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Journal articles on the topic 'Mediated modelling'

Author: Grafiati

Published: 4 June 2021

Last updated: 3 February 2022

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1

Šulc, Petr, Thomas E. Ouldridge, Flavio Romano, Jonathan P. K. Doye, and Ard A. Louis. "Modelling Toehold-Mediated RNA Strand Displacement." Biophysical Journal 108, no. 5 (2015): 1238–47. http://dx.doi.org/10.1016/j.bpj.2015.01.023.

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2

Metaxas, Georgios, Panos Markopoulos, and Emile H. L. Aarts. "Modelling social translucency in mediated environments." Universal Access in the Information Society 11, no. 3 (2011): 311–21. http://dx.doi.org/10.1007/s10209-011-0241-0.

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3

Richards, Shane A., Hugh P. Possingham, and John Noye. "Diel vertical migration: modelling light-mediated mechanisms." Journal of Plankton Research 18, no. 12 (1996): 2199–222. http://dx.doi.org/10.1093/plankt/18.12.2199.

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4

Forgie, Vicky, and Emma Richardson. "The community outcomes process and mediated modelling." International Journal of Sustainable Development 10, no. 4 (2007): 365. http://dx.doi.org/10.1504/ijsd.2007.017910.

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5

Kobe, Bostjan, and Mikael Boden. "Computational Modelling of Linear Motif-Mediated Protein Interactions." Current Topics in Medicinal Chemistry 12, no. 14 (2012): 1553–61. http://dx.doi.org/10.2174/156802612802652439.

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6

Pandey, Sushil Kumar, and Tridib Kumar Goswami. "Modelling perforated mediated modified atmospheric packaging of capsicum." International Journal of Food Science & Technology 47, no. 3 (2012): 556–63. http://dx.doi.org/10.1111/j.1365-2621.2011.02877.x.

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7

Robertson, Christopher, and Graham A. Worth. "Modelling the vibrationally mediated photo-dissociation of acetylene." Physical Chemistry Chemical Physics 19, no. 43 (2017): 29483–97. http://dx.doi.org/10.1039/c7cp05684b.

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8

Liu, Ying Hu, De Li Liu, Min An, et al. "Modelling tritrophic interactions mediated by induced defence volatiles." Ecological Modelling 220, no. 23 (2009): 3241–47. http://dx.doi.org/10.1016/j.ecolmodel.2009.07.003.

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9

Kushagra, Arindam, and V. Ramgopal Rao. "Anomalous diffusion mediated kinetic modelling of surface-stress sensors." Sensors and Actuators B: Chemical 222 (January 2016): 525–30. http://dx.doi.org/10.1016/j.snb.2015.08.107.

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10

Baker, M., S. Denman-Johnson, B. S. Brook, I. Gaywood, and M. R. Owen. "Mathematical modelling of cytokine-mediated inflammation in rheumatoid arthritis." Mathematical Medicine and Biology 30, no. 4 (2012): 311–37. http://dx.doi.org/10.1093/imammb/dqs026.

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11

Beckie, Hugh J., and Linda M. Hall. "Simple to complex: Modelling crop pollen-mediated gene flow." Plant Science 175, no. 5 (2008): 615–28. http://dx.doi.org/10.1016/j.plantsci.2008.05.021.

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12

Beckie, Hugh J., and Linda M. Hall. "Simple to complex: Modelling crop pollen-mediated gene flow." Plant Science 175, no. 5 (2008): 630. http://dx.doi.org/10.1016/j.plantsci.2008.07.006.

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13

Févotte, G., and N. Sheibat-Othman. "MODELLING SOLVENT-MEDIATED POLYMORPHIC TRANSITIONS DURING COOLING SOLUTION CRYSTALLIZATION." IFAC Proceedings Volumes 38, no. 1 (2005): 141–46. http://dx.doi.org/10.3182/20050703-6-cz-1902.02227.

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14

Lai, Xin, Olaf Wolkenhauer, and Julio Vera. "Understanding microRNA-mediated gene regulatory networks through mathematical modelling." Nucleic Acids Research 44, no. 13 (2016): 6019–35. http://dx.doi.org/10.1093/nar/gkw550.

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15

Gujjala, Lohit K. S., Tapas K. Bandyopadhyay, and Rintu Banerjee. "Kinetic modelling of laccase mediated delignification of Lantana camara." Bioresource Technology 212 (July 2016): 47–54. http://dx.doi.org/10.1016/j.biortech.2016.04.006.

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16

Lewis, David F. V. "Structural Models for Cytochrome P450�Mediated Catalysis." Scientific World JOURNAL 3 (2003): 536–45. http://dx.doi.org/10.1100/tsw.2003.41.

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This review focuses on the structural models for cytochrome P450 that are improving our knowledge and understanding of the P450 catalytic cycle, and the way in which substrates bind to the enzyme leading to catalytic conversion and subsequent formation of mono-oxygenated metabolites. Various stages in the P450 reaction cycle have now been investigated using X-ray crystallography and electronic structure calculations, whereas homology modelling of mammalian P450s is currently revealing important aspects of pharmaceutical and other xenobiotic metabolism mediated by P450 involvement. These features are explored in the current review on P450-based catalysis, which emphasises the importance of structural modelling to our understanding of this enzyme's function. In addition, the results of various QSAR analyses on series of chemicals, which are metabolised via P450 enzymes, are presented such that the importance of electronic and other structural factors in explaining variations in rates of metabolism can be appreciated.

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17

Brunner, J. D., and N. Chia. "Metabolite-mediated modelling of microbial community dynamics captures emergent behaviour more effectively than species–species modelling." Journal of The Royal Society Interface 16, no. 159 (2019): 20190423. http://dx.doi.org/10.1098/rsif.2019.0423.

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Personalized models of the gut microbiome are valuable for disease prevention and treatment. For this, one requires a mathematical model that predicts microbial community composition and the emergent behaviour of microbial communities. We seek a modelling strategy that can capture emergent behaviour when built from sets of universal individual interactions. Our investigation reveals that species–metabolite interaction (SMI) modelling is better able to capture emergent behaviour in community composition dynamics than direct species–species modelling. Using publicly available data, we examine the ability of species–species models and species–metabolite models to predict trio growth experiments from the outcomes of pair growth experiments. We compare quadratic species–species interaction models and quadratic SMI models and conclude that only species–metabolite models have the necessary complexity to explain a wide variety of interdependent growth outcomes. We also show that general species–species interaction models cannot match the patterns observed in community growth dynamics, whereas species–metabolite models can. We conclude that species–metabolite modelling will be important in the development of accurate, clinically useful models of microbial communities.

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18

Frenz, Christopher M., and Philippe P. Lefebvre. "Molecular modelling insights into DFNA15 mediated enhancement of POU4F3 stability." International Journal of Computational Biology and Drug Design 1, no. 3 (2008): 295. http://dx.doi.org/10.1504/ijcbdd.2008.021429.

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19

D'hooge, Dagmar R., Marco Fantin, Andrew J. D. Magenau, Dominik Konkolewicz, and Krzysztof Matyjaszewski. "Two-compartment kinetic Monte Carlo modelling of electrochemically mediated ATRP." Reaction Chemistry & Engineering 3, no. 6 (2018): 866–74. http://dx.doi.org/10.1039/c8re00156a.

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20

Richards, Sarah, Rene H. Wink, and Rüdiger Simon. "Mathematical modelling ofWOX5- andCLE40-mediated columella stem cell homeostasis inArabidopsis." Journal of Experimental Botany 66, no. 17 (2015): 5375–84. http://dx.doi.org/10.1093/jxb/erv257.

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21

Storck, Tomas, Bernardino Virdis, and Damien J. Batstone. "Modelling extracellular limitations for mediated versus direct interspecies electron transfer." ISME Journal 10, no. 3 (2015): 621–31. http://dx.doi.org/10.1038/ismej.2015.139.

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22

Rohwetter, P., J. Kasparian, L. Wöste, and J. P. Wolf. "Modelling of HNO3-mediated laser-induced condensation: A parametric study." Journal of Chemical Physics 135, no. 13 (2011): 134703. http://dx.doi.org/10.1063/1.3644591.

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23

Crociani, Olivia, Andrea Becchetti, Duccio Fanelli, and Annarosa Arcangeli. "Adhesion-Mediated Signalling in Cancer: Recent Advances and Mathematical Modelling." Biophysical Reviews and Letters 09, no. 03 (2014): 285–300. http://dx.doi.org/10.1142/s1793048014300047.

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Cancer can be viewed as a "tissue", where neoplastic cells are immersed into a peculiar microenvironment (the "tumor microenvironment", TME) which modulates tumor cell behaviour during multistep tumorigenesis. Based on this concept, antineoplastic therapy should be tuned to target not only tumor cells but also the cellular constituents of the TME. Such necessity is well exemplified by considering tumor angiogenesis, a major aspect of cancer biology. Ion channels and transporters are increasingly recognized as relevant players in the tumor cell-TME cross-talk. For example, during tumor neo-angiogenesis, soluble factors as well as fixed components of the extracellular matrix (ECM) and membrane proteins determine signal exchange between the TME and the implicated cell types. The signalling network is coordinated by functional "hubs", which may be constituted by integrin receptors associated with other proteins to form macromolecular signalling platforms at the adhesive sites. These complexes often include ion channels. The K + channels encoded by the human ether-à-go-go related gene (Kv11.1, or hERG1) are frequently overexpressed in human cancers and regulate intracellular signalling by physically associating with integrin subunits and growth factor/chemokine receptors. In colorectal cancer (CRC) we recently identified a novel signalling pathway centered on hERG1 channels and integrins. This pathway involves the p53 protein, which is encoded by a tumor suppressor gene often mutated in human cancers. p53 controls angiogenesis, through a mechanism regulated by hERG1 K + channels. The central role played by hERG1 in CRC angiogenesis suggests that targeting hERG1 may be an effective therapeutic option in patients with advanced CRC. To better understand the above process, it is necessary to study the interlaced dynamics of the key microscopic actors by using dedicated mathematical models. We here review a simple model, of reductionist inspiration, that explores the intimate connections between apoptosis and hypoxia, passing through angiogenesis. We show that a dynamical switch takes place between the normoxia and cellular death conditions. When oxygen lacks, cells can cross the transition line and so gain their way towards the normoxia regime, by implementing point mutations that affect the p53 production and activation rate, with the involvement of K + ion homeostasis, in agreement with the experimental observations.

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24

Jyoti, Jeevan, Hardeep Chahal, and Asha Rani. "Role of Organizational Learning and Innovation in between High-performance HR Practices and Business Performance: A Study of Telecommunication Sector." Vision: The Journal of Business Perspective 21, no. 3 (2017): 259–73. http://dx.doi.org/10.1177/0972262917716766.

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The purpose of this study is to explore the role of the organizational learning (OL) and innovation as mediators between high-performance human resource practices (HPHRPs) and business performance (BP) in telecommunication sector. Census method has been used for data collection from employees working in telecommunication organizations in Jammu and Kashmir (North India). Reliability and validity have been proven with the help of confirmatory factor analysis. Structural equation modelling has been used for hypotheses testing. The results indicate that OL mediates the relationship between HPHRPs and innovation, whereas innovation does not mediate but moderates the relationship between OL and BP. So the final model evaluated the mediated-moderation effect of OL and innovation in between HPHRPs and BP. The theoretical and managerial implications have also been discussed.

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25

VELARDE, MANUEL G., and CHRISTIAN NEIßNER. "SOLITON-MEDIATED ELECTRON PAIRING." International Journal of Bifurcation and Chaos 18, no. 03 (2008): 885–90. http://dx.doi.org/10.1142/s0218127408020744.

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We study electron-electron pairing in an one-dimensional model lattice system embedded into a three-dimensional environment. The electron pair potential is lowered by a single, localized lattice deformation. Such a deformation is related to solitons moving along the lattice. Yet the exact form and the time evolution of the lattice excitation are of secondary relevance as the electron pair is stable for sufficiently wide deformations which propagate on molecular time scales, e.g. velocity of sound ≪ electron velocity. The spatial structure of the pair potential and the electron-electron wave function bring a mechanism of pairing different from the exchange of phonons between the electrons and the lattice which leads to Cooper pairs, and different also from the formation of bipolarons.

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26

Adamec, Robert. "Modelling Anxiety Disorders Following Chemical Exposures." Toxicology and Industrial Health 10, no. 4-5 (1994): 391–420. http://dx.doi.org/10.1177/074823379401000513.

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The effects of kindling and inverse benzodiazepine receptor agonist -carbolines on animal models of anxiety are briefly reviewed in relation to affective disorder associated with chemical exposure. Recent experimental results are described. In the present study, cats were given the inverse benzodiazepine receptor agonist, FG-7142, a powerful anxiogenic compound in humans and animals. Neural transmission in pathways involved in defensive behavior in the cat was monitored using evoked potential techniques. Change in these pathways was related to behavioral changes induced by the drug. It was found that a single dose offG-7142 lastingly increased defensive response to rodents for at least 40 days after drug administration. Behavioral change was specific to defensive response, since approach-attack behavior remained unchanged, replicating previous studies. The benzodiazepine receptor antagonist, Flumazenil, reversed the increase in defensiveness in a drug-dependent manner, replicating previous findings. Increased defensiveness was paralleled by a delayed onset potentiation of neural transmission between the amygdala and the medial hypothalamus of the left hemisphere. Potentiation in the left hemisphere was transient, decaying between 6 and 12 days after the drug. There was a longer lasting potentiation (LTP) of activity evoked in the left and right amygdalo-periacqueductal gray pathways and in the right amygdalo-medial hypothalamic pathway. Potentiation in these pathways appeared at the time of behavioral change. Potentiation of the right amygdalo-periacqueductal gray and right amygdalo-medial hypothalamic pathways persisted until the end of the experiment. In contrast, potentiation of the left amygdalo-periacqueductal gray pathway faded by 40 days after the drug. Flumazenil decreased potentiation only in the right amygdalo-periacqueductal gray pathway. These data strongly suggest that lasting affective change is mediated by lasting changes in particular efferents of the amygdala of the right hemisphere. Behavioral and physiological effects offG-7142 were blocked by the N-methyl-D-Aspartate (NMDA) receptor blocker, AP7. The data suggest that failure of neural inhibition induced by FG-7142 engages NMDA receptor processes to produce lasting potentiation of transmission in neural circuits that mediate defensive response with behavioral consequences. Since FG-7142 interferes with GABA mediated neural inhibition and is proconvulsant, its action might mimic the action of other environmental chemicals with similar properties, such as chlorinated hydrocarbon insecticides. The relationship of the present data to the literature on the neural and behavioral effects of insecticide exposure is discussed. The significance of these findings for multiple chemical sensitivity disorder is also briefly discussed.

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27

Tekieh, T., S. McCloskey, S. W. Lockley, P. A. Robinson, M. S. Zobaer, and S. Postnova. "Modelling melanopsin-mediated effects of light on circadian phase and sleepiness." Sleep Medicine 64 (December 2019): S379. http://dx.doi.org/10.1016/j.sleep.2019.11.1056.

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28

Robson, Barbara J., Rebecca E. Lester, Darren S. Baldwin, et al. "Modelling food-web mediated effects of hydrological variability and environmental flows." Water Research 124 (November 2017): 108–28. http://dx.doi.org/10.1016/j.watres.2017.07.031.

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29

LEÓN, KALET, ROLANDO PERÉZ, AGUSTIN LAGE, and JORGE CARNEIRO. "Modelling T-cell-Mediated Suppression Dependent on Interactions in Multicellular Conjugates." Journal of Theoretical Biology 207, no. 2 (2000): 231–54. http://dx.doi.org/10.1006/jtbi.2000.2169.

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30

Stanaway, M. A., R. Reeves, and K. L. Mengersen. "Hierarchical Bayesian modelling of plant pest invasions with human-mediated dispersal." Ecological Modelling 222, no. 19 (2011): 3531–40. http://dx.doi.org/10.1016/j.ecolmodel.2011.08.013.

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31

Pretti, Evan, Runfang Mao, and Jeetain Mittal. "Modelling and simulation of DNA-mediated self-assembly for superlattice design." Molecular Simulation 45, no. 14-15 (2019): 1203–10. http://dx.doi.org/10.1080/08927022.2019.1610951.

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32

Ringrose, Leonie, and Martin Howard. "Dissecting chromatin-mediated gene regulation and epigenetic memory through mathematical modelling." Current Opinion in Systems Biology 3 (June 2017): 7–14. http://dx.doi.org/10.1016/j.coisb.2017.02.003.

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33

Asteasuain, Mariano. "Deterministic Approaches for Simulation of Nitroxide-Mediated Radical Polymerization." International Journal of Polymer Science 2018 (August 9, 2018): 1–16. http://dx.doi.org/10.1155/2018/7803702.

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Since its development in the last decades, controlled radical polymerization (CRP) has become a very promising option for the synthesis of polymers with controlled structure. The design and production of tailor-made materials can be significantly improved by developing models capable of predicting the polymer properties from the operating conditions. Nitroxide-mediated polymerization (NMP) was the first of the three main variants of CRP to be discovered. Although it has lost preference over the years against other CRP alternatives, NMP is still an attractive synthesis method because of its simple experimental implementation and environmental friendliness. This review focuses on deterministic methods employed in mathematical models of NMP. It presents an overview of the different techniques that have been reported for modelling NMP processes in homogeneous and heterogeneous media, covering from the prediction of average properties to the latest techniques for modelling univariate and multivariate distributions of polymer properties. Finally, an outlook of model-based design studies of NMP processes is given.

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34

Payne, Adam G., Carl Smith, and Andrew C. Campbell. "A model of oxygen-mediated filial cannibalism in fishes." Ecological Modelling 174, no. 3 (2004): 253–66. http://dx.doi.org/10.1016/j.ecolmodel.2003.09.026.

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35

Richter, Jan, Gerhard Metzner, and Ulrich Behn. "Mathematical Modelling of Venom Immunotherapy." Journal of Theoretical Medicine 4, no. 2 (2002): 119–32. http://dx.doi.org/10.1080/10273660290022172.

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Allergic hypersensitivity of type I for hymenoptera venoms is the most frequent reason for acute IgE-mediated anaphylactic reactions. The subcutaneous injection of increasing doses of purified allergen followed by long-term administration of an adequate maintenance dose over a period of 3–5 years called venom immunotherapy (VIT) has been proven to be a very effective treatment achieving protection in about 96% of allergic patients. Even though the principle of hyposensitisation has been introduced already 90 years ago, the underlying immunoregulatory mechanisms of VIT remain poorly understood. Recent studies suggest a shift in cytokine production from a Th2 to a Th1 cytokine profile during therapy. In this paper, a mathematical model for T-cell regulation and a model for mast cell/basophil desensitisation are presented and analysed to explain the mechanism of conventional rush and ultra-rush VIT.

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36

Adimya, Mostafa, Fabien Craustea, and Shigui Ruanb. "Modelling Hematopoiesis Mediated by Growth Factors With Applications to Periodic Hematological Diseases." Bulletin of Mathematical Biology 68, no. 8 (2006): 2321–51. http://dx.doi.org/10.1007/s11538-006-9121-9.

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37

Carr, John P., Trisna Tungadi, Ruairí Donnelly, et al. "Modelling and manipulation of aphid-mediated spread of non-persistently transmitted viruses." Virus Research 277 (February 2020): 197845. http://dx.doi.org/10.1016/j.virusres.2019.197845.

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38

Nabaei, Malikeh, and Nasser Fatouraee. "Microstructural modelling of cerebral aneurysm evolution through effective stress mediated destructive remodelling." Journal of Theoretical Biology 354 (August 2014): 60–71. http://dx.doi.org/10.1016/j.jtbi.2014.03.020.

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39

Antunes, Paula, Rui Santos, and Nuno Videira. "Participatory decision making for sustainable development—the use of mediated modelling techniques." Land Use Policy 23, no. 1 (2006): 44–52. http://dx.doi.org/10.1016/j.landusepol.2004.08.014.

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40

Zhang, Changyong, Di He, Jinxing Ma, and T. David Waite. "Active chlorine mediated ammonia oxidation revisited: Reaction mechanism, kinetic modelling and implications." Water Research 145 (November 2018): 220–30. http://dx.doi.org/10.1016/j.watres.2018.08.025.

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41

Nguyen, Lan K. "Dynamics of ubiquitin-mediated signalling: insights from mathematical modelling and experimental studies." Briefings in Bioinformatics 17, no. 3 (2015): 479–93. http://dx.doi.org/10.1093/bib/bbv052.

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42

Woolf, D. K., I. S. Leifer, P. D. Nightingale, et al. "Modelling of bubble-mediated gas transfer: Fundamental principles and a laboratory test." Journal of Marine Systems 66, no. 1-4 (2007): 71–91. http://dx.doi.org/10.1016/j.jmarsys.2006.02.011.

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43

Chen, Bing H., F. Baganz, and John M. Woodley. "Modelling and optimisation of a transketolase-mediated carbon–carbon bond formation reaction." Chemical Engineering Science 62, no. 12 (2007): 3178–84. http://dx.doi.org/10.1016/j.ces.2007.02.025.

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44

Verzi, D. W., and S. M. Baer. "Calcium-mediated spine stem restructuring." Mathematical and Computer Modelling 42, no. 1-2 (2005): 151–65. http://dx.doi.org/10.1016/j.mcm.2004.02.040.

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45

Rajić, Tamara, Ana Rakić, and Isidora Milošević. "Modelling health care customer satisfaction: Evidence from Serbia." Serbian Journal of Management 16, no. 1 (2021): 125–45. http://dx.doi.org/10.5937/sjm16-25961.

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Customer loyalty, with satisfaction of customers as its main precondition, has long been regarded as an overarching goal of service businesses. With the proliferation of health care providers, which brought about rising competitive pressures on the market, the issue of how to satisfy and keep patients has been attracting increasing attention of researchers and health care management. Therefore, this study aims to examine the antecedents of patient satisfaction and its direct and mediated impact on patients' behavioural intentions in thus far under-studied context of emerging economy's health care system. The study has been conducted in a primary health care setting, on a convenience sample of 300 patients, by means of structured questionnaire. The application of structural equation modelling (SEM) revealed direct impact of health care service quality on patient satisfaction and its mediated impact on satisfaction, via perceived value of health care services. In addition to direct influence of satisfaction on patients' behavioural intentions, its total effect on positive intentions of patients is increased by the impact of patient commitment to a health care provider, which, as evidenced by this study's findings, increases with patient's rising trust into a health care provider. Implications for theory and practice are discussed and further research directions are provided.

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46

Ito, Hiroaki, Toshihiro Omori, and Takuji Ishikawa. "Swimming mediated by ciliary beating: comparison with a squirmer model." Journal of Fluid Mechanics 874 (July 12, 2019): 774–96. http://dx.doi.org/10.1017/jfm.2019.490.

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The squirmer model of Lighthill and Blake has been widely used to analyse swimming ciliates. However, real ciliates are covered by hair-like organelles, called cilia; the differences between the squirmer model and real ciliates remain unclear. Here, we developed a ciliate model incorporating the distinct ciliary apparatus, and analysed motion using a boundary element–slender-body coupling method. This methodology allows us to accurately calculate hydrodynamic interactions between cilia and the cell body under free-swimming conditions. Results showed that an antiplectic metachronal wave was optimal in the swimming speed with various cell-body aspect ratios, which is consistent with former theoretical studies. Exploiting oblique wave propagation, we reproduced a helical trajectory, like Paramecium, although the cell body was spherical. We confirmed that the swimming velocity of model ciliates was well represented by the squirmer model. However, squirmer modelling outside the envelope failed to estimate the energy costs of swimming; over 90 % of energy was dissipated inside the ciliary envelope. The optimal swimming efficiency was given by the antiplectic wave; the value was 6.7 times larger than in-phase beating. Our findings provide a fundamental basis for modelling swimming micro-organisms.

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47

Kent, Maud I. A., Ryan Lukeman, Joseph T. Lizier, and Ashley J. W. Ward. "Speed-mediated properties of schooling." Royal Society Open Science 6, no. 2 (2019): 181482. http://dx.doi.org/10.1098/rsos.181482.

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Collectively moving animals often display a high degree of synchronization and cohesive group-level formations, such as elongated schools of fish. These global patterns emerge as the result of localized rules of interactions. However, the exact relationship between speed, polarization, neighbour positioning and group structure has produced conflicting results and is largely limited to modelling approaches. This hinders our ability to understand how information spreads between individuals, which may determine the collective functioning of groups. We tested how speed interacts with polarization and positional composition to produce the elongation observed in moving groups of fish as well as how this impacts information flow between individuals. At the local level, we found that increases in speed led to increases in alignment and shifts from lateral to linear neighbour positioning. At the global level, these increases in linear neighbour positioning resulted in elongation of the group. Furthermore, mean pairwise transfer entropy increased with speed and alignment, implying an adaptive value to forming faster, more polarized and linear groups. Ultimately, this research provides vital insight into the mechanisms underlying the elongation of moving animal groups and highlights the functional significance of cohesive and coordinated movement.

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48

Kong, Jianping, Douglas B. Stairs, and John P. Lynch. "Modelling Barrett's oesophagus." Biochemical Society Transactions 38, no. 2 (2010): 321–26. http://dx.doi.org/10.1042/bst0380321.

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Barrett's oesophagus is the replacement of normal squamous oesophageal epithelium with an intestinalized columnar epithelium. Although some insight has been gained as to what Barrett's oesophagus is, how this columnar epithelium emerges from within a stratified squamous epithelium remains an unanswered question. We have sought to determine whether oesophageal keratinocytes can be trans-differentiated into Barrett's oesophagus cells. Using an Affymetrix microarray, we found unexpectedly that gene-expression patterns in the Barrett's oesophagus were only slightly more similar to the normal small intestine than they were to the normal oesophagus. Thus gene-expression patterns suggest significant molecular similarities remain between Barrett's oesophagus cells and normal squamous oesophageal epithelium, despite their histological resemblance with intestine. We next determined whether directed expression of intestine-specific transcription factors could induce intestinalization of keratinocytes. Retroviral-mediated Cdx2 (Caudal-type homeobox 2) expression in immortalized human oesophageal keratinocytes engineered with human telomerase reverse transcriptase (EPC2-hTERT cells) could be established transiently, but not maintained, and was associated with a reduction in cell proliferation. Co-expression of cyclin D1 rescued proliferation in the Cdx2-expressing cells, but co-expression of dominant-negative p53 did not. Cdx2 expression in the EPC2-hTERT.D1 cells did not induce intestinalization. However, when combined with treatments that induce chromatin remodelling, there was a significant induction of Barrett's oesophagus-associated genes. Studies are ongoing to determine whether other intestinal transcription factors, either alone or in combination, can provoke greater intestinalization of oesophageal keratinocytes. We conclude that, on the basis of gene-expression patterns, Barrett's oesophagus epithelial cells may represent an intermediate between oesophageal keratinocytes and intestinal epithelial cells. Moreover, our findings suggest that it may be possible to induce Barrett's oesophagus epithelial cells from oesophageal keratinocytes by altering the expression of certain critical genes.

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Cowan, Catherine M., Megan A. Sealey, Shmma Quraishe, et al. "Modelling Tauopathies inDrosophila: Insights from the Fruit Fly." International Journal of Alzheimer's Disease 2011 (2011): 1–16. http://dx.doi.org/10.4061/2011/598157.

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Abstract:

Drosophila melanogasteris an experimentally tractable model organism that has been used successfully to model aspects of many human neurodegenerative diseases.Drosophilamodels of tauopathy have provided valuable insights into tau-mediated mechanisms of neuronal dysfunction and death. Here we review the findings fromDrosophilamodels of tauopathy reported over the past ten years and discuss how they have furthered our understanding of the pathogenesis of tauopathies. We also discuss the multitude of technical advantages thatDrosophilaoffers, which make it highly attractive as a model for such studies.

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Filipovic, N., M. Kojic, and A. Tsuda. "Modelling thrombosis using dissipative particle dynamics method." Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 366, no. 1879 (2008): 3265–79. http://dx.doi.org/10.1098/rsta.2008.0097.

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Abstract:

Aim . Arterial occlusion is a leading cause of cardiovascular disease. The main mechanism causing vessel occlusion is thrombus formation, which may be initiated by the activation of platelets. The focus of this study is on the mechanical aspects of platelet-mediated thrombosis which includes the motion, collision, adhesion and aggregation of activated platelets in the blood. A review of the existing continuum-based models is given. A mechanical model of platelet accumulation onto the vessel wall is developed using the dissipative particle dynamics (DPD) method in which the blood (i.e. colloidal-composed medium) is treated as a group of mesoscale particles interacting through conservative, dissipative, attractive and random forces. Methods . Colloidal fluid components (plasma and platelets) are discretized by mesoscopic (micrometre-size) particles that move according to Newton's law. The size of each mesoscopic particle is small enough to allow tracking of each constituent of the colloidal fluid, but significantly larger than the size of atoms such that, in contrast to the molecular dynamics approach, detailed atomic level analysis is not required. Results . To test this model, we simulated the deposition of platelets onto the wall of an expanded tube and compared our computed results with the experimental data of Karino et al . ( Miscrovasc. Res. 17 , 238–269, 1977). By matching our simulations to the experimental results, the platelet aggregation/adhesion binding force (characterized by an effective spring constant) was determined and found to be within a physiologically reasonable range. Conclusion . Our results suggest that the DPD method offers a promising new approach to the modelling of platelet-mediated thrombosis. The DPD model includes interaction forces between platelets both when they are in the resting state (non-activated) and when they are activated, and therefore it can be extended to the analysis of kinetics of binding and other phenomena relevant to thrombosis.

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