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https://www.readbyqxmd.com/read/28226722/fast-analytical-spectral-filtering-methods-for-magnetic-resonance-perfusion-quantification
#1
Kasireddy V Reddy, Abhishek Mitra, Phaneendra K Yalavarthy, Kasireddy V Reddy, Abhishek Mitra, Phaneendra K Yalavarthy, Abhishek Mitra, Kasireddy V Reddy, Phaneendra K Yalavarthy
The deconvolution in the perfusion weighted imaging (PWI) plays an important role in quantifying the MR perfusion parameters. The PWI application to stroke and brain tumor studies has become a standard clinical practice. The standard approach for this deconvolution is oscillatory-limited singular value decomposition (oSVD) and frequency domain deconvolution (FDD). The FDD is widely recognized as the fastest approach currently available for deconvolution of MR perfusion data. In this work, two fast deconvolution methods (namely analytical fourier filtering and analytical showalter spectral filtering) are proposed...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226714/a-unified-bayesian-based-compensated-magnetic-resonance-imaging
#2
Ameneh Boroomand, Edward Li, Mohammad Javad Shafiee, Masoom A Haider, Farzad Khalvati, Alexander Wong, Ameneh Boroomand, Edward Li, Mohammad Javad Shafiee, Masoom A Haider, Farzad Khalvati, Alexander Wong, Alexander Wong, Mohammad Javad Shafiee, Edward Li, Masoom A Haider, Ameneh Boroomand, Farzad Khalvati
Magnetic resonance (MR) images of higher quality is demanded for helping with more accurate and earlier diagnosis of different diseases. The overall quality of MR images is limited due to the existence of different degradation factors such as (1) MR aberrations due to intrinsic properties of the MR scanner, (2) magnetic field inhomogeneity, and (3) inherent MRI noise. Correcting each MRI degradation factor could be solely useful for the quality enhancement of MR imaging with a limited impact. Here, we propose a unified Bayesian based compensated MR imaging (CMRI) system which jointly corrects for the different aforementioned MR aberrations as well as MR noise and hence generates compensated MR (CMR) images with a higher quality...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226710/quantitative-analysis-of-histological-tissue-image-based-on-cytological-profiles-and-spatial-statistics
#3
Young Hwan Chang, Guillaume Thibault, Vahid Azimi, Brett Johnson, Danielle Jorgens, Jason Link, Adam Margolin, Joe W Gray, Young Hwan Chang, Guillaume Thibault, Vahid Azimi, Brett Johnson, Danielle Jorgens, Jason Link, Adam Margolin, Joe W Gray, Danielle Jorgens, Brett Johnson, Adam Margolin, Young Hwan Chang, Vahid Azimi, Jason Link, Joe W Gray, Guillaume Thibault
The cellular heterogeneity and complex tissue architecture of most tumor samples is a major obstacle in image analysis on standard hematoxylin and eosin-stained (H&E) tissue sections. A mixture of cancer and normal cells complicates the interpretation of their cytological profiles. Furthermore, spatial arrangement and architectural organization of cells are generally not reflected in cellular characteristics analysis. To address these challenges, first we describe an automatic nuclei segmentation of H&E tissue sections...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226531/bayesian-deconvolution-of-scanning-electron-microscopy-images-using-point-spread-function-estimation-and-non-local-regularization
#4
Joris Roels, Jan Aelterman, Jonas De Vylder, Hiep Luong, Yvan Saeys, Wilfried Philips, Joris Roels, Jan Aelterman, Jonas De Vylder, Hiep Luong, Yvan Saeys, Wilfried Philips, Hiep Luong, Wilfried Philips, Jan Aelterman, Jonas De Vylder, Yvan Saeys, Joris Roels
Microscopy is one of the most essential imaging techniques in life sciences. High-quality images are required in order to solve (potentially life-saving) biomedical research problems. Many microscopy techniques do not achieve sufficient resolution for these purposes, being limited by physical diffraction and hardware deficiencies. Electron microscopy addresses optical diffraction by measuring emitted or transmitted electrons instead of photons, yielding nanometer resolution. Despite pushing back the diffraction limit, blur should still be taken into account because of practical hardware imperfections and remaining electron diffraction...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28223349/identification-of-antibody-targets-for-tuberculosis-serology-using-high-density-nucleic-acid-programmable-protein-arrays
#5
Lusheng Song, Garrick Wallstrom, Xiaobo Yu, Marika Hopper, Jennifer Van Duine, Jason Steel, Jin Park, Peter Wiktor, Peter Khan, Al Brunner, Douglas Wilson, Elizabeth R Jenny-Avital, Ji Qiu, Joshua LaBaer, D Mitchell Magee, Jacqueline M Achkar
Better and more diverse biomarkers for the development of simple point-of-care tests for active tuberculosis (TB), a clinically heterogeneous disease, are urgently needed. We generated a proteomic Mycobacterium tuberculosis (Mtb) High-Density Nucleic Acid Programmable Protein Array (HD-NAPPA) that used a novel multiplexed strategy for expedited high-throughput screening for antibody responses to the Mtb proteome. We screened sera from HIV uninfected and co-infected TB patients and controls (n = 120) from the US and South Africa (SA) using the multiplex HD-NAPPA for discovery, followed by deconvolution and validation through single protein HD-NAPPA with biologically independent samples (n=124)...
February 21, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28221356/terahertz-echoes-reveal-the-inhomogeneity-of-aqueous-salt-solutions
#6
Andrey Shalit, Saima Ahmed, Janne Savolainen, Peter Hamm
The structural and dynamical properties of water are known to be affected by ion solvation. However, a consistent molecular picture that describes how and to what extent ions perturb the water structure is still missing. Here we apply 2D Raman-terahertz spectroscopy to investigate the impact of monatomic cations on the relaxation dynamics of the hydrogen-bond network in aqueous salt solutions. The inherent ability of multidimensional spectroscopy to deconvolute heterogeneous relaxation dynamics is used to reveal the correlation between the inhomogeneity of the collective intermolecular hydrogen-bond modes and the viscosity of a salt solution...
March 2017: Nature Chemistry
https://www.readbyqxmd.com/read/28220842/image-processing-in-digital-pathology-an-opportunity-to-solve-inter-batch-variability-of-immunohistochemical-staining
#7
Yves-Rémi Van Eycke, Justine Allard, Isabelle Salmon, Olivier Debeir, Christine Decaestecker
Immunohistochemistry (IHC) is a widely used technique in pathology to evidence protein expression in tissue samples. However, this staining technique is known for presenting inter-batch variations. Whole slide imaging in digital pathology offers a possibility to overcome this problem by means of image normalisation techniques. In the present paper we propose a methodology to objectively evaluate the need of image normalisation and to identify the best way to perform it. This methodology uses tissue microarray (TMA) materials and statistical analyses to evidence the possible variations occurring at colour and intensity levels as well as to evaluate the efficiency of image normalisation methods in correcting them...
February 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28218397/segmentation-of-digitized-histological-sections-for-quantification-of-the-muscularized-vasculature-in-the-mouse-hind-limb
#8
Yiwen Xu, J Geoffrey Pickering, Zengxuan Nong, Aaron D Ward
Immunohistochemical tissue staining enhances microvasculature characteristics, including the smooth muscle in the medial layer of the vessel walls that is responsible for regulation of blood flow. The vasculature can be imaged in a comprehensive fashion using whole-slide scanning. However, since each such image potentially contains hundreds of small vessels, manual vessel delineation and quantification is not practically feasible. In this work, we present a fully automatic segmentation and vasculature quantification algorithm for whole-slide images...
February 20, 2017: Journal of Microscopy
https://www.readbyqxmd.com/read/28216647/an-adaptive-decorrelation-method-removes-illumina-dna-base-calling-errors-caused-by-crosstalk-between-adjacent-clusters
#9
Bo Wang, Lin Wan, Anqi Wang, Lei M Li
Base-calling accuracy is crucial for high-throughput DNA sequencing and downstream analysis such as read mapping and genome assembly. Accordingly, we made an endeavor to reduce DNA sequencing errors of Illumina systems by correcting three kinds of crosstalk in the cluster intensity data. We discovered that signal crosstalk between adjacent clusters accounts for a large portion of sequencing errors in Illumina systems, even after correcting color crosstalk caused by the overlap of dye emission spectra and phasing/pre-phasing caused by out-of-step nucleotide synthesis...
February 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28214548/global-stability-of-an-%C3%AE-ketoglutarate-dependent-dioxygenase-taud-and-its-related-complexes
#10
Kate L Henderson, Mingjie Li, Salette Martinez, Edwin A Lewis, Robert P Hausinger, Joseph P Emerson
BACKGROUND: TauD is a nonheme iron(II) and α-ketoglutarate (αKG) dependent dioxygenase, and a member of a broader family of enzymes that oxidatively decarboxylate αKG to succinate and carbon dioxide thereby activating O2 to perform a range of oxidation reactions. However before O2 activation can occur, these enzymes bind both substrate and cofactor in an effective manner. Here the thermodynamics associated with substrate and cofactor binding to FeTauD are explored. METHODS: Thermal denaturation of TauD and its enzyme-taurine, enzyme-αKG, and enzyme-taurine-αKG complexes are explored using circular dichroism (CD) spectroscopy and differential scanning calorimetry (DSC)...
February 15, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28207900/classification-and-identification-of-rhodobryum-roseum-limpr-and-its-adulterants-based-on-fourier-transform-infrared-spectroscopy-ftir-and-chemometrics
#11
Zhen Cao, Zhenjie Wang, Zhonglin Shang, Jiancheng Zhao
Fourier-transform infrared spectroscopy (FTIR) with the attenuated total reflectance technique was used to identify Rhodobryum roseum from its four adulterants. The FTIR spectra of six samples in the range from 4000 cm-1 to 600 cm-1 were obtained. The second-derivative transformation test was used to identify the small and nearby absorption peaks. A cluster analysis was performed to classify the spectra in a dendrogram based on the spectral similarity. Principal component analysis (PCA) was used to classify the species of six moss samples...
2017: PloS One
https://www.readbyqxmd.com/read/28207386/detection-and-compensation-of-periodic-motion-in-magnetic-particle-imaging
#12
Nadine Gdaniec, Matthias Schluter, Martin Hofmann, Michael Kaul, Kannan Krishnan, Alexander Schlafer, Tobias Knopp
The temporal resolution of the tomographic imaging method magnetic particle imaging (MPI) is remarkably high. The spatial resolution is degraded for measured voltage signal with low signal-to-noise ratio, because the regularization in the image reconstruction step needs to be increased for system-matrix approaches and for deconvolution steps in x-space approaches. To improve the signal-to-noise ratio, block-wise averaging of the signal over time can be advantageous. However, since block-wise averaging decreases the temporal resolution, it prevents resolving the motion...
February 9, 2017: IEEE Transactions on Medical Imaging
https://www.readbyqxmd.com/read/28199790/an-integrated-microfluidic-processor-for-dna-encoded-combinatorial-library-functional-screening
#13
Andrew B MacConnell, Alexander K Price, Brian M Paegel
DNA-encoded synthesis is rekindling interest in combinatorial compound libraries for drug discovery and in technology for automated and quantitative library screening. Here, we disclose a microfluidic circuit that enables functional screens of DNA-encoded compound beads. The device carries out library bead distribution into picoliter-scale assay reagent droplets, photochemical cleavage of compound from the bead, assay incubation, laser-induced fluorescence-based assay detection, and fluorescence-activated droplet sorting to isolate hits...
February 22, 2017: ACS Combinatorial Science
https://www.readbyqxmd.com/read/28194944/achieving-high-spatial-resolution-surface-plasmon-resonance-microscopy-with-image-reconstruction
#14
Hui Yu, Xiaonan Shan, Shaopeng Wang, Nongjian Tao
Surface plasmon resonance microscopy (SPRM) is a powerful platform for biomedical imaging and molecular binding kinetics analysis. However, the spatial resolution of SPRM along the plasmon propagation direction (longitudinal) is determined by the decaying length of the plasmonic wave, which can be as large as tens of microns. Different methods have been proposed to improve the spatial resolution but each at the expense of decreased sensitivity or temporal resolution. Here we present a method to achieve high spatial resolution SPRM based on deconvolution of complex field...
February 8, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28193155/a-comparison-of-reference-based-algorithms-for-correcting-cell-type-heterogeneity-in-epigenome-wide-association-studies
#15
Andrew E Teschendorff, Charles E Breeze, Shijie C Zheng, Stephan Beck
BACKGROUND: Intra-sample cellular heterogeneity presents numerous challenges to the identification of biomarkers in large Epigenome-Wide Association Studies (EWAS). While a number of reference-based deconvolution algorithms have emerged, their potential remains underexplored and a comparative evaluation of these algorithms beyond tissues such as blood is still lacking. RESULTS: Here we present a novel framework for reference-based inference, which leverages cell-type specific DNAse Hypersensitive Site (DHS) information from the NIH Epigenomics Roadmap to construct an improved reference DNA methylation database...
February 13, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28193052/characterization-of-chain-pairing-variants-of-bispecific-igg-expressed-in-a-single-host-cell-by-high-resolution-native-and-denaturing-mass-spectrometry
#16
Luis Schachner, Guanghui Han, Michael Dillon, Jianhui Zhou, Luke McCarty, Diego Ellerman, Yiyuan Yin, Christoph Spiess, Jennie R Lill, Paul J Carter, Wendy Sandoval
Bispecific antibodies, including bispecific IgG, show some promise in clinical trials as a means to extend the therapeutic potential of antibodies. Bispecific IgG can be made by separate expression and purification of each parent half antibody followed by in vitro reconstitution. Generating bispecific IgG by coexpression of two different light and heavy chains in a single host cell is potentially more efficient because it obviates the need for two separate cell lines and purification processes. However, this workflow may produce unwanted mispaired IgG species in addition to the desired bispecific IgG...
December 20, 2016: Analytical Chemistry
https://www.readbyqxmd.com/read/28190837/analysis-of-distribution-and-intraparticle-diffusion-of-a-fluorescent-dye-in-mesoporous-silica-gel-by-confocal-fluorescence-microspectroscopy
#17
Tatsumi Sato, Kiyoharu Nakatani
A micrometer-sized spherical silica gel microparticle (pore diameter, ∼7 nm) was injected into an aqueous rhodamine 6G solution using microcapillary manipulation-injection technique, and the dye distribution in the single microparticle was measured as the fluorescence depth profile by confocal fluorescence microspectroscopy. The fluorescence depth profile was simulated by the convolution and deconvolution methods to correct the contribution of the spatial resolution of the experimental system. The dye homogeneously or heterogeneously distributed in the microparticle at the adsorption equilibrium, dependent on the type of silica gel...
2017: Analytical Sciences: the International Journal of the Japan Society for Analytical Chemistry
https://www.readbyqxmd.com/read/28187332/elimination-of-digital-and-analog-artefacts-from-time-domain-signals
#18
Günter Hempel
A method is described for the elimination of artefacts that arise in time-domain signals because of the presence of digital and analogous filters. Such artefacts are mostly located at the beginning of the free-induction decay (FID). The procedure introduced here is particularly important if at least one signal component decays rather quickly, i.e. if there is only a small number of data containing this component (as for solid-state (1)H or (2)H FIDs). The method is able to restore the original signal by deconvolution of the spectrometer output from the transfer function of the spectrometer console...
February 3, 2017: Solid State Nuclear Magnetic Resonance
https://www.readbyqxmd.com/read/28184256/immunomethylomic-approach-to-explore-the-blood-neutrophil-lymphocyte-ratio-nlr-in-glioma-survival
#19
John K Wiencke, Devin C Koestler, Lucas A Salas, Joseph L Wiemels, Ritu P Roy, Helen M Hansen, Terri Rice, Lucie S McCoy, Paige M Bracci, Annette M Molinaro, Karl T Kelsey, Margaret R Wrensch, Brock C Christensen
BACKGROUND: Differentially methylated regions (DMRs) within DNA isolated from whole blood can be used to estimate the proportions of circulating leukocyte subtypes. We use the term "immunomethylomics" to describe the application of these immune lineage DMRs to studying leukocyte profiles. Here, we applied this approach to peripheral blood DNA from 72 glioma patients with molecularly defined brain tumors, representing common patient groups with defined characteristic survival times and risk factors...
2017: Clinical Epigenetics
https://www.readbyqxmd.com/read/28182582/accelerated-susceptibility-based-positive-contrast-imaging-of-mr-compatible-metallic-devices-based-on-modified-fast-spin-echo-sequences
#20
Caiyun Shi, Guoxi Xie, Yongqin Zhang, Xiaoyong Zhang, Min Chen, Shi Su, Ying Dong, Xin Liu, Jim Ji
This study aims to develop an accelerated susceptibility-based positive contrast MR imaging method for visualizing MR compatible metallic devices. A modified fast spin echo sequence is used to accelerate data acquisition. Each readout gradient in the modified fast spin echo is slightly shifted by a short distance Tshift. Phase changes accumulated within Tshift are then used to calculate the susceptibility map by using a kernel deconvolution algorithm with a regularized ℓ1 minimization. To evaluate the proposed fast spin echo method, three phantom experiments were conducted and compared to a spin echo based technique and the gold standard CT for visualizing biopsy needles and brachytherapy seeds...
February 9, 2017: Physics in Medicine and Biology
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