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https://www.readbyqxmd.com/read/28445999/crystal-orientation-effect-on-the-subsurface-deformation-of-monocrystalline-germanium-in-nanometric-cutting
#1
Min Lai, Xiaodong Zhang, Fengzhou Fang
Molecular dynamics simulations of nanometric cutting on monocrystalline germanium are conducted to investigate the subsurface deformation during and after nanometric cutting. The continuous random network model of amorphous germanium is established by molecular dynamics simulation, and its characteristic parameters are extracted to compare with those of the machined deformed layer. The coordination number distribution and radial distribution function (RDF) show that the machined surface presents the similar amorphous state...
December 2017: Nanoscale Research Letters
https://www.readbyqxmd.com/read/28445954/a-clinically-feasible-multiplex-proteomic-immunoassay-as-a-novel-functional-diagnostic-for-pancreatic-ductal-adenocarcinoma
#2
Kian-Huat Lim, Emma Langley, Feng Gao, Jingqin Luo, Lin Li, Gary Meyer, Phillip Kim, Sharat Singh, Vladamir M Kushnir, Dayna S Early, Daniel K Mullady, Steven A Edmundowicz, Sachin Wani, Faris M Murad, Dengfeng Cao, Riad R Azar, Andrea Wang-Gillam
To date, targeted therapy for pancreatic ductal adenocarcinoma (PDAC) remains largely unsuccessful in the clinic. Current genomics-based technologies are unable to reflect the quantitative, dynamic signaling changes in the tumor, and require larger tumor samples that are difficult to obtain in PDAC patients. Therefore, a highly sensitive functional tool that can reliably and comprehensively inform intra-tumoral signaling events is direly needed to guide treatment decision. We tested the utility of a highly sensitive proteomics-based functional diagnostic platform, Collaborative Enzyme Enhanced Reactive-immunoassay (CEERTM), on fine-needle aspiration (FNA) samples obtained from 102 patients with radiographically-evident pancreatic tumors...
April 11, 2017: Oncotarget
https://www.readbyqxmd.com/read/28445928/regulation-of-angiogenic-behaviors-by-oxytocin-receptor-through-gli1-indcued-transcription-of-hif-1%C3%AE-in-human-umbilical-vein-endothelial-cells
#3
Ji Zhu, Huiyan Wang, Xiaoyan Zhang, Yin Xie
Angiogenesis is a dynamic hypoxia-stimulated process playing a key role in tissue growth and repair under various pathophysiological circumstances. Abnormal angiogenesis contributes to the pathogenesis of many human diseases. Oxytocin receptor is a classical G-protein-coupled receptor expressed on endothelial cells. The present study was aimed to investigate how oxytocin receptor regulated the angiogenic behaviors of human umbilical vein endothelial cells (HUVECs). We found that oxytocin at 0.1μM significantly increased cell proliferation, upregulated the mRNA and protein expression of CD31 and vWF (two important endothelial markers), and enhanced the tuber formation capacity in HUVECs...
April 22, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/28445909/transient-severe-motion-artifact-related-to-gadoxetate-disodium-enhanced-liver-mri-frequency-and-risk-evaluation-at-a-german-institution
#4
Lennart Well, Vanessa Hanna Rausch, Gerhard Adam, Frank Oliver Henes, Peter Bannas
Purpose Varying frequencies (5 - 18 %) of contrast-related transient severe motion (TSM) imaging artifacts during gadoxetate disodium-enhanced arterial phase liver MRI have been reported. Since previous reports originated from the United States and Japan, we aimed to determine the frequency of TSM at a German institution and to correlate it with potential risk factors and previously published results. Materials and Methods Two age- and sex-matched groups were retrospectively selected (gadoxetate disodium n = 89; gadobenate dimeglumine n = 89) from dynamic contrast-enhanced MRI examinations in a single center...
April 26, 2017: RöFo: Fortschritte Auf Dem Gebiete der Röntgenstrahlen und der Nuklearmedizin
https://www.readbyqxmd.com/read/28445881/absence-of-decline-of-kidney-function-in-human-immunodeficiency-virus-infected-patients-under-routine-clinical-management
#5
Julie Boucquemont, Sylvie Lawson-Ayayi, Claire Rigothier, Fabrice Bonnet, Cécile Proust-Lima, Didier Neau, Carine Greib, Ghada Miremont-Salamé, François Dabis, Michel Dupon, Frédéric-Antoine Dauchy
BACKGROUND: Since the introduction of antiretroviral therapy (ART), human immunodeficiency virus (HIV)-infected patients have a drastically improved prognosis but at the same time they are also more affected by non-HIV related complications, such as chronic kidney disease. The objective of our study was to investigate the effect of proteinuria and tenofovir (TDF)-containing ART regimens on the temporal evolution of estimated glomerular filtration rate (eGFR). METHODS: Between April 2008 and October 2012, we enrolled 395 patients with a complete renal evaluation among patients from the ANRS C03 Aquitaine cohort, a prospective hospital-based cohort of HIV-1-infected patients under routine clinical management in southwestern France...
April 26, 2017: Nephron
https://www.readbyqxmd.com/read/28445879/cytokine-and-chemokine-profiles-in-patients-with-neuromyelitis-optica-spectrum-disorder
#6
Yuge Wang, Yifan Zhou, Xiaobo Sun, Tingting Lu, Lei Wei, Ling Fang, Chen Chen, Qiao Huang, Xueqiang Hu, Zhengqi Lu, Lisheng Peng, Wei Qiu
OBJECTIVE: To screen cytokines and chemokines and determine their dynamic changes in the serum and cerebrospinal fluid (CSF) of patients with neuromyelitis optica spectrum disorder (NMOSD). METHODS: Eight NMOSD with seropositive aquaporin-4 antibody (AQP4-IgG) were enrolled, as well as 8 matched patients with multiple sclerosis (MS) and 8 with noninflammatory neurological diseases, who were included as controls. In total, 102 cytokines and 34 chemokines were detected in the CSF and serum of NMOSD patients and controls...
April 27, 2017: Neuroimmunomodulation
https://www.readbyqxmd.com/read/28445861/the-application-of-silicon-sol-gel-technology-to-forensic-blood-substitute-development-investigation-of-the-spreading-dynamics-onto-a-paper-surface
#7
Theresa Stotesbury, Mike Illes, Paul Wilson, Andrew J Vreugdenhil
This work investigates the spreading dynamics of three candidate sol-gel solutions, of ranging viscosities, surface tensions and densities, and compares them with water and two commercial blood substitute products. Droplets were created with different sizes (10 to75μL) and impact velocities (1.4 to 6.0m/s) to strike 176gsm cardstock. Over 2200 droplets were created using the six different fluids and their final dried stain diameter was measured. Droplet spread was plotted using the Scheller and Bousfield correlation and uses effective viscosity as a parameter for non-Newtonian fluids...
April 1, 2017: Forensic Science International
https://www.readbyqxmd.com/read/28445854/balance-training-in-individuals-with-parkinson-s-disease-therapist-supervised-vs-home-based-exercise-programme
#8
Elizabeth Maria Atterbury, Karen Estelle Welman
BACKGROUND: Poor locomotion and balance in Parkinson's disease (PD) often diminishes independence. Accordingly, gait is considered one of the most relevant rehabilitation outcomes, and home-based balance exercises might be a viable mode of exercise delivery for individuals with PD. However, research on PD interventions rarely indicate best practices to deliver exercises. Therefore, this study endeavoured to compare the efficacy of a home-based and therapist-supervised balance programme on gait parameters, dynamic balance, balance confidence and motivation in individuals diagnosed with PD...
April 4, 2017: Gait & Posture
https://www.readbyqxmd.com/read/28445832/study-of-the-mechanism-of-protonated-histidine-induced-conformational-changes-in-the-zika-virus-dimeric-envelope-protein-using-accelerated-molecular-dynamic-simulations
#9
Jixue Sun, Yang Li, Pi Liu, Jianping Lin
The Zika virus has drawn worldwide attention because of the epidemic diseases it causes. It is a flavivirus that has an icosahedral protein shell constituted by an envelope glycoprotein (E-protein) and membrane protein (M-protein) in the mature virion. The multistep process of membrane fusion to infect the host cell is pH-induced. To understand the mechanism of the conformational changes in the (E-M)2 protein homodimer embedded in the membrane, two 200-ns accelerated dynamic simulations were performed under different pH conditions...
April 13, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28445813/microfluidic-integrated-patterned-ito-immunosensor-for-rapid-detection-of-prostate-specific-membrane-antigen-biomarker-in-prostate-cancer
#10
Rajesh Seenivasan, Chandra K Singh, Jay W Warrick, Nihal Ahmad, Sundaram Gunasekaran
An optically transparent patterned indium tin oxide (ITO) three-electrode sensor integrated with a microfluidic channel was designed for label-free immunosensing of prostate-specific membrane antigen (PSMA), a prostate cancer (PCa) biomarker, expressed on prostate tissue and circulating tumor cells but also found in serum. The sensor relies on cysteamine capped gold nanoparticles (N-AuNPs) covalently linked with anti-PSMA antibody (Ab) for target specificity. A polydimethylsiloxane (PDMS) microfluidic channel is used to efficiently and reproducibly introduce sample containing soluble proteins/cells to the sensor...
April 11, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28445778/the-impact-of-bilateral-vagotomy-on-the-physostigmine-induced-airway-constriction-in-ferrets
#11
Burim Neziri, Armond Daci, Shaip Krasniqi, Ramadan Sopi, Musa A Haxhiu
Vagal innervations have a great role in the respiratory function and are the main route of signal transmission from respiratory neural centers into the trachea and others conducting airways. We have investigated the role of central mechanisms related to vagal neural pathways and the cholinergic outflow in tracheobronchial smooth muscle tone and lung mechanics parameters. Parameters of lung mechanics such as lung resistance (RL), dynamic compliance (Cdyn) and pressure in bypassed tracheal segment (Ptseg) were measured before and after vagotomy and asphyxia test...
April 23, 2017: Respiratory Physiology & Neurobiology
https://www.readbyqxmd.com/read/28445762/analysis-of-active-transport-by-fluorescence-recovery-after-photobleaching
#12
Maria-Veronica Ciocanel, Jill A Kreiling, James A Gagnon, Kimberly L Mowry, Björn Sandstede
Fluorescence recovery after photobleaching (FRAP) is a well-established experimental technique to study binding and diffusion of molecules in cells. Although a large number of analytical and numerical models have been developed to extract binding and diffusion rates from FRAP recovery curves, active transport of molecules is typically not included in the existing models that are used to estimate these rates. Here we present a validated numerical method for estimating diffusion, binding/unbinding rates, and active transport velocities using FRAP data that captures intracellular dynamics through partial differential equation models...
April 25, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28445761/live-cell-super-resolution-reveals-f-actin-and-plasma-membrane-dynamics-at-the-t-cell-synapse
#13
George W Ashdown, Garth L Burn, David J Williamson, Elvis Pandžić, Ruby Peters, Michael Holden, Helge Ewers, Lin Shao, Paul W Wiseman, Dylan M Owen
The cortical actin cytoskeleton has been shown to be critical for the reorganization and heterogeneity of plasma membrane components of many cells, including T cells. Building on previous studies at the T cell immunological synapse, we quantitatively assess the structure and dynamics of this meshwork using live-cell superresolution fluorescence microscopy and spatio-temporal image correlation spectroscopy. We show for the first time, to our knowledge, that not only does the dense actin cortex flow in a retrograde fashion toward the synapse center, but the plasma membrane itself shows similar behavior...
April 25, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28445759/pulsatile-lipid-vesicles-under-osmotic-stress
#14
Morgan Chabanon, James C S Ho, Bo Liedberg, Atul N Parikh, Padmini Rangamani
The response of lipid bilayers to osmotic stress is an important part of cellular function. Recent experimental studies showed that when cell-sized giant unilamellar vesicles (GUVs) are exposed to hypotonic media, they respond to the osmotic assault by undergoing a cyclical sequence of swelling and bursting events, coupled to the membrane's compositional degrees of freedom. Here, we establish a fundamental and quantitative understanding of the essential pulsatile behavior of GUVs under hypotonic conditions by advancing a comprehensive theoretical model of vesicle dynamics...
April 25, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28445755/mapping-ryanodine-binding-sites-in-the-pore-cavity-of-ryanodine-receptors
#15
Van A Ngo, Laura L Perissinotti, Williams Miranda, S R Wayne Chen, Sergei Y Noskov
Ryanodine (Ryd) irreversibly targets ryanodine receptors (RyRs), a family of intracellular calcium release channels essential for many cellular processes ranging from muscle contraction to learning and memory. Little is known of the atomistic details about how Ryd binds to RyRs. In this study, we used all-atom molecular dynamics simulations with both enhanced and bidirectional sampling to gain direct insights into how Ryd interacts with major residues in RyRs that were experimentally determined to be critical for its binding...
April 25, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28445754/probing-the-dynamics-of-clot-bound-thrombin-at-venous-shear-rates
#16
Laura M Haynes, Thomas Orfeo, Kenneth G Mann, Stephen J Everse, Kathleen E Brummel-Ziedins
In closed system models of fibrin formation, exosite-mediated thrombin binding to fibrin contributes to clot stability and is resistant to inhibition by antithrombin/heparin while still susceptible to small, active-site inhibitors. Each molecule of fibrin can bind ∼1.6 thrombin molecules at low-affinity binding sites (Kd = 2.8 μM) and ∼0.3 molecules of thrombin at high-affinity binding sites (Kd = 0.15 μM). The goal of this study is to assess the stability of fibrin-bound thrombin under venous flow conditions and to determine both its accessibility and susceptibility to inhibition...
April 25, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28445750/effect-of-phosphorylation-on-a-human-like-osteopontin-peptide
#17
Samuel Lenton, Marco Grimaldo, Felix Roosen-Runge, Frank Schreiber, Tommy Nylander, Roger Clegg, Carl Holt, Michael Härtlein, Victoria García Sakai, Tilo Seydel, Susana C Marujo Teixeira
The last decade established that the dynamic properties of the phosphoproteome are central to function and its modulation. The temporal dimension of phosphorylation effects remains nonetheless poorly understood, particularly for intrinsically disordered proteins. Osteopontin, selected for this study due to its key role in biomineralization, is expressed in many species and tissues to play a range of distinct roles. A notable property of highly phosphorylated isoforms of osteopontin is their ability to sequester nanoclusters of calcium phosphate to form a core-shell structure, in a fluid that is supersaturated but stable...
April 25, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28445746/crosstalk-and-the-dynamical-modularity-of%C3%A2-feed-forward-loops-in-transcriptional-regulatory-networks
#18
Michael A Rowland, Ahmed Abdelzaher, Preetam Ghosh, Michael L Mayo
Network motifs, such as the feed-forward loop (FFL), introduce a range of complex behaviors to transcriptional regulatory networks, yet such properties are typically determined from their isolated study. We characterize the effects of crosstalk on FFL dynamics by modeling the cross regulation between two different FFLs and evaluate the extent to which these patterns occur in vivo. Analytical modeling suggests that crosstalk should overwhelmingly affect individual protein-expression dynamics. Counter to this expectation we find that entire FFLs are more likely than expected to resist the effects of crosstalk (≈20% for one crosstalk interaction) and remain dynamically modular...
April 25, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28445744/nmrbox-a-resource-for-biomolecular-nmr-computation
#19
Mark W Maciejewski, Adam D Schuyler, Michael R Gryk, Ion I Moraru, Pedro R Romero, Eldon L Ulrich, Hamid R Eghbalnia, Miron Livny, Frank Delaglio, Jeffrey C Hoch
Advances in computation have been enabling many recent advances in biomolecular applications of NMR. Due to the wide diversity of applications of NMR, the number and variety of software packages for processing and analyzing NMR data is quite large, with labs relying on dozens, if not hundreds of software packages. Discovery, acquisition, installation, and maintenance of all these packages is a burdensome task. Because the majority of software packages originate in academic labs, persistence of the software is compromised when developers graduate, funding ceases, or investigators turn to other projects...
April 25, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28445723/mosquitoes-transmit-unique-west-nile-virus-populations-during-each-feeding-episode
#20
Nathan D Grubaugh, Joseph R Fauver, Claudia Rückert, James Weger-Lucarelli, Selene Garcia-Luna, Reyes A Murrieta, Alex Gendernalik, Darci R Smith, Doug E Brackney, Gregory D Ebel
Arthropod-borne viruses (arboviruses), such as Zika virus, chikungunya virus, and West Nile virus (WNV), pose continuous threats to emerge and cause large epidemics. Often, these events are associated with novel virus variants optimized for local transmission that first arise as minorities within a host. Thus, the conditions that regulate the frequency of intrahost variants are important determinants of emergence. Here, we describe the dynamics of WNV genetic diversity during its transmission cycle. By temporally sampling saliva from individual mosquitoes, we demonstrate that virus populations expectorated by mosquitoes are highly diverse and unique to each feeding episode...
April 25, 2017: Cell Reports
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