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https://www.readbyqxmd.com/read/29151216/practical-nonuniform-sampling-and-non-fourier-spectral-reconstruction-for-multidimensional-nmr
#1
Mark W Maciejewski, Adam D Schuyler, Jeffrey C Hoch
A general approach to accelerating multidimensional NMR experiments via nonuniform sampling and maximum entropy spectral reconstruction was first demonstrated by Laue and colleagues in 1987. Following decades of continual improvements involving dozens of software packages for non-Fourier spectral analysis and many different schemes for nonuniform sampling, we still lack a clear consensus on best practices for sampling or spectral reconstruction, and programs for processing nonuniformly sampled data are not particularly user-friendly...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29150622/evidence-of-quantum-phase-transition-in-real-space-vacuum-entanglement-of-higher-derivative-scalar-quantum-field-theories
#2
S Santhosh Kumar, S Shankaranarayanan
In a bipartite set-up, the vacuum state of a free Bosonic scalar field is entangled in real space and satisfies the area-law- entanglement entropy scales linearly with area of the boundary between the two partitions. In this work, we show that the area law is violated in two spatial dimensional model Hamiltonian having dynamical critical exponent z = 3. The model physically corresponds to next-to-next-to-next nearest neighbour coupling terms on a lattice. The result reported here is the first of its kind of violation of area law in Bosonic systems in higher dimensions and signals the evidence of a quantum phase transition...
November 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29149564/binding-thermodynamics-and-kinetics-calculations-using-chemical-host-and-guest-a-comprehensive-picture-of-molecular-recognition
#3
Zhiye Tang, Chia-En A Chang
Understanding the fine balance between changes of entropy and enthalpy and the competition between a guest and water molecules in molecular binding is crucial in fundamental studies and practical applications. Experiments provide measurements. However, illustrating the binding/unbinding processes gives a complete picture of molecular recognition not directly available from experiments, and computational methods bridge the gaps. Here, we investigated guest association/dissociation with β-cyclodextrin (β-CD) by using microsecond-timescale molecular dynamics (MD) simulations, post-analysis and numerical calculations...
November 17, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29149201/the-influence-of-filtering-and-downsampling-on-the-estimation-of-transfer-entropy
#4
Immo Weber, Esther Florin, Michael von Papen, Lars Timmermann
Transfer entropy (TE) provides a generalized and model-free framework to study Wiener-Granger causality between brain regions. Because of its nonparametric character, TE can infer directed information flow also from nonlinear systems. Despite its increasing number of applications in neuroscience, not much is known regarding the influence of common electrophysiological preprocessing on its estimation. We test the influence of filtering and downsampling on a recently proposed nearest neighborhood based TE estimator...
2017: PloS One
https://www.readbyqxmd.com/read/29148560/complex-formation-of-nickel-ii-with-dimethyl-sulfoxide-methanol-and-acetonitrile-in-a-tfsa-based-ionic-liquid-of-c2mim-tfsa
#5
Yutaro Kawazu, Hiroshi Hoke, Yasunori Yamada, Tatsuya Umecky, Kazuhiko Ozutsumi, Toshiyuki Takamuku
The thermodynamics of complex formation of Ni(2+) with molecular liquids (ML), dimethyl sulfoxide (DMSO), methanol (MeOH), and acetonitrile (AN) in the ionic liquid (IL) of 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)amide ([C2mim][TFSA]) has been elucidated using ultraviolet (UV)-visible spectroscopy. X-ray structural analyses for single crystals grown from Ni(2+)-[C2mim][TFSA]-DMSO and -AN solutions at high ML contents have shown that six DMSO oxygen or AN nitrogen atoms coordinate with Ni(2+) to form octahedral structures of [Ni(dmso)6](TFSA)2 and [Ni(an)6](TFSA)2, respectively...
November 17, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29147146/relationships-between-short-and-fast-brain-timescales
#6
Eva Déli, Arturo Tozzi, James F Peters
Brain electric activity exhibits two important features: oscillations with different timescales, characterized by diverse functional and psychological outcomes, and a temporal power law distribution. In order to further investigate the relationships between low- and high- frequency spikes in the brain, we used a variant of the Borsuk-Ulam theorem which states that, when we assess the nervous activity as embedded in a sphere equipped with a fractal dimension, we achieve two antipodal points with similar features (the slow and fast, scale-free oscillations)...
December 2017: Cognitive Neurodynamics
https://www.readbyqxmd.com/read/29146982/photonic-simulation-of-entanglement-growth-and-engineering-after-a-spin-chain-quench
#7
Ioannis Pitsios, Leonardo Banchi, Adil S Rab, Marco Bentivegna, Debora Caprara, Andrea Crespi, Nicolò Spagnolo, Sougato Bose, Paolo Mataloni, Roberto Osellame, Fabio Sciarrino
The time evolution of quantum many-body systems is one of the most important processes for benchmarking quantum simulators. The most curious feature of such dynamics is the growth of quantum entanglement to an amount proportional to the system size (volume law) even when interactions are local. This phenomenon has great ramifications for fundamental aspects, while its optimisation clearly has an impact on technology (e.g., for on-chip quantum networking). Here we use an integrated photonic chip with a circuit-based approach to simulate the dynamics of a spin chain and maximise the entanglement generation...
November 17, 2017: Nature Communications
https://www.readbyqxmd.com/read/29144529/driving-dynamic-colloidal-assembly-using-eccentric-self-propelled-colloids
#8
Zhan Ma, Qun-Li Lei, Ran Ni
Designing protocols to dynamically direct the self-assembly of colloidal particles has become an important direction in soft matter physics because of promising applications in the fabrication of dynamic responsive functional materials. Here, using computer simulations, we found that in the mixture of passive colloids and eccentric self-propelled active particles, when the eccentricity and self-propulsion of active particles are high enough, the eccentric active particles can push passive colloids to form a large dense dynamic cluster, and the system undergoes a novel dynamic demixing transition...
November 16, 2017: Soft Matter
https://www.readbyqxmd.com/read/29143152/electrochemical-and-theoretical-studies-of-the-interactions-of-a-pyridyl-based-corrosion-inhibitor-with-iron-clusters-fe15-fe30-fe45-and-fe60
#9
Julian Cruz-Borbolla, Esteban Garcia-Ochoa, Jayanthi Narayanan, Pablo Maldonado-Rivas, Thangarasu Pandiyan, José M Vásquez-Pérez
The capacity of 2,6-bis[((2-pyridylmethyl)oxy)methyl)]pyridine (BPMMP) to inhibit the corrosion of mild carbon steel in HCl was analyzed. In a polarization study, both the cathodic and anodic currents were appreciably decreased in the presence of BPMMP, suggesting that this ligand is effective at inhibiting corrosion at the metal surface. This conclusion is consistent with the results of impedance analysis, where only one time constant corresponding to one depressed capacitive loop was detected, and the diameter of the impedance plot was directly related to the concentration of BPMMP...
November 15, 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/29142240/robust-segmentation-of-the-full-cerebral-vasculature-in-4d-ct-of-suspected-stroke-patients
#10
Midas Meijs, Ajay Patel, Sil C van de Leemput, Mathias Prokop, Ewoud J van Dijk, Frank-Erik de Leeuw, Frederick J A Meijer, Bram van Ginneken, Rashindra Manniesing
A robust method is presented for the segmentation of the full cerebral vasculature in 4-dimensional (4D) computed tomography (CT). The method consists of candidate vessel selection, feature extraction, random forest classification and postprocessing. Image features include among others the weighted temporal variance image and parameters, including entropy, of an intensity histogram in a local region at different scales. These histogram parameters revealed to be a strong feature in the detection of vessels regardless of shape and size...
November 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29141431/development-of-isothermal-isobaric-replica-permutation-method-for-molecular-dynamics-and-monte-carlo-simulations-and-its-application-to-reveal-temperature-and-pressure-dependence-of-folded-misfolded-and-unfolded-states-of-chignolin
#11
Masataka Yamauchi, Hisashi Okumura
We developed a two-dimensional replica-permutation molecular dynamics method in the isothermal-isobaric ensemble. The replica-permutation method is a better alternative to the replica-exchange method. It was originally developed in the canonical ensemble. This method employs the Suwa-Todo algorithm, instead of the Metropolis algorithm, to perform permutations of temperatures and pressures among more than two replicas so that the rejection ratio can be minimized. We showed that the isothermal-isobaric replica-permutation method performs better sampling efficiency than the isothermal-isobaric replica-exchange method and infinite swapping method...
November 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29140606/mr-textural-analysis-on-t2-flair-images-for-the-prediction-of-true-oligodendroglioma-by-the-2016-who-genetic-classification
#12
Wenting Rui, Yan Ren, Yin Wang, Xinyi Gao, Xiao Xu, Zhenwei Yao
BACKGROUND: The genetic status of 1p/19q is important for differentiating oligodendroglioma, isocitrate-dehydrogenase (IDH)-mutant, and 1p/19q-codeleted from diffuse astrocytoma, IDH-mutant according to the 2016 World Health Organization (WHO) criteria. PURPOSE: To assess the value of magnetic resonance textural analysis (MRTA) on T2 fluid-attenuated inversion recovery (FLAIR) images for making a genetically integrated diagnosis of true oligodendroglioma by WHO guidelines...
November 15, 2017: Journal of Magnetic Resonance Imaging: JMRI
https://www.readbyqxmd.com/read/29140296/microstructure-mechanical-and-tribological-properties-of-oxide-dispersion-strengthened-high-entropy-alloys
#13
Xinyu Liu, Hangboce Yin, Yi Xu
A novel metal matrix composite CrMnFeCoNi with Y₂O₃ as reinforcement phase was designed and manufactured by mechanical alloying and spark plasma sintering. After sintering at 900 °C for 5 min, the microstructure consisted of a FCC matrix and Y₂O₃ nanoparticles. The addition of 0.25 wt % Y₂O₃ increased the room temperature tensile strength of the CrMnFeCoNi base from 868 MPa to 1001 MPa, while the mechanical properties of the addition of 0.5 wt % Y₂O₃ composite decreased. In the meantime, the addition of Y₂O₃ had no significant influence on the coefficient of friction, while the addition of 0...
November 15, 2017: Materials
https://www.readbyqxmd.com/read/29140113/prediction-of-pancreatic-neuroendocrine-tumor-grade-based-on-ct-features-and-texture-analysis
#14
Rodrigo Canellas, Kristine S Burk, Anushri Parakh, Dushyant V Sahani
OBJECTIVE: The purposes of this study were to assess whether CT texture analysis and CT features are predictive of pancreatic neuroendocrine tumor (PNET) grade based on the World Health Organization (WHO) classification and to identify features related to disease progression after surgery. MATERIALS AND METHODS: Preoperative contrast-enhanced CT images of 101 patients with PNETs were assessed. The images were evaluated for tumor location, tumor size, tumor pattern, predominantly solid or cystic composition, presence of calcification, presence of heterogeneous enhancement on contrast-enhanced images, presence of pancreatic duct dilatation, presence of pancreatic atrophy, presence of vascular involvement by the tumor, and presence of lymphadenopathy...
November 15, 2017: AJR. American Journal of Roentgenology
https://www.readbyqxmd.com/read/29139171/structural-insights-into-a-thermostable-variant-of-human-carbonic-anhydrase-ii
#15
Kelsey M Kean, Joseph J Porter, Ryan A Mehl, P Andrew Karplus
Carbonic anhydrase is an enzyme of interest for many biotechnological developments including carbon sequestration. These applications often require harsh conditions, so there is a need for the development of thermostable variants. One of the most thermostable human carbonic anhydrase II variants (HCAIIts) was patented in 2006. Here, we report the ultra-high resolution crystal structure of HCAIIts. The structural changes seen are consistent with each of the six mutations involved acting largely independently and variously resulting in increased H-bonding, improved packing, and reduced side chain entropy loss upon folding to yield the increased stability...
November 15, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/29138873/effects-of-cognitive-load-on-the-amount-and-temporal-structure-of-postural-sway-variability-in-stroke-survivors
#16
Hajar Mehdizadeh, Kinda Khalaf, Hamed Ghomashchi, Ghorban Taghizadeh, Ismaeil Ebrahimi, Parvaneh Taghavi Azar Sharabiani, Seyed Javad Mousavi, Mohamad Parnianpour
This study aimed to investigate the variability in postural sway patterns during quiet standing in stroke survivors. The postural sway was measured in 19 stroke survivors, as well as 19 healthy demographically matched participants, at 3 levels of postural difficulty (rigid surface with closed and open eyes, and foam surface with closed eyes), and 3 levels of cognitive difficulty (without a cognitive task, easy and difficult cognitive tasks). Both linear analyses (the amount of postural sway variability, including the standard deviation of the COP velocity in both the anteroposterior (AP) and mediolateral (ML) directions), as well as non-linear analyses [the temporal structure of the COP variability, including % Recurrence, % Determinism, Shannon Entropy, Trend and the maximum diagonal line (D max)] were employed...
November 14, 2017: Experimental Brain Research. Experimentelle Hirnforschung. Expérimentation Cérébrale
https://www.readbyqxmd.com/read/29137749/exceptionally-high-cavitation-erosion-and-corrosion-resistance-of-a-high-entropy-alloy
#17
R B Nair, H S Arora, Sundeep Mukherjee, S Singh, H Singh, H S Grewal
Cavitation erosion and corrosion of structural materials are serious concerns for marine and offshore industries. Durability and performance of marine components are severely impaired due to degradation from erosion and corrosion. Utilization of advanced structural materials can play a vital role in limiting such degradation. High entropy alloys (HEAs) are a relatively new class of advanced structural materials with exceptional properties. In the present work, we report on the cavitation erosion behavior of Al0...
March 2018: Ultrasonics Sonochemistry
https://www.readbyqxmd.com/read/29137637/molecular-evolution-of-hiv-1-integrase-during-the-20%C3%A2-years-prior-to-the-first-approval-of-integrase-inhibitors
#18
Karolin Meixenberger, Kaveh Pouran Yousef, Maureen Rebecca Smith, Sybille Somogyi, Stefan Fiedler, Barbara Bartmeyer, Osamah Hamouda, Norbert Bannert, Max von Kleist, Claudia Kücherer
BACKGROUND: Detailed knowledge of the evolutionary potential of polymorphic sites in a viral protein is important for understanding the development of drug resistance in the presence of an inhibitor. We therefore set out to analyse the molecular evolution of the HIV-1 subtype B integrase at the inter-patient level in Germany during a 20-year period prior to the first introduction of integrase strand inhibitors (INSTIs). METHODS: We determined 337 HIV-1 integrase subtype B sequences (amino acids 1-278) from stored plasma samples of antiretroviral treatment-naïve individuals newly diagnosed with HIV-1 between 1986 and 2006...
November 14, 2017: Virology Journal
https://www.readbyqxmd.com/read/29135467/univariate-and-multivariate-conditional-entropy-measures-for-the-characterization-of-short-term-cardiovascular-complexity-under-physiological-stress
#19
Martina Valente, Michal Javorka, Alberto Porta, Vlasta Bari, Jana Krohova, Barbora Czippelova, Zuzana Turianikova, Giandomenico Nollo, Luca Faes
A defining feature of physiological systems under the neuroautonomic regulation is their dynamical complexity. The most common approach to assess physiological complexity from short-term recordings, i.e. to compute the rate of entropy generation of an individual system by means of measures of conditional entropy (CE), does not consider that complexity may change when the investigated system is part of a network of physiological interactions. This study aims at extending the concept of short-term complexity towards the perspective of network physiology, defining multivariate CE measures whereby multiple physiological processes are accounted for in the computation of entropy rates...
November 14, 2017: Physiological Measurement
https://www.readbyqxmd.com/read/29134324/trend-to-equilibrium-for-a-reaction-diffusion-system-modelling-reversible-enzyme-reaction
#20
Ján Eliaš
A spatio-temporal evolution of chemicals appearing in a reversible enzyme reaction and modelled by a four-component reaction-diffusion system with the reaction terms obtained by the law of mass action is considered. The large time behaviour of the system is studied by means of entropy methods.
November 13, 2017: Bulletin of Mathematical Biology
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