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Deconvolution

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https://www.readbyqxmd.com/read/28096312/analysis-of-thermoluminescence-glow-curves-using-derivatives-of-different-orders
#1
Mahua Karmakar, S Bhattacharyya, A Sarkar, P S Mazumdar, S D Singh
The suitability of the second derivative method for locating component peaks in complex thermoluminescence (TL) glow curves has been investigated in this work by considering both numerically simulated and experimental TL peaks. This technique is useful to acquire knowledge of the number of component peaks in a complex TL curve which in turn serves as a basic information before applying the deconvolution technique to the glow curve. To check the consistency of the results so obtained, we have also applied the first derivative technique to TL glow curves...
January 16, 2017: Radiation Protection Dosimetry
https://www.readbyqxmd.com/read/28094357/kinetic-analysis-of-non-isothermal-solid-state-reactions-multi-stage-modeling-without-assumptions-in-the-reaction-mechanism
#2
Alexey L Pomerantsev, Alla V Kutsenova, Oxana Ye Rodionova
A novel non-linear regression method for modeling non-isothermal thermogravimetric data is proposed. Experiments for several heating rates are analyzed simultaneously. The method is applicable to complex multi-stage processes when the number of stages is unknown. Prior knowledge of the type of kinetics is not required. The main idea is a consequent estimation of parameters when the overall model is successively changed from one level of modeling to another. At the first level, the Avrami-Erofeev functions are used...
January 17, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28092460/a-three-dimensional-lymphatic-endothelial-cell-tube-formation-assay-to-identify-novel-kinases-involved-in-lymphatic-vessel-remodeling
#3
T Jessica Gambino, Steven P Williams, Carol Caesar, Daniel Resnick, Cameron J Nowell, Rae H Farnsworth, Marc G Achen, Steven A Stacker, Tara Karnezis
The lymphatic system is a series of vessels that transport cells and excess fluid from tissues to the blood vascular system. Normally quiescent, the lymphatics can grow or remodel in response to developmental, immunological, or cells pathological stimuli. Lymphatic vessels comprise lymphatic endothelial cells (LECs) that can respond to external growth factors by undergoing proliferation, migration, adhesion, and tube and lumen formation into new vessel structures, a process known as lymphangiogenesis. To understand the key gene and signaling pathways necessary for lymphangiogenesis and lymphatic vessel remodeling, we have developed a three-dimensional LEC tube formation assay to explore the role of kinase signaling in these processes...
January 2017: Assay and Drug Development Technologies
https://www.readbyqxmd.com/read/28090665/can-patel-s-%C3%AF-accurately-estimate-directionality-of-connections-in-brain-networks-from-fmri
#4
Yunzhi Wang, Olivier David, Xiaoping Hu, Gopikrishna Deshpande
PURPOSE: Investigating directional interactions between brain regions plays a critical role in fully understanding brain function. Consequently, multiple methods have been developed for noninvasively inferring directional connectivity in human brain networks using functional MRI (fMRI). Recent simulations by Smith et al showed that Patel's τ, a method based on higher-order statistics, was the best approach for inferring directional interactions from fMRI. Because simulations make restrictive assumptions about reality, we set out to verify this finding using experimental fMRI data obtained from a three-region network in a rat model with electrophysiological validation...
January 16, 2017: Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine
https://www.readbyqxmd.com/read/28088172/ecotilling-by-sequencing-reveals-polymorphisms-in-genes-encoding-starch-synthases-that-are-associated-with-low-glycemic-response-in-rice
#5
Ramadoss Bharathi Raja, Somanath Agasimani, Sarita Jaiswal, Venkatesan Thiruvengadam, Robin Sabariappan, Ravindra N Chibbar, Sundaram Ganesh Ram
BACKGROUND: Glycemic response, a trait that is tedious to be assayed in cereal staples, has been identified as a factor correlated with alarmingly increasing prevalence of Type II diabetes. Reverse genetics based discovery of allelic variants associated with this nutritional trait gains significance as they can provide scope for genetic improvement of this factor which is otherwise difficult to target through routine screening methods. RESULTS: Through EcoTILLING by sequencing in 512 rice accessions, we report the discovery of six deleterious variants in the genes with potential to increase Resistant Starch (RS) and reduce Hydrolysis Index (HI) of starch...
January 14, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28081561/a-novel-richardson-lucy-model-with-dictionary-basis-and-spatial-regularization-for-isolating-isotropic-signals
#6
Tiantian Xu, Yuanjing Feng, Ye Wu, Qingrun Zeng, Jun Zhang, Jianzhong He, Qichuan Zhuge
Diffusion-weighted magnetic resonance imaging is a non-invasive imaging method that has been increasingly used in neuroscience imaging over the last decade. Partial volume effects (PVEs) exist in sampling signal for many physical and actual reasons, which lead to inaccurate fiber imaging. We overcome the influence of PVEs by separating isotropic signal from diffusion-weighted signal, which can provide more accurate estimation of fiber orientations. In this work, we use a novel response function (RF) and the correspondent fiber orientation distribution function (fODF) to construct different signal models, in which case the fODF is represented using dictionary basis function...
2017: PloS One
https://www.readbyqxmd.com/read/28077880/interleukin-2-receptor-%C3%AE-proximal-promoter-hypomethylation-is-associated-with-multiple-sclerosis
#7
J Field, A Fox, M A Jordan, A G Baxter, T Spelman, M Gresle, H Butzkueven, T J Kilpatrick, J P Rubio
Genetic studies have demonstrated association between single-nucleotide polymorphisms within the IL2RA (interleukin-2 receptor α-subunit) gene and risk of developing multiple sclerosis (MS); however, these variants do not have obvious functional consequences. DNA methylation is a source of genetic variation that could impact on autoimmune disease risk. We investigated DNA methylation of the IL2RA promoter in genomic DNA obtained from peripheral blood mononuclear cells and neural tissue using matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry...
January 12, 2017: Genes and Immunity
https://www.readbyqxmd.com/read/28076381/stain-deconvolution-using-statistical-analysis-of-multi-resolution-stain-colour-representation
#8
Najah Alsubaie, Nicholas Trahearn, Shan E Ahmed Raza, David Snead, Nasir M Rajpoot
Stain colour estimation is a prominent factor of the analysis pipeline in most of histology image processing algorithms. Providing a reliable and efficient stain colour deconvolution approach is fundamental for robust algorithm. In this paper, we propose a novel method for stain colour deconvolution of histology images. This approach statistically analyses the multi-resolutional representation of the image to separate the independent observations out of the correlated ones. We then estimate the stain mixing matrix using filtered uncorrelated data...
2017: PloS One
https://www.readbyqxmd.com/read/28075412/the-antagonistic-effect-of-mycotoxins-deoxynivalenol-and-zearalenone-on-metabolic-profiling-in-serum-and-liver-of-mice
#9
Jian Ji, Pei Zhu, Fangchao Cui, Fuwei Pi, Yinzhi Zhang, Yun Li, Jiasheng Wang, Xiulan Sun
Metabolic profiling in liver and serum of mice was studied for the combined toxic effects of deoxynivalenol (DON) and zearalenone (ZEN), through gas chromatography mass spectrum. The spectrum of serum and liver sample of mice, treated with individual 2 mg/kg DON, 20 mg/kg ZEN, and the combined DON + ZEN with final concentration 2 mg/kg DON and 20 mg/kg ZEN for 21 days, were deconvoluted, aligned and identified with MS DIAL. The data matrix was processed with univariate analysis and multivariate analysis for selection of metabolites with variable importance for the projection (VIP) > 1, t-test p value < 0...
January 10, 2017: Toxins
https://www.readbyqxmd.com/read/28075132/discovery-of-imidazo-1-2-a-pyridine-ethers-and-squaramides-as-selective-and-potent-inhibitors-of-mycobacterial-adenosine-triphosphate-atp-synthesis
#10
Subramanyam J Tantry, Shankar D Markad, Vikas Shinde, Jyothi Bhat, Gayathri Balakrishnan, Amit K Gupta, Anisha Ambady, Anandkumar V Raichurkar, Chaitanyakumar Kedari, Sreevalli Sharma, Naina V Mudugal, Ashwini Narayan, C N Naveen Kumar, Robert Nanduri, Sowmya Bharath, Jitendar Reddy, Vijender Panduga, Prabhakar K R, Karthikeyan Kandaswamy, Ramanatha Saralaya, Parvinder Kaur, Neela Dinesh, Supreeth Guptha, Kirsty Rich, David Murray, Helen Plant, Marian Preston, Helen Ashton, Darren Plant, Jarrod Walsh, Peter Alcock, Kathryn Naylor, Matthew Collier, James Whiteaker, Robert E McLaughlin, Meenakshi Mallya, Manoranjan Panda, Suresh Rudrapatna, Vasanthi Ramachandran, Radha K Shandil, Vasan K Sambandamurthy, Khisimuzi Mdluli, Christopher B Cooper, Harvey Rubin, Takahiro Yano, Pravin S Iyer, Shridhar Narayanan, Stefan Kavanagh, Kakoli Mukherjee, V Balasubramanian, Vinayak P Hosagrahara, Suresh Solapure, Sudha Ravishankar, Shahul Hameed P
The approval of bedaquiline to treat tuberculosis has validated adenosine triphosphate (ATP) synthase as an attractive target to kill Mycobacterium tuberculosis. Herein, we report the discovery of two diverse lead series imidazo[1,2-a]pyridine ethers (IPE) and squaramides (SQA) as inhibitors of mycobacterial ATP-synthesis. Through medicinal chemistry exploration, we established a robust structure activity relationship of these two scaffolds resulting in nanomolar potencies in an ATP-synthesis inhibition assay...
January 11, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28070897/stable-spline-deconvolution-for-dynamic-susceptibility-contrast-mri
#11
Denis Peruzzo, Marco Castellaro, Gianluigi Pillonetto, Alessandra Bertoldo
PURPOSE: To present the stable spline (SS) deconvolution method for the quantification of the cerebral blood flow (CBF) from dynamic susceptibility contrast MRI. METHODS: The SS method was compared with both the block-circulant singular value decomposition (oSVD) and nonlinear stochastic regularization (NSR) methods. oSVD is one of the most popular deconvolution methods in dynamic susceptibility contrast MRI (DSC-MRI). NSR is an alternative approach that we proposed previously...
January 9, 2017: Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine
https://www.readbyqxmd.com/read/28070841/reproducibility-of-dynamic-contrast-enhanced-mri-and-dynamic-susceptibility-contrast-mri-in-the-study-of-brain-gliomas-a-comparison-of-data-obtained-using-different-commercial-software
#12
Gian Marco Conte, Antonella Castellano, Luisa Altabella, Antonella Iadanza, Marcello Cadioli, Andrea Falini, Nicoletta Anzalone
PURPOSE: Dynamic susceptibility contrast MRI (DSC) and dynamic contrast-enhanced MRI (DCE) are useful tools in the diagnosis and follow-up of brain gliomas; nevertheless, both techniques leave the open issue of data reproducibility. We evaluated the reproducibility of data obtained using two different commercial software for perfusion maps calculation and analysis, as one of the potential sources of variability can be the software itself. METHODS: DSC and DCE analyses from 20 patients with gliomas were tested for both the intrasoftware (as intraobserver and interobserver reproducibility) and the intersoftware reproducibility, as well as the impact of different postprocessing choices [vascular input function (VIF) selection and deconvolution algorithms] on the quantification of perfusion biomarkers plasma volume (Vp), volume transfer constant (K (trans)) and rCBV...
January 9, 2017: La Radiologia Medica
https://www.readbyqxmd.com/read/28067513/evolution-of-quantitative-measures-in-nmr-quantum-mechanical-qhnmr-advances-chemical-standardization-of-a-red-clover-trifolium-pratense-extract
#13
Rasika S Phansalkar, Charlotte Simmler, Jonathan Bisson, Shao-Nong Chen, David C Lankin, James B McAlpine, Matthias Niemitz, Guido F Pauli
Chemical standardization, along with morphological and DNA analysis ensures the authenticity and advances the integrity evaluation of botanical preparations. Achievement of a more comprehensive, metabolomic standardization requires simultaneous quantitation of multiple marker compounds. Employing quantitative (1)H NMR (qHNMR), this study determined the total isoflavone content (TIfCo; 34.5-36.5% w/w) via multimarker standardization and assessed the stability of a 10-year-old isoflavone-enriched red clover extract (RCE)...
January 9, 2017: Journal of Natural Products
https://www.readbyqxmd.com/read/28059287/ultrashort-pulses-characterization-by-quantum-state-tomography
#14
Stefan Lerch, André Stefanov
We apply the method of quantum state tomography for the reconstruction of classical laser pulses. The scheme is based on linear inversion, has no need for iterative inversion algorithm or deconvolution, and accounts for partial coherence. The reconstruction protocol is successfully tested on amplitude and phase shaped femtosecond pulses.
December 26, 2016: Optics Express
https://www.readbyqxmd.com/read/28059149/volumetric-light-field-encryption-at-the-microscopic-scale
#15
Haoyu Li, Changliang Guo, Inbarasan Muniraj, Bryce C Schroeder, John T Sheridan, Shu Jia
We report a light-field based method that allows the optical encryption of three-dimensional (3D) volumetric information at the microscopic scale in a single 2D light-field image. The system consists of a microlens array and an array of random phase/amplitude masks. The method utilizes a wave optics model to account for the dominant diffraction effect at this new scale, and the system point-spread function (PSF) serves as the key for encryption and decryption. We successfully developed and demonstrated a deconvolution algorithm to retrieve both spatially multiplexed discrete data and continuous volumetric data from 2D light-field images...
January 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28058728/untargeted-metabolomic-profiling-of-seminal-plasma-in-non-obstructive-azoospermia-men-a-non-invasive-detection-of-spermatogenesis
#16
Kambiz Gilany, Ahmad Mani-Varnosfaderani, Arash Minai-Tehrani, Fateme Mirzajani, Alireza Ghassempour, Mohammed Reza Sadeghi, Mehdi Amini, Hassan Rezadoost
Male factor infertility is involved in almost half of all infertile couples. Lack of the ejaculated sperm due to testicular malfunction has been reported in 6-10% of infertile, a condition named non-obstructive azoospermia (NOA). In this study, we investigated untargeted metabolomic profiling of the seminal plasma in NOA men using gas chromatography-mass spectrometry (GC-MS) and advance chemometrics. In this regard, the seminal plasma fluids of 11 NOA men with TESE-negative (AZN), 9 NOA men with TESE-positive (AZP) and 10 fertile (F) healthy men (as a control group) were collected...
January 6, 2017: Biomedical Chromatography: BMC
https://www.readbyqxmd.com/read/28057586/deconvolutionlab2-an-open-source-software-for-deconvolution-microscopy
#17
REVIEW
Daniel Sage, Lauréne Donati, Ferréol Soulez, Denis Fortun, Guillaume Schmit, Arne Seitz, Romain Guiet, Cédric Vonesch, Michael Unser
Images in fluorescence microscopy are inherently blurred due to the limit of diffraction of light. The purpose of deconvolution microscopy is to compensate numerically for this degradation. Deconvolution is widely used to restore fine details of 3D biological samples. Unfortunately, dealing with deconvolution tools is not straightforward. Among others, end users have to select the appropriate algorithm, calibration and parametrization, while potentially facing demanding computational tasks. To make deconvolution more accessible, we have developed a practical platform for deconvolution microscopy called DeconvolutionLab...
January 2, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28054674/oxidation-defunctionalization-and-catalyst-life-cycle-of-carbon-nanotubes-a-raman-spectroscopy-view
#18
Sergei A Chernyak, Anton S Ivanov, Konstantin I Maslakov, Alexander V Egorov, Zexiang Shen, Serguei S Savilov, Valery V Lunin
Pristine, oxidized and defunctionalized carbon nanotubes (CNTs) were studied by Raman spectroscopy, X-ray diffraction, transmission electron microscopy and low temperature nitrogen adsorption. The Raman spectra of the studied samples in the range of 900-1800 cm(-1) were deconvoluted into five components to reveal the CNT oxidation mechanism. It was found that the oxidation resulted in the reduction of graphite components and ordering of both the structured and defect part of CNTs. Acid treatment also led to different types of disorders in the surface layers of CNTs...
January 18, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28048880/su-f-r-34-quantitative-perfusion-measurement-in-rectal-cancer-using-three-different-pharmacokinetic-models-implications-for-prospective-study-design
#19
K Nie, T Mao, L Shi, N Yue, S Jabbour, S Kim, X Hu, L Qian, X Sun, T Niu
PURPOSE: To compare three different pharmacokinetic models for analysis of dynamic-contrast-enhanced (DCE)-CT data with respect to different acquisition times and location of region of interest. METHODS: Eight rectal cancer patients with pre-treatment DCE-CTs were included. The dynamic sequence started 4-10seconds(s) after the injection of contrast agent. The scan included a 110s acquisition with intervals of 40×1s+15×3s+4×6s. An experienced oncologist outlined the tumor region...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28048584/su-c-207a-04-accuracy-of-acoustic-based-proton-range-verification-in-water
#20
K C Jones, F Vander Stappen, C M Sehgal, S Avery
PURPOSE: To determine the accuracy and dose required for acoustic-based proton range verification (protoacoustics) in water. METHODS: Proton pulses with 17 µs FWHM and instantaneous currents of 480 nA (5.6 × 10(7) protons/pulse, 8.9 cGy/pulse) were generated by a clinical, hospital-based cyclotron at the University of Pennsylvania. The protoacoustic signal generated in a water phantom by the 190 MeV proton pulses was measured with a hydrophone placed at multiple known positions surrounding the dose deposition...
June 2016: Medical Physics
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