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Deconvolution

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https://www.readbyqxmd.com/read/28813413/polylox-barcoding-reveals-haematopoietic-stem-cell-fates-realized-in-vivo
#1
Weike Pei, Thorsten B Feyerabend, Jens Rössler, Xi Wang, Daniel Postrach, Katrin Busch, Immanuel Rode, Kay Klapproth, Nikolaus Dietlein, Claudia Quedenau, Wei Chen, Sascha Sauer, Stephan Wolf, Thomas Höfer, Hans-Reimer Rodewald
Developmental deconvolution of complex organs and tissues at the level of individual cells remains challenging. Non-invasive genetic fate mapping has been widely used, but the low number of distinct fluorescent marker proteins limits its resolution. Much higher numbers of cell markers have been generated using viral integration sites, viral barcodes, and strategies based on transposons and CRISPR-Cas9 genome editing; however, temporal and tissue-specific induction of barcodes in situ has not been achieved. Here we report the development of an artificial DNA recombination locus (termed Polylox) that enables broadly applicable endogenous barcoding based on the Cre-loxP recombination system...
August 16, 2017: Nature
https://www.readbyqxmd.com/read/28811614/retarded-saturation-of-the-areal-capacitance-using-3d-aligned-mno2-thin-film-nanostructures-as-a-supercapacitor-electrode
#2
Green Kim, Ilhwan Ryu, Sanggyu Yim
The supercapacitive properties of manganese oxide (MnO2) thin films electrodeposited on three-dimensionally (3D) aligned inverse-opal nickel nanostructures are investigated. Compared to conventional planar or two-dimensionally (2D) aligned nanostructures, 3D-aligned nanostructures can provide considerably increased and controllable contacts between the electrode and electrolyte. As a result, saturation of the areal capacitance with the electrode thickness and associated decrease of the specific capacitance, C sp , become much slower than those of the planar and 2D-aligned electrode systems...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28811031/bayesian-approach-to-peak-deconvolution-and-library-search-for-high-resolution-gas-chromatography-mass-spectrometry
#3
A Barcaru, H G J Mol, M Tienstra, G Vivó-Truyols
A novel probabilistic Bayesian strategy is proposed to resolve highly coeluting peaks in high-resolution GC-MS (Orbitrap) data. Opposed to a deterministic approach, we propose to solve the problem probabilistically, using a complete pipeline. First, the retention time(s) for a (probabilistic) number of compounds for each mass channel are estimated. The statistical dependency between m/z channels was implied by including penalties in the model objective function. Second, Bayesian Information Criterion (BIC) is used as Occam's razor for the probabilistic assessment of the number of components...
August 29, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/28811030/targeted-analyte-deconvolution-and-identification-by-four-way-parallel-factor-analysis-using-three-dimensional-gas-chromatography-with-mass-spectrometry-data
#4
Nathanial E Watson, Sarah E Prebihalo, Robert E Synovec
Comprehensive three-dimensional gas chromatography with time-of-flight mass spectrometry (GC(3)-TOFMS) creates an opportunity to explore a new paradigm in chemometric analysis. Using this newly described instrument and the well understood Parallel Factor Analysis (PARAFAC) model we present one option for utilization of the novel GC(3)-TOFMS data structure. We present a method which builds upon previous work in both GC(3) and targeted analysis using PARAFAC to simplify some of the implementation challenges previously discovered...
August 29, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/28809493/macroscopic-structural-compositions-of-%C3%AF-conjugated-polymers-combined-insights-from-solid-state-nmr-and-molecular-dynamics-simulations
#5
Anton Melnyk, Matthias Junk, Michael D McGehee, Bradley F Chmelka, Michael Ryan Hansen, Denis Andrienko
Molecular dynamics simulations are combined with solid-state NMR measurements to gain insight into the macroscopic structural composition of the π-conjugated polymer poly(2,5-bis(3-tetradecyl-thiophen-2-yl)thieno[3,2-b]thiophene) (PBTTT). The structural and dynamical properties, as established by the NMR analyses, were used to test the local structure of three constitutient mesophases with: (i) crystalline backbones and side chains, (ii) lamellar backbones and disordered side chains, or (iii) amorphous backbones and side chains...
August 15, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28808992/a-photoaffinity-labeling-based-chemoproteomics-strategy-for-unbiased-target-deconvolution-of-small-molecule-drug-candidates
#6
Jason R Thomas, Scott M Brittain, Jennifer Lipps, Luis Llamas, Rishi K Jain, Markus Schirle
The combination of photoaffinity labeling (PAL) and quantitative chemoproteomics enables the comprehensive, unbiased determination of protein interaction profiles to support target identification of bioactive small molecules. This approach is amenable to cells in culture and compatible with pharmacologically relevant transmembrane target classes like G-protein coupled receptors and ions channels which have been notoriously hard to access by conventional chemoproteomics approaches. Here, we describe a strategy that combines PAL probe titration and competition with excess parental compounds with the goal of enabling the identification of specific interactors as well as assessing the functional relevance of a binding event for the phenotype under investigation...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28806601/influence-of-sublethal-doses-of-acetamiprid-and-halosulfuron-methyl-on-metabolites-of-zebra-fish-brachydanio-rerio
#7
Hong Zhang, Lijuan Zhao
Acetamiprid, a neonicotinoid pesticide, is reported to have adverse sublethal effects on non-target beneficial organisms. Halosulfuron-methyl (HM), one of the most widely used herbicides in agriculture, has high ecotoxicity to aquatic plants and animals. In this study, a GC-MS-based metabolomics approach was used to investigate the toxicity of acetamiprid and HM. The Automated Mass Spectral Deconvolution and Identification System (AMDIS) software program and the retention index method were used to identify 51 metabolites in zebra fish (Brachydanio rerio)...
August 4, 2017: Aquatic Toxicology
https://www.readbyqxmd.com/read/28804973/a-useful-method-for-preparing-mixed-brush-polymer-grafted-nanoparticles-by-polymerizing-block-copolymers-from-surfaces-with-reversed-monomer-addition-sequence
#8
Yang Zheng, Yucheng Huang, Brian C Benicewicz
The preparation of well-defined block copolymers using controlled radical polymerization depends on the proper order of monomer addition. The reversed order of monomer addition results in a mixture of block copolymer and homopolymer and thus has typically been avoided. In this paper, the low blocking efficiency of reversed monomer addition order is utilized in combination with surface initiated reversible addition-fragmentation chain-transfer polymerization to establish a facile procedure toward mixed polymer brush grafted nanoparticles SiO2 -g-(PS (polystyrene), PS-b-PMAA (polymethacrylic acid))...
August 14, 2017: Macromolecular Rapid Communications
https://www.readbyqxmd.com/read/28803903/structured-illumination-microscopy-reveals-actin-i-localization-in-discreet-foci-in-plasmodium-berghei-gametocytes
#9
Chiara Curra, Paul J McMillan, Lefteris Spanos, Vanessa Mollard, Elena Deligianni, Geoffrey McFadden, Leann Tilley, Inga Siden-Kiamos
Actin has important roles in Plasmodium parasites but its exact function in different life stages is not yet fully elucidated. Here we report the localization of ubiquitous actin I in gametocytes of the rodent model parasite P. berghei. Using an antibody specifically recognizing F-actin and deconvolution microscopy we detected actin I in a punctate pattern in gametocytes. 3D-Structured Illumination Microscopy which allows sub-diffraction limit imaging resolved the signal into structures of less than 130 nm length...
August 10, 2017: Experimental Parasitology
https://www.readbyqxmd.com/read/28803647/determination-of-selected-endogenous-anabolic-androgenic-steroids-and-ratios-in-urine-by-ultra-high-performance-liquid-chromatography-tandem-mass-spectrometry-and-isotope-pattern-deconvolution
#10
J Pitarch-Motellón, J V Sancho, M Ibáñez, O Pozo, A F Roig-Navarro
An isotope dilution mass spectrometry (IDMS) method for the determination of selected endogenous anabolic androgenic steroids (EAAS) in urine by UHPLC-MS/MS has been developed using the isotope pattern deconvolution (IPD) mathematical tool. The method has been successfully validated for testosterone, epitestosterone, androsterone and etiocholanolone, employing their respective deuterated analogs using two certified reference materials (CRM). Accuracy was evaluated as recovery of the certified values and ranged from 75% to 108%...
August 3, 2017: Journal of Chromatography. A
https://www.readbyqxmd.com/read/28802083/phase-contrast-hard-x-ray-microscopy-using-synchrotron-radiation-for-the-properties-of-skeletal-muscle-in-mouse-hind-limbs
#11
Sanghun Jang, Jaehong Lim, Onseok Lee
Radiation beam interface contrast X-ray microscopy provides resolution of a few dozen nanometers from fixed whole muscle biopsies, allowing better reconstruction of the microstructure of the muscle than is currently possible with classic histological techniques. Fixed soleus muscle biopsies have been evaluated from the walk-in mouse model using phase-contrast X-ray microscopy, and results presented that corroborate the accuracy of the method used, and its potential for application in physiotherapy and occupational therapy studies...
August 12, 2017: Microscopy Research and Technique
https://www.readbyqxmd.com/read/28801250/decoding-fmri-activity-in-the-time-domain-improves-classification-performance
#12
REVIEW
João Loula, Gaël Varoquaux, Bertrand Thirion
Most current functional Magnetic Resonance Imaging (fMRI) decoding analyses rely on statistical summaries of the data resulting from a deconvolution approach: each stimulation event is associated with a brain response. This standard approach leads to simple learning procedures, yet it is ill-suited for decoding events with short inter-stimulus intervals. In order to overcome this issue, we propose a novel framework that separates the spatial and temporal components of the prediction by decoding the fMRI time-series continuously, i...
August 8, 2017: NeuroImage
https://www.readbyqxmd.com/read/28800494/a-time-domain-model-and-experimental-validation-of-the-acoustic-field-radiated-by-air-coupled-transducers
#13
Ji Li, Bogdan Piwakowski
This paper presents a time-domain model for the prediction of an acoustic field in an air-coupled, non-contact, ultrasonic setup, which includes an air-coupled Emitter, the Propagation space and an air-coupled Receiver (EPR). The model takes into account the finite size of the aperture receiver, attenuation in air, and the electric response of the emitter-receiver set he. The attenuation is characterized by a causal time-domain Green's function, allowing the wideband attenuation of a lossy medium obeying the power law α(ω)=α0ω(η),1⩽η⩽2 to be included...
August 1, 2017: Ultrasonics
https://www.readbyqxmd.com/read/28800490/oxytocin-secretion-is-pulsatile-in-men-and-is-related-to-social-emotional-functioning
#14
Charumathi Baskaran, Franziska Plessow, Lisseth Silva, Elisa Asanza, Dean Marengi, Kamryn T Eddy, Patrick M Sluss, Michael L Johnson, Madhusmita Misra, Elizabeth A Lawson
The hypothalamic hormone oxytocin (OXT) plays an important role in a range of physiological processes and social-emotional functioning in both sexes. In women, physiological stimuli, such as suckling and parturition, result in pulsatile release of OXT into the peripheral circulation via the posterior pituitary gland. However, data regarding OXT secretory patterns in men during a state of rest are limited. Further, the relationship between secretory dynamics of OXT and emotional measures has never been evaluated...
July 24, 2017: Psychoneuroendocrinology
https://www.readbyqxmd.com/read/28799755/polypharmacology-of-n6-3-iodobenzyl-adenosine-5-n-methyluronamide-ib-meca-and-related-a3-adenosine-receptor-ligands-peroxisome-proliferator-activated-receptor-ppar-%C3%AE-partial-agonist-and-ppar-%C3%AE-antagonist-activity-suggests-their-anti-diabetic-potential
#15
Jinha Yu, Seyeon Ahn, Hee Jin Kim, Moonyoung Lee, Sungjin Ahn, Jungmin Kim, Sun Hee Jin, Eunyoung Lee, Gyudong Kim, Jae Hoon Cheong, Kenneth A Jacobson, Lak Shin Jeong, Minsoo Noh
A3 adenosine receptor (AR) ligands including A3 AR agonist, N6-(3-iodobenzyl)adenosine-5'-N-methyluronamide 1a (IB-MECA) were examined for adiponectin production in human bone marrow mesenchymal stem cells (hBM-MSCs). In this model, 1a significantly increased adiponectin production, which is associated with improved insulin sensitivity. However, A3 AR antagonists also promoted adiponectin production in hBM-MSCs, indicating that the A3 AR pathway may not be directly involved in the adiponectin promoting activity...
August 11, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28798660/human-summating-potential-using-continuous-loop-averaging-deconvolution-response-amplitudes-vary-with-tone-burst-repetition-rate-and-duration
#16
Alana E Kennedy, Wafaa A Kaf, John A Ferraro, Rafael E Delgado, Jeffery T Lichtenhan
Electrocochleography (ECochG) to high repetition rate tone bursts may have advantages over ECochG to clicks with standard slow rates. Tone burst stimuli presented at a high repetition rate may enhance summating potential (SP) measurements by reducing neural contributions resulting from neural adaptation to high stimulus repetition rates. To allow for the analysis of the complex ECochG responses to high rates, we deconvolved responses using the Continuous Loop Averaging Deconvolution (CLAD) technique. We examined the effect of high stimulus repetition rate and stimulus duration on SP amplitude measurements made with extratympanic ECochG to tone bursts in 20 adult females with normal hearing...
2017: Frontiers in Neuroscience
https://www.readbyqxmd.com/read/28796605/pulse-inversion-subharmonic-ultrafast-active-cavitation-imaging-in-tissue-using-fast-eigenspace-based-adaptive-beamforming-and-cavitation-deconvolution
#17
Chen Bai, Shanshan Xu, Junbo Duan, Bowen Jing, Miao Yang, Mingxi Wan
Pulse-inversion subharmonic (PISH) imaging can display information relating to pure cavitation bubbles while excluding that of tissue. Although plane-wave-based ultrafast active cavitation imaging (UACI) can monitor the transient activities of cavitation bubbles, its resolution and cavitation-to-tissue ratio (CTR) are barely satisfactory but can be significantly improved by introducing eigenspace-based (ESB) adaptive beamforming. PISH and UACI are a natural combination for imaging of pure cavitation activity in tissue; however, it raises two problems: 1) the ESB beamforming is hard to implement in real time due to the enormous amount of computation associated with the covariance matrix inversion and eigendecomposition and 2) the narrowband characteristic of the subharmonic filter will incur a drastic degradation in resolution...
August 2017: IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control
https://www.readbyqxmd.com/read/28795710/quantification-of-nucleobases-gold-nanoparticles-interactions-energetics-of-the-interactions-through-apparent-binding-constants-determination
#18
J M Carnerero, A Sánchez-Coronilla, E I Martín, A Jimenez-Ruiz, R Prado-Gotor
We explore the possibilities of quantifying the interaction of both adenine and thymine with non-functionalized, anionic citrate gold nanoparticles (AuNPs). Following the plasmon absorbance band's red shifts, dependent of the AuNPs aggregation state, apparent binding free energies of the system are obtained for the sum of the two processes (nucleobase interaction plus nanoparticle aggregation). A deconvolution procedure confirms those results. Those apparent binding free energies are, in both cases, in good agreement with previous studies indicating an increased reactivity for adenine...
August 10, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28792892/eemd-domain-ar-spectral-method-for-mean-scatterer-spacing-estimation-of-breast-tumors-from-ultrasound-backscattered-rf-data
#19
Navid Ibtehaj Nizam, S Kaisar Alam, Md Kamrul Hasan
We present a novel method for estimating the mean scatterer spacing (MSS) of breast tumours using ensemble empirical mode decomposition (EEMD) domain analysis of deconvolved backscattered radio-frequency (RF) data. The autoregressive (AR) spectrum from which the MSS is estimated is obtained from the intrinsic mode functions (IMFs) due to regular scatterers embedded in RF data corrupted by the diffuse scatterers. The IMFs are chosen by giving priority to the presence of an enhanced fundamental harmonic and the presence of a greater number of higher harmonics in the AR spectrum estimated from the IMFs...
August 3, 2017: IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control
https://www.readbyqxmd.com/read/28767373/mixed-neural-network-approach-for-temporal-sleep-stage-classification
#20
Hao Dong, Akara Supratak, Wei Pan, Chao Wu, Paul M Matthews, Yike Guo
This paper proposes a practical approach to addressing limitations posed by using of single-channel electroencephalography (EEG) for sleep stage classification. EEG-based characterizations of sleep stage progression contribute the diagnosis and monitoring of the many pathologies of sleep. Several prior reports explored ways of automating the analysis of sleep EEG and of reducing the complexity of the data needed for reliable discrimination of sleep stages at lower cost in the home. However, these reports have involved recordings from electrodes placed on the cranial vertex or occiput, which are both uncomfortable and difficult to position...
July 28, 2017: IEEE Transactions on Neural Systems and Rehabilitation Engineering
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