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Deconvolution

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https://www.readbyqxmd.com/read/28527313/afm-reconstruction-of-complex-shaped-chiral-plasmonic-nanostructures
#1
A V Kondratov, O Y Rogov, R V Gainutdinov
A significant part of the optical metamaterial phenomena has the plasmonic nature and their investigation requires very accurate knowledge of the fabricated structures shape with a focus on the periodical features. We describe a consistent approach to the shape reconstruction of the plasmonic nanostructures. This includes vertical and tilted spike AFM probes fabrication, AFM imaging and specific post-processing. We studied a complex-shaped chiral metamaterial and conclude that the described post-processing routine extends possibilities of the existing deconvolution algorithms in the case of periodical structures with known rotational symmetry, by providing valuable information about periodical features...
May 11, 2017: Ultramicroscopy
https://www.readbyqxmd.com/read/28523998/uncovering-drug-mechanism-of-action-by-proteome-wide-identification-of-drug-binding-proteins
#2
Tao Cui, Hai Hou, Yao Sun, Huaixing Cang, Xiangxi Wang
Small molecule drugs obtained from synthetic compounds or natural products show their therapeutic effects by specifically binding to one or a few target proteins and modulating their functions. In contrast, undesirable drug-protein interactions may provoke harmful side effects. Furthermore, drug-protein interactions also play roles in drug activation, transport, metabolism and regulation of drug resistance. Therefore, systematically identifying binding proteins of a drug molecule is critical for understanding the mechanism of action of the drug at molecular level...
May 18, 2017: Medicinal Chemistry
https://www.readbyqxmd.com/read/28523284/enhanced-axial-and-lateral-resolution-using-stabilized-pulses
#3
Shujie Chen, Kevin J Parker
Ultrasound B-scan imaging systems operate under some well-known resolution limits. To improve resolution, the concept of stable pulses, having bounded inverse filters, was previously utilized for the lateral deconvolution. This framework has been extended to the axial direction, enabling a two-dimensional deconvolution. The modeling of the two-way response in the axial direction is discussed, and the deconvolution is performed in the in-phase quadrature data domain. Stable inverse filters are generated and applied for the deconvolution of the image data from Field II simulation, a tissue-mimicking phantom, and in vivo imaging of a carotid artery, where resolution enhancement is observed...
April 2017: Journal of Medical Imaging
https://www.readbyqxmd.com/read/28518081/determining-glucose-metabolism-kinetics-using-18f-fdg-micro-pet-ct
#4
Blake J Cochran, William J Ryder, Arvind Parmar, Kerstin Klaeser, Anthonin Reilhac, Georgios I Angelis, Steven R Meikle, Philip J Barter, Kerry-Anne Rye
This paper describes the use of (18)F-FDG and micro-PET/CT imaging to determine in vivo glucose metabolism kinetics in mice (and is transferable to rats). Impaired uptake and metabolism of glucose in multiple organ systems due to insulin resistance is a hallmark of type 2 diabetes. The ability of this technique to extract an image-derived input function from the vena cava using an iterative deconvolution method eliminates the requirement of the collection of arterial blood samples. Fitting of tissue and vena cava time activity curves to a two-tissue, three compartment model permits the estimation of kinetic micro-parameters related to the (18)F-FDG uptake from the plasma to the intracellular space, the rate of transport from intracellular space to plasma and the rate of (18)F-FDG phosphorylation...
May 2, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28517979/cell-type-deconvolution-in-epigenome-wide-association-studies-a-review-and-recommendations
#5
Andrew E Teschendorff, Shijie C Zheng
A major challenge faced by epigenome-wide association studies (EWAS) is cell-type heterogeneity. As many EWAS have already demonstrated, adjusting for changes in cell-type composition can be critical when analyzing and interpreting findings from such studies. Because of their importance, a great number of different statistical algorithms, which adjust for cell-type composition, have been proposed. Some of the methods are 'reference based' in that they require a priori defined reference DNA methylation profiles of cell types that are present in the tissue of interest, while other algorithms are 'reference free...
May 2017: Epigenomics
https://www.readbyqxmd.com/read/28513674/molecular-organization-in-the-twist-bend-nematic-phase-by-resonant-x-ray-scattering-at-the-se-k-edge-and-by-saxs-waxs-and-gixrd
#6
W D Stevenson, Z Ahmed, X B Zeng, C Welch, G Ungar, G H Mehl
Using a magnetically aligned liquid crystal mixture containing a novel Se-labelled dimer and the difluoroterphenyl dimer DTC5C7, the twist-bend nematic phase (Ntb) was studied by the resonant scattering of hard X-rays and by conventional small and wide-angle X-ray scattering (SAXS, WAXS). Resonant diffraction spots indicated a helix with a 9-12 nm pitch in the Ntb phase and an unprecedentedly high helix orientation. This enabled deconvolution of global and local order parameters. These findings, combined with the simultaneously recorded resonant and non-resonant SAXS and WAXS data, allowed us to construct a locally layered molecular model of the Ntb phase, where the average twisted conformation of each molecule was idealised as a helical segment, matching the local heliconical director field...
May 17, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28512739/normal-develompent-of-spinal-axons-in-early-embryo-stages-and-posterior-locomotor-function-is-independent-of-gal-1
#7
Juana M Pasquini, Francisco J Barrantes, Héctor R Quintá
It was recently described that Galectin-1 (Gal-1) promotes axonal growth after spinal cord injury. This effect depends on protein dimerization, since monomeric Gal-1 fails to stimulate axonal re-growth. Gal-1 is expressed in vivo at concentrations that favor the monomeric species. The aim of the present study is to investigate whether endogenous Gal-1 is required for spinal axon development and normal locomotor behavior in mice. In order to characterize axonal development, we used a novel combination of 3-DISCO technique with 1-photon microscopy and epifluorescence microscopy under high power LED illumination, followed by serial image section deconvolution and 3-D reconstruction...
May 17, 2017: Journal of Comparative Neurology
https://www.readbyqxmd.com/read/28503340/administration-frequency-as-well-as-dosage-of-pth-are-associated-with-development-of-cortical-porosity-in-ovariectomized-rats
#8
Aya Takakura, Ji-Won Lee, Kyoko Hirano, Yukihiro Isogai, Toshinori Ishizuya, Ryoko Takao-Kawabata, Tadahiro Iimura
To investigate whether the administration frequency of parathyroid hormone (PTH) is associated with the development of cortical porosity, this study established 15 dosage regimens of teriparatide [human PTH(1-34), TPTD] with four distinct concentrations and four distinct administration frequencies of TPTD to 16-week-old ovariectomized rats. Our analyses demonstrated that the bone mineral density, mechanical properties, and bone turnover were associated with the total amount of TPTD administered. Our observations further revealed that the cortical porosity was markedly developed as a result of an increased administration frequency with a lower concentration of total TPTD administration in our setting, although the highest concentration also induced cortical porosity...
2017: Bone Research
https://www.readbyqxmd.com/read/28500991/thermoluminescence-characteristics-of-a-chondrite-holbrook-and-an-aubrite-achondrite-norton-county-meteorites
#9
Lily Bossin, Nikolaos A Kazakis, George Kitis, Nestor C Tsirliganis
The present study constitutes the first part of a meteorite project, currently in progress, towards the full and thorough dosimetric study (TL and OSL) of two different meteorites of recent fall, Norton County and Holbrook. Both meteorites exhibit strong TL sensitivity, linear dose response and no saturation for doses up to 2kGy. However, the two meteorites exhibited a very dissimilar TL glow curve and behaviour regarding sensitization and fading. Notably, the Norton County aubrite achondrite was found to exhibit a strong fading of the high-temperature peak (~300°C), attributed to anomalous fading, whereas Holbrook did not seem to show signs of anomalous fading...
May 4, 2017: Applied Radiation and Isotopes
https://www.readbyqxmd.com/read/28499599/gas-chromatography-mass-spectrometry-data-processing-made-easy
#10
Lea G Johnsen, Peter B Skou, Bekzod Khakimov, Rasmus Bro
Evaluation of GC-MS data may be challenging due to the high complexity of data including overlapped, embedded, retention time shifted and low S/N ratio peaks. In this work, we demonstrate a new approach, PARAFAC2 based Deconvolution and Identification System (PARADISe), for processing raw GC-MS data. PARADISe is a computer platform independent freely available software incorporating a number of newly developed algorithms in a coherent framework. It offers a solution for analysts dealing with complex chromatographic data...
April 27, 2017: Journal of Chromatography. A
https://www.readbyqxmd.com/read/28497294/a-two-step-deconvolution-analysis-informed-population-pharmacodynamic-modeling-approach-for-drugs-targeting-pulsatile-endogenous-compounds
#11
Michiel J van Esdonk, Jacobus Burggraaf, Piet H van der Graaf, Jasper Stevens
Pharmacodynamic modeling of pulsatile endogenous compounds (e.g. growth hormone [GH]) is currently limited to the identification of a low number of pulses. Commonly used pharmacodynamic models are not able to capture the complexity of pulsatile secretion and therefore non-compartmental analyses are performed to extract summary statistics (mean, AUC, Cmax). The aim of this study was to develop a new quantification method that deals with highly variable pulsatile data by using a deconvolution-analysis-informed population pharmacodynamic modeling approach...
May 11, 2017: Journal of Pharmacokinetics and Pharmacodynamics
https://www.readbyqxmd.com/read/28495876/a-subcellular-map-of-the-human-proteome
#12
Peter J Thul, Lovisa Åkesson, Mikaela Wiking, Diana Mahdessian, Aikaterini Geladaki, Hammou Ait Blal, Tove Alm, Anna Asplund, Lars Björk, Lisa M Breckels, Anna Bäckström, Frida Danielsson, Linn Fagerberg, Jenny Fall, Laurent Gatto, Christian Gnann, Sophia Hober, Martin Hjelmare, Fredric Johansson, Sunjae Lee, Cecilia Lindskog, Jan Mulder, Claire M Mulvey, Peter Nilsson, Per Oksvold, Johan Rockberg, Rutger Schutten, Jochen M Schwenk, Åsa Sivertsson, Evelina Sjöstedt, Marie Skogs, Charlotte Stadler, Devin P Sullivan, Hanna Tegel, Casper Winsnes, Cheng Zhang, Martin Zwahlen, Adil Mardinoglu, Fredrik Pontén, Kalle von Feilitzen, Kathryn S Lilley, Mathias Uhlén, Emma Lundberg
Resolving the spatial distribution of the human proteome at a subcellular level greatly increases our understanding of human biology and disease. Here, we present a comprehensive image-based map of the subcellular protein distribution, the Cell Atlas, built by integrating transcriptomics and antibody-based immunofluorescence microscopy with validation by mass spectrometry. Mapping the in situ localization of 12,003 human proteins at a single-cell level to 30 subcellular structures enabled the definition of 13 major organelle proteomes...
May 11, 2017: Science
https://www.readbyqxmd.com/read/28493232/anthracycline-induced-cardiotoxicity-biomarkers-and-omics-technology-in-the-era-of-patient-specific-care
#13
REVIEW
Shayan Moazeni, Martin Cadeiras, Eric H Yang, Mario C Deng, Kim-Lien Nguyen
Anthracyclines are highly effective against a variety of malignancies. However, their dose-dependent cardiotoxic effects can potentially limit their use. In the past decade, serum biomarkers have been used to diagnose, monitor, predict, and prognosticate disease. Biomarkers such as cardiac troponin and natriuretic peptides have some predictive value, but still lack reliability in this patient population. Novel biomarkers such as galectin-3, soluble ST-2 proteins, myeloperoxidase, and fibrocytes are being explored as potential biomarkers to reliably predict the onset of cardiotoxicity...
December 2017: Clinical and Translational Medicine
https://www.readbyqxmd.com/read/28489730/improved-hiv-1-viral-load-monitoring-capacity-using-pooled-testing-with-marker-assisted-deconvolution
#14
Tao Liu, Joseph W Hogan, Michael J Daniels, Mia Coetzer, Yizhen Xu, Gerald Bove, Allison K Delong, Lauren Ledingham, Millicent Orido, Lameck Diero, Rami Kantor
OBJECTIVE: Improve pooled viral load (VL) testing to increase HIV treatment monitoring capacity, particularly relevant for resource-limited settings. DESIGN: We developed mMPA (marker-assisted mini-pooling with algorithm), a new VL pooling deconvolution strategy that utilizes information from low-cost, routinely-collected clinical markers to determine an efficient order of sequential individual VL testing and dictates when the sequential testing can be stopped. METHODS: We simulated the use of pooled testing to ascertain virological failure status on 918 participants from three studies conducted at the Academic Model Providing Access to Healthcare (AMPATH) in Eldoret, Kenya, and estimated the number of assays needed when using mMPA and other pooling methods...
April 25, 2017: Journal of Acquired Immune Deficiency Syndromes: JAIDS
https://www.readbyqxmd.com/read/28486216/ionization-chamber-radial-response-deconvolution-in-megavoltage-photon-beam
#15
Antti Juhani Kulmala, Mikko Tenhunen
The aim of this paper is to study a radial response model as a method, to correct output factor results gathered with ionization chambers of different size and shape in cone collimated RT fields. An enhanced version of a non-parametric super-resolution deconvolution method able to model a radial response function of a small cylinder symmetric ionization chamber is described and demonstrated. The radial response of four ionization chambers with different geometry and radius are estimated using 6 MV photon beam in water at the isocentre plane...
May 9, 2017: Physics in Medicine and Biology
https://www.readbyqxmd.com/read/28483704/genome-wide-analysis-of-ar-binding-and-comparison-with-transcript-expression-in-primary-human-fetal-prostate-fibroblasts-and-cancer-associated-fibroblasts
#16
REVIEW
Claire Nash, Nadia Boufaied, Ian G Mills, Omar E Franco, Simon W Hayward, Axel A Thomson
The androgen receptor (AR) is a transcription factor, and key regulator of prostate development and cancer, which has discrete functions in stromal versus epithelial cells. AR expressed in mesenchyme is necessary and sufficient for prostate development while loss of stromal AR is predictive of prostate cancer progression. Many studies have characterized genome-wide binding of AR in prostate tumour cells but none have used primary mesenchyme or stroma. We applied ChIPseq to identify genomic AR binding sites in primary human fetal prostate fibroblasts and patient derived cancer associated fibroblasts, as well as the WPMY1 cell line overexpressing AR...
May 5, 2017: Molecular and Cellular Endocrinology
https://www.readbyqxmd.com/read/28480893/precise-determination-of-graphene-functionalization-by-in-situ-raman-spectroscopy
#17
Philipp Vecera, Julio C Chacón-Torres, Thomas Pichler, Stephanie Reich, Himadri R Soni, Andreas Görling, Konstantin Edelthalhammer, Herwig Peterlik, Frank Hauke, Andreas Hirsch
The verification of a successful covalent functionalization of graphene and related carbon allotropes can easily be carried out by Raman spectroscopy. Nevertheless, the unequivocal assignment and resolution of individual lattice modes associated with the covalent binding of addends was elusive up to now. Here we present an in situ Raman study of a controlled functionalization of potassium intercalated graphite, revealing several new bands appearing in the D-region of the spectrum. The evolution of these bands with increasing degree of functionalization from low to moderate levels provides a basis for the deconvolution of the different components towards quantifying the extent of functionalization...
May 8, 2017: Nature Communications
https://www.readbyqxmd.com/read/28477028/whole-tumor-rna-sequencing-and-deconvolution-reveal-a-clinically-prognostic-pten-pi3k-regulated-glioma-transcriptional-signature
#18
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...
April 18, 2017: Oncotarget
https://www.readbyqxmd.com/read/28476016/direct-measurement-of-alpha-emission-probabilities-in-the-decay-of-226-ra
#19
M Marouli, S Pommé, R Van Ammel, E García-Toraño, T Crespo, S Pierre
High-resolution alpha-particle spectrometry was performed to determine the main alpha-particle emission probabilities in the decay of (226)Ra. Thin, homogeneous sources were prepared by electrodeposition on stainless steel disks. Alpha spectra with an energy resolution of 20keV were obtained in three laboratories and analysed with different deconvolution algorithms. In two set-ups, a magnet system was used to deflect conversion electrons to avoid their coincidental detection with the alpha particles. Spectra taken at close range without a magnet system yielded biased results which cannot be fully compensated by statistical corrections for coincidence summing...
April 27, 2017: Applied Radiation and Isotopes
https://www.readbyqxmd.com/read/28474019/direct-observation-of-active-material-interactions-in-flowable-electrodes-using-x-ray-tomography
#20
Kelsey B Hatzell, Jens Eller, Samantha L Morelly, Maureen H Tang, Nicolas J Alvarez, Yury Gogotsi
Understanding electrical percolation and charging mechanisms in electrochemically active biphasic flowable electrodes is critical for enabling scalable deionization (desalination) and energy storage. Flowable electrodes are dynamic material systems which store charge (remove ions) and have the ability to flow. This flow process can induce structural changes in the underlying material arrangement and result in transient and non-uniform material properties. Carbon-based suspensions are opaque, multi-phase, and three dimensional, and thus prior characterization of the structural properties has been limited to indirect methods (electrochemical and rheology)...
May 5, 2017: Faraday Discussions
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