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https://www.readbyqxmd.com/read/28340525/enhanced-dielectric-environment-sensitivity-of-surface-plasmon-polariton-in-the-surface-barrier-heterostructures-based-on-corrugated-thin-metal-films-with-quasi-anticorrelated-interfaces
#1
Alexander V Korovin, Nicolas L Dmitruk, Sergii V Mamykin, Viktor I Myn'ko, Mariya V Sosnova
A new approach to the formation of a 1D planar periodicity on the front of a plasmonic photodetector based on Schottky barrier is proposed. It allows forming a 1D planar periodicity with corrugation at the "metal/environment" interface by laser interference lithography using embedded chalcogenide wires, whereas the "metal/semiconductor" interface is flat that leads to reducing of surface recombination losses at Shottky barrier in contrary to the conventional technology for forming corrugated metal films on the semiconductor surface requiring chemical etching of the semiconductor substrate...
December 2017: Nanoscale Research Letters
https://www.readbyqxmd.com/read/28340512/activation-mechanisms-of-%C3%AE-v%C3%AE-3-integrin-by-binding-to-fibronectin-a-computational-study
#2
Lingyun Wang, Di Pan, Qi Yan, Yuhua Song
Integrin αVβ3 plays an important role in regulating cellular activities and in human diseases. Although the structure of αVβ3 has been studied by crystallography and electron microscopy, the detailed activation mechanism of integrin αVβ3 induced by fibronectin (Fn) remains unclear. In this study, we investigated the conformational and dynamical motion changes of Mn(2+) -bound integrin αVβ3 by binding to Fn with molecular dynamics simulations. Results showed that Fn binding to integrin αVβ3 caused the changes of the conformational flexibility of αVβ3 domains, the essential mode of motion for the domains of αV subunit and β3 subunit and the degrees of correlated motion of residues between the domains of αV subunit and β3 subunit of integrin αVβ3...
March 24, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28340484/engineering-of-layered-lipid-encapsulated-drug-nanoparticles-through-spray-drying
#3
Mahak Sapra, Y S Mayya, Chandra Venkataraman
Drug-containing nanoparticles have been synthesized through the spray-drying of submicron droplet aerosols by using matrix materials such as lipids and biopolymers. Understanding layer formation in composite nanoparticles is essential for the appropriate engineering of particle substructures. The present study developed a droplet-shrinkage model for predicting the solid-phase formation of two non-volatile solutes-stearic acid lipid and a set of drugs, by considering molecular volume and solubility. Nanoparticle formation was simulated to define the parameter space of material properties and process conditions for the formation of a layered structure with the preferential accumulation of the lipid in the outer layer...
March 18, 2017: Colloids and Surfaces. B, Biointerfaces
https://www.readbyqxmd.com/read/28340415/uncertainty-analysis-for-effluent-trading-planning-using-a-bayesian-estimation-based-simulation-optimization-modeling-approach
#4
J L Zhang, Y P Li, G H Huang, B W Baetz, J Liu
In this study, a Bayesian estimation-based simulation-optimization modeling approach (BESMA) is developed for identifying effluent trading strategies. BESMA incorporates nutrient fate modeling with soil and water assessment tool (SWAT), Bayesian estimation, and probabilistic-possibilistic interval programming with fuzzy random coefficients (PPI-FRC) within a general framework. Based on the water quality protocols provided by SWAT, posterior distributions of parameters can be analyzed through Bayesian estimation; stochastic characteristic of nutrient loading can be investigated which provides the inputs for the decision making...
March 6, 2017: Water Research
https://www.readbyqxmd.com/read/28340413/design-synthesis-and-biological-evaluation-of-novel-coumarin-based-benzamides-as-potent-histone-deacetylase-inhibitors-and-anticancer-agents
#5
Tooba Abdizadeh, Mohammad Reza Kalani, Khalil Abnous, Zahra Tayarani-Najaran, Bibi Zahra Khashyarmanesh, Rahman Abdizadeh, Razieh Ghodsi, Farzin Hadizadeh
Histone deacetylases (HDACs) are attractive therapeutic targets for the treatment of cancer and other diseases. It has four classes (I-IV), among them especially class I isozyme are involved in promoting tumor cells proliferation, angiogenesis, differentiation, invasion and metastasis and also viable targets for cancer therapeutics. A novel series of coumarin-based benzamides was designed and synthesized as HDAC inhibitors. The cytotoxic activity of the synthesized compounds (8a-u) was evaluated against six human cancer cell lines including HCT116, A2780, MCF7, PC3, HL60 and A549 and a single normal cell line (Huvec)...
March 18, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28340406/a-local-adjustment-strategy-for-the-initialization-of-dynamic-causal-modelling-to-infer-effective-connectivity-in-brain-epileptic-structures
#6
Wentao Xiang, Ahmad Karfoul, Huazhong Shu, Régine Le Bouquin Jeannès
This paper addresses the question of effective connectivity in the human cerebral cortex in the context of epilepsy. Among model based approaches to infer brain connectivity, spectral Dynamic Causal Modelling is a conventional technique for which we propose an alternative to estimate cross spectral density. The proposed strategy we investigated tackles the sub-estimation of the free energy using the well-known variational Expectation-Maximization algorithm highly sensitive to the initialization of the parameters vector by a permanent local adjustment of the initialization process...
March 7, 2017: Computers in Biology and Medicine
https://www.readbyqxmd.com/read/28340400/pharmacoinformatics-exploration-of-polyphenol-oxidases-leading-to-novel-inhibitors-by-virtual-screening-and-molecular-dynamic-simulation-study
#7
Mubashir Hassan, Qamar Abbas, Zaman Ashraf, Ahmed A Moustafa, Sung-Yum Seo
Polyphenol oxidases (PPOs)/tyrosinases are metal-dependent enzymes and known as important targets for melanogenesis. Although considerable attempts have been conducted to control the melanin-associated diseases by using various inhibitors. However, the exploration of the best anti-melanin inhibitor without side effect still remains a challenge in drug discovery. In present study, protein structure prediction, ligand-based pharmacophore modeling, virtual screening, molecular docking and dynamic simulation study were used to screen the strong novel inhibitor to cure melanogenesis...
March 15, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28340395/a-quint-wavelength-uv-spectroscopy-for-simultaneous-determination-of-dichlorobenzene-chlorobenzene-and-benzene-in-simulated-water-reduced-by-nanoscale-zero-valent-fe-ni-bimetal
#8
Xiaofang Wan, Yu Liu, Xin-Sheng Chai, Youming Li, Congbao Guo
A quint-wavelength UV spectroscopy for rapid determination of dichlorobenzene (DCB), chlorobenzene (CB) and benzene (B) was developed for the dechlorination process of DCB reduced by nanoscale zero-valent Fe/Ni bimetal. Based on the absorbance measurements at 260, 269, 277, 290 and 300nm, the equations for calculating the concentration of DCB and CB and B were established, in which the spectral interference from the nanoparticles could be effectively minimized. The results show that the present method has a good measurement precision (the relative standard deviations are within 2...
March 18, 2017: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/28340381/studying-the-adsorption-of-dna-nanostructures-on-graphene-in-the-aqueous-phase-using-molecular-dynamic-simulations
#9
Jixue Sun, Yang Li, Jianping Lin
DNA nanostructures can undergo large structural fluctuations and deviate from their intended configurations. In this work, two model DNA nanostructures (i.e., Nan and Kai) were designed based on the shape of the two Chinese characters of the name of Nankai University, and additional single-stranded DNA fragments were added to interact with graphene. During four 50-ns molecular dynamic simulations in aqueous solution, the DNA nanostructures adsorbed onto graphene demonstrated more stable conformations with lower root mean square deviations and smaller coordinate changes in the z-axis direction than the DNA nanostructures that were not adsorbed onto graphene...
March 9, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28340354/mechanism-of-substrate-translocation-in-an-alternating-access-transporter
#10
Naomi R Latorraca, Nathan M Fastman, A J Venkatakrishnan, Wolf B Frommer, Ron O Dror, Liang Feng
Transporters shuttle molecules across cell membranes by alternating among distinct conformational states. Fundamental questions remain about how transporters transition between states and how such structural rearrangements regulate substrate translocation. Here, we capture the translocation process by crystallography and unguided molecular dynamics simulations, providing an atomic-level description of alternating access transport. Simulations of a SWEET-family transporter initiated from an outward-open, glucose-bound structure reported here spontaneously adopt occluded and inward-open conformations...
March 23, 2017: Cell
https://www.readbyqxmd.com/read/28340333/the-randomized-crm-an-approach-to-overcoming-the-long-memory-property-of-the-crm
#11
Joseph S Koopmeiners, Andrew Wey
The primary object of a Phase I clinical trial is to determine the maximum tolerated dose (MTD). Typically, the MTD is identified using a dose-escalation study, where initial subjects are treated at the lowest dose level and subsequent subjects are treated at progressively higher dose levels until the MTD is identified. The continual reassessment method (CRM) is a popular model-based dose-escalation design, which utilizes a formal model for the relationship between dose and toxicity to guide dose finding. Recently, it was shown that the CRM has a tendency to get "stuck" on a dose level, with little escalation or de-escalation in the late stages of the trial, due to the long-memory property of the CRM...
March 1, 2017: Journal of Biopharmaceutical Statistics
https://www.readbyqxmd.com/read/28340329/a-close-up-view-of-codon-selection-in-eukaryotic-initiation
#12
Christoffer Lind, Mauricio Esguerra, Johan Åqvist
When given an option to choose among a set of alternatives and only one selection is right, one might stop and reflect over which one is best. However, the ribosome has no time to stop and make such reflections, proteins need to be produced and very fast. Eukaryotic translation initiation is an example of such a conundrum. Here, scanning for the correct codon match must be fast, efficient and accurate. We highlight our recent computational findings, which show how the initiation machinery manages to recognize one specific codon among many possible challengers, by fine-tuning the energetic landscape of base-pairing with the aid of the initiation factors eIF1 and eIF1A...
March 24, 2017: RNA Biology
https://www.readbyqxmd.com/read/28340274/regularized-quantile-regression-applied-to-genome-enabled-prediction-of-quantitative-traits
#13
M Nascimento, F F E Silva, M D V de Resende, C D Cruz, A C C Nascimento, J M S Viana, C F Azevedo, L M A Barroso
Genomic selection (GS) is a variant of marker-assisted selection, in which genetic markers covering the whole genome predict individual genetic merits for breeding. GS increases the accuracy of breeding values (BV) prediction. Although a variety of statistical models have been proposed to estimate BV in GS, few methodologies have examined statistical challenges based on non-normal phenotypic distributions, e.g., skewed distributions. Traditional GS models estimate changes in the phenotype distribution mean, i...
March 22, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28340153/establishing-a-stand-alone-laboratory-dedicated-to-the-care-of-patients-with-ebola-virus-disease
#14
Jing Cao, Christine Senn, Pedro Castaneda, Sheree Humphries, Amy B Karger
Objective: To describe the process for establishment of a stand-alone laboratory dedicated to testing for Ebola virus disease (EVD). Methods: We selected 2 neighboring rooms for the EVD unit: 1 for patient care and 1 for laboratory testing. A limited test menu was developed after consultation with the team of healthcare providers treating patients with EVD, Centers for Disease Control and Prevention (CDC) recommendations, and other sites with EVD expertise. Results: We selected several point-of-care (POC) devices and manual assays to provide necessary testing...
March 13, 2017: Laboratory Medicine
https://www.readbyqxmd.com/read/28340034/estimating-demand-and-cross-price-elasticity-for-very-low-nicotine-content-vlnc-cigarettes-using-a-simulated-demand-task
#15
Megan R Tucker, Murray Laugesen, Randolph C Grace
Introduction: Very Low Nicotine Content (VLNC) cigarettes might be useful as part of a tobacco control strategy, but relatively little is known about their acceptability as substitutes for regular cigarettes. We compared subjective effects and demand for regular cigarettes and Very Low Nicotine Content (VLNC) cigarettes, and estimated cross-price elasticity for VLNC cigarettes, using simulated demand tasks. Methods: 40 New Zealand smokers sampled a VLNC cigarette and completed Cigarette Purchase Tasks to indicate their demand for regular cigarettes and VLNC cigarettes at a range of prices, and a cross-price task indicating how many regular cigarettes and VLNC cigarettes they would purchase at 0...
March 3, 2017: Nicotine & Tobacco Research: Official Journal of the Society for Research on Nicotine and Tobacco
https://www.readbyqxmd.com/read/28340009/designing-an-optimal-screening-program-for-unknown-atrial-fibrillation-a-cost-effectiveness-analysis
#16
Mattias Aronsson, Emma Svennberg, Mårten Rosenqvist, Johan Engdahl, Faris Al-Khalili, Leif Friberg, Viveka Frykman, Lars-Åke Levin
Aims: The primary objective of this study was to use computer simulations to suggest an optimal age for initiation of screening for unknown atrial fibrillation and to evaluate if repeated screening will add value. Methods and results: In the absence of relevant clinical studies, this analysis was based on a simulation model. More than two billion different designs of screening programs for unknown atrial fibrillation were simulated and analysed. Data from the published scientific literature and registries were used to construct the model and estimate lifelong effects and costs...
March 1, 2017: Europace: European Pacing, Arrhythmias, and Cardiac Electrophysiology
https://www.readbyqxmd.com/read/28339846/estimation-of-whole-body-radiation-exposure-from-brachytherapy-for-oral-cancer-using-a-monte-carlo-simulation
#17
Y Ozaki, H Watanabe, A Kaida, M Miura, K Nakagawa, K Toda, R Yoshimura, Y Sumi, T Kurabayashi
Early stage oral cancer can be cured with oral brachytherapy, but whole-body radiation exposure status has not been previously studied. Recently, the International Commission on Radiological Protection Committee (ICRP) recommended the use of ICRP phantoms to estimate radiation exposure from external and internal radiation sources. In this study, we used a Monte Carlo simulation with ICRP phantoms to estimate whole-body exposure from oral brachytherapy. We used a Particle and Heavy Ion Transport code System (PHITS) to model oral brachytherapy with 192Ir hairpins and 198Au grains and to perform a Monte Carlo simulation on the ICRP adult reference computational phantoms...
February 24, 2017: Journal of Radiation Research
https://www.readbyqxmd.com/read/28339836/differences-in-textural-properties-of-cooked-caponized-and-broiler-chicken-breast-meat
#18
J U-Chupaj, Y Malila, C Gamonpilas, K Kijroongrojana, M Petracci, S Benjakul, W Visessanguan
This study was aimed at evaluating textural properties of cooked chicken breast meats obtained from 3 production systems (conventional raising, feed modification, and caponization) and determining the relationship between instrumental parameters and sensory attributes associated with the texture of capon meat. Texture of cooked breast meats was determined using 3 instrumental methods: Warner-Bratzler Shear (WBS), texture profile analysis (TPA), and uniaxial compression (UC), and sensory analysis by trained panelists...
February 23, 2017: Poultry Science
https://www.readbyqxmd.com/read/28339770/characterization-of-indigenous-aseel-chicken-breed-for-morphological-growth-production-and-meat-composition-traits-from-india
#19
U Rajkumar, S Haunshi, C Paswan, M V L N Raju, S V Rama Rao, R N Chatterjee
Aseel is an important native chicken breed of India, known for its martial qualities (aggressive fighting abilities), pugnacity, and majestic gait. The aim of the study is to conserve and characterize the Aseel germplasm, which is considered to be endangered. The birds were maintained on deep litter under a simulated backyard type of housing having night shelter and a free-range area. A total of 313 chicks produced in the second generation from the flock collected from native tract in Andhra Pradesh was characterized for morphological, growth, production, and meat quality parameters...
February 23, 2017: Poultry Science
https://www.readbyqxmd.com/read/28339723/leveraging-molecular-datasets-for-biomarker-based-clinical-trial-design-in-glioblastoma
#20
Shyam K Tanguturi, Lorenzo Trippa, Shakti H Ramkissoon, Kristine Pelton, David Knoff, David Sandak, Neal I Lindeman, Azra H Ligon, Rameen Beroukhim, Giovanni Parmigiani, Patrick Y Wen, Keith L Ligon, Brian M Alexander
Background.: Biomarkers can improve clinical trial efficiency, but designing and interpreting biomarker-driven trials require knowledge of relationships among biomarkers, clinical covariates, and endpoints. We investigated these relationships across genomic subgroups of glioblastoma (GBM) within our institution (DF/BWCC), validated results in The Cancer Genome Atlas (TCGA), and demonstrated potential impacts on clinical trial design and interpretation. Methods.: We identified genotyped patients at DF/BWCC, and clinical associations across 4 common GBM genomic biomarker groups were compared along with overall survival (OS), progression-free survival (PFS), and survival post-progression (SPP)...
February 20, 2017: Neuro-oncology
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