Maximum Systematic Error Research Articles

On the symmetry of photon detection arrays: A directionally sensitive 3D model

A detector's ability to obtain the direction of a radioactive source is an invaluable operational asset. A 2D/3D model was developed based on directionally sensitive arrays. The average location of photon interactions within a symmetrical array yields the direction of the source. The model is validated with simulations and laboratory measurements, maximum systematic error being 5–10° at energies >200 keV and approaching zero at lower energies. The symmetry model yields the direction of a shielded source even when no full energy photons could be detected.

Technical note: Clinical evaluation of a newly released surface-guided radiation therapy system on DIBH for left breast radiation therapy.

It has been shown that a significant reduction of mean heart dose and left anterior descending artery (LAD) dose can be achieved through the use of DIBH for left breast radiation therapy. Surface-guided DIBH has been widely adopted during the last decade, and there are mainly three commercially available SGRT systems. The reports of the performance of a newly released SGRT system for DIBH application are currently very limited. To evaluate the clinical performance of a newly released SGRT system on DIBH for left breast radiation therapy. Twenty-five left breast cancer patients treated with DIBH utilizing Varian's Identify system were included (total 493-fraction treatments). Four aspects of the clinical performance were evaluated: Identify offsets of free breathing post patient setup from tattoos, Identify offsets during DIBH, Identify agreement with radiographic ports during DIBH, and DIBH reference surface re-capture post patient shifts. The systematic and random errors of free breathing Identify offsets post patient setup were calculated for each patient, as well as for offsets during DIBH. Radiographic ports were taken when the patient's DIBH position was within the clinical tolerance of (±0.3cm,±30 ), and these were then compared with treatment field DRRs. If the ports showed that the patient alignment did not agree with the DRRs within 3mm, a patient shift was performed. A new reference surface was captured and verification ports were taken. The all-patient average systematic and random errors of Identify offsets for free breathing were within (0.4cm, 1.50 ) post tattoo setup. The maximum per-patient systematic and random errors were (1.1cm, 6.20 ) and (0.9cm, 20 ), and the maximum amplitude of Identify offsets were (2.59cm, 90 ). All 493-fraction DIBH treatments were delivered and successfully guided by the Identify SGRT system. The systematic and random errors of Identify offsets for DIBH were within (0.2cm, 2.30 ). Seven patients needed re-captured surface references due to surface variation or position shifts based on the ports. All patient DIBH verification ports guided by Identify were approved by attending physicians. This evaluation showed that the Identify system performed effectively for surface-guided patient setup and surface-guided DIBH imaging and treatment delivery. The feature of color-coded real-time patient surface matching feedback facilitated the evaluation of the patient alignment accuracy and the adjustment of the patient position to match the reference.

Gaussian variational method to Fermi-Hubbard model in one and two dimensions

The study of ground-state properties of the Fermi-Hubbard model is a long-lasting task in the research of strongly correlated systems, and is crucial for the understanding of notable quantum phenomena including superconductivity and magnetism. Owing to the exponentially growing complexity of the system, a quantitative analysis usually demands high computational cost and is restricted to small samples, especially in two or higher dimensions. Here, we introduce a variational method in the frame of fermionic Gaussian states, and obtain the ground states of one- and two-dimensional attractive Hubbard models via imaginary-time evolution. We calculate the total energy and benchmark the results in a wide range of interaction strength and filling factor with those obtained via exact two-body results, the density matrix renormalization group based on matrix product states (MPS), and projector Quantum Monte Carlo (QMC) method. For both 1D and 2D cases, the Gaussian variational method presents accurate results for total energy with a maximum systematic error in the intermediate interaction region. The accuracy of these results has negligible dependence on the system size. We further calculate the double occupancy and find excellent agreement with MPS and QMC, as well as the experimental results of cold quantum gases in optical lattices. The results suggest that the Gaussian pairing state is a good approximation to the ground states of attractive Hubbard model, in particular in the strong and weak coupling limits. Moreover, we generalize the method to the attractive Hubbard model with a finite spin-polarization, which can be mapped to the repulsive interaction case via particle-hole transformation, and obtain accurate results of ground state energy and double occupancy. Our work demonstrates the ability of the Gaussian variational method to extract ground state properties of strongly correlated many-body systems with negligible computational cost, especially of large size and in higher dimensions.

Design rules for Background Oriented Schlieren experiments with least-squares based displacement calculation

Background Oriented Schlieren (BOS) is a non-intrusive optical method used to visualize density variations in fluids. A camera is used to measure the distortion of a background image displaying a random pattern due to the refraction of the light induced by the local gradients in the refractive index of the under study. In contrast to conventional schlieren, for which direct observation is possible, the images obtained with the BOS technique have to be processed. In this contribution, a computationally affordable approach based on linear least-squares minimization and adapted from optical flow techniques is presented in detail and tested in the context of BOS with the Matlab GUI application comBOS. A series of synthetic images are first analyzed to devise design rules for the definition of an optimal random Gaussian dot background pattern. Tests are performed for comBOS, the commercial BOS module included in DaVis 10, and the free PIV tool PIVlab. It is found that the diameter of the dot images on the camera sensor should be at least 3 pixels, but can be larger without affecting the accuracy of the measurement with comBOS and DaVis 10, while PIVlab severely degrades the quality of the results for dots larger than 5 pixels. The contrast and the density of dots must also be sufficient such that a minimum of 75 % of the surface of the background is shaded. If these conditions are met, the maximum systematic error in the measured distortions is 0.006 pixel for comBOS and 0.001 pixel with DaVis 10 when local gradients are small. Similar errors are found with PIVlab for dots smaller than 5 pixels in diameter, but they increase rapidly for larger dots. The random error is typically smaller than 0.004 pixel in optimal conditions, but it increases significantly for images affected by a random noise or local gradients of the distortion. Finally, it is concluded with a realistic test case that both comBOS and DaVis 10 are well suited to capture the main features of a complex compressible flow with Schlieren imaging. Thus, the main advantage of comBOS is its affordability and robustness for researchers and educators willing to implement BOS, for example in educational contexts.

Direct Interface Circuit for Capacitive Sensors Affected by Parasitic Series Resistances

This article presents a novel circuit to directly interface a capacitive sensor affected by parasitic series resistances to a digital processor (DP). The presence of such resistances distorts the estimation of the capacitance to be measured. Current measurement procedures for these sensors, such as impedance-frequency characteristics, are complex and require significant hardware resources, power consumption, and time. To eliminate these drawbacks, a new circuit based on the so-called direct interface circuits (DICs) is introduced, which performs the digital reading of the sensors taking advantage of the presence of DPs in many applications. The hardware requirements in the new design are minimal: just two resistors and an operational amplifier in addition to the DP. The circuit requires only two time measurements to estimate sensor capacitance. These are obtained during a single capacitor charging-discharging process, simultaneously reducing power consumption and measurement time. The circuit has been implemented using a field-programmable gate array (FPGA), as the DP, in a general-purpose board to evaluate its performance. Although it is not an application-specific design, the circuit shows a maximum systematic error of 0.37% for capacitances in the 100 pF–96 nF range with parasitic series resistances up to 1200 <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\Omega $ </tex-math></inline-formula> . The maximum measurement time for this range is just 4.5 ms.

Sensitivity of the large muon detector with the Tibet air-shower array to measure the primary proton spectrum between 40 and 630 TeV

Abstract The Tibet ASγ group has been continuously observing cosmic rays and cosmic gamma rays above several TeV using the muon detector array (MD) and high-density Tibet air-shower array (Tibet-III) installed on the Tibet plateau at an altitude of 4300 m. The MD is a water Cherenkov pool array with a large effective area of 3400 m2 and has an excellent capability of primary selection using the number of muons in the shower. We report the sensitivity of the proton spectrum measurements for energies 40–630 TeV obtained via Monte Carlo simulations for an air-shower experiment. It was found that protons could be separated with a purity of 90%, and the survival ratio of protons including model dependence was 14.2%–19.1% and 3.7%–7.4% at about 35 TeV and about 450 TeV, respectively. The maximum total systematic error of the proton flux depending on interaction models in air-shower development and composition models was ±37%. With a large effective area and high proton separation capability, the Tibet ASγ experiment can measure the proton spectrum in the energy range from tens to hundreds of TeV with high statistical accuracy.

Enhancement of Contour Smoothness by Substitution of Interpolated Sub-Pixel Points for Edge Pixels

This study designed a sub-pixel precision edge detecting algorithm to enhance contour smoothness. First, the coordinate value of RGB pixel is projected on the space line of R=G=B to obtain gray image. Then, pixel edges are located using a Canny detector. Next, the edge width is thinned to a single pixel using a morphological thinning operation. Finally, sub-pixel-level smooth contours are extracted by interpolation. In this sub-pixel level contour extraction process, a Single-Pixel-Multi-Point interpolation method was developed to enhance edge smoothness and obtain high precision in edge estimation. This method divides edges in a $3\times 3$ pixels block into nine arrangement modes. According to the arrangement of the eight neighborhoods of a centered edge pixel, different locations of interpolated sub-pixel points are calculated by interpolation with Bezier curves. For symmetrically arranged linear edge pixels, this method can be used to determine the exact contour. Experimental results showed that the proposed algorithm can improve the smoothness of image edge contour. As the curvature of the edge increases, the maximum systematic error will increase. For the edge pixel centered in the $3\times 3$ pixels block and two pixels located at the corner of one side, the max systematic error is 0.5 pixel. For two edge pixels aligned in a single row or column with one located at a corner, the max systematic error is 0.25 pixel.

Halcyon clinical performance evaluation: A log file-based study in comparison with a C-arm Linac

PurposeThe aim of this study is to compare the dosimetric and mechanical accuracy of Volumetric Modulation Arc Therapy (VMAT) delivery on the Halcyon, a recent ring-shaped Treatment Delivery System (TDS) featuring fast rotating gantry, with a conventional C-arm Linac. MethodsThe comparison was performed via log file analysis, where mechanical parameters of related components was extracted. 480 and 3951 VMAT log files of clinically delivered fractions from a Halcyon and a TrueBeam Linac were analyzed respectively. The relations between mechanical parameters and errors were extensively explored to further investigate the differences between the two Linacs. The mechanical parameter fluctuations were taken into account for dose recalculations, and the Dose Volume Parameters (DVP) on the PTV were evaluated to quantify such dosimetric variations. ResultsThe Multi-Leaf Collimator (MLC) leaf mean Root Mean Square (RMS) errors were 0.028 mm and 0.031 mm for Halcyon and TrueBeam respectively. Maximum systematic error on the MLC leaves introduced by the gravity effect were 0.04 mm and 0.01 mm for the Halcyon and TrueBeam respectively. Thanks to the O-ring design, the Halcyon achieved 0.035° in mean RMS error in gantry angle compared with the 0.065° of the TrueBeam. Overall mechanical errors introduced similar levels of dose-volume parameter variations (about 0.1%) on both Linacs. Conclusion: The Halcyon TDS can achieve similar mechanical leaf positioning accuracy compared with the TrueBeam TDS with a doubled delivery speed. In terms of dosimetric accuracy, The DVP standard deviations on the studied TB are generally larger than that on the Halcyon.

The MIPAS/Envisat climatology (2002–2012) of polar stratospheric cloud volume density profiles

Abstract. A global data set of vertical profiles of polar stratospheric cloud (PSC) volume density has been derived from Michelson Interferometer for Passive Atmospheric Sounding (MIPAS) space-borne infrared limb measurements between 2002 and 2012. To develop a well characterized and efficient retrieval scheme, systematic tests based on limb-radiance simulations for PSCs from in situ balloon observations have been performed. The finally selected wavenumber range was 831–832.5 cm−1. Optical constants of nitric acid trihydrate (NAT) have been used to derive maximum and minimum profiles of volume density which are compatible with MIPAS observations under the assumption of small, non-scattering and larger, scattering PSC particles. These max/min profiles deviate from their mean value at each altitude by about 40 %–45 %, which is attributed as the maximum systematic error of the retrieval. Further, the retrieved volume density profiles are characterized by a random error due to instrumental noise of 0.02–0.05 µm3 cm−3, a detection limit of about 0.1–0.2 µm3 cm−3 and a vertical resolution of around 3 km. Comparisons with coincident observations by the Cloud-Aerosol Lidar with Orthogonal Polarization (CALIOP) on the CALIPSO (Cloud-Aerosol Lidar and Infrared Pathfinder Satellite Observations) satellite showed good agreement regarding the vertical profile shape. Quantitatively, in the case of supercooled ternary solution (STS) PSCs, the CALIOP dataset fits to the MIPAS retrievals obtained under the assumptions of small particles. Unlike for STS and NAT, in the case of ice PSCs the MIPAS retrievals are limited by the clouds becoming optically thick in the limb-direction. In these cases, the MIPAS volume densities represent lower limits. Among other interesting features, this climatology helps to study quantitatively the on-set of PSC formation very near to the South Pole and the large variability of the PSC volume densities between different Arctic stratospheric winters.

A Single Layer 3-D Touch Sensing System for Mobile Devices Application

Touch sensing has been widely implemented as a main methodology to bridge human and machine interactions. The traditional touch sensing range is 2-D and therefore limits the user experience. To overcome these limitations, we propose a novel 3-D contactless touch sensing called Airtouch system, which improves user experience by remotely detecting single/multi-finger position. A single layer touch panel with triangle-shaped electrodes is proposed to achieve multitouch detection capability as well as manufacturing cost reduction. Moreover, an oscillator-based-capacitive touch sensing circuit is implemented as the sensing hardware with the bootstrapping technique to eliminate the interchannel coupling effects. To further improve the system accuracy, a grouping algorithm is proposed to group the useful channels’ data and filter out hardware noise impact. Finally, improved algorithms are proposed to eliminate the fringing capacitance effect and achieve accurate finger position estimation. EM simulation proved that the proposed algorithm reduced the maximum systematic error by 11 dB in the horizontal position detection. The proposed system consumes 2.3 mW and is fully compatible with existing mobile device environments. A prototype is built to demonstrate that the system can successfully detect finger movement in a vertical direction up to 6 cm and achieve a horizontal resolution up to 0.6 cm at 1 cm finger-height. As a new interface for human and machine interactions, this system offers great potential in finger movement detection and gesture recognition for small-sized electronics and advanced human interactive games for mobile device.

Voltammetric Determination of Diffusion Coefficients in Polymer Membranes: Guidelines to Minimize Errors

AbstractDiffusion coefficients are important in the design, optimization, and selection of membranes used in many applications including chemical and biosensors. Since the diffusion‐controlled transport of the analyte and interfering ions and molecules through polymer membranes may affect the rate of response, detection limit, selectivity, lifetime, etc. of chemical and biosensors, having a rapid and accurate method for the determination of diffusion coefficients of different compounds in a variety of membranes is uniquely important. In our contribution, we present a simple protocol for the rapid determination of the diffusion coefficients of electrochemically active analytes by linear sweep voltammetry. The expected errors in the estimated coefficients have been analyzed through modeling and the correlation between the magnitude of the unknown diffusion coefficients and the method's related maximum error is presented as a contour plot for different working electrode dimensions. It is also shown that our analysis protocol can be used to estimate the diffusion coefficient in complex membrane matrices and non‐ideal experimental conditions with a maximum systematic error of 14 % even without any experimental parameter optimization.

BEING WISE II: REDUCING THE INFLUENCE OF STAR FORMATION HISTORY ON THE MASS-TO-LIGHT RATIO OF QUIESCENT GALAXIES

ABSTRACT Stellar population synthesis models can now reproduce the photometry of old stellar systems (age 2 Gyr) in the near-infrared (NIR) bands at 3.4 and 4.6 μm (WISE W1 and W2 or IRAC 1 and 2). In this paper, we derive stellar mass-to-light ratios for these and optical bands, and confirm that the NIR M/L shows dramatically reduced sensitivity to both age and metallicity compared to optical bands, and further, that this behavior leads to significantly more robust stellar masses for quiescent galaxies with [Fe/H] −0.5 regardless of star-formation history (SFH). We then use realistic early-type galaxy SFHs and metallicity distributions from the EAGLE simulations of galaxy formation to investigate two methods to determine the appropriate M/L for a galaxy. (1) We show that the uncertainties introduced by an unknown SFH can be largely removed using a spectroscopically inferred luminosity-weighted age and metallicity for the population to select the appropriate single stellar population (SSP) equivalent M/L. Using this method, the maximum systematic error due to SFH on the M/L of an early-type galaxy is at 3.4 μm and typical uncertainties due to errors in the age and metallicity create a scatter of . The equivalent values for optical bands are more than two to three times greater, even before considering uncertainties associated with internal dust extinction. (2) We demonstrate that if the EAGLE SFHs and metallicities accurately reproduce the true properties of early-type galaxies, the use of an iterative approach to select a mass dependent M/L can provide even more accurate stellar masses for early-type galaxies, with typical uncertainties of .

Interferencia en las determinaciones de 24 constituyentes bioquímicos en el autoanalizador ADVIA 1800, causada por adición in vitro de emulsión comercial de nutrición parenteral a un pool de sueros

Introducción. Las interferencias analíticas por turbidez pueden causar errores clínicamente significativos en los resultados de una magnitud biológica. Objetivos. Conocer y cuantificar la posible interferencia producida por la turbidez (lipemia) en la medición rutinaria de 24 constituyentes bioquímicos, empleando para ello el criterio de interferencia clínicamente relevante cuando se supera el máximo error sistemático deseable. Diseño. Estudio experimental con pre y pos-prueba. Institución. Hospital Edgardo Rebagliati Martins, Lima, Perú. Material biológico. Pool de sueros proveniente de muestras procesadas en el laboratorio central del hospital. Intervenciones. Se añadieron cantidades crecientes de una emulsión lipídica comercial de nutrición parenteral a siete diferentes alícuotas de una mezcla de sueros y se determinó en ellas, por triplicado, la influencia del interferente en los 24 constituyentes. Para lo cual se ha seguido el protocolo de la Sociedad Española de Química Clínica. Principales medidas de resultados. Porcentaje relativo de desviación de la concentración del constituyente por influencia de la turbidez, con respecto a una muestra sin interferente. Resultados. Los constituyentes: glucosa, creatinina, potasio, colesterol total, HDL colesterol, fosfatasa alcalina, gammaglutamil transferasa, amilasa y lipasa, no presentaron interferencia en todas las alícuotas con cantidades crecientes del interferente empleado en el ensayo. Se observó interferencia para urea, ácido úrico, proteínas totales, albúmina, bilirrubina total, LDL colesterol, transferrina, fósforo, hierro, láctico deshidrogenasa, aspartato aminotransferasa, alanino aminotransferasa, creatinfosfocinasa, calcio y magnesio. Conclusiones. De los 24 constituyentes estudiados, 15 presentaron interferencia clínicamente significativa. Se recomienda que cada laboratorio investigue los efectos de dicha interferencia empleando sus propios métodos, reactivos o instrumentos.

The systematic and random errors determination using realtime 3D surface tracking system in breast cancer

The purpose of this study to determine the patient setup uncertainties in deep inspiration breath-hold (DIBH) radiation therapy for left breast cancer patients using real-time 3D surface tracking system. The six breast cancer patients treated by 6 MV photon beams from TrueBeam linear accelerator were selected. The patient setup errors and motion during treatment were observed and calculated for interfraction and intrafraction motions. The systematic and random errors were calculated in vertical, longitudinal and lateral directions. From 180 images tracking before and during treatment, the maximum systematic error of interfraction and intrafraction motions were 0.56 mm and 0.23 mm, the maximum random error of interfraction and intrafraction motions were 1.18 mm and 0.53 mm, respectively. The interfraction was more pronounce than the intrafraction, while the systematic error was less impact than random error. In conclusion the intrafraction motion error from patient setup uncertainty is about half of interfraction motion error, which is less impact due to the stability in organ movement from DIBH. The systematic reproducibility is also half of random error because of the high efficiency of modern linac machine that can reduce the systematic uncertainty effectively, while the random errors is uncontrollable.

Interferencia causada por hemólisis en la determinación de 25 constituyentes bioquímicos en el autoanalizador ADVIA 1800

Introducción. La interferencia por hemólisis es la principal causa de rechazo preanalítico demuestras de suero en el laboratorio clínico. Objetivos. Conocer y cuantificar la posible interferencia producida por hemólisis en la medición rutinaria de 25 constituyentes bioquímicos en el autoanalizador ADVIA 1800, empleando para ello el criterio de interferencia clínicamente relevante, cuando se supera el máximo error sistemático deseable. Diseño. Estudio descriptivo comparativo. Institución. Hospital Edgardo Rebagliati Martins, EsSalud, Lima, Perú. Material biológico. Muestras sanguíneas proveniente de sujetos voluntarios. Intervenciones. Se añadió cantidades crecientes de hemoglobina (0,26 g/L, 0,53 g/L, 1,05 g/L, 2,10 g/L, 3,25 g/L, 4,30 g/L y 5,25 g/L) a siete diferentes alícuotas de una mezcla de sueros y se determinó en ellas por duplicado la influencia del interferente en los 25 constituyentes. Se ha seguido el protocolo de la Sociedad Española de Química Clínica. Principales medidas de resultados. Porcentaje relativo de desviación de la concentración del constituyente por influencia de la hemólisis, con respecto a la muestra sin interferente. Resultados. Los constituyentes urea, creatinina, ácido úrico, bilirrubina total, HDL colesterol, LDL colesterol, triglicéridos, calcio y gammaglutamiltransferasa, no presentaron interferencia, mientras que se observó interferencia para glucosa, proteínas, albúmina, colesterol, potasio, fósforo, magnesio, láctico deshidrogenasa, creatinfosfocinasa, aspartato aminotransferasa, alanino aminotransferasa, lipasa, sodio, cloro, fosfatasa alcalina y amilasa. Conclusiones. De los 25 constituyentes estudiados, 16 presentaron interferencia clínicamente significativa. Se recomienda que cada laboratorio investigue los efectos de dicha interferencia empleando sus propios métodos, reactivos o instrumentos.

Automated stereo-photogrammetric DEM generation at high latitudes: Surface Extraction with TIN-based Search-space Minimization (SETSM) validation and demonstration over glaciated regions

Digital elevation models (DEMs) are critical to a wide range of geoscience investigations. High-latitude and polar regions are particularly challenging for automated, stereo-photogrammetric DEM extraction due to the abundance of surfaces that are low-contrast and repetitively textured, such as snow and shadowed terrain, and have discontinuities such as in crevasse fields, glacier calving faces or iceberg edges. Sub-meter, stereo-mode satellite imagery of high geometric and radiometric quality is becoming increasingly accessible, offering the potential for dramatically increasing the spatial coverage and quality of high-latitude DEMs. Here we demonstrate and validate automated DEMs generated from the Surface Extraction with Triangulated Irregular Network-based Search-space Minimization (SETSM) algorithm designed for these challenging terrains using only the satellite rational polynomial coefficients (RPCs). Comparison between 2-m DEMs created from WorldView image pairs and low-altitude LiDAR point clouds in west Greenland give DEM biases of less than 5 m, which is the maximum systematic RPC error. Co-registration with the LiDAR data reduces the DEM RMS error to ~20 cm, which is comparable to the uncertainty of the LiDAR data. We demonstrate SETSM’s automatic RPC refinement and bias reduction by successfully extracting a high-quality DEM from Pleiades stereo pair images with large RPC errors. Finally, we provide examples of SETSM DEMs that demonstrate their utility for a range of applications of interest to polar scientists.

Effects of Bronchoconstriction, Minute Ventilation, and Deep Inspiration on the Composition of Exhaled Breath Condensate

Exhaled breath condensate (EBC) is composed of droplets of airway surface liquid (ASL) diluted by water vapor. The goal of this study was to determine if the composition of EBC is affected by changes in airway caliber, minute ventilation, or forceful exhalation, factors that may differ among subjects with asthma in cross-sectional studies. In a group of subjects with asthma, we measured the effects of the following: (1) a series of three deep-inspiration and forceful-exhalation maneuvers; (2) a doubling of minute ventilation; and (3) acute bronchoconstriction induced by methacholine on EBC volume, dilution of ASL, and concentration of cysteinyl leukotrienes (CysLTs). With the exception of an increase in EBC volume with increased minute ventilation, there were no significant changes in the volume, dilution, or levels of CysLTs in EBC introduced by each of these factors. The CIs surrounding the differences introduced by each factor showed that the maximum systematic errors due to these factors were modest. These results indicate that changes in airway caliber, minute ventilation, or breathing pattern among subjects with asthma do not significantly alter the measurements of mediator concentrations in EBC.

An empirical method to estimate the viscosity of mineral oil by means of ultrasonic attenuation

This paper presents an empirical method for measuring the viscosity of mineral oil. In a built-in pipeline application, conventional ultrasonic methods using shear reflectance or rheological and acoustical phenomena may fail because of attenuated shear wave propagation and an unpredictable spreading loss caused by protective housings and comparable main flows. The empirical method utilizing longitudinal waves eliminates the unknown spreading loss from attenuation measurements on the object fluid by removing the normalized spreading loss per focal length with the measurement of a reference fluid of a known acoustic absorption coefficient. The ultrasonic attenuation of fresh water as the reference fluid and mineral oil as the object fluid were measured along with the sound speed and effective frequency. The empirical equation for the spreading loss in the reference fluid is determined by high-order polynomial fitting. To estimate the shear viscosity of the mineral oil, a linear fit is applied to the total loss difference between the two fluids, whose slope (the absorption coefficient) is combined with an assumed shear-to-volume viscosity relation. The empirical method predicted the viscosities of two types of the mineral oil with a maximum statistical uncertainty of 8.8% and a maximum systematic error of 12.5% compared with directly measured viscosity using a glass-type viscometer. The validity of this method was examined by comparison with the results from theoretical far-field spreading.

TargetSearch - a Bioconductor package for the efficient preprocessing of GC-MS metabolite profiling data

BackgroundMetabolite profiling, the simultaneous quantification of multiple metabolites in an experiment, is becoming increasingly popular, particularly with the rise of systems-level biology. The workhorse in this field is gas-chromatography hyphenated with mass spectrometry (GC-MS). The high-throughput of this technology coupled with a demand for large experiments has led to data pre-processing, i.e. the quantification of metabolites across samples, becoming a major bottleneck. Existing software has several limitations, including restricted maximum sample size, systematic errors and low flexibility. However, the biggest limitation is that the resulting data usually require extensive hand-curation, which is subjective and can typically take several days to weeks.ResultsWe introduce the TargetSearch package, an open source tool which is a flexible and accurate method for pre-processing even very large numbers of GC-MS samples within hours. We developed a novel strategy to iteratively correct and update retention time indices for searching and identifying metabolites. The package is written in the R programming language with computationally intensive functions written in C for speed and performance. The package includes a graphical user interface to allow easy use by those unfamiliar with R.ConclusionsTargetSearch allows fast and accurate data pre-processing for GC-MS experiments and overcomes the sample number limitations and manual curation requirements of existing software. We validate our method by carrying out an analysis against both a set of known chemical standard mixtures and of a biological experiment. In addition we demonstrate its capabilities and speed by comparing it with other GC-MS pre-processing tools. We believe this package will greatly ease current bottlenecks and facilitate the analysis of metabolic profiling data.

Quantitative proton magnetic resonance spectroscopy without water suppression

The suppression of the abundant water signal has been traditionally employed to decrease the dynamic range of the NMR signal in proton MRS (1H MRS) in vivo. When using this approach, if the intent is to utilize the water signal as an internal reference for the absolute quantification of metabolites, additional measurements are required for the acquisition of the water signal. This can be prohibitively time-consuming and is not desired clinically. Additionally, traditional water suppression can lead to metabolite alterations. This can be overcome by performing quantitative 1H MRS without water suppression. However, the non-water-suppressed spectra suffer from gradient-induced frequency modulations, resulting in sidebands in the spectrum. Sidebands may overlap with the metabolites, which renders the spectral analysis and quantification problematic. In this paper, we performed absolute quantification of metabolites without water suppression. Sidebands were removed by utilizing the phase of an external reference signal of single resonance to observe the time-varying the static field fluctuations induced by gradient-vibration and deconvolving this phase contamination from the desired NMR signal. The quantification of metabolites was determined after sideband correction by calibrating the metabolite signal intensities against the recorded water signal. The method was evaluated by phantom and in vivo measurements in human brain. The maximum systematic error for the quantified metabolite concentrations was found to be 10.8%, showing the feasibility of the quantification after sideband correction.