Читать книгу Diatom Morphogenesis - Группа авторов - Страница 44
References
Оглавление[2.1] Albrecht-Buehler, G., Daughter 3T3 cells. Are they mirror images of each other? J. Cell Biol. ,72, 3, 595–603, 1977.
[2.2] Alicea, B. and Gordon, R., Toy models for macroevolutionary patterns and trends. BioSystems, 122, Special Issue: Patterns of Evolution, 25–37, 2014.
[2.3] Alicea, B. and Gordon, R., Cell differentiation processes as spatial networks: Identifying four-dimensional structure in embryogenesis. BioSystems, 173, 235–246, 2018.
[2.4] Alvare, G. and Gordon, R., CT Brush and CancerZap!: Two video games for computed tomography dose minimization. Theor. Biol. Med. Modell., 12, 1, 7, 2015.
[2.5] Amr, I.I., Amin, M., El-Kafrawy, P., Sauber, A.M., Using Statistical Moment Invariants and Entropy in Image Retrieval. Int. J. Comput. Sci. Inf. Secur., 7, 1, 160–164, 2010.
[2.6] Aragon, J., Barrio, R., Woolley, T., Baker, R., Maini, P., Nonlinear effects on Turing patterns: Time oscillations and chaos. Phys. Rev. E, 86, 2, 026201, 2012.
[2.7] Astauroff, B.L., Analyse der erblichen Storungsfalle der bilateralen Symmetrie [Analysis of hereditary disorders of bilateral symmetry] [German]. Z. Indukt. Abstamm. Vererbungsl., 55, I, 183–262, 1930.
[2.8] Atay, F.M., Jalan, S., Jost, J., Randomness, Chaos, and Structure. Complexity, 15, 1, 29–35, 2009.
[2.9] Attneave, F., Some informational aspects of visual perception. Psychol. Rev., 61, 3, 183–193, 1954.
[2.10] Benci, V. and Menconi, G., Some remarks on the definition of Boltzmann, Shannon and Kolmogorov entropy. Milan J. Math., 73, 1, 187–209, 2005.
[2.11] Bentley, K., Clack, C., Cox, E.J., Diatom colony formation: A computational study predicts a single mechanism can produce both linkage and separation valves due to an environmental switch. J. Phycol., 48, 3, 716–728, 2012.
[2.12] Bentley, K., Cox, E.J., Bentley, P.J., Nature’s batik: A computer evolution model of diatom valve morphogenesis. J. Nanosci. Nanotechnol., 5, 1, 25–34, 2005.
[2.13] Biederman, I., Recognition-by-components: A theory of human image understanding. Psychol. Rev., 94, 2, 115–147, 1987.
[2.14] Biederman, I., Mezzanotte, R.J., Rabinowitz, J.C., Scene perception: Detecting and judging objects undergoing relational violations. Cogn. Psychol., 14, 2, 143–177, 1982.
[2.15] Bissantz, N., Holzmann, H., Pawlak, M., Testing for image symmetries-with application to confocal microscopy. IEEE Trans. Inf. Theory, 55, 4, 1841–1855, 2009.
[2.16] Boltzmann, L., Uber die Mechanische Bedeutung des Zweiten Hauptsatzes der Warmetheorie [On the Mechanical Meaning of the Second Law of Heat Theory] [German]. Wien. Ber., 53, 195–220, 1866.
[2.17] Boltzmann, L., Vorlesungen uber Gastheorie, vol. I [Lectures on Gas Theory] [German], vol. 1, J. A. Barth, Leipzig, Germany, 1896.
[2.18] Boltzmann, L., Vorlesungen uber Gastheorie, [Lectures on Gas Theory] [German], vol. II, J. A. Barth, Leipzig, Germany, 1898.
[2.19] Bredov, D. and Volodyaev, I., Increasing complexity: Mechanical guidance and feedback loops as a basis for self-organization in morphogenesis. BioSystems, 173, 133–156, 2018.
[2.20] Burge, J., McCann, B.C., Geisler, W.S., Estimating 3D tilt from local image cues in natural scenes. J. Vision, 16, 13, 2, 1–25, 2016.
[2.21] Chaitin, G.J., Algorithmic information theory. Ibm J. Res. Dev., 21, 4, 350–359, 1977.
[2.22] Chakrabarti, C.G. and Ghosh, K., Biological evolution: Entropy, complexity and stability. J. Mod. Phys., 2, 6, 621–626, 2011.
[2.23] Chen, C.T., Linear System Theory and Design, 4th ed, Oxford University Press, New York, NY, USA, 2013.
[2.24] Chen, Q., Shi, J.C., Tao, Y., Zernicka-Goetz, M., Tracing the origin of heterogeneity and symmetry breaking in the early mammalian embryo. Nat. Commun., 9, 1819, 2018.
[2.25] Cox, E.J., Willis, L., Bentley, K., Integrated simulation with experimentation is a powerful tool for understanding diatom valve morphogenesis. BioSystems, 109, 3, Special Issue on Biological Morphogenesis, 450–459, 2012.
[2.26] Crutchfield, J.P. and Feldman, D.P., Regularities unseen, randomness observed: Levels of entropy convergence. Chaos, 13, 1, 25–54, 2003.
[2.27] Dammig, M. and Mitschke, F., Estimation of Lyapunov exponents from time series: The stochastic case. Phys. Lett. A, 178, 5–6, 385–394, 1993.
[2.28] De Martino, A., Amato, A., Bowler, C., Mitosis in diatoms: Rediscovering an old model for cell division. Bioessays, 31, 8, 874–884, 2009.
[2.29] Eckmann, J.P. and Ruelle, D., Ergodic theory of chaos and strange attractors. Rev. Mod. Phys., 57, 3, 617–656, 1985.
[2.30] Fernandes, L.F., New observations on frustule morphology of Eupodiscus radiatus Bailey and Fryxelliella floridana Prasad. Braz. J. Biol., 63, 3, 411–421, 2003.
[2.31] Fernandes, L.F. and de Souza-Mosimann, R.M., Triceratium moreirae sp. nov. and Triceratium dubium (Triceratiaceae-Bacillariophyta) from estuarine environments of southern Brazil, with comments on the genus Triceratium C. G. Ehrenberg. Braz. J. Biol., 61, 1, 159–170, 2001.
[2.32] Ferrell Jr., J.E., Bistability, bifurcations, and Waddington’s epigenetic landscape. Curr. Biol., 22, 11, R458-R466, 2012.
[2.33] Frey, F.M., Robertson, A., Bukoski, M., A method for quantifying rotational symmetry. New Phytol., 175, 4, 785–791, 2007.
[2.34] Gan, C.C. and Learmonth, G., Comparing entropy with tests for randomness as a measure of complexity in time series. arXiv preprint arXiv:1512.00725, 2015.
[2.35] Gao, J., Hu, J., Tun, W-w., Blasch, E., Multiscale analysis of biological data by scale-dependent Lyapunov exponent. Front. Physiol., 2, 110, 2012.
[2.36] Garrido, A., Symmetry in complex networks. Symmetry-Basel, 3, 1, 1–15, 2011.
[2.37] Ghobara, M.M., Mazumder, N., Vinayak, V., Reissig, L., Gebeshuber, I.C., Tiffany, M.A., Gordon, R., On light and diatoms: A photonics and photobiology review [Chapter 7], in: Diatoms: Fundamentals & Applications [DIFA, Volume 1 in the series: Diatoms: Biology & Applications, series editors: Richard Gordon & Joseph Seckbach], J. Seckbach and R. Gordon (Eds.), pp. 129–190, Wiley-Scrivener, Beverly, MA, USA, 2019.
[2.38] Gibson, R.A. and Mahoney, R.K., Comparative valve and cingular structure in Biddulphia titiana (Grunow) Grunow in Van Heurck and Trigonium arcticum (Brightwell) Cleve (Bacillariophyceae). Proc. Acad. Nat. Sci. Philadelphia, 136, 200–217, 1984.
[2.39] Ginelli, F., Chate, H., Livi, R., Politi, A., Covariant Lyapunov vectors. J. Phys. a-Math. Theor., 46, 25, 254005, 2013.
[2.40] Golubitsky, M. and Stewart, I., Recent advances in symmetric and network dynamics. Chaos, 25, 9, 097612, 2015.
[2.41] Gordon, R., The Hierarchical Genome and Differentiation Waves: Novel Unification of Development, Genetics and Evolution, World Scientific & Imperial College Press, Singapore & London, 1999.
[2.42] Gordon, R., Diatoms and nanotechnology: Early history and imagined future as seen through patents, in: The Diatoms: Applications for the EnVironmental and Earth Sciences, 2nd, J.P. Smol and E.F. Stoermer (Eds.), pp. 585–602, Cambridge University Press, Cambridge, 2010.
[2.43] Gordon, R., Part Three: The reverse engineering road to computing life. Chapter 10: Walking the tightrope: the dilemmas of hierarchical instabilities in Turing’s morphogenesis [invited], in: The Once and Future Turing: Computing the World, S.B. Cooper and A. Hodges (Eds.), pp. 144–159, Cambridge University Press, Cambridge, 2016.
[2.44] Gordon, R. and Aguda, B.D., Diatom morphogenesis: Natural fractal fabrication of a complex microstructure, in: Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, Part 1/4: Cardiology and Imaging, New Orleans, LA, USA, 4-7 Nov. 1988, Institute of Electrical and Electronics Engineers, New York, pp. 273–274, 1988.
[2.45] Gordon, R., Bjorklund, N.K., Robinson, G.G.C., Kling, H.J., Sheared drops and pennate diatoms. Nova Hedwig., 112, Festschrift for Prof. T.V. Desikachary, 287–297, 1996.
[2.46] Gordon, R. and Brodland, G.W., On square holes in pennate diatoms. Diatom Res., 5, 2, 409–413, 1990.
[2.47] Gordon, R. and Drum, R.W., The chemical basis of diatom morphogenesis. Int. Rev. Cytol., 150, 243–372421–422, 1994.
[2.48] Gordon, R., Hanczyc, M.M., Denkov, N.D., Tiffany, M.A., Smoukov, S.K., Chapter 18: Emergence of polygonal shapes in oil droplets and living cells: The potential role of tensegrity in the origin of life, in: Habitability of the Universe Before Earth [Volume 1 in series: Astrobiology: Exploring Life on Earth and Beyond, eds. Pabulo Henrique Rampelotto, Joseph Seckbach & Richard Gordon], R. Gordon and A.A. Sharov (Eds.), pp. 427–490, Elsevier B.V., Amsterdam, 2017.
[2.49] Gordon, R. and Jacobson, A.G., The shaping of tissues in embryos. Sci. Am., 238, 6, 106–113, 160, 1978.
[2.50] Gordon, R., Losic, D., Tiffany, M.A., Nagy, S.S., Sterrenburg, F.A.S., The Glass Menagerie: Diatoms for novel applications in nanotechnology. Trends Biotechnol., 27, 2, 116–127, 2009.
[2.51] Gordon, R., Sterrenburg, F.A.S., Sandhage, K., A Special Issue on Diatom Nanotechnology. J. Nanosci. Nanotechnol., 5, 1, 1–4, 2005.
[2.52] Gordon, R. and Tiffany, M.A., Possible buckling phenomena in diatom morphogenesis, in: The Diatom World, J. Seckbach and J.P. Kociolek (Eds.), pp. 245–272, Springer, Dordrecht, The Netherlands, 2011.
[2.53] Graham, J.H., Freeman, D.C., Emlen, J.M., Antisymmetry, directional asymmetry, and dynamic morphogenesis. Genetica, 89, 1–3, 121–137, 1993.
[2.54] Graham, J.H., Raz, S., Hel-Or, H., Nevo, E., Fluctuating asymmetry: Methods, theory, and applications. Symmetry-Basel, 2, 2, 466–540, 2010.
[2.55] Guan, K., Important notes on Lyapunov exponents. arXiv preprint arXiv:1401.3315., 2014.
[2.56] Hakansson, H. and Chepurnov, V., A study of variation in valve morphology of the diatom Cyclotella meneghiniana in monoclonal cultures: effect of auxospore formation and different salinity conditions. Diatom Res., 14, 2, 251–272, 1999.
[2.57] Hasle, G.R. and Sims, P.A., The diatom genera Stellarima and Symbolophora with comments on the genus Actinoptychus. Br. Phycol. J., 21, 97–114, 1986.
[2.58] Herve, V., Derr, J., Douady, S., Quinet, M., Moisan, L., Lopez, P.J., Multiparametric analyses reveal the pH-dependence of silicon biomineralization in diatoms. PLoS One, 7, 10, e46722, 2012.
[2.59] Hildebrand, M., Lerch, S.J.L., Shrestha, R.P., Understanding diatom cell wall silicification— moving forward. Front. Mar. Sci., 5, 125, 2018.
[2.60] Hollo, G. and Novak, M., The manoeuvrability hypothesis to explain the maintenance of bilateral symmetry in animal evolution. Biol. Direct, 7, 7, 22, 2012.
[2.61] Jacobson, A.G., Some forces that shape the nervous system. Zoon, 6, 13–21, 1978.
[2.62] Jacobson, A.G., Computer modeling of morphogenesis. Am. Zool., 20, 4, 669–677, 1980.
[2.63] Jacobson, A.G. and Gordon, R., Changes in the shape of the developing vertebrate nervous system analyzed experimentally, mathematically and by computer simulation. J. Exp. Zool., 197, 2, 191–246, 1976.
[2.64] Jacobson, A.G. and Gordon, R., Nature and origin of patterns of changes in cell shape in embryos. J. Supramol. Struct., 5, 4, 371–380, 1976.
[2.65] Jaynes, E.T., Information theory and statistical mechanics. Phys. Rev., 106, 620–630, 1957.
[2.66] Jaynes, E.T., Gibbs vs Boltzmann entropies. Am. J. Phys., 33, 5, 391–398, 1965.
[2.67] Jaynes, E.T., Prior probabilities. IEEE Trans. Syst. Sci. Cybern. SSC, 4, 3, 227–241, 1968.
[2.68] Jones, J.S., Evolution: An asymmetrical view of fitness. Nature, 325, 6102, 298–299, 1987.
[2.69] Kaczmarska, I. and Ehrman, J.M., Auxosporulation in Paralia guyana MacGillivary (Bacillariophyta) and possible new insights into the habit of the earliest diatoms. PLoS One, 10, 10, e0141150, 2015.
[2.70] Kadir, T., Boukerroui, D., Brady, M., An analysis of the scale saliency algorithm [Technical report TR-2264-03], Robotics Research Laboratory, Department of Engineering Science, University of Oxford, Oxford, UK, 2003.
[2.71] Klimontovich, Y.L., Entropy, information and ordering criteria in open systems, in: Nonlinear Dynamics in the Life and Social Sciences, vol. 320, W. Sulis and I. Trofimova (Eds.), pp. 13–32, IOS Press, Amsterdam, 2001.
[2.72] Koenderink, J.J., vanDoorn, A.J., Kappers, A.M.L., Todd, J.T., The visual contour in depth. Percept. Psychophys., 59, 6, 828–838, 1997.
[2.73] Korabel, N. and Barkai, E., Pesin-type identity for intermittent dynamics with a zero Lyaponov exponent. Phys. Rev. Lett., 102, 5, 050601, 2009.
[2.74] Korabel, N. and Barkai, E., Separation of trajectories and its relation to entropy for intermittent systems with a zero Lyapunov exponent. Phys. Rev. E, 82, 016209, 2010.
[2.75] Kotzsch, A., Pawolski, D., Milentyev, A., Shevchenko, A., Scheffel, A., Poulsen, N., Shevchenko, A., Kroger, N., Biochemical composition and assembly of biosilica-associated insoluble organic matrices from the diatom Thalassiosira pseudonana. J. Biol. Chem., 291, 10, 4982–4997, 2016.
[2.76] Kroger, N., Prescribing diatom morphology: toward genetic engineering of biological nanomaterials. Curr. Opin. Chem. Biol., 11, 6, 662–669, 2007.
[2.77] Kuptsov, P.V. and Parlitz, U., Theory and computation of covariant Lyapunov vectors. J. Nonlinear Sci., 22, 5, 727–762, 2012.
[2.78] Laffargue, T., Tailleur, J., van Wijland, F., Lyapunov exponents of stochastic systems-from micro to macro. J. Stat. Mech.-Theory Exp., 2016, 034001, 2016.
[2.79] Lee, J.-H. and Chang, M., Morphological variations of the marine diatom genus Actinoptychus in the coastal waters of Korea. Algae, 11, 4, 365–374, 1996.
[2.80] Leeuwenberg, E., The perception of assimilation and brightness contrast as derived from code theory. Percept. Psychophys., 32, 4, 345–352, 1982.
[2.81] Lenoci, L. and Camp, P.J., Self-assembly of peptide scaffolds in biosilica formation: computer simulations of a coarse-grained model. J. Am. Chem. Soc., 128, 31, 10111–10117, 2006.
[2.82] Lenoci, L. and Camp, P.J., Diatom structures templated by phase-separated fluids. Langmuir, 24, 1, 217–223, 2008.
[2.83] Libbrecht, K. and Rasmussen, P., The Snowflake, Winter’s Secret Beauty, Voyageur Press, Stillwater, Minnesota, USA, 2003.
[2.84] Lin, S.K., Correlation of entropy with similarity and symmetry. J. Chem. Inf. Comput. Sci., 36, 3, 367–376, 1996.
[2.85] Losic, D. (Ed.), Diatom Nanotechnology: Progress and Emerging Applications, Royal Society of Chemistry, London, 2018.
[2.86] Loy, G. and Eklundh, J.O., Detecting symmetry and symmetric constellations of features. Lect. Notes Comput. Sci., 3952, 508–521, 2006.
[2.87] Ludwig, W., Das Recht-Links-Problem im Tierreich und beim Menschen: Mit einem Anhang: Rechts-Links-Merkmale der Pflanzen [The Right-Left Problem in the Animal Kingdom and in Humans: With an Appendix: Right-Left Characteristics of Plants] [German], Verlag von Julius Springer, Berlin, Germany, 1932.
[2.88] Lyapunov, A.M., The general problem of the stability of motion [Reprinted translation of: Probleme generale de la stabilite du mouvement. Commun. Soc. Math. Kharkov, 2, 1892, 265–272, 1992.
[2.89] MacArthur, B.D., Sanchez-Garcia, R.J., Anderson, J.W., Symmetry in complex networks. Discrete Appl. Math., 156, 18, 3525–3531, 2008.
[2.90] MacDonald, J.D., On the structure of the diatomaceous frustule, and its genetic cycle. Ann. Mag. Nat. Hist. Ser., 4, 3, 1–8, 1869.
[2.91] Maini, P.K., Baker, R.E., Chuong, C.M., Developmental biology. The Turing model comes of molecular age. Science, 314, 5804, 1397–1398, 2006.
[2.92] Maini, P.K., Woolley, T.E., Baker, R.E., Gaffney, E.A., Lee, S.S., Turing’s model for biological pattern formation and the robustness problem. Interface Focus, 2, 4, 487–496, 2012.
[2.93] Mann, D.G., Specifying a morphogenetic model for diatoms: an analysis of pattern faults in the Voigt zone. Nova Hedwig., Suppl., 130, 97–117, 2006.
[2.94] Mather, K., Genetical control of stability in development. Heredity, 7, 3, 297–336, 1953.
[2.95] Matsumoto, E.A. and Kamien, R.D., Elastic-instability triggered pattern formation. Phys. Rev. E, 80, 2, 15, #021604, 2009.
[2.96] Meinhardt, H. and Gierer, A., Pattern formation by local self-activation and lateral inhibition. Bioessays, 22, 8, 753–760, 2000.
[2.97] Mihelich, M., Dubrulle, B., Paillard, D., Herbert, C., Maximum entropy production vs. Kolmogorov-Sinai entropy in constrained ASEP model. Entropy, 16, 2, 1037–1046, 2014.
[2.98] Mitchell, J.G., Whence is the diversity of diatom frustules derived?, in: Diatom Nanotechnology: Progress and Emerging Applications, D. Losic (Ed.), pp. 1–13, Royal Society of Chemistry, Cambridge, 2018.
[2.99] Nesterenko, A.M., Kuznetsov, M.B., Korotkova, D.D., Zaraisky, A.G., Morphogene adsorption as a Turing instability regulator: Theoretical analysis and possible applications in multicellular embryonic systems. PLoS One, 12, 2, e0171212, 2017.
[2.100] Ornstein, D.S., Ergodic theory, randomness, and “chaos”. Science, 243, 4888, 182–187, 1989.
[2.101] Oseledec, V.I., A multiplicative ergodic theorem. Lyapunov characteristic numbers for dynamical systems. Trans. Moscow Math. Soc., 19, 197–231, 1968.
[2.102] Palmer, A.R., Symmetry breaking and the evolution of development. Science, 306, 5697, 828–833, 2004.
[2.103] Palmer, A.R. and Strobeck, C., Fluctuating asymmetry analyses revisited, Oxford University Press, Oxford, UK, 2003.
[2.104] Pappas, J.L., Geometry and topology of diatom shape and surface morphogenesis for use in applications of nanotechnology. J. Nanosci. Nanotechnol., 5, 1, 120–130, 2005.
[2.105] Pappas, J.L., Theoretical morphospace and its relation to freshwater gomphonemoid-cymbelloid diatom (Bacillariophyta) lineages. J. Biol. Syst., 13, 4, 385–398, 2005.
[2.106] Pappas, J.L., More on theoretical morphospace and its relation to freshwater gomphonemoid-cymbelloid diatom (Bacillariophyta) lineages. J. Biol. Syst., 16, 1, 119–137, 2008.
[2.107] Pappas, J.L., Multivariate complexity analysis of 3D surface form and function of centric diatoms at the Eocene-Oligocene transition. Mar. Micropaleontol., 122, 67–86, 2016.
[2.108] Pappas, J.L. and Miller, D.J., A generalized approach to the modeling and analysis of 3D surface morphology in organisms. PLoS One, 8, 10, e77551, 2013.
[2.109] Parkinson, J., Brechet, Y., Gordon, R., Centric diatom morphogenesis: A model based on a DLA algorithm investigating the potential role of microtubules. Biochim. Biophys. Acta - Mol. Cell Res., 1452, 1, 89–102, 1999.
[2.110] Pesin, J.B., Families of invariant manifolds corresponding to nonzero characteristic exponents. Math. USSR-Izv., 10, 1261–1305, 1976.
[2.111] Pfitzer, E., Untersuchungen uber Bau und Entwicklung der Bacillariaceen (Diatomaceen) [Studies on construction and development of Bacillariaceae (Diatomaceae)] [German], in: Botanische Abhandlungen aus dem Gebiete der Morphologie und Physiologie [Botanical Treatises in the Field of Morphology and Physiology], vol. [i]-vi, J.L.E.R. von Hanstein (Ed.), pp. 1–189, 186 pls, Adolph Marcus, Bonn, Germany, 1871.
[2.112] Pfitzer, E., Die Bacillariaceen (Diatomaceae) [Bacillariaceae (Diatomaceae)] [German], in: Encyklopaedie der Naturwissenschaften. I. Abteilung. I. Thiel: Handbuch der Botanik, vol. 2, A. Schenk (Ed.), pp. 403–445, Verlag von Eduard Trewendt, Breslau, 1882.
[2.113] Pickett-Heaps, J.D., The evolution of the mitotic apparatus: An attempt at comparative ultrastructural cytology in dividing plant cells. Cytobios, 1, 3, 257–280, 1969.
[2.114] Pickett-Heaps, J.D., Schmid, A.M.M., Edgar, L.A., The cell biology of diatom valve formation. Prog. Phycol. Res., 7, 1–168, 1990.
[2.115] Prasad, A. and Ramaswamy, R., Characteristic distributions of finite-time Lyapunov exponents. Phys. Rev. E, 60, 3, 2761–2766, 1999.
[2.116] Rogerson, A., Defreitas, A.S.W., Mclnnes, A.G., Observations on wall morphogenesis in Coscinodiscus asteromphalus (Bacillariophyceae). Trans. Am. Microsc. Soc., 105, 1, 59–67, 1986.
[2.117] Rose, D.T. and Cox, E.J., Some diatom species do not show a gradual decrease in cell size as they reproduce. Fundam. Appl. Limnol., 182, 2, 117–122, 2013.
[2.118] Rosenstein, M.T., Collins, J.J., De Luca, C.J., A practical method for calculating largest Lyapunov exponents from small data sets. Physica D-Nonlinear Phenomena, 65, 1–2, 117–134, 1993.
[2.119] Round, F.E., Crawford, R.M., Mann, D.G., The Diatoms, Biology & Morphology of the Genera, Cambridge University Press, Cambridge, 1990.
[2.120] Sapriel, G., Quinet, M., Heijde, M., Jourdren, L., Tanty, V., Luo, G.Z., Le Crom, S., Lopez, P.J., Genome-wide transcriptome analyses of silicon metabolism in Phaeodactylum tricornutum reveal the multilevel regulation of silicic acid transporters. PLoS One, 4, 10, e7458, 2009.
[2.121] Savriama, Y. and Klingenberg, C.P., Beyond bilateral symmetry: Geometric morphometric methods for any type of symmetry. BMC Evol. Biol., 11, 280, 2011.
[2.122] Schmid, A.-M.M., Morphogenetic forces in diatom cell wall formation, in: Cytomechanics: The Mechanical Basis of Cell Form and Structure, J. Bereiter-Hahn, O.R. Anderson, W.E. Reif (Eds.), pp. 183–199, Springer-Verlag, Berlin, 1987.
[2.123] Schmid, A.-M.M., Aspects of morphogenesis and function of diatom cell walls with implications for taxonomy. Protoplasma, 181, 1–4, 43–60, 1994.
[2.124] Schmid, A.-M.M., The wall & membrane systems in diatoms: Comment in reply to Medlin (2004). Diatom Res., 20, 1, 211–216, 2005.
[2.125] Schmid, A.-M.M. and Crawford, R.M., Ellerbeckia arenaria (Bacillariophyceae): Formation of auxospores and initial cells. Eur. J. Phycol., 36, 4, 307–320, 2001.
[2.126] Schmid, A.-M.M. and Volcani, B.E., Wall morphogenesis in Coscinodiscus wailesii Gran and Angst. I. Valve morphology and development of its architecture. J. Phycol., 19, 4, 387–402, 1983.
[2.127] Schmidt, F. and Fleming, R.W., Visual perception of complex shape-transforming processes. Cogn. Psychol., 90, 48–70, 2016.
[2.128] Shadrina, E.G. and Vol’pert, Y.L., Experience of applying plant and animal fluctuating asymmetry in assessment of environmental quality in terrestrial ecosystems: Results of 20-year studies of wildlife and anthropogenically transformed territories. Russ. J. Dev. Biol., 49, 1, 23–35, 2018.
[2.129] Shannon, C.E., A mathematical theory of communication [corrected version]. Bell Syst. Tech. J., 27, 379–423, 623–656, 1948.
[2.130] Shimada, Y., Tagagi, E., Ikeguchi, T., Symmetry of Lyapunov exponents in bifurcation structures of one-dimensional maps. Chaos, 26, 123119, 2016.
[2.131] Shirokawa, Y. and Shimada, M., Cytoplasmic inheritance of parent - offspring cell structure in the clonal diatom Cyclotella meneghiniana. Proc. R. Soc. B-Biol. Sci., 283, 1842, 20161632, 2016.
[2.132] Shubnikov, A.V. and Belov, N.V., Colored Symmetry, Pergamon Press, New York, 1964.
[2.133] Steinsaltz, D., Random logistic maps and Lyapunov exponents. Indagationes Mathematicae, 12, 4, 557–584, 2001.
[2.134] Sterrenburg, F.A.S., Gordon, R., Tiffany, M.A., Nagy, S.S., Diatoms: Living in a constructal environment, in: Algae and Cyanobacteria in Extreme Environments. Series: Cellular Origin, Life in Extreme Habitats and Astrobiology, vol. 11, J. Seckbach (Ed.), pp. 141–172, Springer, Dordrecht, The Netherlands, 2007.
[2.135] Stevens, K.A., Surface tilt (the direction of slant): A neglected psychophysical variable. Percept. Psychophys., 33, 3, 241–250, 1983.
[2.136] Stewart, M., Introduction to the computer image processing of electron micrographs of two-dimensionally ordered biological structures. J. Electron Microsc. Tech., 9, 4, 301–324, 1988.
[2.137] Sui, N., Li, M., He, P., Statistical computation of Boltzmann entropy and estimation of the optimal probability density function from statistical sample. Mon. Not. R. Astron. Soc., 445, 4, 4211–4218, 2014.
[2.138] Sumper, M., A phase separation model for the nanopatterning of diatom biosilica. Science, 295, 5564, 2430–2433, 2002.
[2.139] Sumper, M. and Brunner, E., Learning from diatoms: Nature’s tools for the production of nanostructured silica. Adv. Funct. Mater., 16, 1, 17–26, 2006.
[2.140] Sun, C.M. and Si, D.Y., Skew and slant correction for document images using gradient direction, in: Proceedings of the Fourth International Conference on Document Analysis and Recognition, vol. 1 and 2, IEEE, Computer Society Press, Los Alamitos, California, USA, pp. 142–146, 1997.
[2.141] Taylor, R.L.V., Attractors: nonstrange to chaotic. SIAM Undergraduate Research Online (SIURO). Soc. Ind. Appl. Math., 21, 6, 72–80, 2011.
[2.142] Tesson, B., Lerch, S.J.L., Hildebrand, M., Characterization of a new protein family associated with the silica deposition vesicle membrane enables genetic manipulation of diatom silica. Sci. Rep., 7, 13457, 2017.
[2.143] Tiffany, M.A., Development of valves in the marine diatom genus Trigonium. J. Phycol., 38, s1, 35, 2002.
[2.144] Tiffany, M.A., Valve development in Aulacodiscus. Diatom Res., 23, 1, 185–212, 2008.
[2.145] Tiffany, M.A., Valve and girdle band morphogenesis in the pseudocellate diatom species Biddulphia biddulphiana J.E. Smith (Boyer) and Isthmia nervosa Kütz. Nova Hedwig. Beih., 144, 61–95, 2015.
[2.146] Tiffany, M.A. and Hernandez-Becerril, D.U., Valve development in the diatom family Asterolampraceae H. L Smith 1872. Micropaleontology, 51, 3, 217–258, 2005.
[2.147] Tonelli, R., Mezzorani, G., Meloni, F., Lissia, M., Coraddu, M., Entropy production and Pesin-like identity at the onset of chaos. Prog. Theor. Phys., 115, 1, 23–29, 2006.
[2.148] Turing, A.M., The chemical basis of morphogenesis. Philos. Trans. R. Soc. Lond. Ser. B, Biol. Sci., B237, 641, 37–72, 1952.
[2.149] Tuszynski, J.A. and Gordon, R., A mean field Ising model for cortical rotation in amphibian one-cell stage embryos. BioSystems, 109, 3, Special Issue on Biological Morphogenesis, 381–389, 2012.
[2.150] Van De Meene, A.M.L. and Pickett-Heaps, J.D., Valve morphogenesis in the centric diIatom Proboscia alata Sundstrom. J. Phycol., 38, 2, 351–363, 2002.
[2.151] Van De Meene, A.M.L. and Pickett-Heaps, J.D., Valve morphogenesis in the centric diatom Rhizosolenia setigera (Bacillariophyceae, Centrales) and its taxonomic implications. Eur. J. Phycol., 39, 1, 93–104, 2004.
[2.152] Van Valen, L.M., A study of fluctuating asymmetry. Evolution, 16, 125–142, 1962.
[2.153] Vanag, V.K. and Epstein, I.R., Pattern formation mechanisms in reaction-diffusion systems. Int. J. Dev. Biol., 53, 5–6, 673–681, 2009.
[2.154] Vartanian, M., Descles, J., Quinet, M., Douady, S., Lopez, P.J., Plasticity and robustness of pattern formation in the model diatom Phaeodactylum tricornutum. New Phytol., 182, 2, 429–442, 2009.
[2.155] Volcani, B.E., Cell wall formation in diatoms: Morphogenesis and biochemistry, in: Silicon and Siliceous Structures in Biological Systems, T.L. Simpson and B.E. Volcani (Eds.), pp. 157–200, Springer-Verlag, New York, 1981.
[2.156] von Stosch, H.A., On auxospore envelopes in diatoms. Bacillaria, 5, 127–156, 1982.
[2.157] Vrieling, E.G., Sun, Q.Y., Tian, M., Kooyman, P.J., Gieskes, W.W.C., van Santen, R.A., Sommerdijk, N., Salinity-dependent diatom biosilicification implies an important role of external ionic strength. Proc. Natl. Acad. Sci. U. S. A., 104, 25, 10441–10446, 2007.
[2.158] Weibel, E.R., Fractal geometry: a design principle for living organisms. Am. J. Physiol., 261, 6.1, L361–L369, 1991.
[2.159] Weisstein, E.W., CRC Concise Encyclopedia of Mathematics, 2nd ed., Chapman & Hall/CRC, London, United Kingdom, 2002.
[2.160] Weyl, H., Symmetry, Princeton University Press, Princeton, New Jersey, USA, 1952.
[2.161] Willis, L., Cox, E.J., Duke, T., A simple probabilistic model of submicroscopic diatom morphogenesis. J. R. Soc. Interface, 10, 83, 20130067, 2013.
[2.162] Willis, L., Page, K.M., Broomhead, D.S., Cox, E.J., Discrete free-boundary reaction-diffusion model of diatom pore occlusions. Plant Ecol. Evol., 143, 3, 297–306, 2010.
[2.163] Wolf, A., Swift, J.B., Swinney, H.L., Vastano, J.A., Determining Lyapunov exponents from a time series. Physica D-Nonlinear Phenomena, 16, 3, 285–317, 1985.
[2.164] Xiao, Y.H., Xiong, M.M., Wang, W., Wang, H., Emergence of symmetry in complex networks. Phys. Rev. E, 77, 6, 066108, 2008.
[2.165] Yang, W., Lopez, P.J., Rosengarten, G., Diatoms: Self assembled silica nanostructures, and templates for bio/chemical sensors and biomimetic membranes. Analyst, 136, 1, 42–53, 2011.
[2.166] Yang, X.-Y., Chen, L.-H., Li, Y., Rooke, J.C., Sanchez, C., Su, B.-L., Hierarchically porous materials: Synthesis strategies and structure design. Chem. Soc. Rev., 46, 2, 481–558, 2017.
[2.167] Zabrodsky, H., Peleg, S., Avnir, D., Symmetry as a continuous feature. IEEE Trans. Pattern Anal. Mach. Intell., 17, 12, 1154–1166, 1995.
1 *Dedicated to the memory of the late Antone G. Jacobson and his life pursuing the puzzle of morphogenesis.
2 +Corresponding author: jlpappas@umich.edu
