Coupling Liquid Research Articles

Computational approaches to protein inference in shotgun proteomics

Shotgun proteomics has recently emerged as a powerful approach to characterizing proteomes in biological samples. Its overall objective is to identify the form and quantity of each protein in a high-throughput manner by coupling liquid chromatography with tandem mass spectrometry. As a consequence of its high throughput nature, shotgun proteomics faces challenges with respect to the analysis and interpretation of experimental data. Among such challenges, the identification of proteins present in a sample has been recognized as an important computational task. This task generally consists of (1) assigning experimental tandem mass spectra to peptides derived from a protein database, and (2) mapping assigned peptides to proteins and quantifying the confidence of identified proteins. Protein identification is fundamentally a statistical inference problem with a number of methods proposed to address its challenges. In this review we categorize current approaches into rule-based, combinatorial optimization and probabilistic inference techniques, and present them using integer programing and Bayesian inference frameworks. We also discuss the main challenges of protein identification and propose potential solutions with the goal of spurring innovative research in this area.

Perceiving the chemical language of Gram-negative bacteria: listening by high-resolution mass spectrometry

Gram-negative bacteria use N-acylhomoserine lactones (AHLs) as their command language to coordinate population behavior during invasion and colonization of higher organisms. Although many different bacterial bioreporters are available for AHLs monitoring, in which a phenotypic response, e.g. bioluminescence, violacin production, and β-galactosidase activity, is exploited, mass spectrometry (MS) is the most versatile detector for rapid analysis of AHLs in complex microbial samples, with or without prior separation steps. In this paper we critically review recent advances in the application of high-resolution MS to analysis of the quorum sensing (QS) signaling molecules used by Gram-negative bacteria, with much emphasis on AHLs. A critical review of the use of bioreporters in the study of AHLs is followed by a short methodological survey of the capabilities of high-resolution mass spectrometry (HRMS), including Fourier-transform ion cyclotron resonance (FTICR) MS and quadrupole time-of-flight (qTOF) MS. Use of infusion electrospray ultrahigh-resolution FTICR MS (12 Tesla) enables accurate mass measurements for determination of the elemental formulas of AHLs in Acidovorax sp. N35 and Burkholderia ubonensis AB030584. Results obtained by coupling liquid chromatography with a hybrid quadrupole linear ion trap-FTICR mass spectrometer (LC-LTQ-FTICRMS, 7-T) for characterization of acylated homoserine lactones in the human pathogen Pseudomonas aeruginosa are presented. UPLC-ESI-qTOF MS has also proved to be suitable for identification of 3O-C(10)HSL in Pseudomonas putida IsoF cell culture supernatant. Aspects of sample preparation and the avoidance of analytical pitfalls are also emphasized.

Planar array of corrugated tapered slot antennas for ultrawideband biomedical microwave imaging system

A planar antenna array that includes 12 corrugated tapered slot elements for use in ultrawideband (UWB) biomedical microwave imaging systems is presented. The used corrugate tapered slot antenna has a compact size, low profile, moderate gain, and distortionless performance in the time domain. The array is immersed in a carefully designed matching liquid of suitable dielectric constant to improve the matching between the array and the imaged object, and thus, to increase the dynamic range of the imaging system. A suitable platform is designed and fabricated to accommodate the array, breast phantom, and a coupling liquid for the case of UWB breast imaging. The design of the whole system is optimized using trust-region framework method in the simulation tool CST Microwave Studio. The performance of the designed array is confirmed via measurements in a realistic imaging environment. © 2012 Wiley Periodicals, Inc. Int J RF and Microwave CAE, 2013. © 2013 Wiley Periodicals, Inc.

Interactive coupling between a tree and raindrops

ABSTRACTThis paper presents a novel approach for simulating the dynamic coupling between a tree and raindrops based on physical deformation and fluid simulation. By the approach, tree animation in the rain can be simulated in a two‐resolution way: branch motion and leaf motion. The branch is represented by the Euler–Bernoulli beam model, and the leaf petiole is represented by the three‐prism elastic model. Interaction coupling liquid motion on the hydrophilic surface with a flexible petiole is well implemented by a special design. To simplify the computation process, instead of the computation‐intensive three‐dimensional Navier–Stokes equations, shallow water equations are used to simulate the water dynamics together with the whole leaf deformation. Simulation has been also made to various phenomena incurred from the interactive coupling. These include, among others, part of impacting raindrops splashing into the air with the remaining flowing along the slant of the leaf and merging into larger ones or hanging on the blade boundary, with the leaf rebounding and vibrating after the drops fall off the leaf. A level‐of‐detail approach is exploited to accelerate rendering in views of different distances. The experimental results illustrate that the approach can be applied to efficiently generate realistic details of the interactive coupling between a tree and raindrops. Copyright © 2012 John Wiley & Sons, Ltd.

Collective Modes in Strongly Coupled Binary Liquids

AbstractWe analyze the collective excitations in two‐ and three‐dimensional binary Yukawa systems, consisting of two components with different masses. Theoretical analysis reveals a profound difference between the weakly and strongly correlated limits: at weak coupling the two components interact via the mean field only and the oscillation frequency is governed by the light component. In the strongly correlated limit the mode frequency is governed by the combined mass, where the heavy component dominates. Computer simulations in the full coupling range extend and confirm the theoretical results (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)

Three-Dimensional Near-Field Microwave Holography for Tissue Imaging

This paper reports the progress toward a fast and reliable microwave imaging setup for tissue imaging exploiting near-field holographic reconstruction. The setup consists of two wideband TEM horn antennas aligned along each other's boresight and performing a rectangular aperture raster scan. The tissue sensing is performed without coupling liquids. At each scanning position, wideband data is acquired. Then, novel holographic imaging algorithms are implemented to provide three-dimensional images of the inspected domain. In these new algorithms, the required incident field and Green's function are obtained from numerical simulations. They replace the plane (or spherical) wave assumption in the previous holographic methods and enable accurate near-field imaging results. Here, we prove that both the incident field and Green's function can be obtained from a single numerical simulation. This eliminates the need for optimization-based deblurring which was previously employed to remove the effect of realistic non-point-wise antennas.

COMPACT WIDEBAND ANTENNA FOR MICROWAVE IMAGING OF BRAIN

This article reports on the design of a wideband compact microstrip-fed tapered slot antenna aimed at microwave imaging of a brain stroke. The antenna is immersed in a carefully designed coupling liquid that is used to facilitate higher signal penetration in the brain and thus increased dynamic range of the imaging system. A parametric analysis is used to find out the required properties of the coupling liquid. A suitable mixture of materials is then used to implement those properties. In order to protect the antenna from the adverse effects of the coupling medium, dielectric sheets are used to cover the radiator and the ground plane. To verify the proposed design in brain imaging, the antenna is tested using a suitable head model. It is shown that the antenna with a compact size (24 mm × 24 mm) on RT6010 substrate (dielectric constant = 10.2) operates efficiently over the band from 1 GHz to more than 4 GHz with more than 10 dB return loss. The time domain performance of the antenna supports its capability to transmit a distortion-less pulse with a high fidelity factor inside the head tissues.

Mathematical modeling of process liquid flow and acetoclastic methanogenesis under mesophilic conditions in a two-phase biogas reactor

Acetoclastic methanogenesis in the second stage of a two-phase biogas reactor is investigated. A mathematical model coupling chemical reactions with transport of process liquid and with the variation of population of the microorganisms living on the plastic tower packing of the reactor is proposed. The evolution of the liquid is described by an advection–diffusion–reaction equation, while a monod-type kinetic is used for the reactions. Moreover, a new inhibition factor MO max is introduced, which hinders the growth of microorganisms when the plastic tower packing is overpopulated. After estimating the reaction parameters, the acetate outflow measured experimentally is in good agreement with that predicted by simulations. For coupling liquid transport with reaction processes, a spatial discretization of the reactor is performed. This yields essential information about the distribution of acetate and the production of methane in the reactor. This information allows for defining a measure of the effectiveness of the reactor.

Development of a simultaneous liquid chromatography/tandem mass spectrometric method for the determination of type B trichothecenes, their derivatives, and precursors in wheat

A method coupling liquid chromatography with tandem mass spectrometry (LC/MS/MS) was developed for the simultaneous quantitative determination of trichothecenes, nivalenol, deoxynivalenol, deoxynivalenol-3-glucoside, fusarenon-X, 3-acetyldeoxynivalenol, 15-acetyldeoxynivalenol, isotrichodermin, calonectrin, 3-deacetylcalonectrin, 15-deacetylcalonectrin, 3,15-diacetylnivalenol, 4,15-diacetylnivalenol, 3,15-diacetyldeoxynivalenol, and 3,4,15-triacetylnivalenol. The analytical parameters of trichothecenes and their derivatives were optimized to enable their highly sensitive detection. Evaluation of clean-up procedures using Multisep #226 and #227 indicated that Multisep #227 was more suitable for their simultaneous detection in wheat. In performance validation studies using the LC/MS/MS method with Multisep #227 cleanup, good recoveries ranging from 84% to 115% with relative standard deviations from 0.4% to 7.2% were measured. The limits of detection and quantification ranged from 0.03 to 1.4 ng·g(-1) and from 0.1 to 4.7 ng·g(-1) , respectively. The effect of matrices using matrix-matched calibration was estimated to range from 80% to 117% after Multisep #227 cleanup. Multisep #227 clean-up procedure with matrix-free standard calibration achieved accurate quantification without having a considerable effect on matrix compounds. Using the developed method, several trichothecene derivatives and precursors were detected in fungally inoculated wheat samples. The developed LC/MS/MS method is a practical technique that can be used for the quantification of trichothecenes in wheat. This study is the first report of an analytical method used for the simultaneous quantification of major trichothecenes, their derivatives and precursors.

Systematic fragmentation patterns of archaeal intact polar lipids by high‐performance liquid chromatography/electrospray ionization ion‐trap mass spectrometry

Archaea are ubiquitous and abundant microorganisms on Earth that mediate key global biogeochemical cycles. The headgroup attached to the sn-1 position of the glycerol backbone and the ether-linked isoprenoid lipids are among the diagnostic traits that distinguish Archaea from Bacteria and Eukarya. Over the last 30 years, numerous archaeal lipids have been purified and described in pure cultures. Coupled high-performance liquid chromatography (HPLC) ion-trap mass spectrometry (ITMS) now enables the detection and rapid identification of intact polar lipids in relatively small and complex samples, revealing a wide range of archaeal lipids in natural environments. Although major structural groups have been identified, the lack of a systematic evaluation of MS/MS fragmentation patterns has hindered the characterization of several atypical components that are therefore considered as unknowns. Here, we examined mass spectra resulting from lipid analysis of natural microbial communities using HPLC/electrospray ionization (ESI)-ITMS(n), and depicted the systematics in MS(2) fragmentation of intact archaeal lipids. This report will be particularly useful for environmental scientists interested in a rapid and straightforward characterization of intact archaeal membrane lipids.

A Noncontact Ultrasonic Platform for Structural Inspection

Miniature robotic vehicles are receiving increasing attention for use in nondestructive testing (NDE) due to their attractiveness in terms of cost, safety, and their accessibility to areas where manual inspection is not practical. Conventional ultrasonic inspection requires the provision of a suitable coupling liquid between the probe and the structure under test. This necessitates either an on board reservoir or umbilical providing a constant flow of coupling fluid, neither of which are practical for a fleet of miniature robotic inspection vehicles. Air-coupled ultrasound offers the possibility of couplant-free ultrasonic inspection. This paper describes the sensing methodology, hardware platform and algorithms used to integrate an air-coupled ultrasonic inspection payload into a miniature robotic vehicle platform. The work takes account of the robot's inherent positional uncertainty when constructing an image of the test specimen from aggregated sensor measurements. This paper concludes with the results of an automatic inspection of a aluminium sample.

Liquid chromatography/mass spectrometry stable isotope analysis of dissolved organic carbon in stream and soil waters

A commercial interface coupling liquid chromatography (LC) to a continuous-flow isotope ratio mass spectrometry (CF-IRMS) instrument was used to determine the δ(13) C of dissolved organic carbon (DOC) in natural waters. Stream and soil waters from a farmland plot in a hedgerow landscape were studied. Based on wet chemical oxidation of dissolved organics the LC/IRMS interface allows the on-line injection of small volumes of water samples, an oxidation reaction to produce CO(2) and gas transfer to the isotope ratio mass spectrometer. In flow injection analysis (FIA) mode, bulk DOC δ(13)C analysis was performed on aqueous samples of up to 100 μL in volume in the range of DOC concentration in fresh waters (1-10 mg C.L(-1)). Mapping the DOC δ(13)C spatial distribution at the plot scale was made possible by this fairly quick method (10 min for triplicate analyses) with little sample manipulation. The relative contributions of different plot sectors to the DOC pool in the stream draining the plot were tentatively inferred on the basis of δ(13)C differences between the hydrophilic and hydrophobic components.

Coupled Liquid Water, Water Vapor, and Heat Transport Simulations in an Unsaturated Zone of a Sandy Loam Field

Information on the coupled liquid water, water vapor, and heat transport under arable field conditions is still limited, particularly for unsaturated soils of semi-arid and arid regions such as New Mexico. HYDRUS-1D model was applied to evaluate various transport mechanisms associated with temporal variations in water content and soil temperature in the unsaturated zone of a sandy loam furrow-irrigated field located at Leyendecker Plant Science Research Center, Las Cruces, New Mexico. The model was calibrated using measured soil water content and soil temperature at 5-, 10-, 20-, and 50-cm depths during a 19-day period (day of the year [DOY] 85 to DOY 103, 2009) and validated for a 31-day period (DOY 104 to DOY 134, 2009). Measured and optimized soil hydraulic and thermal properties and hourly meteorological data were used in model simulations. HYDRUS-1D simulated water contents and soil temperatures correlated well with the measured data at each depth. The total liquid water flux, composed of isothermal and thermal liquid water flux, dominated the soil water movement during early periods after irrigation, whereas the contribution of total water vapor flux, composed of primarily thermal and much smaller isothermal water vapor flux, increased with increasing soil drying. During the soil drying process, the total liquid flux within 15-cm depth eventually changed to water vapor flux near the surface. The upward total liquid and vapor fluxes decreased from 5 cm, indicating that vapor flux was much higher in the layer near the soil surface. The total vapor flux in this unsaturated soil layer was approximately 10.4% of the total liquid and vapor fluxes during the simulation period.

Numerical studies of electrically induced pattern formation by coupling liquid dielectrophoresis and two‐phase flow

Electrically induced patterning process, as a novel micro- or nano-structuring approach for fabrication of various micro- or nano-systems, is usually implemented by applying a voltage to an electrode pair consisting of a patterned or non-patterned template and a polymer-coated substrate separated in parallel by an air gap, followed by photo- or thermo-curing of the fluidic and dielectric polymer. The analyses performed so far to characterize this patterning process have been based on linear thermodynamics for a thermally instable thin film perturbed by an electrostatically induced hydraulic pressure. For mathematical simplicity, these analyses were formulated only for a flat template and a flat film surface with infinite planar area, demonstrating the tendency of initial pattern growth on the polymer film, but being unable to visualize the dynamic evolution of micro- or nano-structure growth throughout the patterning process for a real-life template in practical applications. This paper attempts to provide another insight into this patterning process from a viewpoint of liquid dielectrophoresis (L-DEP), by presenting an approach for numerical simulation of the patterning process based on a coupling of L-DEP and two-phase flow theories. First, a numerical analysis has been made for the electrocoalescence of a water droplet with bottom water in silicone oil to benchmark effectiveness of the proposed numerical approach against published experimental observations. More numerical results have then been provided to show effects of some process variables on the evolution of the polymer micro- or nano-structures for this patterning process.

Coherent Vortices in Strongly Coupled Liquids

Strongly coupled liquids are ubiquitous in both nature and laboratory plasma experiments. They are unique in the sense that their average potential energy per particle dominates over the average kinetic energy. Using "first principles" molecular dynamics (MD) simulations, we report for the first time the emergence of isolated coherent tripolar vortices from the evolution of axisymmetric flows in a prototype two-dimensional (2D) strongly coupled liquid, namely, the Yukawa liquid. Linear growth rates directly obtained from MD simulations are compared with a generalized hydrodynamic model. Our MD simulations reveal that the tripolar vortices persist over several turn over times and hence may be observed in strongly coupled liquids such as complex plasma, liquid metals and astrophysical systems such as white dwarfs and giant planetary interiors, thereby making the phenomenon universal.

Coupling liquid phase electrochemistry with nuclear magnetic resonance spectroscopy and its applications

The combination of liquid nuclear magnetic resonance spectroscopy (NMR) and electrochemistry (EC) is a new technique with promising prospect which provides novel, exciting, and crucial insights into the processes near or on the electrode surface at a molecular or atomic level. The development of in situ EC-NMR spectroscopy with flow or static electrolysis was summarized, the structures of the electrolysis cell and the characteristics of the NMR spectra were analyzed, and the feature of the in situ EC-NMR spectroscopy in practice was described in detail. The electrolysis electrode located at radio-frequency detection area of the NMR spectrometer reduced homogeneity of the magnetic field. Furthermore, the electrolysis current results in broadened spectral lines and loss of resolution. The working electrode consisting of a thin metal film and the electrolysis current parallel to the static magnetic field can overcome such shortcomings. Besides, several high-resolution methods in inhomogeneous fields were discussed and compared, such as intramolecular multiple quantum coherences, nutation echos, intermolecular nuclear Overhauser effects, and intermolecular multiple quantum coherences.

Analysis of wax esters in edible oils by automated on-line coupling liquid chromatography–gas chromatography using the through oven transfer adsorption desorption (TOTAD) interface

An automated method for the direct analysis of wax esters in edible oils is presented. The proposed method uses the TOTAD (through oven transfer adsorption desorption) interface for the on-line coupling of normal phase liquid chromatography and gas chromatography. In this fully automated system, the oil with C32 wax ester as internal standard and diluted with heptane is injected directly with no sample pre-treatment step other than filtration. The proposed method allows analysis of different wax esters, and is simpler and faster than the European Union Official Method, which is tedious and time-consuming. The obtained results closely match the certified values obtained from the median of the analytical results of the inter-labs certification study. Relative standard deviations of the concentrations are less than 5%. The method is appropriate for routine analysis as it is totally automated.

Elastic properties determination of CuInSe2 polycrystalline thin films via a dynamic method

Developing and using a simulation program based on the spectrum angular model, we first determine reflectance functions and acoustic signatures for bulk as well as for different thickness of CuInSe2 films. For bulk material, it is found that the longitudinal and Rayleigh modes are excited at incidence angles of 23.4° and 47°, respectively. This result reveals the great difficulties to characterize CuInSe2 with a conventional scanning acoustic microscope that uses a lens half- opening angle of 50° and water as a coupling liquid. Hence, Freon is used as alternative coupling liquid. Consequently, the effect of thickness on reflection coefficient and acoustic signature variations are quantified for both bulk and thin material. It is shown that as the thickness increases: (i) the critical angle of mode excitation increases, (ii) the periods of acoustic signature curves decrease and (iii) the Rayleigh velocity, VR, mode shifts towards lower values. Hence, a velocity dispersion curve is established in terms of VR as a function of film thickness; it decreases initially from the velocity value of the glass substrate then saturates when it reaches that of CuInSe2. The importance of such curve lies in the possibility of velocity determination by just knowing the thickness, and vice versa. Moreover, elastic constants are straight forward deduced from such a velocity.

Pitfalls encountered during quantitative determination of 3-alkyl-2-methoxypyrazines in grape must and wine using gas chromatography–mass spectrometry with stable isotope dilution analysis. Comprehensive two-dimensional gas chromatography–mass spectrometry and on-line liquid chromatography-multidimensional gas chromatography–mass spectrometry as potential loopholes

The analysis of 3-alkyl-2-methoxypyrazines in Vitis vinifera grape must or wine at the low nanogram per liter level failed in several situations when applying a one-dimensional gas chromatographic analysis with mass spectrometric detection (GC–MS). Sample preparation methods such as headspace solid phase microextraction or solid phase extraction were convenient procedures, however lacking extraction selectivity for complex matrices. Analysis by comprehensive two-dimensional gas chromatography with mass spectrometric detection clearly demonstrated the potential for co-elution in such matrices and the risk for erroneous results when applying one-dimensional GC–MS. In one example, matrix problems would have been a challenge even for a comprehensive two-dimensional chromatographic approach with MS detection (GC × GC–MS). A solution to matrix problems was found by protonating the 3-alkyl-2-methoxypyrazines in acidic pH and sample clean-up using solid phase extraction with a mixed-mode polymeric cation-exchange sorbent. Quantification was performed by a stable isotope dilution assay, following analysis by on-line coupled high performance liquid chromatography with multidimensional gas chromatography and detection with mass spectrometry (on-line LC–MDGC–MS). This new approach allowed trace-level analysis of 3-alkyl-2-methoxypyrazines in grape musts and wines and is described for V. vinifera Sauvignon blanc, following 3-alkyl-2-methoxypyrazines concentrations during ripening and in the processed wines.

Effects of Zeta Potential and Fiber Diameter on Coupled Heat and Liquid Moisture Transfer in Porous Polymer Materials

This study is a theoretical investigation of the liquid water transport coupled with moisture and heat transfer in porous polymer materials. The solid surface zeta potential and the fiber diameter are investigated to reveal the mechanisms of the coupling effects. Based on the PoissonBoltzmann equation for electric double layers and Navier-Stokes equation of liquid flows, a mathematical model to simulate the complex coupled heat and moisture transfer in porous polymer materials is reported in this paper.