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https://www.readbyqxmd.com/read/28437008/effects-from-metal-ion-in-tumor-endothelial-marker-8-and-anthrax-protective-antigen-biolayer-interferometry-experiment-and-molecular-dynamics-simulation-study
#1
Zhe Jia, Christine Ackroyd, Tingting Han, Vibhor Agrawal, Yinling Liu, Kenneth Christensen, Brian Dominy
One of the anthrax receptors, tumor endothelial marker 8 (TEM8), is reported to be a potential anticancer target due to its over-expression during tumor angiogenesis. To extend our BioLayer Interferometry study in PA-TEM8 binding, we present a computational approach to reveal the role of an integral metal ion on receptor structure and binding thermodynamics. We estimated the interaction energy between PA and TEM8 using computer simulation. Consistent with experimental study, computational results indicate the metal ion in TEM8 contributes significantly to the binding affinity, and PA-TEM8 binding is more favorable in the presence of Mg(2+) than Ca(2+) ...
June 5, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28436594/cassandra-an-open-source-monte-carlo-package-for-molecular-simulation
#2
Jindal K Shah, Eliseo Marin-Rimoldi, Ryan Gotchy Mullen, Brian P Keene, Sandip Khan, Andrew S Paluch, Neeraj Rai, Lucienne L Romanielo, Thomas W Rosch, Brian Yoo, Edward J Maginn
Cassandra is an open source atomistic Monte Carlo software package that is effective in simulating the thermodynamic properties of fluids and solids. The different features and algorithms used in Cassandra are described, along with implementation details and theoretical underpinnings to various methods used. Benchmark and example calculations are shown, and information on how users can obtain the package and contribute to it are provided. © 2017 Wiley Periodicals, Inc.
April 24, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28432287/advantages-of-unfair-quantum-ground-state-sampling
#3
Brian Hu Zhang, Gene Wagenbreth, Victor Martin-Mayor, Itay Hen
The debate around the potential superiority of quantum annealers over their classical counterparts has been ongoing since the inception of the field. Recent technological breakthroughs, which have led to the manufacture of experimental prototypes of quantum annealing optimizers with sizes approaching the practical regime, have reignited this discussion. However, the demonstration of quantum annealing speedups remains to this day an elusive albeit coveted goal. We examine the power of quantum annealers to provide a different type of quantum enhancement of practical relevance, namely, their ability to serve as useful samplers from the ground-state manifolds of combinatorial optimization problems...
April 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28431242/structural-and-functional-analysis-of-a-%C3%AE-2-adrenergic-receptor-complex-with-grk5
#4
Konstantin E Komolov, Yang Du, Nguyen Minh Duc, Robin M Betz, João P G L M Rodrigues, Ryan D Leib, Dhabaleswar Patra, Georgios Skiniotis, Christopher M Adams, Ron O Dror, Ka Young Chung, Brian K Kobilka, Jeffrey L Benovic
The phosphorylation of agonist-occupied G-protein-coupled receptors (GPCRs) by GPCR kinases (GRKs) functions to turn off G-protein signaling and turn on arrestin-mediated signaling. While a structural understanding of GPCR/G-protein and GPCR/arrestin complexes has emerged in recent years, the molecular architecture of a GPCR/GRK complex remains poorly defined. We used a comprehensive integrated approach of cross-linking, hydrogen-deuterium exchange mass spectrometry (MS), electron microscopy, mutagenesis, molecular dynamics simulations, and computational docking to analyze GRK5 interaction with the β2-adrenergic receptor (β2AR)...
April 20, 2017: Cell
https://www.readbyqxmd.com/read/28429939/solute-rotation-in-ionic-liquids-size-shape-and-electrostatic-effects
#5
Christopher A Rumble, Caleb Uitvlugt, Brian Conway, Mark Maroncelli
Herein are reported temperature-dependent measurements and molecular dynamics simulations designed to investigate the effects of molecular size, shape, and electrostatics on rotational dynamics in ionic liquids. Experiments were performed in the representative ionic liquid 1-butyl-3-methylimadazolium tetrafluoroborate ([Im41][BF4]) and simulations in the generic ionic liquid model ILM2 as well as a more detailed representation of [Im41][BF4]. 2H longitudinal spin relaxation times were measured for deuterated versions of 1,4-dimethylbenzene, 1-cyano-4-methylbenzene, and 1,4-dimethylpyridinium between 296-337 K...
April 21, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28429276/enhancing-thermal-stability-of-a-highly-concentrated-insulin-formulation-with-pluronic-f-127-for-long-term-use-in-microfabricated-implantable-devices
#6
Jason Li, Michael K Chu, Brian Lu, Sako Mirzaie, Kuan Chen, Claudia R Gordijo, Oliver Plettenburg, Adria Giacca, Xiao Yu Wu
Development of highly concentrated formulations of protein and peptide drugs is a major challenge due to increased susceptibility to aggregation and precipitation. Numerous drug delivery systems including implantable and wearable controlled-release devices require thermally stable formulations with high concentrations due to limited device sizes and long-term use. Herein we report a highly concentrated insulin gel formulation (up to 80 mg/mL, corresponding to 2200 IU/mL), stabilized with a non-ionic amphiphilic triblock copolymer (i...
April 20, 2017: Drug Delivery and Translational Research
https://www.readbyqxmd.com/read/28428910/role-of-the-interosseous-membrane-in-preventing-distal-radioulnar-gapping
#7
Frederick W Werner, Matthew R LeVasseur, Brian J Harley, Ashley Anderson
Background Damage to the interosseous membrane (IOM) can alter load transmission between the radius and ulna and decrease their axial stability. Less is known about the effect of IOM sectioning on the transverse stability between the radius and ulna. Purpose The purpose of this study was to quantify the radioulnar gapping at the distal radioulnar joint (DRUJ) during forearm rotation when the IOM was experimentally sectioned while maintaining the integrity of the distal radioulnar ligaments. Methods In 12 fresh-frozen cadaver forearms tested in a combined wrist-forearm simulator, the increase in gap between the radius and ulna, at the level of the DRUJ, was determined during cyclic forearm rotation following IOM sectioning...
May 2017: Journal of Wrist Surgery
https://www.readbyqxmd.com/read/28425502/revealing-hidden-conformational-space-of-lov-protein-vivid-through-rigid-residue-scan-simulations
#8
Hongyu Zhou, Brian D Zoltowski, Peng Tao
VIVID(VVD) protein is a Light-Oxygen-Voltage(LOV) domain in circadian clock system. Upon blue light activation, a covalent bond is formed between VVD residue Cys108 and its cofactor flavin adenine dinucleotide(FAD), and prompts VVD switching from Dark state to Light state with significant conformational deviation. However, the mechanism of this local environment initiated global protein conformational change remains elusive. We employed a recently developed computational approach, rigid residue scan(RRS), to systematically probe the impact of the internal degrees of freedom in each amino acid residue of VVD on its overall dynamics by applying rigid body constraint on each residue in molecular dynamics simulations...
April 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28422779/the-utility-of-high-fidelity-simulation-for-training-critical-care-fellows-in-the-management-of-extracorporeal-membrane-oxygenation-emergencies-a-randomized-controlled-trial
#9
Bishoy M Zakhary, Lily M Kam, Brian S Kaufman, Kevin J Felner
OBJECTIVE: Although extracorporeal membrane oxygenation volume has increased, proficiency in the technology requires extensive training. We compared traditional water-drill-based extracorporeal membrane oxygenation training with simulation-based extracorporeal membrane oxygenation training with the hypothesis that simulation-based training is superior. DESIGN: Randomized controlled trial. SETTING: Academic medical center. SUBJECTS: Pulmonary/critical care fellows...
April 18, 2017: Critical Care Medicine
https://www.readbyqxmd.com/read/28415349/decorrelation-correction-for-nanoparticle-tracking-analysis-of-dilute-polydisperse-suspensions-in-bulk-flow
#10
John Hartman, Brian Kirby
Nanoparticle tracking analysis, a multiprobe single particle tracking technique, is a widely used method to quickly determine the concentration and size distribution of colloidal particle suspensions. Many popular tools remove non-Brownian components of particle motion by subtracting the ensemble-average displacement at each time step, which is termed dedrifting. Though critical for accurate size measurements, dedrifting is shown here to introduce significant biasing error and can fundamentally limit the dynamic range of particle size that can be measured for dilute heterogeneous suspensions such as biological extracellular vesicles...
March 2017: Physical Review. E
https://www.readbyqxmd.com/read/28415324/scale-dependence-of-multiplier-distributions-for-particle-concentration-enstrophy-and-dissipation-in-the-inertial-range-of-homogeneous-turbulence
#11
Thomas Hartlep, Jeffrey N Cuzzi, Brian Weston
Turbulent flows preferentially concentrate inertial particles depending on their stopping time or Stokes number, which can lead to significant spatial variations in the particle concentration. Cascade models are one way to describe this process in statistical terms. Here, we use a direct numerical simulation (DNS) dataset of homogeneous, isotropic turbulence to determine probability distribution functions (PDFs) for cascade multipliers, which determine the ratio by which a property is partitioned into subvolumes as an eddy is envisioned to decay into smaller eddies...
March 2017: Physical Review. E
https://www.readbyqxmd.com/read/28411601/kinetic-monte-carlo-simulations-of-gan-homoepitaxy-on-c-and-m-plane-surfaces
#12
Dongwei Xu, Peter Zapol, G Brian Stephenson, Carol Thompson
The surface orientation can have profound effects on the atomic-scale processes of crystal growth and is essential to such technologies as GaN-based light-emitting diodes and high-power electronics. We investigate the dependence of homoepitaxial growth mechanisms on the surface orientation of a hexagonal crystal using kinetic Monte Carlo simulations. To model GaN metal-organic vapor phase epitaxy, in which N species are supplied in excess, only Ga atoms on a hexagonal close-packed (HCP) lattice are considered...
April 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28410277/use-of-population-pharmacokinetics-and-electronic-health-records-to-assess-piperacillin-tazobactam-safety-in-infants
#13
Sara Salerno, Christoph P Hornik, Michael Cohen-Wolkowiez, P Brian Smith, Lawrence C Ku, Matthew S Kelly, Reese Clark, Daniel Gonzalez
BACKGROUND: Piperacillin, in combination with tazobactam, is frequently used in infants for treating nosocomial infections, although safety data in this population are limited. Electronic health record (EHR) data can be used to evaluate drug safety in infants, but measures of drug exposure are lacking. METHODS: To relate simulated piperacillin exposure with adverse events (AEs) in infants using EHR data, we identified infants discharged from 333 neonatal intensive care units managed by the Pediatrix Medical Group between 1997 and 2012...
April 13, 2017: Pediatric Infectious Disease Journal
https://www.readbyqxmd.com/read/28409514/neck-strength-and-self-reported-neck-dysfunction-what-is-the-impact-of-a-season-of-rugby-union
#14
Danielle M Salmon, S John Sullivan, Phil Handcock, Nancy J Rehrer, Brian Niven
BACKGROUND: Neck strength has been reported to reduce the incidence of concussions and neck injuries. However little is known about how neck strength changes over a playing season. AIM: To understand the impact a 20-week rugby season has on neck strength, neck pain (NP) and neck stiffness (NS) in a cohort of rugby players, relative to a non-contact control group. METHODS: This prospective cohort study employed a fixed-frame dynamometer to measure neck strength in a simulated contact posture in rugby players (n=32) and controls (n=15)...
April 13, 2017: Journal of Sports Medicine and Physical Fitness
https://www.readbyqxmd.com/read/28408233/securing-a-chest-tube-properly-a-simple-framework-for-teaching-emergency-medicine-residents-and-assessing-their-technical-abilities
#15
Raaj K Ruparel, Torrey A Laack, Rushin D Brahmbhatt, Phillip G Rowse, Johnathon M Aho, Yazan N AlJamal, Brian D Kim, David S Morris, David R Farley, Ronna L Campbell
BACKGROUND: Quality-improvement efforts at our institution have identified chest tube dislodgement as a preventable complication of tube thoracostomy. Because proper fixation techniques are not well described in the literature and are seldom formally taught, techniques vary among residents. OBJECTIVE: Our aim was to develop and test a framework for teaching and assessing chest tube securement. METHODS: A repeated-measures study design was used...
April 10, 2017: Journal of Emergency Medicine
https://www.readbyqxmd.com/read/28407264/microvascular-anastomosis-simulation-using-a-chicken-thigh-model-interval-versus-massed-training
#16
Stephen Schoeff, Brian Hernandez, Derek J Robinson, Mark J Jameson, David C Shonka
OBJECTIVES/HYPOTHESIS: To compare the effectiveness of massed versus interval training when teaching otolaryngology residents microvascular suturing on a validated microsurgical model. STUDY DESIGN: Otolaryngology residents were placed into interval (n = 7) or massed (n = 7) training groups. The interval group performed three separate 30-minute practice sessions separated by at least 1 week, and the massed group performed a single 90-minute practice session. Both groups viewed a video demonstration and recorded a pretest prior to the first training session...
April 13, 2017: Laryngoscope
https://www.readbyqxmd.com/read/28401399/intelligent-viewpoint-selection-for-efficient-ct-to-video-registration-in-laparoscopic-liver-surgery
#17
Maria R Robu, Philip Edwards, João Ramalhinho, Stephen Thompson, Brian Davidson, David Hawkes, Danail Stoyanov, Matthew J Clarkson
PURPOSE: Minimally invasive surgery offers advantages over open surgery due to a shorter recovery time, less pain and trauma for the patient. However, inherent challenges such as lack of tactile feedback and difficulty in controlling bleeding lower the percentage of suitable cases. Augmented reality can show a better visualisation of sub-surface structures and tumour locations by fusing pre-operative CT data with real-time laparoscopic video. Such augmented reality visualisation requires a fast and robust video to CT registration that minimises interruption to the surgical procedure...
April 11, 2017: International Journal of Computer Assisted Radiology and Surgery
https://www.readbyqxmd.com/read/28397787/correlated-mutation-in-the-evolution-of-catalysis-in-uracil-dna-glycosylase-superfamily
#18
Bo Xia, Yinling Liu, Jose Guevara, Jing Li, Celeste Jilich, Ye Yang, Liangjiang Wang, Brian N Dominy, Weiguo Cao
Enzymes in Uracil DNA glycosylase (UDG) superfamily are essential for the removal of uracil. Family 4 UDGa is a robust uracil DNA glycosylase that only acts on double-stranded and single-stranded uracil-containing DNA. Based on mutational, kinetic and modeling analyses, a catalytic mechanism involving leaving group stabilization by H155 in motif 2 and water coordination by N89 in motif 3 is proposed. Mutual Information analysis identifies a complexed correlated mutation network including a strong correlation in the EG doublet in motif 1 of family 4 UDGa and in the QD doublet in motif 1 of family 1 UNG...
April 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28384707/shape-based-reconstruction-for-transrectal-diffuse-optical-tomography-monitoring-of-photothermal-focal-therapy-of-prostate-cancer-simulation-studies
#19
Robert A Weersink, Sahil Chaudhary, Kenwrick Mayo, Jie He, Brian C Wilson
No abstract text is available yet for this article.
April 1, 2017: Journal of Biomedical Optics
https://www.readbyqxmd.com/read/28384085/an-overview-of-research-and-evaluation-designs-for-dissemination-and-implementation
#20
C Hendricks Brown, Geoffrey Curran, Lawrence A Palinkas, Gregory A Aarons, Kenneth B Wells, Loretta Jones, Linda M Collins, Naihua Duan, Brian S Mittman, Andrea Wallace, Rachel G Tabak, Lori Ducharme, David A Chambers, Gila Neta, Tisha Wiley, John Landsverk, Ken Cheung, Gracelyn Cruden
The wide variety of dissemination and implementation designs now being used to evaluate and improve health systems and outcomes warrants review of the scope, features, and limitations of these designs. This article is one product of a design workgroup that was formed in 2013 by the National Institutes of Health to address dissemination and implementation research, and whose members represented diverse methodologic backgrounds, content focus areas, and health sectors. These experts integrated their collective knowledge on dissemination and implementation designs with searches of published evaluations strategies...
March 20, 2017: Annual Review of Public Health
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