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Jin-Ping Li, Guang-Long Feng, Da-Qing Li, Hai-Bo Wang, De-Li Zhao, Yong Wan, Hui-Jie Jiang
BACKGROUND: Functional imaging such as CT perfusion can detect morphological and hemodynamic changes in hepatocellular carcinoma (HCC). Pre-carcinoma and early HCC nodules are difficult to differentiate by observing only their hemodynamics changes. The present study aimed to investigate hemodynamic parameters and evaluate their differential diagnostic cut-off between pre-carcinoma and early HCC nodules using CT perfusion and receiver operating characteristic (ROC) curves. METHODS: Male Wistar rats were randomly divided into control (n=20) and experimental (n=70) groups...
December 2016: Hepatobiliary & Pancreatic Diseases International: HBPD INT
Franz-Philipp Schmidt, Ferdinand Hofer, Joachim R Krenn
Spectrum imaging techniques, gaining simultaneously structural (image) and spectroscopic data, require appropriate and careful processing to extract information of the dataset. In this article we introduce a MATLAB based software that uses three dimensional data (EEL/CL spectrum image in dm3 format (Gatan Inc.'s DigitalMicrograph(®))) as input. A graphical user interface enables a fast and easy mapping of spectral dependent images and position dependent spectra. First, data processing such as background subtraction, deconvolution and denoising, second, multiple display options including an EEL/CL moviemaker and, third, the applicability on a large amount of data sets with a small work load makes this program an interesting tool to visualize otherwise hidden details...
November 21, 2016: Micron: the International Research and Review Journal for Microscopy
Junbo Duan, Hui Zhong, Bowen Jing, Siyuan Zhang, Mingxi Wan
The axial resolution of ultrasonic imaging is confined by the temporal width of acoustic pulse generated by the transducer, which has a limited bandwidth. Deconvolution can eliminate this effect and, therefore, improve the resolution. However, most ultrasonic imaging methods perform deconvolution scan line by scan line, and therefore the information embedded within the neighbor scan lines is unexplored, especially for those materials with layered structures such as blood vessels. In this paper, a joint sparse representation model is proposed to increase the axial resolution of ultrasonic imaging...
December 2016: IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control
Rita Santos, Oleg Ursu, Anna Gaulton, A Patrícia Bento, Ramesh S Donadi, Cristian G Bologa, Anneli Karlsson, Bissan Al-Lazikani, Anne Hersey, Tudor I Oprea, John P Overington
The success of mechanism-based drug discovery depends on the definition of the drug target. This definition becomes even more important as we try to link drug response to genetic variation, understand stratified clinical efficacy and safety, rationalize the differences between drugs in the same therapeutic class and predict drug utility in patient subgroups. However, drug targets are often poorly defined in the literature, both for launched drugs and for potential therapeutic agents in discovery and development...
December 2, 2016: Nature Reviews. Drug Discovery
E Stefanikova, M Peterka, P Bohm, P Bilkova, M Aftanas, M Sos, J Urban, M Hron, R Panek
A new technique for fitting the full radial profiles of electron density and temperature obtained by the Thomson scattering diagnostic in H-mode discharges on the COMPASS tokamak is described. The technique combines the conventionally used modified hyperbolic tangent function for the edge transport barrier (pedestal) fitting and a modification of a Gaussian function for fitting the core plasma. Low number of parameters of this combined function and their straightforward interpretability and controllability provide a robust method for obtaining physically reasonable profile fits...
November 2016: Review of Scientific Instruments
A B Zylstra, H-S Park, J S Ross, F Fiuza, J A Frenje, D P Higginson, C Huntington, C K Li, R D Petrasso, B Pollock, B Remington, H G Rinderknecht, D Ryutov, F H Séguin, D Turnbull, S C Wilks
Pinhole imaging of large (mm scale) carbon-deuterium (CD) plasmas by proton self-emission has been used for the first time to study the microphysics of shock formation, which is of astrophysical relevance. The 3 MeV deuterium-deuterium (DD) fusion proton self-emission from these plasmas is imaged using a novel pinhole imaging system, with up to five different 1 mm diameter pinholes positioned 25 cm from target-chamber center. CR39 is used as the detector medium, positioned at 100 cm distance from the pinhole for a magnification of 4 ×...
November 2016: Review of Scientific Instruments
Oguzhan Balki, Hani E Elsayed-Ali
Carbon ions generated by ablation of a carbon target using an Nd:YAG laser pulse (wavelength λ = 1064 nm, pulse width τ = 7 ns, and laser fluence of 10-110 J cm(-2)) are characterized. Time-of-flight analyzer, a three-mesh retarding field analyzer, and an electrostatic ion energy analyzer are used to study the charge and energy of carbon ions generated by laser ablation. The dependencies of the ion signal on the laser fluence, laser focal point position relative to target surface, and the acceleration voltage are described...
November 2016: Review of Scientific Instruments
E P Hartouni, B Beeman, J A Caggiano, C Cerjan, M J Eckart, G P Grim, R Hatarik, A S Moore, D H Munro, T Phillips, D B Sayre
A common analysis procedure minimizes the ln-likelihood that a set of experimental observables matches a parameterized model of the observation. The model includes a description of the underlying physical process as well as the instrument response function (IRF). In the case investigated here, the National Ignition Facility (NIF) neutron time-of-flight (nTOF) spectrometers, the IRF is constructed from measurements and models. IRF measurements have a finite precision that can make significant contributions to determine the uncertainty estimate of the physical model's parameters...
November 2016: Review of Scientific Instruments
Inês C Santos, Kevin A Schug
The vacuum ultraviolet spectrophotometer was developed recently as an alternative to existing gas chromatography detectors. This detector measures the absorption of gas-phase chemical species in the range of 120-240 nm, where all chemical compounds present unique absorption spectra. Therefore, qualitative analysis can be performed and quantification follows standard Beer-Lambert law principles. Different fields of application, such as petrochemical, food, and environmental analysis have been explored. Commonly demonstrated is the capability for facile deconvolution of co-eluting analytes...
November 7, 2016: Journal of Separation Science
Aliaksei Z Holik, Charity W Law, Ruijie Liu, Zeya Wang, Wenyi Wang, Jaeil Ahn, Marie-Liesse Asselin-Labat, Gordon K Smyth, Matthew E Ritchie
Carefully designed control experiments provide a gold standard for benchmarking different genomics research tools. A shortcoming of many gene expression control studies is that replication involves profiling the same reference RNA sample multiple times. This leads to low, pure technical noise that is atypical of regular studies. To achieve a more realistic noise structure, we generated a RNA-sequencing mixture experiment using two cell lines of the same cancer type. Variability was added by extracting RNA from independent cell cultures and degrading particular samples...
November 29, 2016: Nucleic Acids Research
Noushin Hadadi, Jasmin Hafner, Keng Cher Soh, Vassily Hatzimanikatis
Reaction atom mappings track the positional changes of all of the atoms between the substrates and the products as they undergo the biochemical transformation. However, information on atom transitions in the context of metabolic pathways is not widely available in the literature. The understanding of metabolic pathways at the atomic level is of great importance as it can deconvolute the overlapping catabolic/anabolic pathways resulting in the observed metabolic phenotype. The automated identification of atom transitions within a metabolic network is a very challenging task since the degree of complexity of metabolic networks dramatically increases when we transit from metabolite-level studies to atom-level studies...
November 29, 2016: Biotechnology Journal
Kristen I Fread, William D Strickland, Garry P Nolan, Eli R Zunder
Pooled sample analysis by mass cytometry barcoding carries many advantages: reduced antibody consumption, increased sample throughput, removal of cell doublets, reduction of cross-contamination by sample carryover, and the elimination of tube-to-tube-variability in antibody staining. A single-cell debarcoding algorithm was previously developed to improve the accuracy and yield of sample deconvolution, but this method was limited to using fixed parameters for debarcoding stringency filtering, which could introduce cell-specific or sample-specific bias to cell yield in scenarios where barcode staining intensity and variance are not uniform across the pooled samples...
2016: Pacific Symposium on Biocomputing
Jaebum Chung, Hangwen Lu, Xiaoze Ou, Haojiang Zhou, Changhuei Yang
Fourier ptychographic (FP) microscopy is a coherent imaging method that can synthesize an image with a higher bandwidth using multiple low-bandwidth images captured at different spatial frequency regions. The method's demand for multiple images drives the need for a brighter illumination scheme and a high-frame-rate camera for a faster acquisition. We report the use of a guided laser beam as an illumination source for an FP microscope. It uses a mirror array and a 2-dimensional scanning Galvo mirror system to provide a sample with plane-wave illuminations at diverse incidence angles...
November 1, 2016: Biomedical Optics Express
Peng Li, Jianxin Chen, Wuxia Zhang, Bangze Fu, Wei Wang
ETHNOPHARMACOLOGICAL RELEVANCE: Herbal medicine is a concoction of numerous chemical ingredients, and it exhibits polypharmacological effects to act on multiple pharmacological targets, regulating different biological mechanisms and treating a variety of diseases. Thus, this complexity is impossible to deconvolute by the reductionist method of extracting one active ingredient acting on one biological target. AIM OF THE STUDY: To dissect the polypharmacological effects of herbal medicines and their underling pharmacological targets as well as their corresponding active ingredients...
November 25, 2016: Journal of Ethnopharmacology
Mariana N Levandowski, Thiago C Rozada, Ulisses Z Melo, Ernani A Basso, Barbara C Fiorin
This paper presents a study on the conformational preferences of phenylacetic acid (PA) and its halogenated analogues (FPA, CPA, BPA). To clarify the effects that rule these molecules' behaviour, theoretical calculations were used, for both the isolated phase and solution, combined with nuclear magnetic resonance (NMR) and infrared (IR) spectroscopy. Most conformations of phenylacetic acid and its halogenated derivatives are stabilized through the hyperconjugative effect, which rules the conformational preference...
November 9, 2016: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
Nicolas A Karakatsanis, Charalampos Tsoumpas, Habib Zaidi
Bulk body motion may randomly occur during PET acquisitions introducing blurring, attenuation-emission mismatches and, in dynamic PET, discontinuities in the measured time activity curves between consecutive frames. Meanwhile, dynamic PET scans are longer, thus increasing the probability of bulk motion. In this study, we propose a streamlined 3D PET motion-compensated image reconstruction (3D-MCIR) framework, capable of robustly deconvolving intra-frame motion from a static or dynamic 3D sinogram. The presented 3D-MCIR methods need not partition the data into multiple gates, such as 4D MCIR algorithms, or access list-mode (LM) data, such as LM MCIR methods, both associated with increased computation or memory resources...
November 16, 2016: Computerized Medical Imaging and Graphics: the Official Journal of the Computerized Medical Imaging Society
Chuihan Chen, Wei Miao, Cheng Zhou, Hongjuan Wu
Thermogravimetric kinetic of bamboo waste (BW) pyrolysis has been studied using Asymmetric Double Sigmoidal (Asym2sig) function deconvolution. Through deconvolution, BW pyrolytic profiles could be separated into three reactions well, each of which corresponded to pseudo hemicelluloses (P-HC), pseudo cellulose (P-CL), and pseudo lignin (P-LG) decomposition. Based on Friedman method, apparent activation energy of P-HC, P-CL, P-LG was found to be 175.6kJ/mol, 199.7kJ/mol, and 158.4kJ/mol, respectively. Energy compensation effects (lnk0,z vs...
November 5, 2016: Bioresource Technology
Marta Menicatti, Luca Guandalini, Silvia Dei, Elisa Floriddia, Elisabetta I Teodor, Pietro Traldi, Gianluca Bartolucci
A series of N-alkanol-N-cyclohexanol amine aryl esters cis/trans isomers that showed high efficacy to reverse the acquired resistance of cancer cells during chemotherapeutic therapy (MDR mechanism) was studied. These compounds were two 1,4 cyclohexane cis/trans derivatives (named ELF26A and ELF26B, respectively), and their positional isomers (named ELF34A and ELF34B, respectively) where the aryl-moieties were exchanged. In order to evaluate the behaviour of these compounds during biological tests, a method based on liquid chromatography coupled with mass spectrometry (LC-MS), operating in tandem mass spectrometry (MS/MS) mode, was developed...
2016: European Journal of Mass Spectrometry
Simona Fiori, Andrea Guzzetta, Jhimli Mitra, Kerstin Pannek, Rosa Pasquariello, Paola Cipriani, Michela Tosetti, Giovanni Cioni, Stephen E Rose, Anna Chilosi
Childhood apraxia of speech (CAS) is a paediatric speech sound disorder in which precision and consistency of speech movements are impaired. Most children with idiopathic CAS have normal structural brain MRI. We hypothesize that children with CAS have altered structural connectivity in speech/language networks compared to controls and that these altered connections are related to functional speech/language measures. Whole brain probabilistic tractography, using constrained spherical deconvolution, was performed for connectome generation in 17 children with CAS and 10 age-matched controls...
2016: NeuroImage: Clinical
Evie van der Spoel, Ferdinand Roelfsema, Steffy W Jansen, Abimbola A Akintola, Bart E Ballieux, Christa M Cobbaert, Gerard J Blauw, P Eline Slagboom, Rudi G J Westendorp, Hanno Pijl, Diana van Heemst
CONTEXT: A trade-off between fertility and longevity possibly exists. The association of the male hypothalamic-pituitary-gonadal (HPG) axis with familial longevity has not yet been investigated. OBJECTIVE: To study 24-h hormone concentration profiles of the HPG axis in men enriched for familial longevity and controls. DESIGN: We frequently sampled blood over 24 h in 10 healthy middle-aged male offspring of nonagenarian participants from the Leiden Longevity Study together with 10 male age-matched controls...
2016: Frontiers in Endocrinology
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