor's particle dispersion argument. The strongest dispersion of heavy particles is announced when the Stokes number is of order 1, which is similar to the scenario in incompressible turbulence. The dispersion tends to be suppressed as the Mach number increases. When hybrid solenoidal and compressive forcing at a ratio of 1/2 is employed, the flow field shows apparent anisotropic property, characterized by the appearance of large shock wave structures. Accordingly, the single-particle dispersion shows extremely different behavior from the solenoidal forcing case.

Development of novel ibuprofen-loaded solid dispersion with enhanced bioavailability using cycloamylose.

PubMed

Baek, Hyung Hee; Kim, Dae-Hwan; Kwon, So Young; Rho, Shin-Joung; Kim, Dong-Wuk; Choi, Han-Gon; Kim, Yong-Ro; Yong, Chul Soon

2012-03-01

To develop a novel ibuprofen-loaded solid dispersion with enhanced bioavailability using cycloamylose, it was prepared using spray-drying techniques with cycloamylose at a weight ratio of 1:1. The effect of cycloamylose on aqueous solubility of ibuprofen was investigated. The physicochemical properties of solid dispersions were investigated using scanning electron microscopy (SEM), differential scanning calorimetry (DSC), and X-ray diffraction. The dissolution and bioavailability in rats were evaluated compared with ibuprofen powder. This ibuprofen-loaded solid dispersion improved about 14-fold drug solubility. Ibuprofen was present in an unchanged crystalline state, and cycloamylose played the simple role of a solubilizing agent in this solid dispersion. Moreover, the dispersion gave 2-fold higher AUC (area under the drug concentration-time curve) value compared with a ibuprofen powder, indicating that it improved the oral bioavailability of ibuprofen in rats. Thus, the solid dispersion may be useful to deliver ibuprofen with enhanced bioavailability without crystalline change.

Single-mode dispersive waves and soliton microcomb dynamics

PubMed Central

Yi, Xu; Yang, Qi-Fan; Zhang, Xueyue; Yang, Ki Youl; Li, Xinbai; Vahala, Kerry

2017-01-01

Dissipative Kerr solitons are self-sustaining optical wavepackets in resonators. They use the Kerr nonlinearity to both compensate dispersion and offset optical loss. Besides providing insights into nonlinear resonator physics, they can be applied in frequency metrology, precision clocks, and spectroscopy. Like other optical solitons, the dissipative Kerr soliton can radiate power as a dispersive wave through a process that is the optical analogue of Cherenkov radiation. Dispersive waves typically consist of an ensemble of optical modes. Here, a limiting case is studied in which the dispersive wave is concentrated into a single cavity mode. In this limit, its interaction with the soliton induces hysteresis behaviour in the soliton's spectral and temporal properties. Also, an operating point of enhanced repetition-rate stability occurs through balance of dispersive-wave recoil and Raman-induced soliton-self-frequency shift. The single-mode dispersive wave can therefore provide quiet states of soliton comb operation useful in many applications. PMID:28332495

Droplets size evolution of dispersion in a stirred tank

NASA Astrophysics Data System (ADS)

Kysela, Bohus; Konfrst, Jiri; Chara, Zdenek; Sulc, Radek; Jasikova, Darina

2018-06-01

Dispersion of two immiscible liquids is commonly used in chemical industry as wall as in metallurgical industry e. g. extraction process. The governing property is droplet size distribution. The droplet sizes are given by the physical properties of both liquids and flow properties inside a stirred tank. The first investigation stage is focused on in-situ droplet size measurement using image analysis and optimizing of the evaluation method to achieve maximal result reproducibility. The obtained experimental results are compared with multiphase flow simulation based on Euler-Euler approach combined with PBM (Population Balance Modelling). The population balance model was, in that specific case, simplified with assumption of pure breakage of droplets.

Clustering-based spot segmentation of cDNA microarray images.

PubMed

Uslan, Volkan; Bucak, Ihsan Ömür

2010-01-01

Microarrays are utilized as that they provide useful information about thousands of gene expressions simultaneously. In this study segmentation step of microarray image processing has been implemented. Clustering-based methods, fuzzy c-means and k-means, have been applied for the segmentation step that separates the spots from the background. The experiments show that fuzzy c-means have segmented spots of the microarray image more accurately than the k-means.

A perspective on microarrays: current applications, pitfalls, and potential uses

PubMed Central

Jaluria, Pratik; Konstantopoulos, Konstantinos; Betenbaugh, Michael; Shiloach, Joseph

2007-01-01

With advances in robotics, computational capabilities, and the fabrication of high quality glass slides coinciding with increased genomic information being available on public databases, microarray technology is increasingly being used in laboratories around the world. In fact, fields as varied as: toxicology, evolutionary biology, drug development and production, disease characterization, diagnostics development, cellular physiology and stress responses, and forensics have benefiting from its use. However, for many researchers not familiar with microarrays, current articles and reviews often address neither the fundamental principles behind the technology nor the proper designing of experiments. Although, microarray technology is relatively simple, conceptually, its practice does require careful planning and detailed understanding of the limitations inherently present. Without these considerations, it can be exceedingly difficult to ascertain valuable information from microarray data. Therefore, this text aims to outline key features in microarray technology, paying particular attention to current applications as outlined in recent publications, experimental design, statistical methods, and potential uses. Furthermore, this review is not meant to be comprehensive, but rather substantive; highlighting important concepts and detailing steps necessary to conduct and interpret microarray experiments. Collectively, the information included in this text will highlight the versatility of microarray technology and provide a glimpse of what the future may hold. PMID:17254338

A Platform for Combined DNA and Protein Microarrays Based on Total Internal Reflection Fluorescence

PubMed Central

Asanov, Alexander; Zepeda, Angélica; Vaca, Luis

2012-01-01

We have developed a novel microarray technology based on total internal reflection fluorescence (TIRF) in combination with DNA and protein bioassays immobilized at the TIRF surface. Unlike conventional microarrays that exhibit reduced signal-to-background ratio, require several stages of incubation, rinsing and stringency control, and measure only end-point results, our TIRF microarray technology provides several orders of magnitude better signal-to-background ratio, performs analysis rapidly in one step, and measures the entire course of association and dissociation kinetics between target DNA and protein molecules and the bioassays. In many practical cases detection of only DNA or protein markers alone does not provide the necessary accuracy for diagnosing a disease or detecting a pathogen. Here we describe TIRF microarrays that detect DNA and protein markers simultaneously, which reduces the probabilities of false responses. Supersensitive and multiplexed TIRF DNA and protein microarray technology may provide a platform for accurate diagnosis or enhanced research studies. Our TIRF microarray system can be mounted on upright or inverted microscopes or interfaced directly with CCD cameras equipped with a single objective, facilitating the development of portable devices. As proof-of-concept we applied TIRF microarrays for detecting molecular markers from Bacillus anthracis, the pathogen responsible for anthrax. PMID:22438738

Variance stabilization and normalization for one-color microarray data using a data-driven multiscale approach.

PubMed

Motakis, E S; Nason, G P; Fryzlewicz, P; Rutter, G A

2006-10-15

Many standard statistical techniques are effective on data that are normally distributed with constant variance. Microarray data typically violate these assumptions since they come from non-Gaussian distributions with a non-trivial mean-variance relationship. Several methods have been proposed that transform microarray data to stabilize variance and draw its distribution towards the Gaussian. Some methods, such as log or generalized log, rely on an underlying model for the data. Others, such as the spread-versus-level plot, do not. We propose an alternative data-driven multiscale approach, called the Data-Driven Haar-Fisz for microarrays (DDHFm) with replicates. DDHFm has the advantage of being 'distribution-free' in the sense that no parametric model for the underlying microarray data is required to be specified or estimated; hence, DDHFm can be applied very generally, not just to microarray data. DDHFm achieves very good variance stabilization of microarray data with replicates and produces transformed intensities that are approximately normally distributed. Simulation studies show that it performs better than other existing methods. Application of DDHFm to real one-color cDNA data validates these results. The R package of the Data-Driven Haar-Fisz transform (DDHFm) for microarrays is available in Bioconductor and CRAN.

Validation of MIMGO: a method to identify differentially expressed GO terms in a microarray dataset

PubMed Central

2012-01-01

Background We previously proposed an algorithm for the identification of GO terms that commonly annotate genes whose expression is upregulated or downregulated in some microarray data compared with in other microarray data. We call these “differentially expressed GO terms” and have named the algorithm “matrix-assisted identification method of differentially expressed GO terms” (MIMGO). MIMGO can also identify microarray data in which genes annotated with a differentially expressed GO term are upregulated or downregulated. However, MIMGO has not yet been validated on a real microarray dataset using all available GO terms. Findings We combined Gene Set Enrichment Analysis (GSEA) with MIMGO to identify differentially expressed GO terms in a yeast cell cycle microarray dataset. GSEA followed by MIMGO (GSEA + MIMGO) correctly identified (p < 0.05) microarray data in which genes annotated to differentially expressed GO terms are upregulated. We found that GSEA + MIMGO was slightly less effective than, or comparable to, GSEA (Pearson), a method that uses Pearson’s correlation as a metric, at detecting true differentially expressed GO terms. However, unlike other methods including GSEA (Pearson), GSEA + MIMGO can comprehensively identify the microarray data in which genes annotated with a differentially expressed GO term are upregulated or downregulated. Conclusions MIMGO is a reliable method to identify differentially expressed GO terms comprehensively. PMID:23232071

Microintaglio Printing for Soft Lithography-Based in Situ Microarrays

PubMed Central

Biyani, Manish; Ichiki, Takanori

2015-01-01

Advances in lithographic approaches to fabricating bio-microarrays have been extensively explored over the last two decades. However, the need for pattern flexibility, a high density, a high resolution, affordability and on-demand fabrication is promoting the development of unconventional routes for microarray fabrication. This review highlights the development and uses of a new molecular lithography approach, called “microintaglio printing technology”, for large-scale bio-microarray fabrication using a microreactor array (µRA)-based chip consisting of uniformly-arranged, femtoliter-size µRA molds. In this method, a single-molecule-amplified DNA microarray pattern is self-assembled onto a µRA mold and subsequently converted into a messenger RNA or protein microarray pattern by simultaneously producing and transferring (immobilizing) a messenger RNA or a protein from a µRA mold to a glass surface. Microintaglio printing allows the self-assembly and patterning of in situ-synthesized biomolecules into high-density (kilo-giga-density), ordered arrays on a chip surface with µm-order precision. This holistic aim, which is difficult to achieve using conventional printing and microarray approaches, is expected to revolutionize and reshape proteomics. This review is not written comprehensively, but rather substantively, highlighting the versatility of microintaglio printing for developing a prerequisite platform for microarray technology for the postgenomic era. PMID:27600226

An Introduction to MAMA (Meta-Analysis of MicroArray data) System.

PubMed

Zhang, Zhe; Fenstermacher, David

2005-01-01

Analyzing microarray data across multiple experiments has been proven advantageous. To support this kind of analysis, we are developing a software system called MAMA (Meta-Analysis of MicroArray data). MAMA utilizes a client-server architecture with a relational database on the server-side for the storage of microarray datasets collected from various resources. The client-side is an application running on the end user's computer that allows the user to manipulate microarray data and analytical results locally. MAMA implementation will integrate several analytical methods, including meta-analysis within an open-source framework offering other developers the flexibility to plug in additional statistical algorithms.

Methods to study legionella transcriptome in vitro and in vivo.

PubMed

Faucher, Sebastien P; Shuman, Howard A

2013-01-01

The study of transcriptome responses can provide insight into the regulatory pathways and genetic factors that contribute to a specific phenotype. For bacterial pathogens, it can identify putative new virulence systems and shed light on the mechanisms underlying the regulation of virulence factors. Microarrays have been previously used to study gene regulation in Legionella pneumophila. In the past few years a sharp reduction of the costs associated with microarray experiments together with the availability of relatively inexpensive custom-designed commercial microarrays has made microarray technology an accessible tool for the majority of researchers. Here we describe the methodologies to conduct microarray experiments from in vitro and in vivo samples.

The effect of polysaccharides on the gelatinization properties of cornstarch dispersions

USDA-ARS?s Scientific Manuscript database

Konjac glucomannan (neutral), CMC (negatively charged) and chitosan (positively charged) were added to cornstarch dis- persions, in order to study the effect of polysaccharide-starch interactions on the starch gelatinization properties. Pasting and retrogradation properties were measured with the rh...

Nontronite Particle Aggregation Induced by Microbial Fe(III) Reduction and Exopolysaccharide Production

DTIC Science & Technology

2007-01-01

polymers to achieve desired properties (such Chenu el al., 1979; Kimn el al., 2005). Among these as aggregation. dispersion ) without any structural...performed with and without Na pyrophosphate as a term ’aggregation’ broadly to include all processes that dispersant (25 mM) with shaking in a water...coagulation, at 25 mM was found to be optimal to disperse individual flocculation, agglutination, etc.). The results of this clay particles without

Evaluation of microarray data normalization procedures using spike-in experiments

PubMed Central

Rydén, Patrik; Andersson, Henrik; Landfors, Mattias; Näslund, Linda; Hartmanová, Blanka; Noppa, Laila; Sjöstedt, Anders

2006-01-01

Background Recently, a large number of methods for the analysis of microarray data have been proposed but there are few comparisons of their relative performances. By using so-called spike-in experiments, it is possible to characterize the analyzed data and thereby enable comparisons of different analysis methods. Results A spike-in experiment using eight in-house produced arrays was used to evaluate established and novel methods for filtration, background adjustment, scanning, channel adjustment, and censoring. The S-plus package EDMA, a stand-alone tool providing characterization of analyzed cDNA-microarray data obtained from spike-in experiments, was developed and used to evaluate 252 normalization methods. For all analyses, the sensitivities at low false positive rates were observed together with estimates of the overall bias and the standard deviation. In general, there was a trade-off between the ability of the analyses to identify differentially expressed genes (i.e. the analyses' sensitivities) and their ability to provide unbiased estimators of the desired ratios. Virtually all analysis underestimated the magnitude of the regulations; often less than 50% of the true regulations were observed. Moreover, the bias depended on the underlying mRNA-concentration; low concentration resulted in high bias. Many of the analyses had relatively low sensitivities, but analyses that used either the constrained model (i.e. a procedure that combines data from several scans) or partial filtration (a novel method for treating data from so-called not-found spots) had with few exceptions high sensitivities. These methods gave considerable higher sensitivities than some commonly used analysis methods. Conclusion The use of spike-in experiments is a powerful approach for evaluating microarray preprocessing procedures. Analyzed data are characterized by properties of the observed log-ratios and the analysis' ability to detect differentially expressed genes. If bias is not a major problem; we recommend the use of either the CM-procedure or partial filtration. PMID:16774679

Enhanced solubility of piperine using hydrophilic carrier-based potent solid dispersion systems.

PubMed

Thenmozhi, Kathavarayan; Yoo, Young Je

2017-09-01

Piperine alkaloid, an important constituent of black pepper, exhibits numerous therapeutic properties, whereas its usage as a drug is limited due to its poor solubility in aqueous medium, which leads to poor bioavailability. Herein, a new method has been developed to improve the solubility of this drug based on the development of solid dispersions with improved dissolution rate using hydrophilic carriers such as sorbitol (Sor), polyethylene glycol (PEG) and polyvinyl pyrrolidone K30 (PVP) by solvent method. Physical mixtures of piperine and carriers were also prepared for comparison. The physicochemical properties of the prepared solid dispersions were examined using SEM, TEM, DSC, XRD and FT-IR. In vitro dissolution profile of the solid dispersions was recorded and compared with that of the pure piperine and physical mixtures. The effect of these carriers on the aqueous solubility of piperine has been investigated. The solid dispersions of piperine with Sor, PEG and PVP exhibited superior performance for the dissolution of piperine with a drug release of 70%, 76% and 89%, respectively after 2 h compared to physical mixtures and pure piperine, which could be due to its transformation from crystalline to amorphous form as well as the attachment of hydrophilic carriers to the surface of poorly water-soluble piperine. Results suggest that the piperine solid dispersions prepared with improved in vitro release exhibit potential advantage in delivering poorly water-soluble piperine as an oral supplement.

Investigation of thermal conductivity and rheological properties of nanofluids containing graphene nanoplatelets

PubMed Central

2014-01-01

In the present study, stable homogeneous graphene nanoplatelet (GNP) nanofluids were prepared without any surfactant by high-power ultrasonic (probe) dispersion of GNPs in distilled water. The concentrations of nanofluids were maintained at 0.025, 0.05, 0.075, and 0.1 wt.% for three different specific surface areas of 300, 500, and 750 m2/g. Transmission electron microscopy image shows that the suspensions are homogeneous and most of the materials have been well dispersed. The stability of nanofluid was investigated using a UV-visible spectrophotometer in a time span of 600 h, and zeta potential after dispersion had been investigated to elucidate its role on dispersion characteristics. The rheological properties of GNP nanofluids approach Newtonian and non-Newtonian behaviors where viscosity decreases linearly with the rise of temperature. The thermal conductivity results show that the dispersed nanoparticles can always enhance the thermal conductivity of the base fluid, and the highest enhancement was obtained to be 27.64% in the concentration of 0.1 wt.% of GNPs with a specific surface area of 750 m2/g. Electrical conductivity of the GNP nanofluids shows a significant enhancement by dispersion of GNPs in distilled water. This novel type of nanofluids shows outstanding potential for replacements as advanced heat transfer fluids in medium temperature applications including solar collectors and heat exchanger systems. PMID:24410867

Effect of side-chain structure of rigid polyimide dispersant on mechanical properties of single-walled carbon nanotube/cyanate ester composite.

PubMed

Yuan, Wei; Li, Weifeng; Mu, Yuguang; Chan-Park, Mary B

2011-05-01

Three kinds of polymer, polyimide without side-chain (PI), polyimide-graft-glyceryl 4-nonylphenyl ether (PI-GNE), and polyimide-graft-bisphenol A diglyceryl acrylate (PI-BDA), have been synthesized and used to disperse single-walled carbon nanotubes (SWNTs) and to improve the interfacial bonding between SWNTs and cyanate ester (CE) matrix. Visual observation, UV-vis-near-IR (UV-vis-NIR) spectra, and atomic force microscopy (AFM) images show that both PI-GNE and PI-BDA are highly effective at dispersing and debundling SWNTs in DMF, whereas PI is less effective. Interaction between SWNTs and PI, PI-GNE or PI-BDA was confirmed by computer simulation and Raman spectra. A series of CE-based composite films reinforced with different loadings of SWNTs, SWNTs/PI, SWNTs/PI-GNE and SWNTs/PI-BDA were prepared by solution casting. It was found that, because of the unique side-chain structure of PI-BDA, SWNTs/PI-BDA disperse better in CE matrix than do SWNTs/PI-GNE, SWNTs/PI, and SWNTs. As a result, SWNTs/PI-BDA/CE composites have the greatest improvement in mechanical properties of the materials tested. These results imply that the choice of side-chain on a dispersant is very important to the dispersion of SWNTs in matrix and the filler/matrix interfacial adhesion, which are two key requirements for achieving effective reinforcement.

A comparative study of the effect of spray drying and hot-melt extrusion on the properties of amorphous solid dispersions containing felodipine.

PubMed

Mahmah, Osama; Tabbakh, Rami; Kelly, Adrian; Paradkar, Anant

2014-02-01

To compare the properties of solid dispersions of felodipine for oral bioavailability enhancement using two different polymers, polyvinylpyrrolidone (PVP) and hydroxypropyl methylcellulose acetate succinate (HPMCAS), by hot-melt extrusion (HME) and spray drying. Felodipine solid dispersions were prepared by HME and spray drying techniques. PVP and HPMCAS were used as polymer matrices at different drug : polymer ratios (1 : 1, 1 : 2 and 1 : 3). Detailed characterization was performed using differential scanning calorimetry, powder X-ray diffractometry, scanning electron microscopy and in-vitro dissolution testing. Dissolution profiles were evaluated in the presence of sodium dodecyl sulphate. Stability of different solid dispersions was studied under accelerated conditions (40°C/75% RH) over 8 weeks. Spray-dried formulations were found to release felodipine faster than melt extruded formulations for both polymer matrices. Solid dispersions containing HMPCAS exhibited higher drug release rates and better wettability than those produced with a PVP matrix. No significant differences in stability were observed except with HPMCAS at a 1 : 1 ratio, where crystallization was detected in spray-dried formulations. Solid dispersions of felodipine produced by spray drying exhibited more rapid drug release than corresponding melt extruded formulations, although in some cases improved stability was observed for melt extruded formulations. © 2013 Royal Pharmaceutical Society.

[Web-ring of sites for pathologists in the internet: a computer-mediated communication environment].

PubMed

Khramtsov, A I; Isianov, N N; Khorzhevskiĭ, V A

2009-01-01

The recently developed Web-ring of pathology-related Web-sites has transformed computer-mediated communications for Russian-speaking pathologists. Though the pathologists may be geographically dispersed, the network provides a complex of asynchronous and synchronous conferences for the purposes of diagnosis, consultations, education, communication, and collaboration in the field of pathology. This paper describes approaches to be used by participants of the pathology-related Web-ring. The approaches are analogous to the tools employed in telepathology and digital microscopy. One of the novel methodologies is the use of Web-based conferencing systems, in which the whole slide digital images of tissue microarrays were jointly reviewed online by pathologists at distant locations. By using ImageScope (Aperio Technologies) and WebEx connect desktop management technology, they shared presentations and images and communicated in realtime. In this manner, the Web-based forums and conferences will be a powerful addition to a telepathology.

DNA Microarray-Based Identification of Genes Controlled by Autoinducer 2-Stimulated Quorum Sensing in Escherichia Coli

DTIC Science & Technology

2001-09-01

and pathogenicity in Erwinia carotovora (rsmA) (12). Additionally, csrA has been documented to affect cell size and surface properties, which is in...machinery to cell wall 13.1 b1502 Putative adhesin; similar to FimH protein 13.0 tap Methyl-accepting chemotaxis protein IV, peptide sensor receptor...oxohexanoyl)-L-homoserine lactone 5246 DELISA ET AL. J. BACTERIOL. regulates carbapenem antibiotic production in Erwinia carotovora . Biochem. J. 288:997

GeneXplorer: an interactive web application for microarray data visualization and analysis.

PubMed

Rees, Christian A; Demeter, Janos; Matese, John C; Botstein, David; Sherlock, Gavin

2004-10-01

When publishing large-scale microarray datasets, it is of great value to create supplemental websites where either the full data, or selected subsets corresponding to figures within the paper, can be browsed. We set out to create a CGI application containing many of the features of some of the existing standalone software for the visualization of clustered microarray data. We present GeneXplorer, a web application for interactive microarray data visualization and analysis in a web environment. GeneXplorer allows users to browse a microarray dataset in an intuitive fashion. It provides simple access to microarray data over the Internet and uses only HTML and JavaScript to display graphic and annotation information. It provides radar and zoom views of the data, allows display of the nearest neighbors to a gene expression vector based on their Pearson correlations and provides the ability to search gene annotation fields. The software is released under the permissive MIT Open Source license, and the complete documentation and the entire source code are freely available for download from CPAN http://search.cpan.org/dist/Microarray-GeneXplorer/.

Fluorescence-based bioassays for the detection and evaluation of food materials.

PubMed

Nishi, Kentaro; Isobe, Shin-Ichiro; Zhu, Yun; Kiyama, Ryoiti

2015-10-13

We summarize here the recent progress in fluorescence-based bioassays for the detection and evaluation of food materials by focusing on fluorescent dyes used in bioassays and applications of these assays for food safety, quality and efficacy. Fluorescent dyes have been used in various bioassays, such as biosensing, cell assay, energy transfer-based assay, probing, protein/immunological assay and microarray/biochip assay. Among the arrays used in microarray/biochip assay, fluorescence-based microarrays/biochips, such as antibody/protein microarrays, bead/suspension arrays, capillary/sensor arrays, DNA microarrays/polymerase chain reaction (PCR)-based arrays, glycan/lectin arrays, immunoassay/enzyme-linked immunosorbent assay (ELISA)-based arrays, microfluidic chips and tissue arrays, have been developed and used for the assessment of allergy/poisoning/toxicity, contamination and efficacy/mechanism, and quality control/safety. DNA microarray assays have been used widely for food safety and quality as well as searches for active components. DNA microarray-based gene expression profiling may be useful for such purposes due to its advantages in the evaluation of pathway-based intracellular signaling in response to food materials.

Fluorescence-Based Bioassays for the Detection and Evaluation of Food Materials

PubMed Central

Nishi, Kentaro; Isobe, Shin-Ichiro; Zhu, Yun; Kiyama, Ryoiti

2015-01-01

We summarize here the recent progress in fluorescence-based bioassays for the detection and evaluation of food materials by focusing on fluorescent dyes used in bioassays and applications of these assays for food safety, quality and efficacy. Fluorescent dyes have been used in various bioassays, such as biosensing, cell assay, energy transfer-based assay, probing, protein/immunological assay and microarray/biochip assay. Among the arrays used in microarray/biochip assay, fluorescence-based microarrays/biochips, such as antibody/protein microarrays, bead/suspension arrays, capillary/sensor arrays, DNA microarrays/polymerase chain reaction (PCR)-based arrays, glycan/lectin arrays, immunoassay/enzyme-linked immunosorbent assay (ELISA)-based arrays, microfluidic chips and tissue arrays, have been developed and used for the assessment of allergy/poisoning/toxicity, contamination and efficacy/mechanism, and quality control/safety. DNA microarray assays have been used widely for food safety and quality as well as searches for active components. DNA microarray-based gene expression profiling may be useful for such purposes due to its advantages in the evaluation of pathway-based intracellular signaling in response to food materials. PMID:26473869

Microarray Data Processing Techniques for Genome-Scale Network Inference from Large Public Repositories.

PubMed

Chockalingam, Sriram; Aluru, Maneesha; Aluru, Srinivas

2016-09-19

Pre-processing of microarray data is a well-studied problem. Furthermore, all popular platforms come with their own recommended best practices for differential analysis of genes. However, for genome-scale network inference using microarray data collected from large public repositories, these methods filter out a considerable number of genes. This is primarily due to the effects of aggregating a diverse array of experiments with different technical and biological scenarios. Here we introduce a pre-processing pipeline suitable for inferring genome-scale gene networks from large microarray datasets. We show that partitioning of the available microarray datasets according to biological relevance into tissue- and process-specific categories significantly extends the limits of downstream network construction. We demonstrate the effectiveness of our pre-processing pipeline by inferring genome-scale networks for the model plant Arabidopsis thaliana using two different construction methods and a collection of 11,760 Affymetrix ATH1 microarray chips. Our pre-processing pipeline and the datasets used in this paper are made available at http://alurulab.cc.gatech.edu/microarray-pp.

Dispersion analysis of passive surface-wave noise generated during hydraulic-fracturing operations

USGS Publications Warehouse

Forghani-Arani, Farnoush; Willis, Mark; Snieder, Roel; Haines, Seth S.; Behura, Jyoti; Batzle, Mike; Davidson, Michael

2014-01-01

Surface-wave dispersion analysis is useful for estimating near-surface shear-wave velocity models, designing receiver arrays, and suppressing surface waves. Here, we analyze whether passive seismic noise generated during hydraulic-fracturing operations can be used to extract surface-wave dispersion characteristics. Applying seismic interferometry to noise measurements, we extract surface waves by cross-correlating several minutes of passive records; this approach is distinct from previous studies that used hours or days of passive records for cross-correlation. For comparison, we also perform dispersion analysis for an active-source array that has some receivers in common with the passive array. The active and passive data show good agreement in the dispersive character of the fundamental-mode surface-waves. For the higher mode surface waves, however, active and passive data resolve the dispersive properties at different frequency ranges. To demonstrate an application of dispersion analysis, we invert the observed surface-wave dispersion characteristics to determine the near-surface, one-dimensional shear-wave velocity.

Alpha-dispersion in human tissue

NASA Astrophysics Data System (ADS)

Grimnes, Sverre; Martinsen, Ørjan G.

2010-04-01

Beta dispersion is found in living tissue in the kilohertz - megahertz range and is caused by the cellular structure of biological materials with low frequency properties caused by cell membranes. Alpha dispersion is found in the hertz range and the causes are not so well known. Alpha dispersions are the first to disappear when tissue dies. Tissue data have often been based upon excised specimen from animals and are therefore not necessarily representative for human tissue alpha dispersions. Here we present data obtained with non-invasive skin surface electrodes for different segments of the living human body. We found alpha dispersions in all cases; the ankle-wrist results had the smallest. Large alpha dispersions were found where the distance between the electrodes and muscle masses was small, e.g. on the calf. Further studies on electrode technique and reciprocity, electrode positioning, statistical variations, gender, age and bodily constitutions are necessary in order to reveal more about the alpha dispersion, its appearance and disappearance.

Oil palm phenolics confer neuroprotective effects involving cognitive and motor functions in mice

PubMed Central

Leow, Soon-Sen; Sekaran, Shamala Devi; Tan, YewAi; Sundram, Kalyana; Sambanthamurthi, Ravigadevi

2013-01-01

Objectives Phenolics are important phytochemicals which have positive effects on chronic diseases, including neurodegenerative ailments. The oil palm (Elaeis guineensis) is a rich source of water-soluble phenolics. This study was carried out to discover the effects of administering oil palm phenolics (OPP) to mice, with the aim of identifying whether these compounds possess significant neuroprotective properties. Methods OPP was given to BALB/c mice on a normal diet as fluids for 6 weeks while the controls were given distilled water. These animals were tested in a water maze and on a rotarod weekly to assess the effects of OPP on cognitive and motor functions, respectively. Using Illumina microarrays, we further explored the brain gene expression changes caused by OPP in order to determine the molecular mechanisms involved. Real-time quantitative reverse transcription-polymerase chain reaction experiments were then carried out to validate the microarray data. Results We found that mice given OPP showed better cognitive function and spatial learning when tested in a water maze, and their performance also improved when tested on a rotarod, possibly due to better motor function and balance. Microarray gene expression analysis showed that these compounds up-regulated genes involved in brain development and activity, such as those under the regulation of the brain-derived neurotrophic factor. OPP also down-regulated genes involved in inflammation. Discussion These results suggest that the improvement of mouse cognitive and motor functions by OPP is caused by the neuroprotective and anti-inflammatory effects of the extract. PMID:23433062

CMOS Imaging of Temperature Effects on Pin-Printed Xerogel Sensor Microarrays.

PubMed

Lei Yao; Ka Yi Yung; Chodavarapu, Vamsy P; Bright, Frank V

2011-04-01

In this paper, we study the effect of temperature on the operation and performance of a xerogel-based sensor microarrays coupled to a complementary metal-oxide semiconductor (CMOS) imager integrated circuit (IC) that images the photoluminescence response from the sensor microarray. The CMOS imager uses a 32 × 32 (1024 elements) array of active pixel sensors and each pixel includes a high-gain phototransistor to convert the detected optical signals into electrical currents. A correlated double sampling circuit and pixel address/digital control/signal integration circuit are also implemented on-chip. The CMOS imager data are read out as a serial coded signal. The sensor system uses a light-emitting diode to excite target analyte responsive organometallic luminophores doped within discrete xerogel-based sensor elements. As a proto type, we developed a 3 × 3 (9 elements) array of oxygen (O2) sensors. Each group of three sensor elements in the array (arranged in a column) is designed to provide a different and specific sensitivity to the target gaseous O2 concentration. This property of multiple sensitivities is achieved by using a mix of two O2 sensitive luminophores in each pin-printed xerogel sensor element. The CMOS imager is designed to be low noise and consumes a static power of 320.4 μW and an average dynamic power of 624.6 μW when operating at 100-Hz sampling frequency and 1.8-V dc power supply.

Translating standards into practice - one Semantic Web API for Gene Expression.

PubMed

Deus, Helena F; Prud'hommeaux, Eric; Miller, Michael; Zhao, Jun; Malone, James; Adamusiak, Tomasz; McCusker, Jim; Das, Sudeshna; Rocca Serra, Philippe; Fox, Ronan; Marshall, M Scott

2012-08-01

Sharing and describing experimental results unambiguously with sufficient detail to enable replication of results is a fundamental tenet of scientific research. In today's cluttered world of "-omics" sciences, data standards and standardized use of terminologies and ontologies for biomedical informatics play an important role in reporting high-throughput experiment results in formats that can be interpreted by both researchers and analytical tools. Increasing adoption of Semantic Web and Linked Data technologies for the integration of heterogeneous and distributed health care and life sciences (HCLSs) datasets has made the reuse of standards even more pressing; dynamic semantic query federation can be used for integrative bioinformatics when ontologies and identifiers are reused across data instances. We present here a methodology to integrate the results and experimental context of three different representations of microarray-based transcriptomic experiments: the Gene Expression Atlas, the W3C BioRDF task force approach to reporting Provenance of Microarray Experiments, and the HSCI blood genomics project. Our approach does not attempt to improve the expressivity of existing standards for genomics but, instead, to enable integration of existing datasets published from microarray-based transcriptomic experiments. SPARQL Construct is used to create a posteriori mappings of concepts and properties and linking rules that match entities based on query constraints. We discuss how our integrative approach can encourage reuse of the Experimental Factor Ontology (EFO) and the Ontology for Biomedical Investigations (OBIs) for the reporting of experimental context and results of gene expression studies. Copyright © 2012 Elsevier Inc. All rights reserved.

Methods for processing microarray data.

PubMed

Ares, Manuel

2014-02-01

Quality control must be maintained at every step of a microarray experiment, from RNA isolation through statistical evaluation. Here we provide suggestions for analyzing microarray data. Because the utility of the results depends directly on the design of the experiment, the first critical step is to ensure that the experiment can be properly analyzed and interpreted. What is the biological question? What is the best way to perform the experiment? How many replicates will be required to obtain the desired statistical resolution? Next, the samples must be prepared, pass quality controls for integrity and representation, and be hybridized and scanned. Also, slides with defects, missing data, high background, or weak signal must be rejected. Data from individual slides must be normalized and combined so that the data are as free of systematic bias as possible. The third phase is to apply statistical filters and tests to the data to determine genes (1) expressed above background, (2) whose expression level changes in different samples, and (3) whose RNA-processing patterns or protein associations change. Next, a subset of the data should be validated by an alternative method, such as reverse transcription-polymerase chain reaction (RT-PCR). Provided that this endorses the general conclusions of the array analysis, gene sets whose expression, splicing, polyadenylation, protein binding, etc. change in different samples can be classified with respect to function, sequence motif properties, as well as other categories to extract hypotheses for their biological roles and regulatory logic.

Microfluidic microarray systems and methods thereof

DOEpatents

West, Jay A. A. [Castro Valley, CA; Hukari, Kyle W [San Ramon, CA; Hux, Gary A [Tracy, CA

2009-04-28

Disclosed are systems that include a manifold in fluid communication with a microfluidic chip having a microarray, an illuminator, and a detector in optical communication with the microarray. Methods for using these systems for biological detection are also disclosed.

Chitosan-magnesium aluminum silicate composite dispersions: characterization of rheology, flocculate size and zeta potential.

PubMed

Khunawattanakul, Wanwisa; Puttipipatkhachorn, Satit; Rades, Thomas; Pongjanyakul, Thaned

2008-03-03

Composite dispersions of chitosan (CS), a positively charged polymer, and magnesium aluminum silicate (MAS), a negatively charged clay, were prepared and rheology, flocculate size and zeta potential of the CS-MAS dispersions were investigated. High and low molecular weights of CS (HCS and LCS, respectively) were used in this study. Moreover, the effects of heat treatment at 60 degrees C on the characteristics of the CS-MAS dispersions and the zeta potential of MAS upon addition of CS at different pHs were examined. Incorporation of MAS into CS dispersions caused an increase in viscosity and a shift of CS flow type from Newtonian to pseudoplastic flow with thixotropic properties. Heat treatment brought about a significant decrease in viscosity and hysteresis area of the composite dispersions. Microscopic studies showed that flocculation of MAS occurred after mixing with CS. The size and polydispersity index of the HCS-MAS flocculate were greater than those of the LCS-MAS flocculate. However, a narrower size distribution and the smaller size of the HCS-MAS flocculate were found after heating at 60 degrees C. Zeta potentials of the CS-MAS flocculates were positive and slightly increased with increasing MAS content. In the zeta potential studies, the negative charge of the MAS could be neutralized by the addition of CS. Increasing the pH and molecular weight of CS resulted in higher CS concentrations required to neutralize the charge of MAS. These findings suggest that the electrostatic interaction between CS and MAS caused a change in flow behavior and flocculation of the composite dispersions, depending on the molecular weight of CS. Heat treatment affected the rheological properties and the flocculate size of the composite dispersions. Moreover, pH of medium and molecular weight of CS influence the zeta potential of MAS.

cDNA Microarray Screening in Food Safety

PubMed Central

ROY, SASHWATI; SEN, CHANDAN K

2009-01-01

The cDNA microarray technology and related bioinformatics tools presents a wide range of novel application opportunities. The technology may be productively applied to address food safety. In this mini-review article, we present an update highlighting the late breaking discoveries that demonstrate the vitality of cDNA microarray technology as a tool to analyze food safety with reference to microbial pathogens and genetically modified foods. In order to bring the microarray technology to mainstream food safety, it is important to develop robust user-friendly tools that may be applied in a field setting. In addition, there needs to be a standardized process for regulatory agencies to interpret and act upon microarray-based data. The cDNA microarray approach is an emergent technology in diagnostics. Its values lie in being able to provide complimentary molecular insight when employed in addition to traditional tests for food safety, as part of a more comprehensive battery of tests. PMID:16466843

Functional comparison of microarray data across multiple platforms using the method of percentage of overlapping functions.

PubMed

Li, Zhiguang; Kwekel, Joshua C; Chen, Tao

2012-01-01

Functional comparison across microarray platforms is used to assess the comparability or similarity of the biological relevance associated with the gene expression data generated by multiple microarray platforms. Comparisons at the functional level are very important considering that the ultimate purpose of microarray technology is to determine the biological meaning behind the gene expression changes under a specific condition, not just to generate a list of genes. Herein, we present a method named percentage of overlapping functions (POF) and illustrate how it is used to perform the functional comparison of microarray data generated across multiple platforms. This method facilitates the determination of functional differences or similarities in microarray data generated from multiple array platforms across all the functions that are presented on these platforms. This method can also be used to compare the functional differences or similarities between experiments, projects, or laboratories.

ArrayNinja: An Open Source Platform for Unified Planning and Analysis of Microarray Experiments.

PubMed

Dickson, B M; Cornett, E M; Ramjan, Z; Rothbart, S B

2016-01-01

Microarray-based proteomic platforms have emerged as valuable tools for studying various aspects of protein function, particularly in the field of chromatin biochemistry. Microarray technology itself is largely unrestricted in regard to printable material and platform design, and efficient multidimensional optimization of assay parameters requires fluidity in the design and analysis of custom print layouts. This motivates the need for streamlined software infrastructure that facilitates the combined planning and analysis of custom microarray experiments. To this end, we have developed ArrayNinja as a portable, open source, and interactive application that unifies the planning and visualization of microarray experiments and provides maximum flexibility to end users. Array experiments can be planned, stored to a private database, and merged with the imaged results for a level of data interaction and centralization that is not currently attainable with available microarray informatics tools. © 2016 Elsevier Inc. All rights reserved.

Control of stain geometry by drop evaporation of surfactant containing dispersions.

PubMed

Erbil, H Yildirim

2015-08-01

Control of stain geometry by drop evaporation of surfactant containing dispersions is an important topic of interest because it plays a crucial role in many applications such as forming templates on solid surfaces, in ink-jet printing, spraying of pesticides, micro/nano material fabrication, thin film coatings, biochemical assays, deposition of DNA/RNA micro-arrays, and manufacture of novel optical and electronic materials. This paper presents a review of the published articles on the diffusive drop evaporation of pure liquids (water), the surfactant stains obtained from evaporating drops that do not contain dispersed particles and deposits obtained from drops containing polymer colloids and carbon based particles such as carbon nanotubes, graphite and fullerenes. Experimental results of specific systems and modeling attempts are discussed. This review also has some special subtopics such as suppression of coffee-rings by surfactant addition and "stick-slip" behavior of evaporating nanosuspension drops. In general, the drop evaporation process of a surfactant/particle/substrate system is very complex since dissolved surfactants adsorb on both the insoluble organic/inorganic micro/nanoparticles in the drop, on the air/solution interface and on the substrate surface in different extends. Meanwhile, surfactant adsorbed particles interact with the substrate giving a specific contact angle, and free surfactants create a solutal Marangoni flow in the drop which controls the location of the particle deposition together with the rate of evaporation. In some cases, the presence of a surfactant monolayer at the air/solution interface alters the rate of evaporation. At present, the magnitude of each effect cannot be predicted adequately in advance and consequently they should be carefully studied for any system in order to control the shape and size of the final deposit. Copyright © 2014 Elsevier B.V. All rights reserved.

Organically Modified Nanoclay-Reinforced Rigid Polyurethane Films

NASA Astrophysics Data System (ADS)

Park, Yong Tae; Qian, Yuqiang; Lindsay, Chris; Stein, Andreas; Macosko, Christopher

2012-02-01

The nanodispersion of vermiculite in polyurethanes was investigated to produce organoclay-reinforced rigid gas barrier films. Reducing gas transport can improve the insulation performance of closed cell polyurethane foam. In a previous study, the dispersion of vermiculite in polyurethanes without organic modification was not sufficient due to the non-uniform dispersion morphology. When vermiculite was modified by cation exchange with long-chain quaternary ammonium cations, the dispersion in methylene diphenyl diisocyanate (MDI) was significantly improved. Dispersion was improved by combining high intensity dispersive mixing with efficient distributive mixing. Polymerization conditions were also optimized in order to provide a high state of nanodispersion in the polyurethane nanocomposite. The dispersions were characterized using rheological, microscopic and scattering/diffraction techniques. The final nanocomposites showed enhancement of mechanical properties and reduction in permeability to carbon dioxide at low clay concentration (around 2 wt percent).

Theoretical analyses of resonant frequency shift in anomalous dispersion enhanced resonant optical gyroscopes.

PubMed

Lin, Jian; Liu, Jiaming; Zhang, Hao; Li, Wenxiu; Zhao, Lu; Jin, Junjie; Huang, Anping; Zhang, Xiaofu; Xiao, Zhisong

2016-12-12

Rigorous expressions of resonant frequency shift (RFS) in anomalous dispersion enhanced resonant optical gyroscopes (ADEROGs) are deduced without making approximation, which provides a precise theoretical guidance to achieve ultra-sensitive ADEROGs. A refractive index related modification factor is introduced when considering special theory of relativity (STR). We demonstrate that the RFS will not be "infinitely large" by using critical anomalous dispersion (CAD) and negative modification does not exist, which make the mechanism of anomalous dispersion enhancement clear and coherent. Although step change of RFS will happen when the anomalous dispersion condition varies, the amplification of RFS is limited by attainable variation of refractive index in practice. Moreover, it is shown that the properties of anomalous dispersion will influence not only the amplification of RFS, but also the detection range of ADEROGs.

Damage Tolerance Enhancement of Carbon Fiber Reinforced Polymer Composites by Nanoreinforcement of Matrix

NASA Astrophysics Data System (ADS)

Fenner, Joel Stewart

Nanocomposites are a relatively new class of materials which incorporate exotic, engineered nanoparticles to achieve superior material properties. Because of their extremely small size and well-ordered structure, many nanoparticles possess properties that exceed those offered by a wide range of other known materials, making them attractive candidates for novel materials engineering development. Their small size is also an impediment to their practical use, as they typically cannot be employed by themselves to realize those properties in large structures. Furthermore, nanoparticles typically possess strong self-affinity, rendering them difficult to disperse uniformly into a composite. However, contemporary research has shown that, if well-dispersed, nanoparticles have great capacity to improve the mechanical properties of composites, especially damage tolerance, in the form of fracture toughness, fatigue life, and impact damage mitigation. This research focuses on the development, manufacturing, and testing of hybrid micro/nanocomposites comprised of woven carbon fibers with a carbon nanotube reinforced epoxy matrix. Material processing consisted of dispersant-and-sonication based methods to disperse nanotubes into the matrix, and a vacuum-assisted wet lay-up process to prepare the hybrid composite laminates. Various damage tolerance properties of the hybrid composite were examined, including static strength, fracture toughness, fatigue life, fatigue crack growth rate, and impact damage behavior, and compared with similarly-processed reference material produced without nanoreinforcement. Significant improvements were obtained in interlaminar shear strength (15%), Mode-I fracture toughness (180%), shear fatigue life (order of magnitude), Mode-I fatigue crack growth rate (factor of 2), and effective impact damage toughness (40%). Observations by optical microscopy, scanning electron microscopy, and ultrasonic imaging showed significant differences in failure behavior and fracture morphology between the two materials, related to the differences in properties. Altogether these results provided a means for proposing an explanation of the mechanism of reinforcement (and damage tolerance enhancement) provided by carbon nanotubes in hybrid composite materials.

Emerging Use of Gene Expression Microarrays in Plant Physiology

DOE PAGES

Wullschleger, Stan D.; Difazio, Stephen P.

2003-01-01

Microarrays have become an important technology for the global analysis of gene expression in humans, animals, plants, and microbes. Implemented in the context of a well-designed experiment, cDNA and oligonucleotide arrays can provide highthroughput, simultaneous analysis of transcript abundance for hundreds, if not thousands, of genes. However, despite widespread acceptance, the use of microarrays as a tool to better understand processes of interest to the plant physiologist is still being explored. To help illustrate current uses of microarrays in the plant sciences, several case studies that we believe demonstrate the emerging application of gene expression arrays in plant physiology weremore » selected from among the many posters and presentations at the 2003 Plant and Animal Genome XI Conference. Based on this survey, microarrays are being used to assess gene expression in plants exposed to the experimental manipulation of air temperature, soil water content and aluminium concentration in the root zone. Analysis often includes characterizing transcript profiles for multiple post-treatment sampling periods and categorizing genes with common patterns of response using hierarchical clustering techniques. In addition, microarrays are also providing insights into developmental changes in gene expression associated with fibre and root elongation in cotton and maize, respectively. Technical and analytical limitations of microarrays are discussed and projects attempting to advance areas of microarray design and data analysis are highlighted. Finally, although much work remains, we conclude that microarrays are a valuable tool for the plant physiologist interested in the characterization and identification of individual genes and gene families with potential application in the fields of agriculture, horticulture and forestry.« less

Profiling In Situ Microbial Community Structure with an Amplification Microarray

PubMed Central

Knickerbocker, Christopher; Bryant, Lexi; Golova, Julia; Wiles, Cory; Williams, Kenneth H.; Peacock, Aaron D.; Long, Philip E.

2013-01-01

The objectives of this study were to unify amplification, labeling, and microarray hybridization chemistries within a single, closed microfluidic chamber (an amplification microarray) and verify technology performance on a series of groundwater samples from an in situ field experiment designed to compare U(VI) mobility under conditions of various alkalinities (as HCO3−) during stimulated microbial activity accompanying acetate amendment. Analytical limits of detection were between 2 and 200 cell equivalents of purified DNA. Amplification microarray signatures were well correlated with 16S rRNA-targeted quantitative PCR results and hybridization microarray signatures. The succession of the microbial community was evident with and consistent between the two microarray platforms. Amplification microarray analysis of acetate-treated groundwater showed elevated levels of iron-reducing bacteria (Flexibacter, Geobacter, Rhodoferax, and Shewanella) relative to the average background profile, as expected. Identical molecular signatures were evident in the transect treated with acetate plus NaHCO3, but at much lower signal intensities and with a much more rapid decline (to nondetection). Azoarcus, Thaurea, and Methylobacterium were responsive in the acetate-only transect but not in the presence of bicarbonate. Observed differences in microbial community composition or response to bicarbonate amendment likely had an effect on measured rates of U reduction, with higher rates probable in the part of the field experiment that was amended with bicarbonate. The simplification in microarray-based work flow is a significant technological advance toward entirely closed-amplicon microarray-based tests and is generally extensible to any number of environmental monitoring applications. PMID:23160129

On tide-induced Lagrangian residual current and residual transport: 2. Residual transport with application in south San Francisco Bay, California

USGS Publications Warehouse

Feng, Shizuo; Cheng, Ralph T.; Pangen, Xi

1986-01-01

The transports of solutes and other tracers are fundamental to estuarine processes. The apparent transport mechanisms are convection by tidal current and current-induced shear effect dispersion for processes which take place in a time period of the order of a tidal cycle. However, as emphasis is shifted toward the effects of intertidal processes, the net transport is mainly determined by tide-induced residual circulation and by residual circulation due to other processes. The commonly used intertidal conservation equation takes the form of a convection-dispersion equation in which the convective velocity is the Eulerian residual current, and the dispersion terms are often referred to as the phase effect dispersion or, sometimes, as the “tidal dispersion.” The presence of these dispersion terms is merely the result of a Fickian type hypothesis. Since the actual processes are not Fickian, thus a Fickian hypothesis obscures the physical significance of this equation. Recent research results on residual circulation have suggested that long-term transport phenomena are closely related to the Lagrangian residual current or the Lagrangian residual transport. In this paper a new formulation of an intertidal conservation equation is presented and examined in detail. In a weakly nonlinear tidal estuary the resultant intertidal transport equation also takes the form of a convection-dispersion equation without the ad hoc introduction of phase effect dispersion in a form of dispersion tensor. The convective velocity in the resultant equation is the first-order Lagrangian residual current (the sum of the Eulerian residual current and the Stokes drift). The remaining dispersion terms are important only in higher-order solutions; they are due to shear effect dispersion and turbulent mixing. There exists a dispersion boundary layer adjacent to shoreline boundaries. An order of magnitude estimate of the properties in the dispersion boundary layer is given. The present treatment of intertidal transport processes is illustrated by an analytical solution for an amphidromic system and by a numerical application in South San Francisco Bay, California. The present formulation reveals that the mechanism for long-term transport of solutes is mainly convection due to the Lagrangian residual current in the interior of a tidal estuary. This result also points out the weakness in the tidal dispersion formulation, and explains the large variability of the observed values for tidal dispersion coefficients. Further research on properties of the dispersion boundary layer is needed.

PRACTICAL STRATEGIES FOR PROCESSING AND ANALYZING SPOTTED OLIGONUCLEOTIDE MICROARRAY DATA

EPA Science Inventory

Thoughtful data analysis is as important as experimental design, biological sample quality, and appropriate experimental procedures for making microarrays a useful supplement to traditional toxicology. In the present study, spotted oligonucleotide microarrays were used to profile...

DNA Microarray-based Ecotoxicological Biomarker Discovery in a Small Fish Model Species

EPA Science Inventory

This paper addresses several issues critical to use of zebrafish oligonucleotide microarrays for computational toxicology research on endocrine disrupting chemicals using small fish models, and more generally, the use of microarrays in aquatic toxicology.

IMPROVING THE RELIABILITY OF MICROARRAYS FOR TOXICOLOGY RESEARCH: A COLLABORATIVE APPROACH

EPA Science Inventory

Microarray-based gene expression profiling is a critical tool to identify molecular biomarkers of specific chemical stressors. Although current microarray technologies have progressed from their infancy, biological and technical repeatability and reliability are often still limit...

Physicochemical characterization of tacrolimus-loaded solid dispersion with sodium carboxylmethyl cellulose and sodium lauryl sulfate.

PubMed

Park, Young-Joon; Ryu, Dong-Sung; Li, Dong Xun; Quan, Qi Zhe; Oh, Dong Hoon; Kim, Jong Oh; Seo, Youn Gee; Lee, Young-Im; Yong, Chul Soon; Woo, Jong Soo; Choi, Han-Gon

2009-06-01

To develop a novel tacrolimus-loaded solid dispersion with improved solubility, various solid dispersions were prepared with various ratios of water, sodium lauryl sulfate, citric acid and carboxylmethylcellulose-Na using spray drying technique. The physicochemical properties of solid dispersions were investigated using scanning electron microscopy, differential scanning calorimetery and powder X-ray diffraction. Furthermore, their solubility and dissolution were evaluated compared to drug powder. The solid dispersion at the tacrolimus/CMC-Na/sodium lauryl sulfate/citric acid ratio of 3/24/3/0.2 significantly improved the drug solubility and dissolution compared to powder. The scanning electron microscopy result suggested that carriers might be attached to the surface of drug in this solid dispersion. Unlike traditional solid dispersion systems, the crystal form of drug in this solid dispersion could not be converted to amorphous form, which was confirmed by the analysis of DSC and powder X-ray diffraction. Thus, the solid dispersion system with water, sodium lauryl sulfate, citric acid and CMC-Na should be a potential candidate for delivering a poorly water-soluble tacrolimus with enhanced solubility and no convertible crystalline.

Bright, dark and W-shaped solitons with extended nonlinear Schrödinger's equation for odd and even higher-order terms

NASA Astrophysics Data System (ADS)

Bendahmane, Issam; Triki, Houria; Biswas, Anjan; Saleh Alshomrani, Ali; Zhou, Qin; Moshokoa, Seithuti P.; Belic, Milivoj

2018-02-01

We present solitary wave solutions of an extended nonlinear Schrödinger equation with higher-order odd (third-order) and even (fourth-order) terms by using an ansatz method. The including high-order dispersion terms have significant physical applications in fiber optics, the Heisenberg spin chain, and ocean waves. Exact envelope solutions comprise bright, dark and W-shaped solitary waves, illustrating the potentially rich set of solitary wave solutions of the extended model. Furthermore, we investigate the properties of these solitary waves in nonlinear and dispersive media. Moreover, specific constraints on the system parameters for the existence of these structures are discussed exactly. The results show that the higher-order dispersion and nonlinear effects play a crucial role for the formation and properties of propagating waves.

Mimicking glide symmetry dispersion with coupled slot metasurfaces

NASA Astrophysics Data System (ADS)

Camacho, Miguel; Mitchell-Thomas, Rhiannon C.; Hibbins, Alastair P.; Sambles, J. Roy; Quevedo-Teruel, Oscar

2017-09-01

In this letter, we demonstrate that the dispersion properties associated with glide symmetry can be achieved in systems that only possess reflection symmetry by balancing the influence of two sublattices. We apply this approach to a pair of coupled slots cut into an infinite perfectly conducting plane. Each slot is notched on either edge, with the complete two-slot system having only mirror symmetry. By modifying the relative size of the notches on either side of the slots, we show that a linear dispersion relation with a degeneracy with non-zero group velocity at the Brillouin zone boundary can be achieved. These properties, until now, only found in systems with glide symmetry are numerically and experimentally validated. We also show that these results can be used for the design of ultra-wideband one-dimensional leaky wave antennas in coplanar waveguide technology.

Effect of Acid Oxidation on the Dispersion Property of Multiwalled Carbon Nanotubes

NASA Astrophysics Data System (ADS)

Goh, P. S.; Ismail, A. F.; Aziz, M.

2009-06-01

A means of dispersion of multiwalled carbon nanotube (MWCNT) via mixed acid (HNO3 and H2SO4) oxidation with different treatment durations was investigated through the solubility study of the treated carbon nanotubes in some common solvents. Fourier transformed infrared (FTIR) characterization of the reaction products revealed that the surface of MWCNTs was successfully functionalized with surface acidic groups. The acid-base titration demonstrated that the amount of surface acidic groups increased in parallel with the refluxing duration. The acid modified MWCNTs were found to be well dispersed in polar solvents, such as ethanol and water due to the presence of the hydrophilic acid functional groups on the surface of raw MWCNTs. Such chemical modification of carbon nanotube properties will pave the way towards the realistic applications in the nanotechnology world.

Thermoelectric properties of SrTiO3 nano-particles dispersed indium selenide bulk composites

NASA Astrophysics Data System (ADS)

Lee, Min Ho; Rhyee, Jong-Soo; Vaseem, Mohammad; Hahn, Yoon-Bong; Park, Su-Dong; Jin Kim, Hee; Kim, Sung-Jin; Lee, Hyeung Jin; Kim, Chilsung

2013-06-01

We investigated the thermoelectric properties of the InSe, InSe/In4Se3 composite, and SrTiO3 (STO) nano-particles dispersed InSe/In4Se3 bulk composites. The electrical conductivity of the InSe/In4Se3 composite with self-assembled phase separation is significantly increased compared with those of InSe and In4Se3-δ implying the enhancement of surface conductivity between grain boundaries. The thermal conductivity of InSe/In4Se3 composite is decreased compared to those of InSe. When the STO nano-particle dispersion was employed in the InSe/In4Se3 composite, a coherent interface was observed between nano-particle precipitates and the InSe bulk matrix with a reduction of the thermal conductivity.

Measurement and Modeling of Dispersive Pulse Propagation in Drawn Wire Waveguides

NASA Technical Reports Server (NTRS)

Madaras, Eric I.; Kohl, Thomas W.; Rogers, Wayne P.

1995-01-01

An analytical model of dispersive pulse propagation in semi-infinite cylinders due to transient axially symmetric end conditions has been experimentally investigated. Specifically, the dispersive propagation of the first axially symmetric longitudinal mode in thin wire waveguides, which have ends in butt contact with longitudinal piezoelectric ultrasonic transducers, is examined. The method allows for prediction of a propagated waveform given a measured source waveform, together with the material properties of the cylinder. Alternatively, the source waveform can be extracted from measurement of the propagated waveform. The material properties required for implementation of the pulse propagation model are determined using guided wave phase velocity measurements. Hard tempered aluminum 1100 and 304 stainless steel wires, with 127, 305, and 406 micron diam., were examined. In general, the drawn wires were found to behave as transversely isotropic media.

Measurement and modeling of dispersive pulse propagation in draw wire waveguides

NASA Technical Reports Server (NTRS)

Madaras, Eric I.; Kohl, Thomas W.; Rogers, Wayne P.

1995-01-01

An analytical model of dispersive pulse propagation in semi-infinite cylinders due to transient axially symmetric end conditions has been experimentally investigated. Specifically, the dispersive propagation of the first axially symmetric longitudinal mode in thin wire waveguides, which have ends in butt contact with longitudinal piezoelectric ultrasonic transducers, is examined. The method allows for prediction of a propagated waveform given a measured source waveform, together with the material properties of the cylinder. Alternatively, the source waveform can be extracted from measurement of the propagated waveform. The material properties required for implementation of the pulse propagation model are determined using guided wave phase velocity measurements. Hard tempered aluminum 1100 and 304 stainless steel wires, with 127, 305, and 406 micron diam., were examined. In general, the drawn wires were found to behave as transversely isotropic media.

Direct labeling of serum proteins by fluorescent dye for antibody microarray.

PubMed

Klimushina, M V; Gumanova, N G; Metelskaya, V A

2017-05-06

Analysis of serum proteome by antibody microarray is used to identify novel biomarkers and to study signaling pathways including protein phosphorylation and protein-protein interactions. Labeling of serum proteins is important for optimal performance of the antibody microarray. Proper choice of fluorescent label and optimal concentration of protein loaded on the microarray ensure good quality of imaging that can be reliably scanned and processed by the software. We have optimized direct serum protein labeling using fluorescent dye Arrayit Green 540 (Arrayit Corporation, USA) for antibody microarray. Optimized procedure produces high quality images that can be readily scanned and used for statistical analysis of protein composition of the serum. Copyright © 2017 Elsevier Inc. All rights reserved.

Transfection microarray and the applications.

PubMed

Miyake, Masato; Yoshikawa, Tomohiro; Fujita, Satoshi; Miyake, Jun

2009-05-01

Microarray transfection has been extensively studied for high-throughput functional analysis of mammalian cells. However, control of efficiency and reproducibility are the critical issues for practical use. By using solid-phase transfection accelerators and nano-scaffold, we provide a highly efficient and reproducible microarray-transfection device, "transfection microarray". The device would be applied to the limited number of available primary cells and stem cells not only for large-scale functional analysis but also reporter-based time-lapse cellular event analysis.

A Human Lectin Microarray for Sperm Surface Glycosylation Analysis *

PubMed Central

Sun, Yangyang; Cheng, Li; Gu, Yihua; Xin, Aijie; Wu, Bin; Zhou, Shumin; Guo, Shujuan; Liu, Yin; Diao, Hua; Shi, Huijuan; Wang, Guangyu; Tao, Sheng-ce

2016-01-01

Glycosylation is one of the most abundant and functionally important protein post-translational modifications. As such, technology for efficient glycosylation analysis is in high demand. Lectin microarrays are a powerful tool for such investigations and have been successfully applied for a variety of glycobiological studies. However, most of the current lectin microarrays are primarily constructed from plant lectins, which are not well suited for studies of human glycosylation because of the extreme complexity of human glycans. Herein, we constructed a human lectin microarray with 60 human lectin and lectin-like proteins. All of the lectins and lectin-like proteins were purified from yeast, and most showed binding to human glycans. To demonstrate the applicability of the human lectin microarray, human sperm were probed on the microarray and strong bindings were observed for several lectins, including galectin-1, 7, 8, GalNAc-T6, and ERGIC-53 (LMAN1). These bindings were validated by flow cytometry and fluorescence immunostaining. Further, mass spectrometry analysis showed that galectin-1 binds several membrane-associated proteins including heat shock protein 90. Finally, functional assays showed that binding of galectin-8 could significantly enhance the acrosome reaction within human sperms. To our knowledge, this is the first construction of a human lectin microarray, and we anticipate it will find wide use for a range of human or mammalian studies, alone or in combination with plant lectin microarrays. PMID:27364157

The general dispersion relation of induced streaming instabilities in quantum outflow systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mehdian, H., E-mail: mehdian@khu.ac.ir; Hajisharifi, K.; Hasanbeigi, A.

2015-11-15

In this manuscript the dispersion relations of streaming instabilities, by using the unique property (neutralized in charge and current by default) of plasma shells colliding, have been generalized and studied. This interesting property for interpenetrating beams enables one to find the general dispersion relations without any restrictions used in the previous works in this area. In our previous work [H. Mehdian et al., ApJ. 801, 89 (2015)], employing the plasma shell concept and boost frame method, the general dispersion relation for filamentation instability has been derived in the relativistic classical regime. But in this paper, using the above mentioned concepts,more » the general dispersion relations (for each of streaming instabilities, filamentation, two-stream and multi-stream) in the non-relativistic quantum regime have been derived by employing the quantum fluid equations together with Maxwell equations. The derived dispersion relations enable to describe any arbitrary system of interacting two and three beams, justified neutralization condition, by choosing the inertial reference frame embedded on the one of the beams. Furthermore, by the numerical and analytical study of these dispersion relations, many new features of streaming instabilities (E.g. their cut-off wave numbers and growth rates) in terms of all involved parameters have been illustrated. The obtained results in this paper can be used to describe many astrophysical systems and laboratory astrophysics setting, such as collision of non-parallel plasma shells over a background plasma or the collision of three neutralized plasma slabs, and justifying the many plasma phenomena such as particle accelerations and induced fields.« less

The general dispersion relation of induced streaming instabilities in quantum outflow systems

NASA Astrophysics Data System (ADS)

Mehdian, H.; Hajisharifi, K.; Hasanbeigi, A.

2015-11-01

In this manuscript the dispersion relations of streaming instabilities, by using the unique property (neutralized in charge and current by default) of plasma shells colliding, have been generalized and studied. This interesting property for interpenetrating beams enables one to find the general dispersion relations without any restrictions used in the previous works in this area. In our previous work [H. Mehdian et al., ApJ. 801, 89 (2015)], employing the plasma shell concept and boost frame method, the general dispersion relation for filamentation instability has been derived in the relativistic classical regime. But in this paper, using the above mentioned concepts, the general dispersion relations (for each of streaming instabilities, filamentation, two-stream and multi-stream) in the non-relativistic quantum regime have been derived by employing the quantum fluid equations together with Maxwell equations. The derived dispersion relations enable to describe any arbitrary system of interacting two and three beams, justified neutralization condition, by choosing the inertial reference frame embedded on the one of the beams. Furthermore, by the numerical and analytical study of these dispersion relations, many new features of streaming instabilities (E.g. their cut-off wave numbers and growth rates) in terms of all involved parameters have been illustrated. The obtained results in this paper can be used to describe many astrophysical systems and laboratory astrophysics setting, such as collision of non-parallel plasma shells over a background plasma or the collision of three neutralized plasma slabs, and justifying the many plasma phenomena such as particle accelerations and induced fields.

EMAAS: An extensible grid-based Rich Internet Application for microarray data analysis and management

PubMed Central

Barton, G; Abbott, J; Chiba, N; Huang, DW; Huang, Y; Krznaric, M; Mack-Smith, J; Saleem, A; Sherman, BT; Tiwari, B; Tomlinson, C; Aitman, T; Darlington, J; Game, L; Sternberg, MJE; Butcher, SA

2008-01-01

Background Microarray experimentation requires the application of complex analysis methods as well as the use of non-trivial computer technologies to manage the resultant large data sets. This, together with the proliferation of tools and techniques for microarray data analysis, makes it very challenging for a laboratory scientist to keep up-to-date with the latest developments in this field. Our aim was to develop a distributed e-support system for microarray data analysis and management. Results EMAAS (Extensible MicroArray Analysis System) is a multi-user rich internet application (RIA) providing simple, robust access to up-to-date resources for microarray data storage and analysis, combined with integrated tools to optimise real time user support and training. The system leverages the power of distributed computing to perform microarray analyses, and provides seamless access to resources located at various remote facilities. The EMAAS framework allows users to import microarray data from several sources to an underlying database, to pre-process, quality assess and analyse the data, to perform functional analyses, and to track data analysis steps, all through a single easy to use web portal. This interface offers distance support to users both in the form of video tutorials and via live screen feeds using the web conferencing tool EVO. A number of analysis packages, including R-Bioconductor and Affymetrix Power Tools have been integrated on the server side and are available programmatically through the Postgres-PLR library or on grid compute clusters. Integrated distributed resources include the functional annotation tool DAVID, GeneCards and the microarray data repositories GEO, CELSIUS and MiMiR. EMAAS currently supports analysis of Affymetrix 3' and Exon expression arrays, and the system is extensible to cater for other microarray and transcriptomic platforms. Conclusion EMAAS enables users to track and perform microarray data management and analysis tasks through a single easy-to-use web application. The system architecture is flexible and scalable to allow new array types, analysis algorithms and tools to be added with relative ease and to cope with large increases in data volume. PMID:19032776

The underlying biological mechanisms of biocompatibility differences between bare and TiN-coated NiTi alloys.

PubMed

Lifeng, Zhao; Yan, Hong; Dayun, Yang; Xiaoying, Lü; Tingfei, Xi; Deyuan, Zhang; Ying, Hong; Jinfeng, Yuan

2011-04-01

TiN coating has been demonstrated to improve the biocompatibility of bare NiTi alloys; however, essential biocompatibility differences between NiTi alloys before and after TiN coating are not known so far. In this study, to explore the underlying biological mechanisms of biocompatibility differences between them, the changes of bare and TiN-coated NiTi alloys in surface chemical composition, morphology, hydrophilicity, Ni ions release, cytotoxicity, apoptosis, and gene expression profiles were compared using energy-dispersive spectroscopy, scanning electron microscopy, contact angle, surface energy, Ni ions release analysis, the methylthiazoltetrazolium (MTT) method, flow cytometry and microarray methods, respectively. Pathways binding to networks and real-time polymerase chain reaction (PCR) were employed to analyze and validate the microarray data, respectively. It was found that, compared with the bare NiTi alloys, TiN coating significantly decreased Ni ions content on the surfaces of the NiTi alloys and reduced the release of Ni ions from the alloys, attenuated the inhibition of Ni ions to the expression of genes associated with anti-inflammatory, and also suppressed the promotion of Ni ions to the expression of apoptosis-related genes. Moreover, TiN coating distinctly improved the hydrophilicity and uniformity of the surfaces of the NiTi alloys, and contributed to the expression of genes participating in cell adhesion and other physiological activities. These results indicate that the TiN-coated NiTi alloys will help overcome the shortcomings of NiTi alloys used in clinical application currently, and can be expected to be a replacement of biomaterials for a medical device field.

Microarray Analysis of Iris Gene Expression in Mice with Mutations Influencing Pigmentation

PubMed Central

Trantow, Colleen M.; Cuffy, Tryphena L.; Fingert, John H.; Kuehn, Markus H.

2011-01-01

Purpose. Several ocular diseases involve the iris, notably including oculocutaneous albinism, pigment dispersion syndrome, and exfoliation syndrome. To screen for candidate genes that may contribute to the pathogenesis of these diseases, genome-wide iris gene expression patterns were comparatively analyzed from mouse models of these conditions. Methods. Iris samples from albino mice with a Tyr mutation, pigment dispersion–prone mice with Tyrp1 and Gpnmb mutations, and mice resembling exfoliation syndrome with a Lyst mutation were compared with samples from wild-type mice. All mice were strain (C57BL/6J), age (60 days old), and sex (female) matched. Microarrays were used to compare transcriptional profiles, and differentially expressed transcripts were described by functional annotation clustering using DAVID Bioinformatics Resources. Quantitative real-time PCR was performed to validate a subset of identified changes. Results. Compared with wild-type C57BL/6J mice, each disease context exhibited a large number of statistically significant changes in gene expression, including 685 transcripts differentially expressed in albino irides, 403 in pigment dispersion–prone irides, and 460 in exfoliative-like irides. Conclusions. Functional annotation clusterings were particularly striking among the overrepresented genes, with albino and pigment dispersion–prone irides both exhibiting overall evidence of crystallin-mediated stress responses. Exfoliative-like irides from mice with a Lyst mutation showed overall evidence of involvement of genes that influence immune system processes, lytic vacuoles, and lysosomes. These findings have several biologically relevant implications, particularly with respect to secondary forms of glaucoma, and represent a useful resource as a hypothesis-generating dataset. PMID:20739468

THE MAQC PROJECT: ESTABLISHING QC METRICS AND THRESHOLDS FOR MICROARRAY QUALITY CONTROL

EPA Science Inventory

Microarrays represent a core technology in pharmacogenomics and toxicogenomics; however, before this technology can successfully and reliably be applied in clinical practice and regulatory decision-making, standards and quality measures need to be developed. The Microarray Qualit...

Angular dispersion of oblique phonon modes in BiFeO3 from micro-Raman scattering

NASA Astrophysics Data System (ADS)

Hlinka, J.; Pokorny, J.; Karimi, S.; Reaney, I. M.

2011-01-01

The angular dispersion of oblique phonon modes in a multiferroic BiFeO3 has been obtained from a micro-Raman spectroscopic investigation of a coarse grain ceramic sample. Continuity of the measured angular dispersion curves allows conclusive identification of all pure zone-center polar modes. The method employed here to reconstruct the anisotropic crystal property from a large set of independent local measurements on a macroscopically isotropic ceramic sample profits from the considerable dispersion of the oblique modes in ferroelectric perovskites and it can be in principle conveniently applied to any other optically uniaxial ferroelectric material.

Application of transglycosylated stevia and hesperidin as drug carriers to enhance biopharmaceutical properties of poorly-soluble artemisinin.

PubMed

Letchmanan, Kumaran; Shen, Shou-Cang; Ng, Wai Kiong; Tan, Reginald B H

2018-01-01

Biopharmaceutical properties of poorly water-soluble antimalarial drug, Artemisinin (ART), were improved by formulating amorphous solid dispersions with transglycosylated food additives (Hsp-G and Stevia-G) via co-spray drying. Both the formulated ART/Hsp-G and ART/Stevia-G showed superior dissolution properties with a burst release of more than 95% of drug within 5 min, whereas untreated ART dissolved only 4% in 5min. The supersaturation solubility of the formulated ART was enhanced by 2-fold as compared with untreated counterpart. The storage stability tests indicated that these formulations chemically stable at room temperature and under low humidity (<18% RH) conditions. However, high humidity (75% RH) induced re-crystallization and caused changes in the physical appearance of the solid dispersions. In addition, both the food additives and ART formulated samples showed low cytotoxicity to Caco-2 cell line suggesting their good biocompatibility. Thus, the formation of solid dispersions of ART with transglycosylated food additives is a potentially safe and effective approach to enhance the bioavailability of poorly water-soluble ART. Copyright © 2017 Elsevier B.V. All rights reserved.

Thiolated citrus low-methoxyl pectin: Synthesis, characterization and rheological and oxidation-responsive gelling properties.

PubMed

Chen, Jinfeng; Ye, Fayin; Zhou, Yun; Zhao, Guohua

2018-02-01

In the present study, citrus low-methoxyl pectin was modified by conjugating cysteine via amide bonds, and the resultant polymer (CYS-PEC) was characterized. CYS-PEC conjugates with thiol contents varying from 77.8μmol/g to 296μmol/g were synthesized, and the successful conjugation was evidenced by elemental, and FT-IR analyses. The sulfur in CYS-PEC is predominately in the thiol form, with a minor fraction forming disulfide bonds (∼15%), which occur when thiol/disulfide interchange interrupts the intended thiolation. Both native and modified pectin dispersions exhibited strong pseudoplastic properties, and the frequency sweeps revealed them to be dispersions containing microgel particles. Dynamic viscoelastic analysis was used to determine the oxidation-response gelling capacities of polymer dispersions containing H 2 O 2 , especially those that are highly thiolated and have cross-linked gel properties. For oxidation-induced CYS-PEC gels, their gelation time, hardness, viscosity and elastic moduli and swelling-disintegration ratio are dependent on the thiol group content, H 2 O 2 concentration and polymer concentration. Copyright © 2017 Elsevier Ltd. All rights reserved.

The influence of the use of viscosifying agents as dispersion media on the drug release properties from PLGA nanoparticles.

PubMed

Dillen, Kathleen; Weyenberg, Wim; Vandervoort, Jo; Ludwig, Annick

2004-11-01

Poly(lactide-co-glycolide) nanoparticles incorporating ciprofloxacin HCl were prepared by means of a W/O/W emulsification solvent evaporation method. The physicochemical properties of these particles were evaluated by measuring particle size, zeta potential and drug loading efficiency. Gamma-sterilised nanoparticles were dispersed in different isoviscous polymer solutions, commonly used as vehicles in eye drops. The influence of gamma-irradiation of the viscosifying agents on the drug release properties of the dispersed nanoparticles was evaluated with respect to release in mannitol solution. The viscosity of the polymer solutions prepared was measured by flow rheometry and thereby the influence of temperature and sterilisation by autoclaving on viscosity was examined. Before and after freeze-drying and subsequent sterilisation by gamma-irradiation, the polymer solutions were also characterised by dynamic stress sweep and dynamic frequency sweep oscillation measurements to deduce possible structural changes. A possible relationship between the differences in ciprofloxacin release from the nanoparticles suspended in the various media and the network structure or rheological behaviour of the polymers was investigated.

Thermophysical properties and rheological behavior of electro-rheological fluids at different temperatures

NASA Astrophysics Data System (ADS)

Korobko, Evguenia V.; Korobko, Yulia O.

2000-04-01

Fluid disperse systems, sensitive to the external electric field-electrorheological fluids, are finding increasing use in various areas of industry and technology. Their physicomechanical, electrophysical characteristics determine the valuable specific properties of the materials with assigned structure, obtainable with everwide use of electric fields, which makes it possible to substantially enhance efficiency and productiveness of technological processes and to improve the control of operational regimes of the equipment which employ fluid disperse media. The present investigations has been undertaken with the aim of studying thermophysical properties and rheophysical behavior of low-concentration ER- fluid (diatomite in transformer oil) at different temperatures. It was shown that the electric field, which changes considerably the structure of electrorheological fluid, influences effective thermal conductivity and diffusivity coefficients. Their increase with electric field intensity and the increase of the effective viscosity with temperature are connected with the increase of the conductive component of the overall heat transfer through the contact spots between the solid particles, and with intensification of electric convection in the spaces between the dispersed particles.

Mechanical and morphological properties of polypropylene/nano α-Al2O3 composites.

PubMed

Mirjalili, F; Chuah, L; Salahi, E

2014-01-01

A nanocomposite containing polypropylene (PP) and nano α-Al2O3 particles was prepared using a Haake internal mixer. Mechanical tests, such as tensile and flexural tests, showed that mechanical properties of the composite were enhanced by addition of nano α-Al2O3 particles and dispersant agent to the polymer. Tensile strength was approximately ∼ 16% higher than pure PP by increasing the nano α-Al2O3 loading from 1 to 4 wt% into the PP matrix. The results of flexural analysis indicated that the maximum values of flexural strength and flexural modulus for nanocomposite without dispersant were 50.5 and 1954 MPa and for nanocomposite with dispersant were 55.88 MPa and 2818 MPa, respectively. However, higher concentration of nano α-Al2O3 loading resulted in reduction of those mechanical properties that could be due to agglomeration of nano α-Al2O3 particles. Transmission and scanning electron microscopic observations of the nanocomposites also showed that fracture surface became rougher by increasing the content of filler loading from 1 to 4% wt.

Osmotic Pressure in Ionic Microgel Dispersions

NASA Astrophysics Data System (ADS)

Denton, Alan R.; Tang, Qiyun

2015-03-01

Microgels are microscopic gel particles, typically 10-1000 nm in size, that are swollen by a solvent. Hollow microgels (microcapsules) can encapsulate cargo, such as dye molecules or drugs, in their solvent-filled cavities. Their sensitive response to environmental conditions (e.g., temperature, pH) and influence on flow properties suit microgels to widespread applications in the chemical, pharmaceutical, food, and consumer care industries. When dispersed in water, polyelectrolyte gels become charged through dissociation of counterions. The electrostatic contribution to the osmotic pressure inside and outside of ionic microgels influences particle swelling and bulk materials properties, including thermodynamic, structural, optical, and rheological properties. Within the primitive and cell models of polyelectrolyte solutions, we derive an exact statistical mechanical formula for the contribution of mobile microions to the osmotic pressure within ionic microgels. Using Poisson-Boltzmann theory, we validate this result by explicitly calculating ion distributions across the surface of an ionic microgel and the electrostatic contribution to the osmotic pressure. Within a coarse-grained one-component model, we further chart the limits of the cell model for salty dispersions. This work was supported by the National Science Foundation under Grant No. DMR-1106331.

Dispersion Corrected Structural Properties and Quasiparticle Band Gaps of Several Organic Energetic Solids.

PubMed

Appalakondaiah, S; Vaitheeswaran, G; Lebègue, S

2015-06-18

We have performed ab initio calculations for a series of energetic solids to explore their structural and electronic properties. To evaluate the ground state volume of these molecular solids, different dispersion correction methods were accounted in DFT, namely the Tkatchenko-Scheffler method (with and without self-consistent screening), Grimme's methods (D2, D3(BJ)), and the vdW-DF method. Our results reveal that dispersion correction methods are essential in understanding these complex structures with van der Waals interactions and hydrogen bonding. The calculated ground state volumes and bulk moduli show that the performance of each method is not unique, and therefore a careful examination is mandatory for interpreting theoretical predictions. This work also emphasizes the importance of quasiparticle calculations in predicting the band gap, which is obtained here with the GW approximation. We find that the obtained band gaps are ranging from 4 to 7 eV for the different compounds, indicating their insulating nature. In addition, we show the essential role of quasiparticle band structure calculations to correlate the gap with the energetic properties.

Assessing differential expression in two-color microarrays: a resampling-based empirical Bayes approach.

PubMed

Li, Dongmei; Le Pape, Marc A; Parikh, Nisha I; Chen, Will X; Dye, Timothy D

2013-01-01

Microarrays are widely used for examining differential gene expression, identifying single nucleotide polymorphisms, and detecting methylation loci. Multiple testing methods in microarray data analysis aim at controlling both Type I and Type II error rates; however, real microarray data do not always fit their distribution assumptions. Smyth's ubiquitous parametric method, for example, inadequately accommodates violations of normality assumptions, resulting in inflated Type I error rates. The Significance Analysis of Microarrays, another widely used microarray data analysis method, is based on a permutation test and is robust to non-normally distributed data; however, the Significance Analysis of Microarrays method fold change criteria are problematic, and can critically alter the conclusion of a study, as a result of compositional changes of the control data set in the analysis. We propose a novel approach, combining resampling with empirical Bayes methods: the Resampling-based empirical Bayes Methods. This approach not only reduces false discovery rates for non-normally distributed microarray data, but it is also impervious to fold change threshold since no control data set selection is needed. Through simulation studies, sensitivities, specificities, total rejections, and false discovery rates are compared across the Smyth's parametric method, the Significance Analysis of Microarrays, and the Resampling-based empirical Bayes Methods. Differences in false discovery rates controls between each approach are illustrated through a preterm delivery methylation study. The results show that the Resampling-based empirical Bayes Methods offer significantly higher specificity and lower false discovery rates compared to Smyth's parametric method when data are not normally distributed. The Resampling-based empirical Bayes Methods also offers higher statistical power than the Significance Analysis of Microarrays method when the proportion of significantly differentially expressed genes is large for both normally and non-normally distributed data. Finally, the Resampling-based empirical Bayes Methods are generalizable to next generation sequencing RNA-seq data analysis.

Development of a DNA microarray for species identification of quarantine aphids.

PubMed

Lee, Won Sun; Choi, Hwalran; Kang, Jinseok; Kim, Ji-Hoon; Lee, Si Hyeock; Lee, Seunghwan; Hwang, Seung Yong

2013-12-01

Aphid pests are being brought into Korea as a result of increased crop trading. Aphids exist on growth areas of plants, and thus plant growth is seriously affected by aphid pests. However, aphids are very small and have several sexual morphs and life stages, so it is difficult to identify species on the basis of morphological features. This problem was approached using DNA microarray technology. DNA targets of the cytochrome c oxidase subunit I gene were generated with a fluorescent dye-labelled primer and were hybridised onto a DNA microarray consisting of specific probes. After analysing the signal intensity of the specific probes, the unique patterns from the DNA microarray, consisting of 47 species-specific probes, were obtained to identify 23 aphid species. To confirm the accuracy of the developed DNA microarray, ten individual blind samples were used in blind trials, and the identifications were completely consistent with the sequencing data of all individual blind samples. A microarray has been developed to distinguish aphid species. DNA microarray technology provides a rapid, easy, cost-effective and accurate method for identifying aphid species for pest control management. © 2013 Society of Chemical Industry.

Evaluating concentration estimation errors in ELISA microarray experiments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Daly, Don S.; White, Amanda M.; Varnum, Susan M.

Enzyme-linked immunosorbent assay (ELISA) is a standard immunoassay to predict a protein concentration in a sample. Deploying ELISA in a microarray format permits simultaneous prediction of the concentrations of numerous proteins in a small sample. These predictions, however, are uncertain due to processing error and biological variability. Evaluating prediction error is critical to interpreting biological significance and improving the ELISA microarray process. Evaluating prediction error must be automated to realize a reliable high-throughput ELISA microarray system. Methods: In this paper, we present a statistical method based on propagation of error to evaluate prediction errors in the ELISA microarray process. Althoughmore » propagation of error is central to this method, it is effective only when comparable data are available. Therefore, we briefly discuss the roles of experimental design, data screening, normalization and statistical diagnostics when evaluating ELISA microarray prediction errors. We use an ELISA microarray investigation of breast cancer biomarkers to illustrate the evaluation of prediction errors. The illustration begins with a description of the design and resulting data, followed by a brief discussion of data screening and normalization. In our illustration, we fit a standard curve to the screened and normalized data, review the modeling diagnostics, and apply propagation of error.« less

Lignin-Based Electrospun Nanofibers Reinforced with Cellulose Nanocrystals

Treesearch

Mariko Ago; Kunihiko Okajima; Joseph E. Jakes; Park Sunkyu; Orlando J. Rojas

2012-01-01

Lignin-based fibers were produced by electrospinning aqueous dispersions of lignin, poly(vinyl alcohol) (PVA), and cellulose nanocrystals (CNCs). Defect-free nanofibers with up to 90 wt % lignin and 15% CNCs were achieved. The properties of the aqueous dispersions, including viscosity, electrical conductivity, and surface tension, were examined and correlated to the...

Properties of extruded starch-poly(methyl acrylate) graft copolymers prepared from spherulites formed from amylose-oleic acid inclusion complexes

USDA-ARS?s Scientific Manuscript database

Mixtures of high amylose corn starch and oleic acid were processed by steam jet-cooking, and the dispersions were rapidly cooled to yield amylose-oleic acid inclusion complexes as sub-micron spherulites and spherulite aggregates. Dispersions of these spherulite particles were then graft polymerized ...

Effect of amylopectin on the rheological properties of aqueous dispersions of starch-sodium palmitate complexes

USDA-ARS?s Scientific Manuscript database

Aqueous dispersions of normal and high-amylose corn starch were steam jet cooked and blended with aqueous solutions of sodium palmitate to form amylose inclusion complexes. Partial conversion of complexed sodium palmitate to palmitic acid by addition of acetic acid led to the formation of gels. Bl...

Acoustic Typology of Vowel Inventories and Dispersion Theory: Insights from a Large Cross-Linguistic Corpus

ERIC Educational Resources Information Center

Becker-Kristal, Roy

2010-01-01

This dissertation examines the relationship between the structural, phonemic properties of vowel inventories and their acoustic phonetic realization, with particular focus on the adequacy of Dispersion Theory, which maintains that inventories are structured so as to maximize perceptual contrast between their component vowels. In order to assess…

Glass Reinforcement of Various Epoxy Resins-Polyurea Systems

NASA Astrophysics Data System (ADS)

Joshi, Medha; Jauhari, Smita

2012-07-01

Polyureas (PUs) were prepared by the polycondensation reaction of disperse dyes containing -NH2 group and toluene 2, 4-diisocyanate. The disperse dyes have been prepared by coupling of various 2-diazobenzothiazoles with 1,3-benzenediamine. All the PUs were characterized by elemental analysis, spectral studies, number average molecular weight ( {overline{{Mn}} } ), and thermogravimetry. Further reaction of PUs was carried out with an epoxy resin (i.e., DGEBA). The curing study of prepared resins was monitored by differential scanning calorimeter (DSC). Based on DSC, thermograms glass fiber-reinforced composites have been laminated and characterized by chemical, mechanical, and electrical properties. The unreinforced cured resins were subjected to thermogravimetric analysis (TGA). The laminated composites showed excellent resistance properties against chemicals and good mechanical and electrical properties.

Improved mechanical and electrical properties in electrospun polyimide/multiwalled carbon nanotubes nanofibrous composites

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zha, Jun-Wei; Sun, Fang; Wang, Si-Jiao

2014-10-07

Highly aligned polyimide (PI) and PI/multi-walled carbon nanotubes (PI/MWCNTs) nanofibrous composites by incorporating poly(ethylene oxide) as the dispersing medium were fabricated using electrospinning technique. The morphology, mechanical, and electrical properties of the electrospun nanofibrous composites were investigated. Scanning electron microscope showed that the functionalized MWCNTs (f-MWCNTs) were well dispersed and oriented along the nanofiber axis. Analysis of electrical properties indicated a remarkable improvement on the alternating current conductivity by introduction of the aligned f-MWCNTs. Besides, with addition of 3 vol. % f-MWCNTs, the obvious enhancement of tensile modulus and strength was achieved. Thus, the electrospun PI/MWCNTs nanofibrous composites have greatmore » potential applications in multifunctional engineering materials.« less

Structure and optical properties of noble metal and oxide nanoparticles dispersed in various polysaccharide biopolymers

NASA Astrophysics Data System (ADS)

Djoković, V.; Božanic, D. K.; Vodnik, V. V.; Krsmanović, R. M.; Trandafilovic, L. V.; Dimitrijević-Branković, S.

2011-10-01

We present the results on the structure and the optical properties of noble metal (Ag, Au) and oxide (ZnO) nanoparticles synthesized by various methods in different polysaccharide matrices such as chitosan, glycogen, alginate and starch. The structure of the obtained nanoparticles was studied in detail with microscopic techniques (TEM, SEM), while the XPS spectroscopy was used to investigate the effects at the nanoparticle-biomolecule interfaces. The antimicrobial activity of the nanocomposite films with Ag nanoparticles was tested against the Staphylococcus aureus, Escherichia coli and Candida albicans pathogens. In addition, we will present the results on the structure and optical properties of the tryptophan amino acid functionalized silver nanoparticles dispersed in water soluble polymer matrices.

Synthesis and dielectric properties of zinc oxide nanoparticles using a biotemplate

DOE Office of Scientific and Technical Information (OSTI.GOV)

P, Sharmila P, E-mail: sharmilavishram@gmail.com; Tharayil, Nisha J., E-mail: nishajohntharayil@gmail.com

Zinc Oxide nanoparticles are synthesized using DNA as capping agent. Zinc oxide nanoparticles are synthesized using DNA as a capping agent. Structural and morphological characterizations are done using SEM, FTIR and XRD. The particle size and lattice parameters are calculated from the diffraction data. The optical properties are studied using UV-Vis absorption spectroscopy and bandgap variation with temperature is determined. The dielectric property of nanoparticles is studied by varying temperature and frequency. The dielectric constant and dispersion parameters are found out. Method of Cole-Cole analysis is used to study the high temperature dispersion of relaxation time. The variation of bothmore » AC and DC conductivity are studied and activation energy calculated.« less

Effect of magnetic field on the optical properties of an inhomogeneously broadened multilevel Λ-system in Rb vapor

NASA Astrophysics Data System (ADS)

Kaur, Paramjit; Wasan, Ajay

2017-03-01

We present a theoretical model, using density matrix approach, to study the effect of external longitudinal and transverse magnetic fields on the optical properties of an inhomogeneously broadened multilevel Λ-system using the D2 line in 85Rb and 87Rb atoms. The presence of closely spaced multiple excited states causes asymmetry in the absorption and dispersion profiles. We observe a wide EIT window with a positive slope at the line center for a stationary atom. While for a moving atom, the linewidth of EIT window reduces and positive dispersion becomes steeper. When magnetic field is applied, our calculations show multiple EIT subwindows that are significantly narrower and shallow than single EIT window. The number of EIT subwindows depend on the orientation of the magnetic field. We also obtain multiple positive dispersive regions for subluminal propagation in the medium. The anomalous dispersion exists in between two subwindows showing the superluminal light propagation. Our theoretical analysis explain the experiments performed by Wei et al. [Phys. Rev. A 72, 023806 (2005)] and Iftiquar et al. [Phys. Rev. A 79, 013808 (2009)].

Measurement of chalcogenide glass optical dispersion using a mid-infrared prism coupler

DOE Office of Scientific and Technical Information (OSTI.GOV)

Qiao, Hong; Anheier, Norman C.; Musgraves, Jonathan D.

2011-05-01

Physical properties of chalcogenide glass, including broadband infrared transparency, high refractive index, low glass transition temperature, and nonlinear properties, make them attractive candidates for advanced mid-infrared (3 to 12 {micro}m) optical designs. Efforts focused at developing new chalcogenide glass formulations and processing methods require rapid quantitative evaluation of their optical contents to guide the materials research. However, characterization of important optical parameters such as optical dispersion remains a slow and costly process, generally with limited accuracy. The recent development of a prism coupler at the Pacific Northwest National Laboratory (PNNL) now enables rapid, high precision measurement of refractive indices atmore » discrete wavelengths from the visible to the mid-infrared. Optical dispersion data of several chalcogenide glass families were collected using this method. Variations in the optical dispersion were correlated to glass composition and compared against measurements using other methods. While this work has been focused on facilitating chalcogenide glass synthesis, mid-infrared prism coupler analysis has broader applications to other mid-infrared optical material development efforts, including oxide glasses and crystalline materials.« less

A low-dispersion, exactly energy-charge-conserving semi-implicit relativistic particle-in-cell algorithm

NASA Astrophysics Data System (ADS)

Chen, Guangye; Luis, Chacon; Bird, Robert; Stark, David; Yin, Lin; Albright, Brian

2017-10-01

Leap-frog based explicit algorithms, either ``energy-conserving'' or ``momentum-conserving'', do not conserve energy discretely. Time-centered fully implicit algorithms can conserve discrete energy exactly, but introduce large dispersion errors in the light-wave modes, regardless of timestep sizes. This can lead to intolerable simulation errors where highly accurate light propagation is needed (e.g. laser-plasma interactions, LPI). In this study, we selectively combine the leap-frog and Crank-Nicolson methods to produce a low-dispersion, exactly energy-and-charge-conserving PIC algorithm. Specifically, we employ the leap-frog method for Maxwell equations, and the Crank-Nicolson method for particle equations. Such an algorithm admits exact global energy conservation, exact local charge conservation, and preserves the dispersion properties of the leap-frog method for the light wave. The algorithm has been implemented in a code named iVPIC, based on the VPIC code developed at LANL. We will present numerical results that demonstrate the properties of the scheme with sample test problems (e.g. Weibel instability run for 107 timesteps, and LPI applications.

Chaotic Lagrangian models for turbulent relative dispersion.

PubMed

Lacorata, Guglielmo; Vulpiani, Angelo

2017-04-01

A deterministic multiscale dynamical system is introduced and discussed as a prototype model for relative dispersion in stationary, homogeneous, and isotropic turbulence. Unlike stochastic diffusion models, here trajectory transport and mixing properties are entirely controlled by Lagrangian chaos. The anomalous "sweeping effect," a known drawback common to kinematic simulations, is removed through the use of quasi-Lagrangian coordinates. Lagrangian dispersion statistics of the model are accurately analyzed by computing the finite-scale Lyapunov exponent (FSLE), which is the optimal measure of the scaling properties of dispersion. FSLE scaling exponents provide a severe test to decide whether model simulations are in agreement with theoretical expectations and/or observation. The results of our numerical experiments cover a wide range of "Reynolds numbers" and show that chaotic deterministic flows can be very efficient, and numerically low-cost, models of turbulent trajectories in stationary, homogeneous, and isotropic conditions. The mathematics of the model is relatively simple, and, in a geophysical context, potential applications may regard small-scale parametrization issues in general circulation models, mixed layer, and/or boundary layer turbulence models as well as Lagrangian predictability studies.

Importance of network density of nanotube: Effect on nitrogen dioxide gas sensing by solid state resistive sensor

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mishra, Prabhash; Grachyova, D. V.; Moskalenko, A. S.

2016-04-13

Dispersion of single-walled carbon nanotubes (SWCNTs) is an established fact, however, its effect on toxic gas sensing for the development of solid state resistive sensor was not well reported. In this report, the dispersion quality of SWCNTs has been investigated and improved, and this well-dispersed SWCNTs network was used for sensor fabrication to monitor nitrogen dioxide gas. Ultraviolet (UV)-visible spectroscopic studies shows the strength of SWNTs dispersion and scanning electron microscopy (SEM) imaging provides the morphological properties of the sensor device. In this gas sensor device, two sets of resistive type sensors were fabricated that consisting of a pair ofmore » interdigitated electrodes (IDEs) using dielectrophoresis technique with different SWCNTs network density. With low-density SWCNTs networks, this fabricated sensor exhibits a high response for nitrogen dioxide sensing. The sensing of nitrogen dioxide is mainly due to charge transfer from absorbed molecules to sidewalls of nanotube and tube-tube screening acting a major role for the transport properties of charge carriers.« less

Chaotic Lagrangian models for turbulent relative dispersion

NASA Astrophysics Data System (ADS)

Lacorata, Guglielmo; Vulpiani, Angelo

2017-04-01

A deterministic multiscale dynamical system is introduced and discussed as a prototype model for relative dispersion in stationary, homogeneous, and isotropic turbulence. Unlike stochastic diffusion models, here trajectory transport and mixing properties are entirely controlled by Lagrangian chaos. The anomalous "sweeping effect," a known drawback common to kinematic simulations, is removed through the use of quasi-Lagrangian coordinates. Lagrangian dispersion statistics of the model are accurately analyzed by computing the finite-scale Lyapunov exponent (FSLE), which is the optimal measure of the scaling properties of dispersion. FSLE scaling exponents provide a severe test to decide whether model simulations are in agreement with theoretical expectations and/or observation. The results of our numerical experiments cover a wide range of "Reynolds numbers" and show that chaotic deterministic flows can be very efficient, and numerically low-cost, models of turbulent trajectories in stationary, homogeneous, and isotropic conditions. The mathematics of the model is relatively simple, and, in a geophysical context, potential applications may regard small-scale parametrization issues in general circulation models, mixed layer, and/or boundary layer turbulence models as well as Lagrangian predictability studies.

A Molecular Dynamics Study of Single-Walled Carbon Nanotubes (SWCNTs) Dispersed in Bile Salt Surfactants

NASA Astrophysics Data System (ADS)

Phelan, Frederick, Jr.; Sun, Huai

2014-03-01

Single-walled carbon nanotubes (SWNCTs) are materials with structural, electronic and optical properties that make them attractive for a myriad of advanced technology applications. A practical barrier to their use is that SWCNT synthesis techniques produce heterogeneous mixtures of varying lengths and chirality, whereas applications generally require tubes with narrow size distributions and individual type. Most separation techniques currently in use to obtain monodisperse tube fractions rely on dispersion of these materials in aqueous solution using surfactants. The dispersion process results in a mixture of colloidal structures in which individual tubes are dispersed and contained in a surfactant shell. Understanding the structure and properties of the SWCNT-surfactant complex at the molecular level, and how this is affected by chirality, is key to understanding and improving separations processes. In this study, we use molecular dynamics (MD) simulations to study the structure and properties of SWCNT-surfactant colloidal complexes. We tested a number of methods and protocols in order to build an accurate model for simulating SWCNT systems for a variety of bile salt surfactants as well as anionic co-surfactants, components that are widely used and important in experimental separation studies at NIST. The custom force field parameters used here will be stored in WebFF, a Web-hosted smart force-field repository for polymeric and organic materials being developed at NIST for the Materials Genome Initiative.

Molecular simulation study of dynamical properties of room temperature ionic liquids with carbon pieces

DOE PAGES

Feng, Guang; Zhao, Wei; Cummings, Peter T.; ...

2016-03-29

Room temperature ionic liquids (RTILs) with dispersed carbon pieces exhibit distinctive physiochemical properties. In order to explore the molecular mechanism, RTILs/carbon pieces mixture we investigated it by molecular dynamics (MD) simulation in this work. Rigid and flexible carbon pieces in the form of graphene with different thicknesses and carbon nanotubes in different sizes were dispersed in a representative RTIL 1-butyl-3-methyl-imidazolium dicyanamide ([Bmim][DCA]). Our study demonstrated that the diffusion coefficients of RTILs in the presence of flexible carbons are similar to those of bulk RTILs at varying temperatures, which is in contrast to the decreased diffusion of RTILs in the presencemore » of rigid carbons. In addition, interfacial ion number density at rigid carbon surfaces was higher than that at flexible ones, which is correlated with the accessible external surface area of carbon pieces. The life time of cation-anion pair in the presence of carbon pieces also exhibited a dependence on carbon flexibility. RTILs with dispersed rigid carbon pieces showed longer ion pair life time than those with flexible ones, in consistence with the observation in diffusion coefficients. Furthermore, this work highlights the necessity of including the carbon flexibility when performing MD simulation of RTILs in the presence of dispersed carbon pieces in order to obtain the reliable dynamical and interfacial structural properties.« less

Conservation laws and rogue waves for a higher-order nonlinear Schrödinger equation with variable coefficients in the inhomogeneous fiber

NASA Astrophysics Data System (ADS)

Du, Zhong; Tian, Bo; Wu, Xiao-Yu; Liu, Lei; Sun, Yan

2017-07-01

Subpicosecond or femtosecond optical pulse propagation in the inhomogeneous fiber can be described by a higher-order nonlinear Schrödinger equation with variable coefficients, which is investigated in the paper. Via the Ablowitz-Kaup-Newell-Segur system and symbolic computation, the Lax pair and infinitely-many conservation laws are deduced. Based on the Lax pair and a modified Darboux transformation technique, the first- and second-order rogue wave solutions are constructed. Effects of the groupvelocity dispersion and third-order dispersion on the properties of the first- and second-order rouge waves are graphically presented and analyzed: The groupvelocity dispersion and third-order dispersion both affect the ranges and shapes of the first- and second-order rogue waves: The third-order dispersion can produce a skew angle of the first-order rogue wave and the skew angle rotates counterclockwise with the increase of the groupvelocity dispersion, when the groupvelocity dispersion and third-order dispersion are chosen as the constants; When the groupvelocity dispersion and third-order dispersion are taken as the functions of the propagation distance, the linear, X-shaped and parabolic trajectories of the rogue waves are obtained.

The Importance of Normalization on Large and Heterogeneous Microarray Datasets

EPA Science Inventory

DNA microarray technology is a powerful functional genomics tool increasingly used for investigating global gene expression in environmental studies. Microarrays can also be used in identifying biological networks, as they give insight on the complex gene-to-gene interactions, ne...

SIMULATION AND VISUALIZATION OF FLOW PATTERN IN MICROARRAYS FOR LIQUID PHASE OLIGONUCLEOTIDE AND PEPTIDE SYNTHESIS

PubMed Central

O-Charoen, Sirimon; Srivannavit, Onnop; Gulari, Erdogan

2008-01-01

Microfluidic microarrays have been developed for economical and rapid parallel synthesis of oligonucleotide and peptide libraries. For a synthesis system to be reproducible and uniform, it is crucial to have a uniform reagent delivery throughout the system. Computational fluid dynamics (CFD) is used to model and simulate the microfluidic microarrays to study geometrical effects on flow patterns. By proper design geometry, flow uniformity could be obtained in every microreactor in the microarrays. PMID:17480053

The application of DNA microarrays in gene expression analysis.

PubMed

van Hal, N L; Vorst, O; van Houwelingen, A M; Kok, E J; Peijnenburg, A; Aharoni, A; van Tunen, A J; Keijer, J

2000-03-31

DNA microarray technology is a new and powerful technology that will substantially increase the speed of molecular biological research. This paper gives a survey of DNA microarray technology and its use in gene expression studies. The technical aspects and their potential improvements are discussed. These comprise array manufacturing and design, array hybridisation, scanning, and data handling. Furthermore, it is discussed how DNA microarrays can be applied in the working fields of: safety, functionality and health of food and gene discovery and pathway engineering in plants.

Sandwich ELISA Microarrays: Generating Reliable and Reproducible Assays for High-Throughput Screens

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gonzalez, Rachel M.; Varnum, Susan M.; Zangar, Richard C.

The sandwich ELISA microarray is a powerful screening tool in biomarker discovery and validation due to its ability to simultaneously probe for multiple proteins in a miniaturized assay. The technical challenges of generating and processing the arrays are numerous. However, careful attention to possible pitfalls in the development of your antibody microarray assay can overcome these challenges. In this chapter, we describe in detail the steps that are involved in generating a reliable and reproducible sandwich ELISA microarray assay.

Living on the Edge: Re-shaping the Interface of Synthetic Biology and Nanotechnology.

PubMed

Wu, Shang-Jung; Boghossian, Ardemis A

2016-11-30

A new team of researchers at EPFL is taking an 'anti-disciplinary' approach to creating optical devices. These devices take advantage of the synergy in tuning both nano- and bio-material properties, coupling the advantages of two growing, albeit traditionally distinct, fields. With applications spanning from biosensing and microarray assays to living photovoltaics, the Laboratory of NanoBiotechnology (LNB) is uncovering an unexplored space for the next generation of chemical analytics and light-harvesting technologies.

Comparison of RNA-seq and microarray-based models for clinical endpoint prediction.

PubMed

Zhang, Wenqian; Yu, Ying; Hertwig, Falk; Thierry-Mieg, Jean; Zhang, Wenwei; Thierry-Mieg, Danielle; Wang, Jian; Furlanello, Cesare; Devanarayan, Viswanath; Cheng, Jie; Deng, Youping; Hero, Barbara; Hong, Huixiao; Jia, Meiwen; Li, Li; Lin, Simon M; Nikolsky, Yuri; Oberthuer, André; Qing, Tao; Su, Zhenqiang; Volland, Ruth; Wang, Charles; Wang, May D; Ai, Junmei; Albanese, Davide; Asgharzadeh, Shahab; Avigad, Smadar; Bao, Wenjun; Bessarabova, Marina; Brilliant, Murray H; Brors, Benedikt; Chierici, Marco; Chu, Tzu-Ming; Zhang, Jibin; Grundy, Richard G; He, Min Max; Hebbring, Scott; Kaufman, Howard L; Lababidi, Samir; Lancashire, Lee J; Li, Yan; Lu, Xin X; Luo, Heng; Ma, Xiwen; Ning, Baitang; Noguera, Rosa; Peifer, Martin; Phan, John H; Roels, Frederik; Rosswog, Carolina; Shao, Susan; Shen, Jie; Theissen, Jessica; Tonini, Gian Paolo; Vandesompele, Jo; Wu, Po-Yen; Xiao, Wenzhong; Xu, Joshua; Xu, Weihong; Xuan, Jiekun; Yang, Yong; Ye, Zhan; Dong, Zirui; Zhang, Ke K; Yin, Ye; Zhao, Chen; Zheng, Yuanting; Wolfinger, Russell D; Shi, Tieliu; Malkas, Linda H; Berthold, Frank; Wang, Jun; Tong, Weida; Shi, Leming; Peng, Zhiyu; Fischer, Matthias

2015-06-25

Gene expression profiling is being widely applied in cancer research to identify biomarkers for clinical endpoint prediction. Since RNA-seq provides a powerful tool for transcriptome-based applications beyond the limitations of microarrays, we sought to systematically evaluate the performance of RNA-seq-based and microarray-based classifiers in this MAQC-III/SEQC study for clinical endpoint prediction using neuroblastoma as a model. We generate gene expression profiles from 498 primary neuroblastomas using both RNA-seq and 44 k microarrays. Characterization of the neuroblastoma transcriptome by RNA-seq reveals that more than 48,000 genes and 200,000 transcripts are being expressed in this malignancy. We also find that RNA-seq provides much more detailed information on specific transcript expression patterns in clinico-genetic neuroblastoma subgroups than microarrays. To systematically compare the power of RNA-seq and microarray-based models in predicting clinical endpoints, we divide the cohort randomly into training and validation sets and develop 360 predictive models on six clinical endpoints of varying predictability. Evaluation of factors potentially affecting model performances reveals that prediction accuracies are most strongly influenced by the nature of the clinical endpoint, whereas technological platforms (RNA-seq vs. microarrays), RNA-seq data analysis pipelines, and feature levels (gene vs. transcript vs. exon-junction level) do not significantly affect performances of the models. We demonstrate that RNA-seq outperforms microarrays in determining the transcriptomic characteristics of cancer, while RNA-seq and microarray-based models perform similarly in clinical endpoint prediction. Our findings may be valuable to guide future studies on the development of gene expression-based predictive models and their implementation in clinical practice.

The efficacy of microarray screening for autosomal recessive retinitis pigmentosa in routine clinical practice

PubMed Central

van Huet, Ramon A. C.; Pierrache, Laurence H.M.; Meester-Smoor, Magda A.; Klaver, Caroline C.W.; van den Born, L. Ingeborgh; Hoyng, Carel B.; de Wijs, Ilse J.; Collin, Rob W. J.; Hoefsloot, Lies H.

2015-01-01

Purpose To determine the efficacy of multiple versions of a commercially available arrayed primer extension (APEX) microarray chip for autosomal recessive retinitis pigmentosa (arRP). Methods We included 250 probands suspected of arRP who were genetically analyzed with the APEX microarray between January 2008 and November 2013. The mode of inheritance had to be autosomal recessive according to the pedigree (including isolated cases). If the microarray identified a heterozygous mutation, we performed Sanger sequencing of exons and exon–intron boundaries of that specific gene. The efficacy of this microarray chip with the additional Sanger sequencing approach was determined by the percentage of patients that received a molecular diagnosis. We also collected data from genetic tests other than the APEX analysis for arRP to provide a detailed description of the molecular diagnoses in our study cohort. Results The APEX microarray chip for arRP identified the molecular diagnosis in 21 (8.5%) of the patients in our cohort. Additional Sanger sequencing yielded a second mutation in 17 patients (6.8%), thereby establishing the molecular diagnosis. In total, 38 patients (15.2%) received a molecular diagnosis after analysis using the microarray and additional Sanger sequencing approach. Further genetic analyses after a negative result of the arRP microarray (n = 107) resulted in a molecular diagnosis of arRP (n = 23), autosomal dominant RP (n = 5), X-linked RP (n = 2), and choroideremia (n = 1). Conclusions The efficacy of the commercially available APEX microarray chips for arRP appears to be low, most likely caused by the limitations of this technique and the genetic and allelic heterogeneity of RP. Diagnostic yields up to 40% have been reported for next-generation sequencing (NGS) techniques that, as expected, thereby outperform targeted APEX analysis. PMID:25999674

Perimysial fibroblasts of extraocular muscle, as unique as the muscle fibers.

PubMed

Kusner, Linda L; Young, Andrew; Tjoe, Steven; Leahy, Patrick; Kaminski, Henry J

2010-01-01

Extraocular muscle (EOM) has a distinct skeletal muscle phenotype. The hypothesis for the study was that fibroblasts support the unique EOM phenotype and that perimysial fibroblasts derived from EOM have properties that distinguish them from fibroblasts derived from other skeletal muscle. Perimysial fibroblasts from leg muscle (LM-Fibro) and EOM (EOM-Fibro) of mice were derived and maintained in culture. EOM- and LM-Fibro were assessed morphologically and for vimentin, smooth muscle actin, and Thy-1 immunoreactivity. DNA microarray analysis was performed on LM- and EOM-Fibro grown in conditions that support myoblast differentiation. To assess trophic interactions, co-cultures of myoblasts from established cell lines, CL-EOM and CL-LM with, EOM- or LM-Fibro were performed in direct contact and in a permeable filter support culture. The degree of myotube maturation was assessed by the percentage of myotubes with more than three myonuclei per myotube. EOM- and LM-Fibro cells exhibited distinct morphologies. Both cell types proliferated as a monolayer and expressed vimentin. Fifty-five percent (SD 4.4%) of EOM-Fibro were Thy-1 positive compared with only 24% (SD 4.4%) of LM-Fibro. DNA microarray analysis demonstrated differential expression of structural, immune response, and metabolism-related genes between EOM- and LM-Fibro. Co-cultures demonstrated that mature myotube formation in EOM-derived cell lines was supported to a greater extent by EOM-Fibro than by LM-Fibro, compared with CL-EOM grown with LM-Fibro. Fibroblasts from EOM demonstrate distinct properties that distinguish them from leg muscle-derived fibroblasts. The distinct properties of EOM-Fibro may support the unique EOM phenotype and contribute to their differential involvement in disease.

Best practices for hybridization design in two-colour microarray analysis.

PubMed

Knapen, Dries; Vergauwen, Lucia; Laukens, Kris; Blust, Ronny

2009-07-01

Two-colour microarrays are a popular platform of choice in gene expression studies. Because two different samples are hybridized on a single microarray, and several microarrays are usually needed in a given experiment, there are many possible ways to combine samples on different microarrays. The actual combination employed is commonly referred to as the 'hybridization design'. Different types of hybridization designs have been developed, all aimed at optimizing the experimental setup for the detection of differentially expressed genes while coping with technical noise. Here, we first provide an overview of the different classes of hybridization designs, discussing their advantages and limitations, and then we illustrate the current trends in the use of different hybridization design types in contemporary research.

Enhancing the bioavailability of magnolol in rabbits using melting solid dispersion with polyvinylpyrrolidone.

PubMed

Lin, Shiuan-Pey; Hou, Yu-Chi; Liao, Tzu-Yun; Tsai, Shang-Yuan

2014-03-01

Preparation of magnolol-loaded amorphous solid dispersion was investigated for improving the bioavailability. A solid dispersion of magnolol was prepared with polyvinylpyrrolidone K-30 (PVP) by melting method, and the physical properties were characterized by using differential scanning calorimetry, powder X-ray diffractometry, Fourier transformation-infrared spectroscopy and scanning electron microscope. In addition, dissolution test was also performed. Subsequently, the bioavailability of magnolol pure compound, its physical mixture and solid dispersion were compared in rabbits. The blood samples withdrawn via marginal ear vein at specific time points were assayed by HPLC method. Oral administration of the solid dispersion of magnolol with PVP significantly increased the systemic exposures of magnolol and magnolol sulfates/glucuronides by 80.1% and 142.8%, respectively, compared to those given with magnolol pure compound. Magnolol-loaded amorphous solid dispersion with PVP has demonstrated enhanced bioavailability of magnolol in rabbits.

Bright and dark solitons in the normal dispersion regime of inhomogeneous optical fibers: Soliton interaction and soliton control

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu Wenjun; Tian Bo, E-mail: tian.bupt@yahoo.com.c; State Key Laboratory of Software Development Environment, Beijing University of Aeronautics and Astronautics, Beijing 100191

2010-08-15

Symbolically investigated in this paper is a nonlinear Schroedinger equation with the varying dispersion and nonlinearity for the propagation of optical pulses in the normal dispersion regime of inhomogeneous optical fibers. With the aid of the Hirota method, analytic one- and two-soliton solutions are obtained. Relevant properties of physical and optical interest are illustrated. Different from the previous results, both the bright and dark solitons are hereby derived in the normal dispersion regime of the inhomogeneous optical fibers. Moreover, different dispersion profiles of the dispersion-decreasing fibers can be used to realize the soliton control. Finally, soliton interaction is discussed withmore » the soliton control confirmed to have no influence on the interaction. The results might be of certain value for the study of the signal generator and soliton control.« less

MAVEN Observations of Energy-Time Dispersed Electron Signatures in Martian Crustal Magnetic Fields

NASA Technical Reports Server (NTRS)

Harada, Y.; Mitchell, D. L.; Halekas, J. S.; McFadden, J. P.; Mazelle, C.; Connerney, J. E. P.; Espley, J.; Brain, D. A.; Larson, D. E.; Lillis, R. J.;

Effect of electric field induced alignment and dispersion of functionalized carbon nanotubes on properties of natural rubber

NASA Astrophysics Data System (ADS)

Gao, Jiangshan; He, Yan; Gong, Xiubin

2018-06-01

The original equipment and method for orienting multi-walled carbon nanotubes (MWCNTs) in natural rubber (NR) by alternating current (AC) electric field were reported in the present study. MWCNTs with various volume fractions were dispersed in the mixture latex which composed of natural rubber, additives and methylbenzene. The application of AC electric field during nanocomposites curing process was used to induce the formation of aligned conductive nanotube networks between the electrodes. The aligned MWCNTs in the composites have a better orientation performance and dispersion quality than these of random MWCNTs by analyzing TEM and SEM images. The effects of MWCNTs anisotropy on thermal conductivity, dielectric properties, and dynamic mechanical properties of NR were studied. The mean value of thermal conductivity of composites loading with aligned MWCNTs was 8.67% higher than that of composites with random MWCNTs due to the anisotropy of aligned MWCNTs. The compounds with aligned MWCNTs possessed low dielectric constant, loss tangents and conductivity, namely a good insulativity. The compounds loading with aligned MWCNTs had lower loss modulus and better dynamic mechanical properties than those with random MWCNTs. This method can make full use of the high thermal conductivity of MWCNTs axis, and expand the application areas of natural rubber like conducting heat in a certain direction with a high efficiency.

Co-Processed Chitin-Mannitol as a New Excipient for Oro-Dispersible Tablets

PubMed Central

Daraghmeh, Nidal; Chowdhry, Babur Z.; Leharne, Stephen A.; Al Omari, Mahmoud M. H.; Badwan, Adnan A.

2015-01-01

This study describes the preparation, characterization and performance of a novel excipient for use in oro-dispersible tablets (ODT). The excipient (Cop–CM) consists of chitin and mannitol. The excipient with optimal physicochemical properties was obtained at a chitin: mannitol ratio of 2:8 (w/w) and produced by roll compaction (RC). Differential scanning calorimetry (DSC), Fourier transform-Infrared (FT-IR), X-ray powder diffraction (XRPD) and scanning electron microscope (SEM) techniques were used to characterize Cop–CM, in addition to characterization of its powder and ODT dosage form. The effect of particle size distribution of Cop–CM was investigated and found to have no significant influence on the overall tablet physical properties. The compressibility parameter (a) for Cop–CM was calculated from a Kawakita plot and found to be higher (0.661) than that of mannitol (0.576) due to the presence of the highly compressible chitin (0.818). Montelukast sodium and domperidone ODTs produced, using Cop–CM, displayed excellent physicochemical properties. The exceptional binding, fast wetting and superdisintegration properties of Cop–CM, in comparison with commercially available co-processed ODT excipients, results in a unique multifunctional base which can successfully be used in the formulation of oro-dispersible and fast immediate release tablets. PMID:25830680

The symmetry and coupling properties of solutions in general anisotropic multilayer waveguides.

PubMed

Hernando Quintanilla, F; Lowe, M J S; Craster, R V

2017-01-01

Multilayered plate and shell structures play an important role in many engineering settings where, for instance, coated pipes are commonplace such as in the petrochemical, aerospace, and power generation industries. There are numerous demands, and indeed requirements, on nondestructive evaluation (NDE) to detect defects or to measure material properties using guided waves; to choose the most suitable inspection approach, it is essential to know the properties of the guided wave solutions for any given multilayered system and this requires dispersion curves computed reliably, robustly, and accurately. Here, the circumstances are elucidated, and possible layer combinations, under which guided wave solutions, in multilayered systems composed of generally anisotropic layers in flat and cylindrical geometries, have specific properties of coupling and parity; the partial wave decomposition of the wave field is utilised to unravel the behaviour. A classification into five families is introduced and the authors claim that this is the fundamental way to approach generally anisotropic waveguides. This coupling and parity provides information to be used in the design of more efficient and robust dispersion curve tracing algorithms. A critical benefit is that the analysis enables the separation of solutions into categories for which dispersion curves do not cross; this allows the curves to be calculated simply and without ambiguity.

Experimental Approaches to Microarray Analysis of Tumor Samples

ERIC Educational Resources Information Center

Furge, Laura Lowe; Winter, Michael B.; Meyers, Jacob I.; Furge, Kyle A.

2008-01-01

Comprehensive measurement of gene expression using high-density nucleic acid arrays (i.e. microarrays) has become an important tool for investigating the molecular differences in clinical and research samples. Consequently, inclusion of discussion in biochemistry, molecular biology, or other appropriate courses of microarray technologies has…

Challenges of microarray applications for microbial detection and gene expression profiling in food

USDA-ARS?s Scientific Manuscript database

Microarray technology represents one of the latest advances in molecular biology. The diverse types of microarrays have been applied to clinical and environmental microbiology, microbial ecology, and in human, veterinary, and plant diagnostics. Since multiple genes can be analyzed simultaneously, ...

CEM-designer: design of custom expression microarrays in the post-ENCODE Era.

PubMed

Arnold, Christian; Externbrink, Fabian; Hackermüller, Jörg; Reiche, Kristin

2014-11-10

Microarrays are widely used in gene expression studies, and custom expression microarrays are popular to monitor expression changes of a customer-defined set of genes. However, the complexity of transcriptomes uncovered recently make custom expression microarray design a non-trivial task. Pervasive transcription and alternative processing of transcripts generate a wealth of interweaved transcripts that requires well-considered probe design strategies and is largely neglected in existing approaches. We developed the web server CEM-Designer that facilitates microarray platform independent design of custom expression microarrays for complex transcriptomes. CEM-Designer covers (i) the collection and generation of a set of unique target sequences from different sources and (ii) the selection of a set of sensitive and specific probes that optimally represents the target sequences. Probe design itself is left to third party software to ensure that probes meet provider-specific constraints. CEM-Designer is available at http://designpipeline.bioinf.uni-leipzig.de. Copyright © 2014 Elsevier B.V. All rights reserved.

Multiplex cDNA quantification method that facilitates the standardization of gene expression data

PubMed Central

Gotoh, Osamu; Murakami, Yasufumi; Suyama, Akira

2011-01-01

Microarray-based gene expression measurement is one of the major methods for transcriptome analysis. However, current microarray data are substantially affected by microarray platforms and RNA references because of the microarray method can provide merely the relative amounts of gene expression levels. Therefore, valid comparisons of the microarray data require standardized platforms, internal and/or external controls and complicated normalizations. These requirements impose limitations on the extensive comparison of gene expression data. Here, we report an effective approach to removing the unfavorable limitations by measuring the absolute amounts of gene expression levels on common DNA microarrays. We have developed a multiplex cDNA quantification method called GEP-DEAN (Gene expression profiling by DCN-encoding-based analysis). The method was validated by using chemically synthesized DNA strands of known quantities and cDNA samples prepared from mouse liver, demonstrating that the absolute amounts of cDNA strands were successfully measured with a sensitivity of 18 zmol in a highly multiplexed manner in 7 h. PMID:21415008

Spot detection and image segmentation in DNA microarray data.

PubMed

Qin, Li; Rueda, Luis; Ali, Adnan; Ngom, Alioune

2005-01-01

Following the invention of microarrays in 1994, the development and applications of this technology have grown exponentially. The numerous applications of microarray technology include clinical diagnosis and treatment, drug design and discovery, tumour detection, and environmental health research. One of the key issues in the experimental approaches utilising microarrays is to extract quantitative information from the spots, which represent genes in a given experiment. For this process, the initial stages are important and they influence future steps in the analysis. Identifying the spots and separating the background from the foreground is a fundamental problem in DNA microarray data analysis. In this review, we present an overview of state-of-the-art methods for microarray image segmentation. We discuss the foundations of the circle-shaped approach, adaptive shape segmentation, histogram-based methods and the recently introduced clustering-based techniques. We analytically show that clustering-based techniques are equivalent to the one-dimensional, standard k-means clustering algorithm that utilises the Euclidean distance.

Caryoscope: An Open Source Java application for viewing microarray data in a genomic context

PubMed Central

Awad, Ihab AB; Rees, Christian A; Hernandez-Boussard, Tina; Ball, Catherine A; Sherlock, Gavin

2004-01-01

Background Microarray-based comparative genome hybridization experiments generate data that can be mapped onto the genome. These data are interpreted more easily when represented graphically in a genomic context. Results We have developed Caryoscope, which is an open source Java application for visualizing microarray data from array comparative genome hybridization experiments in a genomic context. Caryoscope can read General Feature Format files (GFF files), as well as comma- and tab-delimited files, that define the genomic positions of the microarray reporters for which data are obtained. The microarray data can be browsed using an interactive, zoomable interface, which helps users identify regions of chromosomal deletion or amplification. The graphical representation of the data can be exported in a number of graphic formats, including publication-quality formats such as PostScript. Conclusion Caryoscope is a useful tool that can aid in the visualization, exploration and interpretation of microarray data in a genomic context. PMID:15488149

Evaluation of a Field-Portable DNA Microarray Platform and Nucleic Acid Amplification Strategies for the Detection of Arboviruses, Arthropods, and Bloodmeals

PubMed Central

Grubaugh, Nathan D.; Petz, Lawrence N.; Melanson, Vanessa R.; McMenamy, Scott S.; Turell, Michael J.; Long, Lewis S.; Pisarcik, Sarah E.; Kengluecha, Ampornpan; Jaichapor, Boonsong; O'Guinn, Monica L.; Lee, John S.

2013-01-01

Highly multiplexed assays, such as microarrays, can benefit arbovirus surveillance by allowing researchers to screen for hundreds of targets at once. We evaluated amplification strategies and the practicality of a portable DNA microarray platform to analyze virus-infected mosquitoes. The prototype microarray design used here targeted the non-structural protein 5, ribosomal RNA, and cytochrome b genes for the detection of flaviviruses, mosquitoes, and bloodmeals, respectively. We identified 13 of 14 flaviviruses from virus inoculated mosquitoes and cultured cells. Additionally, we differentiated between four mosquito genera and eight whole blood samples. The microarray platform was field evaluated in Thailand and successfully identified flaviviruses (Culex flavivirus, dengue-3, and Japanese encephalitis viruses), differentiated between mosquito genera (Aedes, Armigeres, Culex, and Mansonia), and detected mammalian bloodmeals (human and dog). We showed that the microarray platform and amplification strategies described here can be used to discern specific information on a wide variety of viruses and their vectors. PMID:23249687

A molecular beacon microarray based on a quantum dot label for detecting single nucleotide polymorphisms.

PubMed

Guo, Qingsheng; Bai, Zhixiong; Liu, Yuqian; Sun, Qingjiang

2016-03-15

In this work, we report the application of streptavidin-coated quantum dot (strAV-QD) in molecular beacon (MB) microarray assays by using the strAV-QD to label the immobilized MB, avoiding target labeling and meanwhile obviating the use of amplification. The MBs are stem-loop structured oligodeoxynucleotides, modified with a thiol and a biotin at two terminals of the stem. With the strAV-QD labeling an "opened" MB rather than a "closed" MB via streptavidin-biotin reaction, a sensitive and specific detection of label-free target DNA sequence is demonstrated by the MB microarray, with a signal-to-background ratio of 8. The immobilized MBs can be perfectly regenerated, allowing the reuse of the microarray. The MB microarray also is able to detect single nucleotide polymorphisms, exhibiting genotype-dependent fluorescence signals. It is demonstrated that the MB microarray can perform as a 4-to-2 encoder, compressing the genotype information into two outputs. Copyright © 2015 Elsevier B.V. All rights reserved.

MIGS-GPU: Microarray Image Gridding and Segmentation on the GPU.

PubMed

Katsigiannis, Stamos; Zacharia, Eleni; Maroulis, Dimitris

2017-05-01

Complementary DNA (cDNA) microarray is a powerful tool for simultaneously studying the expression level of thousands of genes. Nevertheless, the analysis of microarray images remains an arduous and challenging task due to the poor quality of the images that often suffer from noise, artifacts, and uneven background. In this study, the MIGS-GPU [Microarray Image Gridding and Segmentation on Graphics Processing Unit (GPU)] software for gridding and segmenting microarray images is presented. MIGS-GPU's computations are performed on the GPU by means of the compute unified device architecture (CUDA) in order to achieve fast performance and increase the utilization of available system resources. Evaluation on both real and synthetic cDNA microarray images showed that MIGS-GPU provides better performance than state-of-the-art alternatives, while the proposed GPU implementation achieves significantly lower computational times compared to the respective CPU approaches. Consequently, MIGS-GPU can be an advantageous and useful tool for biomedical laboratories, offering a user-friendly interface that requires minimum input in order to run.

The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements

PubMed Central

2012-01-01

Over the last decade, the introduction of microarray technology has had a profound impact on gene expression research. The publication of studies with dissimilar or altogether contradictory results, obtained using different microarray platforms to analyze identical RNA samples, has raised concerns about the reliability of this technology. The MicroArray Quality Control (MAQC) project was initiated to address these concerns, as well as other performance and data analysis issues. Expression data on four titration pools from two distinct reference RNA samples were generated at multiple test sites using a variety of microarray-based and alternative technology platforms. Here we describe the experimental design and probe mapping efforts behind the MAQC project. We show intraplatform consistency across test sites as well as a high level of interplatform concordance in terms of genes identified as differentially expressed. This study provides a resource that represents an important first step toward establishing a framework for the use of microarrays in clinical and regulatory settings. PMID:16964229

Application of carbohydrate microarray technology for the detection of Burkholderia pseudomallei, Bacillus anthracis and Francisella tularensis antibodies.

PubMed

Parthasarathy, N; Saksena, R; Kováč, P; Deshazer, D; Peacock, S J; Wuthiekanun, V; Heine, H S; Friedlander, A M; Cote, C K; Welkos, S L; Adamovicz, J J; Bavari, S; Waag, D M

2008-11-03

We developed a microarray platform by immobilizing bacterial 'signature' carbohydrates onto epoxide modified glass slides. The carbohydrate microarray platform was probed with sera from non-melioidosis and melioidosis (Burkholderia pseudomallei) individuals. The platform was also probed with sera from rabbits vaccinated with Bacillus anthracis spores and Francisella tularensis bacteria. By employing this microarray platform, we were able to detect and differentiate B. pseudomallei, B. anthracis and F. tularensis antibodies in infected patients, and infected or vaccinated animals. These antibodies were absent in the sera of naïve test subjects. The advantages of the carbohydrate microarray technology over the traditional indirect hemagglutination and microagglutination tests for the serodiagnosis of melioidosis and tularemia are discussed. Furthermore, this array is a multiplex carbohydrate microarray for the detection of all three biothreat bacterial infections including melioidosis, anthrax and tularemia with one, multivalent device. The implication is that this technology could be expanded to include a wide array of infectious and biothreat agents.

Split-plot microarray experiments: issues of design, power and sample size.

PubMed

Tsai, Pi-Wen; Lee, Mei-Ling Ting

2005-01-01

This article focuses on microarray experiments with two or more factors in which treatment combinations of the factors corresponding to the samples paired together onto arrays are not completely random. A main effect of one (or more) factor(s) is confounded with arrays (the experimental blocks). This is called a split-plot microarray experiment. We utilise an analysis of variance (ANOVA) model to assess differentially expressed genes for between-array and within-array comparisons that are generic under a split-plot microarray experiment. Instead of standard t- or F-test statistics that rely on mean square errors of the ANOVA model, we use a robust method, referred to as 'a pooled percentile estimator', to identify genes that are differentially expressed across different treatment conditions. We illustrate the design and analysis of split-plot microarray experiments based on a case application described by Jin et al. A brief discussion of power and sample size for split-plot microarray experiments is also presented.

Women's experiences receiving abnormal prenatal chromosomal microarray testing results.

PubMed

Bernhardt, Barbara A; Soucier, Danielle; Hanson, Karen; Savage, Melissa S; Jackson, Laird; Wapner, Ronald J

2013-02-01

Genomic microarrays can detect copy-number variants not detectable by conventional cytogenetics. This technology is diffusing rapidly into prenatal settings even though the clinical implications of many copy-number variants are currently unknown. We conducted a qualitative pilot study to explore the experiences of women receiving abnormal results from prenatal microarray testing performed in a research setting. Participants were a subset of women participating in a multicenter prospective study "Prenatal Cytogenetic Diagnosis by Array-based Copy Number Analysis." Telephone interviews were conducted with 23 women receiving abnormal prenatal microarray results. We found that five key elements dominated the experiences of women who had received abnormal prenatal microarray results: an offer too good to pass up, blindsided by the results, uncertainty and unquantifiable risks, need for support, and toxic knowledge. As prenatal microarray testing is increasingly used, uncertain findings will be common, resulting in greater need for careful pre- and posttest counseling, and more education of and resources for providers so they can adequately support the women who are undergoing testing.

Fuzzy support vector machine: an efficient rule-based classification technique for microarrays.

PubMed

Hajiloo, Mohsen; Rabiee, Hamid R; Anooshahpour, Mahdi

2013-01-01

The abundance of gene expression microarray data has led to the development of machine learning algorithms applicable for tackling disease diagnosis, disease prognosis, and treatment selection problems. However, these algorithms often produce classifiers with weaknesses in terms of accuracy, robustness, and interpretability. This paper introduces fuzzy support vector machine which is a learning algorithm based on combination of fuzzy classifiers and kernel machines for microarray classification. Experimental results on public leukemia, prostate, and colon cancer datasets show that fuzzy support vector machine applied in combination with filter or wrapper feature selection methods develops a robust model with higher accuracy than the conventional microarray classification models such as support vector machine, artificial neural network, decision trees, k nearest neighbors, and diagonal linear discriminant analysis. Furthermore, the interpretable rule-base inferred from fuzzy support vector machine helps extracting biological knowledge from microarray data. Fuzzy support vector machine as a new classification model with high generalization power, robustness, and good interpretability seems to be a promising tool for gene expression microarray classification.

Phonon properties of lutetium pnictides

NASA Astrophysics Data System (ADS)

Arya, Balwant Singh; Aynyas, Mahendra; Sanyal, Sankar P.

2018-05-01

Phonon properties of Lutetium pnictides (LuX : X = P, As) have been studied by using breathing shell model (BSM) which includes breathing motion of electrons of the Lu atoms due to f-d hybridization to establish their predominant ionic nature. The calculated phonon dispersion curves of these compounds are presented follow the same trend as observed in ytterbium pnictides (YbP and YbAs). We also report one phonon density of states and specific heat for these compounds. We discuss the significance of this approach in predicting the phonon dispersion curves and examine the role of electron-phonon interaction.

Shaping the relation between the mass of supermassive black holes and the velocity dispersion of galactic bulges

NASA Astrophysics Data System (ADS)

Chan, M. H.

2013-05-01

I use the fact that the radiation emitted by the accretion disk of supermassive black hole can heat up the surrounding gas in the protogalaxy to achieve hydrostatic equilibrium during the galaxy formation. The correlation between the black hole mass M BH and velocity dispersion σ thus naturally arises. The result generally agrees with empirical fittings from observational data, even with M BH ≤106 M ⊙. This model provides a clear picture on how the properties of the galactic supermassive black holes are connected with the kinetic properties of the galactic bulges.

Effects of different processing techniques on multi-walled carbon nanotubes/silicone rubber nanocomposite on tensile strength properties

NASA Astrophysics Data System (ADS)

Mazlan, N.; Jaafar, M.; Aziz, A.; Ismail, H.; Busfield, J. J. C.

2016-10-01

In this work, two different processing techniques were approached to identify the properties of the multi-walled carbon nanotubes (MWCNT) reinforced polydimethylsiloxane (PDMS). The MWCNT was dispersed in the polymer by using the ultrasonic and twin screw extruder mixer. The final composite showed different manner of dispersed tubes in the silicone rubber matrix. High shear twin screw extruder tends to fragment the tubes during processing compound, which can be observed by scanning electron microscope (SEM). Tensile strength of the extrusion MWCNT/PDMS nanocomposites was found to be higher compared to ultrasonic MWCNT/PDMS nanocomposites.

Crystals for astronomical X-ray spectroscopy

NASA Technical Reports Server (NTRS)

Burek, A.

1976-01-01

Crystal spectrometric properties and the factors that affect their measurement are discussed. Theoretical and experimental results on KAP are summarized and theoretical results based on the dynamical theory of X-ray diffraction are given for the acid phthalates as well as for the commonly used planes of ADP, PET and EDDT. Anomalous dispersion is found to be important for understanding the details of crystal Bragg reflection properties at long X-ray wavelengths and some important effects are pointed out. The theory of anomalous dispersion is applied to explain the anomalous reflectivity exhibited by KAP at 23.3 A.

Nonaqueous slip casting of YBa2Cu3O(7-x) superconductive ceramics. Ph.D. Thesis - 1993

NASA Technical Reports Server (NTRS)

Hooker, Matthew W.; Taylor, Theodore D.

1994-01-01

This study investigates the slip casting of YBa2Cu3O(7-x) powders using nonaqueous carrier liquids and fired ceramic molds. The parameters of the process examined here include the rheological properties of YBa2Cu3O(7-x) powder dispersed in various solvent/dispersant systems, the combination of nonaqueous slips with fired ceramic molds to form the superconductive ceramics, the process-property relationships using a four-factor factorial experiment, and the applicability of magnetic fields to align the YBa2Cu3O(7-x) grains during the casting process.

Generation of shrimp waste-based dispersant for oil spill response.

PubMed

Zhang, Kedong; Zhang, Baiyu; Song, Xing; Liu, Bo; Jing, Liang; Chen, Bing

2018-04-01

In this study, shrimp waste was enzymatically hydrolyzed to generate a green dispersant and the product was tested for crude oil dispersion in seawater. The hydrolysis process was first optimized based on the dispersant effectiveness (DE) of the product. The functional properties of the product were identified including stability, critical micelle concentration, and emulsification activity. Water was confirmed as a good solvent for dispersant generation when compared with three chemical solvents. The effects of salinity, mixing energy, and temperature on the dispersion of the Alaska North Slope (ANS) crude oil were examined. Microtox acute toxicity test was also conducted to evaluate the toxicity of the produced dispersant. In addition, DE of the product on three different types of crude oil, including ANS crude oil, Prudhoe Bay crude oil (PBC), and Arabian Light crude oil (ALC) was compared with that of the Corexit 9500, respectively. The research output could lead to a promising green solution to the oil spill problem and might result in many other environmental applications.

Solution aging and degradation of a transparent conducting polymer dispersion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Jun; Jacobs, Ian E.; Friedrich, Stephan

As organic electronics improve, there is increased research interest on the longevity and stability of both the device and individual material components. Most of these studies focus on post deposition degradation and aging of the film. In this article, we examine the stability of polyelectrolyte dispersions before film coating. We observe substantial differences in the solution properties of the transparent conducting polymer, S-P3MEET, when comparing fresh versus aged dispersions and relate these solution differences to film properties. The aged dispersion contains large agglomerates and exhibits a typical shear-thinning rheological behavior, which results in non-uniformity of the spin-coated films. Near edgemore » X-ray absorption fine structure measurements were used to differentiate the changes in bonding and oxidation states and show that aged S-P3MEET is more highly self-doped than fresh S-P3MEET. We also show that addition of acid, salt or heat to fresh S-P3MEET can accelerate the degradation/aging process but are subjected to different mechanisms. Conductivity measurements of S-P3MEET films illustrate that there is a tradeoff between increased work function and decreased conductivity upon perfluorinated ionomer (PFI) loading. The formation of nanostructure in solution is also correlated to film morphology variations obtained from atomic force microscopy. Here, we expect that dispersion aging is a process that commonly exists in most solution-dispersed polyelectrolyte materials and that the methodologies presented in this paper might be beneficial to future degradation/stability studies.« less

Influence of gamma ray irradiation and annealing temperature on the optical constants and spectral dispersion parameters of metal-free and zinc tetraphenylporphyrin thin films: A comparative study.

PubMed

Zeyada, H M; Makhlouf, M M; El-Nahass, M M

2015-09-05

In this work, we report on the effect of γ-ray irradiation and annealing temperature on the optical properties of metal-free tetraphenylporphyrin, H2TPP, and zinc tetraphenylporphyrin, ZnTPP, thin films. Thin films of H2TPP and ZnTPP were successfully prepared by the thermal evaporation technique. The optical properties of H2TPP and ZnTPP films were investigated using spectrophotometric measurements of the transmittance and reflectance at normal incidence of light in the wavelength range from 200 to 2500 nm. The absorption spectra of H2TPP showed four absorption bands, namely the Q, B, N and M bands. The effect of inserting Zn atom into the cavity of porphyrin macrocycle in ZnTPP molecule distorted the Q and B bands, reduced the width of absorption region and influenced the optical constants and dispersion parameters. In all conditions, the type of electron transition is indirect allowed transition. Anomalous dispersion is observed in the absorption region but normal dispersion occurs in the transparent region of spectra. We adopted multi-oscillator model and the single oscillator model to interpret the anomalous and normal dispersion, respectively. We have found that the annealing temperature has mostly the opposite effect of γ-ray irradiation on absorption and dispersion characteristics of these films. Copyright © 2015 Elsevier B.V. All rights reserved.

Optimization of nanolime solvent for the consolidation of coarse porous limestone

NASA Astrophysics Data System (ADS)

Borsoi, Giovanni; Lubelli, Barbara; van Hees, Rob; Veiga, Rosário; Silva, António Santos

2016-09-01

The potentialities of nanomaterials for application in the field of conservation have been widely investigated in the last two decades. Among nanomaterials, nanolimes, i.e., dispersions of lime nanoparticles in alcohols are promising consolidating products for calcareous materials. Nanolimes are effective in recovering the very superficial loss of cohesion of decayed materials, but they do not always provide sufficient mass consolidation. This limitation is mainly related to the deposition of the nanoparticles nearby the surface of the material. Experimental research has been set up with the aim of improving the in-depth deposition of lime nanoparticles. Previous research by the authors has shown that nanolime deposition within a substrate can be controlled by adapting the nanolimes properties (kinetic stability and evaporation rate) to the moisture transport behavior of the substrate. Nanolime properties can be modified by the use of different solvents. In this research, nanolime dispersions have been further optimized for application on Maastricht limestone, a coarse porous limestone. Firstly, nanolimes were synthesized and dispersed in ethanol and/or water, both pure and mixed in different percentages. Subsequently, based on the kinetic stability of the nanolime dispersions, the most promising solvent mixtures were selected and applied on the limestone. The deposition of lime nanoparticles within the limestone was studied by phenolphthalein test, optical microscopy and scanning electron microscopy. The results confirm that nanolime dispersed in a mixture of ethanol (95 %) and water (5 %) can guarantee a better nanoparticles in-depth deposition within coarse porous substrates, when compared to dispersions in pure ethanol.

Solution aging and degradation of a transparent conducting polymer dispersion

DOE PAGES

Li, Jun; Jacobs, Ian E.; Friedrich, Stephan; ...

2016-04-23

As organic electronics improve, there is increased research interest on the longevity and stability of both the device and individual material components. Most of these studies focus on post deposition degradation and aging of the film. In this article, we examine the stability of polyelectrolyte dispersions before film coating. We observe substantial differences in the solution properties of the transparent conducting polymer, S-P3MEET, when comparing fresh versus aged dispersions and relate these solution differences to film properties. The aged dispersion contains large agglomerates and exhibits a typical shear-thinning rheological behavior, which results in non-uniformity of the spin-coated films. Near edgemore » X-ray absorption fine structure measurements were used to differentiate the changes in bonding and oxidation states and show that aged S-P3MEET is more highly self-doped than fresh S-P3MEET. We also show that addition of acid, salt or heat to fresh S-P3MEET can accelerate the degradation/aging process but are subjected to different mechanisms. Conductivity measurements of S-P3MEET films illustrate that there is a tradeoff between increased work function and decreased conductivity upon perfluorinated ionomer (PFI) loading. The formation of nanostructure in solution is also correlated to film morphology variations obtained from atomic force microscopy. Here, we expect that dispersion aging is a process that commonly exists in most solution-dispersed polyelectrolyte materials and that the methodologies presented in this paper might be beneficial to future degradation/stability studies.« less

Coptis chinensis Franch. exhibits neuroprotective properties against oxidative stress in human neuroblastoma cells.

PubMed

Friedemann, Thomas; Otto, Benjamin; Klätschke, Kristin; Schumacher, Udo; Tao, Yi; Leung, Alexander Kai-Man; Efferth, Thomas; Schröder, Sven

2014-08-08

The dried rhizome of Coptis chinensis Franch. (family Ranunculaceae) is traditionally used in Chinese medicine for the treatment of inflammatory diseases and diabetes. Recent studies showed a variety of activities of Coptis chinensis Franch. alkaloids, including neuroprotective, neuroregenerative, anti-diabetic, anti-oxidative and anti-inflammatory effects. However, there is no report on the neuroprotective effect of Coptis chinensis Franch. watery extract against tert-butylhydroperoxide (t-BOOH) induced oxidative damage. The aim of the study is to investigate neuroprotective properties of Coptis chinensis Franch. rhizome watery extract (CRE) and to evaluate its potential mechanism of action. Neuroprotective properties on t-BOOH induced oxidative stress were investigated in SH-SY5Y human neuroblastoma cells. Cells were pretreated with CRE for 2 h or 24 h followed by 2 h of treatment with t-BOOH. To evaluate the neuroprotective effect of CRE, cell viability, cellular reactive oxygen species (ROS), mitochondrial membrane potential (MMP) and the apoptotic rate were determined and microarray analyses, as well as qRT-PCR analyses were conducted. Two hours of exposure to 100 µM t-BOOH resulted in a significant reduction of cell viability, increased apoptotic rate, declined mitochondrial membrane potential (MMP) and increased ROS production. Reduction of cell viability, increased apoptotic rate and declined mitochondrial membrane potential (MMP) could be significantly reduced in cells pretreated with CRE (100 µg/ml) for 2h or 24h ahead of t-BOOH exposure with the greatest effect after 24h of pretreatment; however ROS production was not changed significantly. Furthermore, microarray analyses revealed that the expressions of 2 genes; thioredoxin-interacting protein (TXNIP) and mitochondrially encoded NADH dehydrogenase 1, were significantly regulated. Down regulation of TXNIP was confirmed by qRT-PCR. Due to its neuroprotective properties CRE might be a potential therapeutic agent for the prevention or amelioration of diseases like diabetic neuropathy and neurodegenerative disorders like Alzheimer and Parkinsons disease. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Mapping the affinity landscape of Thrombin-binding aptamers on 2΄F-ANA/DNA chimeric G-Quadruplex microarrays

PubMed Central

Abou Assi, Hala; Gómez-Pinto, Irene; González, Carlos

2017-01-01

Abstract In situ fabricated nucleic acids microarrays are versatile and very high-throughput platforms for aptamer optimization and discovery, but the chemical space that can be probed against a given target has largely been confined to DNA, while RNA and non-natural nucleic acid microarrays are still an essentially uncharted territory. 2΄-Fluoroarabinonucleic acid (2΄F-ANA) is a prime candidate for such use in microarrays. Indeed, 2΄F-ANA chemistry is readily amenable to photolithographic microarray synthesis and its potential in high affinity aptamers has been recently discovered. We thus synthesized the first microarrays containing 2΄F-ANA and 2΄F-ANA/DNA chimeric sequences to fully map the binding affinity landscape of the TBA1 thrombin-binding G-quadruplex aptamer containing all 32 768 possible DNA-to-2΄F-ANA mutations. The resulting microarray was screened against thrombin to identify a series of promising 2΄F-ANA-modified aptamer candidates with Kds significantly lower than that of the unmodified control and which were found to adopt highly stable, antiparallel-folded G-quadruplex structures. The solution structure of the TBA1 aptamer modified with 2΄F-ANA at position T3 shows that fluorine substitution preorganizes the dinucleotide loop into the proper conformation for interaction with thrombin. Overall, our work strengthens the potential of 2΄F-ANA in aptamer research and further expands non-genomic applications of nucleic acids microarrays. PMID:28100695

Development of a rapid microarray-based DNA subtyping assay for the alleles of Shiga toxins 1 and 2 of Escherichia coli.

PubMed

Geue, Lutz; Stieber, Bettina; Monecke, Stefan; Engelmann, Ines; Gunzer, Florian; Slickers, Peter; Braun, Sascha D; Ehricht, Ralf

2014-08-01

In this study, we developed a new rapid, economic, and automated microarray-based genotyping test for the standardized subtyping of Shiga toxins 1 and 2 of Escherichia coli. The microarrays from Alere Technologies can be used in two different formats, the ArrayTube and the ArrayStrip (which enables high-throughput testing in a 96-well format). One microarray chip harbors all the gene sequences necessary to distinguish between all Stx subtypes, facilitating the identification of single and multiple subtypes within a single isolate in one experiment. Specific software was developed to automatically analyze all data obtained from the microarray. The assay was validated with 21 Shiga toxin-producing E. coli (STEC) reference strains that were previously tested by the complete set of conventional subtyping PCRs. The microarray results showed 100% concordance with the PCR results. Essentially identical results were detected when the standard DNA extraction method was replaced by a time-saving heat lysis protocol. For further validation of the microarray, we identified the Stx subtypes or combinations of the subtypes in 446 STEC field isolates of human and animal origin. In summary, this oligonucleotide array represents an excellent diagnostic tool that provides some advantages over standard PCR-based subtyping. The number of the spotted probes on the microarrays can be increased by additional probes, such as for novel alleles, species markers, or resistance genes, should the need arise. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements

EPA Science Inventory

Over the last decade, the introduction of microarray technology has had a profound impact on gene expression research. The publication of studies with dissimilar or altogether contradictory results, obtained using different microarray platforms to analyze identical RNA samples, ...

Corresponding-states behavior of a dipolar model fluid with variable dispersion interactions and its relevance to the anomalies of hydrogen fluoride

NASA Astrophysics Data System (ADS)

Weiss, Volker C.; Leroy, Frédéric

2016-06-01

More than two decades ago, the elusiveness of a liquid-vapor equilibrium and a corresponding critical point in simulations of the supposedly simple model of dipolar hard spheres came as a surprise to many liquid matter theorists. van Leeuwen and Smit [Phys. Rev. Lett. 71, 3991 (1993)] showed that a minimum of attractive dispersion interactions among the dipolar particles may be needed to observe regular fluid behavior. Here, we adopt their approach and use an only slightly modified model, in which the original point dipole is replaced by a dipole moment produced by charges that are separated in space, to study the influence of dispersion interactions of variable strength on the coexistence and interfacial properties of a polar fluid. The thermophysical properties are discussed in terms of Guggenheim's corresponding-states approach. In this way, the coexistence curve, the critical compressibility factor, the surface tension, Guggenheim's ratio, and modifications of Guldberg's and Trouton's rules (related to the vapor pressure and the enthalpy of vaporization) are analyzed. As the importance of dispersion is decreased, a crossover from simple-fluid behavior to that characteristic of strongly dipolar systems takes place; for some properties, this transition is monotonic, but for others it occurs non-monotonically. For strongly dipolar systems, the reduced surface tension is very low, whereas Guggenheim's ratio and Guldberg's ratio are found to be high. The critical compressibility factor is smaller, and the coexistence curve is wider and more skewed than for simple fluids. For very weak dispersion, liquid-vapor equilibrium is still observable, but the interfacial tension is extremely low and may, eventually, vanish marking the end of the existence of a liquid phase. We discuss the implications of our findings for real fluids, in particular, for hydrogen fluoride.

Investigation of a novel approach for the cross-linking characterization of SU-8 photoresist materials by means of optical dispersion measurements

NASA Astrophysics Data System (ADS)

Taudt, Ch.; Baselt, T.; Koch, E.; Hartmann, P.

2014-03-01

The increase in efficiency and precision in the production of semiconductor structures under the use of polymeric materials like SU-8 is crucial in securing the technological innovation within this industry. The manufacturing of structures on wafers demands a high quality of materials, tools and production processes. In particular, deviations in the materials' parameters (e.g. cross-linking state, density or mechanical properties) could lead to subsequent problems such as a reduced lifetime of structures and systems. In particular problems during the soft and post-exposure bake process can lead to an inhomogeneous distribution of material properties. This paper describes a novel approach for the characterization of SU-8 material properties in relation to a second epoxy-based material of different cross-linking by the measurement of optical dispersion within the material. A white-light interferometer was used. In particular the setup consisted of a white-light source, a Michelson-type interferometer and a spectrometer. The investigation of the dispersion characteristics was carried out by the detection of the equalization wavelength for different positions of the reference arm in a range from 400 to 900 nm. The measured time delay due to dispersion ranges from 850 to 1050 ps/m. For evaluation purposes a 200μm SU-8 sample was characterized in the described setup regarding its dispersion characteristics in relation to bulk epoxy material. The novel measurement approach allowed a fast and high-resolution material characterization for SU-8 micro structures which was suitable for integration in production lines. The outlook takes modifications of the experimental setup regarding on-wafer measurements into account.

Quantum Drude oscillator model of atoms and molecules: Many-body polarization and dispersion interactions for atomistic simulation

NASA Astrophysics Data System (ADS)

Jones, Andrew P.; Crain, Jason; Sokhan, Vlad P.; Whitfield, Troy W.; Martyna, Glenn J.

2013-04-01

Treating both many-body polarization and dispersion interactions is now recognized as a key element in achieving the level of atomistic modeling required to reveal novel physics in complex systems. The quantum Drude oscillator (QDO), a Gaussian-based, coarse grained electronic structure model, captures both many-body polarization and dispersion and has linear scale computational complexity with system size, hence it is a leading candidate next-generation simulation method. Here, we investigate the extent to which the QDO treatment reproduces the desired long-range atomic and molecular properties. We present closed form expressions for leading order polarizabilities and dispersion coefficients and derive invariant (parameter-free) scaling relationships among multipole polarizability and many-body dispersion coefficients that arise due to the Gaussian nature of the model. We show that these “combining rules” hold to within a few percent for noble gas atoms, alkali metals, and simple (first-row hydride) molecules such as water; this is consistent with the surprising success that models with underlying Gaussian statistics often exhibit in physics. We present a diagrammatic Jastrow-type perturbation theory tailored to the QDO model that serves to illustrate the rich types of responses that the QDO approach engenders. QDO models for neon, argon, krypton, and xenon, designed to reproduce gas phase properties, are constructed and their condensed phase properties explored via linear scale diffusion Monte Carlo (DMC) and path integral molecular dynamics (PIMD) simulations. Good agreement with experimental data for structure, cohesive energy, and bulk modulus is found, demonstrating a degree of transferability that cannot be achieved using current empirical models or fully ab initio descriptions.

Optical properties of an inhomogeneously broadened ΛV-system with multiple excited states

NASA Astrophysics Data System (ADS)

Kaur, Paramjit; Bharti, Vineet; Wasan, Ajay

2014-09-01

We present a theoretical model using a density matrix approach to show the influence of multiple excited states on the optical properties of an inhomogeneously broadened ?V-system of the ?Rb D2 line. These closely spaced multiple excited states cause asymmetry in absorption and dispersion profiles. We observe the reduced absorption profiles, due to dressed state interactions of the applied electromagnetic fields, which results the Mollow sideband-like transparency windows. In a room temperature vapor, we obtain a narrow enhanced absorption and steep positive dispersion at the line center when the strengths of control and pump fields are equal. Here, we show how the probe transmittance varies when it passes through the atomic medium. We also discuss the transient behavior of our system which agrees well with the corresponding absorption and dispersion profiles. This study has potential applications in controllability of group velocity, and for optical and quantum information processing.

Effect of Graphite Nanoplate Morphology on the Dispersion and Physical Properties of Polycarbonate Based Composites.

PubMed

Müller, Michael Thomas; Hilarius, Konrad; Liebscher, Marco; Lellinger, Dirk; Alig, Ingo; Pötschke, Petra

2017-05-18

The influence of the morphology of industrial graphite nanoplate (GNP) materials on their dispersion in polycarbonate (PC) is studied. Three GNP morphology types were identified, namely lamellar, fragmented or compact structure. The dispersion evolution of all GNP types in PC is similar with varying melt temperature, screw speed, or mixing time during melt mixing. Increased shear stress reduces the size of GNP primary structures, whereby the GNP aspect ratio decreases. A significant GNP exfoliation to individual or few graphene layers could not be achieved under the selected melt mixing conditions. The resulting GNP macrodispersion depends on the individual GNP morphology, particle sizes and bulk density and is clearly reflected in the composite's electrical, thermal, mechanical, and gas barrier properties. Based on a comparison with carbon nanotubes (CNT) and carbon black (CB), CNT are recommended in regard to electrical conductivity, whereas, for thermal conductive or gas barrier application, GNP is preferred.

Nano-Disperse Borides and Carbides: Plasma Technology Production, Specific Properties, Economic Evaluation

NASA Astrophysics Data System (ADS)

Galevskii, G. V.; Rudneva, V. V.; Galevskii, S. G.; Tomas, K. I.; Zubkov, M. S.

2016-04-01

The experience of production and study on properties of nano-disperse chromium and titanium borides and carbides, and silicon carbide has been generalized. The structure and special service aspects of utilized plasma-metallurgical complex equipped with a three-jet direct-flow reactor with a capacity of 150 kW have been outlined. Processing, heat engineering and service life characteristics of the reactor are specified. The synthesis parameters of borides and carbides, as well as their basic characteristics in nano-disperse condition and their production flow diagram are outlined. Engineering and economic performance of synthesizing borides in laboratory and industrial conditions is assessed, and the respective segment of the international market as well. The work is performed at State Siberian Industrial University as a project part of the State Order of Ministry of Science and Education of the Russian Federation No. 11.1531/2014/K.

Reinforcement of natural rubber latex by nanosize montmorillonite clay

NASA Astrophysics Data System (ADS)

Tantatherdtam, Rattana

Based on the unique character of montmorillonite namely its layer structure and the ability of silicate particles to separate into nanometer-size platelets, natural rubber (polyisoprene)/clay composites were obtained by mixing rubber latex with clay-water dispersion and coagulating the mixture. The resulting film had greatly improved mechanical properties compared with films using micron-sized fillers. Further, both modulus and toughness were improved; in many composite system an improvement in modulus leads to a loss of toughness. X-ray diffraction results indicated that clay platelets dispersed in the rubber matrix on the nanoscale level with some macromolecules intercalated into the clay gallery. The observed considerable improvement in mechanical properties, coupled with a theoretical model of composite modulus suggests a dispersed structure of clay in the composite. While not all clay particles are exfoliated, data suggest that a reasonable fraction of exfoliated materials is required to explain the experimental results.

Considerations for spectroscopy of liquid-exfoliated 2D materials: emerging photoluminescence of N-methyl-2-pyrrolidone.

PubMed

Ogilvie, Sean P; Large, Matthew J; Fratta, Giuseppe; Meloni, Manuela; Canton-Vitoria, Ruben; Tagmatarchis, Nikos; Massuyeau, Florian; Ewels, Christopher P; King, Alice A K; Dalton, Alan B

2017-12-01

N-methyl-2-pyrrolidone (NMP) has been shown to be the most effective solvent for liquid phase exfoliation and dispersion of a range of 2D materials including graphene, molybdenum disulphide (MoS 2 ) and black phosphorus. However, NMP is also known to be susceptible to sonochemical degradation during exfoliation. We report that this degradation gives rise to strong visible photoluminescence of NMP. Sonochemical modification is shown to influence exfoliation of layered materials in NMP and the optical absorbance of the solvent in the dispersion. The emerging optical properties of the degraded solvent present challenges for spectroscopy of nanomaterial dispersions; most notably the possibility of observing solvent photoluminescence in the spectra of 2D materials such as MoS 2 , highlighting the need for stable solvents and exfoliation processes to minimise the influence of solvent degradation on the properties of liquid-exfoliated 2D materials.

Highly birefringent elliptical core photonic crystal fiber for terahertz application

NASA Astrophysics Data System (ADS)

Sultana, Jakeya; Islam, Md. Saiful; Faisal, Mohammad; Islam, Mohammad Rakibul; Ng, Brian W.-H.; Ebendorff-Heidepriem, Heike; Abbott, Derek

2018-01-01

We present a novel strategy for designing a highly birefringent photonic crystal fiber (PCF) with near zero flattened dispersion properties by applying elliptical air holes in the core area. The elliptical structure of the air holes in the porous-core region introduces asymmetry between x and y polarization modes, which consequently offers ultra-high birefringence. Also the compact geometry of the conventional hexagonal structure in the cladding confines most of the useful power. The optical properties including birefringence, dispersion, confinement loss, effective material loss (EML) and single modeness of the fiber are investigated using a full-vector finite element method. Simulation results show an ultra-high birefringence of 0 . 086 ultra-flattened near zero dispersion of 0 . 53 ± 0 . 07 ps/THz/cm in a broad frequency range. The practical implementation of the proposed fiber is feasible using existing fabrication technology and is applicable to the areas of terahertz sensing and polarization maintaining systems.

Linear dispersion properties of ring velocity distribution functions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vandas, Marek, E-mail: marek.vandas@asu.cas.cz; Hellinger, Petr; Institute of Atmospheric Physics, AS CR, Bocni II/1401, CZ-14100 Prague

2015-06-15

Linear properties of ring velocity distribution functions are investigated. The dispersion tensor in a form similar to the case of a Maxwellian distribution function, but for a general distribution function separable in velocities, is presented. Analytical forms of the dispersion tensor are derived for two cases of ring velocity distribution functions: one obtained from physical arguments and one for the usual, ad hoc ring distribution. The analytical expressions involve generalized hypergeometric, Kampé de Fériet functions of two arguments. For a set of plasma parameters, the two ring distribution functions are compared. At the parallel propagation with respect to the ambientmore » magnetic field, the two ring distributions give the same results identical to the corresponding bi-Maxwellian distribution. At oblique propagation, the two ring distributions give similar results only for strong instabilities, whereas for weak growth rates their predictions are significantly different; the two ring distributions have different marginal stability conditions.« less

Surface plasmon oscillations in a semi-bounded semiconductor plasma

NASA Astrophysics Data System (ADS)

M, SHAHMANSOURI; A, P. MISRA

2018-02-01

We study the dispersion properties of surface plasmon (SP) oscillations in a semi-bounded semiconductor plasma with the effects of the Coulomb exchange (CE) force associated with the spin polarization of electrons and holes as well as the effects of the Fermi degenerate pressure and the quantum Bohm potential. Starting from a quantum hydrodynamic model coupled to the Poisson equation, we derive the general dispersion relation for surface plasma waves. Previous results in this context are recovered. The dispersion properties of the surface waves are analyzed in some particular cases of interest and the relative influence of the quantum forces on these waves are also studied for a nano-sized GaAs semiconductor plasma. It is found that the CE effects significantly modify the behaviors of the SP waves. The present results are applicable to understand the propagation characteristics of surface waves in solid density plasmas.

Electronic properties of two inequivalent surfaces in MoTe2 studied by quasi-particle interference

NASA Astrophysics Data System (ADS)

Iaia, Davide; Shichao, Yan; Madhavan, Vidya

MoTe2 has received renewed interest due to its topological properties. At a temperature below 250 K, MoTe2 is a type II Weyl semimetal hosting three-dimensional (3D) linearly dispersing states with well defined chirality. Nodes in this 3D dispersion are called Weyl points. Weyl points of opposite chirality are expected to be connected by topologically protected Fermi arcs. In this talk we discuss low temperature scanning tunneling microscopy studies of the electronic structure of MoTe2. The electronic properties are studied using quasi-particle interference technique which allows us to resolve Fermi arcs features and to clearly distinguish between two inequivalent MoTe2 surfaces. Our results provide important contributions to further our understanding of the electronic properties of this new and exotic class of materials. National Science Foundation (NSF).

Mechanical Properties of Graphene Nanoplatelet/Carbon Fiber/Epoxy Hybrid Composites: Multiscale Modeling and Experiments

NASA Technical Reports Server (NTRS)

Hadden, C. M.; Klimek-McDonald, D. R.; Pineda, E. J.; King, J. A.; Reichanadter, A. M.; Miskioglu, I.; Gowtham, S.; Odegard, G. M.

2015-01-01

Because of the relatively high specific mechanical properties of carbon fiber/epoxy composite materials, they are often used as structural components in aerospace applications. Graphene nanoplatelets (GNPs) can be added to the epoxy matrix to improve the overall mechanical properties of the composite. The resulting GNP/carbon fiber/epoxy hybrid composites have been studied using multiscale modeling to determine the influence of GNP volume fraction, epoxy crosslink density, and GNP dispersion on the mechanical performance. The hierarchical multiscale modeling approach developed herein includes Molecular Dynamics (MD) and micromechanical modeling, and it is validated with experimental testing of the same hybrid composite material system. The results indicate that the multiscale modeling approach is accurate and provides physical insight into the composite mechanical behavior. Also, the results quantify the substantial impact of GNP volume fraction and dispersion on the transverse mechanical properties of the hybrid composite while the effect on the axial properties is shown to be insignificant.

Mechanical Properties of Graphene Nanoplatelet/Carbon Fiber/Epoxy Hybrid Composites: Multiscale Modeling and Experiments

NASA Technical Reports Server (NTRS)

Hadden, C. M.; Klimek-McDonald, D. R.; Pineda, E. J.; King, J. A.; Reichanadter, A. M.; Miskioglu, I.; Gowtham, S.; Odegard, G. M.

2015-01-01

Because of the relatively high specific mechanical properties of carbon fiber/epoxy composite materials, they are often used as structural components in aerospace applications. Graphene nanoplatelets (GNPs) can be added to the epoxy matrix to improve the overall mechanical properties of the composite. The resulting GNP/carbon fiber/epoxy hybrid composites have been studied using multiscale modeling to determine the influence of GNP volume fraction, epoxy crosslink density, and GNP dispersion on the mechanical performance. The hierarchical multiscale modeling approach developed herein includes Molecular Dynamics (MD) and micromechanical modeling, and it is validated with experimental testing of the same hybrid composite material system. The results indicate that the multiscale modeling approach is accurate and provides physical insight into the composite mechanical behavior. Also, the results quantify the substantial impact of GNP volume fraction and dispersion on the transverse mechanical properties of the hybrid composite, while the effect on the axial properties is shown to be insignificant.

Mechanical Properties of Graphene Nanoplatelet Carbon Fiber Epoxy Hybrid Composites: Multiscale Modeling and Experiments

NASA Technical Reports Server (NTRS)

Hadden, Cameron M.; Klimek-McDonald, Danielle R.; Pineda, Evan J.; King, Julie A.; Reichanadter, Alex M.; Miskioglu, Ibrahim; Gowtham, S.; Odegard, Gregory M.

2015-01-01

Because of the relatively high specific mechanical properties of carbon fiber/epoxy composite materials, they are often used as structural components in aerospace applications. Graphene nanoplatelets (GNPs) can be added to the epoxy matrix to improve the overall mechanical properties of the composite. The resulting GNP/carbon fiber/epoxy hybrid composites have been studied using multiscale modeling to determine the influence of GNP volume fraction, epoxy crosslink density, and GNP dispersion on the mechanical performance. The hierarchical multiscale modeling approach developed herein includes Molecular Dynamics (MD) and micromechanical modeling, and it is validated with experimental testing of the same hybrid composite material system. The results indicate that the multiscale modeling approach is accurate and provides physical insight into the composite mechanical behavior. Also, the results quantify the substantial impact of GNP volume fraction and dispersion on the transverse mechanical properties of the hybrid composite, while the effect on the axial properties is shown to be insignificant.

Substructure Versus Property-Level Dispersed Modes Calculation

NASA Technical Reports Server (NTRS)

Stewart, Eric C.; Peck, Jeff A.; Bush, T. Jason; Fulcher, Clay W.

2016-01-01

This paper calculates the effect of perturbed finite element mass and stiffness values on the eigenvectors and eigenvalues of the finite element model. The structure is perturbed in two ways: at the "subelement" level and at the material property level. In the subelement eigenvalue uncertainty analysis the mass and stiffness of each subelement is perturbed by a factor before being assembled into the global matrices. In the property-level eigenvalue uncertainty analysis all material density and stiffness parameters of the structure are perturbed modified prior to the eigenvalue analysis. The eigenvalue and eigenvector dispersions of each analysis (subelement and property-level) are also calculated using an analytical sensitivity approximation. Two structural models are used to compare these methods: a cantilevered beam model, and a model of the Space Launch System. For each structural model it is shown how well the analytical sensitivity modes approximate the exact modes when the uncertainties are applied at the subelement level and at the property level.

Whey protein isolate modified by transglutaminase aggregation and emulsion gel properties

NASA Astrophysics Data System (ADS)

Qi, Weiwei; Chen, Chong; Liu, Mujun; Yu, Guoping; Cai, Xinghang; Guo, Peipei; Yao, Yuxiu; Mei, Sijie

2015-07-01

Whey protein isolate and commercial soybean salad oil were used to produce the WPI emulsion dispersions. The properties of TG-catalyzed emulsion gelation produced from WPI emulsion dispersions were investigated by the amount of TG, temperature, pH and reaction time. Specifically, the texture properties (hardness and springiness), water-holding capacity and rheological properties (G' and G") were assessed. The result of Orthogonal tests showed WPI emulsion can form better hardness and springiness gel when the ratio of TG and WPI was 20U/g, pH 7.5, treatment temperature and time were 50°C and 3 h, respectively. The microstructure of TG emulsion gels was more compact, gel pore is smaller, distribution more uniform, the oil droplets size smaller compared with untreated emulsion gels. Compared to the control of rheological properties, G' and G" were significantly increased and G' > G", results showed that the gel was solid state, and TG speeded up the process of gelation.

Creep and tensile properties of several oxide-dispersion-strengthened nickel-base alloys at 1365 K

NASA Technical Reports Server (NTRS)

Wittenberger, J. D.

1977-01-01

The tensile properties at room temperature and at 1365 K and the tensile creep properties at low strain rates at 1365 K were measured for several oxide-dispersion-strengthened (ODS) alloys. The alloys examined included ODS Ni, ODS Ni-20Cr, and ODS Ni-16Cr-Al. Metallography of creep tested, large grain size ODS alloys indicated that creep of these alloys is an inhomogeneous process. All alloys appear to possess a threshold stress for creep. This threshold stress is believed to be associated with diffusional creep in the large grain size ODS alloys and normal dislocation motion in perfect single crystal (without transverse low angle boundaries) ODS alloys. Threshold stresses for large grain size ODS Ni-20Cr and Ni-16Cr-Al type alloys are dependent on the grain aspect ratio. Because of the deleterious effect of prior creep on room temperature mechanical properties of large grain size ODS alloys, it is speculated that the threshold stress may be the design limiting creep strength property.

Ripple-modulated electronic structure of a 3D topological insulator.

PubMed

Okada, Yoshinori; Zhou, Wenwen; Walkup, D; Dhital, Chetan; Wilson, Stephen D; Madhavan, V

2012-01-01

Three-dimensional topological insulators host linearly dispersing states with unique properties and a strong potential for applications. An important ingredient in realizing some of the more exotic states in topological insulators is the ability to manipulate local electronic properties. Direct analogy to the Dirac material graphene suggests that a possible avenue for controlling local properties is via a controlled structural deformation such as the formation of ripples. However, the influence of such ripples on topological insulators is yet to be explored. Here we use scanning tunnelling microscopy to determine the effects of one-dimensional buckling on the electronic properties of Bi(2)Te(3.) By tracking spatial variations of the interference patterns generated by the Dirac electrons we show that buckling imposes a periodic potential, which locally modulates the surface-state dispersion. This suggests that forming one- and two-dimensional ripples is a viable method for creating nanoscale potential landscapes that can be used to control the properties of Dirac electrons in topological insulators.

Fluorescent microarray for multiplexed quantification of environmental contaminants in seawater samples

USDA-ARS?s Scientific Manuscript database

The development of a fluorescent multiplexed microarray platform able to detect and quantify a wide variety of pollutants in seawater is reported. The microarray platform has been manufactured by spotting 6 different bioconjugate competitors and it uses a cocktail of 6 monoclonal and polyclonal anti...

Use of Microarray to Analyze Gene Expression Profiles of Acute Effects of Prochloraz on Fathead Minnows Pimephales promelas

EPA Science Inventory

Microarray technology is a powerful tool to investigate the gene expression profiles for thousands of genes simultaneously. In recent years, microarrays have been used to characterize environmental pollutants and identify molecular mode(s) of action of chemicals including endocri...

Gene Expression Browser: Large-Scale and Cross-Experiment Microarray Data Management, Search & Visualization

USDA-ARS?s Scientific Manuscript database

The amount of microarray gene expression data in public repositories has been increasing exponentially for the last couple of decades. High-throughput microarray data integration and analysis has become a critical step in exploring the large amount of expression data for biological discovery. Howeve...

Microarrays Made Simple: "DNA Chips" Paper Activity

ERIC Educational Resources Information Center

Barnard, Betsy

2006-01-01

DNA microarray technology is revolutionizing biological science. DNA microarrays (also called DNA chips) allow simultaneous screening of many genes for changes in expression between different cells. Now researchers can obtain information about genes in days or weeks that used to take months or years. The paper activity described in this article…

MICROARRAY QUALITY CONTROL PROJECT: A COMPREHENSIVE GENE EXPRESSION TECHNOLOGY SURVEY DEMONSTRATES MEASURABLE CONSISTENCY AND CONCORDANT RESULTS BETWEEN PLATFORMS

EPA Science Inventory

Over the last decade, the introduction of microarray technology has had a profound impact on gene expression research. The publication of studies with dissimilar or altogether contradictory results, obtained using different microarray platforms to analyze identical RNA samples, h...

Microarrays

ERIC Educational Resources Information Center

Plomin, Robert; Schalkwyk, Leonard C.

2007-01-01

Microarrays are revolutionizing genetics by making it possible to genotype hundreds of thousands of DNA markers and to assess the expression (RNA transcripts) of all of the genes in the genome. Microarrays are slides the size of a postage stamp that contain millions of DNA sequences to which single-stranded DNA or RNA can hybridize. This…

Microarray Technology for the Diagnosis of Fetal Chromosomal Aberrations: Which Platform Should We Use?

PubMed Central

Karampetsou, Evangelia; Morrogh, Deborah; Chitty, Lyn

2014-01-01

The advantage of microarray (array) over conventional karyotype for the diagnosis of fetal pathogenic chromosomal anomalies has prompted the use of microarrays in prenatal diagnostics. In this review we compare the performance of different array platforms (BAC, oligonucleotide CGH, SNP) and designs (targeted, whole genome, whole genome, and targeted, custom) and discuss their advantages and disadvantages in relation to prenatal testing. We also discuss the factors to consider when implementing a microarray testing service for the diagnosis of fetal chromosomal aberrations. PMID:26237396

A Perspective on DNA Microarrays in Pathology Research and Practice

PubMed Central

Pollack, Jonathan R.

2007-01-01

DNA microarray technology matured in the mid-1990s, and the past decade has witnessed a tremendous growth in its application. DNA microarrays have provided powerful tools for pathology researchers seeking to describe, classify, and understand human disease. There has also been great expectation that the technology would advance the practice of pathology. This review highlights some of the key contributions of DNA microarrays to experimental pathology, focusing in the area of cancer research. Also discussed are some of the current challenges in translating utility to clinical practice. PMID:17600117

Constructing Tissue Microarrays: Protocols and Methods Considering Potential Advantages and Disadvantages for Downstream Use.

PubMed

Bingle, Lynne; Fonseca, Felipe P; Farthing, Paula M

2017-01-01

Tissue microarrays were first constructed in the 1980s but were used by only a limited number of researchers for a considerable period of time. In the last 10 years there has been a dramatic increase in the number of publications describing the successful use of tissue microarrays in studies aimed at discovering and validating biomarkers. This, along with the increased availability of both manual and automated microarray builders on the market, has encouraged even greater use of this novel and powerful tool. This chapter describes the basic techniques required to build a tissue microarray using a manual method in order that the theory behind the practical steps can be fully explained. Guidance is given to ensure potential disadvantages of the technique are fully considered.

Identification of differentially expressed genes and false discovery rate in microarray studies.

PubMed

Gusnanto, Arief; Calza, Stefano; Pawitan, Yudi

2007-04-01

To highlight the development in microarray data analysis for the identification of differentially expressed genes, particularly via control of false discovery rate. The emergence of high-throughput technology such as microarrays raises two fundamental statistical issues: multiplicity and sensitivity. We focus on the biological problem of identifying differentially expressed genes. First, multiplicity arises due to testing tens of thousands of hypotheses, rendering the standard P value meaningless. Second, known optimal single-test procedures such as the t-test perform poorly in the context of highly multiple tests. The standard approach of dealing with multiplicity is too conservative in the microarray context. The false discovery rate concept is fast becoming the key statistical assessment tool replacing the P value. We review the false discovery rate approach and argue that it is more sensible for microarray data. We also discuss some methods to take into account additional information from the microarrays to improve the false discovery rate. There is growing consensus on how to analyse microarray data using the false discovery rate framework in place of the classical P value. Further research is needed on the preprocessing of the raw data, such as the normalization step and filtering, and on finding the most sensitive test procedure.

Systematic spatial bias in DNA microarray hybridization is caused by probe spot position-dependent variability in lateral diffusion.

PubMed

Steger, Doris; Berry, David; Haider, Susanne; Horn, Matthias; Wagner, Michael; Stocker, Roman; Loy, Alexander

2011-01-01

The hybridization of nucleic acid targets with surface-immobilized probes is a widely used assay for the parallel detection of multiple targets in medical and biological research. Despite its widespread application, DNA microarray technology still suffers from several biases and lack of reproducibility, stemming in part from an incomplete understanding of the processes governing surface hybridization. In particular, non-random spatial variations within individual microarray hybridizations are often observed, but the mechanisms underpinning this positional bias remain incompletely explained. This study identifies and rationalizes a systematic spatial bias in the intensity of surface hybridization, characterized by markedly increased signal intensity of spots located at the boundaries of the spotted areas of the microarray slide. Combining observations from a simplified single-probe block array format with predictions from a mathematical model, the mechanism responsible for this bias is found to be a position-dependent variation in lateral diffusion of target molecules. Numerical simulations reveal a strong influence of microarray well geometry on the spatial bias. Reciprocal adjustment of the size of the microarray hybridization chamber to the area of surface-bound probes is a simple and effective measure to minimize or eliminate the diffusion-based bias, resulting in increased uniformity and accuracy of quantitative DNA microarray hybridization.

Systematic Spatial Bias in DNA Microarray Hybridization Is Caused by Probe Spot Position-Dependent Variability in Lateral Diffusion

PubMed Central

Haider, Susanne; Horn, Matthias; Wagner, Michael; Stocker, Roman; Loy, Alexander

2011-01-01

Background The hybridization of nucleic acid targets with surface-immobilized probes is a widely used assay for the parallel detection of multiple targets in medical and biological research. Despite its widespread application, DNA microarray technology still suffers from several biases and lack of reproducibility, stemming in part from an incomplete understanding of the processes governing surface hybridization. In particular, non-random spatial variations within individual microarray hybridizations are often observed, but the mechanisms underpinning this positional bias remain incompletely explained. Methodology/Principal Findings This study identifies and rationalizes a systematic spatial bias in the intensity of surface hybridization, characterized by markedly increased signal intensity of spots located at the boundaries of the spotted areas of the microarray slide. Combining observations from a simplified single-probe block array format with predictions from a mathematical model, the mechanism responsible for this bias is found to be a position-dependent variation in lateral diffusion of target molecules. Numerical simulations reveal a strong influence of microarray well geometry on the spatial bias. Conclusions Reciprocal adjustment of the size of the microarray hybridization chamber to the area of surface-bound probes is a simple and effective measure to minimize or eliminate the diffusion-based bias, resulting in increased uniformity and accuracy of quantitative DNA microarray hybridization. PMID:21858215

Crossword: A Fully Automated Algorithm for the Segmentation and Quality Control of Protein Microarray Images

PubMed Central

2015-01-01

Biological assays formatted as microarrays have become a critical tool for the generation of the comprehensive data sets required for systems-level understanding of biological processes. Manual annotation of data extracted from images of microarrays, however, remains a significant bottleneck, particularly for protein microarrays due to the sensitivity of this technology to weak artifact signal. In order to automate the extraction and curation of data from protein microarrays, we describe an algorithm called Crossword that logically combines information from multiple approaches to fully automate microarray segmentation. Automated artifact removal is also accomplished by segregating structured pixels from the background noise using iterative clustering and pixel connectivity. Correlation of the location of structured pixels across image channels is used to identify and remove artifact pixels from the image prior to data extraction. This component improves the accuracy of data sets while reducing the requirement for time-consuming visual inspection of the data. Crossword enables a fully automated protocol that is robust to significant spatial and intensity aberrations. Overall, the average amount of user intervention is reduced by an order of magnitude and the data quality is increased through artifact removal and reduced user variability. The increase in throughput should aid the further implementation of microarray technologies in clinical studies. PMID:24417579

The detection and differentiation of canine respiratory pathogens using oligonucleotide microarrays.

PubMed

Wang, Lih-Chiann; Kuo, Ya-Ting; Chueh, Ling-Ling; Huang, Dean; Lin, Jiunn-Horng

2017-05-01

Canine respiratory diseases are commonly seen in dogs along with co-infections with multiple respiratory pathogens, including viruses and bacteria. Virus infections in even vaccinated dogs were also reported. The clinical signs caused by different respiratory etiological agents are similar, which makes differential diagnosis imperative. An oligonucleotide microarray system was developed in this study. The wild type and vaccine strains of canine distemper virus (CDV), influenza virus, canine herpesvirus (CHV), Bordetella bronchiseptica and Mycoplasma cynos were detected and differentiated simultaneously on a microarray chip. The detection limit is 10, 10, 100, 50 and 50 copy numbers for CDV, influenza virus, CHV, B. bronchiseptica and M. cynos, respectively. The clinical test results of nasal swab samples showed that the microarray had remarkably better efficacy than the multiplex PCR-agarose gel method. The positive detection rate of microarray and agarose gel was 59.0% (n=33) and 41.1% (n=23) among the 56 samples, respectively. CDV vaccine strain and pathogen co-infections were further demonstrated by the microarray but not by the multiplex PCR-agarose gel. The oligonucleotide microarray provides a highly efficient diagnosis alternative that could be applied to clinical usage, greatly assisting in disease therapy and control. Copyright © 2017 Elsevier B.V. All rights reserved.

Gene selection for microarray data classification via subspace learning and manifold regularization.

PubMed

Tang, Chang; Cao, Lijuan; Zheng, Xiao; Wang, Minhui

2017-12-19

With the rapid development of DNA microarray technology, large amount of genomic data has been generated. Classification of these microarray data is a challenge task since gene expression data are often with thousands of genes but a small number of samples. In this paper, an effective gene selection method is proposed to select the best subset of genes for microarray data with the irrelevant and redundant genes removed. Compared with original data, the selected gene subset can benefit the classification task. We formulate the gene selection task as a manifold regularized subspace learning problem. In detail, a projection matrix is used to project the original high dimensional microarray data into a lower dimensional subspace, with the constraint that the original genes can be well represented by the selected genes. Meanwhile, the local manifold structure of original data is preserved by a Laplacian graph regularization term on the low-dimensional data space. The projection matrix can serve as an importance indicator of different genes. An iterative update algorithm is developed for solving the problem. Experimental results on six publicly available microarray datasets and one clinical dataset demonstrate that the proposed method performs better when compared with other state-of-the-art methods in terms of microarray data classification. Graphical Abstract The graphical abstract of this work.

A platform for the advanced spatial and temporal control of biomolecules

NASA Astrophysics Data System (ADS)

Hook, Andrew L.; Thissen, Helmut; Hayes, Jason P.; Voelcker, Nicolas H.

2007-01-01

Manipulating biomolecules at solid/liquid interfaces is important for the development of various biodevices including microarrays. Smart materials that enable both spatial and temporal control of biomolecules by combining switchability with patterned surface chemistry offer unprecedented levels of control of biomolecule manipulation. Such a system has been developed for the microscale spatial control over both DNA and cell growth on highly doped p-type silicon. Surface modification, involving plasma polymerisation of allylamine and poly(ethlylene glycol) grafting with subsequent laser ablation, led to the production of a patterned surface with dual biomolecule adsorption and desorption properties. On patterned surfaces, preferential electro-stimulated adsorption of DNA to the allylamine plasma polymer surface and subsequent desorption by the application of a negative bias was observed. The ability of this surface to control both DNA and cell attachment in four dimensions has been demonstrated, exemplifying its capacity to be used for complex biological studies such as gene function analysis. This system has been successfully applied to living microarray applications and is an exciting platform for any system incorporating biomolecules.