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Sample records for integrated multiple capillary

  1. Multiple capillary biochemical analyzer

    DOEpatents

    Dovichi, Norman J.; Zhang, Jian Z.

    1995-01-01

    A multiple capillary analyzer allows detection of light from multiple capillaries with a reduced number of interfaces through which light must pass in detecting light emitted from a sample being analyzed, using a modified sheath flow cuvette. A linear or rectangular array of capillaries is introduced into a rectangular flow chamber. Sheath fluid draws individual sample streams through the cuvette. The capillaries are closely and evenly spaced and held by a transparent retainer in a fixed position in relation to an optical detection system. Collimated sample excitation radiation is applied simultaneously across the ends of the capillaries in the retainer. Light emitted from the excited sample is detected by the optical detection system. The retainer is provided by a transparent chamber having inward slanting end walls. The capillaries are wedged into the chamber. One sideways dimension of the chamber is equal to the diameter of the capillaries and one end to end dimension varies from, at the top of the chamber, slightly greater than the sum of the diameters of the capillaries to, at the bottom of the chamber, slightly smaller than the sum of the diameters of the capillaries. The optical system utilizes optic fibres to deliver light to individual photodetectors, one for each capillary tube. A filter or wavelength division demultiplexer may be used for isolating fluorescence at particular bands.

  2. Multiple capillary biochemical analyzer

    DOEpatents

    Dovichi, N.J.; Zhang, J.Z.

    1995-08-08

    A multiple capillary analyzer allows detection of light from multiple capillaries with a reduced number of interfaces through which light must pass in detecting light emitted from a sample being analyzed, using a modified sheath flow cuvette. A linear or rectangular array of capillaries is introduced into a rectangular flow chamber. Sheath fluid draws individual sample streams through the cuvette. The capillaries are closely and evenly spaced and held by a transparent retainer in a fixed position in relation to an optical detection system. Collimated sample excitation radiation is applied simultaneously across the ends of the capillaries in the retainer. Light emitted from the excited sample is detected by the optical detection system. The retainer is provided by a transparent chamber having inward slanting end walls. The capillaries are wedged into the chamber. One sideways dimension of the chamber is equal to the diameter of the capillaries and one end to end dimension varies from, at the top of the chamber, slightly greater than the sum of the diameters of the capillaries to, at the bottom of the chamber, slightly smaller than the sum of the diameters of the capillaries. The optical system utilizes optic fibers to deliver light to individual photodetectors, one for each capillary tube. A filter or wavelength division demultiplexer may be used for isolating fluorescence at particular bands. 21 figs.

  3. An integrated multiple capillary array electrophoresis system for high-throughput DNA sequencing

    SciTech Connect

    Lu, X.

    1998-03-27

    A capillary array electrophoresis system was chosen to perform DNA sequencing because of several advantages such as rapid heat dissipation, multiplexing capabilities, gel matrix filling simplicity, and the mature nature of the associated manufacturing technologies. There are two major concerns for the multiple capillary systems. One concern is inter-capillary cross-talk, and the other concern is excitation and detection efficiency. Cross-talk is eliminated through proper optical coupling, good focusing and immersing capillary array into index matching fluid. A side-entry excitation scheme with orthogonal detection was established for large capillary array. Two 100 capillary array formats were used for DNA sequencing. One format is cylindrical capillary with 150 {micro}m o.d., 75 {micro}m i.d and the other format is square capillary with 300 {micro}m out edge and 75 {micro}m inner edge. This project is focused on the development of excitation and detection of DNA as well as performing DNA sequencing. The DNA injection schemes are discussed for the cases of single and bundled capillaries. An individual sampling device was designed. The base-calling was performed for a capillary from the capillary array with the accuracy of 98%.

  4. Integrated multiplexed capillary electrophoresis system

    DOEpatents

    Yeung, Edward S.; Tan, Hongdong

    2002-05-14

    The present invention provides an integrated multiplexed capillary electrophoresis system for the analysis of sample analytes. The system integrates and automates multiple components, such as chromatographic columns and separation capillaries, and further provides a detector for the detection of analytes eluting from the separation capillaries. The system employs multiplexed freeze/thaw valves to manage fluid flow and sample movement. The system is computer controlled and is capable of processing samples through reaction, purification, denaturation, pre-concentration, injection, separation and detection in parallel fashion. Methods employing the system of the invention are also provided.

  5. Laser illumination of multiple capillaries that form a waveguide

    DOEpatents

    Dhadwal, H.S.; Quesada, M.A.; Studier, F.W.

    1998-08-04

    A system and method are disclosed for efficient laser illumination of the interiors of multiple capillaries simultaneously, and collection of light emitted from them. Capillaries in a parallel array can form an optical waveguide wherein refraction at the cylindrical surfaces confines side-on illuminating light to the core of each successive capillary in the array. Methods are provided for determining conditions where capillaries will form a waveguide and for assessing and minimizing losses due to reflection. Light can be delivered to the arrayed capillaries through an integrated fiber optic transmitter or through a pair of such transmitters aligned coaxially at opposite sides of the array. Light emitted from materials within the capillaries can be carried to a detection system through optical fibers, each of which collects light from a single capillary, with little cross talk between the capillaries. The collection ends of the optical fibers can be in a parallel array with the same spacing as the capillary array, so that the collection fibers can all be aligned to the capillaries simultaneously. Applicability includes improving the efficiency of many analytical methods that use capillaries, including particularly high-throughput DNA sequencing and diagnostic methods based on capillary electrophoresis. 35 figs.

  6. Laser illumination of multiple capillaries that form a waveguide

    DOEpatents

    Dhadwal, Harbans S.; Quesada, Mark A.; Studier, F. William

    1998-08-04

    A system and method are disclosed for efficient laser illumination of the interiors of multiple capillaries simultaneously, and collection of light emitted from them. Capillaries in a parallel array can form an optical waveguide wherein refraction at the cylindrical surfaces confines side-on illuminating light to the core of each successive capillary in the array. Methods are provided for determining conditions where capillaries will form a waveguide and for assessing and minimizing losses due to reflection. Light can be delivered to the arrayed capillaries through an integrated fiber optic transmitter or through a pair of such transmitters aligned coaxially at opposite sides of the array. Light emitted from materials within the capillaries can be carried to a detection system through optical fibers, each of which collects light from a single capillary, with little cross talk between the capillaries. The collection ends of the optical fibers can be in a parallel array with the same spacing as the capillary array, so that the collection fibers can all be aligned to the capillaries simultaneously. Applicability includes improving the efficiency of many analytical methods that use capillaries, including particularly high-throughput DNA sequencing and diagnostic methods based on capillary electrophoresis.

  7. Multiple capillary biochemical analyzer with barrier member

    DOEpatents

    Dovichi, Norman J.; Zhang, Jian Z.

    1996-01-01

    A multiple capillary biochemical analyzer for sequencing DNA and performing other analyses, in which a set of capillaries extends from wells in a microtiter plate into a cuvette. In the cuvette the capillaries are held on fixed closely spaced centers by passing through a sandwich construction having a pair of metal shims which squeeze between them a rubber gasket, forming a leak proof seal for an interior chamber in which the capillary ends are positioned. Sheath fluid enters the chamber and entrains filament sample streams from the capillaries. The filament sample streams, and sheath fluid, flow through aligned holes in a barrier member spaced close to the capillary ends, into a collection chamber having a lower glass window. The filament streams are illuminated above the barrier member by a laser, causing them to fluoresce. The fluorescence is viewed end-on by a CCD camera chip located below the glass window. The arrangement ensures an equal optical path length from all fluorescing spots to the CCD chip and also blocks scattered fluorescence illumination, providing more uniform results and an improved signal to noise ratio.

  8. Multiple capillary biochemical analyzer with barrier member

    DOEpatents

    Dovichi, N.J.; Zhang, J.Z.

    1996-10-22

    A multiple capillary biochemical analyzer is disclosed for sequencing DNA and performing other analyses, in which a set of capillaries extends from wells in a microtiter plate into a cuvette. In the cuvette the capillaries are held on fixed closely spaced centers by passing through a sandwich construction having a pair of metal shims which squeeze between them a rubber gasket, forming a leak proof seal for an interior chamber in which the capillary ends are positioned. Sheath fluid enters the chamber and entrains filament sample streams from the capillaries. The filament sample streams, and sheath fluid, flow through aligned holes in a barrier member spaced close to the capillary ends, into a collection chamber having a lower glass window. The filament streams are illuminated above the barrier member by a laser, causing them to fluoresce. The fluorescence is viewed end-on by a CCD camera chip located below the glass window. The arrangement ensures an equal optical path length from all fluorescing spots to the CCD chip and also blocks scattered fluorescence illumination, providing more uniform results and an improved signal-to-noise ratio. 12 figs.

  9. Multiple beam interference model for measuring parameters of a capillary.

    PubMed

    Xu, Qiwei; Tian, Wenjing; You, Zhihong; Xiao, Jinghua

    2015-08-01

    A multiple beam interference model based on the ray tracing method and interference theory is built to analyze the interference patterns of a capillary tube filled with a liquid. The relations between the angular widths of the interference fringes and the parameters of both the capillary and liquid are derived. Based on these relations, an approach is proposed to simultaneously determine four parameters of the capillary, i.e., the inner and outer radii of the capillary, the refractive indices of the liquid, and the wall material. PMID:26368114

  10. Multiple beam interference model for measuring parameters of a capillary.

    PubMed

    Xu, Qiwei; Tian, Wenjing; You, Zhihong; Xiao, Jinghua

    2015-08-01

    A multiple beam interference model based on the ray tracing method and interference theory is built to analyze the interference patterns of a capillary tube filled with a liquid. The relations between the angular widths of the interference fringes and the parameters of both the capillary and liquid are derived. Based on these relations, an approach is proposed to simultaneously determine four parameters of the capillary, i.e., the inner and outer radii of the capillary, the refractive indices of the liquid, and the wall material.

  11. Integrated chip-based capillary electrophoresis.

    PubMed

    Effenhauser, C S; Bruin, G J; Paulus, A

    1997-11-01

    Integrated capillary electrophoresis (ICE) is emerging as a new analytical tool allowing fast, automated, miniaturized and multiplexed assays, thus meeting the needs of the pharmaceutical industry in drug development. The current state-of-the-art of ICE is described with an emphasis on the choice of the support material (glass or polymeric materials), electrokinetic fluid handling, and injection and detection issues. Strategies and chip designs for pre- or post-column derivatization, DNA sequencing, on-line PCR analysis, on-chip enzymatic sample digestion, fraction isolation, and immunoassays are presented. The review concludes with a brief outlook.

  12. Hybrid integrated PDMS microfluidics with a silica capillary.

    PubMed

    Dimov, Ivan K; Riaz, Asif; Ducrée, Jens; Lee, Luke P

    2010-06-01

    To harness the properties of both PDMS and silica, we have demonstrated hybrid integrated PDMS microfluidic systems with fused silica capillaries. The hybrid integrated PDMS microfluidics and silica capillary (iPSC) modules exhibit a novel architecture and method for leakage free CE sample injection merely requiring a single high voltage source and one pair of electrodes. The use of the iPSC device is based on a modular approach which allows the capillary to be reused extensively whilst replacing the attached fluidic module for different experiments. Integrating fused silica capillaries with PDMS microfluidic modules allows the direct application of a wide variety of well established conventional CE protocols for separations of complex analytes. Furthermore it bears the potential for facile coupling to standard electro-spray ionization mass spectrometry (ESI-MS), letting users focus on the sample analysis rather than the development of new separation protocols. The fabrication of the iPSC module consists of a simple and quick three-step method that submerges a fused silica capillary in PDMS prepolymer. After cross linking the prepolymer and punching the inlets, the iPSC module layer can be mounted onto a microfluidic device for CE separation.

  13. Integration of amperometric sensors for microchip capillary electrophoresis application

    NASA Astrophysics Data System (ADS)

    Dicorato, F.; Moore, E.; Glennon, J.

    2011-08-01

    Capillary electrophoresis is a technique for the separation and analysis of chemical compounds. Techniques adopted from the microchip technology knowledge have led to recent developments of electrophoresis system with integration on microchip. Microchip Capillary Electrophoresis (μCE) systems offer a series of advantages as easy integration for Lab-on-a-chip applications, high performance, portability, speed, minimal solvent and sample requirements. A new technological challenge aims at the development of an economic modular microchip capillary electrophoresis systems using separable and independent units concerning the sensor. In this project we worked on the development of an interchangeable amperometric sensor in order to provide a solution to such electrode passivation and facilitating the use of tailored sensors for specific analyte detection besides. Fluidic chips have been machined from cyclic olefin polymer pallets (Zeonor®) using a micro-injection molding machine.

  14. Induced hydraulic pumping via integrated submicrometer cylindrical glass capillaries.

    PubMed

    Cao, Zhen; Yobas, Levent

    2014-08-01

    Here, we report on a micropump that generates hydraulic pressure owing to a mismatch in EOF rates of microchannels and submicrometer cylindrical glass capillaries integrated on silicon. The electrical conductance of such capillaries in the dilute limit departs from bulk linear behavior as well as from the surface-charge-governed saturation in nanoslits that is well described by the assumption of a constant surface charge density. The capillaries show rather a gradual decrease in conduction at low salt concentrations, which can be explained more aptly by a variable surface charge density that accounts for chemical equilibrium of the surface. The micropump uses a traditional cross-junction structure with ten identical capillaries integrated in parallel on a side arm and each with a 750 nm diameter and 3 mm length. For an applied voltage of 700 V, a hydraulic pressure up to 5 kPa is generated with a corresponding flow velocity nearly 3 mm/s in a straight field-free branch 20 μm wide, 10 μm deep, and 10 mm long. The micropump utility has been demonstrated in an open tubular LC of three fluorescently labeled amino acids in just less than 20 s with minimal plate height values between 3 and 7 μm. The submicrometer capillaries are self-enclosed and produced through a unique process that does not require high-resolution advanced lithography or wafer-bonding techniques to define their highly controlled precise structures. PMID:24917552

  15. Heat Load Sharing in a Capillary Pumped Loop with Multiple Evaporators and Multiple Condensers

    NASA Technical Reports Server (NTRS)

    Ku, Jentung

    2005-01-01

    This paper describes the heat load sharing function among multiple parallel evaporators in a capillary pumped loop (CPL). In the normal mode of operation, the evaporators cool the instruments by absorbing the waste heat. When an instruments is turned off, the attached evaporator can keep it warm by receiving heat from other evaporators serving the operating instruments. This is referred to as heat load sharing. A theoretical basis of heat load sharing is given first. The fact that the wicks in the powered evaporators will develop capillary pressure to force the generated vapor to flow to cold locations where the pressure is lower leads to the conclusion that heat load sharing is an inherent function of a CPL with multiple evaporators. Heat load sharing has been verified with many CPLs in ground tests. Experimental results of the Capillary Pumped Loop 3 (CAPL 3) Flight Experiment are presented in this paper. Factors that affect the amount of heat being shared are discussed. Some constraints of heat load sharing are also addressed.

  16. DNA sequencing by multiple capillaries that form a waveguide

    SciTech Connect

    Dhadwal, S.H.; Quesada, M.A.; Studier, F.W.

    1997-05-01

    A 12-capillary prototype electrophoresis system for DNA sequencing has been constructed. Laser illumination is introduced into an optical waveguide that is formed by an array of individual capillaries that serve both as the optical elements of the periodic array and as the channels containing sieving media for electrophoresis. A theoretical framework and experimental data will be presented to illustrate the viability of this approach.

  17. [A novel multiple-channel apparatus for packing capillary chromatographic column and its application].

    PubMed

    Lü, Yayao; Hao, Feiran; Wang, Huanhuan; Fu, Bin; Qian, Xiaohong; Zhang, Yangjun

    2015-11-01

    A novel multiple-channel apparatus for packing capillary chromatographic column was designed and manufactured for packing six capillary chromatographic columns with close column efficiency at the same time. Briefly, it consists of a magnetic stirrer, a liquid chromatographic pump and a multiple-channel can. The reagents used for preparing ODS (C18) slurry and stirring condition of the magnetic stirrer were optimized in the study. Two batches of capillary chromatographic columns were packed under the optimum condition, and these packed capillary chromatographic columns were evaluated in the terms of peak capacity, sequence coverage, retention times of three peptide ions and column pressure using the tryptic digest of a bovine serum albumin (BSA) and detected by LC-MS in electrospray ionization (ESI) mode. The experimental results showed that the six capillary chromatographic columns packed at the same time had close column efficiencies, however, the column efficiencies of twelve capillary chromatographic columns packed at two times were significantly different. In addition, there was no significant column efficiency difference when packing one or six capillary chromatographic columns at the same time. The multiple-channel apparatus designed by us is simple, time-saving, and can be applied to pack capillary chromatographic columns with similar column efficiencies, thus it is of evident advantage over traditional one-channel apparatus.

  18. Enantiomeric resolution of multiple chiral centres racemates by capillary electrophoresis.

    PubMed

    Ali, Imran; Suhail, Mohd; Al-Othman, Zeid A; Alwarthan, Abdulrahman; Aboul-Enein, Hassan Y

    2016-05-01

    Enantiomeric resolution of multichiral centre racemates is an important area as some multichiral centre racemates are of great medicinal importance. However, enantioseparation of such types of racemates is a challenging task. Amongst many analytical techniques, capillary electrophoresis is a powerful technique and may be used to resolve such racemates. Only few papers are available describing enantiomeric resolution of such racemates. Therefore, efforts have been made to describe the enantiomeric resolution of multichiral centre racemates by capillary electrophoresis. This article discusses the importance of multichiral racemates, the need for capillary electrophoresis in enantiomeric resolution and chiral resolution of multichiral centre racemates using various chiral selectors. Further, attempts have been made to discuss the future challenges and prospects of enantiomeric resolution of multichiral racemates. The various chiral selectors used for the purpose are chiral crown ether, cyclodextrins, polysaccharides, macrocyclic glycopeptide antibiotics and ligand exchange.

  19. Microfabricated capillary electrophoresis chip and method for simultaneously detecting multiple redox labels

    DOEpatents

    Mathies, Richard A.; Singhal, Pankaj; Xie, Jin; Glazer, Alexander N.

    2002-01-01

    This invention relates to a microfabricated capillary electrophoresis chip for detecting multiple redox-active labels simultaneously using a matrix coding scheme and to a method of selectively labeling analytes for simultaneous electrochemical detection of multiple label-analyte conjugates after electrophoretic or chromatographic separation.

  20. Integration of rapid DNA hybridization and capillary zone electrophoresis using bidirectional isotachophoresis.

    PubMed

    Bahga, Supreet S; Han, Crystal M; Santiago, Juan G

    2013-01-01

    We present a method for rapid, sequence-specific detection of multiple DNA fragments by integrating isotachophoresis (ITP) based DNA hybridization and capillary zone electrophoresis (CZE) using bidirectional ITP. Our method leverages the high preconcentration ability of ITP to accelerate slow, second-order DNA hybridization kinetics, and the high resolving power of CZE to separate and identify reaction products. We demonstrate the speed and sensitivity of our assay by detecting 5 pM, 39 nt ssDNA target within 3 min, using a molecular beacon probe. We also demonstrate the feasibility of our assay for multiplexed detection of multiple-length ssDNA targets by simultaneously detecting 39 and 90 nt ssDNA targets.

  1. Calculating alveolar capillary conductance and pulmonary capillary blood volume: comparing the multiple- and single-inspired oxygen tension methods

    PubMed Central

    Ceridon, Maile L.; Beck, Kenneth C.; Olson, Thomas P.; Bilezikian, Jordan A.

    2010-01-01

    Key elements for determining alveolar-capillary membrane conductance (Dm) and pulmonary capillary blood volume (Vc) from the lung diffusing capacity (Dl) for carbon monoxide (DlCO) or for nitric oxide (DlNO) are the reaction rate of carbon monoxide with hemoglobin (θCO) and the DmCO/DlNO relationship (α-ratio). Although a range of values have been reported, currently there is no consensus regarding these parameters. The study purpose was to define optimal parameters (θCO, α-ratio) that would experimentally substantiate calculations of Dm and Vc from the single-inspired O2 tension [inspired fraction of O2 (FiO2)] method relative to the multiple-FiO2 method. Eight healthy men were studied at rest and during moderate exercise (80-W cycle). Dm and Vc were determined by the multiple-FiO2 and single-FiO2 methods (rebreathe technique) and were tabulated by applying previously reported θCO equations (both methods) and by varying the α-ratio (single-FiO2 method) from 1.90 to 2.50. Values were then compared between methods throughout the examined α-ratios. Dm and Vc were critically dependent on the applied θCO equation. For the multiple-FiO2 method, Dm was highly variable between θCO equations (rest and exercise); the range of Vc was less widespread. For the single-FiO2 method, the θCO equation by Reeves and Park (1992) combined with an α-ratio between 2.08 and 2.26 gave values for Dm and Vc that most closely matched those from the multiple-FiO2 method and were also physiologically plausible compared with predicted values. We conclude that the parameters used to calculate Dm and Vc values from the single-FiO2 method (using DlCO and DlNO) can significantly influence results and should be evaluated within individual laboratories to obtain optimal values. PMID:20538842

  2. Calculating alveolar capillary conductance and pulmonary capillary blood volume: comparing the multiple- and single-inspired oxygen tension methods.

    PubMed

    Ceridon, Maile L; Beck, Kenneth C; Olson, Thomas P; Bilezikian, Jordan A; Johnson, Bruce D

    2010-09-01

    Key elements for determining alveolar-capillary membrane conductance (Dm) and pulmonary capillary blood volume (Vc) from the lung diffusing capacity (Dl) for carbon monoxide (DlCO) or for nitric oxide (DlNO) are the reaction rate of carbon monoxide with hemoglobin (thetaCO) and the DmCO/DlNO relationship (alpha-ratio). Although a range of values have been reported, currently there is no consensus regarding these parameters. The study purpose was to define optimal parameters (thetaCO, alpha-ratio) that would experimentally substantiate calculations of Dm and Vc from the single-inspired O2 tension [inspired fraction of O2 (FiO2)] method relative to the multiple-FiO2 method. Eight healthy men were studied at rest and during moderate exercise (80-W cycle). Dm and Vc were determined by the multiple-FiO2 and single-FiO2 methods (rebreathe technique) and were tabulated by applying previously reported thetaCO equations (both methods) and by varying the alpha-ratio (single-FiO2 method) from 1.90 to 2.50. Values were then compared between methods throughout the examined alpha-ratios. Dm and Vc were critically dependent on the applied thetaCO equation. For the multiple-FiO2 method, Dm was highly variable between thetaCO equations (rest and exercise); the range of Vc was less widespread. For the single-FiO2 method, the thetaCO equation by Reeves and Park (1992) combined with an alpha-ratio between 2.08 and 2.26 gave values for Dm and Vc that most closely matched those from the multiple-FiO2 method and were also physiologically plausible compared with predicted values. We conclude that the parameters used to calculate Dm and Vc values from the single-FiO2 method (using DlCO and DlNO) can significantly influence results and should be evaluated within individual laboratories to obtain optimal values.

  3. Multiple response optimization applied to the development of a capillary electrophoretic method for pharmaceutical analysis.

    PubMed

    Candioti, Luciana Vera; Robles, Juan C; Mantovani, Víctor E; Goicoechea, Héctor C

    2006-03-15

    Multiple response simultaneous optimization by using the desirability function was used for the development of a capillary electrophoresis method for the simultaneous determination of four active ingredients in pharmaceutical preparations: vitamins B(6) and B(12), dexamethasone and lidocaine hydrochloride. Five responses were simultaneously optimized: the three resolutions, the analysis time and the capillary current. This latter response was taken into account in order to improve the quality of the separations. The separation was carried out by using capillary zone electrophoresis (CZE) with a silica capillary and UV detection (240 nm). The optimum conditions were: 57.0 mmol l(-1) sodium phosphate buffer solution, pH 7.0 and voltage=17.2 kV. Good results concerning precision (CV lower than 2%), accuracy (recoveries ranged between 98.5 and 102.6%) and selectivity were obtained in the concentration range studied for the four compounds. These results are comparable to those provided by the reference high performance liquid chromatography (HPLC) technique.

  4. Multiple capillary isotachophoresis with repetitive hydrodynamic injections for performance improvement of the electromigration preconcentration.

    PubMed

    Mai, Thanh Duc; Oukacine, Farid; Taverna, Myriam

    2016-07-01

    A novel electrokinetic preconcentration technique based on multiple isotachophoresis (M-ITP) realised in a micro-bored capillary to improve sensitivity for capillary electrophoresis with hydrodynamic injection was developed. The M-ITP operation relies on pressure-assisted pushing of a preconcentrated sample plug after the first ITP process back to the injection end of the capillary, followed by a large volume hydrodynamic injection prior to application of the second ITP step. This operational cycle was repeated as many times as desired with very good repeatability of the peak areas and peak heights at each ITP round (RSD less than 8%). Using imidazole and benzoate as models for cationic and anionic analytes, important insights into the mechanism of this electrokinetic preconcentration process with and without the presence of the electro-osmotic flow (EOF) at acidic and basic conditions were provided. Stacking of the benzoate ion, selected as one model analyte, in the presence of EOF and from a sample plug representing up to 300% of the total capillary length was successfully demonstrated. M-ITP was then demonstrated through the enrichment of the Aβ 1-40 amyloid peptide, considered as one of the biomarkers for biochemical diagnosis of Alzheimer's disease. Quantification of Aβ 1-40 down to 50nM with UV detection was made possible with 6 M-ITP cycles. PMID:27236482

  5. A luminescence lifetime-based capillary oxygen sensor utilizing monolithically integrated organic photodiodes.

    PubMed

    Lamprecht, Bernhard; Tschepp, Andreas; Čajlaković, Merima; Sagmeister, Martin; Ribitsch, Volker; Köstler, Stefan

    2013-10-21

    A novel optical sensor device monolithically integrated on a glass capillary is presented. Therefore, we took advantage of the ability to fabricate organic optoelectronic devices on non-planar substrates. The functionality of the concept is demonstrated by realizing an integrated oxygen sensor based on luminescence decay time measurement.

  6. Charging YOYO-1 on capillary wall for online DNA intercalation and integrating this approach with multiplex PCR and bare narrow capillary-hydrodynamic chromatography for online DNA analysis.

    PubMed

    Chen, Huang; Zhu, Zaifang; Lu, Joann Juan; Liu, Shaorong

    2015-02-01

    Multiplex polymerase chain reaction (PCR) has been widely utilized for high-throughput pathogen identification. Often, a dye is used to intercalate the amplified DNA fragments, and identifications of the pathogens are carried out by DNA melting curve analysis or gel electrophoresis. Integrating DNA amplification and identification is a logic path toward maximizing the benefit of multiplex PCR. Although PCR and gel electrophoresis have been integrated, replenishing the gels after each run is tedious and time-consuming. In this technical note, we develop an approach to address this issue. We perform multiplex PCR inside a capillary, transfer the amplified fragments to a bare narrow capillary, and measure their lengths online using bare narrow capillary-hydrodynamic chromatography (BaNC-HDC), a new technique recently developed in our laboratory for free-solution DNA separation. To intercalate the DNA with YOYO-1 (a fluorescent dye) for BaNC-HDC, we flush the capillary column with a YOYO-1 solution; positively charged YOYO-1 is adsorbed (or charged) onto the negatively charged capillary wall. As DNA molecules are driven down the column for separation, they react with the YOYO-1 stored on the capillary wall and are online-intercalated with the dye. With a single YOYO-1 charging, the column can be used for more than 40 runs, although the fluorescence signal intensities of the DNA peaks decrease gradually. Although the dye-DNA intercalation occurs during the separation, it does not affect the retention times, separation efficiencies, or resolutions. PMID:25555111

  7. Mathematical Modeling of Loop Heat Pipes with Multiple Capillary Pumps and Multiple Condensers. Part 1; Stead State Stimulations

    NASA Technical Reports Server (NTRS)

    Hoang, Triem T.; OConnell, Tamara; Ku, Jentung

    2004-01-01

    Loop Heat Pipes (LHPs) have proven themselves as reliable and robust heat transport devices for spacecraft thermal control systems. So far, the LHPs in earth-orbit satellites perform very well as expected. Conventional LHPs usually consist of a single capillary pump for heat acquisition and a single condenser for heat rejection. Multiple pump/multiple condenser LHPs have shown to function very well in ground testing. Nevertheless, the test results of a dual pump/condenser LHP also revealed that the dual LHP behaved in a complicated manner due to the interaction between the pumps and condensers. Thus it is redundant to say that more research is needed before they are ready for 0-g deployment. One research area that perhaps compels immediate attention is the analytical modeling of LHPs, particularly the transient phenomena. Modeling a single pump/single condenser LHP is difficult enough. Only a handful of computer codes are available for both steady state and transient simulations of conventional LHPs. No previous effort was made to develop an analytical model (or even a complete theory) to predict the operational behavior of the multiple pump/multiple condenser LHP systems. The current research project offered a basic theory of the multiple pump/multiple condenser LHP operation. From it, a computer code was developed to predict the LHP saturation temperature in accordance with the system operating and environmental conditions.

  8. Chemotherapy-Induced Changes in Cardiac Capillary Permeability Measured by Fluorescent Multiple Indicator Dilution

    PubMed Central

    Fernandez-Fernandez, Alicia; Carvajal, Denny A.; Lei, Tingjun; McGoron, Anthony J.

    2014-01-01

    Anthracyclines cause severe irreversible cardiac toxicity. The study of changes in cardiac permeability with chemotherapy could enhance the understanding of mechanisms behind cardiac damage, and provide useful information to evaluate anthracycline cardiotoxicity. Thirty-six rats (12 Sprague-Dawley, 12 Wistar, 12 Fischer-344) were randomly assigned to control (n= 21) or doxorubicin (n = 15), and injected i.p. with a cumulative dose of 18 mg/kg doxorubicin in saline (vehicle) or vehicle over 12 days. Echocardiography was performed at baseline and on day 11. An isolated heart experiment was done on day 12 to obtain perfused heart pressure values, and to measure cardiac capillary permeability using a Texas Red/sodium fluorescein multiple indicator dilution method. Control animals had significantly lower average permeability-surface-area-products (0.035±0.013 cm3/s) than doxorubicin animals (0.066±0.023 cm3/s), PSP±SD, p<0.001. These permeability changes correlated with significant functional changes. There was a significant decline in cardiac function with a deleterious effect of chemotherapy on fractional shortening (p<0.001), left ventricular developed pressure (p<0.001), contractility (p<0.001), and relaxation (p=0.02). Based on our results, cardiac capillary permeability changes can be detected after in vivo chemotherapy treatment using our fluorescent multiple indicator dilution technique, and may provide valuable information in evaluating cardiotoxicity of novel drugs. PMID:25224075

  9. Preparation of a dual-enzyme co-immobilized capillary microreactor and simultaneous screening of multiple enzyme inhibitors by capillary electrophoresis.

    PubMed

    Lin, Pingtan; Zhao, Shulin; Lu, Xin; Ye, Fanggui; Wang, Hengshan

    2013-08-01

    A CE method based on a dual-enzyme co-immobilized capillary microreactor was developed for the simultaneous screening of multiple enzyme inhibitors. The capillary microreactor was prepared by co-immobilizing adenosine deaminase and xanthine oxidase on the inner wall at the inlet end of the separation capillary. The enzymes were first immobilized on gold nanoparticles, and the functionalized gold nanoparticles were then assembled on the inner wall at the inlet end of the separation capillary treated with polyethyleneimine. With the developed CE method, the substrates and products were baseline separated within 3 min. The activity of the immobilized enzyme can be directly detected by measuring the peak height of the products. A statistical parameter Z' factor was recommended for evaluation of the accuracy of a drug screening system. In the present study, it was calculated to be larger than 0.5, implying a good accuracy. Finally, screening a small compound library containing two known enzyme inhibitors and 20 natural extracts by the proposed method was demonstrated. The known inhibitors were identified, and some natural extracts were found to be positive for two-enzyme inhibition by the present method.

  10. High-Throughput Proteomics Using High Efficiency Multiple-Capillary Liquid Chromatography With On-Line High-Performance ESI FTICR Mass Spectrometry

    SciTech Connect

    Shen, Yufeng ); Tolic, Nikola ); Zhao, Rui; Pasa Tolic, Ljiljana ); Li, Lingjun; Berger, Scott J.; Harkewicz, Richard ); Anderson, Gordon A. ); Belov, Mikhail E. ); Smith, Richard D. )

    2000-12-01

    We report on the design and application of a high-efficiency multiple-capillary liquid chromatography (LC) system for high-throughput proteome analysis. The multiple-capillary LC system was operated at the pressure of 10,000 psi using commercial LC pumps to deliver the mobile phase and newly developed passive feedback valves to switch the mobile phase flow and introduce samples. The multiple-capillary LC system was composed of several serially connected dual-capillary column devices. The dual-capillary column approach was designed to eliminate the time delay for regeneration (or equilibrium) of the capillary column after its use under the mobile phase gradient condition (i.e. one capillary column was used in separation and the other was washed using mobile phase A). The serially connected dual-capillary columns and ESI sources were operated independently, and could be used for either''backup'' operation or with other mass spectrometer(s). This high-efficiency multiple-capillary LC system uses switching valves for all operations and is highly amenable to automation. The separations efficiency of dual-capillary column device, optimal capillary dimensions (column length and packed particle size), suitable mobile phases for electrospray, and the capillary re-generation were investigated. A high magnetic field (11.5 tesla) Fourier transform ion cyclotron resonance (FTICR) mass spectrometer was coupled on-line with this high-efficiency multiple-capillary LC system through an electrospray ionization source. The capillary LC provided a peak capacity of {approx}600, and the 2-D capillary LC-FTICR provided a combined resolving power of > 6 x 10 7 polypeptide isotopic distributions. For yeast cellular tryptic digests, > 100,000 polypeptides were typically detected, and {approx}1,000 proteins can be characterized in a single run.

  11. Magneto-capillary valve for integrated purification and enrichment of nucleic acids and proteins.

    PubMed

    den Dulk, Remco C; Schmidt, Kristiane A; Sabatté, Gwénola; Liébana, Susana; Prins, Menno W J

    2013-01-01

    We describe the magneto-capillary valve (MCV) technology, a flexible approach for integrated biological sample preparation within the concept of stationary microfluidics. Rather than moving liquids in a microfluidic device, discrete units of liquid are present at fixed positions in the device and magnetic particles are actuated between the fluids. The MCV concept is characterized by the use of two planar surfaces at a capillary mutual distance, with specific features to confine the fluids by capillary forces, and the use of a gas or a phase-change material separating the stationary aqueous liquids. We have studied the physics of magneto-capillary valving by quantifying the magnetic force as a function of time and position, which reveals the balance of magnetic, capillary and frictional forces in the system. By purification experiments with a fluorescent tracer we have measured the amount of co-transported liquid, which is a key parameter for efficient purification. To demonstrate the versatility of the technology, several MCV device architectures were tested in a series of biological assays, showing the purification and enrichment of nucleic acids and proteins. Target recovery comparable to non-miniaturized commercial kits was observed for the extraction of DNA from human cells in buffer, using a device architecture with patterned air valves. Experiments using an enrichment module and patterned air valves demonstrate a 40-fold effective enrichment of DNA in buffer. DNA was also successfully purified from blood plasma using paraffin phase-change valves. Finally, the enrichment of a protein biomarker (prostate-specific antigen) using geometrical air valves resulted in a 7-fold increase of detection signal. The MCV technology is versatile, offers extensive freedom for the design of fully integrated systems, and is expected to be manufacturable in a cost-effective way. We conclude that the MCV technology can become an important enabling technology for point

  12. Multiple-capillary measurement of RBC speed, flux, and density with optical coherence tomography.

    PubMed

    Lee, Jonghwan; Wu, Weicheng; Lesage, Frederic; Boas, David A

    2013-11-01

    As capillaries exhibit heterogeneous and fluctuating dynamics even during baseline, a technique measuring red blood cell (RBC) speed and flux over many capillaries at the same time is needed. Here, we report that optical coherence tomography can capture individual RBC passage simultaneously over many capillaries located at different depths. Further, we demonstrate the ability to quantify RBC speed, flux, and linear density. This technique will provide a means to monitor microvascular flow dynamics over many capillaries at different depths at the same time.

  13. An air-pressure-free elastomeric valve for integrated nucleic acid analysis by capillary electrophoresis

    NASA Astrophysics Data System (ADS)

    Jung, Wooseok; Barrett, Matthew; Brooks, Carla; Rivera, Andrew; Birdsell, Dawn N.; Wagner, David M.; Zenhausern, Frederic

    2015-12-01

    We present a new elastomeric valve for integrated nucleic acid analysis by capillary electrophoresis. The valve functions include metering to capture a designated volume of biological sample into a polymerase chain reaction (PCR) chamber, sealing to preserve the sample during PCR cycling, and transfer of the PCR-products and on-chip formamide post-processing for the analysis of DNA fragments by capillary gel electrophoresis. This new valve differs from prior art polydimethylsiloxane (PDMS) valves in that the valve is not actuated externally by air-pressure or vacuum so that it simplifies a DNA analysis system by eliminating the need for an air-pressure or vacuum source, and off-cartridge solenoid valves, control circuit boards and software. Instead, the new valve is actuated by a thermal cycling peltier assembly integrated within the hardware instrument that tightly comes in contact with a microfluidic cartridge for thermal activation during PCR, so that it spontaneously closes the valve without an additional actuator system. The valve has bumps in the designated locations so that it has a self-alignment that does not require precise alignment of a valve actuator. Moreover, the thickness of the new valve is around 600 μm with an additional bump height of 400 μm so that it is easy to handle and very feasible to fabricate by injection molding compared to other PDMS valves whose thicknesses are around 30-100 μm. The new valve provided over 95% of metering performance in filling the fixed volume of the PCR chamber, preserved over 97% of the sample volume during PCR, and showed very comparable capillary electrophoresis peak heights to the benchtop assay tube controls with very consistent transfer volume of the PCR-product and on-chip formamide. The new valve can perform a core function for integrated nucleic acid analysis by capillary electrophoresis.

  14. Multiple-stage integrating accelerometer

    DOEpatents

    Devaney, Howard F.

    1986-01-01

    An accelerometer assembly is provided for use in activating a switch in response to multiple acceleration pulses in series. The accelerometer includes a housing forming a chamber. An inertial mass or piston is slidably disposed in the chamber and spring biased toward a first or reset position. A damping system is also provided to damp piston movement in response to first and subsequent acceleration pulses. Additionally, a cam, including a Z-shaped slot, and cooperating follower pin slidably received therein are mounted to the piston and the housing. The middle or cross-over leg of the Z-shaped slot cooperates with the follower pin to block or limit piston movement and prevent switch activation in response to a lone acceleration pulse. The switch of the assembly is only activated after two or more separate acceleration pulses are sensed and the piston reaches the end of the chamber opposite the reset position.

  15. Multiple-stage integrating accelerometer

    DOEpatents

    Devaney, H.F.

    1984-06-27

    An accelerometer assembly is provided for use in activating a switch in response to multiple acceleration pulses in series. The accelerometer includes a housing forming a chamber. An inertial mass or piston is slidably disposed in the chamber and spring biased toward a first or reset position. A damping system is also provided to damp piston movement in response to first and subsequent acceleration pulses. Additionally, a cam, including a Z-shaped slot, and cooperating follower pin slidably received therein are mounted to the piston and the housing. The middle or cross-over leg of the Z-shaped slot cooperates with the follower pin to block or limit piston movement and prevent switch activation in response to a lone acceleration pulse. The switch of the assembly is only activated after two or more separate acceleration pulses are sensed and the piston reaches the end of the chamber opposite the reset position.

  16. An Experimental Study of Pressure Oscillation in a Capillary Pumped Loop with Multiple Evaporators and Condensers

    NASA Technical Reports Server (NTRS)

    Ku, Jen-Tung; Hoang, Triem T.

    1998-01-01

    The heat transport capability of a capillary pumped loop (CPL) is limited by the pressure drop that its evaporator wick can sustain. The pressure drop in a CPL is not constant even under seemingly steady operation, but rather exhibits an oscillatory behavior. A hydrodynamic theory based on a mass-spring-dashpot model was previously developed to predict the pressure oscillation in a CPL with a single evaporator and a single condenser. The theory states that the pressure oscillation is a function of physical dimensions of the CPL components and operating conditions. Experimental data agreed very well with theoretical predictions. The hydrodynamic stability theory has recently been extended to predict the pressure oscillations in CPLs with multiple evaporators and multiple condensers. Concurrently, an experimental study was conducted to verify the theory and to investigate the effects of various parameters on the pressure oscillation. Four evaporators with different wick properties were tested using a test loop containing two condenser plates. The test loop allowed the four evaporators to be tested in a single-pump, two-pump or four-pump configuration, and the two condenser plates to be plumbed either in parallel or in series. Test conditions included varying the power input, the reservoir set point temperature, the condenser sink temperature, and the flow resistance between the reservoir and the loop. Experimental results agreed well with theoretical predictions.

  17. [Electron-microscopy studies of capillaries of the dialyser C-DAK 4 with reference to multiple use].

    PubMed

    Stein, G; Linss, W; Völksch, G

    1977-12-01

    The results of the examinations show that the integrity of the wall of the capillary is not impaired by the process of purification, but, on the other hand, functional changes by thrombotic occlusion as well as disseminated deposits of protein may be expected. The temporary regime of dialysis mus consider this fact in order to achieve a constant effect. But on principle from the clinical experience and on the basis of these results of examinations a manifold use of the dialysator of the capillary in carrying out the purification measures mentioned may be recommended.

  18. Fabrication of a miniaturized capillary waveguide integrated fiber-optic sensor for fluoride determination.

    PubMed

    Xiong, Yan; Wang, Chengjie; Tao, Tao; Duan, Ming; Tan, Jun; Wu, Jiayi; Wang, Dong

    2016-05-10

    Fluoride concentration is a key aspect of water quality and essential for human health. Too much or too little fluoride intake from water supplies is harmful to public health. In this study, a capillary waveguide integrated fiber-optic sensor was fabricated for fluoride measurement in water samples. The sensor was modularly designed with three parts, i.e., a light source, capillary flow cell and detector. When light propagated from a light emitting diode (LED) to the capillary waveguide cell through an excitation fiber, it interacted with the sensing reagent, and its intensity changed with different fluoride concentrations. Then, the light propagated to the detector through a detection fiber for absorption determination of fluoride according to Beer's law. This miniaturized sensor showed advantages of fast analysis (9.2 s) and small reagent demand (200 μL) per sample, and it also had a low detection limit (8 ppb) and high selectivity for fluoride determination. The sensor was applied to fluoride determination in different water samples. The results obtained were compared with those obtained by conventional spectrophotometry and ion chromatography, showing agreement and validating the sensor's potential application.

  19. Fabrication of a miniaturized capillary waveguide integrated fiber-optic sensor for fluoride determination.

    PubMed

    Xiong, Yan; Wang, Chengjie; Tao, Tao; Duan, Ming; Tan, Jun; Wu, Jiayi; Wang, Dong

    2016-05-10

    Fluoride concentration is a key aspect of water quality and essential for human health. Too much or too little fluoride intake from water supplies is harmful to public health. In this study, a capillary waveguide integrated fiber-optic sensor was fabricated for fluoride measurement in water samples. The sensor was modularly designed with three parts, i.e., a light source, capillary flow cell and detector. When light propagated from a light emitting diode (LED) to the capillary waveguide cell through an excitation fiber, it interacted with the sensing reagent, and its intensity changed with different fluoride concentrations. Then, the light propagated to the detector through a detection fiber for absorption determination of fluoride according to Beer's law. This miniaturized sensor showed advantages of fast analysis (9.2 s) and small reagent demand (200 μL) per sample, and it also had a low detection limit (8 ppb) and high selectivity for fluoride determination. The sensor was applied to fluoride determination in different water samples. The results obtained were compared with those obtained by conventional spectrophotometry and ion chromatography, showing agreement and validating the sensor's potential application. PMID:27067512

  20. Gene analysis of multiple oral bacteria by the polymerase chain reaction coupled with capillary polymer electrophoresis.

    PubMed

    Liu, Chenchen; Yamaguchi, Yoshinori; Sekine, Shinichi; Ni, Yi; Li, Zhenqing; Zhu, Xifang; Dou, Xiaoming

    2016-03-01

    Capillary polymer electrophoresis is identified as a promising technology for the analysis of DNA from bacteria, virus and cell samples. In this paper, we propose an innovative capillary polymer electrophoresis protocol for the quantification of polymerase chain reaction products. The internal standard method was modified and applied to capillary polymer electrophoresis. The precision of our modified internal standard protocol was evaluated by measuring the relative standard deviation of intermediate capillary polymer electrophoresis experiments. Results showed that the relative standard deviation was reduced from 12.4-15.1 to 0.6-2.3%. Linear regression tests were also implemented to validate our protocol. The modified internal standard method showed good linearity and robust properties. Finally, the ease of our method was illustrated by analyzing a real clinical oral sample using a one-run capillary polymer electrophoresis experiment. PMID:26648455

  1. Monitoring antigenic protein integrity during glycoconjugate vaccine synthesis using capillary electrophoresis-mass spectrometry.

    PubMed

    Tengattini, Sara; Domínguez-Vega, Elena; Temporini, Caterina; Terreni, Marco; Somsen, Govert W

    2016-09-01

    A capillary electrophoresis-mass spectrometry (CE-MS) method was developed for the characterization and integrity assessment of the Mycobacterium tuberculosis (MTB) antigens TB10.4 and Ag85B and their chemically produced glycoconjugates, which are glycovaccine candidates against tuberculosis (TB). In order to prevent protein adsorption to the inner capillary wall and to achieve efficient separation of the antigen proteoforms, a polyionic multilayer coating of polybrene-dextran sulfate-polybrene (PB-DS-PB) was used in combination with 1.5 M acetic acid as background electrolyte (BGE). Coupling of CE to high-resolution time-of-flight MS was achieved by a coaxial interface employing a sheath liquid of isopropanol-water (50:50, v/v) containing 0.1 % formic acid. The MTB antigens were exposed to experimental conditions used for chemical glycosylation (but no activated saccharide was added) in order to investigate their stability during glycovaccine production. CE-MS analysis revealed the presence of several closely related degradation products, including truncated, oxidized and conformational variants, which were assigned by accurate mass. Analysis of synthesized mannose conjugates of TB10.4 and Ag85B allowed the determination of the glycoform composition of the neo-glycoproteins next to the characterization of degradation products which were shown to be partly glycoconjugated. Moreover, the selectivity of CE-MS allowed specific detection of deamidated species (protein mass change of 1.0 Da only), indicating that chemical glycosylation increased susceptibility to deamidation. Overall, the results show that CE-MS represents a useful analytical tool for the detailed characterization and optimization of neo-glycoconjugate products. Graphical Abstract Flowchart illustrating Mycobacterium tuberculosis (MTB) antigen glycosylation, glycoconjugate variant and degradation product separation by capillary electrophoresis (CE) and their characterization by intact mass

  2. Vertically Integrated Multiple Nanowire Field Effect Transistor.

    PubMed

    Lee, Byung-Hyun; Kang, Min-Ho; Ahn, Dae-Chul; Park, Jun-Young; Bang, Tewook; Jeon, Seung-Bae; Hur, Jae; Lee, Dongil; Choi, Yang-Kyu

    2015-12-01

    A vertically integrated multiple channel-based field-effect transistor (FET) with the highest number of nanowires reported ever is demonstrated on a bulk silicon substrate without use of wet etching. The driving current is increased by 5-fold due to the inherent vertically stacked five-level nanowires, thus showing good feasibility of three-dimensional integration-based high performance transistor. The developed fabrication process, which is simple and reproducible, is used to create multiple stiction-free and uniformly sized nanowires with the aid of the one-route all-dry etching process (ORADEP). Furthermore, the proposed FET is revamped to create nonvolatile memory with the adoption of a charge trapping layer for enhanced practicality. Thus, this research suggests an ultimate design for the end-of-the-roadmap devices to overcome the limits of scaling.

  3. Vertically Integrated Multiple Nanowire Field Effect Transistor.

    PubMed

    Lee, Byung-Hyun; Kang, Min-Ho; Ahn, Dae-Chul; Park, Jun-Young; Bang, Tewook; Jeon, Seung-Bae; Hur, Jae; Lee, Dongil; Choi, Yang-Kyu

    2015-12-01

    A vertically integrated multiple channel-based field-effect transistor (FET) with the highest number of nanowires reported ever is demonstrated on a bulk silicon substrate without use of wet etching. The driving current is increased by 5-fold due to the inherent vertically stacked five-level nanowires, thus showing good feasibility of three-dimensional integration-based high performance transistor. The developed fabrication process, which is simple and reproducible, is used to create multiple stiction-free and uniformly sized nanowires with the aid of the one-route all-dry etching process (ORADEP). Furthermore, the proposed FET is revamped to create nonvolatile memory with the adoption of a charge trapping layer for enhanced practicality. Thus, this research suggests an ultimate design for the end-of-the-roadmap devices to overcome the limits of scaling. PMID:26544156

  4. Wide-field imaging design for a multiple-capillary DNA-sequencing system

    NASA Astrophysics Data System (ADS)

    Nay, Lyle M.; Sinclair, Robert; Swerdlow, Harold

    1997-05-01

    A laser-induced fluorescence detection system compatible with a capillary electrophoresis array was developed. The design incorporates fiber-optic excitation and a detection system including a diffraction grating and a CCD camera. The system employs no moving parts and is capable of producing data comparable to commercially available systems. It is based on a spectrally-resolved four-dye sequencing scheme. The conceptual design was proven, however, refinements must be made to optimize performance for high-throughput capillary-array DNA sequencing. Automated sample preparation and loading in combination with a refillable separation- matrix capillary-array system could prove to be an invaluable tool for completion of the Human Genome Project.

  5. Modification of narrow ablating capillaries under the influence of multiple femtosecond laser pulses

    NASA Astrophysics Data System (ADS)

    Gubin, K. V.; Lotov, K. V.; Trunov, V. I.; Pestryakov, E. V.

    2016-09-01

    Powerful femtosecond laser pulses that propagate through narrow ablating capillaries cause modification of capillary walls, which is studied experimentally and theoretically. At low intensities, the laser-induced periodic surface structures and porous coating composed of sub-micron particles appear on the walls. At higher intensities, the surface is covered by deposited droplets of the size up to 10 μm. In both cases, the ablated material forms a solid plug that completely blocks the capillary after several hundreds or thousands of pulses. The suggested theoretical model indicates that the plug formation is a universal effect. It must take place in any narrow tube subject to ablation under the action of short laser pulses.

  6. Integrating multiple networks for protein function prediction

    PubMed Central

    2015-01-01

    Background High throughput techniques produce multiple functional association networks. Integrating these networks can enhance the accuracy of protein function prediction. Many algorithms have been introduced to generate a composite network, which is obtained as a weighted sum of individual networks. The weight assigned to an individual network reflects its benefit towards the protein functional annotation inference. A classifier is then trained on the composite network for predicting protein functions. However, since these techniques model the optimization of the composite network and the prediction tasks as separate objectives, the resulting composite network is not necessarily optimal for the follow-up protein function prediction. Results We address this issue by modeling the optimization of the composite network and the prediction problems within a unified objective function. In particular, we use a kernel target alignment technique and the loss function of a network based classifier to jointly adjust the weights assigned to the individual networks. We show that the proposed method, called MNet, can achieve a performance that is superior (with respect to different evaluation criteria) to related techniques using the multiple networks of four example species (yeast, human, mouse, and fly) annotated with thousands (or hundreds) of GO terms. Conclusion MNet can effectively integrate multiple networks for protein function prediction and is robust to the input parameters. Supplementary data is available at https://sites.google.com/site/guoxian85/home/mnet. The Matlab code of MNet is available upon request. PMID:25707434

  7. High-Throughput Analysis of Lidocaine in Pharmaceutical Formulation by Capillary Zone Electrophoresis Using Multiple Injections in a Single Run

    PubMed Central

    Valese, Andressa C.; Spudeit, Daniel A.; Dolzan, Maressa D.; Bretanha, Lizandra C.; Micke, Gustavo A.

    2016-01-01

    This paper reports the development of a subminute separation method by capillary zone electrophoresis in an uncoated capillary using multiple injection procedure for the determination of lidocaine in samples of pharmaceutical formulations. The separation was performed in less than a minute leading to doing four injections in a single run. The cathodic electroosmotic flow contributed to reducing the analyses time. The background electrolyte was composed of 20 mmol L−1 2-amino-2-(hydroxymethyl)-1,3-propanediol and 40 mmol L−1 2-(N-morpholino)ethanesulfonic acid at pH 6.1. The internal standard used was benzylamine. Separations were performed in a fused uncoated silica capillary (32 cm total length, 23.5 cm effective length, and 50 μm internal diameter) with direct UV detection at 200 nm. Samples and standards were injected hydrodynamically using 40 mbar/3 s interspersed with spacer electrolyte using 40 mbar/7 s. The electrophoretic system was operated under constant voltage of 30 kV with positive polarity on the injection side. The evaluation of some analytical parameters of the method showed good linearity (r2 > 0.999), a limit of detection 0.92 mg L−1, intermediate precision better than 3.2% (peak area), and recovery in the range of 92–102%. PMID:27069712

  8. Chemosensory function of amphibian skin: integrating epithelial transport, capillary blood flow and behaviour.

    PubMed

    Hillyard, S D; Willumsen, N J

    2011-07-01

    Terrestrial anuran amphibians absorb water across specialized regions of skin on the posterioventral region of their bodies. Rapid water absorption is mediated by the insertion of aquaporins into the apical membrane of the outermost cell layer. Water moves out of the epithelium via aquaglyceroporins in the basolateral membrane and into the circulation in conjunction with increased capillary blood flow to the skin and aquaporins in the capillary endothelial cells. These physiological responses are activated by intrinsic stimuli relating to the animals' hydration status and extrinsic stimuli relating to the detection of osmotically available water. The integration of these processes has been studied using behavioural observations in conjunction with neurophysiological recordings and studies of epithelial transport. These studies have identified plasma volume and urinary bladder stores as intrinsic stimuli that activate the formation of angiotensin II (AII) to stimulate water absorption behaviour. The coordinated increase in water permeability and capillary blood flow appears to be mediated primarily by sympathetic stimulation of beta adrenergic receptors, although the neurohypopyseal hormone arginine vasotocin (AVT) may also play a role. Extrinsic stimuli relate primarily to the ionic and osmotic properties of hydration sources. Toads avoid NaCl solutions that have been shown to be harmful in acute exposure, approx. 200-250 mm. The avoidance is partially attenuated by amiloride raising the hypothesis that the mechanism for salt detection by toads resembles that for salt taste in mammals that take in water by mouth. In this model, depolarization of the basolateral membrane of taste cells is coupled to afferent neural stimulation. In toad skin we have identified innervation of skin epithelial cells by branches of spinal nerves and measured neural responses to NaCl solutions that elicit behavioural avoidance. These same concentrations produce depolarization of the

  9. Mesangial cell αvβ8-integrin regulates glomerular capillary integrity and repair

    PubMed Central

    Lakhe-Reddy, Sujata; Li, Vincent; Arnold, Thomas D.; Khan, Shenaz

    2014-01-01

    αvβ8-Integrin is most abundantly expressed in the kidney, brain, and female reproductive organs, and its cognate ligand is latent transforming growth factor (LTGF)-β. Kidney αvβ8-integrin localizes to mesangial cells, and global β8-integrin gene (Itgb8) deletion results in embryonic lethality due to impaired placentation and cerebral hemorrhage. To circumvent the lethality and better define kidney αvβ8-integrin function, Cre-lox technology was used to generate mesangial-specific Itgb8-null mice. Platelet-derived growth factor-β receptor (PDGFBR)-Cre mice crossed with a reporter strain revealed functional Cre recombinase activity in a predicted mesangial pattern. However, mating between two different PDGFBR-Cre or Ren1d-Cre strains with Itgb8 flox/− mice consistently resulted in incomplete recombination, with no renal phenotype in mosaic offspring. Induction of a renal phenotype with Habu snake venom, a reversible mesangiolytic agent, caused exaggerated glomerular capillary microaneurysms and delayed recovery in Cre+/− PDGFRB flox/− mice compared with Cre+/− PDGFRB flox/+ control mice. To establish the mechanism, in vitro experiments were conducted in Itgb8-null versus Itgb8-expressing mesangial cells and fibroblasts, which revealed β8-integrin-regulated adhesion to Arg-Gly-Asp (RGD) peptides within a mesangial-conditioned matrix as well as β8-integrin-dependent migration on RGD-containing LTGF-β or vitronectin matrices. We speculate that kidney αvβ8-integrin indirectly controls glomerular capillary integrity through mechanical tension generated by binding RGD peptides in the mesangial matrix, and healing after glomerular injury may be facilitated by mesangial cell migration, which is guided by transient β8-integrin interactions with RGD ligands. PMID:24740792

  10. Mesangial cell αvβ8-integrin regulates glomerular capillary integrity and repair.

    PubMed

    Lakhe-Reddy, Sujata; Li, Vincent; Arnold, Thomas D; Khan, Shenaz; Schelling, Jeffrey R

    2014-06-15

    αvβ8-Integrin is most abundantly expressed in the kidney, brain, and female reproductive organs, and its cognate ligand is latent transforming growth factor (LTGF)-β. Kidney αvβ8-integrin localizes to mesangial cells, and global β8-integrin gene (Itgb8) deletion results in embryonic lethality due to impaired placentation and cerebral hemorrhage. To circumvent the lethality and better define kidney αvβ8-integrin function, Cre-lox technology was used to generate mesangial-specific Itgb8-null mice. Platelet-derived growth factor-β receptor (PDGFBR)-Cre mice crossed with a reporter strain revealed functional Cre recombinase activity in a predicted mesangial pattern. However, mating between two different PDGFBR-Cre or Ren1(d)-Cre strains with Itgb8 (flox/-) mice consistently resulted in incomplete recombination, with no renal phenotype in mosaic offspring. Induction of a renal phenotype with Habu snake venom, a reversible mesangiolytic agent, caused exaggerated glomerular capillary microaneurysms and delayed recovery in Cre(+/-) PDGFRB (flox/-) mice compared with Cre(+/-) PDGFRB (flox/+) control mice. To establish the mechanism, in vitro experiments were conducted in Itgb8-null versus Itgb8-expressing mesangial cells and fibroblasts, which revealed β8-integrin-regulated adhesion to Arg-Gly-Asp (RGD) peptides within a mesangial-conditioned matrix as well as β8-integrin-dependent migration on RGD-containing LTGF-β or vitronectin matrices. We speculate that kidney αvβ8-integrin indirectly controls glomerular capillary integrity through mechanical tension generated by binding RGD peptides in the mesangial matrix, and healing after glomerular injury may be facilitated by mesangial cell migration, which is guided by transient β8-integrin interactions with RGD ligands.

  11. Planar lens integrated capillary action microfluidic immunoassay device for the optical detection of troponin I.

    PubMed

    Mohammed, Mazher-Iqbal; Desmulliez, Marc P Y

    2013-01-01

    Optical based analysis in microfluidic and lab-on-a-chip systems are currently considered the gold standard methodology for the determination of end point reactions for various chemical and biological reaction processes. Typically, assays are performed using bulky ancillary apparatus such as microscopes and complex optical excitation and detection systems. Such instrumentation negates many of the advantages offered by device miniaturisation, particularly with respect to overall portability. In this article, we present a CO2 laser ablation technique for rapidly prototyping on-chip planar lenses, in conjunction with capillary action based autonomous microfluidics, to create a miniaturised and fully integrated optical biosensing platform. The presented self-aligned on-chip optical components offer an efficient means to direct excitation light within microfluidics and to directly couple light from a LED source. The device has been used in conjunction with a miniaturised and bespoke fluorescence detection platform to create a complete, palm sized system (≈60 × 80 × 60 mm) capable of performing fluoro-immunoassays. The system has been applied to the detection of cardiac Troponin I, one of the gold standard biomarkers for the diagnosis of acute myocardial infarction, achieving a lower detection limit of 0.08 ng/ml, which is at the threshold of clinically applicable concentrations. The portable nature of the complete system and the biomarker detection capabilities demonstrate the potential of the devised instrumentation for use as a medical diagnostics device at the point of care.

  12. Integrating Whispering Gallery Mode Refractive Index Sensing with Capillary Electrophoresis Separations Using Phase Sensitive Detection.

    PubMed

    Kim, Daniel C; Dunn, Robert C

    2016-01-19

    Whispering gallery mode (WGM) resonators are small, radially symmetric dielectrics that recirculate light through continuous total internal reflection. High-Q resonances are observed that shift in response to changes in surrounding refractive index, leading to many applications in label-free sensing. Surface binding measurements with WGM resonators have demonstrated competitive analytical detection metrics compared to other sensing schemes. Similar figures of merit for detecting bulk refractive index changes, however, have proven more challenging. This has limited their use in applications such as capillary electrophoresis (CE), where their compact footprint and refractive index sensitivity offers advantages in nondestructive, universal detection. Here we couple WGM detection with CE by introducing a modulation scheme to improve detection limits. Phase sensitive WGM (PS-WGM) detection is developed to monitor real-time shifts in the WGM spectrum due to changes in surrounding refractive index. We directly compare phase sensitive detection with spectral measurements normally used to track WGM shifts. We report an improvement in detection limits by almost 300-fold using the PS-WGM method. The integrated CE with PS-WGM approach is demonstrated by detecting the separation of a three-component mixture of cations (Na(+), Li(+), and K(+)).

  13. Planar lens integrated capillary action microfluidic immunoassay device for the optical detection of troponin I

    PubMed Central

    Mohammed, Mazher-Iqbal; Desmulliez, Marc P. Y.

    2013-01-01

    Optical based analysis in microfluidic and lab-on-a-chip systems are currently considered the gold standard methodology for the determination of end point reactions for various chemical and biological reaction processes. Typically, assays are performed using bulky ancillary apparatus such as microscopes and complex optical excitation and detection systems. Such instrumentation negates many of the advantages offered by device miniaturisation, particularly with respect to overall portability. In this article, we present a CO2 laser ablation technique for rapidly prototyping on-chip planar lenses, in conjunction with capillary action based autonomous microfluidics, to create a miniaturised and fully integrated optical biosensing platform. The presented self-aligned on-chip optical components offer an efficient means to direct excitation light within microfluidics and to directly couple light from a LED source. The device has been used in conjunction with a miniaturised and bespoke fluorescence detection platform to create a complete, palm sized system (≈60 × 80 × 60 mm) capable of performing fluoro-immunoassays. The system has been applied to the detection of cardiac Troponin I, one of the gold standard biomarkers for the diagnosis of acute myocardial infarction, achieving a lower detection limit of 0.08 ng/ml, which is at the threshold of clinically applicable concentrations. The portable nature of the complete system and the biomarker detection capabilities demonstrate the potential of the devised instrumentation for use as a medical diagnostics device at the point of care. PMID:24396546

  14. Capillary Hemangioma

    MedlinePlus

    ... Why do capillary hemangiomas on the eyelids cause vision problems? Capillary Hemangiomas of the eyelid can cause ... a capillary hemangioma in the eye socket cause vision problems? A capillary hemangioma in the eye socket ( ...

  15. Simultaneous determination of multiple constituents in real beer samples of different origins by capillary zone electrophoresis.

    PubMed

    Cortacero-Ramírez, Sonia; Segura-Carretero, Antonio; Cruces-Blanco, Carmen; Romero-Romero, Maria Luisa; Fernández-Gutiérrez, Alberto

    2004-11-01

    Simultaneous determination of alcohols, amines, amino acids, flavonoids, and purine and pyrimidine bases in bottled beer samples directly without any pre-treatment was carried out by capillary zone electrophoresis with diode-array detection. Electrolyte conditions such as pH, composition and concentration of the buffer, working voltage and type and time of injection were checked. The best separation of the cited analytes was achieved in 70 mM sodium borate solution and pH 10.25. The detection limits were from 2.1 to 5.6 mg L(-1) for the 18 compounds studied. The developed method is rapid, sensitive and quantitative and has been applied to seven types of international bottled beers of different origins bought locally. PMID:15490130

  16. Automation and integration of multiplexed on-line sample preparation with capillary electrophoresis for DNA sequencing

    SciTech Connect

    Tan, H.

    1999-03-31

    The purpose of this research is to develop a multiplexed sample processing system in conjunction with multiplexed capillary electrophoresis for high-throughput DNA sequencing. The concept from DNA template to called bases was first demonstrated with a manually operated single capillary system. Later, an automated microfluidic system with 8 channels based on the same principle was successfully constructed. The instrument automatically processes 8 templates through reaction, purification, denaturation, pre-concentration, injection, separation and detection in a parallel fashion. A multiplexed freeze/thaw switching principle and a distribution network were implemented to manage flow direction and sample transportation. Dye-labeled terminator cycle-sequencing reactions are performed in an 8-capillary array in a hot air thermal cycler. Subsequently, the sequencing ladders are directly loaded into a corresponding size-exclusion chromatographic column operated at {approximately} 60 C for purification. On-line denaturation and stacking injection for capillary electrophoresis is simultaneously accomplished at a cross assembly set at {approximately} 70 C. Not only the separation capillary array but also the reaction capillary array and purification columns can be regenerated after every run. DNA sequencing data from this system allow base calling up to 460 bases with accuracy of 98%.

  17. Integrated continuous flow polymerase chain reaction and micro-capillary electrophoresis system with bioaffinity preconcentration.

    PubMed

    Njoroge, Samuel K; Witek, Magorzata A; Battle, Katrina N; Immethun, Vicki E; Hupert, Mateusz L; Soper, Steven A

    2011-11-01

    An integrated and modular DNA analysis system is reported that consists of two modules: (i) A continuous flow polymerase chain reaction (CFPCR) module fabricated in a high T(g) (150°C) polycarbonate substrate in which selected gene fragments were amplified using biotin and fluorescently labeled primers accomplished by continuously shuttling small packets of PCR reagents and template through isothermal zones as opposed to heating and cooling large thermal masses typically performed in batch-type thermal reactors. (ii) μCE (micro-capillary electrophoresis) module fabricated in poly(methylmethacrylate) (PMMA), which utilized a bioaffinity selection and purification bed (2.9  μL) to preconcentrate and purify the PCR products generated from the CFPCR module prior to electrophoretic sorting. Biotin-labeled CFPCR products were hydrostatically pumped through the streptavidin-modified bed, where they were extracted onto the surface of micropillars. The affinity bed was also fabricated in PMMA and was populated with an array of microposts (50  μm width; 100  μm height) yielding a total surface area of ∼117  mm(2). This solid-phase extraction (SPE) process demonstrated high selectivity for biotinylated amplicons and utilized the strong streptavidin/biotin interaction (K(d) = 10(-15)  M) to generate high recoveries. The SPE selected CFPCR products were thermally denatured and single-stranded DNA released for injection into a 7-cm-long μCE channel for size-based separations and fluorescence detection. The utility of the system was demonstrated using Alu DNA typing for gender and ethnicity determinations as a model. Compared with the traditional cross-T injection procedure typically used for μCE, the affinity pre-concentration and injection procedure generated signal enhancements of 17- to 40-fold, critical for CFPCR thermal cyclers due to Taylor dispersion associated with their operation. PMID:22038569

  18. Pore-scale Simulations of Capillary Trapping of Supercritical CO2 after Multiple Drainage and Imbibition Cycles

    NASA Astrophysics Data System (ADS)

    Schaap, M. G.

    2015-12-01

    Carbon capture and storage (CCS) of carbon dioxide emissions generated by production or combustion of fossil fuels is a technologically viable means to reduce the build-up of CO2 in the atmosphere and oceans. On a fundamental level, capillary trapping of scCO2 is a pore-scale process that shares mechanisms that are relevant, for example in oil recovery and remediation of NAPL-contaminated aquifers. Capillary trapping of scCO2 differs rather significantly from trapping of oil recovery and NAPL remediation in that the goal is to maximize the amount of NWP storage, whereas the objective of the other applications is to minimize the amount of residual NWP. This difference makes research into capillary trapping of scCO2 unique, but also complex because scCO2 phase properties (e.g. viscosity, density, and interfacial tension) exhibit large shifts with pressure and temperature which can strongly alter the trapping potential and efficiency. In this presentation we compare direct pore-scale observations of the Brine-CO2 drainage and imbibition process with lattice Boltzmann model simulations. The observations were conducted with the synchrotron-based x-ray microtomography facility at the Advanced Photon Source (APS) at Argonne National Laboratory using a novel x-ray compatible, high-pressure, elevated temperature setup. The "large" volumes (~1200 mm3; 6.3 mm diameter and 40 mm in length) were segmented into solid phase (Bentheimer Sandstone), Brine (KI, 1140 kg/m3) and scCO2. We will present LB simulations of small (64^3 voxels) and large sections of the scanned cores with a simple Shan-Chen-type model and a more advanced Equation of State-type model and compare model results to pressure and CO2 saturation levels that were observed for the CO2 invasion and Brine re-imbibition process. We will present results for the smaller sections under multiple drainage and imbibition cycles to investigate whether this will lead to enhanced trapping of scCO2 as found in earlier research.

  19. Multiple-locus variable-number tandem repeat (VNTR) analysis (MLVA) using multiplex PCR and multicolor capillary electrophoresis: application to the genotyping of Brucella species.

    PubMed

    Garofolo, Giuliano

    2015-01-01

    The multiple-locus variable-number tandem repeat (VNTR) analysis (MLVA) is a genetic typing method based on the evaluation of the number of repeated sequences in multiple selected loci of microbial DNA. Although several MLVA typing panels have been proposed for brucellae, the 16-loci panel is recognized as the standard genotyping method, also used for the Brucella international online database. This chapter describes a high-throughput MLVA-16 protocol using multiplex PCRs and multicolor capillary electrophoresis.

  20. Sapphire decelerating capillary channel integrated with antenna at frequency 0.675 THz

    NASA Astrophysics Data System (ADS)

    Ashanin, I. A.; Polozov, S. M.

    2016-07-01

    In recent years, there has been an increasing interest in THz-radiation for application in medicine (THz tomographs), in pharmaceutics (composition analysis for medicines), in introscopy of large-scale objects (ships, trains, containers) and others. THz-radiation can be generated by relativistic electron bunches passing through the Cherenkov decelerating capillary channel (circular waveguide with dielectric filling) with horn extraction. Relativistic electron beams having ∼100 µm in diameter and pulse durations of 1 ps or less (as in photoinjectors) are capable of producing substantial power of THz-radiation. High-peak power coherent Cherenkov radiation can be produced by a properly modulated high-brightness electron beam or by a single, high-density bunch having sub-wavelength dimension. The aperture of a Cherenkov decelerating structure should be comparable with the mm or sub-mm wavelength (0.1-3 mm). Different dielectric materials for the internal surface coating of the capillary channel of mm-sub-mm cross-section can be used. As is known, a frequency of 0.675 THz corresponds to the atmospheric window with high transparency. This report presents the results of electrodynamics study of the metallized sapphire decelerating Cherenkov capillary. A horn antenna attached to the metallized sapphire capillary channel at the 0.675 THz resonant frequency will be considered.

  1. Integrating Multiple Intelligences in EFL/ESL Classrooms

    ERIC Educational Resources Information Center

    Bas, Gokhan

    2008-01-01

    This article deals with the integration of the theory of Multiple Intelligences in EFL/ESL classrooms. In this study, after the theory of multiple intelligences was presented shortly, the integration of this theory into English classrooms. Intelligence types in MI Theory were discussed and some possible application ways of these intelligence types…

  2. Integrated optical detection of autonomous capillary microfluidic immunoassays:a hand-held point-of-care prototype.

    PubMed

    Novo, P; Chu, V; Conde, J P

    2014-07-15

    The miniaturization of biosensors using microfluidics has potential in enabling the development of point-of-care devices, with the added advantages of reduced time and cost of analysis with limits-of-detection comparable to those obtained through traditional laboratory techniques. Interfacing microfluidic devices with the external world can be difficult especially in aspects involving fluid handling and the need for simple sample insertion that avoids special equipment or trained personnel. In this work we present a point-of-care prototype system by integrating capillary microfluidics with a microfabricated photodiode array and electronic instrumentation into a hand-held unit. The capillary microfluidic device is capable of autonomous and sequential fluid flow, including control of the average fluid velocity at any given point of the analysis. To demonstrate the functionality of the prototype, a model chemiluminescence ELISA was performed. The performance of the integrated optical detection in the point-of-care prototype is equal to that obtained with traditional bench-top instrumentation. The photodiode signals were acquired, displayed and processed by a simple graphical user interface using a computer connected to the microcontroller through USB. The prototype performed integrated chemiluminescence ELISA detection in about 15 min with a limit-of-detection of ≈2 nM with an antibody-antigen affinity constant of ≈2×10(7) M(-1). PMID:24607579

  3. Capillary sample

    MedlinePlus

    ... using capillary blood sampling. Disadvantages to capillary blood sampling include: Only a limited amount of blood can be drawn using this method. The procedure has some risks (see below). Capillary ...

  4. Detection of intrathecal immunoglobulin G synthesis by capillary isoelectric focusing immunoassay in oligoclonal band negative multiple sclerosis.

    PubMed

    Halbgebauer, Steffen; Huss, André; Buttmann, Mathias; Steinacker, Petra; Oeckl, Patrick; Brecht, Isabel; Weishaupt, Andreas; Tumani, Hayrettin; Otto, Markus

    2016-05-01

    Oligoclonal immunoglobulin G bands (OCBs) restricted to the cerebrospinal fluid indicate intrathecal inflammation. Using isoelectric focusing and immunoblotting, they are detected in about 95 % of patients with clinically definite multiple sclerosis (MS). To elucidate whether in the remaining 5 % OCBs are truly absent or alternatively missed due to insufficient sensitivity of the routine measurement, we employed a new, highly sensitive nanoscale method for OCB detection. Capillary isoelectric focusing followed by immunological detection served to analyze OCBs in 33 well-characterized OCB-negative and 10 OCB-positive MS patients as well as in 100 OCB-negative control patients with non-inflammatory neurological diseases and 30 OCB-positive control patients with inflammatory neurological diseases. We detected intrathecal immunoglobulin G production in 10 out of 33 MS patients (30 %), initially diagnosed as being OCB-negative, and in all 10 OCB-positive MS patients, but in only 3 out of 100 non-inflammatory neurological controls (3 %) and in 29 of 30 inflammatory neurological controls (97 %). At least about one-third of MS patients without intrathecal immunoglobulin G synthesis according to standard methods are OCB-positive. Advanced methods for OCB detection may increase the analytical sensitivity for detecting OCB in patients with MS who are OCB-negative according to current routine methods.

  5. Highly Sensitive and Multiple Enzyme Activity Assay Using Reagent-release Capillary-Isoelectric Focusing with Rhodamine 110-based Substrates.

    PubMed

    Sueyoshi, Kenji; Nogawa, Yuto; Sugawara, Kasumi; Endo, Tatsuro; Hisamoto, Hideaki

    2015-01-01

    In this study, a simple and highly sensitive enzyme activity assay based on reagent-release capillary-isoelectric focusing is described. Reagent-release capillaries containing a fluorescent substrate, which produces fluorescent products possessing an isoelectric point after reaction with enzymes, provides a simple procedure. This is because it allows to spontaneously inject a sample solution into the capillary by capillary action, mixing reagents, and subsequently concentrating the fluorescent products based on isoelectric focusing. Fluorescent rhodamine 110 and its monoamide derivative, which were generated as a final product and an intermediate, respectively, were then focused and separated by reagent-release capillary-isoelectric focusing. After 30 min of enzyme reactions, two focused fluorescent bands were clearly isolated along the prepared capillaries. Employing the focused band of rhodamine 110 monoamide allowed for highly sensitive detection of enzyme activity in the 10 pg mL(-1) order, while that of the conventional assay using a microplate was in the ng mL(-1) order. Furthermore, arraying reagent-release capillaries of different substrates on a chip allowed for simultaneous multi-assay of enzyme activity with good sensitivity in the pg mL(-1) order for each protein.

  6. Building a cognitive map by assembling multiple path integration systems.

    PubMed

    Wang, Ranxiao Frances

    2016-06-01

    Path integration and cognitive mapping are two of the most important mechanisms for navigation. Path integration is a primitive navigation system which computes a homing vector based on an animal's self-motion estimation, while cognitive map is an advanced spatial representation containing richer spatial information about the environment that is persistent and can be used to guide flexible navigation to multiple locations. Most theories of navigation conceptualize them as two distinctive, independent mechanisms, although the path integration system may provide useful information for the integration of cognitive maps. This paper demonstrates a fundamentally different scenario, where a cognitive map is constructed in three simple steps by assembling multiple path integrators and extending their basic features. The fact that a collection of path integration systems can be turned into a cognitive map suggests the possibility that cognitive maps may have evolved directly from the path integration system.

  7. Screening of neuraminidase inhibitors from traditional Chinese medicines by integrating capillary electrophoresis with immobilized enzyme microreactor.

    PubMed

    Zhao, Haiyan; Chen, Zilin

    2014-05-01

    A simple and effective neuraminidase-immobilized capillary microreactor was fabricated by glutaraldehyde cross-linking technology for screening the neuraminidase inhibitors from traditional Chinese medicines. The substrate and product were separated by CE in short-end injection mode within 2 min. Dual-wavelength ultraviolet detection was employed to eliminate the interference from the screened compounds. The parameters relating to the separation efficiency and the activity of immobilized neuraminidase were systematically evaluated. The activity of the immobilized neuraminidase remained 90% after 30 days storage at 4°C. The immobilized NA microreactor could be continuously used for more than 200 runs. The Michaelis-Menten constant of neuraminidase was determined by the microreactor as 136.6 ± 10.8 μM. In addition, six in eighteen natural products were found as potent inhibitors and the inhibition potentials were ranked in the following order: bavachinin>bavachin>baicalein>baicalin>chrysin and vitexin. The half-maximal inhibitory concentrations were 59.52 ± 4.12, 65.28 ± 1.07, 44.79 ± 1.21 and 31.62 ± 2.04 for baicalein, baicalin, bavachin and bavachinin, respectively. The results demonstrated that the neuraminidase-immobilized capillary microreactor was a very effective tool for screening neuraminidase inhibitors from traditional Chinese medicines.

  8. Integral Methodological Pluralism in Science Education Research: Valuing Multiple Perspectives

    ERIC Educational Resources Information Center

    Davis, Nancy T.; Callihan, Laurie P.

    2013-01-01

    This article examines the multiple methodologies used in educational research and proposes a model that includes all of them as contributing to understanding educational contexts and research from multiple perspectives. The model, based on integral theory (Wilber in a theory of everything. Shambhala, Boston, 2000) values all forms of research as…

  9. Applying Quadrature Rules with Multiple Nodes to Solving Integral Equations

    SciTech Connect

    Hashemiparast, S. M.; Avazpour, L.

    2008-09-01

    There are many procedures for the numerical solution of Fredholm integral equations. The main idea in these procedures is accuracy of the solution. In this paper, we use Gaussian quadrature with multiple nodes to improve the solution of these integral equations. The application of this method is illustrated via some examples, the related tables are given at the end.

  10. The Effects of Tasks on Integrating Information from Multiple Documents

    ERIC Educational Resources Information Center

    Cerdan, Raquel; Vidal-Abarca, Eduardo

    2008-01-01

    The authors examine 2 issues: (a) how students integrate information from multiple scientific documents to describe and explain a physical phenomenon that represents a subset of the information in the documents; and (b) the role of 2 sorts of tasks to achieve this type of integration, either writing an essay on a question requiring integration…

  11. Interstitial integrals in the multiple-scattering model

    SciTech Connect

    Swanson, J.R.; Dill, D.

    1982-08-15

    We present an efficient method for the evaluation of integrals involving multiple-scattering wave functions over the interstitial region. Transformation of the multicenter interstitial wave functions to a single center representation followed by a geometric projection reduces the integrals to products of analytic angular integrals and numerical radial integrals. The projection function, which has the value 1 in the interstitial region and 0 elsewhere, has a closed-form partial-wave expansion. The method is tested by comparing its results with exact normalization and dipole integrals; the differences are 2% at worst and typically less than 1%. By providing an efficient means of calculating Coulomb integrals, the method allows treatment of electron correlations using a multiple scattering basis set.

  12. Portable, Battery Operated Capillary Electrophoresis with Optical Isomer Resolution Integrated with Ionization Source for Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Moini, Mehdi; Rollman, Christopher M.

    2016-03-01

    We introduce a battery operated capillary electrophoresis electrospray ionization (CE/ESI) source for mass spectrometry with optical isomer separation capability. The source fits in front of low or high resolution mass spectrometers similar to a nanospray source with about the same weight and size. The source has two high voltage power supplies (±25 kV HVPS) capable of operating in forward or reverse polarity modes and powered by a 12 V rechargeable lithium ion battery with operation time of ~10 h. In ultrafast CE mode, in which short narrow capillaries (≤15 μm i.d., 15-25 cm long) and field gradients ≥1000 V/cm are used, peak widths at the base are <1 s wide. Under these conditions, the source provides high resolution separation, including optical isomer resolution in ~1 min. Using a low resolution mass spectrometer (LTQ Velos) with a scan time of 0.07 s/scan, baseline separation of amino acids and their optical isomers were achieved in ~1 min. Moreover, bovine serum albumin (BSA) was analyzed in ~1 min with 56% coverage using the data-dependent MS/MS. Using a high resolution mass spectrometer (Thermo Orbitrap Elite) with 15,000 resolution, the fastest scan time achieved was 0.15 s, which was adequate for CE-MS analysis when optical isomer separation is not required or when the optical isomers were well separated. Figures of merit including a detection limit of 2 fmol and linear dynamic range of two orders of magnitude were achieved for amino acids.

  13. Portable, Battery Operated Capillary Electrophoresis with Optical Isomer Resolution Integrated with Ionization Source for Mass Spectrometry.

    PubMed

    Moini, Mehdi; Rollman, Christopher M

    2016-03-01

    We introduce a battery operated capillary electrophoresis electrospray ionization (CE/ESI) source for mass spectrometry with optical isomer separation capability. The source fits in front of low or high resolution mass spectrometers similar to a nanospray source with about the same weight and size. The source has two high voltage power supplies (±25 kV HVPS) capable of operating in forward or reverse polarity modes and powered by a 12 V rechargeable lithium ion battery with operation time of ~10 h. In ultrafast CE mode, in which short narrow capillaries (≤15 μm i.d., 15-25 cm long) and field gradients ≥1000 V/cm are used, peak widths at the base are <1 s wide. Under these conditions, the source provides high resolution separation, including optical isomer resolution in ~1 min. Using a low resolution mass spectrometer (LTQ Velos) with a scan time of 0.07 s/scan, baseline separation of amino acids and their optical isomers were achieved in ~1 min. Moreover, bovine serum albumin (BSA) was analyzed in ~1 min with 56% coverage using the data-dependent MS/MS. Using a high resolution mass spectrometer (Thermo Orbitrap Elite) with 15,000 resolution, the fastest scan time achieved was 0.15 s, which was adequate for CE-MS analysis when optical isomer separation is not required or when the optical isomers were well separated. Figures of merit including a detection limit of 2 fmol and linear dynamic range of two orders of magnitude were achieved for amino acids. PMID:26644308

  14. Contribution of capillary electrophoresis to an integrated vision of humic substances size and charge characterizations

    SciTech Connect

    D'Orlye, Fanny; Reiller, Pascal E.

    2014-02-15

    The physicochemical properties of three different humic substances (HS) are probed using capillary zone electrophoresis in alkaline carbonate buffers, pH 10. Special attention is drawn to the impact of the electrolyte ionic strength and counter-ion nature, chosen within the alkali-metal series, on HS electrophoretic mobility. Taylor-Aris dispersion analysis provides insights into the hydrodynamic radius (R-H) distributions of HS. The smallest characterized entities are of nano-metric dimensions, showing neither ionic strength- nor alkali-metal-induced aggregation. These results are compared with the entities evidenced in dynamic light scattering measurements, the size of which is two order of magnitude higher, ca. 100 nm. The extended Onsager model provides a reasonable description of measured electrophoretic mobilities in the ionic strength range 1-50 mM, thus allowing the estimation of limiting mobilities and ionic charge numbers for the different HS samples. An unexpected HS electrophoretic mobility increase (in absolute value) is observed in the order Li{sup +} ≤ Na{sup +} ≤ K{sup +} ≤ Cs{sup +} and discussed either in terms of retarding forces or in terms of ion-ion interactions. (authors)

  15. An overview of on-line systems using drug metabolizing enzymes integrated into capillary electrophoresis.

    PubMed

    Nowak, Paweł; Woźniakiewicz, Michał; Kościelniak, Paweł

    2013-09-01

    Enzymatic assays using CE are now among the most noteworthy applications of this analytical technique in pharmacology-related investigations. Studies of metabolic pathways of new chemical entities mediated by drug metabolizing enzymes are attracting particular attention. Conventional CE-based enzymatic in vitro assays are generally restricted to the separation of reagents after incubation performed off-line. EMMA represents an alternative and fully prospective approach, allowing injection, reaction, separation, and detection to be conducted in a single capillary. Such an on-line system-in contrast to the standard approach-enables automation, miniaturization, and a significant reduction in reagent volumes, resulting in a very robust and cost-efficient method. Hence, EMMA could be a method of choice for the screening of new drugs, enzymatic inhibitors, and putative drug-drug interactions. This review provides a summary of reports covering the area of EMMA-based and related methods implemented into in vitro studies of drug metabolizing enzymes. A general description of the EMMA framework, enzyme families, and a concise discussion of the prognosis for the development of this methodology are given as well.

  16. Noise suppressing capillary separation system

    DOEpatents

    Yeung, Edward S.; Xue, Yongjun

    1996-07-30

    A noise-suppressing capillary separation system for detecting the real-time presence or concentration of an analyte in a sample is provided. The system contains a capillary separation means through which the analyte is moved, a coherent light source that generates a beam which is split into a reference beam and a sample beam that irradiate the capillary, and a detector for detecting the reference beam and the sample beam light that transmits through the capillary. The laser beam is of a wavelength effective to be absorbed by a chromophore in the capillary. The system includes a noise suppressing system to improve performance and accuracy without signal averaging or multiple scans.

  17. Trajectory of isoelectric focusing from gels to capillaries to immobilized gradients in capillaries

    PubMed Central

    Koshel, Brooke M.; Wirth, Mary J.

    2013-01-01

    This review presents the need for replacing gels in 2D separations for proteomics, where speed, high-throughput, and the ability to characterize trace level proteins or small samples are the current desires. The theme of the review is isoelectric focusing, which is a valuable tool because it pre-concentrates proteins in addition to separating with high peak capacity. The review traces the technological progress from gel IEF to cIEF to packed capillaries with immobilized gradients for cIEF. Multiple capillary techniques are progressing toward meeting the current desires, providing extremely high sensitivity with regard to concentration and to small samples, integrated automation, and high peak capacity from multiple dimensions of separation. Capillaries with immobilized pH gradients for cIEF are emerging, which will alleviate interference from ampholytes and improve reproducibility in separation times when this valuable technique can be used as one of the dimensions. PMID:22930445

  18. High-Throughput Analysis With 96-Capillary Array Electrophoresis and Integrated Sample Preparation for DNA Sequencing Based on Laser Induced Fluorescence Detection

    SciTech Connect

    Gang Xue

    2001-12-31

    The purpose of this research was to improve the fluorescence detection for the multiplexed capillary array electrophoresis, extend its use beyond the genomic analysis, and to develop an integrated micro-sample preparation system for high-throughput DNA sequencing. The authors first demonstrated multiplexed capillary zone electrophoresis (CZE) and micellar electrokinetic chromatography (MEKC) separations in a 96-capillary array system with laser-induced fluorescence detection. Migration times of four kinds of fluoresceins and six polyaromatic hydrocarbons (PAHs) are normalized to one of the capillaries using two internal standards. The relative standard deviations (RSD) after normalization are 0.6-1.4% for the fluoresceins and 0.1-1.5% for the PAHs. Quantitative calibration of the separations based on peak areas is also performed, again with substantial improvement over the raw data. This opens up the possibility of performing massively parallel separations for high-throughput chemical analysis for process monitoring, combinatorial synthesis, and clinical diagnosis. The authors further improved the fluorescence detection by step laser scanning. A computer-controlled galvanometer scanner is adapted for scanning a focused laser beam across a 96-capillary array for laser-induced fluorescence detection. The signal at a single photomultiplier tube is temporally sorted to distinguish among the capillaries. The limit of detection for fluorescein is 3 x 10{sup -11} M (S/N = 3) for 5-mW of total laser power scanned at 4 Hz. The observed cross-talk among capillaries is 0.2%. Advantages include the efficient utilization of light due to the high duty-cycle of step scan, good detection performance due to the reduction of stray light, ruggedness due to the small mass of the galvanometer mirror, low cost due to the simplicity of components, and flexibility due to the independent paths for excitation and emission.

  19. Integrated optical-fiber capillary electrophoresis microchips with novel spin-on-glass surface modification.

    PubMed

    Lin, Che-Hsin; Lee, Gwo-Bin; Fu, Lung-Ming; Chen, Shu-Hui

    2004-07-30

    This paper presents a novel micro-capillary electrophoresis (CE) chip with embedded optical fibers for the on-line detection of DNA samples. The optical fibers are pre-etched and then inserted directly into fiber channels incorporated within low-cost soda-lime glass substrates. The embedded optical fibers are precisely aligned with the microfluidic channels such that the induced fluorescence signals from labeled bio-samples can be detected. This arrangement avoids the requirement for delicate optical alignment procedures and equipment. Surface modification of the CE channels is accomplished by means of a simple and reliable organic-based spin-on-glass (SOG) method. The zeta potential distribution and the corresponding electroosmotic mobility of the fluid are simulated numerically for the modified and non-modified channel surfaces, and then both sets of results are verified experimentally. The present results indicate that the value of the zeta potential for a surface with an SOG coating is 19.3 times smaller than that of an untreated surface. A phiX-174 DNA marker fluid is used to evaluate the injection and separation performance of the developed micro-CE device. Furthermore, the long-term stability of the SOG-coated surface is also investigated. The experimental data reveal that the microchip device is capable of providing highly efficient separations of bio-molecules, and that the SOG layer retains its low zeta potential characteristics for at least 45 days. The present results confirm the effectiveness of the proposed micro-CE chip in performing the on-line detection of DNA samples, and indicate that the SOG process represents a simple and reliable solution for the surface modification of glass-based microchannels. PMID:15142580

  20. Method and system of integrating information from multiple sources

    DOEpatents

    Alford, Francine A.; Brinkerhoff, David L.

    2006-08-15

    A system and method of integrating information from multiple sources in a document centric application system. A plurality of application systems are connected through an object request broker to a central repository. The information may then be posted on a webpage. An example of an implementation of the method and system is an online procurement system.

  1. Integrative prescreening in analysis of multiple cancer genomic studies

    PubMed Central

    2012-01-01

    Background In high throughput cancer genomic studies, results from the analysis of single datasets often suffer from a lack of reproducibility because of small sample sizes. Integrative analysis can effectively pool and analyze multiple datasets and provides a cost effective way to improve reproducibility. In integrative analysis, simultaneously analyzing all genes profiled may incur high computational cost. A computationally affordable remedy is prescreening, which fits marginal models, can be conducted in a parallel manner, and has low computational cost. Results An integrative prescreening approach is developed for the analysis of multiple cancer genomic datasets. Simulation shows that the proposed integrative prescreening has better performance than alternatives, particularly including prescreening with individual datasets, an intensity approach and meta-analysis. We also analyze multiple microarray gene profiling studies on liver and pancreatic cancers using the proposed approach. Conclusions The proposed integrative prescreening provides an effective way to reduce the dimensionality in cancer genomic studies. It can be coupled with existing analysis methods to identify cancer markers. PMID:22799431

  2. Integration of multiple sensor fusion in controller design.

    PubMed

    Abdelrahman, Mohamed; Kandasamy, Parameshwaran

    2003-04-01

    The main focus of this research is to reduce the risk of a catastrophic response of a feedback control system when some of the feedback data from the system sensors are not reliable, while maintaining a reasonable performance of the control system. In this paper a methodology for integrating multiple sensor fusion into the controller design is presented. The multiple sensor fusion algorithm produces, in addition to the estimate of the measurand, a parameter that measures the confidence in the estimated value. This confidence is integrated as a parameter into the controller to produce fast system response when the confidence in the estimate is high, and a slow response when the confidence in the estimate is low. Conditions for the stability of the system with the developed controller are discussed. This methodology is demonstrated on a cupola furnace model. The simulations illustrate the advantages of the new methodology.

  3. Downsizing of an integrated tracking unit for multiple applications

    NASA Astrophysics Data System (ADS)

    Steinway, William J.; Thomas, James E.; Nicoloff, Michael J.; Patz, Mark D.

    1997-02-01

    This paper describes the specifications and capabilities of the integrated tracking unit (ITU) and its multiple applications are presented. The original ITU was developed by Coleman Research Corporation (CRC) for several federal law enforcement agencies over a four-year period and it has been used for friendly and unfriendly vehicle and person position tracking. The ITU has been down-sized to reduce its physical size, weight, and power requirements with respect to the first generation unit. The ITU consists of a global positioning system (GPS) receiver for precise position location and a cellular phone to transmit voice and data to a PC base station with a modem interface. This paper describes the down-sizing of the unit introduced in CRC's 'An Integrated Tracking Unit for Multiple Applications' paper presented at the 1995 Counterdrug Technology Assessment Center's symposium in Nashua, NH. This paper provides a description of the ITU and tested applications.

  4. Multiscale fabrication of multiple proteins and topographical structures by combining capillary force lithography and microscope projection photolithography.

    PubMed

    Kwon, Keon Woo; Choi, Jong-Cheol; Suh, Kahp-Yang; Doh, Junsang

    2011-04-01

    We present new methods that enable the fabrication of multiscale, multicomponent protein-patterned surfaces and multiscale topologically structured surfaces by exploiting the merits of two well-established techniques: capillary force lithography (CFL) and microscope projection photolithography (MPP) based on a protein-friendly photoresist. We further demonstrate that, when hierarchically organized micro- and nanostructures were used as a cell culture platform, human colon cancer cells (cell line SW480) preferentially adhere and migrate onto the area with nanoscale topography over the one with microscale topography. These methods will provide many exciting opportunities for the study of cellular responses to multiscale physicochemical cues.

  5. Multilayer polymer microchip capillary array electrophoresis devices with integrated on-chip labeling for high-throughput protein analysis

    PubMed Central

    Yu, Ming; Wang, Qingsong; Patterson, James E.; Woolley, Adam T.

    2011-01-01

    It is desirable to have inexpensive, high-throughput systems that integrate multiple sample analysis processes and procedures, for applications in biology, chemical analysis, drug discovery, and disease screening. In this paper, we demonstrate multilayer polymer microfluidic devices with integrated on-chip labeling and parallel electrophoretic separation of up to 8 samples. Microchannels were distributed in two different layers and connected through interlayer through-holes in the middle layer. A single set of electrophoresis reservoirs and one fluorescent label reservoir address parallel analysis units for up to 8 samples. Individual proteins and a mixture of cancer biomarkers have been successfully labeled on-chip and separated in parallel with this system. A detection limit of 600 ng/mL was obtained for heat shock protein 90. Our integrated on-chip labeling microdevices show great potential for low-cost, simplified, rapid and high-throughput analysis. PMID:21449615

  6. NEXT Propellant Management System Integration With Multiple Ion Thrusters

    NASA Technical Reports Server (NTRS)

    Sovey, James S.; Soulas, George C.; Herman, Daniel A.

    2011-01-01

    As a critical part of the NEXT test validation process, a multiple-string integration test was performed on the NEXT propellant management system and ion thrusters. The objectives of this test were to verify that the PMS is capable of providing stable flow control to multiple thrusters operating over the NEXT system throttling range and to demonstrate to potential users that the NEXT PMS is ready for transition to flight. A test plan was developed for the sub-system integration test for verification of PMS and thruster system performance and functionality requirements. Propellant management system calibrations were checked during the single and multi-thruster testing. The low pressure assembly total flow rates to the thruster(s) were within 1.4 percent of the calibrated support equipment flow rates. The inlet pressures to the main, cathode, and neutralizer ports of Thruster PM1R were measured as the PMS operated in 1-thruster, 2-thruster, and 3-thruster configurations. It was found that the inlet pressures to Thruster PM1R for 2-thruster and 3-thruster operation as well as single thruster operation with the PMS compare very favorably indicating that flow rates to Thruster PM1R were similar in all cases. Characterizations of discharge losses, accelerator grid current, and neutralizer performance were performed as more operating thrusters were added to the PMS. There were no variations in these parameters as thrusters were throttled and single and multiple thruster operations were conducted. The propellant management system power consumption was at a fixed voltage to the DCIU and a fixed thermal throttle temperature of 75 C. The total power consumed by the PMS was 10.0, 17.9, and 25.2 W, respectively, for single, 2-thruster, and 3-thruster operation with the PMS. These sub-system integration tests of the PMS, the DCIU Simulator, and multiple thrusters addressed, in part, the NEXT PMS and propulsion system performance and functionality requirements.

  7. Integrative metabolomics for characterizing unknown low-abundance metabolites by capillary electrophoresis-mass spectrometry with computer simulations.

    PubMed

    Lee, Richard; Ptolemy, Adam S; Niewczas, Liliana; Britz-McKibbin, Philip

    2007-01-15

    Characterization of unknown low-abundance metabolites in biological samples is one the most significant challenges in metabolomic research. In this report, an integrative strategy based on capillary electrophoresis-electrospray ionization-ion trap mass spectrometry (CE-ESI-ITMS) with computer simulations is examined as a multiplexed approach for studying the selective nutrient uptake behavior of E. coli within a complex broth medium. On-line sample preconcentration with desalting by CE-ESI-ITMS was performed directly without off-line sample pretreatment in order to improve detector sensitivity over 50-fold for cationic metabolites with nanomolar detection limits. The migration behavior of charged metabolites were also modeled in CE as a qualitative tool to support MS characterization based on two fundamental analyte physicochemical properties, namely, absolute mobility (muo) and acid dissociation constant (pKa). Computer simulations using Simul 5.0 were used to better understand the dynamics of analyte electromigration, as well as aiding de novo identification of unknown nutrients. There was excellent agreement between computer-simulated and experimental electropherograms for several classes of cationic metabolites as reflected by their relative migration times with an average error of <2.0%. Our studies revealed differential uptake of specific amino acids and nucleoside nutrients associated with distinct stages of bacterial growth. Herein, we demonstrate that CE can serve as an effective preconcentrator, desalter, and separator prior to ESI-MS, while providing additional qualitative information for unambiguous identification among isobaric and isomeric metabolites. The proposed strategy is particularly relevant for characterizing unknown yet biologically relevant metabolites that are not readily synthesized or commercially available.

  8. Integrative metabolomics for characterizing unknown low-abundance metabolites by capillary electrophoresis-mass spectrometry with computer simulations.

    PubMed

    Lee, Richard; Ptolemy, Adam S; Niewczas, Liliana; Britz-McKibbin, Philip

    2007-01-15

    Characterization of unknown low-abundance metabolites in biological samples is one the most significant challenges in metabolomic research. In this report, an integrative strategy based on capillary electrophoresis-electrospray ionization-ion trap mass spectrometry (CE-ESI-ITMS) with computer simulations is examined as a multiplexed approach for studying the selective nutrient uptake behavior of E. coli within a complex broth medium. On-line sample preconcentration with desalting by CE-ESI-ITMS was performed directly without off-line sample pretreatment in order to improve detector sensitivity over 50-fold for cationic metabolites with nanomolar detection limits. The migration behavior of charged metabolites were also modeled in CE as a qualitative tool to support MS characterization based on two fundamental analyte physicochemical properties, namely, absolute mobility (muo) and acid dissociation constant (pKa). Computer simulations using Simul 5.0 were used to better understand the dynamics of analyte electromigration, as well as aiding de novo identification of unknown nutrients. There was excellent agreement between computer-simulated and experimental electropherograms for several classes of cationic metabolites as reflected by their relative migration times with an average error of <2.0%. Our studies revealed differential uptake of specific amino acids and nucleoside nutrients associated with distinct stages of bacterial growth. Herein, we demonstrate that CE can serve as an effective preconcentrator, desalter, and separator prior to ESI-MS, while providing additional qualitative information for unambiguous identification among isobaric and isomeric metabolites. The proposed strategy is particularly relevant for characterizing unknown yet biologically relevant metabolites that are not readily synthesized or commercially available. PMID:17222002

  9. Multiple cue use and integration in pigeons (Columba livia).

    PubMed

    Legge, Eric L G; Madan, Christopher R; Spetch, Marcia L; Ludvig, Elliot A

    2016-05-01

    Encoding multiple cues can improve the accuracy and reliability of navigation and goal localization. Problems may arise, however, if one cue is displaced and provides information which conflicts with other cues. Here we investigated how pigeons cope with cue conflict by training them to locate a goal relative to two landmarks and then varying the amount of conflict between the landmarks. When the amount of conflict was small, pigeons tended to integrate both cues in their search patterns. When the amount of conflict was large, however, pigeons used information from both cues independently. This context-dependent strategy for resolving spatial cue conflict agrees with Bayes optimal calculations for using information from multiple sources.

  10. Multiplexed fluorescence detector system for capillary electrophoresis

    DOEpatents

    Yeung, E.S.; Taylor, J.A.

    1996-03-12

    A fluorescence detection system for capillary electrophoresis is provided wherein the detection system can simultaneously excite fluorescence and substantially simultaneously monitor separations in multiple capillaries. This multiplexing approach involves laser irradiation of a sample in a plurality of capillaries through optical fibers that are coupled individually with the capillaries. The array is imaged orthogonally through a microscope onto a charge-coupled device camera for signal analysis. 14 figs.

  11. Multiplexed fluorescence detector system for capillary electrophoresis

    DOEpatents

    Yeung, Edward S.; Taylor, John A.

    1994-06-28

    A fluorescence detection system for capillary electrophoresis is provided wherein the detection system can simultaneously excite fluorescence and substantially simultaneously monitor separations in multiple capillaries. This multiplexing approach involves laser irradiation of a sample in a plurality of capillaries through optical fibers that are coupled individually with the capillaries. The array is imaged orthogonally through a microscope onto a charge-coupled device camera for signal analysis.

  12. Multiplexed fluorescence detector system for capillary electrophoresis

    DOEpatents

    Yeung, E.S.; Taylor, J.A.

    1994-06-28

    A fluorescence detection system for capillary electrophoresis is provided wherein the detection system can simultaneously excite fluorescence and substantially simultaneously monitor separations in multiple capillaries. This multiplexing approach involves laser irradiation of a sample in a plurality of capillaries through optical fibers that are coupled individually with the capillaries. The array is imaged orthogonally through a microscope onto a charge-coupled device camera for signal analysis. 14 figures.

  13. Multiplexed fluorescence detector system for capillary electrophoresis

    DOEpatents

    Yeung, Edward S.; Taylor, John A.

    1996-03-12

    A fluorescence detection system for capillary electrophoresis is provided wherein the detection system can simultaneously excite fluorescence and substantially simultaneously monitor separations in multiple capillaries. This multiplexing approach involves laser irradiation of a sample in a plurality of capillaries through optical fibers that are coupled individually with the capillaries. The array is imaged orthogonally through a microscope onto a charge-coupled device camera for signal analysis.

  14. Pt@AuNPs integrated quantitative capillary-based biosensors for point-of-care testing application.

    PubMed

    Wu, Ze; Fu, Qiangqiang; Yu, Shiting; Sheng, Liangrong; Xu, Meng; Yao, Cuize; Xiao, Wei; Li, Xiuqing; Tang, Yong

    2016-11-15

    Current diagnostic technologies primarily rely on bulky and costly analytical instruments. Therefore, cost-effective and portable diagnosis tools that can be used for point-of-care tests (POCT) are highly desirable. In this study, we report a cost-effective, portable capillary-based biosensor for quantitative detection of biomarkers by the naked eye. This capillary-based biosensor was tested by measuring the distance of blue ink movement, which was directly correlated with the oxygen (O2) produced by efficient core-shell Pt@Au nanoparticles (Pt@AuNPs) catalysts decomposed hydrogen peroxide (H2O2). By linking the Pt@AuNPs with antibodies, capillary-based biosensor sandwich immunoassays were constructed. The concentrations of the target proteins were positively correlated with the distances of ink movement. To demonstrate their performance, the biosensors were used to detect the cancer biomarker sprostate-specific antigen (PSA) and carcinoembryonic antigen (CEA). The linear detection range (LDR) of the capillary-based biosensor for detecting PSA was from 0.02 to 2.5ng/mL, and the limit of detection (LOD) was 0.017ng/mL. LDR of the biosensor for detecting CEA was from 0.063 to 16ng/mL, and the LOD was 0.044ng/mL. For detection of PSA and CEA in clinical serum samples, the detection results of the capillary-based biosensor were well correlate with the results from of chemiluminescence immunoassays (CLIAs). Thus, the capillary-based biosensor may potentially be a useful strategy for point-of-care testing, in addition to being portable and cost effective. PMID:27240013

  15. Integrated presentation of ecological risk from multiple stressors

    PubMed Central

    Goussen, Benoit; Price, Oliver R.; Rendal, Cecilie; Ashauer, Roman

    2016-01-01

    Current environmental risk assessments (ERA) do not account explicitly for ecological factors (e.g. species composition, temperature or food availability) and multiple stressors. Assessing mixtures of chemical and ecological stressors is needed as well as accounting for variability in environmental conditions and uncertainty of data and models. Here we propose a novel probabilistic ERA framework to overcome these limitations, which focusses on visualising assessment outcomes by construct-ing and interpreting prevalence plots as a quantitative prediction of risk. Key components include environmental scenarios that integrate exposure and ecology, and ecological modelling of relevant endpoints to assess the effect of a combination of stressors. Our illustrative results demonstrate the importance of regional differences in environmental conditions and the confounding interactions of stressors. Using this framework and prevalence plots provides a risk-based approach that combines risk assessment and risk management in a meaningful way and presents a truly mechanistic alternative to the threshold approach. Even whilst research continues to improve the underlying models and data, regulators and decision makers can already use the framework and prevalence plots. The integration of multiple stressors, environmental conditions and variability makes ERA more relevant and realistic. PMID:27782171

  16. Integral methodological pluralism in science education research: valuing multiple perspectives

    NASA Astrophysics Data System (ADS)

    Davis, Nancy T.; Callihan, Laurie P.

    2013-09-01

    This article examines the multiple methodologies used in educational research and proposes a model that includes all of them as contributing to understanding educational contexts and research from multiple perspectives. The model, based on integral theory (Wilber in a theory of everything. Shambhala, Boston, 2000) values all forms of research as true, but partial. Consideration of objective (exterior) forms of research and data and subjective (interior) forms of research and data are further divided into individual and collective domains. Taking this categorization system one step further reveals eight indigenous perspectives that form a framework for considering research methodologies. Each perspective has unique questions, data sources, methods and quality criteria designed to reveal what is "true" from that view. As science educators who guide our students' research, this framework offers a useful guide to explain differences in types of research, the purpose and validity of each. It allows professional science educators to appreciate multiple forms of research while maintaining rigorous quality criteria. Use of this framework can also help avoid problems of imposing quality criteria of one methodology on research data and questions gathered using another methodology. This model is explored using the second author's dissertation research. Finally a decision chart is provided to use with those who are starting inquiries to guide their thinking and choice of appropriate methodologies to use when conducting research.

  17. Automation and integration of polymerase chain reaction with capillary electrophoresis for high throughput genotyping and disease diagnosis

    SciTech Connect

    Zhang, N.

    1999-02-12

    Genotyping is to detect specific loci in the human genome. These loci provide important information for forensic testing, construction of genetic linkage maps, gene related disease diagnosis and pharmacogenetic research. Genotyping is becoming more and more popular after these loci can be easily amplified by polymerase chain reaction (PCR). Capillary electrophoresis has its unique advantages for DNA analysis due to its fast heat dissipation and ease of automation. Four projects are described in which genotyping is performed by capillary electrophoresis emphasizing different aspects. First, the author demonstrates a principle to determine the genotype based on capillary electrophoresis system. VNTR polymorphism in the human D1S80 locus was studied. Second, the separation of four short tandem repeat (STR) loci vWF, THO1, TPOX and CSF1PO (CTTv) by using poly(ethylene oxide) (PEO) was studied in achieving high resolution and preventing rehybridization of the DNA fragments. Separation under denaturing, non-denaturing conditions and at elevated temperature was discussed. Third, a 250 {micro}m i.d., 365 {micro}m o.d. fused silica capillary was used as the microreactor for PCR. Fourth, direct PCR from blood was studied to simplify the sample preparation for genotyping to minimum.

  18. One-step multiple component isolation from the oil of Crinitaria tatarica (Less.) Sojak. by preparative capillary gas with characterization by spectroscopic and spectrometric techniques and evaluation of biological activity

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In the present work multiple component isolation from the oil of Crinitaria tatarica (Less.) Sojak. by Preparative Capillary Gas Chromatography (PCGC) with characterization by mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy have been carried out. Gas chromatography (GC-FID) ...

  19. A multiple index integrating different levels of organization.

    PubMed

    Cortes, Rui; Hughes, Samantha; Coimbra, Ana; Monteiro, Sandra; Pereira, Vítor; Lopes, Marisa; Pereira, Sandra; Pinto, Ana; Sampaio, Ana; Santos, Cátia; Carrola, João; de Jesus, Joaquim; Varandas, Simone

    2016-10-01

    Many methods in freshwater biomonitoring tend to be restricted to a few levels of biological organization, limiting the potential spectrum of measurable of cause-effect responses to different anthropogenic impacts. We combined distinct organisational levels, covering biological biomarkers (histopathological and biochemical reactions in liver and fish gills), community based bioindicators (fish guilds, invertebrate metrics/traits and chironomid pupal exuviae) and ecosystem functional indicators (decomposition rates) to assess ecological status at designated Water Framework Directive monitoring sites, covering a gradient of human impact across several rivers in northern Portugal. We used Random Forest to rank the variables that contributed more significantly to successfully predict the different classes of ecological status and also to provide specific cut levels to discriminate each WFD class based on reference condition. A total of 59 Biological Quality Elements and functional indicators were determined using this procedure and subsequently applied to develop the integrated Multiple Ecological Level Index (MELI Index), a potentially powerful bioassessment tool. PMID:27344015

  20. Noise suppressing capillary separation system

    DOEpatents

    Yeung, E.S.; Xue, Y.

    1996-07-30

    A noise-suppressing capillary separation system for detecting the real-time presence or concentration of an analyte in a sample is provided. The system contains a capillary separation means through which the analyte is moved, a coherent light source that generates a beam which is split into a reference beam and a sample beam that irradiate the capillary, and a detector for detecting the reference beam and the sample beam light that transmits through the capillary. The laser beam is of a wavelength effective to be absorbed by a chromophore in the capillary. The system includes a noise suppressing system to improve performance and accuracy without signal averaging or multiple scans. 13 figs.

  1. Integrating Multiple Criteria Evaluation and GIS in Ecotourism: a Review

    NASA Astrophysics Data System (ADS)

    Mohd, Z. H.; Ujang, U.

    2016-09-01

    The concept of 'Eco-tourism' is increasingly heard in recent decades. Ecotourism is one adventure that environmentally responsible intended to appreciate the nature experiences and cultures. Ecotourism should have low impact on environment and must contribute to the prosperity of local residents. This article reviews the use of Multiple Criteria Evaluation (MCE) and Geographic Information System (GIS) in ecotourism. Multiple criteria evaluation mostly used to land suitability analysis or fulfill specific objectives based on various attributes that exist in the selected area. To support the process of environmental decision making, the application of GIS is used to display and analysis the data through Analytic Hierarchy Process (AHP). Integration between MCE and GIS tool is important to determine the relative weight for the criteria used objectively. With the MCE method, it can resolve the conflict between recreation and conservation which is to minimize the environmental and human impact. Most studies evidences that the GIS-based AHP as a multi criteria evaluation is a strong and effective in tourism planning which can aid in the development of ecotourism industry effectively.

  2. Multiple Integrated Complementary Healing Approaches: Energetics & Light for bone.

    PubMed

    Gray, Michael G; Lackey, Brett R; Patrick, Evelyn F; Gray, Sandra L; Hurley, Susan G

    2016-01-01

    A synergistic-healing strategy that combines molecular targeting within a system-wide perspective is presented as the Multiple Integrated Complementary Healing Approaches: Energetics And Light (MICHAEL). The basis of the MICHAEL approach is the realization that environmental, nutritional and electromagnetic factors form a regulatory framework involved in bone and nerve healing. The interactions of light, energy, and nutrition with neural, hormonal and cellular pathways will be presented. Energetic therapies including electrical, low-intensity pulsed ultrasound and light based treatments affect growth, differentiation and proliferation of bone and nerve and can be utilized for their healing benefits. However, the benefits of these therapies can be impaired by the absence of nutritional, hormonal and organismal factors. For example, lack of sleep, disrupted circadian rhythms and vitamin-D deficiency can impair healing. Molecular targets, such as the Wnt pathway, protein kinase B and glucocorticoid signaling systems can be modulated by nutritional components, including quercetin, curcumin and Mg(2+) to enhance the healing process. The importance of water and water-regulation will be presented as an integral component. The effects of exercise and acupuncture on bone healing will also be discussed within the context of the MICHAEL approach. PMID:26804592

  3. Tools and Models for Integrating Multiple Cellular Networks

    SciTech Connect

    Gerstein, Mark

    2015-11-06

    In this grant, we have systematically investigated the integrated networks, which are responsible for the coordination of activity between metabolic pathways in prokaryotes. We have developed several computational tools to analyze the topology of the integrated networks consisting of metabolic, regulatory, and physical interaction networks. The tools are all open-source, and they are available to download from Github, and can be incorporated in the Knowledgebase. Here, we summarize our work as follow. Understanding the topology of the integrated networks is the first step toward understanding its dynamics and evolution. For Aim 1 of this grant, we have developed a novel algorithm to determine and measure the hierarchical structure of transcriptional regulatory networks [1]. The hierarchy captures the direction of information flow in the network. The algorithm is generally applicable to regulatory networks in prokaryotes, yeast and higher organisms. Integrated datasets are extremely beneficial in understanding the biology of a system in a compact manner due to the conflation of multiple layers of information. Therefore for Aim 2 of this grant, we have developed several tools and carried out analysis for integrating system-wide genomic information. To make use of the structural data, we have developed DynaSIN for protein-protein interactions networks with various dynamical interfaces [2]. We then examined the association between network topology with phenotypic effects such as gene essentiality. In particular, we have organized E. coli and S. cerevisiae transcriptional regulatory networks into hierarchies. We then correlated gene phenotypic effects by tinkering with different layers to elucidate which layers were more tolerant to perturbations [3]. In the context of evolution, we also developed a workflow to guide the comparison between different types of biological networks across various species using the concept of rewiring [4], and Furthermore, we have developed

  4. Capillary ratchet: Hydrodynamics of capillary feeding in shorebirds

    NASA Astrophysics Data System (ADS)

    Prakash, Manu; Quere, David; Bush, John

    2008-03-01

    Bill morphologies are highly specialized to particular foraging strategies in birds, as is apparent from the large diversity of beak shapes observed in nature. Here we present an experimental and analytical study of capillary feeding in shorebirds. We highlight the critical role of contact angle hysteresis in capillary feeding. Our study provides a simple physical rationalization for the observation of multiple mandibular spreading cycles in feeding, necessary to overcome contact line resistance. We also find a unique geometrical optima in beak opening and closing angles for the most efficient drop transport. This capillary ratchet mechanism may also find applications in micro scale fluid transport, such as valveless pumping of fluid drops.

  5. High integrity carrier phase navigation using multiple civil GPS signals

    NASA Astrophysics Data System (ADS)

    Jung, Jaewoo

    2000-11-01

    A navigation system should guide users to their destinations accurately and reliably. Among the many available navigation aids, the Global Positioning System stands out due to its unique capabilities. It is a satellite-based navigation system which covers the entire Earth with horizontal accuracy of 20 meters for stand alone civil users. Today, the GPS provides only one civil signal, but two more signals will be available in the near future. GPS will provide a second signal at 1227.60 MHz (L2) and a third signal at 1176.45 MHz (Lc), in addition to the current signal at 1575.42 MHz (L1). The focus of this thesis is exploring the possibility of using beat frequencies of these signals to provide navigation aid to users with high accuracy and integrity. To achieve high accuracy, the carrier phase differential GPS is used. The integer ambiguity is resolved using the Cascade Integer Resolution (CIR), which is defined in this thesis. The CIR is an instantaneous, geometry-free integer resolution method utilizing beat frequencies of GPS signals. To insure high integrity, the probability of incorrect integer ambiguity resolution using the CIR is analyzed. The CIR can immediately resolve the Lc integer ambiguity up to 2.4 km from the reference receiver, the Widelane (L1-L2) integer ambiguity up to 22 km, and the Extra Widelane (L2-Lc) integer ambiguity from there on, with probability of incorrect integer resolution of 10-4 . The optimal use of algebraic combinations of multiple GPS signals are also investigated in this thesis. Finally, the gradient of residual differential ionospheric error is estimated to stimated to increase performance of the CIR.

  6. Development of Multiple-Locus Variable-Number Tandem-Repeat Analysis for Molecular Subtyping of Campylobacter jejuni by Using Capillary Electrophoresis

    PubMed Central

    Techaruvichit, Punnida; Vesaratchavest, Mongkol; Keeratipibul, Suwimon; Kuda, Takashi; Kimura, Bon

    2015-01-01

    Campylobacter jejuni is a common cause of the frequently reported food-borne diseases in developed and developing nations. This study describes the development of multiple-locus variable-number tandem-repeat (VNTR) analysis (MLVA) using capillary electrophoresis as a novel typing method for microbial source tracking and epidemiological investigation of C. jejuni. Among 36 tandem repeat loci detected by the Tandem Repeat Finder program, 7 VNTR loci were selected and used for characterizing 60 isolates recovered from chicken meat samples from retail shops, samples from chicken meat processing factory, and stool samples. The discrimination ability of MLVA was compared with that of multilocus sequence typing (MLST). MLVA (diversity index of 0.97 with 31 MLVA types) provided slightly higher discrimination than MLST (diversity index of 0.95 with 25 MLST types). The overall concordance between MLVA and MLST was estimated at 63% by adjusted Rand coefficient. MLVA predicted MLST type better than MLST predicted MLVA type, as reflected by Wallace coefficient (Wallace coefficient for MLVA to MLST versus MLST to MLVA, 86% versus 51%). MLVA is a useful tool and can be used for effective monitoring of C. jejuni and investigation of epidemics caused by C. jejuni. PMID:26025899

  7. Simultaneous determination of free and total glycerol in biodiesel by capillary electrophoresis using multiple short-end injection.

    PubMed

    Spudeit, Daniel Alfonso; Piovezan, Marcel; Dolzan, Maressa D; Vistuba, Jacqueline Pereira; Azevedo, Mônia Stremel; Vitali, Luciano; Leal Oliveira, Marcone Augusto; Oliveira Costa, Ana Carolina; Micke, Gustavo Amadeu

    2013-12-01

    A rapid method for the simultaneous determination of free glycerol (FG) and total glycerol (TG) in biodiesel by CE using a short-end multiple injection (SE/MI) configuration system is described. The sample preparation for FG involves the extraction of glycerol with water and for TG a saponification reaction is carried out followed by extraction as in the case of FG. The glycerol extracted in both cases is submitted to periodate oxidation and the iodate ions formed are measured on a CE-SE/MI system. The relevance of this study lies in the fact that no analytical procedure has been previously reported for the determination of TG (or of FG and TG simultaneously) by CE. The optimum conditions for the saponification/extraction process were 1.25% KOH and 25°C, with a time of only 5 min, and biodiesel mass in the range of 50.0-200.0 mg can be used. Multiple injections were performed hydrodynamically with negative pressure as follows: 50 mbar/3s (FG sample); 50 mbar/6s (electrolyte spacer); 50 mbar/3s (TG sample). The linear range obtained was 1.55-46.5 mg/L with R(2) > 0.99. The LOD and LOQ were 0.16 mg/L and 0.47 mg/L, respectively for TG. The method provides acceptable throughput for application in quality control and monitoring biodiesel synthesis process. In addition, it offers simple sample preparation (saponification process), it can be applied to a variety biodiesel samples (soybean, castor, and waste cooking oils) and it can be used for the determination of two key parameters related to the biodiesel quality with a fast separation (less than 30 s) using an optimized CE-SE/MI system.

  8. Simultaneous determination of free and total glycerol in biodiesel by capillary electrophoresis using multiple short-end injection.

    PubMed

    Spudeit, Daniel Alfonso; Piovezan, Marcel; Dolzan, Maressa D; Vistuba, Jacqueline Pereira; Azevedo, Mônia Stremel; Vitali, Luciano; Leal Oliveira, Marcone Augusto; Oliveira Costa, Ana Carolina; Micke, Gustavo Amadeu

    2013-12-01

    A rapid method for the simultaneous determination of free glycerol (FG) and total glycerol (TG) in biodiesel by CE using a short-end multiple injection (SE/MI) configuration system is described. The sample preparation for FG involves the extraction of glycerol with water and for TG a saponification reaction is carried out followed by extraction as in the case of FG. The glycerol extracted in both cases is submitted to periodate oxidation and the iodate ions formed are measured on a CE-SE/MI system. The relevance of this study lies in the fact that no analytical procedure has been previously reported for the determination of TG (or of FG and TG simultaneously) by CE. The optimum conditions for the saponification/extraction process were 1.25% KOH and 25°C, with a time of only 5 min, and biodiesel mass in the range of 50.0-200.0 mg can be used. Multiple injections were performed hydrodynamically with negative pressure as follows: 50 mbar/3s (FG sample); 50 mbar/6s (electrolyte spacer); 50 mbar/3s (TG sample). The linear range obtained was 1.55-46.5 mg/L with R(2) > 0.99. The LOD and LOQ were 0.16 mg/L and 0.47 mg/L, respectively for TG. The method provides acceptable throughput for application in quality control and monitoring biodiesel synthesis process. In addition, it offers simple sample preparation (saponification process), it can be applied to a variety biodiesel samples (soybean, castor, and waste cooking oils) and it can be used for the determination of two key parameters related to the biodiesel quality with a fast separation (less than 30 s) using an optimized CE-SE/MI system. PMID:24310857

  9. A Fuzzy Logic Framework for Integrating Multiple Learned Models

    SciTech Connect

    Bobi Kai Den Hartog

    1999-03-01

    The Artificial Intelligence field of Integrating Multiple Learned Models (IMLM) explores ways to combine results from sets of trained programs. Aroclor Interpretation is an ill-conditioned problem in which trained programs must operate in scenarios outside their training ranges because it is intractable to train them completely. Consequently, they fail in ways related to the scenarios. We developed a general-purpose IMLM solution, the Combiner, and applied it to Aroclor Interpretation. The Combiner's first step, Scenario Identification (M), learns rules from very sparse, synthetic training data consisting of results from a suite of trained programs called Methods. S1 produces fuzzy belief weights for each scenario by approximately matching the rules. The Combiner's second step, Aroclor Presence Detection (AP), classifies each of three Aroclors as present or absent in a sample. The third step, Aroclor Quantification (AQ), produces quantitative values for the concentration of each Aroclor in a sample. AP and AQ use automatically learned empirical biases for each of the Methods in each scenario. Through fuzzy logic, AP and AQ combine scenario weights, automatically learned biases for each of the Methods in each scenario, and Methods' results to determine results for a sample.

  10. Capillary origami

    NASA Astrophysics Data System (ADS)

    Py, Charlotte; Doppler, Lionel; Bico, Jose; Roman, Benoit; Reverdy, Paul; Baroud, Charles

    2006-11-01

    The wet fur of a dog coming out of a pond assembles into bunches: this is the most common effect of capillary forces on elasticity structures (the hairs). From a practical point of view, the deformation of flexible elements by surface tension forces dramatically damages mechanical microsystems or lung airways, but also allows the self-organization of nanotube carpets into well defined clump patterns. But capillary forces may generate even more complex structures when flexible sheets are brought to contact with a liquid interface. Here we present experiments where surface tension folds up an elastic sheet around a deposited water droplet, and discuss the different possible shapes obtained. These self-folding origami may be used in microsy stems design as a convenient and robust way to fold two-dimensional planar patterns into 3-dimensional structures, since surface tension effects are enhanced at small scales.

  11. On-line sample preconcentration with chemical derivatization of bacterial biomarkers by capillary electrophoresis: a dual strategy for integrating sample pretreatment with chemical analysis.

    PubMed

    Ptolemy, Adam S; Le Bihan, Marianne; Britz-McKibbin, Philip

    2005-11-01

    Simple, selective yet sensitive methods to quantify low-abundance bacterial biomarkers derived from complex samples are required in clinical, biological, and environmental applications. In this report, a new strategy to integrate sample pretreatment with chemical analysis is investigated using on-line preconcentration with chemical derivatization by CE and UV detection. Single-step enantioselective analysis of muramic acid (MA) and diaminopimelic acid (DAP) was achieved by CE via sample enrichment by dynamic pH junction with ortho-phthalaldehyde/N-acetyl-L-cysteine labeling directly in-capillary. The optimized method resulted in up to a 100-fold enhancement in concentration sensitivity compared to conventional off-line derivatization procedures. The method was also applied toward the detection of micromolar levels of MA and DAP excreted in the extracellular medium of Escherichia coli bacterial cell cultures. On-line preconcentration with chemical derivatization by CE represents a unique approach for conducting rapid, sensitive, and high-throughput analyses of other classes of amino acid and amino sugar metabolites with reduced sample handling, where the capillary functions simultaneously as a concentrator, microreactor, and chiral selector.

  12. On-line sample preconcentration with chemical derivatization of bacterial biomarkers by capillary electrophoresis: a dual strategy for integrating sample pretreatment with chemical analysis.

    PubMed

    Ptolemy, Adam S; Le Bihan, Marianne; Britz-McKibbin, Philip

    2005-11-01

    Simple, selective yet sensitive methods to quantify low-abundance bacterial biomarkers derived from complex samples are required in clinical, biological, and environmental applications. In this report, a new strategy to integrate sample pretreatment with chemical analysis is investigated using on-line preconcentration with chemical derivatization by CE and UV detection. Single-step enantioselective analysis of muramic acid (MA) and diaminopimelic acid (DAP) was achieved by CE via sample enrichment by dynamic pH junction with ortho-phthalaldehyde/N-acetyl-L-cysteine labeling directly in-capillary. The optimized method resulted in up to a 100-fold enhancement in concentration sensitivity compared to conventional off-line derivatization procedures. The method was also applied toward the detection of micromolar levels of MA and DAP excreted in the extracellular medium of Escherichia coli bacterial cell cultures. On-line preconcentration with chemical derivatization by CE represents a unique approach for conducting rapid, sensitive, and high-throughput analyses of other classes of amino acid and amino sugar metabolites with reduced sample handling, where the capillary functions simultaneously as a concentrator, microreactor, and chiral selector. PMID:16200529

  13. Liposome behavior in capillary electrophoresis.

    PubMed

    Roberts, M A; Locascio-Brown, L; Maccrehan, W A; Durst, R A

    1996-10-01

    The behavior of liposomes in capillary electrophoresis is studied for the purpose of developing a potential method for characterizing liposomes prepared for use in industrial and analytical applications. This study characterizes the electrophoretic behavior of liposomes under various conditions to provide information about electrophoretic mobility and liposome-capillary surface interactions. The results of this method are compared with the results obtained using traditional laser light-scattering methods to obtain size information about liposome preparations. Additionally, reactions of liposomes and the surfactant n-octyl-β-d-glucopyranoside are performed off-line in bulk solution experiments and on-line in the capillary. Automated delivery of lysis agents by multiple electrokinetic injections is demonstrated as a general method for inducing on-capillary reactions between liposomes and other reagents. Furthermore, some preliminary evidence on the use of liposomes as a hydrophobic partitioning medium for analytical separations is presented.

  14. Generating nonlinear FM chirp radar signals by multiple integrations

    DOEpatents

    Doerry, Armin W.

    2011-02-01

    A phase component of a nonlinear frequency modulated (NLFM) chirp radar pulse can be produced by performing digital integration operations over a time interval defined by the pulse width. Each digital integration operation includes applying to a respectively corresponding input parameter value a respectively corresponding number of instances of digital integration.

  15. Information Integration in Multiple Cue Judgment: A Division of Labor Hypothesis

    ERIC Educational Resources Information Center

    Juslin, Peter; Karlsson, Linnea; Olsson, Henrik

    2008-01-01

    There is considerable evidence that judgment is constrained to additive integration of information. The authors propose an explanation of why serial and additive cognitive integration can produce accurate multiple cue judgment both in additive and non-additive environments in terms of an adaptive division of labor between multiple representations.…

  16. Pre-employment integrity testing across multiple industries.

    PubMed

    Fine, Saul

    2010-10-01

    Despite the robust meta-analytic data available, very little comparative research exists on validities of integrity measures within specific industries. Among a sample of 2456 Israeli job applicants, integrity scores were found to be significantly correlated with self-reported counterproductive work behaviors across eight different industries, with no evidence of adverse impact by gender, age, or national origin. These results are believed to be of practical importance to the diverse organizations administering integrity tests. PMID:21117489

  17. Improving the accuracy of multiple integral evaluation by applying Romberg's method

    NASA Astrophysics Data System (ADS)

    Zhidkov, E. P.; Lobanov, Yu. Yu.; Rushai, V. D.

    2009-02-01

    Romberg’s method, which is used to improve the accuracy of one-dimensional integral evaluation, is extended to multiple integrals if they are evaluated using the product of composite quadrature formulas. Under certain conditions, the coefficients of the Romberg formula are independent of the integral’s multiplicity, which makes it possible to use a simple evaluation algorithm developed for one-dimensional integrals. As examples, integrals of multiplicity two to six are evaluated by Romberg’s method and the results are compared with other methods.

  18. 77 FR 33486 - Certain Integrated Circuit Packages Provided With Multiple Heat-Conducting Paths and Products...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-06-06

    ... COMMISSION Certain Integrated Circuit Packages Provided With Multiple Heat- Conducting Paths and Products... With Multiple Heat-Conducting Paths and Products Containing Same, DN 2899; the Commission is soliciting... multiple heat-conducting paths and products containing same. The complaint names as respondents...

  19. Capillary muscle

    PubMed Central

    Cohen, Caroline; Mouterde, Timothée; Quéré, David; Clanet, Christophe

    2015-01-01

    The contraction of a muscle generates a force that decreases when increasing the contraction velocity. This “hyperbolic” force–velocity relationship has been known since the seminal work of A. V. Hill in 1938 [Hill AV (1938) Proc R Soc Lond B Biol Sci 126(843):136–195]. Hill’s heuristic equation is still used, and the sliding-filament theory for the sarcomere [Huxley H, Hanson J (1954) Nature 173(4412):973–976; Huxley AF, Niedergerke R (1954) Nature 173(4412):971–973] suggested how its different parameters can be related to the molecular origin of the force generator [Huxley AF (1957) Prog Biophys Biophys Chem 7:255–318; Deshcherevskiĭ VI (1968) Biofizika 13(5):928–935]. Here, we develop a capillary analog of the sarcomere obeying Hill’s equation and discuss its analogy with muscles. PMID:25944938

  20. Curriculum Integration in Arts Education: Connecting Multiple Art Forms through the Idea of "Space"

    ERIC Educational Resources Information Center

    Bautista, Alfredo; Tan, Liang See; Ponnusamy, Letchmi Devi; Yau, Xenia

    2016-01-01

    Arts integration research has focused on documenting how the teaching of specific art forms can be integrated with "core" academic subject matters (e.g. science, mathematics and literacy). However, the question of how the teaching of multiple art forms themselves can be integrated in schools remains to be explored by educational…

  1. Integrative Data Analysis: The Simultaneous Analysis of Multiple Data Sets

    ERIC Educational Resources Information Center

    Curran, Patrick J.; Hussong, Andrea M.

    2009-01-01

    There are both quantitative and methodological techniques that foster the development and maintenance of a cumulative knowledge base within the psychological sciences. Most noteworthy of these techniques is meta-analysis, which allows for the synthesis of summary statistics drawn from multiple studies when the original data are not available.…

  2. Identifying multiple submissions in Internet research: preserving data integrity.

    PubMed

    Bowen, Anne M; Daniel, Candice M; Williams, Mark L; Baird, Grayson L

    2008-11-01

    Internet-based sexuality research with hidden populations has become increasingly popular. Respondent anonymity may encourage participation and lower social desirability, but associated disinhibition may promote multiple submissions, especially when incentives are offered. The goal of this study was to identify the usefulness of different variables for detecting multiple submissions from repeat responders and to explore incentive effects. The data included 1,900 submissions from a three-session Internet intervention with a pretest and three post-test questionnaires. Participants were men who have sex with men and incentives were offered to rural participants for completing each questionnaire. The final number of submissions included 1,273 "unique", 132 first submissions by "repeat responders" and 495 additional submissions by the "repeat responders" (N = 1,900). Four categories of repeat responders were identified: "infrequent" (2-5 submissions), "persistent" (6-10 submissions), "very persistent" (11-30 submissions), and "hackers" (more than 30 submissions). Internet Provider (IP) addresses, user names, and passwords were the most useful for identifying "infrequent" repeat responders. "Hackers" often varied their IP address and identifying information to prevent easy identification, but investigating the data for small variations in IP, using reverse telephone look up, and patterns across usernames and passwords were helpful. Incentives appeared to play a role in stimulating multiple submissions, especially from the more sophisticated "hackers". Finally, the web is ever evolving and it will be necessary to have good programmers and staff who evolve as fast as "hackers".

  3. Spectrometer capillary vessel and method of making same

    DOEpatents

    Linehan, John C.; Yonker, Clement R.; Zemanian, Thomas S.; Franz, James A.

    1995-01-01

    The present invention is an arrangement of a glass capillary tube for use in spectroscopy. In particular, the invention is a capillary arranged in a manner permitting a plurality or multiplicity of passes of a sample material through a spectroscopic measurement zone. In a preferred embodiment, the multi-pass capillary is insertable within a standard NMR sample tube. The present invention further includes a method of making the multi-pass capillary tube and an apparatus for spinning the tube.

  4. Spectrometer capillary vessel and method of making same

    DOEpatents

    Linehan, J.C.; Yonker, C.R.; Zemanian, T.S.; Franz, J.A.

    1995-11-21

    The present invention is an arrangement of a glass capillary tube for use in spectroscopy. In particular, the invention is a capillary arranged in a manner permitting a plurality or multiplicity of passes of a sample material through a spectroscopic measurement zone. In a preferred embodiment, the multi-pass capillary is insertable within a standard NMR sample tube. The present invention further includes a method of making the multi-pass capillary tube and an apparatus for spinning the tube. 13 figs.

  5. Total integrated slidable and valveless solid phase extraction-polymerase chain reaction-capillary electrophoresis microdevice for mini Y chromosome short tandem repeat genotyping.

    PubMed

    Kim, Yong Tae; Lee, Dohwan; Heo, Hyun Young; Sim, Jeong Eun; Woo, Kwang Man; Kim, Do Hyun; Im, Sung Gap; Seo, Tae Seok

    2016-04-15

    A fully integrated slidable and valveless microsystem, which performs solid phase DNA extraction (SPE), micro-polymerase chain reaction (μPCR) and micro-capillary electrophoresis (μCE) coupled with a portable genetic analyser, has been developed for forensic genotyping. The use of a slidable chip, in which a 1 μL-volume of the PCR chamber was patterned at the center, does not necessitate any microvalves and tubing systems for fluidic control. The functional micro-units of SPE, μPCR, and μCE were fabricated on a single glass wafer by conventional photolithography, and the integrated microdevice consists of three layers: from top to bottom, a slidable chip, a channel wafer in which a SPE chamber, a mixing microchannel, and a CE microchannel were fabricated, and a Ti/Pt resistance temperature detector (RTD) wafer. The channel glass wafer and the RTD glass wafer were thermally bonded, and the slidable chip was placed on the designated functional unit. The entire process from the DNA extraction using whole human blood sample to identification of target Y chromosomal short tandem repeat (STR) loci was serially carried out with simply sliding the slidable chamber from one to another functional unit. Monoplex and multiplex detection of amelogenin and mini Y STR loci were successfully analysed on the integrated slidable SPE-μPCR-μCE microdevice by using 1 μL whole human blood within 60 min. The proposed advanced genetic analysis microsystem is capable of point-of-care DNA testing with sample-in-answer-out capability, more importantly, without use of complicated microvalves and microtubing systems for liquid transfer.

  6. Multiple integral representation for the trigonometric SOS model with domain wall boundaries

    NASA Astrophysics Data System (ADS)

    Galleas, W.

    2012-05-01

    Using the dynamical Yang-Baxter algebra we derive a functional equation for the partition function of the trigonometric SOS model with domain wall boundary conditions. The solution of the equation is given in terms of a multiple contour integral.

  7. Two-Dimensional Integral Combustion for Multiple Phase Flow

    1997-05-05

    This ANL multiphase two-dimensional combustion computer code solves conservation equations for gaseous species and solid particles (or droplets) of various sizes. General conservation laws, expressed by ellipitic-type partial differential equations are used in conjunction with rate equations governing the mass, momentum, enthaply, species, turbulent kinetic energy, and turbulent dissipation for a two-phase reacting flow. Associated submodels include an integral combustion, a two-parameter turbulence, a particle evaporation, and interfacial submodels. A newly-developed integral combustion submodel replacingmore » an Arrhenius-type differential reaction submodel is implemented to improve numerical convergence and enhance numerical stability. The two-parameter turbulence submodel is modified for both gas and solid phases. The evaporation submodel treats size dispersion as well as particle evaporation. Interfacial submodels use correlations to model interfacial momentum and energy transfer.« less

  8. Identifying Multiple Submissions in Internet Research: Preserving Data Integrity

    PubMed Central

    Bowen, Anne M.; Daniel, Candice M.; Williams, Mark L.; Baird, Grayson L.

    2008-01-01

    Internet-based sexuality research with hidden populations has become increasingly popular. Respondent anonymity may encourage participation and lower social desirability, but associated disinhibition may promote multiple submissions, especially when incentives are offered. The goal of this study was to identify the usefulness of different variables for detecting multiple submissions from repeat responders and to explore incentive effects. The data included 1,900 submissions from a three-session Internet intervention with a pretest and three post-test questionnaires. Participants were men who have sex with men and incentives were offered to rural participants for completing each questionnaire. The final number of submissions included 1,273 “unique”, 132 first submissions by “repeat responders” and 495 additional submissions by the “repeat responders” (N = 1,900). Four categories of repeat responders were identified: “infrequent” (2–5 submissions), “persistent” (6–10 submissions), “very persistent” (11–30 submissions), and “hackers” (more than 30 submissions). Internet Provider (IP) addresses, user names, and passwords were the most useful for identifying “infrequent” repeat responders. “Hackers” often varied their IP address and identifying information to prevent easy identification, but investigating the data for small variations in IP, using reverse telephone look up, and patterns across usernames and passwords were helpful. Incentives appeared to play a role in stimulating multiple submissions, especially from the more sophisticated “hackers”. Finally, the web is ever evolving and it will be necessary to have good programmers and staff who evolve as fast as “hackers”. PMID:18240015

  9. Multiple time step integrators in ab initio molecular dynamics

    SciTech Connect

    Luehr, Nathan; Martínez, Todd J.; Markland, Thomas E.

    2014-02-28

    Multiple time-scale algorithms exploit the natural separation of time-scales in chemical systems to greatly accelerate the efficiency of molecular dynamics simulations. Although the utility of these methods in systems where the interactions are described by empirical potentials is now well established, their application to ab initio molecular dynamics calculations has been limited by difficulties associated with splitting the ab initio potential into fast and slowly varying components. Here we present two schemes that enable efficient time-scale separation in ab initio calculations: one based on fragment decomposition and the other on range separation of the Coulomb operator in the electronic Hamiltonian. We demonstrate for both water clusters and a solvated hydroxide ion that multiple time-scale molecular dynamics allows for outer time steps of 2.5 fs, which are as large as those obtained when such schemes are applied to empirical potentials, while still allowing for bonds to be broken and reformed throughout the dynamics. This permits computational speedups of up to 4.4x, compared to standard Born-Oppenheimer ab initio molecular dynamics with a 0.5 fs time step, while maintaining the same energy conservation and accuracy.

  10. The Role of Epistemic Beliefs in the Comprehension of Multiple Expository Texts: Toward an Integrated Model

    ERIC Educational Resources Information Center

    Braten, Ivar; Britt, M. Anne; Stromso, Helge I.; Rouet, Jean-Francois

    2011-01-01

    In present-day knowledge societies, competent reading involves the integration of information from multiple sources into a coherent, meaningful representation of a topic, issue, or situation. This article reviews research and theory concerning the comprehension of multiple textual resources, focusing especially on linkages recently established…

  11. Empathetic, Critical Integrations of Multiple Perspectives: A Core Practice for Language Teacher Education?

    ERIC Educational Resources Information Center

    Daniel, Shannon M.

    2015-01-01

    In this self-study, the author reflects on her implementation of empathetic, critical integrations of multiple perspectives (ECI), which she designed to afford preservice teachers the opportunity to discuss and collectively reflect upon the oft-diverging multiple perspectives, values, and practices they experience during their practicum (Daniel,…

  12. Revised Capillary Breakup Rheometer Method

    NASA Astrophysics Data System (ADS)

    Lu, Louise; Schultz, William; Solomon, Michael

    2014-11-01

    Rather than integrate the one-dimensional equation of motion for a capillary breakup rheometer, we take the axial derivative of that equation. This avoids the determination of the axial force with all of its complications and correction factors. The resulting evolutionary equation that involves either two or four derivatives of the capillary radius as a function of the axial coordinate determines the ratio of elongational viscosity to surface tension coefficient. We examine several silicone and olive oils to show the accuracy of the method for Newtonian fluids. We will discuss our surface tension measurement techniques and briefly describe measurements of viscoelastic materials, including saliva.

  13. Students' integration of multiple representations in a titration experiment

    NASA Astrophysics Data System (ADS)

    Kunze, Nicole M.

    A complete understanding of a chemical concept is dependent upon a student's ability to understand the microscopic or particulate nature of the phenomenon and integrate the microscopic, symbolic, and macroscopic representations of the phenomenon. Acid-base chemistry is a general chemistry topic requiring students to understand the topics of chemical reactions, solutions, and equilibrium presented earlier in the course. In this study, twenty-five student volunteers from a second semester general chemistry course completed two interviews. The first interview was completed prior to any classroom instruction on acids and bases. The second interview took place after classroom instruction, a prelab activity consisting of a titration calculation worksheet, a titration computer simulation, or a microscopic level animation of a titration, and two microcomputer-based laboratory (MBL) titration experiments. During the interviews, participants were asked to define and describe acid-base concepts and in the second interview they also drew the microscopic representations of four stages in an acid-base titration. An analysis of the data showed that participants had integrated the three representations of an acid-base titration to varying degrees. While some participants showed complete understanding of acids, bases, titrations, and solution chemistry, other participants showed several alternative conceptions concerning strong acid and base dissociation, the formation of titration products, and the dissociation of soluble salts. Before instruction, participants' definitions of acid, base, and pH were brief and consisted of descriptive terms. After instruction, the definitions were more scientific and reflected the definitions presented during classroom instruction.

  14. Predicting White Matter Integrity from Multiple Common Genetic Variants

    PubMed Central

    Kohannim, Omid; Jahanshad, Neda; Braskie, Meredith N; Stein, Jason L; Chiang, Ming-Chang; Reese, April H; Hibar, Derrek P; Toga, Arthur W; McMahon, Katie L; de Zubicaray, Greig I; Medland, Sarah E; Montgomery, Grant W; Martin, Nicholas G; Wright, Margaret J; Thompson, Paul M

    2012-01-01

    Several common genetic variants have recently been discovered that appear to influence white matter microstructure, as measured by diffusion tensor imaging (DTI). Each genetic variant explains only a small proportion of the variance in brain microstructure, so we set out to explore their combined effect on the white matter integrity of the corpus callosum. We measured six common candidate single-nucleotide polymorphisms (SNPs) in the COMT, NTRK1, BDNF, ErbB4, CLU, and HFE genes, and investigated their individual and aggregate effects on white matter structure in 395 healthy adult twins and siblings (age: 20–30 years). All subjects were scanned with 4-tesla 94-direction high angular resolution diffusion imaging. When combined using mixed-effects linear regression, a joint model based on five of the candidate SNPs (COMT, NTRK1, ErbB4, CLU, and HFE) explained ∼6% of the variance in the average fractional anisotropy (FA) of the corpus callosum. This predictive model had detectable effects on FA at 82% of the corpus callosum voxels, including the genu, body, and splenium. Predicting the brain's fiber microstructure from genotypes may ultimately help in early risk assessment, and eventually, in personalized treatment for neuropsychiatric disorders in which brain integrity and connectivity are affected. PMID:22510721

  15. Promoting return of function in multiple sclerosis: An integrated approach

    PubMed Central

    Gacias, Mar; Casaccia, Patrizia

    2013-01-01

    Multiple sclerosis is a disease characterized by inflammatory demyelination, axonal degeneration and progressive brain atrophy. Most of the currently available disease modifying agents proved to be very effective in managing the relapse rate, however progressive neuronal damage continues to occur and leads to progressive accumulation of irreversible disability. For this reason, any therapeutic strategy aimed at restoration of function must take into account not only immunomodulation, but also axonal protection and new myelin formation. We further highlight the importance of an holistic approach, which considers the variability of therapeutic responsiveness as the result of the interplay between genetic differences and the epigenome, which is in turn affected by gender, age and differences in life style including diet, exercise, smoking and social interaction. PMID:24363985

  16. Exercise in multiple sclerosis -- an integral component of disease management.

    PubMed

    Döring, Andrea; Pfueller, Caspar F; Paul, Friedemann; Dörr, Jan

    2011-12-24

    Multiple sclerosis (MS) is the most common chronic inflammatory disorder of the central nervous system (CNS) in young adults. The disease causes a wide range of symptoms depending on the localization and characteristics of the CNS pathology. In addition to drug-based immunomodulatory treatment, both drug-based and non-drug approaches are established as complementary strategies to alleviate existing symptoms and to prevent secondary diseases. In particular, physical therapy like exercise and physiotherapy can be customized to the individual patient's needs and has the potential to improve the individual outcome. However, high quality systematic data on physical therapy in MS are rare. This article summarizes the current knowledge on the influence of physical activity and exercise on disease-related symptoms and physical restrictions in MS patients. Other treatment strategies such as drug treatments or cognitive training were deliberately excluded for the purposes of this article.

  17. Promoting return of function in multiple sclerosis: An integrated approach.

    PubMed

    Gacias, Mar; Casaccia, Patrizia

    2013-10-01

    Multiple sclerosis is a disease characterized by inflammatory demyelination, axonal degeneration and progressive brain atrophy. Most of the currently available disease modifying agents proved to be very effective in managing the relapse rate, however progressive neuronal damage continues to occur and leads to progressive accumulation of irreversible disability. For this reason, any therapeutic strategy aimed at restoration of function must take into account not only immunomodulation, but also axonal protection and new myelin formation. We further highlight the importance of an holistic approach, which considers the variability of therapeutic responsiveness as the result of the interplay between genetic differences and the epigenome, which is in turn affected by gender, age and differences in life style including diet, exercise, smoking and social interaction. PMID:24363985

  18. Nonlinear gravity-capillary water waves

    NASA Astrophysics Data System (ADS)

    Jiang, Lei

    1997-11-01

    Two-dimensional gravity-capillary water waves are analyzed using a fully-nonlinear Cauchy-integral method with spectral accuracy. Standing waves are generated in experiments by vertical oscillation and measured by a non-intrusive optical system along with a wave probe. Nonlinear resonance of standing waves with non-wetting contact line effects are discussed in detail. Amplitude- dependent wave frequency and damping in a glass rectangular tank suggest a new contact-line model. A new type of sideband resonance due to modulated forcing is discovered and explained by weakly-nonlinear analysis. This analytical solution is verified by our numerical simulations and physical experiments. New standing waveforms with dimpled or sharp crests are observed in experiments and computations. These new waveforms have strong symmetry breaking in time as a result of nonlinear harmonic interaction. With increasing wave steepness, steep standing waves experience period- tripling with three distinct forms: sharp crest, dimpled or flat crest, and round crest. Significant breaking occurs in the sharp-crest mode and the dimpled-crest mode. Using a complex-demodulation technique, I find that these breaking waves are related to the same 1:2 internal resonance (harmonic interaction) that causes the new steep waveforms. Novel approaches are used to estimate the (breaking and non-breaking) wave dissipation in steep and breaking standing waves. The breaking events (spray, air entrainment, and plunging) approximately double the wave dissipation. Weak capillarity significantly affects the limiting wave height and the form of standing waves, as demonstrated by both computations and small-scale Faraday-wave experiments. Capillary ripple generation on traveling waves is shown to be significant even at moderate wave steepness. The ubiquitous horizontal asymmetry of traveling waves is shown to be critical to capillary ripple generation. Two new asymmetric modes are identified and are shown to have an

  19. Multiple roles of atm in monitoring and maintaining dna integrity

    PubMed Central

    Derheimer, Frederick A; Kastan, Michael B

    2010-01-01

    The ability of our cells to maintain genomic integrity is fundamental for protection from cancer development. Central to this process is the ability of cells to recognize and repair DNA damage and progress through the cell cycle in a regulated and orderly manner. In addition, protection of chromosome ends through the proper assembly of telomeres prevents loss of genetic information and aberrant chromosome fusions. Cells derived from patients with ataxia-telangiectasia (A-T) show defects in cell cycle regulation, abnormal responses to DNA breakage, and chromosomal end-to-end fusions. The identification and characterization of the ATM (ataxia-telangiectasia, mutated) gene product has provided an essential tool for researchers in elucidating cellular mechanisms involved in cell cycle control, DNA repair, and chromosomal stability. PMID:20580718

  20. A boundary-integral representation for biphasic mixture theory, with application to the post-capillary glycocalyx

    PubMed Central

    Sumets, P. P.; Cater, J. E.; Long, D. S.; Clarke, R. J.

    2015-01-01

    We describe a new boundary-integral representation for biphasic mixture theory, which allows us to efficiently solve certain elastohydrodynamic–mobility problems using boundary element methods. We apply this formulation to model the motion of a rigid particle through a microtube which has non-uniform wall shape, is filled with a viscous Newtonian fluid, and is lined with a thin poroelastic layer. This is relevant to scenarios such as the transport of small rigid cells (such as neutrophils) through microvessels that are lined with an endothelial glycocalyx layer (EGL). In this context, we examine the impact of geometry upon some recently reported phenomena, including the creation of viscous eddies, fluid flux into the EGL, as well as the role of the EGL in transmitting mechanical signals to the underlying endothelial cells. PMID:26345494

  1. Integrating regional conservation priorities for multiple objectives into national policy.

    PubMed

    Beger, Maria; McGowan, Jennifer; Treml, Eric A; Green, Alison L; White, Alan T; Wolff, Nicholas H; Klein, Carissa J; Mumby, Peter J; Possingham, Hugh P

    2015-01-01

    Multinational conservation initiatives that prioritize investment across a region invariably navigate trade-offs among multiple objectives. It seems logical to focus where several objectives can be achieved efficiently, but such multi-objective hotspots may be ecologically inappropriate, or politically inequitable. Here we devise a framework to facilitate a regionally cohesive set of marine-protected areas driven by national preferences and supported by quantitative conservation prioritization analyses, and illustrate it using the Coral Triangle Initiative. We identify areas important for achieving six objectives to address ecosystem representation, threatened fauna, connectivity and climate change. We expose trade-offs between areas that contribute substantially to several objectives and those meeting one or two objectives extremely well. Hence there are two strategies to guide countries choosing to implement regional goals nationally: multi-objective hotspots and complementary sets of single-objective priorities. This novel framework is applicable to any multilateral or global initiative seeking to apply quantitative information in decision making. PMID:26364769

  2. Integrating regional conservation priorities for multiple objectives into national policy

    PubMed Central

    Beger, Maria; McGowan, Jennifer; Treml, Eric A.; Green, Alison L.; White, Alan T.; Wolff, Nicholas H.; Klein, Carissa J.; Mumby, Peter J.; Possingham, Hugh P.

    2015-01-01

    Multinational conservation initiatives that prioritize investment across a region invariably navigate trade-offs among multiple objectives. It seems logical to focus where several objectives can be achieved efficiently, but such multi-objective hotspots may be ecologically inappropriate, or politically inequitable. Here we devise a framework to facilitate a regionally cohesive set of marine-protected areas driven by national preferences and supported by quantitative conservation prioritization analyses, and illustrate it using the Coral Triangle Initiative. We identify areas important for achieving six objectives to address ecosystem representation, threatened fauna, connectivity and climate change. We expose trade-offs between areas that contribute substantially to several objectives and those meeting one or two objectives extremely well. Hence there are two strategies to guide countries choosing to implement regional goals nationally: multi-objective hotspots and complementary sets of single-objective priorities. This novel framework is applicable to any multilateral or global initiative seeking to apply quantitative information in decision making. PMID:26364769

  3. DictyBase 2013: integrating multiple Dictyostelid species.

    PubMed

    Basu, Siddhartha; Fey, Petra; Pandit, Yogesh; Dodson, Robert; Kibbe, Warren A; Chisholm, Rex L

    2013-01-01

    dictyBase (http://dictybase.org) is the model organism database for the social amoeba Dictyostelium discoideum. This contribution provides an update on dictyBase that has been previously presented. During the past 3 years, dictyBase has taken significant strides toward becoming a genome portal for the whole Amoebozoa clade. In its latest release, dictyBase has scaled up to host multiple Dictyostelids, including Dictyostelium purpureum [Sucgang, Kuo, Tian, Salerno, Parikh, Feasley, Dalin, Tu, Huang, Barry et al.(2011) (Comparative genomics of the social amoebae Dictyostelium discoideum and Dictyostelium purpureum. Genome Biol., 12, R20)], Dictyostelium fasciculatum and Polysphondylium pallidum [Heidel, Lawal, Felder, Schilde, Helps, Tunggal, Rivero, John, Schleicher, Eichinger et al. (2011) (Phylogeny-wide analysis of social amoeba genomes highlights ancient origins for complex intercellular communication. Genome Res., 21, 1882-1891)]. The new release includes a new Genome Browser with RNAseq expression, interspecies Basic Local Alignment Search Tool alignments and a unified Basic Local Alignment Search Tool search for cross-species comparisons.

  4. "Getting the best sensitivity from on-capillary fluorescence detection in capillary electrophoresis" - A tutorial.

    PubMed

    Galievsky, Victor A; Stasheuski, Alexander S; Krylov, Sergey N

    2016-09-01

    Capillary electrophoresis with Laser-Induced Fluorescence (CE-LIF) detection is being applied to new analytical problems which challenge both the power of CE separation and the sensitivity of LIF detection. On-capillary LIF detection is much more practical than post-capillary detection in a sheath-flow cell. Therefore, commercial CE instruments utilize solely on-capillary CE-LIF detection with a Limit of Detection (LOD) in the nM range, while there are multiple applications of CE-LIF that require pM or lower LODs. This tutorial analyzes all aspects of on-capillary LIF detection in CE in an attempt to identify means for improving LOD of CE-LIF with on-capillary detection. We consider principles of signal enhancement and noise reduction, as well as relevant areas of fluorophore photochemistry and fluorescent microscopy. PMID:27543015

  5. Integrating multiple scientific computing needs via a Private Cloud infrastructure

    NASA Astrophysics Data System (ADS)

    Bagnasco, S.; Berzano, D.; Brunetti, R.; Lusso, S.; Vallero, S.

    2014-06-01

    In a typical scientific computing centre, diverse applications coexist and share a single physical infrastructure. An underlying Private Cloud facility eases the management and maintenance of heterogeneous use cases such as multipurpose or application-specific batch farms, Grid sites catering to different communities, parallel interactive data analysis facilities and others. It allows to dynamically and efficiently allocate resources to any application and to tailor the virtual machines according to the applications' requirements. Furthermore, the maintenance of large deployments of complex and rapidly evolving middleware and application software is eased by the use of virtual images and contextualization techniques; for example, rolling updates can be performed easily and minimizing the downtime. In this contribution we describe the Private Cloud infrastructure at the INFN-Torino Computer Centre, that hosts a full-fledged WLCG Tier-2 site and a dynamically expandable PROOF-based Interactive Analysis Facility for the ALICE experiment at the CERN LHC and several smaller scientific computing applications. The Private Cloud building blocks include the OpenNebula software stack, the GlusterFS filesystem (used in two different configurations for worker- and service-class hypervisors) and the OpenWRT Linux distribution (used for network virtualization). A future integration into a federated higher-level infrastructure is made possible by exposing commonly used APIs like EC2 and by using mainstream contextualization tools like CloudInit.

  6. Integrating stakeholder values with multiple attributes to quantify watershed performance

    NASA Astrophysics Data System (ADS)

    Shriver, Deborah M.; Randhir, Timothy O.

    2006-08-01

    Integrating stakeholder values into the process of quantifying impairment of ecosystem functions is an important aspect of watershed assessment and planning. This study develops a classification and prioritization model to assess potential impairment in watersheds. A systematic evaluation of a broad set of abiotic, biotic, and human indicators of watershed structure and function was used to identify the level of degradation at a subbasin scale. Agencies and communities can use the method to effectively target and allocate resources to areas of greatest restoration need. The watershed performance measure (WPM) developed in this study is composed of three major components: (1) hydrologic processes (water quantity and quality), (2) biodiversity at a species scale (core and priority habitat for rare and endangered species and species richness) and landscape scale (impacts of fragmentation), and (3) urban impacts as assessed in the built environment (effective impervious area) and population effects (densities and density of toxic waste sites). Simulation modeling using the Soil and Water Assessment Tool (SWAT), monitoring information, and spatial analysis with GIS were used to assess each criterion in developing this model. Weights for attributes of potential impairment were determined through the use of the attribute prioritization procedure with a panel of expert stakeholders. This procedure uses preselected attributes and corresponding stakeholder values and is data intensive. The model was applied to all subbasins of the Chicopee River Watershed of western Massachusetts, an area with a mixture of rural, heavily forested lands, suburban, and urbanized areas. Highly impaired subbasins in one community were identified using this methodology and evaluated for principal forms of degradation and potential restoration policies and BMPs. This attribute-based prioritization method could be used in identifying baselines, prioritization policies, and adaptive community

  7. An Integrated Approach for Accessing Multiple Datasets through LANCE

    NASA Astrophysics Data System (ADS)

    Murphy, K. J.; Teague, M.; Conover, H.; Regner, K.; Beaumont, B.; Masuoka, E.; Vollmer, B.; Theobald, M.; Durbin, P.; Michael, K.; Boller, R. A.; Schmaltz, J. E.; Davies, D.; Horricks, K.; Ilavajhala, S.; Thompson, C. K.; Bingham, A.

    2011-12-01

    The NASA/GSFC Land Atmospheres Near-real time Capability for EOS (LANCE) provides imagery for approximately 40 data products from MODIS, AIRS, AMSR-E and OMI to support the applications community in the study of a variety of phenomena. Thirty-six of these products are available within 2.5 hours of observation at the spacecraft. The data set includes the population density data provided by the EOSDIS Socio-Economic Data and Applications Center (SEDAC). The purpose of this paper is to describe the variety of tools that have been developed by LANCE to support user access to the imagery. The long-standing Rapid Response system has been integrated into LANCE and is a major vehicle for the distribution of the imagery to end users. There are presently approximately 10,000 anonymous users per month accessing these imagery. The products are grouped into 14 applications categories such as Smoke Plumes, Pollution, Fires, Agriculture and the selection of any category will make relevant subsets of the 40 products available as possible overlays in an interactive Web Client utilizing Web Mapping Service (WMS) to support user investigations (http://lance2.modaps.eosdis.nasa.gov/wms/). For example, selecting Severe Storms will include 6 products for MODIS, OMI, AIRS, and AMSR-E plus the SEDAC population density data. The client and WMS were developed using open-source technologies such as OpenLayers and MapServer and provides a uniform, browser-based access to data products. All overlays are downloadable in PNG, JPEG, or GeoTiff form up to 200MB per request. The WMS was beta-tested with the user community and substantial performance improvements were made through the use of such techniques as tile-caching. LANCE established a partnership with Physical Oceanography Distributed Active Archive Center (PO DAAC) to develop an alternative presentation for the 40 data products known as the State of the Earth (SOTE). This provides a Google Earth-based interface to the products grouped in

  8. An integrated quality by design and mixture-process variable approach in the development of a capillary electrophoresis method for the analysis of almotriptan and its impurities.

    PubMed

    Orlandini, S; Pasquini, B; Stocchero, M; Pinzauti, S; Furlanetto, S

    2014-04-25

    The development of a capillary electrophoresis (CE) method for the assay of almotriptan (ALM) and its main impurities using an integrated Quality by Design and mixture-process variable (MPV) approach is described. A scouting phase was initially carried out by evaluating different CE operative modes, including the addition of pseudostationary phases and additives to the background electrolyte, in order to approach the analytical target profile. This step made it possible to select normal polarity microemulsion electrokinetic chromatography (MEEKC) as operative mode, which allowed a good selectivity to be achieved in a low analysis time. On the basis of a general Ishikawa diagram for MEEKC methods, a screening asymmetric matrix was applied in order to screen the effects of the process variables (PVs) voltage, temperature, buffer concentration and buffer pH, on critical quality attributes (CQAs), represented by critical separation values and analysis time. A response surface study was then carried out considering all the critical process parameters, including both the PVs and the mixture components (MCs) of the microemulsion (borate buffer, n-heptane as oil, sodium dodecyl sulphate/n-butanol as surfactant/cosurfactant). The values of PVs and MCs were simultaneously changed in a MPV study, making it possible to find significant interaction effects. The design space (DS) was defined as the multidimensional combination of PVs and MCs where the probability for the different considered CQAs to be acceptable was higher than a quality level π=90%. DS was identified by risk of failure maps, which were drawn on the basis of Monte-Carlo simulations, and verification points spanning the design space were tested. Robustness testing of the method, performed by a D-optimal design, and system suitability criteria allowed a control strategy to be designed. The optimized method was validated following ICH Guideline Q2(R1) and was applied to a real sample of ALM coated tablets.

  9. [Integrated risk evaluation of multiple disasters affecting longyan yield in Fujian Province, East China].

    PubMed

    Chen, Jia-Jin; Wang, Jia-Yi; Li, Li-Chun; Lin, Jing; Yang, Kai; Ma, Zhi-Guo; Xu, Zong-Huan

    2012-03-01

    In this study, an index system for the integrated risk evaluation of multiple disasters on the Longyan production in Fujian Province was constructed, based on the analysis of the major environmental factors affecting the Longyan growth and yield, and from the viewpoints of potential hazard of disaster-causing factors, vulnerability of hazard-affected body, and disaster prevention and mitigation capability of Longyan growth regions in the Province. In addition, an integrated evaluation model of multiple disasters was established to evaluate the risks of the major agro-meteorological disasters affecting the Longyan yield, based on the yearly meteorological data, Longyan planting area and yield, and other socio-economic data in Longyan growth region in Fujian, and by using the integral weight of risk indices determined by AHP and entropy weight coefficient methods. In the Province, the Longyan growth regions with light integrated risk of multiple disasters were distributed in the coastal counties (except Dongshan County) with low elevation south of Changle, the regions with severe and more severe integrated risk were mainly in Zhangping of Longyan, Dongshan, Pinghe, Nanjin, and Hua' an of Zhangzhou, Yongchun and Anxi of Quanzhou, north mountainous areas of Putian and Xianyou, Minqing, Minhou, Luoyuan, and mountainous areas of Fuzhou, and Fuan, Xiapu, and mountainous areas of Ninde, among which, the regions with severe integrated risk were in Dongshan, Zhangping, and other mountainous areas with high altitudes, and the regions with moderate integrated risk were distributed in the other areas of the Province.

  10. Numerical solution of optimal control problems using multiple-interval integral Gegenbauer pseudospectral methods

    NASA Astrophysics Data System (ADS)

    Tang, Xiaojun

    2016-04-01

    The main purpose of this work is to provide multiple-interval integral Gegenbauer pseudospectral methods for solving optimal control problems. The latest developed single-interval integral Gauss/(flipped Radau) pseudospectral methods can be viewed as special cases of the proposed methods. We present an exact and efficient approach to compute the mesh pseudospectral integration matrices for the Gegenbauer-Gauss and flipped Gegenbauer-Gauss-Radau points. Numerical results on benchmark optimal control problems confirm the ability of the proposed methods to obtain highly accurate solutions.

  11. Technology Integration in a One-to-One Laptop Initiative: A Multiple Case Study Analysis

    ERIC Educational Resources Information Center

    Jones, Marsha B.

    2013-01-01

    The purpose of this multiple case study analysis was to examine teachers' experiences and perceptions in order to understand what actions and interactions supported or inhibited technology integration during a one-to-one laptop initiative. This research sought to gain teachers' perspectives on the challenges and successes they faced as classroom…

  12. The Effect of Sensory Integration Treatment on Children with Multiple Disabilities.

    ERIC Educational Resources Information Center

    Din, Feng S.; Lodato, Donna M.

    Six children with multiple disabilities (ages 5 to 8) participated in this evaluation of the effect of sensory integration treatment on sensorimotor function and academic learning. The children had cognitive abilities ranging from sub-average to significantly sub-average, three were non-ambulatory, one had severe behavioral problems, and each…

  13. STRUCTURE OF THE EGF RECEPTOR TRANSACTIVATION CIRCUIT INTEGRATES MULTIPLE SIGNALS WITH CELL CONTEXT

    PubMed Central

    Joslin, Elizabeth J.; Shankaran, Harish; Opresko, Lee K.; Bollinger, Nikki; Lauffenburger, Douglas A.; Wiley, H. Steven

    2012-01-01

    Summary Transactivation of the epidermal growth factor receptor (EGFR) is thought to be a process by which a variety of cellular inputs can be integrated into a single signaling pathway through either stimulated proteolysis (shedding) of membrane-anchored EGFR ligands or by modification of the activity of the EGFR. As a first step towards building a predictive model of the EGFR transactivation circuit, we quantitatively defined how signals from multiple agonists were integrated both upstream and downstream of the EGFR to regulate extracellular signal regulated kinase (ERK) activity in human mammary epithelial cells. By using a “non-binding” reporter of ligand shedding, we found that transactivation triggers a positive feedback loop from ERK back to the EGFR such that ligand shedding drives EGFR-stimulated ERK that in turn drives further ligand shedding. Importantly, activated Ras and ERK levels were nearly linear functions of ligand shedding and the effect of multiple, sub-saturating inputs was additive. Simulations showed that ERK-mediated feedback through ligand shedding resulted in a stable steady-state level of activated ERK, but also showed that the extracellular environment can modulate the level of feedback. Our results suggest that the transactivation circuit acts as a context-dependent integrator and amplifier of multiple extracellular signals and that signal integration can effectively occur at multiple points in the EGFR pathway. PMID:20458382

  14. Multiplicity and Self-Identity: Trauma and Integration in Shirley Mason's Art

    ERIC Educational Resources Information Center

    Thompson, Geoffrey

    2011-01-01

    This viewpoint appeared in its original form as the catalogue essay that accompanied the exhibition "Multiplicity and Self-Identity: Trauma and Integration in Shirley Mason's Art," curated by the author for Gallery 2110, Sacramento, CA, and the 2010 Annual Conference of the American Art Therapy Association. The exhibition featured 17 artworks by…

  15. Fostering Creativity in Advertising Students: Incorporating the Theories of Multiple Intelligences and Integrative Learning.

    ERIC Educational Resources Information Center

    Rega, Bonney

    Noting that linguistic and mathematical/logical are the two kinds of intelligences the educational system encourages and that the educational system, as well as science in general, tends to neglect the nonverbal form of intellect, this paper describes Howard Gardner's multiple intelligences theory and Peter Kline's theory of integrative learning…

  16. Combining versus Analyzing Multiple Causes: How Domain Assumptions and Task Context Affect Integration Rules

    ERIC Educational Resources Information Center

    Waldmann, Michael R.

    2007-01-01

    In everyday life, people typically observe fragments of causal networks. From this knowledge, people infer how novel combinations of causes they may never have observed together might behave. I report on 4 experiments that address the question of how people intuitively integrate multiple causes to predict a continuously varying effect. Most…

  17. Understanding and Integrating Multiple Science Texts: Summary Tasks Are Sometimes Better than Argument Tasks

    ERIC Educational Resources Information Center

    Gil, Laura; Braten, Ivar; Vidal-Abarca, Eduardo; Stromso, Helge I.

    2010-01-01

    One of the major challenges of a knowledge society is that students as well as other citizens must learn to understand and integrate information from multiple textual sources. Still, task and reader characteristics that may facilitate or constrain such intertextual processes are not well understood by researchers. In this study, we compare the…

  18. Integration of graphene oxide and DNA as a universal platform for multiple arithmetic logic units.

    PubMed

    Wang, Kun; Ren, Jiangtao; Fan, Daoqing; Liu, Yaqing; Wang, Erkang

    2014-11-28

    By a combination of graphene oxide and DNA, a universal platform was developed for integration of multiple logic gates to implement both half adder and half subtractor functions. A constant undefined threshold range between high and low fluorescence output signals was set for all the developed logic gates.

  19. Multiple proviral integration events after virological synapse-mediated HIV-1 spread

    SciTech Connect

    Russell, Rebecca A.; Martin, Nicola; Mitar, Ivonne; Jones, Emma; Sattentau, Quentin J.

    2013-08-15

    HIV-1 can move directly between T cells via virological synapses (VS). Although aspects of the molecular and cellular mechanisms underlying this mode of spread have been elucidated, the outcomes for infection of the target cell remain incompletely understood. We set out to determine whether HIV-1 transfer via VS results in productive, high-multiplicity HIV-1 infection. We found that HIV-1 cell-to-cell spread resulted in nuclear import of multiple proviruses into target cells as seen by fluorescence in-situ hybridization. Proviral integration into the target cell genome was significantly higher than that seen in a cell-free infection system, and consequent de novo viral DNA and RNA production in the target cell detected by quantitative PCR increased over time. Our data show efficient proviral integration across VS, implying the probability of multiple integration events in target cells that drive productive T cell infection. - Highlights: • Cell-to-cell HIV-1 infection delivers multiple vRNA copies to the target cell. • Cell-to-cell infection results in productive infection of the target cell. • Cell-to-cell transmission is more efficient than cell-free HIV-1 infection. • Suggests a mechanism for recombination in cells infected with multiple viral genomes.

  20. A technique for constructing an integrated scene from multiple viewing angles using a tactical ranging sensor

    NASA Astrophysics Data System (ADS)

    VanMaasdam, Peter J.; Riddle, Jack G.

    2003-09-01

    The problem of seamless scene integration from multiple 3-dimensional views of a location for surveillance or recognition purposes is one that continues to receive much interest. This technique holds the promise of increased ability to detect concealed targets, as well as better visualization of the scene itself. The process of creating an integrated scene 'model' from multiple range images taken at different views of the scene consists of several basic steps: (1) Matching of scene points across views, (2) Registration of the multiple views to a common reference frame, and (3) Integration of the multiple views into a complete 3D representation (such as a mesh or voxel space). We propose using a technique known as spin-map correlation to compute the initial scene point correspondences between views. This technique has the advantage of being able to perform the registration with minimal knowledge of viewing geometry or viewer location - the only requirement is that there is overlap between views. Registration is performed using the correspondences generated from spin-map matching to seed an Iterative Closest Point (ICP) algorithm. The ICP algorithm grows the list of correspondences and estimates the rigid transformation between the multiple views. Following registration of the disparate views, the surface is represented probabilistically in a voxel space that is then polygonised into a triangular facet model using the well-known marching cubes algorithm. We demonstrate this procedure using LADAR range images of an armored vehicle of interest.

  1. Integrating Multiple Evidence Sources to Predict Adverse Drug Reactions Based on a Systems Pharmacology Model

    PubMed Central

    Cao, D-S; Xiao, N; Li, Y-J; Zeng, W-B; Liang, Y-Z; Lu, A-P; Xu, Q-S; Chen, AF

    2015-01-01

    Identifying potential adverse drug reactions (ADRs) is critically important for drug discovery and public health. Here we developed a multiple evidence fusion (MEF) method for the large-scale prediction of drug ADRs that can handle both approved drugs and novel molecules. MEF is based on the similarity reference by collaborative filtering, and integrates multiple similarity measures from various data types, taking advantage of the complementarity in the data. We used MEF to integrate drug-related and ADR-related data from multiple levels, including the network structural data formed by known drug–ADR relationships for predicting likely unknown ADRs. On cross-validation, it obtains high sensitivity and specificity, substantially outperforming existing methods that utilize single or a few data types. We validated our prediction by their overlap with drug–ADR associations that are known in databases. The proposed computational method could be used for complementary hypothesis generation and rapid analysis of potential drug–ADR interactions. PMID:26451329

  2. Information integration in multiple cue judgment: a division of labor hypothesis.

    PubMed

    Juslin, Peter; Karlsson, Linnea; Olsson, Henrik

    2008-01-01

    There is considerable evidence that judgment is constrained to additive integration of information. The authors propose an explanation of why serial and additive cognitive integration can produce accurate multiple cue judgment both in additive and non-additive environments in terms of an adaptive division of labor between multiple representations. It is hypothesized that, whereas the additive, independent linear effect of each cue can be explicitly abstracted and integrated by a serial, additive judgment process, a variety of sophisticated task properties, like non-additive cue combination, non-linear relations, and inter-cue correlation, are carried implicitly by exemplar memory. Three experiments investigating the effect of additive versus non-additive cue combination verify the predicted shift in cognitive representations as a function of the underlying combination rule. PMID:17376423

  3. Intranasal lobular capillary haemangioma

    PubMed Central

    Nayak, Dipak Ranjan; Bhandarkar, Ajay M; Shivamurthy, Archana; Joy, Jasmi

    2014-01-01

    Lobular capillary haemangioma (LCH) is a benign proliferation of capillaries with a characteristic lobular architecture on microscopy; it has an affinity for mucous membrane and skin of the head and neck. It is extremely rare in the nasal cavity. We present the case of a 45-year-old man who presented with epistaxis without any predisposing factors, which was diagnosed as lobular capillary haemangioma. PMID:25304675

  4. Capillary zone electrophoresis

    SciTech Connect

    Jorgenson, J.W.; Lukacs, K.D.

    1983-10-21

    Zone electrophoresis in capillaries is a technique complementary to electrophoresis in supporting media, and each approach has its own particular advantages. Efficient heat transfer from small-diameter capillaries permits use of unusually high voltages, resulting in both high resolution and rapid analysis. Capillaries also seem well suited for automation. Our present electromigration injection technique is relatively straightforward and should be simple to automate. Capillaries are reusable, which is an advantage over gels. On-line electronic detection permits good quantification, further enhancing possibilities for fully automatic operation. The greatest obstacle to further development and utilization of capillaries is the requirement of extremely sensitive detectors, and more types of detectors with higher sensitivity are greatly needed. A better understanding of capillary surface modification will also be important, both for improved capillary surface deactivation and for better control over electroosmotic flow. Capillaries should provide an ideal system in which to explore nonaqueous separation media. The prospects for nonaqueous media in electrophoresis are similar to those in electrochemistry, and capillaries should prove an excellent system in which to begin their study. 18 refs., 8 figs.

  5. Hollow fiber integrated microfluidic platforms for in vitro Co-culture of multiple cell types.

    PubMed

    Huang, Jen-Huang; Harris, Jennifer F; Nath, Pulak; Iyer, Rashi

    2016-10-01

    This study demonstrates a rapid prototyping approach for fabricating and integrating porous hollow fibers (HFs) into microfluidic device. Integration of HF can enhance mass transfer and recapitulate tubular shapes for tissue-engineered environments. We demonstrate the integration of single or multiple HFs, which can give the users the flexibility to control the total surface area for tissue development. We also present three microfluidic designs to enable different co-culture conditions such as the ability to co-culture multiple cell types simultaneously on a flat and tubular surface, or inside the lumen of multiple HFs. Additionally, we introduce a pressurized cell seeding process that can allow the cells to uniformly adhere on the inner surface of HFs without losing their viabilities. Co-cultures of lung epithelial cells and microvascular endothelial cells were demonstrated on the different platforms for at least five days. Overall, these platforms provide new opportunities for co-culturing of multiple cell types in a single device to reconstruct native tissue micro-environment for biomedical and tissue engineering research. PMID:27613401

  6. An ontology for the integration of multiple genetic disorder data sources.

    PubMed

    Gong, P; Qu, W; Feng, D D

    2005-01-01

    As a huge amount of gene disorder information is available on the Internet, there is an increasing requirement to integrate these data sources. The integration of gene disorder data sources provides an important tool in the research of life science, therapeutics, and genetic disease prevention and inhibition. The key challenge of such integration is how to deal with semantic heterogeneity of multiple information resources. The paper proposes an ontology-based approach to describe and extract the semantics of genetic disorder terminologies and provides a mechanism for sharing and reusing genetic disorder knowledge. According to this unified meta model, heterogeneous gene disorder data sources can be integrated, and a semantic middleware has the ability to do reasoning on the knowledge base of gene disorder for users and applications' various queries.

  7. Orthogonal matrix factorization enables integrative analysis of multiple RNA binding proteins

    PubMed Central

    Stražar, Martin; Žitnik, Marinka; Zupan, Blaž; Ule, Jernej; Curk, Tomaž

    2016-01-01

    Motivation: RNA binding proteins (RBPs) play important roles in post-transcriptional control of gene expression, including splicing, transport, polyadenylation and RNA stability. To model protein–RNA interactions by considering all available sources of information, it is necessary to integrate the rapidly growing RBP experimental data with the latest genome annotation, gene function, RNA sequence and structure. Such integration is possible by matrix factorization, where current approaches have an undesired tendency to identify only a small number of the strongest patterns with overlapping features. Because protein–RNA interactions are orchestrated by multiple factors, methods that identify discriminative patterns of varying strengths are needed. Results: We have developed an integrative orthogonality-regularized nonnegative matrix factorization (iONMF) to integrate multiple data sources and discover non-overlapping, class-specific RNA binding patterns of varying strengths. The orthogonality constraint halves the effective size of the factor model and outperforms other NMF models in predicting RBP interaction sites on RNA. We have integrated the largest data compendium to date, which includes 31 CLIP experiments on 19 RBPs involved in splicing (such as hnRNPs, U2AF2, ELAVL1, TDP-43 and FUS) and processing of 3’UTR (Ago, IGF2BP). We show that the integration of multiple data sources improves the predictive accuracy of retrieval of RNA binding sites. In our study the key predictive factors of protein–RNA interactions were the position of RNA structure and sequence motifs, RBP co-binding and gene region type. We report on a number of protein-specific patterns, many of which are consistent with experimentally determined properties of RBPs. Availability and implementation: The iONMF implementation and example datasets are available at https://github.com/mstrazar/ionmf. Contact: tomaz.curk@fri.uni-lj.si Supplementary information: Supplementary data are available

  8. High sensitivity detection of NO2 employing off-axis integrated cavity output spectroscopy coupled with multiple line integrated spectroscopy

    NASA Astrophysics Data System (ADS)

    Rao, Gottipaty N.; Karpf, Andreas

    2011-05-01

    We report on the development of a new sensor for NO2 with ultrahigh sensitivity of detection. This has been accomplished by combining off-axis integrated cavity output spectroscopy (OA-ICOS) (which can provide large path lengths of the order of several km in a small volume cell) with multiple line integrated absorption spectroscopy (MLIAS) (where we integrate the absorption spectra over a large number of rotational-vibrational transitions of the molecular species to further improve the sensitivity). Employing an external cavity tunable quantum cascade laser operating in the 1601 - 1670 cm-1 range and a high-finesse optical cavity, the absorption spectra of NO2 over 100 transitions in the R-band have been recorded. From the observed linear relationship between the integrated absorption vs. concentration of NO2, we report an effective sensitivity of detection of 10 ppt for NO2. To the best of our knowledge, this is among the most sensitive levels of detection of NO2 to date. A sensitive sensor for the detection of NO2 will be helpful to monitor the ambient air quality, combustion emissions from the automobiles, power plants, aircraft and for the detection of nitrate based explosives (which are commonly used in improvised explosives (IEDs)). Additionally such a sensor would be valuable for the study of complex chemical reactions that undergo in the atmosphere resulting in the formation of photochemical smog, tropospheric ozone and acid rain.

  9. Integrated strong cation-exchange hybrid monolith coupled with capillary zone electrophoresis and simultaneous dynamic pH junction for large-volume proteomic analysis by mass spectrometry.

    PubMed

    Zhang, Zhenbin; Sun, Liangliang; Zhu, Guijie; Yan, Xiaojing; Dovichi, Norman J

    2015-06-01

    A sulfonate-silica hybrid strong cation-exchange (SCX) monolith was synthesized at the proximal end of a capillary zone electrophoresis column and used for on-line solid-phase extraction (SPE) sample preconcentration. Sample was prepared in an acidic buffer and deposited onto the SCX-SPE monolith and eluted using a basic buffer. Electrophoresis was performed in an acidic buffer. This combination of buffers results in formation of a dynamic pH junction, which allows use of relatively large elution buffer volume while maintaining peak efficiency and resolution. All experiments were performed with a 50 µm ID capillary, a 1cm long SCX-SPE monolith, a 60cm long separation capillary, and a electrokinetically pumped nanospray interface. The volume of the capillary is 1.1 µL. By loading 21 µL of a 1×10(-7) M angiotensin II solution, an enrichment factor of 3000 compared to standard electrokinetic injection was achieved on this platform while retaining efficient electrophoretic performance (N=44,000 plates). The loading capacity of the sulfonate SCX hybrid monolith was determined to be ~15 pmol by frontal analysis with 10(-5) M angiotensin II. The system was also applied to the analysis of a 10(-4) mg/mL bovine serum albumin tryptic digest; the protein coverage was 12% and 11 peptides were identified. Finally, by loading 5.5 µL of a 10(-3) mg/mL E. coli digest, 109 proteins and 271 peptides were identified in a 20 min separation; the median separation efficiency generated by these peptides was 25,000 theoretical plates.

  10. A graph-based integrative method of detecting consistent protein functional modules from multiple data sources.

    PubMed

    Zhang, Yuan; Cheng, Yue; Ge, Liang; Du, Nan; Jia, Kebin; Zhang, Aidong

    2015-01-01

    Many clustering methods have been developed to identify functional modules in Protein-Protein Interaction (PPI) networks but the results are far from satisfaction. To overcome the noise and incomplete problems of PPI networks and find more accurate and stable functional modules, we propose an integrative method, bipartite graph-based Non-negative Matrix Factorisation method (BiNMF), in which we adopt multiple biological data sources as different views that describe PPIs. Specifically, traditional clustering models are adopted as preliminary analysis of different views of protein functional similarity. Then the intermediate clustering results are represented by a bipartite graph which can comprehensively represent the relationships between proteins and intermediate clusters and finally overlapping clustering results are achieved. Through extensive experiments, we see that our method is superior to baseline methods and detailed analysis has demonstrated the benefits of integrating diverse clustering methods and multiple biological information sources. PMID:26547971

  11. Scientific concepts and applications of integrated discrete multiple organ co-culture technology

    PubMed Central

    Gayathri, Loganathan; Dhanasekaran, Dharumadurai; Akbarsha, Mohammad A.

    2015-01-01

    Over several decades, animals have been used as models to investigate the human-specific drug toxicity, but the outcomes are not always reliably extrapolated to the humans in vivo. Appropriate in vitro human-based experimental system that includes in vivo parameters is required for the evaluation of multiple organ interaction, multiple organ/organ-specific toxicity, and metabolism of xenobiotic compounds to avoid the use of animals for toxicity testing. One such versatile in vitro technology in which human primary cells could be used is integrated discrete multiple organ co-culture (IdMOC). IdMOC system adopts wells-within-well concept that facilitates co-culture of cells from different organs in a discrete manner, separately in the respective media in the smaller inner wells which are then interconnected by an overlay of a universal medium in the large containing well. This novel in vitro approach mimics the in vivo situation to a great extent, and employs cells from multiple organs that are physically separated but interconnected by a medium that mimics the systemic circulation and provides for multiple organ interaction. Applications of IdMOC include assessment of multiple organ toxicity, drug distribution, organ-specific toxicity, screening of anticancer drugs, metabolic cytotoxicity, etc. PMID:25969651

  12. PIF4 Integrates Multiple Environmental and Hormonal Signals for Plant Growth Regulation in Arabidopsis

    PubMed Central

    Choi, Hyunmo; Oh, Eunkyoo

    2016-01-01

    As sessile organisms, plants must be able to adapt to the environment. Plants respond to the environment by adjusting their growth and development, which is mediated by sophisticated signaling networks that integrate multiple environmental and endogenous signals. Recently, increasing evidence has shown that a bHLH transcription factor PIF4 plays a major role in the multiple signal integration for plant growth regulation. PIF4 is a positive regulator in cell elongation and its activity is regulated by various environmental signals, including light and temperature, and hormonal signals, including auxin, gibberellic acid and brassinosteroid, both transcriptionally and post-translationally. Moreover, recent studies have shown that the circadian clock and metabolic status regulate endogenous PIF4 level. The PIF4 transcription factor cooperatively regulates the target genes involved in cell elongation with hormone-regulated transcription factors. Therefore, PIF4 is a key integrator of multiple signaling pathways, which optimizes growth in the environment. This review will discuss our current understanding of the PIF4-mediated signaling networks that control plant growth. PMID:27432188

  13. PIF4 Integrates Multiple Environmental and Hormonal Signals for Plant Growth Regulation in Arabidopsis.

    PubMed

    Choi, Hyunmo; Oh, Eunkyoo

    2016-08-31

    As sessile organisms, plants must be able to adapt to the environment. Plants respond to the environment by adjusting their growth and development, which is mediated by sophisticated signaling networks that integrate multiple environmental and endogenous signals. Recently, increasing evidence has shown that a bHLH transcription factor PIF4 plays a major role in the multiple signal integration for plant growth regulation. PIF4 is a positive regulator in cell elongation and its activity is regulated by various environmental signals, including light and temperature, and hormonal signals, including auxin, gibberellic acid and brassinosteroid, both transcriptionally and post-translationally. Moreover, recent studies have shown that the circadian clock and metabolic status regulate endogenous PIF4 level. The PIF4 transcription factor cooperatively regulates the target genes involved in cell elongation with hormone-regulated transcription factors. Therefore, PIF4 is a key integrator of multiple signaling pathways, which optimizes growth in the environment. This review will discuss our current understanding of the PIF4-mediated signaling networks that control plant growth. PMID:27432188

  14. The eye in hand: predicting others' behavior by integrating multiple sources of information

    PubMed Central

    Pezzulo, Giovanni; Costantini, Marcello

    2015-01-01

    The ability to predict the outcome of other beings' actions confers significant adaptive advantages. Experiments have assessed that human action observation can use multiple information sources, but it is currently unknown how they are integrated and how conflicts between them are resolved. To address this issue, we designed an action observation paradigm requiring the integration of multiple, potentially conflicting sources of evidence about the action target: the actor's gaze direction, hand preshape, and arm trajectory, and their availability and relative uncertainty in time. In two experiments, we analyzed participants' action prediction ability by using eye tracking and behavioral measures. The results show that the information provided by the actor's gaze affected participants' explicit predictions. However, results also show that gaze information was disregarded as soon as information on the actor's hand preshape was available, and this latter information source had widespread effects on participants' prediction ability. Furthermore, as the action unfolded in time, participants relied increasingly more on the arm movement source, showing sensitivity to its increasing informativeness. Therefore, the results suggest that the brain forms a robust estimate of the actor's motor intention by integrating multiple sources of information. However, when informative motor cues such as a preshaped hand with a given grip are available and might help in selecting action targets, people tend to capitalize on such motor cues, thus turning out to be more accurate and fast in inferring the object to be manipulated by the other's hand. PMID:25568158

  15. A Methodology for Multiple Rule System Integration and Resolution Within a Singular Knowledge Base

    NASA Technical Reports Server (NTRS)

    Kautzmann, Frank N., III

    1988-01-01

    Expert Systems which support knowledge representation by qualitative modeling techniques experience problems, when called upon to support integrated views embodying description and explanation, especially when other factors such as multiple causality, competing rule model resolution, and multiple uses of knowledge representation are included. A series of prototypes are being developed to demonstrate the feasibility of automating the process of systems engineering, design and configuration, and diagnosis and fault management. A study involves not only a generic knowledge representation; it must also support multiple views at varying levels of description and interaction between physical elements, systems, and subsystems. Moreover, it will involve models of description and explanation for each level. This multiple model feature requires the development of control methods between rule systems and heuristics on a meta-level for each expert system involved in an integrated and larger class of expert system. The broadest possible category of interacting expert systems is described along with a general methodology for the knowledge representation and control of mutually exclusive rule systems.

  16. A hybrid fluorous monolithic capillary column with integrated nanoelectrospray ionization emitter for determination of perfluoroalkyl acids by nano-liquid chromatography-nanoelectrospray ionization-mass spectrometry/mass spectrometry.

    PubMed

    Zhang, Haiyang; Ou, Junjie; Wei, Yinmao; Wang, Hongwei; Liu, Zhongshan; Zou, Hanfa

    2016-04-01

    A hybrid fluorous monolithic column was simply prepared via photo-initiated free radical polymerization of an acrylopropyl polyhedral oligomeric silsesquioxane (acryl-POSS) and a perfluorous monomer (2,2,3,3,4,4,5,5,6,6,7,7-dodecafluoroheptyl acrylate) in UV-transparent fused-silica capillaries within 5min. The physical characterization of hybrid fluorous monolith, including scanning electron microscopy (SEM), Fourier transform infrared (FT-IR) spectroscopy, mercury intrusion porosimetry (MIP) and nitrogen adsorption/desorption measurement was performed. Chromatographic performance was also evaluated by capillary liquid chromatography (cLC). Due to the fluorous-fluorous interaction between fluorous monolith and analytes, fluorobenzenes could well be separated, and the column efficiencies reached 86,600-92,500plates/m at the velocity of 0.87mm/s for alkylbenzenes and 51,900-76,000plates/m at the velocity of 1.10mm/s for fluorobenzenes. Meanwhile, an approach to integrate nanoelectrospray ionization (ESI) emitter with hybrid fluorous monolithic column was developed for quantitative determination of perfluoroalkyl acids by nanoHPLC-ESI-MS/MS. The integration design could minimize extracolumn volume, thus excluding undesirable peak broadening and improving separation performance. PMID:26916593

  17. A hybrid fluorous monolithic capillary column with integrated nanoelectrospray ionization emitter for determination of perfluoroalkyl acids by nano-liquid chromatography-nanoelectrospray ionization-mass spectrometry/mass spectrometry.

    PubMed

    Zhang, Haiyang; Ou, Junjie; Wei, Yinmao; Wang, Hongwei; Liu, Zhongshan; Zou, Hanfa

    2016-04-01

    A hybrid fluorous monolithic column was simply prepared via photo-initiated free radical polymerization of an acrylopropyl polyhedral oligomeric silsesquioxane (acryl-POSS) and a perfluorous monomer (2,2,3,3,4,4,5,5,6,6,7,7-dodecafluoroheptyl acrylate) in UV-transparent fused-silica capillaries within 5min. The physical characterization of hybrid fluorous monolith, including scanning electron microscopy (SEM), Fourier transform infrared (FT-IR) spectroscopy, mercury intrusion porosimetry (MIP) and nitrogen adsorption/desorption measurement was performed. Chromatographic performance was also evaluated by capillary liquid chromatography (cLC). Due to the fluorous-fluorous interaction between fluorous monolith and analytes, fluorobenzenes could well be separated, and the column efficiencies reached 86,600-92,500plates/m at the velocity of 0.87mm/s for alkylbenzenes and 51,900-76,000plates/m at the velocity of 1.10mm/s for fluorobenzenes. Meanwhile, an approach to integrate nanoelectrospray ionization (ESI) emitter with hybrid fluorous monolithic column was developed for quantitative determination of perfluoroalkyl acids by nanoHPLC-ESI-MS/MS. The integration design could minimize extracolumn volume, thus excluding undesirable peak broadening and improving separation performance.

  18. Jacobian integration method increases the statistical power to measure gray matter atrophy in multiple sclerosis☆

    PubMed Central

    Nakamura, Kunio; Guizard, Nicolas; Fonov, Vladimir S.; Narayanan, Sridar; Collins, D. Louis; Arnold, Douglas L.

    2013-01-01

    Gray matter atrophy provides important insights into neurodegeneration in multiple sclerosis (MS) and can be used as a marker of neuroprotection in clinical trials. Jacobian integration is a method for measuring volume change that uses integration of the local Jacobian determinants of the nonlinear deformation field registering two images, and is a promising tool for measuring gray matter atrophy. Our main objective was to compare the statistical power of the Jacobian integration method to commonly used methods in terms of the sample size required to detect a treatment effect on gray matter atrophy. We used multi-center longitudinal data from relapsing–remitting MS patients and evaluated combinations of cross-sectional and longitudinal pre-processing with SIENAX/FSL, SPM, and FreeSurfer, as well as the Jacobian integration method. The Jacobian integration method outperformed these other commonly used methods, reducing the required sample size by a factor of 4–5. The results demonstrate the advantage of using the Jacobian integration method to assess neuroprotection in MS clinical trials. PMID:24266007

  19. A Nonparametric, Multiple Imputation-Based Method for the Retrospective Integration of Data Sets.

    PubMed

    Carrig, Madeline M; Manrique-Vallier, Daniel; Ranby, Krista W; Reiter, Jerome P; Hoyle, Rick H

    2015-01-01

    Complex research questions often cannot be addressed adequately with a single data set. One sensible alternative to the high cost and effort associated with the creation of large new data sets is to combine existing data sets containing variables related to the constructs of interest. The goal of the present research was to develop a flexible, broadly applicable approach to the integration of disparate data sets that is based on nonparametric multiple imputation and the collection of data from a convenient, de novo calibration sample. We demonstrate proof of concept for the approach by integrating three existing data sets containing items related to the extent of problematic alcohol use and associations with deviant peers. We discuss both necessary conditions for the approach to work well and potential strengths and weaknesses of the method compared to other data set integration approaches.

  20. Traction boundary integral equation (BIE) formulations and applications to nonplanar and multiple cracks

    NASA Astrophysics Data System (ADS)

    Cruse, Thomas A.; Novati, Giorgio

    The hypersingular Somigliana identity for the stress tensor is used as the basis for a traction boundary integral equation (BIE) suitable for numerical application to nonplanar cracks and to multiple cracks. The variety of derivations of hypersingular traction BIE formulations is reviewed and extended for this problem class. Numerical implementation is accomplished for piecewise-flat models of curved cracks, using local coordinate system integrations. A nonconforming, triangular boundary element implementation of the integral equations is given. Demonstration problems include several three-dimensional approximations to plane-strain fracture mechanics problems, for which exact or highly accurate numerical solutions exist. In all cases, the use of a piecewise-flat traction BIE implementation is shown to give excellent results.

  1. Capillary micro-switches

    NASA Astrophysics Data System (ADS)

    Steen, Paul; Matalanis, Claude; Hirsa, Amir; Cox, Christhopher

    2002-11-01

    A capillary surface is a liquid/liquid or liquid/gas interface whose shape is determined by surface tension. Capillary surfaces occur when the capillary length is large compared to the container scale, as happens for typical liquids against gas on the sub-millimeter scale on Earth and on the meter scale in the micro-gravity environment of space vehicles. Manipulating capillary surfaces has emerged as a leading strategy for moving liquids on the micro-scale [1]. Practitioners have yet to take advantage of capillary instability in their design of devices, though. We illustrate how the response diagram of a single switch (bi-stable device) can be constructed from that of two capillary elements, how that of a system of switches (a pair) can be built from that of a single switch and finally how understanding the response of the system guides us to observations of new behavior in the laboratory. Experiments on capillary surfaces use either a soap-film analog (10 centimeter scale) or a liquid/gas (millimeter scale) apparatus. Progress is reported on the application of an array of micro-switches to make a controllable adhesion device, with the aim of effecting droplet transport. 1. Cho, Fan, Moon and Kim, "Towards digital microfluidic circuits: creating, transporting, cutting and merging liquid droplets by electrowetting-based actuation." Proc. 15th IEEE Int'l Conf. on MEMS, January 2002.

  2. Multiplexed capillary electrophoresis system

    DOEpatents

    Yeung, E.S.; Li, Q.; Lu, X.

    1998-04-21

    The invention provides a side-entry optical excitation geometry for use in a multiplexed capillary electrophoresis system. A charge-injection device is optically coupled to capillaries in the array such that the interior of a capillary is imaged onto only one pixel. In Sanger-type 4-label DNA sequencing reactions, nucleotide identification (``base calling``) is improved by using two long-pass filters to split fluorescence emission into two emission channels. A binary poly(ethyleneoxide) matrix is used in the electrophoretic separations. 19 figs.

  3. Multiplexed capillary electrophoresis system

    DOEpatents

    Yeung, E.S.; Chang, H.T.; Fung, E.N.; Li, Q.; Lu, X.

    1996-12-10

    The invention provides a side-entry optical excitation geometry for use in a multiplexed capillary electrophoresis system. A charge-injection device is optically coupled to capillaries in the array such that the interior of a capillary is imaged onto only one pixel. In Sanger-type 4-label DNA sequencing reactions, nucleotide identification (``base calling``) is improved by using two long-pass filters to split fluorescence emission into two emission channels. A binary poly(ethyleneoxide) matrix is used in the electrophoretic separations. 19 figs.

  4. Multiplexed capillary electrophoresis system

    DOEpatents

    Yeung, Edward S.; Li, Qingbo; Lu, Xiandan

    1998-04-21

    The invention provides a side-entry optical excitation geometry for use in a multiplexed capillary electrophoresis system. A charge-injection device is optically coupled to capillaries in the array such that the interior of a capillary is imaged onto only one pixel. In Sanger-type 4-label DNA sequencing reactions, nucleotide identification ("base calling") is improved by using two long-pass filters to split fluorescence emission into two emission channels. A binary poly(ethyleneoxide) matrix is used in the electrophoretic separations.

  5. Multiplexed capillary electrophoresis system

    DOEpatents

    Yeung, Edward S.; Chang, Huan-Tsang; Fung, Eliza N.; Li, Qingbo; Lu, Xiandan

    1996-12-10

    The invention provides a side-entry optical excitation geometry for use in a multiplexed capillary electrophoresis system. A charge-injection device is optically coupled to capillaries in the array such that the interior of a capillary is imaged onto only one pixel. In Sanger-type 4-label DNA sequencing reactions, nucleotide identification ("base calling") is improved by using two long-pass filters to split fluorescence emission into two emission channels. A binary poly(ethyleneoxide) matrix is used in the electrophoretic separations.

  6. Nasal Lobular Capillary Hemangioma

    PubMed Central

    Patil, Prashant; Singla, Saurabh; Mane, Ranoji; Jagdeesh, K. S.

    2013-01-01

    Nasal lobular capillary hemangioma is a rare benign tumor of the paranasal sinuses. This lesion is believed to grow rapidly in size over time. The exact etiopathogenesis is still a dilemma. We discuss a case of nasal lobular capillary hemangioma presenting with a history of epistaxis. Contrast enhanced computed tomography of paranasal sinuses revealed an intensely enhancing soft-tissue mass in the left nasal cavity and left middle and inferior meati with no obvious bony remodeling or destruction. We present imaging and pathologic features of nasal lobular capillary hemangioma and differentiate it from other entities like nasal angiofibroma. PMID:24228209

  7. High-precision, automated integration of multiple isothermal titration calorimetric thermograms: new features of NITPIC

    PubMed Central

    Scheuermann, Thomas H.; Brautigam, Chad A.

    2014-01-01

    Isothermal titration calorimetry (ITC) has become a standard and widely available tool to measure the thermodynamic parameters of macromolecular associations. Modern applications of the method, including global analysis and drug screening, require the acquisition of multiple sets of data; sometimes these data sets number in the hundreds. Therefore, there is a need for quick, precise, and automated means to process the data, particularly at the first step of data analysis, which is commonly the integration of the raw data to yield an interpretable isotherm. Herein, we describe enhancements to an algorithm that previously has been shown to provide an automated, unbiased, and high-precision means to integrate ITC data. These improvements allow for the speedy and precise serial integration of an unlimited number of ITC data sets, and they have been implemented in the freeware program NITPIC, version 1.1.0. We present a comprehensive comparison of the performance of this software against an older version of NITPIC and a current version of Origin, which is commonly used for integration. The new methods recapitulate the excellent performance of the previous versions of NITPIC while speeding it up substantially, and their precision is significantly better than that of Origin. This new version of NITPIC is therefore well suited to the serial integration of many ITC data sets. PMID:25524420

  8. High-precision, automated integration of multiple isothermal titration calorimetric thermograms: new features of NITPIC.

    PubMed

    Scheuermann, Thomas H; Brautigam, Chad A

    2015-04-01

    Isothermal titration calorimetry (ITC) has become a standard and widely available tool to measure the thermodynamic parameters of macromolecular associations. Modern applications of the method, including global analysis and drug screening, require the acquisition of multiple sets of data; sometimes these data sets number in the hundreds. Therefore, there is a need for quick, precise, and automated means to process the data, particularly at the first step of data analysis, which is commonly the integration of the raw data to yield an interpretable isotherm. Herein, we describe enhancements to an algorithm that previously has been shown to provide an automated, unbiased, and high-precision means to integrate ITC data. These improvements allow for the speedy and precise serial integration of an unlimited number of ITC data sets, and they have been implemented in the freeware program NITPIC, version 1.1.0. We present a comprehensive comparison of the performance of this software against an older version of NITPIC and a current version of Origin, which is commonly used for integration. The new methods recapitulate the excellent performance of the previous versions of NITPIC while speeding it up substantially, and their precision is significantly better than that of Origin. This new version of NITPIC is therefore well suited to the serial integration of many ITC data sets. PMID:25524420

  9. Identification of genes for complex diseases using integrated analysis of multiple types of genomic data.

    PubMed

    Cao, Hongbao; Lei, Shufeng; Deng, Hong-Wen; Wang, Yu-Ping

    2012-01-01

    Various types of genomic data (e.g., SNPs and mRNA transcripts) have been employed to identify risk genes for complex diseases. However, the analysis of these data has largely been performed in isolation. Combining these multiple data for integrative analysis can take advantage of complementary information and thus can have higher power to identify genes (and/or their functions) that would otherwise be impossible with individual data analysis. Due to the different nature, structure, and format of diverse sets of genomic data, multiple genomic data integration is challenging. Here we address the problem by developing a sparse representation based clustering (SRC) method for integrative data analysis. As an example, we applied the SRC method to the integrative analysis of 376821 SNPs in 200 subjects (100 cases and 100 controls) and expression data for 22283 genes in 80 subjects (40 cases and 40 controls) to identify significant genes for osteoporosis (OP). Comparing our results with previous studies, we identified some genes known related to OP risk (e.g., 'THSD4', 'CRHR1', 'HSD11B1', 'THSD7A', 'BMPR1B' 'ADCY10', 'PRL', 'CA8','ESRRA', 'CALM1', 'CALM1', 'SPARC', and 'LRP1'). Moreover, we uncovered novel osteoporosis susceptible genes ('DICER1', 'PTMA', etc.) that were not found previously but play functionally important roles in osteoporosis etiology from existing studies. In addition, the SRC method identified genes can lead to higher accuracy for the diagnosis/classification of osteoporosis subjects when compared with the traditional T-test and Fisher-exact test, which further validates the proposed SRC approach for integrative analysis.

  10. Identification of Genes for Complex Diseases Using Integrated Analysis of Multiple Types of Genomic Data

    PubMed Central

    Cao, Hongbao; Lei, Shufeng; Deng, Hong-Wen; Wang, Yu-Ping

    2012-01-01

    Various types of genomic data (e.g., SNPs and mRNA transcripts) have been employed to identify risk genes for complex diseases. However, the analysis of these data has largely been performed in isolation. Combining these multiple data for integrative analysis can take advantage of complementary information and thus can have higher power to identify genes (and/or their functions) that would otherwise be impossible with individual data analysis. Due to the different nature, structure, and format of diverse sets of genomic data, multiple genomic data integration is challenging. Here we address the problem by developing a sparse representation based clustering (SRC) method for integrative data analysis. As an example, we applied the SRC method to the integrative analysis of 376821 SNPs in 200 subjects (100 cases and 100 controls) and expression data for 22283 genes in 80 subjects (40 cases and 40 controls) to identify significant genes for osteoporosis (OP). Comparing our results with previous studies, we identified some genes known related to OP risk (e.g., ‘THSD4’, ‘CRHR1’, ‘HSD11B1’, ‘THSD7A’, ‘BMPR1B’ ‘ADCY10’, ‘PRL’, ‘CA8’,’ESRRA’, ‘CALM1’, ‘CALM1’, ‘SPARC’, and ‘LRP1’). Moreover, we uncovered novel osteoporosis susceptible genes (‘DICER1’, ‘PTMA’, etc.) that were not found previously but play functionally important roles in osteoporosis etiology from existing studies. In addition, the SRC method identified genes can lead to higher accuracy for the diagnosis/classification of osteoporosis subjects when compared with the traditional T-test and Fisher-exact test, which further validates the proposed SRC approach for integrative analysis. PMID:22957024

  11. Capillary pumped loop application guide

    NASA Astrophysics Data System (ADS)

    Cullimore, Brent A.

    Capillary pumped loops (CPLs) have undergone extensive development since the late 1970's, and represent a maturing technology that is beginning to appear in spacecraft designs. Perhaps because most CPL literature is intended for CPL and heat pipe dedvelopers, or perhaps because of the myriad of component design and layout options available, many thermal control designers are either unfamiliar with the capabilities offered by CPLs, or are confused about their limitations. This survey paper is targeted toward thermal control designers who must decide when and where to use CPLs, or having chosen a CPL solution, must deal with system-level integration and test issues.

  12. MSblender: A probabilistic approach for integrating peptide identifications from multiple database search engines.

    PubMed

    Kwon, Taejoon; Choi, Hyungwon; Vogel, Christine; Nesvizhskii, Alexey I; Marcotte, Edward M

    2011-07-01

    Shotgun proteomics using mass spectrometry is a powerful method for protein identification but suffers limited sensitivity in complex samples. Integrating peptide identifications from multiple database search engines is a promising strategy to increase the number of peptide identifications and reduce the volume of unassigned tandem mass spectra. Existing methods pool statistical significance scores such as p-values or posterior probabilities of peptide-spectrum matches (PSMs) from multiple search engines after high scoring peptides have been assigned to spectra, but these methods lack reliable control of identification error rates as data are integrated from different search engines. We developed a statistically coherent method for integrative analysis, termed MSblender. MSblender converts raw search scores from search engines into a probability score for every possible PSM and properly accounts for the correlation between search scores. The method reliably estimates false discovery rates and identifies more PSMs than any single search engine at the same false discovery rate. Increased identifications increment spectral counts for most proteins and allow quantification of proteins that would not have been quantified by individual search engines. We also demonstrate that enhanced quantification contributes to improve sensitivity in differential expression analyses.

  13. Real object-based 360-degree integral-floating display using multiple depth camera

    NASA Astrophysics Data System (ADS)

    Erdenebat, Munkh-Uchral; Dashdavaa, Erkhembaatar; Kwon, Ki-Chul; Wu, Hui-Ying; Yoo, Kwan-Hee; Kim, Young-Seok; Kim, Nam

    2015-03-01

    A novel 360-degree integral-floating display based on the real object is proposed. The general procedure of the display system is similar with conventional 360-degree integral-floating displays. Unlike previously presented 360-degree displays, the proposed system displays the 3D image generated from the real object in 360-degree viewing zone. In order to display real object in 360-degree viewing zone, multiple depth camera have been utilized to acquire the depth information around the object. Then, the 3D point cloud representations of the real object are reconstructed according to the acquired depth information. By using a special point cloud registration method, the multiple virtual 3D point cloud representations captured by each depth camera are combined as single synthetic 3D point cloud model, and the elemental image arrays are generated for the newly synthesized 3D point cloud model from the given anamorphic optic system's angular step. The theory has been verified experimentally, and it shows that the proposed 360-degree integral-floating display can be an excellent way to display real object in the 360-degree viewing zone.

  14. A fast and high performance multiple data integration algorithm for identifying human disease genes

    PubMed Central

    2015-01-01

    Background Integrating multiple data sources is indispensable in improving disease gene identification. It is not only due to the fact that disease genes associated with similar genetic diseases tend to lie close with each other in various biological networks, but also due to the fact that gene-disease associations are complex. Although various algorithms have been proposed to identify disease genes, their prediction performances and the computational time still should be further improved. Results In this study, we propose a fast and high performance multiple data integration algorithm for identifying human disease genes. A posterior probability of each candidate gene associated with individual diseases is calculated by using a Bayesian analysis method and a binary logistic regression model. Two prior probability estimation strategies and two feature vector construction methods are developed to test the performance of the proposed algorithm. Conclusions The proposed algorithm is not only generated predictions with high AUC scores, but also runs very fast. When only a single PPI network is employed, the AUC score is 0.769 by using F2 as feature vectors. The average running time for each leave-one-out experiment is only around 1.5 seconds. When three biological networks are integrated, the AUC score using F3 as feature vectors increases to 0.830, and the average running time for each leave-one-out experiment takes only about 12.54 seconds. It is better than many existing algorithms. PMID:26399620

  15. Capillary rise of superspreaders.

    PubMed

    Radulovic, Jovana; Sefiane, Khellil; Shanahan, Martin E R

    2011-09-15

    Trisiloxane surfactants, known as 'superspreaders', are commonly employed in numerous applications where enhanced wetting is of the utmost importance. The underlying mechanisms of superspreader wetting have been a focus of scientific interest for ca. 2 decades, and a number of mechanisms have been proposed to explain the unique trisiloxane dynamics. We have studied trisiloxane behaviour in thin capillaries to get further insight into their interfacial activity. Additionally, our knowledge of the capillary rise of superspreaders is surprisingly limited, and the effect of this extraordinary group of surfactants on capillary phenomena has been largely overlooked. Diffusion was confirmed to be the limiting factor of trisiloxane behaviour. A tentative theoretical explanation for the phenomenon studied and an appropriate mathematical model are presented. It is concluded that the enhancement of wetting due to surfactant addition is also a function of geometry: the effect is clear for a sessile drop, but more complex and less beneficial in a capillary.

  16. Displaced capillary dies

    DOEpatents

    Kalejs, Juris P.; Chalmers, Bruce; Surek, Thomas

    1984-01-01

    An asymmetrical shaped capillary die made exclusively of graphite is used to grow silicon ribbon which is capable of being made into solar cells that are more efficient than cells produced from ribbon made using a symmetrically shaped die.

  17. Displaced capillary dies

    DOEpatents

    Kalejs, Juris P.; Chalmers, Bruce; Surek, Thomas

    1982-01-01

    An asymmetrical shaped capillary die made exclusively of graphite is used to grow silicon ribbon which is capable of being made into solar cells that are more efficient than cells produced from ribbon made using a symmetrically shaped die.

  18. Integration of Symptom Ratings from Multiple Informants in ADHD Diagnosis: A Psychometric Model with Clinical Utility

    PubMed Central

    Martel, Michelle M.; Schimmack, Ulrich; Nikolas, Molly; Nigg, Joel T.

    2015-01-01

    The Diagnostic and Statistical Manual of Mental Disorder—Fifth Edition explicitly requires that Attention-Deficit/Hyperactivity Disorder (ADHD) symptoms should be apparent across settings, taking into account reports from multiple informants. Yet, it provides no guidelines how information from different raters should be combined in ADHD diagnosis. We examined the validity of different approaches using structural equation modeling (SEM) for multiple-informant data. Participants were 725 children, 6 to 17 years old, and their primary caregivers and teachers, recruited from the community and completing a thorough research-based diagnostic assessment, including a clinician-administered diagnostic interview, parent and teacher standardized rating scales and cognitive testing. A best-estimate ADHD diagnosis was generated by a diagnostic team. An SEM model demonstrated convergent validity among raters. We found relatively weak symptom-specific agreement among raters, suggesting that a general average scoring algorithm is preferable to symptom-specific scoring algorithms such as the “or” and “and” algorithms. Finally, to illustrate the validity of this approach, we show that averaging makes it possible to reduce the number of items from 18 items to 8 items without a significant decrease in validity. In conclusion, information from multiple raters increases the validity of ADHD diagnosis, and averaging appears to be the optimal way to integrate information from multiple raters. PMID:25730162

  19. Integration of multiple view plus depth data for free viewpoint 3D display

    NASA Astrophysics Data System (ADS)

    Suzuki, Kazuyoshi; Yoshida, Yuko; Kawamoto, Tetsuya; Fujii, Toshiaki; Mase, Kenji

    2014-03-01

    This paper proposes a method for constructing a reasonable scale of end-to-end free-viewpoint video system that captures multiple view and depth data, reconstructs three-dimensional polygon models of objects, and display them on virtual 3D CG spaces. This system consists of a desktop PC and four Kinect sensors. First, multiple view plus depth data at four viewpoints are captured by Kinect sensors simultaneously. Then, the captured data are integrated to point cloud data by using camera parameters. The obtained point cloud data are sampled to volume data that consists of voxels. Since volume data that are generated from point cloud data are sparse, those data are made dense by using global optimization algorithm. Final step is to reconstruct surfaces on dense volume data by discrete marching cubes method. Since accuracy of depth maps affects to the quality of 3D polygon model, a simple inpainting method for improving depth maps is also presented.

  20. ePRISM: A case study in multiple proxy and mixed temporal resolution integration

    USGS Publications Warehouse

    Robinson, Marci M.; Dowsett, Harry J.

    2010-01-01

    As part of the Pliocene Research, Interpretation and Synoptic Mapping (PRISM) Project, we present the ePRISM experiment designed I) to provide climate modelers with a reconstruction of an early Pliocene warm period that was warmer than the PRISM interval (similar to 3.3 to 3.0 Ma), yet still similar in many ways to modern conditions and 2) to provide an example of how best to integrate multiple-proxy sea surface temperature (SST) data from time series with varying degrees of temporal resolution and age control as we begin to build the next generation of PRISM, the PRISM4 reconstruction, spanning a constricted time interval. While it is possible to tie individual SST estimates to a single light (warm) oxygen isotope event, we find that the warm peak average of SST estimates over a narrowed time interval is preferential for paleoclimate reconstruction as it allows for the inclusion of more records of multiple paleotemperature proxies.

  1. [The academic education in nursing and multiple-victim incidents: an integrative review].

    PubMed

    Salvador, Pétala Tuani Candido de Oliveira; Dantas, Rodrigo Assis Neves; Dantas, Daniele Vieira; Torres, Gilson de Vasconcelos

    2012-06-01

    The objective of this study is to reflect on the knowledge, competencies and skill that must be promoted during the academic education of nurses for an effective professional practice in view of a multiple-victim incident (MVI). This is an integrative literature review regarding academic nursing education. The literature survey was performed on the BDENF, LILACS, SciELO, MEDLINE, Web of Knowledge and HighWire Press databases, using the following descriptors: higher education; nursing education; emergency nursing; and mass casualty incidents. The publications permitted considerations regarding the following themes: particularities; competencies and skills essential in nursing practice in view of multiple-victim incidents; and the professors' strategies to promote those competencies and skills. The literature analysis demonstrated that nursing education should be configured as a space to develop critical thinking skills, which requires professors to have an eclectic educational background.

  2. Characterization of multiple-bit errors from single-ion tracks in integrated circuits

    NASA Technical Reports Server (NTRS)

    Zoutendyk, J. A.; Edmonds, L. D.; Smith, L. S.

    1989-01-01

    The spread of charge induced by an ion track in an integrated circuit and its subsequent collection at sensitive nodal junctions can cause multiple-bit errors. The authors have experimentally and analytically investigated this phenomenon using a 256-kb dynamic random-access memory (DRAM). The effects of different charge-transport mechanisms are illustrated, and two classes of ion-track multiple-bit error clusters are identified. It is demonstrated that ion tracks that hit a junction can affect the lateral spread of charge, depending on the nature of the pull-up load on the junction being hit. Ion tracks that do not hit a junction allow the nearly uninhibited lateral spread of charge.

  3. Integrated multiple patch-clamp array chip via lateral cell trapping junctions

    NASA Astrophysics Data System (ADS)

    Seo, J.; Ionescu-Zanetti, C.; Diamond, J.; Lal, R.; Lee, L. P.

    2004-03-01

    We present an integrated multiple patch-clamp array chip by utilizing lateral cell trapping junctions. The intersectional design of a microfluidic network provides multiple cell addressing and manipulation sites for efficient electrophysiological measurements at a number of patch sites. The patch pores consist of openings in the sidewall of a main fluidic channel, and a membrane patch is drawn into a smaller horizontal channel. This device geometry not only minimizes capacitive coupling between the cell reservoir and the patch channel, but also allows simultaneous optical and electrical measurements of ion channel proteins. Evidence of the hydrodynamic placement of mammalian cells at the patch sites as well as measurements of patch sealing resistance is presented. Device fabrication is based on micromolding of polydimethylsiloxane, thus allowing inexpensive mass production of disposable high-throughput biochips.

  4. A Tri-Factor Model for Integrating Ratings Across Multiple Informants

    PubMed Central

    Bauer, Daniel J.; Howard, Andrea L.; Baldasaro, Ruth E.; Curran, Patrick J.; Hussong, Andrea M.; Chassin, Laurie; Zucker, Robert A.

    2014-01-01

    Psychologists often obtain ratings for target individuals from multiple informants such as parents or peers. In this paper we propose a tri-factor model for multiple informant data that separates target-level variability from informant-level variability and item-level variability. By leveraging item-level data, the tri-factor model allows for examination of a single trait rated on a single target. In contrast to many psychometric models developed for multitrait-multimethod data, the tri-factor model is predominantly a measurement model. It is used to evaluate item quality in scale development, test hypotheses about sources of target variability (e.g., sources of trait differences) versus informant variability (e.g., sources of rater bias), and generate integrative scores that are purged of the subjective biases of single informants. PMID:24079932

  5. Integrated airborne lidar and multiple endmember spectral mixture analysis (MESMA) for plant species mapping across multiple functional groups

    NASA Astrophysics Data System (ADS)

    Dahlin, K.; Asner, G. P.

    2010-12-01

    The ability to map plant species distributions has long been one of the key goals of terrestrial remote sensing. Achieving this goal has been challenging, however, due to technical constraints and the difficulty in relating remote observations to ground measurements. Advances in both the types of data that can be collected remotely and in available analytical tools like multiple endmember spectral mixture analysis (MESMA) are allowing for rapid improvements in this field. In 2007 the Carnegie Airborne Observatory (CAO) acquired high resolution lidar and hyperspectral imagery of Jasper Ridge Biological Preserve (Woodside, California). The site contains a mosaic of vegetation types, from grassland to chaparral to evergreen forest. To build a spectral library, 415 GPS points were collected in the field, made up of 44 plant species, six plant categories (for nonphotosynthetic vegetation), and four substrate types. Using the lidar data to select the most illuminated pixels as seen from the aircraft (based on canopy shape and viewing angle), we then reduced the spectral library to only the most fully lit pixels. To identify individual plant species in the imagery, first the hyperspectral data was used to calculate the normalized difference vegetation index (NDVI), and then pixels with an NDVI less than 0.15 were removed from further analysis. The remaining image was stratified into five classes based on vegetation height derived from the lidar data. For each class, a suite of possible endmembers was identified and then three endmember selection procedures (endmember average RMS, minimum average spectral angle, and count based endmember selection) were employed to select the most representative endmembers from each species in each class. Two and three endmember models were then applied and each pixel was assigned a species or plant category based on the highest endmember fraction. To validate the approach, an independent set of 200 points was collected throughout the

  6. Method for Visually Integrating Multiple Data Acquisition Technologies for Real Time and Retrospective Analysis

    NASA Technical Reports Server (NTRS)

    Bogart, Edward H. (Inventor); Pope, Alan T. (Inventor)

    2000-01-01

    A system for display on a single video display terminal of multiple physiological measurements is provided. A subject is monitored by a plurality of instruments which feed data to a computer programmed to receive data, calculate data products such as index of engagement and heart rate, and display the data in a graphical format simultaneously on a single video display terminal. In addition live video representing the view of the subject and the experimental setup may also be integrated into the single data display. The display may be recorded on a standard video tape recorder for retrospective analysis.

  7. Capillary discharge source

    DOEpatents

    Bender, III, Howard Albert

    2003-11-25

    Debris generation from an EUV electric discharge plasma source device can be significantly reduced or essentially eliminated by encasing the electrodes with dielectric or electrically insulating material so that the electrodes are shielded from the plasma, and additionally by providing a path for the radiation to exit wherein the electrodes are not exposed to the area where the radiation is collected. The device includes: (a) a body, which is made of an electrically insulating material, that defines a capillary bore that has a proximal end and a distal end and that defines at least one radiation exit; (b) a first electrode that defines a first channel that has a first inlet end that is connected to a source of gas and a first outlet end that is in communication with the capillary bore, wherein the first electrode is positioned at the distal end of the capillary bore; (c) a second electrode that defines a second channel that has a second inlet end that is in communication with the capillary bore and an outlet end, wherein the second electrode is positioned at the proximal end of the capillary bore; and (d) a source of electric potential that is connected across the first and second electrodes, wherein radiation generated within the capillary bore is emitted through the at least one radiation exit and wherein the first electrode and second electrode are shielded from the emitted radiation.

  8. Capillary saturation and desaturation.

    PubMed

    Hilfer, R; Armstrong, R T; Berg, S; Georgiadis, A; Ott, H

    2015-12-01

    Capillary desaturation experiments produce disconnected (trapped) ganglia of mesoscopic sizes intermediate between pore size and system size. Experimental evidence for interactions between these mesoscale clusters during desaturation is analyzed and discussed within the established microscopic and macroscopic laws of Newton, Young-Laplace, and Darcy. A theoretical expression for capillary number correlations is introduced that seems to have remained unnoticed. It expresses capillary desaturation curves in terms of stationary capillary pressures and relative permeabilities. The theoretical expression shows that the plateau saturation in capillary desaturation curves may in general differ from the residual nonwetting saturation defined through the saturation limit of the main hysteresis loop. Hysteresis effects as well as the difference between wetting and nonwetting fluids are introduced into the analysis of capillary desaturation experiments. The article examines experiments with different desaturation protocols and discusses the existence of a mesoscopic length scale intermediate between pore scale and sample scale. The theoretical expression is derived entirely within the existing traditional theory of two-phase flow in porous media and compared to a recent experiment. PMID:26764820

  9. Cortical mechanisms for trans-saccadic memory and integration of multiple object features

    PubMed Central

    Prime, Steven L.; Vesia, Michael; Crawford, J. Douglas

    2011-01-01

    Constructing an internal representation of the world from successive visual fixations, i.e. separated by saccadic eye movements, is known as trans-saccadic perception. Research on trans-saccadic perception (TSP) has been traditionally aimed at resolving the problems of memory capacity and visual integration across saccades. In this paper, we review this literature on TSP with a focus on research showing that egocentric measures of the saccadic eye movement can be used to integrate simple object features across saccades, and that the memory capacity for items retained across saccades, like visual working memory, is restricted to about three to four items. We also review recent transcranial magnetic stimulation experiments which suggest that the right parietal eye field and frontal eye fields play a key functional role in spatial updating of objects in TSP. We conclude by speculating on possible cortical mechanisms for governing egocentric spatial updating of multiple objects in TSP. PMID:21242142

  10. One-step integration of multiple genes into the oleaginous yeast Yarrowia lipolytica.

    PubMed

    Gao, Shuliang; Han, Linna; Zhu, Li; Ge, Mei; Yang, Sheng; Jiang, Yu; Chen, Daijie

    2014-12-01

    Yarrowia lipolytica is an unconventional yeast, and is generally recognized as safe (GRAS). It provides a versatile fermentation platform that is used commercially to produce many added-value products. Here we report a multiple fragment assembly method that allows one-step integration of an entire β-carotene biosynthesis pathway (~11 kb, consisting of four genes) via in vivo homologous recombination into the rDNA locus of the Y. lipolytica chromosome. The highest efficiency was 21%, and the highest production of β-carotene was 2.2 ± 0.3 mg per g dry cell weight. The total procedure was completed in less than one week, as compared to a previously reported sequential gene integration method that required n weeks for n genes. This time-saving method will facilitate synthetic biology, metabolic engineering and functional genomics studies of Y. lipolytica. PMID:25216641

  11. An integrated probabilistic approach for gene function prediction using multiple sources of high-throughput data.

    PubMed

    Zhang, Chao; Joshi, Trupti; Lin, Guan Ning; Xu, Dong

    2008-01-01

    Characterising gene function is one of the major challenging tasks in the post-genomic era. Various approaches have been developed to integrate multiple sources of high-throughput data to predict gene function. Most of those approaches are just used for research purpose and have not been implemented as publicly available tools. Even for those implemented applications, almost all of them are still web-based 'prediction servers' that have to be managed by specialists. This paper introduces a systematic method for integrating various sources of high-throughput data to predict gene function and analyse our prediction results and evaluates its performances based on the competition for mouse gene function prediction (MouseFunc). A stand-alone Java-based software package 'GeneFAS' is freely available at http://digbio. missouri.eduigenefas.

  12. Studying morphological integration and modularity at multiple levels: concepts and analysis

    PubMed Central

    Klingenberg, Christian Peter

    2014-01-01

    Although most studies on integration and modularity have focused on variation among individuals within populations or species, this is not the only level of variation for which integration and modularity exist. Multiple levels of biological variation originate from distinct sources: genetic variation, phenotypic plasticity resulting from environmental heterogeneity, fluctuating asymmetry from random developmental variation and, at the interpopulation or interspecific levels, evolutionary change. The processes that produce variation at all these levels can impart integration or modularity on the covariance structure among morphological traits. In turn, studies of the patterns of integration and modularity can inform about the underlying processes. In particular, the methods of geometric morphometrics offer many advantages for such studies because they can characterize the patterns of morphological variation in great detail and maintain the anatomical context of the structures under study. This paper reviews biological concepts and analytical methods for characterizing patterns of variation and for comparing across levels. Because research comparing patterns across level has only just begun, there are relatively few results, generalizations are difficult and many biological and statistical questions remain unanswered. Nevertheless, it is clear that research using this approach can take advantage of an abundance of new possibilities that are so far largely unexplored. PMID:25002695

  13. Pragmatic Metadata Management for Integration into Multiple Spatial Data Infrastructure Systems and Platforms

    NASA Astrophysics Data System (ADS)

    Benedict, K. K.; Scott, S.

    2013-12-01

    While there has been a convergence towards a limited number of standards for representing knowledge (metadata) about geospatial (and other) data objects and collections, there exist a variety of community conventions around the specific use of those standards and within specific data discovery and access systems. This combination of limited (but multiple) standards and conventions creates a challenge for system developers that aspire to participate in multiple data infrastrucutres, each of which may use a different combination of standards and conventions. While Extensible Markup Language (XML) is a shared standard for encoding most metadata, traditional direct XML transformations (XSLT) from one standard to another often result in an imperfect transfer of information due to incomplete mapping from one standard's content model to another. This paper presents the work at the University of New Mexico's Earth Data Analysis Center (EDAC) in which a unified data and metadata management system has been developed in support of the storage, discovery and access of heterogeneous data products. This system, the Geographic Storage, Transformation and Retrieval Engine (GSTORE) platform has adopted a polyglot database model in which a combination of relational and document-based databases are used to store both data and metadata, with some metadata stored in a custom XML schema designed as a superset of the requirements for multiple target metadata standards: ISO 19115-2/19139/19110/19119, FGCD CSDGM (both with and without remote sensing extensions) and Dublin Core. Metadata stored within this schema is complemented by additional service, format and publisher information that is dynamically "injected" into produced metadata documents when they are requested from the system. While mapping from the underlying common metadata schema is relatively straightforward, the generation of valid metadata within each target standard is necessary but not sufficient for integration into

  14. Structure of the EGF receptor transactivation circuit integrates multiple signals with cell context

    SciTech Connect

    Joslin, Elizabeth J.; Shankaran, Harish; Opresko, Lee K.; Bollinger, Nikki; Lauffenburger, Douglas A.; Wiley, H. S.

    2010-05-10

    Transactivation of the epidermal growth factor receptor (EGFR) has been proposed to be a mechanism by which a variety of cellular inputs can be integrated into a single signaling pathway, but the regulatory topology of this important system is unclear. To understand the transactivation circuit, we first created a “non-binding” reporter for ligand shedding. We then quantitatively defined how signals from multiple agonists were integrated both upstream and downstream of the EGFR into the extracellular signal regulated kinase (ERK) cascade in human mammary epithelial cells. We found that transactivation is mediated by a recursive autocrine circuit where ligand shedding drives EGFR-stimulated ERK that in turn drives further ligand shedding. The time from shedding to ERK activation is fast (<5 min) whereas the recursive feedback is slow (>15 min). Simulations showed that this delay in positive feedback greatly enhanced system stability and robustness. Our results indicate that the transactivation circuit is constructed so that the magnitude of ERK signaling is governed by the sum of multiple direct inputs, while recursive, autocrine ligand shedding controls signal duration.

  15. Critical Velocities in Open Capillary Flow

    NASA Technical Reports Server (NTRS)

    Dreyer, Michael; Langbein, Dieter; Rath, Hans J.

    1996-01-01

    This paper describes the proposed research program on open capillary flow and the preliminary work performed theoretically and in drop tower experiments. The work focuses on the fundamental physical understanding of the flow through capillary bound geometries, where the circumference of the cross section of the flow path contains free surfaces. Examples for such a flow configuration are capillary vanes in surface tension tanks, flow along edges and corners and flow through liquid bridges. The geometries may be classified by their cross section areas, wetted circumferences and the radii of curvature of the free surfaces. In the streaming float zone the flow path is bound by a free surface only. The ribbon vane is a model for vane types used in surface tension tanks, where a structure in proximity to the tank wall forms a capillary gap. A groove is used in heat pipes for the transportation of the condensed working fluid to the heat source and a wedge may occur in a spaceborne experiment where fluid has to be transported by the means of surface tension. The research objectives are the determination of the maximum volume flux, the observation of the free surfaces and the liquid flow inside the flow path as well as the evaluation of the limiting capillary wave speed. The restriction of the maximum volume flux is due to convective forces (flow velocity exceeding the capillary wave speed) and/or viscous forces, i.e. the viscous head loss along the flow path must be compensated by the capillary pressure due to the curved free surface. Exceeding the maximum volume flux leads to the choking of the flow path, thus the free surface collapses and.gas ingestion occurs at the outlet. The means are ground-based experimental work with plateau tanks and in a drop tower, a sounding rocket flight, and theoretical analysis with integral balances as well as full three dimensional CFD solutions for flow with free surfaces.

  16. Cumulative health risk assessment: integrated approaches for multiple contaminants, exposures, and effects

    SciTech Connect

    Rice, Glenn; Teuschler, Linda; MacDonel, Margaret; Butler, Jim; Finster, Molly; Hertzberg, Rick; Harou, Lynne

    2007-07-01

    Available in abstract form only. Full text of publication follows: As information about environmental contamination has increased in recent years, so has public interest in the combined effects of multiple contaminants. This interest has been highlighted by recent tragedies such as the World Trade Center disaster and hurricane Katrina. In fact, assessing multiple contaminants, exposures, and effects has long been an issue for contaminated sites, including U.S. Department of Energy (DOE) legacy waste sites. Local citizens have explicitly asked the federal government to account for cumulative risks, with contaminants moving offsite via groundwater flow, surface runoff, and air dispersal being a common emphasis. Multiple exposures range from ingestion and inhalation to dermal absorption and external gamma irradiation. Three types of concerns can lead to cumulative assessments: (1) specific sources or releases - e.g., industrial facilities or accidental discharges; (2) contaminant levels - in environmental media or human tissues; and (3) elevated rates of disease - e.g., asthma or cancer. The specific initiator frames the assessment strategy, including a determination of appropriate models to be used. Approaches are being developed to better integrate a variety of data, extending from environmental to internal co-location of contaminants and combined effects, to support more practical assessments of cumulative health risks. (authors)

  17. 360 degree viewable floating autostereoscopic display using integral photography and multiple semitransparent mirrors.

    PubMed

    Zhao, Dong; Su, Baiquan; Chen, Guowen; Liao, Hongen

    2015-04-20

    In this paper, we present a polyhedron-shaped floating autostereoscopic display viewable from 360 degrees using integral photography (IP) and multiple semitransparent mirrors. IP combined with polyhedron-shaped multiple semitransparent mirrors is used to achieve a 360 degree viewable floating three-dimensional (3D) autostereoscopic display, having the advantage of being able to be viewed by several observers from various viewpoints simultaneously. IP is adopted to generate a 3D autostereoscopic image with full parallax property. Multiple semitransparent mirrors reflect corresponding IP images, and the reflected IP images are situated around the center of the polyhedron-shaped display device for producing the floating display. The spatial reflected IP images reconstruct a floating autostereoscopic image viewable from 360 degrees. We manufactured two prototypes for producing such displays and performed two sets of experiments to evaluate the feasibility of the method described above. The results of our experiments showed that our approach can achieve a floating autostereoscopic display viewable from surrounding area. Moreover, it is shown the proposed method is feasible to facilitate the continuous viewpoint of a whole 360 degree display without flipping.

  18. 360 degree viewable floating autostereoscopic display using integral photography and multiple semitransparent mirrors.

    PubMed

    Zhao, Dong; Su, Baiquan; Chen, Guowen; Liao, Hongen

    2015-04-20

    In this paper, we present a polyhedron-shaped floating autostereoscopic display viewable from 360 degrees using integral photography (IP) and multiple semitransparent mirrors. IP combined with polyhedron-shaped multiple semitransparent mirrors is used to achieve a 360 degree viewable floating three-dimensional (3D) autostereoscopic display, having the advantage of being able to be viewed by several observers from various viewpoints simultaneously. IP is adopted to generate a 3D autostereoscopic image with full parallax property. Multiple semitransparent mirrors reflect corresponding IP images, and the reflected IP images are situated around the center of the polyhedron-shaped display device for producing the floating display. The spatial reflected IP images reconstruct a floating autostereoscopic image viewable from 360 degrees. We manufactured two prototypes for producing such displays and performed two sets of experiments to evaluate the feasibility of the method described above. The results of our experiments showed that our approach can achieve a floating autostereoscopic display viewable from surrounding area. Moreover, it is shown the proposed method is feasible to facilitate the continuous viewpoint of a whole 360 degree display without flipping. PMID:25969022

  19. Energy Simulation of Integrated Multiple-Zone Variable Refrigerant Flow System

    SciTech Connect

    Shen, Bo; Rice, C Keith; Baxter, Van D

    2013-01-01

    We developed a detailed steady-state system model, to simulate the performance of an integrated five-zone variable refrigerant flow (VRF)heat pump system. The system is multi-functional, capable of space cooling, space heating, combined space cooling and water heating, and dedicated water heating. Methods were developed to map the VRF performance in each mode, based on the abundant data produced by the equipment system model. The performance maps were used in TRNSYS annual energy simulations. Using TRNSYS, we have successfully setup and run cases for a multiple-split, VRF heat pump and dehumidifier combination in 5-zone houses in 5 climates that control indoor dry-bulb temperature and relative humidity. We compared the calculated energy consumptions for the VRF heat pump against that of a baseline central air source heat pump, coupled with electric water heating and the standalone dehumidifiers. In addition, we investigated multiple control scenarios for the VRF heat pump, i.e. on/off control, variable indoor air flow rate, and using different zone temperature setting schedules, etc. The energy savings for the multiple scenarios were assessed.

  20. A microfluidic localized, multiple cell culture array using vacuum actuated cell seeding: integrated anticancer drug testing.

    PubMed

    Gao, Yan; Li, Peng; Pappas, Dimitri

    2013-12-01

    In this study, we introduced a novel and convenient approach to culture multiple cells in localized arrays of microfluidic chambers using one-step vacuum actuation. In one device, we integrated 8 individually addressable regions of culture chambers, each only requiring one simple vacuum operation to seed cell lines. Four cell lines were seeded in designated regions in one device via sequential injection with high purity (99.9 %-100 %) and cultured for long-term. The on-chip simultaneous culture of HuT 78, Ramos, PC-3 and C166-GFP cells for 48 h was demonstrated with viabilities of 92 %+/-2 %, 94 %+/-4 %, 96 %+/-2 % and 97 %+/-2 %, respectively. The longest culture period for C166-GFP cells in this study was 168 h with a viability of 96 %+/-10 %. Cell proliferation in each individual side channel can be tracked. Mass transport between the main channel and side channels was achieved through diffusion and studied using fluorescein solution. The main advantage of this device is the capability to perform multiple cell-based assays on the same device for better comparative studies. After treating cells with staurosporine or anti-human CD95 for 16 h, the apoptotic cell percentage of HuT 78, CCRF-CEM, PC-3 and Ramos cells were 36 %+/-3 %, 24 %+/-4 %, 12 %+/-2 %, 18 %+/-4 % for staurosporine, and 63 %+/-2 %, 45 %+/-1 %, 3 %+/-3 %, 27 %+/-12 % for anti-human CD95, respectively. With the advantages of enhanced integration, ease of use and fabrication, and flexibility, this device will be suitable for long-term multiple cell monitoring and cell based assays.

  1. Assessing District Energy Systems Performance Integrated with Multiple Thermal Energy Storages

    NASA Astrophysics Data System (ADS)

    Rezaie, Behnaz

    The goal of this study is to examine various energy resources in district energy (DE) systems and then DE system performance development by means of multiple thermal energy storages (TES) application. This study sheds light on areas not yet investigated precisely in detail. Throughout the research, major components of the heat plant, energy suppliers of the DE systems, and TES characteristics are separately examined; integration of various configurations of the multiple TESs in the DE system is then analysed. In the first part of the study, various sources of energy are compared, in a consistent manner, financially and environmentally. The TES performance is then assessed from various aspects. Then, TES(s) and DE systems with several sources of energy are integrated, and are investigated as a heat process centre. The most efficient configurations of the multiple TESs integrated with the DE system are investigated. Some of the findings of this study are applied on an actual DE system. The outcomes of this study provide insight for researchers and engineers who work in this field, as well as policy makers and project managers who are decision-makers. The accomplishments of the study are original developments TESs and DE systems. As an original development the Enviro-Economic Function, to balance the economic and environmental aspects of energy resources technologies in DE systems, is developed; various configurations of multiple TESs, including series, parallel, and general grid, are developed. The developed related functions are discharge temperature and energy of the TES, and energy and exergy efficiencies of the TES. The TES charging and discharging behavior of TES instantaneously is also investigated to obtain the charging temperature, the maximum charging temperature, the charging energy flow, maximum heat flow capacity, the discharging temperature, the minimum charging temperature, the discharging energy flow, the maximum heat flow capacity, and performance

  2. Capillary rise in a microchannel of arbitrary shape and wettability: hysteresis loop.

    PubMed

    Wang, Zhengjia; Chang, Cheng-Chung; Hong, Siang-Jie; Sheng, Yu-Jane; Tsao, Heng-Kwong

    2012-12-11

    Capillary rise in an asymmetric microchannel, in which both contact angle (wettability) and open angle (geometry) can vary with position, is investigated based on free-energy minimization. The integration of the Young-Laplace equation yields the general force balance between surface tension and gravity. The former is surface tension times the integration of cos θ(u) along the contact line, where θ(u) depicts the local difference between contact angle and open angle. The latter comes from the total volume right underneath the meniscus. For the same channel height, multiple solutions can be obtained from the force balance. However, the stable height of capillary rise must satisfy stability analysis. Several interesting cases have been studied, including short capillary, truncated cone, hyperboloid, and two different plates. As the tube length is smaller than Jurin's height, the angle of contact will be tuned to fulfill the force balance. While only one stable state is seen for divergent channels, two stable states can be observed for convergent channels. Three regimes can be identified for the plot of the stable height of capillary rise against the channel height. The higher height dominates in the short channel regime, while the lower height prevails in the tall channel regime. However, both solutions are stable in the intermediate regime. Surface Evolver simulations and experiments are performed to validate our theoretical predictions. Our results offer some implications for water transport to the tops of tall trees. A small bore at the uppermost leaf connected to a larger xylem conduit corresponds to a convergent channel, and two stable heights are possible. The slow growth of the tree can be regarded as a gradual rise of the convergent channel. Consequently, the stable height of capillary rise to the top of a tall tree can always be achieved. PMID:23171321

  3. Integration of multiple determinants in the neuronal computation of economic values.

    PubMed

    Raghuraman, Anantha P; Padoa-Schioppa, Camillo

    2014-08-27

    Economic goods may vary on multiple dimensions (determinants). A central conjecture in decision neuroscience is that choices between goods are made by comparing subjective values computed through the integration of all relevant determinants. Previous work identified three groups of neurons in the orbitofrontal cortex (OFC) of monkeys engaged in economic choices: (1) offer value cells, which encode the value of individual offers; (2) chosen value cells, which encode the value of the chosen good; and (3) chosen juice cells, which encode the identity of the chosen good. In principle, these populations could be sufficient to generate a decision. Critically, previous work did not assess whether offer value cells (the putative input to the decision) indeed encode subjective values as opposed to physical properties of the goods, and/or whether offer value cells integrate multiple determinants. To address these issues, we recorded from the OFC while monkeys chose between risky outcomes. Confirming previous observations, three populations of neurons encoded the value of individual offers, the value of the chosen option, and the value-independent choice outcome. The activity of both offer value cells and chosen value cells encoded values defined by the integration of juice quantity and probability. Furthermore, both populations reflected the subjective risk attitude of the animals. We also found additional groups of neurons encoding the risk associated with a particular option, the risky nature of the chosen option, and whether the trial outcome was positive or negative. These results provide substantial support for the conjecture described above and for the involvement of OFC in good-based decisions. PMID:25164656

  4. Integrating multiple evidences in taxonomy: species diversity and phylogeny of mustached bats (Mormoopidae: Pteronotus).

    PubMed

    Pavan, Ana Carolina; Marroig, Gabriel

    2016-10-01

    A phylogenetic systematic perspective is instrumental in recovering new species and their evolutionary relationships. The advent of new technologies for molecular and morphological data acquisition and analysis, allied to the integration of knowledge from different areas, such as ecology and population genetics, allows for the emergence of more rigorous, accurate and complete scientific hypothesis on species diversity. Mustached bats (genus Pteronotus) are a good model for the application of this integrative approach. They are a widely distributed and a morphologically homogeneous group, but comprising species with remarkable differences in their echolocation strategy and feeding behavior. The latest systematic review suggested six species with 17 subspecies in Pteronotus. Subsequent studies using discrete morphological characters supported the same arrangement. However, recent papers reported high levels of genetic divergence among conspecific taxa followed by bioacoustic and geographic agreement, suggesting an underestimated diversity in the genus. To date, no study merging genetic evidences and morphometric variation along the entire geographic range of this group has been attempted. Based on a comprehensive sampling including representatives of all current taxonomic units, we attempt to delimit species in Pteronotus through the application of multiple methodologies and hierarchically distinct datasets. The molecular approach includes six molecular markers from three genetic transmission systems; morphological investigations used 41 euclidean distances estimated through three-dimensional landmarks collected from 1628 skulls. The phylogenetic analysis reveals a greater diversity than previously reported, with a high correspondence among the genetic lineages and the currently recognized subspecies in the genus. Discriminant analysis of variables describing size and shape of cranial bones support the rising of the genetic groups to the specific status. Based on

  5. No double-dissociation between optic ataxia and visual agnosia: multiple sub-streams for multiple visuo-manual integrations.

    PubMed

    Pisella, L; Binkofski, F; Lasek, K; Toni, I; Rossetti, Y

    2006-01-01

    The current dominant view of the visual system is marked by the functional and anatomical dissociation between a ventral stream specialised for perception and a dorsal stream specialised for action. The "double-dissociation" between visual agnosia (VA), a deficit of visual recognition, and optic ataxia (OA), a deficit of visuo-manual guidance, considered as consecutive to ventral and dorsal damage, respectively, has provided the main argument for this dichotomic view. In the first part of this paper, we show that the currently available empirical data do not suffice to support a double-dissociation between OA and VA. In the second part, we review evidence coming from human neuropsychology and monkey data, which cast further doubts on the validity of a simple double-dissociation between perception and action because they argue for a far more complex organisation with multiple parallel visual-to-motor connections: 1. A dorso-dorsal pathway (involving the most dorsal part of the parietal and pre-motor cortices): for immediate visuo-motor control--with OA as typical disturbance. The latest research about OA is reviewed, showing how these patients exhibit deficits restricted to the most direct and fast visuo-motor transformations. We also propose that mild mirror ataxia, consisting of misreaching errors when the controlesional hand is guided to a visual goal though a mirror, could correspond to OA with an isolated "hand effect". 2. A ventral stream-prefrontal pathway (connections from the ventral visual stream to pre-frontal areas, by-passing the parietal areas): for "mediate" control (involving spatial or temporal transpositions [Rossetti, Y., & Pisella, L. (2003). Mediate responses as direct evidence for intention: Neuropsychology of Not to-, Not now- and Not there-tasks. In S. Johnson (Ed.), Cognitive Neuroscience perspectives on the problem of intentional action (pp. 67-105). MIT Press.])--with VA as typical disturbance. Preserved visuo-manual guidance in patients

  6. An Integrative Framework for the Analysis of Multiple and Multimodal Representations for Meaning-Making in Science Education

    ERIC Educational Resources Information Center

    Tang, Kok-Sing; Delgado, Cesar; Moje, Elizabeth Birr

    2014-01-01

    This paper presents an integrative framework for analyzing science meaning-making with representations. It integrates the research on multiple representations and multimodal representations by identifying and leveraging the differences in their units of analysis in two dimensions: timescale and compositional grain size. Timescale considers the…

  7. DNA Sequencing Using capillary Electrophoresis

    SciTech Connect

    Dr. Barry Karger

    2011-05-09

    The overall goal of this program was to develop capillary electrophoresis as the tool to be used to sequence for the first time the Human Genome. Our program was part of the Human Genome Project. In this work, we were highly successful and the replaceable polymer we developed, linear polyacrylamide, was used by the DOE sequencing lab in California to sequence a significant portion of the human genome using the MegaBase multiple capillary array electrophoresis instrument. In this final report, we summarize our efforts and success. We began our work by separating by capillary electrophoresis double strand oligonucleotides using cross-linked polyacrylamide gels in fused silica capillaries. This work showed the potential of the methodology. However, preparation of such cross-linked gel capillaries was difficult with poor reproducibility, and even more important, the columns were not very stable. We improved stability by using non-cross linked linear polyacrylamide. Here, the entangled linear chains could move when osmotic pressure (e.g. sample injection) was imposed on the polymer matrix. This relaxation of the polymer dissipated the stress in the column. Our next advance was to use significantly lower concentrations of the linear polyacrylamide that the polymer could be automatically blown out after each run and replaced with fresh linear polymer solution. In this way, a new column was available for each analytical run. Finally, while testing many linear polymers, we selected linear polyacrylamide as the best matrix as it was the most hydrophilic polymer available. Under our DOE program, we demonstrated initially the success of the linear polyacrylamide to separate double strand DNA. We note that the method is used even today to assay purity of double stranded DNA fragments. Our focus, of course, was on the separation of single stranded DNA for sequencing purposes. In one paper, we demonstrated the success of our approach in sequencing up to 500 bases. Other

  8. Integrating multiple lines of evidence into historical biogeography hypothesis testing: a Bison bison case study.

    PubMed

    Metcalf, Jessica L; Prost, Stefan; Nogués-Bravo, David; DeChaine, Eric G; Anderson, Christian; Batra, Persaram; Araújo, Miguel B; Cooper, Alan; Guralnick, Robert P

    2014-02-22

    One of the grand goals of historical biogeography is to understand how and why species' population sizes and distributions change over time. Multiple types of data drawn from disparate fields, combined into a single modelling framework, are necessary to document changes in a species's demography and distribution, and to determine the drivers responsible for change. Yet truly integrated approaches are challenging and rarely performed. Here, we discuss a modelling framework that integrates spatio-temporal fossil data, ancient DNA, palaeoclimatological reconstructions, bioclimatic envelope modelling and coalescence models in order to statistically test alternative hypotheses of demographic and potential distributional changes for the iconic American bison (Bison bison). Using different assumptions about the evolution of the bioclimatic niche, we generate hypothetical distributional and demographic histories of the species. We then test these demographic models by comparing the genetic signature predicted by serial coalescence against sequence data derived from subfossils and modern populations. Our results supported demographic models that include both climate and human-associated drivers of population declines. This synthetic approach, integrating palaeoclimatology, bioclimatic envelopes, serial coalescence, spatio-temporal fossil data and heterochronous DNA sequences, improves understanding of species' historical biogeography by allowing consideration of both abiotic and biotic interactions at the population level.

  9. Integrating multiple lines of evidence into historical biogeography hypothesis testing: a Bison bison case study

    PubMed Central

    Metcalf, Jessica L.; Prost, Stefan; Nogués-Bravo, David; DeChaine, Eric G.; Anderson, Christian; Batra, Persaram; Araújo, Miguel B.; Cooper, Alan; Guralnick, Robert P.

    2014-01-01

    One of the grand goals of historical biogeography is to understand how and why species' population sizes and distributions change over time. Multiple types of data drawn from disparate fields, combined into a single modelling framework, are necessary to document changes in a species's demography and distribution, and to determine the drivers responsible for change. Yet truly integrated approaches are challenging and rarely performed. Here, we discuss a modelling framework that integrates spatio-temporal fossil data, ancient DNA, palaeoclimatological reconstructions, bioclimatic envelope modelling and coalescence models in order to statistically test alternative hypotheses of demographic and potential distributional changes for the iconic American bison (Bison bison). Using different assumptions about the evolution of the bioclimatic niche, we generate hypothetical distributional and demographic histories of the species. We then test these demographic models by comparing the genetic signature predicted by serial coalescence against sequence data derived from subfossils and modern populations. Our results supported demographic models that include both climate and human-associated drivers of population declines. This synthetic approach, integrating palaeoclimatology, bioclimatic envelopes, serial coalescence, spatio-temporal fossil data and heterochronous DNA sequences, improves understanding of species' historical biogeography by allowing consideration of both abiotic and biotic interactions at the population level. PMID:24403338

  10. Integrating syndromic surveillance data across multiple locations: effects on outbreak detection performance.

    PubMed

    Reis, Ben Y; Mandl, Kenneth D

    2003-01-01

    Syndromic surveillance systems are being deployed widely to monitor for signals of covert bioterrorist attacks. Regional systems are being established through the integration of local surveillance data across multiple facilities. We studied how different methods of data integration affect outbreak detection performance. We used a simulation relying on a semi-synthetic dataset, introducing simulated outbreaks of different sizes into historical visit data from two hospitals. In one simulation, we introduced the synthetic outbreak evenly into both hospital datasets (aggregate model). In the second, the outbreak was introduced into only one or the other of the hospital datasets (local model). We found that the aggregate model had a higher sensitivity for detecting outbreaks that were evenly distributed between the hospitals. However, for outbreaks that were localized to one facility, maintaining individual models for each location proved to be better. Given the complementary benefits offered by both approaches, the results suggest building a hybrid system that includes both individual models for each location, and an aggregate model that combines all the data. We also discuss options for multi-level signal integration hierarchies. PMID:14728233

  11. Passive Reactor Cooling Using Capillary Porous Wick

    SciTech Connect

    Miller, Christopher G.; Lin, Thomas F.

    2006-07-01

    Long-term reliability of actively pumped cooling systems is a concern in space-based nuclear reactors. Capillary-driven passive cooling systems are being considered as an alternative to gravity-driven systems. The high surface tension of liquid lithium makes it attractive as the coolant in a capillary-driven cooling system. A system has been conceived in which the fuel rod of a reactor is surrounded by a concentric wick through which liquid lithium flows to provide cooling under normal and emergency operating conditions. Unheated wicking experiments at three pressures using four layered screen mesh wicks of different porosities and three relatively high surface tension fluids have been conducted to gain insight into capillary phenomena for such a capillary cooling system. All fluids tested demonstrated wicking ability in each of the wick structures for all pressures, and wicking ability for each fluid increased with decreasing wick pore size. An externally heated wicking experiment with liquid lithium as the wicking fluid was also conducted. In addition to wicking experiments, a heater rod is under development to simulate the fuel rod of a space based nuclear reactor by providing a heat flux of up to 110 kW/m{sup 2}. Testing of this heater rod has shown its ability to undergo repeated cycling from below 533 K to over 1255 K without failure. This heater rod will be integrated into lithium wicking experiments to provide more realistic simulation of the proposed capillary-driven space nuclear reactor cooling system. (authors)

  12. Multiple kernel learning with random effects for predicting longitudinal outcomes and data integration.

    PubMed

    Chen, Tianle; Zeng, Donglin; Wang, Yuanjia

    2015-12-01

    Predicting disease risk and progression is one of the main goals in many clinical research studies. Cohort studies on the natural history and etiology of chronic diseases span years and data are collected at multiple visits. Although, kernel-based statistical learning methods are proven to be powerful for a wide range of disease prediction problems, these methods are only well studied for independent data, but not for longitudinal data. It is thus important to develop time-sensitive prediction rules that make use of the longitudinal nature of the data. In this paper, we develop a novel statistical learning method for longitudinal data by introducing subject-specific short-term and long-term latent effects through a designed kernel to account for within-subject correlation of longitudinal measurements. Since the presence of multiple sources of data is increasingly common, we embed our method in a multiple kernel learning framework and propose a regularized multiple kernel statistical learning with random effects to construct effective nonparametric prediction rules. Our method allows easy integration of various heterogeneous data sources and takes advantage of correlation among longitudinal measures to increase prediction power. We use different kernels for each data source taking advantage of the distinctive feature of each data modality, and then optimally combine data across modalities. We apply the developed methods to two large epidemiological studies, one on Huntington's disease and the other on Alzheimer's Disease (Alzheimer's Disease Neuroimaging Initiative, ADNI) where we explore a unique opportunity to combine imaging and genetic data to study prediction of mild cognitive impairment, and show a substantial gain in performance while accounting for the longitudinal aspect of the data.

  13. Gas-Filled Capillary Model

    NASA Astrophysics Data System (ADS)

    Steinhauer, L. C.; Kimura, W. D.

    2006-11-01

    We have developed a 1-D, quasi-steady-state numerical model for a gas-filled capillary discharge that is designed to aid in selecting the optimum capillary radius in order to guide a laser beam with the required intensity through the capillary. The model also includes the option for an external solenoid B-field around the capillary, which increases the depth of the parabolic density channel in the capillary, thereby allowing for propagation of smaller laser beam waists. The model has been used to select the parameters for gas-filled capillaries to be utilized during the Staged Electron Laser Acceleration — Laser Wakefield (STELLA-LW) experiment.

  14. A compact short-capillary based high-speed capillary electrophoresis bioanalyzer.

    PubMed

    Fang, Xiao-Xia; Fang, Pan; Pan, Jian-Zhang; Fang, Qun

    2016-09-01

    Here, a compact high-speed CE bioanalyzer based on a short capillary has been developed. Multiple modules of picoliter scale sample injection, high-speed CE separation, sample changing, LIF detection, as well as a custom designed tablet computer for data processing, instrument controlling, and result displaying were integrated in the bioanalyzer with a total size of 23 × 17 × 19 cm (length × width × height). The high-speed CE bioanalyzer is capable of performing automated sample injection and separation for multiple samples and has been successfully applied in fast separations of amino acids, chiral amino acids, proteins and DNA fragments. For instance, baseline separation of six FITC-labeled amino acids and ultrahigh-speed separation of three amino acids could be achieved within 7 and 1 s, respectively. The separation speed and efficiency of the optimized high-speed CE system are comparable to or even better than those reported in microchip-based CE systems. We believe this bioanalyzer could provide an advanced platform for fundamental research in bioscience and clinical diagnosis, as well as in quality control for drugs, foods, and feeds. PMID:27377052

  15. Derivatization in Capillary Electrophoresis.

    PubMed

    Marina, M Luisa; Castro-Puyana, María

    2016-01-01

    Capillary electrophoresis is a well-established separation technique in analytical research laboratories worldwide. Its interesting advantages make CE an efficient and potent alternative to other chromatographic techniques. However, it is also recognized that its main drawback is the relatively poor sensitivity when using optical detection. One way to overcome this limitation is to perform a derivatization reaction which is intended to provide the analyte more suitable analytical characteristics enabling a high sensitive detection. Based on the analytical step where the CE derivatization takes place, it can be classified as precapillary (before separation), in-capillary (during separation), or postcapillary (after separation). This chapter describes the application of four different derivatization protocols (in-capillary and precapillary modes) to carry out the achiral and chiral analysis of different compounds in food and biological samples with three different detection modes (UV, LIF, and MS). PMID:27645730

  16. Capillary stretching of fibers

    NASA Astrophysics Data System (ADS)

    Duprat, C.; Protiere, S.

    2015-09-01

    We study the interaction of a finite volume of liquid with two parallel thin flexible fibers. A tension along the fibers is imposed and may be varied. We report two morphologies, i.e. two types of wet adhesion: a weak capillary adhesion, where a liquid drop bridges the fibers, and a strong elastocapillary adhesion where the liquid is spread between two collapsed fibers. We show that geometry, capillarity and stretching are the key parameters at play. We describe the collapse and detachment of the fibers as a function of two nondimensional parameters, arising from the geometry of the system and a balance between capillary and stretching energies. In addition, we show that the morphology, thus the capillary adhesion, can be controlled by changing the tension within the fibers.

  17. Capillary condenser/evaporator

    NASA Technical Reports Server (NTRS)

    Valenzuela, Javier A. (Inventor)

    2010-01-01

    A heat transfer device is disclosed for transferring heat to or from a fluid that is undergoing a phase change. The heat transfer device includes a liquid-vapor manifold in fluid communication with a capillary structure thermally connected to a heat transfer interface, all of which are disposed in a housing to contain the vapor. The liquid-vapor manifold transports liquid in a first direction and conducts vapor in a second, opposite direction. The manifold provides a distributed supply of fluid (vapor or liquid) over the surface of the capillary structure. In one embodiment, the manifold has a fractal structure including one or more layers, each layer having one or more conduits for transporting liquid and one or more openings for conducting vapor. Adjacent layers have an increasing number of openings with decreasing area, and an increasing number of conduits with decreasing cross-sectional area, moving in a direction toward the capillary structure.

  18. Integrated microfluidic device using a single universal aptamer to detect multiple types of influenza viruses.

    PubMed

    Wang, Chih-Hung; Chang, Chih-Peng; Lee, Gwo-Bin

    2016-12-15

    DNA aptamers that can bind specific molecular targets have great potential as probes for microbial diagnostic applications. However, aptamers may change their conformation under different operating conditions, thus affecting their affinity and specificity towards the target molecules. In this study, a new integrated microfluidic system was developed that exploited the predictable change in conformation of a single universal influenza aptamer exposed to differing ion concentrations in order to detect multiple types of the influenza virus. Furthermore, the fluorescent-labeled universal aptamer used in this system could distinguish and detect three different influenza viruses (influenza A H1N1, H3N2, and influenza B) at the same time in 20min and therefore has great potential for point-of-care applications requiring rapid diagnosis of influenza viruses.

  19. MR-elastography reveals degradation of tissue integrity in multiple sclerosis.

    PubMed

    Wuerfel, Jens; Paul, Friedemann; Beierbach, Bernd; Hamhaber, Uwe; Klatt, Dieter; Papazoglou, Sebastian; Zipp, Frauke; Martus, Peter; Braun, Jürgen; Sack, Ingolf

    2010-02-01

    In multiple sclerosis (MS), diffuse brain parenchymal damage exceeding focal inflammation is increasingly recognized to be present from the very onset of the disease, and, although occult to conventional imaging techniques, may present a major cause of permanent neurological disability. Subtle tissue alterations significantly influence biomechanical properties given by stiffness and internal friction, that--in more accessible organs than the brain--are traditionally assessed by manual palpation during the clinical exam. The brain, however, is protected from our sense of touch, and thus our current knowledge on cerebral viscoelasticity is very limited. We developed a clinically feasible magnetic resonance elastography setup sensitive to subtle alterations of brain parenchymal biomechanical properties. Investigating 45 MS patients revealed a significant decrease (13%, P<0.001) of cerebral viscoelasticity compared to matched healthy volunteers, indicating a widespread tissue integrity degradation, while structure-geometry defining parameters remained unchanged. Cerebral viscoelasticity may represent a novel in vivo marker of neuroinflammatory and neurodegenerative pathology. PMID:19539039

  20. System and method for integrating and accessing multiple data sources within a data warehouse architecture

    DOEpatents

    Musick, Charles R.; Critchlow, Terence; Ganesh, Madhaven; Slezak, Tom; Fidelis, Krzysztof

    2006-12-19

    A system and method is disclosed for integrating and accessing multiple data sources within a data warehouse architecture. The metadata formed by the present method provide a way to declaratively present domain specific knowledge, obtained by analyzing data sources, in a consistent and useable way. Four types of information are represented by the metadata: abstract concepts, databases, transformations and mappings. A mediator generator automatically generates data management computer code based on the metadata. The resulting code defines a translation library and a mediator class. The translation library provides a data representation for domain specific knowledge represented in a data warehouse, including "get" and "set" methods for attributes that call transformation methods and derive a value of an attribute if it is missing. The mediator class defines methods that take "distinguished" high-level objects as input and traverse their data structures and enter information into the data warehouse.

  1. Generalized Additive Mixed-Models for Pharmacology Using Integrated Discrete Multiple Organ Co-Culture

    PubMed Central

    Ingersoll, Thomas; Cole, Stephanie; Madren-Whalley, Janna; Booker, Lamont; Dorsey, Russell; Li, Albert; Salem, Harry

    2016-01-01

    Integrated Discrete Multiple Organ Co-culture (IDMOC) is emerging as an in-vitro alternative to in-vivo animal models for pharmacology studies. IDMOC allows dose-response relationships to be investigated at the tissue and organoid levels, yet, these relationships often exhibit responses that are far more complex than the binary responses often measured in whole animals. To accommodate departure from binary endpoints, IDMOC requires an expansion of analytic techniques beyond simple linear probit and logistic models familiar in toxicology. IDMOC dose-responses may be measured at continuous scales, exhibit significant non-linearity such as local maxima or minima, and may include non-independent measures. Generalized additive mixed-modeling (GAMM) provides an alternative description of dose-response that relaxes assumptions of independence and linearity. We compared GAMMs to traditional linear models for describing dose-response in IDMOC pharmacology studies. PMID:27110941

  2. A quantitative approach for integrating multiple lines of evidence for the evaluation of environmental health risks

    PubMed Central

    Schleier III, Jerome J.; Marshall, Lucy A.; Davis, Ryan S.

    2015-01-01

    Decision analysis often considers multiple lines of evidence during the decision making process. Researchers and government agencies have advocated for quantitative weight-of-evidence approaches in which multiple lines of evidence can be considered when estimating risk. Therefore, we utilized Bayesian Markov Chain Monte Carlo to integrate several human-health risk assessment, biomonitoring, and epidemiology studies that have been conducted for two common insecticides (malathion and permethrin) used for adult mosquito management to generate an overall estimate of risk quotient (RQ). The utility of the Bayesian inference for risk management is that the estimated risk represents a probability distribution from which the probability of exceeding a threshold can be estimated. The mean RQs after all studies were incorporated were 0.4386, with a variance of 0.0163 for malathion and 0.3281 with a variance of 0.0083 for permethrin. After taking into account all of the evidence available on the risks of ULV insecticides, the probability that malathion or permethrin would exceed a level of concern was less than 0.0001. Bayesian estimates can substantially improve decisions by allowing decision makers to estimate the probability that a risk will exceed a level of concern by considering seemingly disparate lines of evidence. PMID:25648367

  3. Improved detection of differentially expressed genes in microarray experiments through multiple scanning and image integration

    PubMed Central

    Romualdi, Chiara; Trevisan, Silvia; Celegato, Barbara; Costa, Germano; Lanfranchi, Gerolamo

    2003-01-01

    The variability of results in microarray technology is in part due to the fact that independent scans of a single hybridised microarray give spot images that are not quite the same. To solve this problem and turn it to our advantage, we introduced the approach of multiple scanning and of image integration of microarrays. To this end, we have developed specific software that creates a virtual image that statistically summarises a series of consecutive scans of a microarray. We provide evidence that the use of multiple imaging (i) enhances the detection of differentially expressed genes; (ii) increases the image homogeneity; and (iii) reveals false-positive results such as differentially expressed genes that are detected by a single scan but not confirmed by successive scanning replicates. The increase in the final number of differentially expressed genes detected in a microarray experiment with this approach is remarkable; 50% more for microarrays hybridised with targets labelled by reverse transcriptase, and 200% more for microarrays developed with the tyramide signal amplification (TSA) technique. The results have been confirmed by semi-quantitative RT–PCR tests. PMID:14627839

  4. Multiple-mode Lamb wave scattering simulations using 3D elastodynamic finite integration technique.

    PubMed

    Leckey, Cara A C; Rogge, Matthew D; Miller, Corey A; Hinders, Mark K

    2012-02-01

    We have implemented three-dimensional (3D) elastodynamic finite integration technique (EFIT) simulations to model Lamb wave scattering for two flaw-types in an aircraft-grade aluminum plate, a rounded rectangle flat-bottom hole and a disbond of the same shape. The plate thickness and flaws explored in this work include frequency-thickness regions where several Lamb wave modes exist and sometimes overlap in phase and/or group velocity. For the case of the flat-bottom hole the depth was incrementally increased to explore progressive changes in multiple-mode Lamb wave scattering due to the damage. The flat-bottom hole simulation results have been compared to experimental data and are shown to provide key insight for this well-defined experimental case by explaining unexpected results in experimental waveforms. For the rounded rectangle disbond flaw, which would be difficult to implement experimentally, we found that Lamb wave behavior differed significantly from the flat-bottom hole flaw. Most of the literature in this field is restricted to low frequency-thickness regions due to difficulties in interpreting data when multiple modes exist. We found that benchmarked 3D EFIT simulations can yield an understanding of scattering behavior for these higher frequency-thickness regions and in cases that would be difficult to set up experimentally. Additionally, our results show that 2D simulations would not have been sufficient for modeling the complicated scattering that occurred. PMID:21908011

  5. Elderly patient refractory to multiple pain medications successfully treated with integrative East–West medicine

    PubMed Central

    Tu, Bill; Johnston, Michael; Hui, Ka-Kit

    2008-01-01

    Background: Polypharmacy is a common and serious problem in the elderly today. Few solutions have been effective in reducing its incidence. Case summary: An 87-year-old female with a history of osteoarthritis and spinal stenosis presented with a five month history of severe right hip pain. She had been seen by multiple specialists and hospitalized many times. During these encounters, she was prescribed a long list of pain medications. However, these medications did not improve her pain and added to her risk of adverse drug events. After exhausting traditional Western medical therapies, she received a referral to the UCLA Center for East–West Medicine. There, clinicians treated her with a nonpharmacological integrative East-West medicine approach that included acupuncture, dry needling of trigger points, and education on self-acupressure. Her pain began improving and she was able to cut back on analgesic use under physician supervision. Ultimately, she improved to the point where she was able to discontinue all of her pain medications. Symptomatic relief was evidenced by improvement in health-related quality of life (HRQOL). Conclusions: This case study suggests that integrative East–West medicine may have the potential to reduce the incidence of polypharmacy in elderly patients presenting with pain conditions and improve their quality of life. PMID:20428398

  6. Optimal Operation System of the Integrated District Heating System with Multiple Regional Branches

    NASA Astrophysics Data System (ADS)

    Kim, Ui Sik; Park, Tae Chang; Kim, Lae-Hyun; Yeo, Yeong Koo

    This paper presents an optimal production and distribution management for structural and operational optimization of the integrated district heating system (DHS) with multiple regional branches. A DHS consists of energy suppliers and consumers, district heating pipelines network and heat storage facilities in the covered region. In the optimal management system, production of heat and electric power, regional heat demand, electric power bidding and sales, transport and storage of heat at each regional DHS are taken into account. The optimal management system is formulated as a mixed integer linear programming (MILP) where the objectives is to minimize the overall cost of the integrated DHS while satisfying the operation constraints of heat units and networks as well as fulfilling heating demands from consumers. Piecewise linear formulation of the production cost function and stairwise formulation of the start-up cost function are used to compute nonlinear cost function approximately. Evaluation of the total overall cost is based on weekly operations at each district heat branches. Numerical simulations show the increase of energy efficiency due to the introduction of the present optimal management system.

  7. Robust control of multiple integrators subject to input saturation and disturbance

    NASA Astrophysics Data System (ADS)

    Ding, Shihong; Zheng, Wei Xing

    2015-04-01

    This paper is concerned with the problem of robust stabilisation of multiple integrators systems subject to input saturation and disturbance from the viewpoint of state feedback and output feedback. First of all, without considering the disturbance, a backstepping-like method in conjunction with a series of saturation functions with different saturation levels is employed to design a nested-saturation based state-feedback controller with pre-chosen parameters. On this basis, taking the disturbance into account, a sliding mode disturbance observer (DOB) is adopted to estimate the states and the disturbance. Then, by combining the above state-feedback controller and the estimated states together, a composite controller with disturbance compensation is developed. With the removal of the non-increasing restriction on the saturation levels, the controller design becomes very flexible and the convergence performance of the closed-loop system is much improved. Meanwhile, with the aid of the estimated values by the DOB, we obtain not only the output-feedback control scheme but also the better disturbance rejection property for the closed-loop system. A simulation example of a triple integrators system is presented to substantiate the usefulness of the proposed technique.

  8. The blackboard model - A framework for integrating multiple cooperating expert systems

    NASA Technical Reports Server (NTRS)

    Erickson, W. K.

    1985-01-01

    The use of an artificial intelligence (AI) architecture known as the blackboard model is examined as a framework for designing and building distributed systems requiring the integration of multiple cooperating expert systems (MCXS). Aerospace vehicles provide many examples of potential systems, ranging from commercial and military aircraft to spacecraft such as satellites, the Space Shuttle, and the Space Station. One such system, free-flying, spaceborne telerobots to be used in construction, servicing, inspection, and repair tasks around NASA's Space Station, is examined. The major difficulties found in designing and integrating the individual expert system components necessary to implement such a robot are outlined. The blackboard model, a general expert system architecture which seems to address many of the problems found in designing and building such a system, is discussed. A progress report on a prototype system under development called DBB (Distributed BlackBoard model) is given. The prototype will act as a testbed for investigating the feasibility, utility, and efficiency of MCXS-based designs developed under the blackboard model.

  9. Capillary action liquid chromatography.

    PubMed

    Zhang, Bo; Bergström, Edmund T; Goodall, David M; Myers, Peter

    2009-06-01

    Capillary action LC (caLC) is introduced as a technique using capillary action as the driving force to perform LC in capillary columns packed with HPLC type microparticulate materials. A dry packing method with centrifugal force was developed to prepare capillary columns in parallel (10 columns per 3 min) to support their disposable use in caLC. Using a digital microscope for real-time imaging and recording separations of components in a dye mixture, caLC was found to have flow characteristics similar to TLC. Based on the investigation of microparticulate HPLC silica gels of different size (1.5-10 microm) and a typical TLC grade irregular medium, Merck 60G silica, the van Deemter curves suggested molecular diffusion as the major contribution to band broadening in caLC. With Waters Xbridge 2.6 microm silica, plate heights down to 8.8 microm were obtained, comparable to those achievable in HPLC. Assisted by an image-processing method, the visual caLC separation was converted to a classical chromatogram for further data analysis and such a facility confirmed the observation of highly efficient bands.

  10. Chemical derivatization combined with capillary LC or MALDI-TOF MS for trace determination of lipoic acid in cosmetics and integrated protein expression profiling in human keratinocytes.

    PubMed

    Tsai, Chia-Ju; Lin, Ying-Chi; Chen, Yen-Ling; Feng, Chia-Hsien

    2014-12-01

    Lipoic acid (LA) is an essential cofactor in mitochondrial enzymes and an ideal antioxidant in prokaryotic and eukaryotic cells. Capillary liquid chromatography coupled with ultraviolet detection (CapLC-UV) and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) are two environmentally friendly methods for determining LA. In this study, a pre-column microwave-assisted derivatization with 4-bromomethyl-6,7-dimethoxycoumarin enhanced the UV absorbance of LA and was monitored at 345 nm by CapLC-UV. Gradient separation was performed using a reversed-phase C18 column with a mobile phase consisting of acetonitrile-0.1% formic acid solution. The ionization of LA was increased, and the LA derivative was detected by MALDI-TOF MS at m/z 683 with an α-cyano-4-hydroxycinnamic acid matrix. The linear response ranged from 0.1 to 40 μM with a correlation coefficient of 0.999. The CapLC-UV and MALDI-TOF MS had detection limits of 5 and 4 fmol, respectively. These methods effectively detected LA in dietary supplements and cosmetics. Cellular proteomes of a human keratinocyte cell line (HaCaT) irradiated with UV radiation were also compared with and without LA treatment. The cellular proteomes were identified by nanoultra performance LC with LTQ Orbitrap system after trypsin digestion. Protein identification was performed by simultaneous peptide sequencing and MASCOT search. The analysis revealed changes in several proteins, including CDC42, TPI1, HNRPA2B1, PRDX1, PTGES3 and MYL6.

  11. Integrating multiple evidences in taxonomy: species diversity and phylogeny of mustached bats (Mormoopidae: Pteronotus).

    PubMed

    Pavan, Ana Carolina; Marroig, Gabriel

    2016-10-01

    A phylogenetic systematic perspective is instrumental in recovering new species and their evolutionary relationships. The advent of new technologies for molecular and morphological data acquisition and analysis, allied to the integration of knowledge from different areas, such as ecology and population genetics, allows for the emergence of more rigorous, accurate and complete scientific hypothesis on species diversity. Mustached bats (genus Pteronotus) are a good model for the application of this integrative approach. They are a widely distributed and a morphologically homogeneous group, but comprising species with remarkable differences in their echolocation strategy and feeding behavior. The latest systematic review suggested six species with 17 subspecies in Pteronotus. Subsequent studies using discrete morphological characters supported the same arrangement. However, recent papers reported high levels of genetic divergence among conspecific taxa followed by bioacoustic and geographic agreement, suggesting an underestimated diversity in the genus. To date, no study merging genetic evidences and morphometric variation along the entire geographic range of this group has been attempted. Based on a comprehensive sampling including representatives of all current taxonomic units, we attempt to delimit species in Pteronotus through the application of multiple methodologies and hierarchically distinct datasets. The molecular approach includes six molecular markers from three genetic transmission systems; morphological investigations used 41 euclidean distances estimated through three-dimensional landmarks collected from 1628 skulls. The phylogenetic analysis reveals a greater diversity than previously reported, with a high correspondence among the genetic lineages and the currently recognized subspecies in the genus. Discriminant analysis of variables describing size and shape of cranial bones support the rising of the genetic groups to the specific status. Based on

  12. Integrating Multiple Autonomous Underwater Vessels, Surface Vessels and Aircraft into Oceanographic Research Vessel Operations

    NASA Astrophysics Data System (ADS)

    McGillivary, P. A.; Borges de Sousa, J.; Martins, R.; Rajan, K.

    2012-12-01

    Autonomous platforms are increasingly used as components of Integrated Ocean Observing Systems and oceanographic research cruises. Systems deployed can include gliders or propeller-driven autonomous underwater vessels (AUVs), autonomous surface vessels (ASVs), and unmanned aircraft systems (UAS). Prior field campaigns have demonstrated successful communication, sensor data fusion and visualization for studies using gliders and AUVs. However, additional requirements exist for incorporating ASVs and UASs into ship operations. For these systems to be optimally integrated into research vessel data management and operational planning systems involves addressing three key issues: real-time field data availability, platform coordination, and data archiving for later analysis. A fleet of AUVs, ASVs and UAS deployed from a research vessel is best operated as a system integrated with the ship, provided communications among them can be sustained. For this purpose, Disruptive Tolerant Networking (DTN) software protocols for operation in communication-challenged environments help ensure reliable high-bandwidth communications. Additionally, system components need to have considerable onboard autonomy, namely adaptive sampling capabilities using their own onboard sensor data stream analysis. We discuss Oceanographic Decision Support System (ODSS) software currently used for situational awareness and planning onshore, and in the near future event detection and response will be coordinated among multiple vehicles. Results from recent field studies from oceanographic research vessels using AUVs, ASVs and UAS, including the Rapid Environmental Picture (REP-12) cruise, are presented describing methods and results for use of multi-vehicle communication and deliberative control networks, adaptive sampling with single and multiple platforms, issues relating to data management and archiving, and finally challenges that remain in addressing these technological issues. Significantly, the

  13. Quantitative Integration of Multiple Geophysical Techniques for Reducing Uncertainty in Discrete Anomaly Detection

    NASA Astrophysics Data System (ADS)

    Carr, M. C.; Baker, G. S.; Herrmann, N.; Yerka, S.; Angst, M.

    2008-12-01

    The objectives of this project are to (1) utilize quantitative integration of multiple geophysical techniques, (2) determine geophysical anomalies that may indicate locations of various archaeological structures, and (3) develop techniques of quantifying causes of uncertainty. Two sites are used to satisfy these objectives. The first, representing a site with unknown target features, is an archaeological site on the Tennessee River floodplain. The area is divided into 437 (20 x 20 m) plots with 0.5 m spacing where magnetic gradiometry profiles were collected in a zig-zag pattern, resulting in 350 km of line data. Once anomalies are identified in the magnetics data, potential excavation sites for archeological features are determined and other geophysical techniques are utilized to gain confidence in choosing which anomalies to excavate. Several grids are resurveyed using Ground Penetrating Radar (GPR) and EM-31 with a 0.25 m spacing in a grid pattern. A quantitative method of integrating data into one comprehensive set is developed, enhancing interpretation because each geophysical technique utilized within this study produced a unique response to noise and the targets. Spatial visualization software is used to interpolate irregularly spaced XYZ data into a regularly spaced grid and display the geophysical data in 3D representations. Once all data are exported from each individual instrument, grid files are created for quantitative merging of the data and to create grid-based maps including contour, image, shaded relief, and surface maps. Statistics were calculated from anomaly classification in the data and excavated features present. To study this methodology in a more controlled setting, a second site is used. This site is analogous to the first in that it is along the Tennessee River floodplain on the same bedrock units. However, this analog site contains known targets (previously buried and accurately located) including size, shape, and orientation. Four

  14. Multiple-source spatial data fusion and integration research in the region unified planning management information system

    NASA Astrophysics Data System (ADS)

    Liu, Zhijun; Zhang, Liangpei; Liu, Zhenmin; Jiao, Hongbo; Chen, Liqun

    2008-12-01

    In order to manage the internal resources of Gulf of Tonkin and integrate multiple-source spatial data, the establishment of region unified plan management system is needed. The data fusion and the integrated research should be carried on because there are some difficulties in the course of the system's establishment. For example, kinds of planning and the project data format are different, and data criterion is not unified. Besides, the time state property is strong, and spatial reference is inconsistent, etc. In this article the ARCGIS ENGINE is introduced as the developing platform, key technologies are researched, such as multiple-source data transformation and fusion, remote sensing data and DEM fusion and integrated, plan and project data integration, and so on. Practice shows that the system improves the working efficiency of Guangxi Gulf of Tonkin Economic Zone Management Committee significantly and promotes planning construction work of the economic zone remarkably.

  15. A multiple hypotheses uncertainty analysis in hydrological modelling: about model structure, landscape parameterization, and numerical integration

    NASA Astrophysics Data System (ADS)

    Pilz, Tobias; Francke, Till; Bronstert, Axel

    2016-04-01

    Until today a large number of competing computer models has been developed to understand hydrological processes and to simulate and predict streamflow dynamics of rivers. This is primarily the result of a lack of a unified theory in catchment hydrology due to insufficient process understanding and uncertainties related to model development and application. Therefore, the goal of this study is to analyze the uncertainty structure of a process-based hydrological catchment model employing a multiple hypotheses approach. The study focuses on three major problems that have received only little attention in previous investigations. First, to estimate the impact of model structural uncertainty by employing several alternative representations for each simulated process. Second, explore the influence of landscape discretization and parameterization from multiple datasets and user decisions. Third, employ several numerical solvers for the integration of the governing ordinary differential equations to study the effect on simulation results. The generated ensemble of model hypotheses is then analyzed and the three sources of uncertainty compared against each other. To ensure consistency and comparability all model structures and numerical solvers are implemented within a single simulation environment. First results suggest that the selection of a sophisticated numerical solver for the differential equations positively affects simulation outcomes. However, already some simple and easy to implement explicit methods perform surprisingly well and need less computational efforts than more advanced but time consuming implicit techniques. There is general evidence that ambiguous and subjective user decisions form a major source of uncertainty and can greatly influence model development and application at all stages.

  16. Integrated defense system overlaps as a disease model: with examples for multiple chemical sensitivity.

    PubMed Central

    Rowat, S C

    1998-01-01

    The central nervous, immune, and endocrine systems communicate through multiple common messengers. Over evolutionary time, what may be termed integrated defense system(s) (IDS) have developed to coordinate these communications for specific contexts; these include the stress response, acute-phase response, nonspecific immune response, immune response to antigen, kindling, tolerance, time-dependent sensitization, neurogenic switching, and traumatic dissociation (TD). These IDSs are described and their overlap is examined. Three models of disease production are generated: damage, in which IDSs function incorrectly; inadequate/inappropriate, in which IDS response is outstripped by a changing context; and evolving/learning, in which the IDS learned response to a context is deemed pathologic. Mechanisms of multiple chemical sensitivity (MCS) are developed from several IDS disease models. Model 1A is pesticide damage to the central nervous system, overlapping with body chemical burdens, TD, and chronic zinc deficiency; model 1B is benzene disruption of interleukin-1, overlapping with childhood developmental windows and hapten-antigenic spreading; and model 1C is autoimmunity to immunoglobulin-G (IgG), overlapping with spreading to other IgG-inducers, sudden spreading of inciters, and food-contaminating chemicals. Model 2A is chemical and stress overload, including comparison with the susceptibility/sensitization/triggering/spreading model; model 2B is genetic mercury allergy, overlapping with: heavy metals/zinc displacement and childhood/gestational mercury exposures; and model 3 is MCS as evolution and learning. Remarks are offered on current MCS research. Problems with clinical measurement are suggested on the basis of IDS models. Large-sample patient self-report epidemiology is described as an alternative or addition to clinical biomarker and animal testing. Images Figure 1 Figure 2 Figure 3 Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 PMID:9539008

  17. A multi-disciplinary approach for the integrated assessment of multiple risks in delta areas.

    NASA Astrophysics Data System (ADS)

    Sperotto, Anna; Torresan, Silvia; Critto, Andrea; Marcomini, Antonio

    2016-04-01

    The assessment of climate change related risks is notoriously difficult due to the complex and uncertain combinations of hazardous events that might happen, the multiplicity of physical processes involved, the continuous changes and interactions of environmental and socio-economic systems. One important challenge lies in predicting and modelling cascades of natural and man -made hazard events which can be triggered by climate change, encompassing different spatial and temporal scales. Another regard the potentially difficult integration of environmental, social and economic disciplines in the multi-risk concept. Finally, the effective interaction between scientists and stakeholders is essential to ensure that multi-risk knowledge is translated into efficient adaptation and management strategies. The assessment is even more complex at the scale of deltaic systems which are particularly vulnerable to global environmental changes, due to the fragile equilibrium between the presence of valuable natural ecosystems and relevant economic activities. Improving our capacity to assess the combined effects of multiple hazards (e.g. sea-level rise, storm surges, reduction in sediment load, local subsidence, saltwater intrusion) is therefore essential to identify timely opportunities for adaptation. A holistic multi-risk approach is here proposed to integrate terminology, metrics and methodologies from different research fields (i.e. environmental, social and economic sciences) thus creating shared knowledge areas to advance multi risk assessment and management in delta regions. A first testing of the approach, including the application of Bayesian network analysis for the assessment of impacts of climate change on key natural systems (e.g. wetlands, protected areas, beaches) and socio-economic activities (e.g. agriculture, tourism), is applied in the Po river delta in Northern Italy. The approach is based on a bottom-up process involving local stakeholders early in different

  18. Defective sensorimotor integration in preparation for reaction time tasks in patients with multiple sclerosis.

    PubMed

    Cabib, Christopher; Llufriu, Sara; Casanova-Molla, Jordi; Saiz, Albert; Valls-Solé, Josep

    2015-03-01

    Slowness of voluntary movements in patients with multiple sclerosis (MS) may be due to various factors, including attentional and cognitive deficits, delays in motor conduction time, and impairment of specific central nervous system circuits. In 13 healthy volunteers and 20 mildly disabled, relapsing-remitting MS patients, we examined simple reaction time (SRT) tasks requiring sensorimotor integration in circuits involving the corpus callosum and the brain stem. A somatosensory stimulus was used as the imperative signal (IS), and subjects were requested to react with either the ipsilateral or the contralateral hand (uncrossed vs. crossed SRT). In 33% of trials, a startling auditory stimulus was presented together with the IS, and the percentage reaction time change with respect to baseline SRT trials was measured (StartReact effect). The difference between crossed and uncrossed SRT, which requires interhemispheric conduction, was significantly larger in patients than in healthy subjects (P = 0.021). The StartReact effect, which involves activation of brain stem motor pathways, was reduced significantly in patients with respect to healthy subjects (uncrossed trials: P = 0.015; crossed trials: P = 0.005). In patients, a barely significant correlation was found between SRT delay and conduction abnormalities in motor and sensory pathways (P = 0.02 and P = 0.04, respectively). The abnormalities found specifically in trials reflecting interhemispheric transfer of information, as well as the evidence for reduced subcortical motor preparation, indicate that a delay in reaction time execution in MS patients cannot be explained solely by conduction slowing in motor and sensory pathways but suggest, instead, defective sensorimotor integration mechanisms in at least the two circuits examined.

  19. Integrating Multiple Distribution Models to Guide Conservation Efforts of an Endangered Toad

    PubMed Central

    Treglia, Michael L.; Fisher, Robert N.; Fitzgerald, Lee A.

    2015-01-01

    Species distribution models are used for numerous purposes such as predicting changes in species’ ranges and identifying biodiversity hotspots. Although implications of distribution models for conservation are often implicit, few studies use these tools explicitly to inform conservation efforts. Herein, we illustrate how multiple distribution models developed using distinct sets of environmental variables can be integrated to aid in identification sites for use in conservation. We focus on the endangered arroyo toad (Anaxyrus californicus), which relies on open, sandy streams and surrounding floodplains in southern California, USA, and northern Baja California, Mexico. Declines of the species are largely attributed to habitat degradation associated with vegetation encroachment, invasive predators, and altered hydrologic regimes. We had three main goals: 1) develop a model of potential habitat for arroyo toads, based on long-term environmental variables and all available locality data; 2) develop a model of the species’ current habitat by incorporating recent remotely-sensed variables and only using recent locality data; and 3) integrate results of both models to identify sites that may be employed in conservation efforts. We used a machine learning technique, Random Forests, to develop the models, focused on riparian zones in southern California. We identified 14.37% and 10.50% of our study area as potential and current habitat for the arroyo toad, respectively. Generally, inclusion of remotely-sensed variables reduced modeled suitability of sites, thus many areas modeled as potential habitat were not modeled as current habitat. We propose such sites could be made suitable for arroyo toads through active management, increasing current habitat by up to 67.02%. Our general approach can be employed to guide conservation efforts of virtually any species with sufficient data necessary to develop appropriate distribution models. PMID:26125634

  20. Integration of Multiple Genomic and Phenotype Data to Infer Novel miRNA-Disease Associations

    PubMed Central

    Zhou, Meng; Cheng, Liang; Yang, Haixiu; Wang, Jing; Sun, Jie; Wang, Zhenzhen

    2016-01-01

    MicroRNAs (miRNAs) play an important role in the development and progression of human diseases. The identification of disease-associated miRNAs will be helpful for understanding the molecular mechanisms of diseases at the post-transcriptional level. Based on different types of genomic data sources, computational methods for miRNA-disease association prediction have been proposed. However, individual source of genomic data tends to be incomplete and noisy; therefore, the integration of various types of genomic data for inferring reliable miRNA-disease associations is urgently needed. In this study, we present a computational framework, CHNmiRD, for identifying miRNA-disease associations by integrating multiple genomic and phenotype data, including protein-protein interaction data, gene ontology data, experimentally verified miRNA-target relationships, disease phenotype information and known miRNA-disease connections. The performance of CHNmiRD was evaluated by experimentally verified miRNA-disease associations, which achieved an area under the ROC curve (AUC) of 0.834 for 5-fold cross-validation. In particular, CHNmiRD displayed excellent performance for diseases without any known related miRNAs. The results of case studies for three human diseases (glioblastoma, myocardial infarction and type 1 diabetes) showed that all of the top 10 ranked miRNAs having no known associations with these three diseases in existing miRNA-disease databases were directly or indirectly confirmed by our latest literature mining. All these results demonstrated the reliability and efficiency of CHNmiRD, and it is anticipated that CHNmiRD will serve as a powerful bioinformatics method for mining novel disease-related miRNAs and providing a new perspective into molecular mechanisms underlying human diseases at the post-transcriptional level. CHNmiRD is freely available at http://www.bio-bigdata.com/CHNmiRD. PMID:26849207

  1. Integration of Multiple Genomic and Phenotype Data to Infer Novel miRNA-Disease Associations.

    PubMed

    Shi, Hongbo; Zhang, Guangde; Zhou, Meng; Cheng, Liang; Yang, Haixiu; Wang, Jing; Sun, Jie; Wang, Zhenzhen

    2016-01-01

    MicroRNAs (miRNAs) play an important role in the development and progression of human diseases. The identification of disease-associated miRNAs will be helpful for understanding the molecular mechanisms of diseases at the post-transcriptional level. Based on different types of genomic data sources, computational methods for miRNA-disease association prediction have been proposed. However, individual source of genomic data tends to be incomplete and noisy; therefore, the integration of various types of genomic data for inferring reliable miRNA-disease associations is urgently needed. In this study, we present a computational framework, CHNmiRD, for identifying miRNA-disease associations by integrating multiple genomic and phenotype data, including protein-protein interaction data, gene ontology data, experimentally verified miRNA-target relationships, disease phenotype information and known miRNA-disease connections. The performance of CHNmiRD was evaluated by experimentally verified miRNA-disease associations, which achieved an area under the ROC curve (AUC) of 0.834 for 5-fold cross-validation. In particular, CHNmiRD displayed excellent performance for diseases without any known related miRNAs. The results of case studies for three human diseases (glioblastoma, myocardial infarction and type 1 diabetes) showed that all of the top 10 ranked miRNAs having no known associations with these three diseases in existing miRNA-disease databases were directly or indirectly confirmed by our latest literature mining. All these results demonstrated the reliability and efficiency of CHNmiRD, and it is anticipated that CHNmiRD will serve as a powerful bioinformatics method for mining novel disease-related miRNAs and providing a new perspective into molecular mechanisms underlying human diseases at the post-transcriptional level. CHNmiRD is freely available at http://www.bio-bigdata.com/CHNmiRD.

  2. Integrated dementia care in The Netherlands: a multiple case study of case management programmes.

    PubMed

    Minkman, Mirella M N; Ligthart, Suzanne A; Huijsman, Robbert

    2009-09-01

    The number of dementia patients is growing, and they require a variety of services, making integrated care essential for the ability to continue living in the community. Many healthcare systems in developed countries are exploring new approaches for delivering health and social care. The purpose of this study was to describe and analyse a new approach in extensive case management programmes concerned with long-term dementia care in The Netherlands. The focus is on the characteristics, and success and failure factors of these programmes.A multiple case study was conducted in eight regional dementia care provider networks in The Netherlands. Based on a literature study, a questionnaire was developed for the responsible managers and case managers of the eight case management programmes. During 16 semistructured face-to-face interviews with both respondent groups, a deeper insight into the dementia care programmes was provided. Project documentation for all the cases was studied. The eight programmes were developed independently to improve the quality and continuity of long-term dementia care. The programmes show overlap in terms of their vision, tasks of case managers, case management process and the participating partners in the local dementia care networks. Differences concern the targeted dementia patient groups as well as the background of the case managers and their position in the local dementia care provider network. Factors for success concern the expert knowledge of case managers, investment in a strong provider network and coherent conditions for effective inter-organizational cooperation to deliver integrated care. When explored, caregiver and patient satisfaction was high. Further research into the effects on client outcomes, service use and costs is recommended in order to further analyse the impact of this approach in long-term care. To facilitate implementation, with a focus on joint responsibilities of the involved care providers, policy

  3. Integrating multiple distribution models to guide conservation efforts of an endangered toad

    USGS Publications Warehouse

    Treglia, Michael L.; Fisher, Robert N.; Fitzgerald, Lee A.

    2015-01-01

    Species distribution models are used for numerous purposes such as predicting changes in species’ ranges and identifying biodiversity hotspots. Although implications of distribution models for conservation are often implicit, few studies use these tools explicitly to inform conservation efforts. Herein, we illustrate how multiple distribution models developed using distinct sets of environmental variables can be integrated to aid in identification sites for use in conservation. We focus on the endangered arroyo toad (Anaxyrus californicus), which relies on open, sandy streams and surrounding floodplains in southern California, USA, and northern Baja California, Mexico. Declines of the species are largely attributed to habitat degradation associated with vegetation encroachment, invasive predators, and altered hydrologic regimes. We had three main goals: 1) develop a model of potential habitat for arroyo toads, based on long-term environmental variables and all available locality data; 2) develop a model of the species’ current habitat by incorporating recent remotely-sensed variables and only using recent locality data; and 3) integrate results of both models to identify sites that may be employed in conservation efforts. We used a machine learning technique, Random Forests, to develop the models, focused on riparian zones in southern California. We identified 14.37% and 10.50% of our study area as potential and current habitat for the arroyo toad, respectively. Generally, inclusion of remotely-sensed variables reduced modeled suitability of sites, thus many areas modeled as potential habitat were not modeled as current habitat. We propose such sites could be made suitable for arroyo toads through active management, increasing current habitat by up to 67.02%. Our general approach can be employed to guide conservation efforts of virtually any species with sufficient data necessary to develop appropriate distribution models.

  4. Integrating Multiple Distribution Models to Guide Conservation Efforts of an Endangered Toad.

    PubMed

    Treglia, Michael L; Fisher, Robert N; Fitzgerald, Lee A

    2015-01-01

    Species distribution models are used for numerous purposes such as predicting changes in species' ranges and identifying biodiversity hotspots. Although implications of distribution models for conservation are often implicit, few studies use these tools explicitly to inform conservation efforts. Herein, we illustrate how multiple distribution models developed using distinct sets of environmental variables can be integrated to aid in identification sites for use in conservation. We focus on the endangered arroyo toad (Anaxyrus californicus), which relies on open, sandy streams and surrounding floodplains in southern California, USA, and northern Baja California, Mexico. Declines of the species are largely attributed to habitat degradation associated with vegetation encroachment, invasive predators, and altered hydrologic regimes. We had three main goals: 1) develop a model of potential habitat for arroyo toads, based on long-term environmental variables and all available locality data; 2) develop a model of the species' current habitat by incorporating recent remotely-sensed variables and only using recent locality data; and 3) integrate results of both models to identify sites that may be employed in conservation efforts. We used a machine learning technique, Random Forests, to develop the models, focused on riparian zones in southern California. We identified 14.37% and 10.50% of our study area as potential and current habitat for the arroyo toad, respectively. Generally, inclusion of remotely-sensed variables reduced modeled suitability of sites, thus many areas modeled as potential habitat were not modeled as current habitat. We propose such sites could be made suitable for arroyo toads through active management, increasing current habitat by up to 67.02%. Our general approach can be employed to guide conservation efforts of virtually any species with sufficient data necessary to develop appropriate distribution models.

  5. Integrating Multiple Distribution Models to Guide Conservation Efforts of an Endangered Toad.

    PubMed

    Treglia, Michael L; Fisher, Robert N; Fitzgerald, Lee A

    2015-01-01

    Species distribution models are used for numerous purposes such as predicting changes in species' ranges and identifying biodiversity hotspots. Although implications of distribution models for conservation are often implicit, few studies use these tools explicitly to inform conservation efforts. Herein, we illustrate how multiple distribution models developed using distinct sets of environmental variables can be integrated to aid in identification sites for use in conservation. We focus on the endangered arroyo toad (Anaxyrus californicus), which relies on open, sandy streams and surrounding floodplains in southern California, USA, and northern Baja California, Mexico. Declines of the species are largely attributed to habitat degradation associated with vegetation encroachment, invasive predators, and altered hydrologic regimes. We had three main goals: 1) develop a model of potential habitat for arroyo toads, based on long-term environmental variables and all available locality data; 2) develop a model of the species' current habitat by incorporating recent remotely-sensed variables and only using recent locality data; and 3) integrate results of both models to identify sites that may be employed in conservation efforts. We used a machine learning technique, Random Forests, to develop the models, focused on riparian zones in southern California. We identified 14.37% and 10.50% of our study area as potential and current habitat for the arroyo toad, respectively. Generally, inclusion of remotely-sensed variables reduced modeled suitability of sites, thus many areas modeled as potential habitat were not modeled as current habitat. We propose such sites could be made suitable for arroyo toads through active management, increasing current habitat by up to 67.02%. Our general approach can be employed to guide conservation efforts of virtually any species with sufficient data necessary to develop appropriate distribution models. PMID:26125634

  6. Integration of Multiple Genomic and Phenotype Data to Infer Novel miRNA-Disease Associations.

    PubMed

    Shi, Hongbo; Zhang, Guangde; Zhou, Meng; Cheng, Liang; Yang, Haixiu; Wang, Jing; Sun, Jie; Wang, Zhenzhen

    2016-01-01

    MicroRNAs (miRNAs) play an important role in the development and progression of human diseases. The identification of disease-associated miRNAs will be helpful for understanding the molecular mechanisms of diseases at the post-transcriptional level. Based on different types of genomic data sources, computational methods for miRNA-disease association prediction have been proposed. However, individual source of genomic data tends to be incomplete and noisy; therefore, the integration of various types of genomic data for inferring reliable miRNA-disease associations is urgently needed. In this study, we present a computational framework, CHNmiRD, for identifying miRNA-disease associations by integrating multiple genomic and phenotype data, including protein-protein interaction data, gene ontology data, experimentally verified miRNA-target relationships, disease phenotype information and known miRNA-disease connections. The performance of CHNmiRD was evaluated by experimentally verified miRNA-disease associations, which achieved an area under the ROC curve (AUC) of 0.834 for 5-fold cross-validation. In particular, CHNmiRD displayed excellent performance for diseases without any known related miRNAs. The results of case studies for three human diseases (glioblastoma, myocardial infarction and type 1 diabetes) showed that all of the top 10 ranked miRNAs having no known associations with these three diseases in existing miRNA-disease databases were directly or indirectly confirmed by our latest literature mining. All these results demonstrated the reliability and efficiency of CHNmiRD, and it is anticipated that CHNmiRD will serve as a powerful bioinformatics method for mining novel disease-related miRNAs and providing a new perspective into molecular mechanisms underlying human diseases at the post-transcriptional level. CHNmiRD is freely available at http://www.bio-bigdata.com/CHNmiRD. PMID:26849207

  7. [Venoruton and capillary permeability].

    PubMed

    Cesarone, M R; Laurora, G; Gabini, M; Errichi, B M; Candiani, C; Belcaro, G

    1989-05-01

    A new system to evaluate capillary permeability, the vacuum suction chamber (VSC) device, was used to assess the effects of Venoruton in patients with venous hypertension. A temporary, superficial skin lesion (wheal) was produced with the VSC device by negative pressure (30 mmHg) applied for 10 minutes on the internal, perimalleolar region. Wheals disappear in less than 60 minutes in normals while in patients with venous hypertension the wheal is more persistent, requiring a significantly longer time to disappear. This new technique was used in association with laser-Doppler flowmetry to evaluate the efficacy of Venoruton (1000 mgs t.i.d.) administered for 2 weeks on venous hypertension. Results indicate a positive effect of Venoruton in reducing the abnormally increased capillary permeability in venous hypertension and are proportional to the changes observed in signs and symptoms after treatment.

  8. Enantioseparations by capillary electrochromatography.

    PubMed

    Fanali, S; Catarcini, P; Blaschke, G; Chankvetadze, B

    2001-09-01

    The review summarizes recent developments in enantioseparations by capillary electrochromatography (CEC). Selected fundamental aspects of CEC are discussed in order to stress those features which may allow the success of this technique in the competitive field of enantioseparations. In addition, the comparative characteristics of the different modes of chiral CEC and the stationary phases are presented. The effects of the characteristics of the stationary and liquid phases and operational conditions on the separation results are discussed. Finally, some future trends are briefly addressed.

  9. Integrating Multiple Scales of Hydraulic Conductivity Measurements in Training Image-Based Stochastic Models

    NASA Astrophysics Data System (ADS)

    Mahmud, K.; Mariethoz, G.; Baker, A.

    2013-12-01

    It has been widely demonstrated that the hydraulic conductivity of an aquifer increases with a larger portion of the aquifer tested. This poses a challenge when different hydraulic conductivity measurements coexist in a field study and have to be integrated simultaneously (e.g. core analysis, slug tests and well tests). While the scaling of hydraulic conductivity can be analytically derived in multiGaussian media, there is no general methodology to simultaneously integrate hydraulic conductivity measurements taken at different scales in highly heterogeneous media. Here we address this issue in the context of multiple-point statistics simulations (MPS). In MPS, the spatial continuity is based on a training image (TI) that contains the variability, connectivity, and structural properties of the medium. The key principle of our methodology is to consider the different scales of hydraulic conductivity as joint variables which are simulated together. Based on a TI that represents the fine-scale spatial variability, we use a classical upscaling method to obtain a series of upscaled TIs that correspond to the different scales at which measurements are available. In our case, the renormalization method is used for this upscaling step, but any upscaling method could be employed. Considered together, the different scales obtained are considered a single multi-scale representation of the initial TI, in a similar fashion as the multiscale pyramids used in image processing. We then use recent MPS simulation methods that allow dealing with multivariate TIs to generate conditional realizations of the different scales together. One characteristic of these realizations is that the possible non-linear relationships between the different simulated scales are statistically similar to the relationships observed in the multiscale TI. Therefore these relationships are considered a reasonable approximation of the renormalization results that were used on the TI. Another characteristic of

  10. Integrated modeling of flow and residence times at the catchment scale with multiple interacting pathways

    NASA Astrophysics Data System (ADS)

    Davies, J.; Beven, K.; Rodhe, A.; Nyberg, L.; Bishop, K.

    2013-08-01

    There is still a need for catchment hydrological and transport models that properly integrate the effects of preferential flows while accounting for differences in velocities and celerities. A modeling methodology is presented here which uses particle tracking methods to simulate both flow and transport in multiple pathways in a single consistent solution. Water fluxes and storages are determined by the volume and density of particles and transport is attained by labeling the particles with information that may be tracked throughout the lifetime of that particle in the catchment. The methodology allows representation of preferential flows through the use of particle velocity distributions, and mixing between pathways can be achieved with pathway transition probabilities. A transferable 3-D modeling methodology is presented for the first time and applied to a unique step-shift isotope experiment that was carried out at the 0.63 ha G1 catchment in Gårdsjön, Sweden. This application highlights the importance of combining flow and transport in hydrological representations, and the importance of pathway velocity distributions and interactions in obtaining a satisfactory representation of the observations.

  11. An integrated economic model of multiple types and uses of water

    NASA Astrophysics Data System (ADS)

    Luckmann, Jonas; Grethe, Harald; McDonald, Scott; Orlov, Anton; Siddig, Khalid

    2014-05-01

    Water scarcity is an increasing problem in many parts of the world and the management of water has become an important issue on the political economy agenda in many countries. As water is used in most economic activities and the allocation of water is often a complex problem involving different economic agents and sectors, Computable General Equilibrium (CGE) models have been proven useful to analyze water allocation problems, although their adaptation to include water is still relatively undeveloped. This paper provides a description of an integrated water-focused CGE model (STAGE_W) that includes multiple types and uses of water, and for the first time, the reclamation of wastewater as well as the provision of brackish groundwater as separate, independent activities with specific cost structures. The insights provided by the model are illustrated with an application to the Israeli water sector assuming that freshwater resources available to the economy are cut by 50%. We analyze how the Israeli economy copes with this shock if it reduces potable water supply compared with further investments in the desalination sector. The results demonstrate that the effects on the economy are slightly negative under both scenarios. Counter intuitively, the provision of additional potable water to the economy through desalination does not substantively reduce the negative outcomes. This is mainly due to the high costs of desalination, which are currently subsidized, with the distribution of the negative welfare effect over household groups dependent on how these subsidies are financed.

  12. Efficient implicit integration for finite-strain viscoplasticity with a nested multiplicative split

    NASA Astrophysics Data System (ADS)

    Shutov, A. V.

    2016-07-01

    An efficient and reliable stress computation algorithm is presented, which is based on implicit integration of the local evolution equations of multiplicative finite-strain plasticity/viscoplasticity. The algorithm is illustrated by an example involving a combined nonlinear isotropic/kinematic hardening; numerous backstress tensors are employed for a better description of the material behavior. The considered material model exhibits the so-called weak invariance under arbitrary isochoric changes of the reference configuration, and the presented algorithm retains this useful property. Even more: the weak invariance serves as a guide in constructing this algorithm. The constraint of inelastic incompressibility is exactly preserved as well. The proposed method is first-order accurate. Concerning the accuracy of the stress computation, the new algorithm is comparable to the Euler Backward method with a subsequent correction of incompressibility (EBMSC) and the classical exponential method (EM). Regarding the computational efficiency, the new algorithm is superior to the EBMSC and EM. Some accuracy tests are presented using parameters of the aluminum alloy 5754-O and the 42CrMo4 steel. FEM solutions of two boundary value problems using MSC.MARC are presented to show the correctness of the numerical implementation.

  13. Optimized breeding strategies for multiple trait integration: II. Process efficiency in event pyramiding and trait fixation.

    PubMed

    Peng, Ting; Sun, Xiaochun; Mumm, Rita H

    2014-01-01

    Multiple trait integration (MTI) is a multi-step process of converting an elite variety/hybrid for value-added traits (e.g. transgenic events) through backcross breeding. From a breeding standpoint, MTI involves four steps: single event introgression, event pyramiding, trait fixation, and version testing. This study explores the feasibility of marker-aided backcross conversion of a target maize hybrid for 15 transgenic events in the light of the overall goal of MTI of recovering equivalent performance in the finished hybrid conversion along with reliable expression of the value-added traits. Using the results to optimize single event introgression (Peng et al. Optimized breeding strategies for multiple trait integration: I. Minimizing linkage drag in single event introgression. Mol Breed, 2013) which produced single event conversions of recurrent parents (RPs) with ≤8 cM of residual non-recurrent parent (NRP) germplasm with ~1 cM of NRP germplasm in the 20 cM regions flanking the event, this study focused on optimizing process efficiency in the second and third steps in MTI: event pyramiding and trait fixation. Using computer simulation and probability theory, we aimed to (1) fit an optimal breeding strategy for pyramiding of eight events into the female RP and seven in the male RP, and (2) identify optimal breeding strategies for trait fixation to create a 'finished' conversion of each RP homozygous for all events. In addition, next-generation seed needs were taken into account for a practical approach to process efficiency. Building on work by Ishii and Yonezawa (Optimization of the marker-based procedures for pyramiding genes from multiple donor lines: I. Schedule of crossing between the donor lines. Crop Sci 47:537-546, 2007a), a symmetric crossing schedule for event pyramiding was devised for stacking eight (seven) events in a given RP. Options for trait fixation breeding strategies considered selfing and doubled haploid approaches to achieve homozygosity

  14. Automated Parallel Capillary Electrophoretic System

    DOEpatents

    Li, Qingbo; Kane, Thomas E.; Liu, Changsheng; Sonnenschein, Bernard; Sharer, Michael V.; Kernan, John R.

    2000-02-22

    An automated electrophoretic system is disclosed. The system employs a capillary cartridge having a plurality of capillary tubes. The cartridge has a first array of capillary ends projecting from one side of a plate. The first array of capillary ends are spaced apart in substantially the same manner as the wells of a microtitre tray of standard size. This allows one to simultaneously perform capillary electrophoresis on samples present in each of the wells of the tray. The system includes a stacked, dual carousel arrangement to eliminate cross-contamination resulting from reuse of the same buffer tray on consecutive executions from electrophoresis. The system also has a gel delivery module containing a gel syringe/a stepper motor or a high pressure chamber with a pump to quickly and uniformly deliver gel through the capillary tubes. The system further includes a multi-wavelength beam generator to generate a laser beam which produces a beam with a wide range of wavelengths. An off-line capillary reconditioner thoroughly cleans a capillary cartridge to enable simultaneous execution of electrophoresis with another capillary cartridge. The streamlined nature of the off-line capillary reconditioner offers the advantage of increased system throughput with a minimal increase in system cost.

  15. Using Images, Metaphor, and Hypnosis in Integrating Multiple Personality and Dissociative States: A Review of the Literature.

    ERIC Educational Resources Information Center

    Crawford, Carrie L.

    1990-01-01

    Reviews literature on hypnosis, imagery, and metaphor as applied to the treatment and integration of those with multiple personality disorder (MPD) and dissociative states. Considers diagnostic criteria of MPD; explores current theories of etiology and treatment; and suggests specific examples of various clinical methods of treatment using…

  16. Integrated photonic decoder with complementary code processing and balanced detection for two-dimensional optical code division multiple access.

    PubMed

    Takiguchi, K; Okuno, M; Takahashi, H; Moriwaki, O

    2007-04-01

    We propose a novel integrated photonic decoder for two-dimensional (time spreading, wavelength hopping) optical code division multiple access. The decoder is composed of multiplexers-demultiplexers, variable delay lines, and a coupler, which processes complementary codes and utilizes balanced detection to reduce unwanted cross-correlation interference. We successfully carried out a 10 Gbit/s transmission that demonstrated its effectiveness.

  17. Determination of cloud effective particle size from the multiple-scattering effect on lidar integration-method temperature measurements.

    PubMed

    Reichardt, Jens; Reichardt, Susanne

    2006-04-20

    A method is presented that permits the determination of the cloud effective particle size from Raman- or Rayleigh-integration temperature measurements that exploits the dependence of the multiple-scattering contributions to the lidar signals from heights above the cloud on the particle size of the cloud. Independent temperature information is needed for the determination of size. By use of Raman-integration temperatures, the technique is applied to cirrus measurements. The magnitude of the multiple-scattering effect and the above-cloud lidar signal strength limit the method's range of applicability to cirrus optical depths from 0.1 to 0.5. Our work implies that records of stratosphere temperature obtained with lidar may be affected by multiple scattering in clouds up to heights of 30 km and beyond.

  18. Integration of Multiple Non-Normal Checklist Procedures into a Single Checklist Procedure for Transport Aircraft: A Preliminary Investigation

    NASA Technical Reports Server (NTRS)

    Foernsler, Lynda J.

    1996-01-01

    Checklists are used by the flight crew to properly configure an aircraft for safe flight and to ensure a high level of safety throughout the duration of the flight. In addition, the checklist provides a sequential framework to meet cockpit operational requirements, and it fosters cross-checking of the flight deck configuration among crew members. This study examined the feasibility of integrating multiple checklists for non-normal procedures into a single procedure for a typical transport aircraft. For the purposes of this report, a typical transport aircraft is one that represents a midpoint between early generation aircraft (B-727/737-200 and DC-10) and modern glass cockpit aircraft (B747-400/777 and MD-11). In this report, potential conflicts among non-normal checklist items during multiple failure situations for a transport aircraft are identified and analyzed. The non-normal checklist procedure that would take precedence for each of the identified multiple failure flight conditions is also identified. The rationale behind this research is that potential conflicts among checklist items might exist when integrating multiple checklists for non-normal procedures into a single checklist. As a rule, multiple failures occurring in today's highly automated and redundant system transport aircraft are extremely improbable. In addition, as shown in this analysis, conflicts among checklist items in a multiple failure flight condition are exceedingly unlikely. The possibility of a multiple failure flight condition occurring with a conflict among checklist items is so remote that integration of the non-normal checklists into a single checklist appears to be a plausible option.

  19. Capillary solitons on a levitated medium.

    PubMed

    Perrard, S; Deike, L; Duchêne, C; Pham, C-T

    2015-07-01

    A water cylinder deposited on a heated channel levitates on its own generated vapor film owing to the Leidenfrost effect. This experimental setup permits the study of the one-dimensional propagation of surface waves in a free-to-move liquid system. We report the observation of gravity-capillary waves under a dramatic reduction of gravity (up to a factor 30), leading to capillary waves at the centimeter scale. The generated nonlinear structures propagate without deformation and undergo mutual collisions and reflections at the boundaries of the domain. They are identified as Korteweg-de Vries solitons with negative amplitude and subsonic velocity. The typical width and amplitude-dependent velocities are in excellent agreement with theoretical predictions based on a generalized Korteweg-de Vries equation adapted to any substrate geometry. When multiple solitons are present, they interact and form a soliton turbulencelike spectrum.

  20. Capillary solitons on a levitated medium.

    PubMed

    Perrard, S; Deike, L; Duchêne, C; Pham, C-T

    2015-07-01

    A water cylinder deposited on a heated channel levitates on its own generated vapor film owing to the Leidenfrost effect. This experimental setup permits the study of the one-dimensional propagation of surface waves in a free-to-move liquid system. We report the observation of gravity-capillary waves under a dramatic reduction of gravity (up to a factor 30), leading to capillary waves at the centimeter scale. The generated nonlinear structures propagate without deformation and undergo mutual collisions and reflections at the boundaries of the domain. They are identified as Korteweg-de Vries solitons with negative amplitude and subsonic velocity. The typical width and amplitude-dependent velocities are in excellent agreement with theoretical predictions based on a generalized Korteweg-de Vries equation adapted to any substrate geometry. When multiple solitons are present, they interact and form a soliton turbulencelike spectrum. PMID:26274114

  1. Capillary solitons on a levitated medium

    NASA Astrophysics Data System (ADS)

    Perrard, S.; Deike, L.; Duchêne, C.; Pham, C.-T.

    2015-07-01

    A water cylinder deposited on a heated channel levitates on its own generated vapor film owing to the Leidenfrost effect. This experimental setup permits the study of the one-dimensional propagation of surface waves in a free-to-move liquid system. We report the observation of gravity-capillary waves under a dramatic reduction of gravity (up to a factor 30), leading to capillary waves at the centimeter scale. The generated nonlinear structures propagate without deformation and undergo mutual collisions and reflections at the boundaries of the domain. They are identified as Korteweg-de Vries solitons with negative amplitude and subsonic velocity. The typical width and amplitude-dependent velocities are in excellent agreement with theoretical predictions based on a generalized Korteweg-de Vries equation adapted to any substrate geometry. When multiple solitons are present, they interact and form a soliton turbulencelike spectrum.

  2. Integration of Multiple Components in Polystyrene-based Microfluidic Devices Part 2: Cellular Analysis

    PubMed Central

    Anderson, Kari B.; Halpin, Stephen T.; Johnson, Alicia S.; Martin, R. Scott; Spence, Dana M.

    2012-01-01

    In Part II of this series describing the use of polystyrene (PS) devices for microfluidic-based cellular assays, various cellular types and detection strategies are employed to determine three fundamental assays often associated with cells. Specifically, using either integrated electrochemical sensing or optical measurements with a standard multi-well plate reader, cellular uptake, production, or release of important cellular analytes are determined on a PS-based device. One experiment involved the fluorescence measurement of nitric oxide (NO) produced within an endothelial cell line following stimulation with ATP. The result was a four-fold increase in NO production (as compared to a control), with this receptor-based mechanism of NO production verifying the maintenance of cell receptors following immobilization onto the PS substrate. The ability to monitor cellular uptake was also demonstrated by optical determination of Ca2+ into endothelial cells following stimulation with the Ca2+ ionophore A20317. The result was a significant increase (42%) in the calcium uptake in the presence of the ionophore, as compared to a control (17%) (p < 0.05). Finally, the release of catecholamines from a dopaminergic cell line (PC 12 cells) was electrochemically monitored, with the electrodes being embedded into the PS-based device. The PC 12 cells had better adherence on the PS devices, as compared to use of PDMS. Potassium-stimulation resulted in the release of 114 ± 11 µM catecholamines, a significant increase (p < 0.05) over the release from cells that had been exposed to an inhibitor (reserpine, 20 ± 2 µM of catecholamines). The ability to successfully measure multiple analytes, generated in different means from various cells under investigation, suggests that PS may be a useful material for microfluidic device fabrication, especially considering the enhanced cell adhesion to PS, its enhanced rigidity/amenability to automation, and its ability to enable a wider range of

  3. Integration of multiple intraguild predator cues for oviposition decisions by a predatory mite

    PubMed Central

    Walzer, Andreas; Schausberger, Peter

    2012-01-01

    In mutual intraguild predation (IGP), the role of individual guild members is strongly context dependent and, during ontogeny, can shift from an intraguild (IG) prey to a food competitor or to an IG predator. Consequently, recognition of an offspring's predator is more complex for IG than classic prey females. Thus, IG prey females should be able to modulate their oviposition decisions by integrating multiple IG predator cues and by experience. Using a guild of plant-inhabiting predatory mites sharing the spider mite Tetranychus urticae as prey and passing through ontogenetic role shifts in mutual IGP, we assessed the effects of single and combined direct cues of the IG predator Amblyseius andersoni (eggs and traces left by a female on the substrate) on prey patch selection and oviposition behaviour of naïve and IG predator-experienced IG prey females of Phytoseiulus persimilis. The IG prey females preferentially resided in patches without predator cues when the alternative patch contained traces of predator females or the cue combination. Preferential egg placement in patches without predator cues was only apparent in the choice situation with the cue combination. Experience increased the responsiveness of females exposed to the IG predator cue combination, indicated by immediate selection of the prey patch without predator cues and almost perfect oviposition avoidance in patches with the cue combination. We argue that the evolution of the ability of IG prey females to evaluate offspring's IGP risk accurately is driven by the irreversibility of oviposition and the functionally complex relationships between predator guild members. PMID:23264692

  4. Capillary reference half-cell

    DOEpatents

    Hall, Stephen H.

    1996-01-01

    The present invention is a reference half-cell electrode wherein intermingling of test fluid with reference fluid does not affect the performance of the reference half-cell over a long time. This intermingling reference half-cell may be used as a single or double junction submersible or surface reference electrode. The intermingling reference half-cell relies on a capillary tube having a first end open to reference fluid and a second end open to test fluid wherein the small diameter of the capillary tube limits free motion of fluid within the capillary to diffusion. The electrode is placed near the first end of the capillary in contact with the reference fluid. The method of operation of the present invention begins with filling the capillary tube with a reference solution. After closing the first end of the capillary, the capillary tube may be fully submerged or partially submerged with the second open end inserted into test fluid. Since the electrode is placed near the first end of the capillary, and since the test fluid may intermingle with the reference fluid through the second open end only by diffusion, this intermingling capillary reference half-cell provides a stable voltage potential for long time periods.

  5. Capillary reference half-cell

    DOEpatents

    Hall, S.H.

    1996-02-13

    The present invention is a reference half-cell electrode wherein intermingling of test fluid with reference fluid does not affect the performance of the reference half-cell over a long time. This intermingling reference half-cell may be used as a single or double junction submersible or surface reference electrode. The intermingling reference half-cell relies on a capillary tube having a first end open to reference fluid and a second end open to test fluid wherein the small diameter of the capillary tube limits free motion of fluid within the capillary to diffusion. The electrode is placed near the first end of the capillary in contact with the reference fluid. The method of operation of the present invention begins with filling the capillary tube with a reference solution. After closing the first end of the capillary, the capillary tube may be fully submerged or partially submerged with the second open end inserted into test fluid. Since the electrode is placed near the first end of the capillary, and since the test fluid may intermingle with the reference fluid through the second open end only by diffusion, this intermingling capillary reference half-cell provides a stable voltage potential for long time periods. 11 figs.

  6. Stability of Constrained Capillary Surfaces

    NASA Astrophysics Data System (ADS)

    Bostwick, J. B.; Steen, P. H.

    2015-01-01

    A capillary surface is an interface between two fluids whose shape is determined primarily by surface tension. Sessile drops, liquid bridges, rivulets, and liquid drops on fibers are all examples of capillary shapes influenced by contact with a solid. Capillary shapes can reconfigure spontaneously or exhibit natural oscillations, reflecting static or dynamic instabilities, respectively. Both instabilities are related, and a review of static stability precedes the dynamic case. The focus of the dynamic case here is the hydrodynamic stability of capillary surfaces subject to constraints of (a) volume conservation, (b) contact-line boundary conditions, and (c) the geometry of the supporting surface.

  7. Alveolar Capillary Dysplasia

    PubMed Central

    Stankiewicz, Pawel; Steinhorn, Robin H.

    2011-01-01

    Alveolar capillary dysplasia with misalignment of the pulmonary veins (ACD/MPV) is a rare, fatal developmental lung disorder of neonates and infants. This review aims to address recent findings in the etiology and genetics of ACD/MPV and to raise awareness of this poorly known disease, which may also present as milder, unclassified forms. Successively discussed are what is known about the epidemiology, pathogenesis, pathophysiology, diagnostic indicators and approaches, genetic testing, treatment, and cases of delayed onset. The review concludes with suggestions for future directions to answer the many unknowns about this disorder. PMID:21471096

  8. Future Directions in Vulnerability to Depression among Youth: Integrating Risk Factors and Processes across Multiple Levels of Analysis

    PubMed Central

    Hankin, Benjamin L.

    2014-01-01

    Depression is a developmental phenomenon. Considerable progress has been made in describing the syndrome, establishing its prevalence and features, providing clues as to its etiology, and developing evidence-based treatment and prevention options. Despite considerable headway in distinct lines of vulnerability research, there is an explanatory gap in the field ability to more comprehensively explain and predict who is likely to become depressed, when, and why. Still, despite clear success in predicting moderate variance for future depression, especially with empirically rigorous methods and designs, the heterogeneous and multi-determined nature of depression suggests that additional etiologies need to be included to advance knowledge on developmental pathways to depression. This paper advocates for a multiple levels of analysis approach to investigating vulnerability to depression across the lifespan and providing a more comprehensive understanding of its etiology. One example of a multiple levels of analysis model of vulnerabilities to depression is provided that integrates the most accessible, observable factors (e.g., cognitive and temperament risks), intermediate processes and endophenotypes (e.g., information processing biases, biological stress physiology, and neural activation and connectivity), and genetic influences (e.g., candidate genes and epigenetics). Evidence for each of these factors as well as their cross-level integration is provided. Methodological and conceptual considerations important for conducting integrative, multiple levels of depression vulnerability research are discussed. Finally, translational implications for how a multiple levels of analysis perspective may confer additional leverage to reduce the global burden of depression and improve care are considered. PMID:22900513

  9. Capillary suspensions: Particle networks formed through the capillary force

    PubMed Central

    Koos, Erin

    2014-01-01

    The addition of small amounts of a secondary fluid to a suspension can, through the attractive capillary force, lead to particle bridging and network formation. The capillary bridging phenomenon can be used to stabilize particle suspensions and precisely tune their rheological properties. This effect can even occur when the secondary fluid wets the particles less well than the bulk fluid. These materials, so-called capillary suspensions, have been the subject of recent research studying the mechanism for network formation, the properties of these suspensions, and how the material properties can be modified. Recent work in colloidal clusters is summarized and the relationship to capillary suspensions is discussed. Capillary suspensions can also be used as a pathway for new material design and some of these applications are highlighted. Results obtained to date are summarized and central questions that remain to be answered are proposed in this review. PMID:25729316

  10. Tapered capillary optics

    DOEpatents

    Hirsch, Gregory

    1998-01-01

    A metal or glass wire is etched with great precision into a very narrowly tapering cone which has the shape of the desired final capillary-optics bore. By controlling the rate of removal of the wire from an etchant bath, a carefully controlled taper is produced. A sensor measures the diameter of the wire as it leaves the surface of the etchant. This signal is used for feedback control of the withdrawal speed. The etched wire undergoes a treatment to produce an extremely low surface-roughness. The etched and smoothed wire is coated with the material of choice for optimizing the reflectivity of the radiation being focused. This could be a vacuum evaporation, sputtering, CVD or aqueous chemical process. The coated wire is either electroplated, built up with electroless plating, or encapsulated in a polymer cylinder such as epoxy to increase the diameter of the wire for easier handling and greater robustness. During this process, the wire is vertically oriented and tensioned to assure that the wire is absolutely straight. The coated and electroformed wire is bonded to a flat, rigid substrate and is then periodically segmented by cutting or etching a series of narrow slits or grooves into the wire. The wire is vertically oriented and tensioned during the bonding process to assure that it is straight. The original wire material is then chemically etched away through the slits or otherwise withdrawn to leave the hollow internal bore of the final tapered-capillary optical element.

  11. Capillary Electrophoresis in Metabolomics.

    PubMed

    Maier, Tanja Verena; Schmitt-Kopplin, Philippe

    2016-01-01

    Metabolomics is an analytical toolbox to describe (all) low-molecular-weight compounds in a biological system, as cells, tissues, urine, and feces, as well as in serum and plasma. To analyze such complex biological samples, high requirements on the analytical technique are needed due to the high variation in compound physico-chemistry (cholesterol derivatives, amino acids, fatty acids as SCFA, MCFA, or LCFA, or pathway-related metabolites belonging to each individual organism) and concentration dynamic range. All main separation techniques (LC-MS, GC-MS) are applied in routine to metabolomics hyphenated or not to mass spectrometry, and capillary electrophoresis is a powerful high-resolving technique but still underused in this field of complex samples. Metabolomics can be performed in the non-targeted way to gain an overview on metabolite profiles in biological samples. Targeted metabolomics is applied to analyze quantitatively pre-selected metabolites. This chapter reviews the use of capillary electrophoresis in the field of metabolomics and exemplifies solutions in metabolite profiling and analysis in urine and plasma. PMID:27645748

  12. EasyCloneMulti: A Set of Vectors for Simultaneous and Multiple Genomic Integrations in Saccharomyces cerevisiae

    PubMed Central

    Baallal Jacobsen, Simo Abdessamad; Jensen, Niels B.; Kildegaard, Kanchana R.; Herrgård, Markus J.; Schneider, Konstantin; Koza, Anna; Forster, Jochen; Nielsen, Jens; Borodina, Irina

    2016-01-01

    Saccharomyces cerevisiae is widely used in the biotechnology industry for production of ethanol, recombinant proteins, food ingredients and other chemicals. In order to generate highly producing and stable strains, genome integration of genes encoding metabolic pathway enzymes is the preferred option. However, integration of pathway genes in single or few copies, especially those encoding rate-controlling steps, is often not sufficient to sustain high metabolic fluxes. By exploiting the sequence diversity in the long terminal repeats (LTR) of Ty retrotransposons, we developed a new set of integrative vectors, EasyCloneMulti, that enables multiple and simultaneous integration of genes in S. cerevisiae. By creating vector backbones that combine consensus sequences that aim at targeting subsets of Ty sequences and a quickly degrading selective marker, integrations at multiple genomic loci and a range of expression levels were obtained, as assessed with the green fluorescent protein (GFP) reporter system. The EasyCloneMulti vector set was applied to balance the expression of the rate-controlling step in the β-alanine pathway for biosynthesis of 3-hydroxypropionic acid (3HP). The best 3HP producing clone, with 5.45 g.L-1 of 3HP, produced 11 times more 3HP than the lowest producing clone, which demonstrates the capability of EasyCloneMulti vectors to impact metabolic pathway enzyme activity. PMID:26934490

  13. Formulation of an explicit-multiple-time-step time integration method for use in a global primitive equation grid model

    NASA Technical Reports Server (NTRS)

    Chao, W. C.

    1982-01-01

    With appropriate modifications, a recently proposed explicit-multiple-time-step scheme (EMTSS) is incorporated into the UCLA model. In this scheme, the linearized terms in the governing equations that generate the gravity waves are split into different vertical modes. Each mode is integrated with an optimal time step, and at periodic intervals these modes are recombined. The other terms are integrated with a time step dictated by the CFL condition for low-frequency waves. This large time step requires a special modification of the advective terms in the polar region to maintain stability. Test runs for 72 h show that EMTSS is a stable, efficient and accurate scheme.

  14. Multiple timescale stochastic optimization with application to integrating renewable resources in power systems

    NASA Astrophysics Data System (ADS)

    Gangammanavar, Harsha

    The contribution of renewable resources to the energy portfolio across the world has been steadily increasing over the past few years. Several studies predict the continuation of this trend in the future leading to large scale integration of renewable resources into energy networks. A principal challenge associated with this is the intermittency and non-dispatchability of the renewable sources. This necessitates incorporation of faster reserves, storage devices and similar services operating alongside the slow ramping conventional generators in the energy network. To maintain the robustness of such a network, there are proposals to require hourly planning for some resources, and sub-hourly planning for others: an hourly scale may be used for conventional generator production levels and a sub-hourly scale for renewable generator levels and/or storage and transmission network utilization. This dissertation will present a multiple time scale stochastic programming formulation of the economic dispatch problem and algorithmic frameworks to tackle it. The first approach highlights the difference between hourly and sub-hourly planning of economic dispatch and uses the two-stage Stochastic Decomposition (SD) algorithm. The second framework combines three principal components: optimization, dynamic control and simulation. The conventional generator decisions are obtained iteratively by solving a regularized linear problem in the first stage of SD. For these first stage decisions, a policy for recommending the dispatch decisions is identified using an Approximate Dynamic Programming based controller. A vector autoregression based simulator is used to provide the sub-hourly wind generation scenarios. The performance of these algorithms was tested on the IEEE model energy networks and the Illinois energy network. The insights gained regarding the benefits of sub-hourly planning and role of operating reserves/storage in energy network with high renewable penetration will be

  15. On Capillary Rise and Nucleation

    ERIC Educational Resources Information Center

    Prasad, R.

    2008-01-01

    A comparison of capillary rise and nucleation is presented. It is shown that both phenomena result from a balance between two competing energy factors: a volume energy and a surface energy. Such a comparison may help to introduce nucleation with a topic familiar to the students, capillary rise. (Contains 1 table and 3 figures.)

  16. Capillary optics for radiation focusing

    SciTech Connect

    Peurrung, A.J.; Reeder, P.L.; Bliss, M.; Craig, R.A.; Lepel, E.A.; Stromswold, D.C.; Stoffels, J.; Sunberg, D.S.; Tenny, H.

    1996-11-01

    Capillary lens technology may ultimately bring benefits to neutron and x-ray-based science like conventional lenses with visible light. Although the technology is not yet 10 years old, these lenses have already had a significant impact in engineering, science, and medicine. Capillary lenses are advantageous when it is desirable to increase the radiation flux at a location without regard to its angular divergence. PNNL has worked to improve the technology in several ways. A single, optimally tapered capillary was manufactured, which allows intensity gains of a factor of 270 for an initially parallel, incident x-ray beam. Feasibility of constructing neutron lenses using {sup 58}Ni (particularly effective at reflecting neutrons) has been explored. Three applications for capillary optics have been identified and studied: neutron telescope, Gandolphi x-ray diffractometry, and neutron radiotherapy. A brief guide is given for determining which potential applications are likely to be helped by capillary optics.

  17. Biomedical applications of capillary electrophoresis

    NASA Astrophysics Data System (ADS)

    Kartsova, L. A.; Bessonova, E. A.

    2015-08-01

    The review deals with modern analytical approaches used in capillary electrophoresis for solving medical and biological problems: search for biomarkers of various diseases and rapid diagnosis based on characteristic profiles of biologically active compounds by capillary electrophoresis with mass spectrometric detection; monitoring of the residual drugs in biological fluids for evaluating the efficiency of drug therapy; testing of the enantiomeric purity of pharmaceutical products; the use of novel materials as components of stationary and pseudo-stationary phases in capillary electrophoresis and capillary electrochromatography to increase the selectivity of separation of components of complex matrices; and identification of various on-line preconcentration techniques to reduce the detection limits of biologically active analytes. A topical trend in capillary electrophoresis required in clinical practice, viz., the design of microfluidic systems, is discussed. The bibliography includes 173 references.

  18. The use of artificial intelligence techniques to improve the multiple payload integration process

    NASA Technical Reports Server (NTRS)

    Cutts, Dannie E.; Widgren, Brian K.

    1992-01-01

    A maximum return of science and products with a minimum expenditure of time and resources is a major goal of mission payload integration. A critical component then, in successful mission payload integration is the acquisition and analysis of experiment requirements from the principal investigator and payload element developer teams. One effort to use artificial intelligence techniques to improve the acquisition and analysis of experiment requirements within the payload integration process is described.

  19. Multiple Strategies for Spatial Integration of 2D Layouts within Working Memory

    PubMed Central

    Meilinger, Tobias; Watanabe, Katsumi

    2016-01-01

    Prior results on the spatial integration of layouts within a room differed regarding the reference frame that participants used for integration. We asked whether these differences also occur when integrating 2D screen views and, if so, what the reasons for this might be. In four experiments we showed that integrating reference frames varied as a function of task familiarity combined with processing time, cues for spatial transformation, and information about action requirements paralleling results in the 3D case. Participants saw part of an object layout in screen 1, another part in screen 2, and reacted on the integrated layout in screen 3. Layout presentations between two screens coincided or differed in orientation. Aligning misaligned screens for integration is known to increase errors/latencies. The error/latency pattern was thus indicative of the reference frame used for integration. We showed that task familiarity combined with self-paced learning, visual updating, and knowing from where to act prioritized the integration within the reference frame of the initial presentation, which was updated later, and from where participants acted respectively. Participants also heavily relied on layout intrinsic frames. The results show how humans flexibly adjust their integration strategy to a wide variety of conditions. PMID:27101011

  20. Multiple Strategies for Spatial Integration of 2D Layouts within Working Memory.

    PubMed

    Meilinger, Tobias; Watanabe, Katsumi

    2016-01-01

    Prior results on the spatial integration of layouts within a room differed regarding the reference frame that participants used for integration. We asked whether these differences also occur when integrating 2D screen views and, if so, what the reasons for this might be. In four experiments we showed that integrating reference frames varied as a function of task familiarity combined with processing time, cues for spatial transformation, and information about action requirements paralleling results in the 3D case. Participants saw part of an object layout in screen 1, another part in screen 2, and reacted on the integrated layout in screen 3. Layout presentations between two screens coincided or differed in orientation. Aligning misaligned screens for integration is known to increase errors/latencies. The error/latency pattern was thus indicative of the reference frame used for integration. We showed that task familiarity combined with self-paced learning, visual updating, and knowing from where to act prioritized the integration within the reference frame of the initial presentation, which was updated later, and from where participants acted respectively. Participants also heavily relied on layout intrinsic frames. The results show how humans flexibly adjust their integration strategy to a wide variety of conditions.

  1. Multiple Strategies for Spatial Integration of 2D Layouts within Working Memory.

    PubMed

    Meilinger, Tobias; Watanabe, Katsumi

    2016-01-01

    Prior results on the spatial integration of layouts within a room differed regarding the reference frame that participants used for integration. We asked whether these differences also occur when integrating 2D screen views and, if so, what the reasons for this might be. In four experiments we showed that integrating reference frames varied as a function of task familiarity combined with processing time, cues for spatial transformation, and information about action requirements paralleling results in the 3D case. Participants saw part of an object layout in screen 1, another part in screen 2, and reacted on the integrated layout in screen 3. Layout presentations between two screens coincided or differed in orientation. Aligning misaligned screens for integration is known to increase errors/latencies. The error/latency pattern was thus indicative of the reference frame used for integration. We showed that task familiarity combined with self-paced learning, visual updating, and knowing from where to act prioritized the integration within the reference frame of the initial presentation, which was updated later, and from where participants acted respectively. Participants also heavily relied on layout intrinsic frames. The results show how humans flexibly adjust their integration strategy to a wide variety of conditions. PMID:27101011

  2. Flight Testing of the Capillary Pumped Loop 3 Experiment

    NASA Technical Reports Server (NTRS)

    Ottenstein, Laura; Butler, Dan; Ku, Jentung; Cheung, Kwok; Baldauff, Robert; Hoang, Triem

    2002-01-01

    The Capillary Pumped Loop 3 (CAPL 3) experiment was a multiple evaporator capillary pumped loop experiment that flew in the Space Shuttle payload bay in December 2001 (STS-108). The main objective of CAPL 3 was to demonstrate in micro-gravity a multiple evaporator capillary pumped loop system, capable of reliable start-up, reliable continuous operation, and heat load sharing, with hardware for a deployable radiator. Tests performed on orbit included start-ups, power cycles, low power tests (100 W total), high power tests (up to 1447 W total), heat load sharing, variable/fixed conductance transition tests, and saturation temperature change tests. The majority of the tests were completed successfully, although the experiment did exhibit an unexpected sensitivity to shuttle maneuvers. This paper describes the experiment, the tests performed during the mission, and the test results.

  3. Steady Capillary Driven Flow

    NASA Technical Reports Server (NTRS)

    Weislogel, Mark M.

    1996-01-01

    A steady capillary driven flow is developed for a liquid index in a circular tube which is partially coated with a surface modifier to produce a discontinuous wetting condition from one side of the tube to the other. The bulk flow is novel in that it is truly steady, and controlled solely by the physics associated with dynamic wetting. The influence of gravity on the flow is minimized through the use of small diameter tubes approximately O(1 mm) tested horizontally in a laboratory and larger tubes approximately O(10 mm) tested in the low gravity environment of a drop tower. Average steady velocities are predicted and compared against a large experimental data set which includes the effects of tube dimensions and fluid properties. The sensitivity of the velocity to surface cleanliness is dramatic and the advantages of experimentation in a microgravity environment are discussed.

  4. Benign sinonasal capillary haemangioma

    PubMed Central

    Stubbs, Darren; Poulios, Aristotelis; Khalil, Hisham

    2014-01-01

    Haemangiomas are benign fibrovascular tumours relatively that are common in the head and neck, where 60% of them occur Among the various categories of haemangiomas, lobular capillary haemangiomas (LCH) occur frequently on the skin, lips, buccal mucosa, tongue and gingiva. However, they are vanishingly rare in the paranasal sinuses. The imaging features of LCH are non-specific. The histological characteristics of LCH can also make diagnosis difficult as sometimes resemble highly vascular malignant tumours. This leads to the false preoperative diagnosis of suspected malignancy in many cases, which places the patient under unnecessary distress and anxiety. We present a case of LCH appearing as a suspicious nasal lesion of the lateral nasal wall with unilateral nasal obstruction, necrotic centre and epistaxis. The tumour was excised endoscopically in one operation including endoscopic medial maxillectomy. Further education about this lesion is deemed important as preoperative embolisation may be needed for a safe operation. PMID:25287393

  5. Capillaries for use in a multiplexed capillary electrophoresis system

    DOEpatents

    Yeung, E.S.; Chang, H.T.; Fung, E.N.

    1997-12-09

    The invention provides a side-entry optical excitation geometry for use in a multiplexed capillary electrophoresis system. A charge-injection device is optically coupled to capillaries in the array such that the interior of a capillary is imaged onto only one pixel. In Sanger-type 4-label DNA sequencing reactions, nucleotide identification (``base calling``) is improved by using two long-pass filters to split fluorescence emission into two emission channels. A binary poly(ethyleneoxide) matrix is used in the electrophoretic separations. 19 figs.

  6. Capillaries for use in a multiplexed capillary electrophoresis system

    DOEpatents

    Yeung, Edward S.; Chang, Huan-Tsang; Fung, Eliza N.

    1997-12-09

    The invention provides a side-entry optical excitation geometry for use in a multiplexed capillary electrophoresis system. A charge-injection device is optically coupled to capillaries in the array such that the interior of a capillary is imaged onto only one pixel. In Sanger-type 4-label DNA sequencing reactions, nucleotide identification ("base calling") is improved by using two long-pass filters to split fluorescence emission into two emission channels. A binary poly(ethyleneoxide) matrix is used in the electrophoretic separations.

  7. Integrated p-n junction InGaN/GaN multiple-quantum-well devices with diverse functionalities

    NASA Astrophysics Data System (ADS)

    Cai, Wei; Gao, Xumin; Yuan, Wei; Yang, Yongchao; Yuan, Jialei; Zhu, Hongbo; Wang, Yongjin

    2016-05-01

    We propose, fabricate, and demonstrate integrated p-n junction InGaN/GaN multiple-quantum-well devices with diverse functionalities on a GaN-on-silicon platform. Suspended devices with a common n-contact are realized using a wafer-level process. For the integrated devices, part of the light emitted by a light-emitting diode (LED) is guided in-plane through a suspended waveguide and is sensed by another photodiode. The induced photocurrent is tuned by the LED. The integrated devices can act as two independent LEDs to deliver different signals simultaneously for free-space visible light communication. Furthermore, the suspended devices can be used as two separate photodiodes to detect incident light with a distinct on/off switching performance.

  8. Accurate and efficient Nyström volume integral equation method for the Maxwell equations for multiple 3-D scatterers

    NASA Astrophysics Data System (ADS)

    Chen, Duan; Cai, Wei; Zinser, Brian; Cho, Min Hyung

    2016-09-01

    In this paper, we develop an accurate and efficient Nyström volume integral equation (VIE) method for the Maxwell equations for a large number of 3-D scatterers. The Cauchy Principal Values that arise from the VIE are computed accurately using a finite size exclusion volume together with explicit correction integrals consisting of removable singularities. Also, the hyper-singular integrals are computed using interpolated quadrature formulae with tensor-product quadrature nodes for cubes, spheres and cylinders, that are frequently encountered in the design of meta-materials. The resulting Nyström VIE method is shown to have high accuracy with a small number of collocation points and demonstrates p-convergence for computing the electromagnetic scattering of these objects. Numerical calculations of multiple scatterers of cubic, spherical, and cylindrical shapes validate the efficiency and accuracy of the proposed method.

  9. Applications of capillary optical fibers

    NASA Astrophysics Data System (ADS)

    Romaniuk, Ryszard

    2006-10-01

    The paper updates and summarizes contemporary applications of capillary optical fibers. Some of these applications are straight consequence of the classical capillary properties and capillary devices like: rheometry, electrophoresis, column chromatography (gas and liquid). Some new applications are tightly connected with co-propagation (or counter-propagation) of micro-mass together with optical wave - evanescent or of considerable intensity. In the first case, the optical wave is propagated in a narrow (more and more frequently single-mode) optical ring core adjacent to the capillary hole. The optical propagation is purely refractive. In the second case, the intensity maximum of optical wave is on the capillary long axis, i.e. in the center of the hole. The optical propagation is purely photonic, i.e. in a Bragg waveguide (one dimensional photonic band-gap). The capillary hole is filled with vacuum or with propagated matter (gas, liquid, single atoms, continuous particle arrangement). Optical capillaries, filamentary and embedded, are turning to a fundamental component of nano- and micro-MOEMS.

  10. Instability of the capillary bridge

    NASA Astrophysics Data System (ADS)

    Pare, Gounseti; Hoepffner, Jerome

    2014-11-01

    Capillary adhesion is a physical mechanism that maintains two bodies in contact by capillarity through a liquid ligament. The capillary bridge is an idealization of this capillary adhesion. In this study we first focus on the classical case of the stability of the capillary bridge. Secondly we study a slightly more complex configuration, imagining a flow in the capillary bridge as in the case of the dynamics of the neck of a liquid ligament, in its withdrawal under the effect of capillarity. Inspired by the experiments on soap films of Plateau, the configuration analyzed consists of an initially axisymmetric, mass of fluid held by surface tension forces between two parallel, coaxial, solid pipes of the same diameter. The results presented are obtained by numerical simulations using the free software, Gerris Flow Solver. We first focus on the capillary Venturi. In the static configuration the stability diagram of the capillary bridge obtained is in perfect agreement with the results of Lev A. Slobozhanin. In the dynamic case we develop a matlab code based on the one dimensional equations of Eggers and Dupont. The comparison of the bifurcation diagram obtained and the numerical simulations shows a good agreement.

  11. Multiple Integration of the Heat-Conduction Equation for a Space Bounded From the Inside

    NASA Astrophysics Data System (ADS)

    Kot, V. A.

    2016-03-01

    An N-fold integration of the heat-conduction equation for a space bounded from the inside has been performed using a system of identical equalities with definition of the temperature function by a power polynomial with an exponential factor. It is shown that, in a number of cases, the approximate solutions obtained can be considered as exact because their errors comprise hundredths and thousandths of a percent. The method proposed for N-fold integration represents an alternative to classical integral transformations.

  12. Capillary Array Waveguide Amplified Fluorescence Detector for mHealth.

    PubMed

    Balsam, Joshua; Bruck, Hugh Alan; Rasooly, Avraham

    2013-09-01

    array can potentially be used for sensitive analysis of multiple fluorescent detection assays simultaneously. The simple phone based capillary array approach presented in this paper is capable of amplifying weak fluorescent signals thereby improving the sensitivity of optical detectors based on mobile phones. This may allow sensitive biological assays to be measured with low sensitivity detectors and may make mHealth practical for many diagnostics applications, especially in resource-poor and global health settings.

  13. Capillary Array Waveguide Amplified Fluorescence Detector for mHealth

    PubMed Central

    Balsam, Joshua; Bruck, Hugh Alan; Rasooly, Avraham

    2013-01-01

    array can potentially be used for sensitive analysis of multiple fluorescent detection assays simultaneously. The simple phone based capillary array approach presented in this paper is capable of amplifying weak fluorescent signals thereby improving the sensitivity of optical detectors based on mobile phones. This may allow sensitive biological assays to be measured with low sensitivity detectors and may make mHealth practical for many diagnostics applications, especially in resource-poor and global health settings. PMID:24039345

  14. A fully integrated and automated microsystem for rapid pharmacogenetic typing of multiple warfarin-related single-nucleotide polymorphisms.

    PubMed

    Zhuang, Bin; Han, Junping; Xiang, Guangxin; Gan, Wupeng; Wang, Shuaiqin; Wang, Dong; Wang, Lei; Sun, Jing; Li, Cai-Xia; Liu, Peng

    2016-01-01

    A fully integrated and automated microsystem consisting of low-cost, disposable plastic chips for DNA extraction and PCR amplification combined with a reusable glass capillary array electrophoresis chip in a modular-based format was successfully developed for warfarin pharmacogenetic testing. DNA extraction was performed by adopting a filter paper-based method, followed by "in situ" PCR that was carried out directly in the same reaction chamber of the chip without elution. PCR products were then co-injected with sizing standards into separation channels for detection using a novel injection electrode. The entire process was automatically conducted on a custom-made compact control and detection instrument. The limit of detection of the microsystem for the singleplex amplification of amelogenin was determined to be 0.625 ng of standard K562 DNA and 0.3 μL of human whole blood. A two-color multiplex allele-specific PCR assay for detecting the warfarin-related single-nucleotide polymorphisms (SNPs) 6853 (-1639G>A) and 6484 (1173C>T) in the VKORC1 gene and the *3 SNP (1075A>C) in the CYP2C9 gene was developed and used for validation studies. The fully automated genetic analysis was completed in two hours with a minimum requirement of 0.5 μL of input blood. Samples from patients with different genotypes were all accurately analyzed. In addition, both dried bloodstains and oral swabs were successfully processed by the microsystem with a simple modification to the DNA extraction and amplification chip. The successful development and operation of this microsystem establish the feasibility of rapid warfarin pharmacogenetic testing in routine clinical practice. PMID:26568290

  15. Capillary flow solder wettability test

    SciTech Connect

    Vianco, P.T.; Rejent, J.A.

    1996-01-01

    A test procedure was developed to assess the capillary flow wettability of solders inside of a confined geometry. The test geometry was comprised of two parallel plates with a controlled gap of constant thickness (0.008 cm, 0.018 cm, 0.025 cm, and 0.038 cm). Capillary flow was assessed by: (1) the meniscus or capillary rise of the solder within the gap, (2) the extent of void formation in the gap, and (3) the time-dependence of the risen solder film. Tests were performed with the lead-free solders.

  16. Integration and Testing Challenges of Small, Multiple Satellite Missions: Experiences from the Space Technology 5 Project

    NASA Technical Reports Server (NTRS)

    Sauerwein, Timothy A.; Gostomski, Thomas

    2008-01-01

    The ST5 technology demonstration mission led by GSFC of NASA's New Millennium Program managed by JPL consisted of three micro satellites (approximately 30 kg each) deployed into orbit from the Pegasus XL launch vehicle. In order to meet the launch date schedule of ST5, a different approach was required rather than the standard I&T approach used for single, room-sized satellites. The three spacecraft were designed, integrated, and tested at NASA Goddard Space Flight Center. It was determined that there was insufficient time in the schedule to perform three spacecraft I&T activities in series using standard approaches. The solution was for spacecraft #1 to undergo integration and test first, followed by spacecraft #2 and #3 simultaneously. This simultaneous integration was successful for several reasons. Each spacecraft had a Lead Test Conductor who planned and coordinated their spacecraft through its integration and test activities. One team of engineers and technicians executed the integration of all three spacecraft, learning and gaining knowledge and efficiency as spacecraft #1 integration and testing progressed. They became acutely familiar with the hardware, operation and processes for I&T, thus had the experience and knowledge to safely execute I&T for spacecraft #2 and #3. The integration team was extremely versatile; each member could perform many different activities or work any spacecraft, when needed. ST5 was successfully integrated, tested and shipped to the launch site per the I&T schedule that was planned three years previously. The I&T campaign was completed with ST5's successful launch on March 22, 2006.

  17. Investigation of interference in multiple-input multiple-output wireless transmission at W band for an optical wireless integration system.

    PubMed

    Li, Xinying; Yu, Jianjun; Dong, Ze; Zhang, Junwen; Chi, Nan; Yu, Jianguo

    2013-03-01

    We experimentally investigate the interference in multiple-input multiple-output (MIMO) wireless transmission by adjusting the relative locations of horn antennas (HAs) in a 100 GHz optical wireless integration system, which can deliver a 50 Gb/s polarization-division-multiplexing quadrature-phase-shift-keying signal over 80 km single-mode fiber-28 and a 2×2 MIMO wireless link. For the parallel 2×2 MIMO wireless link, each receiver HA can only get wireless power from the corresponding transmitter HA, while for the crossover ones, the receiver HA can get wireless power from two transmitter HAs. At the wireless receiver, polarization demultiplexing is realized by the constant modulus algorithm (CMA) in the digital-signal-processing part. Compared to the parallel case, wireless interference causes about 2 dB optical signal-to-noise ratio penalty at a bit-error ratio (BER) of 3.8×10(-3) for the crossover cases if similar CMA taps are employed. The increase in CMA tap length can reduce wireless interference and improve BER performance. Furthermore, more CMA taps should be adopted to overcome the severe wireless interference when two pairs of transmitter and receiver HAs have different wireless distances.

  18. Analysis of Capillary Rise in Asymmetric Branch-Like Capillary

    NASA Astrophysics Data System (ADS)

    Li, Caoxiong; Shen, Yinghao; Ge, Hongkui; Yang, Zhihui; Su, Shuai; Ren, Kai; Huang, Heyu

    2016-05-01

    Transport in porous media is common in nature, attracting many attentions for a long time. Tree-like network model is often used as a simplification for porous space, expressing the complexity of pore spaces instead of capillary bundle. To investigate spontaneous imbibition characteristics in this network, a dynamic asymmetric branch-like capillary model is used to represent basic network structure, using fractal method to represent tortuosity. This work investigates the influence of parameters on imbibition process in the branch-like capillary model. An analytical equation for the imbibition mass versus time is derived. Parameters from capillary structures to liquid properties are taken into account and analyzed based on the numerical solution of the equation. It is found that the imbibition process in asymmetric branch-like capillary model can be recognized by four sections and brunching tubes are positive for imbibition process. Concomitantly, meniscus arrest event is simulated and discussed. Moreover, the influence of parameters on imbibition process is discussed. These parameters can be classified as static and dynamic. Static parameters mainly change the capillary force, which are related to the ultimate imbibition mass or imbibition ability, while dynamic parameters mainly have influence on resistance of flowing fluid, which are related to the imbibition speed in the imbibition process.

  19. Multiple Sensory Inputs Are Extensively Integrated to Modulate Nociception in C. elegans

    PubMed Central

    Summers, Philip J.; Layne, Robert M.; Ortega, Amanda C.; Harris, Gareth P.; Bamber, Bruce A.

    2015-01-01

    Sensory inputs are integrated extensively before decision making, with altered multisensory integration being associated with disorders such as autism. We demonstrate that the two C. elegans AIB interneurons function as a biphasic switch, integrating antagonistic, tonic, and acute inputs from three distinct pairs of sensory neurons to modulate nociception. Off food, animals reverse away from a noxious stimulus. In contrast, on food or serotonin, AIB signaling is inhibited and, although animals initiate an aversive response more rapidly, they continue forward after the initial backward locomotion is complete. That is, animals continue to move forward and feed even when presented with a noxious repellant, with AIB inhibition decreasing the repellant concentration evoking a maximal response. These studies demonstrate that the AIBs serve as an integrating hub, receiving inputs from different sensory neurons to modulate locomotory decision making differentially, and highlight the utility of this model to analyze the complexities of multisensory integration. SIGNIFICANCE STATEMENT Dysfunctional sensory signaling and perception are associated with a number of disease states, including autism spectrum disorders, schizophrenia, and anxiety. We have used the C. elegans model to examine multisensory integration at the interneuron level to better understand the modulation of this complex, multicomponent process. C. elegans responds to a repulsive odorant by first backing up and then either continuing forward or turning and moving away from the odorant. This decision-making process is modulated extensively by the activity state of the two AIB interneurons, with the AIBs integrating an array of synergistic and antagonistic glutamatergic inputs, from sensory neurons responding directly to the odorant to others responding to a host of additional environmental variables to ultimately fine tune aversive behaviors. PMID:26180208

  20. Biomimetic aqueous-core lipid nanoballoons integrating a multiple emulsion formulation: a suitable housing system for viable lytic bacteriophages.

    PubMed

    Balcão, Victor M; Glasser, Cássia A; Chaud, Marco V; del Fiol, Fernando S; Tubino, Matthieu; Vila, Marta M D C

    2014-11-01

    The emergence of antibiotic-resistant bacterial strains and the weak penetration of antibiotics into bacterial biofilms put an emphasis in the need for safe and effective alternatives for antimicrobial treatments. The application of strictly lytic bacteriophages (or phages) has been proposed as an alternative (or complement) to conventional antibiotics, allowing release of the natural predators of bacteria directly to the site of infection. In the present research effort, production of bacteriophage derivatives (starting from lytic phage particle isolates), encompassing full stabilization of their three-dimensional structure, has been attempted via housing said bacteriophage particles within lipid nanovesicles integrating a multiple water-in-oil-in-water (W/O/W) emulsion. As a proof-of-concept for the aforementioned strategy, bacteriophage particles with broad lytic spectrum were entrapped within the aqueous core of lipid nanoballoons integrating a W/O/W multiple emulsion. Long-term storage of the multiple emulsions produced did not lead to leaching of phage particles, thus proving the effectiveness of the encapsulation procedure.

  1. Integrating Multiple Identities: Narrative in the Formation and Maintenance of the Self in International School Students

    ERIC Educational Resources Information Center

    Sears, Coreen

    2011-01-01

    This article reports on an investigation into the formation and maintenance of identity in globally mobile children and young people in the setting of an international school. The findings suggest that students at the school sustain composite identities that encompass their multiple experiences. The school itself offers a milieu which recognizes…

  2. SOUND SURVEY DESIGNS CAN FACILITATE INTEGRATING STREAM MONITORING DATA ACROSS MULTIPLE PROGRAMS

    EPA Science Inventory

    Multiple agencies in the Pacific Northwest monitor the condition of stream networks or their watersheds. Some agencies use a stream "network" perspective to report on the fraction or length of the network that either meets or violates particular criteria. Other agencies use a "wa...

  3. Selecting an Appropriate Multiple Comparison Technique: An Integration of Monte Carlo Studies.

    ERIC Educational Resources Information Center

    Myette, Beverly M.; White, Karl R.

    Twenty Monte Carlo studies on multiple comparison (MC) techniques were conducted to examine which MC technique was the "method of choice." The results from these studies had several apparent contradictions when different techniques were investigated under varying sample size and variance conditions. Box's coefficient of variance variation and bias…

  4. Diffusion Weighted Callosal Integrity Reflects Interhemispheric Communication Efficiency in Multiple Sclerosis

    ERIC Educational Resources Information Center

    Warlop, Nele P.; Achten, Eric; Debruyne, Jan; Vingerhoets, Guy

    2008-01-01

    We aimed to investigate the relation between damage in the corpus callosum and the performance on an interhemispheric communication task in patients with multiple sclerosis (MS). Relative callosal lesion load defined as the ratio between callosal area and the total lesion load in the total corpus callosum, and the diffusion tensor imaging (DTI)…

  5. The Multiple Menu Model: A Successful Marriage for Integrating Content and Process.

    ERIC Educational Resources Information Center

    Renzulli, Joseph S.

    1997-01-01

    The Multiple Menu Model is a practical set of planning guides that teachers can use to design indepth curriculum units. This model differs from traditional approaches by balancing content and process, involving students as inquirers, and exploring knowledge's structure and interconnectedness. Components include menus for knowledge, instructional…

  6. Meaning, Memory, and Multiplication: Integrating Patterns and Properties with Basic Facts

    ERIC Educational Resources Information Center

    Ploger, Don; Hecht, Steven

    2012-01-01

    Although learning mathematics certainly depends upon accurate understanding of the facts of multiplication, it requires much more. This study examines the relationship between a meaningful understanding of arithmetic operations and the mastery of basic facts. The study began with a joke about a mistaken mathematical fact. The children appreciated…

  7. Impulsive synchronization of Markovian jumping randomly coupled neural networks with partly unknown transition probabilities via multiple integral approach.

    PubMed

    Chandrasekar, A; Rakkiyappan, R; Cao, Jinde

    2015-10-01

    This paper studies the impulsive synchronization of Markovian jumping randomly coupled neural networks with partly unknown transition probabilities via multiple integral approach. The array of neural networks are coupled in a random fashion which is governed by Bernoulli random variable. The aim of this paper is to obtain the synchronization criteria, which is suitable for both exactly known and partly unknown transition probabilities such that the coupled neural network is synchronized with mixed time-delay. The considered impulsive effects can be synchronized at partly unknown transition probabilities. Besides, a multiple integral approach is also proposed to strengthen the Markovian jumping randomly coupled neural networks with partly unknown transition probabilities. By making use of Kronecker product and some useful integral inequalities, a novel Lyapunov-Krasovskii functional was designed for handling the coupled neural network with mixed delay and then impulsive synchronization criteria are solvable in a set of linear matrix inequalities. Finally, numerical examples are presented to illustrate the effectiveness and advantages of the theoretical results.

  8. DNA typing by capillary electrophoresis

    SciTech Connect

    Zhang, N.

    1997-10-08

    Capillary electrophoresis is becoming more and more important in nucleic acid analysis including DNA sequencing, typing and disease gene measurements. This work summarized the background of DNA typing. The recent development of capillary electrophoresis was also discussed. The second part of the thesis showed the principle of DNA typing based on using the allelic ladder as the absolute standard ladder in capillary electrophoresis system. Future work will be focused on demonstrating DNA typing on multiplex loci and examples of disease diagnosis in the on-line format of PCR-CE. Also capillary array electrophoresis system should allow high throughput, fast speed DNA typing. Only the introduction and conclusions for this report are available here. A reprint was removed for separate processing.

  9. Capillary Electrophoresis in Wine Science.

    PubMed

    Coelho, Christian; Bagala, Franck; Gougeon, Régis D; Schmitt-Kopplin, Philippe

    2016-01-01

    Capillary electrophoresis appeared to be a powerful and reliable technique to analyze the diversity of wine compounds. Wine presents a great variety of natural chemicals coming from the grape berry extraction and the fermentation processes. The first and more abundant after water, ethanol has been quantified in wines via capillary electrophoresis. Other families like organic acids, neutral and acid sugars, polyphenols, amines, thiols, vitamins, and soluble proteins are electrophoretically separated from the complex matrix.Here, we will focus on the different methodologies that have been employed to conduct properly capillary electrophoresis in wine analysis.Two examples informing on wine chemistry obtained by capillary electrophoresis will be detailed. They concern polyphenol analysis and protein profiling. The first category is a well-developed quantitative approach important for the quality and the antioxidant properties conferred to wine. The second aspect involves more research aspects dealing with microbiota infections in the vineyard or in the grape as well as enological practices. PMID:27645750

  10. Surface Tension and Capillary Rise

    ERIC Educational Resources Information Center

    Walton, Alan J.

    1972-01-01

    Discussion of the shortcomings of textbook explanations of surface tension, distinguishing between concepts of tension and capillary rise. The arguments require only a clear understanding of Newtonian mechanics, notably potential energy. (DF)

  11. Capillary electrophoresis electrospray ionization mass spectrometry interface

    DOEpatents

    Smith, Richard D.; Severs, Joanne C.

    1999-01-01

    The present invention is an interface between a capillary electrophoresis separation capillary end and an electrospray ionization mass spectrometry emitter capillary end, for transporting an anolyte sample from a capillary electrophoresis separation capillary to a electrospray ionization mass spectrometry emitter capillary. The interface of the present invention has: (a) a charge transfer fitting enclosing both of the capillary electrophoresis capillary end and the electrospray ionization mass spectrometry emitter capillary end; (b) a reservoir containing an electrolyte surrounding the charge transfer fitting; and (c) an electrode immersed into the electrolyte, the electrode closing a capillary electrophoresis circuit and providing charge transfer across the charge transfer fitting while avoiding substantial bulk fluid transfer across the charge transfer fitting. Advantages of the present invention have been demonstrated as effective in providing high sensitivity and efficient analyses.

  12. Design and Integration of an All-Magnetic Attitude Control System for FASTSAT-HSV01's Multiple Pointing Objectives

    NASA Technical Reports Server (NTRS)

    DeKock, Brandon; Sanders, Devon; Vanzwieten, Tannen; Capo-Lugo, Pedro

    2011-01-01

    The FASTSAT-HSV01 spacecraft is a microsatellite with magnetic torque rods as it sole attitude control actuator. FASTSAT s multiple payloads and mission functions require the Attitude Control System (ACS) to maintain Local Vertical Local Horizontal (LVLH)-referenced attitudes without spin-stabilization, while the pointing errors for some attitudes be significantly smaller than the previous best-demonstrated for this type of control system. The mission requires the ACS to hold multiple stable, unstable, and non-equilibrium attitudes, as well as eject a 3U CubeSat from an onboard P-POD and recover from the ensuing tumble. This paper describes the Attitude Control System, the reasons for design choices, how the ACS integrates with the rest of the spacecraft, and gives recommendations for potential future applications of the work.

  13. Multiple Integrated Examinations: An Observational Study of Different Academic Curricula Based on a Business Administration Assessment

    ERIC Educational Resources Information Center

    Ardolino, Piermatteo; Noventa, Stefano; Formicuzzi, Maddalena; Cubico, Serena; Favretto, Giuseppe

    2016-01-01

    An observational study has been carried out to analyse differences in performance between students of different undergraduate curricula in the same written business administration examination, focusing particularly on possible effects of "integrated" or "multi-modular" examinations, a recently widespread format in Italian…

  14. Integration and Testing Challenges of Small, Multiple Satellite Missions: Experiences from the Space Technology 5 Project

    NASA Technical Reports Server (NTRS)

    Sauerwein, Timothy A.; Gostomski, Thomas

    2007-01-01

    The ST5 payload, part of NASA s New Millennium Program headquartered at JPL, consisted of three micro satellites (approx. 30 kg each) deployed into orbit from the Pegasus XL launch. ST5 was a technology demonstration mission, intended to test new technologies for potential use for future missions. In order to meet the launch date schedule of ST 5, a different approach was required rather than the standard I&T approach used for single, room-sized satellites. The I&T phase was planned for spacecraft #1 to undergo integration and test first, followed by spacecraft #2 and #3 in tandem. A team of engineers and technicians planned and executed the integration of all three spacecraft emphasizing versatility and commonality. They increased their knowledge and efficiency through spacecraft #1 integration and testing and utilized their experience and knowledge to safely execute I&T for spacecraft #2 and #3. Each integration team member could perform many different roles and functions and thus better support activities on any of the three spacecraft. The I&T campaign was completed with STS s successful launch on March 22,2006

  15. Comic Relief: Graduate Students Address Multiple Meanings for Technology Integration with Digital Comic Creation

    ERIC Educational Resources Information Center

    Sockman, Beth Rajan; Sutton, Rhonda; Herrmann, Michele

    2016-01-01

    This study determined the usefulness of digital comic creation with 77 graduate students in a teacher technology course. Students completed an assigned reading and created digital comics that addressed technology integration concerns in the schools and society. Using practical action research, 77 student-created comics were analyzed. The findings…

  16. Integration and Testing Challenges of Small, Multiple Satellite Missions: Experiences From The Space Technology 5 Project

    NASA Technical Reports Server (NTRS)

    Sauerwein, Timothy A.; Gostomski, Thomas

    2007-01-01

    This brief presentation describes the mechanical and electrical integration activities and environmental testing challenges of the Space Technology 5 (ST5) Project. Lessons learned during this process are highlighted, including performing mechanical activities serially to gain efficiency through repetition and performing electrical activities based on the level of subsystem expertise available.

  17. Understanding Introductory Students' Application of Integrals in Physics from Multiple Perspectives

    ERIC Educational Resources Information Center

    Hu, Dehui

    2013-01-01

    Calculus is used across many physics topics from introductory to upper-division level college courses. The concepts of differentiation and integration are important tools for solving real world problems. Using calculus or any mathematical tool in physics is much more complex than the straightforward application of the equations and algorithms that…

  18. Integrating Gender on Multiple Levels: A Conceptual Model for Teaching Gender Issues in Family Therapy

    ERIC Educational Resources Information Center

    Williams, Lee; McBain, Heidi

    2006-01-01

    As the field of family therapy has evolved, there has been growing recognition as to the importance of gender in family therapy. To prepare the next generation of family therapists adequately, it is important that they recognize the many and complex ways in which gender permeates their work. In this article we present an integrative model to help…

  19. An integrated modeling approach to support management decisions of coupled groundwater-agricultural systems under multiple uncertainties

    NASA Astrophysics Data System (ADS)

    Hagos Subagadis, Yohannes; Schütze, Niels; Grundmann, Jens

    2015-04-01

    The planning and implementation of effective water resources management strategies need an assessment of multiple (physical, environmental, and socio-economic) issues, and often requires new research in which knowledge of diverse disciplines are combined in a unified methodological and operational frameworks. Such integrative research to link different knowledge domains faces several practical challenges. Such complexities are further compounded by multiple actors frequently with conflicting interests and multiple uncertainties about the consequences of potential management decisions. A fuzzy-stochastic multiple criteria decision analysis tool was developed in this study to systematically quantify both probabilistic and fuzzy uncertainties associated with complex hydrosystems management. It integrated physical process-based models, fuzzy logic, expert involvement and stochastic simulation within a general framework. Subsequently, the proposed new approach is applied to a water-scarce coastal arid region water management problem in northern Oman, where saltwater intrusion into a coastal aquifer due to excessive groundwater extraction for irrigated agriculture has affected the aquifer sustainability, endangering associated socio-economic conditions as well as traditional social structure. Results from the developed method have provided key decision alternatives which can serve as a platform for negotiation and further exploration. In addition, this approach has enabled to systematically quantify both probabilistic and fuzzy uncertainties associated with the decision problem. Sensitivity analysis applied within the developed tool has shown that the decision makers' risk aversion and risk taking attitude may yield in different ranking of decision alternatives. The developed approach can be applied to address the complexities and uncertainties inherent in water resources systems to support management decisions, while serving as a platform for stakeholder participation.

  20. Unexpected inheritance: multiple integrations of ancient bornavirus and ebolavirus/marburgvirus sequences in vertebrate genomes.

    PubMed

    Belyi, Vladimir A; Levine, Arnold J; Skalka, Anna Marie

    2010-01-01

    Vertebrate genomes contain numerous copies of retroviral sequences, acquired over the course of evolution. Until recently they were thought to be the only type of RNA viruses to be so represented, because integration of a DNA copy of their genome is required for their replication. In this study, an extensive sequence comparison was conducted in which 5,666 viral genes from all known non-retroviral families with single-stranded RNA genomes were matched against the germline genomes of 48 vertebrate species, to determine if such viruses could also contribute to the vertebrate genetic heritage. In 19 of the tested vertebrate species, we discovered as many as 80 high-confidence examples of genomic DNA sequences that appear to be derived, as long ago as 40 million years, from ancestral members of 4 currently circulating virus families with single strand RNA genomes. Surprisingly, almost all of the sequences are related to only two families in the Order Mononegavirales: the Bornaviruses and the Filoviruses, which cause lethal neurological disease and hemorrhagic fevers, respectively. Based on signature landmarks some, and perhaps all, of the endogenous virus-like DNA sequences appear to be LINE element-facilitated integrations derived from viral mRNAs. The integrations represent genes that encode viral nucleocapsid, RNA-dependent-RNA-polymerase, matrix and, possibly, glycoproteins. Integrations are generally limited to one or very few copies of a related viral gene per species, suggesting that once the initial germline integration was obtained (or selected), later integrations failed or provided little advantage to the host. The conservation of relatively long open reading frames for several of the endogenous sequences, the virus-like protein regions represented, and a potential correlation between their presence and a species' resistance to the diseases caused by these pathogens, are consistent with the notion that their products provide some important biological

  1. Integrating multiple health behavior theories into program planning: the PER worksheet.

    PubMed

    Langlois, Marietta A; Hallam, Jeffrey S

    2010-03-01

    The foundation of a logic model or any theory-based planning model is the identification of the behavioral antecedents and the relationship of these variables to the target behavior. Applying theoretical concepts to specific behaviors and populations is often challenging for practitioners and program planning students. The challenge comes from the abstract definition of theoretical constructs, the duplication of similar constructs in multiple theories, and the need to combine multiple theories. To simplify the planning process when utilizing logic models and health behavior theory, we recommend the use of the PER Worksheet. The PER Worksheet is a planning tool that provides layman-term prompts for identifying health behavior antecedents. It encompasses five common health behavior theories-health belief model, theory of planned behavior, social cognitive theory, an ecological perspective, and transtheoretical model. The PER Worksheet is organized into three columns: Predisposing, Enabling, and Reinforcing factors, terms of the PRECEDE/PROCEED model.

  2. Integration of multiple PCR amplification and DNA mutation analyses by using oligonucleotide microchip.

    SciTech Connect

    Tillib, S. V.; Strizhkov, B. N.; Mirzabekov, A. D.; Biochip Technology Center; Russian Academy of Sciences

    2001-05-01

    We have developed a method for parallel independent on-chip amplification and the following sequence variation analysis of multiple DNA regions directly using microchip with an array of nanoliter gel pads containing specific sets of tethered primers. The method has three key features. First, DNA to be amplified is enriched at gel pads by its hybridization with immobilized primers. Second, different sets of specific primers are immobilized within various gel pads, and primers are detached within gel pads just before polymerase chain reaction to enhance the amplification. A gel pad may contain an additional permanently immobilized dormant primer that is activated to carry out the allele-specific primer extension reaction to detect mutations. Third, multiple polymerase chain reactions are confined within nanoliter gel pads covered and separated from each other with mineral oil. The method was applied to simultaneously identify several abundant drug-resistant mutations in three genes of Mycobacterium tuberculosis.

  3. Multiple abiotic stimuli are integrated in the regulation of rice gene expression under field conditions.

    PubMed

    Plessis, Anne; Hafemeister, Christoph; Wilkins, Olivia; Gonzaga, Zennia Jean; Meyer, Rachel Sarah; Pires, Inês; Müller, Christian; Septiningsih, Endang M; Bonneau, Richard; Purugganan, Michael

    2015-01-01

    Plants rely on transcriptional dynamics to respond to multiple climatic fluctuations and contexts in nature. We analyzed the genome-wide gene expression patterns of rice (Oryza sativa) growing in rainfed and irrigated fields during two distinct tropical seasons and determined simple linear models that relate transcriptomic variation to climatic fluctuations. These models combine multiple environmental parameters to account for patterns of expression in the field of co-expressed gene clusters. We examined the similarities of our environmental models between tropical and temperate field conditions, using previously published data. We found that field type and macroclimate had broad impacts on transcriptional responses to environmental fluctuations, especially for genes involved in photosynthesis and development. Nevertheless, variation in solar radiation and temperature at the timescale of hours had reproducible effects across environmental contexts. These results provide a basis for broad-based predictive modeling of plant gene expression in the field. PMID:26609814

  4. Tuning cell migration: contractility as an integrator of intracellular signals from multiple cues

    PubMed Central

    Bordeleau, Francois; Reinhart-King, Cynthia A.

    2016-01-01

    There has been immense progress in our understanding of the factors driving cell migration in both two-dimensional and three-dimensional microenvironments over the years. However, it is becoming increasingly evident that even though most cells share many of the same signaling molecules, they rarely respond in the same way to migration cues. To add to the complexity, cells are generally exposed to multiple cues simultaneously, in the form of growth factors and/or physical cues from the matrix. Understanding the mechanisms that modulate the intracellular signals triggered by multiple cues remains a challenge. Here, we will focus on the molecular mechanism involved in modulating cell migration, with a specific focus on how cell contractility can mediate the crosstalk between signaling initiated at cell-matrix adhesions and growth factor receptors. PMID:27508074

  5. Multi-model inference in comparative phylogeography: an integrative approach based on multiple lines of evidence

    PubMed Central

    Collevatti, Rosane G.; Terribile, Levi C.; Diniz-Filho, José A. F.; Lima-Ribeiro, Matheus S.

    2015-01-01

    Comparative phylogeography has its roots in classical biogeography and, historically, relies on a pattern-based approach. Here, we present a model-based framework for comparative phylogeography. Our framework was initially developed for statistical phylogeography based on a multi-model inference approach, by coupling ecological niche modeling, coalescent simulation and direct spatio-temporal reconstruction of lineage diffusion using a relaxed random walk model. This multi-model inference framework is particularly useful to investigate the complex dynamics and current patterns in genetic diversity in response to processes operating on multiple taxonomic levels in comparative phylogeography. In addition, because of the lack, or incompleteness of fossil record, the understanding of the role of biogeographical events (vicariance and dispersal routes) in most regions worldwide is barely known. Thus, we believe that the expansion of that framework for multiple species under a comparative approach may give clues on genetic legacies in response to Quaternary climate changes and other biogeographical processes. PMID:25741360

  6. Multi-model inference in comparative phylogeography: an integrative approach based on multiple lines of evidence.

    PubMed

    Collevatti, Rosane G; Terribile, Levi C; Diniz-Filho, José A F; Lima-Ribeiro, Matheus S

    2015-01-01

    Comparative phylogeography has its roots in classical biogeography and, historically, relies on a pattern-based approach. Here, we present a model-based framework for comparative phylogeography. Our framework was initially developed for statistical phylogeography based on a multi-model inference approach, by coupling ecological niche modeling, coalescent simulation and direct spatio-temporal reconstruction of lineage diffusion using a relaxed random walk model. This multi-model inference framework is particularly useful to investigate the complex dynamics and current patterns in genetic diversity in response to processes operating on multiple taxonomic levels in comparative phylogeography. In addition, because of the lack, or incompleteness of fossil record, the understanding of the role of biogeographical events (vicariance and dispersal routes) in most regions worldwide is barely known. Thus, we believe that the expansion of that framework for multiple species under a comparative approach may give clues on genetic legacies in response to Quaternary climate changes and other biogeographical processes. PMID:25741360

  7. Simulating multiple diffraction in imaging systems using a path integration method.

    PubMed

    Mout, Marco; Wick, Michael; Bociort, Florian; Petschulat, Jörg; Urbach, Paul

    2016-05-10

    We present a method for simulating multiple diffraction in imaging systems based on the Huygens-Fresnel principle. The method accounts for the effects of both aberrations and diffraction and is entirely performed using Monte Carlo ray tracing. We compare the results of this method to those of reference simulations for field propagation through optical systems and for the calculation of point spread functions. The method can accurately model a wide variety of optical systems beyond the exit pupil approximation. PMID:27168302

  8. 'Unite and conquer': enhanced prediction of protein subcellular localization by integrating multiple specialized tools

    PubMed Central

    Shen, Yao Qing; Burger, Gertraud

    2007-01-01

    Background Knowing the subcellular location of proteins provides clues to their function as well as the interconnectivity of biological processes. Dozens of tools are available for predicting protein location in the eukaryotic cell. Each tool performs well on certain data sets, but their predictions often disagree for a given protein. Since the individual tools each have particular strengths, we set out to integrate them in a way that optimally exploits their potential. The method we present here is applicable to various subcellular locations, but tailored for predicting whether or not a protein is localized in mitochondria. Knowledge of the mitochondrial proteome is relevant to understanding the role of this organelle in global cellular processes. Results In order to develop a method for enhanced prediction of subcellular localization, we integrated the outputs of available localization prediction tools by several strategies, and tested the performance of each strategy with known mitochondrial proteins. The accuracy obtained (up to 92%) surpasses by far the individual tools. The method of integration proved crucial to the performance. For the prediction of mitochondrion-located proteins, integration via a two-layer decision tree clearly outperforms simpler methods, as it allows emphasis of biologically relevant features such as the mitochondrial targeting peptide and transmembrane domains. Conclusion We developed an approach that enhances the prediction accuracy of mitochondrial proteins by uniting the strength of specialized tools. The combination of machine-learning based integration with biological expert knowledge leads to improved performance. This approach also alleviates the conundrum of how to choose between conflicting predictions. Our approach is easy to implement, and applicable to predicting subcellular locations other than mitochondria, as well as other biological features. For a trial of our approach, we provide a webservice for mitochondrial protein

  9. Integrated Model of Multiple Kernel Learning and Differential Evolution for EUR/USD Trading

    PubMed Central

    Deng, Shangkun; Sakurai, Akito

    2014-01-01

    Currency trading is an important area for individual investors, government policy decisions, and organization investments. In this study, we propose a hybrid approach referred to as MKL-DE, which combines multiple kernel learning (MKL) with differential evolution (DE) for trading a currency pair. MKL is used to learn a model that predicts changes in the target currency pair, whereas DE is used to generate the buy and sell signals for the target currency pair based on the relative strength index (RSI), while it is also combined with MKL as a trading signal. The new hybrid implementation is applied to EUR/USD trading, which is the most traded foreign exchange (FX) currency pair. MKL is essential for utilizing information from multiple information sources and DE is essential for formulating a trading rule based on a mixture of discrete structures and continuous parameters. Initially, the prediction model optimized by MKL predicts the returns based on a technical indicator called the moving average convergence and divergence. Next, a combined trading signal is optimized by DE using the inputs from the prediction model and technical indicator RSI obtained from multiple timeframes. The experimental results showed that trading using the prediction learned by MKL yielded consistent profits. PMID:25097891

  10. The dynamics of capillary-driven two-phase flow: the role of nanofluid structural forces.

    PubMed

    Nikolov, Alex; Zhang, Hua

    2015-07-01

    Capillary-driven flows are fundamental phenomena and are involved in many key technological processes, such as oil recovery through porous rocks, ink-jet printing, the bubble dynamics in a capillary, microfluidic devices and labs on chips. Here, we discuss and propose a model for the oil displacement dynamics from the capillary by the nanofluid (which is composed of a liquid suspension of nanoparticles); we elucidate the physics of the novelty of the phenomenon and its application. The oil displacement by the nanofluid flow is a multi-stage phenomenon, first leading to the oil film formation on the capillary wall, its break-up, and retraction over the capillary wall; this lead to the formation of the oil double concave meniscus. With time, the process repeats itself, leading to the formation of a regular "necklace" of oil droplets inside the capillary. Finally, the oil droplets are separated by the nanofluid film from the capillary wall. The light reflected differential interferometry technique is applied to investigate the nanofluid interactions with the glass wall. We find nanoparticles tend to self-structure into multiple layers close to the solid wall, which cause the structural forces to arise that lead to the oil displacement from the capillary. This research is expected to benefit the understanding of nanofluid phenomena in a capillary and promote their use in technological applications. PMID:25465201

  11. Curating and Integrating Data from Multiple Sources to Support Healthcare Analytics.

    PubMed

    Ng, Kenney; Kakkanatt, Chris; Benigno, Michael; Thompson, Clay; Jackson, Margaret; Cahan, Amos; Zhu, Xinxin; Zhang, Ping; Huang, Paul

    2015-01-01

    As the volume and variety of healthcare related data continues to grow, the analysis and use of this data will increasingly depend on the ability to appropriately collect, curate and integrate disparate data from many different sources. We describe our approach to and highlight our experiences with the development of a robust data collection, curation and integration infrastructure that supports healthcare analytics. This system has been successfully applied to the processing of a variety of data types including clinical data from electronic health records and observational studies, genomic data, microbiomic data, self-reported data from surveys and self-tracked data from wearable devices from over 600 subjects. The curated data is currently being used to support healthcare analytic applications such as data visualization, patient stratification and predictive modeling. PMID:26262355

  12. Curating and Integrating Data from Multiple Sources to Support Healthcare Analytics.

    PubMed

    Ng, Kenney; Kakkanatt, Chris; Benigno, Michael; Thompson, Clay; Jackson, Margaret; Cahan, Amos; Zhu, Xinxin; Zhang, Ping; Huang, Paul

    2015-01-01

    As the volume and variety of healthcare related data continues to grow, the analysis and use of this data will increasingly depend on the ability to appropriately collect, curate and integrate disparate data from many different sources. We describe our approach to and highlight our experiences with the development of a robust data collection, curation and integration infrastructure that supports healthcare analytics. This system has been successfully applied to the processing of a variety of data types including clinical data from electronic health records and observational studies, genomic data, microbiomic data, self-reported data from surveys and self-tracked data from wearable devices from over 600 subjects. The curated data is currently being used to support healthcare analytic applications such as data visualization, patient stratification and predictive modeling.

  13. A Case Study in Integrating Multiple E-commerce Standards via Semantic Web Technology

    NASA Astrophysics Data System (ADS)

    Yu, Yang; Hillman, Donald; Setio, Basuki; Heflin, Jeff

    Internet business-to-business transactions present great challenges in merging information from different sources. In this paper we describe a project to integrate four representative commercial classification systems with the Federal Cataloging System (FCS). The FCS is used by the US Defense Logistics Agency to name, describe and classify all items under inventory control by the DoD. Our approach uses the ECCMA Open Technical Dictionary (eOTD) as a common vocabulary to accommodate all different classifications. We create a semantic bridging ontology between each classification and the eOTD to describe their logical relationships in OWL DL. The essential idea is that since each classification has formal definitions in a common vocabulary, we can use subsumption to automatically integrate them, thus mitigating the need for pairwise mappings. Furthermore our system provides an interactive interface to let users choose and browse the results and more importantly it can translate catalogs that commit to these classifications using compiled mapping results.

  14. ICOMFLO2. Two-Dimensional Integral Combustion for Multiple Phase Flow

    SciTech Connect

    S.L. Chang; S. Lottes

    1990-05-01

    This ANL multiphase two-dimensional combustion computer code solves conservation equations for gaseous species and solid particles (or droplets) of various sizes. General conservation laws, expressed by ellipitic-type partial differential equations are used in conjunction with rate equations governing the mass, momentum, enthaply, species, turbulent kinetic energy, and turbulent dissipation for a two-phase reacting flow. Associated submodels include an integral combustion, a two-parameter turbulence, a particle evaporation, and interfacial submodels. A newly-developed integral combustion submodel replacing an Arrhenius-type differential reaction submodel is implemented to improve numerical convergence and enhance numerical stability. The two-parameter turbulence submodel is modified for both gas and solid phases. The evaporation submodel treats size dispersion as well as particle evaporation. Interfacial submodels use correlations to model interfacial momentum and energy transfer.

  15. Microfluidic flow counterbalanced capillary electrophoresis.

    PubMed

    Xia, Ling; Dutta, Debashis

    2013-04-01

    Flow counterbalanced capillary electrophoresis (FCCE) offers a powerful approach to realizing difficult charge based separations in compact microchip devices with application of relatively small electrical voltages. The need for dynamically controlling the pressure-gradient in the FCCE column however presents a significant challenge in implementing this technique on the microchip platform. In this article, we report the use of a simple on-chip pumping unit that allows precise introduction of a periodic pressure-driven backflow into a microfluidic separation channel enabling an FCCE analysis. The backflow in our device was produced by fabricating a shallow segment (0.5 μm deep) downstream of the analysis column (5 μm deep) and applying an electric field across it. A mismatch in the electroosmotic transport rate at the interface of this segment was shown to yield a pressure-gradient that could reverse the flow of the analyte bands without inverting the direction of the electric field. Although such a pressure-gradient also led to additional band broadening in the system, overall, the separation resolution of our device was observed to improve with an increasing number of back-and-forth sample passes through the analysis channel. For our current design, the corresponding improvement in the effective separation length was as much as 52% of the actual distance travelled by the chosen FITC-labeled amino acid samples. The reported device is well suited for further miniaturization of the FCCE method to the nanofluidic length scale which likely would improve its performance, and is easily integrable to other analytical procedures on the microchip platform for lab-on-a-chip applications. PMID:23420375

  16. Identification of Genes for Complex Diseases by Integrating Multiple Types of Genomic Data

    PubMed Central

    Cao, Hongbao; Lei, Shufeng; Deng, Hong-Wen; Wang, Yu-Ping

    2014-01-01

    Combining multi-type of genomic data for integrative analyses can take advantage of complementary information and thus can have higher power to identify genes/variables that would otherwise be impossible with individual data analysis. Here we proposed a sparse representation based clustering (SRC) method for integrative data analyses, and applied to the analysis of 376821 SNPs in 200 subjects (100 cases and 100 controls) and expression data for 22283 genes in 80 subjects (40 cases and 40 controls) to identify significant genes for osteoporosis (OP). Comparing our results with previous studies, we identified some genes known related to OP risk, as well as some uncovered novel osteoporosis susceptible genes (‘DICER1’, ‘PTMA’, etc.) that may function importantly in osteoporosis etiology. In addition, the identified genes can lead to higher accuracy for the identification of osteoporosis subjects when compared with the traditional T-test and Fisher-exact test, which further validate the proposed SRC approach for integrative analysis. PMID:23367184

  17. Integration of Multiple Components in Polystyrene-based Microfluidic Devices Part 1: Fabrication and Characterization

    PubMed Central

    Johnson, Alicia S.; Anderson, Kari B.; Halpin, Stephen T.; Kirkpatrick, Douglas C.; Spence, Dana M.; Martin, R. Scott

    2012-01-01

    In Part I of a two-part series, we describe a simple, and inexpensive approach to fabricate polystyrene devices that is based upon melting polystyrene (from either a Petri dish or powder form) against PDMS molds or around electrode materials. The ability to incorporate microchannels in polystyrene and integrate the resulting device with standard laboratory equipment such as an optical plate reader for analyte readout and micropipettors for fluid propulsion is first described. A simple approach for sample and reagent delivery to the device channels using a standard, multi-channel micropipette and a PDMS-based injection block is detailed. Integration of the microfluidic device with these off-chip functions (sample delivery and readout) enables high throughput screens and analyses. An approach to fabricate polystyrene-based devices with embedded electrodes is also demonstrated, thereby enabling the integration of microchip electrophoresis with electrochemical detection through the use of a palladium electrode (for a decoupler) and carbon-fiber bundle (for detection). The device was sealed against a PDMS-based microchannel and used for the electrophoretic separation and amperometric detection of dopamine, epinephrine, catechol, and 3,4-dihydroxyphenylacetic acid. Finally, these devices were compared against PDMS-based microchips in terms of their optical transparency and absorption of an anti-platelet drug, clopidogrel. Part I of this series lays the foundation for Part II, where these devices were utilized for various on-chip cellular analysis. PMID:23120747

  18. Integration of multiple land surface models into NASA's Carbon Monitoring System

    NASA Astrophysics Data System (ADS)

    Sikka, M.; Fisher, J. B.; Schwalm, C. R.; Liu, J.; Bowman, K. W.; Huntzinger, D. N.

    2013-12-01

    NASA's Carbon Monitoring System Flux (CMS-Flux) integrates NASA remote sensing and modeling capabilities with emphasis on CO2 fluxes between the land (incl. fossil fuel), ocean, and atmosphere. CMS-Flux is distinguished by two foci: cross-component expertise, and exploitation of new global satellite observations of atmospheric CO2 (XCO2) from JAXA's GOSAT and NASA's imminent OCO-2. Critical objectives of CMS-Flux include the spatiotemporal representation of flux uncertainty within the carbon cycle and the assessment of where the integration of remote sensing carbon data across components can reduce that uncertainty. One of the largest uncertainties in the global carbon cycle is from the terrestrial biosphere, and we asked how atmospheric CO2 observations can constrain terrestrial biosphere carbon flux estimates. To address this, we provided the CMS-Flux atmospheric inversion model (which is driven by XCO2) with terrestrial biosphere flux estimates using 10 process models from the Multi-Scale Synthesis and Terrestrial Model Intercomparison Project (MsTMIP) as a prior estimate of land flux. We show here the system of integrating the benchmark-weighted multi-model mean and variability of MsTMIP land models into the atmospheric system, and present results on how coupling these two cutting-edge land and atmospheric components reduces uncertainty in the global carbon cycle.

  19. Towards a Better Understanding of CMMI and Agile Integration - Multiple Case Study of Four Companies

    NASA Astrophysics Data System (ADS)

    Pikkarainen, Minna

    The amount of software is increasing in the different domains in Europe. This provides the industries in smaller countries good opportunities to work in the international markets. Success in the global markets however demands the rapid production of high quality, error free software. Both CMMI and agile methods seem to provide a ready solution for quality and lead time improvements. There is not, however, much empirical evidence available either about 1) how the integration of these two aspects can be done in practice or 2) what it actually demands from assessors and software process improvement groups. The goal of this paper is to increase the understanding of CMMI and agile integration, in particular, focusing on the research question: how to use ‘lightweight’ style of CMMI assessments in agile contexts. This is done via four case studies in which assessments were conducted using the goals of CMMI integrated project management and collaboration and coordination with relevant stakeholder process areas and practices from XP and Scrum. The study shows that the use of agile practices may support the fulfilment of the goals of CMMI process areas but there are still many challenges for the agile teams to be solved within the continuous improvement programs. It also identifies practical advices to the assessors and improvement groups to take into consideration when conducting assessment in the context of agile software development.

  20. Microsystem capillary separations

    DOEpatents

    TeGrotenhuis, Ward E [Kennewick, WA; Wegeng, Robert S [Richland, WA; Whyatt, Greg A [West Richland, WA; Stenkamp, Victoria S [Richland, WA; Gauglitz, Phillip A [Richland, WA

    2003-12-23

    Laminated, multiphase separators and contactors having wicking structures and gas flow channels are described. Some preferred embodiments are combined with microchannel heat exchange. Integrated systems containing these components are also part of the present invention.

  1. Curvature capillary migration of microspheres.

    PubMed

    Sharifi-Mood, Nima; Liu, Iris B; Stebe, Kathleen J

    2015-09-14

    We address the question: how does capillarity propel microspheres along curvature gradients? For a particle on a fluid interface, there are two conditions that can apply at the three phase contact line: either the contact line adopts an equilibrium contact angle, or it can be pinned by kinetic trapping, e.g. at chemical heterogeneities, asperities, or other pinning sites on the particle surface. We formulate the curvature capillary energy for both scenarios for particles smaller than the capillary length and far from any pinning boundaries. The scale and range of the distortion made by the particle are set by the particle radius; we use singular perturbation methods to find the distortions and to rigorously evaluate the associated capillary energies. For particles with equilibrium contact angles, contrary to the literature, we find that the capillary energy is negligible, with the first contribution bounded to fourth order in the product of the particle radius and the deviatoric curvature of the host interface. For pinned contact lines, we find curvature capillary energies that are finite, with a functional form investigated previously by us for disks and microcylinders on curved interfaces. In experiments, we show microspheres migrate along deterministic trajectories toward regions of maximum deviatoric curvature with curvature capillary energies ranging from 6 × 10(3)-5 × 10(4)kBT. These data agree with the curvature capillary energy for the case of pinned contact lines. The underlying physics of this migration is a coupling of the interface deviatoric curvature with the quadrupolar mode of nanometric disturbances in the interface owing to the particle's contact line undulations. This work is an example of the major implications of nanometric roughness and contact line pinning for colloidal dynamics.

  2. On the performance of capillary barriers as landfill cover

    NASA Astrophysics Data System (ADS)

    Kämpf, M.; Montenegro, H.

    Landfills and waste heaps require an engineered surface cover upon closure. The capping system can vary from a simple soil cover to multiple layers of earth and geosynthetic materials. Conventional design features a compacted soil layer, which suffers from drying out and cracking, as well as root and animal intrusion. Capillary barriers consisting of inclined fine-over-coarse soil layers are investigated as an alternative cover system. Under unsaturated conditions, the textural contrast delays vertical drainage by capillary forces. The moisture that builds up above the contact will flow downdip along the interface of the layers. Theoretical studies of capillary barriers have identified the hydraulic properties of the layers, the inclination angle, the length of the field and the infiltration rate as the fundamental characteristics of the system. However, it is unclear how these findings can lead to design criteria for capillary barriers. To assess the uncertainty involved in such approaches, experiments have been carried out in a 8 m long flume and on large scale test sites (40 m x 15 m). In addition, the ability of a numerical model to represent the relevant flow processes in capillary barriers has been examined.

  3. FDRAnalysis: a tool for the integrated analysis of tandem mass spectrometry identification results from multiple search engines.

    PubMed

    Wedge, David C; Krishna, Ritesh; Blackhurst, Paul; Siepen, Jennifer A; Jones, Andrew R; Hubbard, Simon J

    2011-04-01

    Confident identification of peptides via tandem mass spectrometry underpins modern high-throughput proteomics. This has motivated considerable recent interest in the postprocessing of search engine results to increase confidence and calculate robust statistical measures, for example through the use of decoy databases to calculate false discovery rates (FDR). FDR-based analyses allow for multiple testing and can assign a single confidence value for both sets and individual peptide spectrum matches (PSMs). We recently developed an algorithm for combining the results from multiple search engines, integrating FDRs for sets of PSMs made by different search engine combinations. Here we describe a web-server and a downloadable application that makes this routinely available to the proteomics community. The web server offers a range of outputs including informative graphics to assess the confidence of the PSMs and any potential biases. The underlying pipeline also provides a basic protein inference step, integrating PSMs into protein ambiguity groups where peptides can be matched to more than one protein. Importantly, we have also implemented full support for the mzIdentML data standard, recently released by the Proteomics Standards Initiative, providing users with the ability to convert native formats to mzIdentML files, which are available to download.

  4. The effect of training image and secondary data integration with multiple-point geostatistics in groundwater modelling

    NASA Astrophysics Data System (ADS)

    He, X. L.; Sonnenborg, T. O.; Jørgensen, F.; Jensen, K. H.

    2014-08-01

    Multiple-point geostatistical simulation (MPS) has recently become popular in stochastic hydrogeology, primarily because of its capability to derive multivariate distributions from a training image (TI). However, its application in three-dimensional (3-D) simulations has been constrained by the difficulty of constructing a 3-D TI. The object-based unconditional simulation program TiGenerator may be a useful tool in this regard; yet the applicability of such parametric training images has not been documented in detail. Another issue in MPS is the integration of multiple geophysical data. The proper way to retrieve and incorporate information from high-resolution geophysical data is still under discussion. In this study, MPS simulation was applied to different scenarios regarding the TI and soft conditioning. By comparing their output from simulations of groundwater flow and probabilistic capture zone, TI from both sources (directly converted from high-resolution geophysical data and generated by TiGenerator) yields comparable results, even for the probabilistic capture zones, which are highly sensitive to the geological architecture. This study also suggests that soft conditioning in MPS is a convenient and efficient way of integrating secondary data such as 3-D airborne electromagnetic data (SkyTEM), but over-conditioning has to be avoided.

  5. The effect of training image and secondary data integration with multiple-point geostatistics in groundwater modeling

    NASA Astrophysics Data System (ADS)

    He, X.; Sonnenborg, T. O.; Jørgensen, F.; Jensen, K. H.

    2013-09-01

    Multiple-point geostatistic simulation (MPS) has recently become popular in stochastic hydrogeology, primarily because of its capability to derive multivariate distributions from the training image (TI). However, its application in three dimensional simulations has been constrained by the difficulty of constructing 3-D TI. The object-based TiGenerator may be a useful tool in this regard; yet the sensitivity of model predictions to the training image has not been documented. Another issue in MPS is the integration of multiple geophysical data. The best way to retrieve and incorporate information from high resolution geophysical data is still under discussion. This work shows that TI from TiGenerator delivers acceptable results when used for groundwater modeling, although the TI directly converted from high resolution geophysical data leads to better simulation. The model results also indicate that soft conditioning in MPS is a convenient and efficient way of integrating secondary data such as 3-D airborne electromagnetic data, but over conditioning has to be avoided.

  6. Integrating multiple disturbance aspects: management of an invasive thistle, Carduus nutans

    PubMed Central

    Zhang, Rui; Shea, Katriona

    2012-01-01

    Background and Aims Disturbances occur in most ecological systems, and play an important role in biological invasions. We delimit five key disturbance aspects: intensity, frequency, timing, duration and extent. Few studies address more than one of these aspects, yet interactions and interdependence between aspects may lead to complex outcomes. Methods In a two-cohort experimental study, we examined how multiple aspects (intensity, frequency and timing) of a mowing disturbance regime affect the survival, phenology, growth and reproduction of an invasive thistle Carduus nutans (musk thistle). Key Results Our results show that high intensity and late timing strongly delay flowering phenology and reduce plant survival, capitulum production and plant height. A significant interaction between intensity and timing further magnifies the main effects. Unexpectedly, high frequency alone did not effectively reduce reproduction. However, a study examining only frequency and intensity, and not timing, would have erroneously attributed the importance of timing to frequency. Conclusions We used management of an invasive species as an example to demonstrate the importance of a multiple-aspect disturbance framework. Failure to consider possible interactions, and the inherent interdependence of certain aspects, could result in misinterpretation and inappropriate management efforts. This framework can be broadly applied to improve our understanding of disturbance effects on individual responses, population dynamics and community composition. PMID:22199031

  7. Hybrid MCDA Methods to Integrate Multiple Ecosystem Services in Forest Management Planning: A Critical Review

    NASA Astrophysics Data System (ADS)

    Uhde, Britta; Andreas Hahn, W.; Griess, Verena C.; Knoke, Thomas

    2015-08-01

    Multi-criteria decision analysis (MCDA) is a decision aid frequently used in the field of forest management planning. It includes the evaluation of multiple criteria such as the production of timber and non-timber forest products and tangible as well as intangible values of ecosystem services (ES). Hence, it is beneficial compared to those methods that take a purely financial perspective. Accordingly, MCDA methods are increasingly popular in the wide field of sustainability assessment. Hybrid approaches allow aggregating MCDA and, potentially, other decision-making techniques to make use of their individual benefits and leading to a more holistic view of the actual consequences that come with certain decisions. This review is providing a comprehensive overview of hybrid approaches that are used in forest management planning. Today, the scientific world is facing increasing challenges regarding the evaluation of ES and the trade-offs between them, for example between provisioning and regulating services. As the preferences of multiple stakeholders are essential to improve the decision process in multi-purpose forestry, participatory and hybrid approaches turn out to be of particular importance. Accordingly, hybrid methods show great potential for becoming most relevant in future decision making. Based on the review presented here, the development of models for the use in planning processes should focus on participatory modeling and the consideration of uncertainty regarding available information.

  8. SoftSearch: Integration of Multiple Sequence Features to Identify Breakpoints of Structural Variations

    PubMed Central

    Hart, Steven N.; Sarangi, Vivekananda; Moore, Raymond; Baheti, Saurabh; Bhavsar, Jaysheel D.; Couch, Fergus J.; Kocher, Jean-Pierre A.

    2013-01-01

    Background Structural variation (SV) represents a significant, yet poorly understood contribution to an individual’s genetic makeup. Advanced next-generation sequencing technologies are widely used to discover such variations, but there is no single detection tool that is considered a community standard. In an attempt to fulfil this need, we developed an algorithm, SoftSearch, for discovering structural variant breakpoints in Illumina paired-end next-generation sequencing data. SoftSearch combines multiple strategies for detecting SV including split-read, discordant read-pair, and unmated pairs. Co-localized split-reads and discordant read pairs are used to refine the breakpoints. Results We developed and validated SoftSearch using real and synthetic datasets. SoftSearch’s key features are 1) not requiring secondary (or exhaustive primary) alignment, 2) portability into established sequencing workflows, and 3) is applicable to any DNA-sequencing experiment (e.g. whole genome, exome, custom capture, etc.). SoftSearch identifies breakpoints from a small number of soft-clipped bases from split reads and a few discordant read-pairs which on their own would not be sufficient to make an SV call. Conclusions We show that SoftSearch can identify more true SVs by combining multiple sequence features. SoftSearch was able to call clinically relevant SVs in the BRCA2 gene not reported by other tools while offering significantly improved overall performance. PMID:24358278

  9. Multiple abiotic stimuli are integrated in the regulation of rice gene expression under field conditions

    PubMed Central

    Plessis, Anne; Hafemeister, Christoph; Wilkins, Olivia; Gonzaga, Zennia Jean; Meyer, Rachel Sarah; Pires, Inês; Müller, Christian; Septiningsih, Endang M; Bonneau, Richard; Purugganan, Michael

    2015-01-01

    Plants rely on transcriptional dynamics to respond to multiple climatic fluctuations and contexts in nature. We analyzed the genome-wide gene expression patterns of rice (Oryza sativa) growing in rainfed and irrigated fields during two distinct tropical seasons and determined simple linear models that relate transcriptomic variation to climatic fluctuations. These models combine multiple environmental parameters to account for patterns of expression in the field of co-expressed gene clusters. We examined the similarities of our environmental models between tropical and temperate field conditions, using previously published data. We found that field type and macroclimate had broad impacts on transcriptional responses to environmental fluctuations, especially for genes involved in photosynthesis and development. Nevertheless, variation in solar radiation and temperature at the timescale of hours had reproducible effects across environmental contexts. These results provide a basis for broad-based predictive modeling of plant gene expression in the field. DOI: http://dx.doi.org/10.7554/eLife.08411.001 PMID:26609814

  10. Carotenoid-based bill colour is an integrative signal of multiple parasite infection in blackbird

    NASA Astrophysics Data System (ADS)

    Biard, Clotilde; Saulnier, Nicolas; Gaillard, Maria; Moreau, Jérôme

    2010-11-01

    In the study of parasite-mediated sexual selection, there has been controversial evidence for the prediction that brighter males should have fewer parasites. Most of these studies have focused on one parasite species. Our aim was to investigate the expression of carotenoid-based coloured signals in relation to patterns of multiple parasite infections, to determine whether colour reflects parasite load of all parasite species, or whether different relationships might be found when looking at each parasite species independently. We investigated the relationship between bill colour, body mass and plasma carotenoids and parasite load (feather chewing lice, blood parasite Plasmodium sp., intestinal parasites cestodes and coccidia) in the blackbird ( Turdus merula). Bill colour on its own appeared to be a poor predictor of parasite load when investigating its relationships with individual parasite species. Variation in parasite intensities at the community level was summarised using principal component analysis to derive synthetic indexes of relative parasite species abundance and absolute parasite load. The relative abundance of parasite species was strongly related to bill colour, plasma carotenoid levels and body mass: birds with relatively more cestodes and chewing lice and relatively less Plasmodium and coccidia had a more colourful bill, circulated more carotenoids and were heavier. These results suggest that bill colour more accurately reflects the relative intensities of parasite infection, rather than one-by-one relationships with parasites or absolute parasite burden. Investigating patterns of multiple parasite infection would thus improve our understanding of the information conveyed by coloured signals on parasite load.

  11. Hybrid MCDA Methods to Integrate Multiple Ecosystem Services in Forest Management Planning: A Critical Review.

    PubMed

    Uhde, Britta; Hahn, W Andreas; Griess, Verena C; Knoke, Thomas

    2015-08-01

    Multi-criteria decision analysis (MCDA) is a decision aid frequently used in the field of forest management planning. It includes the evaluation of multiple criteria such as the production of timber and non-timber forest products and tangible as well as intangible values of ecosystem services (ES). Hence, it is beneficial compared to those methods that take a purely financial perspective. Accordingly, MCDA methods are increasingly popular in the wide field of sustainability assessment. Hybrid approaches allow aggregating MCDA and, potentially, other decision-making techniques to make use of their individual benefits and leading to a more holistic view of the actual consequences that come with certain decisions. This review is providing a comprehensive overview of hybrid approaches that are used in forest management planning. Today, the scientific world is facing increasing challenges regarding the evaluation of ES and the trade-offs between them, for example between provisioning and regulating services. As the preferences of multiple stakeholders are essential to improve the decision process in multi-purpose forestry, participatory and hybrid approaches turn out to be of particular importance. Accordingly, hybrid methods show great potential for becoming most relevant in future decision making. Based on the review presented here, the development of models for the use in planning processes should focus on participatory modeling and the consideration of uncertainty regarding available information.

  12. Integrative analysis of multiple diverse omics datasets by sparse group multitask regression.

    PubMed

    Lin, Dongdong; Zhang, Jigang; Li, Jingyao; He, Hao; Deng, Hong-Wen; Wang, Yu-Ping

    2014-01-01

    A variety of high throughput genome-wide assays enable the exploration of genetic risk factors underlying complex traits. Although these studies have remarkable impact on identifying susceptible biomarkers, they suffer from issues such as limited sample size and low reproducibility. Combining individual studies of different genetic levels/platforms has the promise to improve the power and consistency of biomarker identification. In this paper, we propose a novel integrative method, namely sparse group multitask regression, for integrating diverse omics datasets, platforms, and populations to identify risk genes/factors of complex diseases. This method combines multitask learning with sparse group regularization, which will: (1) treat the biomarker identification in each single study as a task and then combine them by multitask learning; (2) group variables from all studies for identifying significant genes; (3) enforce sparse constraint on groups of variables to overcome the "small sample, but large variables" problem. We introduce two sparse group penalties: sparse group lasso and sparse group ridge in our multitask model, and provide an effective algorithm for each model. In addition, we propose a significance test for the identification of potential risk genes. Two simulation studies are performed to evaluate the performance of our integrative method by comparing it with conventional meta-analysis method. The results show that our sparse group multitask method outperforms meta-analysis method significantly. In an application to our osteoporosis studies, 7 genes are identified as significant genes by our method and are found to have significant effects in other three independent studies for validation. The most significant gene SOD2 has been identified in our previous osteoporosis study involving the same expression dataset. Several other genes such as TREML2, HTR1E, and GLO1 are shown to be novel susceptible genes for osteoporosis, as confirmed from other

  13. Multiple-viewing-zone integral imaging using a dynamic barrier array for three-dimensional displays

    NASA Astrophysics Data System (ADS)

    Choi, Heejin; Min, Sung-Wook; Jung, Sungyong; Park, Jae-Hyeung; Lee, Byoungho

    2003-04-01

    In spite of many advantages of integral imaging, the viewing zone in which an observer can see three-dimensional images is limited within a narrow range. Here, we propose a novel method to increase the number of viewing zones by using a dynamic barrier array. We prove our idea by fabricating and locating the dynamic barrier array between a lens array and a display panel. By tilting the barrier array, it is possible to distribute images for each viewing zone. Thus, the number of viewing zones can be increased with an increment of the states of the barrier array tilt.

  14. Integration of multiple DICOM Web servers into an enterprise-wide Web-based electronic medical record

    NASA Astrophysics Data System (ADS)

    Stewart, Brent K.; Langer, Steven G.; Martin, Kelly P.

    1999-07-01

    The purpose of this paper is to integrate multiple DICOM image webservers into the currently existing enterprises- wide web-browsable electronic medical record. Over the last six years the University of Washington has created a clinical data repository combining in a distributed relational database information from multiple departmental databases (MIND). A character cell-based view of this data called the Mini Medical Record (MMR) has been available for four years, MINDscape, unlike the text-based MMR. provides a platform independent, dynamic, web browser view of the MIND database that can be easily linked with medical knowledge resources on the network, like PubMed and the Federated Drug Reference. There are over 10,000 MINDscape user accounts at the University of Washington Academic Medical Centers. The weekday average number of hits to MINDscape is 35,302 and weekday average number of individual users is 1252. DICOM images from multiple webservers are now being viewed through the MINDscape electronic medical record.

  15. Performance Analysis of Fault Detection and Identification for Multiple Faults in GNSS and GNSS/INS Integration

    NASA Astrophysics Data System (ADS)

    Alqurashi, Muwaffaq; Wang, Jinling

    2015-03-01

    For positioning, navigation and timing (PNT) purposes, GNSS or GNSS/INS integration is utilised to provide real-time solutions. However, any potential sensor failures or faulty measurements due to malfunctions of sensor components or harsh operating environments may cause unsatisfactory estimation for PNT parameters. The inability for immediate detecting faulty measurements or sensor component failures will reduce the overall performance of the system. So, real time detection and identification of faulty measurements is required to make the system more accurate and reliable for different applications that need real time solutions such as real time mapping for safety or emergency purposes. Consequently, it is necessary to implement an online fault detection and isolation (FDI) algorithm which is a statistic-based approach to detect and identify multiple faults.However, further investigations on the performance of the FDI for multiple fault scenarios is still required. In this paper, the performance of the FDI method under multiple fault scenarios is evaluated, e.g., for two, three and four faults in the GNSS and GNSS/INS measurements under different conditions of visible satellites and satellites geometry. Besides, the reliability (e.g., MDB) and separability (correlation coefficients between faults detection statistics) measures are also investigated to measure the capability of the FDI method. A performance analysis of the FDI method is conducted under the geometric constraints, to show the importance of the FDI method in terms of fault detectability and separability for robust positioning and navigation for real time applications.

  16. A hyphenated optical trap capillary electrophoresis laser induced native fluorescence system for single-cell chemical analysis

    PubMed Central

    Cecala, Christine; Rubakhin, Stanislav S.; Mitchell, Jennifer W.; Gillette, Martha U.; Sweedler, Jonathan V.

    2013-01-01

    Single-cell measurements allow a unique glimpse into cell-to-cell heterogeneity; even small changes in selected cells can have a profound impact on an organism’s physiology. Here an integrated approach to single-cell chemical sampling and assay are described. Capillary electrophoresis (CE) with laser-induced native fluorescence (LINF) has the sensitivity to characterize natively-fluorescent indoles and catechols within individual cells. While the separation and detection approaches are well established, the sampling and injection of individually selected cells requires new approaches. We describe an optimized system that interfaces a single-beam optical trap with CE and multichannel LINF detection. A cell is localized within the trap and then the capillary inlet is positioned near the cell using a computer-controlled micromanipulator. Hydrodynamic injection allows cell lysis to occur within the capillary inlet, followed by the CE separation and LINF detection. The use of multiple emission wavelengths allows improved analyte identification based on differences in analyte fluorescence emission profiles and migration time. The system enables injections of individual rat pinealocytes and quantification of their endogenous indoles, including serotonin, N-acetyl-serotonin, 5-hydroxyindole-3-acetic acid, tryptophol and others. The amounts detected in individual cells incubated in 5-hydroxytryptophan ranged from 10−14 mol to 10−16 mol, an order of magnitude higher than observed in untreated pinealocytes. PMID:22543409

  17. The value of integrating information from multiple hazards for flood risk management

    NASA Astrophysics Data System (ADS)

    Castillo-Rodríguez, J. T.; Escuder-Bueno, I.; Altarejos-García, L.; Serrano-Lombillo, A.

    2013-07-01

    This article presents a methodology for estimating flood risk in urban areas integrating pluvial flooding, river flooding and failure of both small and large dams. The first part includes a review of basic concepts and existing methods on flood risk analysis, evaluation and management. Traditionally, flood risk analyses have focused on specific site studies and qualitative or semi-quantitative approaches. However, in this context, a general methodology to perform a quantitative flood risk analysis including different flood hazards was still required. The second part describes the proposed methodology, which presents an integrated approach - combining pluvial, river flooding and dam failure, as applied to a case study: a urban area located downstream a dam under construction. Such methodology represents an upgrade of the methodological piece developed within the SUFRI project. This article shows how outcomes from flood risk analysis provide better and more complete information to inform authorities, local entities and the stakeholders involved on decision-making with regard to flood risk management.

  18. The value of integrating information from multiple hazards for flood risk analysis and management

    NASA Astrophysics Data System (ADS)

    Castillo-Rodríguez, J. T.; Escuder-Bueno, I.; Altarejos-García, L.; Serrano-Lombillo, A.

    2014-02-01

    This article presents a methodology for estimating flood risk in urban areas integrating pluvial flooding, river flooding and failure of both small and large dams. The first part includes a review of basic concepts on flood risk analysis, evaluation and management. Flood risk analyses may be developed at local, regional and national level, however a general methodology to perform a quantitative flood risk analysis including different flood hazards is still required. The second part describes the proposed methodology, which presents an integrated approach - combining pluvial, river flooding and flooding from dam failure, as applied to a case study: an urban area located downstream of a dam under construction. The methodology enhances the approach developed within the SUFRI project ("Sustainable Strategies of Urban Flood Risk Management to cope with the residual risk", 2009-2011). This article also shows how outcomes from flood risk analysis provide better and more complete information to inform authorities, local entities and the stakeholders involved in decision-making with regard to flood risk management.

  19. Two-Dimensional Integral Reacting Computer Code for Multiple Phase Flows

    1997-05-05

    ICRKFLO solves conservation equations for gaseous species, droplets, and solid particles of various sizes. General conservation laws, expressed by ellipitic-type partial differential equations, are used in conjunction with rate equations governing the mass, momentum, enthalpy, species, turbulent kinetic energy and dissipation for a three-phase reacting flow. Associated sub-models include integral combustion, two-parameter turbulence, particle melting and evaporation, droplet evaporation, and interfacial submodels. An evolving integral reaction submodel, originally designed for ICOMFLO2 to solve numerical stabilitymore » problems associated with Arrhenius type differential reaction submodels, was expanded and enhanced to handle petroleum cracking applications. A two-parameter turbulence submodel accounts for droplet and particle dispersion by gas phase turbulence with feedback effects on the gas phase. The evaporation submodel treats not only particle evaporation but the droplet size distribution shift caused by evaporation. Interfacial submodels correlate momentum and energy transfer between phases. Three major upgrades, adding new capabilities and improved physical modeling, were implemnted in IRCKFLO Version 2.0. They are :(1) particle-particle and particle wall interactions; (2) a two-step process for computing the reaction kinetics for a very large number of chemical reactions within a complex non-isothermal hydrodynamic flow field; and (3) a sectional coupling method combined with a triangular blocked cell technique for computing reacting multiphase flow systems of complex geometry while preserving the advantages of grid orthogonality.« less

  20. Capillary instability of jets

    NASA Astrophysics Data System (ADS)

    Chauhan, Anuj

    This thesis studies the capillary instability of a compound jet. A compound jet comprises an inner core of a primary fluid surrounded by an annulus of an immiscible secondary fluid. The compound jet is unstable due to capillarity. A compound jet finds applications in a variety of fields, such as, ink jet printing, particle sorting, extrusion, molding, particle production etc. In some of these applications such as molding, the disturbances that could cause the jet breakup start as periodic spatial disturbances of Fourier wave number k and grow in time. This is the temporal instability. In some other applications, such as, ink-jet printing, the disturbances initiate at the edge of the nozzle from which the jet issues out. These disturbances grow in space. This is the spatial instability. At small velocities, even if the initial disturbances are periodic in time, they grow exponentially in time. This is the absolute instability. We perform the temporal, spatial and the absolute stability analysis of an inviscid compound jet in a unified framework using the theory of transforms. Further, we solve the temporal instability problem for a viscous jet to understand the effect of viscosity on breakup dynamics. In the temporal analysis, we show that each interface of the compound jet contributes one mode to the instability. The modes contributed by the inner and outer interfaces grow for waves longer than the inner and the outer circumference of the undisturbed jet, respectively. The inner interface mode has a higher growth rate and hence dominates the breakup. The two interfaces grow exactly in phase in this mode and hence it is refereed to as the stretching mode. The other mode is the squeezing mode because the two interfaces grow exactly out of phase. The same two modes are also present in the spatial analysis. At high Weber numbers the predictions of the spatial theory reduce to those of the temporal theory because the waves simply convect with the jet velocity and there

  1. Real-time trace gas sensor using a multimode diode laser and multiple-line integrated cavity enhanced absorption spectroscopy.

    PubMed

    Karpf, Andreas; Rao, Gottipaty N

    2015-07-01

    We describe and demonstrate a highly sensitive trace gas sensor based on a simplified design that is capable of measuring sub-ppb concentrations of NO2 in tens of milliseconds. The sensor makes use of a relatively inexpensive Fabry-Perot diode laser to conduct off-axis cavity enhanced spectroscopy. The broad frequency range of a multimode Fabry-Perot diode laser spans a large number of absorption lines, thereby removing the need for a single-frequency tunable laser source. The use of cavity enhanced absorption spectroscopy enhances the sensitivity of the sensor by providing a pathlength on the order of 1 km in a small volume. Off-axis alignment excites a large number of cavity modes simultaneously, thereby reducing the sensor's susceptibility to vibration. Multiple-line integrated absorption spectroscopy (where one integrates the absorption spectra over a large number of rovibronic transitions of the molecular species) further improves the sensitivity of detection. Relatively high laser power (∼400  mW) is used to compensate for the low coupling efficiency of a broad linewidth laser to the optical cavity. The approach was demonstrated using a 407 nm diode laser to detect trace quantities of NO2 in zero air. Sensitivities of 750 ppt, 110 ppt, and 65 ppt were achieved using integration times of 50 ms, 5 s, and 20 s respectively.

  2. Multiple-body simulation with emphasis on integrated Space Shuttle vehicle

    NASA Technical Reports Server (NTRS)

    Chiu, Ing-Tsau

    1993-01-01

    The program to obtain intergrid communications - Pegasus - was enhanced to make better use of computing resources. Periodic block tridiagonal and penta-diagonal diagonal routines in OVERFLOW were modified to use a better algorithm to speed up the calculation for grids with periodic boundary conditions. Several programs were added to collar grid tools and a user friendly shell script was developed to help users generate collar grids. User interface for HYPGEN was modified to cope with the changes in HYPGEN. ET/SRB attach hardware grids were added to the computational model for the space shuttle and is currently incorporated into the refined shuttle model jointly developed at Johnson Space Center and Ames Research Center. Flow simulation for the integrated space shuttle vehicle at flight Reynolds number was carried out and compared with flight data as well as the earlier simulation for wind tunnel Reynolds number.

  3. A planning study of simultaneous integrated boost with forward IMRT for multiple brain metastases

    SciTech Connect

    Liang, Xiaodong; Ni, Lingqin; Hu, Wei; Chen, Weijun; Ying, Shenpeng; Gong, Qiangjun; Liu, Yanmei

    2013-07-01

    The objective of this study was to evaluate the dose conformity and feasibility of whole-brain radiotherapy with a simultaneous integrated boost by forward intensity-modulated radiation therapy in patients with 1 to 3 brain metastases. Forward intensity-modulated radiation therapy plans were generated for 10 patients with 1 to 3 brain metastases on Pinnacle 6.2 Treatment Planning System. The prescribed dose was 30 Gy to the whole brain (planning target volume [PTV]{sub wbrt}) and 40 Gy to individual brain metastases (PTV{sub boost}) simultaneously, and both doses were given in 10 fractions. The maximum diameters of individual brain metastases ranged from 1.6 to 6 cm, and the summated PTVs per patient ranged from 1.62 to 69.81 cm{sup 3}. Conformity and feasibility were evaluated regarding conformation number and treatment delivery time. One hundred percent volume of the PTV{sub boost} received at least 95% of the prescribed dose in all cases. The maximum doses were less than 110% of the prescribed dose to the PTV{sub boost}, and all of the hot spots were within the PTV{sub boost}. The volume of the PTV{sub wbrt} that received at least 95% of the prescribed dose ranged from 99.2% to 100%. The mean values of conformation number were 0.682. The mean treatment delivery time was 2.79 minutes. Ten beams were used on an average in these plans. Whole-brain radiotherapy with a simultaneous integrated boost by forward intensity-modulated radiation therapy in 1 to 3 brain metastases is feasible, and treatment delivery time is short.

  4. Soil mapping at regional scale using Remote Sensing - integrating multiple research methods

    NASA Astrophysics Data System (ADS)

    Mulder, V. L.; de Bruin, S.; Schaepman, M. E.

    2012-04-01

    Initiated by renewed interest in soil resources because of their role in supporting food security and climate change adaptation and mitigation, this research aims to provide a coherent methodology for soil and terrain mapping using remote sensing data. The work particularly addresses data acquisition for extensive areas where information about soils is sparse while at the same time resources are limited. The methodology aims to fully exploit data from current missions as well as the Sentinel-2 satellite mission (to be launched in 2014) for delivering soil data. The project aims to establish a coherent methodology where RS is integrated within each part of the soil mapping process on a regional scale; (1) A sampling method (constrained Latin hypercube sampling) that aims to acquire soil sample data representing soil variability in the study area under time and budgetary constraints. (2) Retrieval of composite soil mineralogy from spectroscopic data using linear mixing and non-linear methods. (3) Soil property prediction at regional scale using remote sensing data and a small primary data set. Employing regression trees and related methods along with spatial interpolation, this part integrates the above components and produces soil property maps as well as confidence intervals for these. The methodologies are demonstrated in a 1500 km2 study area in Northern Morocco offering a combination of landscape diversity, sparse vegetation cover and limited availability of existing data. With this research, we demonstrate that remote sensing plays a fundamental role for delivering detailed soil data on global and regional scale which is required for research focussing on food security and climate change adaptation and mitigation.

  5. Decay of capillary wave turbulence.

    PubMed

    Deike, Luc; Berhanu, Michael; Falcon, Eric

    2012-06-01

    We report on the observation of freely decaying capillary wave turbulence on the surface of a fluid. The capillary wave turbulence spectrum decay is found to be self-similar in time with the same power law exponent as the one found in the stationary regime, in agreement with weak turbulence predictions. The amplitude of all Fourier modes are found to decrease exponentially with time at the same damping rate. The longest wavelengths involved in the system are shown to be damped by a viscous surface boundary layer. These long waves play the role of an energy source during the decay that sustains nonlinear interactions to keep capillary waves in a wave turbulent state.

  6. Paramecium swimming in capillary tube

    NASA Astrophysics Data System (ADS)

    Jana, Saikat; Um, Soong Ho; Jung, Sunghwan

    2012-04-01

    Swimming organisms in their natural habitat need to navigate through a wide range of geometries and chemical environments. Interaction with boundaries in such situations is ubiquitous and can significantly modify the swimming characteristics of the organism when compared to ideal laboratory conditions. We study the different patterns of ciliary locomotion in glass capillaries of varying diameter and characterize the effect of the solid boundaries on the velocities of the organism. Experimental observations show that Paramecium executes helical trajectories that slowly transition to straight lines as the diameter of the capillary tubes decreases. We predict the swimming velocity in capillaries by modeling the system as a confined cylinder propagating longitudinal metachronal waves that create a finite pressure gradient. Comparing with experiments, we find that such pressure gradient considerations are necessary for modeling finite sized ciliary organisms in restrictive geometries.

  7. Facile integration of multiple magnetite nanoparticles for theranostics combining efficient MRI and thermal therapy

    NASA Astrophysics Data System (ADS)

    Huang, Guoming; Zhu, Xianglong; Li, Hui; Wang, Lirong; Chi, Xiaoqin; Chen, Jiahe; Wang, Xiaomin; Chen, Zhong; Gao, Jinhao

    2015-01-01

    Multifunctional nanostructures with both diagnostic and therapeutic capabilities have attracted considerable attention in biomedical research because they can offer great advantages in disease management and prognosis. In this work, a facile way to transfer the hydrophobic iron oxide (IO) nanoparticles into aqueous media by employing carboxylic graphene oxide (GO-COOH) as the transferring agent has been reported. In this one-step process, IO nanoparticles adhere to GO-COOH and form water-dispersible clusters via hydrophobic interactions between the hydrophobic ligands of IO nanoparticles and the basal plane of GO-COOH. The multiple IO nanoparticles on GO-COOH sheets (IO/GO-COOH) present a significant increase in T2 contrast enhancement. Moreover, the IO/GO-COOH nanoclusters also display a high photothermal conversion efficiency and can effectively inhibit tumor growth through the photothermal effects. It is envisioned that such IO/GO-COOH nanocomposites combining efficient MRI and photothermal therapy hold great promise in theranostic applications.Multifunctional nanostructures with both diagnostic and therapeutic capabilities have attracted considerable attention in biomedical research because they can offer great advantages in disease management and prognosis. In this work, a facile way to transfer the hydrophobic iron oxide (IO) nanoparticles into aqueous media by employing carboxylic graphene oxide (GO-COOH) as the transferring agent has been reported. In this one-step process, IO nanoparticles adhere to GO-COOH and form water-dispersible clusters via hydrophobic interactions between the hydrophobic ligands of IO nanoparticles and the basal plane of GO-COOH. The multiple IO nanoparticles on GO-COOH sheets (IO/GO-COOH) present a significant increase in T2 contrast enhancement. Moreover, the IO/GO-COOH nanoclusters also display a high photothermal conversion efficiency and can effectively inhibit tumor growth through the photothermal effects. It is envisioned

  8. An Integrated MRI and MRS Approach to Evaluation of Multiple Sclerosis with Cognitive Impairment

    NASA Astrophysics Data System (ADS)

    Liang, Zhengrong; Li, Lihong; Lu, Hongbing; Huang, Wei; Tudorica, Alina; Krupp, Lauren

    Magnetic resonance imaging and spectroscopy (MRI/MRS) plays a unique role in multiple sclerosis (MS) evaluation, because of its ability to provide both high image contrast and significant chemical change among brain tissues. The image contrast renders the possibility of quantifying the tissue volumetric and texture variations, e.g., cerebral atrophy and progressing speed, reflecting the ongoing destructive pathologic processes. Any chemical change reflects an early sign of pathological alteration, e.g., decreased N-acetyl aspartate (NAA) in lesions and normal appearing white matter, related to axonal damage or dysfunction. Both MRI and MRS encounter partial volume (PV) effect, which compromises the quantitative capability, especially for MRS. This work aims to develop a statistical framework to segment the tissue mixtures inside each image element, eliminating theoretically the PV effect, and apply the framework to the evaluation of MS with cognitive impairment. The quantitative measures from MRI/MRS neuroimaging are strongly correlated with the qualitative neuropsychological scores of Brief Repeatable Battery (BRB) test on cognitive impairment, demonstrating the usefulness of the PV image segmentation framework in this clinically significant problem.

  9. Multiple components are integrated to determine leaf complexity in Lotus japonicus.

    PubMed

    Wang, Zhenhua; Chen, Jianghua; Weng, Lin; Li, Xin; Cao, Xianglin; Hu, Xiaohe; Luo, Da; Yang, Jun

    2013-05-01

    Transcription factors and phytohormones have been reported to play crucial roles to regulate leaf complexity among plant species. Using the compound-leafed species Lotus japonicus, a model legume plant with five visible leaflets, we characterized four independent mutants with reduced leaf complexity, proliferating floral meristem (pfm), proliferating floral organ-2 (pfo-2), fused leaflets1 (ful1) and umbrella leaflets (uml), which were further identified as loss-of-function mutants of Arabidopsis orthologs LEAFY (LFY), UNUSUAL FLORAL ORGANS (UFO), CUP-SHAPED COTYLEDON 2 (CUC2) and PIN-FORMED 1 (PIN1), respectively. Comparing the leaf development of wild-type and mutants by a scanning electron microscopy approach, leaflet initiation and/or dissection were found to be affected in these mutants. Expression and phenotype analysis indicated that PFM/LjLFY and PFO/LjUFO determined the basipetal leaflet initiation manner in L. japonicus. Genetic analysis of ful1 and uml mutants and their double mutants revealed that the CUC2-like gene and auxin pathway also participated in leaflet dissection in L. japonicus, and their functions might influence cytokinin biogenesis directly or indirectly. Our results here suggest that multiple genes were interplayed and played conserved functions in controlling leaf complexity during compound leaf development in L. japonicus.

  10. Multiple components are integrated to determine leaf complexity in Lotus japonicus.

    PubMed

    Wang, Zhenhua; Chen, Jianghua; Weng, Lin; Li, Xin; Cao, Xianglin; Hu, Xiaohe; Luo, Da; Yang, Jun

    2013-05-01

    Transcription factors and phytohormones have been reported to play crucial roles to regulate leaf complexity among plant species. Using the compound-leafed species Lotus japonicus, a model legume plant with five visible leaflets, we characterized four independent mutants with reduced leaf complexity, proliferating floral meristem (pfm), proliferating floral organ-2 (pfo-2), fused leaflets1 (ful1) and umbrella leaflets (uml), which were further identified as loss-of-function mutants of Arabidopsis orthologs LEAFY (LFY), UNUSUAL FLORAL ORGANS (UFO), CUP-SHAPED COTYLEDON 2 (CUC2) and PIN-FORMED 1 (PIN1), respectively. Comparing the leaf development of wild-type and mutants by a scanning electron microscopy approach, leaflet initiation and/or dissection were found to be affected in these mutants. Expression and phenotype analysis indicated that PFM/LjLFY and PFO/LjUFO determined the basipetal leaflet initiation manner in L. japonicus. Genetic analysis of ful1 and uml mutants and their double mutants revealed that the CUC2-like gene and auxin pathway also participated in leaflet dissection in L. japonicus, and their functions might influence cytokinin biogenesis directly or indirectly. Our results here suggest that multiple genes were interplayed and played conserved functions in controlling leaf complexity during compound leaf development in L. japonicus. PMID:23331609

  11. Endocannabinoid Signaling within the Basolateral Amygdala Integrates Multiple Stress Hormone Effects on Memory Consolidation

    PubMed Central

    Atsak, Piray; Hauer, Daniela; Campolongo, Patrizia; Schelling, Gustav; Fornari, Raquel V; Roozendaal, Benno

    2015-01-01

    Glucocorticoid hormones are known to act synergistically with other stress-activated neuromodulatory systems, such as norepinephrine and corticotropin-releasing factor (CRF), within the basolateral complex of the amygdala (BLA) to induce optimal strengthening of the consolidation of long-term memory of emotionally arousing experiences. However, as the onset of these glucocorticoid actions appear often too rapid to be explained by genomic regulation, the neurobiological mechanism of how glucocorticoids could modify the memory-enhancing properties of norepinephrine and CRF remained elusive. Here, we show that the endocannabinoid system, a rapidly activated retrograde messenger system, is a primary route mediating the actions of glucocorticoids, via a glucocorticoid receptor on the cell surface, on BLA neural plasticity and memory consolidation. Furthermore, glucocorticoids recruit downstream endocannabinoid activity within the BLA to interact with both the norepinephrine and CRF systems in enhancing memory consolidation. These findings have important implications for understanding the fine-tuned crosstalk between multiple stress hormone systems in the coordination of (mal)adaptive stress and emotional arousal effects on neural plasticity and memory consolidation. PMID:25547713

  12. Conformation-sensitive capillary electrophoresis.

    PubMed

    Ashton, Emma Jane

    2011-01-01

    Conformation-sensitive capillary electrophoresis (CSCE) is a rapid, high-throughput screening method that can be applied to any region of a genome for detection of sequence variants. Slab gel-based conformation-sensitive gel electrophoresis was first described by Ganguly et al., and the transfer from slab gels to capillaries for higher throughput was reported by Rozycka et al. CSCE is based on the principle that DNA homoduplexes and heteroduplexes migrate at different rates during electrophoresis under mildly denaturing conditions. Fragments showing an altered peak morphology compared to the wild type are then sequenced to determine the precise nature of the sequence variant detected.

  13. Nonsteady Flow in Capillary Tubes

    NASA Astrophysics Data System (ADS)

    Hara, Ayako

    2000-03-01

    Surface phenomena in the field of electron devices and the problem of how long. It takes plants to absorb water during their growth in hydroponic cultivation is attraching the attention of riseachers. However, the related study of non-steady flow in capillary tubes has a number of issues that require investigation. In response to this situation, we made attempted to assess nonsteady fiow in capillary tubes, the liquid rise time and other issues, using a motion equation that takes factors including the friction force of the tube and the surface tension into consideration.

  14. Capillary interactions in Pickering emulsions

    NASA Astrophysics Data System (ADS)

    Guzowski, J.; Tasinkevych, M.; Dietrich, S.

    2011-09-01

    The effective capillary interaction potentials for small colloidal particles trapped at the surface of liquid droplets are calculated analytically. Pair potentials between capillary monopoles and dipoles, corresponding to particles floating on a droplet with a fixed center of mass and subjected to external forces and torques, respectively, exhibit a repulsion at large angular separations and an attraction at smaller separations, with the latter resembling the typical behavior for flat interfaces. This change of character is not observed for quadrupoles, corresponding to free particles on a mechanically isolated droplet. The analytical results are compared with the numerical minimization of the surface free energy of the droplet in the presence of spherical or ellipsoidal particles.

  15. Integrated QSAR study for inhibitors of hedgehog signal pathway against multiple cell lines:a collaborative filtering method

    PubMed Central

    2012-01-01

    Background The Hedgehog Signaling Pathway is one of signaling pathways that are very important to embryonic development. The participation of inhibitors in the Hedgehog Signal Pathway can control cell growth and death, and searching novel inhibitors to the functioning of the pathway are in a great demand. As the matter of fact, effective inhibitors could provide efficient therapies for a wide range of malignancies, and targeting such pathway in cells represents a promising new paradigm for cell growth and death control. Current research mainly focuses on the syntheses of the inhibitors of cyclopamine derivatives, which bind specifically to the Smo protein, and can be used for cancer therapy. While quantitatively structure-activity relationship (QSAR) studies have been performed for these compounds among different cell lines, none of them have achieved acceptable results in the prediction of activity values of new compounds. In this study, we proposed a novel collaborative QSAR model for inhibitors of the Hedgehog Signaling Pathway by integration the information from multiple cell lines. Such a model is expected to substantially improve the QSAR ability from single cell lines, and provide useful clues in developing clinically effective inhibitors and modifications of parent lead compounds for target on the Hedgehog Signaling Pathway. Results In this study, we have presented: (1) a collaborative QSAR model, which is used to integrate information among multiple cell lines to boost the QSAR results, rather than only a single cell line QSAR modeling. Our experiments have shown that the performance of our model is significantly better than single cell line QSAR methods; and (2) an efficient feature selection strategy under such collaborative environment, which can derive the commonly important features related to the entire given cell lines, while simultaneously showing their specific contributions to a specific cell-line. Based on feature selection results, we have

  16. Simulating mesoscale coastal evolution for decadal coastal management: A new framework integrating multiple, complementary modelling approaches

    NASA Astrophysics Data System (ADS)

    van Maanen, Barend; Nicholls, Robert J.; French, Jon R.; Barkwith, Andrew; Bonaldo, Davide; Burningham, Helene; Brad Murray, A.; Payo, Andres; Sutherland, James; Thornhill, Gillian; Townend, Ian H.; van der Wegen, Mick; Walkden, Mike J. A.

    2016-03-01

    Coastal and shoreline management increasingly needs to consider morphological change occurring at decadal to centennial timescales, especially that related to climate change and sea-level rise. This requires the development of morphological models operating at a mesoscale, defined by time and length scales of the order 101 to 102 years and 101 to 102 km. So-called 'reduced complexity' models that represent critical processes at scales not much smaller than the primary scale of interest, and are regulated by capturing the critical feedbacks that govern landform behaviour, are proving effective as a means of exploring emergent coastal behaviour at a landscape scale. Such models tend to be computationally efficient and are thus easily applied within a probabilistic framework. At the same time, reductionist models, built upon a more detailed description of hydrodynamic and sediment transport processes, are capable of application at increasingly broad spatial and temporal scales. More qualitative modelling approaches are also emerging that can guide the development and deployment of quantitative models, and these can be supplemented by varied data-driven modelling approaches that can achieve new explanatory insights from observational datasets. Such disparate approaches have hitherto been pursued largely in isolation by mutually exclusive modelling communities. Brought together, they have the potential to facilitate a step change in our ability to simulate the evolution of coastal morphology at scales that are most relevant to managing erosion and flood risk. Here, we advocate and outline a new integrated modelling framework that deploys coupled mesoscale reduced complexity models, reductionist coastal area models, data-driven approaches, and qualitative conceptual models. Integration of these heterogeneous approaches gives rise to model compositions that can potentially resolve decadal- to centennial-scale behaviour of diverse coupled open coast, estuary and inner

  17. Integration and Visualization of Multiple Sensors in Generating the NOAA Operational Snow and Ice Cover Products

    NASA Astrophysics Data System (ADS)

    Li, M.; Helfrich, S.

    2011-12-01

    Global snow and ice cover is a key component in the climate and hydrologic system as well as daily weather forecasting. The National Oceanic and Atmospheric Administration (NOAA) has produced a daily northern hemisphere snow and ice cover chart since 1997 through the Interactive Multisensor Snow and Ice Mapping System (IMS). The IMS integrates and visualizes a wide variety of satellite data, as well as derived snow/ice products and surface observations, to provide meteorologists with the ability to interactively prepare the daily northern hemisphere snow and ice cover chart. These products are presently used as operational inputs into several weather prediction models and are applied in climate monitoring. The IMS is currently on its second version (released in 2004) and scheduled to be upgraded to the third version (V3) in 2013. The IMS V3 will have nearly 40 external inputs as data sources processed by the IMS, which fall into five data formats: binary image, HDF file, GeoTIFF image, Shapefile image and ASCII file. With the exception of the GeoTIFF and Shapefile files, which are used directly by IMS, all other types of data are pre-processed to ENVI image file format and "sectorized" for different areas around the northern hemisphere. The IMS V3 will generate daily snow and ice cover maps in five formats: ASCII, ENVI, GeoTIFF, GIF and GRIB2 and three resolutions: 24km, 4km and 1km. In this presentation, the methods are discussed for accessing and processing satellite data, model results and surface reports. All input data with varying formats and resolutions are processed to a fixed projection. The visualization methodology for IMS are provided for five different resolutions of 48km, 24km, 8km, 4km, 2km and 1km. This work will facilitate the future enhancement of IMS, provide users with an understanding of the software architecture, provide a prospectus on future data sources, and help to preserve the integrity of the long-standing satellite-derived snow and ice

  18. Integrated optic chemical sensor for the simultaneous detection and quantification of multiple ions. Final report, March--September 1995

    SciTech Connect

    Mendoza, E.

    1995-09-01

    This final report summarizes the work performed by Physical Optics Corporation (POC) on the DOE contract entitled {open_quotes}Integrated Optic Chemical Sensor for the Simultaneous Detection and Quantification of Multiple Metal Ions{close_quotes}. This project successfully demonstrated a multi-element integrated optic chemical sensor (IOCS) system capable of simultaneous detection and quantification of metal ions in a water flow stream. POC`s innovative integrated optic chemical sensor technology uses an array of chemically active optical waveguides integrated in parallel in a single small IOCS chip. The IOCS technique uses commonly available materials and straightforward processing to produce channel waveguides in porous glass, each channel treated with a chemical indicator that responds optically to heavy metal ions in a water flow stream. The porosity of the glass allows metal ions present in the water to diffuse into the glass and interact with the immobilized indicators, producing a measurable optical chance. For the {open_quotes}proof-of-concept{close_quotes} demonstration, POC designed and fabricated two types of IOCS chips. Type I uses an array of four straight channel waveguides, three of which are doped with a metal sensitive indicator, an ionophore. The undoped fourth channel is used as the reference channel. Type II uses a 1 x 4 star coupler structure with three sensing channels and a reference channel. Successful implementation of the IOCS technology is expected to have a broad impact on water quality control as well as in the commercial environmental monitoring market. Because of the self-referenced, multidetection capability of the IOCS technique, POC`s water quality sensors are expected to find markets in environmental monitoring and protection, ground water monitoring, and in-line process control. Specific applications include monitoring of chromium, copper, and iron ions in water discharged by the metal plating industry.

  19. Infant, Control Thyself: Infants’ Integration of Multiple Social Cues to Regulate Their Imitative Behavior

    PubMed Central

    Repacholi, Betty M.; Meltzoff, Andrew N.; Rowe, Hillary; Toub, Tamara Spiewak

    2016-01-01

    This study investigated 15-month-old infants’ (N = 150) ability to self-regulate based on observing a social interaction between two adults. Infants were bystanders to a social exchange in which an Experimenter performed actions on objects and an Emoter expressed anger, as if they were forbidden acts. Next, the Emoter became neutral and her visual access to the infant was experimentally manipulated. The Emoter either: (a) left the room, (b) turned her back, (c) faced the infant but looked down at a magazine, or (d) faced and looked toward the infant. Infants were then presented with the test objects. When the previously angry Emoter was facing them, infants were hesitant to imitate the demonstrated acts in comparison to the other conditions. We hypothesize that infants integrated the emotional and visual-perceptual cues to determine whether the Emoter would get angry at them, and then regulated their behavior accordingly. Temperament was related to infants’ self-regulation –infants with higher impulsivity scores were more likely to perform the forbidden acts. Taken together, these findings provide insight into the roots of executive functions in late infancy.

  20. Using Multiple Instrument Measurements To Assess Integrated Water Vapor Path From A Multispectral Microwave Radiometer

    NASA Astrophysics Data System (ADS)

    Fallon, J.; Han, Z. T.; Gross, B.; Moshary, F.

    2013-12-01

    Microwave Radiometers are mounted on satellites and the ground to collect climatological data. While they provide very useful information about temperature, RH, and water vapor, radiometers should periodically be cross-referenced with other instruments to gauge the veracity of the data. Data available from the closest ground-based GPS receivers and sun photometers was plotted alongside, and used to analyze, data from City College's Microwave Radiometer. Observing all of the data together in a graph allows one to see some of the general advantages and disadvantages of each instrument. The GPS-MET seems to be accurate continuously, while AERONET data is not even available during the night and while there is cloud cover. Lastly, the microwave radiometer collects data continuously, but at certain times the data are about five times higher than the expected values, based on the values given by GPS-MET and AERONET. A good explanation for those spikes is rainfall. For times when it is not raining, the microwave radiometer at City College is sufficiently close to the integrated water vapor data collected by City College's sun photometer and data from Union, New Jersey and East Moriches, New York, as proven by statistical tools.

  1. ChIP-Array 2: integrating multiple omics data to construct gene regulatory networks

    PubMed Central

    Wang, Panwen; Qin, Jing; Qin, Yiming; Zhu, Yun; Wang, Lily Yan; Li, Mulin Jun; Zhang, Michael Q.; Wang, Junwen

    2015-01-01

    Transcription factors (TFs) play an important role in gene regulation. The interconnections among TFs, chromatin interactions, epigenetic marks and cis-regulatory elements form a complex gene transcription apparatus. Our previous work, ChIP-Array, combined TF binding and transcriptome data to construct gene regulatory networks (GRNs). Here we present an enhanced version, ChIP-Array 2, to integrate additional types of omics data including long-range chromatin interaction, open chromatin region and histone modification data to dissect more comprehensive GRNs involving diverse regulatory components. Moreover, we substantially extended our motif database for human, mouse, rat, fruit fly, worm, yeast and Arabidopsis, and curated large amount of omics data for users to select as input or backend support. With ChIP-Array 2, we compiled a library containing regulatory networks of 18 TFs/chromatin modifiers in mouse embryonic stem cell (mESC). The web server and the mESC library are publicly free and accessible athttp://jjwanglab.org/chip-array. PMID:25916854

  2. An Integrated Cell Purification and Genomics Strategy Reveals Multiple Regulators of Pancreas Development

    PubMed Central

    Benitez, Cecil M.; Qu, Kun; Sugiyama, Takuya; Pauerstein, Philip T.; Liu, Yinghua; Tsai, Jennifer; Gu, Xueying; Ghodasara, Amar; Arda, H. Efsun; Zhang, Jiajing; Dekker, Joseph D.; Tucker, Haley O.; Chang, Howard Y.; Kim, Seung K.

    2014-01-01

    The regulatory logic underlying global transcriptional programs controlling development of visceral organs like the pancreas remains undiscovered. Here, we profiled gene expression in 12 purified populations of fetal and adult pancreatic epithelial cells representing crucial progenitor cell subsets, and their endocrine or exocrine progeny. Using probabilistic models to decode the general programs organizing gene expression, we identified co-expressed gene sets in cell subsets that revealed patterns and processes governing progenitor cell development, lineage specification, and endocrine cell maturation. Purification of Neurog3 mutant cells and module network analysis linked established regulators such as Neurog3 to unrecognized gene targets and roles in pancreas development. Iterative module network analysis nominated and prioritized transcriptional regulators, including diabetes risk genes. Functional validation of a subset of candidate regulators with corresponding mutant mice revealed that the transcription factors Etv1, Prdm16, Runx1t1 and Bcl11a are essential for pancreas development. Our integrated approach provides a unique framework for identifying regulatory genes and functional gene sets underlying pancreas development and associated diseases such as diabetes mellitus. PMID:25330008

  3. BioZone Exploting Source-Capability Information for Integrated Access to Multiple Bioinformatics Data Sources

    SciTech Connect

    Liu, L; Buttler, D; Paques, H; Pu, C; Critchlow

    2002-01-28

    Modern Bioinformatics data sources are widely used by molecular biologists for homology searching and new drug discovery. User-friendly and yet responsive access is one of the most desirable properties for integrated access to the rapidly growing, heterogeneous, and distributed collection of data sources. The increasing volume and diversity of digital information related to bioinformatics (such as genomes, protein sequences, protein structures, etc.) have led to a growing problem that conventional data management systems do not have, namely finding which information sources out of many candidate choices are the most relevant and most accessible to answer a given user query. We refer to this problem as the query routing problem. In this paper we introduce the notation and issues of query routing, and present a practical solution for designing a scalable query routing system based on multi-level progressive pruning strategies. The key idea is to create and maintain source-capability profiles independently, and to provide algorithms that can dynamically discover relevant information sources for a given query through the smart use of source profiles. Compared to the keyword-based indexing techniques adopted in most of the search engines and software, our approach offers fine-granularity of interest matching, thus it is more powerful and effective for handling queries with complex conditions.

  4. Integrating aerial geophysical data in multiple-point statistics simulations to assist groundwater flow models

    NASA Astrophysics Data System (ADS)

    Dickson, Neil E. M.; Comte, Jean-Christophe; Renard, Philippe; Straubhaar, Julien A.; McKinley, Jennifer M.; Ofterdinger, Ulrich

    2015-08-01

    The process of accounting for heterogeneity has made significant advances in statistical research, primarily in the framework of stochastic analysis and the development of multiple-point statistics (MPS). Among MPS techniques, the direct sampling (DS) method is tested to determine its ability to delineate heterogeneity from aerial magnetics data in a regional sandstone aquifer intruded by low-permeability volcanic dykes in Northern Ireland, UK. The use of two two-dimensional bivariate training images aids in creating spatial probability distributions of heterogeneities of hydrogeological interest, despite relatively `noisy' magnetics data (i.e. including hydrogeologically irrelevant urban noise and regional geologic effects). These distributions are incorporated into a hierarchy system where previously published density function and upscaling methods are applied to derive regional distributions of equivalent hydraulic conductivity tensor K. Several K models, as determined by several stochastic realisations of MPS dyke locations, are computed within groundwater flow models and evaluated by comparing modelled heads with field observations. Results show a significant improvement in model calibration when compared to a simplistic homogeneous and isotropic aquifer model that does not account for the dyke occurrence evidenced by airborne magnetic data. The best model is obtained when normal and reverse polarity dykes are computed separately within MPS simulations and when a probability threshold of 0.7 is applied. The presented stochastic approach also provides improvement when compared to a previously published deterministic anisotropic model based on the unprocessed (i.e. noisy) airborne magnetics. This demonstrates the potential of coupling MPS to airborne geophysical data for regional groundwater modelling.

  5. Optimized particle-mesh Ewald/multiple-time step integration for molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Batcho, Paul F.; Case, David A.; Schlick, Tamar

    2001-09-01

    We develop an efficient multiple time step (MTS) force splitting scheme for biological applications in the AMBER program in the context of the particle-mesh Ewald (PME) algorithm. Our method applies a symmetric Trotter factorization of the Liouville operator based on the position-Verlet scheme to Newtonian and Langevin dynamics. Following a brief review of the MTS and PME algorithms, we discuss performance speedup and the force balancing involved to maximize accuracy, maintain long-time stability, and accelerate computational times. Compared to prior MTS efforts in the context of the AMBER program, advances are possible by optimizing PME parameters for MTS applications and by using the position-Verlet, rather than velocity-Verlet, scheme for the inner loop. Moreover, ideas from the Langevin/MTS algorithm LN are applied to Newtonian formulations here. The algorithm's performance is optimized and tested on water, solvated DNA, and solvated protein systems. We find CPU speedup ratios of over 3 for Newtonian formulations when compared to a 1 fs single-step Verlet algorithm using outer time steps of 6 fs in a three-class splitting scheme; accurate conservation of energies is demonstrated over simulations of length several hundred ps. With modest Langevin forces, we obtain stable trajectories for outer time steps up to 12 fs and corresponding speedup ratios approaching 5. We end by suggesting that modified Ewald formulations, using tailored alternatives to the Gaussian screening functions for the Coulombic terms, may allow larger time steps and thus further speedups for both Newtonian and Langevin protocols; such developments are reported separately.

  6. Using an integrated COC index and multilevel measurements to verify the care outcome of patients with multiple chronic conditions

    PubMed Central

    2012-01-01

    Background The increasing prevalence of multiple chronic conditions has accentuated the importance of coordinating and integrating health care services. Patients with better continuity of care (COC) have a lower utilization rate of emergency department (ED) services, lower hospitalization and better care outcomes. Previous COC studies have focused on the care outcome of patients with a single chronic condition or that of physician-patient relationships; few studies have investigated the care outcome of patients with multiple chronic conditions. Using multi-chronic patients as subjects, this study proposes an integrated continuity of care (ICOC) index to verify the association between COC and care outcomes for two scopes of chronic conditions, at physician and medical facility levels. Methods This study used a dataset of 280,840 subjects, obtained from the Longitudinal Health Insurance Database (LHID 2005), compiled by the National Health Research Institutes, of the National Health Insurance Bureau of Taiwan. Principal Component Analysis (PCA) was used to integrate the indices of density, dispersion and sequence into ICOC to measure COC outcomes - the utilization rate of ED services and hospitalization. A Generalized Estimating Equations model was used to verify the care outcomes. Results We discovered that the higher the COC at medical facility level, the lower the utilization rate of ED services and hospitalization for patients; by contrast, the higher the COC at physician level, the higher the utilization rate of ED services (odds ratio > 1; Exp(β) = 2.116) and hospitalization (odds ratio > 1; Exp(β) = 1.688). When only those patients with major chronic conditions with the highest number of medical visits were considered, it was found that the higher the COC at both medical facility and physician levels, the lower the utilization rate of ED services and hospitalization. Conclusions The study shows that ICOC is more stable than single indices and

  7. Integrated Systems View on Networking by Hormones in Arabidopsis Immunity Reveals Multiple Crosstalk for Cytokinin[W

    PubMed Central

    Naseem, Muhammad; Philippi, Nicole; Hussain, Anwar; Wangorsch, Gaby; Ahmed, Nazeer; Dandekar, Thomas

    2012-01-01

    Phytohormones signal and combine to maintain the physiological equilibrium in the plant. Pathogens enhance host susceptibility by modulating the hormonal balance of the plant cell. Unlike other plant hormones, the detailed role of cytokinin in plant immunity remains to be fully elucidated. Here, extensive data mining, including of pathogenicity factors, host regulatory proteins, enzymes of hormone biosynthesis, and signaling components, established an integrated signaling network of 105 nodes and 163 edges. Dynamic modeling and system analysis identified multiple cytokinin-mediated regulatory interactions in plant disease networks. This includes specific synergism between cytokinin and salicylic acid pathways and previously undiscovered aspects of antagonism between cytokinin and auxin in plant immunity. Predicted interactions and hormonal effects on plant immunity are confirmed in subsequent experiments with Pseudomonas syringae pv tomato DC3000 and Arabidopsis thaliana. Our dynamic simulation is instrumental in predicting system effects of individual components in complex hormone disease networks and synergism or antagonism between pathways. PMID:22643121

  8. Cooperative suction by vertical capillary array pump for controlling flow profiles of microfluidic sensor chips.

    PubMed

    Horiuchi, Tsutomu; Hayashi, Katsuyoshi; Seyama, Michiko; Inoue, Suzuyo; Tamechika, Emi

    2012-10-18

    A passive pump consisting of integrated vertical capillaries has been developed for a microfluidic chip as an useful component with an excellent flow volume and flow rate. A fluidic chip built into a passive pump was used by connecting the bottoms of all the capillaries to a top surface consisting of a thin layer channel in the microfluidic chip where the thin layer channel depth was smaller than the capillary radius. As a result the vertical capillaries drew fluid cooperatively rather than independently, thus exerting the maximum suction efficiency at every instance. This meant that a flow rate was realized that exhibited little variation and without any external power or operation. A microfluidic chip built into this passive pump had the ability to achieve a quasi-steady rather than a rapidly decreasing flow rate, which is a universal flow characteristic in an ordinary capillary.

  9. An integrated pan-tropical biomass map using multiple reference datasets.

    PubMed

    Avitabile, Valerio; Herold, Martin; Heuvelink, Gerard B M; Lewis, Simon L; Phillips, Oliver L; Asner, Gregory P; Armston, John; Ashton, Peter S; Banin, Lindsay; Bayol, Nicolas; Berry, Nicholas J; Boeckx, Pascal; de Jong, Bernardus H J; DeVries, Ben; Girardin, Cecile A J; Kearsley, Elizabeth; Lindsell, Jeremy A; Lopez-Gonzalez, Gabriela; Lucas, Richard; Malhi, Yadvinder; Morel, Alexandra; Mitchard, Edward T A; Nagy, Laszlo; Qie, Lan; Quinones, Marcela J; Ryan, Casey M; Ferry, Slik J W; Sunderland, Terry; Laurin, Gaia Vaglio; Gatti, Roberto Cazzolla; Valentini, Riccardo; Verbeeck, Hans; Wijaya, Arief; Willcock, Simon

    2016-04-01

    We combined two existing datasets of vegetation aboveground biomass (AGB) (Proceedings of the National Academy of Sciences of the United States of America, 108, 2011, 9899; Nature Climate Change, 2, 2012, 182) into a pan-tropical AGB map at 1-km resolution using an independent reference dataset of field observations and locally calibrated high-resolution biomass maps, harmonized and upscaled to 14 477 1-km AGB estimates. Our data fusion approach uses bias removal and weighted linear averaging that incorporates and spatializes the biomass patterns indicated by the reference data. The method was applied independently in areas (strata) with homogeneous error patterns of the input (Saatchi and Baccini) maps, which were estimated from the reference data and additional covariates. Based on the fused map, we estimated AGB stock for the tropics (23.4 N-23.4 S) of 375 Pg dry mass, 9-18% lower than the Saatchi and Baccini estimates. The fused map also showed differing spatial patterns of AGB over large areas, with higher AGB density in the dense forest areas in the Congo basin, Eastern Amazon and South-East Asia, and lower values in Central America and in most dry vegetation areas of Africa than either of the input maps. The validation exercise, based on 2118 estimates from the reference dataset not used in the fusion process, showed that the fused map had a RMSE 15-21% lower than that of the input maps and, most importantly, nearly unbiased estimates (mean bias 5 Mg dry mass ha(-1) vs. 21 and 28 Mg ha(-1) for the input maps). The fusion method can be applied at any scale including the policy-relevant national level, where it can provide improved biomass estimates by integrating existing regional biomass maps as input maps and additional, country-specific reference datasets.

  10. An integrated pan-tropical biomass map using multiple reference datasets.

    PubMed

    Avitabile, Valerio; Herold, Martin; Heuvelink, Gerard B M; Lewis, Simon L; Phillips, Oliver L; Asner, Gregory P; Armston, John; Ashton, Peter S; Banin, Lindsay; Bayol, Nicolas; Berry, Nicholas J; Boeckx, Pascal; de Jong, Bernardus H J; DeVries, Ben; Girardin, Cecile A J; Kearsley, Elizabeth; Lindsell, Jeremy A; Lopez-Gonzalez, Gabriela; Lucas, Richard; Malhi, Yadvinder; Morel, Alexandra; Mitchard, Edward T A; Nagy, Laszlo; Qie, Lan; Quinones, Marcela J; Ryan, Casey M; Ferry, Slik J W; Sunderland, Terry; Laurin, Gaia Vaglio; Gatti, Roberto Cazzolla; Valentini, Riccardo; Verbeeck, Hans; Wijaya, Arief; Willcock, Simon

    2016-04-01

    We combined two existing datasets of vegetation aboveground biomass (AGB) (Proceedings of the National Academy of Sciences of the United States of America, 108, 2011, 9899; Nature Climate Change, 2, 2012, 182) into a pan-tropical AGB map at 1-km resolution using an independent reference dataset of field observations and locally calibrated high-resolution biomass maps, harmonized and upscaled to 14 477 1-km AGB estimates. Our data fusion approach uses bias removal and weighted linear averaging that incorporates and spatializes the biomass patterns indicated by the reference data. The method was applied independently in areas (strata) with homogeneous error patterns of the input (Saatchi and Baccini) maps, which were estimated from the reference data and additional covariates. Based on the fused map, we estimated AGB stock for the tropics (23.4 N-23.4 S) of 375 Pg dry mass, 9-18% lower than the Saatchi and Baccini estimates. The fused map also showed differing spatial patterns of AGB over large areas, with higher AGB density in the dense forest areas in the Congo basin, Eastern Amazon and South-East Asia, and lower values in Central America and in most dry vegetation areas of Africa than either of the input maps. The validation exercise, based on 2118 estimates from the reference dataset not used in the fusion process, showed that the fused map had a RMSE 15-21% lower than that of the input maps and, most importantly, nearly unbiased estimates (mean bias 5 Mg dry mass ha(-1) vs. 21 and 28 Mg ha(-1) for the input maps). The fusion method can be applied at any scale including the policy-relevant national level, where it can provide improved biomass estimates by integrating existing regional biomass maps as input maps and additional, country-specific reference datasets. PMID:26499288

  11. Regulation of skeletal muscle capillary growth in exercise and disease.

    PubMed

    Haas, Tara L; Nwadozi, Emmanuel

    2015-12-01

    Capillaries, which are the smallest and most abundant type of blood vessel, form the primary site of gas, nutrient, and waste transfer between the vascular and tissue compartments. Skeletal muscle exhibits the capacity to generate new capillaries (angiogenesis) as an adaptation to exercise training, thus ensuring that the heightened metabolic demand of the active muscle is matched by an improved capacity for distribution of gases, nutrients, and waste products. This review summarizes the current understanding of the regulation of skeletal muscle capillary growth. The multi-step process of angiogenesis is coordinated through the integration of a diverse array of signals associated with hypoxic, metabolic, hemodynamic, and mechanical stresses within the active muscle. The contributions of metabolic and mechanical factors to the modulation of key pro- and anti-angiogenic molecules are discussed within the context of responses to a single aerobic exercise bout and short-term and long-term training. Finally, the paradoxical lack of angiogenesis in peripheral artery disease and diabetes and the implications for disease progression and muscle health are discussed. Future studies that emphasize an integrated analysis of the mechanisms that control skeletal muscle capillary growth will enable development of targeted exercise programs that effectively promote angiogenesis in healthy individuals and in patient populations. PMID:26554747

  12. Regulation of skeletal muscle capillary growth in exercise and disease.

    PubMed

    Haas, Tara L; Nwadozi, Emmanuel

    2015-12-01

    Capillaries, which are the smallest and most abundant type of blood vessel, form the primary site of gas, nutrient, and waste transfer between the vascular and tissue compartments. Skeletal muscle exhibits the capacity to generate new capillaries (angiogenesis) as an adaptation to exercise training, thus ensuring that the heightened metabolic demand of the active muscle is matched by an improved capacity for distribution of gases, nutrients, and waste products. This review summarizes the current understanding of the regulation of skeletal muscle capillary growth. The multi-step process of angiogenesis is coordinated through the integration of a diverse array of signals associated with hypoxic, metabolic, hemodynamic, and mechanical stresses within the active muscle. The contributions of metabolic and mechanical factors to the modulation of key pro- and anti-angiogenic molecules are discussed within the context of responses to a single aerobic exercise bout and short-term and long-term training. Finally, the paradoxical lack of angiogenesis in peripheral artery disease and diabetes and the implications for disease progression and muscle health are discussed. Future studies that emphasize an integrated analysis of the mechanisms that control skeletal muscle capillary growth will enable development of targeted exercise programs that effectively promote angiogenesis in healthy individuals and in patient populations.

  13. A novel instrument for studying the flow behaviour of erythrocytes through microchannels simulating human blood capillaries.

    PubMed

    Sutton, N; Tracey, M C; Johnston, I D; Greenaway, R S; Rampling, M W

    1997-05-01

    A novel instrument has been developed to study the microrheology of erythrocytes as they flow through channels of dimensions similar to human blood capillaries. The channels are produced in silicon substrates using microengineering technology. Accurately defined, physiological driving pressures and temperatures are employed whilst precise, real-time image processing allows individual cells to be monitored continuously during their transit. The instrument characterises each cell in a sample of ca. 1000 in terms of its volume and flow velocity profile during its transit through a channel. The unique representation of the data in volume/velocity space provides new insight into the microrheological behaviour of blood. The image processing and subsequent data analysis enable the system to reject anomalous events such as multiple cell transits, thereby ensuring integrity of the resulting data. By employing an array of microfluidic flow channels we can integrate a number of different but precise and highly reproducible channel sizes and geometries within one array, thereby allowing multiple, concurrent isobaric measurements on one sample. As an illustration of the performance of the system, volume/velocity data sets recorded in a microfluidic device incorporating multiple channels of 100 microns length and individual widths ranging between 3.0 and 4.0 microns are presented. PMID:9211405

  14. On-chip integration of suspended InGaN/GaN multiple-quantum-well devices with versatile functionalities.

    PubMed

    Cai, Wei; Yang, Yongchao; Gao, Xumin; Yuan, Jialei; Yuan, Wei; Zhu, Hongbo; Wang, Yongjin

    2016-03-21

    We propose, fabricate and demonstrate on-chip photonic integration of suspended InGaN/GaN multiple quantum wells (MQWs) devices on the GaN-on-silicon platform. Both silicon removal and back wafer etching are conducted to obtain membrane-type devices, and suspended waveguides are used for the connection between p-n junction InGaN/GaN MQWs devices. As an in-plane data transmission system, the middle p-n junction InGaN/GaN MQWs device is used as a light emitting diode (LED) to deliver signals by modulating the intensity of the emitted light, and the other two devices act as photodetectors (PDs) to sense the light guided by the suspended waveguide and convert the photons into electrons, achieving 1 × 2 in-plane information transmission via visible light. Correspondingly, the three devices can function as independent PDs to realize multiple receivers for free space visible light communication. Further, the on-chip photonic platform can be used as an active electro-optical sensing system when the middle device acts as a PD and the other two devices serve as LEDs. The experimental results show that the auxiliary LED sources can enhance the amplitude of the induced photocurrent. PMID:27136794

  15. On-chip integration of suspended InGaN/GaN multiple-quantum-well devices with versatile functionalities.

    PubMed

    Cai, Wei; Yang, Yongchao; Gao, Xumin; Yuan, Jialei; Yuan, Wei; Zhu, Hongbo; Wang, Yongjin

    2016-03-21

    We propose, fabricate and demonstrate on-chip photonic integration of suspended InGaN/GaN multiple quantum wells (MQWs) devices on the GaN-on-silicon platform. Both silicon removal and back wafer etching are conducted to obtain membrane-type devices, and suspended waveguides are used for the connection between p-n junction InGaN/GaN MQWs devices. As an in-plane data transmission system, the middle p-n junction InGaN/GaN MQWs device is used as a light emitting diode (LED) to deliver signals by modulating the intensity of the emitted light, and the other two devices act as photodetectors (PDs) to sense the light guided by the suspended waveguide and convert the photons into electrons, achieving 1 × 2 in-plane information transmission via visible light. Correspondingly, the three devices can function as independent PDs to realize multiple receivers for free space visible light communication. Further, the on-chip photonic platform can be used as an active electro-optical sensing system when the middle device acts as a PD and the other two devices serve as LEDs. The experimental results show that the auxiliary LED sources can enhance the amplitude of the induced photocurrent.

  16. Decadal trends in global pelagic ocean chlorophyll: A new assessment integrating multiple satellites, in situ data, and models

    PubMed Central

    Gregg, Watson W; Rousseaux, Cécile S

    2014-01-01

    Quantifying change in ocean biology using satellites is a major scientific objective. We document trends globally for the period 1998–2012 by integrating three diverse methodologies: ocean color data from multiple satellites, bias correction methods based on in situ data, and data assimilation to provide a consistent and complete global representation free of sampling biases. The results indicated no significant trend in global pelagic ocean chlorophyll over the 15 year data record. These results were consistent with previous findings that were based on the first 6 years and first 10 years of the SeaWiFS mission. However, all of the Northern Hemisphere basins (north of 10° latitude), as well as the Equatorial Indian basin, exhibited significant declines in chlorophyll. Trend maps showed the local trends and their change in percent per year. These trend maps were compared with several other previous efforts using only a single sensor (SeaWiFS) and more limited time series, showing remarkable consistency. These results suggested the present effort provides a path forward to quantifying global ocean trends using multiple satellite missions, which is essential if we are to understand the state, variability, and possible changes in the global oceans over longer time scales. PMID:26213675

  17. Multiple levels of impaired neural plasticity and cellular resilience in bipolar disorder: Developing treatments using an integrated translational approach

    PubMed Central

    Machado-Vieira, Rodrigo; Soeiro-De-Souza, Marcio G.; Richards, Erica M.; Teixeira, Antonio L.; Zarate, Carlos A.

    2014-01-01

    Objectives This paper reviews the neurobiology of bipolar disorder (BD), particularly findings associated with impaired cellular resilience and plasticity. Methods PubMed/Medline articles and book chapters published over the last 20 years were identified using the following keyword combinations: BD, calcium, cytokines, endoplasmic reticulum (ER), genetics, glucocorticoids, glutamate, imaging, ketamine, lithium, mania, mitochondria, neuroplasticity, neuroprotection, neurotrophic, oxidative stress, plasticity, resilience, and valproate. Results BD is associated with impaired cellular resilience and synaptic dysfunction at multiple levels, associated with impaired cellular resilience and plasticity. These findings were partially prevented or even reversed with the use of mood stabilizers, but longitudinal studies associated with clinical outcome remain scarce. Conclusions Evidence consistently suggests that BD involves impaired neural plasticity and cellular resilience at multiple levels. This includes the genetic and intra- and intercellular signalling levels, their impact on brain structure and function, as well as the final translation into behaviour/cognitive changes. Future studies are expected to adopt integrated translational approaches using a variety of methods (e.g., microarray approaches, neuroimaging, genetics, electrophysiology, and the new generation of –omics techniques). These studies will likely focus on more precise diagnoses and a personalized medicine paradigm in order to develop better treatments for those who need them most. PMID:23998912

  18. Temporal averaging across multiple response options: insight into the mechanisms underlying integration.

    PubMed

    De Corte, Benjamin J; Matell, Matthew S

    2016-03-01

    Rats trained on a dual-duration, dual-modality peak-interval procedure (e.g., tone = 10 s/light = 20 s) often show unimodal response distributions with peaks that fall in between the anchor durations when both cues are presented as a simultaneous compound. Two hypotheses can explain this finding. According to the averaging hypothesis, rats integrate the anchor durations into an average during compound trials, with each duration being weighted by its respective reinforcement probability. According to the simultaneous temporal processing hypothesis, rats time both durations veridically and simultaneously during compound trials and respond continuously across both durations, thereby producing a unimodal response distribution with a peak falling in between the anchor durations. In the present compounding experiment, rats were trained to associate a tone and light with two different durations (e.g., 5 and 20 s, respectively). However, in contrast to previous experiments, each cue was also associated with a distinct response requirement (e.g., left nosepoke for tone/right nosepoke for light). On the majority of compound trials, responding on a given nosepoke fell close to its respective duration, but was shifted in the direction of the other cue's duration, suggesting rats timed an average of the two durations. However, more weight appeared to be given to the duration associated with the manipulandum on which the rat responded, rather than the duration associated with a higher reinforcement probability as predicted by the averaging hypothesis. Group differences were also observed, with rats trained to associate the tone and light with the short and long durations, respectively, being more likely to show these shifts than the counterbalanced modality-duration group (i.e., light-short/tone-long). This parallels group differences observed in past studies and suggest that cue weighting in response to stimulus compounds is influenced by the modality-duration relationship of

  19. Capillary electrophoresis for drug analysis

    NASA Astrophysics Data System (ADS)

    Lurie, Ira S.

    1999-02-01

    Capillary electrophoresis (CE) is a high resolution separation technique which is amenable to a wide variety of solutes, including compounds which are thermally degradable, non-volatile and highly polar, and is therefore well suited for drug analysis. Techniques which have been used in our laboratory include electrokinetic chromatography (ECC), free zone electrophoresis (CZE) and capillary electrochromatography (CEC). ECC, which uses a charged run buffer additive which migrates counter to osmotic flow, is excellent for many applications, including, drug screening and analyses of heroin, cocaine and methamphetamine samples. ECC approaches include the use of micelles and charged cyclodextrins, which allow for the separation of complex mixtures. Simultaneous separation of acidic, neutral and basic solutes and the resolution of optical isomers and positional isomers are possible. CZE has been used for the analysis of small ions (cations and anions) in heroin exhibits. For the ECC and CZE experiments performed in our laboratory, uncoated capillaries were used. In contrast, CEC uses capillaries packed with high performance liquid chromatography stationary phases, and offers both high peak capacities and unique selectivities. Applications include the analysis of cannabinoids and drug screening. Although CE suffers from limited concentration sensitivity, it is still applicable to trace analysis of drug samples, especially when using injection techniques such as stacking, or detection schemes such as laser induced fluorescence and extended pathlength UV.

  20. Capillary Rise in a Wedge

    ERIC Educational Resources Information Center

    Piva, M.

    2009-01-01

    In introductory-level physics courses, the concept of surface tension is often illustrated using the example of capillary rise in thin tubes. In this paper the author describes experiments conducted using a planar geometry created with two small plates forming a thin wedge. The distribution of the fluid entering the wedge can be studied as a…

  1. Simulations of shearing of capillary bridges.

    PubMed

    Wiklund, H S; Uesaka, T

    2012-03-01

    Capillary bridges are considered as the major source of interaction forces acting in wet particulate systems. We study the dynamic shear resistance by using a lattice Boltzmann numerical scheme for a binary fluid. The shear resistance force showed very little dependence on surface tension and contact angle. Instead, the shear resistance is a dynamic phenomenon and a major contributing factor is the distortion of the flow field caused by the presence of interfaces. This distortion of the flow field is geometry-dependent: in smaller diameter bridges the proportion of this distorted flow field becomes larger and it makes a major contribution to the shear resistance force. In other words multiple bridges have an enhancement effect on shear resistance. PMID:22401464

  2. Capillary blood viscosity in microcirculation.

    PubMed

    Cortinovis, A; Crippa, A; Cavalli, R; Corti, M; Cattaneo, L

    2006-01-01

    As known, at the arteriolar level there is the highest resistance to the flow due to the section and to the velocity with an average pressure fall of 50 mmHg (from 85 to 35 mmHg). This resistance is expressed in sec(-1) by the ratio W/2r. This ratio is very high with an average value of 332 sec(-1) and viscosity at this high shear-rate is negligible. At the capillary level the pressure fall is 11.5 mmHg but the vascular resistance W/2r is much lower, on average 32 sec(-1). We can say that if a resistance of 333 sec(-1) corresponds with a pressure fall of 50 mmHg, then a resistance of 32 sec(-1) should correspond with a pressure fall of 4.8 mmHg. The highest pressure fall is due to another kind of resistance which we can define as "Capillary Blood Viscosity" because it depends on the rheological and structural characteristics of the blood. Our instrument reproduces the structure of the capillary district in an experimental model and measures the General Blood Viscosity (GBV) and the Capillary Blood Viscosity (CBV) at the same shear-rate and in particular at the low shear-rate when in non-Newtonian fluids the highest increase in viscosity appears. Consequently, at the capillary, viscosity is dominant with respect to the other geometric and physical resistances. Moreover, the percentage ratio between the GBV and the CBV gives a physical measure of erythrocyte deformability. Knowing viscosity at shear-rate present in the circulatory system, we can obtain the size of RBCs aggregates in the different circulatory districts and their characteristics expressed like "aggregation bond". Changes in CBV are the only possibility in clinical practice to improve the circulatory flow in the capillary district because it is not sure that changes in the arteriolar section can improve the capillary flow or rather open arterio-venous anastomosis. Moreover, in the systemic circulation the aggregate size allows us to point out the phenomenon of cell adhesion because the presence of

  3. Analysis of microRNA and Gene Expression Profiles in Multiple Sclerosis: Integrating Interaction Data to Uncover Regulatory Mechanisms

    PubMed Central

    Freiesleben, Sherry; Hecker, Michael; Zettl, Uwe Klaus; Fuellen, Georg; Taher, Leila

    2016-01-01

    MicroRNAs (miRNAs) have been reported to contribute to the pathophysiology of multiple sclerosis (MS), an inflammatory disorder of the central nervous system. Here, we propose a new consensus-based strategy to analyse and integrate miRNA and gene expression data in MS as well as other publically available data to gain a deeper understanding of the role of miRNAs in MS and to overcome the challenges posed by studies with limited patient sample sizes. We processed and analysed microarray datasets, and compared the expression of genes and miRNAs in the blood of MS patients and controls. We then used our consensus and integration approach to construct two molecular networks dysregulated in MS: a miRNA- and a gene-based network. We identified 18 differentially expressed (DE) miRNAs and 128 DE genes that may contribute to the regulatory alterations behind MS. The miRNAs were linked to immunological and neurological pathways, and we exposed let-7b-5p and miR-345-5p as promising blood-derived disease biomarkers in MS. The results suggest that DE miRNAs are more informative than DE genes in uncovering pathways potentially involved in MS. Our findings provide novel insights into the regulatory mechanisms and networks underlying MS. PMID:27694855

  4. Development of a Multiple Input Integrated Pole-to-Pole Global CMORPH

    NASA Astrophysics Data System (ADS)

    Joyce, R.; Xie, P.

    2013-12-01

    A test system is being developed at NOAA Climate Prediction Center (CPC) to produce a passive microwave (PMW), IR-based, and model integrated high-resolution precipitation estimation on a 0.05olat/lon grid covering the entire globe from pole to pole. Experiments have been conducted for a summer Test Bed period using data for July and August of 2009. The pole-to-pole global CMORPH system is built upon the Kalman Filter based CMORPH algorithm of Joyce and Xie (2011). First, retrievals of instantaneous precipitation rates from PMW observations aboard nine low earth orbit (LEO) satellites are decoded and pole-to-pole mapped onto a 0.05olat/lon grid over the globe. Also precipitation estimates from LEO AVHRR retrievals are derived using a PDF matching of LEO IR with calibrated microwave combined (MWCOMB) precipitation retrievals. The motion vectors for the precipitating cloud systems are defined using information from both satellite IR observations and precipitation fields generated by the NCEP Climate Forecast System Reanalysis (CFSR). To this end, motion vectors are first computed for the CFSR hourly precipitation fields through cross-correlation analysis of consecutive hourly precipitation fields on the global T382 (~35 km) grid. In a similar manner, separate processing is also performed on satellite IR-based precipitation estimates to derive motion vectors from observations. A blended analysis of precipitating cloud motion vectors is then constructed through the combination of CFSR and satellite-derived vectors utilizing a two-dimensional optimal interpolation (2D-OI) method, in which CFSR-derived motion vectors are used as the first guess and subsequently satellite derived vectors modify the first guess. Weights used to generate the combinations are defined under the OI framework as a function of error statistics for the CFSR and satellite IR based motion vectors. The screened and calibrated PMW and AVHRR derived precipitation estimates are then separately

  5. Gradient elution in capillary electrochromatography

    SciTech Connect

    Anex, D.; Rakestraw, D.J.; Yan, Chao; Dadoo, R.; Zare, R.N.

    1997-08-01

    In analogy to pressure-driven gradient techniques in high-performance liquid chromatography, a system has been developed for delivering electroosmotically-driven solvent gradients for capillary electrochromatography (CEC). Dynamic gradients with sub-mL/min flow rates are generated by merging two electroosmotic flows that are regulated by computer-controlled voltages. These flows are delivered by two fused-silica capillary arms attached to a T-connector, where they mix and then flow into a capillary column that has been electrokinetically packed with 3-mm reversed-phase particles. The inlet of one capillary arm is placed in a solution reservoir containing one mobile phase and the inlet of the other is placed in a second reservoir containing a second mobile phase. Two independent computer-controlled programmable high-voltage power supplies (0-50 kV)--one providing an increasing ramp and the other providing a decreasing ramp--are used to apply variable high-voltage potentials to the mobile phase reservoirs to regulate the electroosmotic flow in each arm. The ratio of the electroosmotic flow rates between the two arms is changed with time according to the computer-controlled voltages to deliver the required gradient profile to the separation column. Experiments were performed to confirm the composition of the mobile phase during a gradient run and to determine the change of the composition in response to the programmed voltage profile. To demonstrate the performance of electroosmotically-driven gradient elution in CEC, a mixture of 16 polycyclic aromatic hydrocarbons (PAHs) was separated in less than 90 minutes. This gradient technique is expected to be well-suited for generating not only solvent gradients in CEC, but also other types of gradients such as pH- and ionic-strength gradients in capillary electrokinetic separations and analyses.

  6. Fabrication of a capillary immunosensor in polymethyl methacrylate.

    PubMed

    Holt, David B; Gauger, Paul R; Kusterbeck, Anne W; Ligler, Frances S

    2002-01-01

    A method for fabricating capillary-based immunosensors in a coupon milled from an inexpensive, commodity plastic (PMMA, plexiglass) is demonstrated. The key feature of the technique is the use of sol-gel technology to deposit a glass-like (Si [bond] OH) film on surfaces of the plastic capillary channels to facilitate antibody immobilization. The utility of this method was demonstrated in the context of continuous flow displacement immunosensors for the explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX). These sensors exhibited sensitivity to low microg/l RDX concentrations and peak-to-peak signal variations that were generally less than 10% for multiple injections at a single RDX concentration. The useful lifetime of the coupons in these experiments was greater than 10 h even after multiple exposures to high (1000 microg/l) RDX levels. This sensor platform has the physical characteristics needed for a portable field instrument: small, light-weight, and rugged.

  7. Capillary filling dynamics of viscoelastic fluids

    NASA Astrophysics Data System (ADS)

    Bandopadhyay, Aditya; Ghosh, Uddipta; Chakraborty, Suman

    2014-05-01

    We consider the filling of a capillary by a viscoelastic fluid described by the Phan-Thien-Tanner (PTT) constitutive behavior. By considering both vertical capillary filling and horizontal capillary filling, we demarcate the role played by gravity and fluid rheology towards long-time oscillations in the capillary penetration depth. We also consider the isothermal filling of the capillary for a closed channel and thus bring out the fundamental differences in the nature of capillary filling for PTT and Newtonian fluids for closed channels in comparison to open channels. Through a scaling analysis, we highlight a distinct viscoelastic regime in the horizontal capillary filling which is in contrast to the Washburn scaling seen in the case of Newtonian fluids. Such an analysis with a very general constitutive behavior is therefore expected to shed light on many areas of microfluidics which focus on biofluids that are often well described by the PTT constitutive behavior.

  8. [Determination of serum proteins by high performance capillary zone electrophoresis].

    PubMed

    Zhang, N; Tang, Y; Hao, D M; Zheng, L; Qiu, G B

    1999-11-01

    The separation method of serum proteins was established with an untreared 50 microns i.d. x 47 cm (40 cm to detector) capillary and detection of absorbance at 200 nm. Analysis was performed by pressure injectction 17.23 kPa.s and by applying 23 kV in the constant voltage mode. Serum samples were diluted 40-folds with assay buffer (12.5 mmol/L sodium borate, 1 mmol/L calcium lactate, 0.7 mmol/L magnesium sulfate, 1 mmol/L EDTA were mixed). A normal control serum protein was separated into 6 fractions. In pregnant serum, the alpha 0 was an additionally unknown fraction. Comparison of capillary electrophoresis with conventional cellulose acetate electrophoresis for analysis of serum proteins from normal control, pregnant women multiple myeloma and tonic rachitis patients indicates that capillary clectrophoresis is a new technique for the analysis of serum proteins because of its high efficiency, on-line data processing and automation. Capillary electrophoresis is the reliable technique for clinical diagnosis of serum protein abnormalities.

  9. Performance of single particle fritted capillary columns in electrochromatography.

    PubMed

    Zhang, Bo; Liu, Qing; Yang, Lijun; Wang, Qiuquan

    2013-01-11

    Development of capillary electrochromatography (CEC) largely depends on column technology. The past ten years or so have seen a great number of CEC works performed on monolithic columns, due to simplicity and robustness in column fabrication. Monolithic columns eliminate the issue of column fritting, which conventionally made particle-packed capillary columns fragile and introduced nonuniformity to the chromatographic bed. The particulate packing material, however, is still a popular type of stationary phase widely used in CEC, as the rich library of HPLC packing material provides a wide range of choices for chromatographic separations performed in electrodriven mode. In this study, we investigated a purely physical fritting method, single particle fritting technology, to immobilize particulate chromatographic material inside capillary tube in a sinter-free manner to produce robust capillary columns. Single particle fritted columns present significantly improved column-to-column reproducibility (n=10) in peak efficiency, retention factor, peak area and asymmetry (%RSD=5.4, 7.7, 6.2 and 6.1, respectively, at 26 kV), enabling their practical application in high throughput parallel analysis using multiple columns.

  10. Interfacial velocities and capillary pressure gradients during Haines jumps.

    PubMed

    Armstrong, Ryan T; Berg, Steffen

    2013-10-01

    Drainage is typically understood as a process where the pore space is invaded by a nonwetting phase pore-by-pore, the controlling parameters of which are represented by capillary number and mobility ratio. However, what is less understood and where experimental data are lacking is direct knowledge of the dynamics of pore drainage and the associated intrinsic time scales since the rate dependencies often observed with displacement processes are potentially dependent on these time scales. Herein, we study pore drainage events with a high speed camera in a micromodel system and analyze the dependency of interfacial velocity on bulk flow rate and spatial fluid configurations. We find that pore drainage events are cooperative, meaning that capillary pressure differences which extend over multiple pores directly affect fluid topology and menisci dynamics. Results suggest that not only viscous forces but also capillarity acts in a nonlocal way. Lastly, the existence of a pore morphological parameter where pore drainage transitions from capillary to inertial and/or viscous dominated is discussed followed by a discussion on capillary dispersion and time scale dependencies. We show that the displacement front is disperse when volumetric flow rate is less than the intrinsic time scale for a pore drainage event and becomes sharp when the flow rate is greater than the intrinsic time scale (i.e., overruns the pore drainage event), which clearly shows how pore-scale parameters influence macroscale flow behavior. PMID:24229279

  11. Efficient multiple-time-step integrators with distance-based force splitting for particle-mesh-Ewald molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Qian, Xiaoliang; Schlick, Tamar

    2002-04-01

    We develop an efficient multiple-time-step force splitting scheme for particle-mesh-Ewald molecular dynamics simulations. Our method exploits smooth switch functions effectively to regulate direct and reciprocal space terms for the electrostatic interactions. The reciprocal term with the near field contributions removed is assigned to the slow class; the van der Waals and regulated particle-mesh-Ewald direct-space terms, each associated with a tailored switch function, are assigned to the medium class. All other bonded terms are assigned to the fast class. This versatile protocol yields good stability and accuracy for Newtonian algorithms, with temperature and pressure coupling, as well as for Langevin dynamics. Since the van der Waals interactions need not be cut at short distances to achieve moderate speedup, this integrator represents an enhancement of our prior multiple-time-step implementation for microcanonical ensembles. Our work also tests more rigorously the stability of such splitting schemes, in combination with switching methodology. Performance of the algorithms is optimized and tested on liquid water, solvated DNA, and solvated protein systems over 400 ps or longer simulations. With a 6 fs outer time step, we find computational speedup ratios of over 6.5 for Newtonian dynamics, compared with 0.5 fs single-time-step simulations. With modest Langevin damping, an outer time step of up to 16 fs can be used with a speedup ratio of 7.5. Theoretical analyses in our appendices produce guidelines for choosing the Langevin damping constant and show the close relationship among the leapfrog Verlet, velocity Verlet, and position Verlet variants.

  12. Scaling filtering and multiplicative cascade information integration techniques for geological, geophysical and geochemical data processing and geological feature recognition

    NASA Astrophysics Data System (ADS)

    Cheng, Q.

    2013-12-01

    This paper introduces several techniques recently developed based on the concepts of multiplicative cascade processes and multifractals for processing exploration geochemical and geophysical data for recognition of geological features and delineation of target areas for undiscovered mineral deposits. From a nonlinear point of view extreme geo-processes such as cloud formation, rainfall, hurricanes, flooding, landslides, earthquakes, igneous activities, tectonics and mineralization often show singular property that they may result in anomalous amounts of energy release or mass accumulation that generally are confined to narrow intervals in space or time. The end products of these non-linear processes have in common that they can be modeled as fractals or multifractals. Here we show that the three fundamental concepts of scaling in the context of multifractals: singularity, self-similarity and fractal dimension spectrum, make multifractal theory and methods useful for geochemical and geophysical data processing for general purposes of geological features recognition. These methods include: a local singularity analysis based on a area-density (C-A) multifractal model used as a scaling high-pass filtering technique capable of extracting weak signals caused by buried geological features; a suite of multifractal filtering techniques based on spectrum density - area (S-A) multifractal models implemented in various domain including frequency domain can be used for unmixing geochemical or geophysical fields according to distinct generalized self-similarities characterized in certain domain; and multiplicative cascade processes for integration of diverse evidential layers of information for prediction of point events such as location of mineral deposits. It is demonstrated by several case studies involving Fe, Sn, Mo-Ag and Mo-W mineral deposits that singularity method can be utilized to process stream sediment/soil geochemical data and gravity/aeromagnetic data as high

  13. A New Method for Simultaneous Measurement of the Integrated Reflectivity of Crystals at Multiple Orders of Reflection and Comparison with New Theoretical Calculations

    SciTech Connect

    S.G. Lee; J.G. Bak; Y.S. Jung; M. Bitter; K.W. Hill; G. Hoelzer; O. Wehrhan; E. Foerster

    2003-04-09

    This paper describes a new method for the simultaneous measurement of the integrated reflectivity of a crystal for multiple orders of reflection at a predefined Bragg angle. The technique is demonstrated with a mica crystal for Bragg angles of 43{sup o}, 47{sup o}, and 50{sup o}. The measured integrated reflectivity for Bragg reflections up to the 24th order is compared with new theoretical predictions, which are also presented in this paper.

  14. A rectangular capillary suction apparatus

    SciTech Connect

    Lee, D.J. . Dept. of Chemical Engineering); Hsu, Y.H. . Dept. of Chemical Engineering)

    1994-06-01

    Fluid flow and cake formation in a rectangular capillary suction apparatus (RCSA) are investigated experimentally and theoretically. Water, methanol, ethanol, and ethylene glycol are used to study the effects of liquid properties, and CaCO[sub 3], kaolin, and bentonite slurries are employed for studying the effects of cake formation on capillary suction-time (CST). A theory based on a diffusion-like approach is developed. The liquid saturation under the inner cell will approach a constant value when the wet front distance is large. A method based on this experimental finding for estimating the cake specific resistance is proposed. The agreement between experiments and calculations is close. The RCSA is superior to the cylindrical CSA when treating liquids with small diffusivities or slurries with high solid concentration and/or with high averaged specific resistance.

  15. Capillary electrophoresis in food authenticity.

    PubMed

    Kvasnicka, Frantisek

    2005-06-01

    Food authenticity is a term which simply refers to whether the food purchased by the consumer matches its description. False description can occur in many forms, from the undeclared addition of water or other cheaper materials, or the wrong declaration of the amount of a particular ingredient in the product, to making false statements about the source of ingredients i.e., their geographic, plant, or animal origin. The aim of this review is to summarize applications of capillary electrophoresis in food authentication.

  16. Capillary electrophoresis systems and methods

    SciTech Connect

    Dorairaj, Rathissh; Keynton, Robert S.; Roussel, Thomas J.; Crain, Mark M.; Jackson, Douglas J.; Walsh, Kevin M.; Naber, John F.; Baldwin, Richard P.; Franco, Danielle B.

    2011-08-02

    An embodiment of the invention is directed to a capillary electrophoresis apparatus comprising a plurality of separation micro-channels. A sample loading channel communicates with each of the plurality of separation channels. A driver circuit comprising a plurality of electrodes is configured to induce an electric field across each of the plurality of separation channels sufficient to cause analytes in the samples to migrate along each of the channels. The system further comprises a plurality of detectors configured to detect the analytes.

  17. Ionic Liquids in Capillary Electrophoresis.

    PubMed

    Holzgrabe, Ulrike; Wahl, Joachim

    2016-01-01

    Recently, a great interest was drawn toward ionic liquids (ILs) in analytical separation techniques. ILs possess many properties making them excellent additives in capillary electrophoresis (CE) background electrolytes (BGE). The most important property is the charge of the dissolved ions in BGE enabling the cations to interact with deprotonated silanol groups on the capillary surface and thereby modifying the electroosmotic flow (EOF). Ionic and/or proton donor-acceptor interactions between analyte and IL are possible interactions facilitating new kinds of separation mechanisms in CE. Further advantages of ILs are the high conductivity, the environmentally friendliness, and the good solubility for organic and inorganic compounds. The most commonly used ILs in capillary electrophoresis are dialkylimidazolium-based ILs, whereas for enantioseparation a lot of innovative chiral cations and anions were investigated.ILs are reported to be additives to a normal CE background electrolyte or the sole electrolyte in CE, nonaqueous CE (NACE), micellar electrokinetic chromatography (MEKC), and in enantioseparation. An overview of applications and separation mechanisms reported in the literature is given here, in addition to the enantioseparation of pseudoephedrine using tetrabutylammonium chloride (TBAC) as IL additive to an ammonium formate buffer containing β-cyclodextrin (β-CD). PMID:27645735

  18. Capillary Electrophoresis - Optical Detection Systems

    SciTech Connect

    Sepaniak, M. J.

    2001-08-06

    Molecular recognition systems are developed via molecular modeling and synthesis to enhance separation performance in capillary electrophoresis and optical detection methods for capillary electrophoresis. The underpinning theme of our work is the rational design and development of molecular recognition systems in chemical separations and analysis. There have been, however, some subtle and exciting shifts in our research paradigm during this period. Specifically, we have moved from mostly separations research to a good balance between separations and spectroscopic detection for separations. This shift is based on our perception that the pressing research challenges and needs in capillary electrophoresis and electrokinetic chromatography relate to the persistent detection and flow rate reproducibility limitations of these techniques (see page 1 of the accompanying Renewal Application for further discussion). In most of our work molecular recognition reagents are employed to provide selectivity and enhance performance. Also, an emerging trend is the use of these reagents with specially-prepared nano-scale materials. Although not part of our DOE BES-supported work, the modeling and synthesis of new receptors has indirectly supported the development of novel microcantilevers-based MEMS for the sensing of vapor and liquid phase analytes. This fortuitous overlap is briefly covered in this report. Several of the more significant publications that have resulted from our work are appended. To facilitate brevity we refer to these publications liberally in this progress report. Reference is also made to very recent work in the Background and Preliminary Studies Section of the Renewal Application.

  19. Treelike networks accelerating capillary flow

    NASA Astrophysics Data System (ADS)

    Shou, Dahua; Ye, Lin; Fan, Jintu

    2014-05-01

    Transport in treelike networks has received wide attention in natural systems, oil recovery, microelectronic cooling systems, and textiles. Existing studies are focused on transport behaviors under a constant potential difference (including pressure, temperature, and voltage) in a steady state [B. Yu and B. Li, Phys. Rev. E 73, 066302 (2006), 10.1103/PhysRevE.73.066302; J. Chen, B. Yu, P. Xu, and Y. Li, Phys. Rev. E 75, 056301 (2007), 10.1103/PhysRevE.75.056301]. However, dynamic (time-dependent) transport in such systems has rarely been concerned. In this work, we theoretically investigate the dynamics of capillary flow in treelike networks and design the distribution of radius and length of local branches for the fastest capillary flow. It is demonstrated that capillary flow in the optimized tree networks is faster than in traditional parallel tube nets under fixed constraints. As well, the flow time of the liquid is found to increase approximately linearly with penetration distance, which differs from Washburn's classic description that flow time increases as the square of penetration distance in a uniform tube.

  20. Capillary-driven automatic packaging.

    PubMed

    Ding, Yuzhe; Hong, Lingfei; Nie, Baoqing; Lam, Kit S; Pan, Tingrui

    2011-04-21

    Packaging continues to be one of the most challenging steps in micro-nanofabrication, as many emerging techniques (e.g., soft lithography) are incompatible with the standard high-precision alignment and bonding equipment. In this paper, we present a simple-to-operate, easy-to-adapt packaging strategy, referred to as Capillary-driven Automatic Packaging (CAP), to achieve automatic packaging process, including the desired features of spontaneous alignment and bonding, wide applicability to various materials, potential scalability, and direct incorporation in the layout. Specifically, self-alignment and self-engagement of the CAP process induced by the interfacial capillary interactions between a liquid capillary bridge and the top and bottom substrates have been experimentally characterized and theoretically analyzed with scalable implications. High-precision alignment (of less than 10 µm) and outstanding bonding performance (up to 300 kPa) has been reliably obtained. In addition, a 3D microfluidic network, aligned and bonded by the CAP technique, has been devised to demonstrate the applicability of this facile yet robust packaging technique for emerging microfluidic and bioengineering applications.

  1. Development of semi-sphere field-of-view sun sensor integrated with multiple linear CMOS image sensor

    NASA Astrophysics Data System (ADS)

    Zhao, Yao-kun; Li, Bin; Zhang, Fan

    2014-11-01

    Sun sensor is a key device in satellite's attitude determination system. It acquires satellite's attitude information by measuring sun light direction. Compared with area array CMOS sun sensor, the linear CMOS sun sensor has the advantages of low power consumption, light weight and relatively simple algorithm. Considering the pixel number, power consumption and efficiency of output, most sun sensors equipped with a single photosensitive unit usually have (+/-60)x(+/-60) field of view(FOV). Satellites usually use multiple sun sensors for semi-sphere field of view in total to meet the need of attitude measurement in all directions. Considering the need of large-scale FOV measurement and high integration level, this paper proposes a semi-sphere FOV sun sensor, of which coverage area can be (+/-90)x(+/-90) . A prototype has been made and the calibration of key component has been conducted. By integrating four photosensitive units, the semi-sphere FOV sun sensor is achieved, as a result, the demand of high integration can be realized for a micro-satellite device. The photosensitive unit consists of an N-shape slit mask and a linear CMOS image sensor. An N-shape slit model is established to acquire biaxial sun angles from analyzing the shift of 3 peak values from the image of the linear sensor. Embedded system has been designed and developed, in which the MCU control four photosensitive units. Calibration of one photosensitive unit, which is the key step in the process of the whole calibration of semi-sphere FOV sun sensor, has been conducted. As a result of the symmetry of N-shape slit, initial position of the linear image sensor can be fixed. Due to the installation error and machining deviation, centroid algorithm and data gridding technique is adopted to improve the accuracy. Experiments show that the single photosensitive unit can reach an angle accuracy of 0.1625°. Consequently, from the point of significant component in the sun sensor, initial calibration ensures

  2. Validation of STR typing by capillary electrophoresis.

    PubMed

    Moretti, T R; Baumstark, A L; Defenbaugh, D A; Keys, K M; Brown, A L; Budowle, B

    2001-05-01

    With the use of capillary electrophoresis (CE), high-resolution electrophoretic separation of short tandem repeat (STR) loci can be achieved in a semiautomated fashion. Laser-induced detection of fluorescently labeled PCR products and multicolor analysis enable the rapid generation of multilocus DNA profiles. In this study, conditions for typing PCR-amplified STR loci by capillary electrophoresis were investigated using the ABI Prism 310 Genetic Analyzer (Applied Biosystems). An internal size standard was used with each run to effectively normalize mobility differences among injections. Alleles were designated by comparison to allelic ladders that were run with each sample set. Multiple runs of allelic ladders and of amplified samples demonstrate that allele sizes were reproducible, with standard deviations typically less than 0.12 bases for fragments up to 317 bases in length (largest allele analyzed) separated in a 47 cm capillary. Therefore, 99.7% of all alleles that are the same length should fall within the measurement error window of +/- 0.36 bases. Microvariants of the tetranucleotide repeats were also accurately typed by the analytical software. Alleles differing in size by one base could be resolved in two-donor DNA mixtures in which the minor component comprised > or = 5% of the total DNA. Furthermore, the quantitative data format (i.e., peak amplitude) can in some instances assist in determining individual STR profiles in mixed samples. DNA samples from previously typed cases (typed for RFLP, AmpliType PM+DQA1, and/or D1S80) were amplified using AmpFlSTR Profiler Plus and COfiler and were evaluated using the ABI Prism 310. Most samples yielded typable results. Compared with previously determined results for other loci, there were no discrepancies as to the inclusion or exclusion of suspects or victims. CE thus provides efficient separation, resolution, sensitivity and precision, and the analytical software provides reliable genotyping of STR loci. The

  3. Progression of Diabetic Capillary Occlusion: A Model

    PubMed Central

    Gens, John Scott; Glazier, James A.; Burns, Stephen A.; Gast, Thomas J.

    2016-01-01

    An explanatory computational model is developed of the contiguous areas of retinal capillary loss which play a large role in diabetic maculapathy and diabetic retinal neovascularization. Strictly random leukocyte mediated capillary occlusion cannot explain the occurrence of large contiguous areas of retinal ischemia. Therefore occlusion of an individual capillary must increase the probability of occlusion of surrounding capillaries. A retinal perifoveal vascular sector as well as a peripheral retinal capillary network and a deleted hexagonal capillary network are modelled using Compucell3D. The perifoveal modelling produces a pattern of spreading capillary loss with associated macular edema. In the peripheral network, spreading ischemia results from the progressive loss of the ladder capillaries which connect peripheral arterioles and venules. System blood flow was elevated in the macular model before a later reduction in flow in cases with progression of capillary occlusions. Simulations differing only in initial vascular network structures but with identical dynamics for oxygen, growth factors and vascular occlusions, replicate key clinical observations of ischemia and macular edema in the posterior pole and ischemia in the retinal periphery. The simulation results also seem consistent with quantitative data on macular blood flow and qualitative data on venous oxygenation. One computational model applied to distinct capillary networks in different retinal regions yielded results comparable to clinical observations in those regions. PMID:27300722

  4. Fluid Delivery System For Capillary Electrophoretic Applications.

    DOEpatents

    Li, Qingbo; Liu, Changsheng; Kane, Thomas E.; Kernan, John R.; Sonnenschein, Bernard; Sharer, Michael V.

    2002-04-23

    An automated electrophoretic system is disclosed. The system employs a capillary cartridge having a plurality of capillary tubes. The cartridge has a first array of capillary ends projecting from one side of a plate. The first array of capillary ends are spaced apart in substantially the same manner as the wells of a microtitre tray of standard size. This allows one to simultaneously perform capillary electrophoresis on samples present in each of the wells of the tray. The system includes a stacked, dual carrousel arrangement to eliminate cross-contamination resulting from reuse of the same buffer tray on consecutive executions from electrophoresis. The system also has a gel delivery module containing a gel syringe/a stepper motor or a high pressure chamber with a pump to quickly and uniformly deliver gel through the capillary tubes. The system further includes a multi-wavelength beam generator to generate a laser beam which produces a beam with a wide range of wavelengths. An off-line capillary reconditioner thoroughly cleans a capillary cartridge to enable simultaneous execution of electrophoresis with another capillary cartridge. The streamlined nature of the off-line capillary reconditioner offers the advantage of increased system throughput with a minimal increase in system cost.

  5. Identification of novel adhesins of M. tuberculosis H37Rv using integrated approach of multiple computational algorithms and experimental analysis.

    PubMed

    Kumar, Sanjiv; Puniya, Bhanwar Lal; Parween, Shahila; Nahar, Pradip; Ramachandran, Srinivasan

    2013-01-01

    Pathogenic bacteria interacting with eukaryotic host express adhesins on their surface. These adhesins aid in bacterial attachment to the host cell receptors during colonization. A few adhesins such as Heparin binding hemagglutinin adhesin (HBHA), Apa, Malate Synthase of M. tuberculosis have been identified using specific experimental interaction models based on the biological knowledge of the pathogen. In the present work, we carried out computational screening for adhesins of M. tuberculosis. We used an integrated computational approach using SPAAN for predicting adhesins, PSORTb, SubLoc and LocTree for extracellular localization, and BLAST for verifying non-similarity to human proteins. These steps are among the first of reverse vaccinology. Multiple claims and attacks from different algorithms were processed through argumentative approach. Additional filtration criteria included selection for proteins with low molecular weights and absence of literature reports. We examined binding potential of the selected proteins using an image based ELISA. The protein Rv2599 (membrane protein) binds to human fibronectin, laminin and collagen. Rv3717 (N-acetylmuramoyl-L-alanine amidase) and Rv0309 (L,D-transpeptidase) bind to fibronectin and laminin. We report Rv2599 (membrane protein), Rv0309 and Rv3717 as novel adhesins of M. tuberculosis H37Rv. Our results expand the number of known adhesins of M. tuberculosis and suggest their regulated expression in different stages.

  6. Overcoming inherent resistance to histone deacetylase inhibitors in multiple myeloma cells by targeting pathways integral to the actin cytoskeleton

    PubMed Central

    Mithraprabhu, S; Khong, T; Spencer, A

    2014-01-01

    Histone deacetylase inhibitors (HDACi) are novel chemotherapeutics undergoing evaluation in clinical trials for the potential treatment of patients with multiple myeloma (MM). Although HDACi have demonstrable synergy when combined with proteasome inhibitors (PIs), recent evidence indicates that combination of HDACi and PI is beneficial only in a subset of patients with advanced MM, clearly indicating that other rational combinations should be explored. In this context we hypothesized that understanding the molecular signature associated with inherent resistance to HDACi would provide a basis for the identification of therapeutic combinations with improved clinical efficacy. Using human myeloma cell lines (HMCL) categorized as sensitive, intermediate or resistant to HDACi, gene expression profiling (GEP) and gene ontology enrichment analyses were performed to determine if a genetic signature associated with inherent resistance to HDACi-resistance could be identified. Correlation of GEP to increasing or decreasing sensitivity to HDACi indicated a unique 35-gene signature that was significantly enriched for two pathways – regulation of actin cytoskeleton and protein processing in endoplasmic reticulum. When HMCL and primary MM samples were treated with a combination of HDACi and agents targeting the signaling pathways integral to the actin cytoskeleton, synergistic cell death was observed in all instances, thus providing a rationale for combining these agents with HDACi for the treatment of MM to overcome resistance. This report validates a molecular approach for the identification of HDACi partner drugs and provides an experimental framework for the identification of novel therapeutic combinations for anti-MM treatment. PMID:24651437

  7. Comparing and combining data across multiple sources via integration of paired-sample data to correct for measurement error.

    PubMed

    Huang, Yunda; Huang, Ying; Moodie, Zoe; Li, Sue; Self, Steve

    2012-12-10

    In biomedical research such as the development of vaccines for infectious diseases or cancer, study outcomes measured by an assay or device are often collected from multiple sources or laboratories. Measurement error that may vary between laboratories needs to be adjusted for when combining samples across data sources. We incorporate such adjustment in the main study by comparing and combining independent samples from different laboratories via integration of external data, collected on paired samples from the same two laboratories. We propose the following: (i) normalization of individual-level data from two laboratories to the same scale via the expectation of true measurements conditioning on the observed; (ii) comparison of mean assay values between two independent samples in the main study accounting for inter-source measurement error; and (iii) sample size calculations of the paired-sample study so that hypothesis testing error rates are appropriately controlled in the main study comparison. Because the goal is not to estimate the true underlying measurements but to combine data on the same scale, our proposed methods do not require that the true values for the error-prone measurements are known in the external data. Simulation results under a variety of scenarios demonstrate satisfactory finite sample performance of our proposed methods when measurement errors vary. We illustrate our methods using real enzyme-linked immunosorbent spot assay data generated by two HIV vaccine laboratories.

  8. Comparing and Combining Data across Multiple Sources via Integration of Paired-sample Data to Correct for Measurement Error

    PubMed Central

    Huang, Yunda; Huang, Ying; Moodie, Zoe; Li, Sue; Self, Steve

    2014-01-01

    Summary In biomedical research such as the development of vaccines for infectious diseases or cancer, measures from the same assay are often collected from multiple sources or laboratories. Measurement error that may vary between laboratories needs to be adjusted for when combining samples across laboratories. We incorporate such adjustment in comparing and combining independent samples from different labs via integration of external data, collected on paired samples from the same two laboratories. We propose: 1) normalization of individual level data from two laboratories to the same scale via the expectation of true measurements conditioning on the observed; 2) comparison of mean assay values between two independent samples in the Main study accounting for inter-source measurement error; and 3) sample size calculations of the paired-sample study so that hypothesis testing error rates are appropriately controlled in the Main study comparison. Because the goal is not to estimate the true underlying measurements but to combine data on the same scale, our proposed methods do not require that the true values for the errorprone measurements are known in the external data. Simulation results under a variety of scenarios demonstrate satisfactory finite sample performance of our proposed methods when measurement errors vary. We illustrate our methods using real ELISpot assay data generated by two HIV vaccine laboratories. PMID:22764070

  9. Integrated analysis of phenome, genome, and transcriptome of hybrid rice uncovered multiple heterosis-related loci for yield increase

    PubMed Central

    Li, Dayong; Huang, Zhiyuan; Song, Shuhui; Xin, Yeyun; Mao, Donghai; Lv, Qiming; Zhou, Ming; Tian, Dongmei; Tang, Mingfeng; Wu, Qi; Liu, Xue; Chen, Tingting; Song, Xianwei; Fu, Xiqin; Zhao, Bingran; Liang, Chengzhi; Li, Aihong; Liu, Guozhen; Li, Shigui; Hu, Songnian; Cao, Xiaofeng; Yu, Jun; Yuan, Longping; Chen, Caiyan; Zhu, Lihuang

    2016-01-01

    Hybrid rice is the dominant form of rice planted in China, and its use has extended worldwide since the 1970s. It offers great yield advantages and has contributed greatly to the world’s food security. However, the molecular mechanisms underlying heterosis have remained a mystery. In this study we integrated genetics and omics analyses to determine the candidate genes for yield heterosis in a model two-line rice hybrid system, Liang-you-pei 9 (LYP9) and its parents. Phenomics study revealed that the better parent heterosis (BPH) of yield in hybrid is not ascribed to BPH of all the yield components but is specific to the BPH of spikelet number per panicle (SPP) and paternal parent heterosis (PPH) of effective panicle number (EPN). Genetic analyses then identified multiple quantitative trait loci (QTLs) for these two components. Moreover, a number of differentially expressed genes and alleles in the hybrid were mapped by transcriptome profiling to the QTL regions as possible candidate genes. In parallel, a major QTL for yield heterosis, rice heterosis 8 (RH8), was found to be the DTH8/Ghd8/LHD1 gene. Based on the shared allelic heterozygosity of RH8 in many hybrid rice cultivars, a common mechanism for yield heterosis in the present commercial hybrid rice is proposed. PMID:27663737

  10. Many Is Better Than One: An Integration of Multiple Simple Strategies for Accurate Lung Segmentation in CT Images.

    PubMed

    Shi, Zhenghao; Ma, Jiejue; Zhao, Minghua; Liu, Yonghong; Feng, Yaning; Zhang, Ming; He, Lifeng; Suzuki, Kenji

    2016-01-01

    Accurate lung segmentation is an essential step in developing a computer-aided lung disease diagnosis system. However, because of the high variability of computerized tomography (CT) images, it remains a difficult task to accurately segment lung tissue in CT slices using a simple strategy. Motived by the aforementioned, a novel CT lung segmentation method based on the integration of multiple strategies was proposed in this paper. Firstly, in order to avoid noise, the input CT slice was smoothed using the guided filter. Then, the smoothed slice was transformed into a binary image using an optimized threshold. Next, a region growing strategy was employed to extract thorax regions. Then, lung regions were segmented from the thorax regions using a seed-based random walk algorithm. The segmented lung contour was then smoothed and corrected with a curvature-based correction method on each axis slice. Finally, with the lung masks, the lung region was automatically segmented from a CT slice. The proposed method was validated on a CT database consisting of 23 scans, including a number of 883 2D slices (the number of slices per scan is 38 slices), by comparing it to the commonly used lung segmentation method. Experimental results show that the proposed method accurately segmented lung regions in CT slices. PMID:27635395

  11. Many Is Better Than One: An Integration of Multiple Simple Strategies for Accurate Lung Segmentation in CT Images

    PubMed Central

    Zhao, Minghua; Liu, Yonghong; Feng, Yaning; Zhang, Ming; He, Lifeng; Suzuki, Kenji

    2016-01-01

    Accurate lung segmentation is an essential step in developing a computer-aided lung disease diagnosis system. However, because of the high variability of computerized tomography (CT) images, it remains a difficult task to accurately segment lung tissue in CT slices using a simple strategy. Motived by the aforementioned, a novel CT lung segmentation method based on the integration of multiple strategies was proposed in this paper. Firstly, in order to avoid noise, the input CT slice was smoothed using the guided filter. Then, the smoothed slice was transformed into a binary image using an optimized threshold. Next, a region growing strategy was employed to extract thorax regions. Then, lung regions were segmented from the thorax regions using a seed-based random walk algorithm. The segmented lung contour was then smoothed and corrected with a curvature-based correction method on each axis slice. Finally, with the lung masks, the lung region was automatically segmented from a CT slice. The proposed method was validated on a CT database consisting of 23 scans, including a number of 883 2D slices (the number of slices per scan is 38 slices), by comparing it to the commonly used lung segmentation method. Experimental results show that the proposed method accurately segmented lung regions in CT slices. PMID:27635395

  12. MULTIPASS, a rice R2R3-type MYB transcription factor, regulates adaptive growth by integrating multiple hormonal pathways.

    PubMed

    Schmidt, Romy; Schippers, Jos H M; Mieulet, Delphine; Obata, Toshihiro; Fernie, Alisdair R; Guiderdoni, Emmanuel; Mueller-Roeber, Bernd

    2013-10-01

    Growth regulation is an important aspect of plant adaptation during environmental perturbations. Here, the role of MULTIPASS (OsMPS), an R2R3-type MYB transcription factor of rice, was explored. OsMPS is induced by salt stress and expressed in vegetative and reproductive tissues. Over-expression of OsMPS reduces growth under non-stress conditions, while knockdown plants display increased biomass. OsMPS expression is induced by abscisic acid and cytokinin, but is repressed by auxin, gibberellin and brassinolide. Growth retardation caused by OsMPS over-expression is partially restored by auxin application. Expression profiling revealed that OsMPS negatively regulates the expression of EXPANSIN (EXP) and cell-wall biosynthesis as well as phytohormone signaling genes. Furthermore, the expression of OsMPS-dependent genes is regulated by auxin, cytokinin and abscisic acid. Moreover, we show that OsMPS is a direct upstream regulator of OsEXPA4, OsEXPA8, OsEXPB2, OsEXPB3, OsEXPB6 and the endoglucanase genes OsGLU5 and OsGLU14. The multiple responses of OsMPS and its target genes to various hormones suggest an integrative function of OsMPS in the cross-talk between phytohormones and the environment to regulate adaptive growth.

  13. Quantifying the cleanliness of glass capillaries.

    PubMed

    Bowman, C L

    1998-01-01

    I used capillary rise methods to investigate the lumenal surface properties of quartz (fused silica, Amersil T-08), borosilicate (Corning 7800), and high-lead glass (Corning 0010) capillaries commonly used to make patch pipets. I calculated the capillary rise and contact angle for water and methanol from weight measurements. The capillary rise was compared with the theoretical maximum value calculated by assuming each fluid perfectly wetted the lumenal surface of the glass (i.e., zero contact angle, which reflects the absence of surface contamination). For borosilicate, high-lead, and quartz capillaries, the rise for water was substantially less than the theoretical maximum rise. Exposure of the borosilicate, lead, and quartz capillaries to several cleaning methods resulted in substantially better--but not perfect--agreement between the theoretical maximum rise and calculated capillary rise. By contrast, the capillary rise for methanol was almost identical in untreated and cleaned capillaries, but less than its theoretical maximum rise. The residual discrepancy between the observed and theoretical rise for water could not be improved on by trying a variety of cleaning procedures, but some cleaning methods were superior to others. The water solubility of the surface contaminants, deduced from the effectiveness of repeated rinsing, was different for each of the three types of capillaries examined: Corning 7800 > quartz > Corning 0010. A surface film was also detected in quatz tubing with an internal filament. I conclude that these borosilicate, quartz, and high-lead glass capillaries have a film on the lumenal surface, which can be removed using appropriate cleaning methods. The surface contaminants may be unique to each type of capillary and may also be hydrophobic. Two simple methods are presented to quantitate the cleanliness of glass capillary tubing commonly used to make pipets for studies of biological membranes. It is not known if the surface film is of

  14. Detachable strong cation exchange monolith, integrated with capillary zone electrophoresis and coupled with pH gradient elution, produces improved sensitivity and numbers of peptide identifications during bottom-up analysis of complex proteomes.

    PubMed

    Zhang, Zhenbin; Yan, Xiaojing; Sun, Liangliang; Zhu, Guijie; Dovichi, Norman J

    2015-04-21

    A detachable sulfonate-silica hybrid strong cation-exchange monolith was synthesized in a fused silica capillary, and used for solid phase extraction with online pH gradient elution during capillary zone electrophoresis-tandem mass spectrometry (CZE-MS/MS) proteomic analysis. Tryptic digests were prepared in 50 mM formic acid and loaded onto the strong cation-exchange monolith. Fractions were eluted using a series of buffers with lower concentration but higher pH values than the 50 mM formic acid background electrolyte. This combination of elution and background electrolytes results in both sample stacking and formation of a dynamic pH junction and allows use of relatively large elution buffer volumes while maintaining reasonable peak efficiency and resolution. A series of five pH bumps were applied to elute E. coli tryptic peptides from the monolith, followed by analysis using CZE coupled to an LTQ-Orbitrap Velos mass spectrometer; 799 protein groups and 3381 peptides were identified from 50 ng of the digest in a 2.5 h analysis, which approaches the identification rate for this organism that was obtained with an Orbitrap Fusion. We attribute the improved numbers of peptide and protein identifications to the efficient fractionation by the online pH gradient elution, which decreased the complexity of the sample in each elution step and improved the signal intensity of low abundance peptides. We also performed a comparative analysis using a nanoACQUITY UltraPerformance LCH system. Similar numbers of protein and peptide identifications were produced by the two methods. Protein identifications showed significant overlap between the two methods, whereas peptide identifications were complementary.

  15. A detachable strong cation exchange monolith, integrated with capillary zone electrophoresis and coupled with pH gradient elution, produces improved sensitivity and numbers of peptide identifications during bottom-up analysis of complex proteomes

    PubMed Central

    Zhang, Zhenbin; Yan, Xiaojing; Sun, Liangliang; Zhu, Guijie; Dovichi, Norman J.

    2015-01-01

    A detachable sulfonate-silica hybrid strong cation-exchange monolith was synthesized in a fused silica capillary, and used for solid phase extraction with on-line pH gradient elution during capillary zone electrophoresis-tandem mass spectrometry (CZE-MS/MS) proteomic analysis. Tryptic digests were prepared in 50 mM formic acid and loaded onto the strong cation-exchange monolith. Fractions were eluted using a series of buffers with lower concentration but higher pH values than the 50 mM formic acid background electrolyte. This combination of elution and background electrolytes results in both sample stacking and formation of a dynamic pH junction, and allows use of relatively large elution buffer volumes while maintaining reasonable peak efficiency and resolution. A series of five pH bumps were applied to elute E. coli tryptic peptides from the monolith, followed by analysis using CZE coupled to an LTQ-Orbitrap Velos mass spectrometer; 799 protein groups and 3,381 peptides were identified from 50 ng of the digest in a 2.5 hour analysis, which approaches the identification rate for this organism that was obtained with an Orbitrap Fusion. We attribute the improved numbers of peptide and protein identifications to the efficient fractionation by the on-line pH gradient elution, which decreased the complexity of the sample in each elution step and improved the signal intensity of low abundance peptides. We also performed a comparative analysis using a nanoACQUITY UltraPerformance LCH system. Similar numbers of protein and peptide identifications were produced by the two methods. Protein identifications showed significant overlap between the two methods, whereas peptide identifications were complementary. PMID:25822566

  16. Solid-phase based on-chip DNA purification through a valve-free stepwise injection of multiple reagents employing centrifugal force combined with a hydrophobic capillary barrier pressure.

    PubMed

    Zhang, Hainan; Tran, Hong Hanh; Chung, Bong Hyun; Lee, Nae Yoon

    2013-03-21

    In this paper, we demonstrate a simple technique for sequentially introducing multiple sample liquids into microchannels driven by centrifugal force combined with a hydrophobic barrier pressure and apply the technique for performing solid-phase based on-chip DNA purification. Three microchannels with varying widths, all equipped with independent sample reservoirs at the inlets, were fabricated on a hydrophobic elastomer, poly(dimethylsiloxane) (PDMS). First, glass beads were packed inside the reaction chamber, and a whole cell containing the DNA extract was introduced into the widest channel by applying centrifugal force for physical adsorption of the DNA onto the glass beads. Next, washing and elution solutions were sequentially introduced into the intermediate and narrowest microchannels, respectively, by gradually increasing the amount of centrifugal force. Through a precise manipulation of the centrifugal force, the DNA adsorbed onto the glass beads was successfully washed and eluted in a continuous manner without the need to introduce each solution manually. A stepwise injection of liquids was successfully demonstrated using multiple ink solutions, the results of which corresponded well with the theoretical analyses. As a practical application, the D1S80 locus of human genomic DNA, which is widely used for forensic purposes, was successfully purified using the microdevice introduced in this study, as demonstrated through successful target amplification. This will pave the way for the construction of a control-free valve system for realizing on-chip DNA purification, which is one of the most labor-intensive and hard-to-miniaturize components, on a greatly simplified and miniaturized platform employing hydrophobic PDMS.

  17. Capillary Versus Aspiration Biopsy: Effect of Needle Size and Length on the Cytopathological Specimen Quality

    SciTech Connect

    Hopper, Kenneth D.; Grenko, Ronald T.; Fisher, Alicia I.; TenHave, Thomas R.

    1996-09-15

    Purpose: To test the value of the nonaspiration, or capillary, biopsy technique by experimental comparison with the conventional fine-needle aspiration technique using various needle gauges and lengths. Methods: On fresh hepatic and renal tissue from five autopsies, multiple biopsy specimens were taken with 20, 22, and 23-gauge Chiba needles of 5, 10, 15, and 20-cm length, using the aspiration technique and the capillary technique. The resultant specimens were graded on the basis of a grading scheme by a cytopathologist who was blinded to the biopsy technique. Results: The capillary technique obtained less background blood or clot which could obscure diagnostic tissue, although not significantly different from the aspiration technique (p= 0.2). However, for the amount of cellular material obtained, retention of appropriate architecture, and mean score, the capillary technique performed statistically worse than aspiration biopsy (p < 0.01). In addition, with decreasing needle caliber (increasing needle gauge) and increasing length, the capillary biopsy was inferior to the aspiration biopsy. Conclusion: The capillary biopsy technique is inferior to the aspiration technique according to our study. When the capillary technique is to be applied, preference should be given to larger caliber, shorter needles.

  18. The Effects of Student Multiple Intelligence Preference on Integration of Earth Science Concepts and Knowledge within a Middle Grades Science Classroom.

    ERIC Educational Resources Information Center

    Cutshall, Lisa Christine

    This research was conducted in an eastern Tennessee 8th grade science classroom with 99 students participating. The action research project attempted to examine an adolescent science student's integration of science concepts within a project-based setting using the multiple intelligence theory. In an effort to address the national science…

  19. Integrating Multiple Intelligences and Learning Styles on Solving Problems, Achievement in, and Attitudes towards Math in Six Graders with Learning Disabilities in Cooperative Groups

    ERIC Educational Resources Information Center

    Eissa, Mourad Ali; Mostafa, Amaal Ahmed

    2013-01-01

    This study investigated the effect of using differentiated instruction by integrating multiple intelligences and learning styles on solving problems, achievement in, and attitudes towards math in six graders with learning disabilities in cooperative groups. A total of 60 students identified with LD were invited to participate. The sample was…

  20. Capillary Phenomena at Nanoscales: Electrowetting and Capillary Adhesion

    NASA Astrophysics Data System (ADS)

    Robbins, Mark

    2011-11-01

    Theories of capillary phenomena have traditionally been based on continuum approximations that break down as dimensions shrink to nanometer scales. Molecular simulations are used to test the limits of continuum theory in electrowetting on dielectric (EWOD) and capillary adhesion between solids. In EWOD, a fluid drop is separated from an electrode by a dielectric. Increasing the voltage V between drop and electrode, decreases the contact angle θ, allowing the droplet to be manipulated. Simulations of nanoscale drops show the same behavior as experiments on millimeter drops. The contact angle follows the continuum Young-Lippmann equation (YLE) at low voltages and then saturates. The saturation mechanism has been difficult to identify in experiments. Simulations show that charged molecules are pulled from the drop by large electrostatic forces near the contact line. Saturation can be delayed by increasing molecular binding, lowering temperature or increasing dielectric constant. A local force balance equation is derived that agrees with the YLE below saturation and remains valid after saturation. Simulations of capillary adhesion examined the force between a spherical tip of radius R and a flat substrate. The shape of the meniscus agrees remarkably well with continuum theory down to nanometer separations, as does the adhesive force from interfacial tension. However, the total force may deviate by factors of two or have the opposite sign. While the component of the pressure along the substrate agrees with the Laplace pressure from continuum theory, the out-of âplane component does not. There may also be significant force oscillations associated with layering near the solids. The elastic response of the solid has little affect on adhesive forces. This material is based upon work supported by National Science Foundation Grant No. CMS-0103408.

  1. Capillary pumped loop body heat exchanger

    NASA Technical Reports Server (NTRS)

    Swanson, Theodore D. (Inventor); Wren, deceased, Paul (Inventor)

    1998-01-01

    A capillary pumped loop for transferring heat from one body part to another body part, the capillary pumped loop comprising a capillary evaporator for vaporizing a liquid refrigerant by absorbing heat from a warm body part, a condenser for turning a vaporized refrigerant into a liquid by transferring heat from the vaporized liquid to a cool body part, a first tube section connecting an output port of the capillary evaporator to an input of the condenser, and a second tube section connecting an output of the condenser to an input port of the capillary evaporator. A wick may be provided within the condenser. A pump may be provided between the second tube section and the input port of the capillary evaporator. Additionally, an esternal heat source or heat sink may be utilized.

  2. Capillary electrophoresis analysis of a wide variety of seized drugs using the same capillary with dynamic coatings.

    PubMed

    Lurie, Ira S; Hays, Patrick A; Parker, Kimberly

    2004-06-01

    Capillary electrophoresis methodology is presented for the routine analysis of a wide variety of seized drugs using the same capillary with dynamic coatings and multiple run buffers. The types of exhibits analyzed using diode array UV detection include phenethylamines, cocaine, oxycodone, heroin, lysergic acid diethylamide (LSD), opium, hallucinogenic mushrooms, and gamma-hydroxybutyrate-gamma-butyrolactone (GHB-GBL). Both qualitative and quantitative analyses are achieved using run buffers that contain additives that provide for secondary equilibrium and/or dynamic coating of the capillary. Dynamic coating of the capillary surface is accomplished by rapid flushes of 0.1 N sodium hydroxide, water, buffer containing polycation coating reagent, and a buffer containing a polyanionic coating reagent (with or without cyclodextrin(s)) or a micelle coating reagent. Dynamic coating with a polyanionic coating reagent is used for the analysis of moderately basic seized drugs and adulterants. The use of cyclodextrin in the run buffer not only allows for chiral analysis but also greatly enhances separation selectivity for achiral solutes. A capillary dynamically coated with a micelle allows for the analysis of neutral, acidic, and weakly basic drugs (GHB, GBL and neutral, acidic, and weakly basic adulterants). Dynamic coating, which gives rise to a relatively high and robust electroosmotic flow at pH < 7, allows for rapid, precise and reproducible separations. For a wide variety of drugs, excellent linearity and migration time precision and good peak area precision (external and internal standard) is obtained. Quantitative results for synthetic mixtures are in good agreement with actual values. Screening for adulterants is greatly enhanced by the use of automated library searches.

  3. Measurement of Liquid Viscosities in Tapered or Parabolic Capillaries.

    PubMed

    Ershov; Zorin; Starov

    1999-08-01

    The possibility of using tapered or parabolic capillaries for measurement of liquid viscosities is investigated both experimentally and theoretically. It is demonstrated that even small deviations in capillary radius from a constant value may substantially affect measurement results. Equations are derived which allow correct analysis of the measurement results in tapered or parabolic capillaries. The following cases are analyzed: a water imbibition into a tapered or parabolic capillary and displacement of one liquid by another immiscible liquid in tapered or parabolic capillaries. Two possibilities are considered: (a) the narrow end of the capillary as capillary inlet and (b) the wide end of the capillary as capillary inlet. Copyright 1999 Academic Press.

  4. Transmission of slow highly charged ions through glass capillaries: Role of the capillary shape

    NASA Astrophysics Data System (ADS)

    Zhou, C. L.; Simon, M.; Ikeda, T.; Guillous, S.; Iskandar, W.; Méry, A.; Rangama, J.; Lebius, H.; Benyagoub, A.; Grygiel, C.; Müller, A.; Döbeli, M.; Tanis, J. A.; Cassimi, A.

    2013-11-01

    Comparison of the transmission of 27-keV Ar9+ ions through insulating funnel- and conical-shaped glass capillaries of outlet diameters of ˜22 μm is reported. Beam intensities of 1, 5, and 10 pA were injected into both capillaries. Transmission at the untilted angle of 0° was measured as well as at a tilt angle of ˜0.5° for the funnel capillary and a tilt angle of ˜1.1° for the conical capillary. For the funnel capillary, blocking of transmission was observed, whereas, the transmission was continuous for the conical capillary. These measurements suggest that conical-shaped capillaries have transport properties that are different than funnel-shaped capillaries for slow highly charged ions.

  5. Malpighi and the discovery of capillaries.

    PubMed

    Pearce, J M S

    2007-01-01

    Leonardo da Vinci clearly observed and described capillaries. Using the microscope, Marcello Malpighi examined the brain and major organs to demonstrate their finer anatomical features. This led to his discovery in 1661, of capillaries that proved fundamental to our understanding of the vascular system in the brain and cord. He hypothesized that capillaries were the connection between arteries and veins that allowed blood to flow back to the heart in the circulation of the blood, as first asserted by William Harvey.

  6. Analysis of Small Ions with Capillary Electrophoresis.

    PubMed

    Aulakh, Jatinder Singh; Kaur, Ramandeep; Malik, Ashok Kumar

    2016-01-01

    Small inorganic ions are easily separated through capillary electrophoresis because they have a high charge-to-mass ratio and suffer little from some of the undesired phenomenon affecting higher molecular weight species like adsorption to the capillary wall, decomposition, and precipitation. This chapter is focused on the analysis of small ions other than metal ions using capillary electrophoresis. Methods are described for the determination of ions of nitrogen, phosphorus, sulfur, fluorine, chlorine, bromine, and iodine. PMID:27645739

  7. Non-contact acoustic trapping in circular cross-section glass capillaries: a numerical study.

    PubMed

    Gralinski, Ian; Alan, Tuncay; Neild, Adrian

    2012-11-01

    Ultrasonic particle manipulation has many applications in microfluidic systems. Such manipulation is achievable by establishing an ultrasonic standing wave in fluid filled micromachined chambers. In this work, the focus is on analyzing the trapping potential of water filled capillary tubes actuated ultrasonically. The curved walls necessitate the use of a finite element modeling approach. Multiple arrangements of the piezoelectric transducers were studied along with the effects of changing the capillary and piezoelectric transducer thicknesses. Additionally, different modes of driving the piezoelectric transducers were investigated. It was found that positioning four piezoelectric transducers equally spaced around the capillary tube provided the best force potential field for trapping polystyrene spheres in the center of the capillary. PMID:23145585

  8. Modelling the effect of pore structure and wetting angles on capillary rise in soils having different wettabilities

    NASA Astrophysics Data System (ADS)

    Czachor, Henryk

    2006-09-01

    SummaryCapillary rise in axis symmetrical sinusoidal capillary (SC) has been modelled. Analytical formula for meniscus radius, capillary pressure and meniscus rate in SC have been found. Capillary shape described by wall waviness highly influences all of them. The limit between wettability and repellency in such capillary is described by critical value of contact angle θc which is related to the pore geometry by the equation ctg( θc) = πd2, where d2 - pore wall waviness. Kinetics of capillary rise in sinusoidal capillary has been determined by numerical integration of meniscus rate equation for a wide range of pore wall waviness and several values of contact angles. Application of Washburn theory to the data obtained from simulation gives the contact angle value much higher than the true one. In contrast, the obtained pore radius value is usually well correlated with capillary neck. However, in some cases a calculated radius can be even smaller. Above conclusions have been qualitatively confirmed by experiments performed on glass beads and soils. Contact angle measured on flat glass was 27.4°. The calculations concerning the data from capillary rise experiments on 90-1000 μm fraction of glass powder and Washburn theory gave values ca. 80°. The contact angle values for peat soils and loamy sand have close values, which supports the opinion that non-cylindrical shape of soil pores highly influences both the wettability/repellency and the water flux in soils.

  9. Transient studies of capillary-induced flow

    NASA Technical Reports Server (NTRS)

    Reagan, M. K.; Bowman, W. J.

    1993-01-01

    This paper presents the numerical and experimental results of a study performed on the transient rise of fluid in a capillary tube. The capillary tube problem provides an excellent mechanism from which to launch an investigation into the transient flow of a fluid in a porous wick structure where capillary forces must balance both adverse gravitational effects and frictional losses. For the study, a capillary tube, initially charged with a small volume of water, was lowered into a pool of water. The behavior of the column of fluid during the transient that followed as more water entered the tube from the pool was both numerically and experimentally studied.

  10. Patient- and family-centered care coordination: a framework for integrating care for children and youth across multiple systems.

    PubMed

    2014-05-01

    Understanding a care coordination framework, its functions, and its effects on children and families is critical for patients and families themselves, as well as for pediatricians, pediatric medical subspecialists/surgical specialists, and anyone providing services to children and families. Care coordination is an essential element of a transformed American health care delivery system that emphasizes optimal quality and cost outcomes, addresses family-centered care, and calls for partnership across various settings and communities. High-quality, cost-effective health care requires that the delivery system include elements for the provision of services supporting the coordination of care across settings and professionals. This requirement of supporting coordination of care is generally true for health systems providing care for all children and youth but especially for those with special health care needs. At the foundation of an efficient and effective system of care delivery is the patient-/family-centered medical home. From its inception, the medical home has had care coordination as a core element. In general, optimal outcomes for children and youth, especially those with special health care needs, require interfacing among multiple care systems and individuals, including the following: medical, social, and behavioral professionals; the educational system; payers; medical equipment providers; home care agencies; advocacy groups; needed supportive therapies/services; and families. Coordination of care across settings permits an integration of services that is centered on the comprehensive needs of the patient and family, leading to decreased health care costs, reduction in fragmented care, and improvement in the patient/family experience of care.

  11. Time resolved EUV spectra from Zpinching capillary discharge plasma

    NASA Astrophysics Data System (ADS)

    Jancarek, Alexandr; Nevrkla, Michal; Nawaz, Fahad

    2015-09-01

    We developed symmetrically charged driver to obtain high voltage, high current Z-pinching capillary discharge. Plasma is created by up to 70 kA, 29 ns risetime current pulse passing through a 5 mm inner diameter, 224 mm long capillary filled with gas to initial pressure in the range of 1 kPa. Due to the low inductance design of the driver, the pinch is observable directly from the measured current curve. Time-integrated and time-resolved spectra of discharge plasma radiation are recorded together with the capillary current and analyzed. The most encouraging spectra were captured in the wavelength range 8.3 ÷ 14 nm. This spectral region contains nitrogen Balmer series lines including potentially lasing NVII 2 - 3 transition. Spectral lines are identified in the NIST database using the FLY kinetic code. The line of 13.38 nm wavelength, transition NVII 2 - 3, was observed in gated, and also in time-integrated spectra for currents >60 kA. This work has been supported by the Ministry of Education, Youth and Sports of the Czech Republic grants LG13029.

  12. Enantiomer Separations by Capillary Electrophoresis.

    PubMed

    Scriba, Gerhard K E; Harnisch, Henrik; Zhu, Qingfu

    2016-01-01

    Capillary electrophoresis (CE) is a versatile and flexible technique for analytical enantioseparations. This is due to the large variety of chiral selectors as well as the different operation modes including electrokinetic chromatography, micellar electrokinetic chromatography, and microemulsion electrokinetic chromatography. The chiral selector, which is added to the background electrolyte, represents a pseudostationary phase with its own electrophoretic mobility allowing a variety of different separation protocols. The present chapter briefly addresses the basic fundamentals of CE enantioseparations as well as the most frequently applied chiral selectors and separation modes. The practical example illustrates the separation of the enantiomers of a positively charged analyte using native and charged cyclodextrin derivatives as chiral selectors. PMID:27645742

  13. Capillary surfaces in exotic containers

    SciTech Connect

    Concus, P. ); Finn, R. . Dept. of Mathematics)

    1991-07-01

    A survey is presented of results to date for capillary surfaces in exotic'' containers. These containers have the property that each one admits a continuum of distinct equilibrium free surfaces, all bounding with the container walls the same volume of fluid, making the same contact angle at the trip interface curve, and having identical mechanical energies. The containers can be so designed that they are themselves axially symmetric but that the fluid configurations of minimizing energy cannot be axially symmetric. 9 refs., 2 figs.

  14. Capillary rafts and their destabilization

    NASA Astrophysics Data System (ADS)

    Protiere, Suzie; Abkarian, Manouk; Aristoff, Jeffrey; Stone, Howard

    2010-11-01

    Small objects trapped at an interface are very common in Nature (insects walking on water, ant rafts, bubbles or pollen at the water-air interface, membranes...) and are found in many multiphase industrial processes. The study of such particle-laden interfaces is therefore of practical as well as fundamental importance. Here we report experiments on the self-assembly of spherical particles into capillary rafts at an oil-water interface and elucidate how such rafts sink. We characterize different types of sinking behavior and show that it is possible to obtain "armored droplets," whereby the sinking oil is encapsulated within a shell of particles.

  15. High pressure pulsed capillary viscometry

    NASA Technical Reports Server (NTRS)

    Smith, R. L.; Walowitt, J. A.; Pan, C. H. T.

    1972-01-01

    An analytical and test program was conducted in order to establish the feasibility of a multichamber pulsed-capillary viscometer. The initial design incorporated a piston, ram, and seals which produced measured pulses up to 30,000 psi in the closed chamber system. Pressure pulses from one to ten milliseconds were investigated in a system volume of 1 cuin. Four test fluids: a MIL-L-7808, a 5P4E polyphenyl ether, a MIL-L-23699A, and a synthetic hydrocarbon were examined in the test pressure assembly. The pressure-viscosity coefficient and viscosity delay time were determined for the MIL-L-7808 lubricant tested.

  16. Capillary electrophoresis in metallodrug development.

    PubMed

    Holtkamp, Hannah; Hartinger, Christian G

    2015-09-01

    Capillary electrophoresis (CE) is a separation method based on differential migration of analytes in electric fields. The compatibility with purely aqueous separation media makes it a versatile tool in metallodrug research. Many metallodrugs undergo ligand exchange reactions that can easily be followed with this method and the information gained can even be improved by coupling the CE to advanced detectors, such as mass spectrometers. This gives the method high potential to facilitate the development of metallodrugs, especially when combined with innovative method development and experimental design. PMID:26547417

  17. Tissue proteomics using capillary isoelectric focusing-based multidimensional separations.

    PubMed

    Wang, Yueju; Balgley, Brian M; Lee, Cheng S

    2005-10-01

    The capabilities of capillary isoelectric focusing-based multidimensional separations for performing proteome analysis from minute samples create new opportunities in the pursuit of biomarker discovery using enriched and selected cell populations procured from tissue specimens. In this article, recent advances in online integration of capillary isoelectric focusing with nano-reversed phase liquid chromatography for achieving high-resolution peptide and protein separations prior to mass spectrometry analysis are reviewed, along with its potential application to tissue proteomics. These proteome technological advances combined with recently developed tissue microdissection techniques, provide powerful tools for those seeking to gain a greater understanding at the global level of the cellular machinery associated with human diseases such as cancer.

  18. Evaluation of capillary reinforced composites

    NASA Technical Reports Server (NTRS)

    Cahill, J. E.; Halase, J. F.; South, W. K.; Stoffer, L. J.

    1985-01-01

    Anti-icing of the inlet of jet engines is generally performed with high pressure heated air that is directed forward from the compressor through a series of pipes to various manifolds located near the structures to be anti-iced. From these manifolds, the air is directed to all flowpath surfaces that may be susceptible to ice formation. There the anti-icing function may be performed by either heat conduction or film heating. Unfortunately, the prospect of utilizing lighweight, high strength composites for inlet structures of jet engines has been frustrated by the low transverse thermal conductivity of such materials. It was the objective of this program to develop an advanced materials and design concept for anti-icing composite structures. The concept that was evaluated used capillary glass tubes embedded on the surface of a composite structure with heated air ducted through the tubes. An analytical computer program was developed to predict the anti-icing performance of such tubes and a test program was conducted to demonstrate actual performance of this system. Test data and analytical code results were in excellent agreement. Both indicate feasibility of using capillary tubes for surface heating as a means for composite engine structures to combat ice accumulation.

  19. Cryogenic Capillary Screen Heat Entrapment

    NASA Technical Reports Server (NTRS)

    Bolshinskiy, L.G.; Hastings, L.J.; Stathman, G.

    2007-01-01

    Cryogenic liquid acquisition devices (LADs) for space-based propulsion interface directly with the feed system, which can be a significant heat leak source. Further, the accumulation of thermal energy within LAD channels can lead to the loss of sub-cooled propellant conditions and result in feed system cavitation during propellant outflow. Therefore, the fundamental question addressed by this program was: "To what degree is natural convection in a cryogenic liquid constrained by the capillary screen meshes envisioned for LADs.?"Testing was first conducted with water as the test fluid, followed by LN2 tests. In either case, the basic experimental approach was to heat the bottom of a cylindrical column of test fluid to establish stratification patterns measured by temperature sensors located above and below a horizontal screen barrier position. Experimentation was performed without barriers, with screens, and with a solid barrier. The two screen meshes tested were those typically used by LAD designers, "200x1400" and "325x2300", both with Twill Dutch Weave. Upon consideration of both the water and LN2 data it was concluded that heat transfer across the screen meshes was dependent upon barrier thermal conductivity and that the capillary screen meshes were impervious to natural convection currents.

  20. Nonaqueous Capillary Electrophoresis Mass Spectrometry.

    PubMed

    Klampfl, Christian W; Himmelsbach, Markus

    2016-01-01

    The term nonaqueous capillary electrophoresis (NACE) commonly refers to capillary electrophoresis with purely nonaqueous background electrolytes (BGE). Main advantages of NACE are the possibility to analyze substances with very low solubility in aqueous media as well as separation selectivity that can be quite different in organic solvents (compared to water)-a property that can be employed for manipulation of separation selectivities. Mass spectrometry (MS) has become more and more popular as a detector in CE a fact that applies also for NACE. In the present chapter, the development of NACE-MS since 2004 is reviewed. Relevant parameters like composition of BGE and its influence on separation and detection in NACE as well as sheath liquid for NACE-MS are discussed. Finally, an overview of the papers published in the field of NACE-MS between 2004 and 2014 is given. Applications are grouped according to the field (analysis of natural products, biomedical analysis, food analysis, analysis of industrial products, and fundamental investigations). PMID:27645734

  1. Capillary Rise in Porous Media.

    PubMed

    Lago, Marcelo; Araujo, Mariela

    2001-02-01

    Capillary rise experiments were performed in columns filled with glass beads and Berea sandstones, using visual methods to register the advance of the water front. For the glass bead filled columns, early time data are well fitted by the Washburn equation. However, in the experiments, the advancing front exceeded the predicted equilibrium height. For large times, an algebraic behavior of the velocity of the front is observed (T. Delker et al., Phys. Rev. Lett. 76, 2902 (1996)). A model for studying the capillary pressure evolution in a regular assembly of spheres is proposed and developed. It is based on a quasi-static advance of the meniscus with a piston-like motion and allows us to estimate the hydraulic equilibrium height, with values very close to those obtained by fitting early time data to a Washburn equation. The change of regime is explained as a transition in the mechanism of advance of the meniscus. On the other hand, only the Washburn regime was observed for the sandstones. The front velocity was fitted to an algebraical form with an exponent close to 0.5, a value expected from the asymptotic limit of the Washburn equation. Copyright 2001 Academic Press. PMID:11161488

  2. Atomic Force Controlled Capillary Electrophoresis

    NASA Astrophysics Data System (ADS)

    Lewis, Aaron; Yeshua, Talia; Palchan, Mila; Lovsky, Yulia; Taha, Hesham

    2010-03-01

    Lithography based on scanning probe microscopic techniques has considerable potential for accurate & localized deposition of material on the nanometer scale. Controlled deposition of metallic features with high purity and spatial accuracy is of great interest for circuit edit applications in the semiconductor industry, for plasmonics & nanophotonics and for basic research in surface enhanced Raman scattering & nanobiophysics. Within the context of metal deposition we will review the development of fountain pen nanochemistry and its most recent emulation Atomic Force Controlled Capillary Electrophoresis (ACCE). Using this latter development we will demonstrate achievement of unprecedented control of nanoparticle deposition using a three-electrode geometry. Three electrodes are attached: one on the outside of a metal coated glass probe, one on the inside of a hollow probe in a solution containing Au nanoparticles in the capillary, and a third on the surface where the writing takes place. The three electrodes provide electrical pulses for accurate control of deposition and retraction of the liquid from the surface overcoming the lack of control seen in both dip pen lithography & fountain pen nanochemistry when the tip contacts the surface. With this development, we demonstrate depositing a single 1.3 nm Au nanoparticle onto surfaces such as semiconductors.

  3. Single-step co-integration of multiple expressible heterologous genes into the ribosomal DNA of the methylotrophic yeast Hansenula polymorpha.

    PubMed

    Klabunde, J; Diesel, A; Waschk, D; Gellissen, G; Hollenberg, C P; Suckow, M

    2002-05-01

    We have investigated the methylotrophic yeast Hansenula polymorpha as a host for the co-integration and expression of multiple heterologous genes using an rDNA integration approach. The ribosomal DNA (rDNA) of H. polymorpha was found to consist of a single rDNA cluster of about 50-60 repeats of an 8-kb unit located on chromosome II. A 2.4-kb segment of H. polymorpha rDNA encompassing parts of the 25S, the complete 5S and the non-transcribed spacer region between 25S and 18S rDNA was isolated and inserted into conventional integrative H. polymorpha plasmids harboring the Saccharomyces- cerevisiae-derived URA3 gene for selection. These rDNA plasmids integrated homologously into the rDNA repeats of a H. polymorpha (odc1) host as several independent clusters. Anticipating that this mode of multiple-cluster integration could be used for the simultaneous integration of several distinct rDNA plasmids, the host strain was co-transformed with a mixture of up to three different plasmids, all bearing the same URA3 selection marker. Transformations indeed resulted in mitotically stable strains harboring one, two, or all three plasmids integrated into the rDNA. The overall copy number of the plasmids integrated did not exceed the number of rDNA repeats present in the untransformed host strain, irrespective of the number of different plasmids involved. Strains harboring different plasmids co-expressed the introduced genes, resulting in functional proteins. Thus, this approach provides a new and attractive tool for the rapid generation of recombinant strains that simultaneously co-produce several proteins in desired stoichiometric ratios. PMID:12021801

  4. A loudspeaker-driven system for rapid and multiple solution exchanges in patch-clamp experiments.

    PubMed

    Méry, P F; Lechêne, P; Fischmeister, R

    1992-04-01

    A new and inexpensive system allowing rapid and synchronized changes of solutions around a membrane patch or a cell under voltage-clamp conditions is described. Four plastic capillary tubings (OD 640 microns; ID 430 microns) were glued together horizontally and attached to a coil of a commercially available loudspeaker. Servo-control of the position of the coil allowed the mouth of any of the capillaries to be positioned near the pipette tip within 6 ms. A high flow speed of the test solution was crucial to achieve rapid solution exchange. At a flow speed of 5 cm/s, complete exchange of the external environment of a frog ventricular cell was achieved within 20-30 ms. The time course of solution change was found to be 3-5 times faster at the tip of an open patch pipette. To preserve the physical integrity of the cell, the cell was usually perfused by a control capillary at a slow velocity (0.2-0.4 cm/s) and test solutions flowing out of adjacent capillaries at high velocity (4-5 cm/s) were applied to the cell only for short periods. Determination of the three-dimensional contamination profile around the mouth of the control capillary allowed the optimal conditions for the use of the system to be established and possible sources of contamination to be avoided between adjacent capillaries with unmatched flow speeds. Successive and multiple changes in external solutions could be easily synchronized with voltage-clamp depolarizations to examine the time course of the effect of drugs on voltage-operated ion channels.(ABSTRACT TRUNCATED AT 250 WORDS)

  5. Sheathless interface for coupling capillary electrophoresis with mass spectrometry

    SciTech Connect

    Wang, Chenchen; Tang, Keqi; Smith, Richard D.

    2014-06-17

    A sheathless interface for coupling capillary electrophoresis (CE) with mass spectrometry is disclosed. The sheathless interface includes a separation capillary for performing CE separation and an emitter capillary for electrospray ionization. A portion of the emitter capillary is porous or, alternatively, is coated to form an electrically conductive surface. A section of the emitter capillary is disposed within the separation capillary, forming a joint. A metal tube, containing a conductive liquid, encloses the joint.

  6. Enzymophoresis of nucleic acids by tandem capillary enzyme reactor-capillary zone electrophoresis.

    PubMed

    Nashabeh, W; el Rassi, Z

    1992-04-10

    Enzymophoresis with coupled heterogeneous capillary enzyme reactor-capillary zone electrophoresis was developed and evaluated in the area of nucleic acids. Ribonuclease T1, hexokinase and adenosine deaminase were successfully immobilized on the inner walls of short fused-silica capillaries through glutaraldehyde attachment. These open-tubular capillary enzyme reactors were quite stable for a prolonged period of use under operation conditions normally used in capillary zone electrophoresis. The capillary enzyme reactors coupled in series with capillary zone electrophoresis served as peak locator on the electropherogram, improved the system selectivity, and facilitated the quantitative determination of the analytes with good accuracy. Also, they allowed the on-line digestion and mapping of minute amounts of transfer ribonucleic acids, and the simultaneous synthesis and separation of nanogram quantities of oligonucleotides.

  7. The performance of integrated health care networks in continuity of care: a qualitative multiple case study of COPD patients

    PubMed Central

    Waibel, Sina; Vargas, Ingrid; Aller, Marta-Beatriz; Gusmão, Renata; Henao, Diana; Vázquez, M. Luisa

    2015-01-01

    Background Integrated health care networks (IHN) are promoted in numerous countries as a response to fragmented care delivery by providing a coordinated continuum of services to a defined population. However, evidence on their effectiveness and outcome is scarce, particularly considering continuity across levels of care; that is the patient's experience of connected and coherent care received from professionals of the different care levels over time. The objective was to analyse the chronic obstructive pulmonary disease (COPD) patients’ perceptions of continuity of clinical management and information across care levels and continuity of relation in IHN of the public health care system of Catalonia. Methods A qualitative multiple case study was conducted, where the cases are COPD patients. A theoretical sample was selected in two stages: (1) study contexts: IHN and (2) study cases consisting of COPD patients. Data were collected by means of individual, semi-structured interviews to the patients, their general practitioners and pulmonologists and review of records. A thematic content analysis segmented by IHN and cases with a triangulation of sources and analysists was carried out. Results COPD patients of all networks perceived that continuity of clinical management was existent due to clear distribution of roles for COPD care across levels, rapid access to care during exacerbations and referrals to secondary care when needed; nevertheless, patients of some networks highlighted too long waiting times to non-urgent secondary care. Physicians generally agreed with patients, however, also indicated unclear distribution of roles, some inadequate referrals and long waiting times to primary care in some networks. Concerning continuity of information, patients across networks considered that their clinical information was transferred across levels via computer and that physicians also used informal communication mechanisms (e-mail, telephone); whereas physicians

  8. Monitoring the Lavina di Roncovetro (RE, Italy) landslide by integrating traditional monitoring systems and multiple high-resolution topographic datasets

    NASA Astrophysics Data System (ADS)

    Fornaciai, Alessandro; Favalli, Massimiliano; Gigli, Giovanni; Nannipieri, Luca; Mucchi, Lorenzo; Intieri, Emanuele; Agostini, Andrea; Pizziolo, Marco; Bertolini, Giovanni; Trippi, Federico; Casagli, Nicola; Schina, Rosa; Carnevale, Ennio

    2016-04-01

    Roncovetro Landslide were generated at different times. The 3D models are then georeferenced and the digital elevation models (DEMs) created. By comparing the obtained DEMs, changes in the investigated area were detected and the sediment volumes, as well as the 3D displacement at the most active parts of the landslide quantified. In this work, we test the performance of the SFM techniques applied on active landslide by comparing them with the traditional monitoring systems, highlighting the strengths and weaknesses of both methods. In addition, we show the preliminary results obtained integrating the traditional monitoring systems and the multiple high-resolution topographic datasets, over a period of more than one year, used for investigating the spatial and the temporal evolution of the upper sector of the Roncovetro landslide.

  9. Intracranial capillary hemangioma in an elderly patient

    PubMed Central

    Okamoto, Ai; Nakagawa, Ichiro; Matsuda, Ryosuke; Nishimura, Fumihiko; Motoyama, Yasushi; Park, Young-Su; Nakamura, Mitsutoshi; Nakase, Hiroyuki

    2015-01-01

    Background: Capillary hemangiomas are neoplasms involving skin and soft tissue in infants. These lesions rarely involved an intracranial space and reported age distribution ranges from infancy to middle age. We report an extremely rare case of rapidly rising intracranial capillary hemangioma in an elderly woman. Case Description: The 82-year-old woman presented with vomiting, reduced level of consciousness, and worsening mental state. Computed tomography showed a contrast-enhanced extra-axial lesion in the left frontal operculum, although no intracranial mass lesion was identifiable from magnetic resonance imaging taken 2 years earlier. Complete surgical excision was performed and histopathological examination diagnosed benign capillary hemangioma consisting of a variety of dilated capillary blood vessels lined by endothelial cells. Conclusion: This is the first description of rapid growth of an intracranial capillary hemangioma in an elderly woman. These lesions are exceedingly rare in the elderly population, but still show the capacity for rapid growth. Complete excision would prevent further recurrence. PMID:26664868

  10. Modeling capillary barriers in unsaturated fractured rock

    NASA Astrophysics Data System (ADS)

    Wu, Yu-Shu; Zhang, W.; Pan, Lehua; Hinds, Jennifer; Bodvarsson, G. S.

    2002-11-01

    This work presents a series of numerical modeling studies that investigate the hydrogeologic conditions required to form capillary barriers and the effect that capillary barriers have on fluid flow and tracer transport processes in the unsaturated fractured rock of Yucca Mountain, Nevada, a potential site for storing high-level radioactive waste. The modeling approach is based on a dual-continuum formulation of coupled multiphase fluid and tracer transport through fractured porous rock. The numerical modeling results showed that effective capillary barriers can develop where both matrix and fracture capillary gradients tend to move water upward. Under the current hydrogeologic conceptualization of Yucca Mountain, strong capillary barrier effects exist for diverting a significant amount of moisture flow through the relatively shallow Paintbrush nonwelded unit, with major faults observed at the site serving as major downward pathways for laterally diverted percolation fluxes. In addition, we used observed field liquid saturation and goechemical isotopic data to check model results and found consistent agreement.

  11. Use of capillary electrophoresis to study methylation patterns in DNA

    NASA Astrophysics Data System (ADS)

    Voss, Karl; Roos, Pieter; Zhang, Jian Z.; Dovichi, Norman J.

    1996-04-01

    A four-color multiple capillary DNA sequencer is used to determine the methylation pattern of double stranded DNA. The DNA sample is treated with bisulfite under conditions that convert cytosine to uracil. Methyl-cytosine is inert under these reaction conditions. After PCR amplification, the reaction products are subjected to a four-color fluorescent Sanger sequencing reaction. The sequence is then determined by use of capillary electrophoresis. Comparison of the sequence obtained after bisulfite treatment with the original sequence reveals that certain of the Cs in the original sequence are converted to Ts. This conversion occurs only if the original C was not methylated. Those Cs that are common to both sequences were methylated in the original sequence. Methylation patterns have been implicated in aging, developmental biology, and cancer; however, there has been no simple and rapid method for determining the methylation pattern in genomic DNA. The method described in this paper is quick, simple, and accurate, and demonstrates an exciting application of capillary electrophoresis DNA sequencing.

  12. Chiral structures from achiral liquid crystals in cylindrical capillaries.

    PubMed

    Jeong, Joonwoo; Kang, Louis; Davidson, Zoey S; Collings, Peter J; Lubensky, Tom C; Yodh, A G

    2015-04-14

    We study chiral symmetry-broken configurations of nematic liquid crystals (LCs) confined to cylindrical capillaries with homeotropic anchoring on the cylinder walls (i.e., perpendicular surface alignment). Interestingly, achiral nematic LCs with comparatively small twist elastic moduli relieve bend and splay deformations by introducing twist deformations. In the resulting twisted and escaped radial (TER) configuration, LC directors are parallel to the cylindrical axis near the center, but to attain radial orientation near the capillary wall, they escape along the radius through bend and twist distortions. Chiral symmetry-breaking experiments in polymer-coated capillaries are carried out using Sunset Yellow FCF, a lyotropic chromonic LC with a small twist elastic constant. Its director configurations are investigated by polarized optical microscopy and explained theoretically with numerical calculations. A rich phenomenology of defects also arises from the degenerate bend/twist deformations of the TER configuration, including a nonsingular domain wall separating domains of opposite twist handedness but the same escape direction and singular point defects (hedgehogs) separating domains of opposite escape direction. We show the energetic preference for singular defects separating domains of opposite twist handedness compared with those of the same handedness, and we report remarkable chiral configurations with a double helix of disclination lines along the cylindrical axis. These findings show archetypally how simple boundary conditions and elastic anisotropy of confined materials lead to multiple symmetry breaking and how these broken symmetries combine to create a variety of defects. PMID:25825733

  13. Droplet microfluidics for postcolumn reactions in capillary electrophoresis.

    PubMed

    Abdul Keyon, Aemi S; Guijt, Rosanne M; Bolch, Christopher J; Breadmore, Michael C

    2014-12-01

    A postcolumn reaction system based on droplet microfluidics was developed for capillary electrophoresis (CE). Analytes were separated using capillary zone electrophoresis (CZE) and electrophoretically transferred into droplets. The use of a micro cross for positioning a salt bridge-electrode opposite the separation capillary outlet is the key element for maintaining the electrical connection during electrophoretic separation. As the first of its kind, positioning the droplets in the electric field eliminated the need for electroosmotic flow (EOF) or hydrodynamic flow for droplet compartmentalization. Depending on the total flow rate of both aqueous and oil phases, droplets of water-in-oil could be formed having frequencies between 0.7 and 3.7 Hz with a size of approximately 14 nL per droplet. Compartmentalized in the droplets, analytes reacted with reagents already present in the droplets to facilitate detection. The periodate oxidation of paralytic shellfish toxins (PSTs) was demonstrated, overcoming the limitation of precolumn oxidation, which results in multiple and sometimes identical oxidation products formed from the different PSTs. Compartmentalization allows the oxidation products for each peak to be contained and to contribute to a single fluorescence signal, preserving the selectivity of CZE separation while gaining the sensitivity of fluorescence detection.

  14. Chiral structures from achiral liquid crystals in cylindrical capillaries

    NASA Astrophysics Data System (ADS)

    Jeong, Joonwoo; Kang, Louis; Davidson, Zoey S.; Collings, Peter J.; Lubensky, Tom C.; Yodh, A. G.

    2015-04-01

    We study chiral symmetry-broken configurations of nematic liquid crystals (LCs) confined to cylindrical capillaries with homeotropic anchoring on the cylinder walls (i.e., perpendicular surface alignment). Interestingly, achiral nematic LCs with comparatively small twist elastic moduli relieve bend and splay deformations by introducing twist deformations. In the resulting twisted and escaped radial (TER) configuration, LC directors are parallel to the cylindrical axis near the center, but to attain radial orientation near the capillary wall, they escape along the radius through bend and twist distortions. Chiral symmetry-breaking experiments in polymer-coated capillaries are carried out using Sunset Yellow FCF, a lyotropic chromonic LC with a small twist elastic constant. Its director configurations are investigated by polarized optical microscopy and explained theoretically with numerical calculations. A rich phenomenology of defects also arises from the degenerate bend/twist deformations of the TER configuration, including a nonsingular domain wall separating domains of opposite twist handedness but the same escape direction and singular point defects (hedgehogs) separating domains of opposite escape direction. We show the energetic preference for singular defects separating domains of opposite twist handedness compared with those of the same handedness, and we report remarkable chiral configurations with a double helix of disclination lines along the cylindrical axis. These findings show archetypally how simple boundary conditions and elastic anisotropy of confined materials lead to multiple symmetry breaking and how these broken symmetries combine to create a variety of defects.

  15. Chiral structures from achiral liquid crystals in cylindrical capillaries

    PubMed Central

    Jeong, Joonwoo; Kang, Louis; Davidson, Zoey S.; Collings, Peter J.; Lubensky, Tom C.; Yodh, A. G.

    2015-01-01

    We study chiral symmetry-broken configurations of nematic liquid crystals (LCs) confined to cylindrical capillaries with homeotropic anchoring on the cylinder walls (i.e., perpendicular surface alignment). Interestingly, achiral nematic LCs with comparatively small twist elastic moduli relieve bend and splay deformations by introducing twist deformations. In the resulting twisted and escaped radial (TER) configuration, LC directors are parallel to the cylindrical axis near the center, but to attain radial orientation near the capillary wall, they escape along the radius through bend and twist distortions. Chiral symmetry-breaking experiments in polymer-coated capillaries are carried out using Sunset Yellow FCF, a lyotropic chromonic LC with a small twist elastic constant. Its director configurations are investigated by polarized optical microscopy and explained theoretically with numerical calculations. A rich phenomenology of defects also arises from the degenerate bend/twist deformations of the TER configuration, including a nonsingular domain wall separating domains of opposite twist handedness but the same escape direction and singular point defects (hedgehogs) separating domains of opposite escape direction. We show the energetic preference for singular defects separating domains of opposite twist handedness compared with those of the same handedness, and we report remarkable chiral configurations with a double helix of disclination lines along the cylindrical axis. These findings show archetypally how simple boundary conditions and elastic anisotropy of confined materials lead to multiple symmetry breaking and how these broken symmetries combine to create a variety of defects. PMID:25825733

  16. Integration of a sensor based multiple robot environment for space applications: The Johnson Space Center Teleoperator Branch Robotics Laboratory

    NASA Technical Reports Server (NTRS)

    Hwang, James; Campbell, Perry; Ross, Mike; Price, Charles R.; Barron, Don

    1989-01-01

    An integrated operating environment was designed to incorporate three general purpose robots, sensors, and end effectors, including Force/Torque Sensors, Tactile Array sensors, Tactile force sensors, and Force-sensing grippers. The design and implementation of: (1) the teleoperation of a general purpose PUMA robot; (2) an integrated sensor hardware/software system; (3) the force-sensing gripper control; (4) the host computer system for dual Robotic Research arms; and (5) the Ethernet integration are described.

  17. Copolymers For Capillary Gel Electrophoresis

    DOEpatents

    Liu, Changsheng; Li, Qingbo

    2005-08-09

    This invention relates to an electrophoresis separation medium having a gel matrix of at least one random, linear copolymer comprising a primary comonomer and at least one secondary comonomer, wherein the comonomers are randomly distributed along the copolymer chain. The primary comonomer is an acrylamide or an acrylamide derivative that provides the primary physical, chemical, and sieving properties of the gel matrix. The at least one secondary comonomer imparts an inherent physical, chemical, or sieving property to the copolymer chain. The primary and secondary comonomers are present in a ratio sufficient to induce desired properties that optimize electrophoresis performance. The invention also relates to a method of separating a mixture of biological molecules using this gel matrix, a method of preparing the novel electrophoresis separation medium, and a capillary tube filled with the electrophoresis separation medium.

  18. Scaling of brain metabolism and blood flow in relation to capillary and neural scaling.

    PubMed

    Karbowski, Jan

    2011-01-01

    Brain is one of the most energy demanding organs in mammals, and its total metabolic rate scales with brain volume raised to a power of around 5/6. This value is significantly higher than the more common exponent 3/4 relating whole body resting metabolism with body mass and several other physiological variables in animals and plants. This article investigates the reasons for brain allometric distinction on a level of its microvessels. Based on collected empirical data it is found that regional cerebral blood flow CBF across gray matter scales with cortical volume V as CBF ~ V(-1/6), brain capillary diameter increases as V(1/12), and density of capillary length decreases as V(-1/6). It is predicted that velocity of capillary blood is almost invariant (~V(ε)), capillary transit time scales as V(1/6), capillary length increases as V(1/6+ε), and capillary number as V(2/3-ε), where ε is typically a small correction for medium and large brains, due to blood viscosity dependence on capillary radius. It is shown that the amount of capillary length and blood flow per cortical neuron are essentially conserved across mammals. These results indicate that geometry and dynamics of global neuro-vascular coupling have a proportionate character. Moreover, cerebral metabolic, hemodynamic, and microvascular variables scale with allometric exponents that are simple multiples of 1/6, rather than 1/4, which suggests that brain metabolism is more similar to the metabolism of aerobic than resting body. Relation of these findings to brain functional imaging studies involving the link between cerebral metabolism and blood flow is also discussed.

  19. Capillary malformation--arteriovenous malformation syndrome: review of the literature, proposed diagnostic criteria, and recommendations for management.

    PubMed

    Orme, Charisse M; Boyden, Lynn M; Choate, Keith A; Antaya, Richard J; King, Brett A

    2013-01-01

    Capillary malformation-arteriovenous malformation syndrome is an autosomal dominant disorder caused by mutations in the RASA1 gene and characterized by multiple small, round to oval capillary malformations with or without arteriovenous malformations. Ateriovenous malformations occur in up to one-third of patients and may involve the brain and spine. Although making the diagnosis is straightforward in some patients, there are other patients for whom diagnostic criteria may be helpful in their evaluation. Here we review the literature regarding capillary malformation-arteriovenous malformation syndrome, propose diagnostic criteria, and discuss the care of patients with this condition.

  20. Gardening for Homonyms: Integrating Science and Language Arts to Support Children's Creative Use of Multiple Meaning Words

    ERIC Educational Resources Information Center

    Luna, Melissa J.; Rye, James Andrew; Forinash, Melissa; Minor, Alana

    2015-01-01

    Curriculum integration can increase the presence of science at the elementary level. The purpose of this article is to share how two second-grade teachers have integrated language arts content as a part of science-language arts instruction in a garden-based learning context. One application was a teacher-designed "Gardening for Homonyms"…