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PyDREAM: high-dimensional parameter inference for biological models in python.
Shockley EM, Vrugt JA, Lopez CF
(2018) Bioinformatics 34: 695-697
MeSH Terms: Algorithms, Calibration, Computational Biology, Markov Chains, Models, Biological, Monte Carlo Method, Software, Uncertainty
Show Abstract · Added March 14, 2018
Summary - Biological models contain many parameters whose values are difficult to measure directly via experimentation and therefore require calibration against experimental data. Markov chain Monte Carlo (MCMC) methods are suitable to estimate multivariate posterior model parameter distributions, but these methods may exhibit slow or premature convergence in high-dimensional search spaces. Here, we present PyDREAM, a Python implementation of the (Multiple-Try) Differential Evolution Adaptive Metropolis [DREAM(ZS)] algorithm developed by Vrugt and ter Braak (2008) and Laloy and Vrugt (2012). PyDREAM achieves excellent performance for complex, parameter-rich models and takes full advantage of distributed computing resources, facilitating parameter inference and uncertainty estimation of CPU-intensive biological models.
Availability and implementation - PyDREAM is freely available under the GNU GPLv3 license from the Lopez lab GitHub repository at http://github.com/LoLab-VU/PyDREAM.
Contact - c.lopez@vanderbilt.edu.
Supplementary information - Supplementary data are available at Bioinformatics online.
© The Author(s) 2017. Published by Oxford University Press.
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8 MeSH Terms
An Interlaboratory Evaluation of Drift Tube Ion Mobility-Mass Spectrometry Collision Cross Section Measurements.
Stow SM, Causon TJ, Zheng X, Kurulugama RT, Mairinger T, May JC, Rennie EE, Baker ES, Smith RD, McLean JA, Hann S, Fjeldsted JC
(2017) Anal Chem 89: 9048-9055
MeSH Terms: Calibration, Ion Mobility Spectrometry, Laboratories, Lipids, Mass Spectrometry, Molecular Structure, Nitrogen, Proteins, Reproducibility of Results
Show Abstract · Added December 17, 2018
Collision cross section (CCS) measurements resulting from ion mobility-mass spectrometry (IM-MS) experiments provide a promising orthogonal dimension of structural information in MS-based analytical separations. As with any molecular identifier, interlaboratory standardization must precede broad range integration into analytical workflows. In this study, we present a reference drift tube ion mobility mass spectrometer (DTIM-MS) where improvements on the measurement accuracy of experimental parameters influencing IM separations provide standardized drift tube, nitrogen CCS values (CCS) for over 120 unique ion species with the lowest measurement uncertainty to date. The reproducibility of these CCS values are evaluated across three additional laboratories on a commercially available DTIM-MS instrument. The traditional stepped field CCS method performs with a relative standard deviation (RSD) of 0.29% for all ion species across the three additional laboratories. The calibrated single field CCS method, which is compatible with a wide range of chromatographic inlet systems, performs with an average, absolute bias of 0.54% to the standardized stepped field CCS values on the reference system. The low RSD and biases observed in this interlaboratory study illustrate the potential of DTIM-MS for providing a molecular identifier for a broad range of discovery based analyses.
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9 MeSH Terms
Evaluation of Collision Cross Section Calibrants for Structural Analysis of Lipids by Traveling Wave Ion Mobility-Mass Spectrometry.
Hines KM, May JC, McLean JA, Xu L
(2016) Anal Chem 88: 7329-36
MeSH Terms: Calibration, Ions, Nitrogen, Peptides, Phosphatidylcholines, Phosphatidylethanolamines, Spectrometry, Mass, Electrospray Ionization
Show Abstract · Added December 17, 2018
Collision cross section (CCS) measurement of lipids using traveling wave ion mobility-mass spectrometry (TWIM-MS) is of high interest to the lipidomics field. However, currently available calibrants for CCS measurement using TWIM are predominantly peptides that display quite different physical properties and gas-phase conformations from lipids, which could lead to large CCS calibration errors for lipids. Here we report the direct CCS measurement of a series of phosphatidylcholines (PCs) and phosphatidylethanolamines (PEs) in nitrogen using a drift tube ion mobility (DTIM) instrument and an evaluation of the accuracy and reproducibility of PCs and PEs as CCS calibrants for phospholipids against different classes of calibrants, including polyalanine (PolyAla), tetraalkylammonium salts (TAA), and hexakis(fluoroalkoxy)phosphazines (HFAP), in both positive and negative modes in TWIM-MS analysis. We demonstrate that structurally mismatched calibrants lead to larger errors in calibrated CCS values while the structurally matched calibrants, PCs and PEs, gave highly accurate and reproducible CCS values at different traveling wave parameters. Using the lipid calibrants, the majority of the CCS values of several classes of phospholipids measured by TWIM are within 2% error of the CCS values measured by DTIM. The development of phospholipid CCS calibrants will enable high-accuracy structural studies of lipids and add an additional level of validation in the assignment of identifications in untargeted lipidomics experiments.
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MeSH Terms
Automatic tracking of intraoperative brain surface displacements in brain tumor surgery.
Kumar AN, Miga MI, Pheiffer TS, Chambless LB, Thompson RC, Dawant BM
(2014) Conf Proc IEEE Eng Med Biol Soc 2014: 1509-12
MeSH Terms: Algorithms, Brain, Brain Mapping, Brain Neoplasms, Calibration, Humans, Image Processing, Computer-Assisted, Imaging, Three-Dimensional, Microscopy, Video, Models, Statistical, Neurosurgery, Neurosurgical Procedures, Reproducibility of Results, Surgery, Computer-Assisted, Video Recording
Show Abstract · Added February 12, 2015
In brain tumor surgery, soft-tissue deformation, known as brain shift, introduces inaccuracies in the application of the preoperative surgical plan and impedes the advancement of image-guided surgical (IGS) systems. Considerable progress in using patient-specific biomechanical models to update the preoperative images intraoperatively has been made. These model-update methods rely on accurate intraoperative 3D brain surface displacements. In this work, we investigate and develop a fully automatic method to compute these 3D displacements for lengthy (~15 minutes) stereo-pair video sequences acquired during neurosurgery. The first part of the method finds homologous points temporally in the video and the second part computes the nonrigid transformation between these homologous points. Our results, based on parts of 2 clinical cases, show that this speedy and promising method can robustly provide 3D brain surface measurements for use with model-based updating frameworks.
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15 MeSH Terms
Standardizing accelerometer-based activity monitor calibration and output reporting.
Coolbaugh CL, Hawkins DA
(2014) J Appl Biomech 30: 594-7
MeSH Terms: Acceleration, Accelerometry, Calibration, Equipment Failure Analysis, Reference Standards, Reproducibility of Results, Sensitivity and Specificity, Transducers, United States
Show Abstract · Added September 15, 2014
Wearable accelerometer-based activity monitors (AMs) are used to estimate energy expenditure and ground reaction forces in free-living environments, but a lack of standardized calibration and data reporting methods limits their utility. The objectives of this study were to (1) design an inexpensive and easily reproducible AM testing system, (2) develop a standardized calibration method for accelerometer-based AMs, and (3) evaluate the utility of the system and accuracy of the calibration method. A centrifuge-type device was constructed to apply known accelerations (0-8g) to each sensitive axis of 30 custom and two commercial AMs. Accelerometer data were recorded and matrix algebra and a least squares solution were then used to determine a calibration matrix for the custom AMs to convert raw accelerometer output to units of g's. Accuracy was tested by comparing applied and calculated accelerations for custom and commercial AMs. AMs were accurate to within 4% of applied accelerations. The relatively inexpensive AM testing system (< $100) and calibration method has the potential to improve the sharing of AM data, the ability to compare data from different studies, and the accuracy of AM-based models to estimate various physiological and biomechanical quantities of interest in field-based assessments of physical activity.
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9 MeSH Terms
Toward rapid, high-sensitivity, volume-constrained biomarker quantification and validation using backscattering interferometry.
Olmsted IR, Hassanein M, Kussrow A, Hoeksema M, Li M, Massion PP, Bornhop DJ
(2014) Anal Chem 86: 7566-74
MeSH Terms: Antigens, Neoplasm, Biomarkers, Tumor, Calibration, Enzyme-Linked Immunosorbent Assay, Galectins, Humans, Keratin-19, Limit of Detection, Lung Neoplasms
Show Abstract · Added February 2, 2015
Realizing personalized medicine, which promises to enable early disease detection, efficient diagnostic staging, and therapeutic efficacy monitoring, hinges on biomarker quantification in patient samples. Yet, the lack of a sensitive technology and assay methodology to rapidly validate biomarker candidates continues to be a bottleneck for clinical translation. In our first direct and quantitative comparison of backscattering interferometry (BSI) to fluorescence sensing by ELISA, we show that BSI could aid in overcoming this limitation. The analytical validation study was performed against ELISA for two biomarkers for lung cancer detection: Cyfra 21-1 and Galectin-7. Spiked serum was used for calibration and comparison of analytical figures of merit, followed by analysis of blinded patient samples. Using the ELISA antibody as the probe chemistry in a mix-and-read assay, BSI provided significantly lower detection limits for spiked serum samples with each of the biomarkers. The limit of quantification (LOQ) for Cyrfa-21-1 was measured to be 230 pg/mL for BSI versus 4000 pg/mL for ELISA, and for Galectin-7, it was 13 pg/mL versus 500 pg/mL. The coefficient of variation for 5 day, triplicate determinations was <15% for BSI and <10% for ELISA. The two techniques correlated well, ranging from 3-29% difference for Cyfra 21-1 in a blinded patient sample analysis. The label-free and free-solution operation of BSI allowed for a significant improvement in analysis speed, with greater ease, improved LOQ values, and excellent day-to-day reproducibility. In this unoptimized format, BSI required 5.5-fold less sample quantity needed for ELISA (a 10 point calibration curve measured in triplicate required 36 μL of serum for BSI vs 200 μL for ELISA). The results indicate that the BSI platform can enable rapid, sensitive analytical validation of serum biomarkers and should significantly impact the validation bottleneck of biomarkers.
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9 MeSH Terms
Quantum dot-based single-molecule microscopy for the study of protein dynamics.
Chang JC, Rosenthal SJ
(2013) Methods Mol Biol 1026: 71-84
MeSH Terms: Calibration, Cell Survival, HeLa Cells, Humans, Microscopy, Proteins, Quantum Dots
Show Abstract · Added May 27, 2014
Real-time microscopic visualization of single molecules in living cells provides a molecular perspective of cellular dynamics, which is difficult to be observed by conventional ensemble techniques. Among various classes of fluorescent tags used in single-molecule tracking, quantum dots are particularly useful due to their unique photophysical properties. This chapter provides an overview of single quantum dot tracking for protein dynamic studies. First, we review the fundamental diffraction limit of conventional optical systems and recent developments in single-molecule detection beyond the diffraction barrier. Second, we describe methods to prepare water-soluble quantum dots for biological labeling and single-molecule microscopy experimental design. Third, we provide detailed methods to perform quantum dot-based single-molecule microscopy. This technical section covers three protocols including (1) imaging system calibration using spin-coated single quantum dots, (2) single quantum dot labeling in living cells, and (3) tracking algorithms for single-molecule analysis.
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7 MeSH Terms
Calibrating a population-based job-exposure matrix using inspection measurements to estimate historical occupational exposure to lead for a population-based cohort in Shanghai, China.
Koh DH, Bhatti P, Coble JB, Stewart PA, Lu W, Shu XO, Ji BT, Xue S, Locke SJ, Portengen L, Yang G, Chow WH, Gao YT, Rothman N, Vermeulen R, Friesen MC
(2014) J Expo Sci Environ Epidemiol 24: 9-16
MeSH Terms: Adult, Aged, Air Pollutants, Occupational, Calibration, China, Cohort Studies, Dust, Female, Humans, Industry, Lead, Middle Aged, Occupational Exposure, Occupations, Retrospective Studies
Show Abstract · Added March 24, 2014
The epidemiologic evidence for the carcinogenicity of lead is inconsistent and requires improved exposure assessment to estimate risk. We evaluated historical occupational lead exposure for a population-based cohort of women (n=74,942) by calibrating a job-exposure matrix (JEM) with lead fume (n=20,084) and lead dust (n=5383) measurements collected over four decades in Shanghai, China. Using mixed-effect models, we calibrated intensity JEM ratings to the measurements using fixed-effects terms for year and JEM rating. We developed job/industry-specific estimates from the random-effects terms for job and industry. The model estimates were applied to subjects' jobs when the JEM probability rating was high for either job or industry; remaining jobs were considered unexposed. The models predicted that exposure increased monotonically with JEM intensity rating and decreased 20-50-fold over time. The cumulative calibrated JEM estimates and job/industry-specific estimates were highly correlated (Pearson correlation=0.79-0.84). Overall, 5% of the person-years and 8% of the women were exposed to lead fume; 2% of the person-years and 4% of the women were exposed to lead dust. The most common lead-exposed jobs were manufacturing electronic equipment. These historical lead estimates should enhance our ability to detect associations between lead exposure and cancer risk in the future epidemiologic analyses.
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15 MeSH Terms
Quantitative metrics in clinical radiology reporting: a snapshot perspective from a single mixed academic-community practice.
Abramson RG, Su PF, Shyr Y
(2012) Magn Reson Imaging 30: 1357-66
MeSH Terms: Academic Medical Centers, Calibration, Data Interpretation, Statistical, Decision Making, Diagnostic Imaging, Humans, Magnetic Resonance Imaging, Prevalence, Radiographic Image Interpretation, Computer-Assisted, Radiology, Reproducibility of Results, Retrospective Studies, Tomography, X-Ray Computed
Show Abstract · Added March 7, 2014
Quantitative imaging has emerged as a leading priority on the imaging research agenda, yet clinical radiology has traditionally maintained a skeptical attitude toward numerical measurement in diagnostic interpretation. To gauge the extent to which quantitative reporting has been incorporated into routine clinical radiology practice, and to offer preliminary baseline data against which the evolution of quantitative imaging can be measured, we obtained all clinical computed tomography (CT) and magnetic resonance imaging (MRI) reports from two randomly selected weekdays in 2011 at a single mixed academic-community practice and evaluated those reports for the presence of quantitative descriptors. We found that 44% of all reports contained at least one "quantitative metric" (QM), defined as any numerical descriptor of a physical property other than quantity, but only 2% of reports contained an "advanced quantitative metric" (AQM), defined as a numerical parameter reporting on lesion function or composition, excluding simple size and distance measurements. Possible reasons for the slow translation of AQMs into routine clinical radiology reporting include perceptions that the primary clinical question may be qualitative in nature or that a qualitative answer may be sufficient; concern that quantitative approaches may obscure important qualitative information, may not be adequately validated, or may not allow sufficient expression of uncertainty; the feeling that "gestalt" interpretation may be superior to quantitative paradigms; and practical workflow limitations. We suggest that quantitative imaging techniques will evolve primarily as dedicated instruments for answering specific clinical questions requiring precise and standardized interpretation. Validation in real-world settings, ease of use, and reimbursement economics will all play a role in determining the rate of translation of AQMs into broad practice.
Copyright © 2012 Elsevier Inc. All rights reserved.
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13 MeSH Terms
Advances in preclinical SPECT instrumentation.
Peterson TE, Shokouhi S
(2012) J Nucl Med 53: 841-4
MeSH Terms: Animals, Calibration, Humans, Image Processing, Computer-Assisted, Tomography, Emission-Computed, Single-Photon
Show Abstract · Added May 30, 2014
Preclinical SPECT of rodents is both in demand and very demanding. The need for high spatial resolution in combination with good sensitivity has given rise to considerable innovation in the areas of detectors, collimation, acquisition geometry, and image reconstruction. Some of the developments described herein are beginning to carry over into clinical imaging as well.
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5 MeSH Terms