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https://www.readbyqxmd.com/read/29151221/quantitative-determination-of-interacting-protein-surfaces-in-prokaryotes-and-eukaryotes-by-using-in-cell-nmr-spectroscopy
#1
David S Burz, Christopher M DeMott, Asma Aldousary, Stephen Dansereau, Alexander Shekhtman
This paper describes three protocols for identifying interacting surfaces on (15)N-labeled target proteins of known structure by using in-cell NMR spectroscopy. The first protocol describes how to identify protein quinary structure interaction surfaces in prokaryotes by using cross-relaxation-induced polarization transfer, CRIPT, based in-cell NMR. The second protocol describes how to introduce labeled protein into eukaryotic (HeLa) cells via electroporation for CRIPT-based in-cell studies. The third protocol describes how to quantitatively map protein interacting surfaces by utilizing singular value decomposition, SVD, analysis of STructural INTeractions by in-cell NMR, STINT-NMR, data...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29150809/molecular-properties-of-metal-difluorides-and-their-interactions-with-co2-and-h2o-molecules-a-dft-investigation
#2
Agnes Lincy Arokiyanathan, Senthilkumar Lakshmipathi
A computational study of metal difluorides (MF2; M = Ca to Zn) and their interactions with carbon dioxide and water molecules was performed. The structural parameter values obtained and the results of AIM analysis and energy decomposition analysis indicated that the Ca-F bond is weaker and less ionic than the bonds in the transition metal difluorides. A deformation density plot revealed the stablizing influence of the Jahn-Teller effect in nonlinear MF2 molecules (e.g., where M= Sc, Ti, Cr). An anaysis of the metal K-edge peaks of the difluorides showed that shifts in the edge energy were due to the combined effects of the ionicity, effective nuclear charge, and the spin state of the metal...
November 18, 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/29150618/lexical-processing-of-chinese-sub-character-components-semantic-activation-of-phonetic-radicals-as-revealed-by-the-stroop-effect
#3
Su-Ling Yeh, Wei-Lun Chou, Pokuan Ho
Most Chinese characters are compounds consisting of a semantic radical indicating semantic category and a phonetic radical cuing the pronunciation of the character. Controversy surrounds whether radicals also go through the same lexical processing as characters and, critically, whether phonetic radicals involve semantic activation since they can also be characters when standing alone. Here we examined these issues using the Stroop task whereby participants responded to the ink color of the character. The key finding was that Stroop effects were found when the character itself had a meaning unrelated to color, but contained a color name phonetic radical (e...
November 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29149686/preliminary-application-of-structure-from-motion-and-gis-to-document-decomposition-and-taphonomic-processes
#4
Connor D Carlton, Samantha Mitchell, Patrick Lewis
Over the past decade, Structure from Motion (SfM) has increasingly been used as a means of digital preservation and for documenting archaeological excavations, architecture, and cultural material. However, few studies have tapped the potential of using SfM to document and analyze taphonomic processes affecting burials for forensic sciences purposes. This project utilizes SfM models to elucidate specific post-depositional events that affected a series of three human cadavers deposited at the South East Texas Applied Forensic Science Facility (STAFS)...
November 2, 2017: Forensic Science International
https://www.readbyqxmd.com/read/29148432/a-singular-value-decomposition-linear-programming-svdlp-optimization-technique-for-circular-cone-based-robotic-radiotherapy
#5
Bin Liang, Yongbao Li, Wei Ran, Bin Guo, Xuang Xu, Bo Liu, Jiafeng Li, Qiuwen Wu, Fugen Zhou
With robot-controlled linac positioning, the robotic radiotherapy system such as CyberKnife significantly increases the freedom in radiation beam placement, but also imposes more challenges on treatment plan optimization. The resampling mechanism in vendor supplied treatment planning system (MultiPlan) could not fully explore the increased beam direction search space. Besides, a sparse treatment plan (using fewer beams) is desired to improve the treatment efficiency. This study proposes a singular value decomposition linear programming (SVDLP) optimization technique for circular collimator based robotic radiotherapy...
November 17, 2017: Physics in Medicine and Biology
https://www.readbyqxmd.com/read/29147828/a-reliable-spectral-method-to-reaction-diffusion-equations-in-entrapped-cell-photobioreactor-packed-with-gel-granules-using-chebyshev-wavelets
#6
M Salai Mathi Selvi, G Hariharan, K Kannan
A mathematical model of a reaction-diffusion within an entrapped-cell photobioreactor packed with gel granules containing immobilized photosynthetic bacterial cells is discussed. A theoretical model is based on a system of coupled nonlinear reaction-diffusion equations. In this research work, we have developed an efficient wavelet-based spectral approach for solving the proposed model. Analytical expressions for the concentration of substrate and product are established for all values of reaction-diffusion parameters using second kind Chebyshev wavelet method...
November 17, 2017: Journal of Membrane Biology
https://www.readbyqxmd.com/read/29147563/a-novel-microaneurysms-detection-approach-based-on-convolutional-neural-networks-with-reinforcement-sample-learning-algorithm
#7
Umit Budak, Abdulkadir Şengür, Yanhui Guo, Yaman Akbulut
Microaneurysms (MAs) are known as early signs of diabetic-retinopathy which are called red lesions in color fundus images. Detection of MAs in fundus images needs highly skilled physicians or eye angiography. Eye angiography is an invasive and expensive procedure. Therefore, an automatic detection system to identify the MAs locations in fundus images is in demand. In this paper, we proposed a system to detect the MAs in colored fundus images. The proposed method composed of three stages. In the first stage, a series of pre-processing steps are used to make the input images more convenient for MAs detection...
December 2017: Health Information Science and Systems
https://www.readbyqxmd.com/read/29147561/synthesis-and-reactivity-of-a-4his-enzyme-model-complex
#8
Jia Li, Atanu Banerjee, Timothy A Hasse, Reza Loloee, Shannon M Biros, Richard J Staples, Ferman A Chavez
A new iron(II) complex has been prepared and characterized. [Fe(TrIm)4(OTf)2] (1, TrIm = 1-Tritylimidazole). The solid state structure of 1 has been determined by X-ray crystallography. Compound 1 crystallizes in triclinic space group P1̄, with a = 13.342(7) Å, b = 13.5131(7) Å and c = 13.7025(7) Å. The iron center resides in distorted octahedral geometry coordinated to four equatorial imidazole groups and two axial triflate oxygens groups. The complex is high spin between 20 K and 300 K as indicated by variable field variable temperature magnetic measurements...
2017: RSC Advances
https://www.readbyqxmd.com/read/29145420/effects-of-increased-levels-of-atmospheric-co2-and-high-temperatures-on-rice-growth-and-quality
#9
Shuo Liu, Muhammad Ahmed Waqas, Song-He Wang, Xiang-Yang Xiong, Yun-Fan Wan
The increased atmospheric temperatures resulting from the increased concentration of atmospheric carbon dioxide (CO2) have had a profound influence on global rice production. China serves as an important area for producing and consuming rice. Therefore, exploring the effects of the simultaneously rising levels of atmospheric CO2 and temperatures on rice growth and quality in the future is very important. The present study was designed to measure the most important aspects of variation for rice-related physiological, ecological and quality indices in different growing periods under a simultaneous increase of CO2 and temperature, through simulation experiments in climate-controlled growth chambers, with southern rice as the study object...
2017: PloS One
https://www.readbyqxmd.com/read/29145081/elimination-of-chlorine-refractory-carbamazepine-by-breakpoint-chlorination-reactive-species-and-oxidation-byproducts
#10
Wen-Long Wang, Qian-Yuan Wu, Ye Du, Nan Huang, Hong-Ying Hu
Breakpoint chlorination can be commonly observed in the chlorination of water treatments when ammonia is present. In this study, it was found that breakpoint chlorination can remarkably eliminate a ubiquitous and chlorine-refractory micropollutant, carbamazepine (CBZ), with the removal of 72% at neutral condition. At neutral pH, low CBZ elimination was observed at a chlorine/ammonia molar ratio (Cl/N) of 1.0 and higher CBZ elimination was observed as Cl/N ratio increased from 1.0 to 1.6 (breakpoint), indicating that CBZ elimination was closely related to the generation and decomposition of chloramines...
November 7, 2017: Water Research
https://www.readbyqxmd.com/read/29145003/the-importance-of-saprinus-semistriatus-coleoptera-histeridae-for-estimating-the-minimum-post-mortem-interval
#11
I Szelecz, N Feddern, C V W Seppey, J Amendt, E A D Mitchell
In forensic science, the use of entomological evidence to estimate the minimum post-mortem interval can be crucial. However, not all cadaver-visiting insects are equally useful. Our focus is on the histerid beetle Saprinus semistriatus (Scriba 1790) (Histeridae; Coleoptera). Histeridae are common predators that feed mainly on dipteran larvae on carrion and dung. We review 23 publications mentioning this species and provide new experimental data on its temporal pattern beneath and on hanging pig cadavers. In a field experiment near Neuchâtel, Switzerland, we recorded the abundance of S...
November 10, 2017: Legal Medicine
https://www.readbyqxmd.com/read/29144747/structural-variability-of-4f-and-5f-thiocyanate-complexes-and-dissociation-of-uranium-iii-thiocyanate-bonds-with-increased-ionicity
#12
Saptarshi Biswas, Shuwen Ma, Stefano Nuzzo, Brendan Twamley, Andrew T Russell, James A Platts, František Hartl, Robert J Baker
A series of complexes [Et4N][Ln(NCS)4(H2O)4] (Ln = Pr, Tb, Dy, Ho, Yb) have been structurally characterized, all showing the same structure, namely a distorted square antiprismatic coordination geometry, and the Ln-O and Ln-N bond lengths following the expected lanthanide contraction. When the counterion is Cs(+), a different structural motif is observed and the eight-coordinate complex Cs5[Nd(NCS)8] isolated. The thorium compounds [Me4N]4[Th(NCS)7(NO3)] and [Me4N]4[Th(NCS)6(NO3)2] have been characterized, and high coordination numbers are also observed...
November 16, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/29144300/enhancing-dewaterability-of-waste-activated-sludge-by-combined-oxidative-conditioning-process-with-zero-valent-iron-and-peroxymonosulfate
#13
Xu Zhou, Wenbiao Jin, Hongyi Chen, Chuan Chen, Songfang Han, Renjie Tu, Wei Wei, Shu-Hong Gao, Guo-Jun Xie, Qilin Wang
The enhancement of sludge dewaterability is of great importance for facilitating the sludge disposal during the operation of wastewater treatment plants. In this study, a novel oxidative conditioning approach was applied to enhance the dewaterability of waste activated sludge by the combination of zero-valent iron (ZVI) and peroxymonosulfate (PMS). It was found that the dewaterability of sludge was significantly improved after the addition of ZVI (0-4 g/g TSS) (TSS: total suspended solids) and PMS (0-1 g/g TSS)...
November 2017: Water Science and Technology: a Journal of the International Association on Water Pollution Research
https://www.readbyqxmd.com/read/29143772/fault-detection-of-bearing-systems-through-eemd-and-optimization-algorithm
#14
Dong-Han Lee, Jong-Hyo Ahn, Bong-Hwan Koh
This study proposes a fault detection and diagnosis method for bearing systems using ensemble empirical mode decomposition (EEMD) based feature extraction, in conjunction with particle swarm optimization (PSO), principal component analysis (PCA), and Isomap. First, a mathematical model is assumed to generate vibration signals from damaged bearing components, such as the inner-race, outer-race, and rolling elements. The process of decomposing vibration signals into intrinsic mode functions (IMFs) and extracting statistical features is introduced to develop a damage-sensitive parameter vector...
October 28, 2017: Sensors
https://www.readbyqxmd.com/read/29143214/cellular-processing-of-gold-nanoparticles-ce-icp-ms-evidence-for-the-speciation-changes-in-human-cytosol
#15
Joanna Legat, Magdalena Matczuk, Andrei R Timerbaev, Maciej Jarosz
The cellular uptake of gold nanoparticles (AuNPs) may (or may not) affect their speciation, but information on the chemical forms in which the particles exist in the cell remains obscure. An analytical method based on the use of capillary electrophoresis hyphenated with inductively coupled plasma mass spectrometry (ICP-MS) has been proposed to shed light on the intracellular processing of AuNPs. It was observed that when being introduced into normal cytosol, the conjugates of 10-50 nm AuNPs with albumin evolved in human serum stayed intact...
November 15, 2017: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/29143041/joint-experimental-and-theoretical-studies-of-the-surprising-stability-of-the-aryl-pentazole-upon-noncovalent-binding-to-%C3%AE-cyclodextrin
#16
Yu-Zhang Yang, Xiao-Feng Liu, Ru-Bo Zhang, Si-Ping Pang
Herein, binding of the β-cyclodextrin (β-CD) host to the unstable aryl pentazole guest has been confirmed experimentally and theoretically. After the confinement of aryl pentazole, electron density reorganization was studied by M06-2X dispersion-corrected DFT and further reflected in the characteristic shift in the NMR spectra. Among the host-guest complexes, the inclusion complex is favored with the phenyl ring expectedly encapsulated within the cavity through noncovalent interactions such as hydrogen bonding, C-Hπ, and the special Csp(2)-HH-Csp(3) bonding discovered by the NBO, QTAIM, and NCI-RDG theories...
November 16, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29142740/combined-empirical-mode-decomposition-and-texture-features-for-skin-lesion-classification-using-quadratic-support-vector-machine
#17
Maram A Wahba, Amira S Ashour, Sameh A Napoleon, Mustafa M Abd Elnaby, Yanhui Guo
Purpose: Basal cell carcinoma is one of the most common malignant skin lesions. Automated lesion identification and classification using image processing techniques is highly required to reduce the diagnosis errors. Methods: In this study, a novel technique is applied to classify skin lesion images into two classes, namely the malignant Basal cell carcinoma and the benign nevus. A hybrid combination of bi-dimensional empirical mode decomposition and gray-level difference method features is proposed after hair removal...
December 2017: Health Information Science and Systems
https://www.readbyqxmd.com/read/29141438/synthesis-and-stability-of-hydrogen-selenide-compounds-at-high-pressure
#18
Edward J Pace, Jack Binns, Miriam Peña Alvarez, Philip Dalladay-Simpson, Eugene Gregoryanz, Ross T Howie
The observation of high-temperature superconductivity in hydride sulfide (H2S) at high pressures has generated considerable interest in compressed hydrogen-rich compounds. High-pressure hydrogen selenide (H2Se) has also been predicted to be superconducting at high temperatures; however, its behaviour and stability upon compression remains unknown. In this study, we synthesize H2Se in situ from elemental Se and molecular H2 at pressures of 0.4 GPa and temperatures of 473 K. On compression at 300 K, we observe the high-pressure solid phase sequence (I-I'-IV) of H2Se through Raman spectroscopy and x-ray diffraction measurements, before dissociation into its constituent elements...
November 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29141427/tensor-structured-coupled-cluster-theory
#19
Roman Schutski, Jinmo Zhao, Thomas M Henderson, Gustavo E Scuseria
We derive and implement a new way of solving coupled cluster equations with lower computational scaling. Our method is based on the decomposition of both amplitudes and two electron integrals, using a combination of tensor hypercontraction and canonical polyadic decomposition. While the original theory scales as O(N(6)) with respect to the number of basis functions, we demonstrate numerically that we achieve sub-millihartree difference from the original theory with O(N(4)) scaling. This is accomplished by solving directly for the factors that decompose the cluster operator...
November 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29141415/contribution-to-viscosity-from-the-structural-relaxation-via-the-atomic-scale-green-kubo-stress-correlation-function
#20
V A Levashov
We studied the connection between the structural relaxation and viscosity for a binary model of repulsive particles in the supercooled liquid regime. The used approach is based on the decomposition of the macroscopic Green-Kubo stress correlation function into the correlation functions between the atomic level stresses. Previously we used the approach to study an iron-like single component system of particles. The role of vibrational motion has been addressed through the demonstration of the relationship between viscosity and the shear waves propagating over large distances...
November 14, 2017: Journal of Chemical Physics
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