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https://www.readbyqxmd.com/read/27911400/visualizing-stromule-frequency-with-fluorescence-microscopy
#1
Jacob O Brunkard, Anne M Runkel, Patricia Zambryski
Stromules, or "stroma-filled tubules", are narrow, tubular extensions from the surface of the chloroplast that are universally observed in plant cells but whose functions remain mysterious. Alongside growing attention on the role of chloroplasts in coordinating plant responses to stress, interest in stromules and their relationship to chloroplast signaling dynamics has increased in recent years, aided by advances in fluorescence microscopy and protein fluorophores that allow for rapid, accurate visualization of stromule dynamics...
November 23, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/27910998/aurora-a-shines-on-t-cell-activation-through-the-regulation-of-lck
#2
Noelia Blas-Rus, Eugenio Bustos-Morán, Noa B Martín-Cófreces, Francisco Sánchez-Madrid
Different protein kinases control signaling emanating from the T cell receptor (TCR) during antigen-specific T cell activation. Mitotic kinases, e.g. Aurora-A, have been widely studied in the context of mitosis due to their role during microtubule (MT) nucleation, becoming critical regulators of cell cycle progression. We have recently described a specific role for Aurora-A kinase in antigenic T cell activation. Blockade of Aurora-A in T cells severely disrupts the dynamics of MTs and CD3ζ-bearing signaling vesicles during T cell activation...
December 2, 2016: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/27910892/dynamic-microenvironment-induces-phenotypic-plasticity-of-esophageal-cancer-cells-under-flow
#3
Gizem Calibasi Kocal, Sinan Güven, Kira Foygel, Aaron Goldman, Pu Chen, Shiladitya Sengupta, Ramasamy Paulmurugan, Yasemin Baskin, Utkan Demirci
Cancer microenvironment is a remarkably heterogeneous composition of cellular and non-cellular components, regulated by both external and intrinsic physical and chemical stimuli. Physical alterations driven by increased proliferation of neoplastic cells and angiogenesis in the cancer microenvironment result in the exposure of the cancer cells to elevated levels of flow-based shear stress. We developed a dynamic microfluidic cell culture platform utilizing eshopagael cancer cells as model cells to investigate the phenotypic changes of cancer cells upon exposure to fluid shear stress...
December 2, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27910824/accelerated-high-resolution-photoacoustic-tomography-via-compressed-sensing
#4
Simon Arridge, Paul Beard, Marta Betcke, Ben Cox, Nam Huynh, Felix Lucka, Olumide Ogunlade, Edward Zhang
Current 3D photoacoustic tomography (PAT) systems offer either high image quality or high frame rates but are not able to deliver high spatial and temporal resolution simultaneously, which limits their ability to image dynamic processes in living tissue (4D PAT). A particular example is the planar Fabry-Pérot (FP) photoacoustic scanner, which yields high-resolution 3D images but takes several minutes to sequentially map the incident photoacoustic field on the 2D sensor plane, point-by-point. However, as the spatio-temporal complexity of many absorbing tissue structures is rather low, the data recorded in such a conventional, regularly sampled fashion is often highly redundant...
December 21, 2016: Physics in Medicine and Biology
https://www.readbyqxmd.com/read/27910620/a-novel-technique-for-real-time-estimation-of-edge-pedestal-density-gradients-via-reflectometer-time-delay-data
#5
L Zeng, E J Doyle, T L Rhodes, G Wang, C Sung, W A Peebles, M Bobrek
A new model-based technique for fast estimation of the pedestal electron density gradient has been developed. The technique uses ordinary mode polarization profile reflectometer time delay data and does not require direct profile inversion. Because of its simple data processing, the technique can be readily implemented via a Field-Programmable Gate Array, so as to provide a real-time density gradient estimate, suitable for use in plasma control systems such as envisioned for ITER, and possibly for DIII-D and Experimental Advanced Superconducting Tokamak...
November 2016: Review of Scientific Instruments
https://www.readbyqxmd.com/read/27910588/online-measurements-of-surface-tensions-and-viscosities-based-on-the-hydrodynamics-of-taylor-flow-in-a-microchannel
#6
Yanhong Sun, Chaohong Guo, Yuyan Jiang, Tao Wang, Lei Zhang
This paper demonstrates an online measurement technique which can measure both surface tension and viscosity for confined fluids in microfluidic systems. The surface tension and viscosity are determined by monitoring the liquid film thickness deposited in a microchannel based on the hydrodynamics of Taylor flow. Measurements were carried out for pure liquids and binary aqueous liquid mixtures. The results agreed well with reference data and theoretical models. This novel method has considerable potential for measuring dynamic interfacial tension of complex mixtures...
November 2016: Review of Scientific Instruments
https://www.readbyqxmd.com/read/27910491/measurement-of-high-dynamic-range-x-ray-thomson-scattering-spectra-for-the-characterization-of-nano-plasmas-at-lcls
#7
M J MacDonald, T Gorkhover, B Bachmann, M Bucher, S Carron, R N Coffee, R P Drake, K R Ferguson, L B Fletcher, E J Gamboa, S H Glenzer, S Göde, S P Hau-Riege, D Kraus, J Krzywinski, A L Levitan, K-H Meiwes-Broer, C P O'Grady, T Osipov, T Pardini, C Peltz, S Skruszewicz, M Swiggers, C Bostedt, T Fennel, T Döppner
Atomic clusters can serve as ideal model systems for exploring ultrafast (∼100 fs) laser-driven ionization dynamics of dense matter on the nanometer scale. Resonant absorption of optical laser pulses enables heating to temperatures on the order of 1 keV at near solid density conditions. To date, direct probing of transient states of such nano-plasmas was limited to coherent x-ray imaging. Here we present the first measurement of spectrally resolved incoherent x-ray scattering from clusters, enabling measurements of transient temperature, densities, and ionization...
November 2016: Review of Scientific Instruments
https://www.readbyqxmd.com/read/27909574/characterization-of-5-2-18-f-fluoroethoxy-l-tryptophan-for-pet-imaging-of-the-pancreas
#8
Ahmed Abbas, Christine Beamish, Rebecca McGirr, John Demarco, Neil Cockburn, Dawid Krokowski, Ting-Yim Lee, Michael Kovacs, Maria Hatzoglou, Savita Dhanvantari
Purpose: In diabetes, pancreatic beta cell mass declines significantly prior to onset of fasting hyperglycemia. This decline may be due to endoplasmic reticulum (ER) stress, and the system L amino acid transporter LAT1 may be a biomarker of this process. In this study, we used 5-(2- (18)F-fluoroethoxy)-L-tryptophan ( (18)F-L-FEHTP) to target LAT1 as a potential biomarker of beta cell function in diabetes. Procedures: Uptake of (18)F-L-FEHTP was determined in wild-type C57BL/6 mice by ex vivo biodistribution...
2016: F1000Research
https://www.readbyqxmd.com/read/27909395/reversal-learning-in-humans-and-gerbils-dynamic-control-network-facilitates-learning
#9
Christian Jarvers, Tobias Brosch, André Brechmann, Marie L Woldeit, Andreas L Schulz, Frank W Ohl, Marcel Lommerzheim, Heiko Neumann
Biologically plausible modeling of behavioral reinforcement learning tasks has seen great improvements over the past decades. Less work has been dedicated to tasks involving contingency reversals, i.e., tasks in which the original behavioral goal is reversed one or multiple times. The ability to adjust to such reversals is a key element of behavioral flexibility. Here, we investigate the neural mechanisms underlying contingency-reversal tasks. We first conduct experiments with humans and gerbils to demonstrate memory effects, including multiple reversals in which subjects (humans and animals) show a faster learning rate when a previously learned contingency re-appears...
2016: Frontiers in Neuroscience
https://www.readbyqxmd.com/read/27909095/dynamic-shifts-in-large-scale-brain-network-balance-as-a-function-of-arousal
#10
Christina B Young, Gal Raz, Daphne Everaerd, Christian F Beckmann, Indira Tendolkar, Talma Hendler, Guillén Fernández, Erno J Hermans
: The ability to temporarily prioritize rapid and vigilant reactions over slower higher-order cognitive functions is essential for adaptive responding to threat. This reprioritization is believed to reflect shifts in resource allocation between large-scale brain networks that support these cognitive functions, including the salience and executive control networks. How changes in communication within and between such networks dynamically unfold as a function of threat-related arousal, however, remains unknown...
December 1, 2016: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/27908138/stochastic-simulation-of-anharmonic-dissipation-i-linear-response-regime
#11
Yun-An Yan
Over decades, the theoretical study of the quantum dissipative dynamics was mainly based on the linear dissipation model. The study of the nonlinear dissipative dynamics in condensed phases, where there exist an infinite number of bath modes, is extremely difficult even if not impossible. This work put forward a stochastic scheme for the simulation of the nonlinear dissipative dynamics. In the linear response regime, the second-order cumulant expansion becomes exact to reproduce the effect of the bath on the evolution of the reduced system...
November 28, 2016: Journal of Chemical Physics
https://www.readbyqxmd.com/read/27908131/molecular-dynamics-investigation-of-desorption-and-ion-separation-following-picosecond-infrared-laser-pirl-ablation-of-an-ionic-aqueous-protein-solution
#12
J Zou, C Wu, W D Robertson, L V Zhigilei, R J D Miller
Molecular dynamics simulations were performed to characterize the ablation process induced by a picosecond infrared laser (PIRL) operating in the regime of desorption by impulsive vibrational excitation (DIVE) of a model peptide (lysozyme)/counter-ion system in aqueous solution. The simulations were performed for ablation under typical experimental conditions found within a time-of-flight mass spectrometer (TOF-MS), that is in vacuum with an applied electric field (E = ± 10(7) V/m), for up to 2 ns post-ablation and compared to the standard PIRL-DIVE ablation condition (E = 0 V/m)...
November 28, 2016: Journal of Chemical Physics
https://www.readbyqxmd.com/read/27908129/self-consistent-molecular-dynamics-calculation-of-diffusion-in-higher-n-alkanes
#13
Nikolay D Kondratyuk, Genri E Norman, Vladimir V Stegailov
Diffusion is one of the key subjects of molecular modeling and simulation studies. However, there is an unresolved lack of consistency between Einstein-Smoluchowski (E-S) and Green-Kubo (G-K) methods for diffusion coefficient calculations in systems of complex molecules. In this paper, we analyze this problem for the case of liquid n-triacontane. The non-conventional long-time tails of the velocity autocorrelation function (VACF) are found for this system. Temperature dependence of the VACF tail decay exponent is defined...
November 28, 2016: Journal of Chemical Physics
https://www.readbyqxmd.com/read/27908110/effects-of-herzberg-teller-vibronic-coupling-on-coherent-excitation-energy-transfer
#14
Hou-Dao Zhang, Qin Qiao, Rui-Xue Xu, YiJing Yan
In this work, we study the effects of non-Condon vibronic coupling on the quantum coherence of excitation energy transfer, via the exact dissipaton-equation-of-motion evaluations on excitonic model systems. Field-triggered excitation energy transfer dynamics and two dimensional coherent spectroscopy are simulated for both Condon and non-Condon vibronic couplings. Our results clearly demonstrate that the non-Condon vibronic coupling intensifies the dynamical electronic-vibrational energy transfer and enhances the total system-and-bath quantum coherence...
November 28, 2016: Journal of Chemical Physics
https://www.readbyqxmd.com/read/27908108/dual-hydrogen-bonding-motifs-in-complexes-formed-between-tropolone-and-formic-acid
#15
Deacon J Nemchick, Michael K Cohen, Patrick H Vaccaro
The near-ultraviolet π(*)←π absorption system of weakly bound complexes formed between tropolone (TrOH) and formic acid (FA) under cryogenic free-jet expansion conditions has been interrogated by exploiting a variety of fluorescence-based laser-spectroscopic probes, with synergistic quantum-chemical calculations built upon diverse model chemistries being enlisted to unravel the structural and dynamical properties of the pertinent ground [X̃(1)A(')] and excited [Ã(1)A(')π(*)π] electronic states. For binary TrOH ⋅ FA adducts, the presence of dual hydrogen-bond linkages gives rise to three low-lying isomers designated (in relative energy order) as INT, EXT1, and EXT2 depending on whether docking of the FA ligand to the TrOH substrate takes place internal or external to the five-membered reaction cleft of tropolone...
November 28, 2016: Journal of Chemical Physics
https://www.readbyqxmd.com/read/27908103/non-equilibrium-dynamics-from-rpmd-and-cmd
#16
Ralph Welsch, Kai Song, Qiang Shi, Stuart C Althorpe, Thomas F Miller
We investigate the calculation of approximate non-equilibrium quantum time correlation functions (TCFs) using two popular path-integral-based molecular dynamics methods, ring-polymer molecular dynamics (RPMD) and centroid molecular dynamics (CMD). It is shown that for the cases of a sudden vertical excitation and an initial momentum impulse, both RPMD and CMD yield non-equilibrium TCFs for linear operators that are exact for high temperatures, in the t = 0 limit, and for harmonic potentials; the subset of these conditions that are preserved for non-equilibrium TCFs of non-linear operators is also discussed...
November 28, 2016: Journal of Chemical Physics
https://www.readbyqxmd.com/read/27908084/a-robust-automatic-birdsong-phrase-classification-a-template-based-approach
#17
Kantapon Kaewtip, Abeer Alwan, Colm O'Reilly, Charles E Taylor
Automatic phrase detection systems of bird sounds are useful in several applications as they reduce the need for manual annotations. However, birdphrase detection is challenging due to limited training data and background noise. Limited data occur because of limited recordings or the existence of rare phrases. Background noise interference occurs because of the intrinsic nature of the recording environment such as wind or other animals. This paper presents a different approach to birdsong phrase classification using template-based techniques suitable even for limited training data and noisy environments...
November 2016: Journal of the Acoustical Society of America
https://www.readbyqxmd.com/read/27908025/geometry-of-behavioral-spaces-a-computational-approach-to-analysis-and-understanding-of-agent-based-models-and-agent-behaviors
#18
Martin Cenek, Spencer K Dahl
Systems with non-linear dynamics frequently exhibit emergent system behavior, which is important to find and specify rigorously to understand the nature of the modeled phenomena. Through this analysis, it is possible to characterize phenomena such as how systems assemble or dissipate and what behaviors lead to specific final system configurations. Agent Based Modeling (ABM) is one of the modeling techniques used to study the interaction dynamics between a system's agents and its environment. Although the methodology of ABM construction is well understood and practiced, there are no computational, statistically rigorous, comprehensive tools to evaluate an ABM's execution...
November 2016: Chaos
https://www.readbyqxmd.com/read/27908021/finding-equilibrium-in-the-spatiotemporal-chaos-of-the-complex-ginzburg-landau-equation
#19
Christopher C Ballard, C Clark Esty, David A Egolf
Equilibrium statistical mechanics allows the prediction of collective behaviors of large numbers of interacting objects from just a few system-wide properties; however, a similar theory does not exist for far-from-equilibrium systems exhibiting complex spatial and temporal behavior. We propose a method for predicting behaviors in a broad class of such systems and apply these ideas to an archetypal example, the spatiotemporal chaotic 1D complex Ginzburg-Landau equation in the defect chaos regime. Building on the ideas of Ruelle and of Cross and Hohenberg that a spatiotemporal chaotic system can be considered a collection of weakly interacting dynamical units of a characteristic size, the chaotic length scale, we identify underlying, mesoscale, chaotic units and effective interaction potentials between them...
November 2016: Chaos
https://www.readbyqxmd.com/read/27908011/principal-dynamic-mode-analysis-of-neural-mass-model-for-the-identification-of-epileptic-states
#20
Yuzhen Cao, Liu Jin, Fei Su, Jiang Wang, Bin Deng
The detection of epileptic seizures in Electroencephalography (EEG) signals is significant for the diagnosis and treatment of epilepsy. In this paper, in order to obtain characteristics of various epileptiform EEGs that may differentiate different states of epilepsy, the concept of Principal Dynamic Modes (PDMs) was incorporated to an autoregressive model framework. First, the neural mass model was used to simulate the required intracerebral EEG signals of various epileptiform activities. Then, the PDMs estimated from the nonlinear autoregressive Volterra models, as well as the corresponding Associated Nonlinear Functions (ANFs), were used for the modeling of epileptic EEGs...
November 2016: Chaos
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