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https://www.readbyqxmd.com/read/29351280/a-generic-framework-for-individual-based-modelling-and-physical-biological-interaction
#1
Asbjørn Christensen, Patrizio Mariani, Mark R Payne
The increased availability of high-resolution ocean data globally has enabled more detailed analyses of physical-biological interactions and their consequences to the ecosystem. We present IBMlib, which is a versatile, portable and computationally effective framework for conducting Lagrangian simulations in the marine environment. The purpose of the framework is to handle complex individual-level biological models of organisms, combined with realistic 3D oceanographic model of physics and biogeochemistry describing the environment of the organisms without assumptions about spatial or temporal scales...
2018: PloS One
https://www.readbyqxmd.com/read/29350955/rate-dependence-of-elementary-rearrangements-and-spatiotemporal-correlations-in-the-3d-flow-of-soft-solids
#2
Vishwas V Vasisht, Sudeep K Dutta, Emanuela Del Gado, Daniel L Blair
We use a combination of confocal microscopy, rheology, and molecular dynamics simulations to investigate jammed emulsions under shear, by analyzing the 3D droplets rearrangements in the shear frame. Our quantitative analysis of local dynamics reveals elementary nonaffine rearrangements that underlie the onset of the flow at small strains. We find that the mechanism of unjamming and the upturn in the material flow curve are associated to a qualitative change in spatiotemporal correlations of such rearrangements with the applied shear rate...
January 5, 2018: Physical Review Letters
https://www.readbyqxmd.com/read/29350620/trions-in-bulk-and-monolayer-materials-faddeev-equations-and-hyperspherical-harmonics
#3
I Filikhin, Roman Ya Kezerashvili, Shalva M Tsiklauri, Bravislav Vlahovic
The negatively T<sup>- </sup>and positively T<sup>+</sup> charged trions in bulk and monolayer semiconductors are studied in the effective mass approximation within the framework of a potential model. The binding energies of trions in various semiconductors are calculated by employing Faddeev equation with the Coulomb potential in three-dimensional (3D) configuration space. Results of calculations of the binding energies for T<sup>-</sup> are consistent with previous computational studies while the T<sup>+</sup> is unbound for all considered cases...
January 19, 2018: Nanotechnology
https://www.readbyqxmd.com/read/29350616/a-disassembly-driven-mechanism-explains-f-actin-mediated-chromosome-transport-in-starfish-oocytes
#4
Philippe Bun, Serge Dmitrieff, Julio M Belmonte, François J Nédélec, Péter Lénárt
While contraction of sarcomeric actomyosin assemblies is well understood, this is not the case for disordered networks of actin filaments (F-actin) driving diverse essential processes in animal cells. For example, at the onset of meiosis in starfish oocytes a contractile F-actin network forms in the nuclear region transporting embedded chromosomes to the assembling microtubule spindle. Here, we addressed the mechanism driving contraction of this 3D disordered F-actin network by comparing quantitative observations to computational models...
January 19, 2018: ELife
https://www.readbyqxmd.com/read/29350579/evaluation-of-respiratory-motion-corrected-cone-beam-ct-at-end-expiration-in-abdominal-radiotherapy-sites-a-prospective-study
#5
Russell E Kincaid, Agung E Hertanto, Yu-Chi Hu, Abraham J Wu, Karyn A Goodman, Hai D Pham, Ellen D Yorke, Qinghui Zhang, Qing Chen, Gig S Mageras
BACKGROUND: Cone beam computed tomography (CBCT) for radiotherapy image guidance suffers from respiratory motion artifacts. This limits soft tissue visualization and localization accuracy, particularly in abdominal sites. We report on a prospective study of respiratory motion-corrected (RMC)-CBCT to evaluate its efficacy in localizing abdominal organs and improving soft tissue visibility at end expiration. MATERIAL AND METHODS: In an IRB approved study, 11 patients with gastroesophageal junction (GEJ) cancer and five with pancreatic cancer underwent a respiration-correlated CT (4DCT), a respiration-gated CBCT (G-CBCT) near end expiration and a one-minute free-breathing CBCT scan on a single treatment day...
January 19, 2018: Acta Oncologica
https://www.readbyqxmd.com/read/29350559/visualizing-3d-food-microstructure-using-tomographic-methods-advantages-and-disadvantages
#6
Zi Wang, Els Herremans, Siem Janssen, Dennis Cantre, Pieter Verboven, Bart Nicolaï
X-ray micro-computed tomography (micro-CT) provides the unique ability to capture intact internal microstructure data without significant preparation of the sample. The fundamentals of micro-CT technology are briefly described along with a short introduction to basic image processing, quantitative analysis, and derivative computational modeling. The applications and limitations of micro-CT in industries such as meat, dairy, postharvest, and bread/confectionary are discussed to serve as a guideline to the plausibility of utilizing the technique for detecting features of interest...
January 18, 2018: Annual Review of Food Science and Technology
https://www.readbyqxmd.com/read/29350495/the-current-landscape-of-3d-in-vitro-tumor-models-what-cancer-hallmarks-are-accessible-for-drug-discovery
#7
REVIEW
Darren Rodenhizer, Teresa Dean, Elisa D'Arcangelo, Alison P McGuigan
Cancer prognosis remains a lottery dependent on cancer type, disease stage at diagnosis, and personal genetics. While investment in research is at an all-time high, new drugs are more likely to fail in clinical trials today than in the 1970s. In this review, a summary of current survival statistics in North America is provided, followed by an overview of the modern drug discovery process, classes of models used throughout different stages, and challenges associated with drug development efficiency are highlighted...
January 19, 2018: Advanced Healthcare Materials
https://www.readbyqxmd.com/read/29350308/the-ppar%C3%AE-agonist-efatutazone-delays-invasive-progression-and-induces-differentiation-of-ductal-carcinoma-in-situ
#8
Virginie Ory, William B Kietzman, Jacob Boeckelman, Bhaskar V Kallakury, Anton Wellstein, Priscilla A Furth, Anna T Riegel
PURPOSE: Ductal carcinoma in situ (DCIS) is a pre-invasive lesion of the breast considered a precursor of invasive ductal carcinoma. This study aimed to determine whether activated PPARγ acts as a tumor suppressor in human DCIS progression. METHODS: We utilized the high-affinity PPARγ agonist, efatutazone, to activate endogenous PPARγ in a well-defined model for the progression of basal (triple negative) DCIS, MCFDCIS cells, cultured under 2D and 3D conditions...
January 19, 2018: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/29350197/a-three-dimensional-correction-method-for-predicting-the-readings-of-a-pinpoint-chamber-on-the-cyberknife-sup-%C3%A2-sup-m6%C3%A2-machine
#9
Yongqian Zhang, Edward Brandner, Cihat Ozhasoglu, Ron Lalonde, Dwight E Heron, M Saiful Huq
The use of small fields in radiation therapy techniques has increased substantially in particular in stereotactic radiosurgery (SRS) and stereotactic body radiation therapy (SBRT). However, as field size reduces further still, the response of the detector changes more rapidly with field size, and the effects of measurement uncertainties become increasingly significant. This work presents a novel 3D dose volume-to-point correction method to predict the readings of a 0.015cc PinPoint chamber (PTW 31014) for both small static-fields and composite-field dosimetry formed by fixed cones on the CyberKnife® M6™ machine...
January 19, 2018: Physics in Medicine and Biology
https://www.readbyqxmd.com/read/29350183/integrated-biocircuits-engineering-functional-multicellular-circuits-and-devices
#10
Jordan Prox, Tory Smith, Chad Holl, Nick Chehade, Liang Guo
Novel in vitro platforms are currently revolutionizing the study and reconstruction of cellular circuitry to bypass the pertaining obstacles of data retrieval in vivo. While earlier approaches have provided great insights into culturing circuits in planar dissociated cell culture systems, the lack of full control over network activity and formation limits our understanding of their functionality. Thus, integrating various controllable parameters are required in creating a suitable microenvironment including cell patterning, highly-specified electrical and chemical stimuli, and rational circuit formation via logic functions...
January 19, 2018: Journal of Neural Engineering
https://www.readbyqxmd.com/read/29349885/a-hierarchical-z-scheme-%C3%AE-fe2-o3-g-c3-n4-hybrid-for-enhanced-photocatalytic-co2-reduction
#11
Zhifeng Jiang, Weiming Wan, Huaming Li, Shouqi Yuan, Huijun Zhao, Po Keung Wong
The challenge in the artificial photosynthesis of fossil resources from CO2 by utilizing solar energy is to achieve stable photocatalysts with effective CO2 adsorption capacity and high charge-separation efficiency. A hierarchical direct Z-scheme system consisting of urchin-like hematite and carbon nitride provides an enhanced photocatalytic activity of reduction of CO2 to CO, yielding a CO evolution rate of 27.2 µmol g-1 h-1 without cocatalyst and sacrifice reagent, which is >2.2 times higher than that produced by g-C3 N4 alone (10...
January 19, 2018: Advanced Materials
https://www.readbyqxmd.com/read/29349513/3d-qsar-study-of-steroidal-and-azaheterocyclic-human-aromatase-inhibitors-using-quantitative-profile-of-protein-ligand-interactions
#12
Sehan Lee, Mace G Barron
Aromatase is a member of the cytochrome P450 superfamily responsible for a key step in the biosynthesis of estrogens. As estrogens are involved in the control of important reproduction-related processes, including sexual differentiation and maturation, aromatase is a potential target for endocrine disrupting chemicals as well as breast cancer therapy. In this work, 3D-QSAR combined with quantitative profile of protein-ligand interactions was employed in the identification and characterization of critical steric and electronic features of aromatase-inhibitor complexes and the estimation of their quantitative contribution to inhibition potency...
January 18, 2018: Journal of Cheminformatics
https://www.readbyqxmd.com/read/29349447/theoretical-study-on-the-charge-transport-in-single-crystals-of-tcnq-f2-tcnq-and-f4-tcnq
#13
Li-Fei Ji, Jian-Xun Fan, Shou-Feng Zhang, Ai-Min Ren
2,5-Difluoro-7,7,8,8-tetracyanoquinodimethane (F2-TCNQ) was recently reported to display excellent electron transport properties in single crystal field-effect transistors (FETs). Its carrier mobility can reach 25 cm2 V-1 s-1 in devices. However, its counterparts TCNQ and F4-TCNQ (tetrafluoro-7,7,8,8-tetracyanoquinodimethane) do not exhibit the same highly efficient behavior. To better understand this significant difference in charge carrier mobility, a multiscale approach combining semiclassical Marcus hopping theory, a quantum nuclear enabled hopping model and molecular dynamics simulations was performed to assess the electron mobilities of the Fn-TCNQ (n = 0, 2, 4) systems in this work...
January 19, 2018: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29348860/silencing-ror1-and-ror2-inhibits-invasion-and-adhesion-in-an-organotypic-model-of-ovarian-cancer-metastasis
#14
Claire Henry, Neville Hacker, Caroline Ford
OBJECTIVE: Elevated expression of the ROR1 and ROR2 Wnt receptors has been noted in both the tumour and stromal compartments of ovarian cancer patient tissue samples. In vitro studies have suggested these receptors play a role in ovarian cancer metastasis. However, these previous studies have utilised simple 2D in vitro models to investigate cancer cell growth and migration, which does not allow investigation of stromal involvement in Wnt driven metastasis. AIM: To investigate targeting ROR1 and ROR2 using a primary co-culture 3D model of epithelial ovarian cancer dissemination to the omentum...
December 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/29348853/3d-cultivation-of-nsclc-cell-lines-induce-gene-expression-alterations-of-key-cancer-associated-pathways-and-mimic-in-vivo-conditions
#15
Gabriele Gamerith, Johannes Rainer, Julia M Huber, Hubert Hackl, Zlatko Trajanoski, Stefan Koeck, Edith Lorenz, Johann Kern, Reinhard Kofler, Jens M Kelm, Heinz Zwierzina, Arno Amann
This work evaluated gene expression differences between a hanging-drop 3D NSCLC model and 2D cell cultures and their in-vivo relevance by comparison to patient-derived data from The Cancer Genome Atlas. Gene expression of 2D and 3D cultures for Colo699 and A549 were assessed using Affymetrix HuGene 1.0 ST gene chips. Biostatistical analyses tested for reproducibility, comparability and significant differences in gene expression profiles between cell lines, experiments and culture methods. The analyses revealed a high interassay correlation within specific culture systems proving a high validity...
December 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/29348534/anti-cancer-activities-of-allyl-isothiocyanate-and-its-conjugated-silicon-quantum-dots
#16
Peng Liu, Mehrnaz Behray, Qi Wang, Wei Wang, Zhigang Zhou, Yimin Chao, Yongping Bao
Allyl isothiocyanate (AITC), a dietary phytochemical in some cruciferous vegetables, exhibits promising anticancer activities in many cancer models. However, previous data showed AITC to have a biphasic effect on cell viability, DNA damage and migration in human hepatoma HepG2 cells. Moreover, in a 3D co-culture of HUVEC with pericytes, it inhibited tube formation at high doses but promoted this at low doses, which confirmed its biphasic effect on angiogenesis. siRNA knockdown of Nrf2 and glutathione inhibition abolished the stimulation effect of AITC on cell migration and DNA damage...
January 18, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29347597/general-purpose-graphics-processing-unit-implementation-of-cosmological-domain-wall-network-evolution
#17
J R C C C Correia, C J A P Martins
Topological defects unavoidably form at symmetry breaking phase transitions in the early universe. To probe the parameter space of theoretical models and set tighter experimental constraints (exploiting the recent advances in astrophysical observations), one requires more and more demanding simulations, and therefore more hardware resources and computation time. Improving the speed and efficiency of existing codes is essential. Here we present a general purpose graphics-processing-unit implementation of the canonical Press-Ryden-Spergel algorithm for the evolution of cosmological domain wall networks...
October 2017: Physical Review. E
https://www.readbyqxmd.com/read/29347292/boundary-conditions-for-a-one-sided-numerical-model-of-evaporative-instabilities-in-sessile-drops-of-ethanol-on-heated-substrates
#18
Sergey Semenov, Florian Carle, Marc Medale, David Brutin
The work is focused on obtaining boundary conditions for a one-sided numerical model of thermoconvective instabilities in evaporating pinned sessile droplets of ethanol on heated substrates. In the one-sided model, appropriate boundary conditions for heat and mass transfer equations are required at the droplet surface. Such boundary conditions are obtained in the present work based on a derived semiempirical theoretical formula for the total droplet's evaporation rate, and on a two-parametric nonisothermal approximation of the local evaporation flux...
December 2017: Physical Review. E
https://www.readbyqxmd.com/read/29347276/generalized-network-modeling-network-extraction-as-a-coarse-scale-discretization-of-the-void-space-of-porous-media
#19
Ali Q Raeini, Branko Bijeljic, Martin J Blunt
A generalized network extraction workflow is developed for parameterizing three-dimensional (3D) images of porous media. The aim of this workflow is to reduce the uncertainties in conventional network modeling predictions introduced due to the oversimplification of complex pore geometries encountered in natural porous media. The generalized network serves as a coarse discretization of the surface generated from a medial-axis transformation of the 3D image. This discretization divides the void space into individual pores and then subdivides each pore into sub-elements called half-throat connections...
July 2017: Physical Review. E
https://www.readbyqxmd.com/read/29346929/numerical-estimation-of-structure-constants-in-the-three-dimensional-ising-conformal-field-theory-through-markov-chain-uv-sampler
#20
Victor Herdeiro
Herdeiro and Doyon [Phys. Rev. E 94, 043322 (2016)2470-004510.1103/PhysRevE.94.043322] introduced a numerical recipe, dubbed uv sampler, offering precise estimations of the conformal field theory (CFT) data of the planar two-dimensional (2D) critical Ising model. It made use of scale invariance emerging at the critical point in order to sample finite sublattice marginals of the infinite plane Gibbs measure of the model by producing holographic boundary distributions. The main ingredient of the Markov chain Monte Carlo sampler is the invariance under dilation...
September 2017: Physical Review. E
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