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https://www.readbyqxmd.com/read/28645069/controlled-single-bubble-cavitation-collapse-results-in-jet-induced-injury-in-brain-tissue
#1
Saranya Canchi, Karen Kelly, Yu Hong, Michael A King, Ghatu Subhash, Malisa Sarntinoranont
Multiscale damage due to cavitation is considered as a potential mechanism of traumatic brain injury (TBI) associated with explosion. In this study, we employed a TBI relevant hippocampal ex vivo slice model to induce bubble cavitation. Placement of single reproducible seed bubbles allowed control of size, number, and tissue location to visualize and measure deformation parameters. Maximum strain value was measured at 45 µs after bubble collapse, presented with a distinct contour and coincided temporally and spatially with the liquid jet...
June 15, 2017: Journal of the Mechanical Behavior of Biomedical Materials
https://www.readbyqxmd.com/read/28644624/extensive-assessment-of-various-computational-methods-for-aspartate-s-pka-shift
#2
Zhaoxi Sun, Xiaohui Wang, Jianing Song
A series of computational methods for pKa shift prediction are extensively tested on a set of benchmark protein systems, aiming at identifying pitfalls and evaluating their performance on high variants. Including 19 ASP residues in 10 protein systems, the benchmark set consists of both residues with highly shifted pKa values as well as those varying little from the reference value, with an experimental RMS free energy differences of 2.49 kcal/mol with respect to blocked amino acid, namely the RMS pKa shift being 1...
June 23, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28644375/gaden-a-3d-gas-dispersion-simulator-for-mobile-robot-olfaction-in-realistic-environments
#3
Javier Monroy, Victor Hernandez-Bennets, Han Fan, Achim Lilienthal, Javier Gonzalez-Jimenez
This work presents a simulation framework developed under the widely used Robot Operating System (ROS) to enable the validation of robotics systems and gas sensing algorithms under realistic environments. The framework is rooted in the principles of computational fluid dynamics and filament dispersion theory, modeling wind flow and gas dispersion in 3D real-world scenarios (i.e., accounting for walls, furniture, etc.). Moreover, it integrates the simulation of different environmental sensors, such as metal oxide gas sensors, photo ionization detectors, or anemometers...
June 23, 2017: Sensors
https://www.readbyqxmd.com/read/28644152/incorporating-hypr-de-noising-within-iterative-pet-reconstruction-hypr-osem
#4
Ju-Chieh Kevin Cheng, Julian C Matthews, Vesna Sossi, Jose Anton-Rodriguez, Andre Salomon, Ronald Boellaard
HighlY constrained back-PRojection (HYPR) is a post-processing de-noising technique originally developed for time-resolved Magnetic Resonance Imaging. It has been recently applied to dynamic imaging for Positron Emission Tomography (PET) and shown promising results. In this work, we have developed an iterative reconstruction algorithm (HYPR-OSEM) which improves the signal-to-noise ratio (SNR) in static imaging (i.e. single frame reconstruction) by incorporating HYPR de-noising directly within the ordered subsets expectation maximization (OSEM) algorithm...
June 23, 2017: Physics in Medicine and Biology
https://www.readbyqxmd.com/read/28643581/a-white-paper-on-global-wheat-health-based-on-scenario-development-and-analysis
#5
Serge Savary, Annika Djurle, Jonathan Yuen, Andrea Ficke, Vittorio Rossi, Paul Esker, Jose M Fernandes, Emerson Del Ponte, Jatindra Kumar, Laurence V Madden, Pierce A Paul, Neil McRoberts, Pawan Kumar Singh, Laurent Huber, Claude Pope de Vallavieille, Sébastien Saint-Jean, Laetitia Willocquet
Scenario analysis constitutes a useful approach to synthesize knowledge and derive hypotheses in the case of complex systems which are documented with mainly qualitative or very diverse information. In this article, a framework for scenario analysis is designed and then, applied to global wheat health within a timeframe from today to 2050. Scenario analysis entails the choice of settings, the definition of scenarios of change, and the analysis of outcomes of these scenarios in the chosen settings. Three idealized agrosystems, representing a large fraction of the global diversity of wheat-based agrosystems, are considered, which represent the settings of the analysis...
June 23, 2017: Phytopathology
https://www.readbyqxmd.com/read/28643242/what-influences-linkage-to-care-after-home-based-hiv-counseling-and-testing
#6
Reshma Naik, Wanga Zembe, Fatima Adigun, Elizabeth Jackson, Hanani Tabana, Debra Jackson, Frank Feeley, Tanya Doherty
To maximize the benefits of test and treat strategies that utilize community-based HIV testing, clients who test positive must link to care in a timely manner. However, linkage rates across the HIV treatment cascade are typically low and little is known about what might facilitate or hinder care-seeking behavior. This qualitative study was conducted within a home-based HIV counseling and testing (HBHCT) intervention in South Africa. In-depth interviews were conducted with 30 HBHCT clients who tested HIV positive to explore what influenced their care-seeking behavior...
June 22, 2017: AIDS and Behavior
https://www.readbyqxmd.com/read/28643235/design-and-evaluation-of-rgd-modified-gemini-surfactant-based-lipoplexes-for-targeted-gene-therapy-in-melanoma-model
#7
Waleed Mohammed-Saeid, Jackson Chitanda, Mays Al-Dulaymi, Ronald Verrall, Ildiko Badea
PURPOSE: We have developed and evaluated novel peptide-targeted gemini surfactant-based lipoplexes designed for melanoma gene therapy. METHODS: Integrin receptor targeting peptide, cyclic-arginylglycylaspartic acid (cRGD), was either chemically coupled to a gemini surfactant backbone or physically co-formulated with lipoplexes. Several formulations and transfection techniques were developed. Transfection efficiency and cellular toxicity of the lipoplexes were evaluated in an in vitro human melanoma model...
June 22, 2017: Pharmaceutical Research
https://www.readbyqxmd.com/read/28642608/ocean-acidification-as-a-driver-of-community-simplification-via-the-collapse-of-higher-order-and-rise-of-lower-order-consumers
#8
S Vizzini, B Martínez-Crego, C Andolina, A Massa-Gallucci, S D Connell, M C Gambi
Increasing oceanic uptake of CO2 is predicted to drive ecological change as both a resource (i.e. CO2 enrichment on primary producers) and stressor (i.e. lower pH on consumers). We use the natural ecological complexity of a CO2 vent (i.e. a seagrass system) to assess the potential validity of conceptual models developed from laboratory and mesocosm research. Our observations suggest that the stressor-effect of CO2 enrichment combined with its resource-effect drives simplified food web structure of lower trophic diversity and shorter length...
June 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28642368/the-influence-of-disulfide-bonds-on-the-mechanical-stability-of-proteins-is-context-dependent
#9
Aitor Manteca, Álvaro Alonso-Caballero, Marie Fertin, Simon Poly, David De Sancho, Raul Perez-Jimenez
Disulfide bonds play a crucial role in proteins, modulating their stability and constraining their conformational dynamics. A particularly important case is that of proteins that need to withstand forces arising from their normal biological function and that are often disulfide bonded. However, the influence of disulfides on the overall mechanical stability of proteins is poorly understood. Here, we used single-molecule force spectroscopy (smFS) to study the role of disulfide bonds in different mechanical proteins in terms of their unfolding forces...
June 22, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28642243/anti-inflammatory-and-anti-osteoarthritis-effects-of-tectorigenin
#10
Cheng-Long Wang, De Li, Chuan-Dong Wang, Fei Xiao, Jun-Feng Zhu, Chao Shen, Bin Zuo, Yi-Min Cui, Hui Wang, Yuan Gao, Guo-Li Hu, Xiao-Ling Zhang, Xiao-Dong Chen
Osteoarthritis (OA) is a common and dynamic joint disease, including the articular cartilage, underlying bones, and synovium. In particular, OA is considered as the degeneration of the cartilage. Tectorigenin (Tec) can affect many biological processes. However, its effect on articular chondrocytes remains unclear. This study aimed to assess the role of Tec in articular cartilage. In vitro, Tec inhibited the expression levels of type X collagen, cyclooxigenase-2, matrix metalloproteinase (MMP)-3, and MMP-13 gene but enhanced those of Runx1, type II collagen, and aggrecan in the presence of IL-1β...
June 22, 2017: Biology Open
https://www.readbyqxmd.com/read/28642126/molecular-and-hydrodynamic-properties-of-human-epidermal-growth-factor-receptor-her2-extracellular-domain-and-its-homodimer-experiments-and-multi-scale-simulations
#11
J F Vega, J Ramos, V Cruz, E Vicente-Alique, E Sánchez-Sánchez, A Sánchez-Fernández, Y Wang, P Hu, J Cortés, J Martínez-Salazar
BACKGROUND: In a broad range of human carcinomas gene amplification leads to HER2 overexpression, which has been proposed to cause spontaneous dimerization and activation in the absence of ligand. This makes HER2 attractive as a therapeutic target. However, the HER2 homodimerization mechanism remains unexplored. It has been suggested that the "back-to-back" homodimer does not form in solution. Notwithstanding, very recently the crystal structure of the HER2 extracellular domain homodimer formed with a "back-to-head" interaction has been resolved...
June 19, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28641819/dynamic-contrast-enhanced-mr-imaging-of-carotid-vasa-vasorum-in-relation-to-coronary-and-cerebrovascular-events
#12
Juan Wang, Huijun Chen, Jie Sun, Daniel S Hippe, Huawei Zhang, Shengyuan Yu, Jianming Cai, Leixing Xie, Bao Cui, Chun Yuan, Xihai Zhao, Weimin Yuan, Hongbin Liu
BACKGROUND AND AIMS: Dynamic contrast-enhanced MR imaging (DCE-MRI) provides a noninvasive approach to the functional status of carotid adventitial vasa vasorum. Contrast extravasation rate, or K(trans), derived from kinetic modeling of adventitial enhancement, has been correlated with plaque neovascularization and inflammation. This study sought to clarify the clinical implications of K(trans) by evaluating its relationship with documented cardiovascular events (CVE). METHODS: Seventy patients with carotid plaque at clinical ultrasound examination were recruited and imaged with a previously-described bright-blood DCE-MRI protocol (spatial resolution: 0...
June 3, 2017: Atherosclerosis
https://www.readbyqxmd.com/read/28641435/validating-and-implementing-modified-filinov-phase-filtration-in-semiclassical-dynamics
#13
Matthew S Church, Sergey V Antipov, Nandini Ananth
The Mixed Quantum-Classical Initial Value Representation (MQC-IVR) is a recently introduced approximate semiclassical (SC) method for the calculation of real-time quantum correlation functions. MQC-IVR employs a modified Filinov filtration (MFF) scheme to control the overall phase of the SC integrand, extending the applicability of SC methods to complex systems while retaining their ability to accurately describe quantum coherence effects. Here, we address questions regarding the effectiveness of the MFF scheme in combination with SC dynamics...
June 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28641189/qualitative-and-quantitative-simulation-of-androgen-receptor-antagonists-a-case-study-of-polybrominated-diphenyl-ethers
#14
Yang Wu, Wei Shi, Pu Xia, Xiaowei Zhang, Hongxia Yu
Recently, great attention has been paid to the identification and prediction of the androgen disrupting potencies of polybrominated diphenyl ethers (PBDEs). However, few existing models can discriminate active and inactive compounds, which make the quantitative prediction process including the quantitative structure-activity relationship (QSAR) technique unreliable. In this study, different grouping methods were investigated and compared for qualitative identification, including molecular docking and molecular dynamics simulations (MD)...
June 19, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28640810/lassim-a-network-inference-toolbox-for-genome-wide-mechanistic-modeling
#15
Rasmus Magnusson, Guido Pio Mariotti, Mattias Köpsén, William Lövfors, Danuta R Gawel, Rebecka Jörnsten, Jörg Linde, Torbjörn Nordling, Elin Nyman, Sylvie Schulze, Colm E Nestor, Huan Zhang, Gunnar Cedersund, Mikael Benson, Andreas Tjärnberg, Mika Gustafsson
Recent technological advancements have made time-resolved, quantitative, multi-omics data available for many model systems, which could be integrated for systems pharmacokinetic use. Here, we present large-scale simulation modeling (LASSIM), which is a novel mathematical tool for performing large-scale inference using mechanistically defined ordinary differential equations (ODE) for gene regulatory networks (GRNs). LASSIM integrates structural knowledge about regulatory interactions and non-linear equations with multiple steady state and dynamic response expression datasets...
June 22, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28640664/%C3%A2-somos-iguales-using-a-structural-violence-framework-to-understand-gender-and-health-inequities-from-an-intersectional-perspective-in-the-peruvian-amazon
#16
Geordan D Shannon, Angelica Motta, Carlos F Cáceres, Jolene Skordis-Worrall, Diana Bowie, Audrey Prost
BACKGROUND: In the Peruvian Amazon, historical events of colonization and political marginalization intersect with identities of ethnicity, class and geography in the construction of gender and health inequities. Gender-based inequalities can manifest in poor health outcomes via discriminatory practices, healthcare system imbalances, inequities in health research, and differential exposures and vulnerabilities to diseases. Structural violence is a comprehensive framework to explain the mechanisms by which social forces such as poverty, racism and gender inequity become embodied as individual experiences and health outcomes, and thus may be a useful tool in structuring an intersectional analysis of gender and health inequities in Amazonian Peru...
January 2017: Global Health Action
https://www.readbyqxmd.com/read/28640260/microscopy-of-the-interacting-harper-hofstadter-model-in-the-two-body-limit
#17
M Eric Tai, Alexander Lukin, Matthew Rispoli, Robert Schittko, Tim Menke, Dan Borgnia, Philipp M Preiss, Fabian Grusdt, Adam M Kaufman, Markus Greiner
The interplay between magnetic fields and interacting particles can lead to exotic phases of matter that exhibit topological order and high degrees of spatial entanglement. Although these phases were discovered in a solid-state setting, recent innovations in systems of ultracold neutral atoms-uncharged atoms that do not naturally experience a Lorentz force-allow the synthesis of artificial magnetic, or gauge, fields. This experimental platform holds promise for exploring exotic physics in fractional quantum Hall systems, owing to the microscopic control and precision that is achievable in cold-atom systems...
June 21, 2017: Nature
https://www.readbyqxmd.com/read/28639942/commissioning-of-the-tongue-and-groove-modelling-in-treatment-planning-systems-from-static-fields-to-vmat-treatments
#18
Victor Hernandez, Juan Antonio Vera-Sánchez, Laure Vieillevigne, Jordi Saez
Adequate modelling of the multi-leaf collimator (MLC) by treatment planning systems (TPS) is essential for accurate dose calculations in intensity-modulated radiation-therapy. For this reason modern TPSs incorporate MLC characteristics such as the leaf end curvature, MLC transmission and the tongue-and-groove. However, the modelling of the tongue-and-groove is often neglected during TPS commissioning and it is not known how accurate it is. This study evaluates the dosimetric consequences of the tongue-and-groove effect for two different MLC models using both film dosimetry and ionisation chambers...
June 22, 2017: Physics in Medicine and Biology
https://www.readbyqxmd.com/read/28639169/the-effects-of-predator-evolution-and-genetic-variation-on-predator-prey-population-level-dynamics
#19
Michael H Cortez, Swati Patel
This paper explores how predator evolution and the magnitude of predator genetic variation alter the population-level dynamics of predator-prey systems. We do this by analyzing a general eco-evolutionary predator-prey model using four methods: Method 1 identifies how eco-evolutionary feedbacks alter system stability in the fast and slow evolution limits; Method 2 identifies how the amount of standing predator genetic variation alters system stability; Method 3 identifies how the phase lags in predator-prey cycles depend on the amount of genetic variation; and Method 4 determines conditions for different cycle shapes in the fast and slow evolution limits using geometric singular perturbation theory...
June 21, 2017: Bulletin of Mathematical Biology
https://www.readbyqxmd.com/read/28638897/adaptive-liquid-flow-behavior-in-3d-nanopores
#20
Mingzhe Li, Weiyi Lu
Liquid flow speed in 2D nanochannel models has previously been characterized, whereas liquid flow behavior in 3D nanostructured materials remains unknown. To fill this gap, we have developed a novel liquid nanofoam (LN) system composed of nanoporous silica gel particles and a non-wettable liquid phase. We demonstrated that the dynamic behavior of the LN sample was strain rate insensitive by impacting it with a drop weight at various incident speeds. Using this experimental setup, we measured the effective liquid flow speed in 3D nanopores and showed that it was 5 orders of magnitude higher than that of quasi-static loading...
June 22, 2017: Physical Chemistry Chemical Physics: PCCP
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