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https://www.readbyqxmd.com/read/28637263/nearly-nondiffracting-electron-lattice-beams-generated-by-polygonal-slits
#1
Hiroki Nambu, Yuuki Noguchi, Koh Saitoh, Masaya Uchida
A method for generating electron lattice beams carrying vortices using nanofabricated polygonal slits in a transmission electron microscope is proposed. Experimental and simulation study of the intensity of the beams verified their Bessel beam-like nearly nondiffracting behavior. Phase analysis using a diffractive imaging method found arrays of quantized vortices, forming an electron beam lattice with cylindrical intensity distribution in the propagation direction. Such vortex lattice beams may be used in a variety of applications including nanofabrication, particle manipulation or a new electron imaging method...
June 15, 2017: Microscopy
https://www.readbyqxmd.com/read/28637261/further-simulations-and-analyses-demonstrate-open-problems-of-phylostratigraphy
#2
Bryan A Moyers, Jianzhi Zhang
Phylostratigraphy, originally designed for gene age estimation by BLAST-based protein homology searches of sequenced genomes, has been widely used for studying patterns and inferring mechanisms of gene origination and evolution. We previously showed by computer simulation that phylostratigraphy underestimates gene age for a non-negligible fraction of genes and that the underestimation is severer for genes with certain properties such as fast evolution and short protein sequences. Consequently, many previously reported age distributions of gene properties may have been methodological artifacts rather than biological realities...
June 14, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28637216/qualitative-analysis-and-detection-of-the-pyrolytic-products-of-jwh-018-and-11-additional-synthetic-cannabinoids-in-the-presence-of-common-herbal-smoking-substrates
#3
Stephen Raso, Suzanne Bell
Synthetic cannabinoids have become a ubiquitous challenge in forensic toxicology and seized drug analysis. Thermal degradation products have yet to be identified and evaluated for toxicity in comparison to parent and metabolic compounds. An investigation into these pyrolytic products, as the major route of ingestion is inhalation, may produce additional insight to understand the toxicity of synthetic cannabinoids. The pyrolysis of JWH-018 and 11 additional synthetic cannabinoids and six herbal plant substrates were conducted using an in-house constructed smoking simulator...
June 20, 2017: Journal of Analytical Toxicology
https://www.readbyqxmd.com/read/28637199/first-ex-vivo-and-preliminary-sheep-model-results-of-the-new-tribio-aortic-valve-bioprosthesis-in-small-aortic-annuli
#4
Sina Stock, Hans-Hinrich Sievers, Doreen Richardt, Michael Scharfschwerdt
OBJECTIVES: : Small aortic annuli are challenging in aortic valve replacement. Prosthesis-patient mismatch, accompanied by high transvalvular gradients and small orifice area, is an often faced problem impairing postoperative outcome. The new TRIBIO bioprosthesis aims to enable enhanced haemodynamics, being increasingly important with decreasing annular size. This study compares ex vivo hydrodynamics of TRIBIO with 2 established bioprostheses in small annuli at different stroke volumes, simulating 'rest' and 'exercise', and evaluates haemodynamics of TRIBIO in a sheep model...
June 20, 2017: Interactive Cardiovascular and Thoracic Surgery
https://www.readbyqxmd.com/read/28637180/participatory-design-of-probability-based-decision-support-tools-for-in-hospital-nurses
#5
Alvin D Jeffery, Laurie L Novak, Betsy Kennedy, Mary S Dietrich, Lorraine C Mion
Objective: To describe nurses' preferences for the design of a probability-based clinical decision support (PB-CDS) tool for in-hospital clinical deterioration. Methods: A convenience sample of bedside nurses, charge nurses, and rapid response nurses ( n  = 20) from adult and pediatric hospitals completed participatory design sessions with researchers in a simulation laboratory to elicit preferred design considerations for a PB-CDS tool. Following theme-based content analysis, we shared findings with user interface designers and created a low-fidelity prototype...
June 19, 2017: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/28637146/instilling-positive-beliefs-about-disabilities-pilot-testing-a-novel-experiential-learning-activity-for-rehabilitation-students
#6
Arielle M Silverman, Jennifer S Pitonyak, Ian K Nelson, Patricia N Matsuda, Deborah Kartin, Ivan R Molton
PURPOSE: To develop and test a novel impairment simulation activity to teach beginning rehabilitation students how people adapt to physical impairments. METHODS: Masters of Occupational Therapy students (n = 14) and Doctor of Physical Therapy students (n = 18) completed the study during the first month of their program. Students were randomized to the experimental or control learning activity. Experimental students learned to perform simple tasks while simulating paraplegia and hemiplegia...
February 25, 2017: Disability and Rehabilitation
https://www.readbyqxmd.com/read/28637053/a-new-analytical-method-for-characterizing-nonlinear-visual-processes-with-stimuli-of-arbitrary-distribution-theory-and-applications
#7
Ryusuke Hayashi, Osamu Watanabe, Hiroki Yokoyama, Shin'ya Nishida
Characterization of the functional relationship between sensory inputs and neuronal or observers' perceptual responses is one of the fundamental goals of systems neuroscience and psychophysics. Conventional methods, such as reverse correlation and spike-triggered data analyses are limited in their ability to resolve complex and inherently nonlinear neuronal/perceptual processes because these methods require input stimuli to be Gaussian with a zero mean. Recent studies have shown that analyses based on a generalized linear model (GLM) do not require such specific input characteristics and have advantages over conventional methods...
June 1, 2017: Journal of Vision
https://www.readbyqxmd.com/read/28637051/teaching-transnasal-endoscopy-to-graduate-students-without-a-hospital-or-simulation-laboratory-pool-noodles-and-cadavers
#8
Shari Salzhauer Berkowitz
Purpose: This study reports on a training opportunity in endoscopy in which speech-language pathology graduate students use inanimate objects and cadavers. Best practices for transnasal endoscopy in vivo require a physician to be nearby, but many graduate programs do not have this access. Method: Endoscopy was offered as a graduate elective. Students (13 women) initially learned to manipulate the endoscope through the lumen of a swimming pool noodle that was embedded with trinkets...
June 20, 2017: American Journal of Speech-language Pathology
https://www.readbyqxmd.com/read/28636971/simulated-long-term-effects-of-varying-tree-retention-on-wood-production-dead-wood-and-carbon-stock-changes
#9
Francesca Santaniello, Line B Djupström, Thomas Ranius, Jan Weslien, Jörgen Rudolphi, Johan Sonesson
Boreal forests are an important source of timber and pulp wood, but provide also other products and services. Utilizing a simulation program and field data from a tree retention experiment in a Scots pine forest in central Sweden, we simulated the consequences during the following 100 years of various levels of retention on production of merchantable wood, dead wood input (as a proxy for biodiversity), and carbon stock changes. At the stand level, wood production decreased with increased retention levels, while dead wood input and carbon stock increased...
June 18, 2017: Journal of Environmental Management
https://www.readbyqxmd.com/read/28636944/transduction-of-repetitive-mechanical-stimuli-by-piezo1-and-piezo2-ion-channels
#10
Amanda H Lewis, Alisa F Cui, Malcolm F McDonald, Jörg Grandl
Several cell types experience repetitive mechanical stimuli, including vein endothelial cells during pulsating blood flow, inner ear hair cells upon sound exposure, and skin cells and their innervating dorsal root ganglion (DRG) neurons when sweeping across a textured surface or touching a vibrating object. While mechanosensitive Piezo ion channels have been clearly implicated in sensing static touch, their roles in transducing repetitive stimulations are less clear. Here, we perform electrophysiological recordings of heterologously expressed mouse Piezo1 and Piezo2 responding to repetitive mechanical stimulations...
June 20, 2017: Cell Reports
https://www.readbyqxmd.com/read/28636918/actin-filament-strain-promotes-severing-and-cofilin-dissociation
#11
Anthony C Schramm, Glen M Hocky, Gregory A Voth, Laurent Blanchoin, Jean-Louis Martiel, Enrique M De La Cruz
Computational and structural studies have been indispensable in investigating the molecular origins of actin filament mechanical properties and modulation by the regulatory severing protein cofilin. All-atom molecular dynamics simulations of cofilactin filament structures determined by electron cryomicroscopy reveal how cofilin enhances the bending and twisting compliance of actin filaments. Continuum mechanics models suggest that buckled cofilactin filaments localize elastic energy at boundaries between bare and cofilin-decorated segments because of their nonuniform elasticity, thereby accelerating filament severing...
June 20, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28636916/structural-behavior-of-the-peptaibol-harzianin-hk-vi-in-a-dmpc-bilayer-insights-from-md-simulations
#12
Marina Putzu, Sezgin Kara, Sergii Afonin, Stephan L Grage, Andrea Bordessa, Grégory Chaume, Thierry Brigaud, Anne S Ulrich, Tomáš Kubař
Microsecond molecular dynamics simulations of harzianin HK VI (HZ) interacting with a dimyristoylphosphatidylcholine bilayer were performed at the condition of low peptide-to-lipid ratio. Two orientations of HZ molecule in the bilayer were found and characterized. In the orientation perpendicular to the bilayer surface, HZ induces a local thinning of the bilayer. When inserted into the bilayer parallel to its surface, HZ is located nearly completely within the hydrophobic region of the bilayer. A combination of solid-state NMR and circular dichroism experiments found the latter orientation to be dominant...
June 20, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28636914/peptide-protein-binding-investigated-by-far-ir-spectroscopy-and-molecular-dynamics-simulations
#13
Yoann Cote, Yves Nominé, Juan Ramirez, Petra Hellwig, Roland H Stote
Molecular dynamics (MD) simulations and far-infrared (far-IR) spectroscopy were combined to study peptide binding by the second PDZ domain (PDZ1) of MAGI1, which has been identified as an important target for the Human Papilloma Virus. PDZ1 recognizes and binds to the C-terminal end of the E6 protein from high-risk Human Papilloma Virus. The far-IR spectra of two forms of the protein, an unbound APO form and a HOLO form (where the PDZ1 is bound to an 11-residue peptide derived from the C terminus of HPV16 E6), were obtained...
June 20, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28636909/electric-field-induced-protein-translocation-via-a-conformational-transition-in-secdf-an-md-study
#14
Emel Ficici, Daun Jeong, Ioan Andricioaei
SecDF is an important component of the Sec protein translocation machinery embedded in the bacterial membrane, which is associated with many functions, such as stabilizing other Sec translocon components within the membrane, maintaining the transmembrane (TM) potential, and facilitating the ATP-independent stage of the translocation mechanism. Related studies suggest that SecDF undergoes functionally important conformational changes that involve mainly its P1-head domain and that these changes are coupled with the proton motive force (Δp)...
June 20, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28636906/flexible-fitting-of-atomic-models-into-cryo-em-density-maps-guided-by-helix-correspondences
#15
Hang Dou, Derek W Burrows, Matthew L Baker, Tao Ju
Although electron cryo-microscopy (cryo-EM) has recently achieved resolutions of better than 3 Å, at which point molecular modeling can be done directly from the density map, analysis and annotation of a cryo-EM density map still primarily rely on fitting atomic or homology models to the density map. In this article, we present, to our knowledge, a new method for flexible fitting of known or modeled protein structures into cryo-EM density maps. Unlike existing methods that are guided by local density gradients, our method is guided by correspondences between the α-helices in the density map and model, and does not require an initial rigid-body fitting step...
June 20, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28636905/a-kepler-workflow-tool-for-reproducible-amber-gpu-molecular-dynamics
#16
Shweta Purawat, Pek U Ieong, Robert D Malmstrom, Garrett J Chan, Alan K Yeung, Ross C Walker, Ilkay Altintas, Rommie E Amaro
With the drive toward high throughput molecular dynamics (MD) simulations involving ever-greater numbers of simulation replicates run for longer, biologically relevant timescales (microseconds), the need for improved computational methods that facilitate fully automated MD workflows gains more importance. Here we report the development of an automated workflow tool to perform AMBER GPU MD simulations. Our workflow tool capitalizes on the capabilities of the Kepler platform to deliver a flexible, intuitive, and user-friendly environment and the AMBER GPU code for a robust and high-performance simulation engine...
June 20, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28636894/effects-of-hpmc-substituent-pattern-on-water-up-take-polymer-and-drug-release-an-experimental-and-modelling-study
#17
Diego Caccavo, Gaetano Lamberti, Anna Angela Barba, Susanna Abrahmsén-Alami, Anna Viridén, Anette Larsson
The purpose of this study was to investigate the hydration behavior of two matrix formulations containing the cellulose derivative hydroxypropyl methylcellulose (HPMC). The two HPMC batches investigated had different substitution pattern along the backbone; the first one is referred to as heterogeneous and the second as homogenous. The release of both the drug molecule theophylline and the polymer was determined. Additionally, the water concentrations at different positions in the swollen gel layers were determined by Magnetic Resonance Imaging...
June 18, 2017: International Journal of Pharmaceutics
https://www.readbyqxmd.com/read/28636825/a-new-mixed-all-atom-coarse-grained-model-application-to-melittin-aggregation-in-aqueous-solution
#18
Mee Y Shelley, Myvizhi Esai Selvan, Jun Zhao, Volodymyr Babin, Chenyi Liao, Jianing Li, John Clarence Shelley
We introduce a new mixed resolution, all-atom/coarse-grained approach (AACG) for modeling peptides in aqueous solution and apply it to characterizing the aggregation of melittin. All of the atoms in peptidic components are represented while a single site is used for each water molecule. With the full flexibility of the peptide retained, our AACG method achieves speedups by a factor of 3-4 for CPU time reduction and another factor of roughly 7 for diffusion. An Ewald treatment permits the inclusion of long-range electrostatic interactions...
June 21, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28636824/bicanonical-ab-initio-molecular-dynamics-for-open-systems
#19
Johannes Frenzel, Bernd Meyer, Dominik Marx
Performing ab initio molecular dynamics simulations of open systems, where the chemical potential rather than the number of both, nuclei and electrons is fixed, still is a challenge. Here, drawing on bicanonical sampling ideas introduced two decades ago by Swope and Andersen to calculate chemical potentials of liquids and solids, an ab initio simulation technique is devised, which introduces a fictitious dynamics of two superimposed but otherwise independent periodic systems including full electronic structure, such that either the chemical potential or the average fractional particle number of a specific chemical species can be kept constant...
June 21, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28636811/performance-evaluation-of-gpu-parallelization-space-time-adaptive-algorithms-and-their-combination-for-simulating-cardiac-electrophysiology
#20
Rafael S Oliveira, Bernardo M Rocha, Denise Burgarelli, Wagner Meira, Christakis Constantinides, Rodrigo Weber Dos Santos
The use of computer models as a tool for the study and understanding of the complex phenomena of cardiac electrophysiology has attained increased importance nowadays. At the same time, the increased complexity of the biophysical processes translates into complex computational and mathematical models. In order to speed up cardiac simulations and to allow more precise and realistic uses, two different techniques have been traditionally exploited: parallel computing and sophisticated numerical methods. In this work, we combine a modern parallel computing technique based on multicore and graphics processing units (GPUs), and a sophisticated numerical method based on a new space-time adaptive algorithm...
June 21, 2017: International Journal for Numerical Methods in Biomedical Engineering
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