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https://www.readbyqxmd.com/read/28640851/ligand-mediated-and-tertiary-interactions-cooperatively-stabilize-the-p1-region-in-the-guanine-sensing-riboswitch
#1
Christian A Hanke, Holger Gohlke
Riboswitches are genetic regulatory elements that control gene expression depending on ligand binding. The guanine-sensing riboswitch (Gsw) binds ligands at a three-way junction formed by paired regions P1, P2, and P3. Loops L2 and L3 cap the P2 and P3 helices and form tertiary interactions. Part of P1 belongs to the switching sequence dictating the fate of the mRNA. Previous studies revealed an intricate relationship between ligand binding and presence of the tertiary interactions, and between ligand binding and influence on the P1 region...
2017: PloS One
https://www.readbyqxmd.com/read/28640748/spike-detection-using-a-multiresolution-entropy-based-method
#2
Sajjad Farashi
Correct interpretation of neural mechanisms depends on the accurate detection of neuronal activities, which become visible as spikes in the electrical activity of neurons. In the present work, a novel entropy based method is proposed for spike detection which employs the fact that transient spike events change the entropy level of the neural time series. In this regard, the time-dependent entropy method can be used for detecting spike times, where the entropy of a selected segment of a neural time series, using a sliding window approach, is calculated and the time of the events are highlighted by sharp peaks in the output of the time-dependent entropy method...
June 22, 2017: Biomedizinische Technik. Biomedical Engineering
https://www.readbyqxmd.com/read/28637203/morphological-diversity-strongly-constrains-synaptic-connectivity-and-plasticity
#3
Michael W Reimann, Anna-Lena Horlemann, Srikanth Ramaswamy, Eilif B Muller, Henry Markram
Synaptic connectivity between neurons is naturally constrained by the anatomical overlap of neuronal arbors, the space on the axon available for synapses, and by physiological mechanisms that form synapses at a subset of potential synapse locations. What is not known is how these constraints impact emergent connectivity in a circuit with diverse morphologies. We investigated the role of morphological diversity within and across neuronal types on emergent connectivity in a model of neocortical microcircuitry...
June 20, 2017: Cerebral Cortex
https://www.readbyqxmd.com/read/28636363/distinct-protein-hydration-water-species-defined-by-spatially-resolved-spectra-of-intermolecular-vibrations
#4
Viren Sureshkumar Pattni, Tatiana Vasilevskaya, Walter Thiel, Matthias Heyden
In this molecular dynamics simulation study, we analyze intermolecular vibrations in the hydration shell of a solvated enyzme, the membrane type 1--matrix metalloproteinase, with high spatial resolution. Our approach allows us to characterize vibrational signatures of the local hydrogen bond network, the translational mobility of water molecules, as well as the molecular entropy, in specific local environments. Our study demonstrates the heterogeneity of water properties within the hydration shell of a complex biomolecule...
June 21, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28636317/downsizing-proto-oncogene-cfos-to-short-helix-constrained-peptides-that-bind-jun
#5
Daniel Baxter, Samuel R Perry, Timothy A Hill, W Mei Kok, Nathan R Zaccai, R Leo Brady, David P Fairlie, Jody M Mason
The oncogenic transcription factor activator protein-1 (AP-1) is a DNA-binding protein that assembles through dimerization of Fos and Jun protein subunits, their leucine-rich helical sequences entwining into a coiled-coil structure. This study reports on downsizing the proto-oncogene cFos protein (380 residues) to shorter peptides (37-25 residues) modified with helix-inducing constraints to enhance binding to Jun. A crystal structure is reported for a 37-residue Fos-derived peptide (FosW) bound to Jun. This guided iterative downsizing of FosW to shorter peptide sequences that were constrained into stable water-soluble α-helices by connecting amino acid side chains to form cyclic pentapeptide components...
June 21, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28635287/configurational-disorder-of-water-hydrogen-bond-network-at-the-protein-dynamical-transition
#6
Obaidur Rahaman, Maria Kalimeri, Marina Katava, Alessandro Paciaroni, Fabio Sterpone
We introduce a novel strategy to quantify the disorder of extended water-water hydrogen-bond (HB) networks sampled in particle-based computer simulations. The method relies on the conformational clustering of the HB connectivity states. We successfully applied it to unveil the fine relationship among the protein dynamical transition in hydrated powder, which marks the activation of protein flexibility at Td∽240 K, and the sudden increase of the configurational disorder of the water HB network enveloping the proteins...
June 21, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28635126/reinterpreting-maximum-entropy-in-ecology-a-null-hypothesis-constrained-by-ecological-mechanism
#7
James P O'Dwyer, Andrew Rominger, Xiao Xiao
Simplified mechanistic models in ecology have been criticised for the fact that a good fit to data does not imply the mechanism is true: pattern does not equal process. In parallel, the maximum entropy principle (MaxEnt) has been applied in ecology to make predictions constrained by just a handful of state variables, like total abundance or species richness. But an outstanding question remains: what principle tells us which state variables to constrain? Here we attempt to solve both problems simultaneously, by translating a given set of mechanisms into the state variables to be used in MaxEnt, and then using this MaxEnt theory as a null model against which to compare mechanistic predictions...
July 2017: Ecology Letters
https://www.readbyqxmd.com/read/28634332/predicting-the-potential-risk-area-of-illegal-vaccine-trade-in-china
#8
Yilan Liao, Yanhui Lei, Zhoupeng Ren, Huiyan Chen, Dongyue Li
Since the disclosure of the "Illegal vaccine operation series case in Jinan, Shandong" in March, 2016, this issue has attracted a great deal of attention and has led to public concerns about the safety and efficacy of the vaccines involved in this case. The main purpose of this paper is to scientifically and scrupulously predict the possible geographic distribution of illegal vaccines in China, and provide a foundation to guide future governmental policies and actions. A species distribution model was used because of the advantages of using presence/pseudo-absence or presence-only data, and it performs well with incomplete species distribution data...
June 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28631793/organic-inorganic-macroion-coacervate-complexation
#9
Benxin Jing, Jie Qiu, Yingxi Zhu
Coacervate complexes that are liquid-liquid separated complex materials are often formed by stoichiometrically mixing oppositely charged polyelectrolytes in salted aqueous solution. Entropy-driven ion pairing, resulting from the release of counterions near polyelectrolytes, has been identified as the primary driving force for coacervate formation between oppositely charged polyelectrolytes, including proteins and DNA, in aqueous solution. In this work we have examined the complexation between net neutral zwitterionic poly(sulfobetaine methacrylate) (PSBMA) and inorganic polyoxometalate (POM) polyanions in LiCl aqueous solutions...
June 20, 2017: Soft Matter
https://www.readbyqxmd.com/read/28631123/modeling-solubility-of-co2-hydrocarbon-gas-in-ionic-liquid-emim-fap-using-aspen-plus-simulations
#10
Bishwadeep Bagchi, Sushmita Sati, Vidyasagar Shilapuram
The Peng-Robinson equation of state with quadratic van der Waals (vdW) mixing rule model was chosen to perform the thermodynamic calculations in Flash3 column of Aspen Plus to predict the solubility of CO2 or any one of the hydrocarbons (HCs) among methane, ethane, propane, and butane in an ionic liquid 1-ethyl-3-methylimidazolium tris(pentafluoroethyl)trifluorophosphate ([emim][FAP]). Bubble point pressure, solubility, bubble point temperature, fugacity, and partial molar volume at infinite dilution were obtained from the simulations, and enthalpy of absorption, Gibbs free energy of solvation, and entropy change of absorption were estimated by thermodynamic relations...
June 19, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28630885/bayesian-framework-inspired-no-reference-region-of-interest-quality-measure-for-brain-mri-images
#11
Michael Osadebey, Marius Pedersen, Douglas Arnold, Katrina Wendel-Mitoraj
We describe a postacquisition, attribute-based quality assessment method for brain magnetic resonance imaging (MRI) images. It is based on the application of Bayes theory to the relationship between entropy and image quality attributes. The entropy feature image of a slice is segmented into low- and high-entropy regions. For each entropy region, there are three separate observations of contrast, standard deviation, and sharpness quality attributes. A quality index for a quality attribute is the posterior probability of an entropy region given any corresponding region in a feature image where quality attribute is observed...
April 2017: Journal of Medical Imaging
https://www.readbyqxmd.com/read/28630680/purely-entropic-self-assembly-of-the-bicontinuous-ia3d-gyroid-phase-in-equilibrium-hard-pear-systems
#12
Philipp W A Schönhöfer, Laurence J Ellison, Matthieu Marechal, Douglas J Cleaver, Gerd E Schröder-Turk
We investigate a model of hard pear-shaped particles which forms the bicontinuous Ia[Formula: see text]d structure by entropic self-assembly, extending the previous observations of Barmes et al. (2003 Phys. Rev. E68, 021708. (doi:10.1103/PhysRevE.68.021708)) and Ellison et al. (2006 Phys. Rev. Lett.97, 237801. (doi:10.1103/PhysRevLett.97.237801)). We specifically provide the complete phase diagram of this system, with global density and particle shape as the two variable parameters, incorporating the gyroid phase as well as disordered isotropic, smectic and nematic phases...
August 6, 2017: Interface Focus
https://www.readbyqxmd.com/read/28630434/metallicity-in-a-holstein-hubbard-chain-at-half-filling-with-gaussian-anharmonicity
#13
Ch Uma Lavanya, I V Sankar, Ashok Chatterjee
The Holstein-Hubbard model with Gaussian phonon anharmonicity is studied in one-dimension at half filling using a variational method based on a series of canonical transformations. A fairly accurate phonon state is chosen to average the transformed Holstein-Hubbard Hamiltonian to obtain an effective Hubbard model which is then solved using the exact Bethe - ansatz following Lieb and Wu to obtain the ground state energy, the average lattice displacement and the renormalized parameters. The Mott-Hubbard criterion, local spin moment and the von Neumann entropy (which is a measure of quantum entanglement) are calculated to determine the ground state phase diagram which shows that the width of the metallic phase flanked by the SDW and CDW phases increases with increasing anharmonicity at low and moderate values of anharmonicity but eventually saturates when the anharmonicity becomes substantially large...
June 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28629778/posture-and-gaze-tracking-of-a-vertically-moving-target-reveals-age-related-constraints-in-visuo-motor-coupling
#14
H Sotirakis, A Kyvelidou, N Stergiou, V Hatzitaki
Previously we have demonstrated that the effect of aging on posture and gaze active tracking of a visual target moving in the horizontal direction is dependent on target's complexity. In this study, we asked whether a similar phenomenon is present when tracking a visual target moving with varying complexity in the vertical direction. Ten young (22.98±2.9years) and 10 older adults (72.45±4.72years) tracked for 120seconds, a visual target moving vertically by shifting their bodyweight in the anterior-posterior direction...
June 16, 2017: Neuroscience Letters
https://www.readbyqxmd.com/read/28629416/ct-texture-features-are-associated-with-overall-survival-in-pancreatic-ductal-adenocarcinoma-a-quantitative-analysis
#15
Armin Eilaghi, Sameer Baig, Yucheng Zhang, Junjie Zhang, Paul Karanicolas, Steven Gallinger, Farzad Khalvati, Masoom A Haider
BACKGROUND: To assess whether CT-derived texture features predict survival in patients undergoing resection for pancreatic ductal adenocarcinoma (PDAC). METHODS: Thirty patients with pre-operative CT from 2007 to 2012 for PDAC were included. Tumor size and five texture features namely uniformity, entropy, dissimilarity, correlation, and inverse difference normalized were calculated. Mann-Whitney rank sum test was used to compare tumor with normal pancreas. Receiver operating characteristics (ROC) analysis, Cox regression and Kaplan-Meier tests were used to assess association of texture features with overall survival (OS)...
June 19, 2017: BMC Medical Imaging
https://www.readbyqxmd.com/read/28628618/solving-the-influence-maximization-problem-reveals-regulatory-organization-of-the-yeast-cell-cycle
#16
David L Gibbs, Ilya Shmulevich
The Influence Maximization Problem (IMP) aims to discover the set of nodes with the greatest influence on network dynamics. The problem has previously been applied in epidemiology and social network analysis. Here, we demonstrate the application to cell cycle regulatory network analysis for Saccharomyces cerevisiae. Fundamentally, gene regulation is linked to the flow of information. Therefore, our implementation of the IMP was framed as an information theoretic problem using network diffusion. Utilizing more than 28,000 regulatory edges from YeastMine, gene expression dynamics were encoded as edge weights using time lagged transfer entropy, a method for quantifying information transfer between variables...
June 19, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28628398/skill-level-changes-the-coordination-and-variability-of-standing-posture-and-movement-in-a-pistol-aiming-task
#17
Ji-Hyun Ko, Dong-Wook Han, Karl M Newell
The study investigated the coordination and variability of posture and pistol motion for skilled pistol shooters and novices in a pistol-aiming task. The participants stood on a force platform and held a pistol with the preferred arm to aim for accuracy to a target on 30 s trials. The results revealed that the amount of the centre of pressure (COP) and pistol motion was lower for the expert than novice group. The time-varying structure of COP as indexed by multiscale entropy (MSE) and detrended fluctuation analysis (DFA) was also lower for the expert than the novice group...
June 19, 2017: Journal of Sports Sciences
https://www.readbyqxmd.com/read/28628313/tunneling-kinetics-and-non-adiabatic-proton-coupled-electron-transfer-in-proteins-the-effect-of-electric-fields-and-anharmonic-donor-acceptor-interactions
#18
Bridget Salna, Abdelkrim Benabbas, Douglas Russo, Paul M Champion
A proper description of proton donor-acceptor (D-A) distance fluctuations is crucial for understanding tunneling in proton-coupled electron transport (PCET). The typical harmonic approximation for the D-A potential results in a Gaussian probability distribution, which does not appropriately reflect the electronic repulsion forces that increase the energetic cost of sampling shorter D-A distances. Because these shorter distances are the primary channel for thermally activated tunneling, the analysis of tunneling kinetics depends sensitively on the inherently anharmonic nature of the D-A interaction...
June 19, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28627561/a-promising-single-atom-catalyst-for-co-oxidation-ag-on-boron-vacancies-of-h-bn-sheets
#19
Zhansheng Lu, Peng Lv, Zongxian Yang, Shuo Li, Dongwei Ma, Ruqian Wu
Single atom catalysts (SACs) have attracted broad research interest in recent years due to their importance in various fields, such as environmental protection and energy conversion. Here, we discuss the mechanisms of CO oxidation to CO2 over single Ag atoms supported on hexagonal boron-nitride sheets (Ag1/BN) through systematic van der Waals inclusive density functional theory (DFT-D) calculations. The Ag adatom can be anchored onto a boron defect (VB), as suggested by the large energy barrier of 3.12 eV for Ag diffusion away from the VB site...
June 19, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28627470/investigation-of-itraconazole-ternary-amorphous-solid-dispersions-based-on-povidone-and-carbopol
#20
Fan Meng, Jordan Meckel, Feng Zhang
We investigate a ternary system that consists of itraconazole (ITZ) and two polymers: povidone K12 and Carbopol 907. The interactions between these two polymers and their effects on the properties of ternary ITZ amorphous solid dispersions (ASDs) are studied. These two polymers can form a water-insoluble complex in acidic aqueous media. The critical pH is determined to be 4.17. The weight percentage of Carbopol 907 in the interpolymer complex range from 59 to 70%, depending on the initial ratios between these two polymers in the starting solutions...
June 13, 2017: European Journal of Pharmaceutical Sciences
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