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Deconvolution

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https://www.readbyqxmd.com/read/28933113/-evaluation-of-pharmacokinetics-and-in-vitro-in-vivo-correlation-of-ibuprofen-with-essential-oils-as-penetration-enhancer-following-transdermal-administration
#1
Qiu-Dong Jiang, Ye-Ming Wu, Hui Zhang, Pei Liu, Jun Chen, Jin-Ao Duan
The study was carried out to investigate the pharmacokinetics and in vitro/in vivo correlation of ibuprofen with essential oils as penetration enhancers (PE) following transdermal administration. With Azone as the positive control, ibuprofen hydrogels containing Chuanxiong oil, Angelica oil or Cinnamon oil as PE were prepared and administered to the rat abdominal skin. Then the pharmacokinetics of ibuprofen following transdermal administration were investigated and compared. In comparison with negative control (no PE was added), the relative bioavailability values with the addition of Chuanxiong oil, Angelica oil, Cinnamon oil and Azone as PE were determined to be 161...
December 2016: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/28932758/iterative-image-processing-for-early-diagnostic-of-beta-amyloid-plaque-deposition-in-pre-clinical-alzheimer-s-disease-studies
#2
Nikolai V Slavine, Padmakar V Kulkarni, Roderick W McColl
PURPOSE: To test and evaluate an efficient iterative image processing strategy to improve the quality of sub-optimal pre-clinical PET images. A novel iterative resolution subsets-based method to reduce noise and enhance resolution (RSEMD) has been demonstrated on examples of PET imaging studies of Alzheimer's disease (AD) plaques deposition in mice brains. MATERIALS AND METHODS: The RSEMD method was applied to imaging studies of non-invasive detection of beta-amyloid plaque in transgenic mouse models of AD...
August 2017: Journal of Applied Bioinformatics & Computational Biology
https://www.readbyqxmd.com/read/28931946/comparison-of-perfusion-models-for-quantitative-t1-weighted-dce-mri-of-rectal-cancer
#3
Tanja Gaa, Wiebke Neumann, Sonja Sudarski, Ulrike I Attenberger, Stefan O Schönberg, Lothar R Schad, Frank G Zöllner
In this work, the two compartment exchange model and two compartment uptake model were applied to obtain quantitative perfusion parameters in rectum carcinoma and the results were compared to those obtained by the deconvolution algorithm. Eighteen patients with newly diagnosed rectal carcinoma underwent 3 T MRI of the pelvis including a T1 weighted dynamic contrastenhanced (DCE) protocol before treatment. Mean values for Plasma Flow (PF), Plasma Volume (PV) and Mean Transit Time (MTT) were obtained for all three approaches and visualized in parameter cards...
September 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28929836/the-relationship-between-blood-flow-impairment-and-oxygen-depletion-in-acute-ischemic-stroke-imaged-with-magnetic-resonance-imaging
#4
Alexander Seiler, Nicholas P Blockley, Ralf Deichmann, Ulrike Nöth, Oliver C Singer, Michael A Chappell, Johannes C Klein, Marlies Wagner
Oxygenation-sensitive spin relaxation time T2' and relaxation rate R2' (1/T2') are presumed to be markers of the cerebral oxygen extraction fraction (OEF) in acute ischemic stroke. In this study, we investigate the relationship of T2'/R2' with dynamic susceptibility contrast-based relative cerebral blood flow (rCBF) in acute ischemic stroke to assess their plausibility as surrogate markers of the ischemic penumbra. Twenty-one consecutive patients with internal carotid artery and/or middle cerebral artery occlusion were studied at 3...
January 1, 2017: Journal of Cerebral Blood Flow and Metabolism
https://www.readbyqxmd.com/read/28929760/a-classic-azo-dye-agglomeration-system-evidence-for-slow-continuous-nucleation-autocatalytic-agglomerative-growth-plus-the-effects-of-dust-removal-by-microfiltration-on-the-kinetics
#5
Saim Özkar, Richard G Finke
An important but virtually ignored 1978 paper by Reeves and co-workers, which examined a dye-OAc hydrolysis and then agglomeration system, is reanalyzed in light of current state of knowledge of nucleation and growth/agglomeration phenomena. The Finke-Watzky two-step mechanism is used to account quantitatively for the kinetics data, in turn providing deconvolution of dye hydrolysis and nucleation of agglomerative growth, from the agglomerative growth step, including their separate rate constants. Significantly, the effects of microfiltration of the removable dust on the two steps and their rate constants are uncovered and quantitated for the first time, including the finding that the presence of dust accelerates both steps by ca...
September 20, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28924329/a-computational-tool-for-accelerated-analysis-of-oligomeric-proanthocyanidins-in-plants
#6
Mengliang Zhang, Jianghao Sun, Pei Chen
A computational tool was developed to facilitate proanthocyanidin analysis using data collected by ultra-high-performance liquid chromatography-diode array detection-high resolution accurate mass-mass spectrometry (UHPLC-DAD-HRAM-MS). Both identification and semi-quantitation of proanthocyanidins can be achieved by the developed computational tool. It can extract proanthocyanidin chromatographic peaks, deconvolute the isotopic patterns of A-type, B-type, and multi-charged proanthocyanidins ions, and predict proanthocyanidin structures...
March 2017: Journal of Food Composition and Analysis
https://www.readbyqxmd.com/read/28922119/pure-let-image-deconvolution
#7
Jizhou Li, Florian Luisier, Thierry Blu
We propose a non-iterative image deconvolution algorithm for data corrupted by Poisson or mixed Poisson-Gaussian noise. Many applications involve such a problem, ranging from astronomical to biological imaging. We parametrize the deconvolution process as a linear combination of elementary functions, termed as linear expansion of thresholds (LET). This parametrization is then optimized by minimizing a robust estimate of the true mean squared error, the Poisson unbiased risk estimate (PURE). Each elementary function consists of a Wiener filtering followed by a pointwise thresholding of undecimated Haar wavelet coefficients...
September 18, 2017: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/28917822/chemgenie-integration-of-chemogenomics-data-for-applications-in-chemical-biology
#8
REVIEW
Peter S Kutchukian, Charlie Chang, Sean J Fox, Erica Cook, Richard Barnard, David Tellers, Huijun Wang, Dante Pertusi, Meir Glick, Robert P Sheridan, Iain Wallace, Anne Mai Wassermann
Increasing amounts of biological data are accumulating in the pharmaceutical industry and academic institutions. However, data do not equal actionable information, and guidelines for appropriate data capture, harmonization, integration, mining, and visualization need to be established to fully harness their potential. Here, we describe ongoing efforts at Merck & Co. to structure data in the area of chemogenomics. We are integrating complementary data from both internal and external data sources into one chemogenomics database (Chemical Genetic Interaction Enterprise; CHEMGENIE)...
September 14, 2017: Drug Discovery Today
https://www.readbyqxmd.com/read/28914966/monte-carlo-methods-for-nonparametric-regression-with-heteroscedastic-measurement-error
#9
Julie McIntyre, Brent A Johnson, Stephen M Rappaport
Nonparametric regression is a fundamental problem in statistics but challenging when the independent variable is measured with error. Among the first approaches was an extension of deconvoluting kernel density estimators for homescedastic measurement error. The main contribution of this article is to propose a new simulation-based nonparametric regression estimator for the heteroscedastic measurement error case. Similar to some earlier proposals, our estimator is built on principles underlying deconvoluting kernel density estimators...
September 15, 2017: Biometrics
https://www.readbyqxmd.com/read/28913326/improvement-in-white-matter-tract-reconstruction-with-constrained-spherical-deconvolution-and-track-density-mapping-in-low-angular-resolution-data-a-pediatric-study-and-literature-review
#10
Benedetta Toselli, Domenico Tortora, Mariasavina Severino, Gabriele Arnulfo, Andrea Canessa, Giovanni Morana, Andrea Rossi, Marco Massimo Fato
INTRODUCTION: Diffusion-weighted magnetic resonance imaging (DW-MRI) allows noninvasive investigation of brain structure in vivo. Diffusion tensor imaging (DTI) is a frequently used application of DW-MRI that assumes a single main diffusion direction per voxel, and is therefore not well suited for reconstructing crossing fiber tracts. Among the solutions developed to overcome this problem, constrained spherical deconvolution with probabilistic tractography (CSD-PT) has provided superior quality results in clinical settings on adult subjects; however, it requires particular acquisition parameters and long sequences, which may limit clinical usage in the pediatric age group...
2017: Frontiers in Pediatrics
https://www.readbyqxmd.com/read/28912426/deconvolution-of-dna-methylation-identifies-differentially-methylated-gene-regions-on-1p36-across-breast-cancer-subtypes
#11
Alexander J Titus, Gregory P Way, Kevin C Johnson, Brock C Christensen
Breast cancer is a complex disease consisting of four distinct molecular subtypes. DNA methylation-based (DNAm) studies in tumors are complicated further by disease heterogeneity. In the present study, we compared DNAm in breast tumors with normal-adjacent breast samples from The Cancer Genome Atlas (TCGA). We constructed models stratified by tumor stage and PAM50 molecular subtype and performed cell-type reference-free deconvolution to control for cellular heterogeneity. We identified nineteen differentially methylated gene regions (DMGRs) in early stage tumors across eleven genes (AGRN, C1orf170, FAM41C, FLJ39609, HES4, ISG15, KLHL17, NOC2L, PLEKHN1, SAMD11, WASH5P)...
September 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28911941/headspace-solid-phase-microextraction-coupled-to-comprehensive-two-dimensional-gas-chromatography-time-of-flight-mass-spectrometry-for-the-analysis-of-aerosol-from-tobacco-heating-product
#12
Benjamin Savareear, Radoslaw Lizak, Michał Brokl, Chris Wright, Chuan Liu, Jean-Francois Focant
A method involving headspace solid-phase microextraction (HS-SPME) and comprehensive two-dimensional gas chromatography coupled to time-of-flight mass spectrometry (GC×GC-TOFMS) was developed and optimised to elucidate the volatile composition of the particulate phase fraction of aerosol produced by tobacco heating products (THPs). Three SPME fiber types were studied in terms of extraction capacity and precision measurements. Divinylbenzene polydimethylsiloxane appeared as the most efficient coating for these measurements...
September 7, 2017: Journal of Chromatography. A
https://www.readbyqxmd.com/read/28904337/toxoplasma-modulates-signature-pathways-of-human-epilepsy-neurodegeneration-cancer
#13
Huân M Ngô, Ying Zhou, Hernan Lorenzi, Kai Wang, Taek-Kyun Kim, Yong Zhou, Kamal El Bissati, Ernest Mui, Laura Fraczek, Seesandra V Rajagopala, Craig W Roberts, Fiona L Henriquez, Alexandre Montpetit, Jenefer M Blackwell, Sarra E Jamieson, Kelsey Wheeler, Ian J Begeman, Carlos Naranjo-Galvis, Ney Alliey-Rodriguez, Roderick G Davis, Liliana Soroceanu, Charles Cobbs, Dennis A Steindler, Kenneth Boyer, A Gwendolyn Noble, Charles N Swisher, Peter T Heydemann, Peter Rabiah, Shawn Withers, Patricia Soteropoulos, Leroy Hood, Rima McLeod
One third of humans are infected lifelong with the brain-dwelling, protozoan parasite, Toxoplasma gondii. Approximately fifteen million of these have congenital toxoplasmosis. Although neurobehavioral disease is associated with seropositivity, causality is unproven. To better understand what this parasite does to human brains, we performed a comprehensive systems analysis of the infected brain: We identified susceptibility genes for congenital toxoplasmosis in our cohort of infected humans and found these genes are expressed in human brain...
September 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28901611/consistency-based-respiratory-motion-estimation-in-rotational-angiography
#14
Mathias Unberath, André Aichert, Stephan Achenbach, Andreas Maier
PURPOSE: Rotational coronary angiography enables 3D reconstruction but suffers from intra-scan cardiac and respiratory motion. While gating handles cardiac motion, respiratory motion requires compensation. State-of-the-art algorithms rely on 3D-2D registration that depends on initial reconstructions of sufficient quality. We propose a compensation method that is applied directly in projection domain. It overcomes the need for reconstruction and thus complements the state-of-the-art. METHODS: Virtual single-frame background subtraction based on vessel segmentation and spectral deconvolution yields non-truncated images of the contrasted lumen...
September 2017: Medical Physics
https://www.readbyqxmd.com/read/28894859/changes-in-dynamics-of-%C3%AE-chymotrypsin-due-to-covalent-inhibitors-investigated-by-elastic-incoherent-neutron-scattering
#15
C D Andersson, N Martinez, D Zeller, S H Rondahl, M M Koza, B Frick, F Ekström, J Peters, A Linusson
An essential role of enzymes is to catalyze various chemical reactions in the human body and inhibition of the enzymatic activity by small molecules is the mechanism of action of many drugs or tool compounds used to study biological processes. Here, we investigate the effect on the dynamics of the serine protease α-chymotrypsin when in complex with two different covalently bound inhibitors using elastic incoherent neutron scattering. The results show that the inhibited enzyme displays enhanced dynamics compared to the free form...
September 12, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28893506/cytochrome-b561-copper-%C3%AE-cleaved-amyloid-precursor-protein-and-niemann-pick-c1-protein-are-involved-in-ascorbate-induced-release-and-membrane-penetration-of-heparan-sulfate-from-endosomal-s-nitrosylated-glypican-1
#16
Fang Cheng, Lars-Åke Fransson, Katrin Mani
Ascorbate-induced release of heparan sulfate from S-nitrosylated heparan sulfate proteoglycan glypican-1 takes place in endosomes. Heparan sulfate penetrates the membrane and is transported to the nucleus. This process is dependent on copper and on expression and processing of the amyloid precursor protein. It remains unclear how exogenously supplied ascorbate can generate HS-anMan in endosomes and how passage through the membrane is facilitated. Here we have examined wild-type, Alzheimer Tg2576 and amyloid precursor protein (-/-) mouse fibroblasts and human fetal and Niemann-Pick C1 fibroblasts by using deconvolution immunofluorescence microscopy, siRNA technology and [S(35)]sulfate-labeling, vesicle isolation and gel chromatography...
September 9, 2017: Experimental Cell Research
https://www.readbyqxmd.com/read/28881745/whole-tumor-rna-sequencing-and-deconvolution-reveal-a-clinically-prognostic-pten-pi3k-regulated-glioma-transcriptional-signature
#17
Yuan Pan, Erin C Bush, Joseph A Toonen, Yu Ma, Anne C Solga, Peter A Sims, David H Gutmann
The concept that solid tumors are maintained by a productive interplay between neoplastic and non-neoplastic elements has gained traction with the demonstration that stromal fibroblasts and immune system cells dictate cancer development and progression. While less studied, brain tumor (glioma) biology is likewise influenced by non-neoplastic immune system cells (macrophages and microglia) which interact with neoplastic glioma cells to create a unique physiological state (glioma ecosystem) distinct from that found in the normal tissue...
August 8, 2017: Oncotarget
https://www.readbyqxmd.com/read/28879082/hemodynamic-variability-in-soldiers-with-trauma-implications-for-functional-mri-connectivity-studies
#18
D Rangaprakash, Michael N Dretsch, Wenjing Yan, Jeffrey S Katz, Thomas S Denney, Gopikrishna Deshpande
Functional MRI (fMRI) is an indirect measure of neural activity as a result of the convolution of the hemodynamic response function (HRF) and latent (unmeasured) neural activity. Recent studies have shown variability of HRF across brain regions (intra-subject spatial variability) and between subjects (inter-subject variability). Ignoring this HRF variability during data analysis could impair the reliability of such fMRI results. Using whole-brain resting-state fMRI (rs-fMRI), we employed hemodynamic deconvolution to estimate voxel-wise HRF...
2017: NeuroImage: Clinical
https://www.readbyqxmd.com/read/28877871/comparative-nmr-and-nirs-analysis-of-oxygen-dependent-metabolism-in-exercising-finger-flexor-muscles
#19
David Bendahan, Benjamin Chatel, Thomas Jue
Muscle contraction requires the physiology to adapt rapidly to meet the surge in energy demand. To investigate the shift in metabolic control, especially between oxygen and metabolism, researchers often depend on near infrared spectroscopy (NIRS) to measure non-invasively the tissue O2 Because NIRS detects the overlapping myoglobin (Mb) and hemoglobin (Hb) signals in muscle, interpreting the data as an index of cellular or vascular O2 requires deconvoluting the relative contribution. Currently, many in the NIRS field ascribe the signal to Hb...
September 6, 2017: American Journal of Physiology. Regulatory, Integrative and Comparative Physiology
https://www.readbyqxmd.com/read/28875035/classification-of-crystal-structure-using-a-convolutional-neural-network
#20
Woon Bae Park, Jiyong Chung, Jaeyoung Jung, Keemin Sohn, Satendra Pal Singh, Myoungho Pyo, Namsoo Shin, Kee-Sun Sohn
A deep machine-learning technique based on a convolutional neural network (CNN) is introduced. It has been used for the classification of powder X-ray diffraction (XRD) patterns in terms of crystal system, extinction group and space group. About 150 000 powder XRD patterns were collected and used as input for the CNN with no handcrafted engineering involved, and thereby an appropriate CNN architecture was obtained that allowed determination of the crystal system, extinction group and space group. In sharp contrast with the traditional use of powder XRD pattern analysis, the CNN never treats powder XRD patterns as a deconvoluted and discrete peak position or as intensity data, but instead the XRD patterns are regarded as nothing but a pattern similar to a picture...
July 1, 2017: IUCrJ
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