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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, 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.

  6. 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.

  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. Stable capillary coating with successive multiple ionic polymer layers.

    PubMed

    Katayama, H; Ishihama, Y; Asakawa, N

    1998-06-01

    A stable modification of the inner wall of a fused silica capillary was established by a simple coating procedure, successive multiple ionic-polymer layer (SMIL) coating. An anionic polymer was tightly fixed to the capillary wall by the SMIL coating, in which a cationic polymer was sandwiched between the anionic polymer and the uncoated fused silica capillary by noncovalent bonding. The SMIL-coated capillary showed a long lifetime. The endurance of the SMIL-coated capillary was more than 100 runs, and it was also tolerant to organic solvents, 1 M NaOH, and a surfactant. The coating efficiency did not depend on capillary sources, and the relative standard deviation of capillary-to-capillary reproducibility was less than 1%. In this study, dextran sulfate (DS) was used as the anionic polymer, and Polybrene was used as the cationic polymer for SMIL modification. The DS-modified capillary (SMIL-DS capillary) exhibited a pH-independent electroosmotic flow (EOF) from anode to cathode in the pH range of 2-11. The SMIL-DS capillary showed good performance for acidic protein analyses under physiological conditions (pH 7.4). Also, the presence of EOF under acidic conditions permitted new applications. Simultaneous separations of cationic, anionic, and neutral amino acids were achieved by capillary zone electrophoresis, and separations of cresol isomers were achieved by micellar electrokinetic chromatography under the acidic conditions. The SMIL-DS capillary was also useful for fast and precise determination of the pKa of acidic functional groups.

  10. Hybrid integrated PDMS microfluidics with a silica capillary.

    PubMed

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

    2010-06-07

    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.

  11. 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.

  12. Selectivity toward multiple predetermined targets in nanoparticle capillary electrochromatography.

    PubMed

    Spégel, Peter; Schweitz, Leif; Nilsson, Staffan

    2003-12-01

    Two unique methods to achieve selectivity toward multiple predetermined targets employing molecular imprinting technology have been developed. Partial filling capillary electrochromatography (CEC) was utilized to evaluate and compare the two techniques. The first approach, the mixed singly templated molecularly imprinted polymer (MIP) nanoparticle approach, is based on the mixing of two types of MIP nanoparticles with inherently different selectivity. The second approach, the multiply templated MIP nanoparticle approach, is based on the incorporation of two different templates during the preparation of the MIP nanoparticles. The use of MIPs in analytical chemistry applications has been extensively investigated during the past years. However, MIP nanoparticles with tailored multiple selectivity toward predetermined enantiomers has not yet been explored. The relative amounts of the two templates studied, i.e., (S)-ropivacaine and (S)-propranolol, were found to strongly affect the affinity of the multiply templated MIP nanoparticles for the predetermined targets. The amount of (S)-propranolol template had to be decreased to concentrations rarely applied in MIP synthesis in order to achieve 2-fold selectivity. Even though strongly decreased to 10% of the usual concentration employed, the MIP could efficiently separate the enantiomers of propranolol when applied in partial filling CEC. This opens up for new possibilities to decrease the need for an initial high amount of template in order to be able to produce an efficient MIP. The multiple enantiomer separation ability of the multiply templated MIP nanoparticles was compared with that of singly templated MIP nanoparticles that were mixed prior to analysis. It was concluded that the multiply templated MIP potentially can offer many new and interesting applications in chromatography as well as in sensor technology and solid-phase extraction.

  13. A prototypic system of parallel electrophoresis in multiple capillaries coupled with microwell arrays.

    PubMed

    Su, Jing; Ren, Kangning; Dai, Wen; Zhao, Yihua; Zhou, Jianhua; Wu, Hongkai

    2011-11-01

    We present a microfluidic system that can be directly coupled with microwell array and perform parallel electrophoresis in multiple capillaries simultaneously. The system is based on an array of glass capillaries, fixed in a polydimethylsiloxane (PDMS) microfluidic scaffold, with one end open for interfacing with microwells. In this capillary array, every two adjacent capillaries act as a pair to be coupled with one microwell; samples in the microwells are introduced and separated by simply applying voltage between two electrodes that are placed at the other ends of capillaries; thus no complicated circuit design is required. We evaluate the performance of this system and perform multiple CE with direct sample introduction from microwell array. Also with this system, we demonstrate the analysis of cellular contents of cells lysed in a microwell array. Our results show that this prototypic system is a promising platform for high-throughput analysis of samples in microwell arrays.

  14. GUcal: An integrated application for capillary electrophoresis based glycan analysis.

    PubMed

    Jarvas, Gabor; Szigeti, Marton; Guttman, Andras

    2015-12-01

    Recent emergence in the use of monoclonal antibody therapeutics and other glycoprotein biopharmaceuticals requires high-throughput, robust, and automated techniques for their glycosylation analysis. Capillary electrophoresis is one of the high-performance methods of choice; however, while the necessary instrumentation is well developed, the related bioinformatics tools are lacked behind. In this paper, we introduce an integrated toolset dubbed as GUcal, to automatically calculate the glucose unit (GU) values for all sample components of interest in an electropherogram with a concomitant database search for structural assignment. The database comprises CE GUs and suggested structures of N-glycans released from human IgG. The app is freely available online (www.lendulet.uni-pannon.hu/gucal) and readily facilitates CE-based glycan analysis.

  15. Multiple, genital lobular capillary haemangioma (pyogenic granuloma) in a young woman: a diagnostic puzzle

    PubMed Central

    Gupta, S.; Radotra, B. D.; Kumar, B.

    2000-01-01

    A 21 year old woman presented with multiple lobulated lesions on the labia majora. The surface of most of the lesions was ulcerated revealing a glistening surface. All lesions were excised. The histopathology revealed features suggestive of lobular capillary haemangioma (pyogenic granuloma). Pyogenic granuloma is considered as a reactive hyperproliferative vascular response to trauma or other stimuli. A literature search revealed reports of a few cases of lobular capillary haemangioma of the glans penis but not on the female genitalia. This case is presented to help physicians become aware that lobular capillary haemangiomas (pyogenic granuloma) may occur at this site. Key Words: pyogenic granuloma; vulva PMID:10817071

  16. The deformation behavior of multiple red blood cells in a capillary vessel.

    PubMed

    Gong, Xiaobo; Sugiyama, Kazuyasu; Takagi, Shu; Matsumoto, Yoichiro

    2009-07-01

    The deformation of multiple red blood cells in a capillary flow was studied numerically. The immersed boundary method was used for the fluid red blood cells interaction. The membrane of the red blood cell was modeled as a hyperelastic thin shell. The numerical results show that the apparent viscosity in the capillary flow is more sensitive to the change of shear coefficient of the membrane than the bending coefficient and surface dilation coefficient, and the increase in the shear coefficient results in an increase in the pressure drop in the blood flow in capillary vessels in order to sustain the same flux rate of red blood cells.

  17. 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.

  18. Microdevices integrating affinity columns and capillary electrophoresis for multi-biomarker analysis in human serum

    PubMed Central

    Yang, Weichun; Yu, Ming; Sun, Xiuhua; Woolley, Adam T.

    2010-01-01

    Summary Biomarkers in human body fluids have great potential for use in screening for diseases such as cancer and diabetes, diagnosis, determining the effectiveness of treatments, and detecting recurrence. Present 96-well immunoassay technology effectively analyzes large numbers of samples; however, this approach is more expensive and less time effective on single or a few samples. In contrast, microfluidic systems are well suited for assaying small numbers of specimens in a point-of-care setting, provided suitable procedures are developed to work within peak capacity constraints when analyzing complex mixtures like human blood serum. Here, we developed integrated microdevices with an affinity column and capillary electrophoresis channels to isolate and quantitate a panel of proteins in complex matrices. To form an affinity column, a thin film of a reactive polymer was photopolymerized in a microchannel, and four antibodies were covalently immobilized to it. The retained protein amounts were consistent from chip to chip, demonstrating reproducibility. Furthermore, the signals from four fluorescently labeled proteins captured on-column were in the same range after rinsing, indicating the column has little bias toward any of the four antibodies or their antigens. These affinity columns have been integrated with capillary electrophoresis separation, enabling us to simultaneously quantify four protein biomarkers in human blood serum in the low ng/mL range using either a calibration curve or standard addition. Our systems provide a fast, integrated and automated platform for multiple biomarker quantitation in complex media such as human blood serum. PMID:20664867

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

    PubMed

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

    2013-01-07

    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.

  20. Integration of valving and sensing on a capillary-assembled microchip.

    PubMed

    Hisamoto, Hideaki; Funano, Shun-ichi; Terabe, Shigeru

    2005-04-01

    A simple integration of both flow control valves and a reaction-based sensing function on a single microchip was performed by using capillary-assembled microchip (CAs-CHIP: Hisamoto, H.; Nakashima, Y.; Kitamura, C.; Funano, S.-i.; Yasuoka, M.; Morishima, K.; Kikutani, Y.; Kitamori, T.; Terabe, S. Anal. Chem. 2004, 76, 3222-3228.). In contrast to the previously reported on-chip valving systems, where the simple valving functions were integrated, our system can integrate not only valving function but also many other chemical functions to perform a complex chemical operation on a single microchip. Here, an enzymatic reaction-based readout system is employed as an example. A square capillary immobilizing N-isopropylacrylamide polymer monolith (referred to as "valving capillary") is used as a thermoresponsive "valving part" and the immobilizing enzyme-modified glycidyl methacrylate polymer monolith (referred to as "sensing capillary") is used as a "sensing part" of the CAs-CHIP. These capillaries are embedded into a lattice microchannel network fabricated on poly(dimethylsiloxane), which has the same channel dimensions as the outer dimensions of the square capillaries. After bonding, a small Peltier device (2 mm x 2 mm) for temperature control is placed on the embedded valving capillaries to control fluid flow. Using this for heating or cooling, fast operation times of 1.4 and 3.2 s for opening and closing valves, respectively, are successfully achieved. Finally, two valving capillaries are independently controlled to trap sample solution within a bypass channel, where the enzyme-immobilized capillary is embedded, and then enzymatic reaction-based sensing of chemical species is performed as an example. The fundamental characteristics of the valve-integrated microchip are fully investigated, and an application to the analysis of an enzyme substrate by using two independent valving capillaries and a sensing capillary is demonstrated.

  1. Visual detection of multiple genetically modified organisms in a capillary array.

    PubMed

    Shao, Ning; Chen, Jianwei; Hu, Jiaying; Li, Rong; Zhang, Dabing; Guo, Shujuan; Hui, Junhou; Liu, Peng; Yang, Litao; Tao, Sheng-Ce

    2017-01-31

    There is an urgent need for rapid, low-cost multiplex methodologies for the monitoring of genetically modified organisms (GMOs). Here, we report a C[combining low line]apillary A[combining low line]rray-based L[combining low line]oop-mediated isothermal amplification for M[combining low line]ultiplex visual detection of nucleic acids (CALM) platform for the simple and rapid monitoring of GMOs. In CALM, loop-mediated isothermal amplification (LAMP) primer sets are pre-fixed to the inner surface of capillaries. The surface of the capillary array is hydrophobic while the capillaries are hydrophilic, enabling the simultaneous loading and separation of the LAMP reaction mixtures into each capillary by capillary forces. LAMP reactions in the capillaries are then performed in parallel, and the results are visually detected by illumination with a hand-held UV device. Using CALM, we successfully detected seven frequently used transgenic genes/elements and five plant endogenous reference genes with high specificity and sensitivity. Moreover, we found that measurements of real-world blind samples by CALM are consistent with results obtained by independent real-time PCRs. Thus, with an ability to detect multiple nucleic acids in a single easy-to-operate test, we believe that CALM will become a widely applied technology in GMO monitoring.

  2. 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

  3. 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.

  4. 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.

  5. From single to multiple microcoil flow probe NMR and related capillary techniques: a review.

    PubMed

    Gökay, Ozan; Albert, Klaus

    2012-01-01

    Nuclear magnetic resonance (NMR) spectroscopy is one of the most important and powerful instrumental analytical techniques for structural elucidation of unknown small and large (complex) isolated and synthesized compounds in organic and inorganic chemistry. X-ray crystallography, neutron scattering (neutron diffraction), and NMR spectroscopy are the only suitable methods for three-dimensional structure determination at atomic resolution. Moreover, these methods are complementary. However, by means of NMR spectroscopy, reaction dynamics and interaction processes can also be investigated. Unfortunately, this technique is very insensitive in comparison with other spectrometric (e.g., mass spectrometry) and spectroscopic (e.g., infrared spectroscopy) methods. Mainly through the development of stronger magnets and more sensitive solenoidal microcoil flow probes, this drawback has been successfully counteracted. Capillary NMR spectroscopy increases the mass-based sensitivity of the NMR spectroscopic analysis up to 100-fold compared with conventional 5-mm NMR probes, and thus can be coupled online and off-line with other microseparation and detection techniques. It offers not only higher sensitivity, but in many cases provides better quality spectra than traditional methods. Owing to the immense number of compounds (e.g., of natural product extracts and compound libraries) to be examined, single microcoil flow probe NMR spectroscopy will soon be far from being sufficiently effective as a screening method. For this reason, an inevitable trend towards coupled microseparation-multiple microcoil flow probe NMR techniques, which allow simultaneous online and off-line detection of several compounds, will occur. In this review we describe the current status and possible future developments of single and multiple microcoil capillary flow probe NMR spectroscopy and its application as a high-throughput tool for the analysis of a large number of mass-limited samples. The advantages

  6. Development and integration of the capillary pumped loop GAS and Hitchhiker flight experiments

    NASA Technical Reports Server (NTRS)

    Butler, D.; Mcintosh, R.

    1990-01-01

    The Capillary Pumped Loop (CPL) is a thermal control system with high density heat acquisition and transport capability. A small spaceflight version of the CPL was built and flown as a GAS experiment on STS 51-D in April 1985 and STS 51-G in June 1985, and as a Hitchhiker-G experiment on STS 61-C in January 1986. The purpose of the experiments was to demonstrate the capability of a capillary pumped system under microgravity conditions for use in the thermal control of large scientific instruments, advanced orbiting spacecraft, and space station components. The development, integration, and test activities of the CPL are described.

  7. 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

    2015-02-03

    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.

  8. Multilayer chitosan-based open tubular capillary anion exchange column with integrated monolithic capillary suppressor.

    PubMed

    Huang, Xiaojia; Foss, Frank W; Dasgupta, Purnendu K

    2011-11-30

    We describe a multilayered open tubular anion exchange column fabricated by alternately pumping solutions of chitosan and glutaraldehyde. The column is terminated in an integrally bonded monolithic suppressor cast around a mandrel of a tungsten wire, composed of an acrylic acid (AA)-ethylene dimethacrylate (EDMA) monolith that is made with sufficient porogen for the monolith to function as a membrane. For a 4.5m long 75 μm bore column coated with 24 successive layers of the condensation polymer (estimated to contain ~72 molecular layers) and coupled to 1cm length of a suppressor fabricated with 55-60% AA, effective separation of several common anions (F(-), Cl(-), NO(2)(-), Br(-), NO(3)(-), average number of theoretical plates ~12,000) and adequate suppression of 1 mM KOH used as eluent was observed at a flow rate of 800 nL min(-1) to obtain sub-picomol detection limits at an operating pressure of ~1 bar. The separation is not time efficient but the system can be meritorious in unique niche applications where a small form factor is desired and liquid volume and power consumption are more important than separation speed.

  9. 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.

  10. 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.

  11. 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.

  12. 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

    2013-01-07

    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

  13. Stereospecific micellar electrokinetic chromatography assay of methionine sulfoxide reductase activity employing a multiple layer coated capillary.

    PubMed

    Zhu, Qingfu; El-Mergawy, Rabab G; Heinemann, Stefan H; Schönherr, Roland; Jáč, Pavel; Scriba, Gerhard K E

    2013-09-01

    A micellar electrokinetic chromatography method for the analysis of the l-methionine sulfoxide diastereomers employing a successive multiple ionic-polymer layer coated fused-silica capillary was developed and validated in order to investigate the stereospecificity of methionine sulfoxide reductases. The capillary coating consisted of a first layer of hexadimethrine and a second layer of dextran sulfate providing a stable strong cathodic EOF and consequently highly repeatable analyte migration times. The methionine sulfoxide diastereomers, methionine as product as well as β-alanine as internal standard were derivatized by dabsyl chloride and separated using a 35 mM sodium phosphate buffer, pH 8.0, containing 25 mM SDS as BGE and a separation voltage of 25 kV. The method was validated in the range of 0.15-2.0 mM with respect to linearity and precision. The LODs of the analytes ranged between 0.04 and 0.10 mM. The assay was subsequently applied to determine the stereospecificity of methionine sulfoxide reductases as well as the enzyme kinetics of human methionine sulfoxide reductase A. Monitoring the decrease of the l-methionine-(S)-sulfoxide Km = 411.8 ± 33.8 μM and Vmax = 307.5 ± 10.8 μM/min were determined.

  14. 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.

  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. 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.

  17. Integrated sample cleanup and microchip capillary array electrophoresis for high-performance forensic STR profiling.

    PubMed

    Liu, Peng; Greenspoon, Susan A; Yeung, Stephanie Hi; Scherer, James R; Mathies, Richard A

    2012-01-01

    Microfluidics has the potential to significantly improve the speed, throughput, and cost performance of electrophoretic short tandem repeat (STR) analysis by translating the process into a miniaturized and integrated format. Current STR analysis bypasses the post-PCR sample cleanup step in order to save time and cost, resulting in poor injection efficiency, bias against larger loci, and delicate injection timing controls. Here we describe the operation of an integrated high-throughput sample cleanup and capillary array electrophoresis microsystem that employs a streptavidin capture gel chemistry coupled to a simple direct-injection geometry for simultaneously analyzing 12 STR samples in less than 30 min with >10-fold improved sensitivity.

  18. Integrated capillary electrophoresis microsystem for multiplex analysis of human respiratory viruses.

    PubMed

    Thaitrong, Numrin; Liu, Peng; Briese, Thomas; Lipkin, W Ian; Chiesl, Thomas N; Higa, Yukiko; Mathies, Richard A

    2010-12-15

    We developed a two-layer, four-channel polymerase chain reaction (PCR)-capillary electrophoresis microdevice that integrates nucleic acid amplification, sample cleanup and concentration, capillary electrophoretic separation, and detection for multiplex analysis of four human respiratory viral pathogens, influenza A, influenza B, coronavirus OC43, and human metapneumovirus. Biotinylated and fluorescently labeled double-stranded (ds) deoxyribonucleic acid (DNA) amplification products are generated in a 100 nL PCR reactor incorporating an integrated heater and a temperature sensor. After amplification, the products are captured and concentrated in a cross-linked acrylamide gel capture matrix copolymerized with acrydite-functionalized streptavidin-capture agents. Thermal dehybridization releases the fluorescently labeled DNA strand for capillary electrophoresis injection, separation, and detection. Using plasmid standards containing the viral genes of interest, each target can be detected starting from as few as 10 copies/reactor. When a two-step reverse transcription PCR amplification is employed, the device can detect ribonucleic acid (RNA) analogues of all four viral targets with detection limits in the range of 25-100 copies/reactor. The utility of the microdevice for analyzing samples from nasopharyngeal swabs is demonstrated. When size-based separation is combined with four-color detection, this platform provides excellent product discrimination, making it readily extendable to higher-order multiplex assays. This portable microsystem is also suitable for performing automated assays in point-of-care diagnostic applications.

  19. 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.

  20. 3D printed LED based on-capillary detector housing with integrated slit.

    PubMed

    Cecil, Farhan; Zhang, Min; Guijt, Rosanne M; Henderson, Alan; Nesterenko, Pavel N; Paull, Brett; Breadmore, Michael C; Macka, Mirek

    2017-05-01

    A 3D printed photometric detector body with integrated slit was fabricated to position a LED and photodiode either side of capillary tubing using a fused deposition modelling (FDM) printer. To make this approach suitable for capillaries down to 50 μm i.d. the dimension of the in-built slit is the critical element of the printed housing. The spatial orientation of the model for printing was found to significantly impact on the resolution of the structures and voids that can be printed. By designing a housing with a slit positioned in the XY plane in parallel with the print direction, the narrowest void (slit) that could be printed was 70 μm. The potential use of the 3D printed slit for photometric detection was characterised using tubing and capillary from 500 down to 50 μm i.d, demonstrating a linear response from 632 to 40 mAU. The effective pathlength and stray light varied from 383 to 22 μm and 3.8% - 50% for 500- 50 μm i.d tubing and capillary. The use of a V-shaped alignment feature allowed for easy and reliable positioning of the tubing inside the detector, as demonstrated by a RSD of 1.9% (n = 10) in peak height when repositioning the tubing between measurements using flow injection analysis (FIA). The performance of the 3D printed housing and 70 μm slit was benchmarked against a commercially available interface using the CE separation of Zn(2+) and Cu(2+) complexes with PAR. The limit of detection with the 3D printed slit was 6.8 and 4.5 μM and is 2.8 and 1.6 μM with the commercial interface.

  1. 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.

  2. A microfluidic circulatory system integrated with capillary-assisted pressure sensors.

    PubMed

    Chen, Yangfan; Chan, Ho Nam; Michael, Sean A; Shen, Yusheng; Chen, Yin; Tian, Qian; Huang, Lu; Wu, Hongkai

    2017-02-14

    The human circulatory system comprises a complex network of blood vessels interconnecting biologically relevant organs and a heart driving blood recirculation throughout this system. Recreating this system in vitro would act as a bridge between organ-on-a-chip and "body-on-a-chip" and advance the development of in vitro models. Here, we present a microfluidic circulatory system integrated with an on-chip pressure sensor to closely mimic human systemic circulation in vitro. A cardiac-like on-chip pumping system is incorporated in the device. It consists of four pumping units and passive check valves, which mimic the four heart chambers and heart valves, respectively. Each pumping unit is independently controlled with adjustable pressure and pump rate, enabling users to control the mimicked blood pressure and heartbeat rate within the device. A check valve is located downstream of each pumping unit to prevent backward leakage. Pulsatile and unidirectional flow can be generated to recirculate within the device by programming the four pumping units. We also report an on-chip capillary-assisted pressure sensor to monitor the pressure inside the device. One end of the capillary was placed in the measurement region, while the other end was sealed. Time-dependent pressure changes were measured by recording the movement of the liquid-gas interface in the capillary and calculating the pressure using the ideal gas law. The sensor covered the physiologically relevant blood pressure range found in humans (0-142.5 mmHg) and could respond to 0.2 s actuation time. With the aid of the sensor, the pressure inside the device could be adjusted to the desired range. As a proof of concept, human normal left ventricular and arterial pressure profiles were mimicked inside this device. Human umbilical vein endothelial cells (HUVECs) were cultured on chip and cells can respond to mechanical forces generated by arterial-like flow patterns.

  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

    2015-12-09

    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.

  4. Integrating Internal Standards into Disposable Capillary Electrophoresis Devices To Improve Quantification

    PubMed Central

    2017-01-01

    To improve point-of-care quantification using microchip capillary electrophoresis (MCE), the chip-to-chip variabilities inherent in disposable, single-use devices must be addressed. This work proposes to integrate an internal standard (ISTD) into the microchip by adding it to the background electrolyte (BGE) instead of the sample—thus eliminating the need for additional sample manipulation, microchip redesigns, and/or system expansions required for traditional ISTD usage. Cs and Li ions were added as integrated ISTDs to the BGE, and their effects on the reproducibility of Na quantification were explored. Results were then compared to the conclusions of our previous publication which used Cs and Li as traditional ISTDs. The in-house fabricated microchips, electrophoretic protocols, and solution matrixes were kept constant, allowing the proposed method to be reliably compared to the traditional method. Using the integrated ISTDs, both Cs and Li improved the Na peak area reproducibility approximately 2-fold, to final RSD values of 2.2–4.7% (n = 900). In contrast (to previous work), Cs as a traditional ISTD resulted in final RSDs of 2.5–8.8%, while the traditional Li ISTD performed poorly with RSDs of 6.3–14.2%. These findings suggest integrated ISTDs are a viable method to improve the precision of disposable MCE devices—giving matched or superior results to the traditional method in this study while neither increasing system cost nor complexity. PMID:28192985

  5. Controlled release of reagents in capillary-driven microfluidics using reagent integrators.

    PubMed

    Hitzbleck, Martina; Gervais, Luc; Delamarche, Emmanuel

    2011-08-21

    The integration and release of reagents in microfluidics as used for point-of-care testing is essential for an easy and accurate operation of these promising diagnostic devices. Here, we present microfluidic functional structures, which we call reagent integrators (RIs), for integrating and releasing small amounts of dried reagents (ng quantities and less) into microlitres of sample in a capillary-driven microfluidic chip. Typically, a RI is less than 1 mm(2) in area and has an inlet splitting into a central reagent channel, in which reagents can be loaded using an inkjet spotter, and two diluter channels. During filling of the microfluidic chip, spotted reagents reconstitute and exit the RI with a dilution factor that relates to the relative hydraulic resistance of the channels forming the RI. We exemplify the working principle of RIs by (i) distributing ∼100 pg of horseradish peroxidase (HRP) in different volume fractions of a 1 μL solution containing a fluorogenic substrate for HRP and (ii) performing an immunoassay for C-reactive protein (CRP) using 450 pg of fluorescently labeled detection antibodies (dAbs) that reconstitute in ∼5 to 30% of a 1 μL sample of human serum. RIs preserve the conceptual simplicity of lateral flow assays while providing a great degree of control over the integration and release of reagents in a stream of sample. We believe RIs to be broadly applicable to microfluidic devices as used for biological assays.

  6. 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.

  7. Functional integral approach for multiplicative stochastic processes.

    PubMed

    Arenas, Zochil González; Barci, Daniel G

    2010-05-01

    We present a functional formalism to derive a generating functional for correlation functions of a multiplicative stochastic process represented by a Langevin equation. We deduce a path integral over a set of fermionic and bosonic variables without performing any time discretization. The usual prescriptions to define the Wiener integral appear in our formalism in the definition of Green's functions in the Grassman sector of the theory. We also study nonperturbative constraints imposed by Becchi, Rouet and Stora symmetry (BRS) and supersymmetry on correlation functions. We show that the specific prescription to define the stochastic process is wholly contained in tadpole diagrams. Therefore, in a supersymmetric theory, the stochastic process is uniquely defined since tadpole contributions cancels at all order of perturbation theory.

  8. 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

  9. Separation of polypeptides by isoelectric point focusing in electrospray-friendly solution using a multiple-junction capillary fractionator.

    PubMed

    Chingin, Konstantin; Astorga-Wells, Juan; Pirmoradian Najafabadi, Mohammad; Lavold, Thorleif; Zubarev, Roman A

    2012-08-07

    We introduce an online multiple-junction capillary isoelectric focusing fractionator (OMJ-CIEF) for separation of biological molecules in solution by pI. In OMJ-CIEF, the separation capillary is divided into seven equal sections joined with each other via tubular Nafion membrane insertions. Each junction is communicated with its own external electrolytic buffer which is used both to supply electrical contact and for solvent exchange. The performance of the fractionator was explored using protein and peptide samples covering broad pI range. Separation was achieved in ionic and ampholytic buffers, including ammonium formate, ammonium hydroxide, histidine, and arginine. By maintaining electric potential across upstream segments of the capillary after the focusing stage, selective release of downstream analyte fractions could be achieved. The selective release mode circumvents the problem of peak broadening during mobilization and enables convenient comprehensive sampling for orthogonal separation methods. Using single-component ampholyte buffers with well-defined pI cutoff values, controlled separation of protein mixture into basic and acidic fractions was demonstrated. The device is cheap and easy to fabricate in-house, simple in operation, and straightforward in interfacing to hyphened analytical platforms. OMJ-CIEF has a potential of becoming a practical add-on unit in a wide range of bioanalytical setups, in particular as a first-dimension separation in mass spectrometry based proteomics or as a preparative tool for analyte purification, fractionation, and preconcentration.

  10. Integrated management of multiple reservoir field developments

    SciTech Connect

    Lyons, S.L.; Chan, H.M.; Harper, J.L.; Boyett, B.A.; Dowson, P.R.; Bette, S.

    1995-10-01

    This paper consists of two sections. The authors first describe the coupling of a pipeline network model to a reservoir simulator and then the application of this new simulator to optimize the production strategy of two Mobil field developments. Mobil`s PEGASUS simulator is an integrated all purpose reservoir simulator that handles black-oil, compositional, faulted and naturally fractured reservoirs. The authors have extended the simulator to simultaneously model multiple reservoirs coupled with surface pipeline networks and processes. This allows them to account for the effects of geology, well placement, and surface production facilities on well deliverability in a fully integrated fashion. They have also developed a gas contract allocation system that takes the user-specified constraints, target rates and swing factors and automatically assigns rates to the individual wells of each reservoir. This algorithm calculates the overall deliverability and automatically reduces the user-specified target rates to meet the deliverability constraints. The algorithm and solution technique are described. This enhanced simulator has been applied to model a Mobil field development in the Southern Gas Basin, offshore United Kingdom, which consists of three separate gas reservoirs connected via a pipeline network. The simulator allowed the authors to accurately determine the impact on individual reservoir and total field performance by varying the development timing of these reservoirs. Several development scenarios are shown to illustrate the capabilities of PEGASUS. Another application of this technology is in the field developments in North Sumatra, Indonesia. Here the objective is to economically optimize the development of multiple fields to feed the PT Arun LNG facility. Consideration of a range of gas compositions, well productivity`s, and facilities constraints in an integrated fashion results in improved management of these assets. Model specifics are discussed.

  11. 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

  12. 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.

  13. Integrated affinity capture, purification, and capillary electrophoresis microdevice for quantitative double-stranded DNA analysis.

    PubMed

    Toriello, Nicholas M; Liu, Chung N; Blazej, Robert G; Thaitrong, Numrin; Mathies, Richard A

    2007-11-15

    A novel injection method is developed that utilizes a thermally switchable oligonucleotide affinity capture gel to mediate the concentration, purification, and injection of dsDNA for quantitative microchip capillary electrophoresis analysis. The affinity capture matrix consists of a 20 base acrydite modified oligonucleotide copolymerized into a 6% linear polyacrylamide gel that captures ssDNA or dsDNA analyte including PCR amplicons and synthetic oligonucleotides. Double stranded PCR amplicons with complementarity to the capture probe up to 81 bases from their 5' terminus are reproducibly captured via helix invasion. By integrating the oligo capture matrix directly with the CE separation channel, the electrophoretically mobilized target fragments are quantitatively captured and injected after thermal release for unbiased, efficient, and quantitative analysis. The capture process exhibits optimal efficiency at 44 degrees C and 100 V/cm with a 20 microM affinity capture probe (TM = 57.7 degrees C). A dsDNA titration assay with 20 bp fragments validated that dsDNA is captured at the same efficiency as ssDNA. Dilution studies with a duplex 20mer show that targets can be successfully captured and analyzed with a limit of detection of 1 pM from 250 nL of solution (approximately 150,000 fluorescent molecules). Simultaneous capture and injection of amplicons from E. coli K12 and M13mp18 using a mixture of two different capture probes demonstrates the feasibility of multiplex target capture. Unlike the traditional cross-injector, this method enables efficient capture and injection of dsDNA amplicons which will facilitate the quantitative analysis of products from integrated nanoliter-scale PCR reactors.

  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. 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%.

  16. 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…

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

    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) ...

  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. 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.

  20. Capillary sample

    MedlinePlus

    ... repeat the test with blood drawn from a vein. Alternative Names Blood sample - capillary; Fingerstick; Heelstick Images Phenylketonuria test Phenylketonuria test Capillary sample References Garza ...

  1. 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.

  2. 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.

  3. Capillary zone electrophoresis-multiple reaction monitoring from 100 pg of RAW 264.7 cell lysate digest

    PubMed Central

    Sun, Liangliang; Li, Yihan; Champion, Matthew M.; Zhu, Guijie; Wojcik, Roza; Dovichi, Norman J.

    2013-01-01

    Capillary zone electrophoresis-multiple/single reaction monitoring (CZE-MRM/SRM), which employed an electrokinetically driven sheath-flow electrospray interface, was used for the rapid and highly sensitive detection of protein analytes in complex tryptic digests. MRM channels were developed against a commercial exponential mixture of bovine proteins. Five proteins spanning four orders of magnitude concentration range were confidently detected from only 2.5 ng of the digest mixture; the mass detection limits (S/N=3) of two detected proteins, alpha-casein and glutamate dehydrogenasewere about 600 zmole and 30 amole, respectively. This technique was then applied to a RAW 264.7 cell lysate digest. Three proteins were confidently and reproducibly detected from 100 pg of this digest. The sample amount corresponds to the approximate protein content from a single cell, which suggests that CZE-MRM may be a useful analytical tool in chemical cytometry. In addition to providing highly sensitive detection of proteins in complex mixtures, this system is highly rapid; migration time of the protein digests was less than 10 min. PMID:23591184

  4. 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.

  5. Multiple crossbar network: Integrated supercomputing framework

    SciTech Connect

    Hoebelheinrich, R. )

    1989-01-01

    At Los Alamos National Laboratory, site of one of the world's most powerful scientific supercomputing facilities, a prototype network for an environment that links supercomputers and workstations is being developed. Driven by a need to provide graphics data at movie rates across a network from a Cray supercomputer to a Sun scientific workstation, the network is called the Multiple Crossbar Network (MCN). It is intended to be coarsely grained, loosely coupled, general-purpose interconnection network that will vastly increase the speed at which supercomputers communicate with each other in large networks. The components of the network are described, as well as work done in collaboration with vendors who are interested in providing commercial products. 9 refs.

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

    PubMed

    Zhao, Haiyan; Chen, Zilin

    2014-05-02

    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.

  7. Integration of multianalyte sensing functions on a capillary-assembled microchip: simultaneous determination of ion concentrations and enzymatic activities by a "drop-and-sip" technique.

    PubMed

    Henares, Terence G; Takaishi, Masayuki; Yoshida, Naoya; Terabe, Shigeru; Mizutani, Fumio; Sekizawa, Ryuichi; Hisamoto, Hideaki

    2007-02-01

    A general and simple implementation of simultaneous multiparametric sensing in a single microchip is presented by using a capillary-assembled microchip (CAs-CHIP) integrated with the plural different reagent-release capillaries (RRCs), acting as various biochemical sensors. A novel "drop-and-sip" technique of fluid handling is performed with a microliter droplet of a model sample solution containing proteases (trypsin, chymotrypsin, thrombin, elastase) and divalent cations (Ca2+, Zn2+, Mg2+) that passes through the microchannel with the aid of a micropipette as a vacuum pump, concurrently filling each RRC via capillary force. To avert the evaporation of the nanoliter sample volume in each capillary, PDMS oil is dropped on the outlet hole of the CAs-CHIP exploiting the capillary force that results in spontaneous sealing of all the RRCs. In addition, this high-speed sample introduction alleviates the possibility of protein adsorption and capillary cross-contamination, allowing a reliable and multianalyte determination of a sample containing many different proteases and divalent cations by using the fluorescence image analysis. Presented results suggested the possible application of this microchip in the field of drug discovery and systems biology.

  8. Multiple methods integration for structural mechanics analysis and design

    NASA Technical Reports Server (NTRS)

    Housner, J. M.; Aminpour, M. A.

    1991-01-01

    A new research area of multiple methods integration is proposed for joining diverse methods of structural mechanics analysis which interact with one another. Three categories of multiple methods are defined: those in which a physical interface are well defined; those in which a physical interface is not well-defined, but selected; and those in which the interface is a mathematical transformation. Two fundamental integration procedures are presented that can be extended to integrate various methods (e.g., finite elements, Rayleigh Ritz, Galerkin, and integral methods) with one another. Since the finite element method will likely be the major method to be integrated, its enhanced robustness under element distortion is also examined and a new robust shell element is demonstrated.

  9. Identification of new oxycodone metabolites in human urine by capillary electrophoresis-multiple-stage ion-trap mass spectrometry.

    PubMed

    Baldacci, A; Caslavska, J; Wey, A B; Thormann, W

    2004-10-08

    Capillary electrophoresis-electrospray ionization multiple-stage ion-trap mass spectrometry (CE-MSn) and computer simulation of fragmentation are demonstrated to be effective tools to detect and identify phase I and phase II metabolites of oxycodone (OCOD) in human urine. OCOD is a strong analgesic used for the management of moderate to severe mainly postoperative or cancer-related pain whose metabolism in man is largely unknown. Using an aqueous pH 9 ammonium acetate buffer and CE-MSn (n < or = 5), OCOD and its phase I metabolites produced by O-demethylation, N-demethylation, 6-ketoreduction and N-oxidation (such as oxymorphone, noroxycodone, noroxymorphone, 6-oxycodol, nor-6-oxycodol, oxycodone-N-oxide and 6-oxycodol-N-oxide) and phase II conjugates with glucuronic acid of several of these compounds could be detected in alkaline solid-phase extracts of a patient urine that was collected during a pharmacotherapy episode with daily ingestion of 240-320 mg of OCOD chloride. The data for three known OCOD metabolites for which the standards had to be synthesized in-house, 6-oxycodol, nor-6-oxycodol and oxycodone-N-oxide, were employed to identify two new metabolites, the N-oxidized derivative of 6-oxycodol and an O-glucuronide of this compound. CE-MSn and computer simulation of fragmentation also led to the identification of the N-glucuronide of noroxymorphone, another novel OCOD metabolite for which no standard compound or mass spectra library data were available.

  10. 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.

  11. 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.

  12. 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)

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

    SciTech Connect

    Xue, Gang

    2001-01-01

    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 10-11 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.

  14. 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.

  15. Capillary electrophoresis and capillary electrophoresis-ion trap multiple-stage mass spectrometry for the differentiation and identification of oxycodone and its major metabolites in human urine.

    PubMed

    Wey, Anita B; Thormann, Wolfgang

    2002-04-25

    Oxycodone (OCOD) and its metabolites, including oxymorphone (OMOR), noroxycodone (NOCOD) and noroxymorphone (NOMOR), are opioids that carry an OH group at position 14. Using capillary electrophoresis (CE) with a binary phosphate buffer containing 60% ethylene glycol (pH 7.9), the migration order of OCOD and OMOR with respect to their N-demethylated analogs was found to be reversed compared to that observed for codeine, dihydrocodeine, morphine and dihydromorphine, compounds that do not have an OH group at position 14. OCOD and structurally related compounds can also be distinguished from these opioids by their absorbance spectra at low wavelengths and via a characteristic neutral H2O loss at the MS2 level. Using the binary phosphate buffer, CE with UV detection is shown to be capable of monitoring OCOD, NOCOD, OMOR (after hydrolysis only) and NOMOR (after hydrolysis and in patient urine only) in alkaline liquid-liquid extracts of urines that were collected after ingestion of 10 mg OCOD hydrochloride and in a patient urine collected at steady state (80 mg OCOD hydrochloride daily). Using an aqueous pH 9 ammonium acetate buffer, these results were confirmed by CE-MS3. Based on CE-MS, MS2 and MS3 data, the absorbance spectra measured across the CE peaks and the relative position within the electropherogram, two peaks monitored in the UV absorbance electropherograms could be assigned to the two keto-reduced metabolites 6oxycodol (60COL) and nor6oxycodol, for which no standards were available. Comparison of data obtained with urines pretreated with two different enzyme products (beta-glucuronidase and beta-glucuronidase/arylsulfatase) suggest that OCOD, NOCOD and 6OCOL are mainly glucuronidated, whereas OMOR mainly forms other conjugates. Furthermore, in a first attempt to directly measure conjugates of the compounds of interest, solid-phase extracts were analyzed by CE-MS4, which revealed the presence of the acyl glucuronides of 6OCOL and OMOR and an unidentified OMOR

  16. Integrating Multiple Teaching Methods into a General Chemistry Classroom.

    ERIC Educational Resources Information Center

    Francisco, Joseph S.; Nicoll, Gayle; Trautmann, Marcella

    1998-01-01

    Four different methods of teaching--cooperative learning, class discussions, concept maps, and lectures--were integrated into a freshman-level general chemistry course to compare students' levels of participation. Findings support the idea that multiple modes of learning foster the metacognitive skills necessary for mastering general chemistry.…

  17. Content Integration across Multiple Documents Reduces Memory for Sources

    ERIC Educational Resources Information Center

    Braasch, Jason L. G.; McCabe, Rebecca M.; Daniel, Frances

    2016-01-01

    The current experiments systematically examined semantic content integration as a mechanism for explaining source inattention and forgetting when reading-to-remember multiple texts. For all 3 experiments, degree of semantic overlap was manipulated amongst messages provided by various information sources. In Experiment 1, readers' source…

  18. Method and system of integrating information from multiple sources

    SciTech Connect

    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.

  19. A simplified poly(dimethylsiloxane) capillary electrophoresis microchip integrated with a low-noise contactless conductivity detector.

    PubMed

    Liu, Benyan; Zhang, Yi; Mayer, Dirk; Krause, Hans-Joachim; Jin, Qinghui; Zhao, Jianlong; Offenhäusser, Andreas

    2011-03-01

    A contactless conductivity detector integrated into a poly(dimethylsiloxane) microchip for electrophoresis is presented. It adopted the simplest configuration of electrodes commonly used in this detection mode for capillary electrophoresis microchips. Although the chip is based on a simple and effective design, it is able to obtain low detection levels due to the low noise of the detection circuit. A circuit based on a lock-in amplifier was designed on printed circuit boards to read out the signal. The property of the detection cell was studied by applying excitation signals of different frequencies and different amplitudes. It was found that the best detection limit could be achieved with a frequency of 50 kHz and amplitude of 20 V. The performance of the detector was demonstrated by successfully separating and detecting several inorganic ions and also a mixture of heavy metal ions. An average detection limit of 0.4 μM was obtained for inorganic cations. This value is significantly improved compared to similar microchip-based detectors. The presented detector could be promising for mass production due to its properties, such as simple construction, high degree of integration, high performance and low cost.

  20. Factors to be considered for robust high-throughput automated DNA sequencing using a multiple-capillary array instrument

    NASA Astrophysics Data System (ADS)

    Carrilho, Emanuel; Miller, Arthur W.; Ruiz-Martinez, Marie C.; Kotler, Lev; Kesilman, Jeffrey; Karger, Barry L.

    1997-05-01

    The overall goal of our program is to develop a robust, high throughput, fully automated DNA sequencing instrument based on replaceable polymer solutions using a multicapillary array. Significant effort has already been devoted to column and polymer chemistry in order to obtain long read lengths per run in fast analysis time. In this paper we report on progress in instrument considerations and data processing software. A simple instrument design, based on no moving parts for continuous illumination of the capillaries and detection of the fluorescent light was used for this study. Our polymer solution replacement system with the permanent connection between the buffer/chamber manifold and capillary columns on the detector side is designed to prevent the trapping of air bubbles during matrix solution replacement. A special construction of a column-electrode couple on the injection side precludes air trapping during sample injection from small sample volumes. Our in-house software now features the significant reduction of the crosstalk signal from neighbor columns, which may be a potential problem in densely packed large capillary array sequencers.

  1. Capillary Electrophoresis – Single Strand Conformation Polymorphism for the Detection of Multiple Mutations Leading to Tuberculosis Drug Resistance

    PubMed Central

    Krothapalli, Sowmya; May, Michael K.; Hestekin, Christa N.

    2013-01-01

    Drug resistant tuberculosis (TB) is a major health problem in both developed and developing countries. Mutations in the Mycobacterium (M.) tuberculosis bacterial genome, such as those to the rpoB gene and mabA-inhA promoter region, have been linked to TB drug resistance in against rifampicin and isoniazid, respectively. The rapid, accurate, and inexpensive identification of these and other mutations leading to TB drug resistance is an essential tool for improving human health. Capillary electrophoresis (CE) single strand conformation polymorphism (SSCP) can be a highly sensitive technique for the detection of genetic mutation that has not been previously explored for drug resistance mutations in M. tuberculosis. This work explores the potential of CE-SSCP through the optimization of variables such as polymer separation matrix concentration, capillary wall coating, electric field strength, and temperature on resolution of mutation detection. The successful detection of an rpoB gene mutation and two mabA-inhA promoter region mutations while simultaneously differentiating a TB-causing mycobacteria from a non-TB bacteria was accomplished using the optimum conditions of 4.5% (w/v) PDMA in a PDMA coated capillary at 20°C using a separation voltage of 278 V/cm. This multiplexed analysis that can be completed in a few hours demonstrates the potential of CE-SSCP to be an inexpensive and rapid analysis method. PMID:22884688

  2. Capillary electrophoresis-single strand conformation polymorphism for the detection of multiple mutations leading to tuberculosis drug resistance.

    PubMed

    Krothapalli, Sowmya; May, Michael K; Hestekin, Christa N

    2012-10-01

    Drug resistant tuberculosis (TB) is a major health problem in both developed and developing countries. Mutations in the Mycobacterium (M.) tuberculosis bacterial genome, such as those to the rpoB gene and mabA-inhA promoter region, have been linked to TB drug resistance in against rifampicin and isoniazid, respectively. The rapid, accurate, and inexpensive identification of these and other mutations leading to TB drug resistance is an essential tool for improving human health. Capillary electrophoresis (CE) single strand conformation polymorphism (SSCP) can be a highly sensitive technique for the detection of genetic mutation that has not been previously explored for drug resistance mutations in M. tuberculosis. This work explores the potential of CE-SSCP through the optimization of variables such as polymer separation matrix concentration, capillary wall coating, electric field strength, and temperature on resolution of mutation detection. The successful detection of an rpoB gene mutation and two mabA-inhA promoter region mutations while simultaneously differentiating a TB-causing mycobacteria from a non-TB bacteria was accomplished using the optimum conditions of 4.5% (w/v) PDMA in a PDMA coated capillary at 20°C using a separation voltage of 278 V/cm. This multiplexed analysis that can be completed in a few hours demonstrates the potential of CE-SSCP to be an inexpensive and rapid analysis method.

  3. HMC algorithm with multiple time scale integration and mass preconditioning

    NASA Astrophysics Data System (ADS)

    Urbach, C.; Jansen, K.; Shindler, A.; Wenger, U.

    2006-01-01

    We present a variant of the HMC algorithm with mass preconditioning (Hasenbusch acceleration) and multiple time scale integration. We have tested this variant for standard Wilson fermions at β=5.6 and at pion masses ranging from 380 to 680 MeV. We show that in this situation its performance is comparable to the recently proposed HMC variant with domain decomposition as preconditioner. We give an update of the "Berlin Wall" figure, comparing the performance of our variant of the HMC algorithm to other published performance data. Advantages of the HMC algorithm with mass preconditioning and multiple time scale integration are that it is straightforward to implement and can be used in combination with a wide variety of lattice Dirac operators.

  4. Predicting Protein Function via Semantic Integration of Multiple Networks.

    PubMed

    Yu, Guoxian; Fu, Guangyuan; Wang, Jun; Zhu, Hailong

    2016-01-01

    Determining the biological functions of proteins is one of the key challenges in the post-genomic era. The rapidly accumulated large volumes of proteomic and genomic data drives to develop computational models for automatically predicting protein function in large scale. Recent approaches focus on integrating multiple heterogeneous data sources and they often get better results than methods that use single data source alone. In this paper, we investigate how to integrate multiple biological data sources with the biological knowledge, i.e., Gene Ontology (GO), for protein function prediction. We propose a method, called SimNet, to Semantically integrate multiple functional association Networks derived from heterogenous data sources. SimNet firstly utilizes GO annotations of proteins to capture the semantic similarity between proteins and introduces a semantic kernel based on the similarity. Next, SimNet constructs a composite network, obtained as a weighted summation of individual networks, and aligns the network with the kernel to get the weights assigned to individual networks. Then, it applies a network-based classifier on the composite network to predict protein function. Experiment results on heterogenous proteomic data sources of Yeast, Human, Mouse, and Fly show that, SimNet not only achieves better (or comparable) results than other related competitive approaches, but also takes much less time. The Matlab codes of SimNet are available at https://sites.google.com/site/guoxian85/simnet.

  5. 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.

  6. Effective Thermo-Capillary Mixing in Droplet Microfluidics Integrated with a Microwave Heater.

    PubMed

    Yesiloz, Gurkan; Boybay, Muhammed S; Ren, Carolyn L

    2017-02-07

    In this study, we present a microwave-based microfluidic mixer that allows rapid mixing within individual droplets efficiently. The designed microwave mixer is a coplanar design with a small footprint, which is fabricated on a glass substrate and integrated with a microfluidic chip. The mixer works essentially as a resonator that accumulates an intensive electromagnetic field into a spiral capacitive gap (around 200 μm), which provides sufficient energy to heat-up droplets that pass through the capacitive gap. This microwave actuation induces nonuniform Marangoni stresses on the interface, which results in three-dimensional motion inside the droplet and thus fast mixing. In order to evaluate the performance of the microwave mixer, droplets with highly viscous fluid, 75% (w/w) glycerol solution, were generated, half of which were seeded with fluorescent dye for imaging purposes. The relative importance of different driving forces for mixing was evaluated qualitatively using magnitude analysis, and the effect of the applied power on mixing performance was also investigated. Mixing efficiency was quantified using the mixing index, which shows as high as 97% mixing efficiency was achieved within the range of milliseconds. This work demonstrates a very unique approach of utilizing microwave technology to facilitate mixing in droplet microfluidics systems, which can potentially open up areas for biochemical synthesis applications.

  7. 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

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

    PubMed

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

    2011-05-01

    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 eight 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 eight 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.

  9. Can the meaning of multiple words be integrated unconsciously?

    PubMed Central

    van Gaal, Simon; Naccache, Lionel; Meuwese, Julia D. I.; van Loon, Anouk M.; Leighton, Alexandra H.; Cohen, Laurent; Dehaene, Stanislas

    2014-01-01

    What are the limits of unconscious language processing? Can language circuits process simple grammatical constructions unconsciously and integrate the meaning of several unseen words? Using behavioural priming and electroencephalography (EEG), we studied a specific rule-based linguistic operation traditionally thought to require conscious cognitive control: the negation of valence. In a masked priming paradigm, two masked words were successively (Experiment 1) or simultaneously presented (Experiment 2), a modifier (‘not’/‘very’) and an adjective (e.g. ‘good’/‘bad’), followed by a visible target noun (e.g. ‘peace’/‘murder’). Subjects indicated whether the target noun had a positive or negative valence. The combination of these three words could either be contextually consistent (e.g. ‘very bad - murder’) or inconsistent (e.g. ‘not bad - murder’). EEG recordings revealed that grammatical negations could unfold partly unconsciously, as reflected in similar occipito-parietal N400 effects for conscious and unconscious three-word sequences forming inconsistent combinations. However, only conscious word sequences elicited P600 effects, later in time. Overall, these results suggest that multiple unconscious words can be rapidly integrated and that an unconscious negation can automatically ‘flip the sign’ of an unconscious adjective. These findings not only extend the limits of subliminal combinatorial language processes, but also highlight how consciousness modulates the grammatical integration of multiple words. PMID:24639583

  10. SPARSE INTEGRATIVE CLUSTERING OF MULTIPLE OMICS DATA SETS

    PubMed Central

    Wang, Sijian; Mo, Qianxing

    2012-01-01

    High resolution microarrays and second-generation sequencing platforms are powerful tools to investigate genome-wide alterations in DNA copy number, methylation, and gene expression associated with a disease. An integrated genomic profiling approach measuring multiple omics data types simultaneously in the same set of biological samples would render an integrated data resolution that would not be available with any single data type. In this study, we use penalized latent variable regression methods for joint modeling of multiple omics data types to identify common latent variables that can be used to cluster patient samples into biologically and clinically relevant disease subtypes. We consider lasso (Tibshirani, 1996), elastic net (Zou and Hastie, 2005), and fused lasso (Tibshirani et al., 2005) methods to induce sparsity in the coefficient vectors, revealing important genomic features that have significant contributions to the latent variables. An iterative ridge regression is used to compute the sparse coefficient vectors. In model selection, a uniform design (Fang and Wang, 1994) is used to seek “experimental” points that scattered uniformly across the search domain for efficient sampling of tuning parameter combinations. We compared our method to sparse singular value decomposition (SVD) and penalized Gaussian mixture model (GMM) using both real and simulated data sets. The proposed method is applied to integrate genomic, epigenomic, and transcriptomic data for subtype analysis in breast and lung cancer data sets. PMID:24587839

  11. 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.

  12. Dissociating conflict adaptation from feature integration: a multiple regression approach.

    PubMed

    Notebaert, Wim; Verguts, Tom

    2007-10-01

    Congruency effects are typically smaller after incongruent than after congruent trials. One explanation is in terms of higher levels of cognitive control after detection of conflict (conflict adaptation; e.g., M. M. Botvinick, T. S. Braver, D. M. Barch, C. S. Carter, & J. D. Cohen, 2001). An alternative explanation for these results is based on feature repetition and/or integration effects (e.g., B. Hommel, R. W. Proctor, & K.-P. Vu, 2004; U. Mayr, E. Awh, & P. Laurey, 2003). Previous attempts to dissociate feature integration from conflict adaptation focused on a particular subset of the data in which feature transitions were held constant (J. G. Kerns et al., 2004) or in which congruency transitions were held constant (C. Akcay & E. Hazeltine, in press), but this has a number of disadvantages. In this article, the authors present a multiple regression solution for this problem and discuss its possibilities and pitfalls.

  13. An integrated passive micromixer-magnetic separation-capillary electrophoresis microdevice for rapid and multiplex pathogen detection at the single-cell level.

    PubMed

    Jung, Jae Hwan; Kim, Gha-Young; Seo, Tae Seok

    2011-10-21

    Here we report an integrated microdevice consisting of an efficient passive mixer, a magnetic separation chamber, and a capillary electrophoretic microchannel in which DNA barcode assay, target pathogen separation, and barcode DNA capillary electrophoretic analysis were performed sequentially within 30 min for multiplex pathogen detection at the single-cell level. The intestine-shaped serpentine 3D micromixer provides a high mixing rate to generate magnetic particle-pathogenic bacteria-DNA barcode labelled AuNP complexes quantitatively. After magnetic separation and purification of those complexes, the barcode DNA strands were released and analyzed by the microfluidic capillary electrophoresis within 5 min. The size of the barcode DNA strand was controlled depending on the target bacteria (Staphylococcus aureus, Escherichia coli O157:H7, and Salmonella typhimurium), and the different elution time of the barcode DNA peak in the electropherogram allows us to recognize the target pathogen with ease in the monoplex as well as in the multiplex analysis. In addition, the quantity of the DNA barcode strand (∼10(4)) per AuNP is enough to be observed in the laser-induced confocal fluorescence detector, thereby making single-cell analysis possible. This novel integrated microdevice enables us to perform rapid, sensitive, and multiplex pathogen detection with sample-in-answer-out capability to be applied for biosafety testing, environmental screening, and clinical trials.

  14. Automated 10-channel capillary chip immunodetector for biological agents detection.

    PubMed

    Yacoub-George, Erwin; Hell, Waltraud; Meixner, Leonhard; Wenninger, Franz; Bock, Karlheinz; Lindner, Petra; Wolf, Hans; Kloth, Tanja; Feller, Klaus A

    2007-02-15

    The automated 10-channel capillary chip immunodetector (10K-IDWG) is a prototype, which has been developed for automatically operated biological agents (BA) point detection. The current technology uses a chemiluminescence capillary immunoassay (EIA) technique in combination with integrated microfluidics and allows the highly sensitive and rapid detection and preliminary identification of multiple BA in aqueous solutions in the laboratory. The chemiluminescence capillary EIA are performed within a disposable capillary chip containing 10 fused-silica capillaries arranged in parallel coated with selected capture antibodies. A multianode-photomultiplier array is used to detect chemiluminescence intensity in each capillary. Reservoirs for reagents and buffers and a waste disposal reservoir are integrated. This paper describes the technology of the 10K-IDWG and its evaluation with three different BA, the toxin staphylococcal enterotoxin B (SEB), the bacterial analyte Escherichia coli (E. coli) O157:H7 as a model for bacterial pathogens, and the bacteriophage M13 as a model for virus pathogens. The 10K-IDWG is able to detect the above mentioned three BA in an aqueous sample within 29 min (single analyte-detection and multiplexing). Limits of detection (LOD) are 0.1 ng/ml for SEB, 10(4)cfu/ml for E. coli O157:H7, and 5x10(5) pfu/ml for M13. Cross reactivities between the three assays were not observed.

  15. 77 FR 74027 - Certain Integrated Circuit Packages Provided with Multiple Heat-Conducting Paths and Products...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-12-12

    ... From the Federal Register Online via the Government Publishing Office INTERNATIONAL TRADE COMMISSION Certain Integrated Circuit Packages Provided with Multiple Heat- Conducting Paths and Products... integrated circuit packages provided with multiple heat-conducting paths and products containing same...

  16. On a New Simple Method for Evaluation of Certain Multiple Definite Integrals

    ERIC Educational Resources Information Center

    Sen Gupta, I.; Debnath, L.

    2006-01-01

    This paper deals with a simple method of evaluation of certain multiple definite integrals. This is followed by two main theorems concerning multiple definite integrals. Some examples of applications are given.

  17. 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

  18. Integrated presentation of ecological risk from multiple stressors

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

    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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.... International Trade Commission has received a complaint entitled Certain Integrated Circuit Packages Provided... sale within the United States after importation of certain integrated circuit packages provided...

  5. Analysis of multiple quaternary ammonium compounds in the brain using tandem capillary column separation and high resolution mass spectrometric detection.

    PubMed

    Falasca, Sara; Petruzziello, Filomena; Kretz, Robert; Rainer, Gregor; Zhang, Xiaozhe

    2012-06-08

    Endogenous quaternary ammonium compounds are involved in various physiological processes in the central nervous system. In the present study, eleven quaternary ammonium compounds, including acetylcholine, choline, carnitine, acetylcarnitine and seven other acylcarnitines of low polarity, were analyzed from brain extracts using a two dimension capillary liquid chromatography-Fourier transform mass spectrometry method. To deal with their large difference in hydrophobicities, tandem coupling between reversed phase and hydrophilic interaction chromatography columns was used to separate all the targeted quaternary ammonium compounds. Using high accuracy mass spectrometry in selected ion monitoring mode, all the compounds could be detected from each brain sample with high selectivity. The developed method was applied for the relative quantification of these quaternary ammonium compounds in three different brain regions of tree shrews: prefrontal cortex, striatum, and hippocampus. The comparative analysis showed that quaternary ammonium compounds were differentially distributed across the three brain areas. The analytical method proved to be highly sensitive and reliable for simultaneous determination of all the targeted analytes from brain samples.

  6. 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.

  7. 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) ...

  8. Integrating Multiple Teaching Methods into a General Chemistry Classroom

    NASA Astrophysics Data System (ADS)

    Francisco, Joseph S.; Nicoll, Gayle; Trautmann, Marcella

    1998-02-01

    In addition to the traditional lecture format, three other teaching strategies (class discussions, concept maps, and cooperative learning) were incorporated into a freshman level general chemistry course. Student perceptions of their involvement in each of the teaching methods, as well as their perceptions of the utility of each method were used to assess the effectiveness of the integration of the teaching strategies as received by the students. Results suggest that each strategy serves a unique purpose for the students and increased student involvement in the course. These results indicate that the multiple teaching strategies were well received by the students and that all teaching strategies are necessary for students to get the most out of the course.

  9. An integrated modelling framework for neural circuits with multiple neuromodulators

    PubMed Central

    Vemana, Vinith

    2017-01-01

    Neuromodulators are endogenous neurochemicals that regulate biophysical and biochemical processes, which control brain function and behaviour, and are often the targets of neuropharmacological drugs. Neuromodulator effects are generally complex partly owing to the involvement of broad innervation, co-release of neuromodulators, complex intra- and extrasynaptic mechanism, existence of multiple receptor subtypes and high interconnectivity within the brain. In this work, we propose an efficient yet sufficiently realistic computational neural modelling framework to study some of these complex behaviours. Specifically, we propose a novel dynamical neural circuit model that integrates the effective neuromodulator-induced currents based on various experimental data (e.g. electrophysiology, neuropharmacology and voltammetry). The model can incorporate multiple interacting brain regions, including neuromodulator sources, simulate efficiently and easily extendable to large-scale brain models, e.g. for neuroimaging purposes. As an example, we model a network of mutually interacting neural populations in the lateral hypothalamus, dorsal raphe nucleus and locus coeruleus, which are major sources of neuromodulator orexin/hypocretin, serotonin and norepinephrine/noradrenaline, respectively, and which play significant roles in regulating many physiological functions. We demonstrate that such a model can provide predictions of systemic drug effects of the popular antidepressants (e.g. reuptake inhibitors), neuromodulator antagonists or their combinations. Finally, we developed user-friendly graphical user interface software for model simulation and visualization for both fundamental sciences and pharmacological studies. PMID:28100828

  10. 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.

  11. Using Multiple Ontologies to Integrate Complex Biological Data

    PubMed Central

    Petri, Victoria; Pasko, Dean; Bromberg, Susan; Wu, Wenhua; Chen, Jiali; Nenasheva, Nataliya; Kwitek, Anne; Twigger, Simon; Jacob, Howard

    2005-01-01

    The strength of the rat as a model organism lies in its utility in pharmacology, biochemistry and physiology research. Data resulting from such studies is difficult to represent in databases and the creation of user-friendly data mining tools has proved difficult. The Rat Genome Database has developed a comprehensive ontology-based data structure and annotation system to integrate physiological data along with environmental and experimental factors, as well as genetic and genomic information. RGD uses multiple ontologies to integrate complex biological information from the molecular level to the whole organism, and to develop data mining and presentation tools. This approach allows RGD to indicate not only the phenotypes seen in a strain but also the specific values under each diet and atmospheric condition, as well as gender differences. Harnessing the power of ontologies in this way allows the user to gather and filter data in a customized fashion, so that a researcher can retrieve all phenotype readings for which a high hypoxia is a factor. Utilizing the same data structure for expression data, pathways and biological processes, RGD will provide a comprehensive research platform which allows users to investigate the conditions under which biological processes are altered and to elucidate the mechanisms of disease. PMID:18629202

  12. 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.

  13. Integrated molecular profiling of SOD2 expression in multiple myeloma.

    PubMed

    Hurt, Elaine M; Thomas, Suneetha B; Peng, Benjamin; Farrar, William L

    2007-05-01

    Reactive oxygen species are known to be involved in several cellular processes, including cell signaling. SOD2 is a key enzyme in the conversion of reactive oxygen species and has been implicated in a host of disease states, including cancer. Using an integrated, whole-cell approach encompassing epigenetics, genomics, and proteomics, we have defined the role of SOD2 in multiple myeloma. We show that the SOD2 promoter is methylated in several cell lines and there is a correlative decrease in expression. Furthermore, myeloma patient samples have decreased SOD2 expression compared with healthy donors. Overexpression of SOD2 results in decreased proliferation and altered sensitivity to 2-methoxyestradiol-induced DNA damage and apoptosis. Genomic profiling revealed regulation of 65 genes, including genes involved in tumorigenesis, and proteomic analysis identified activation of the JAK/STAT pathway. Analysis of nearly 400 activated transcription factors identified 31 transcription factors with altered DNA binding activity, including XBP1, NFAT, forkhead, and GAS binding sites. Integration of data from our gestalt molecular analysis has defined a role for SOD2 in cellular proliferation, JAK/STAT signaling, and regulation of several transcription factors.

  14. 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

  15. Geometric integrators for multiple time-scale simulation

    NASA Astrophysics Data System (ADS)

    Jia, Zhidong; Leimkuhler, Ben

    2006-05-01

    In this paper, we review and extend recent research on averaging integrators for multiple time-scale simulation such as are needed for physical N-body problems including molecular dynamics, materials modelling and celestial mechanics. A number of methods have been proposed for direct numerical integration of multiscale problems with special structure, such as the mollified impulse method (Garcia-Archilla, Sanz-Serna and Skeel 1999 SIAM J. Sci. Comput. 20 930-63) and the reversible averaging method (Leimkuhler and Reich 2001 J. Comput. Phys. 171 95-114). Features of problems of interest, such as thermostatted coarse-grained molecular dynamics, require extension of the standard framework. At the same time, in some applications the computation of averages plays a crucial role, but the available methods have deficiencies in this regard. We demonstrate that a new approach based on the introduction of shadow variables, which mirror physical variables, has promised for broadening the usefulness of multiscale methods and enhancing accuracy of or simplifying computation of averages. The shadow variables must be computed from an auxiliary equation. While a geometric integrator in the extended space is possible, in practice we observe enhanced long-term energy behaviour only through use of a variant of the method which controls drift of the shadow variables using dissipation and sacrifices the formal geometric properties such as time-reversibility and volume preservation in the enlarged phase space, stabilizing the corresponding properties in the physical variables. The method is applied to a gravitational three-body problem as well as a partially thermostatted model problem for a dilute gas of diatomic molecules.

  16. 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.

  17. Capillary electrophoresis.

    PubMed

    Compton, S W; Brownlee, R G

    1988-05-01

    While capillary electrophoresis, or historically related techniques, have been used for over a century, and recognition of the value of this separation methodology has certainly grown rapidly in the past few years, the technique has generally been used by analytical chemists, particularly in Europe and Japan, and small groups of researchers in the United States. Many of the basic instrumentation problems have been solved only relatively recently, and researchers using capillary electrophoresis are now turning their attention to studying specific applications which demonstrate the potential versatility of this electrophoretic technique. The appearance of standardized commercial instrumentation is imminent. With the availability of such technology, capillary electrophoresis will no longer be an academic curiosity, but rather a tool with the potential for routine separations of diverse samples of interest to analyst, researcher, and clinician.

  18. The United States Marine Corps Data Collaboration Requirements: Retrieving and Integrating Data From Multiple Databases

    DTIC Science & Technology

    2004-03-01

    THE UNITED STATES MARINE CORPS DATA COLLABORATION REQUIREMENTS: RETRIEVING AND INTEGRATING DATA FROM...STATES MARINE CORPS DATA COLLABORATION REQUIREMENTS: RETRIEVING AND INTEGRATING DATA FROM MULTIPLE DATABASES THESIS Presented to the...04M-04 THE UNITED STATES MARINE CORPS DATA COLLABORATION REQUIREMENTS: RETRIEVING AND INTEGRATING DATA FROM MULTIPLE DATABASES Pamela J

  19. 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.

  20. Enhanced performance for the interacting multiple model estimator with integrated multiple filters

    NASA Astrophysics Data System (ADS)

    Sabordo, Madeleine G.; Aboutanios, Elias

    2015-05-01

    In this paper, we propose a new approach to target visibility for the Interacting Multiple Model (IMM) algorithm. We introduce the IMM Integrated Multiple Filters (IMF) to selectively engage a suitable filter appropriate for gated clutter density at each time step and investigate five model sets that model the dynamic motion of a manoeuvring target. The model sets are incorporated into the IMM-IMF tracker to estimate the behaviour of the target. We employ the Dynamic Error Spectrum (DES) to assess the effectiveness of the tracker with target visibility concept incorporated and to compare the performance of the model sets in enhancing tracking performance. Results show that the new version of target visibility significantly improves the performance of the tracker. Simulation results also demonstrate that the 2CV-CA-2CT model set proves to be the most robust at the cost of computational resource. The CV-CA model is the fastest tracker. However, it is the least robust in terms of performance. These results assist decision makers and researchers in choosing appropriate models for IMMtrackers. Augmenting the capability of the tracker improves the ability of the platform to identify possible threats and consequently, enhance situational awareness.

  1. A Fuzzy Logic Framework for Integrating Multiple Learned Models

    SciTech Connect

    Hartog, Bobi Kai Den

    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.

  2. Impaired functional integration in multiple sclerosis: a graph theory study.

    PubMed

    Rocca, Maria A; Valsasina, Paola; Meani, Alessandro; Falini, Andrea; Comi, Giancarlo; Filippi, Massimo

    2016-01-01

    Aim of this study was to explore the topological organization of functional brain network connectivity in a large cohort of multiple sclerosis (MS) patients and to assess whether its disruption contributes to disease clinical manifestations. Graph theoretical analysis was applied to resting state fMRI data from 246 MS patients and 55 matched healthy controls (HC). Functional connectivity between 116 cortical and subcortical brain regions was estimated using a bivariate correlation analysis. Global network properties (network degree, global efficiency, hierarchy, path length and assortativity) were abnormal in MS patients vs HC, and contributed to distinguish cognitively impaired MS patients (34%) from HC, but not the main MS clinical phenotypes. Compared to HC, MS patients also showed: (1) a loss of hubs in the superior frontal gyrus, precuneus and anterior cingulum in the left hemisphere; (2) a different lateralization of basal ganglia hubs (mostly located in the left hemisphere in HC, and in the right hemisphere in MS patients); and (3) a formation of hubs, not seen in HC, in the left temporal pole and cerebellum. MS patients also experienced a decreased nodal degree in the bilateral caudate nucleus and right cerebellum. Such a modification of regional network properties contributed to cognitive impairment and phenotypic variability of MS. An impairment of global integration (likely to reflect a reduced competence in information exchange between distant brain areas) occurs in MS and is associated with cognitive deficits. A regional redistribution of network properties contributes to cognitive status and phenotypic variability of these patients.

  3. 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.

  4. Automatic and integrated micro-enzyme assay (AIμEA) platform for highly sensitive thrombin analysis via an engineered fluorescence protein-functionalized monolithic capillary column.

    PubMed

    Lin, Lihua; Liu, Shengquan; Nie, Zhou; Chen, Yingzhuang; Lei, Chunyang; Wang, Zhen; Yin, Chao; Hu, Huiping; Huang, Yan; Yao, Shouzhuo

    2015-04-21

    Nowadays, large-scale screening for enzyme discovery, engineering, and drug discovery processes require simple, fast, and sensitive enzyme activity assay platforms with high integration and potential for high-throughput detection. Herein, a novel automatic and integrated micro-enzyme assay (AIμEA) platform was proposed based on a unique microreaction system fabricated by a engineered green fluorescence protein (GFP)-functionalized monolithic capillary column, with thrombin as an example. The recombinant GFP probe was rationally engineered to possess a His-tag and a substrate sequence of thrombin, which enable it to be immobilized on the monolith via metal affinity binding, and to be released after thrombin digestion. Combined with capillary electrophoresis-laser-induced fluorescence (CE-LIF), all the procedures, including thrombin injection, online enzymatic digestion in the microreaction system, and label-free detection of the released GFP, were integrated in a single electrophoretic process. By taking advantage of the ultrahigh loading capacity of the AIμEA platform and the CE automatic programming setup, one microreaction column was sufficient for many times digestion without replacement. The novel microreaction system showed significantly enhanced catalytic efficiency, about 30 fold higher than that of the equivalent bulk reaction. Accordingly, the AIμEA platform was highly sensitive with a limit of detection down to 1 pM of thrombin. Moreover, the AIμEA platform was robust and reliable to detect thrombin in human serum samples and its inhibition by hirudin. Hence, this AIμEA platform exhibits great potential for high-throughput analysis in future biological application, disease diagnostics, and drug screening.

  5. 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.

  6. Generating nonlinear FM chirp radar signals by multiple integrations

    DOEpatents

    Doerry, Armin W [Albuquerque, NM

    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.

  7. {sf MBsums} -- a {sf Mathematica} Package for the Representation of Mellin-Barnes Integrals by Multiple Sums

    NASA Astrophysics Data System (ADS)

    Ochman, M.; Riemann, T.

    Feynman integrals may be represented by the Mathematica packages AMBRE and MB as multiple Mellin-Barnes integrals. With the Mathematica package MBsums these Mellin-Barnes integrals are transformed into multiple sums.

  8. Demonstration of Nautilus Centripetal Capillary Condenser Technology

    NASA Technical Reports Server (NTRS)

    Wheeler, RIchard; Tang, Linh; Wambolt, Spencer; Golliher, Eric; Agui, Juan

    2016-01-01

    This paper describes the results of a proof of concept effort for development of a Nautilus Centripetal Capillary Condenser (NCCC or NC3) used for microgravity compatible water recovery from moist air with integral passive phase separation. Removal of liquid condensate from the air stream exiting a condenser is readily performed here on Earth. In order to perform this function in space however, without gravity or mechanical action, other tactics including utilization of inertial, drag and capillary forces are required. Within the NC3, liquid water forms via condensation on cold condenser surfaces as humid air passes along multiple spiral channels, each in its own plane, all together forming a stacked plate assembly. Non-mechanical inertial forces are employed to transfer condensate, as it forms, via centripetal action to the outer perimeter of each channel. A V-shaped groove, constructed on this outer edge of the spiral channel, increases local capillary forces thereby retaining the liquid. Air drag then pulls the liquid along to a collection region near the center of the device. Dry air produced by each parallel spiral channel is combined in a common orthogonal, out-of-plane conduit passing down the axial center of the stacked device. Similarly, the parallel condensate streams are combined and removed from the condenser/separator through yet another out-of-plane axial conduit. NC3 is an integration of conventional finned condenser operation, combined with static phase separation and capillary transport phenomena. A Mars' transit mission would be a logical application for this technology where gravity is absent and the use of vibrating, energy-intensive, motor-driven centrifugal separators is undesired. Here a vapor stream from either the Heat Melt Compactor or the Carbon dioxide Reduction Assembly, for example, would be dried to a dew point of 10 deg using a passive NC3 condenser/separator with the precious water condensate recycled to the water bus.

  9. Validating Measurement of Knowledge Integration in Science Using Multiple-Choice and Explanation Items

    ERIC Educational Resources Information Center

    Lee, Hee-Sun; Liu, Ou Lydia; Linn, Marcia C.

    2011-01-01

    This study explores measurement of a construct called knowledge integration in science using multiple-choice and explanation items. We use construct and instructional validity evidence to examine the role multiple-choice and explanation items plays in measuring students' knowledge integration ability. For construct validity, we analyze item…

  10. 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.…

  11. Integration Strategies for Learners with Severe Multiple Disabilities.

    ERIC Educational Resources Information Center

    Eichinger, Joanne; Woltman, Sheila

    1993-01-01

    This article reports the experiences of one school district as it moved from serving students with severe disabilities in segregated programs to a full inclusion model. Year one focused on getting started, planning, and beginning integration efforts and year two on implementation of a structured peer integration program. Applicability of the full…

  12. 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…

  13. 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.…

  14. 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".

  15. Microfluidic PMMA interfaces for rectangular glass capillaries

    NASA Astrophysics Data System (ADS)

    Evander, Mikael; Tenje, Maria

    2014-02-01

    We present the design and fabrication of a polymeric capillary fluidic interface fabricated by micro-milling. The design enables the use of glass capillaries with any kind of cross-section in complex microfluidic setups. We demonstrate two different designs of the interface; a double-inlet interface for hydrodynamic focusing and a capillary interface with integrated pneumatic valves. Both capillary interfaces are presented together with examples of practical applications. This communication shows the design optimization and presents details of the fabrication process. The capillary interface opens up for the use of complex microfluidic systems in single-use glass capillaries. They also enable simple fabrication of glass/polymer hybrid devices that can be beneficial in many research fields where a pure polymer chip negatively affects the device's performance, e.g. acoustofluidics.

  16. 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.

  17. 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,…

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

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

    PubMed Central

    2012-01-01

    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. PMID:22738091

  4. 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.

  5. 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

  6. 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.

  7. 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

  8. Integration of multiple research disciplines on the International Space Station

    NASA Technical Reports Server (NTRS)

    Penley, N. J.; Uri, J.; Sivils, T.; Bartoe, J. D.

    2000-01-01

    The International Space Station will provide an extremely high-quality, long-duration microgravity environment for the conduct of research. In addition, the ISS offers a platform for performing observations of Earth and Space from a high-inclination orbit, outside of the Earth's atmosphere. This unique environment and observational capability offers the opportunity for advancement in a diverse set of research fields. Many of these disciplines do not relate to one another, and present widely differing approaches to study, as well as different resource and operational requirements. Significant challenges exist to ensure the highest quality research return for each investigation. Requirements from different investigations must be identified, clarified, integrated and communicated to ISS personnel in a consistent manner. Resources such as power, crew time, etc. must be apportioned to allow the conduct of each investigation. Decisions affecting research must be made at the strategic level as well as at a very detailed execution level. The timing of the decisions can range from years before an investigation to real-time operations. The international nature of the Space Station program adds to the complexity. Each participating country must be assured that their interests are represented during the entire planning and operations process. A process for making decisions regarding research planning, operations, and real-time replanning is discussed. This process ensures adequate representation of all research investigators. It provides a means for timely decisions, and it includes a means to ensure that all ISS International Partners have their programmatic interests represented. c 2000 Published by Elsevier Science Ltd. All rights reserved.

  9. 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

  10. 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

  11. [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.

  12. 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.

  13. 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.

  14. Multidimensional capillary electrophoresis.

    PubMed

    Grochocki, Wojciech; Markuszewski, Michał J; Quirino, Joselito P

    2015-01-01

    Multidimensional separation where two or more orthogonal displacement mechanisms are combined is a promising approach to increase peak capacity in CE. The combinations allow dramatic improvement of analytical performance since the total peak capacity is given by a product of the peak capacities of all methods. The initial reports were concentrated on the construction of effective connections between capillaries for 2D analysis. Today, 2D and 3D CE systems are now able to separate real complex biological or environmental mixtures with good repeatability, improved resolution with minimal loss of sample. This review will present the developments in the field of multidimensional CE during the last 15 years. The endeavors in this specific field were on the development of interfaces, interface-free techniques including integrated separations, microdevices, and on-line sample concentration techniques to improve detection sensitivity.

  15. 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…

  16. 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…

  17. 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…

  18. 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…

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

    PubMed

    Özek, Gulmira; Ishmuratova, Margarita; Tabanca, Nurhayat; Radwan, Mohammed M; Göger, Fatih; Özek, Temel; Wedge, David E; Becnel, James J; Cutler, Stephen J; Can Başer, Kemal H

    2012-03-01

    Gas chromatographic analysis revealed that the oil of Crinitaria tatarica was rich in sabinene (32.1%), β-pinene (8.8%), and two unknown (M+200) compounds (I) and (II) (21.4% and 3.4%). One-step multiple fractionation of the oil and separation of two unknown constituents were performed using preparative capillary gas chromatography connected to preparative fraction collector system. This combination allowed separation and recover of sufficient quantities of two unknown compounds with high purity from complex oil matrix. Separation conditions (column temperature, cooling temperature, flow rate, injection volume, cut time) were optimized to achieve the best isolation and successful collection. The target compounds were separated from the oil using a HP Innowax (Walt & Jennings Scientific, Wilmington, DE, USA) preparative capillary column in rapid one-step manner with 95.0% purity. Trapping of the isolated compounds in collector system was facilitated by cooling with liquid nitrogen. Structure determination was accomplished by spectral analysis including ultraviolet, nuclear magnetic rezonance, and high-resolution electrospray ionization mass spectrometry. Z- (I) and E-artemidin (II) were isolated for the first time from this species. Crinitaria tatarica oil and Z- (I) and E-artemidin (II) were evaluated for biological activity.

  20. 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.

  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. A rapid and reliable strategy for chromosomal integration of gene(s) with multiple copies

    PubMed Central

    Gu, Pengfei; Yang, Fan; Su, Tianyuan; Wang, Qian; Liang, Quanfeng; Qi, Qingsheng

    2015-01-01

    Direct optimization of the metabolic pathways on the chromosome requires tools that can fine tune the overexpression of a desired gene or optimize the combination of multiple genes. Although plasmid-dependent overexpression has been used for this task, fundamental issues concerning its genetic stability and operational repeatability have not been addressed. Here, we describe a rapid and reliable strategy for chromosomal integration of gene(s) with multiple copies (CIGMC), which uses the flippase from the yeast 2-μm plasmid. Using green fluorescence protein as a model, we verified that the fluorescent intensity was in accordance with the integration copy number of the target gene. When a narrow-host-range replicon, R6K, was used in the integrative plasmid, the maximum integrated copy number of Escherichia coli reached 15. Applying the CIGMC method to optimize the overexpression of single or multiple genes in amino acid biosynthesis, we successfully improved the product yield and stability of the production. As a flexible strategy, CIGMC can be used in various microorganisms other than E. coli. PMID:25851494

  3. The use of multiple oxygen implants for fabrication of bipolar silicon-on-insulator integrated circuits

    NASA Astrophysics Data System (ADS)

    Platteter, Dale G.; Cheek, Tom F., Jr.

    1988-12-01

    A description is given of the radiation improvements obtained by fabricating bipolar integrated circuits on oxygen-implanted silicon-on-insulator substrates that were manufactured with multiple (low-dose) implants. Bipolar 74ALSOO gates fabricated on these substrates showed an improvement in total dose and dose-rate radiation response over identical circuits fabricated in bulk silicon. Defects in SIMOX material were reduced by over four orders of magnitude. The results demonstrate that bipolar devices, fabricated on multiple-implant SIMOX substrates, can compete with conventional dielectric isolation for many radiation-hardened system applications.

  4. Error and timing analysis of multiple time-step integration methods for molecular dynamics

    NASA Astrophysics Data System (ADS)

    Han, Guowen; Deng, Yuefan; Glimm, James; Martyna, Glenn

    2007-02-01

    Molecular dynamics simulations of biomolecules performed using multiple time-step integration methods are hampered by resonance instabilities. We analyze the properties of a simple 1D linear system integrated with the symplectic reference system propagator MTS (r-RESPA) technique following earlier work by others. A closed form expression for the time step dependent Hamiltonian which corresponds to r-RESPA integration of the model is derived. This permits us to present an analytic formula for the dependence of the integration accuracy on short-range force cutoff range. A detailed analysis of the force decomposition for the standard Ewald summation method is then given as the Ewald method is a good candidate to achieve high scaling on modern massively parallel machines. We test the new analysis on a realistic system, a protein in water. Under Langevin dynamics with a weak friction coefficient ( ζ=1 ps) to maintain temperature control and using the SHAKE algorithm to freeze out high frequency vibrations, we show that the 5 fs resonance barrier present when all degrees of freedom are unconstrained is postponed to ≈12 fs. An iso-error boundary with respect to the short-range cutoff range and multiple time step size agrees well with the analytical results which are valid due to dominance of the high frequency modes in determining integrator accuracy. Using r-RESPA to treat the long range interactions results in a 6× increase in efficiency for the decomposition described in the text.

  5. Multiple trim magnets, or magic fingers,'' for insertion device field integral correction

    SciTech Connect

    Hoyer, E.; Marks, S.; Pipersky, P.; Schlueter, R. )

    1995-02-01

    Multiple trim magnets (MTMs), also known as magic fingers,'' are an arrangement of magnets for reducing integrated magnetic-field errors in insertion devices. The idea is to use transverse arrays of permanent magnets, hence the name multiple trim magnets,'' above and below the midplane, to correct both normal and skew longitudinal magnetic-field integral errors in a device. MTMs are typically installed at the ends of an ID. Adjustments are made by changing either the size, position, or orientation of each trim magnet. Application of the MTMs to the ALS undulators reduced both the normal and skew longitudinal field integral errors, over the entire 20 mm[times]60 mm good field region,'' of the beam aperture by as much as an order of magnitude. The requirements included corrections of field and gradients outside the multipole convergence radius. Additionally, these trim magnet arrays provided correction of the linear component of the integrated field gradients for particles with trajectories not parallel to the nominal beam axis. The MTM concept, design, construction, tests that demonstrated feasibility, and magnetic-field integral reduction of ALS undulators are presented.

  6. 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.

  7. 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

  8. 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

  9. Modeling of multiple-optical-axis pattern-integrated interference lithography systems.

    PubMed

    Sedivy, Donald E; Gaylord, Thomas K

    2014-06-01

    The image quality and collimation in a multiple-optical-axis pattern-integrated interference lithography system are evaluated for an elementary optical system composed of single-element lenses. Image quality and collimation are individually and jointly optimized for these lenses. Example images for a jointly optimized system are simulated using a combination of ray tracing and Fourier analysis. Even with these nonoptimized components, reasonable fidelity is shown to be possible.

  10. It is time to integrate: the temporal dynamics of object motion and texture motion integration in multiple object tracking.

    PubMed

    Huff, Markus; Papenmeier, Frank

    2013-01-14

    In multiple-object tracking, participants can track several moving objects among identical distractors. It has recently been shown that the human visual system uses motion information in order to keep track of targets (St. Clair et al., Journal of Vision, 10(4), 1-13). Texture on the surface of an object that moved in the opposite direction to the object itself impaired tracking performance. In this study, we examined the temporal interval at which texture motion and object motion is integrated in dynamic scenes. In two multiple-object tracking experiments, we manipulated the texture motion on the objects: The texture either moved in the same direction as the objects, in the opposite direction, or alternated between the same and opposite direction at varying intervals. In Experiment 1, we show that the integration of object motion and texture motion can take place at intervals as short as 100 ms. In Experiment 2, we show that there is a linear relationship between the proportion of opposite texture motion and tracking performance. We suggest that texture motion might cause shifts in perceived object locations, thus influencing tracking performance.

  11. 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

  12. 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.

  13. Modulation of C. elegans Touch Sensitivity Is Integrated at Multiple Levels

    PubMed Central

    Chen, Xiaoyin

    2014-01-01

    Sensory systems can adapt to different environmental signals. Here we identify four conditions that modulate anterior touch sensitivity in Caenorhabditis elegans after several hours and demonstrate that such sensory modulation is integrated at multiple levels to produce a single output. Prolonged vibration involving integrin signaling directly sensitizes the touch receptor neurons (TRNs). In contrast, hypoxia, the dauer state, and high salt reduce touch sensitivity by preventing the release of long-range neuroregulators, including two insulin-like proteins. Integration of these latter inputs occurs at upstream neurohormonal cells and at the insulin signaling cascade within the TRNs. These signals and those from integrin signaling converge to modulate touch sensitivity by regulating AKT kinases and DAF-16/FOXO. Thus, activation of either the integrin or insulin pathways can compensate for defects in the other pathway. This modulatory system integrates conflicting signals from different modalities, and adapts touch sensitivity to both mechanical and non-mechanical conditions. PMID:24806678

  14. 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.

  15. Capillary rheometry for thermosets

    NASA Technical Reports Server (NTRS)

    Malguarnera, S. C.; Carroll, D. R.

    1982-01-01

    Capillary rheometry is effectively used with thermosets. Most important is providing a uniform temperature in the barrel. This was successfully accomplished by using a circulating hot oil system. Standard capillary rheometry methods provide the dependence of thermoset apparent viscosity on shear rate, temperature and time. Such information is very useful in evaluating resin processability and in setting preliminary fabrication conditions.

  16. An Integrated Experimental Design for the Assessment of Multiple Toxicological End Points in Rat Bioassays

    PubMed Central

    Manservisi, Fabiana; Marquillas, Clara Babot; Buscaroli, Annalisa; Huff, James; Lauriola, Michelina; Mandrioli, Daniele; Manservigi, Marco; Panzacchi, Simona; Silbergeld, Ellen K.; Belpoggi, Fiorella

    2016-01-01

    Background: For nearly five decades long-term studies in rodents have been the accepted benchmark for assessing chronic long-term toxic effects, particularly carcinogenicity, of chemicals. The European Food Safety Authority (EFSA) and the World Health Organization (WHO) have pointed out that the current set of internationally utilized test methods capture only some of the potential adverse effects associated with exposures to these agents over the lifetime. Objectives: In this paper, we propose the adaption of the carcinogenicity bioassay to integrate additional protocols for comprehensive long-term toxicity assessment that includes developmental exposures and long-term outcomes, capable of generating information on a broad spectrum of different end points. Discussion: An integrated study design based on a stepwise process is described that includes the priority end points of the Economic Co-operation and Development and the National Toxicology Program guidelines on carcinogenicity and chronic toxicity and developmental and reproductive toxicity. Integrating a comprehensive set of relevant toxicological end points in a single protocol represents an opportunity to optimize animal use in accordance with the 3Rs (replacement, reduction and refinement). This strategy has the potential to provide sufficient data on multiple windows of susceptibility of specific interest for risk assessments and public health decision-making by including prenatal, lactational, neonatal exposures and evaluating outcomes over the lifespan. Conclusion: This integrated study design is efficient in that the same generational cohort of rats used for evaluating long-term outcomes can be monitored in satellite parallel experiments to measure biomarkers and other parameters related to system-specific responses including metabolic alterations and endocrine disturbances. Citation: Manservisi F, Babot Marquillas C, Buscaroli A, Huff J, Lauriola M, Mandrioli D, Manservigi M, Panzacchi S, Silbergeld

  17. Identification of Functional Modules by Integration of Multiple Data Sources Using a Bayesian Network Classifier

    PubMed Central

    Wang, Jinlian; Zuo, Yiming; Liu, Lun; Man, Yangao; Tadesse, Mahlet G.; Ressom, Habtom W

    2014-01-01

    Background Prediction of functional modules is indispensable for detecting protein deregulation in human complex diseases such as cancer. Bayesian network (BN) is one of the most commonly used models to integrate heterogeneous data from multiple sources such as protein domain, interactome, functional annotation, genome-wide gene expression, and the literature. Methods and Results In this paper, we present a BN classifier that is customized to: 1) increase the ability to integrate diverse information from different sources, 2) effectively predict protein-protein interactions, 3) infer aberrant networks with scale-free and small world properties, and 4) group molecules into functional modules or pathways based on the primary function and biological features. Application of this model on discovering protein biomarkers of hepatocelluar carcinoma (HCC) leads to the identification of functional modules that provide insights into the mechanism of the development and progression of HCC. These functional modules include cell cycle deregulation, increased angiogenesis (e.g., vascular endothelial growth factor, blood vessel morphogenesis), oxidative metabolic alterations, and aberrant activation of signaling pathways involved in cellular proliferation, survival, and differentiation. Conclusion The discoveries and conclusions derived from our customized BN classifier are consistent with previously published results. The proposed approach for determining BN structure facilitates the integration of heterogeneous data from multiple sources to elucidate the mechanisms of complex diseases. PMID:24736851

  18. MSblender: a probabilistic approach for integrating peptide identifications from multiple database search engines

    PubMed Central

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

    2011-01-01

    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 all possible PSMs 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 all detected 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. PMID:21488652

  19. 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.

  20. 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

  1. [Transvascular fluid exchange disturbed by capillary injuries].

    PubMed

    Lugrin, D; Chave, S; Raucoules, M; Grimaud, D

    1996-01-01

    Fluid exchange disorders due to capillary lesions are numerous and their extent depends on the underlying disease as well as the capillary structure of the affected organ. The inflammatory cascade, triggered by sepsis or reperfusion injury, is mediated by several humoral mediators and activated blood cells. These include pro-inflammatory cytokines, arachidonic acid, proteases, oxygen free radicals, polymorphonuclears, procoagulant, complement and fibrinolytic system. The interaction between these mediators leads to a loss of endothelial integrity, a loss of basment membrane and a disruption of the interstitial matrix, with wasting of the endothelial cytoskeleton. The alteration in permeability induces transcapillary exudation of water and protein in the interstitial space, leading to organ dysfunction, mainly the lungs and splanchnic organs. Nitric oxyde, by modulating the response of the endothelium to the cellular interaction may protect against capillary injury. Capillary "stress lesions" following microvascular hypertension are the physiological basis of neurogenic or high altitude pulmonary oedema, and overinflation injury from mechanical ventilation. The anatomic specific features of the cerebral capillaries resulted in the well known concept of blood brain barrier with it's changeing morphology. Under the effect of humoral mediators and cellular interactions, the endothelial cells are able, via a calcium-mediated mechanism, to contract and to modify capillary permeability, leading to vasogenic oedema.

  2. [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.

  3. Pooling Data from Multiple Longitudinal Studies: The Role of Item Response Theory in Integrative Data Analysis

    PubMed Central

    Curran, Patrick J.; Hussong, Andrea M.; Cai, Li; Huang, Wenjing; Chassin, Laurie; Sher, Kenneth J.; Zucker, Robert A.

    2010-01-01

    There are a number of significant challenges encountered when studying development over an extended period of time including subject attrition, changing measurement structures across group and developmental period, and the need to invest substantial time and money. Integrative data analysis is an emerging set of methodologies that overcomes many of the challenges of single sample designs through the pooling of data drawn from multiple existing developmental studies. This approach is characterized by a host of advantages, but this also introduces several new complexities that must be addressed prior to broad adoption by developmental researchers. In this paper we focus on methods for fitting measurement models and creating scale scores using data drawn from multiple longitudinal studies. We present findings from the analysis of repeated measures of internalizing symptomatology that were pooled from three existing developmental studies. We describe and demonstrate each step in the analysis and we conclude with a discussion of potential limitations and directions for future research. PMID:18331129

  4. 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.

  5. 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.

  6. SXR optical diagnostics of capillary discharge plasma

    NASA Astrophysics Data System (ADS)

    Pina, L.; Jancarek, A.; Vrbova, M.; Tamas, M.; Blazej, J.; Havlikova, R.; Vrba, P.; Tomassetti, G.; Ritucci, A.

    2006-08-01

    Pinching capillary discharge in nitrogen is investigated for the purpose of development of laser recombination pumping. An apparatus, previously realized for argon capillary laser pumping, was used to understand details of pinching mechanism and emission characteristics for capillary filled by nitrogen. Time dependences of radiation intensities emitted in the wavelength range 1.9 - 2.5 nm and time integrated in the spectral range 10 - 20 nm were measured under various pressures. A computer model is used to describe the pinch dynamics and to estimate the radiation characteristics. EUV reflection grating spectrometer coupled to BI CCD camera and filtered PIN diode were used for time integrated and time resolved spectral measurements respectively. The measured profiles of radiation intensities are compared with the computer simulations of time dependences of selected energy level populations that correspond to the hydrogen- and helium- like ion line emission in the detected spectral range. Complex method for spectral image restoration was developed.

  7. 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

  8. 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.

  9. Current DOT research on the effect of multiple site damage on structural integrity

    NASA Astrophysics Data System (ADS)

    Tong, P.; Arin, Kemal; Jeong, David Y.; Greif, R.; Brewer, John C.; Bobo, Stephan N.; Sampath, Sam N.

    1992-07-01

    Multiple site damage (MSD) is a type of cracking that may be found in aging airplanes and which may adversely affect their continuing airworthiness. The Volpe National Transportation Systems Center has supported the Federal Aviation Administration Technical Center on structural integrity research for the past two and half years. The work has focused on understanding the behavior of MSD, detection of MSD during airframe inspection, and the avoidance of MSD in future designs. These three elements of the MSD problem are addressed and a summary of the completed work, the current status, and requirements for future research is provided.

  10. Multiple Populations in M31 Globular Clusters: Clues from Infrared High Resolution Integrated Light Spectroscopy

    NASA Astrophysics Data System (ADS)

    Sakari, Charli; APOGEE Team

    2017-01-01

    Abundance variations are a common feature of Milky Way globular clusters. The globular clusters in M31 are too distant for detailed abundance studies of their individual stars; however, cluster abundances can be determined through high resolution, integrated light (IL) spectroscopy. In this talk, I discuss how IL abundances can be interpreted in the context of multiple populations. In particular, I will present new infrared abudances of 25 M31 globular clusters, derived from IL spectra from the Apache Point Observatory Galactic Evolution Experiment (APOGEE). These H band spectra allow determinations of C, N, and O from molecular features, and Fe, Na, Mg, Al, Si, Ca, Ti, and K from atomic features. The integrated abundance ratios are then investigated with cluster [Fe/H] and mass.

  11. Evaluating environmental sustainability: an integration of multiple-criteria decision-making and fuzzy logic.

    PubMed

    Liu, Kevin F R

    2007-05-01

    While pursuing economic development, countries around the world have become aware of the importance of environmental sustainability; therefore, the evaluation of environmental sustainability has become a significant issue. Traditionally, multiple-criteria decision-making (MCDM) was widely used as a way of evaluating environmental sustainability, Recently, several researchers have attempted to implement this evaluation with fuzzy logic since they recognized the assessment of environmental sustainability as a subjective judgment Intuition. This paper outlines a new evaluation-framework of environmental sustainability, which integrates fuzzy logic into MCDM. This evaluation-framework consists of 36 structured and 5 unstructured decision-points, wherein MCDM is used to handle the former and fuzzy logic serves for the latter, With the integrated evaluation-framework, the evaluations of environmental sustainability in 146 countries are calculated, ranked and clustered, and the evaluation results are very helpful to these countries, as they identify their obstacles towards environmental sustainability.

  12. Position synchronised control of multiple robotic manipulators based on integral sliding mode

    NASA Astrophysics Data System (ADS)

    Zhao, Dongya; Zhu, Quanmin

    2014-03-01

    In this study, a new position synchronised control algorithm is developed for multiple robotic manipulator systems. In the merit of system synchronisation and integral sliding mode control, the proposed approach can stabilise position tracking of each robotic manipulator while coordinating its motion with the other manipulators. With the integral sliding mode, the proposed approach has insensitiveness against the lumped system uncertainty within the entire process of operation. Further, a perturbation estimator is proposed to reduce chattering effect. The corresponding stability analysis is presented to lay a foundation for theoretical understanding to the underlying issues as well as safely operating real systems. An illustrative example is bench tested to validate the effectiveness of the proposed approach.

  13. Data integration and systems biology approaches for biomarker discovery: challenges and opportunities for multiple sclerosis.

    PubMed

    Villoslada, Pablo; Baranzini, Sergio

    2012-07-15

    New "omic" technologies and their application to systems biology approaches offer new opportunities for biomarker discovery in complex disorders, including multiple sclerosis (MS). Recent studies using massive genotyping, DNA arrays, antibody arrays, proteomics, glycomics, and metabolomics from different tissues (blood, cerebrospinal fluid, brain) have identified many molecules associated with MS, defining both susceptibility and functional targets (e.g., biomarkers). Such discoveries involve many different levels in the complex organizational hierarchy of humans (DNA, RNA, protein, etc.), and integrating these datasets into a coherent model with regard to MS pathogenesis would be a significant step forward. Given the dynamic and heterogeneous nature of MS, validating biomarkers is mandatory. To develop accurate markers of disease prognosis or therapeutic response that are clinically useful, combining molecular, clinical, and imaging data is necessary. Such an integrative approach would pave the way towards better patient care and more effective clinical trials that test new therapies, thus bringing the paradigm of personalized medicine in MS one step closer.

  14. Monolithic integration of multiple-emission-wavelength laser diodes using low-energy ion implantation

    NASA Astrophysics Data System (ADS)

    Aimez, Vincent; Paquette, Michel; Beauvais, Jacques; Beerens, Jean; Poole, Philip J.; Charbonneau, N. Sylvain

    1998-09-01

    A monolithic optoelectronic chip containing multiple emission wavelength laser diodes has been developed. The semiconductor quantum well lasers have Fabry-Perot cavities of 500 micrometers in length. Electrical insulation between individual integrated devices has been achieved by wet etching the top contact layer and by a lift-off of the surface metal contact between the different lasers. The electroluminescence peak emission spectra of the integrated laser diodes has been shifted over a 25 nm range and 74 nm for discrete devices. Blueshifting of the emission wavelength has been achieved by quantum well intermixing using an industrial low energy ion implanter to generate point defects and a rapid thermal annealer to promote interdiffusion of the barrier and quantum well atoms during the recrystallization anneal. Phosphorus ions were implanted with an energy of 360 keV to precisely defined regions of the heterostructure with SiO2 serving as a masking material. Thus reference and intermixed regions were integrated on a single component. Integrated and discrete laser diodes have been assessed in terms of threshold currents and emission wavelengths.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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

  20. Analysis of bovine milk caseins on organic monolithic columns: an integrated capillary liquid chromatography-high resolution mass spectrometry approach for the study of time-dependent casein degradation.

    PubMed

    Pierri, Giuseppe; Kotoni, Dorina; Simone, Patrizia; Villani, Claudio; Pepe, Giacomo; Campiglia, Pietro; Dugo, Paola; Gasparrini, Francesco

    2013-10-25

    Casein proteins constitute approximately 80% of the proteins present in bovine milk and account for many of its nutritional and technological properties. The analysis of the casein fraction in commercially available pasteurized milk and the study of its time-dependent degradation is of considerable interest in the agro-food industry. Here we present new analytical methods for the study of caseins in fresh and expired bovine milk, based on the use of lab-made capillary organic monolithic columns. An integrated capillary high performance liquid chromatography and high-resolution mass spectrometry (Cap-LC-HRMS) approach was developed, exploiting the excellent resolution, permeability and biocompatibility of organic monoliths, which is easily adaptable to the analysis of intact proteins. The resolution obtained on the lab-made Protein-Cap-RP-Lauryl-γ-Monolithic column (270 mm × 0.250 mm length × internal diameter, L × I.D.) in the analysis of commercial standard caseins (αS-CN, β-CN and κ-CN) through Cap-HPLC-UV was compared to the one observe using two packed capillary C4 columns, the ACE C4 (3 μm, 150 mm × 0.300 mm, L × I.D.) and the Jupiter C4 column (5 μm, 150 mm × 0.300 mm, L × I.D.). Thanks to the higher resolution observed, the monolithic capillary column was chosen for the successive degradation studies of casein fractions extracted from bovine milk 1-4 weeks after expiry date. The comparison of the UV chromatographic profiles of skim, semi-skim and whole milk showed a major stability of whole milk towards time-dependent degradation of caseins, which was further sustained by high-resolution analysis on a 50-cm long monolithic column using a 120-min time gradient. Contemporarily, the exact monoisotopic and average molecular masses of intact αS-CN and β-CN protein standards were obtained through high resolution mass spectrometry and used for casein identification in Cap-LC-HRMS analysis. Finally, the proteolytic degradation of β-CN in skim milk

  1. Functional integration between brain regions at rest occurs in multiple-frequency bands.

    PubMed

    Gohel, Suril R; Biswal, Bharat B

    2015-02-01

    Studies of resting-state fMRI have shown that blood oxygen level dependent (BOLD) signals giving rise to temporal correlation across voxels (or regions) are dominated by low-frequency fluctuations in the range of ∼ 0.01-0.1 Hz. These low-frequency fluctuations have been further divided into multiple distinct frequency bands (slow-5 and -4) based on earlier neurophysiological studies, though low sampling frequency of fMRI (∼ 0.5 Hz) has substantially limited the exploration of other known frequency bands of neurophysiological origins (slow-3, -2, and -1). In this study, we used resting-state fMRI data acquired from 21 healthy subjects at a higher sampling frequency of 1.5 Hz to assess the presence of resting-state functional connectivity (RSFC) across multiple frequency bands: slow-5 to slow-1. The effect of different frequency bands on spatial extent and connectivity strength for known resting-state networks (RSNs) was also evaluated. RSNs were derived using independent component analysis and seed-based correlation. Commonly known RSNs, such as the default mode, the fronto-parietal, the dorsal attention, and the visual networks, were consistently observed at multiple frequency bands. Significant inter-hemispheric connectivity was observed between each seed and its contra lateral brain region across all frequency bands, though overall spatial extent of seed-based correlation maps decreased in slow-2 and slow-1 frequency bands. These results suggest that functional integration between brain regions at rest occurs over multiple frequency bands and RSFC is a multiband phenomenon. These results also suggest that further investigation of BOLD signal in multiple frequency bands for related cognitive processes should be undertaken.

  2. Accelerating Ab Initio Path Integral Simulations via Imaginary Multiple-Timestepping.

    PubMed

    Cheng, Xiaolu; Herr, Jonathan D; Steele, Ryan P

    2016-04-12

    This work investigates the use of multiple-timestep schemes in imaginary time for computationally efficient ab initio equilibrium path integral simulations of quantum molecular motion. In the simplest formulation, only every n(th) path integral replica is computed at the target level of electronic structure theory, whereas the remaining low-level replicas still account for nuclear motion quantum effects with a more computationally economical theory. Motivated by recent developments for multiple-timestep techniques in real-time classical molecular dynamics, both 1-electron (atomic-orbital basis set) and 2-electron (electron correlation) truncations are shown to be effective. Structural distributions and thermodynamic averages are tested for representative analytic potentials and ab initio molecular examples. Target quantum chemistry methods include density functional theory and second-order Møller-Plesset perturbation theory, although any level of theory is formally amenable to this framework. For a standard two-level splitting, computational speedups of 1.6-4.0x are observed when using a 4-fold reduction in time slices; an 8-fold reduction is feasible in some cases. Multitiered options further reduce computational requirements and suggest that quantum mechanical motion could potentially be obtained at a cost not significantly different from the cost of classical simulations.

  3. Capillary nail refill test

    MedlinePlus

    ... may indicate: Dehydration Shock Peripheral vascular disease (PVD) Hypothermia Alternative Names Nail blanch test; Capillary refill time ... Elsevier Saunders; 2016:chap 79. Read More Dehydration Hypothermia Peripheral artery disease - legs Shock Review Date 4/ ...

  4. 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.

  5. 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.

  6. 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.

  7. 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

  8. Encrypting three-dimensional information system based on integral imaging and multiple chaotic maps

    NASA Astrophysics Data System (ADS)

    Xing, Yan; Wang, Qiong-Hua; Xiong, Zhao-Long; Deng, Huan

    2016-02-01

    An encrypting three-dimensional (3-D) information system based on integral imaging (II) and multiple chaotic maps is proposed. In the encrypting process, the elemental image array (EIA) which represents spatial and angular information of the real 3-D scene is picked up by a microlens array. Subsequently, R, G, and B color components decomposed by the EIA are encrypted using multiple chaotic maps. Finally, these three encrypted components are interwoven to obtain the cipher information. The decryption process implements the reverse operation of the encryption process for retrieving the high-quality 3-D images. Since the encrypted EIA has the data redundancy property due to II, and all parameters of the pickup part are the secret keys of the encrypting system, the system sensitivity on the changes of the plaintext and secret keys can be significantly improved. Moreover, the algorithm based on multiple chaotic maps can effectively enhance the security. A preliminary experiment is carried out, and the experimental results verify the effectiveness, robustness, and security of the proposed system.

  9. 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.

  10. 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)

  11. Design of capillary flows with functionally graded porous titanium oxide films fabricated by anodization instability.

    PubMed

    Joung, Young Soo; Figliuzzi, Bruno Michel; Buie, Cullen R

    2014-06-01

    We have developed an electrochemical fabrication method utilizing breakdown anodization (BDA) to yield capillary flows that can be expressed as functions of capillary height. This method uses anodization instability with high electric potentials and mildly acidic electrolytes that are maintained at low temperature. BDA produces highly porous micro- and nano-structured surfaces composed of amorphous titanium oxide on titanium substrates, resulting in high capillary pressure and capillary diffusivity. With this fabrication technique the capillary flow properties can be controlled by varying the applied electric field and electrolyte temperature. Furthermore, they can be expressed as functions of capillary height when customized electric fields are used in BDA. To predict capillary flows on BDA surfaces, we developed a conceptual model of highly wettable porous films, which are modeled as multiple layers of capillary tubes oriented in the flow direction. From the model, we derived a general capillary flow equation of motion in terms of capillary pressure and capillary diffusivity, both of which can be expressed as functions of capillary height. The theoretical model was verified by comparisons with experimental capillary flows, showing good agreement. From investigation of the surface morphology we found that the surface structures were also functionally graded with respect to the capillary height (i.e. applied electric field). The suggested fabrication method and the theoretical model offer novel design methodologies for microscale liquid transport devices requiring control over propagation speed.

  12. 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.

  13. 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.

  14. Capillary saturation and desaturation

    NASA Astrophysics Data System (ADS)

    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.

  15. 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.

  16. 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…

  17. 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

  18. 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.

  19. 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

  20. 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.

  1. The use of the Integrated Discrete Multiple Organ Co-culture (IdMOC) system for the evaluation of multiple organ toxicity.

    PubMed

    Li, Albert P

    2009-09-01

    The application of the Integrated Discrete Multiple Organ Co-culture (IdMOC) system in the evaluation of organ-specific toxicity is reviewed. In vitro approaches to predict in vivo toxicity have met with limited success, mainly because of the complexity of in vivo toxic responses. In vivo properties that are not well-represented in vitro include organ-specific responses, multiple organ metabolism, and multiple organ interactions. The IdMOC system has been developed to address these deficiencies. The system uses a 'wells-within-a-well' concept for the co-culturing of cells or tissue slices from different organs as physically separated (discrete) entities in the small inner wells. These inner wells are nevertheless interconnected (integrated) by overlying culture medium in the large outer containing well. The IdMOC system thereby models the in vivo situation, in which multiple organs are physically separated but interconnected by the systemic circulation, permitting multiple organ interactions. The IdMOC system, with either cells or tissue slices from multiple organs, can be used to evaluate cell type-specific or organ-specific toxicity.

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

    PubMed

    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.

  3. 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

  4. Integration of Multiple Data Sources to Simulate the Dynamics of Land Systems.

    PubMed

    Deng, Xiangzheng; Su, Hongbo; Zhan, Jinyan

    2008-02-04

    In this paper we present and develop a new model, which we have calledDynamics of Land Systems (DLS). The DLS model is capable of integrating multiple datasources to simulate the dynamics of a land system. Three main modules are incorporatedin DLS: a spatial regression module, to explore the relationship between land uses andinfluencing factors, a scenario analysis module of the land uses of a region during thesimulation period and a spatial disaggregation module, to allocate land use changes froma regional level to disaggregated grid cells. A case study on Taips County in North Chinais incorporated in this paper to test the functionality of DLS. The simulation results underthe baseline, economic priority and environmental scenarios help to understand the landsystem dynamics and project near future land-use trajectories of a region, in order tofocus management decisions on land uses and land use planning.

  5. 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.

  6. Integrated Anaerobic-Aerobic Biodegradation of Multiple Contaminants Including Chlorinated Ethylenes, Benzene, Toluene, and Dichloromethane.

    PubMed

    Yoshikawa, Miho; Zhang, Ming; Toyota, Koki

    2017-01-01

    Complete bioremediation of soils containing multiple volatile organic compounds (VOCs) remains a challenge. To explore the possibility of complete bioremediation through integrated anaerobic-aerobic biodegradation, laboratory feasibility tests followed by alternate anaerobic-aerobic and aerobic-anaerobic biodegradation tests were performed. Chlorinated ethylenes, including tetrachloroethylene (PCE), trichloroethylene (TCE), cis-dichloroethylene (cis-DCE), and vinyl chloride (VC), and dichloromethane (DCM) were used for anaerobic biodegradation, whereas benzene, toluene, and DCM were used for aerobic biodegradation tests. Microbial communities involved in the biodegradation tests were analyzed to characterize the major bacteria that may contribute to biodegradation. The results demonstrated that integrated anaerobic-aerobic biodegradation was capable of completely degrading the seven VOCs with initial concentration of each VOC less than 30 mg/L. Benzene and toluene were degraded within 8 days, and DCM was degraded within 20 to 27 days under aerobic conditions when initial oxygen concentrations in the headspaces of test bottles were set to 5.3% and 21.0%. Dehalococcoides sp., generally considered sensitive to oxygen, survived aerobic conditions for 28 days and was activated during the subsequent anaerobic biodegradation. However, degradation of cis-DCE was suppressed after oxygen exposure for more than 201 days, suggesting the loss of viability of Dehalococcoides sp., as they are the only known anaerobic bacteria that can completely biodegrade chlorinated ethylenes to ethylene. Anaerobic degradation of DCM following previous aerobic degradation was complete, and yet-unknown microbes may be involved in the process. The findings may provide a scientific and practical basis for the complete bioremediation of multiple contaminants in situ and a subject for further exploration.

  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. Peritubular capillary rarefaction: a new therapeutic target in chronic kidney disease

    PubMed Central

    Kida, Yujiro; Tchao, Bie Nga; Yamaguchi, Ikuyo

    2013-01-01

    Chronic kidney disease (CKD) is epidemic around the world and desparately needs new therapies. Peritubular capillary (PTC) rarefaction, along with interstitial fibrosis and tubular atorophy, is one of the major hallmarks of CKD and predicts renal outcome in patients with CKD. PTC endothelial cells (ECs) undergo apoptosis during CKD, leading to capillary loss, tissue hypoxia, and oxidant stress. Although the mechanisms of PTC rarefaction are not well understood, the process of PTC rarefaction depends on multiple events that happen during CKD. These events, which lead to an antiangiogenic environment, include deprivation of EC survival factors, increased production of vascular growth inhibitors, malfunction of ECs, dysfunction of endothelial progenitor cells, and loss of EC integrity via pericyte detachment from vasculature. In this review, we focus on major factors regulating angiogenesis and EC survival and describe roles of these factors in PTC rarefaction during CKD and possible therapeutic applications. PMID:23475077

  9. 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.

  10. Integrated Multiple “-omics” Data Reveal Subtypes of Hepatocellular Carcinoma

    PubMed Central

    Liu, Gang; Dong, Chuanpeng; Liu, Lei

    2016-01-01

    Hepatocellular carcinoma is one of the most heterogeneous cancers, as reflected by its multiple grades and difficulty to subtype. In this study, we integrated copy number variation, DNA methylation, mRNA, and miRNA data with the developed “cluster of cluster” method and classified 256 HCC samples from TCGA (The Cancer Genome Atlas) into five major subgroups (S1-S5). We observed that this classification was associated with specific mutations and protein expression, and we detected that each subgroup had distinct molecular signatures. The subclasses were associated not only with survival but also with clinical observations. S1 was characterized by bulk amplification on 8q24, TP53 mutation, low lipid metabolism, highly expressed onco-proteins, attenuated tumor suppressor proteins and a worse survival rate. S2 and S3 were characterized by telomere hypomethylation and a low expression of TERT and DNMT1/3B. Compared to S2, S3 was associated with less copy number variation and some good prognosis biomarkers, including CRP and CYP2E1. In contrast, the mutation rate of CTNNB1 was higher in S3. S4 was associated with bulk amplification and various molecular characteristics at different biological levels. In summary, we classified the HCC samples into five subgroups using multiple “-omics” data. Each subgroup had a distinct survival rate and molecular signature, which may provide information about the pathogenesis of subtypes in HCC. PMID:27806083

  11. Multiple-Time Step Ab Initio Molecular Dynamics Based on Two-Electron Integral Screening.

    PubMed

    Fatehi, Shervin; Steele, Ryan P

    2015-03-10

    A multiple-timestep ab initio molecular dynamics scheme based on varying the two-electron integral screening method used in Hartree-Fock or density functional theory calculations is presented. Although screening is motivated by numerical considerations, it is also related to separations in the length- and timescales characterizing forces in a molecular system: Loose thresholds are sufficient to describe fast motions over short distances, while tight thresholds may be employed for larger length scales and longer times, leading to a practical acceleration of ab initio molecular dynamics simulations. Standard screening approaches can lead, however, to significant discontinuities in (and inconsistencies between) the energy and gradient when the screening threshold is loose, making them inappropriate for use in dynamics. To remedy this problem, a consistent window-screening method that smooths these discontinuities is devised. Further algorithmic improvements reuse electronic-structure information within the dynamics step and enhance efficiency relative to a naı̈ve multiple-timestepping protocol. The resulting scheme is shown to realize meaningful reductions in the cost of Hartree-Fock and B3LYP simulations of a moderately large system, the protonated sarcosine/glycine dipeptide embedded in a 19-water cluster.

  12. High-throughput sequencing of multiple amplicons for barcoding and integrative taxonomy

    PubMed Central

    Cruaud, Perrine; Rasplus, Jean-Yves; Rodriguez, Lillian Jennifer; Cruaud, Astrid

    2017-01-01

    Until now, the potential of NGS for the construction of barcode libraries or integrative taxonomy has been seldom realised. Here, we amplified (two-step PCR) and simultaneously sequenced (MiSeq) multiple markers from hundreds of fig wasp specimens. We also developed a workflow for quality control of the data. Illumina and Sanger sequences accumulated in the past years were compared. Interestingly, primers and PCR conditions used for the Sanger approach did not require optimisation to construct the MiSeq library. After quality controls, 87% of the species (76% of the specimens) had a valid MiSeq sequence for each marker. Importantly, major clusters did not always correspond to the targeted loci. Nine specimens exhibited two divergent sequences (up to 10%). In 95% of the species, MiSeq and Sanger sequences obtained from the same sampling were similar. For the remaining 5%, species were paraphyletic or the sequences clustered into divergent groups on the Sanger + MiSeq trees (>7%). These problematic cases may represent coding NUMTS or heteroplasms. Our results illustrate that Illumina approaches are not artefact-free and confirm that Sanger databases can contain non-target genes. This highlights the importance of quality controls, working with taxonomists and using multiple markers for DNA-taxonomy or species diversity assessment. PMID:28165046

  13. Fuzzy adaptive interacting multiple model nonlinear filter for integrated navigation sensor fusion.

    PubMed

    Tseng, Chien-Hao; Chang, Chih-Wen; Jwo, Dah-Jing

    2011-01-01

    In this paper, the application of the fuzzy interacting multiple model unscented Kalman filter (FUZZY-IMMUKF) approach to integrated navigation processing for the maneuvering vehicle is presented. The unscented Kalman filter (UKF) employs a set of sigma points through deterministic sampling, such that a linearization process is not necessary, and therefore the errors caused by linearization as in the traditional extended Kalman filter (EKF) can be avoided. The nonlinear filters naturally suffer, to some extent, the same problem as the EKF for which the uncertainty of the process noise and measurement noise will degrade the performance. As a structural adaptation (model switching) mechanism, the interacting multiple model (IMM), which describes a set of switching models, can be utilized for determining the adequate value of process noise covariance. The fuzzy logic adaptive system (FLAS) is employed to determine the lower and upper bounds of the system noise through the fuzzy inference system (FIS). The resulting sensor fusion strategy can efficiently deal with the nonlinear problem for the vehicle navigation. The proposed FUZZY-IMMUKF algorithm shows remarkable improvement in the navigation estimation accuracy as compared to the relatively conventional approaches such as the UKF and IMMUKF.

  14. Improved Thermal Behavior of Multiple Linked Arrays of Silicon Nanowires Integrated into Planar Thermoelectric Microgenerators

    NASA Astrophysics Data System (ADS)

    Dávila, Diana; Tarancón, Albert; Calaza, Carlos; Salleras, Marc; Fernández-Regúlez, Marta; Paulo, Alvaro San; Fonseca, Luis

    2013-07-01

    Low-dimensional structures have been shown to be promising candidates for enhancing the thermoelectric properties of semiconductors, paving the way for integration of thermoelectric generators into silicon microtechnology. With this aim, dense arrays of well-oriented and size-controlled silicon nanowires (Si NWs) obtained by the chemical vapor deposition (CVD)-vapor-liquid-solid (VLS) mechanism have been implemented into microfabricated structures to develop planar unileg thermoelectric microgenerators ( μTEGs). Different low-thermal-mass suspended structures have been designed and microfabricated on silicon-on-insulator (SOI) substrates to operate as microthermoelements using p-type Si NW arrays as the thermoelectric material. To obtain nanowire arrays with effective lengths larger than normally attained by the VLS technique, structures composed of multiple ordered arrays consecutively bridged by transversal microspacers have been fabricated. The successive linkage of multiple Si NW arrays enabled the development of larger temperature differences while preserving good electrical contact. This gives rise to small internal thermoelement resistances, enhancing the performance of the devices as energy harvesters.

  15. An integrated voice and data multiple-access scheme for a land-mobile satellite system

    NASA Technical Reports Server (NTRS)

    Li, V. O. K.; Yan, T.-Y.

    1984-01-01

    An analytical study is performed of the satellite requirements for a land mobile satellite system (LMSS). The spacecraft (MSAT-X) would be in GEO and would be compatible with multiple access by mobile radios and antennas and fixed stations. The FCC has received a petition from NASA to reserve the 821-825 and 866-870 MHz frequencies for the LMSS, while communications with fixed earth stations would be in the Ku band. MSAT-X transponders would alter the frequencies of signal and do no processing in the original configuration considered. Channel use would be governed by an integrated demand-assigned, multiple access protocol, which would divide channels into reservation and information channels, governed by a network management center. Further analyses will cover tradeoffs between data and voice users, probability of blocking, and the performance impacts of on-board switching and variable bandwidth assignment. Initial calculations indicate that a large traffic volume can be handled with acceptable delays and voice blocking probabilities.

  16. An integrated decision making approach for assessing healthcare waste treatment technologies from a multiple stakeholder.

    PubMed

    Shi, Hua; Liu, Hu-Chen; Li, Ping; Xu, Xue-Guo

    2017-01-01

    With increased worldwide awareness of environmental issues, healthcare waste (HCW) management has received much attention from both researchers and practitioners over the past decade. The task of selecting the optimum treatment technology for HCWs is a challenging decision making problem involving conflicting evaluation criteria and multiple stakeholders. In this paper, we develop an integrated decision making framework based on cloud model and MABAC method for evaluating and selecting the best HCW treatment technology from a multiple stakeholder perspective. The introduced framework deals with uncertain linguistic assessments of alternatives by using interval 2-tuple linguistic variables, determines decision makers' relative weights based on the uncertainty and divergence degrees of every decision maker, and obtains the ranking of all HCW disposal alternatives with the aid of an extended MABAC method. Finally, an empirical example from Shanghai, China, is provided to illustrate the feasibility and effectiveness of the proposed approach. Results indicate that the methodology being proposed is more suitable and effective to handle the HCW treatment technology selection problem under vague and uncertain information environment.

  17. 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.

  18. Integrated health messaging for multiple neglected zoonoses: Approaches, challenges and opportunities in Morocco.

    PubMed

    Ducrotoy, M J; Yahyaoui Azami, H; El Berbri, I; Bouslikhane, M; Fassi Fihri, O; Boué, F; Petavy, A F; Dakkak, A; Welburn, S; Bardosh, K L

    2015-12-01

    Integrating the control of multiple neglected zoonoses at the community-level holds great potential, but critical data is missing to inform the design and implementation of different interventions. In this paper we present an evaluation of an integrated health messaging intervention, using powerpoint presentations, for five bacterial (brucellosis and bovine tuberculosis) and dog-associated (rabies, cystic echinococcosis and leishmaniasis) zoonotic diseases in Sidi Kacem Province, northwest Morocco. Conducted by veterinary and epidemiology students between 2013 and 2014, this followed a process-based approach that encouraged sequential adaptation of images, key messages, and delivery strategies using auto-evaluation and end-user feedback. We describe the challenges and opportunities of this approach, reflecting on who was targeted, how education was conducted, and what tools and approaches were used. Our results showed that: (1) replacing words with local pictures and using "hands-on" activities improved receptivity; (2) information "overload" easily occurred when disease transmission pathways did not overlap; (3) access and receptivity at schools was greater than at the community-level; and (4) piggy-backing on high-priority diseases like rabies offered an important avenue to increase knowledge of other zoonoses. We conclude by discussing the merits of incorporating our validated education approach into the school curriculum in order to influence long-term behaviour change.

  19. 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.

  20. 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.

  1. 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).

  2. 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.

  3. 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

  4. 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

  5. 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.

  6. 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

  7. 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.

  8. 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.

  9. 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

  10. Extraction of situational meaning by integrating multiple meanings in a complex environment: a functional MRI study.

    PubMed

    Sugiura, Motoaki; Wakusawa, Keisuke; Sekiguchi, Atsushi; Sassa, Yuko; Jeong, Hyeonjeong; Horie, Kaoru; Sato, Shigeru; Kawashima, Ryuta

    2009-08-01

    Humans extract behaviorally significant meaning from a situation by integrating meanings from multiple components of a complex daily environment. To determine the neural underpinnings of this ability, the authors performed functional magnetic resonance imaging of healthy subjects while the latter viewed naturalistic scenes of two people and an object, including a threatening situation of a person being attacked by an offender with an object. The authors used a two-factorial design: the object was either aversive or nonaversive, and the offender's action was either directed to the person or elsewhere. This allowed the authors to examine the neural response to object aversiveness and person-directed intention separately. A task unrelated to threat was also used to address incidental (i.e., subconscious or unintentional) detection. Assuming individual differences in incidental threat detection, the authors used a functional connectivity analysis using principal components analysis of intersubject variability. The left lateral orbitofrontal cortex and medial prefrontal cortex (MPFC) were specifically activated in response to a threatening situation. The threat-related component of intersubject variability was extracted from these data and showed a significant correlation with personality scores. There was also a correlation between threat-related intersubject variability and activation for object aversiveness in the left temporal pole and lateral orbitofrontal cortex; person-directed intention in the left superior frontal gyrus; threatening situations in the left MPFC; and independently for both factors in the right MPFC. Results demonstrate independent processing of object aversiveness and person-directed intention in the left temporal-orbitofrontal and superior frontal networks, respectively, and their integration into situational meaning in the MPFC.

  11. 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.

  12. 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.

  13. Integration of MicroRNA databases to study MicroRNAs associated with multiple sclerosis.

    PubMed

    Angerstein, Charlotte; Hecker, Michael; Paap, Brigitte Katrin; Koczan, Dirk; Thamilarasan, Madhan; Thiesen, Hans-Jürgen; Zettl, Uwe Klaus

    2012-06-01

    MicroRNAs (miRNAs) are small non-coding RNAs which regulate many genes post-transcriptionally. In various contexts of medical science, miRNAs gained increasing attention over the last few years. Analyzing the functions, interactions and cellular effects of miRNAs is a very complex and challenging task. Many miRNA databases with diverse data contents have been developed. Here, we demonstrate how to integrate their information in a reasonable way on a set of miRNAs that were found to be dysregulated in the blood of patients with multiple sclerosis (MS). Using the miR2Disease database, we retrieved 16 miRNAs associated with MS according to four different studies. We studied the predicted and experimentally validated target genes of these miRNAs, their expression profiles in different blood cell types and brain tissues, the pathways and biological processes affected by these miRNAs as well as their regulation by transcription factors. Only miRNA-mRNA interactions that were predicted by at least seven different prediction algorithms were considered. This resulted in a network of 1,498 target genes. In this network, the MS-associated miRNAs hsa-miR-20a-5p and hsa-miR-20b-5p occurred as central hubs regulating about 500 genes each. Strikingly, many of the putative target genes play a role in T cell activation and signaling, and many have transcription factor activity. The latter suggests that miRNAs often act as regulators of regulators with many secondary effects on gene expression. Our present work provides a guideline on how information of different databases can be integrated in the analysis of miRNAs. Future investigations of miRNAs shall help to better understand the mechanisms underlying different diseases and their treatments.

  14. 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

  15. 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.

  16. 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

  17. Neural Network Emulation of the Integral Equation Model with Multiple Scattering

    PubMed Central

    Pulvirenti, Luca; Ticconi, Francesca; Pierdicca, Nazzareno

    2009-01-01

    The Integral Equation Model with multiple scattering (IEMM) represents a well-established method that provides a theoretical framework for the scattering of electromagnetic waves from rough surfaces. A critical aspect is the long computational time required to run such a complex model. To deal with this problem, a neural network technique is proposed in this work. In particular, we have adopted neural networks to reproduce the backscattering coefficients predicted by IEMM at L- and C-bands, thus making reference to presently operative satellite radar sensors, i.e., that aboard ERS-2, ASAR on board ENVISAT (C-band), and PALSAR aboard ALOS (L-band). The neural network-based model has been designed for radar observations of both flat and tilted surfaces, in order to make it applicable for hilly terrains too. The assessment of the proposed approach has been carried out by comparing neural network-derived backscattering coefficients with IEMM-derived ones. Different databases with respect to those employed to train the networks have been used for this purpose. The outcomes seem to prove the feasibility of relying on a neural network approach to efficiently and reliably approximate an electromagnetic model of surface scattering. PMID:22408496

  18. Multiple Roles of MYC in Integrating Regulatory Networks of Pluripotent Stem Cells

    PubMed Central

    Fagnocchi, Luca; Zippo, Alessio

    2017-01-01

    Pluripotent stem cells (PSCs) are defined by their self-renewal potential, which permits their unlimited propagation, and their pluripotency, being able to generate cell of the three embryonic lineages. These properties render PSCs a valuable tool for both basic and medical research. To induce and stabilize the pluripotent state, complex circuitries involving signaling pathways, transcription regulators and epigenetic mechanisms converge on a core transcriptional regulatory network of PSCs, thus determining their cell identity. Among the transcription factors, MYC represents a central hub, which modulates and integrates multiple mechanisms involved both in the maintenance of pluripotency and in cell reprogramming. Indeed, it instructs the PSC-specific cell cycle, metabolism and epigenetic landscape, contributes to limit exit from pluripotency and modulates signaling cascades affecting the PSC identity. Moreover, MYC extends its regulation on pluripotency by controlling PSC-specific non-coding RNAs. In this report, we review the MYC-controlled networks, which support the pluripotent state and discuss how their perturbation could affect cell identity. We further discuss recent finding demonstrating a central role of MYC in triggering epigenetic memory in PSCs, which depends on the establishment of a WNT-centered self-reinforcing circuit. Finally, we comment on the therapeutic implications of the role of MYC in affecting PSCs. Indeed, PSCs are used for both disease and cancer modeling and to derive cells for regenerative medicine. For these reasons, unraveling the MYC-mediated mechanism in those cells is fundamental to exploit their full potential and to identify therapeutic targets. PMID:28217689

  19. 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.

  20. Assessing and predicting protein interactions by combining manifold embedding with multiple information integration

    PubMed Central

    2012-01-01

    Background Protein-protein interactions (PPIs) play crucial roles in virtually every aspect of cellular function within an organism. Over the last decade, the development of novel high-throughput techniques has resulted in enormous amounts of data and provided valuable resources for studying protein interactions. However, these high-throughput protein interaction data are often associated with high false positive and false negative rates. It is therefore highly desirable to develop scalable methods to identify these errors from the computational perspective. Results We have developed a robust computational technique for assessing the reliability of interactions and predicting new interactions by combining manifold embedding with multiple information integration. Validation of the proposed method was performed with extensive experiments on densely-connected and sparse PPI networks of yeast respectively. Results demonstrate that the interactions ranked top by our method have high functional homogeneity and localization coherence. Conclusions Our proposed method achieves better performances than the existing methods no matter assessing or predicting protein interactions. Furthermore, our method is general enough to work over a variety of PPI networks irrespectively of densely-connected or sparse PPI network. Therefore, the proposed algorithm is a much more promising method to detect both false positive and false negative interactions in PPI networks. PMID:22595000

  1. Integrity of the Anterior Visual Pathway and Its Association with Ambulatory Performance in Multiple Sclerosis

    PubMed Central

    Sandroff, Brian M.; Pula, John H.; Motl, Robert W.

    2013-01-01

    Background. Retinal nerve fiber layer thickness (RNFLT) and total macular volume (TMV) represent markers of neuroaxonal degeneration within the anterior visual pathway that might correlate with ambulation in persons with multiple sclerosis (MS). Objective. This study examined the associations between RNFLT and TMV with ambulatory parameters in MS. Methods. Fifty-eight MS patients underwent a neurological examination for generation of an expanded disability status scale (EDSS) score and measurement of RNFLT and TMV using optical coherence tomography (OCT). Participants completed the 6-minute walk (6MW) and the timed 25-foot walk (T25FW). The associations were examined using generalized estimating equation models that accounted for within-patient, inter-eye correlations, and controlled for disease duration, EDSS score, and age. Results. RNFLT was not significantly associated with 6MW (P = 0.99) or T25FW (P = 0.57). TMV was significantly associated with 6MW (P = 0.023) and T25FW (P = 0.005). The coefficients indicated that unit differences in 6MW (100 feet) and T25FW (1 second) were associated with 0.040 and −0.048 unit differences in TMV (mm3), respectively. Conclusion. Integrity of the anterior visual pathway, particularly TMV, might represent a noninvasive measure of neuroaxonal degeneration that is correlated with ambulatory function in MS. PMID:23864950

  2. Optimal multiple-information integration inherent in a ring neural network

    NASA Astrophysics Data System (ADS)

    Takiyama, Ken

    2017-02-01

    Although several behavioral experiments have suggested that our neural system integrates multiple sources of information based on the certainty of each type of information in the manner of maximum-likelihood estimation, it is unclear how the maximum-likelihood estimation is implemented in our neural system. Here, I investigate the relationship between maximum-likelihood estimation and a widely used ring-type neural network model that is used as a model of visual, motor, or prefrontal cortices. Without any approximation or ansatz, I analytically demonstrate that the equilibrium of an order parameter in the neural network model exactly corresponds to the maximum-likelihood estimation when the strength of the symmetrical recurrent synaptic connectivity within a neural population is appropriately stronger than that of asymmetrical connectivity, that of local and external inputs, and that of symmetrical or asymmetrical connectivity between different neural populations. In this case, strengths of local and external inputs or those of symmetrical connectivity between different neural populations exactly correspond to the input certainty in maximum-likelihood estimation. Thus, my analysis suggests appropriately strong symmetrical recurrent connectivity as a possible candidate for implementing the maximum-likelihood estimation within our neural system.

  3. 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

  4. 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…

  5. A retrospective likelihood approach for efficient integration of multiple omics factors in case-control association studies.

    PubMed

    Balliu, Brunilda; Tsonaka, Roula; Boehringer, Stefan; Houwing-Duistermaat, Jeanine

    2015-03-01

    Integrative omics, the joint analysis of outcome and multiple types of omics data, such as genomics, epigenomics, and transcriptomics data, constitute a promising approach for powerful and biologically relevant association studies. These studies often employ a case-control design, and often include nonomics covariates, such as age and gender, that may modify the underlying omics risk factors. An open question is how to best integrate multiple omics and nonomics information to maximize statistical power in case-control studies that ascertain individuals based on the phenotype. Recent work on integrative omics have used prospective approaches, modeling case-control status conditional on omics, and nonomics risk factors. Compared to univariate approaches, jointly analyzing multiple risk factors with a prospective approach increases power in nonascertained cohorts. However, these prospective approaches often lose power in case-control studies. In this article, we propose a novel statistical method for integrating multiple omics and nonomics factors in case-control association studies. Our method is based on a retrospective likelihood function that models the joint distribution of omics and nonomics factors conditional on case-control status. The new method provides accurate control of Type I error rate and has increased efficiency over prospective approaches in both simulated and real data.

  6. 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.

  7. MS-kNN: protein function prediction by integrating multiple data sources

    PubMed Central

    2013-01-01

    ) the k-nearest neighbor algorithm is an efficient and effective model for protein function prediction; (2) it is beneficial to transfer functions across a wide range of organisms; (3) it is helpful to integrate multiple sources of protein information. PMID:23514608

  8. Capillary Isoelectric Focusing

    NASA Astrophysics Data System (ADS)

    Markuszewski, Michał J.; Bujak, Renata; Daghir, Emilia

    Capillary isoelectric focusing (CIEF) is a widespread technique for the analysis of peptides and proteins in biological samples. CIEF is used to separate mixtures of compounds on the basis of differences in their isoelectric point. Aspects of sample preparation, capillary selection, zone mobilization procedures as well as various detection modes used have been described and discussed. Moreover CIEF, coupled to various types of detection techniques (MALDI or LIF), has increasingly been applied to the analysis of variety different high-molecular compounds. CIEF is considered as a highly specific analytical method which may be routinely used in the separation of rare hemoglobin variants. In addition, the application of CIEF in proteomic field have been discussed on the examples of analyses of glycoproteins and immunoglobins due to the meaning in clinical diagnostic.

  9. 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.

  10. 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.

  11. Integrating data from multiple science networks to conduct cross-scale ecohydrological research. (Invited)

    NASA Astrophysics Data System (ADS)

    Tazik, D.; Roehm, C. L.; Atkin, O.; Ayers, E.; Berukoff, S. J.; Fitzgerald, M.; Held, A. A.; Hinckley, E. S.; Kampe, T. U.; Liddell, M.; Phinn, S. R.; Taylor, J. R.; Thibault, K. M.; Thorpe, A.

    2013-12-01

    Distributed standardized sensor networks that collect coordinated airborne- and ground-based observations and are coupled with remotely sensed satellite imagery provide unique insight into complex ecological processes and feedbacks across a range of spatio-temporal scales. Measurements and information transfer at and across scales are key challenges in ecohydrology. A combination of approaches, for example, isotopic signatures of leaves, evapotranspiration using micrometeorological techniques, and water stress from remote sensing imagery, will improve our ability to integrate data across spatial scales. The collaboration among science networks such as the National Ecological Observatory Network (NEON) in the US and Terrestrial Ecosystem Research Network (TERN) in Australia will provide data that enable researchers to address complex questions regarding processes operating within and across systems, at site-to-continental scales and beyond. In this talk, we present several examples demonstrating combinations of remotely sensed and ground-based ecohydrological data collected using standardized methodologies across multiple sensor networks. Examples include: 1) determining ecohydrological controls on plant production at plot to regional scales; 2) interpreting atmospheric chemical and isotopic deposition gradients across geographic domains; 3) using the stable isotope signatures of small mammal tissues to track drought dynamics across space and time; 4) mapping water quality characteristics in optically complex waters using remotely sensed imagery and high temporal frequency ground based sensor calibration data and 5) scaling plot and individual plant level vegetation structure estimates to continental scale maps of vegetation and ground cover dynamics. Australian scientists are using TERN's infrastructure for improving Soil-Vegetation-Atmosphere Transfer (SVAT) modeling for Australian conditions by assessing plant photosynthetic and respiration performance across a

  12. 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

  13. 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

  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. Novel stability analysis for recurrent neural networks with multiple delays via line integral-type L-K functional.

    PubMed

    Liu, Zhenwei; Zhang, Huaguang; Zhang, Qingling

    2010-11-01

    This paper studies the stability problem of a class of recurrent neural networks (RNNs) with multiple delays. By using an augmented matrix-vector transformation for delays and a novel line integral-type Lyapunov-Krasovskii functional, a less conservative delay-dependent global asymptotical stability criterion is first proposed for RNNs with multiple delays. The obtained stability result is easy to check and improve upon the existing ones. Then, two numerical examples are given to verify the effectiveness of the proposed criterion.

  16. Double-layer poly(vinyl alcohol)-coated capillary for highly sensitive and stable capillary electrophoresis and capillary electrophoresis with mass spectrometry glycan analysis.

    PubMed

    Zhang, Yi-Wei; Zhao, Ming-Zhe; Liu, Jing-Xin; Zhou, Ying-Lin; Zhang, Xin-Xiang

    2015-02-01

    Glycosylation plays an important role in protein conformations and functions as well as many biological activities. Capillary electrophoresis combined with various detection methods provided remarkable developments for high-sensitivity glycan profiling. The coating of the capillary is needed for highly polar molecules from complex biosamples. A poly(vinyl alcohol)-coated capillary is commonly utilized in the capillary electrophoresis separation of saccharides sample due to the high-hydrophilicity properties. A modified facile coating workflow was carried out to acquire a novel multiple-layer poly(vinyl alcohol)-coated capillary for highly sensitive and stable analysis of glycans. The migration time fluctuation was used as index in the optimization of layers and a double layer was finally chosen, considering both the effects and simplicity in fabrication. With migration time relative standard deviation less than 1% and theoretical plates kept stable during 100 consecutive separations, the method was presented to be suitable for the analysis of glycosylation with wide linear dynamic range and good reproducibility. The glycan profiling of enzymatically released N-glycans from human serum was obtained by the presented capillary electrophoresis method combined with mass spectrometry detection with acceptable results.

  17. 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.

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

    PubMed

    Maury, Jérôme; Germann, Susanne M; 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.

  19. 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

  20. 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.

  1. 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.

  2. 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.

  3. Radially resolved spectral observations of polyacetal capillary discharge plasmas

    NASA Astrophysics Data System (ADS)

    Morgan, C. A.; Griem, H. R.; Elton, R. C.

    1995-07-01

    The temporal evolution of the radial profile of lithium-like oxygen (OVI or O5+) 3d-4f, 52.0 nm emission from 80 ns rise time, 6-16 kA peak current, pulsed capillary discharges in 1 mm diam, 1 cm long polyacetal capillaries, has been studied. Evidence was seen for a central ``flattening'' in this emission. Extreme-ultraviolet, time-integrated, pinhole transmission grating spectra were taken of discharges at 16 and 23 kA peak currents in 0.5 mm diam, 1 cm long capillaries. Spectra obtained at the higher peak current (23 kA) showed evidence of helium-like (CV or C4+) and/or hydrogen-like carbon (CV or C5+) resonance line emission (4.0 and 3.4 nm wavelength) filling the capillary diameter.

  4. 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.

  5. Capillary rogue waves.

    PubMed

    Shats, M; Punzmann, H; Xia, H

    2010-03-12

    We report the first observation of extreme wave events (rogue waves) in parametrically driven capillary waves. Rogue waves are observed above a certain threshold in forcing. Above this threshold, frequency spectra broaden and develop exponential tails. For the first time we present evidence of strong four-wave coupling in nonlinear waves (high tricoherence), which points to modulation instability as the main mechanism in rogue waves. The generation of rogue waves is identified as the onset of a distinct tail in the probability density function of the wave heights. Their probability is higher than expected from the measured wave background.

  6. 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

  7. Extremely sensitive detection of NO₂ employing off-axis integrated cavity output spectroscopy coupled with multiple-line integrated absorption spectroscopy.

    PubMed

    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 kilometers 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 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 versus concentration of NO₂ and the standard deviation of the integrated absorption signal, we report an effective sensitivity of detection of approximately 28 ppt (parts in 10¹²) for NO₂ To the best of our knowledge, this is among the most sensitive levels of detection of NO₂ to date.

  8. 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

  9. Disruptive Promise: The Links Intervention and Its Impact on Multiple, Multimodal, Internet Text Integration

    ERIC Educational Resources Information Center

    Schira Hagerman, Michelle

    2014-01-01

    This dissertation study presents an instructional intervention called LINKS: Learning to Integrate InterNet Knowledge Strategically. It reports evidence of the intervention's impact on two variables: (a) ninth graders' use of ten online reading and integration strategies while engaged in dyadic online inquiry on science topics in school, and (b)…

  10. An integrative model links multiple inputs and signaling pathways to the onset of DNA synthesis in hepatocytes

    PubMed Central

    Huard, Jérémy; Mueller, Stephanie; Gilles, Ernst D; Klingmüller, Ursula; Klamt, Steffen

    2012-01-01

    During liver regeneration, quiescent hepatocytes re-enter the cell cycle to proliferate and compensate for lost tissue. Multiple signals including hepatocyte growth factor, epidermal growth factor, tumor necrosis factor α, interleukin-6, insulin and transforming growth factor β orchestrate these responses and are integrated during the G1 phase of the cell cycle. To investigate how these inputs influence DNA synthesis as a measure for proliferation, we established a large-scale integrated logical model connecting multiple signaling pathways and the cell cycle. We constructed our model based upon established literature knowledge, and successively improved and validated its structure using hepatocyte-specific literature as well as experimental DNA synthesis data. Model analyses showed that activation of the mitogen-activated protein kinase and phosphatidylinositol 3-kinase pathways was sufficient and necessary for triggering DNA synthesis. In addition, we identified key species in these pathways that mediate DNA replication. Our model predicted oncogenic mutations that were compared with the COSMIC database, and proposed intervention targets to block hepatocyte growth factor-induced DNA synthesis, which we validated experimentally. Our integrative approach demonstrates that, despite the complexity and size of the underlying interlaced network, logical modeling enables an integrative understanding of signaling-controlled proliferation at the cellular level, and thus can provide intervention strategies for distinct perturbation scenarios at various regulatory levels. PMID:22443451

  11. 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.

  12. Membrane-type photonic integration of InGaN/GaN multiple-quantum-well diodes and waveguide

    NASA Astrophysics Data System (ADS)

    Gao, Xumin; Bai, Dan; Cai, Wei; Xu, Yin; Yuan, Jialei; Yang, Yongchao; Zhu, Guixia; Cao, Xun; Zhu, Hongbo; Wang, Yongjin

    2017-02-01

    We report here a membrane-type integration of InGaN/GaN multiple-quantum-well diodes (MQWDs) with a waveguide to build a highly integrated photonic system to perform functionalities on a GaN-on-silicon platform. Suspended MQWDs can be used as either for light-emitting diode (LED) or photodiode. In the fabricated photonic system, part of the LED emission is coupled into a suspended waveguide, and the guided light laterally propagates along the waveguide and is finally sensed by the photodiode. The photonic system can detect the in-plane guided light and the external incident light simultaneously. Planar optical communication experimentally demonstrates that the proof-of-concept monolithic photonic integration system can achieve the in-plane visible light communication. This work paves the way towards novel active electro-optical sensing systems and planar optical communication in the visible range.

  13. 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.)

  14. Optimized breeding strategies for multiple trait integration: I. Minimizing linkage drag in single event introgression.

    PubMed

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

    2014-01-01

    From a breeding standpoint, multiple trait integration (MTI) is a four-step process of converting an elite variety/hybrid for value-added traits (e.g. transgenic events) using backcross breeding, ultimately regaining the performance attributes of the target hybrid along with reliable expression of the value-added traits. In the light of the overarching goal of recovering equivalent performance in the finished conversion, this study focuses on the first step of MTI, single event introgression, exploring the feasibility of marker-aided backcross conversion of a target maize hybrid for 15 transgenic events, incorporating eight events into the female hybrid parent and seven into the male parent. Single event introgression is conducted in parallel streams to convert the recurrent parent (RP) for individual events, with the primary objective of minimizing residual non-recurrent parent (NRP) germplasm, especially in the chromosomal proximity to the event (i.e. linkage drag). In keeping with a defined lower limit of 96.66 % overall RP germplasm recovery (i.e. ≤120 cM NRP germplasm given a genome size of 1,788 cM), a breeding goal for each of the 15 single event conversions was developed: <8 cM of residual NRP germplasm across the genome with ~1 cM in the 20 cM region flanking the event. Using computer simulation, we aimed to identify optimal breeding strategies for single event introgression to achieve this breeding goal, measuring efficiency in terms of number of backcross generations required, marker data points needed, and total population size across generations. Various selection schemes classified as three-stage, modified two-stage, and combined selection conducted from BC1 through BC3, BC4, or BC5 were compared. The breeding goal was achieved with a selection scheme involving five generations of marker-aided backcrossing, with BC1 through BC3 selected for the event of interest and minimal linkage drag at population size of 600, and BC4 and BC5 selected for

  15. 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.

  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. Geometry-induced capillary emptying.

    PubMed

    Rascón, Carlos; Parry, Andrew O; Aarts, Dirk G A L

    2016-10-24

    When a capillary is half-filled with liquid and turned to the horizontal, the liquid may flow out of the capillary or remain in it. For lack of a better criterion, the standard assumption is that the liquid will remain in a capillary of narrow cross-section, and will flow out otherwise. Here, we present a precise mathematical criterion that determines which of the two outcomes occurs for capillaries of arbitrary cross-sectional shape, and show that the standard assumption fails for certain simple geometries, leading to very rich and counterintuitive behavior. This opens the possibility of creating very sensitive microfluidic devices that respond readily to small physical changes, for instance, by triggering the sudden displacement of fluid along a capillary without the need of any external pumping.

  18. 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.

  19. 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.

  20. Understanding Physiology in the Continuum: Integration of Information from Multiple -Omics Levels

    PubMed Central

    Kamisoglu, Kubra; Acevedo, Alison; Almon, Richard R.; Coyle, Susette; Corbett, Siobhan; Dubois, Debra C.; Nguyen, Tung T.; Jusko, William J.; Androulakis, Ioannis P.

    2017-01-01

    In this paper, we discuss approaches for integrating biological information reflecting diverse physiologic levels. In particular, we explore statistical and model-based methods for integrating transcriptomic, proteomic and metabolomics data. Our case studies reflect responses to a systemic inflammatory stimulus and in response to an anti-inflammatory treatment. Our paper serves partly as a review of existing methods and partly as a means to demonstrate, using case studies related to human endotoxemia and response to methylprednisolone (MPL) treatment, how specific questions may require specific methods, thus emphasizing the non-uniqueness of the approaches. Finally, we explore novel ways for integrating -omics information with PKPD models, toward the development of more integrated pharmacology models. PMID:28289389

  1. Statistical Methods for Integrating Multiple Types of High-Throughput Data

    PubMed Central

    Xie, Yang; Ahn, Chul

    2011-01-01

    Large-scale sequencing, copy number, mRNA, and protein data have given great promise to the biomedical research, while posing great challenges to data management and data analysis. Integrating different types of high-throughput data from diverse sources can increase the statistical power of data analysis and provide deeper biological understanding. This chapter uses two biomedical research examples to illustrate why there is an urgent need to develop reliable and robust methods for integrating the heterogeneous data. We then introduce and review some recently developed statistical methods for integrative analysis for both statistical inference and classification purposes. Finally, we present some useful public access databases and program code to facilitate the integrative analysis in practice. PMID:20652519

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. A capillary Archimedes' screw

    NASA Astrophysics Data System (ADS)

    Darbois Texier, Baptiste; Dorbolo, Stephane

    2014-11-01

    As used by Egyptians for irrigation and reported by Archimedes, a screw turning inside a hollow pipe can pull out a fluid againt gravity. At a centimetric scale, an analagous system can be found with a drop pending on a rotating spiral which is tilted toward the horizontal. The ascent of the drop to the top of the spiral is considered and a theoretical model based on geometrical considerations is proposed. The climb of the drop is limited by the fluid deposition on the screw at high capillary number and by a centrifugation phenomenon. We find out the range of fluid proprities and spiral characteristics for which an ascending motion of the drop is possible. Finally we discuss the efficiency of such system to extract a fluid from a bath at a centrimetric scale.

  8. 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.

  9. A modular cell-based biosensor using engineered genetic logic circuits to detect and integrate multiple environmental signals

    PubMed Central

    Wang, Baojun; Barahona, Mauricio; Buck, Martin

    2013-01-01

    Cells perceive a wide variety of cellular and environmental signals, which are often processed combinatorially to generate particular phenotypic responses. Here, we employ both single and mixed cell type populations, pre-programmed with engineered modular cell signalling and sensing circuits, as processing units to detect and integrate multiple environmental signals. Based on an engineered modular genetic AND logic gate, we report the construction of a set of scalable synthetic microbe-based biosensors comprising exchangeable sensory, signal processing and actuation modules. These cellular biosensors were engineered using distinct signalling sensory modules to precisely identify various chemical signals, and combinations thereof, with a quantitative fluorescent output. The genetic logic gate used can function as a biological filter and an amplifier to enhance the sensing selectivity and sensitivity of cell-based biosensors. In particular, an Escherichia coli consortium-based biosensor has been constructed that can detect and integrate three environmental signals (arsenic, mercury and copper ion levels) via either its native two-component signal transduction pathways or synthetic signalling sensors derived from other bacteria in combination with a cell-cell communication module. We demonstrate how a modular cell-based biosensor can be engineered predictably using exchangeable synthetic gene circuit modules to sense and integrate multiple-input signals. This study illustrates some of the key practical design principles required for the future application of these biosensors in broad environmental and healthcare areas. PMID:22981411

  10. A modular cell-based biosensor using engineered genetic logic circuits to detect and integrate multiple environmental signals.

    PubMed

    Wang, Baojun; Barahona, Mauricio; Buck, Martin

    2013-02-15

    Cells perceive a wide variety of cellular and environmental signals, which are often processed combinatorially to generate particular phenotypic responses. Here, we employ both single and mixed cell type populations, pre-programmed with engineered modular cell signalling and sensing circuits, as processing units to detect and integrate multiple environmental signals. Based on an engineered modular genetic AND logic gate, we report the construction of a set of scalable synthetic microbe-based biosensors comprising exchangeable sensory, signal processing and actuation modules. These cellular biosensors were engineered using distinct signalling sensory modules to precisely identify various chemical signals, and combinations thereof, with a quantitative fluorescent output. The genetic logic gate used can function as a biological filter and an amplifier to enhance the sensing selectivity and sensitivity of cell-based biosensors. In particular, an Escherichia coli consortium-based biosensor has been constructed that can detect and integrate three environmental signals (arsenic, mercury and copper ion levels) via either its native two-component signal transduction pathways or synthetic signalling sensors derived from other bacteria in combination with a cell-cell communication module. We demonstrate how a modular cell-based biosensor can be engineered predictably using exchangeable synthetic gene circuit modules to sense and integrate multiple-input signals. This study illustrates some of the key practical design principles required for the future application of these biosensors in broad environmental and healthcare areas.

  11. Multiplicative Word Problems and Intensive Quantities: An Integrated Software Response. Technical Report 85-19.

    ERIC Educational Resources Information Center

    Kaput, James J.

    This document reports on a project that is examining some of the difficulties encountered in teaching word problems involving multiplication, division, and intensive quantities. Some of the various uses of these operations and their structures are considered. Described are discoveries and assumptions regarding students' cognitive models of these…

  12. 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)…

  13. Identity salience model: A paradigm for integrating multiple identities in clinical practice.

    PubMed

    Yakushko, Oksana; Davidson, Meghan M; Williams, Elizabeth Nutt

    2009-06-01

    The manuscript presents an identity salience model for clinical practice and psychotherapy research. The model seeks to incorporate contemporary social identity theory and ecological theory, as well as an appreciation of individuals' multiple identities without necessitating a hierarchy of oppression. A clinical case example utilizing the identity salience model is presented. (PsycINFO Database Record (c) 2010 APA, all rights reserved).

  14. 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…

  15. Utilizing Multiple Frameworks To Integrate Knowledge and Experience in Educational Administration Preparation Programs.

    ERIC Educational Resources Information Center

    Reitzug, Ulrich C.

    An argument for teaching vision development and clarification in educational administration programs through the use of multiple conceptual frameworks is presented in this paper. A review of two conceptual frameworks--reflective practice and leadership forces--concludes that vision, a key ingredient of effective leadership, must be more thoroughly…

  16. 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

  17. 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.

  18. Inertial Rise in Short Capillaries

    NASA Astrophysics Data System (ADS)

    Shardt, Orest; Waghmare, Prashant; Mitra, Sushanta; Derksen, Jos

    2013-11-01

    We investigate the primarily inertial rise of liquid in vertical glass capillaries that are shorter than the equilibrium rise height (Jurin height). We focus on the behavior of the liquid upon reaching the top of the capillary and use high-speed imaging to observe the motion of the liquid-air interface with high spatial and temporal resolution. We examine the dependence of the interface behavior on the meniscus speed and capillary height and describe a new phenomenon. Upon reaching the upper edge of a sufficiently short capillary, the meniscus inverts, rises upward, and bulges out radially. The bulging liquid then wets the external surface of the capillary and slides down. The meniscus inside the capillary retracts, falling below the upper edge, and then oscillates vertically with decaying amplitude, inverting several times before reaching a steady shape. A theoretical analysis is used to interpret the conditions required for this phenomenon to occur. A key assumption in the analysis is that the transient flow is inertial and therefore the capillary driving force is balanced by the weight and inertia of the rising liquid column while viscous forces are comparatively small. The analysis points to the possibility of obtaining previously-unseen behavior under reduced gravity.

  19. Integrating multiple types of data for signaling research: challenges and opportunities.

    PubMed

    Wiley, H Steven

    2011-02-15

    New technologies promise to provide unprecedented amounts of information that can build a foundation for creating predictive models of cell signaling pathways. To be useful, however, this information must be integrated into a coherent framework. In addition, the sheer volume of data gathered from the new technologies requires computational approaches for its analysis. Unfortunately, there are many barriers to data integration and analysis, mostly because of a lack of adequate data standards and their inconsistent use by scientists. However, solving the fundamental issues of data sharing will enable the investigation of entirely new areas of cell signaling research.

  20. 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.

  1. Electrospraying from nanofluidic capillary slot

    NASA Astrophysics Data System (ADS)

    Arscott, Steve; Troadec, David

    2005-09-01

    We present here an original electrospray emitter tip based on a nanofluidic capillary slot. The nanofabrication involves focused ion beam etching to form the slot which has a cross-section of 50×300nm and a length of 4μm. The liquid is deformed into the nanofluidic capillary slot by capillary action; the electrospray is produced by the application of a low voltage. Using a water-methanol-formic acid solution, we have observed an electrospray onset voltage of 125V. At a measured electrospray current of 1nA, the unforced flow-rate is estimated to be 110pLmin-1.

  2. Using Multiple Forms of Data in Principal Evaluations: An Overview with Examples. Integrated Leadership Development Initiative

    ERIC Educational Resources Information Center

    Sanders, Nancy; Kearney, Karen; Vince, Scott

    2012-01-01

    The Integrated Leadership Development Initiative (ILDI) is a cross-agency partnership that focuses on collaboratively guiding and supporting leader development and improving conditions of leadership so that there are highly accomplished leaders in every district and school in California. In this brief, ILDI focuses on Principal Evaluations and…

  3. The Impact of Technology Integration upon Collegiate Pedagogy from the Lens of Multiple Disciplines

    ERIC Educational Resources Information Center

    Swanson, Joan Ann

    2016-01-01

    Technology integration on college campuses has become both a reality and necessity to meet the demands for function and flow in an ever advancing world of learning. This study qualitatively reviewed how a multi-disciplinary sample of collegiate instructors viewed technology and how they incorporated it into their pedagogy. Results indicated a…

  4. 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.

  5. 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…

  6. 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

  7. 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…

  8. 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…

  9. 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.

  10. An introduction and integration of cross-classified, multiple membership, and dynamic group random-effects models.

    PubMed

    Cafri, Guy; Hedeker, Donald; Aarons, Gregory A

    2015-12-01

    In longitudinal studies, time-varying group membership and group effects are important issues that need to be addressed. In this article we describe use of cross-classified and multiple membership random-effects models to address time-varying group membership, and dynamic group random-effects models to address time-varying group effects. We propose new models that integrate features of existing models, evaluate these models through simulation, provide guidance on how to fit these models, and apply the models in 2 real data examples. The discussion focuses on challenges in the application of these models.

  11. MEMS with integrated CMOS read-out circuit based on sub-micrometric cantilevers array for multiple sensing (Invited Paper)

    NASA Astrophysics Data System (ADS)

    Villarroya, Maria; Verd, Jaume; Teva, Jordi; Abadal, Gabriel; Figueras, Eduard; Perez-Murano, Francesc; Esteve, Jaume; Barniol, Nuria

    2005-07-01

    A Micro Electro Mechanical System (MEMS) for mass detection is presented. It has been developed by the monolithic integration of the mechanical transducer with the CMOS control circuit. The sensor transducer consists on an array of four resonating cantilevers; oscillation is achieved by electrostatic excitation. The independent control on each cantilever of the arrays allows multiple sensing on a single device. The microresonators are fabricated on polysilicon in a compatibilized process with the front-end CMOS circuitry. The readout of the cantilevers oscillation is achieved by a current amplifier. Expected Mass resolution in air is 80 ag/Hz.

  12. '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

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

    PubMed

    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.

  14. Stress and the engagement of multiple memory systems: integration of animal and human studies.

    PubMed

    Schwabe, Lars

    2013-11-01

    Learning and memory can be controlled by distinct memory systems. How these systems are coordinated to optimize learning and behavior has long been unclear. Accumulating evidence indicates that stress may modulate the engagement of multiple memory systems. In particular, rodent and human studies demonstrate that stress facilitates dorsal striatum-dependent "habit" memory, at the expense of hippocampus-dependent "cognitive" memory. Based on these data, a model is proposed which states that the impact of stress on the relative use of multiple memory systems is due to (i) differential effects of hormones and neurotransmitters that are released during stressful events on hippocampal and dorsal striatal memory systems, thus changing the relative strength of and the interactions between these systems, and (ii) a modulatory influence of the amygdala which biases learning toward dorsal striatum-based memory after stress. This shift to habit memory after stress can be adaptive with respect to current performance but might contribute to psychopathology in vulnerable individuals.

  15. Genes that integrate multiple adipogenic signaling pathways in human mesenchymal stem cells.

    PubMed

    Ito, Tomoya; Tsuruta, So; Tomita, Koki; Kikuchi, Kunio; Yokoi, Takahide; Aizawa, Yasunori

    2011-06-17

    Adipogenesis is a well-characterized cell differentiation process. A large body of evidence has revealed the core transcription factors and signaling pathways that govern adipogenesis, but cross-talks between these cellular signals and its functional consequences have not been thoroughly investigated. We, therefore, sought to identify genes that are regulated by multiple signaling pathways during adipogenesis of human mesenchymal stem cells. Focusing on the early stage of adipogenesis, microarray analysis and quantitative RT-PCR identified 12 genes whose transcription levels were dramatically affected by the complete adipogenic induction cocktail but not by the cocktail's individual components. Expression kinetics of these genes indicate diverse mechanisms of transcriptional regulation during adipogenesis. Functional relationships between these genes and adipogenic differentiation were frequently unknown. This study thus provided novel adipogenic gene candidates that likely mediate communications among multiple signaling pathways within human mesenchymal stem cells.

  16. 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

  17. 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

  18. APPLICATION OF THE NATURALLY-OCCURRING DEUTERIUM ISOTOPE TO TRACING THE CAPILLARY FRINGE

    EPA Science Inventory

    Naturally-occurring deuterium is a useful tracer of subsurface hydrologic processes. A possible application includes the identification of capillary fringes in the vadose zone. Multiple and discontinuous water tables persist in many temperate regions, under various hydrogeologi...

  19. Integrated model of multiple kernel learning and differential evolution for EUR/USD trading.

    PubMed

    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.

  20. Integrating Multiple Social Statuses in Health Disparities Research: The Case of Lung Cancer

    PubMed Central

    Williams, David R; Kontos, Emily Z; Viswanath, K; Haas, Jennifer S; Lathan, Christopher S; MacConaill, Laura E; Chen, Jarvis; Ayanian, John Z

    2012-01-01

    Objective To illustrate the complex patterns that emerge when race/ethnicity, socioeconomic status (SES), and gender are considered simultaneously in health care disparities research and to outline the needed research to understand them by using disparities in lung cancer risks, treatment, and outcomes as an example. Principal Findings SES, gender, and race/ethnicity are social categories that are robust predictors of variations in health and health services utilization. These are usually considered separately, but intersectionality theory indicates that the impact of each depends on the others. Each reflects historically and culturally contingent variations in social, economic, and political status. Distinct patterns of risk and resilience emerge at the intersections of multiple social categories and shape the experience of health, health care access, utilization, quality, and outcomes where these categories intersect. Intersectional approaches call for greater attention to understand social processes at multiple levels of society and require the collection of relevant data and utilization of appropriate analytic approaches to understand how multiple risk factors and resources combine to affect the distribution of disease and its management. Conclusions Understanding how race/ethnicity, gender, and SES are interactive, interdependent, and social identities can provide new knowledge to enhance our efforts to effectively address health disparities. PMID:22568674

  1. 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.

  2. 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.

  3. 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.

  4. Integrated multiple image GIS application to the regional geologic interpretation of the Llano Uplift region, Texas

    SciTech Connect

    Gobel, V.W.; Clark, M.; McDonald, D. )

    1993-03-01

    GIS applications have been developed that can be used in regional geologic analysis. The techniques can discriminate lithologic boundaries expressed in images that capture morphologic features resulting from the interaction between surface shaping agents and crustal rocks. Study area selected is the Llano Uplift region, central Texas, a highly suitable test site because of (1) the availability of reliable, repeatable ground control; (2) a moderate topography reflecting complex multi-phase deformational periods; and (3) the lack of large scale geologic maps that would allow a unified interpretation of the region. The objectives are (1) the recognition of strain features being the results of deformational processes that affected basement and cover rocks; (2) the development of methodology to perform this recognition involving the integration of multispectral images, space shuttle photography, and geologic ground control in a GIS database. It is demonstrated that it is feasible to undertake regional geologic interpretations utilizing an integrated GIS database.

  5. On the connection generated by the problem of minimizing a multiple integral

    NASA Astrophysics Data System (ADS)

    Zelikin, M. I.

    1997-02-01

    We consider the Dirichlet integral, a functional which depends quadratically on the sections of a vector bundle \\pi \\colon \\xi \\to \\mathfrak{N} over a smooth manifold \\mathfrak{N}. We obtain and investigate a quadratic system of partial differential equations, called the Riccati equation by analogy with the one-dimensional case. We show that the solutions of this system define a connection \

  6. 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.

  7. Capillary fracturing in granular media.

    PubMed

    Holtzman, Ran; Szulczewski, Michael L; Juanes, Ruben

    2012-06-29

    We study the displacement of immiscible fluids in deformable, noncohesive granular media. Experimentally, we inject air into a thin bed of water-saturated glass beads and observe the invasion morphology. The control parameters are the injection rate, the bead size, and the confining stress. We identify three invasion regimes: capillary fingering, viscous fingering, and "capillary fracturing," where capillary forces overcome frictional resistance and induce the opening of conduits. We derive two dimensionless numbers that govern the transition among the different regimes: a modified capillary number and a fracturing number. The experiments and analysis predict the emergence of fracturing in fine-grained media under low confining stress, a phenomenon that likely plays a fundamental role in many natural processes such as primary oil migration, methane venting from lake sediments, and the formation of desiccation cracks.

  8. Capillary Fracturing in Granular Media

    NASA Astrophysics Data System (ADS)

    Holtzman, Ran; Szulczewski, Michael L.; Juanes, Ruben

    2012-06-01

    We study the displacement of immiscible fluids in deformable, noncohesive granular media. Experimentally, we inject air into a thin bed of water-saturated glass beads and observe the invasion morphology. The control parameters are the injection rate, the bead size, and the confining stress. We identify three invasion regimes: capillary fingering, viscous fingering, and “capillary fracturing,” where capillary forces overcome frictional resistance and induce the opening of conduits. We derive two dimensionless numbers that govern the transition among the different regimes: a modified capillary number and a fracturing number. The experiments and analysis predict the emergence of fracturing in fine-grained media under low confining stress, a phenomenon that likely plays a fundamental role in many natural processes such as primary oil migration, methane venting from lake sediments, and the formation of desiccation cracks.

  9. 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.

  10. 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.

  11. 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

  12. MetaTracker: integration and abstraction of 3D motion tracking data from multiple hardware systems

    NASA Astrophysics Data System (ADS)

    Kopecky, Ken; Winer, Eliot

    2014-06-01

    Motion tracking has long been one of the primary challenges in mixed reality (MR), augmented reality (AR), and virtual reality (VR). Military and defense training can provide particularly difficult challenges for motion tracking, such as in the case of Military Operations in Urban Terrain (MOUT) and other dismounted, close quarters simulations. These simulations can take place across multiple rooms, with many fast-moving objects that need to be tracked with a high degree of accuracy and low latency. Many tracking technologies exist, such as optical, inertial, ultrasonic, and magnetic. Some tracking systems even combine these technologies to complement each other. However, there are no systems that provide a high-resolution, flexible, wide-area solution that is resistant to occlusion. While frameworks exist that simplify the use of tracking systems and other input devices, none allow data from multiple tracking systems to be combined, as if from a single system. In this paper, we introduce a method for compensating for the weaknesses of individual tracking systems by combining data from multiple sources and presenting it as a single tracking system. Individual tracked objects are identified by name, and their data is provided to simulation applications through a server program. This allows tracked objects to transition seamlessly from the area of one tracking system to another. Furthermore, it abstracts away the individual drivers, APIs, and data formats for each system, providing a simplified API that can be used to receive data from any of the available tracking systems. Finally, when single-piece tracking systems are used, those systems can themselves be tracked, allowing for real-time adjustment of the trackable area. This allows simulation operators to leverage limited resources in more effective ways, improving the quality of training.

  13. FDRAnalysis: A tool for the integrated analysis of tandem mass spectrometry identification results from multiple search engines

    PubMed Central

    Wedge, David C; Krishna, Ritesh; Blackhurst, Paul; Siepen, Jennifer A; Jones, Andrew R.; Hubbard, Simon J.

    2013-01-01

    Confident identification of peptides via tandem mass spectrometry underpins modern high-throughput proteomics. This has motivated considerable recent interest in the post-processing 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, which 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 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. PMID:21222473

  14. 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.

  15. 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

  16. 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

  17. 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.

  18. 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.

  19. 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.

  20. Integrating the effects of simultaneous multiple stresses on plants using the simulation model TREGRO

    SciTech Connect

    Weinstein, D.A.; Yanai, R.D.

    1994-05-01

    TREGRO, a model of tree physiological response to environmental stress, was developed to examine the details of tree response to the interaction between ozone sum and nutrient deficiency. TREGRO was used to test the hypothesis that the nutrient deficiency would exacerbate growth reductions caused by ozone. When TREGRO was applied to a range of multiple-stress scenarios involving these two stresses, the simulated effects of the combined stresses in reducing red spruce (Rcea rubens Sarg.) tree growth were less than the sum of the effects simulated when each stress was acting alone. Red spruce, a species with a growth strategy involving low maximum potential growth rates and storage in C reserves, showed simulated patterns of allocation that minimized the added effect of ozone when Mg nutrient availability was low. In contrast, ponderosa pine (Pinus ponderosa Dougl.), a species that allocated C to the construction of new tissue preferentially, showed little ability to ameliorate ozone stress under low nutrient conditions. In neither case were the effects of ozone increased by nutrient deficiency. It is speculated that a species which maintains maximum C demand rates considerably below rates of C supply may be better able to adjust to conditions of multiple stresses. 22 refs., 12 figs., 1 tab.

  1. Integrative analysis of multiple diverse omics datasets by sparse group multitask regression

    PubMed Central

    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

  2. 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.

  3. 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.

  4. 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.

  5. Whole-Brain Radiotherapy With Simultaneous Integrated Boost to Multiple Brain Metastases Using Volumetric Modulated Arc Therapy

    SciTech Connect

    Lagerwaard, Frank J. Hoorn, Elles A.P. van der; Verbakel, Wilko; Haasbeek, Cornelis J.A.; Slotman, Ben J.; Senan, Suresh

    2009-09-01

    Purpose: Volumetric modulated arc therapy (RapidArc [RA]; Varian Medical Systems, Palo Alto, CA) allows for the generation of intensity-modulated dose distributions by use of a single gantry rotation. We used RA to plan and deliver whole-brain radiotherapy (WBRT) with a simultaneous integrated boost in patients with multiple brain metastases. Methods and Materials: Composite RA plans were generated for 8 patients, consisting of WBRT (20 Gy in 5 fractions) with an integrated boost, also 20 Gy in 5 fractions, to Brain metastases, and clinically delivered in 3 patients. Summated gross tumor volumes were 1.0 to 37.5 cm{sup 3}. RA plans were measured in a solid water phantom by use of Gafchromic films (International Specialty Products, Wayne, NJ). Results: Composite RA plans could be generated within 1 hour. Two arcs were needed to deliver the mean of 1,600 monitor units with a mean 'beam-on' time of 180 seconds. RA plans showed excellent coverage of planning target volume for WBRT and planning target volume for the boost, with mean volumes receiving at least 95% of the prescribed dose of 100% and 99.8%, respectively. The mean conformity index was 1.36. Composite plans showed much steeper dose gradients outside Brain metastases than plans with a conventional summation of WBRT and radiosurgery. Comparison of calculated and measured doses showed a mean gamma for double-arc plans of 0.30, and the area with a gamma larger than 1 was 2%. In-room times for clinical RA sessions were approximately 20 minutes for each patient. Conclusions: RA treatment planning and delivery of integrated plans of WBRT and boosts to multiple brain metastases is a rapid and accurate technique that has a higher conformity index than conventional summation of WBRT and radiosurgery boost.

  6. Prediction of phosphorylation sites based on the integration of multiple classifiers.

    PubMed

    Han, R Z; Wang, D; Chen, Y H; Dong, L K; Fan, Y L

    2017-02-23

    Phosphorylation is an important part of post-translational modifications of proteins, and is essential for many biological activities. Phosphorylation and dephosphorylation can regulate signal transduction, gene expression, and cell cycle regulation in many cellular processes. Phosphorylation is extremely important for both basic research and drug discovery to rapidly and correctly identify the attributes of a new protein phosphorylation sites. Moreover, abnormal phosphorylation can be used as a key medical feature related to a disease in some cases. The using of computational methods could improve the accuracy of detection of phosphorylation sites, which can provide predictive guidance for the prevention of the occurrence and/or the best course of treatment for certain diseases. Furthermore, this approach can effectively reduce the costs of biological experiments. In this study, a flexible neural tree (FNT), particle swarm optimization, and support vector machine algorithms were used to classify data with secondary encoding according to the physical and chemical properties of amino acids for feature extraction. Comparison of the classification results obtained from the three classifiers showed that the classification of the FNT was the best. The three classifiers were then integrated in the form of a minority subordinate to the majority vote to obtain the results. The performance of the integrated model showed improvement in sensitivity (87.41%), specificity (87.60%), and accuracy (87.50%).

  7. CytoSolve: A Scalable Computational Method for Dynamic Integration of Multiple Molecular Pathway Models.

    PubMed

    Ayyadurai, V A Shiva; Dewey, C Forbes

    2011-03-01

    A grand challenge of computational systems biology is to create a molecular pathway model of the whole cell. Current approaches involve merging smaller molecular pathway models' source codes to create a large monolithic model (computer program) that runs on a single computer. Such a larger model is difficult, if not impossible, to maintain given ongoing updates to the source codes of the smaller models. This paper describes a new system called CytoSolve that dynamically integrates computations of smaller models that can run in parallel across different machines without the need to merge the source codes of the individual models. This approach is demonstrated on the classic Epidermal Growth Factor Receptor (EGFR) model of Kholodenko. The EGFR model is split into four smaller models and each smaller model is distributed on a different machine. Results from four smaller models are dynamically integrated to generate identical results to the monolithic EGFR model running on a single machine. The overhead for parallel and dynamic computation is approximately twice that of a monolithic model running on a single machine. The CytoSolve approach provides a scalable method since smaller models may reside on any computer worldwide, where the source code of each model can be independently maintained and updated.

  8. Facile integration of multiple magnetite nanoparticles for theranostics combining efficient MRI and thermal therapy.

    PubMed

    Huang, Guoming; Zhu, Xianglong; Li, Hui; Wang, Lirong; Chi, Xiaoqin; Chen, Jiahe; Wang, Xiaomin; Chen, Zhong; Gao, Jinhao

    2015-02-14

    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.

  9. Integrative assessment of multiple pesticides as risk factors for non-Hodgkin's lymphoma among men

    PubMed Central

    De Roos, A J; Zahm, S; Cantor, K; Weisenburger, D; Holmes, F; Burmeister, L; Blair, A

    2003-01-01

    Methods: During the 1980s, the National Cancer Institute conducted three case-control studies of NHL in the midwestern United States. These pooled data were used to examine pesticide exposures in farming as risk factors for NHL in men. The large sample size (n = 3417) allowed analysis of 47 pesticides simultaneously, controlling for potential confounding by other pesticides in the model, and adjusting the estimates based on a prespecified variance to make them more stable. Results: Reported use of several individual pesticides was associated with increased NHL incidence, including organophosphate insecticides coumaphos, diazinon, and fonofos, insecticides chlordane, dieldrin, and copper acetoarsenite, and herbicides atrazine, glyphosate, and sodium chlorate. A subanalysis of these "potentially carcinogenic" pesticides suggested a positive trend of risk with exposure to increasing numbers. Conclusion: Consideration of multiple exposures is important in accurately estimating specific effects and in evaluating realistic exposure scenarios. PMID:12937207

  10. Discovering perturbation of modular structure in HIV progression by integrating multiple data sources through non-negative matrix factorization.

    PubMed

    Ray, Sumanta; Maulik, Ujjwal

    2016-12-20

    Detecting perturbation in modular structure during HIV-1 disease progression is an important step to understand stage specific infection pattern of HIV-1 virus in human cell. In this article, we proposed a novel methodology on integration of multiple biological information to identify such disruption in human gene module during different stages of HIV-1 infection. We integrate three different biological information: gene expression information, protein-protein interaction information and gene ontology information in single gene meta-module, through non negative matrix factorization (NMF). As the identified metamodules inherit those information so, detecting perturbation of these, reflects the changes in expression pattern, in PPI structure and in functional similarity of genes during the infection progression. To integrate modules of different data sources into strong meta-modules, NMF based clustering is utilized here. Perturbation in meta-modular structure is identified by investigating the topological and intramodular properties and putting rank to those meta-modules using a rank aggregation algorithm. We have also analyzed the preservation structure of significant GO terms in which the human proteins of the meta-modules participate. Moreover, we have performed an analysis to show the change of coregulation pattern of identified transcription factors (TFs) over the HIV progression stages.

  11. Microfluidic flow counterbalanced capillary electrophoresis.

    PubMed

    Xia, Ling; Dutta, Debashis

    2013-04-07

    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.

  12. A simplified method for capillary embedment into microfluidic devices - exemplified by sol-gel-based preconcentration.

    PubMed

    Thorslund, Sara; Johannesson, Nina; Nikolajeff, Fredrik; Bergquist, Jonas

    2007-12-01

    We here describe an alternative method of embedding functionalized capillaries into microdevices fabricated in PDMS. The capillaries have square-shaped outer dimensions and fit into elastic PDMS channel networks of similar dimensions. By modifying the capillary off-chip, the technique makes it possible to integrate a new chip function without risking contamination of already existing chemically patterned areas because of new reagent solutions. Leak-free insertion of these capillaries has earlier been reported, where a thin layer of uncured PDMS bonded the capillary to the microchannel and the lid structure. In this new approach, oxygen plasma is used to bond the square capillary to the PDMS, eliminating the risk of clogging the microsystem with uncured prepolymer. The new embedding technique was exemplified and evaluated by inserting a square capillary piece containing monolithic sol-gel for sample preconcentration application. The assembled microdevice was run with mass spectrometric detection, showing that peptides were preconcentrated without leakage from either the sol-gel itself or around the inserted capillary. Repeated preconcentration runs showed migration times better than 3% for all peptides. We believe that the presented microchip assembling technique greatly simplifies the insertion of functionalized capillary pieces, e.g., an initial preconcentrator to a PDMS device containing other downstream modules.

  13. Threshold capillary pressure in capillaries with curved sides

    NASA Astrophysics Data System (ADS)

    Lago, Marcelo; Araujo, Mariela

    2003-03-01

    Modeling of fluid flow through permeable media is of great importance in assessing the performance of both hydrocarbon reservoirs and aquifers. In this process, network models based on cylindrical capillaries with circular cross sections are frequently used. This type of capillaries are not able to reproduce interesting physical phenomena observed in the experiments, for example, situations where there is flow by films with the wetting fluid occupying the crevices and wedges of the structure. We present an analysis of the behavior of the capillary pressure of a droplet of non-wetting fluid with an infinite length, inside objects of cylindrical symmetry with curved sides. The calculation is based on a method proposed by Mayer and Stowe and Princen (MS-P). Different capillary geometries are considered, and the behavior of the capillary pressure and transversal fluid saturation as a function of the shape factor is studied. The results found either analytically or numerically, allow to understand the relation between geometry and flow properties, and helps in the building of more realistic pore network models for flow studies at the pore scale.

  14. Two-dimensional capillary electrophoresis using tangentially connected capillaries.

    PubMed

    Sahlin, Eskil

    2007-06-22

    A novel type of fused silica capillary system is described where channels with circular cross-sections are tangentially in contact with each other and connected through a small opening at the contact area. Since the channels are not crossing each other in the same plane, the capillaries can easily be filled with different solutions, i.e. different solutions will be in contact with each other at the contact point. The system has been used to perform different types of two-dimensional separations and the complete system is fully automated where a high voltage switch is used to control the location of the high voltage in the system. Using two model compounds it is demonstrated that a type of two-dimensional separation can be performed using capillary zone electrophoresis at two different pH values. It is also shown that a compound with acid/base properties can be concentrated using a dynamic pH junction mechanism when transferred from the first separation to the second separation. In addition, the system has been used to perform a comprehensive two-dimensional capillary electrophoresis separation of tryptic digest of bovine serum albumin using capillary zone electrophoresis followed by micellar electrokinetic chromatography.

  15. 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.

  16. Integrated, multi-cohort analysis identifies conserved transcriptional signatures across multiple respiratory viruses

    PubMed Central

    Andres-Terre, Marta; McGuire, Helen M; Pouliot, Yannick; Bongen, Erika; Sweeney, Timothy E.; Tato, Cristina M; Khatri, Purvesh

    2015-01-01

    Respiratory viral infections are a significant burden to healthcare worldwide. Many whole genome expression profiles have identified different respiratory viral infection signatures, but these have not translated to clinical practice. Here, we performed two integrated, multi-cohort analyses of publicly available transcriptional data of viral infections. First, we identified a common host signature across different respiratory viral infections that could distinguish (a) individuals with viral infections from healthy controls and from those with bacterial infections, and (b) symptomatic from asymptomatic subjects prior to symptom onset in challenge studies. Second, we identified an influenza-specific host response signature that (a) could distinguish influenza-infected samples from those with bacterial and other respiratory viral infections, (b) was a diagnostic and prognostic marker in influenza-pneumonia patients and influenza challenge studies, and (c) was predictive of response to influenza vaccine. Our results have applications in the diagnosis, prognosis, and identification of drug targets in viral infections. PMID:26682989

  17. 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.

  18. Protein function prediction by massive integration of evolutionary analyses and multiple data sources

    PubMed Central

    2013-01-01

    Background Accurate protein function annotation is a severe bottleneck when utilizing the deluge of high-throughput, next generation sequencing data. Keeping database annotations up-to-date has become a major scientific challenge that requires the development of reliable automatic predictors of protein function. The CAFA experiment provided a unique opportunity to undertake comprehensive 'blind testing' of many diverse approaches for automated function prediction. We report on the methodology we used for this challenge and on the lessons we learnt. Methods Our method integrates into a single framework a wide variety of biological information sources, encompassing sequence, gene expression and protein-protein interaction data, as well as annotations in UniProt entries. The methodology transfers functional categories based on the results from complementary homology-based and feature-based analyses. We generated the final molecular function and biological process assignments by combining the initial predictions in a probabilistic manner, which takes into account the Gene Ontology hierarchical structure. Results We propose a novel scoring function called COmbined Graph-Information Content similarity (COGIC) score for the comparison of predicted functional categories and benchmark data. We demonstrate that our integrative approach provides increased scope and accuracy over both the component methods and the naïve predictors. In line with previous studies, we find that molecular function predictions are more accurate than biological process assignments. Conclusions Overall, the results indicate that there is considerable room for improvement in the field. It still remains for the community to invest a great deal of effort to make automated function prediction a useful and routine component in the toolbox of life scientists. As already witnessed in other areas, community-wide blind testing experiments will be pivotal in establishing standards for the evaluation of

  19. 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.

  20. Capillary and Thermocapillary-Assisted Spreading on Chemically Patterned Substrates

    NASA Astrophysics Data System (ADS)

    Reisner, Walter W.; Darhuber, Anton A.; Troian, Sandra M.

    2001-11-01

    The possibility of creating miniaturized devices integrating electronic, optical and fluidic components for chemical analysis and synthesis has generated significant interest in flow confinement and actuation at the micron scale. Our group has recently suggested how capillary and thermocapillary transport on chemically patterned substrates can serve as a basis for microfluidic devices. From a theoretical perspective, the lateral confinement of static or moving liquid streams by micropatterning techniques introduces an additional curvature which strongly modifies the usual spreading behavior. In this talk we describe the dynamic behavior of a liquid rivulet spreading along a hydrophilic microstripe under capillary and thermocapillary forcing. The influence of the transverse curvature induced by lateral confinement leads to a nonlinear diffusion equation for capillary spreading that can be solved via a similarity transformation. The inclusion of thermocapillary forcing is investigated in a steady-state approximation via an asymptotic expansion in the thermocapillary stress.

  1. 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.

  2. 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.

  3. A unified statistical model of protein multiple sequence alignment integrating direct coupling and insertions

    PubMed Central

    Kinjo, Akira R.

    2016-01-01

    The multiple sequence alignment (MSA) of a protein family provides a wealth of information in terms of the conservation pattern of amino acid residues not only at each alignment site but also between distant sites. In order to statistically model the MSA incorporating both short-range and long-range correlations as well as insertions, I have derived a lattice gas model of the MSA based on the principle of maximum entropy. The partition function, obtained by the transfer matrix method with a mean-field approximation, accounts for all possible alignments with all possible sequences. The model parameters for short-range and long-range interactions were determined by a self-consistent condition and by a Gaussian approximation, respectively. Using this model with and without long-range interactions, I analyzed the globin and V-set domains by increasing the “temperature” and by “mutating” a site. The correlations between residue conservation and various measures of the system’s stability indicate that the long-range interactions make the conservation pattern more specific to the structure, and increasingly stabilize better conserved residues. PMID:27924257

  4. Spatial Self-Organization of Ecosystems: Integrating Multiple Mechanisms of Regular-Pattern Formation.

    PubMed

    Pringle, Robert M; Tarnita, Corina E

    2017-01-31

    Large-scale regular vegetation patterns are common in nature, but their causes are disputed. Whereas recent theory focuses on scale-dependent feedbacks as a potentially universal mechanism, earlier studies suggest that many regular spatial patterns result from territorial interference competition between colonies of social-insect ecosystem engineers, leading to hexagonally overdispersed nest sites and associated vegetation. Evidence for this latter mechanism is scattered throughout decades of disparate literature and lacks a unified conceptual framework, fueling skepticism about its generality in debates over the origins of patterned landscapes. We review these mechanisms and debates, finding evidence that spotted and gapped vegetation patterns generated by ants, termites, and other subterranean animals are globally widespread, locally important for ecosystem functioning, and consistent with models of intraspecific territoriality. Because these and other mechanisms of regular-pattern formation are not mutually exclusive and can coexist and interact at different scales, the prevailing theoretical outlook on spatial self-organization in ecology must expand to incorporate the dynamic interplay of multiple processes.

  5. 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.

  6. 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

  7. Capillary wave measurements on helically-supported capillary channels

    NASA Astrophysics Data System (ADS)

    Chandurwala, Fahim; Thiessen, David

    2010-10-01

    NASA is considering power generation by the Rankine cycle to save weight on long-duration manned missions to the moon or Mars. Phase separation technology is critical to this process in microgravity. Arrays of capillary channels might be useful for filtering liquid drops from a flowing vapor. The efficiency of droplet capture by a helically-supported capillary channel is being studied. A droplet impinging on the channel launches capillary waves that propagate down the channel helping to dissipate some of the drop's kinetic energy. High-speed video of the channel combined with image processing allows for measurement of the amplitude and speed of the wave packets. Increasing the pitch of the support structure decreases the wave speed. An understanding of the dynamic response of the channel to drop impact is a first step in predicting drop-capture efficiency.

  8. Development of a capillary electrophoresis-mass spectrometry method using polymer capillaries for metabolomic analysis of yeast.

    PubMed

    Tanaka, Yoshihide; Higashi, Tetsuji; Rakwal, Randeep; Wakida, Shin-ichi; Iwahashi, Hitoshi

    2008-05-01

    Metabolomics is an emerging field in analytical biochemistry, and the development of such a method for comprehensive and quantitative analysis of organic acids, carbohydrates, and nucleotides is a necessity in the era of functional genomics. When a concentrated yeast extract was analyzed by CE-MS using a successive multiple ionic-polymer layer (SMIL)-coated capillary, the adsorption of the contaminants on the capillary wall caused severe problems such as no elution, band-broadening, and asymmetric peaks. Therefore, an analytical method for the analysis of anionic metabolites in yeast was developed by pressure-assisted CE using an inert polymer capillary made from poly(ether etherketone) (PEEK) and PTFE. We preferred to use the PEEK over the PTFE capillary in CE-MS due to the easy-to-use PEEK capillary and its high durability. The separation of anionic metabolites was successfully achieved with ammonium hydrogencarbonate/formate buffer (pH 6.0) as the electrolyte solution. The use of 2-propanol washing after every electrophoresis run not only eliminated wall-adsorption phenomena, but allowed for good repeatability to be obtained for migration times in the metabolomic analysis.

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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.

  14. Multiple crosstalk between TOR and the cell integrity MAPK signaling pathway in fission yeast

    PubMed Central

    Madrid, Marisa; Vázquez-Marín, Beatriz; Franco, Alejandro; Soto, Teresa; Vicente-Soler, Jero; Gacto, Mariano; Cansado, José

    2016-01-01

    In eukaryotic cells, the highly conserved Target of Rapamycin (TOR) and the Mitogen Activated Protein Kinase (MAPK) signaling pathways elicit adaptive responses to extra- and intracellular conditions by regulating essential cellular functions. However, the nature of the functional relationships between both pathways is not fully understood. In the fission yeast Schizosaccharomyces pombe the cell integrity MAPK pathway (CIP) regulates morphogenesis, cell wall structure and ionic homeostasis. We show that the Rab GTPase Ryh1, a TORC2 complex activator, cross-activates the CIP and its core member, the MAPK Pmk1, by two distinct mechanisms. The first one involves TORC2 and its downstream effector, Akt ortholog Gad8, which together with TORC1 target Psk1 increase protein levels of the PKC ortholog Pck2 during cell wall stress or glucose starvation. Also, Ryh1 activates Pmk1 in a TORC2-independent fashion by prompting plasma membrane trafficking and stabilization of upstream activators of the MAPK cascade, including PDK ortholog Ksg1 or Rho1 GEF Rgf1. Besides, stress-activated Pmk1 cross-inhibits Ryh1 signaling by decreasing the GTPase activation cycle, and this ensures cell growth during alterations in phosphoinositide metabolism. Our results reveal a highly intricate cross-regulatory relationship between both pathways that warrants adequate cell adaptation and survival in response to environmental changes. PMID:27876895

  15. Integrating multiple technologies to understand the foraging behaviour of Hawaiian monk seals

    PubMed Central

    Littnan, Charles; Halpin, Patrick; Read, Andrew

    2017-01-01

    The objective of this research was to investigate and describe the foraging behaviour of monk seals in the main Hawaiian Islands. Specifically, our goal was to identify a metric to classify foraging behaviour from telemetry instruments. We deployed accelerometers, seal-mounted cameras and GPS tags on six monk seals during 2012–2014 on the islands of Molokai, Kauai and Oahu. We used pitch, calculated from the accelerometer, to identify search events and thus classify foraging dives. A search event and consequent ‘foraging dive’ occurred when the pitch was greater than or equal to 70° at a depth less than or equal to −3 m. By integrating data from the accelerometers with video and GPS, we were able to ground-truth this classification method and identify environmental variables associated with each foraging dive. We used Bayesian logistic regression to identify the variables that influenced search events. Dive depth, body motion (mean overall dynamic body acceleration during the dive) and proximity to the sea floor were the best predictors of search events for these seals. Search events typically occurred on long, deep dives, with more time spent at the bottom (more than 50% bottom time). We can now identify where monk seals are foraging in the main Hawaiian Islands (MHI) and what covariates influence foraging behaviour in this region. This increased understanding will inform management strategies and supplement outreach and recovery efforts.

  16. BioZoom: Exploiting Source-Capability Information for Integrated Access to Multiple Bioinformatics Data Sources

    SciTech Connect

    Liu, L; Buttler, D; Critchlow, T J; Han, W; Paques, H; Pu, C; Rocco, D

    2003-01-09

    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.

  17. Integrating Multiple On-line Knowledge Bases for Disease-Lab Test Relation Extraction.

    PubMed

    Zhang, Yaoyun; Soysal, Ergin; Moon, Sungrim; Wang, Jingqi; Tao, Cui; Xu, Hua

    2015-01-01

    A computable knowledge base containing relations between diseases and lab tests would be a great resource for many biomedical informatics applications. This paper describes our initial step towards establishing a comprehensive knowledge base of disease and lab tests relations utilizing three public on-line resources. LabTestsOnline, MedlinePlus and Wikipedia are integrated to create a freely available, computable disease-lab test knowledgebase. Disease and lab test concepts are identified using MetaMap and relations between diseases and lab tests are determined based on source-specific rules. Experimental results demonstrate a high precision for relation extraction, with Wikipedia achieving the highest precision of 87%. Combining the three sources reached a recall of 51.40%, when compared with a subset of disease-lab test relations extracted from a reference book. Moreover, we found additional disease-lab test relations from on-line resources, indicating they are complementary to existing reference books for building a comprehensive disease and lab test relation knowledge base.

  18. 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.

  19. An integrated cell purification and genomics strategy reveals multiple regulators of pancreas development.

    PubMed

    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

    2014-10-01

    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.

  20. Multiple attractors of host-parasitoid models with integrated pest management strategies: eradication, persistence and outbreak.

    PubMed

    Tang, Sanyi; Xiao, Yanni; Cheke, Robert A

    2008-03-01

    Host-parasitoid models including integrated pest management (IPM) interventions with impulsive effects at both fixed and unfixed times were analyzed with regard to host-eradication, host-parasitoid persistence and host-outbreak solutions. The host-eradication periodic solution with fixed moments is globally stable if the host's intrinsic growth rate is less than the summation of the mean host-killing rate and the mean parasitization rate during the impulsive period. Solutions for all three categories can coexist, with switch-like transitions among their attractors showing that varying dosages and frequencies of insecticide applications and the numbers of parasitoids released are crucial. Periodic solutions also exist for models with unfixed moments for which the maximum amplitude of the host is less than the economic threshold. The dosages and frequencies of IPM interventions for these solutions are much reduced in comparison with the pest-eradication periodic solution. Our results, which are robust to inclusion of stochastic effects and with a wide range of parameter values, confirm that IPM is more effective than any single control tactic.

  1. High-throughput microfluidic device for single cell analysis using multiple integrated soft lithographic pumps.

    PubMed

    Patabadige, Damith E W; Mickleburgh, Tom; Ferris, Lorin; Brummer, Gage; Culbertson, Anne H; Culbertson, Christopher T

    2016-05-01

    The ability to accurately control fluid transport in microfluidic devices is key for developing high-throughput methods for single cell analysis. Making small, reproducible changes to flow rates, however, to optimize lysis and injection using pumps external to the microfluidic device are challenging and time-consuming. To improve the throughput and increase the number of cells analyzed, we have integrated previously reported micropumps into a microfluidic device that can increase the cell analysis rate to ∼1000 cells/h and operate for over an hour continuously. In order to increase the flow rates sufficiently to handle cells at a higher throughput, three sets of pumps were multiplexed. These pumps are simple, low-cost, durable, easy to fabricate, and biocompatible. They provide precise control of the flow rate up to 9.2 nL/s. These devices were used to automatically transport, lyse, and electrophoretically separate T-Lymphocyte cells loaded with Oregon green and 6-carboxyfluorescein. Peak overlap statistics predicted the number of fully resolved single-cell electropherograms seen. In addition, there was no change in the average fluorescent dye peak areas indicating that the cells remained intact and the dyes did not leak out of the cells over the 1 h analysis time. The cell lysate peak area distribution followed that expected of an asynchronous steady-state population of immortalized cells.

  2. Model framework for integrating multiple exposure pathways to chemicals in household cleaning products.

    PubMed

    Shin, H-M; McKone, T E; Bennett, D H

    2016-11-17

    We present a screening-level exposure-assessment method which integrates exposure from all plausible exposure pathways as a result of indoor residential use of cleaning products. The exposure pathways we considered are (i) exposure to a user during product use via inhalation and dermal, (ii) exposure to chemical residues left on clothing, (iii) exposure to all occupants from the portion released indoors during use via inhalation and dermal, and (iv) exposure to the general population due to down-the-drain disposal via inhalation and ingestion. We use consumer product volatilization models to account for the chemical fractions volatilized to air (fvolatilized ) and disposed down the drain (fdown-the-drain ) during product use. For each exposure pathway, we use a fate and exposure model to estimate intake rates (iR) in mg/kg/d. Overall, the contribution of the four exposure pathways to the total exposure varies by the type of cleaning activities and with chemical properties. By providing a more comprehensive exposure model and by capturing additional exposures from often-overlooked exposure pathways, our method allows us to compare the relative contribution of various exposure routes and could improve high-throughput exposure assessment for chemicals in cleaning products.

  3. A technique for modelling p- n junction depletion capacitance of multiple doping regions in integrated circuits

    NASA Astrophysics Data System (ADS)

    Pinkham, Raymond; Anderson, Daniel F.

    1986-08-01

    The continuing advancements in integrated circuit technology have placed new burdons on the circuit design engineer, who must rely extensively upon computer simulation to correctly predict circuit behavior. One challenge is to develop better modelling techniques to more accurately deal with complex p- n junction structures often used in modern VLSI designs. This paper presents an easily implemented method for deriving parameters which accurately model the behavior of MOS VLSI structures containing complex p- n junction capacitance components. The methodology is applicable to both planar and laterally diffused junctions, whether formed by direct ion implantation or by diffusion from a finite or infinite source. The theories behind the equations used and results of the application of this new technique are discussed. A flow chart for a fitter program based on the new method is presented and described. The corresponding program written for the TI-59 scientific programmable calculator is available. Final model parameters are given and are shown to produce a numerical capacitance model which is accurate to within 2%.

  4. Integrating Multiple On-line Knowledge Bases for Disease-Lab Test Relation Extraction

    PubMed Central

    Zhang, Yaoyun; Soysal, Ergin; Moon, Sungrim; Wang, Jingqi; Tao, Cui; Xu, Hua

    2015-01-01

    A computable knowledge base containing relations between diseases and lab tests would be a great resource for many biomedical informatics applications. This paper describes our initial step towards establishing a comprehensive knowledge base of disease and lab tests relations utilizing three public on-line resources. LabTestsOnline, MedlinePlus and Wikipedia are integrated to create a freely available, computable disease-lab test knowledgebase. Disease and lab test concepts are identified using MetaMap and relations between diseases and lab tests are determined based on source-specific rules. Experimental results demonstrate a high precision for relation extraction, with Wikipedia achieving the highest precision of 87%. Combining the three sources reached a recall of 51.40%, when compared with a subset of disease-lab test relations extracted from a reference book. Moreover, we found additional disease-lab test relations from on-line resources, indicating they are complementary to existing reference books for building a comprehensive disease and lab test relation knowledge base. PMID:26306271

  5. Leader-following consensus for single-integrator multi-agent systems with multiplicative noises in directed topologies

    NASA Astrophysics Data System (ADS)

    Djaidja, Sabir; Wu, Qinghe

    2015-11-01

    This paper proposes a leader-following consensus control for continuous-time single-integrator multi-agent systems with multiplicative measurement noises under directed fixed and switching topologies. The consensus controller is developed by combining the graph theory and stochastic tools. The control input for each agent relies on its own state and its neighbours' states corrupted by noises, the noises are considered proportional to the relative distance between agents, both of the noisy case and the noise-free case are studied, and conditions to achieve mean square convergence under noisy measurement and asymptotic convergence in absence of noises are derived. Finally, in order to prove the validity of the consensus control, some simulations were carried out.

  6. Integrating multiple data sources in species distribution modeling: a framework for data fusion.

    PubMed

    Pacifici, Krishna; Reich, Brian J; Miller, David A W; Gardner, Beth; Stauffer, Glenn; Singh, Susheela; McKerrow, Alexa; Collazo, Jaime A

    2017-03-01

    The last decade has seen a dramatic increase in the use of species distribution models (SDMs) to characterize patterns of species' occurrence and abundance. Efforts to parameterize SDMs often create a tension between the quality and quantity of data available to fit models. Estimation methods that integrate both standardized and non-standardized data types offer a potential solution to the tradeoff between data quality and quantity. Recently several authors have developed approaches for jointly modeling two sources of data (one of high quality and one of lesser quality). We extend their work by allowing for explicit spatial autocorrelation in occurrence and detection error using a Multivariate Conditional Autoregressive (MVCAR) model and develop three models that share information in a less direct manner resulting in more robust performance when the auxiliary data is of lesser quality. We describe these three new approaches ("Shared," "Correlation," "Covariates") for combining data sources and show their use in a case study of the Brown-headed Nuthatch in the Southeastern U.S. and through simulations. All three of the approaches which used the second data source improved out-of-sample predictions relative to a single data source ("Single"). When information in the second data source is of high quality, the Shared model performs the best, but the Correlation and Covariates model also perform well. When the information quality in the second data source is of lesser quality, the Correlation and Covariates model performed better suggesting they are robust alternatives when little is known about auxiliary data collected opportunistically or through citizen scientists. Methods that allow for both data types to be used will maximize the useful information available for estimating species distributions.

  7. 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.

  8. An investigation of multidisciplinary complex health care interventions - steps towards an integrative treatment model in the rehabilitation of People with Multiple Sclerosis

    PubMed Central

    2012-01-01

    Background The Danish Multiple Sclerosis Society initiated a large-scale bridge building and integrative treatment project to take place from 2004–2010 at a specialized Multiple Sclerosis (MS) hospital. In this project, a team of five conventional health care practitioners and five alternative practitioners was set up to work together in developing and offering individualized treatments to 200 people with MS. The purpose of this paper is to present results from the six year treatment collaboration process regarding the development of an integrative treatment model. Discussion The collaborative work towards an integrative treatment model for people with MS, involved six steps: 1) Working with an initial model 2) Unfolding the different treatment philosophies 3) Discussing the elements of the Intervention-Mechanism-Context-Outcome-scheme (the IMCO-scheme) 4) Phrasing the common assumptions for an integrative MS program theory 5) Developing the integrative MS program theory 6) Building the integrative MS treatment model. The model includes important elements of the different treatment philosophies represented in the team and thereby describes a common understanding of the complexity of the courses of treatment. Summary An integrative team of practitioners has developed an integrative model for combined treatments of People with Multiple Sclerosis. The model unites different treatment philosophies and focuses on process-oriented factors and the strengthening of the patients’ resources and competences on a physical, an emotional and a cognitive level. PMID:22524586

  9. 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

  10. Decadal trends in global pelagic ocean chlorophyll: A new assessment integrating multiple satellites, in situ data, and models.

    PubMed

    Gregg, Watson W; Rousseaux, Cécile S

    2014-09-01

    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.

  11. Effects of complex internal structures on rheology of multiple emulsions particles in 2D from a boundary integral method.

    PubMed

    Wang, Jingtao; Liu, Jinxia; Han, Junjie; Guan, Jing

    2013-02-08

    A boundary integral method is developed to investigate the effects of inner droplets and asymmetry of internal structures on rheology of two-dimensional multiple emulsion particles with arbitrary numbers of layers and droplets within each layer. Under a modest extensional flow, the number increment of layers and inner droplets, and the collision among inner droplets subject the particle to stronger shears. In addition, the coalescence or release of inner droplets changes the internal structure of the multiple emulsion particles. Since the rheology of such particles is sensitive to internal structures and their change, modeling them as the core-shell particles to obtain the viscosity equation of a single particle should be modified by introducing the time-dependable volume fraction Φ(t) of the core instead of the fixed Φ. An asymmetric internal structure induces an oriented contact and merging of the outer and inner interface. The start time of the interface merging is controlled by adjusting the viscosity ratio and enhancing the asymmetry, which is promising in the controlled release of inner droplets through hydrodynamics for targeted drug delivery.

  12. Psychometrically Informed Approach to Integration of Multiple Informant Ratings in Adult ADHD in a Community-Recruited Sample.

    PubMed

    Martel, Michelle M; Nigg, Joel T; Schimmack, Ulrich

    2017-04-01

    Although Diagnostic and Statistical Manual of Mental Disorders-Fifth edition requires that attention-deficit/hyperactivity disorder (ADHD) symptoms are apparent across settings, assessed by multiple informants, there remains no standardized approach to integration of multiple sources in adult ADHD diagnosis. The goal of the study was to evaluate informant effects on adult ADHD symptom ratings. Participants were 406 adults, ages 18 to 37, and identified second reporters, recruited from the community, and completing a comprehensive diagnostic and cognitive assessment, including a clinician-administered diagnostic interview and self- and other-report questionnaires of ADHD symptoms. Structural equation modeling indicated good fit for a trifactor model of ADHD, including general ADHD, specific inattention and hyperactivity-impulsivity, and self- and other-perspective factors. Yet there were a number of symptoms on the specific hyperactive-impulsive and self-factors that exhibited nonsignificant loadings. Significant differential item functioning across self-ratings and informant ratings was also noted. The external validation indices of laboratory executive function and diagnostic team-rated impairment was significantly correlated with the specific inattentive factor. While executive function was marginally significantly correlated with the other perspective factor, impairment was associated with the self-perspective factor. Overall, inattentive symptoms may be more sensitive measures of adult ADHD, and other and self-ratings may provide different information in relation to external criteria.

  13. Capillary imbibition in parallel tubes

    NASA Astrophysics Data System (ADS)

    McRae, Oliver; Ramakrishnan, T. S.; Bird, James

    2016-11-01

    In modeling porous media two distinct approaches can be employed; the sample can be examined holistically, using global variables such as porosity, or it can be treated as a network of capillaries connected in series to various intermediate reservoirs. In forced imbibition this series-based description is sufficient to characterize the flow, due to the presence of an externally maintained pressure difference. However, in spontaneous imbibition, flow is driven by an internal capillary pressure, making it unclear whether a series-based model is appropriate. In this talk, we show using numerical simulations the dynamics of spontaneous imbibition in concentrically arranged capillary tubes. This geometry allows both tubes access to a semi-infinite reservoir but with inlets in close enough proximity to allow for interference. We compare and contrast the results of our simulations with theory and previous experiments. Schlumberger-Doll Research.

  14. Non-Aqueous Capillary Electrophoresis

    NASA Astrophysics Data System (ADS)

    Szumski, Michał; Buszewski, Bogusław

    Non-aqueous capillary electrophoresis and capillary electrochromatography are special variants of these techniques. Here, organic solvents or their mixtures with or without dissolved electrolytes are used as separation buffer or mobile phase, respectively. The most important features of non-aqueous systems are: better solubility of more hydrophobic ionic substances (many natural products) than in water, much less current and Joule heating allows for using highly concentrated buffers and/or larger capillary internal diameters, polar interactions are enhanced in organic solvents which is often highly advantageous in chiral separation systems. This chapter presents most frequently used solvents, their properties, as well as shows pH* scale which is often used in non-aqueous systems.

  15. 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.

  16. 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

  17. The coexistence of multiple receptors in a single nerve terminal provides evidence for pre-synaptic integration.

    PubMed

    Ladera, Carolina; Godino, María Del Carmen; Martín, Ricardo; Luján, Rafael; Shigemoto, Ryuichi; Ciruela, Francisco; Torres, Magdalena; Sánchez-Prieto, José

    2007-12-01

    Excitatory synaptic transmission is inhibited by G protein coupled receptors, including the adenosine A(1), GABA(B), and metabotropic glutamate receptor 7. These receptors are present in nerve terminals where they reduce the release of glutamate through activating signaling pathways negatively coupled to Ca(2+) channels and adenylyl cyclase. However, it is not clear whether these receptors operate in distinct subpopulations of nerve terminals or if they are co-expressed in the same nerve terminals, despite the functional consequences that such distributions may have on synaptic transmission. Applying Ca(2+) imaging and immunocytochemistry, we show that these three G protein coupled receptors coexist in a subpopulation of cerebrocortical nerve terminals. The three receptors share an intracellular signaling pathway through which their inhibitory responses are integrated and coactivation of these receptors produced an integrated response. Indeed, this response was highly variable, from a synergistic response at subthreshold agonist concentrations to an occluded response at high agonist concentrations. The presence of multiple receptors in a nerve terminal could be responsible for the physiological effects of neurotransmitter spillover from neighboring synapses or alternatively, the co-release of transmitters by the same nerve terminal.

  18. 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.

  19. Capillary haemangioma of the testis

    PubMed Central

    Mazal, P; Kratzik, C; Kain, R; Susani, M

    2000-01-01

    A case of testicular capillary haemangioma is reported and the importance of intraoperative examination of this very rare lesion emphasised. Capillary haemangioma of the testis can be similar to malignant testicular tumours on clinical presentation, as well as on ultrasonography and magnetic resonance imaging, and therefore should be included in the intraoperative differential diagnosis. Because of the benign nature of this lesion, conservative surgical treatment by means of tumour enucleation with preservation of the testis is possible, if intraoperative examination of frozen sections of representative tissue can be performed. Key Words: testis • haemangioma PMID:11002773

  20. 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.

  1. Native capillary isoelectric focusing for the separation of protein complex isoforms and subcomplexes

    PubMed Central

    Fonslow, Bryan R.; Kang, Seong A.; Gestaut, Daniel R.; Graczyk, Beth; Davis, Trisha N.; Sabatini, David M.; Yates, John R.

    2010-01-01

    Here we report the use of capillary isoelectric focusing under native conditions for the separation of protein complex isoforms and subcomplexes. Using biologically relevant HIS-tag and FLAG-tag purified protein complexes, we demonstrate the separations of protein complex isoforms of the mammalian target of rapamycin complex (mTORC1 and 2) and the subcomplexes and different phosphorylation states of the Dam1 complex. The high efficiency capillary isoelectric focusing separation allowed for resolution of protein complexes and subcomplexes similar in size and biochemical composition. By performing separations with native buffers and reduced temperature (15°C) we were able to maintain the complex integrity of the more thermolabile mTORC2 during isoelectric focusing and detection (< 45 min). Increasing the separation temperature allowed us to monitor dissociation of the Dam1 complex into its subcomplexes (25°C) and eventually its individual protein components (30°C). The separation of two different phosphorylation states of the Dam1 complex, generated from an in vitro kinase assay with Mps1 kinase, was straightforward due to the large pI shift upon multiple phosphorylation events. The separation of the protein complex isoforms of mTORC, on the other hand, required the addition of a small pI range (4 – 6.5) of ampholytes to improve resolution and stability of the complexes. We show that native capillary isoelectric focusing is a powerful method for the difficult separations of large, similar, unstable protein complexes. This method shows potential for differentiation of protein complex isoform and subcomplex compositions, post-translational modifications, architectures, stabilities, equilibria, and relative abundances under biologically relevant conditions. PMID:20614870

  2. Native capillary isoelectric focusing for the separation of protein complex isoforms and subcomplexes.

    PubMed

    Fonslow, Bryan R; Kang, Seong A; Gestaut, Daniel R; Graczyk, Beth; Davis, Trisha N; Sabatini, David M; Yates, John R

    2010-08-01

    Here we report the use of capillary isoelectric focusing under native conditions for the separation of protein complex isoforms and subcomplexes. Using biologically relevant HIS-tag and FLAG-tag purified protein complexes, we demonstrate the separations of protein complex isoforms of the mammalian target of rapamycin complex (mTORC1 and 2) and the subcomplexes and different phosphorylation states of the Dam1 complex. The high efficiency capillary isoelectric focusing separation allowed for resolution of protein complexes and subcomplexes similar in size and biochemical composition. By performing separations with native buffers and reduced temperature (15 degrees C) we were able to maintain the complex integrity of the more thermolabile mTORC2 during isoelectric focusing and detection (<45 min). Increasing the separation temperature allowed us to monitor dissociation of the Dam1 complex into its subcomplexes (25 degrees C) and eventually its individual protein components (30 degrees C). The separation of two different phosphorylation states of the Dam1 complex, generated from an in vitro kinase assay with Mps1 kinase, was straightforward due to the large pI shift upon multiple phosphorylation events. The separation of the protein complex isoforms of mTORC, on the other hand, required the addition of a small pI range (4-6.5) of ampholytes to improve resolution and stability of the complexes. We show that native capillary isoelectric focusing is a powerful method for the difficult separations of large, similar, unstable protein complexes. This method shows potential for differentiation of protein complex isoform and subcomplex compositions, post-translational modifications, architectures, stabilities, equilibria, and relative abundances under biologically relevant conditions.

  3. Cooperative Suction by Vertical Capillary Array Pump for Controlling Flow Profiles of Microfluidic Sensor Chips

    PubMed Central

    Horiuchi, Tsutomu; Hayashi, Katsuyoshi; Seyama, Michiko; Inoue, Suzuyo; Tamechika, Emi

    2012-01-01

    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. PMID:23202035

  4. 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.

  5. 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.

  6. Comprehensive integrated spirometry using raised volume passive and forced expirations and multiple-breath nitrogen washout in infants.

    PubMed

    Morris, Mohy G

    2010-02-28

    With the rapid somatic growth and development in infants, simultaneous accurate measurements of lung volume and airway function are essential. Raised volume rapid thoracoabdominal compression (RTC) is widely used to generate forced expiration from an airway opening pressure of 30 cmH(2)O (V(30)). The (dynamic) functional residual capacity (FRC(dyn)) remains the lung volume most routinely measured. The aim of this study was to develop comprehensive integrated spirometry that included all subdivisions of lung volume at V(30) or total lung capacity (TLC(30)). Measurements were performed on 17 healthy infants aged 8.6-119.7 weeks. A commercial system for multiple-breath nitrogen washout (MBNW) to measure lung volumes and a custom made system to perform RTC were used in unison. A refined automated raised volume RTC and the following two novel single maneuvers with dual volume measurements were performed from V(30) during a brief post-hyperventilation apneic pause: (1) the passive expiratory flow was integrated to produce the inspiratory capacity (IC) and the static (passive) FRC (FRC(st)) was estimated by initiating MBNW after end-passive expiration; (2) RTC was initiated late during passive expiration, flow was integrated to produce the slow vital capacity ((j)SVC) and the residual volume (RV) was measured by initiating MBNW after end-expiration while the jacket (j) was inflated. Intrasubject FRC(dyn) and FRC(st) measurements overlapped (p=0.6420) but neither did with the RV (p<0.0001). Means (95% confidence interval) of FRC(dyn), IC, FRC(st), (j)SVC, RV, forced vital capacity and tidal volume were 21.2 (19.7-22.7), 36.7 (33.0-40.4), 21.2 (19.6-22.8), 40.7 (37.2-44.2), 18.1 (16.6-19.7), 40.7 (37.1-44.2) and 10.2 (9.6-10.7)ml/kg, respectively. Static lung volumes and capacities at V(30) and variables from the best forced expiratory flow-volume curve were dependent on age, body length and weight. In conclusion, we developed a comprehensive physiologically integrated

  7. 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.

  8. Bacterial motion in narrow capillaries

    PubMed Central

    Ping, Liyan; Wasnik, Vaibhav; Emberly, Eldon

    2014-01-01

    Motile bacteria often have to pass through small tortuous pores in soil or tissue of higher organisms. However, their motion in this prevalent type of niche is not fully understood. Here, we modeled it with narrow glass capillaries and identified a critical radius (Rc) for bacterial motion. Near the surface of capillaries narrower than that, the swimming trajectories are helices. In larger capillaries, they swim in distorted circles. Under non-slip condition, the peritrichous Escherichia coli swam in left-handed helices with an Rc of ∼10 μm near glass surface. However, slipping could occur in the fast monotrichous Pseudomonas fluorescens, when a speed threshold was exceeded, and thus both left-handed and right-handed helices were executed in glass capillaries. In the natural non-cylindrical pores, the near-surface trajectories would be spirals and twisted loops. Engaging in such motions reduces the bacterial migration rate. With a given pore size, the run length and the tumbling angle of the bacterium determine the probability and duration of their near-surface motion. Shear flow and chemotaxis potentially enhance it. Based on this observation, the puzzling previous observations on bacterial migration in porous environments can be interpreted. PMID:25764548

  9. 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…

  10. Development of a new type of imaging detector with capillary plate

    SciTech Connect

    Tsukahara, M.; Sakurai, H.; Saito, S.

    1996-12-31

    We have developed a new type of proportional counter utilizing a capillary plate with the capability of fine imaging power. Light outputs of the CGPC (Capillary Gas Proportional Counter) due to gas proportional scintillation are investigated by an optical imaging apparatus featured an intensified CCD camera to the CGPC. We successfully detected a image of {alpha}-particle track with a fill gas of xenon + 5% methane. It indicates first evidence of the gas multiplication in a thin capillary. We describe in detail the light output of the CGPC and characteristics of the imaging due to the CGPC.

  11. Megalencephaly-capillary malformation-polymicrogyria syndrome: the first case report in Korea

    PubMed Central

    Choi, Yeon-Chul; Yum, Mi-Sun; Kim, Min-Jee; Lee, Yun-Jung

    2016-01-01

    Megalencephaly-capillary malformation-polymicrogyria syndrome (MCAP), previously known as macrocephaly-cutis marmorata telangiectatica congenita and macrocephaly-capillary malformation syndrome, is a rare multiple-malformation syndrome that is characterized by progressive megalencephaly, capillary malformations of the midline face and body, or distal limb anomalies such as syndactyly. Herein, we report a female infant case that satisfies the recently proposed criteria of MCAP and describe the distinctive neuroradiological and morphological features. We have also reviewed recently published reports and the diagnostic criteria proposed by various authors in order to facilitate the clinical diagnosis of these children in pediatric neurology clinics. PMID:28018470

  12. BEAUTY: an enhanced BLAST-based search tool that integrates multiple biological information resources into sequence similarity search results.

    PubMed

    Worley, K C; Wiese, B A; Smith, R F

    1995-09-01

    BEAUTY (BLAST enhanced alignment utility) is an enhanced version of the NCBI's BLAST data base search tool that facilitates identification of the functions of matched sequences. We have created new data bases of conserved regions and functional domains for protein sequences in NCBI's Entrez data base, and BEAUTY allows this information to be incorporated directly into BLAST search results. A Conserved Regions Data Base, containing the locations of conserved regions within Entrez protein sequences, was constructed by (1) clustering the entire data base into families, (2) aligning each family using our PIMA multiple sequence alignment program, and (3) scanning the multiple alignments to locate the conserved regions within each aligned sequence. A separate Annotated Domains Data Base was constructed by extracting the locations of all annotated domains and sites from sequences represented in the Entrez, PROSITE, BLOCKS, and PRINTS data bases. BEAUTY performs a BLAST search of those Entrez sequences with conserved regions and/or annotated domains. BEAUTY then uses the information from the Conserved Regions and Annotated Domains data bases to generate, for each matched sequence, a schematic display that allows one to directly compare the relative locations of (1) the conserved regions, (2) annotated domains and sites, and (3) the locally aligned regions matched in the BLAST search. In addition, BEAUTY search results include World-Wide Web hypertext links to a number of external data bases that provide a variety of additional types of information on the function of matched sequences. This convenient integration of protein families, conserved regions, annotated domains, alignment displays, and World-Wide Web resources greatly enhances the biological informativeness of sequence similarity searches. BEAUTY searches can be performed remotely on our system using the "BCM Search Launcher" World-Wide Web pages (URL is < http:/ /gc.bcm.tmc.edu:8088/ search-launcher/launcher.html > ).

  13. Capillary gas chromatographic analysis of alditol acetates of neutral and amino sugars in bacterial cell walls.

    PubMed

    Fox, A; Morgan, S L; Hudson, J R; Zhu, Z T; Lau, P Y

    1983-02-18

    Several improvements in the preparation of alditol acetates of neutral and amino sugars and in the preparation of glass capillary columns for their separation are described. Modifications in sample preparation permitted the simultaneous processing of multiple samples and eliminated extraneous background peaks. Efficient and inert columns were tailor-made for the separation of alditol acetates of neutral and amino sugars by leaching glass capillaries with aqueous hydrochloric acid and dynamically coating with SP-2330.

  14. Microscale capillary wave turbulence excited by high frequency vibration.

    PubMed

    Blamey, Jeremy; Yeo, Leslie Y; Friend, James R

    2013-03-19

    Low frequency (O(10 Hz-10 kHz)) vibration excitation of capillary waves has been extensively studied for nearly two centuries. Such waves appear at the excitation frequency or at rational multiples of the excitation frequency through nonlinear coupling as a result of the finite displacement of the wave, most often at one-half the excitation frequency in so-called Faraday waves and twice this frequency in superharmonic waves. Less understood, however, are the dynamics of capillary waves driven by high-frequency vibration (>O(100 kHz)) and small interface length scales, an arrangement ideal for a broad variety of applications, from nebulizers for pulmonary drug delivery to complex nanoparticle synthesis. In the few studies conducted to date, a marked departure from the predictions of classical Faraday wave theory has been shown, with the appearance of broadband capillary wave generation from 100 Hz to the excitation frequency and beyond, without a clear explanation. We show that weak wave turbulence is the dominant mechanism in the behavior of the system, as evident from wave height frequency spectra that closely follow the Rayleigh-Jeans spectral response η ≈ ω(-17/12) as a consequence of a period-halving, weakly turbulent cascade that appears within a 1 mm water drop whether driven by thickness-mode or surface acoustic Rayleigh wave excitation. However, such a cascade is one-way, from low to high frequencies. The mechanism of exciting the cascade with high-frequency acoustic waves is an acoustic streaming-driven turbulent jet in the fluid bulk, driving the fundamental capillary wave resonance through the well-known coupling between bulk flow and surface waves. Unlike capillary waves, turbulent acoustic streaming can exhibit subharmonic cascades from high to low frequencies; here it appears from the excitation frequency all the way to the fundamental modes of the capillary wave at some four orders of magnitude in frequency less than the excitation frequency

  15. On-line capillary isoelectric focusing-electrospray mass spectrometry for protein characterization

    SciTech Connect

    Tang, Qing; Harrata, K.A.; Lee, C.S.

    1996-12-31

    The integration of capillary isoelectric focusing (CIEF) with electrospray mass spectrometry (ESMS) as a two-dimensional separation system for protein characterization will be presented. Mixtures of protein variants are focused and cathodically mobilized in a polyacrylamide coated capillary. At the end of CIEF capillary, the mobilized protein zones are analyzed by mass spectrometry coupled on-line to an electrospray interface with a coaxial sheath flow configuration. The effects of carrier ampholyte concentration on the CIEF separation and the protein electrospray mass spectra will be discussed. On-line CIEF-ESMS with superior resolving power, speed, and sensitivity will be demonstrated for the analysis of hemoglobin and glycoprotein variants.

  16. 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

  17. 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

  18. Overcoming inherent resistance to histone deacetylase inhibitors in multiple myeloma cells by targeting pathways integral to the actin cytoskeleton.

    PubMed

    Mithraprabhu, S; Khong, T; Spencer, A

    2014-03-20

    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.

  19. Integrated analysis of phenome, genome, and transcriptome of hybrid rice uncovered multiple heterosis-related loci for yield increase.

    PubMed

    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

    2016-10-11

    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.

  20. 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.

  1. Thermal management in high-power electronics cooled down using capillary pump

    NASA Astrophysics Data System (ADS)

    Wiecek, Boguslaw; Wajman, Tomasz; Felczak, Mariola; Berlinski, Marek

    2003-04-01

    By using the evaporation of working fluid in the capillary it is possible to design and build cooling device, with high cooling effectiveness. This paper presents a preliminary cooling system integrated with electronic device., which is supported by evaporation and capillarity effects. A simplified modeling of conjugate heat transfer including evaporation using FLUENT package is discussed. The experiments for open and close loop capillary pomp are shown to compare and verify the measurements and simulation results.

  2. 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…

  3. Capillary rise in cellulose sponges

    NASA Astrophysics Data System (ADS)

    Kim, Jungchul; Kim, Ho-Young; Mahadevan, L.

    2011-11-01

    A cellulose sponge, commonly used for clean-up jobs, can absorb and hold a significant amount of water within its pores, whose size ranges from micrometers to millimeters. We investigate the dynamics of capillary rise of water in the sponge using a combination of experiment and theory. We find that the rate of the capillary rise is significantly lower than Washburn's rule that assumes the sponge as a row of adjoined pores and the liquid flow to be driven by the Laplace pressure. We introduce a novel theory to model the flow in the hygroscopic porous media by combining Darcy's law based on the moisture concentration and the modified Young-Laplace equation. The scaling law constructed through this work agrees well with the experimental results.

  4. Step-gradient capillary electrochromatography.

    PubMed

    Euerby, M R; Gilligan, D; Johnson, C M; Bartle, K D

    1997-10-01

    The analytical benefits of using a step-gradient in capillary electrochromatography (CEC) are demonstrated. The application of step-gradient CEC to the analysis of six diuretics of widely differing lipophilicities was evaluated and shown to result in a marked reduction in the analysis time and an improvement in the peak shape for later-eluting lipophilic components. When the step-gradient approach was performed in an automated mode, the retention time RSD for repeated injections was below 1%.

  5. Capillary electrophoresis systems and methods

    DOEpatents

    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.

  6. Acceleration of canonical molecular dynamics simulations using macroscopic expansion of the fast multipole method combined with the multiple timestep integrator algorithm

    NASA Astrophysics Data System (ADS)

    Kawata, Masaaki; Mikami, Masuhiro

    A canonical molecular dynamics (MD) simulation was accelerated by using an efficient implementation of the multiple timestep integrator algorithm combined with the periodic fast multiple method (MEFMM) for both Coulombic and van der Waals interactions. Although a significant reduction in computational cost has been obtained previously by using the integrated method, in which the MEFMM was used only to calculate Coulombic interactions (Kawata, M., and Mikami, M., 2000, J. Comput. Chem., in press), the extension of this method to include van der Waals interactions yielded further acceleration of the overall MD calculation by a factor of about two. Compared with conventional methods, such as the velocity-Verlet algorithm combined with the Ewald method (timestep of 0.25fs), the speedup by using the extended integrated method amounted to a factor of 500 for a 100 ps simulation. Therefore, the extended method reduces substantially the computational effort of large scale MD simulations.

  7. 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.

  8. Integration

    ERIC Educational Resources Information Center

    Kalyn, Brenda

    2006-01-01

    Integrated learning is an exciting adventure for both teachers and students. It is not uncommon to observe the integration of academic subjects such as math, science, and language arts. However, educators need to recognize that movement experiences in physical education also can be linked to academic curricula and, may even lead the…

  9. 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.

  10. Capillary stretching of elastic fibers

    NASA Astrophysics Data System (ADS)

    Protiere, Suzie; Stone, Howard A.; Duprat, Camille

    2014-11-01

    Fibrous media consisting of constrained flexible fibers can be found in many engineered systems (membranes in filters, woven textile, matted paper). When such materials interact with a liquid, the presence of liquid/air interfaces induces capillary forces that deform the fibers. To model this interaction we study the behaviour of a finite volume of liquid deposited on two parallel flexible fibers clamped at both ends. A tension along the fibers is imposed and may be varied. We show that the system undergoes various morphological changes as the interfiber distance, the elasticity and the tension of the fibers are varied. For a certain range of parameters, the liquid spreads along the fibers and pulls them together, leading to the ``zipping'' of the fibers. This capillary adhesion can then be enhanced or reduced by changing the tension within the fibers. We will show that balancing stretching and capillary forces allows the prediction of this transition as well as the conditions for which detachment of the fibers occurs. These results may be used to prevent the clogging of fibrous membranes or to optimize the capture of liquids.

  11. 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

  12. Fluid Delivery System For Capillary Electrophoretic Applications.

    SciTech Connect

    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.

  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. 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.

  15. Quantification of normal-appearing white matter tract integrity in multiple sclerosis: a diffusion kurtosis imaging study

    PubMed Central

    de Kouchkovsky, Ivan; Fieremans, Els; Fleysher, Lazar; Herbert, Joseph; Grossman, Robert I.; Inglese, Matilde

    2017-01-01

    Our aim is to characterize the nature and extent of pathological changes in the normal-appearing white matter (NAWM) of patients with multiple sclerosis (MS) using novel diffusion kurtosis imaging-derived white matter tract integrity (WMTI) metrics, and to investigate the association between these WMTI metrics and clinical parameters. 32 patients with relapsing-remitting MS and 19 age- and gender-matched healthy controls underwent MRI and neurological examination. Maps of mean diffusivity, fractional anisotropy and WMTI metrics (intra-axonal diffusivity, axonal water fraction, tortuosity and axial and radial extra-axonal diffusivity) were created. Tract-based spatial statistics analysis was performed to assess for differences in the NAWM between patients and controls. A region of interest analysis of the corpus callosum was also performed to assess for group differences and to evaluate correlations between WMTI metrics and measures of disease severity. Mean diffusivity and radial extra-axonal diffusivity were significantly increased while fractional anisotropy, axonal water fraction, intra-axonal diffusivity and tortuosity were decreased in MS patients compared with controls (p values ranging from <0.001 to < 0.05). Axonal water fraction in the corpus callosum was significantly associated with the expanded disability status scale score (ρ = −0.39, p = 0.035). With the exception of the axial extra-axonal diffusivity, all metrics were correlated with the symbol digits modality test score (p values ranging from 0.001 to < 0.05). WMTI metrics are thus sensitive to changes in the NAWM of MS patients and might provide a more pathologically specific, clinically meaningful and practical complement to standard diffusion tensor imaging-derived metrics. PMID:27094571

  16. 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.

  17. PGC-1α integrates glucose metabolism and angiogenesis in multiple myeloma cells by regulating VEGF and GLUT-4.

    PubMed

    Cao, Dedong; Zhou, Hao; Zhao, Jikai; Jin, Lu; Yu, Wen; Yan, Han; Hu, Yu; Guo, Tao

    2014-03-01

    Human peroxisome proliferator-activated receptor-γ coactivator 1α (PGC-1α) is a key coactivator in the regulation of gene transcriptional activity in normal tissues. However, it is not clear whether it is involved in the angiogenesis and metabolism of multiple myeloma (MM). The aim of the present study was to investigate the role of PGC-1α in MM. Small interfering RNA (siRNA) was used to inhibit PGC-1α expression in RPMI-8226 cells. An endothelial cell migration assay was performed using transwell chambers and the expression of PGC-1α, estrogen-related receptor-α (ERR-α), vascular endothelial growth factor (VEGF) and glucose transporter-4 (GLUT-4) was tested by reverse transcription-polymerase chain reaction (RT-PCR). The protein expression of PGC-1α, ERR-α and GLUT-4 was assayed by western blot analysis. Lastly, RPMI-8226 cell proliferation was evaluated using CCK-8 assay. VEGF and GLUT-4 mRNA levels were decreased in cells treated with siRNA targeting PGC-1α, as was the level of GLUT-4 protein. Endothelial cell migration was significantly reduced when these cells were cultured with culture medium from RPMI-8226 cells treated with siPGC-1α. The proliferation rates at 24 and 48 h were suppressed by PGC-1α inhibition. Our results showed that inhibition of PGC-1α suppresses cell proliferation probably by downregulation of VEGF and GLUT-4. The present study suggests that PGC-1α integrates angiogenesis and glucose metabolism in myeloma through regulation of VEGF and GLUT-4.

  18. Integrative analysis of DNA copy number, DNA methylation and gene expression in multiple myeloma reveals alterations related to relapse

    PubMed Central

    Krzeminski, Patryk; Corchete, Luis A.; García, Juan L.; López-Corral, Lucía; Fermiñán, Encarna; García, Eva M.; Martín, Ana A.; Hernández-Rivas, Jesús M.; García-Sanz, Ramón; Miguel, Jesús F. San; Gutiérrez, Norma C.

    2016-01-01

    Multiple myeloma (MM) remains incurable despite the introduction of novel agents, and a relapsing course is observed in most patients. Although the development of genomic technologies has greatly improved our understanding of MM pathogenesis, the mechanisms underlying relapse have been less thoroughly investigated. In this study, an integrative analysis of DNA copy number, DNA methylation and gene expression was conducted in matched diagnosis and relapse samples from MM patients. Overall, the acquisition of abnormalities at relapse was much more frequent than the loss of lesions present at diagnosis, and DNA losses were significantly more frequent in relapse than in diagnosis samples. Interestingly, copy number abnormalities involving more than 100 Mb of DNA at relapse significantly affect the gene expression of these samples, provoking a particular deregulation of the IL-8 pathway. On the other hand, no significant modifications of gene expression were observed in those samples with less than 100 Mb affected by chromosomal changes. Although several statistical approaches were used to identify genes whose abnormal expression at relapse was regulated by methylation, only two genes that were significantly deregulated in relapse samples (SORL1 and GLT1D1) showed a negative correlation between methylation and expression. Further analysis revealed that DNA methylation was involved in regulating SORL1 expression in MM. Finally, relevant changes in gene expression observed in relapse samples, such us downregulation of CD27 and P2RY8, were most likely not preceded by alterations in the corresponding DNA. Taken together, these results suggest that the genomic heterogeneity described at diagnosis remains at relapse. PMID:27811368

  19. Integrative analysis of DNA copy number, DNA methylation and gene expression in multiple myeloma reveals alterations related to relapse.

    PubMed

    Krzeminski, Patryk; Corchete, Luis A; García, Juan L; López-Corral, Lucía; Fermiñán, Encarna; García, Eva M; Martín, Ana A; Hernández-Rivas, Jesús M; García-Sanz, Ramón; San Miguel, Jesús F; Gutiérrez, Norma C

    2016-12-06

    Multiple myeloma (MM) remains incurable despite the introduction of novel agents, and a relapsing course is observed in most patients. Although the development of genomic technologies has greatly improved our understanding of MM pathogenesis, the mechanisms underlying relapse have been less thoroughly investigated. In this study, an integrative analysis of DNA copy number, DNA methylation and gene expression was conducted in matched diagnosis and relapse samples from MM patients. Overall, the acquisition of abnormalities at relapse was much more frequent than the loss of lesions present at diagnosis, and DNA losses were significantly more frequent in relapse than in diagnosis samples. Interestingly, copy number abnormalities involving more than 100 Mb of DNA at relapse significantly affect the gene expression of these samples, provoking a particular deregulation of the IL-8 pathway. On the other hand, no significant modifications of gene expression were observed in those samples with less than 100 Mb affected by chromosomal changes. Although several statistical approaches were used to identify genes whose abnormal expression at relapse was regulated by methylation, only two genes that were significantly deregulated in relapse samples (SORL1 and GLT1D1) showed a negative correlation between methylation and expression. Further analysis revealed that DNA methylation was involved in regulating SORL1 expression in MM. Finally, relevant changes in gene expression observed in relapse samples, such us downregulation of CD27 and P2RY8, were most likely not preceded by alterations in the corresponding DNA. Taken together, these results suggest that the genomic heterogeneity described at diagnosis remains at relapse.

  20. Sub-wavelength fluorescent polymer coatings to convert standard glass capillaries into robust microfluidic refractometric sensors

    NASA Astrophysics Data System (ADS)

    Rowland, Kristopher J.; François, Alexandre; Hoffmann, Peter; Monro, Tanya M.

    2013-03-01

    A capillary microresonator platform for label-free refractometric sensing is demonstrated by coating the interior of thick-walled silica capillaries with a sub-wavelength layer of high refractive index, dye-doped polymer. No intermediate processing, such as etching or tapering, of the capillary is required. Side illumination and detection of the polymer layer reveals a fluorescence spectrum that is periodically modulated by the presence of whispering gallery modes within the layer. The fabricated capillary resonators exhibited sensitivities to changes in internal refractive index of up to 29.44 nm/RIU, demonstrated by flowing through aqueous dilutions of glucose. Thick walled capillaries are used in order to readily allow interfacing with existing biological and chemical sensing and separation platforms such as capillary electrophoresis or gas chromatography where such capillaries are routinely used. The interior polymer coating method described here could enable the use of a wide range of materials for the design of optofluidic label-free sensors integrated with industry standard (bio)chemical analytical separation platforms.

  1. 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.

  2. Joule heating in packed capillaries used in capillary electrochromatography.

    PubMed

    Rathore, Anurag S; Reynolds, Kimberly J; Colón, Luis A

    2002-09-01

    Effective heat dissipation is critical for reproducible and efficient separations in electrically driven separation systems. Flow rate, retention kinetics, and analyte diffusion rates are some of the characteristics that are affected by variation in the temperature of the mobile phase inside the column. In this study, we examine the issue of Joule heating in packed capillary columns used in capillary electrochromatography (CEC). As almost all commonly used CEC packings are poor thermal conductors, it is assumed that the packing particles do not conduct heat and heat transfer is solely through the mobile phase flowing through the system. The electrical conductivity of various mobile phases was measured at different temperatures by a conductivity meter and the temperature coefficient for each mobile phase was calculated. This was followed by measurement of the electrical current at several applied voltages to calculate the conductivity of the solution within the column as a function of the applied voltage. An overall increase in the conductivity is attributed to Joule heating within the column, while a constant conductivity means good heat dissipation. A plot of conductivity versus applied voltage was used as the indicator of poor heat dissipation. Using theories that have been proposed earlier for modeling of Joule heating effects in capillary electrophoresis (CE), we estimated the temperature within CEC columns. Under mobile and stationary phase conditions typically used in CEC, heat dissipation was found to be not always efficient. Elevated temperatures within the columns in excess of 23 degrees C above ambient temperature were calculated for packed columns, and about 35 degrees C for an open column, under a given set of conditions. The results agree with recently published experimental findings with nuclear magnetic resonance (NMR) thermometry, and Raman spectroscopic measurements.

  3. 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.

  4. Equilibrium capillary forces with atomic force microscopy.

    PubMed

    Sprakel, J; Besseling, N A M; Leermakers, F A M; Cohen Stuart, M A

    2007-09-07

    We present measurements of equilibrium forces resulting from capillary condensation. The results give access to the ultralow interfacial tensions between the capillary bridge and the coexisting bulk phase. We demonstrate this with solutions of associative polymers and an aqueous mixture of gelatin and dextran, with interfacial tensions around 10 microN/m. The equilibrium nature of the capillary forces is attributed to the combination of a low interfacial tension and a microscopic confinement geometry, based on nucleation and growth arguments.

  5. Mixed Refrigerants for a Glass Capillary Micro Cryogenic Cooler

    DTIC Science & Technology

    2010-08-01

    ADDRESS(ES) University of Colorado at Boulder,DARPA Center for Integrated Micro / Nano -Electromechanical Transducers (iMint),Boulder,CO,80309-0427 8...coolerq M.-H. Lin a,*, P.E. Bradley b, Marcia L. Huber b, R. Lewis a, R. Radebaugh b, Y.C. Lee a aDARPA Center for Integrated Micro / Nano ...COVERED 00-00-2009 to 00-00-2009 4. TITLE AND SUBTITLE Mixed refrigerants for a glass capillary micro cryogenic cooler 5a. CONTRACT NUMBER 5b

  6. 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.

  7. Capillaroscopy and the measurement of capillary pressure

    PubMed Central

    Shore, Angela C

    2000-01-01

    Capillaries play a critical role in cardiovascular function as the point of exchange of nutrients and waste products between the tissues and circulation. Studies of capillary function in man are limited by access to the vascular bed. However, skin capillaries can readily be studied by the technique of capillaroscopy which enables the investigator to assess morphology, density and blood flow velocity. It is also possible to estimate capillary pressure by direct cannulation using glass micropipettes. This review will describe the techniques used to make these assessments and will outline some of the changes that are seen in health and disease. PMID:11136289

  8. 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)

  9. Horizontal microscopy in square capillaries

    NASA Astrophysics Data System (ADS)

    Moroz, Pavel E.

    1992-07-01

    Intracellular protoplasmic movements may, due to gravity, have a vertical component greater or different from the horizontal one. This makes horizontal microscopy indispensable in the search for the cellular sensor of gravity. The possibility of the latter being a cell organelle assigns special significance to high-resolution microscopy. A horizontal suction device for picking up a cell and its high-resolution horizontal microscopy in a rectangular capillary may be helpful for detection of gravity-related shifts of cellular organelles in vivo.

  10. Capillary wave spectroscopy on ferrofluids

    NASA Astrophysics Data System (ADS)

    Patzke, J.; Rathke, B.; Will, S.

    2007-12-01

    We investigate the magnetoviscous effect in ferrofluids by Capillary Wave Spectroscopy (CWS, Surface Light Scattering). This technique probes a specific mode of thermally excited surface waves giving information on surface tension and viscosity. In ferrofluids we detect a transition from propagating surface modes to overdamped ones depending on the particle concentration and strength and the orientation of an externally applied magnetic field. We interprete this effect as caused by an increase of the liquid viscosity with an increasing particle concentration and field-strength. Changing the relative orientation of the scattering vector and magnetic field shows that the viscous properties of ferrofluids in a magnetic field are anisotropic. Figs 8, Refs 12.

  11. 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.

  12. Capillary Bridges between Soft Substrates

    NASA Astrophysics Data System (ADS)

    Wexler, Jason S.; Heard, Tiara M.; Stone, Howard A.

    2014-02-01

    A wetting droplet trapped in the thin gap between two elastic bodies will deflect the bodies towards one another. The deformation increases the total capillary adhesion force by increasing the contact radius and narrowing the gap height. For flat droplets, with a large ratio of radius to gap height, the Laplace pressure causes surface deformations that are orders of magnitude larger than those induced by a sessile droplet of the same radius. We present experiments, scalings, and closed-form solutions that describe the deformation. Using variational techniques, we also show that the problem exhibits a bifurcation, where the gap spontaneously closes due to an incremental increase in drop volume.

  13. 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

  14. 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.

  15. The Concept Mastery in the Perspective of Gender of Junior High School Students on Eclipse Theme in Multiple Intelligences-based of Integrated Earth and Space Science Learning

    NASA Astrophysics Data System (ADS)

    Liliawati, W.; Utama, J. A.; Mursydah, L. S.

    2017-03-01

    The purpose of this study is to identify gender-based concept mastery differences of junior high school students after the implementation of multiple intelligences-based integrated earth and space science learning. Pretest-posttest group design was employed to two different classes at one of junior high school on eclipse theme in Tasikmalaya West Java: one class for boys (14 students) and one class of girls (18 students). The two-class received same treatment. The instrument of concepts mastery used in this study was open-ended eight essay questions. Reliability test result of this instrument was 0.9 (category: high) while for validity test results were high and very high category. We used instruments of multiple intelligences identification and learning activity observation sheet for our analysis. The results showed that normalized N-gain of concept mastery for boys and girls were improved, respectively 0.39 and 0.65. Concept mastery for both classes differs significantly. The dominant multiple intelligences for boys were in kinesthetic while girls dominated in the rest of multiple intelligences. Therefor we concluded that the concept mastery was influenced by gender and student’s multiple intelligences. Based on this finding we suggested to considering the factor of gender and students’ multiple intelligences given in the learning activity.

  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. 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.

  18. 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.

  19. 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.

  20. 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.

  1. Sheathless interface for coupling capillary electrophoresis with mass spectrometry

    DOEpatents

    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.

  2. Internal capillary insulation for cryogenic tanks

    NASA Technical Reports Server (NTRS)

    Mcgrew, J. L.

    1972-01-01

    Capillary-type insulation was devised for installation on inside of liquid methane fuel tanks for future aircraft. Insulation consists of honeycomb core of fiberglass cloth impregnated with polyimide resin which is bonded onto metal tank wall using polyimide adhesive. Capillary holes in each honeycomb cell admit methane which provides static pressure in cell.

  3. Capillary waveguide optrodes for Medical applications

    NASA Astrophysics Data System (ADS)

    Kieslinger, Dietmar; Weigl, Bernhard H.; Draxler, Sonja; Lippitsch, Max E.

    1997-01-01

    Glass capillaries with a chemically sensitive coating on the inner surface are used as optical sensors for medical diagnostics. The capillary simultaneously serves as a sample compartment, a sensor element, and an inhomogeneous optical waveguide. Different optical setups have been investigated and compared regarding its waveguiding properties.

  4. Multiple Perspectives on Integrated Education for Children with Disabilities in the Context of Early Childhood Centres in Hong Kong

    ERIC Educational Resources Information Center

    Lai, Yuk Ching; Gill, Judith

    2014-01-01

    The integration of children with disabilities in mainstream early childhood settings is a common practice in many developed and developing countries world-wide. A number of key points have been raised concerning such integration, including the increased attention to civil education about the rights of persons with disabilities, training for…

  5. 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"…

  6. Capillary electrophoresis using core-based hyperbranched polyethyleneimine (CHPEI) static-coated capillaries.

    PubMed

    Boonyakong, Cheerapa; Tucker, Sheryl A

    2009-10-01

    With unique 3-D architecture, the application of core-based hyperbranched polyethyleneimine (CHPEI), as a capillary coating in capillary electrophoresis, is demonstrated by manipulation of the electroosmotic mobility (EOF). CHPEI coatings (CHPEI5, M(w) approximately 5000 and CHPEI25, M(w) approximately 25,000) were physically adsorbed onto the inner surface of bare fused-silica capillary (BFS) via electrostatic interaction of the oppositely charged molecules by rinsing the capillaries with different CHPEI aqueous solutions. The EOF values of the coated capillaries were measured over the pH range of 4.0-9.0. At higher pH (pH >6) the coated capillary surface possesses excess negative charges, which causes the reversal of the EOF. The magnitudes of the EOF obtained from the coated capillaries were three-fold lower than that of BFS capillary. Desirable reproducibility of the EOF with % RSD (n = 5) < or = 2 was obtained. Effect of ionic strength, stability of the coating (% RSD = 0.3) and the dependence of the EOF on pH (% RSD = 0.5) were also investigated. The CHPEI-coated capillaries were successfully utilized to separate phenolic compounds, B vitamins, as well as basic drugs and related compounds with reasonable analysis time (< 20 min) and acceptable migration-time repeatability (< 0.7% RSD for intra-capillary and < 2% RSD for inter-capillary).

  7. Lymphoma-type adult T-cell leukaemia-lymphoma with a bulky cutaneous tumour showing multiple human T-lymphotropic virus-1 DNA integration.

    PubMed

    Kato, N; Sugawara, H; Aoyagi, S; Mayuzumi, M

    2001-06-01

    Human T-lymphotropic virus-1 (HTLV-1) is considered to be the cause of adult T-cell leukaemia-lymphoma (ATL). Monoclonal integration of HTLV-1 proviral DNA, as is analysed by Southern blotting, has been demonstrated in ATL patients. Unusual integration patterns of HTLV-1 proviral DNA have occasionally been described, and it is suggested that the patterns have clinical implications for ATL pathophysiology. Multiple, complete and defective types of integration patterns, in that order, are apparently associated with prognoses from good to poor. We report a 73-year-old Japanese woman with lymphoma-type ATL and a bulky cutaneous tumour on the left thigh. Four bands of slightly differing intensity were seen after EcoRI digestion of skin and lymph node samples on Southern blot analysis of HTLV-1 proviral DNA. Analysis for T-cell receptor-beta gene revealed five novel bands after restriction enzyme digestion with HindIII, indicating that the patient has four separate tumour cell clones, each of which carries one copy of the provirus. She was treated with chemotherapy and radiation and remains under reasonable control despite some relapsing cutaneous nodules. The indolent course in this present case could be related to the multiple integration pattern of HTLV-1 proviral DNA detected.

  8. Study of Capillary-Based Gaseous Detectors

    NASA Astrophysics Data System (ADS)

    Iacobaeus, C.; Francke, T.; Danielsson, M.; Ostling, J.; Peskov, V.

    2004-06-01

    We have studied gain vs. voltage characteristics and position resolutions of multistep capillary plates (two or three capillary plates operating in a cascade), as well as capillary plates operating in a mode when the main amplification occurs between plates or between the capillary plate and the readout plate (parallel plate amplification mode). Results of these studies demonstrated that in the parallel-plate amplification mode one can reach both high gains (>100000) and good position resolutions (~100 micro meter) even with a single step arrangement. It offers a compact amplification structure, which can be used in many applications. For example, in preliminary tests we succeeded to combine it with a photocathode and use it as a position sensitive gaseous photomultiplier. CsI coated capillary plates could also be used as a high position resolution and high rate X-ray converter.

  9. Oximetry of retinal capillaries by multicomponent analysis.

    PubMed

    Furukawa, Hiromitsu; Arimoto, Hidenobu; Shirai, Tomohiro; Ooto, Sotaro; Hangai, Masanori; Yoshimura, Nagahisa

    2012-08-01

    Retinal oximetry of capillaries was performed for early detection of retinal vascular abnormalities, which are caused predominantly by complications of systemic circulatory diseases. As the conventional method for determining absorbance is not applicable to capillaries, multicomponent analysis was used to estimate the absorbance spectra of the retinal blood vessels. In this analysis, the capillary spectrum was classified as intermediate between those of the retinal arteries and veins, enabling relative estimation of oxygen saturation in the capillaries. This method could be useful for early recognition of disturbances in the peripheral circulation. Furthermore, a spectroscopic ophthalmoscope system based on the proposed method was developed to examine the human retina. A clinical trial of this system demonstrated that oximetry of the retinal capillaries may be an improvement over the present diagnosis for patients of malignant hypertension.

  10. An integrated eco-hydrologic modeling framework for assessing the effects of interacting stressors on multiple ecosystem services

    EPA Science Inventory

    The U.S. Environmental Protection Agency recently established the Ecosystem Services Research Program to help formulate methods and models for conducting comprehensive risk assessments that quantify how multiple ecosystem services interact and respond in concert to environmental ...

  11. Fast and Broadband Signal Integrity Analysis of Multiple Vias in Heterogeneous 3D IC and Die-Level Packaging by Using Generalized Foldy-Lax Scattering Method

    NASA Astrophysics Data System (ADS)

    Chang, Xin

    This dissertation proposal is concerned with the use of fast and broadband full-wave electromagnetic methods for modeling high speed interconnects (e.g, vertical vias and horizontal traces) and passive components (e.g, decoupling capacitors) for structures of PCB and packages, in 3D IC, Die-level packaging and SIW based devices, to effectively modeling the designs signal integrity (SI) and power integrity (PI) aspects. The main contributions finished in this thesis is to create a novel methodology, which hybridizes the Foldy-Lax multiple scattering equations based fast full wave method, method of moment (MoM) based 1D technology, modes decoupling based geometry decomposition and cavity modes expansions, to model and simulate the electromagnetic scattering effects for the irregular power/ground planes, multiple vias and traces, for fast and accurate analysis of link level simulation on multilayer electronic structures. For the modeling details, the interior massively-coupled multiple vias problem is modeled most-analytically by using the Foldy-Lax multiple scattering equations. The dyadic Green's functions of the magnetic field are expressed in terms of waveguide modes in the vertical direction and vector cylindrical wave expansions or cavity modes expansions in the horizontal direction, combined with 2D MoM realized by 1D technology. For the incident field of the case of vias in the arbitrarily shaped antipad in finite large cavity/waveguide, the exciting and scattering field coefficients are calculated based on the transformation which converts surface integration of magnetic surface currents in antipad into 1D line integration of surface charges on the vias and on the ground plane. Geometry decomposition method is applied to model and integrate both the vertical and horizontal interconnects/traces in arbitrarily shaped power/ground planes. Moreover, a new form of multiple scattering equations is derived for solving coupling effects among mixed metallic

  12. 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.

  13. 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

  14. A new set of rDNA-NTS-based multiple integrative cassettes for the development of antibiotic-marker-free recombinant yeasts.

    PubMed

    Moon, Hye Yun; Lee, Dong Wook; Sim, Gyu Hun; Kim, Hong-Jin; Hwang, Jee Youn; Kwon, Mun-Gyeong; Kang, Bo-Kyu; Kim, Jong Man; Kang, Hyun Ah

    2016-09-10

    The traditional yeast Saccharomyces cerevisiae has been widely used as a host system to produce recombinant proteins and metabolites of great commercial value. To engineer recombinant yeast that stably maintains expression cassettes without an antibiotic resistance gene, we developed new multiple integration cassettes by exploiting the non-transcribed spacer (NTS) of ribosomal DNA (rDNA) in combination with defective selection markers. The 5' and 3'-fragments of rDNA-NTS2 were used as flanking sequences for the expression cassettes carrying a set of URA3, LEU2, HIS3, and TRP1 selection markers with truncated promoters of different lengths. The integration numbers of NTS-based expression cassettes, ranging from one to ∼30 copies, showed a proportional increase with the extent of decreased expression of the auxotrophic markers. The NTS-based cassettes were used to construct yeast strains expressing the capsid protein of red-spotted grouper necrosis virus (RG-NNVCP) in a copy number-dependent manner. Oral administration of the recombinant yeast, harboring ∼30 copies of the integrated RG-NNVCP cassettes, provoked efficient immune responses in mice. In contrast, for the NTS cassettes expressing a truncated 3-hydroxyl-3-methylglutaryl-CoA reductase, the integrant carrying only 4 copies was screened as the highest producer of squalene, showing a 150-fold increase compared to that of the wild-type strain. The multiple integrated cassettes were stably retained under prolonged nonselective conditions. Altogether, our results strongly support that rDNA-NTS integrative cassettes are useful tools to construct recombinant yeasts carrying optimal copies of a desired expression cassette without an antibiotic marker gene, which are suitable as oral vaccines or feed additives for animal and human consumption.

  15. Interlaboratory study to evaluate the robustness of capillary electrophoresis-mass spectrometry for peptide mapping.

    PubMed

    Wenz, Christian; Barbas, Coral; López-Gonzálvez, Ángeles; Garcia, Antonia; Benavente, Fernando; Sanz-Nebot, Victoria; Blanc, Tim; Freckleton, Gordon; Britz-McKibbin, Philip; Shanmuganathan, Meera; de l'Escaille, Francois; Far, Johann; Haselberg, Rob; Huang, Sean; Huhn, Carolin; Pattky, Martin; Michels, David; Mou, Si; Yang, Feng; Neusuess, Christian; Tromsdorf, Nora; Baidoo, Edward E K; Keasling, Jay D; Park, SungAe Suhr

    2015-07-06

    A collaborative study on the robustness and portability of a capillary electrophoresis-mass spectrometry method for peptide mapping was performed by an international team, consisting of 13 independent laboratories from academia and industry. All participants used the same batch of samples, reagents and coated capillaries to run their assays, whereas they utilized the capillary electrophoresis-mass spectrometry equipment available in their laboratories. The equipment used varied in model, type and instrument manufacturer. Furthermore, different types of sheath-flow capillary electrophoresis-mass spectrometry interfaces were used. Migration time, peak height and peak area of ten representative target peptides of trypsin-digested bovine serum albumin were determined by every laboratory on two consecutive days. The data were critically evaluated to identify outliers and final values for means, repeatability (precision within a laboratory) and reproducibility (precision between laboratories) were established. For relative migration time the repeatability was between 0.05 and 0.18% RSD and the reproducibility between 0.14 and 1.3% RSD. For relative peak area repeatability and reproducibility values obtained were 3-12 and 9-29% RSD, respectively. These results demonstrate that capillary electrophoresis-mass spectrometry is robust enough to allow a method transfer across multiple laboratories and should promote a more widespread use of peptide mapping and other capillary electrophoresis-mass spectrometry applications in biopharmaceutical analysis and related fields.

  16. Time-varying volatility in Malaysian stock exchange: An empirical study using multiple-volatility-shift fractionally integrated model

    NASA Astrophysics Data System (ADS)

    Cheong, Chin Wen

    2008-02-01

    This article investigated the influences of structural breaks on the fractionally integrated time-varying volatility model in the Malaysian stock markets which included the Kuala Lumpur composite index and four major sectoral indices. A fractionally integrated time-varying volatility model combined with sudden changes is developed to study the possibility of structural change in the empirical data sets. Our empirical results showed substantial reduction in fractional differencing parameters after the inclusion of structural change during the Asian financial and currency crises. Moreover, the fractionally integrated model with sudden change in volatility performed better in the estimation and specification evaluations.

  17. Abnormalities of capillary microarchitecture in a rat model of coronary ischemic congestive heart failure.

    PubMed

    Chen, Jiqiu; Yaniz-Galende, Elisa; Kagan, Heather J; Liang, Lifan; Hekmaty, Saboor; Giannarelli, Chiara; Hajjar, Roger

    2015-04-15

    The aim of the present study is to explore the role of capillary disorder in coronary ischemic congestive heart failure (CHF). CHF was induced in rats by aortic banding plus ischemia-reperfusion followed by aortic debanding. Coronary arteries were perfused with plastic polymer containing fluorescent dye. Multiple fluorescent images of casted heart sections and scanning electric microscope of coronary vessels were obtained to characterize changes in the heart. Cardiac function was assessed by echocardiography and in vivo hemodynamics. Stenosis was found in all levels of the coronary arteries in CHF. Coronary vasculature volume and capillary density in remote myocardium were significantly increased in CHF compared with control. This occurred largely in microvessels with a diameter of ≤3 μm. Capillaries in CHF had a tortuous structure, while normal capillaries were linear. Capillaries in CHF had inconsistent diameters, with assortments of narrowed and bulged segments. Their surfaces appeared rough, potentially indicating endothelial dysfunction in CHF. Segments of main capillaries between bifurcations were significantly shorter in length in CHF than in control. Transiently increasing preload by injecting 50 μl of 30% NaCl demonstrated that the CHF heart had lower functional reserve; this may be associated with congestion in coronary microcirculation. Ischemic coronary vascular disorder is not limited to the main coronary arteries, as it occurs in arterioles and capillaries. Capillary disorder in CHF included stenosis, deformed structure, proliferation, and roughened surfaces. This disorder in the coronary artery architecture may contribute to the reduction in myocyte contractility in the setting of heart failure.

  18. Abnormalities of capillary microarchitecture in a rat model of coronary ischemic congestive heart failure

    PubMed Central

    Chen, Jiqiu; Yaniz-Galende, Elisa; Kagan, Heather J.; Liang, Lifan; Hekmaty, Saboor; Giannarelli, Chiara

    2015-01-01

    The aim of the present study is to explore the role of capillary disorder in coronary ischemic congestive heart failure (CHF). CHF was induced in rats by aortic banding plus ischemia-reperfusion followed by aortic debanding. Coronary arteries were perfused with plastic polymer containing fluorescent dye. Multiple fluorescent images of casted heart sections and scanning electric microscope of coronary vessels were obtained to characterize changes in the heart. Cardiac function was assessed by echocardiography and in vivo hemodynamics. Stenosis was found in all levels of the coronary arteries in CHF. Coronary vasculature volume and capillary density in remote myocardium were significantly increased in CHF compared with control. This occurred largely in microvessels with a diameter of ≤3 μm. Capillaries in CHF had a tortuous structure, while normal capillaries were linear. Capillaries in CHF had inconsistent diameters, with assortments of narrowed and bulged segments. Their surfaces appeared rough, potentially indicating endothelial dysfunction in CHF. Segments of main capillaries between bifurcations were significantly shorter in length in CHF than in control. Transiently increasing preload by injecting 50 μl of 30% NaCl demonstrated that the CHF heart had lower functional reserve; this may be associated with congestion in coronary microcirculation. Ischemic coronary vascular disorder is not limited to the main coronary arteries, as it occurs in arterioles and capillaries. Capillary disorder in CHF included stenosis, deformed structure, proliferation, and roughened surfaces. This disorder in the coronary artery architecture may contribute to the reduction in myocyte contractility in the setting of heart failure. PMID:25659485

  19. Symmetric and asymmetric capillary bridges between a rough surface and a parallel surface.

    PubMed

    Wang, Yongxin; Michielsen, Stephen; Lee, Hoon Joo

    2013-09-03

    Although the formation of a capillary bridge between two parallel surfaces has been extensively studied, the majority of research has described only symmetric capillary bridges between two smooth surfaces. In this work, an instrument was built to form a capillary bridge by squeezing a liquid drop on one surface with another surface. An analytical solution that describes the shape of symmetric capillary bridges joining two smooth surfaces has been extended to bridges that are asymmetric about the midplane and to rough surfaces. The solution, given by elliptical integrals of the first and second kind, is consistent with a constant Laplace pressure over the entire surface and has been verified for water, Kaydol, and dodecane drops forming symmetric and asymmetric bridges between parallel smooth surfaces. This solution has been applied to asymmetric capillary bridges between a smooth surface and a rough fabric surface as well as symmetric bridges between two rough surfaces. These solutions have been experimentally verified, and good agreement has been found between predicted and experimental profiles for small drops where the effect of gravity is negligible. Finally, a protocol for determining the profile from the volume and height of the capillary bridge has been developed and experimentally verified.

  20. Capillary waveguide optrodes: an approach to optical sensing in medical diagnostics.

    PubMed

    Lippitsch, M E; Draxler, S; Kieslinger, D; Lehmann, H; Weigl, B H

    1996-07-01

    Glass capillaries with a chemically sensitive coating on the inner surface are used as optical sensors for medical diagnostics. A capillary simultaneously serves as a sample compartment, a sensor element, and an inhomogeneous optical waveguide. Various detection schemes based on absorption, fluorescence intensity, or fluorescence lifetime are described. In absorption-based capillary waveguide optrodes the absorption in the sensor layer is analyte dependent; hence light transmission along the inhomogeneous waveguiding structure formed by the capillary wall and the sensing layer is a function of the analyte concentration. Similarly, in fluorescence-based capillary optrodes the fluorescence intensity or the fluorescence lifetime of an indicator dye fixed in the sensing layer is analyte dependent; thus the specific property of fluorescent light excited in the sensing layer and thereafter guided along the inhomogeneous waveguiding structure is a function of the analyte concentration. Both schemes are experimentally demonstrated, one with carbon dioxide as the analyte and the other one with oxygen. The device combines optical sensors with the standard glass capillaries usually applied to gather blood drops from fingertips, to yield a versatile diagnostic instrument, integrating the sample compartment, the optical sensor, and the light-collecting optics into a single piece. This ensures enhanced sensor performance as well as improved handling compared with other sensors.