Morphology-Induced Collective Behaviors: Dynamic Pattern Formation in Water-Floating Elements

PubMed Central

Nakajima, Kohei; Ngouabeu, Aubery Marchel Tientcheu; Miyashita, Shuhei; Göldi, Maurice; Füchslin, Rudolf Marcel; Pfeifer, Rolf

2012-01-01

Complex systems involving many interacting elements often organize into patterns. Two types of pattern formation can be distinguished, static and dynamic. Static pattern formation means that the resulting structure constitutes a thermodynamic equilibrium whose pattern formation can be understood in terms of the minimization of free energy, while dynamic pattern formation indicates that the system is permanently dissipating energy and not in equilibrium. In this paper, we report experimental results showing that the morphology of elements plays a significant role in dynamic pattern formation. We prepared three different shapes of elements (circles, squares, and triangles) floating in a water-filled container, in which each of the shapes has two types: active elements that were capable of self-agitation with vibration motors, and passive elements that were mere floating tiles. The system was purely decentralized: that is, elements interacted locally, and subsequently elicited global patterns in a process called self-organized segregation. We showed that, according to the morphology of the selected elements, a different type of segregation occurs. Also, we quantitatively characterized both the local interaction regime and the resulting global behavior for each type of segregation by means of information theoretic quantities, and showed the difference for each case in detail, while offering speculation on the mechanism causing this phenomenon. PMID:22715370

Instabilities and spatiotemporal patterns behind predator invasions with nonlocal prey competition.

PubMed

Merchant, Sandra M; Nagata, Wayne

2011-12-01

We study the influence of nonlocal intraspecies prey competition on the spatiotemporal patterns arising behind predator invasions in two oscillatory reaction-diffusion integro-differential models. We use three common types of integral kernels as well as develop a caricature system, to describe the influence of the standard deviation and kurtosis of the kernel function on the patterns observed. We find that nonlocal competition can destabilize the spatially homogeneous state behind the invasion and lead to the formation of complex spatiotemporal patterns, including stationary spatially periodic patterns, wave trains and irregular spatiotemporal oscillations. In addition, the caricature system illustrates how large standard deviation and low kurtosis facilitate the formation of these spatiotemporal patterns. This suggests that nonlocal competition may be an important mechanism underlying spatial pattern formation, particularly in systems where the competition between individuals varies over space in a platykurtic manner. Copyright © 2011 Elsevier Inc. All rights reserved.

Analysis of the Enhanced Stability of R(+)-Alpha Lipoic Acid by the Complex Formation with Cyclodextrins

PubMed Central

Ikuta, Naoko; Sugiyama, Hironori; Shimosegawa, Hiroshi; Nakane, Rie; Ishida, Yoshiyuki; Uekaji, Yukiko; Nakata, Daisuke; Pallauf, Kathrin; Rimbach, Gerald; Terao, Keiji; Matsugo, Seiichi

2013-01-01

R(+)-alpha lipoic acid (RALA) is one of the cofactors for mitochondrial enzymes and, therefore, plays a central role in energy metabolism. RALA is unstable when exposed to low pH or heat, and therefore, it is difficult to use enantiopure RALA as a pharma- and nutra-ceutical. In this study, we have aimed to stabilize RALA through complex formation with cyclodextrins (CDs). α-CD, β-CD and γ-CD were used for the formation of these RALA-CD complexes. We confirmed the complex formation using differential scanning calorimetry and showed by using HPLC analysis that complexed RALA is more stable than free RALA when subjected to humidity and high temperature or acidic pH conditions. Scanning electron microscopy studies showed that the particle size and shape differed depending on the cyclodextrin used for complexation. Further, the complexes of CD and RALA showed a different particle size distribution pattern compared with that of CD itself or that of the physical mixture of RALA and CD. PMID:23434662

Complex-ordered patterns in shaken convection.

PubMed

Rogers, Jeffrey L; Pesch, Werner; Brausch, Oliver; Schatz, Michael F

2005-06-01

We report and analyze complex patterns observed in a combination of two standard pattern forming experiments. These exotic states are composed of two distinct spatial scales, each displaying a different temporal dependence. The system is a fluid layer experiencing forcing from both a vertical temperature difference and vertical time-periodic oscillations. Depending on the parameters these forcing mechanisms produce fluid motion with either a harmonic or a subharmonic temporal response. Over a parameter range where these mechanisms have comparable influence the spatial scales associated with both responses are found to coexist, resulting in complex, yet highly ordered patterns. Phase diagrams of this region are reported and criteria to define the patterns as quasiperiodic crystals or superlattices are presented. These complex patterns are found to satisfy four-mode (resonant tetrad) conditions. The qualitative difference between the present formation mechanism and the resonant triads ubiquitously used to explain complex-ordered patterns in other nonequilibrium systems is discussed. The only exception to quantitative agreement between our analysis based on Boussinesq equations and laboratory investigations is found to be the result of breaking spatial symmetry in a small parameter region near onset.

Directed formation of micro- and nanoscale patterns of functional light-harvesting LH2 complexes.

PubMed

Reynolds, Nicholas P; Janusz, Stefan; Escalante-Marun, Maryana; Timney, John; Ducker, Robert E; Olsen, John D; Otto, Cees; Subramaniam, Vinod; Leggett, Graham J; Hunter, C Neil

2007-11-28

The precision placement of the desired protein components on a suitable substrate is an essential prelude to any hybrid "biochip" device, but a second and equally important condition must also be met: the retention of full biological activity. Here we demonstrate the selective binding of an optically active membrane protein, the light-harvesting LH2 complex from Rhodobacter sphaeroides, to patterned self-assembled monolayers at the micron scale and the fabrication of nanometer-scale patterns of these molecules using near-field photolithographic methods. In contrast to plasma proteins, which are reversibly adsorbed on many surfaces, the LH2 complex is readily patterned simply by spatial control of surface polarity. Near-field photolithography has yielded rows of light-harvesting complexes only 98 nm wide. Retention of the native optical properties of patterned LH2 molecules was demonstrated using in situ fluorescence emission spectroscopy.

On the mechanical theory for biological pattern formation

NASA Astrophysics Data System (ADS)

Bentil, D. E.; Murray, J. D.

1993-02-01

We investigate the pattern-forming potential of mechanical models in embryology proposed by Oster, Murray and their coworkers. We show that the presence of source terms in the tissue extracellular matrix and cell density equations give rise to spatio-temporal oscillations. An extension of one such model to include ‘biologically realistic long range effects induces the formation of stationary spatial patterns. Previous attempts to solve the full system were in one dimension only. We obtain solutions in one dimension and extend our simulations to two dimensions. We show that a single mechanical model alone is capable of generating complex but regular spatial patterns rather than the requirement of model interaction as suggested by Nagorcka et al. and Shaw and Murray. We discuss some biological applications of the models among which are would healing and formation of dermatoglyphic (fingerprint) patterns.

Interactions of Enolizable Barbiturate Dyes.

PubMed

Schade, Alexander; Schreiter, Katja; Rüffer, Tobias; Lang, Heinrich; Spange, Stefan

2016-04-11

The specific barbituric acid dyes 1-n-butyl-5-(2,4-dinitro-phenyl) barbituric acid and 1-n-butyl-5-{4-[(1,3-dioxo-1H-inden-(3 H)-ylidene)methyl]phenyl}barbituric acid were used to study complex formation with nucleobase derivatives and related model compounds. The enol form of both compounds shows a strong bathochromic shift of the UV/Vis absorption band compared to the rarely coloured keto form. The keto-enol equilibria of the five studied dyes are strongly dependent on the properties of the environment as shown by solvatochromic studies in ionic liquids and a set of organic solvents. Enol form development of the barbituric acid dyes is also associated with alteration of the hydrogen bonding pattern from the ADA to the DDA type (A=hydrogen bond acceptor site, D=donor site). Receptor-induced altering of ADA towards DDA hydrogen bonding patterns of the chromophores are utilised to study supramolecular complex formation. As complementary receptors 9-ethyladenine, 1-n-butylcytosine, 1-n-butylthymine, 9-ethylguanidine and 2,6-diacetamidopiridine were used. The UV/Vis spectroscopic response of acid-base reaction compared to supramolecular complex formation is evaluated by (1)H NMR titration experiments and X-ray crystal structure analyses. An increased acidity of the barbituric acid derivative promotes genuine salt formation. In contrast, supramolecular complex formation is preferred for the weaker acidic barbituric acid. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Pattern Formation and Complexity Emergence

NASA Astrophysics Data System (ADS)

Berezin, Alexander A.

2001-03-01

Success of nonlinear modelling of pattern formation and self-organization encourages speculations on informational and number theoretical foundations of complexity emergence. Pythagorean "unreasonable effectiveness of integers" in natural processes is perhaps extrapolatable even to universal emergence "out-of-nothing" (Leibniz, Wheeler). Because rational numbers (R = M/N) are everywhere dense on real axis, any digital string (hence any "book" from "Library of Babel" of J.L.Borges) is "recorded" infinitely many times in arbitrary many rationals. Furthermore, within any arbitrary small interval there are infinitely many Rs for which (either or both) integers (Ms and Ns) "carry" any given string of any given length. Because any iterational process (such as generation of fractal features of Mandelbrot Set) is arbitrary closely approximatable with rational numbers, the infinite pattern of integers expresses itself in generation of complexity of the world, as well as in emergence of the world itself. This "tunnelling" from Platonic World ("Platonia" of J.Barbour) to a real (physical) world is modern recast of Leibniz's motto ("for deriving all from nothing there suffices a single principle").

Pattern formation and collective effects in populations of magnetic microswimmers

NASA Astrophysics Data System (ADS)

Vach, Peter J.; Walker, Debora; Fischer, Peer; Fratzl, Peter; Faivre, Damien

2017-03-01

Self-propelled particles are one prototype of synthetic active matter used to understand complex biological processes, such as the coordination of movement in bacterial colonies or schools of fishes. Collective patterns such as clusters were observed for such systems, reproducing features of biological organization. However, one limitation of this model is that the synthetic assemblies are made of identical individuals. Here we introduce an active system based on magnetic particles at colloidal scales. We use identical but also randomly-shaped magnetic micropropellers and show that they exhibit dynamic and reversible pattern formation.

Self-reduction of a copper complex MOD ink for inkjet printing conductive patterns on plastics.

PubMed

Farraj, Yousef; Grouchko, Michael; Magdassi, Shlomo

2015-01-31

Highly conductive copper patterns on low-cost flexible substrates are obtained by inkjet printing a metal complex based ink. Upon heating the ink, the soluble complex, which is composed of copper formate and 2-amino-2-methyl-1-propanol, decomposes under nitrogen at 140 °C and is converted to pure metallic copper. The decomposition process of the complex is investigated and a suggested mechanism is presented. The ink is stable in air for prolonged periods, with no sedimentation or oxidation problems, which are usually encountered in copper nanoparticle based inks.

Spatial Heterogeneity and Imperfect Mixing in Chemical Reactions: Visualization of Density-Driven Pattern Formation

DOE PAGES

Sobel, Sabrina G.; Hastings, Harold M.; Testa, Matthew

2009-01-01

Imore » mperfect mixing is a concern in industrial processes, everyday processes (mixing paint, bread machines), and in understanding salt water-fresh water mixing in ecosystems. The effects of imperfect mixing become evident in the unstirred ferroin-catalyzed Belousov-Zhabotinsky reaction, the prototype for chemical pattern formation. Over time, waves of oxidation (high ferriin concentration, blue) propagate into a background of low ferriin concentration (red); their structure reflects in part the history of mixing in the reaction vessel. However, it may be difficult to separate mixing effects from reaction effects. We describe a simpler model system for visualizing density-driven pattern formation in an essentially unmixed chemical system: the reaction of pale yellow Fe 3 + with colorless SCN − to form the blood-red Fe ( SCN ) 2 + complex ion in aqueous solution. Careful addition of one drop of Fe ( NO 3 ) 3 to KSCN yields striped patterns after several minutes. The patterns appear reminiscent of Rayleigh-Taylor instabilities and convection rolls, arguing that pattern formation is caused by density-driven mixing.« less

Spatial Heterogeneity and Imperfect Mixing in Chemical Reactions: Visualization of Density-Driven Pattern Formation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sobel, Sabrina G.; Hastings, Harold M.; Testa, Matthew

Imore » mperfect mixing is a concern in industrial processes, everyday processes (mixing paint, bread machines), and in understanding salt water-fresh water mixing in ecosystems. The effects of imperfect mixing become evident in the unstirred ferroin-catalyzed Belousov-Zhabotinsky reaction, the prototype for chemical pattern formation. Over time, waves of oxidation (high ferriin concentration, blue) propagate into a background of low ferriin concentration (red); their structure reflects in part the history of mixing in the reaction vessel. However, it may be difficult to separate mixing effects from reaction effects. We describe a simpler model system for visualizing density-driven pattern formation in an essentially unmixed chemical system: the reaction of pale yellow Fe 3 + with colorless SCN − to form the blood-red Fe ( SCN ) 2 + complex ion in aqueous solution. Careful addition of one drop of Fe ( NO 3 ) 3 to KSCN yields striped patterns after several minutes. The patterns appear reminiscent of Rayleigh-Taylor instabilities and convection rolls, arguing that pattern formation is caused by density-driven mixing.« less

Self-organized pattern formation at organic-inorganic interfaces during deposition: Experiment versus modeling

NASA Astrophysics Data System (ADS)

Szillat, F.; Mayr, S. G.

2011-09-01

Self-organized pattern formation during physical vapor deposition of organic materials onto rough inorganic substrates is characterized by a complex morphological evolution as a function of film thickness. We employ a combined experimental-theoretical study using atomic force microscopy and numerically solved continuum rate equations to address morphological evolution in the model system: poly(bisphenol A carbonate) on polycrystalline Cu. As the key ingredients for pattern formation, (i) curvature and interface potential driven surface diffusion, (ii) deposition noise, and (iii) interface boundary effects are identified. Good agreement of experiments and theory, fitting only the Hamaker constant and diffusivity within narrow physical parameter windows, corroborates the underlying physics and paves the way for computer-assisted interface engineering.

An automated graphics tool for comparative genomics: the Coulson plot generator

PubMed Central

2013-01-01

Background Comparative analysis is an essential component to biology. When applied to genomics for example, analysis may require comparisons between the predicted presence and absence of genes in a group of genomes under consideration. Frequently, genes can be grouped into small categories based on functional criteria, for example membership of a multimeric complex, participation in a metabolic or signaling pathway or shared sequence features and/or paralogy. These patterns of retention and loss are highly informative for the prediction of function, and hence possible biological context, and can provide great insights into the evolutionary history of cellular functions. However, representation of such information in a standard spreadsheet is a poor visual means from which to extract patterns within a dataset. Results We devised the Coulson Plot, a new graphical representation that exploits a matrix of pie charts to display comparative genomics data. Each pie is used to describe a complex or process from a separate taxon, and is divided into sectors corresponding to the number of proteins (subunits) in a complex/process. The predicted presence or absence of proteins in each complex are delineated by occupancy of a given sector; this format is visually highly accessible and makes pattern recognition rapid and reliable. A key to the identity of each subunit, plus hierarchical naming of taxa and coloring are included. A java-based application, the Coulson plot generator (CPG) automates graphic production, with a tab or comma-delineated text file as input and generating an editable portable document format or svg file. Conclusions CPG software may be used to rapidly convert spreadsheet data to a graphical matrix pie chart format. The representation essentially retains all of the information from the spreadsheet but presents a graphically rich format making comparisons and identification of patterns significantly clearer. While the Coulson plot format is highly useful in comparative genomics, its original purpose, the software can be used to visualize any dataset where entity occupancy is compared between different classes. Availability CPG software is available at sourceforge http://sourceforge.net/projects/coulson and http://dl.dropbox.com/u/6701906/Web/Sites/Labsite/CPG.html PMID:23621955

Spontaneous formation of linearly arranged microcraters on sol-gel-derived silica-poly(vinylpyrrolidone) hybrid films induced by Bénard-Marangoni convection.

PubMed

Uchiyama, Hiroaki; Mantani, Yuto; Kozuka, Hiromitsu

2012-07-10

Complex, sophisticated surface patterns on micrometer and nanometer scales are obtained when solvent evaporates from solutions containing nonvolatile solutes dropped on a solid substrate. Such evaporation-driven pattern formation has been utilized as a fabrication process of highly ordered patterns in thin films. Here, we suggested the spontaneous pattern formation induced by Bénard-Marangoni convection triggered by solvent evaporation as a novel patterning process of sol-gel-derived organic-inorganic hybrid films. Microcraters of 1.0-1.5 μm in height and of 100-200 μm in width were spontaneously formed on the surface of silica-poly(vinylpyrrolidone) hybrid films prepared via temperature-controlled dip-coating process, where the surface patterns were linearly arranged parallel to the substrate withdrawal direction. Such highly ordered micropatterns were achieved by Bénard-Marangoni convection activated at high temperatures and the unidirectional flow of the coating solution on the substrate during dip-coating.

Perceptual Visual Grouping under Inattention: Electrophysiological Functional Imaging

ERIC Educational Resources Information Center

Razpurker-Apfeld, Irene; Pratt, Hillel

2008-01-01

Two types of perceptual visual grouping, differing in complexity of shape formation, were examined under inattention. Fourteen participants performed a similarity judgment task concerning two successive briefly presented central targets surrounded by task-irrelevant simple and complex grouping patterns. Event-related potentials (ERPs) were…

Self-organization of network dynamics into local quantized states

DOE PAGES

Nicolaides, Christos; Juanes, Ruben; Cueto-Felgueroso, Luis

2016-02-17

Self-organization and pattern formation in network-organized systems emerges from the collective activation and interaction of many interconnected units. A striking feature of these non-equilibrium structures is that they are often localized and robust: only a small subset of the nodes, or cell assembly, is activated. Understanding the role of cell assemblies as basic functional units in neural networks and socio-technical systems emerges as a fundamental challenge in network theory. A key open question is how these elementary building blocks emerge, and how they operate, linking structure and function in complex networks. Here we show that a network analogue of themore » Swift-Hohenberg continuum model—a minimal-ingredients model of nodal activation and interaction within a complex network—is able to produce a complex suite of localized patterns. Thus, the spontaneous formation of robust operational cell assemblies in complex networks can be explained as the result of self-organization, even in the absence of synaptic reinforcements.« less

Self-organization of network dynamics into local quantized states.

PubMed

Nicolaides, Christos; Juanes, Ruben; Cueto-Felgueroso, Luis

2016-02-17

Self-organization and pattern formation in network-organized systems emerges from the collective activation and interaction of many interconnected units. A striking feature of these non-equilibrium structures is that they are often localized and robust: only a small subset of the nodes, or cell assembly, is activated. Understanding the role of cell assemblies as basic functional units in neural networks and socio-technical systems emerges as a fundamental challenge in network theory. A key open question is how these elementary building blocks emerge, and how they operate, linking structure and function in complex networks. Here we show that a network analogue of the Swift-Hohenberg continuum model-a minimal-ingredients model of nodal activation and interaction within a complex network-is able to produce a complex suite of localized patterns. Hence, the spontaneous formation of robust operational cell assemblies in complex networks can be explained as the result of self-organization, even in the absence of synaptic reinforcements.

Self-organization of network dynamics into local quantized states

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nicolaides, Christos; Juanes, Ruben; Cueto-Felgueroso, Luis

Self-organization and pattern formation in network-organized systems emerges from the collective activation and interaction of many interconnected units. A striking feature of these non-equilibrium structures is that they are often localized and robust: only a small subset of the nodes, or cell assembly, is activated. Understanding the role of cell assemblies as basic functional units in neural networks and socio-technical systems emerges as a fundamental challenge in network theory. A key open question is how these elementary building blocks emerge, and how they operate, linking structure and function in complex networks. Here we show that a network analogue of themore » Swift-Hohenberg continuum model—a minimal-ingredients model of nodal activation and interaction within a complex network—is able to produce a complex suite of localized patterns. Thus, the spontaneous formation of robust operational cell assemblies in complex networks can be explained as the result of self-organization, even in the absence of synaptic reinforcements.« less

Systematic coarse-grained modeling of complexation between small interfering RNA and polycations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wei, Zonghui; Luijten, Erik, E-mail: luijten@northwestern.edu; Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208

All-atom molecular dynamics simulations can provide insight into the properties of polymeric gene-delivery carriers by elucidating their interactions and detailed binding patterns with nucleic acids. However, to explore nanoparticle formation through complexation of these polymers and nucleic acids and study their behavior at experimentally relevant time and length scales, a reliable coarse-grained model is needed. Here, we systematically develop such a model for the complexation of small interfering RNA (siRNA) and grafted polyethyleneimine copolymers, a promising candidate for siRNA delivery. We compare the predictions of this model with all-atom simulations and demonstrate that it is capable of reproducing detailed bindingmore » patterns, charge characteristics, and water release kinetics. Since the coarse-grained model accelerates the simulations by one to two orders of magnitude, it will make it possible to quantitatively investigate nanoparticle formation involving multiple siRNA molecules and cationic copolymers.« less

Pattern Formation on Networks: from Localised Activity to Turing Patterns

PubMed Central

McCullen, Nick; Wagenknecht, Thomas

2016-01-01

Networks of interactions between competing species are used to model many complex systems, such as in genetics, evolutionary biology or sociology and knowledge of the patterns of activity they can exhibit is important for understanding their behaviour. The emergence of patterns on complex networks with reaction-diffusion dynamics is studied here, where node dynamics interact via diffusion via the network edges. Through the application of a generalisation of dynamical systems analysis this work reveals a fundamental connection between small-scale modes of activity on networks and localised pattern formation seen throughout science, such as solitons, breathers and localised buckling. The connection between solutions with a single and small numbers of activated nodes and the fully developed system-scale patterns are investigated computationally using numerical continuation methods. These techniques are also used to help reveal a much larger portion of of the full number of solutions that exist in the system at different parameter values. The importance of network structure is also highlighted, with a key role being played by nodes with a certain so-called optimal degree, on which the interaction between the reaction kinetics and the network structure organise the behaviour of the system. PMID:27273339

Liesegang banding and multiple precipitate formation in cobalt phosphate systems

NASA Astrophysics Data System (ADS)

Karam, Tony; El-Rassy, Houssam; Zaknoun, Farah; Moussa, Zeinab; Sultan, Rabih

2012-02-01

We study a cobalt phosphate Liesegang pattern from cobalt(II) and phosphate ions in a 1D tube. The system yields a complex, multi-component pattern. Characterization of the different precipitates by FTIR, SEM and XRD reveals that they are cobalt phosphate polymorphs with different degrees of hydration.

Hybrid copper complex-derived conductive patterns printed on polyimide substrates

NASA Astrophysics Data System (ADS)

Lee, Byoungyoon; Jeong, Sooncheol; Kim, Yoonhyun; Jeong, Inbum; Woo, Kyoohee; Moon, Jooho

2012-06-01

We synthesized new copper complexes that can be readily converted into highly conductive Cu film. Mechanochemical milling of copper (I) oxide suspended in formic acid resulted in the submicron-sized Cu formate together Cu nanoparticles. The submicrometer-sized Cu formates are reactive toward inter-particle sintering and metallic Cu seeds present in the Cu complexes assist their decomposition and the nucleation of Cu. The hybrid copper complex film printed on polyimide substrate is decomposed into dense and uniform Cu layer after annealing at 250 °C for 30 min under nitrogen atmosphere. The resulting Cu film exhibited a low resistivity of 8.2 μΩ·cm and good adhesion characteristics.

Reaction-diffusion controlled growth of complex structures

NASA Astrophysics Data System (ADS)

Noorduin, Willem; Mahadevan, L.; Aizenberg, Joanna

2013-03-01

Understanding how the emergence of complex forms and shapes in biominerals came about is both of fundamental and practical interest. Although biomineralization processes and organization strategies to give higher order architectures have been studied extensively, synthetic approaches to mimic these self-assembled structures are highly complex and have been difficult to emulate, let alone replicate. The emergence of solution patterns has been found in reaction-diffusion systems such as Turing patterns and the BZ reaction. Intrigued by this spontaneous formation of complexity we explored if similar processes can lead to patterns in the solid state. We here identify a reaction-diffusion system in which the shape of the solidified products is a direct readout of the environmental conditions. Based on insights in the underlying mechanism, we developed a toolbox of engineering strategies to deterministically sculpt patterns and shapes, and combine different morphologies to create a landscape of hierarchical multi scale-complex tectonic architectures with unprecedented levels of complexity. These findings may hold profound implications for understanding, mimicking and ultimately expanding upon nature's morphogenesis strategies, allowing the synthesis of advanced highly complex microscale materials and devices. WLN acknowledges the Netherlands Organization for Scientific Research for financial support

Multi-frequency complex network from time series for uncovering oil-water flow structure.

PubMed

Gao, Zhong-Ke; Yang, Yu-Xuan; Fang, Peng-Cheng; Jin, Ning-De; Xia, Cheng-Yi; Hu, Li-Dan

2015-02-04

Uncovering complex oil-water flow structure represents a challenge in diverse scientific disciplines. This challenge stimulates us to develop a new distributed conductance sensor for measuring local flow signals at different positions and then propose a novel approach based on multi-frequency complex network to uncover the flow structures from experimental multivariate measurements. In particular, based on the Fast Fourier transform, we demonstrate how to derive multi-frequency complex network from multivariate time series. We construct complex networks at different frequencies and then detect community structures. Our results indicate that the community structures faithfully represent the structural features of oil-water flow patterns. Furthermore, we investigate the network statistic at different frequencies for each derived network and find that the frequency clustering coefficient enables to uncover the evolution of flow patterns and yield deep insights into the formation of flow structures. Current results present a first step towards a network visualization of complex flow patterns from a community structure perspective.

Light-driven dynamic Archimedes spirals and periodic oscillatory patterns of topological solitons in anisotropic soft matter

DOE PAGES

Martinez, Angel; Smalyukh, Ivan I.

2015-02-12

Oscillatory and excitable systems very commonly exhibit formation of dynamic non-equilibrium patterns. For example, rotating spiral patterns are observed in biological, chemical, and physical systems ranging from organization of slime mold cells to Belousov-Zhabotinsky reactions, and to crystal growth from nuclei with screw dislocations. Here we describe spontaneous formation of spiral waves and a large variety of other dynamic patterns in anisotropic soft matter driven by low-intensity light. The unstructured ambient or microscope light illumination of thin liquid crystal films in contact with a self-assembled azobenzene monolayer causes spontaneous formation, rich spatial organization, and dynamics of twisted domains and topologicalmore » solitons accompanied by the dynamic patterning of azobenzene group orientations within the monolayer. Linearly polarized incident light interacts with the twisted liquid crystalline domains, mimicking their dynamics and yielding patterns in the polarization state of transmitted light, which can be transformed to similar dynamic patterns in its intensity and interference color. This shows that the delicate light-soft-matter interaction can yield complex self-patterning of both. Finally, we uncover underpinning physical mechanisms and discuss potential uses.« less

Molecular engineering of polymersome surface topology

PubMed Central

Ruiz-Pérez, Lorena; Messager, Lea; Gaitzsch, Jens; Joseph, Adrian; Sutto, Ludovico; Gervasio, Francesco Luigi; Battaglia, Giuseppe

2016-01-01

Biological systems exploit self-assembly to create complex structures whose arrangements are finely controlled from the molecular to mesoscopic level. We report an example of using fully synthetic systems that mimic two levels of self-assembly. We show the formation of vesicles using amphiphilic copolymers whose chemical nature is chosen to control both membrane formation and membrane-confined interactions. We report polymersomes with patterns that emerge by engineering interfacial tension within the polymersome surface. This allows the formation of domains whose topology is tailored by chemical synthesis, paving the avenue to complex supramolecular designs functionally similar to those found in viruses and trafficking vesicles. PMID:27152331

Fabrication of 10 μm-scale conductive Cu patterns by selective laser sintering of Cu complex ink

NASA Astrophysics Data System (ADS)

Min, Hyungsuk; Lee, Byoungyoon; Jeong, Sooncheol; Lee, Myeongkyu

2017-02-01

A Cu complex ink was synthesized using copper formate as a precursor and its potential for laser patterning was investigated. The Cu ink was spin-coated onto a substrate and the coated film was space-selectively sintered using a nanosecond-pulsed ultraviolet laser. The unexposed Cu ink could be removed from the film by rinsing it with the dispersing agent used to synthesize the ink, disclosing a conductive Cu pattern. A minimum resistivity of 8.46×10-5 Ω cm was obtained for the Cu lines with 10-20 μm widths. The feasibility of this method for metallization was demonstrated by fabricating a complex Cu electric circuit on an indium tin oxide-coated glass substrate. The selective laser sintering approach provides a simple, cost-effective alternative to conventional lithography for the production of electrode or metallization patterns.

Core regulatory network motif underlies the ocellar complex patterning in Drosophila melanogaster

NASA Astrophysics Data System (ADS)

Aguilar-Hidalgo, D.; Lemos, M. C.; Córdoba, A.

2015-03-01

During organogenesis, developmental programs governed by Gene Regulatory Networks (GRN) define the functionality, size and shape of the different constituents of living organisms. Robustness, thus, is an essential characteristic that GRNs need to fulfill in order to maintain viability and reproducibility in a species. In the present work we analyze the robustness of the patterning for the ocellar complex formation in Drosophila melanogaster fly. We have systematically pruned the GRN that drives the development of this visual system to obtain the minimum pathway able to satisfy this pattern. We found that the mechanism underlying the patterning obeys to the dynamics of a 3-nodes network motif with a double negative feedback loop fed by a morphogenetic gradient that triggers the inhibition in a French flag problem fashion. A Boolean modeling of the GRN confirms robustness in the patterning mechanism showing the same result for different network complexity levels. Interestingly, the network provides a steady state solution in the interocellar part of the patterning and an oscillatory regime in the ocelli. This theoretical result predicts that the ocellar pattern may underlie oscillatory dynamics in its genetic regulation.

A Complex Network Analysis of Granular Fabric Evolution in Three-Dimensions

DTIC Science & Technology

2011-01-01

organized pattern formation (e.g., strain localization), and co-evolution of emergent in- ternal structures (e.g., force cycles and force chains) [15...these networks, particularly recurring patterns or motifs, and understanding how these co-evolve are crucial to the robust characterization and...the lead up to and during failure. Since failure patterns and boundaries of flow in three-dimensional specimens can be quite complicated and difficult

Formation mechanism of dot-line square superlattice pattern in dielectric barrier discharge

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Weibo; Dong, Lifang, E-mail: donglfhbu@163.com, E-mail: pyy1616@163.com; Wang, Yongjie

We investigate the formation mechanism of the dot-line square superlattice pattern (DLSSP) in dielectric barrier discharge. The spatio-temporal structure studied by using the intensified-charge coupled device camera shows that the DLSSP is an interleaving of three different subpatterns in one half voltage cycle. The dot square lattice discharges first and, then, the two kinds of line square lattices, which form square grid structures discharge twice. When the gas pressure is varied, DLSSP can transform from square superlattice pattern (SSP). The spectral line profile method is used to compare the electron densities, which represent the amounts of surface charges qualitatively. Itmore » is found that the amount of surface charges accumulated by the first discharge of DLSSP is less than that of SSP, leading to a bigger discharge area of the following discharge (lines of DLSSP instead of halos of SSP). The spatial distribution of the electric field of the surface charges is simulated to explain the formation of DLSSP. This paper may provide a deeper understanding for the formation mechanism of complex superlattice patterns in DBD.« less

Dyke-sill relationships in Karoo dolerites as indicators of propagation and emplacement processes of mafic magmas in the shallow crust

NASA Astrophysics Data System (ADS)

Coetzee, A.; Kisters, A. F. M.

2017-04-01

This paper describes the spatial and temporal relationships between Karoo-age (ca. 180 Ma) dolerite dykes and a regional-scale saucer-sill complex from the Secunda (coal mine) Complex in the northeastern parts of the Karoo Basin of South Africa. Unlike parallel dyke swarms of regional extensional settings, mafic dykes commonly show curved geometries and highly variable orientations, short strike extents and complex cross-cutting and intersecting relationships. Importantly, the dyke networks originate from the upper contacts of the first-order dolerite sill-saucer structure and are not the feeders of the saucer complex. Cross-cutting relationships indicate the largely contemporaneous formation of dykes and the inner sill and inclined sheets of the underlying saucer. Systematic dykes form a distinct boxwork-type pattern of two high-angle, interconnected dyke sets. The formation and orientation of this dyke set is interpreted to be related to the stretching of roof strata above elongated magma lobes that facilitated the propagation of the inner sill, similar to the "cracked lid" model described for large saucer complexes in Antarctica. Dyke patterns generally reflect the saucer emplacement process and the associated deformation of wall rocks rather than far-field regional stresses.

The structure and evolution of galacto-detonation waves - Some analytic results in sequential star formation models of spiral galaxies

NASA Technical Reports Server (NTRS)

Cowie, L. L.; Rybicki, G. B.

1982-01-01

Waves of star formation in a uniform, differentially rotating disk galaxy are treated analytically as a propagating detonation wave front. It is shown, that if single solitary waves could be excited, they would evolve asymptotically to one of two stable spiral forms, each of which rotates with a fixed pattern speed. Simple numerical solutions confirm these results. However, the pattern of waves that develop naturally from an initially localized disturbance is more complex and dies out within a few rotation periods. These results suggest a conclusive observational test for deciding whether sequential star formation is an important determinant of spiral structure in some class of galaxies.

Wilson Cycle studies

NASA Technical Reports Server (NTRS)

Burke, Kevin

1987-01-01

Regional lineaments in continental evolution were studied. It was concluded that lineaments within continents are attributed to a small number of processes of continent formation and modification, but interactions among these processes may produce complex patterns.

Spatial-pattern-induced evolution of a self-replicating loop network.

PubMed

Suzuki, Keisuke; Ikegami, Takashi

2006-01-01

We study a system of self-replicating loops in which interaction rules between individuals allow competition that leads to the formation of a hypercycle-like network. The main feature of the model is the multiple layers of interaction between loops, which lead to both global spatial patterns and local replication. The network of loops manifests itself as a spiral structure from which new kinds of self-replicating loops emerge at the boundaries between different species. In these regions, larger and more complex self-replicating loops live for longer periods of time, managing to self-replicate in spite of their slower replication. Of particular interest is how micro-scale interactions between replicators lead to macro-scale spatial pattern formation, and how these macro-scale patterns in turn perturb the micro-scale replication dynamics.

A Chaperone Complex Formed by HSP47, FKBP65 and BiP Modulates Telopeptide Lysyl Hydroxylation of Type I Procollagen

PubMed Central

Duran, Ivan; Martin, Jorge H.; Weis, Mary Ann; Krejci, Pavel; Konik, Peter; Li, Bing; Alanay, Yasemin; Lietman, Caressa; Lee, Brendan; Eyre, David; Cohn, Daniel H.; Krakow, Deborah

2017-01-01

Lysine hydroxylation of type I collagen telopeptides varies from tissue to tissue and these distinct hydroxylation patterns modulate collagen crosslinking to generate a unique extracellular matrix. Abnormalities in these patterns contribute to pathologies that include osteogenesis imperfecta (OI), fibrosis and cancer. Telopeptide procollagen modifications are carried out by lysyl hydroxylase 2 (LH2), however, little is known regarding how this enzyme regulates hydroxylation patterns. We identified an ER complex of resident chaperones that includes HSP47, FKBP65 and BiP regulating the activity of LH2. Our findings show that FKBP65 and HSP47 modulate the activity of LH2 to either favor or repress its activity. BiP was also identified as a member of the complex, playing a role in enhancing the formation of the complex. This newly identified ER chaperone complex contributes to our understanding of how LH2 regulates lysyl hydroxylation of type I collagen C-telopeptides to affect the quality of connective tissues. PMID:28177155

Neuromechanical factors involved in the formation and propulsion of fecal pellets in the guinea-pig colon.

PubMed

Costa, M; Wiklendt, L; Simpson, P; Spencer, N J; Brookes, S J; Dinning, P G

2015-10-01

The neuromechanical processes involved in the formation and propulsion of fecal pellets remain incompletely understood. We analyzed motor patterns in isolated segments of the guinea-pig proximal and distal colon, using video imaging, during oral infusion of liquid, viscous material, or solid pellets. Colonic migrating motor complexes (CMMCs) in the proximal colon divided liquid or natural semisolid contents into elongated shallow boluses. At the colonic flexure these boluses were formed into shorter, pellet-shaped boluses. In the non-distended distal colon, spontaneous CMMCs produced small dilations. Both high- and low-viscosity infusions evoked a distinct motor pattern that produced pellet-shaped boluses. These were propelled at speeds proportional to their surface area. Solid pellets were propelled at a speed that increased with diameter, to a maximum that matched the diameter of natural pellets. Pellet speed was reduced by increasing resistive load. Tetrodotoxin blocked all propulsion. Hexamethonium blocked normal motor patterns, leaving irregular propagating contractions, indicating the existence of neural pathways that did not require nicotinic transmission. Colonic migrating motor complexes are responsible for the slow propulsion of the soft fecal content in the proximal colon, while the formation of pellets at the colonic flexure involves a content-dependent mechanism in combination with content-independent spontaneous CMMCs. Bolus size and consistency affects propulsion speed suggesting that propulsion is not a simple reflex but rather a more complex process involving an adaptable neuromechanical loop. © 2015 John Wiley & Sons Ltd.

Pattern Formation in Complex Fluids

NASA Astrophysics Data System (ADS)

Shelley, Michael

2000-03-01

Classical fluid instabilities -- such as the Saffman-Taylor instability in a Hele-Shaw cell -- are dramatically modified by using complex fluids. For example, polymeric liquids driven in a Hele-Shaw cell yield "dendritic" patterns with an apparent directional anisotropy. The dynamics of complex liquids can also lead to new instabilities and patterns, such as space-filling patterns formed by successive bucklings of growing "elastica" seen in the phase transition of a liquid crystalline material. Understanding such problems requires an interplay between physical modeling, mathematical analysis, and sophisticated nonlinear simulation. For the first problem, I will discuss a non-Newtonian version of Darcy's law for Hele-Shaw flow. This yields a free-boundary problem for the pattern formation, and requires the solution of a nonlinear elliptic equation in a time-dependent domain. This is pushing the development of adaptive grid methods that represent the geometry accurately and efficiently. Our simulations yield insight into how shear-thinning, as is evinced by polymeric liquids, can produce patterns reminiscent of experiment, with "dendritic fingers", side-branching, and reduced tip-splitting. In the second problem, a long filament in a smectic-A phase grows within an isotropic fluid. The splay deformation of the material gives this filament an elastic response. The macroscopic model describes the dynamics of a growing, elastic filament immersed in a Stokesian fluid. The model marries filament elasticity and tensile forces with a numerically tractable nonlocal slender-body theory. Analysis shows that growth of the filament, despite fluid drag, produces a buckling instability. When coupled to a nonlocal hydrodynamic self-interaction, our fully nonlinear simulations show that such instabilities iterate along the filament, and give "space-filling" patterns.

Non-Linear Pattern Formation in Bone Growth and Architecture

PubMed Central

Salmon, Phil

2014-01-01

The three-dimensional morphology of bone arises through adaptation to its required engineering performance. Genetically and adaptively bone travels along a complex spatiotemporal trajectory to acquire optimal architecture. On a cellular, micro-anatomical scale, what mechanisms coordinate the activity of osteoblasts and osteoclasts to produce complex and efficient bone architectures? One mechanism is examined here – chaotic non-linear pattern formation (NPF) – which underlies in a unifying way natural structures as disparate as trabecular bone, swarms of birds flying, island formation, fluid turbulence, and others. At the heart of NPF is the fact that simple rules operating between interacting elements, and Turing-like interaction between global and local signals, lead to complex and structured patterns. The study of “group intelligence” exhibited by swarming birds or shoaling fish has led to an embodiment of NPF called “particle swarm optimization” (PSO). This theoretical model could be applicable to the behavior of osteoblasts, osteoclasts, and osteocytes, seeing them operating “socially” in response simultaneously to both global and local signals (endocrine, cytokine, mechanical), resulting in their clustered activity at formation and resorption sites. This represents problem-solving by social intelligence, and could potentially add further realism to in silico computer simulation of bone modeling. What insights has NPF provided to bone biology? One example concerns the genetic disorder juvenile Pagets disease or idiopathic hyperphosphatasia, where the anomalous parallel trabecular architecture characteristic of this pathology is consistent with an NPF paradigm by analogy with known experimental NPF systems. Here, coupling or “feedback” between osteoblasts and osteoclasts is the critical element. This NPF paradigm implies a profound link between bone regulation and its architecture: in bone the architecture is the regulation. The former is the emergent consequence of the latter. PMID:25653638

Non-linear pattern formation in bone growth and architecture.

PubMed

Salmon, Phil

2014-01-01

The three-dimensional morphology of bone arises through adaptation to its required engineering performance. Genetically and adaptively bone travels along a complex spatiotemporal trajectory to acquire optimal architecture. On a cellular, micro-anatomical scale, what mechanisms coordinate the activity of osteoblasts and osteoclasts to produce complex and efficient bone architectures? One mechanism is examined here - chaotic non-linear pattern formation (NPF) - which underlies in a unifying way natural structures as disparate as trabecular bone, swarms of birds flying, island formation, fluid turbulence, and others. At the heart of NPF is the fact that simple rules operating between interacting elements, and Turing-like interaction between global and local signals, lead to complex and structured patterns. The study of "group intelligence" exhibited by swarming birds or shoaling fish has led to an embodiment of NPF called "particle swarm optimization" (PSO). This theoretical model could be applicable to the behavior of osteoblasts, osteoclasts, and osteocytes, seeing them operating "socially" in response simultaneously to both global and local signals (endocrine, cytokine, mechanical), resulting in their clustered activity at formation and resorption sites. This represents problem-solving by social intelligence, and could potentially add further realism to in silico computer simulation of bone modeling. What insights has NPF provided to bone biology? One example concerns the genetic disorder juvenile Pagets disease or idiopathic hyperphosphatasia, where the anomalous parallel trabecular architecture characteristic of this pathology is consistent with an NPF paradigm by analogy with known experimental NPF systems. Here, coupling or "feedback" between osteoblasts and osteoclasts is the critical element. This NPF paradigm implies a profound link between bone regulation and its architecture: in bone the architecture is the regulation. The former is the emergent consequence of the latter.

Pattern formation in mass conserving reaction-diffusion systems

NASA Astrophysics Data System (ADS)

Brauns, Fridtjof; Halatek, Jacob; Frey, Erwin

We present a rigorous theoretical framework able to generalize and unify pattern formation for quantitative mass conserving reaction-diffusion models. Mass redistribution controls chemical equilibria locally. Separation of diffusive mass redistribution on the level of conserved species provides a general mathematical procedure to decompose complex reaction-diffusion systems into effectively independent functional units, and to reveal the general underlying bifurcation scenarios. We apply this framework to Min protein pattern formation and identify the mechanistic roles of both involved protein species. MinD generates polarity through phase separation, whereas MinE takes the role of a control variable regulating the existence of MinD phases. Hence, polarization and not oscillations is the generic core dynamics of Min proteins in vivo. This establishes an intrinsic mechanistic link between the Min system and a broad class of intracellular pattern forming systems based on bistability and phase separation (wave-pinning). Oscillations are facilitated by MinE redistribution and can be understood mechanistically as relaxation oscillations of the polarization direction.

Experimental investigation of the dynamics of spontaneous pattern formation during dendritic ice crystal growth

NASA Astrophysics Data System (ADS)

Tirmizi, Shakeel H.; Gill, William N.

1989-06-01

The dynamics of spontaneous pattern formation are studied experimentally by observing and recording the evolution of ice crystal patterns which grow freely in a supercooled melt. The sequence of evolution to dendrites is recorded in real time using cine-micrography. In the range of subcoolings from 0.06 to 0.29°C, all the patterns evolved as follows: Smooth disk → Perturbed disk → Disk dendrite → Partially developed dendrite → Fully developed dendrite. The initial smooth disk, the main branch and the side branches all developed perturbations beyond a critical size which depends on the subcooling. The combined effect of the destabilizing thermal gradients ahead of the growing crystal and the stabilizing Gibbs-Thompson capillarity effect dictates the critical size of the unstable structures in terms of the mean curvature of the interface. Detailed analysis of the evolving patterns was done using digital image analysis on the PRIME computer to determine both the manner in which the dendritic growth process replicates itself and the role which the shape and the movement of the interface play in the pattern formation process. Total arc length ST, total area A and the complexity ratio ξ = ST⧸√ A of evolving patterns were computed as a function of time and undercooling for each crystal image. These results permitted us to make some comparisons with theoretical models on pattern evolution. Three distinct phases of evolution were identified: the initial phase when the crystal structure is smooth and free of any perturbations and the complexity ratio is almost a constant, an intermediate phase when the crystal structure develops perturbations which grow quickly in number and in size and the complexity ratio increases rapidly and a final phase when the pattern approaches that of a fully developed dendrite which, on a global scale grows in a shape-perserving manner and has a slowly increasing complexity ratio which seems to approach an asymptote. Two factors were found to be responsible for the symmetric dendritic patterns. These are: first, hexagonal symmetry due to the hexagonal closed packed structure, leads to strong anisotropy in molecular attachment kinetics and in surface free energy; second, the competition among side branches causes smaller side branches to melt when they are trapped between larger ones which generate latent heat and prevent the small branches from gaining access to the fresh cold fluid ahead of them. These two factors lead to a channelling effect which prevents the growth of perturbations from occurring randomly and thus directs the evolving crystal structure into patterns which are regular and reproducible. Theoretical models which are local in nature fail to take into account side branch competition, and this is one of their major weaknesses.

Crustal fingering: solidification on a viscously unstable interface

NASA Astrophysics Data System (ADS)

Fu, Xiaojing; Jimenez-Martinez, Joaquin; Cueto-Felgueroso, Luis; Porter, Mark; Juanes, Ruben

2017-11-01

Motivated by the formation of gas hydrates in seafloor sediments, here we study the volumetric expansion of a less viscous gas pocket into a more viscous liquid when the gas-liquid interfaces readily solidify due to hydrate formation. We first present a high-pressure microfluidic experiment to study the depressurization-controlled expansion of a Xenon gas pocket in a water-filled Hele-Shaw cell. The evolution of the pocket is controlled by three processes: (1) volumetric expansion of the gas; (2) rupturing of existing hydrate films on the gas-liquid interface; and (3) formation of new hydrate films. These result in gas fingering leading to a complex labyrinth pattern. To reproduce these observations, we propose a phase-field model that describes the formation of hydrate shell on viscously unstable interfaces. We design the free energy of the three-phase system to rigorously account for interfacial effects, gas compressibility and phase transitions. We model the hydrate shell as a highly viscous fluid with shear-thinning rheology to reproduce shell-rupturing behavior. We present high-resolution numerical simulations of the model, which illustrate the emergence of complex crustal fingering patterns as a result of gas expansion dynamics modulated by hydrate growth at the interface.

Candidate gene screen in the red flour beetle Tribolium reveals six3 as ancient regulator of anterior median head and central complex development.

PubMed

Posnien, Nico; Koniszewski, Nikolaus Dieter Bernhard; Hein, Hendrikje Jeannette; Bucher, Gregor

2011-12-01

Several highly conserved genes play a role in anterior neural plate patterning of vertebrates and in head and brain patterning of insects. However, head involution in Drosophila has impeded a systematic identification of genes required for insect head formation. Therefore, we use the red flour beetle Tribolium castaneum in order to comprehensively test the function of orthologs of vertebrate neural plate patterning genes for a function in insect head development. RNAi analysis reveals that most of these genes are indeed required for insect head capsule patterning, and we also identified several genes that had not been implicated in this process before. Furthermore, we show that Tc-six3/optix acts upstream of Tc-wingless, Tc-orthodenticle1, and Tc-eyeless to control anterior median development. Finally, we demonstrate that Tc-six3/optix is the first gene known to be required for the embryonic formation of the central complex, a midline-spanning brain part connected to the neuroendocrine pars intercerebralis. These functions are very likely conserved among bilaterians since vertebrate six3 is required for neuroendocrine and median brain development with certain mutations leading to holoprosencephaly.

Candidate Gene Screen in the Red Flour Beetle Tribolium Reveals Six3 as Ancient Regulator of Anterior Median Head and Central Complex Development

PubMed Central

Hein, Hendrikje Jeannette; Bucher, Gregor

2011-01-01

Several highly conserved genes play a role in anterior neural plate patterning of vertebrates and in head and brain patterning of insects. However, head involution in Drosophila has impeded a systematic identification of genes required for insect head formation. Therefore, we use the red flour beetle Tribolium castaneum in order to comprehensively test the function of orthologs of vertebrate neural plate patterning genes for a function in insect head development. RNAi analysis reveals that most of these genes are indeed required for insect head capsule patterning, and we also identified several genes that had not been implicated in this process before. Furthermore, we show that Tc-six3/optix acts upstream of Tc-wingless, Tc-orthodenticle1, and Tc-eyeless to control anterior median development. Finally, we demonstrate that Tc-six3/optix is the first gene known to be required for the embryonic formation of the central complex, a midline-spanning brain part connected to the neuroendocrine pars intercerebralis. These functions are very likely conserved among bilaterians since vertebrate six3 is required for neuroendocrine and median brain development with certain mutations leading to holoprosencephaly. PMID:22216011

Network-based high level data classification.

PubMed

Silva, Thiago Christiano; Zhao, Liang

2012-06-01

Traditional supervised data classification considers only physical features (e.g., distance or similarity) of the input data. Here, this type of learning is called low level classification. On the other hand, the human (animal) brain performs both low and high orders of learning and it has facility in identifying patterns according to the semantic meaning of the input data. Data classification that considers not only physical attributes but also the pattern formation is, here, referred to as high level classification. In this paper, we propose a hybrid classification technique that combines both types of learning. The low level term can be implemented by any classification technique, while the high level term is realized by the extraction of features of the underlying network constructed from the input data. Thus, the former classifies the test instances by their physical features or class topologies, while the latter measures the compliance of the test instances to the pattern formation of the data. Our study shows that the proposed technique not only can realize classification according to the pattern formation, but also is able to improve the performance of traditional classification techniques. Furthermore, as the class configuration's complexity increases, such as the mixture among different classes, a larger portion of the high level term is required to get correct classification. This feature confirms that the high level classification has a special importance in complex situations of classification. Finally, we show how the proposed technique can be employed in a real-world application, where it is capable of identifying variations and distortions of handwritten digit images. As a result, it supplies an improvement in the overall pattern recognition rate.

Reverse and forward engineering of protein pattern formation.

PubMed

Kretschmer, Simon; Harrington, Leon; Schwille, Petra

2018-05-26

Living systems employ protein pattern formation to regulate important life processes in space and time. Although pattern-forming protein networks have been identified in various prokaryotes and eukaryotes, their systematic experimental characterization is challenging owing to the complex environment of living cells. In turn, cell-free systems are ideally suited for this goal, as they offer defined molecular environments that can be precisely controlled and manipulated. Towards revealing the molecular basis of protein pattern formation, we outline two complementary approaches: the biochemical reverse engineering of reconstituted networks and the de novo design, or forward engineering, of artificial self-organizing systems. We first illustrate the reverse engineering approach by the example of the Escherichia coli Min system, a model system for protein self-organization based on the reversible and energy-dependent interaction of the ATPase MinD and its activating protein MinE with a lipid membrane. By reconstituting MinE mutants impaired in ATPase stimulation, we demonstrate how large-scale Min protein patterns are modulated by MinE activity and concentration. We then provide a perspective on the de novo design of self-organizing protein networks. Tightly integrated reverse and forward engineering approaches will be key to understanding and engineering the intriguing phenomenon of protein pattern formation.This article is part of the theme issue 'Self-organization in cell biology'. © 2018 The Author(s).

Comparing DNA damage-processing pathways by computer analysis of chromosome painting data.

PubMed

Levy, Dan; Vazquez, Mariel; Cornforth, Michael; Loucas, Bradford; Sachs, Rainer K; Arsuaga, Javier

2004-01-01

Chromosome aberrations are large-scale illegitimate rearrangements of the genome. They are indicative of DNA damage and informative about damage processing pathways. Despite extensive investigations over many years, the mechanisms underlying aberration formation remain controversial. New experimental assays such as multiplex fluorescent in situ hybridyzation (mFISH) allow combinatorial "painting" of chromosomes and are promising for elucidating aberration formation mechanisms. Recently observed mFISH aberration patterns are so complex that computer and graph-theoretical methods are needed for their full analysis. An important part of the analysis is decomposing a chromosome rearrangement process into "cycles." A cycle of order n, characterized formally by the cyclic graph with 2n vertices, indicates that n chromatin breaks take part in a single irreducible reaction. We here describe algorithms for computing cycle structures from experimentally observed or computer-simulated mFISH aberration patterns. We show that analyzing cycles quantitatively can distinguish between different aberration formation mechanisms. In particular, we show that homology-based mechanisms do not generate the large number of complex aberrations, involving higher-order cycles, observed in irradiated human lymphocytes.

Beyond Molecular Codes: Simple Rules to Wire Complex Brains

PubMed Central

Hassan, Bassem A.; Hiesinger, P. Robin

2015-01-01

Summary Molecular codes, like postal zip codes, are generally considered a robust way to ensure the specificity of neuronal target selection. However, a code capable of unambiguously generating complex neural circuits is difficult to conceive. Here, we re-examine the notion of molecular codes in the light of developmental algorithms. We explore how molecules and mechanisms that have been considered part of a code may alternatively implement simple pattern formation rules sufficient to ensure wiring specificity in neural circuits. This analysis delineates a pattern-based framework for circuit construction that may contribute to our understanding of brain wiring. PMID:26451480

Programming Cells for Dynamic Assembly of Inorganic Nano-Objects with Spatiotemporal Control.

PubMed

Wang, Xinyu; Pu, Jiahua; An, Bolin; Li, Yingfeng; Shang, Yuequn; Ning, Zhijun; Liu, Yi; Ba, Fang; Zhang, Jiaming; Zhong, Chao

2018-04-01

Programming living cells to organize inorganic nano-objects (NOs) in a spatiotemporally precise fashion would advance new techniques for creating ordered ensembles of NOs and new bio-abiotic hybrid materials with emerging functionalities. Bacterial cells often grow in cellular communities called biofilms. Here, a strategy is reported for programming dynamic biofilm formation for the synchronized assembly of discrete NOs or hetero-nanostructures on diverse interfaces in a dynamic, scalable, and hierarchical fashion. By engineering Escherichia coli to sense blue light and respond by producing biofilm curli fibers, biofilm formation is spatially controlled and the patterned NOs' assembly is simultaneously achieved. Diverse and complex fluorescent quantum dot patterns with a minimum patterning resolution of 100 µm are demonstrated. By temporally controlling the sequential addition of NOs into the culture, multilayered heterostructured thin films are fabricated through autonomous layer-by-layer assembly. It is demonstrated that biologically dynamic self-assembly can be used to advance a new repertoire of nanotechnologies and materials with increasing complexity that would be otherwise challenging to produce. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Dermatoglyphics--a possible biomarker in the neurodevelopmental model for the origin of mental disorders.

PubMed

Ahmed-Popova, Ferihan M; Mantarkov, Mladen J; Sivkov, Stefan T; Akabaliev, Valentin H

2014-01-01

Dermatoglyphic pattern formation and differentiation are complex processes which have been in the focus of research interest ever since dermatoglyphics became a science. The patterns' early differentiation and genetic uniqueness as well as the relatively simple methods used to obtain and store fingerprints make it possible to study the relationship between certain dermatoglyphic characteristics and the underlying pathological processes in a number of diseases, including mental disorders. The present review reports published data from fundamental and clinical studies on dermatoglyphics primarily in schizophrenia and bipolar disorder to lend additional support for the neurodevelopmental hypothesis in the etiology of these disorders. Following an analysis of the theories of dermatoglyphics formation and the complex association between ridge patterns and central nervous system in early embryogenesis, an attempt is made to present dermatoglyphics as possible biological markers of impaired neurodevelopment. The contradictory data in the literature on dermatoglyphics in mental disorders suggest the need for further studies on these biological markers in order to identify their place in the neurodevelopmental etiological model of these diseases.

Spatial pattern formation of microbes at the soil microscale affect soil C and N turnover in an individual-based microbial community model

NASA Astrophysics Data System (ADS)

Kaiser, Christina; Evans, Sarah; Dieckmann, Ulf; Widder, Stefanie

2016-04-01

At the μm-scale, soil is a highly structured and complex environment, both in physical as well as in biological terms, characterized by non-linear interactions between microbes, substrates and minerals. As known from mathematics and theoretical ecology, spatial structure significantly affects the system's behaviour by enabling synergistic dynamics, facilitating diversity, and leading to emergent phenomena such as self-organisation and self-regulation. Such phenomena, however, are rarely considered when investigating mechanisms of microbial soil organic matter turnover. Soil organic matter is the largest terrestrial reservoir for organic carbon (C) and nitrogen (N) and plays a pivotal role in global biogeochemical cycles. Still, the underlying mechanisms of microbial soil organic matter buildup and turnover remain elusive. We explored mechanisms of microbial soil organic matter turnover using an individual-based, stoichiometrically and spatially explicit computer model, which simulates the microbial de-composer system at the soil microscale (i.e. on a grid of 100 x 100 soil microsites). Soil organic matter dynamics in our model emerge as the result of interactions among individual microbes with certain functional traits (f.e. enzyme production rates, growth rates, cell stoichiometry) at the microscale. By degrading complex substrates, and releasing labile substances microbes in our model continusly shape their environment, which in turn feeds back to spatiotemporal dynamics of the microbial community. In order to test the effect of microbial functional traits and organic matter input rate on soil organic matter turnover and C and N storage, we ran the model into steady state using continuous inputs of fresh organic material. Surprisingly, certain parameter settings that induce resource limitation of microbes lead to regular spatial pattern formation (f.e. moving spiral waves) of microbes and substrate at the μm-scale at steady-state. The occurrence of these pattern can be explained by the Turing mechanism. These pattern formation had strong consequences for process rates, as well as for C and N storage in the soil at the steady state: Scenarios that exhibited pattern formation were generally associated with higher C storage at steady state compared to those without pattern formation (i.e. at non-limiting conditions for microbes). Moreover, pattern formation lead to a spatial decoupling of C and N turnover processes, and to a spatial decoupling of microbial N mineralization and N immobilization. Taken together, our theoretical analysis shows that self-organisation may be a feature of the soil decomposer system, with consequences for process rates of microbial C and N turnover. Pattern formation through spatial self-organization, which has been observed on larger spatial scales in other resource-limited communities (e.g., vegetation patterns in arid or wetland eco-systems), may also occur at the soil microscale, leaving its mark on the soil's storage capacity for C and N.

Quantitative assessment of Hox complex expression in the indirect development of the polychaete annelid Chaetopterus sp

NASA Technical Reports Server (NTRS)

Peterson, K. J.; Irvine, S. Q.; Cameron, R. A.; Davidson, E. H.

2000-01-01

A prediction from the set-aside theory of bilaterian origins is that pattern formation processes such as those controlled by the Hox cluster genes are required specifically for adult body plan formation. This prediction can be tested in animals that use maximal indirect development, in which the embryonic formation of the larva and the postembryonic formation of the adult body plan are temporally and spatially distinct. To this end, we quantitatively measured the amount of transcripts for five Hox genes in embryos of a lophotrochozoan, the polychaete annelid Chaetopterus sp. The polychaete Hox complex is shown not to be expressed during embryogenesis, but transcripts of all measured Hox complex genes are detected at significant levels during the initial stages of adult body plan formation. Temporal colinearity in the sequence of their activation is observed, so that activation follows the 3'-5' arrangement of the genes. Moreover, Hox gene expression is spatially localized to the region of teloblastic set-aside cells of the later-stage embryos. This study shows that an indirectly developing lophotrochozoan shares with an indirectly developing deuterostome, the sea urchin, a common mode of Hox complex utilization: construction of the larva, whether a trochophore or dipleurula, does not involve Hox cluster expression, but in both forms the complex is expressed in the set-aside cells from which the adult body plan derives.

Integument pattern formation involves genetic and epigenetic controls: feather arrays simulated by digital hormone models

PubMed Central

Jiang, Ting-Xin; Widelitz, Randall B.; Shen, Wei-Min; Will, Peter; Wu, Da-Yu; Lin, Chih-Min; Jung, Han-Sung; Chuong, Cheng-Ming

2015-01-01

Pattern formation is a fundamental morphogenetic process. Models based on genetic and epigenetic control have been proposed but remain controversial. Here we use feather morphogenesis for further evaluation. Adhesion molecules and/or signaling molecules were first expressed homogenously in feather tracts (restrictive mode, appear earlier) or directly in bud or inter-bud regions (de novo mode, appear later). They either activate or inhibit bud formation, but paradoxically co-localize in the bud. Using feather bud reconstitution, we showed that completely dissociated cells can reform periodic patterns without reference to previous positional codes. The patterning process has the characteristics of being self-organizing, dynamic and plastic. The final pattern is an equilibrium state reached by competition, and the number and size of buds can be altered based on cell number and activator/inhibitor ratio, respectively. We developed a Digital Hormone Model which consists of (1) competent cells without identity that move randomly in a space, (2) extracellular signaling hormones which diffuse by a reaction-diffusion mechanism and activate or inhibit cell adhesion, and (3) cells which respond with topological stochastic actions manifested as changes in cell adhesion. Based on probability, the results are cell clusters arranged in dots or stripes. Thus genetic control provides combinational molecular information which defines the properties of the cells but not the final pattern. Epigenetic control governs interactions among cells and their environment based on physical-chemical rules (such as those described in the Digital Hormone Model). Complex integument patterning is the sum of these two components of control and that is why integument patterns are usually similar but non-identical. These principles may be shared by other pattern formation processes such as barb ridge formation, fingerprints, pigmentation patterning, etc. The Digital Hormone Model can also be applied to swarming robot navigation, reaching intelligent automata and representing a self-re-configurable type of control rather than a follow-the-instruction type of control. PMID:15272377

Turing-like structures in a functional model of cortical spreading depression

NASA Astrophysics Data System (ADS)

Verisokin, A. Yu.; Verveyko, D. V.; Postnov, D. E.

2017-12-01

Cortical spreading depression (CSD) along with migraine waves and spreading depolarization events with stroke or injures are the front-line examples of extreme physiological behaviors of the brain cortex which manifest themselves via the onset and spreading of localized areas of neuronal hyperactivity followed by their depression. While much is known about the physiological pathways involved, the dynamical mechanisms of the formation and evolution of complex spatiotemporal patterns during CSD are still poorly understood, in spite of the number of modeling studies that have been already performed. Recently we have proposed a relatively simple mathematical model of cortical spreading depression which counts the effects of neurovascular coupling and cerebral blood flow redistribution during CSD. In the present study, we address the main dynamical consequences of newly included pathways, namely, the changes in the formation and propagation speed of the CSD front and the pattern formation features in two dimensions. Our most notable finding is that the combination of vascular-mediated spatial coupling with local regulatory mechanisms results in the formation of stationary Turing-like patterns during a CSD event.

Using micro-patterned surfaces to inhibit settlement and biofilm formation by Bacillus subtilis.

PubMed

Chang, Siyuan; Chen, Xiaodong; Jiang, Shuo; Chen, Jinchun; Shi, Lin

2017-07-01

Biofilm is a biological complex caused by bacteria attachment to the substrates and their subsequent reproduction and secretion. This phenomenon reduces heat transfer efficiency and causes significant losses in treated sewage heat-recovering systems. This paper describes a physical approach to inhibit bacteria settlement and biofilm formation by Bacillus subtilis, which is the dominant species in treated sewage. Here, micro-patterned surfaces with different characteristics (stripe and cube) and dimensions (1-100 μm) were fabricated as surfaces of interest. Model sewage was prepared and a rotating coupon device was used to form the biofilms. Precision balance, scanning electron microscopy, and confocal laser scanning microscopy (CLSM) were employed to investigate the inhibitory effects and the mechanisms of the biofilm-surface interactions. The results have shown that surfaces with small pattern sizes (1 and 2 μm) all reduced biofilm formation significantly. Interestingly, the CLSM images showed that the surfaces do not play a role in "killing" the bacteria. These findings are useful for future development of new process surfaces on which bacteria settlement and biofilm formation can be inhibited or minimized.

Contribution to the understanding of how principal component analysis-derived dietary patterns emerge from habitual data on food consumption.

PubMed

Schwedhelm, Carolina; Iqbal, Khalid; Knüppel, Sven; Schwingshackl, Lukas; Boeing, Heiner

2018-02-01

Principal component analysis (PCA) is a widely used exploratory method in epidemiology to derive dietary patterns from habitual diet. Such dietary patterns seem to originate from intakes on multiple days and eating occasions. Therefore, analyzing food intake of study populations with different levels of food consumption can provide additional insights as to how habitual dietary patterns are formed. We analyzed the food intake data of German adults in terms of the relations among food groups from three 24-h dietary recalls (24hDRs) on the habitual, single-day, and main-meal levels, and investigated the contribution of each level to the formation of PCA-derived habitual dietary patterns. Three 24hDRs were collected in 2010-2012 from 816 adults for an European Prospective Investigation into Cancer and Nutrition (EPIC)-Potsdam subcohort study. We identified PCA-derived habitual dietary patterns and compared cross-sectional food consumption data in terms of correlation (Spearman), consistency (intraclass correlation coefficient), and frequency of consumption across all days and main meals. Contribution to the formation of the dietary patterns was obtained through Spearman correlation of the dietary pattern scores. Among the meals, breakfast appeared to be the most consistent eating occasion within individuals. Dinner showed the strongest correlations with "Prudent" (Spearman correlation = 0.60), "Western" (Spearman correlation = 0.59), and "Traditional" (Spearman correlation = 0.60) dietary patterns identified on the habitual level, and lunch showed the strongest correlations with the "Cereals and legumes" (Spearman correlation = 0.60) habitual dietary pattern. Higher meal consistency was related to lower contributions to the formation of PCA-derived habitual dietary patterns. Absolute amounts of food consumption did not strongly conform to the habitual dietary patterns by meals, suggesting that these patterns are formed by complex combinations of variable food consumption across meals. Dinner showed the highest contribution to the formation of habitual dietary patterns. This study provided information about how PCA-derived dietary patterns are formed and how they could be influenced.

A Rich Morphological Diversity of Biosaline Drying Patterns Is Generated by Different Bacterial Species, Different Salts and Concentrations: Astrobiological Implications

NASA Astrophysics Data System (ADS)

Gómez Gómez, José María; Medina, Jesús; Rull, Fernando

2016-07-01

Biosaline formations (BSFs) are complex self-organized biomineral patterns formed by "hibernating" bacteria as the biofilm that contains them dries out. They were initially described in drying biofilms of Escherichia coli cells + NaCl. Due to their intricate 3-D morphology and anhydrobiosis, these biomineralogical structures are of great interest in astrobiology. Here we report experimental data obtained with various alkali halide salts (NaF, NaCl, NaBr, LiCl, KCl, CsCl) on BSF formation with E. coli and Bacillus subtilis bacteria at two saline concentrations: 9 and 18 mg/mL. Our results indicate that, except for LiCl, which is inactive, all the salts assayed are active during BSF formation and capable of promoting the generation of distinctive drying patterns at each salt concentration. Remarkably, the BSFs produced by these two bacterial species produce characteristic architectural hallmarks as the BSF dries. The potential biogenicity of these biosaline drying patterns is studied, and the astrobiological implications of these findings are discussed.

The effect of butterfly-scale inspired patterning on leading-edge vortex growth

NASA Astrophysics Data System (ADS)

Wilroy, Jacob; Lang, Amy; Wahidi, Redha

2014-11-01

Leading edge vortices (LEVs) are important for generating thrust and lift in flapping flight, and the surface patterning (scales) on butterfly wings is hypothesized to play a role in the vortex formation of the LEV. To simplify this complex flow problem, we designed an experiment to focus on the alteration of 2-D vortex development with a variation in surface patterning. Specifically we are interested in the secondary vorticity generated by the LEV interacting at the patterned surface and how this can affect the growth rate of the circulation in the LEV. For this experiment we used rapid-prototyped longitudinal and transverse square grooves attached to a flat plate and compared the vortex formation as the plate moved vertically. The plate is impulsively started in quiescent water and flow fields at Re = 1500, 3000, and 6000 are examined using Digital Particle Image Velocimetry (DPIV). The vortex formation time is 0.6 and is based on the flat plate travel length and chord length. Support for this research came from NSF REU Grant 1358991 and CBET 1335848.

The effect of butterfly-scale inspired patterning on leading-edge vortex growth

NASA Astrophysics Data System (ADS)

Wilroy, Jacob; Lang, Amy

2015-11-01

Leading edge vortices (LEVs) are important for generating thrust and lift in flapping flight, and the surface patterning (scales) on butterfly wings is hypothesized to play a role in the vortex formation of the LEV. To simplify this complex flow problem, an experiment was designed to focus on the alteration of 2-D vortex development with a variation in surface patterning. Specifically, the secondary vorticity generated by the LEV interacting at the patterned surface was studied and the subsequent affect on the growth rate of the circulation in the LEV. For this experiment we used butterfly inspired grooves attached to a flat plate and compared the vortex formation to a smooth plate case as the plate moved vertically. The plate is impulsively started in quiescent water and flow fields at Re = 1500, 3000, and 6000 are examined using Digital Particle Image Velocimetry (DPIV). The vortex formation time is 3.0 and is based on the flat plate travel length and chord length. We would like to thank the National Science Foundation REU Site Award 1358991 for funding this research.

Phase separation driven by density-dependent movement: A novel mechanism for ecological patterns.

PubMed

Liu, Quan-Xing; Rietkerk, Max; Herman, Peter M J; Piersma, Theunis; Fryxell, John M; van de Koppel, Johan

2016-12-01

Many ecosystems develop strikingly regular spatial patterns because of small-scale interactions between organisms, a process generally referred to as spatial self-organization. Self-organized spatial patterns are important determinants of the functioning of ecosystems, promoting the growth and survival of the involved organisms, and affecting the capacity of the organisms to cope with changing environmental conditions. The predominant explanation for self-organized pattern formation is spatial heterogeneity in establishment, growth and mortality, resulting from the self-organization processes. A number of recent studies, however, have revealed that movement of organisms can be an important driving process creating extensive spatial patterning in many ecosystems. Here, we review studies that detail movement-based pattern formation in contrasting ecological settings. Our review highlights that a common principle, where movement of organisms is density-dependent, explains observed spatial regular patterns in all of these studies. This principle, well known to physics as the Cahn-Hilliard principle of phase separation, has so-far remained unrecognized as a general mechanism for self-organized complexity in ecology. Using the examples presented in this paper, we explain how this movement principle can be discerned in ecological settings, and clarify how to test this mechanism experimentally. Our study highlights that animal movement, both in isolation and in unison with other processes, is an important mechanism for regular pattern formation in ecosystems. Copyright © 2016 Elsevier B.V. All rights reserved.

A Developmental Framework for Complex Plasmodesmata Formation Revealed by Large-Scale Imaging of the Arabidopsis Leaf Epidermis[W

PubMed Central

Fitzgibbon, Jessica; Beck, Martina; Zhou, Ji; Faulkner, Christine; Robatzek, Silke; Oparka, Karl

2013-01-01

Plasmodesmata (PD) form tubular connections that function as intercellular communication channels. They are essential for transporting nutrients and for coordinating development. During cytokinesis, simple PDs are inserted into the developing cell plate, while during wall extension, more complex (branched) forms of PD are laid down. We show that complex PDs are derived from existing simple PDs in a pattern that is accelerated when leaves undergo the sink–source transition. Complex PDs are inserted initially at the three-way junctions between epidermal cells but develop most rapidly in the anisocytic complexes around stomata. For a quantitative analysis of complex PD formation, we established a high-throughput imaging platform and constructed PDQUANT, a custom algorithm that detected cell boundaries and PD numbers in different wall faces. For anticlinal walls, the number of complex PDs increased with increasing cell size, while for periclinal walls, the number of PDs decreased. Complex PD insertion was accelerated by up to threefold in response to salicylic acid treatment and challenges with mannitol. In a single 30-min run, we could derive data for up to 11k PDs from 3k epidermal cells. This facile approach opens the door to a large-scale analysis of the endogenous and exogenous factors that influence PD formation. PMID:23371949

Complex Dynamic Systems View on Conceptual Change: How a Picture of Students' Intuitive Conceptions Accrue from Dynamically Robust Task Dependent Learning Outcomes

ERIC Educational Resources Information Center

Koponen, Ismo T.; Kokkonen, Tommi; Nousiainen, Maiji

2017-01-01

We discuss here conceptual change and the formation of robust learning outcomes from the viewpoint of complex dynamic systems (CDS). The CDS view considers students' conceptions as context dependent and multifaceted structures which depend on the context of their application. In the CDS view the conceptual patterns (i.e. intuitive conceptions…

Complex structures from patterned cell sheets

PubMed Central

Misra, M.; Audoly, B.; Shvartsman, S. Y.

2017-01-01

The formation of three-dimensional structures from patterned epithelial sheets plays a key role in tissue morphogenesis. An important class of morphogenetic mechanisms relies on the spatio-temporal control of apical cell contractility, which can result in the localized bending of cell sheets and in-plane cell rearrangements. We have recently proposed a modified vertex model that can be used to systematically explore the connection between the two-dimensional patterns of cell properties and the emerging three-dimensional structures. Here we review the proposed modelling framework and illustrate it through the computational analysis of the vertex model that captures the salient features of the formation of the dorsal appendages during Drosophila oogenesis. This article is part of the themed issue ‘Systems morphodynamics: understanding the development of tissue hardware’. PMID:28348251

Recent developments on polyphenol–protein interactions: effects on tea and coffee taste, antioxidant properties and the digestive system.

PubMed

Bandyopadhyay, Prasun; Ghosh, Amit K; Ghosh, Chandrasekhar

2012-06-01

Tea and coffee are widely consumed beverages across the world and they are rich sources of various polyphenols. Polyphenols are responsible for the bitterness and astringency of beverages and are also well known to impart antioxidant properties which is beneficial against several oxidative stress related diseases like cancer, cardiovascular diseases, and aging. On the other hand, proteins are also known to display many important roles in several physiological activities. Polyphenols can interact with proteins through hydrophobic or hydrophilic interactions, leading to the formation of soluble or insoluble complexes. According to recent studies, this complex formation can affect the bioavailability and beneficiary properties of both the individual components, in either way. For example, polyphenol-protein complex formation can reduce or enhance the antioxidant activity of polyphenols; similarly it can also affect the digestion ability of several digestive enzymes present in our body. Surprisingly, no review article has been published recently which has focused on the progress in this area, despite numerous articles having appeared in this field. This review summarizes the recent trends and patterns (2005 onwards) in polyphenol-protein interaction studies focusing on the characterization of the complex, the effect of this complex formation on tea and coffee taste, antioxidant properties and the digestive system.

Pattern Notes.

ERIC Educational Resources Information Center

Fields, Alan

1980-01-01

Looks at an alternative method to linear notes for organizing thoughts when preparing a talk or paper. This method displays the manner in which the relationships of a subject are organized and offers a format for displaying complex inter-dependencies in place of linear notes. (Author/MER)

A competitive complex formation mechanism underlies trichome patterning on Arabidopsis leaves

PubMed Central

Digiuni, Simona; Schellmann, Swen; Geier, Florian; Greese, Bettina; Pesch, Martina; Wester, Katja; Dartan, Burcu; Mach, Valerie; Srinivas, Bhylahalli Purushottam; Timmer, Jens; Fleck, Christian; Hulskamp, Martin

2008-01-01

Trichome patterning in Arabidopsis serves as a model system for de novo pattern formation in plants. It is thought to typify the theoretical activator–inhibitor mechanism, although this hypothesis has never been challenged by a combined experimental and theoretical approach. By integrating the key genetic and molecular data of the trichome patterning system, we developed a new theoretical model that allows the direct testing of the effect of experimental interventions and in the prediction of patterning phenotypes. We show experimentally that the trichome inhibitor TRIPTYCHON is transcriptionally activated by the known positive regulators GLABRA1 and GLABRA3. Further, we demonstrate by particle bombardment of protein fusions with GFP that TRIPTYCHON and CAPRICE but not GLABRA1 and GLABRA3 can move between cells. Finally, theoretical considerations suggest promoter swapping and basal overexpression experiments by means of which we are able to discriminate three biologically meaningful variants of the trichome patterning model. Our study demonstrates that the mutual interplay between theory and experiment can reveal a new level of understanding of how biochemical mechanisms can drive biological patterning processes. PMID:18766177

Desiccation of a Sessile Drop of Blood: Cracks Formation and Delamination

NASA Astrophysics Data System (ADS)

Sobac, Benjamin; Brutin, David

2011-11-01

The evaporation of drops of biological fluids has been studied since few years du to several applications in medical fields such as medical tests, drug screening, biostabilization... The evaporation of a drop of whole blood leads to the formation of final typical pattern of cracks. Flow motion, adhesion, gelation and fracturation all occur during the evaporation of this complex matter. During the drying, a sol-gel transition develops. The drying kinetics is explained by a simple model of evaporation taking account of the evolution of the gelation front. The system solidifies and when stresses are too important, cracks nucleate. The cracks formation and the structure of the crack pattern are investigated. The initial crack spacing is found in good agreement with the implementation in open geometry of the model of cracks formation induced by evaporation proposed by Allain and Limat. Finally, the drop is still drying after the end of the formation of cracks which leads, like in the situation of colloid suspensions, to the observation of a delamination phenomenon.

Structure, recognition and adaptive binding in RNA aptamer complexes.

PubMed

Patel, D J; Suri, A K; Jiang, F; Jiang, L; Fan, P; Kumar, R A; Nonin, S

1997-10-10

Novel features of RNA structure, recognition and discrimination have been recently elucidated through the solution structural characterization of RNA aptamers that bind cofactors, aminoglycoside antibiotics, amino acids and peptides with high affinity and specificity. This review presents the solution structures of RNA aptamer complexes with adenosine monophosphate, flavin mononucleotide, arginine/citrulline and tobramycin together with an example of hydrogen exchange measurements of the base-pair kinetics for the AMP-RNA aptamer complex. A comparative analysis of the structures of these RNA aptamer complexes yields the principles, patterns and diversity associated with RNA architecture, molecular recognition and adaptive binding associated with complex formation.

Module Based Complexity Formation: Periodic Patterning in Feathers and Hairs

PubMed Central

Chuong, Cheng-Ming; Yeh, Chao-Yuan; Jiang, Ting-Xin; Widelitz, Randall

2012-01-01

Patterns describe order which emerges from homogeneity. Complex patterns on the integument are striking because of their visibility throughout an organism's lifespan. Periodic patterning is an effective design because the ensemble of hair or feather follicles (modules) allows the generation of complexity, including regional variations and cyclic regeneration, giving the skin appendages a new lease on life. Spatial patterns include the arrangements of feathers and hairs in specified number, size, and spacing. We explore how a field of equivalent progenitor cells can generate periodically arranged modules based on genetic information, physical-chemical rules and developmental timing. Reconstitution experiments suggest a competitive equilibrium regulated by activators / inhibitors involving Turing reaction-diffusion. Temporal patterns result from oscillating stem cell activities within each module (micro-environment regulation), reflected as growth (anagen) and resting (telogen) phases during the cycling of feather and hair follicles. Stimulating modules with activators initiates the spread of regenerative hair waves, while global inhibitors outside each module (macro-environment) prevent this. Different wave patterns can be simulated by Cellular Automata principles. Hormonal status and seasonal changes can modulate appendage phenotypes, leading to “organ metamorphosis”, with multiple ectodermal organ phenotypes generated from the same precursors. We discuss potential evolutionary novel steps using this module based complexity in several amniote integument organs, exemplified by the spectacular peacock feather pattern. We thus explore the application of the acquired knowledge of patterning in tissue engineering. New hair follicles can be generated after wounding. Hairs and feathers can be reconstituted through self-organization of dissociated progenitor cells. PMID:23539312

Module-based complexity formation: periodic patterning in feathers and hairs.

PubMed

Chuong, Cheng-Ming; Yeh, Chao-Yuan; Jiang, Ting-Xin; Widelitz, Randall

2013-01-01

Patterns describe order which emerges from homogeneity. Complex patterns on the integument are striking because of their visibility throughout an organism’s lifespan. Periodic patterning is an effective design because the ensemble of hair or feather follicles (modules) allows the generation of complexity, including regional variations and cyclic regeneration, giving the skin appendages a new lease on life. Spatial patterns include the arrangements of feathers and hairs in specific number, size, and spacing.We explorehowa field of equivalent progenitor cells can generate periodically arranged modules based on genetic information, physical–chemical rules and developmental timing. Reconstitution experiments suggest a competitive equilibrium regulated by activators/inhibitors involving Turing reaction-diffusion. Temporal patterns result from oscillating stem cell activities within each module (microenvironment regulation), reflected as growth (anagen) and resting (telogen) phases during the cycling of feather and hair follicles. Stimulating modules with activators initiates the spread of regenerative hair waves, while global inhibitors outside each module (macroenvironment) prevent this. Different wave patterns can be simulated by cellular automata principles. Hormonal status and seasonal changes can modulate appendage phenotypes, leading to ‘organ metamorphosis’, with multiple ectodermal organ phenotypes generated from the same precursors. We discuss potential novel evolutionary steps using this module-based complexity in several amniote integument organs, exemplified by the spectacular peacock feather pattern. We thus explore the application of the acquired knowledge of patterning in tissue engineering. New hair follicles can be generated after wounding. Hairs and feathers can be reconstituted through self-organization of dissociated progenitor cells. © 2012 Wiley Periodicals, Inc.

Regulation of Facial Morphogenesis by Endothelin Signaling: Insights from Mice and Fish

PubMed Central

Clouthier, David E.; Garcia, Elvin; Schilling, Thomas F.

2010-01-01

Craniofacial morphogenesis is accomplished through a complex set of developmental events, most of which are initiated in neural crest cells within the pharyngeal arches. Local patterning cues from the surrounding environment induce gene expression within neural crest cells, leading to formation of a diverse set of skeletal elements. Endothelin-1 (Edn1) is one of the primary signals that establish the identities of neural crest cells within the mandibular portion of the first pharyngeal arch. Signaling through its cognate receptor, the endothelin-A receptor, is critical for patterning the ventral/distal portion of the arch (lower jaw) and also participates with Hox genes in patterning more posterior arches. Edn1/Ednra signaling is highly conserved between mouse and zebrafish, and genetic analyses in these two species have provided complementary insights into the patterning cues responsible for establishing the craniofacial complex as well as the genetic basis of facial birth defect syndromes. PMID:20684004

Weak connections form an infinite number of patterns in the brain

NASA Astrophysics Data System (ADS)

Ren, Hai-Peng; Bai, Chao; Baptista, Murilo S.; Grebogi, Celso

2017-04-01

Recently, much attention has been paid to interpreting the mechanisms for memory formation in terms of brain connectivity and dynamics. Within the plethora of collective states a complex network can exhibit, we show that the phenomenon of Collective Almost Synchronisation (CAS), which describes a state with an infinite number of patterns emerging in complex networks for weak coupling strengths, deserves special attention. We show that a simulated neuron network with neurons weakly connected does produce CAS patterns, and additionally produces an output that optimally model experimental electroencephalograph (EEG) signals. This work provides strong evidence that the brain operates locally in a CAS regime, allowing it to have an unlimited number of dynamical patterns, a state that could explain the enormous memory capacity of the brain, and that would give support to the idea that local clusters of neurons are sufficiently decorrelated to independently process information locally.

Two new Bent-toed Geckos of the Cyrtodactylus pulchellus complex from Peninsular Malaysia and multiple instances of convergent adaptation to limestone forest ecosystems.

PubMed

Grismer, L Lee; Wood, Perry L; Anuar, Shahrul; Grismer, Marta S; Quah, Evan S H; Murdoch, Matthew L; Muin, Mohd Abdul; Davis, Hayden R; Aguilar, César; Klabacka, Randy; Cobos, Anthony J; Aowphol, Anchalee; Sites, Jack W

2016-04-25

A new species of limestone cave-adapted gecko of the Cyrtodactylus pulchellus complex, C. hidupselamanya sp. nov., is described from an isolated karst formation at Felda Chiku 7, Kelantan, Peninsular Malaysia. This formation is scheduled to be completely quarried for its mineral content. From what we know about the life history of C. hidupselamanya sp. nov., this will result in its extinction. A new limestone forest-adapted species, C. lenggongensis sp. nov., from the Lenggong Valley, Perak was previously considered to be conspecific with C. bintangrendah but a re-evaluation of morphological, color pattern, molecular, and habitat preference indicates that it too is a unique lineage worthy of specific recognition. Fortunately C. lenggongensis sp. nov. is not facing extinction because its habitat is protected by the UNESCO Archaeological Heritage of the Lenggong Valley due to the archaeological significance of that region. Both new species can be distinguished from all other species of Cyrtodactylus based on molecular evidence from the mitochondrial gene ND2 and its flanking tRNAs as well as having unique combinations of morphological and color pattern characteristics. Using a time-calibrated BEAST analysis we inferred that the evolution of a limestone habitat preference and its apparently attendant morphological and color pattern adaptations evolved independently at least four times in the C. pulchellus complex between 26.1 and 0.78 mya.

Nixtamalization Process Affects Resistant Starch Formation and Glycemic Index of Tamales.

PubMed

Mariscal-Moreno, Rosa María; de Dios Figueroa Cárdenas, Juan; Santiago-Ramos, David; Rayas-Duarte, Patricia; Veles-Medina, José Juan; Martínez-Flores, Héctor Eduardo

2017-05-01

Tamales were prepared with 3 nixtamalization processes (traditional, ecological, and classic) and evaluated for chemical composition, starch properties, and glycemic index. Resistant starch (RS) in tamales increased 1.6 to 3.7 times compared to raw maize. This increment was due to the starch retrogradation (RS3) and amylose-lipid complexes (RS5) formation. Tamales elaborated with classic and ecological nixtamalization processes exhibited the highest total, soluble and insoluble dietary fiber content, and the highest RS content and lower in vivo glycemic index compared to tamales elaborated with traditional nixtamalization process. Thermal properties of tamales showed 3 endotherms: amylopectin retrogradation (42.7 to 66.6 °C), melting of amylose lipid complex type I (78.8 to 105.4), and melting of amylose-lipid complex type II (110.7 to 129.7). Raw maize exhibited X-ray diffraction pattern type A, after nixtamalization and cooking of tamales it changed to V-type polymorph structure, due to amylose-lipid complexes formation. Tamales from ecological nixtamalization processes could represent potential health benefits associated with the reduction on blood glucose response after consumption. © 2017 Institute of Food Technologists®.

Active Curved Polymers Form Vortex Patterns on Membranes.

PubMed

Denk, Jonas; Huber, Lorenz; Reithmann, Emanuel; Frey, Erwin

2016-04-29

Recent in vitro experiments with FtsZ polymers show self-organization into different dynamic patterns, including structures reminiscent of the bacterial Z ring. We model FtsZ polymers as active particles moving along chiral, circular paths by Brownian dynamics simulations and a Boltzmann approach. Our two conceptually different methods point to a generic phase behavior. At intermediate particle densities, we find self-organization into vortex structures including closed rings. Moreover, we show that the dynamics at the onset of pattern formation is described by a generalized complex Ginzburg-Landau equation.

Interdependency of formation and localisation of the Min complex controls symmetric plastid division.

PubMed

Maple, Jodi; Møller, Simon G

2007-10-01

Plastid division represents a fundamental biological process essential for plant development; however, the molecular basis of symmetric plastid division is unclear. AtMinE1 plays a pivotal role in selection of the plastid division site in concert with AtMinD1. AtMinE1 localises to discrete foci in chloroplasts and interacts with AtMinD1, which shows a similar localisation pattern. Here, we investigate the importance of Min protein complex formation during the chloroplast division process. Dissection of the assembly of the Min protein complex and determination of the interdependency of complex assembly and localisation in planta allow us to present a model of the molecular basis of selection of the division site in plastids. Moreover, functional analysis of AtMinE1 in bacteria demonstrates the level of functional conservation and divergence of the plastidic MinE proteins.

Biological pattern formation: from basic mechanisms to complex structures

NASA Astrophysics Data System (ADS)

Koch, A. J.; Meinhardt, H.

1994-10-01

The reliable development of highly complex organisms is an intriguing and fascinating problem. The genetic material is, as a rule, the same in each cell of an organism. How then do cells, under the influence of their common genes, produce spatial patterns? Simple models are discussed that describe the generation of patterns out of an initially nearly homogeneous state. They are based on nonlinear interactions of at least two chemicals and on their diffusion. The concepts of local autocatalysis and of long-range inhibition play a fundamental role. Numerical simulations show that the models account for many basic biological observations such as the regeneration of a pattern after excision of tissue or the production of regular (or nearly regular) arrays of organs during (or after) completion of growth. Very complex patterns can be generated in a reproducible way by hierarchical coupling of several such elementary reactions. Applications to animal coats and to the generation of polygonally shaped patterns are provided. It is further shown how to generate a strictly periodic pattern of units that themselves exhibit a complex and polar fine structure. This is illustrated by two examples: the assembly of photoreceptor cells in the eye of Drosophila and the positioning of leaves and axillary buds in a growing shoot. In both cases, the substructures have to achieve an internal polarity under the influence of some primary pattern-forming system existing in the fly's eye or in the plant. The fact that similar models can describe essential steps in organisms as distantly related as animals and plants suggests that they reveal some universal mechanisms.

Genomic approaches to identifying transcriptional regulators of osteoblast differentiation

NASA Technical Reports Server (NTRS)

Stains, Joseph P.; Civitelli, Roberto

2003-01-01

Recent microarray studies of mouse and human osteoblast differentiation in vitro have identified novel transcription factors that may be important in the establishment and maintenance of differentiation. These findings help unravel the pattern of gene-expression changes that underly the complex process of bone formation.

Complex collective dynamics of active torque-driven colloids at interfaces

DOE Office of Scientific and Technical Information (OSTI.GOV)

Snezhko, Alexey

Modern self-assembly techniques aiming to produce complex structural order or functional diversity often rely on non-equilibrium conditions in the system. Light, electric, or magnetic fields are predominantly used to modify interaction profiles of colloidal particles during self-assembly or induce complex out-of-equilibrium dynamic ordering. The energy injection rate, properties of the environment are important control parameters that influence the outcome of active (dynamic) self-assembly. The current review is focused on a case of collective dynamics and self-assembly of particles with externally driven torques coupled to a liquid or solid interface. The complexity of interactions in such systems is further enriched bymore » strong hydrodynamic coupling between particles. Unconventionally ordered dynamic self-assembled patterns, spontaneous symmetry breaking phenomena, self-propulsion, and collective transport have been reported in torque-driven colloids. Some of the features of the complex collective behavior and dynamic pattern formation in those active systems have been successfully captured in simulations.« less

Can mechanics control pattern formation in plants?

PubMed

Dumais, Jacques

2007-02-01

Development of the plant body entails many pattern forming events at scales ranging from the cellular level to the whole plant. Recent evidence suggests that mechanical forces play a role in establishing some of these patterns. The development of cellular configurations in glandular trichomes and the rippling of leaf surfaces are discussed in depth to illustrate how intricate patterns can emerge from simple and well-established molecular and cellular processes. The ability of plants to sense and transduce mechanical signals suggests that complex interactions between mechanics and chemistry are possible during plant development. The inclusion of mechanics alongside traditional molecular controls offers a more comprehensive view of developmental processes.

Origin of Complexity in Multicellular Organisms

NASA Astrophysics Data System (ADS)

Furusawa, Chikara; Kaneko, Kunihiko

2000-06-01

Through extensive studies of dynamical system modeling cellular growth and reproduction, we find evidence that complexity arises in multicellular organisms naturally through evolution. Without any elaborate control mechanism, these systems can exhibit complex pattern formation with spontaneous cell differentiation. Such systems employ a ``cooperative'' use of resources and maintain a larger growth speed than simple cell systems, which exist in a homogeneous state and behave ``selfishly.'' The relevance of the diversity of chemicals and reaction dynamics to the growth of a multicellular organism is demonstrated. Chaotic biochemical dynamics are found to provide the multipotency of stem cells.

Micro- and nanotechnology in cardiovascular tissue engineering.

PubMed

Zhang, Boyang; Xiao, Yun; Hsieh, Anne; Thavandiran, Nimalan; Radisic, Milica

2011-12-09

While in nature the formation of complex tissues is gradually shaped by the long journey of development, in tissue engineering constructing complex tissues relies heavily on our ability to directly manipulate and control the micro-cellular environment in vitro. Not surprisingly, advancements in both microfabrication and nanofabrication have powered the field of tissue engineering in many aspects. Focusing on cardiac tissue engineering, this paper highlights the applications of fabrication techniques in various aspects of tissue engineering research: (1) cell responses to micro- and nanopatterned topographical cues, (2) cell responses to patterned biochemical cues, (3) controlled 3D scaffolds, (4) patterned tissue vascularization and (5) electromechanical regulation of tissue assembly and function.

Biofilm three-dimensional architecture influences in situ pH distribution pattern on the human enamel surface

PubMed Central

Xiao, Jin; Hara, Anderson T; Kim, Dongyeop; Zero, Domenick T; Koo, Hyun; Hwang, Geelsu

2017-01-01

To investigate how the biofilm three-dimensional (3D) architecture influences in situ pH distribution patterns on the enamel surface. Biofilms were formed on human tooth enamel in the presence of 1% sucrose or 0.5% glucose plus 0.5% fructose. At specific time points, biofilms were exposed to a neutral pH buffer to mimic the buffering of saliva and subsequently pulsed with 1% glucose to induce re-acidification. Simultaneous 3D pH mapping and architecture of intact biofilms was performed using two-photon confocal microscopy. The enamel surface and mineral content characteristics were examined successively via optical profilometry and microradiography analyses. Sucrose-mediated biofilm formation created spatial heterogeneities manifested by complex networks of bacterial clusters (microcolonies). Acidic regions (pH<5.5) were found only in the interior of microcolonies, which impedes rapid neutralization (taking more than 120 min for neutralization). Glucose exposure rapidly re-created the acidic niches, indicating formation of diffusion barriers associated with microcolonies structure. Enamel demineralization (white spots), rougher surface, deeper lesion and more mineral loss appeared to be associated with the localization of these bacterial clusters at the biofilm-enamel interface. Similar 3D architecture was observed in plaque-biofilms formed in vivo in the presence of sucrose. The formation of complex 3D architectures creates spatially heterogeneous acidic microenvironments in close proximity of enamel surface, which might correlate with the localized pattern of the onset of carious lesions (white spot like) on teeth. PMID:28452377

Nonlinear ring resonator: spatial pattern generation

NASA Astrophysics Data System (ADS)

Ivanov, Vladimir Y.; Lachinova, Svetlana L.; Irochnikov, Nikita G.

2000-03-01

We consider theoretically spatial pattern formation processes in a unidirectional ring cavity with thin layer of Kerr-type nonlinear medium. Our method is based on studying of two coupled equations. The first is a partial differential equation for temporal dynamics of phase modulation of light wave in the medium. It describes nonlinear interaction in the Kerr-type lice. The second is a free propagation equation for the intracavity field complex amplitude. It involves diffraction effects of light wave in the cavity.

Neofunctionalization of embryonic head patterning genes facilitates the positioning of novel traits on the dorsal head of adult beetles.

PubMed

Zattara, Eduardo E; Busey, Hannah A; Linz, David M; Tomoyasu, Yoshinori; Moczek, Armin P

2016-07-13

The origin and integration of novel traits are fundamental processes during the developmental evolution of complex organisms. Yet how novel traits integrate into pre-existing contexts remains poorly understood. Beetle horns represent a spectacular evolutionary novelty integrated within the context of the adult dorsal head, a highly conserved trait complex present since the origin of insects. We investigated whether otd1/2 and six3, members of a highly conserved gene network that instructs the formation of the anterior end of most bilaterians, also play roles in patterning more recently evolved traits. Using ablation-based fate-mapping, comparative larval RNA interference (RNAi) and transcript sequencing, we found that otd1/2, but not six3, play a fundamental role in the post-embryonic formation of the adult dorsal head and head horns of Onthophagus beetles. By contrast, neither gene appears to pattern the adult head of Tribolium flour beetles even though all are expressed in the dorsal head epidermis of both Onthophagus and Tribolium We propose that, at least in beetles, the roles of otd genes during post-embryonic development are decoupled from their embryonic functions, and that potentially non-functional post-embryonic expression in the dorsal head facilitated their co-option into a novel horn-patterning network during Onthophagus evolution. © 2016 The Author(s).

Neofunctionalization of embryonic head patterning genes facilitates the positioning of novel traits on the dorsal head of adult beetles

PubMed Central

Busey, Hannah A.; Linz, David M.; Tomoyasu, Yoshinori; Moczek, Armin P.

2016-01-01

The origin and integration of novel traits are fundamental processes during the developmental evolution of complex organisms. Yet how novel traits integrate into pre-existing contexts remains poorly understood. Beetle horns represent a spectacular evolutionary novelty integrated within the context of the adult dorsal head, a highly conserved trait complex present since the origin of insects. We investigated whether otd1/2 and six3, members of a highly conserved gene network that instructs the formation of the anterior end of most bilaterians, also play roles in patterning more recently evolved traits. Using ablation-based fate-mapping, comparative larval RNA interference (RNAi) and transcript sequencing, we found that otd1/2, but not six3, play a fundamental role in the post-embryonic formation of the adult dorsal head and head horns of Onthophagus beetles. By contrast, neither gene appears to pattern the adult head of Tribolium flour beetles even though all are expressed in the dorsal head epidermis of both Onthophagus and Tribolium. We propose that, at least in beetles, the roles of otd genes during post-embryonic development are decoupled from their embryonic functions, and that potentially non-functional post-embryonic expression in the dorsal head facilitated their co-option into a novel horn-patterning network during Onthophagus evolution. PMID:27412276

Spontaneous formation of nanoparticle stripe patterns through dewetting

NASA Astrophysics Data System (ADS)

Huang, Jiaxing; Kim, Franklin; Tao, Andrea R.; Connor, Stephen; Yang, Peidong

2005-12-01

Significant advancement has been made in nanoparticle research, with synthetic techniques extending over a wide range of materials with good control over particle size and shape. A grand challenge is assembling and positioning the nanoparticles in desired locations to construct complex, higher-order functional structures. Controlled positioning of nanoparticles has been achieved in pre-defined templates fabricated by top-down approaches. A self-assembly method, however, is highly desirable because of its simplicity and compatibility with heterogeneous integration processes. Here we report on the spontaneous formation of ordered gold and silver nanoparticle stripe patterns on dewetting a dilute film of polymer-coated nanoparticles floating on a water surface. Well-aligned stripe patterns with tunable orientation, thickness and periodicity at the micrometre scale were obtained by transferring nanoparticles from a floating film onto a substrate in a dip-coating fashion. This facile technique opens up a new avenue for lithography-free patterning of nanoparticle arrays for various applications including, for example, multiplexed surface-enhanced Raman substrates and templated fabrication of higher-order nanostructures.

Patterned Cell Alignment in Response to Macroscale Curvature

NASA Astrophysics Data System (ADS)

Bade, Nathan; Kamien, Randall; Assoian, Richard; Stebe, Kathleen

The formation of spatial behavior patterns in tissues is a long-standing problem in biology. Decades of research have focused on understanding how biochemical signaling and morphogen gradients establish cell patterns during development and tissue morphogenesis. Here, we show that geometry and physical cues can drive organization and pattern formation. We find that mouse embryonic fibroblasts and human vascular smooth muscle cells sense curvature differently when in monolayers than when isolated on surfaces with various amounts of Gaussian curvature. While the long, apical stress fibers within these cells align in the direction of minimum curvature on cylindrical substrates, a subpopulation of stress fibers beneath the nucleus aligns in the circumferential direction and is bent maximally. We find dramatic reorganization of the actin cytoskeleton upon activation of RhoA, which is associated with increased contractility of the fibers. Thus, stress fiber alignment is likely a result of a complex balance between energy penalties associated with stress fiber bending, contractility, and the dynamics of F-actin assembly.

The role of various structures in the head on the formation of the biosonar beam of the baiji (Lipotes vexillifer).

PubMed

Wei, Chong; Au, Whitlow W L; Song, Zhongchang; Zhang, Yu

2016-02-01

The relative role of the various structures in the head of the baiji (Lipotes vexillifer) is examined. A finite element approach was applied to numerically simulate the acoustic propagation through a dolphin's head to examine the relative role of the skull, air sacs, and melon in the formation of the biosonar beam in the vertical plane. The beam pattern obtained with the whole head in place is compared with the beam pattern when the air sac is removed and the other structures (skull and melon) are in place, with only the skull removed, and finally with only the melon removed. The beam pattern with the air sacs and skull intact and the melon removed closely resembled the beam pattern for the complete head, suggesting that the melon has a minor role in the formation of the beam. The beam pattern for the other two cases had very little resemblance to the beam pattern for the whole head. The air sacs seem to have a role of directing propagation of the signal toward the front and the skull prevents the sound propagating below the rostrum. The beam patterns along with a correlation analysis showed that the melon had only a slight influence on the shape and direction of the beam. The resultant beam exiting the head of the dolphin is the result of complex reflection processes within the head of the animal.

Interplay between membrane elasticity and active cytoskeleton forces regulates the aggregation dynamics of the immunological synapse

NASA Astrophysics Data System (ADS)

Dharan, Nadiv; Farago, Oded

Adhesion between a T cell and an antigen presenting cell is achieved by TCR-pMHC and LFA1-ICAM1 protein complexes. These segregate to form a special pattern, known as the immunological synapse (IS), consisting of a central quasi-circular domain of TCR-pMHC bonds surrounded by a peripheral domain of LFA1-ICAM1 complexes. Insights gained from imaging studies had led to the conclusion that the formation of the central adhesion domain in the IS is driven by active (ATP-driven) mechanisms. Recent studies, however, suggested that passive (thermodynamic) mechanisms may also play an important role in this process. Here, we present a simple physical model, taking into account the membrane-mediated thermodynamic attraction between the TCR-pMHC bonds and the effective forces that they experience due to ATP-driven actin retrograde flow and transport by dynein motor proteins. Monte Carlo simulations of the model exhibit a good spatio-temporal agreement with the experimentally observed pattern evolution of the TCR-pMHC microclusters. The agreement is lost when one of the aggregation mechanisms is "muted", which helps to identify the respective roles in the process. We conclude that actin retrograde flow drives the centripetal motion of TCR-pMHC bonds, while the membrane-mediated interactions facilitate microcluster formation and growth. In the absence of dynein motors, the system evolves into a ring-shaped pattern, which highlights the role of dynein motors in the formation of the final concentric pattern. The interplay between the passive and active mechanisms regulates the rate of the accumulation process, which in the absence of one them proceeds either too quickly or slowly.

Lattice-Matched Epitaxial Graphene Grown on Boron Nitride.

PubMed

Davies, Andrew; Albar, Juan D; Summerfield, Alex; Thomas, James C; Cheng, Tin S; Korolkov, Vladimir V; Stapleton, Emily; Wrigley, James; Goodey, Nathan L; Mellor, Christopher J; Khlobystov, Andrei N; Watanabe, Kenji; Taniguchi, Takashi; Foxon, C Thomas; Eaves, Laurence; Novikov, Sergei V; Beton, Peter H

2018-01-10

Lattice-matched graphene on hexagonal boron nitride is expected to lead to the formation of a band gap but requires the formation of highly strained material and has not hitherto been realized. We demonstrate that aligned, lattice-matched graphene can be grown by molecular beam epitaxy using substrate temperatures in the range 1600-1710 °C and coexists with a topologically modified moiré pattern with regions of strained graphene which have giant moiré periods up to ∼80 nm. Raman spectra reveal narrow red-shifted peaks due to isotropic strain, while the giant moiré patterns result in complex splitting of Raman peaks due to strain variations across the moiré unit cell. The lattice-matched graphene has a lower conductance than both the Frenkel-Kontorova-type domain walls and also the topological defects where they terminate. We relate these results to theoretical models of band gap formation in graphene/boron nitride heterostructures.

Positive Disintegration as a Process of Symmetry Breaking.

PubMed

Laycraft, Krystyna

2017-04-01

This article presents an analysis of the positive disintegration as a process of symmetry breaking. Symmetry breaking plays a major role in self-organized patterns formation and correlates directly to increasing complexity and function specialization. According to Dabrowski, a creator of the Theory of Positive Disintegration, the change from lower to higher levels of human development requires a major restructuring of an individual's psychological makeup. Each level of human development is a relatively stable and coherent configuration of emotional-cognitive patterns called developmental dynamisms. Their main function is to restructure a mental structure by breaking the symmetry of a low level and bringing differentiation and then integration to higher levels. The positive disintegration is then the process of transitions from a lower level of high symmetry and low complexity to higher levels of low symmetry and high complexity of mental structure.

Cultured Neuronal Networks Express Complex Patterns of Activity and Morphological Memory

NASA Astrophysics Data System (ADS)

Raichman, Nadav; Rubinsky, Liel; Shein, Mark; Baruchi, Itay; Volman, Vladislav; Ben-Jacob, Eshel

The following sections are included: * Cultured Neuronal Networks * Recording the Network Activity * Network Engineering * The Formation of Synchronized Bursting Events * The Characterization of the SBEs * Highly-Active Neurons * Function-Form Relations in Cultured Networks * Analyzing the SBEs Motifs * Network Repertoire * Network under Hypothermia * Summary * Acknowledgments * References

The expert advantage in dynamic pattern recall persists across both attended and unattended display elements.

PubMed

Gorman, Adam D; Abernethy, Bruce; Farrow, Damian

2013-07-01

We examined how differences in attention influence how expert and novice basketball players encode into memory the specific structural information contained within patterns of play from their sport. Our participants were primed during a typical recall task to focus attention on either attacking or defending player formations before being asked to recall the attended or unattended portion of the pattern. Adherence to the instructional set was confirmed through an analysis of gaze distributions. Recall performance was superior for the experts relative to the novices across both the attended and unattended attacking and defensive pattern structures. Expert recall of attacker positions was unchanged with and without attention, whereas recall accuracy for the positions of defenders diminished without attention, as did the novices' recall of both attack and defense formations. The findings suggest that experienced performers are better than novices at encoding the elements from a complex and dynamic pattern in the absence of focused attention, with this advantage being especially evident in relation to the recall of attacking structure. Some revision of long-term memory theories of expertise will be necessary to accommodate these findings.

Understanding spatial and temporal patterning of astrocyte calcium transients via interactions between network transport and extracellular diffusion

NASA Astrophysics Data System (ADS)

Shtrahman, E.; Maruyama, D.; Olariu, E.; Fink, C. G.; Zochowski, M.

2017-02-01

Astrocytes form interconnected networks in the brain and communicate via calcium signaling. We investigate how modes of coupling between astrocytes influence the spatio-temporal patterns of calcium signaling within astrocyte networks and specifically how these network interactions promote coordination within this group of cells. To investigate these complex phenomena, we study reduced cultured networks of astrocytes and neurons. We image the spatial temporal patterns of astrocyte calcium activity and quantify how perturbing the coupling between astrocytes influences astrocyte activity patterns. To gain insight into the pattern formation observed in these cultured networks, we compare the experimentally observed calcium activity patterns to the patterns produced by a reduced computational model, where we represent astrocytes as simple units that integrate input through two mechanisms: gap junction coupling (network transport) and chemical release (extracellular diffusion). We examine the activity patterns in the simulated astrocyte network and their dependence upon these two coupling mechanisms. We find that gap junctions and extracellular chemical release interact in astrocyte networks to modulate the spatiotemporal patterns of their calcium dynamics. We show agreement between the computational and experimental findings, which suggests that the complex global patterns can be understood as a result of simple local coupling mechanisms.

Interaction and formation mechanism of binary complex between zein and propylene glycol alginate.

PubMed

Sun, Cuixia; Dai, Lei; Gao, Yanxiang

2017-02-10

The anti-solvent co-precipitation method was used to fabricate the zein-propylene glycol alginate (PGA) binary complex with different mass ratios of zein to PGA (20:1, 10:1, 5:1, 2:1 and 1:1) at pH 4.0. Results showed that attractive electrostatic interaction between zein and PGA occurred and negatively charged binary complex with large size and high turbidity was formed due to the charge neutralization. Hydrogen bonding and hydrophobic effects were involved in the interactions between zein and PGA, leading to the changed secondary structure and improved thermal stability of zein. Aggregates in the irregular shape with large size were obviously observed in the AFM images. PGA alone exhibited a fine filamentous network structure, while zein-PGA binary complex showed a rough branch-like pattern and the surface of "branch" was closely adsorbed by lots of spherical zein particles. Q in zein-PGA binary complex dispersions presented the improved photochemical and thermal stability. The potential mechanism of a two-step process was proposed to explain the formation of zein-PGA binary complexes. Copyright © 2016 Elsevier Ltd. All rights reserved.

Emergent Vortex Patterns in Systems of Self-Propelled, Chiral Particles

NASA Astrophysics Data System (ADS)

Huber, Lorenz; Denk, Jonas; Reithmann, Emanuel; Frey, Erwin

Self-organization of FtsZ polymers is vital for Z-ring assembly during bacterial cell division, and has been studied using reconstituted in vitro model systems. Employing Brownian dynamics simulations and a Boltzmann approach, we model FtsZ polymers as active particles moving along chiral circular paths. With both theoretical approaches we find self-organization into vortex structures and characterize different states in parameter states. Our work demonstrates that these patterns are robust and are generic for active chiral matter. Moreover, we show that the dynamics at the onset of pattern formation is described by a generalized complex Ginzburg-Landau equation.

Refinement and Pattern Formation in Neural Circuits by the Interaction of Traveling Waves with Spike-Timing Dependent Plasticity

PubMed Central

Bennett, James E. M.; Bair, Wyeth

2015-01-01

Traveling waves in the developing brain are a prominent source of highly correlated spiking activity that may instruct the refinement of neural circuits. A candidate mechanism for mediating such refinement is spike-timing dependent plasticity (STDP), which translates correlated activity patterns into changes in synaptic strength. To assess the potential of these phenomena to build useful structure in developing neural circuits, we examined the interaction of wave activity with STDP rules in simple, biologically plausible models of spiking neurons. We derive an expression for the synaptic strength dynamics showing that, by mapping the time dependence of STDP into spatial interactions, traveling waves can build periodic synaptic connectivity patterns into feedforward circuits with a broad class of experimentally observed STDP rules. The spatial scale of the connectivity patterns increases with wave speed and STDP time constants. We verify these results with simulations and demonstrate their robustness to likely sources of noise. We show how this pattern formation ability, which is analogous to solutions of reaction-diffusion systems that have been widely applied to biological pattern formation, can be harnessed to instruct the refinement of postsynaptic receptive fields. Our results hold for rich, complex wave patterns in two dimensions and over several orders of magnitude in wave speeds and STDP time constants, and they provide predictions that can be tested under existing experimental paradigms. Our model generalizes across brain areas and STDP rules, allowing broad application to the ubiquitous occurrence of traveling waves and to wave-like activity patterns induced by moving stimuli. PMID:26308406

Refinement and Pattern Formation in Neural Circuits by the Interaction of Traveling Waves with Spike-Timing Dependent Plasticity.

PubMed

Bennett, James E M; Bair, Wyeth

2015-08-01

Traveling waves in the developing brain are a prominent source of highly correlated spiking activity that may instruct the refinement of neural circuits. A candidate mechanism for mediating such refinement is spike-timing dependent plasticity (STDP), which translates correlated activity patterns into changes in synaptic strength. To assess the potential of these phenomena to build useful structure in developing neural circuits, we examined the interaction of wave activity with STDP rules in simple, biologically plausible models of spiking neurons. We derive an expression for the synaptic strength dynamics showing that, by mapping the time dependence of STDP into spatial interactions, traveling waves can build periodic synaptic connectivity patterns into feedforward circuits with a broad class of experimentally observed STDP rules. The spatial scale of the connectivity patterns increases with wave speed and STDP time constants. We verify these results with simulations and demonstrate their robustness to likely sources of noise. We show how this pattern formation ability, which is analogous to solutions of reaction-diffusion systems that have been widely applied to biological pattern formation, can be harnessed to instruct the refinement of postsynaptic receptive fields. Our results hold for rich, complex wave patterns in two dimensions and over several orders of magnitude in wave speeds and STDP time constants, and they provide predictions that can be tested under existing experimental paradigms. Our model generalizes across brain areas and STDP rules, allowing broad application to the ubiquitous occurrence of traveling waves and to wave-like activity patterns induced by moving stimuli.

The formation mechanisms of turbidity maximum in the Pearl River estuary, China.

PubMed

Wai, O W H; Wang, C H; Li, Y S; Li, X D

2004-03-01

The formation and dynamics of turbidity maxima (TM) in the Pearl River estuary (PRE) are not well understood but the existence of TM in the estuary have great potential engineering and environmental impacts. Based on the measurements of two large-scale field surveys conducted in the wet season of 1978 (July of 1978) and the dry season of 1979 (March of 1979), the existence and seasonal variations of TM in the PRE focusing on the two major natural navigation channels have been studied. The sediment transport fluxes over two consecutive tidal cycles have been analyzed in detail. The analysis results reveal that the formation mechanisms of TM in the estuary are rather complex. In general, gravitational circulation, tidal trapping, and sediment resuspension and deposition processes are the primary TM formation mechanisms in the PRE. The clockwise back flow pattern around Lingding Island also leads to the formation of TM in the West channel of the PRE. The occurrence of TM far upstream of the salt water wedge is the result of the complex hydrodynamic and sediment transport processes generated by the runoff of the major rivers.

Pattern Driven Stress Localization

NASA Astrophysics Data System (ADS)

Croll, Andrew; Crosby, Alfred

2010-03-01

The self-assembly of patterns from isotropic initial states is a major driver of modern soft-matter research. This avenue of study is directed by the desire to understand the complex physics of the varied structures found in Nature, and by technological interest in functional materials that may be derived through biomimicry. In this work we show how a simple striped phase can respond with significant complexity to an appropriately chosen perturbation. In particular, we show how a buckled elastic plate transitions into a state of stress localization using a simple, self-assembled variation in surface topography. The collection of topographic boundaries act in concert to change the state from isotropic sinusoidal wrinkles, to sharp folds or creases separated by relatively flat regions. By varying the size of the imposed topographic pattern or the wavelength of the wrinkles, we construct a state diagram of the system. The localized state has implications for both biological systems, and for the control of non-linear pattern formation.

Provenance and metamorphic PT conditions of Cryogenian-Ediacaran metasediments from the Kid metamorphic complex, Sinai, NE Arabian-Nubian Shield: Insights from detrital zircon geochemistry and mineral chemistry

NASA Astrophysics Data System (ADS)

El-Bialy, Mohammed Z.; Ali, Kamal A.; Abu El-Enen, Mahrous M.; Ahmed, Ahmed H.

2015-12-01

The Malhaq and Um Zariq formations occupy the northern part of the Neoproterozoic Kid metamorphic complex of SE Sinai, NE Arabian-Nubian Shield. This study presents new mineral chemistry data and LA-ICP-MS analyses of the trace element concentrations on zircons separated from metapelites from these formations. The detrital zircons of Um Zariq Formation are more enriched in ΣREE, whereas Malhaq Formation zircons are markedly HREE-enriched with strongly fractionated HREE patterns. The quite differences in the overall slope and size of the Eu and Ce anomalies between REE patterns of the two zircon suites provide a robust indication of different sources. The Ti-in-zircon thermometer has revealed that the zircons separated from Malhaq Formation were crystallized within the 916-1018 °C range, while those from Um Zariq Formation exhibit higher range of crystallization temperatures (1084-1154 °C). The detrital zircons of Malhaq Formation were derived mainly from mafic source rocks (basalt and dolerite), whereas Um Zariq Formation zircons have varied and more evolved parent rocks. Most of the investigated zircons from both formations are concluded to be unaltered magmatic that were lately crystallized from a high LREE/HREE melt. All the studied detrital zircon grains show typical trace elements features of crustal-derived zircons. All of the Um Zariq Formation and most of Malhaq Formation detrital zircons are geochemically discriminated as continental zircons. Both formation metapelites record similar, overlapping peak metamorphic temperatures (537-602 °C and 550-579 °C, respectively), and pressures (3.83-4.93 kbar and 3.69-4.07 kbar, respectively). The geothermal gradient, at the peak metamorphic conditions, was quite high (37-41 °C/km) corresponding to metamorphism at burial depth of 14-16 km. The peak regional metamorphism of Um Zariq and Malhaq formations is concluded to be generated during extensional regime and thinning of the lithosphere in an island arc setting with heat flow from the underlying arc granitoids.

A two-step patterning process increases the robustness of periodic patterning in the fly eye.

PubMed

Gavish, Avishai; Barkai, Naama

2016-06-01

Complex periodic patterns can self-organize through dynamic interactions between diffusible activators and inhibitors. In the biological context, self-organized patterning is challenged by spatial heterogeneities ('noise') inherent to biological systems. How spatial variability impacts the periodic patterning mechanism and how it can be buffered to ensure precise patterning is not well understood. We examine the effect of spatial heterogeneity on the periodic patterning of the fruit fly eye, an organ composed of ∼800 miniature eye units (ommatidia) whose periodic arrangement along a hexagonal lattice self-organizes during early stages of fly development. The patterning follows a two-step process, with an initial formation of evenly spaced clusters of ∼10 cells followed by a subsequent refinement of each cluster into a single selected cell. Using a probabilistic approach, we calculate the rate of patterning errors resulting from spatial heterogeneities in cell size, position and biosynthetic capacity. Notably, error rates were largely independent of the desired cluster size but followed the distributions of signaling speeds. Pre-formation of large clusters therefore greatly increases the reproducibility of the overall periodic arrangement, suggesting that the two-stage patterning process functions to guard the pattern against errors caused by spatial heterogeneities. Our results emphasize the constraints imposed on self-organized patterning mechanisms by the need to buffer stochastic effects. Author summary Complex periodic patterns are common in nature and are observed in physical, chemical and biological systems. Understanding how these patterns are generated in a precise manner is a key challenge. Biological patterns are especially intriguing, as they are generated in a noisy environment; cell position and cell size, for example, are subject to stochastic variations, as are the strengths of the chemical signals mediating cell-to-cell communication. The need to generate a precise and robust pattern in this 'noisy' environment restricts the space of patterning mechanisms that can function in the biological setting. Mathematical modeling is useful in comparing the sensitivity of different mechanisms to such variations, thereby highlighting key aspects of their design.We use mathematical modeling to study the periodic patterning of the fruit fly eye. In this system, a highly ordered lattice of differentiated cells is generated in a two-dimensional cell epithelium. The pattern is first observed by the appearance of evenly spaced clusters of ∼10 cells that express specific genes. Each cluster is subsequently refined into a single cell, which initiates the formation and differentiation of a miniature eye unit, the ommatidium. We formulate a mathematical model based on the known molecular properties of the patterning mechanism, and use a probabilistic approach to calculate the errors in cluster formation and refinement resulting from stochastic cell-to-cell variations ('noise') in different quantitative parameters. This enables us to define the parameters most influencing noise sensitivity. Notably, we find that this error is roughly independent of the desired cluster size, suggesting that large clusters are beneficial for ensuring the overall reproducibility of the periodic cluster arrangement. For the stage of cluster refinement, we find that rapid communication between cells is critical for reducing error. Our work provides new insights into the constraints imposed on mechanisms generating periodic patterning in a realistic, noisy environment, and in particular, discusses the different considerations in achieving optimal design of the patterning network.

Theory of domain patterns in systems with long-range interactions of Coulomb type.

PubMed

Muratov, C B

2002-12-01

We develop a theory of the domain patterns in systems with competing short-range attractive interactions and long-range repulsive Coulomb interactions. We take an energetic approach, in which patterns are considered as critical points of a mean-field free energy functional. Close to the microphase separation transition, this functional takes on a universal form, allowing us to treat a number of diverse physical situations within a unified framework. We use asymptotic analysis to study domain patterns with sharp interfaces. We derive an interfacial representation of the pattern's free energy which remains valid in the fluctuating system, with a suitable renormalization of the Coulomb interaction's coupling constant. We also derive integro-differential equations describing stationary domain patterns of arbitrary shapes and their thermodynamic stability, coming from the first and second variations of the interfacial free energy. We show that the length scale of a stable domain pattern must obey a certain scaling law with the strength of the Coulomb interaction. We analyzed the existence and stability of localized (spots, stripes, annuli) and periodic (lamellar, hexagonal) patterns in two dimensions. We show that these patterns are metastable in certain ranges of the parameters and that they can undergo morphological instabilities leading to the formation of more complex patterns. We discuss nucleation of the domain patterns by thermal fluctuations and pattern formation scenarios for various thermal quenches. We argue that self-induced disorder is an intrinsic property of the domain patterns in the systems under consideration.

Reassessing the roles of PIN proteins and anticlinal microtubules during pavement cell morphogenesis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Belteton, Samuel; Sawchuk, Megan G.; Donohoe, Bryon S.

The leaf epidermis is a biomechanical shell that influences the size and shape of the organ. Its morphogenesis is a multiscale process in which nanometer-scale cytoskeletal protein complexes, individual cells, and groups of cells pattern growth and define macroscopic leaf traits. Interdigitated growth of neighboring cells is an evolutionarily conserved developmental strategy. Understanding how signaling pathways and cytoskeletal proteins pattern cell walls during this form of tissue morphogenesis is an important research challenge. The cellular and molecular control of a lobed cell morphology is currently thought to involve PIN-FORMED (PIN)-type plasma membrane efflux carriers that generate subcellular auxin gradients. Auxinmore » gradients were proposed to function across cell boundaries to encode stable offset patterns of cortical microtubules and actin filaments between adjacent cells. Many models suggest that long-lived microtubules along the anticlinal cell wall generate local cell wall heterogeneities that restrict local growth and specify the timing and location of lobe formation. Here we used Arabidopsis reverse genetics and multivariate long-term time-lapse imaging to test current cell shape control models. We found that neither PIN proteins nor microtubules along the anticlinal wall predict the patterns of lobe formation. In fields of lobing cells, anticlinal microtubules are not correlated with cell shape and are unstable at the time scales of cell expansion. Our analyses indicate that anticlinal microtubules have multiple functions in pavement cells, and that lobe initiation is likely controlled by complex interactions among cell geometry, cell wall stress patterns, and transient microtubule networks that span the anticlinal and periclinal walls.« less

Reassessing the Roles of PIN Proteins and Anticlinal Microtubules during Pavement Cell Morphogenesis1[OPEN

PubMed Central

Sawchuk, Megan G.; Scarpella, Enrico

2018-01-01

The leaf epidermis is a biomechanical shell that influences the size and shape of the organ. Its morphogenesis is a multiscale process in which nanometer-scale cytoskeletal protein complexes, individual cells, and groups of cells pattern growth and define macroscopic leaf traits. Interdigitated growth of neighboring cells is an evolutionarily conserved developmental strategy. Understanding how signaling pathways and cytoskeletal proteins pattern cell walls during this form of tissue morphogenesis is an important research challenge. The cellular and molecular control of a lobed cell morphology is currently thought to involve PIN-FORMED (PIN)-type plasma membrane efflux carriers that generate subcellular auxin gradients. Auxin gradients were proposed to function across cell boundaries to encode stable offset patterns of cortical microtubules and actin filaments between adjacent cells. Many models suggest that long-lived microtubules along the anticlinal cell wall generate local cell wall heterogeneities that restrict local growth and specify the timing and location of lobe formation. Here, we used Arabidopsis (Arabidopsis thaliana) reverse genetics and multivariate long-term time-lapse imaging to test current cell shape control models. We found that neither PIN proteins nor long-lived microtubules along the anticlinal wall predict the patterns of lobe formation. In fields of lobing cells, anticlinal microtubules are not correlated with cell shape and are unstable at the time scales of cell expansion. Our analyses indicate that anticlinal microtubules have multiple functions in pavement cells and that lobe initiation is likely controlled by complex interactions among cell geometry, cell wall stress patterns, and transient microtubule networks that span the anticlinal and periclinal walls. PMID:29192026

Effects of gonadoliberin analogue triptorelin on the pituitary-testicular complex in neonatal rats.

PubMed

Dygalo, N N; Shemenkova, T V; Kalinina, T S; Shishkina, G T

2014-02-01

Triptorelin, a synthetic analogue of neurohormone gonadoliberin (gonadotropin-releasing hormone, GnRH) administered daily to rats on postnatal days 5-7 suppressed the expression of GnRH receptor in the pituitary gland, but did not change functioning of the pituitary-testicular complex. Administration of triptorelin on postnatal days 12-14 (i.e. during the formation of pulsatile pattern of GnRH secretion and increasing levels of its mRNA receptor in the pituitary gland) had no effect on receptor expression, but increased the levels of luteinizing hormone mRNA in the pituitary gland and the weight of testes. At that time, blood levels of testosterone were lowered, which indicated disturbed pulsatile pattern of GnRH secretion.

Stripes and belly-spots – a review of pigment cell morphogenesis in vertebrates

PubMed Central

Kelsh, Robert N.; Harris, Melissa L.; Colanesi, Sarah; Erickson, Carol A.

2009-01-01

Pigment patterns in the integument have long-attracted attention from both scientists and non-scientists alike since their natural attractiveness combines with their excellence as models for the general problem of pattern formation. Pigment cells are formed from the neural crest and must migrate to reach their final locations. In this review, we focus on our current understanding of mechanisms underlying the control of pigment cell migration and patterning in diverse vertebrates. The model systems discussed here –chick, mouse, and zebrafish – each provide unique insights into the major morphogenetic events driving pigment pattern formation. In birds and mammals, melanoblasts must be specified before they can migrate on the dorsolateral pathway. Transmembrane receptors involved in guiding them onto this route include EphB2 and Ednrb2 in chick, and Kit in mouse. Terminal migration depends, in part, upon extracellular matrix reorganization by ADAMTS20. Invasion of the ectoderm, especially into the feather germ and hair follicles, requires specific signals that are beginning to be characterized. We summarize our current understanding of the mechanisms regulating melanoblast number and organization in the epidermis. We note the apparent differences in pigment pattern formation in poikilothermic vertebrates when compared with birds and mammals. With more pigment cell types, migration pathways are more complex and largely unexplored; nevertheless, a role for Kit signaling in melanophore migration is clear and indicates that at least some patterning mechanisms may be highly conserved. We summarize the multiple factors thought to contribute to zebrafish embryonic pigment pattern formation, highlighting a recent study identifying Sdf1a as one factor crucial for regulation of melanophore positioning. Finally, we discuss the mechanisms generating a second, metamorphic pigment pattern in adult fish, emphasizing recent studies strengthening the evidence that undifferentiated progenitor cells play a major role in generating adult pigment cells. PMID:18977309

Beaver assisted river valley formation

USGS Publications Warehouse

Westbrook, Cherie J.; Cooper, D.J.; Baker, B.W.

2011-01-01

We examined how beaver dams affect key ecosystem processes, including pattern and process of sediment deposition, the composition and spatial pattern of vegetation, and nutrient loading and processing. We provide new evidence for the formation of heterogeneous beaver meadows on riverine system floodplains and terraces where dynamic flows are capable of breaching in-channel beaver dams. Our data show a 1.7-m high beaver dam triggered overbank flooding that drowned vegetation in areas deeply flooded, deposited nutrient-rich sediment in a spatially heterogeneous pattern on the floodplain and terrace, and scoured soils in other areas. The site quickly de-watered following the dam breach by high stream flows, protecting the deposited sediment from future re-mobilization by overbank floods. Bare sediment either exposed by scouring or deposited by the beaver flood was quickly colonized by a spatially heterogeneous plant community, forming a beaver meadow. Many willow and some aspen seedlings established in the more heavily disturbed areas, suggesting the site may succeed to a willow carr plant community suitable for future beaver re-occupation. We expand existing theory beyond the beaver pond to include terraces within valleys. This more fully explains how beavers can help drive the formation of alluvial valleys and their complex vegetation patterns as was first postulated by Ruedemann and Schoonmaker in 1938. ?? 2010 John Wiley & Sons, Ltd.

Multiple spiral patterns in the transitional disk of HD 100546

NASA Astrophysics Data System (ADS)

Boccaletti, A.; Pantin, E.; Lagrange, A.-M.; Augereau, J.-C.; Meheut, H.; Quanz, S. P.

2013-12-01

Context. Protoplanetary disks around young stars harbor many structures related to planetary formation. Of particular interest, spiral patterns were discovered among several of these disks and are expected to be the sign of gravitational instabilities leading to giant planet formation or gravitational perturbations caused by already existing planets. In this context, the star HD 100546 presents some specific characteristics with a complex gaseous and dusty disk that includes spirals, as well as a possible planet in formation. Aims: The objective of this study is to analyze high-contrast and high angular resolution images of this emblematic system to shed light on critical steps in planet formation. Methods: We retrieved archival images obtained at Gemini in the near IR (Ks band) with the instrument NICI and processed the data using an advanced high contrast imaging technique that takes advantage of the angular differential imaging. Results: These new images reveal the spiral pattern previously identified with Hubble Space Telescope (HST) with an unprecedented resolution, while the large-scale structure of the disk is mostly cancelled by the data processing. The single pattern to the southeast in HST images is now resolved into a multi-armed spiral pattern. Using two models of a gravitational perturber orbiting in a gaseous disk, we attempted to constrain the characteristics of this perturber, assuming that each spiral is independent, and drew qualitative conclusions. The non-detection of the northeast spiral pattern observed in HST allows putting a lower limit on the intensity ratio between the two sides of the disk, which if interpreted as forward scattering, yields a larger anisotropic scattering than is derived in the visible. Also, we find that the spirals are likely to be spatially resolved with a thickness of about 5-10 AU. Finally, we did not detect the candidate planet in formation recently discovered in the Lp band, with a mass upper limit of 16-18 MJ. Based on data retrieved from the Gemini archive.

Visual analysis and exploration of complex corporate shareholder networks

NASA Astrophysics Data System (ADS)

Tekušová, Tatiana; Kohlhammer, Jörn

2008-01-01

The analysis of large corporate shareholder network structures is an important task in corporate governance, in financing, and in financial investment domains. In a modern economy, large structures of cross-corporation, cross-border shareholder relationships exist, forming complex networks. These networks are often difficult to analyze with traditional approaches. An efficient visualization of the networks helps to reveal the interdependent shareholding formations and the controlling patterns. In this paper, we propose an effective visualization tool that supports the financial analyst in understanding complex shareholding networks. We develop an interactive visual analysis system by combining state-of-the-art visualization technologies with economic analysis methods. Our system is capable to reveal patterns in large corporate shareholder networks, allows the visual identification of the ultimate shareholders, and supports the visual analysis of integrated cash flow and control rights. We apply our system on an extensive real-world database of shareholder relationships, showing its usefulness for effective visual analysis.

Resolving protein interactions and organization downstream the T cell antigen receptor using single-molecule localization microscopy: a review

NASA Astrophysics Data System (ADS)

Sherman, Eilon

2016-06-01

Signal transduction is mediated by heterogeneous and dynamic protein complexes. Such complexes play a critical role in diverse cell functions, with the important example of T cell activation. Biochemical studies of signalling complexes and their imaging by diffraction limited microscopy have resulted in an intricate network of interactions downstream the T cell antigen receptor (TCR). However, in spite of their crucial roles in T cell activation, much remains to be learned about these signalling complexes, including their heterogeneous contents and size distribution, their complex arrangements in the PM, and the molecular requirements for their formation. Here, we review how recent advancements in single molecule localization microscopy have helped to shed new light on the organization of signalling complexes in single molecule detail in intact T cells. From these studies emerges a picture where cells extensively employ hierarchical and dynamic patterns of nano-scale organization to control the local concentration of interacting molecular species. These patterns are suggested to play a critical role in cell decision making. The combination of SMLM with more traditional techniques is expected to continue and critically contribute to our understanding of multimolecular protein complexes and their significance to cell function.

Directing the phase behavior of polyelectrolyte complexes using chiral patterned peptides

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pacalin, Naomi M.; Leon, Lorraine; Tirrell, Matthew

Polyelectrolyte complexes (PECs) have a broad range of promising applications as soft materials due to their self-assembly and diversity of structure and chemical composition. Peptide polymer PECs are highly biocompatible and biodegradable, making them particularly useful for encapsulation of food additives and flavors, micellar drug delivery, medical and underwater adhesives, fetal membrane patches, and scaffolds for cell growth in tissue engineering. While parameters affecting PEC formation and stability in regards to charge effects are well researched, little is known about the effects of van der Waals interactions, hydrogen bonding, and secondary structure in these materials. Peptide chirality provides a uniquemore » opportunity to manipulate PEC phase to modulate the amount of solid-like (precipitate) or liquid-like (coacervate) character by influencing hydrogen bonding interactions among peptide chains. In previous work, we showed that chiral peptides form solid complexes, while complexes with even one racemic peptide were fluid. This raised the interesting question of how long a homochiral sequence must be to result in solid phase formation. In this work, we designed chiral patterned peptides of polyglutamic acid and polylysine ranging from 50 to 90% L-chiral residues with increasing numbers of sequential L-chiral residues before a chirality change. These polymers were mixed together to form PECs. We observed that 8 or more sequential L-chiral residues are necessary to achieve both the appearance of a precipitate phase and sustained beta-sheets in the complex, as determined by optical imaging and FTIR Spectroscopy. Less homochiral content results in formation of a coacervate phase. Thus, we show that chiral sequence can be used to control the phase transition of PECs. Understanding how to manipulate PEC phase using chiral sequence as presented here may enable tuning of the material properties to achieve the desired mechanical strength for coatings and polymer brushes, or the most effective molecular release kinetics for drug delivery applications, for example.« less

Directing the phase behavior of polyelectrolyte complexes using chiral patterned peptides

NASA Astrophysics Data System (ADS)

Pacalin, Naomi M.; Leon, Lorraine; Tirrell, Matthew

2016-10-01

Polyelectrolyte complexes (PECs) have a broad range of promising applications as soft materials due to their self-assembly and diversity of structure and chemical composition. Peptide polymer PECs are highly biocompatible and biodegradable, making them particularly useful for encapsulation of food additives and flavors, micellar drug delivery, medical and underwater adhesives, fetal membrane patches, and scaffolds for cell growth in tissue engineering. While parameters affecting PEC formation and stability in regards to charge effects are well researched, little is known about the effects of van der Waals interactions, hydrogen bonding, and secondary structure in these materials. Peptide chirality provides a unique opportunity to manipulate PEC phase to modulate the amount of solid-like (precipitate) or liquid-like (coacervate) character by influencing hydrogen bonding interactions among peptide chains. In previous work, we showed that chiral peptides form solid complexes, while complexes with even one racemic peptide were fluid. This raised the interesting question of how long a homochiral sequence must be to result in solid phase formation. In this work, we designed chiral patterned peptides of polyglutamic acid and polylysine ranging from 50 to 90% L-chiral residues with increasing numbers of sequential L-chiral residues before a chirality change. These polymers were mixed together to form PECs. We observed that 8 or more sequential L-chiral residues are necessary to achieve both the appearance of a precipitate phase and sustained β-sheets in the complex, as determined by optical imaging and FTIR Spectroscopy. Less homochiral content results in formation of a coacervate phase. Thus, we show that chiral sequence can be used to control the phase transition of PECs. Understanding how to manipulate PEC phase using chiral sequence as presented here may enable tuning of the material properties to achieve the desired mechanical strength for coatings and polymer brushes, or the most effective molecular release kinetics for drug delivery applications, for example.

Patterns of calcium oxalate monohydrate crystallization in complex biological systems

NASA Astrophysics Data System (ADS)

Golovanova, O. A.; Korol'kov, V. V.; Kuimova, M. V.

2017-01-01

The paper presents the features of calcium oxalate crystallization in the presence of additives revealed through experimental modeling. The patterns of phase formation are shown for the Ca2+ - C2O4 2- - H2O and Ca2+ - C2O4 2- - PO4 3- - H2O systems with the components and pH of the saline varying over a wide concentrations range. The effect of additives on crystallization of calcium oxalate monohydrate was investigated. It was found that the ionic strength and magnesium ions are inhibitors, and calcium oxalate and hydroxyapatite crystals are catalysts of calcium oxalate monohydrate crystallization. The basic calcium phosphate (apatite) was found to be most thermodynamically stable, which indicates its special role in kidney stone formation since it is found in virtually all stones.

Students Mental Representation of Biology Diagrams/Pictures Conventions Based on Formation of Causal Network

NASA Astrophysics Data System (ADS)

Sampurno, A. W.; Rahmat, A.; Diana, S.

2017-09-01

Diagrams/pictures conventions is one form of visual media that often used to assist students in understanding the biological concepts. The effectiveness of use diagrams/pictures in biology learning at school level has also been mostly reported. This study examines the ability of high school students in reading diagrams/pictures biological convention which is described by Mental Representation based on formation of causal networks. The study involved 30 students 11th grade MIA senior high school Banten Indonesia who are studying the excretory system. MR data obtained by Instrument worksheet, developed based on CNET-protocol, in which there are diagrams/drawings of nephron structure and urinary mechanism. Three patterns formed MR, namely Markov chain, feedback control with a single measurement, and repeated feedback control with multiple measurement. The third pattern is the most dominating pattern, differences in the pattern of MR reveal the difference in how and from which point the students begin to uncover important information contained in the diagram to establish a causal networks. Further analysis shows that a difference in the pattern of MR relate to how complex the students process the information contained in the diagrams/pictures.

N-cadherin in adult rat cardiomyocytes in culture. II. Spatio-temporal appearance of proteins involved in cell-cell contact and communication. Formation of two distinct N-cadherin/catenin complexes.

PubMed

Hertig, C M; Butz, S; Koch, S; Eppenberger-Eberhardt, M; Kemler, R; Eppenberger, H M

1996-01-01

The spatio-temporal appearance and distribution of proteins forming the intercalated disc were investigated in adult rat cardiomyocytes (ARC). The 'redifferentiation model' of ARC involves extensive remodelling of the plasma membrane and of the myofibrillar apparatus. It represents a valuable system to elucidate the formation of cell-cell contact between cardiomyocytes and to assess the mechanisms by which different proteins involved in the cell-cell adhesion process are sorted in a precise manner to the sites of function. Appearance of N-cadherin, the catenins and connexin43 within newly formed adherens and gap junctions was studied. Here first evidence is provided for a formation of two distinct and separable N-cadherin/catenin complexes in cardiomyocytes. Both complexes are composed of N-cadherin and alpha-catenin which bind to either beta-catenin or plakoglobin in a mutually exclusive manner. The two N-cadherin/catenin complexes are assumed to be functionally involved in the formation of cell-cell contacts in ARC; however, the differential appearance and localization of the two types of complexes may also point to a specific role during ARC differentiation. The newly synthesized beta-catenin containing complex is more abundant during the first stages in culture after ARC isolation, while the newly synthesized plakoglobin containing complex progressively accumulates during the morphological changes of ARC. ARC formed a tissue-like pattern in culture whereby the new cell-cell contacts could be dissolved through Ca2+ depletion. Presence of cAMP and replenishment of Ca2+ content in the culture medium not only allowed reformation of cell-cell contacts but also affected the relative protein ratio between the two N-cadherin/catenin complexes, increasing the relative amount of newly synthesized beta-catenin over plakoglobin at a particular stage of ARC differentiation. The clustered N-cadherin/catenin complexes at the plasma membrane appear to be a prerequisite for the following gap junction formation; a temporal sequence of the appearance of adherens junction proteins and of gap junctions forming connexin-43 is suggested.

Effects of short-term tocopherol (T) feeding on structure-localized protein tyrosine nitration (pTN) patterns of mitochondrial ATPase following endotoxin (LPS) challenge in beef calves.

USDA-ARS?s Scientific Manuscript database

Mitochondrial ATPase/Complex-V (MCV) is an electron transport chain (ETC) component needed for ATP synthesis. The ETC, exquisitely sensitive to proinflammatory mediators (PIM), generates oxynitrogen reactants leading to pTN formation as mitochondrial membrane leakage occurs. Immunohistochemical loca...

Self-organization of neural tissue architectures from pluripotent stem cells.

PubMed

Karus, Michael; Blaess, Sandra; Brüstle, Oliver

2014-08-15

Despite being a subject of intensive research, the mechanisms underlying the formation of neural tissue architectures during development of the central nervous system remain largely enigmatic. So far, studies into neural pattern formation have been restricted mainly to animal experiments. With the advent of pluripotent stem cells it has become possible to explore early steps of nervous system development in vitro. These studies have unraveled a remarkable propensity of primitive neural cells to self-organize into primitive patterns such as neural tube-like rosettes in vitro. Data from more advanced 3D culture systems indicate that this intrinsic propensity for self-organization can even extend to the formation of complex architectures such as a multilayered cortical neuroepithelium or an entire optic cup. These novel experimental paradigms not only demonstrate the enormous self-organization capacity of neural stem cells, they also provide exciting prospects for studying the earliest steps of human neural tissue development and the pathogenesis of brain malformations in reductionist in vitro paradigms. © 2014 Wiley Periodicals, Inc.

Active Brownian Particles. From Individual to Collective Stochastic Dynamics

NASA Astrophysics Data System (ADS)

Romanczuk, P.; Bär, M.; Ebeling, W.; Lindner, B.; Schimansky-Geier, L.

2012-03-01

We review theoretical models of individual motility as well as collective dynamics and pattern formation of active particles. We focus on simple models of active dynamics with a particular emphasis on nonlinear and stochastic dynamics of such self-propelled entities in the framework of statistical mechanics. Examples of such active units in complex physico-chemical and biological systems are chemically powered nano-rods, localized patterns in reaction-diffusion system, motile cells or macroscopic animals. Based on the description of individual motion of point-like active particles by stochastic differential equations, we discuss different velocity-dependent friction functions, the impact of various types of fluctuations and calculate characteristic observables such as stationary velocity distributions or diffusion coefficients. Finally, we consider not only the free and confined individual active dynamics but also different types of interaction between active particles. The resulting collective dynamical behavior of large assemblies and aggregates of active units is discussed and an overview over some recent results on spatiotemporal pattern formation in such systems is given.

Human Lipopolysaccharide-binding Protein (LBP) and CD14 Independently Deliver Triacylated Lipoproteins to Toll-like Receptor 1 (TLR1) and TLR2 and Enhance Formation of the Ternary Signaling Complex*

PubMed Central

Ranoa, Diana Rose E.; Kelley, Stacy L.; Tapping, Richard I.

2013-01-01

Bacterial lipoproteins are the most potent microbial agonists for the Toll-like receptor 2 (TLR2) subfamily, and this pattern recognition event induces cellular activation, leading to host immune responses. Triacylated bacterial lipoproteins coordinately bind TLR1 and TLR2, resulting in a stable ternary complex that drives intracellular signaling. The sensitivity of TLR-expressing cells to lipoproteins is greatly enhanced by two lipid-binding serum proteins known as lipopolysaccharide-binding protein (LBP) and soluble CD14 (sCD14); however, the physical mechanism that underlies this increased sensitivity is not known. To address this, we measured the ability of LBP and sCD14 to drive ternary complex formation between soluble extracellular domains of TLR1 and TLR2 and a synthetic triacylated lipopeptide agonist. Importantly, addition of substoichiometric amounts of either LBP or sCD14 significantly enhanced formation of a TLR1·TLR2 lipopeptide ternary complex as measured by size exclusion chromatography. However, neither LBP nor sCD14 was physically associated with the final ternary complex. Similar results were obtained using outer surface protein A (OspA), a naturally occurring triacylated lipoprotein agonist from Borrelia burgdorferi. Activation studies revealed that either LBP or sCD14 sensitized TLR-expressing cells to nanogram levels of either the synthetic lipopeptide or OspA lipoprotein agonist. Together, our results show that either LBP or sCD14 can drive ternary complex formation and TLR activation by acting as mobile carriers of triacylated lipopeptides or lipoproteins. PMID:23430250

Self-Organization of Stem Cell Colonies and of Early Mammalian Embryos: Recent Experiments Shed New Light on the Role of Autonomy vs. External Instructions in Basic Body Plan Development

PubMed Central

Denker, Hans-Werner

2016-01-01

“Organoids”, i.e., complex structures that can develop when pluripotent or multipotent stem cells are maintained in three-dimensional cultures, have become a new area of interest in stem cell research. Hopes have grown that when focussing experimentally on the mechanisms behind this type of in vitro morphogenesis, research aiming at tissue and organ replacements can be boosted. Processes leading to the formation of organoids in vitro are now often addressed as self-organization, a term referring to the formation of complex tissue architecture in groups of cells without depending on specific instruction provided by other cells or tissues. The present article focuses on recent reports using the term self-organization in the context of studies on embryogenesis, specifically addressing pattern formation processes in human blastocysts attaching in vitro, or in colonies of pluripotent stem cells (“gastruloids”). These morphogenetic processes are of particular interest because, during development in vivo, they lead to basic body plan formation and individuation. Since improved methodologies like those employed by the cited authors became available, early embryonic pattern formation/self-organization appears to evolve now as a research topic of its own. This review discusses concepts concerning the involved mechanisms, focussing on autonomy of basic body plan development vs. dependence on external signals, as possibly provided by implantation in the uterus, and it addresses biological differences between an early mammalian embryo, e.g., a morula, and a cluster of pluripotent stem cells. It is concluded that, apart from being of considerable biological interest, the described type of research needs to be contemplated carefully with regard to ethical implications when performed with human cells. PMID:27792143

Self-Organization of Stem Cell Colonies and of Early Mammalian Embryos: Recent Experiments Shed New Light on the Role of Autonomy vs. External Instructions in Basic Body Plan Development.

PubMed

Denker, Hans-Werner

2016-10-25

" Organoids ", i.e., complex structures that can develop when pluripotent or multipotent stem cells are maintained in three-dimensional cultures, have become a new area of interest in stem cell research. Hopes have grown that when focussing experimentally on the mechanisms behind this type of in vitro morphogenesis, research aiming at tissue and organ replacements can be boosted. Processes leading to the formation of organoids in vitro are now often addressed as self-organization , a term referring to the formation of complex tissue architecture in groups of cells without depending on specific instruction provided by other cells or tissues. The present article focuses on recent reports using the term self-organization in the context of studies on embryogenesis , specifically addressing pattern formation processes in human blastocysts attaching in vitro, or in colonies of pluripotent stem cells (" gastruloids "). These morphogenetic processes are of particular interest because, during development in vivo, they lead to basic body plan formation and individuation. Since improved methodologies like those employed by the cited authors became available, early embryonic pattern formation/self-organization appears to evolve now as a research topic of its own. This review discusses concepts concerning the involved mechanisms, focussing on autonomy of basic body plan development vs. dependence on external signals, as possibly provided by implantation in the uterus, and it addresses biological differences between an early mammalian embryo, e.g., a morula, and a cluster of pluripotent stem cells. It is concluded that, apart from being of considerable biological interest, the described type of research needs to be contemplated carefully with regard to ethical implications when performed with human cells.

Formation and biochemical characterization of tube/pelle death domain complexes: critical regulators of postreceptor signaling by the Drosophila toll receptor.

PubMed

Schiffmann, D A; White, J H; Cooper, A; Nutley, M A; Harding, S E; Jumel, K; Solari, R; Ray, K P; Gay, N J

1999-09-07

In Drosophila, the Toll receptor signaling pathway is required for embryonic dorso-ventral patterning and at later developmental stages for innate immune responses. It is thought that dimerization of the receptor by binding of the ligand spätzle causes the formation of a postreceptor activation complex at the cytoplasmic surface of the membrane. Two components of this complex are the adaptor tube and protein kinase pelle. These proteins both have "death domains", protein interaction motifs found in a number of signaling pathways, particularly those involved in apoptotic cell death. It is thought that pelle is bound by tube during formation of the activation complexes, and that this interaction is mediated by the death domains. In this paper, we show using the yeast two-hybrid system that the wild-type tube and pelle death domains bind together. Mutant tube proteins which do not support signaling in the embryo are also unable to bind pelle in the 2-hybrid assay. We have purified proteins corresponding to the death domains of tube and pelle and show that these form corresponding heterodimeric complexes in vitro. Partial proteolysis reveals a smaller core consisting of the minimal death domain sequences. We have studied the tube/pelle interaction with the techniques of surface plasmon resonance, analytical ultracentrifugation and isothermal titration calorimetry. These measurements produce a value of K(d) for the complex of about 0.5 microM.

Reassessing the Roles of PIN Proteins and Anticlinal Microtubules during Pavement Cell Morphogenesis.

PubMed

Belteton, Samuel A; Sawchuk, Megan G; Donohoe, Bryon S; Scarpella, Enrico; Szymanski, Daniel B

2018-01-01

The leaf epidermis is a biomechanical shell that influences the size and shape of the organ. Its morphogenesis is a multiscale process in which nanometer-scale cytoskeletal protein complexes, individual cells, and groups of cells pattern growth and define macroscopic leaf traits. Interdigitated growth of neighboring cells is an evolutionarily conserved developmental strategy. Understanding how signaling pathways and cytoskeletal proteins pattern cell walls during this form of tissue morphogenesis is an important research challenge. The cellular and molecular control of a lobed cell morphology is currently thought to involve PIN-FORMED (PIN)-type plasma membrane efflux carriers that generate subcellular auxin gradients. Auxin gradients were proposed to function across cell boundaries to encode stable offset patterns of cortical microtubules and actin filaments between adjacent cells. Many models suggest that long-lived microtubules along the anticlinal cell wall generate local cell wall heterogeneities that restrict local growth and specify the timing and location of lobe formation. Here, we used Arabidopsis ( Arabidopsis thaliana ) reverse genetics and multivariate long-term time-lapse imaging to test current cell shape control models. We found that neither PIN proteins nor long-lived microtubules along the anticlinal wall predict the patterns of lobe formation. In fields of lobing cells, anticlinal microtubules are not correlated with cell shape and are unstable at the time scales of cell expansion. Our analyses indicate that anticlinal microtubules have multiple functions in pavement cells and that lobe initiation is likely controlled by complex interactions among cell geometry, cell wall stress patterns, and transient microtubule networks that span the anticlinal and periclinal walls. © 2018 American Society of Plant Biologists. All Rights Reserved.

In situ U-Th-Pb ages of the Miaoya carbonatite complex in the South Qinling orogenic belt, central China

NASA Astrophysics Data System (ADS)

Ying, Yuancan; Chen, Wei; Lu, Jue; Jiang, Shao-Yong; Yang, Yueheng

2017-10-01

The Miaoya carbonatite complex in the South Qinling orogenic belt hosts one of the largest rare earth element (REE)-Nb deposits in China that is composed of carbonatite and syenite. The emplacement age of the complex and the geochronological relationship between the carbonatite and syenite have long been debated. In this study, in situ U-Th-Pb ages have been obtained for the constituent minerals zircon, monazite and columbite from carbonatite and syenite of the Miaoya complex, together with their chemical and isotopic compositions. In situ trace element compositions for zircon from carbonatite and syenite are highly variable. The zircon displays slightly heavy REE (HREE)-enriched chondrite-normalized patterns with no Eu anomaly and various light REE (LREE) contents. In situ Th-Pb dating for zircon from the Miaoya complex by laser ablation ICP-MS yields ages of 442.6 ± 4.0 Ma (n = 53) for syenite and 426.5 ± 8.0 Ma (n = 23) for carbonatite. Monazite from carbonatite and syenite shows similar chondrite-normalized REE patterns and yields a consistent Th-Pb age of 240 Ma. Based on petrographic and chemical composition, columbite from the carbonatite can be identified into two groups. The columbite dispersed within carbonatite is characterized by slightly LREE-enriched chondrite-normalized REE patterns, whereas columbite associated with apatite is characterized by LREE-depleted trends. Columbite has been further determined to have a weighted mean 206Pb/238U age of 232.8 ± 4.5 Ma (n = 9) using LA-ICP-MS. Detailed geochronological and chemical investigations suggest that there were two major episodes of magmatic/metasomatic activities in the formational history of the Miaoya carbonatite complex. The early alkaline magmatism emplaced in the Silurian was related to the opening of the Mianlue Ocean, whereas the late metasomatism or hydrothermal overprint occurred during the Triassic South Qinling orogeny. The latter serves as the major ore formation period for both REE (e.g., monazite) and Nb (e.g., columbite).

Coupling nonlinear optical waves to photoreactive and phase-separating soft matter: Current status and perspectives

NASA Astrophysics Data System (ADS)

Biria, Saeid; Morim, Derek R.; An Tsao, Fu; Saravanamuttu, Kalaichelvi; Hosein, Ian D.

2017-10-01

Nonlinear optics and polymer systems are distinct fields that have been studied for decades. These two fields intersect with the observation of nonlinear wave propagation in photoreactive polymer systems. This has led to studies on the nonlinear dynamics of transmitted light in polymer media, particularly for optical self-trapping and optical modulation instability. The irreversibility of polymerization leads to permanent capture of nonlinear optical patterns in the polymer structure, which is a new synthetic route to complex structured soft materials. Over time more intricate polymer systems are employed, whereby nonlinear optical dynamics can couple to nonlinear chemical dynamics, opening opportunities for self-organization. This paper discusses the work to date on nonlinear optical pattern formation processes in polymers. A brief overview of nonlinear optical phenomenon is provided to set the stage for understanding their effects. We review the accomplishments of the field on studying nonlinear waveform propagation in photopolymerizable systems, then discuss our most recent progress in coupling nonlinear optical pattern formation to polymer blends and phase separation. To this end, perspectives on future directions and areas of sustained inquiry are provided. This review highlights the significant opportunity in exploiting nonlinear optical pattern formation in soft matter for the discovery of new light-directed and light-stimulated materials phenomenon, and in turn, soft matter provides a platform by which new nonlinear optical phenomenon may be discovered.

SMC5/6 is required for the formation of segregation-competent bivalent chromosomes during meiosis I in mouse oocytes

PubMed Central

Hwang, Grace; Sun, Fengyun; Eppig, John J.; Handel, Mary Ann

2017-01-01

SMC complexes include three major classes: cohesin, condensin and SMC5/6. However, the localization pattern and genetic requirements for the SMC5/6 complex during mammalian oogenesis have not previously been examined. In mouse oocytes, the SMC5/6 complex is enriched at the pericentromeric heterochromatin, and also localizes along chromosome arms during meiosis. The infertility phenotypes of females with a Zp3-Cre-driven conditional knockout (cKO) of Smc5 demonstrated that maternally expressed SMC5 protein is essential for early embryogenesis. Interestingly, protein levels of SMC5/6 complex components in oocytes decline as wild-type females age. When SMC5/6 complexes were completely absent in oocytes during meiotic resumption, homologous chromosomes failed to segregate accurately during meiosis I. Despite what appears to be an inability to resolve concatenation between chromosomes during meiosis, localization of topoisomerase IIα to bivalents was not affected; however, localization of condensin along the chromosome axes was perturbed. Taken together, these data demonstrate that the SMC5/6 complex is essential for the formation of segregation-competent bivalents during meiosis I, and findings suggest that age-dependent depletion of the SMC5/6 complex in oocytes could contribute to increased incidence of oocyte aneuploidy and spontaneous abortion in aging females. PMID:28302748

Distribution pattern of rare earth ions between water and montmorillonite and its relation to the sorbed species of the ions.

PubMed

Takahashi, Yoshio; Tada, Akisa; Shimizu, Hiroshi

2004-09-01

REE (rare earth element) distribution coefficients (Kd) between the aqueous phase and montmorillonite surface were obtained to investigate the relation between the REE distribution patterns and the species of REE sorbed on the solid-water interface. It was shown that the features in the REE patterns, such as the slope of the REE patterns, the tetrad effect, and the Y/Ho ratio, were closely related to the REE species at the montmorillonite-water interface. In a binary system (REE-montmorillonite) below pH 5, three features (a larger Kd value for a lighter REE, the absence of the tetrad effect, and the Y/Ho ratio being unchanged from its initial value) suggest that hydrated REE are directly sorbed as an outer-sphere complex at the montmorillonite-water interface. Above pH 5.5, the features in the REE patterns, the larger Kd value for heavier REE, the M-type tetrad effect, and the reduced Y/Ho ratio, showed the formation of an inner-sphere complex of REE with -OH group at the montmorillonite surface. In addition, the REE patterns in the presence of humic acid at pH 5.9 were also studied, where the REE patterns became flat, suggesting that the humate complex is dominant as both dissolved and sorbed species of REE in the ternary system. All of these results were consistent with the spectroscopic data (laser-induced fluorescence spectroscopy) showing the local structure of Eu(III) conducted in the same experimental system. The present results suggest that the features in the REE distribution patterns include information on the REE species at the solid-water interface.

An experimental design method leading to chemical Turing patterns.

PubMed

Horváth, Judit; Szalai, István; De Kepper, Patrick

2009-05-08

Chemical reaction-diffusion patterns often serve as prototypes for pattern formation in living systems, but only two isothermal single-phase reaction systems have produced sustained stationary reaction-diffusion patterns so far. We designed an experimental method to search for additional systems on the basis of three steps: (i) generate spatial bistability by operating autoactivated reactions in open spatial reactors; (ii) use an independent negative-feedback species to produce spatiotemporal oscillations; and (iii) induce a space-scale separation of the activatory and inhibitory processes with a low-mobility complexing agent. We successfully applied this method to a hydrogen-ion autoactivated reaction, the thiourea-iodate-sulfite (TuIS) reaction, and noticeably produced stationary hexagonal arrays of spots and parallel stripes of pH patterns attributed to a Turing bifurcation. This method could be extended to biochemical reactions.

Amygdala connections with jaw, tongue and laryngo-pharyngeal premotor neurons.

PubMed

Van Daele, D J; Fazan, V P S; Agassandian, K; Cassell, M D

2011-03-17

As the central nucleus (CE) is the only amygdaloid nucleus to send axons to the pons and medulla, it is thought to be involved in the expression of conditioned responses by accessing hindbrain circuitry generating stereotypic responses to aversive stimuli. Responses to aversive oral stimuli include gaping and tongue protrusion generated by central pattern generators and other premotor neurons in the ponto-medullary reticular formation. We investigated central nucleus connections with the reticular formation by identifying premotor reticular formation neurons through the retrograde trans-synaptic transport of pseudorabies virus (PRV) inoculated into masseter, genioglossus, thyroarytenoid or inferior constrictor muscles in combination with anterograde labeling of CE axons with biotinylated dextran amine. Three dimensional mapping of PRV infected premotor neurons revealed specific clusters of these neurons associated with different oro-laryngo-pharyngeal muscles, particularly in the parvicellular reticular formation. CE axon terminals were concentrated in certain parvicellular clusters but overall putative contacts were identified with premotor neurons associated with all four oro-laryngo-pharyngeal muscles investigated. We also mapped the retrograde trans-synaptic spread of PRV through the various nuclei of the amygdaloid complex. Medial CE was the first amygdala structure infected (4 days post-inoculation) with trans-synaptic spread to the lateral CE and the caudomedial parvicellular basolateral nucleus by day 5 post-inoculation. Infected neurons were only very rarely found in the lateral capsular CE and the lateral nucleus and then at only the latest time points. The data demonstrate that the CE is directly connected with clusters of reticular premotor neurons that may represent complex pattern generators and/or switching elements for the generation of stereotypic oral and laryngo-pharyngeal movements during aversive oral stimulation. Serial connections through the amygdaloid complex linked with the oro-laryngo-pharyngeal musculature appear quite distinct from those believed to sub-serve fear responses, suggesting there are distinct "channels" for the acquisition and expression of particular conditioned behaviors. Copyright © 2011 IBRO. Published by Elsevier Ltd. All rights reserved.

Chemotactic-based adaptive self-organization during colonial development

NASA Astrophysics Data System (ADS)

Cohen, Inon; Czirók, Andras; Ben-Jacob, Eshel

1996-02-01

Bacterial colonies have developed sophisticated modes of cooperative behavior which enable them to respond to adverse growth conditions. It has been shown that such behavior can be manifested in the development of complex colonial patterns. Certain bacterial species exhibit formation of branching patterns during colony development. Here we present a generic model to describe such patterning of swimming (tumbling) bacteria on agar surfaces. The model incorporates: (1) food diffusion, (2) reproduction and sporulation of the cells, (3) movement of the bacterial cells within a self-produced wetting fluid and (4) chemotactic signaling. As a plausible explanation for transitions between different branching morphologies, we propose an interplay between chemotaxis towards food, self-produced short range chemoattractant and long range chemorepellent.

Encapsulation and stabilization of β-carotene by amylose inclusion complexes.

PubMed

Kong, Lingyan; Bhosale, Rajesh; Ziegler, Gregory R

2018-03-01

In the present study, we report a novel composition based on amylose (or starch) inclusion complex with an amphiphilic material as an effective encapsulation platform technology to incorporate guests of interest. Specifically, the encapsulation of β-carotene in amylose-surfactant and amylose/starch-ascorbyl palmitate (AscP) inclusion complexes was investigated. Surfactants of different hydrophilicity/lipophilicity were selected to cover a broad range of HLB values. The formation of the inclusion complexes was characterized by X-ray diffraction and differential scanning calorimetry. The ability of amylose-surfactant system to encapsulate β-carotene was dependent on the HLB value of the surfactants, instead of their ability to induce inclusion complexation. The incorporation of β-carotene hindered amylose-surfactant inclusion complex formation, whereas no significant effect was observed on structural and thermal properties of starch-AscP inclusion complex in the presence of β-carotene. The X-ray diffraction pattern of amylose-AscP-β-carotene showed that β-carotene molecules did not crystallize into a separated phase and thus were suggested to be homogeneously immobilized within the polycrystalline amylose-AscP inclusion complexes. During a storage period of six weeks at 20 and 30°C, the stability of β-carotene was improved by encapsulation in starch-AscP inclusion complexes compared with that in physical mixtures of the three components. Copyright © 2017 Elsevier Ltd. All rights reserved.

Desiccation of a pool of blood: from fluid mechanics to forensic investigations

NASA Astrophysics Data System (ADS)

Nicloux, Celine; Brutin, David

2012-11-01

The evaporation of biological fluids (with droplet configuration) has been studied since a few years due to several applications in medical fields such as medical tests, drug screening, biostabilization... The evaporation of a drop of whole blood leads to the formation of final typical pattern of cracks. Flow motion, adhesion, gelation and fracturation all occur during the evaporation of this complex matter. During the drying, a sol-gel transition develops. The evaporation of a pool of blood is studied in order to link the pattern formation and the evaporation dynamics. We intend to transfer the knowledge acquired for drops on pool to improve the forensic investigations. In this study, we focus on both pool of blood and pure water to determine the transition region from drop to pool and then to characterize the evaporation rate in the pool configuration. The spreading of blood which can be seen as a complex fluid is strongly influenced the substrate nature. The initial contact angle of blood on different substrate nature will influence the maximum thickness of the layer and then will influence the evaporation mass flux. The authors gratefully acknowledge the help and the fruitful discussions raised with A. Boccoz.

Comprehensive microarray-based analysis for stage-specific larval camouflage pattern-associated genes in the swallowtail butterfly, Papilio xuthus

PubMed Central

2012-01-01

Background Body coloration is an ecologically important trait that is often involved in prey-predator interactions through mimicry and crypsis. Although this subject has attracted the interest of biologists and the general public, our scientific knowledge on the subject remains fragmentary. In the caterpillar of the swallowtail butterfly Papilio xuthus, spectacular changes in the color pattern are observed; the insect mimics bird droppings (mimetic pattern) as a young larva, and switches to a green camouflage coloration (cryptic pattern) in the final instar. Despite the wide variety and significance of larval color patterns, few studies have been conducted at a molecular level compared with the number of studies on adult butterfly wing patterns. Results To obtain a catalog of genes involved in larval mimetic and cryptic pattern formation, we constructed expressed sequence tag (EST) libraries of larval epidermis for P. xuthus, and P. polytes that contained 20,736 and 5,376 clones, respectively, representing one of the largest collections available in butterflies. A comparison with silkworm epidermal EST information revealed the high expression of putative blue and yellow pigment-binding proteins in Papilio species. We also designed a microarray from the EST dataset information, analyzed more than five stages each for six markings, and confirmed spatial expression patterns by whole-mount in situ hybridization. Hence, we succeeded in elucidating many novel marking-specific genes for mimetic and cryptic pattern formation, including pigment-binding protein genes, the melanin-associated gene yellow-h3, the ecdysteroid synthesis enzyme gene 3-dehydroecdysone 3b-reductase, and Papilio-specific genes. We also found many cuticular protein genes with marking specificity that may be associated with the unique surface nanostructure of the markings. Furthermore, we identified two transcription factors, spalt and ecdysteroid signal-related E75, as genes expressed in larval eyespot markings. This finding suggests that E75 is a strong candidate mediator of the hormone-dependent coordination of larval pattern formation. Conclusions This study is one of the most comprehensive molecular analyses of complicated morphological features, and it will serve as a new resource for studying insect mimetic and cryptic pattern formation in general. The wide variety of marking-associated genes (both regulatory and structural genes) identified by our screening indicates that a similar strategy will be effective for understanding other complex traits. PMID:22651552

Pattern palette for complex fluid flows

NASA Astrophysics Data System (ADS)

Sandnes, B.

2012-04-01

From landslides to oil and gas recovery to the squeeze of a toothpaste tube, flowing complex fluids are everywhere around us in nature and engineering. That is not to say, though, that they are always well understood. The dissipative interactions, through friction and inelastic collisions, often give rise to nonlinear dynamics and complexity manifested in pattern formation on large scales. The images displayed on this poster illustrate the diverse morphologies found in multiphase flows involving wet granular material: Air is injected into a generic mixture of granular material and fluid contained in a 500 µm gap between two parallel glass plates. At low injection rates, friction between the grains - glass beads averaging 100 µm in diameter - dominates the rheology, producing "stick-slip bubbles" and labyrinthine frictional fingering. A transition to various other morphologies, including "corals" and viscous fingers, emerges for increasing injection rate. At sufficiently high granular packing fractions, the material behaves like a deformable, porous solid, and the air rips through in sudden fractures.

Molecular complexes of alprazolam with carboxylic acids, boric acid, boronic acids, and phenols. Evaluation of supramolecular heterosynthons mediated by a triazole ring.

PubMed

Varughese, Sunil; Azim, Yasser; Desiraju, Gautam R

2010-09-01

A series of molecular complexes, both co-crystals and salts, of a triazole drug-alprazolam-with carboxylic acids, boric acid, boronic acids, and phenols have been analyzed with respect to heterosynthons present in the crystal structures. In all cases, the triazole ring behaves as an efficient hydrogen bond acceptor with the acidic coformers. The hydrogen bond patterns exhibited with aromatic carboxylic acids were found to depend on the nature and position of the substituents. Being a strong acid, 2,6-dihydroxybenzoic acid forms a salt with alprazolam. With aliphatic dicarboxylic acids alprazolam forms hydrates and the water molecules play a central role in synthon formation and crystal packing. The triazole ring makes two distinct heterosynthons in the molecular complex with boric acid. Boronic acids and phenols form consistent hydrogen bond patterns, and these are seemingly independent of the substitutional effects. Boronic acids form noncentrosymmetric cyclic synthons, while phenols form O--H...N hydrogen bonds with the triazole ring.

Self-Organized Lattices of Nonlinear Optochemical Waves in Photopolymerizable Fluids: The Spontaneous Emergence of 3-D Order in a Weakly Correlated System.

PubMed

Ponte, Matthew R; Hudson, Alexander D; Saravanamuttu, Kalaichelvi

2018-03-01

Many of the extraordinary three-dimensional architectures that pattern our physical world emerge from complex nonlinear systems or dynamic populations whose individual constituents are only weakly correlated to each other. Shoals of fish, murmuration behaviors in birds, congestion patterns in traffic, and even networks of social conventions are examples of spontaneous pattern formation, which cannot be predicted from the properties of individual elements alone. Pattern formation at a different scale has been observed or predicted in weakly correlated systems including superconductors, atomic gases near Bose Einstein condensation, and incoherent optical fields. Understanding pattern formation in nonlinear weakly correlated systems, which are often unified through mathematical expression, could pave intelligent self-organizing pathways to functional materials, architectures, and computing technologies. However, it is experimentally difficult to directly visualize the nonlinear dynamics of pattern formation in most populations-especially in three dimensions. Here, we describe the collective behavior of large populations of nonlinear optochemical waves, which are poorly correlated in both space and time. The optochemical waves-microscopic filaments of white light entrapped within polymer channels-originate from the modulation instability of incandescent light traveling in photopolymerizable fluids. By tracing the three-dimensional distribution of optical intensity in the nascent polymerizing system, we find that populations of randomly distributed, optochemical waves synergistically and collectively shift in space to form highly ordered lattices of specific symmetries. These, to our knowledge, are the first three-dimensionally periodic structures to emerge from a system of weakly correlated waves. Their spontaneous formation in an incoherent and effectively chaotic field is counterintuitive, but the apparent contradiction of known behaviors of light including the laws of optical interference can be explained through the soliton-like interactions of optochemical waves with nearest neighbors. Critically, this work casts fundamentally new insight into the collective behaviors of poorly correlated nonlinear waves in higher dimensions and provides a rare, accessible platform for further experimental studies of these previously unexplored behaviors. Furthermore, it defines a self-organization paradigm that, unlike conventional counterparts, could generate polymer microstructures with symmetries spanning all the Bravais lattices.

A carbohydrate-anion recognition system in aprotic solvents.

PubMed

Ren, Bo; Dong, Hai; Ramström, Olof

2014-05-01

A carbohydrate-anion recognition system in nonpolar solvents is reported, in which complexes form at the B-faces of β-D-pyranosides with H1-, H3-, and H5-cis patterns similar to carbohydrate-π interactions. The complexation effect was evaluated for a range of carbohydrate structures; it resulted in either 1:1 carbohydrate-anion complexes, or 1:2 complex formation depending on the protection pattern of the carbohydrate. The interaction was also evaluated with different anions and solvents. In both cases it resulted in significant binding differences. The results indicate that complexation originates from van der Waals interactions or weak CH⋅⋅⋅A(-) hydrogen bonds between the binding partners and is related to electron-withdrawing groups of the carbohydrates as well as increased hydrogen-bond-accepting capability of the anions. © 2014 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA. This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.

Unbound Young Stellar Systems: Star Formation on the Loose

NASA Astrophysics Data System (ADS)

Gouliermis, Dimitrios A.

2018-07-01

Unbound young stellar systems, the loose ensembles of physically related young bright stars, trace the typical regions of recent star formation in galaxies. Their morphologies vary from small few pc-size associations of newly formed stars to enormous few kpc-size complexes composed of stars few 100 Myr old. These stellar conglomerations are located within the disks and along the spiral arms and rings of star-forming disk galaxies, and they are the active star-forming centers of dwarf and starburst galaxies. Being associated with star-forming regions of various sizes, these stellar structures trace the regions where stars form at various length- and timescales, from compact clusters to whole galactic disks. Stellar associations, the prototypical unbound young systems, and their larger counterparts, stellar aggregates, and stellar complexes, have been the focus of several studies for quite a few decades, with special interest on their demographics, classification, and structural morphology. The compiled surveys of these loose young stellar systems demonstrate that the clear distinction of these systems into well-defined classes is not as straightforward as for stellar clusters, due to their low densities, asymmetric shapes and variety in structural parameters. These surveys also illustrate that unbound stellar structures follow a clear hierarchical pattern in the clustering of their stars across various scales. Stellar associations are characterized by significant sub-structure with bound stellar clusters being their most compact parts, while associations themselves are the brighter denser parts of larger stellar aggregates and stellar complexes, which are members of larger super-structures up to the scale of a whole star-forming galaxy. This structural pattern, which is usually characterized as self-similar or fractal, appears to be identical to that of star-forming giant molecular clouds and interstellar gas, driven mainly by turbulence cascade. In this short review, I make a concise compilation of our understanding of unbound young stellar systems across various environments in the local universe, as it is developed during the last 60 years. I present a factual assessment of the clustering behavior of star formation, as revealed from the assembling pattern of stars across loose stellar structures and its relation to the interstellar medium and the environmental conditions. I also provide a consistent account of the processes that possibly play important role in the formation of unbound stellar systems, compiled from both theoretical and observational investigations on the field.

Synthesis, characterization, photoluminescence, and electrochemical studies of novel mononuclear Cu(II) and Zn(II) complexes with the 1-benzylimidazolium ligand

NASA Astrophysics Data System (ADS)

Bibi, Sherino; Mohammad, Sharifah; Manan, Ninie Suhana Abdul; Ahmad, Jimmy; Kamboh, Muhammad Afzal; Khor, Sook Mei; Yamin, Bohari M.; Abdul Halim, Siti Nadiah

2017-08-01

Two new mononuclear coordination complexes [Cu(bim)4Cl2]ṡ2H2O (1) and [Zn(bim)2Cl2] (2) containing the 1-benzylimidazole (bim) ligand were successfully synthesized. Both complexes were characterized by IR, UV-vis, and fluorescence spectroscopies, single crystal and powder X-ray diffraction measurements, and thermogravimetric analysis. Self-assembly during the recrystallization process resulted in the formation of octahedral and tetrahedral Cu(II) and Zn(II) complexes, respectively. The single crystals obtained are representative of the bulk material, as shown by the powder X-ray diffraction patterns. Cyclic voltammetry measurements showed that complex 1 undergoes a quasi-reversible redox reaction, while complex 2 undergoes reduction alone, and no oxidation peak was observed; this is due to the stability of the reduced form of complex 2.

Charge and pressure-tuned surface patterning of surfactant-encapsulated polyoxometalate complexes at the air-water interface.

PubMed

Xu, Miao; Li, Haolong; Zhang, Liying; Wang, Yizhan; Yuan, Yuan; Zhang, Jianming; Wu, Lixin

2012-10-16

In this paper, four organic-inorganic hybrid complexes were prepared using a cationic surfactant dimethyldioctadecylammonium (DODA) to replace the counter cations of four Keggin-type polyoxometalate (POM) clusters with gradually increased negative charges, PW(12)O(40)(3-), SiW(12)O(40)(4-), BW(12)O(40)(5-), and CoW(12)O(40)(6-). The formed surfactant-encapsulated POM (SEP) complexes showed typical amphiphilic properties and can be spread onto the air-water interface to form Langmuir monolayers. The interfacial behavior of the SEP monolayer films was systemically studied by multiple in situ and ex situ characterization methods including Brewster angle microscopy (BAM), atomic force microscopy (AFM), reflection-absorption infrared (RAIR), and X-ray photoelectron spectroscopy (XPS). We found that the increasing alkyl chain density of SEPs leads to an enhanced stability and a higher collapse pressure of SEP Langmuir monolayers. Moreover, a second layer evolved as patterns from the initial monolayers of all the SEPs, when the surface pressures approached the collapse values. The rational combination of alkyl chain density and surface pressure can precisely control the size and the morphology of SEP patterns transforming from disk-like to leaf-like structures on a micrometer scale. The pattern formation was demonstrated to be driven by the self-optimized surface energy of SEP monolayers. This finding can direct a new strategy for the fabrication of POM-hybrid films with controllable patterns, which should be instructive for designing POM-based thin film devices.

Patterned assembly of colloidal particles by confined dewetting lithography.

PubMed

Celio, Hugo; Barton, Emily; Stevenson, Keith J

2006-12-19

We report the assembly of colloidal particles into confined arrangements and patterns on various cleaned and chemically modified solid substrates using a method which we term "confined dewetting lithography" or CDL for short. The experimental setup for CDL is a simple deposition cell where an aqueous suspension of colloidal particles (e.g., polystyrene spheres) is placed between a floating deposition template (i.e., metal microgrid) and the solid substrate. The voids of the deposition template serve as an array of micrometer-sized reservoirs where several hydrodynamic processes are confined. These processes include water evaporation, meniscus formation, convective flow, rupturing, dewetting, and capillary-bridge formation. We discuss the optimal conditions where the CDL has a high efficiency to deposit intricate patterns of colloidal particles using polystyrene spheres (PS; 4.5, 2.0, 1.7, 0.11, 0.064 microm diameter) and square and hexagonal deposition templates as model systems. We find that the optimization conditions of the CDL method, when using submicrometer, sulfate-functionalized PS particles, are primarily dependent on minimizing attractive particle-substrate interactions. The CDL methodology described herein presents a relatively simple and rapid method to assemble virtually any geometric pattern, including more complex patterns assembled using PS particles with different diameters, from aqueous suspensions by choosing suitable conditions and materials.

Mass Spectrometry Profiles Superoxide-Induced Intra-molecular Disulfide in the FMN-binding Subunit of Mitochondrial Complex I

PubMed Central

Zhang, Liwen; Xu, Hua; Chen, Chwen-Lih; Green-Church, Kari B.; Freitas, Michael A.; Chen, Yeong-Renn

2008-01-01

Protein thiols with regulatory functions play a critical role in maintaining the homeostasis of the redox state in mitochondria. One major host of regulatory cysteines in mitochondria is complex I, with the thiols primarily located on its 51 kDa FMN-binding subunit. In response to oxidative stress, these thiols are expected to form intra-molecular disulfide bridges as one of their oxidative post-translational modifications. Here, to test this hypothesis and gain insights into the molecular pattern of disulfide in complex I, the isolated bovine complex I was prepared. Superoxide (O2•−) is generated by complex I under the conditions of enzyme turnover. O2•−-induced intra-molecular disulfide formation at the 51 kDa subunit was determined by tandem mass spectrometry and database searching, with the latter accomplished by adaptation of the in-house developed database search engine, MassMatrix [Xu H., et. al J. Proteome Res. (2008) 7, 138–44]. LC/MS/MS analysis of tryptic/chymotryptic digests of the 51 kDa subunit from alkylated complex I revealed that four specific cysteines (C125, C142, C187, and C206) of the 51 kDa subunit were involved in the formation of mixed intra-molecular disulfide linkages. In all, three cysteine pairs were observed: C125/C142, C187/C206, and C142/C206. The formation of disulfide bond was subsequently inhibited by superoxide dismutase, indicating the involvement of O2•−. These results elucidated by mass spectrometry indicates that the residues of C125, C142, C187, and C206 are the specific regulatory cysteines of complex I, and they participate in the oxidative modification with disulfide formation under the physiological or pathophysiological conditions of oxidative stress. PMID:18789718

Establishment of spatial pattern.

PubMed

Slack, Jonathan

2014-01-01

An overview and perspective are presented of mechanisms for the development of spatial pattern in animal embryos. It is intended both for new entrants to developmental biology and for specialists in other fields, with only a basic knowledge of animal life cycles being required. The first event of pattern formation is normally the localization of a cytoplasmic determinant in the egg, either during oogenesis or post-fertilization. Following cleavage to a multicellular stage, some cells contain the determinant and others do not. The determinant confers a specific developmental pathway on the cells that contain it, often making them the source of the first extracellular signal, or inducing factor. Inducing factors often form concentration gradients to which cells respond by up or downregulating genes at various concentration thresholds. This enables an initial situation consisting of two cell states (with or without the determinant) to generate a multistate pattern. Multiple rounds of gradient signaling, interspersed with phases of morphogenetic movements, can generate a complex pattern using a small number of signals and responding genes. Development proceeds in a hierarchical manner, with broad body subdivisions being specified initially, and becoming successively subdivided to give individual organs and tissues composed of multiple cell types in a characteristic arrangement. Double gradient models can account for embryonic regulation, whereby a similarly proportioned body pattern is formed following removal of material. Processes that are involved at the later stages include the formation of repeating structures by the combination of an oscillator with a gradient, and the formation of tissues with one cell type scattered in a background of another through a process called lateral inhibition. This set of processes make up a 'developmental toolkit' which can be deployed in various sequences and combinations to generate a very wide variety of structures and cell types. © 2014 Wiley Periodicals, Inc.

The formation and distribution of hippocampal synapses on patterned neuronal networks

NASA Astrophysics Data System (ADS)

Dowell-Mesfin, Natalie M.

Communication within the central nervous system is highly orchestrated with neurons forming trillions of specialized junctions called synapses. In vivo, biochemical and topographical cues can regulate neuronal growth. Biochemical cues also influence synaptogenesis and synaptic plasticity. The effects of topography on the development of synapses have been less studied. In vitro, neuronal growth is unorganized and complex making it difficult to study the development of networks. Patterned topographical cues guide and control the growth of neuronal processes (axons and dendrites) into organized networks. The aim of this dissertation was to determine if patterned topographical cues can influence synapse formation and distribution. Standard fabrication and compression molding procedures were used to produce silicon masters and polystyrene replicas with topographical cues presented as 1 mum high pillars with diameters of 0.5 and 2.0 mum and gaps of 1.0 to 5.0 mum. Embryonic rat hippocampal neurons grown unto patterned surfaces. A developmental analysis with immunocytochemistry was used to assess the distribution of pre- and post-synaptic proteins. Activity-dependent pre-synaptic vesicle uptake using functional imaging dyes was also performed. Adaptive filtering computer algorithms identified synapses by segmenting juxtaposed pairs of pre- and post-synaptic labels. Synapse number and area were automatically extracted from each deconvolved data set. In addition, neuronal processes were traced automatically to assess changes in synapse distribution. The results of these experiments demonstrated that patterned topographic cues can induce organized and functional neuronal networks that can serve as models for the study of synapse formation and plasticity as well as for the development of neuroprosthetic devices.

Pattern formation--A missing link in the study of ecosystem response to environmental changes.

PubMed

Meron, Ehud

2016-01-01

Environmental changes can affect the functioning of an ecosystem directly, through the response of individual life forms, or indirectly, through interspecific interactions and community dynamics. The feasibility of a community-level response has motivated numerous studies aimed at understanding the mutual relationships between three elements of ecosystem dynamics: the abiotic environment, biodiversity and ecosystem function. Since ecosystems are inherently nonlinear and spatially extended, environmental changes can also induce pattern-forming instabilities that result in spatial self-organization of life forms and resources. This, in turn, can affect the relationships between these three elements, and make the response of ecosystems to environmental changes far more complex. Responses of this kind can be expected in dryland ecosystems, which show a variety of self-organizing vegetation patterns along the rainfall gradient. This paper describes the progress that has been made in understanding vegetation patterning in dryland ecosystems, and the roles it plays in ecosystem response to environmental variability. The progress has been achieved by modeling pattern-forming feedbacks at small spatial scales and up-scaling their effects to large scales through model studies. This approach sets the basis for integrating pattern formation theory into the study of ecosystem dynamics and addressing ecologically significant questions such as the dynamics of desertification, restoration of degraded landscapes, biodiversity changes along environmental gradients, and shrubland-grassland transitions. Copyright © 2015 Elsevier Inc. All rights reserved.

Artificial Loading of ASC Specks with Cytosolic Antigens

PubMed Central

Sahillioğlu, Ali Can; Özören, Nesrin

2015-01-01

Inflammasome complexes form upon interaction of Nod Like Receptor (NLR) proteins with pathogen associated molecular patterns (PAPMS) inside the cytosol. Stimulation of a subset of inflammasome receptors including NLRP3, NLRC4 and AIM2 triggers formation of the micrometer-sized spherical supramolecular complex called the ASC speck. The ASC speck is thought to be the platform of inflammasome activity, but the reason why a supramolecular complex is preferred against oligomeric platforms remains elusive. We observed that a set of cytosolic proteins, including the model antigen ovalbumin, tend to co-aggregate on the ASC speck. We suggest that co-aggregation of antigenic proteins on the ASC speck during intracellular infection might be instrumental in antigen presentation. PMID:26258904

D2+ Molecular complex in non-uniform height quantum ribbon under crossed electric and magnetic fields

NASA Astrophysics Data System (ADS)

Suaza, Y. A.; Laroze, D.; Fulla, M. R.; Marín, J. H.

2018-05-01

The D2+ molecular complex fundamental properties in a uniform and multi-hilled semiconductor quantum ribbon under orthogonal electric and magnetic fields are theoretically studied. The energy structure is calculated by using adiabatic approximation combined with diagonalization procedure. The D2+ energy structure is more strongly controlled by the geometrical structural hills than the Coulomb interaction. The formation of vibrational and rotational states is discussed. Aharanov-Bohm oscillation patterns linked to rotational states as well as the D2+ molecular complex stability are highly sensitive to the number of hills while electric field breaks the electron rotational symmetry and removes the energy degeneration between low-lying states.

[A NATURAL PLAGUE FOCUS. IN GORNYI ALTAI: FORMATION, DEVELOPMENT, AND FUNCTIONING].

PubMed

Korzun, V M; Balakhoiov, S V; Chpanin, E V; Denisov, A V; Mikhailov, E P; Mischenko, A J; Yarygina, M B; Rozhdestvensky, E N; Fomina, L A

2016-01-01

The paper gives the results of analyzing the data of long-term studies of the natural focal pattern of plague in the Gornyi Altai natural focus. It describes a wide range of biological processes occurring in the focus and shows the most important patterns of its functioning as a complex multilevel ecological system. The key features of the formation of the focus have been revealed. The plague focus in South-Western Altai has formed relatively, recently, about half a century ago, then it has intensively developed and its enzootic area and the activity of epizootic manifestations have considerably increased. This process is due to the space-time transformations of the basic ecological and population characteristics of Pallas' pika (Ochotoma pallasi), the principal vector of the pathogen of plague and fleas parasitizing the mammal, which is in turn related to the aridization of mountain steppes in South-Western Altai.

Topology-generating interfacial pattern formation during liquid metal dealloying

DOE PAGES

Geslin, Pierre -Antoine; McCue, Ian; Gaskey, Bernard; ...

2015-11-19

Liquid metal dealloying has emerged as a novel technique to produce topologically complex nanoporous and nanocomposite structures with ultra-high interfacial area and other unique properties relevant for diverse material applications. This process is empirically known to require the selective dissolution of one element of a multicomponent solid alloy into a liquid metal to obtain desirable structures. However, how structures form is not known. Here we demonstrate, using mesoscale phase-field modelling and experiments, that nano/microstructural pattern formation during dealloying results from the interplay of (i) interfacial spinodal decomposition, forming compositional domain structures enriched in the immiscible element, and (ii) diffusion-coupled growthmore » of the enriched solid phase and the liquid phase into the alloy. We highlight how those two basic mechanisms interact to yield a rich variety of topologically disconnected and connected structures. Furthermore, we deduce scaling laws governing microstructural length scales and dealloying kinetics.« less

Topology-generating interfacial pattern formation during liquid metal dealloying.

PubMed

Geslin, Pierre-Antoine; McCue, Ian; Gaskey, Bernard; Erlebacher, Jonah; Karma, Alain

2015-11-19

Liquid metal dealloying has emerged as a novel technique to produce topologically complex nanoporous and nanocomposite structures with ultra-high interfacial area and other unique properties relevant for diverse material applications. This process is empirically known to require the selective dissolution of one element of a multicomponent solid alloy into a liquid metal to obtain desirable structures. However, how structures form is not known. Here we demonstrate, using mesoscale phase-field modelling and experiments, that nano/microstructural pattern formation during dealloying results from the interplay of (i) interfacial spinodal decomposition, forming compositional domain structures enriched in the immiscible element, and (ii) diffusion-coupled growth of the enriched solid phase and the liquid phase into the alloy. We highlight how those two basic mechanisms interact to yield a rich variety of topologically disconnected and connected structures. Moreover, we deduce scaling laws governing microstructural length scales and dealloying kinetics.

Patterning at the 10 nanometer length scale using a strongly segregating block copolymer thin film and vapor phase infiltration of inorganic precursors

NASA Astrophysics Data System (ADS)

Choi, Jonathan W.; Li, Zhaodong; Black, Charles T.; Sweat, Daniel P.; Wang, Xudong; Gopalan, Padma

2016-06-01

In this work, we demonstrate the use of self-assembled thin films of the cylinder-forming block copolymer poly(4-tert-butylstyrene-block-2-vinylpyridine) to pattern high density features at the 10 nm length scale. This material's large interaction parameter facilitates pattern formation in single-digit nanometer dimensions. This block copolymer's accessible order-disorder transition temperature allows thermal annealing to drive the assembly of ordered 2-vinylpyridine cylinders that can be selectively complexed with the organometallic precursor trimethylaluminum. This unique chemistry converts organic 2-vinylpyridine cylinders into alumina nanowires with diameters ranging from 8 to 11 nm, depending on the copolymer molecular weight. Graphoepitaxy of this block copolymer aligns and registers sub-12 nm diameter nanowires to larger-scale rectangular, curved, and circular features patterned by optical lithography. The alumina nanowires function as a robust hard mask to withstand the conditions required for patterning the underlying silicon by plasma etching. We conclude with a discussion of some of the challenges that arise with using block copolymers for patterning at sub-10 nm feature sizes.In this work, we demonstrate the use of self-assembled thin films of the cylinder-forming block copolymer poly(4-tert-butylstyrene-block-2-vinylpyridine) to pattern high density features at the 10 nm length scale. This material's large interaction parameter facilitates pattern formation in single-digit nanometer dimensions. This block copolymer's accessible order-disorder transition temperature allows thermal annealing to drive the assembly of ordered 2-vinylpyridine cylinders that can be selectively complexed with the organometallic precursor trimethylaluminum. This unique chemistry converts organic 2-vinylpyridine cylinders into alumina nanowires with diameters ranging from 8 to 11 nm, depending on the copolymer molecular weight. Graphoepitaxy of this block copolymer aligns and registers sub-12 nm diameter nanowires to larger-scale rectangular, curved, and circular features patterned by optical lithography. The alumina nanowires function as a robust hard mask to withstand the conditions required for patterning the underlying silicon by plasma etching. We conclude with a discussion of some of the challenges that arise with using block copolymers for patterning at sub-10 nm feature sizes. Electronic supplementary information (ESI) available. See DOI: 10.1039/c6nr01409g

Wilson cycle studies

NASA Technical Reports Server (NTRS)

1987-01-01

Continents originate by the sweeping together of island arcs. Continental and island arc crusts are dominated by rocks of comparable compositional and density ranges, evidence of the operation of this process is abundant in the geological record, and can be seen in action today in Indonesia. Lineaments within continents are attributable to a small number of processes of continent formation and modification, but interactions among these processes may produce complex patterns.

Gigantism in a bacterium, Epulopiscium fishelsoni, correlates with complex patterns in arrangement, quantity, and segregation of DNA.

PubMed

Bresler, V; Montgomery, W L; Fishelson, L; Pollak, P E

1998-11-01

Epulopiscium fishelsoni, gut symbiont of the brown surgeonfish (Acanthurus nigrofuscus) in the Red Sea, attains a larger size than any other eubacterium, varies 10- to 20-fold in length (and >2, 000-fold in volume), and undergoes a complex daily life cycle. In early morning, nucleoids contain highly condensed DNA in elongate, chromosome-like structures which are physically separated from the general cytoplasm. Cell division involves production of two (rarely three) nucleoids within a cell, deposition of cell walls around expanded nucleoids, and emergence of daughter cells from the parent cell. Fluorescence measurements of DNA, RNA, and other cell components indicate the following. DNA quantity is proportional to cell volume over cell lengths of approximately 30 micrometers to >500 micrometers. For cells of a given size, nucleoids of cells with two nucleoids (binucleoid) contain approximately equal amounts of DNA. And each nucleoid of a binucleoid cell contains one-half the DNA of the single nucleoid in a uninucleoid cell of the same size. The life cycle involves approximately equal subdivision of DNA among daughter cells, formation of apical caps of condensed DNA from previously decondensed and diffusely distributed DNA, and "pinching" of DNA near the middle of the cell in the absence of new wall formation. Mechanisms underlying these patterns remain unclear, but formation of daughter nucleoids and cells occurs both during diurnal periods of host feeding and bacterial cell growth and during nocturnal periods of host inactivity when mean bacterial cell size declines.

Intrinsic Membrane Properties of Pre-oromotor Neurons in the Intermediate Zone of the Medullary Reticular Formation

PubMed Central

Venugopal, Sharmila; Boulant, Jack A.; Chen, Zhixiong; Travers, Joseph B.

2010-01-01

Neurons in the lower brainstem that control consummatory behavior are widely distributed in the reticular formation (RF) of the pons and medulla. The intrinsic membrane properties of neurons within this distributed system shape complex excitatory and inhibitory inputs from both orosensory and central structures implicated in homeostatic control to produce coordinated oromotor patterns. The current study explored the intrinsic membrane properties of neurons in the intermediate subdivision of the medullary reticular formation (IRt). Neurons in the IRt receive input from the overlying (gustatory) nucleus of the solitary tract and project to the oromotor nuclei. Recent behavioral pharmacology studies as well as computational modeling suggest that inhibition in the IRt plays an important role in the transition from a taste-initiated oromotor pattern of ingestion to one of rejection. The present study explored the impact of hyperpolarization on membrane properties. In response to depolarization, neurons responded with either a tonic discharge, an irregular/burst pattern or were spike-adaptive. A hyperpolarizing pre-pulse modulated the excitability of most (82%) IRt neurons to subsequent depolarization. Instances of both increased (30%) and decreased (52%) excitability were observed. Currents induced by the hyperpolarization included an outward 4-AP sensitive K+ current that suppressed excitability and an inward cation current that increased excitability. These currents are also present in other subpopulations of RF neurons that influence the oromotor nuclei and we discuss how these currents could alter ring characteristics to impact pattern generation. PMID:20338224

Basic Research of Intrinsic Tamper Indication Markings Defined by Pulsed Laser Irradiation (Quad Chart).

DOE Office of Scientific and Technical Information (OSTI.GOV)

Moody, Neville R.

Objective: We will research how short (ns) and ultrashort (fs) laser pulses interact with the surfaces of various materials to create complex color layers and morphological patterns. Method: We are investigating the site-specific, formation of microcolor features. Also, research includes a fundamental study of the physics underlying periodic ripple formation during femtosecond laser irradiation. Status of effort: Laser induced color markings were demonstrated on an increased number of materials (including metal thin films) and investigated for optical properties and microstructure. Technology that allows for marking curved surfaces (and large areas) has been implemented. We have used electro-magnetic solvers to modelmore » light-solid interactions leading to periodic surface ripple patterns. This includes identifying the roles of surface plasmon polaritons. Goals/Milestones: Research corrosion resistance of oxide color markings (salt spray, fog, polarization tests); Through modeling, investigate effects of multi-source scattering and interference on ripple patterns; Investigate microspectrophotometry for mapping color; and Investigate new methods for laser color marking curved surfaces and large areas.« less

Formation of charge-nanopatterned templates with flexible geometry via layer by layer deposition of polyelectrolytes for directed self-assembly of gold nanoparticles

NASA Astrophysics Data System (ADS)

Sayin, Mustafa; Dahint, Reiner

2017-03-01

Nanostructure formation via self-assembly processes offers a fast and cost-effective approach to generate surface patterns on large lateral scale. In particular, if the high precision of lithographic techniques is not required, a situation typical of many biotechnological and biomedical applications, it may be considered as the method of choice as it does not require any sophisticated instrumentation. However, in many cases the variety and complexity of the surface structures accessible with a single self-assembly based technique is limited. Here, we report on a new approach which combines two different self-assembly strategies, colloidal lithography and layer-by-layer deposition of polyelectrolytes, in order to significantly expand the spectrum of accessible patterns. In particular, flat and donut-like charge-patterned templates have been generated, which facilitate subsequent deposition of gold nanoparticles in dot, grid, ring, out-of-ring and circular patch structures. Potential applications are e.g. in the fields of biofunctional interfaces with well-defined lateral dimensions, optical devices with tuned properties, and controlled three-dimensional material growth.

Nearest pattern interaction and global pattern formation

NASA Astrophysics Data System (ADS)

Jeong, Seong-Ok; Moon, Hie-Tae; Ko, Tae-Wook

2000-12-01

We studied the effect of nearest pattern interaction on a global pattern formation in a two-dimensional space, where patterns are to grow initially from a noise in the presence of a periodic supply of energy. Although our approach is general, we found that this study is relevant in particular to the pattern formation on a periodically vibrated granular layer, as it gives a unified perspective of the experimentally observed pattern dynamics such as oscillon and stripe formations, skew-varicose and crossroll instabilities, and also a kink formation and decoration.

Flo11p-Independent Control of “Mat” Formation by Hsp70 Molecular Chaperones and Nucleotide Exchange Factors in Yeast

PubMed Central

Martineau, Céline N.; Beckerich, Jean-Marie; Kabani, Mehdi

2007-01-01

The yeast Saccharomyces cerevisiae has been used as a model for fungal biofilm formation due to its ability to adhere to plastic surfaces and to form mats on low-density agar petri plates. Mats are complex multicellular structures composed of a network of cables that form a central hub from which emanate multiple radial spokes. This reproducible and elaborate pattern is indicative of a highly regulated developmental program that depends on specific transcriptional programming, environmental cues, and possibly cell–cell communication systems. While biofilm formation and sliding motility were shown to be strictly dependent on the cell-surface adhesin Flo11p, little is known about the cellular machinery that controls mat formation. Here we show that Hsp70 molecular chaperones play key roles in this process with the assistance of the nucleotide exchange factors Fes1p and Sse1p and the Hsp40 family member Ydj1p. The disruption of these cofactors completely abolished mat formation. Furthermore, complex interactions among SSA genes were observed: mat formation depended mostly on SSA1 while minor defects were observed upon loss of SSA2; additional mutations in SSA3 or SSA4 further enhanced these phenotypes. Importantly, these mutations did not compromise invasive growth or Flo11p expression, suggesting that Flo11p-independent pathways are necessary to form mats. PMID:17947402

Self-organized pattern dynamics of somitogenesis model in embryos

NASA Astrophysics Data System (ADS)

Guan, Linan; Shen, Jianwei

2018-09-01

Somitogenesis, the sequential formation of a periodic pattern along the anteroposterior axis of vertebrate embryos, is one of the most obvious examples of the segmental patterning processes that take place during embryogenesis and also one of the major unresolved events in developmental biology. In this paper, we investigate the effect of diffusion on pattern formation use a modified two dimensional model which can be used to explain somitogenesis during embryonic development. This model is suitable for exploring a design space of somitogenesis and can explain many aspects of somitogenesis that previous models cannot. In the present paper, by analyzing the local linear stability of the equation, we acquired the conditions of Hopf bifurcation and Turing bifurcation. In addition, the amplitude equation near the Turing bifurcation point is obtained by using the methods of multi-scale expansion and symmetry analysis. By analyzing the stability of the amplitude equation, we know that there are various complex phenomena, including Spot pattern, mixture of spot-stripe patterns and labyrinthine. Finally, numerical simulation are given to verify the correctness of our theoretical results. Somitogenesis occupies an important position in the process of biological development, and as a pattern process can be used to investigate many aspects of embryogenesis. Therefore, our study helps greatly to cell differentiation, gene expression and embryonic development. What is more, it is of great significance for the diagnosis and treatment of human diseases to study the related knowledge of model biology.

SMC5/6 is required for the formation of segregation-competent bivalent chromosomes during meiosis I in mouse oocytes.

PubMed

Hwang, Grace; Sun, Fengyun; O'Brien, Marilyn; Eppig, John J; Handel, Mary Ann; Jordan, Philip W

2017-05-01

SMC complexes include three major classes: cohesin, condensin and SMC5/6. However, the localization pattern and genetic requirements for the SMC5/6 complex during mammalian oogenesis have not previously been examined. In mouse oocytes, the SMC5/6 complex is enriched at the pericentromeric heterochromatin, and also localizes along chromosome arms during meiosis. The infertility phenotypes of females with a Zp3-Cre -driven conditional knockout (cKO) of Smc5 demonstrated that maternally expressed SMC5 protein is essential for early embryogenesis. Interestingly, protein levels of SMC5/6 complex components in oocytes decline as wild-type females age. When SMC5/6 complexes were completely absent in oocytes during meiotic resumption, homologous chromosomes failed to segregate accurately during meiosis I. Despite what appears to be an inability to resolve concatenation between chromosomes during meiosis, localization of topoisomerase IIα to bivalents was not affected; however, localization of condensin along the chromosome axes was perturbed. Taken together, these data demonstrate that the SMC5/6 complex is essential for the formation of segregation-competent bivalents during meiosis I, and findings suggest that age-dependent depletion of the SMC5/6 complex in oocytes could contribute to increased incidence of oocyte aneuploidy and spontaneous abortion in aging females. © 2017. Published by The Company of Biologists Ltd.

Definitions of Complexity are Notoriously Difficult

NASA Astrophysics Data System (ADS)

Schuster, Peter

Definitions of complexity are notoriously difficult if not impossible at all. A good working hypothesis might be: Everything is complex that is not simple. This is precisely the way in which we define nonlinear behavior. Things appear complex for different reasons: i) Complexity may result from lack of insight, ii) complexity may result from lack of methods, and (iii) complexity may be inherent to the system. The best known example for i) is celestial mechanics: The highly complex Pythagorean epicycles become obsolete by the introduction of Newton's law of universal gravitation. To give an example for ii), pattern formation and deterministic chaos became not really understandable before extensive computer simulations became possible. Cellular metabolism may serve as an example for iii) and is caused by the enormous complexity of biochemical reaction networks with up to one hundred individual reaction fluxes. Nevertheless, only few fluxes are dominant in the sense that using Pareto optimal values for them provides near optimal values for all the others...

Elongator complex is critical for cell cycle progression and leaf patterning in Arabidopsis.

PubMed

Xu, Deyang; Huang, Weihua; Li, Yang; Wang, Hua; Huang, Hai; Cui, Xiaofeng

2012-03-01

The mitotic cell cycle in higher eukaryotes is of pivotal importance for organ growth and development. Here, we report that Elongator, an evolutionarily conserved histone acetyltransferase complex, acts as an important regulator of mitotic cell cycle to promote leaf patterning in Arabidopsis. Mutations in genes encoding Elongator subunits resulted in aberrant cell cycle progression, and the altered cell division affects leaf polarity formation. The defective cell cycle progression is caused by aberrant DNA replication and increased DNA damage, which activate the DNA replication checkpoint to arrest the cell cycle. Elongator interacts with proliferating cell nuclear antigen (PCNA) and is required for efficient histone 3 (H3) and H4 acetylation coupled with DNA replication. Levels of chromatin-bound H3K56Ac and H4K5Ac known to associate with replicons during DNA replication were reduced in the mutants of both Elongator and chromatin assembly factor 1 (CAF-1), another protein complex that physically interacts with PCNA for DNA replication-coupled chromatin assembly. Disruptions of CAF-1 also led to severe leaf polarity defects, which indicated that Elongator and CAF-1 act, at least partially, in the same pathway to promote cell cycle progression. Collectively, our results demonstrate that Elongator is an important regulator of mitotic cell cycle, and the Elongator pathway plays critical roles in promoting leaf polarity formation. © 2011 The Authors. The Plant Journal © 2011 Blackwell Publishing Ltd.

Anatomy and growth pattern of Amazon deep-sea fan as revealed by long-range side-scan sonar (GLORIA) and high-resolution seismic studies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Damuth, J.E.; Flood, R.D.; Kowsmann, R.O.

1988-08-01

Imaging of the Amazon deep-sea fan with long-range side-scan sonar (GLORIA) has, for the first time, revealed the anatomy, trends, and growth pattern of distributary channels on this fan. Only one channel-levee system was active at any given time and extended from the Amazon Submarine Canyon downslope onto the lower fan (> 4,200 m). Formation of new channel-levee systems occurred when a currently active channel-levee system was cut off and abandoned through avulsion, and a new channel-levee system was established nearby. Through time, successive channel-levee formation and abandonment built two broad levee complexes consisting of groups of overlapping, coalescing segmentsmore » of channel-levee systems across the present fan surface. These, plus older, now buried levee complexes, indicate that fan growth is radially outward and downslope through development of successive levee complexes. The most striking characteristic of the distributary channels is their intricate, often recurving, meanders with sinuosities of up to 2.5. Cutoffs and abandoned meander loops indicate that the channels migrate laterally through time. Channel bifurcation results predominantly from avulsion when flows breach a channel levee, thereby abandoning the present channel and establishing a new channel-levee segment nearby. No clear evidence of channel branching (i.e., division of a single channel into two active segments) or braiding was observed. 22 figs.« less

Cytoskeletal self-organization in neuromorphogenesis.

PubMed

Dehmelt, Leif

2014-01-01

Self-organization of dynamic microtubules via interactions with associated motors plays a critical role in spindle formation. The microtubule-based mechanisms underlying other aspects of cellular morphogenesis, such as the formation and development of protrusions from neuronal cells is less well understood. In a recent study, we investigated the molecular mechanism that underlies the massive reorganization of microtubules induced in non-neuronal cells by expression of the neuronal microtubule stabilizer MAP2c. In that study we directly observed cortical dynein complexes and how they affect the dynamic behavior of motile microtubules in living cells. We found that stationary dynein complexes transiently associate with motile microtubules near the cell cortex and that their rapid turnover facilitates efficient microtubule transport. Here, we discuss our findings in the larger context of cellular morphogenesis with specific focus on self-organizing principles from which cellular shape patterns such as the thin protrusions of neurons can emerge.

Cytoskeletal self-organization in neuromorphogenesis

PubMed Central

Dehmelt, Leif

2014-01-01

Self-organization of dynamic microtubules via interactions with associated motors plays a critical role in spindle formation. The microtubule-based mechanisms underlying other aspects of cellular morphogenesis, such as the formation and development of protrusions from neuronal cells is less well understood. In a recent study, we investigated the molecular mechanism that underlies the massive reorganization of microtubules induced in non-neuronal cells by expression of the neuronal microtubule stabilizer MAP2c. In that study we directly observed cortical dynein complexes and how they affect the dynamic behavior of motile microtubules in living cells. We found that stationary dynein complexes transiently associate with motile microtubules near the cell cortex and that their rapid turnover facilitates efficient microtubule transport. Here, we discuss our findings in the larger context of cellular morphogenesis with specific focus on self-organizing principles from which cellular shape patterns such as the thin protrusions of neurons can emerge. PMID:24847718

Posttranslational modifications of Sindbis virus glycoproteins: electrophoretic analysis of pulse-chase-labeled infected cells.

PubMed

Bonatti, S; Cancedda, F D

1982-04-01

Cytoplasmic extracts prepared from Sindbis virus-infected chicken embryo fibroblasts pulse-chase-labeled with [35S]methionine 6 h postinfection were analyzed on a highly resolving sodium dodecyl sulfate-gel either directly or after various treatments. The results we obtained suggest that (i) the proteolytic cleavage which converts PE2 to E2 glycoprotein takes place intracellularly, before or at least during the formation of complex-type oligosaccharide side chains; and (ii) E1 glycoprotein undergoes a complex maturation pattern. Newly synthesized E1 has a molecular weight of 53,000: shortly thereafter, this 53,000 (53K) form was converted to a 50K form. Subsequently, the 50K form decreased its apparent molecular weight progressively and eventually comigrated with E1 glycoprotein present in the extracellular virus, which displays a molecular weight of 51,000 to 52,000. The conversion of the 53K to the 50K form was not the result of a proteolytic processing and did not depend on glycosylation or disulfide bridge formation and exchange. The possible mechanisms of this conversion are discussed. The second conversion step (from the 50K to the 51-52K form) was due to the formation of complex-type oligosaccharide and was reversed by incubating the cellular extracts with neuraminidase before electrophoretic analysis.

Complex furrows in a 2D epithelial sheet code the 3D structure of a beetle horn.

PubMed

Matsuda, Keisuke; Gotoh, Hiroki; Tajika, Yuki; Sushida, Takamichi; Aonuma, Hitoshi; Niimi, Teruyuki; Akiyama, Masakazu; Inoue, Yasuhiro; Kondo, Shigeru

2017-10-24

The external organs of holometabolous insects are generated through two consecutive processes: the development of imaginal primordia and their subsequent transformation into the adult structures. During the latter process, many different phenomena at the cellular level (e.g. cell shape changes, cell migration, folding and unfolding of epithelial sheets) contribute to the drastic changes observed in size and shape. Because of this complexity, the logic behind the formation of the 3D structure of adult external organs remains largely unknown. In this report, we investigated the metamorphosis of the horn in the Japanese rhinoceros beetle Trypoxylus dichotomus. The horn primordia is essentially a 2D epithelial cell sheet with dense furrows. We experimentally unfolded these furrows using three different methods and found that the furrow pattern solely determines the 3D horn structure, indicating that horn formation in beetles occurs by two distinct processes: formation of the furrows and subsequently unfolding them. We postulate that this developmental simplicity offers an inherent advantage to understanding the principles that guide 3D morphogenesis in insects.

Mechanical Model of Geometric Cell and Topological Algorithm for Cell Dynamics from Single-Cell to Formation of Monolayered Tissues with Pattern

PubMed Central

Kachalo, Sëma; Naveed, Hammad; Cao, Youfang; Zhao, Jieling; Liang, Jie

2015-01-01

Geometric and mechanical properties of individual cells and interactions among neighboring cells are the basis of formation of tissue patterns. Understanding the complex interplay of cells is essential for gaining insight into embryogenesis, tissue development, and other emerging behavior. Here we describe a cell model and an efficient geometric algorithm for studying the dynamic process of tissue formation in 2D (e.g. epithelial tissues). Our approach improves upon previous methods by incorporating properties of individual cells as well as detailed description of the dynamic growth process, with all topological changes accounted for. Cell size, shape, and division plane orientation are modeled realistically. In addition, cell birth, cell growth, cell shrinkage, cell death, cell division, cell collision, and cell rearrangements are now fully accounted for. Different models of cell-cell interactions, such as lateral inhibition during the process of growth, can be studied in detail. Cellular pattern formation for monolayered tissues from arbitrary initial conditions, including that of a single cell, can also be studied in detail. Computational efficiency is achieved through the employment of a special data structure that ensures access to neighboring cells in constant time, without additional space requirement. We have successfully generated tissues consisting of more than 20,000 cells starting from 2 cells within 1 hour. We show that our model can be used to study embryogenesis, tissue fusion, and cell apoptosis. We give detailed study of the classical developmental process of bristle formation on the epidermis of D. melanogaster and the fundamental problem of homeostatic size control in epithelial tissues. Simulation results reveal significant roles of solubility of secreted factors in both the bristle formation and the homeostatic control of tissue size. Our method can be used to study broad problems in monolayered tissue formation. Our software is publicly available. PMID:25974182

Numerical models of caldera deformation: Effects of multiphase and multicomponent hydrothermal fluid flow

USGS Publications Warehouse

Hutnak, M.; Hurwitz, S.; Ingebritsen, S.E.; Hsieh, P.A.

2009-01-01

Ground surface displacement (GSD) in large calderas is often interpreted as resulting from magma intrusion at depth. Recent advances in geodetic measurements of GSD, notably interferometric synthetic aperture radar, reveal complex and multifaceted deformation patterns that often require complex source models to explain the observed GSD. Although hydrothermal fluids have been discussed as a possible deformation agent, very few quantitative studies addressing the effects of multiphase flow on crustal mechanics have been attempted. Recent increases in the power and availability of computing resources allow robust quantitative assessment of the complex time-variant thermal interplay between aqueous fluid flow and crustal deformation. We carry out numerical simulations of multiphase (liquid-gas), multicomponent (H 2O-CO2) hydrothermal fluid flow and poroelastic deformation using a range of realistic physical parameters and processes. Hydrothermal fluid injection, circulation, and gas formation can generate complex, temporally and spatially varying patterns of GSD, with deformation rates, magnitudes, and geometries (including subsidence) similar to those observed in several large calderas. The potential for both rapid and gradual deformation resulting from magma-derived fluids suggests that hydrothermal fluid circulation may help explain deformation episodes at calderas that have not culminated in magmatic eruption.

Stratal stacking patterns and tectono-sedimentary evolution of hyperextended magma-poor rifted margins

NASA Astrophysics Data System (ADS)

Ribes, C.; Gillard, M.; Epin, M. E.; Ghienne, J. F.; Manatschal, G.; Karner, G. D.; Johnson, C. A.

2016-12-01

Research on the formation and evolution of deep-water rifted margins has undergone a major paradigm shift in recent years. An increasing number of studies of present-day and fossil rifted margins allow us to identify and characterize the structural architecture of the most distal parts of rifted margins, the so-called hyperextended, magma-poor rifted margins. However, at present, little is known about the depositional environments, sedimentary facies, stacking patterns, subsidence and thermal history within these domains. In this context, characterizing the stratal stacking patterns and understanding their spatial and temporal evolution is a new challenge. The major difficulty comes from the fact that the observed stratigraphic geometries and facies relationships are a result of the complex interplay between sediment supply and available accommodation, which is controlled by not only the regional generation of accommodation, but also by local tectono-magmatic processes. These parameters are poorly constrained or even sufficiently known in these tectonic settings. Indeed, the complex structural evolution of hyperextended magma-poor rifted margins, including the development of poly-phase in-sequence and out of sequence extensional detachment faults and associated mantle exhumation and magmatic activity, can generate complex accommodation patterns over a highly structured top basement. The presentation summarizes early results concerning the controlling parameters on ultra-deep water stratigraphic stacking patterns and to provide a conceptual framework. This observation-driven approach combines fieldwork from fossil Alpine Tethys margins exposed in the Alps and the analysis of seismic reflection data from present-day deep water rifted margins such as the Australian-Antarctic, East India and Iberia-Newfoundland margins.

Post-Self-Assembly Cross-Linking to Integrate Molecular Nanofibers with Copolymers in Oscillatory Hydrogels

DTIC Science & Technology

2013-05-09

The BZ reaction provides a model system to mimic a variety of complex processes, such as biological morphogenesis, in monodisperse microemulsions .15...surfaces, ion-exchange resins, membranes, and microemulsions . For example, in addition to minimizing the hydrodynamic effects and formation of bubbles...Reaction-Diffusion Microemulsions Reveals Three-Dimensional Tu- ring Patterns. Science (Washington, DC, U.S.) 2011, 331, 1309−1312. (16) Agladze, K. I

Multi-channels coupling-induced pattern transition in a tri-layer neuronal network

NASA Astrophysics Data System (ADS)

Wu, Fuqiang; Wang, Ya; Ma, Jun; Jin, Wuyin; Hobiny, Aatef

2018-03-01

Neurons in nerve system show complex electrical behaviors due to complex connection types and diversity in excitability. A tri-layer network is constructed to investigate the signal propagation and pattern formation by selecting different coupling channels between layers. Each layer is set as different states, and the local kinetics is described by Hindmarsh-Rose neuron model. By changing the number of coupling channels between layers and the state of the first layer, the collective behaviors of each layer and synchronization pattern of network are investigated. A statistical factor of synchronization on each layer is calculated. It is found that quiescent state in the second layer can be excited and disordered state in the third layer is suppressed when the first layer is controlled by a pacemaker, and the developed state is dependent on the number of coupling channels. Furthermore, the collapse in the first layer can cause breakdown of other layers in the network, and the mechanism is that disordered state in the third layer is enhanced when sampled signals from the collapsed layer can impose continuous disturbance on the next layer.

Spatial inventory integrating raster databases and point sample data. [Geographic Information System for timber inventory

NASA Technical Reports Server (NTRS)

Strahler, A. H.; Woodcock, C. E.; Logan, T. L.

1983-01-01

A timber inventory of the Eldorado National Forest, located in east-central California, provides an example of the use of a Geographic Information System (GIS) to stratify large areas of land for sampling and the collection of statistical data. The raster-based GIS format of the VICAR/IBIS software system allows simple and rapid tabulation of areas, and facilitates the selection of random locations for ground sampling. Algorithms that simplify the complex spatial pattern of raster-based information, and convert raster format data to strings of coordinate vectors, provide a link to conventional vector-based geographic information systems.

The effects of task difficulty and resource requirements on attention strategies

NASA Technical Reports Server (NTRS)

King, Teresa

1991-01-01

The patterns of attention strategies for task difficulty/resource tasks for which experimental results are presented and analyzed support the hypothesis that subjects may adopt an alternating (rather than concurrent one) when compelled to do so by either the size or the complexity of a visual display. According to the multiple resource model, if subjects had been performing the two tasks concurrently, the cost of this strategy would have been shown by a decrement in the spatial format, rather than the verbal format, due to competition for the same resource. Subjects may apply different strategies as a function of task difficulty and/or resource demand.

Nucleosome Positioning and Epigenetics

NASA Astrophysics Data System (ADS)

Schwab, David; Bruinsma, Robijn

2008-03-01

The role of chromatin structure in gene regulation has recently taken center stage in the field of epigenetics, phenomena that change the phenotype without changing the DNA sequence. Recent work has also shown that nucleosomes, a complex of DNA wrapped around a histone octamer, experience a sequence dependent energy landscape due to the variation in DNA bend stiffness with sequence composition. In this talk, we consider the role nucleosome positioning might play in the formation of heterochromatin, a compact form of DNA generically responsible for gene silencing. In particular, we discuss how different patterns of nucleosome positions, periodic or random, could either facilitate or suppress heterochromatin stability and formation.

Regulation of endoderm formation and left-right asymmetry by miR-92 during early zebrafish development

PubMed Central

Li, Nan; Wei, Chunyao; Olena, Abigail F.; Patton, James G.

2011-01-01

microRNAs (miRNAs) are a family of 21-23 nucleotide endogenous non-coding RNAs that post-transcriptionally regulate gene expression in a sequence-specific manner. Typically, miRNAs downregulate target genes by recognizing and recruiting protein complexes to 3′UTRs, followed by translation repression or mRNA degradation. miR-92 is a well-studied oncogene in mammalian systems. Here, using zebrafish as a model system, we uncovered a novel tissue-inductive role for miR-92 during early vertebrate development. Overexpression resulted in reduced endoderm formation during gastrulation with consequent cardia and viscera bifida. By contrast, depletion of miR-92 increased endoderm formation, which led to abnormal Kupffer's vesicle development and left-right patterning defects. Using target prediction algorithms and reporter constructs, we show that gata5 is a target of miR-92. Alteration of gata5 levels reciprocally mirrored the effects of gain and loss of function of miR-92. Moreover, genetic epistasis experiments showed that miR-92-mediated defects could be substantially suppressed by modulating gata5 levels. We propose that miR-92 is a critical regulator of endoderm formation and left-right asymmetry during early zebrafish development and provide the first evidence for a regulatory function for gata5 in the formation of Kupffer's vesicle and left-right patterning. PMID:21447552

SVP-like MADS-box protein from Carya cathayensis forms higher-order complexes.

PubMed

Wang, Jingjing; Hou, Chuanming; Huang, Jianqin; Wang, Zhengjia; Xu, Yingwu

2015-03-01

To properly regulate plant flowering time and construct floral pattern, MADS-domain containing transcription factors must form multimers including homo- and hetero-dimers. They are also active in forming hetero-higher-order complexes with three to five different molecules. However, it is not well known if a MADS-box protein can also form homo-higher-order complex. In this study a biochemical approach is utilized to provide insight into the complex formation for an SVP-like MADS-box protein cloned from hickory. The results indicated that the protein is a heterogeneous higher-order complex with the peak population containing over 20 monomers. Y2H verified the protein to form homo-complex in yeast cells. Western blot of the hickory floral bud sample revealed that the protein exists in higher-order polymers in native. Deletion assays indicated that the flexible C-terminal residues are mainly responsible for the higher-order polymer formation and the heterogeneity. Current results provide direct biochemical evidences for an active MADS-box protein to be a high order complex, much higher than a quartermeric polymer. Analysis suggests that a MADS-box subset may be able to self-assemble into large complexes, and thereby differentiate one subfamily from the other in a higher-order structural manner. Present result is a valuable supplement to the action of mechanism for MADS-box proteins in plant development. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

Behavior of implanted hydrogen in ferritic/martensitic steels under irradiation

NASA Astrophysics Data System (ADS)

Wan, F.; Takahashi, H.; Ohnuki, S.; Nagasaki, R.

1988-07-01

The aim of this study was to clarify the behavior of hydrogen under irradiation in ferritic/martensitic stainless steel Fe-10Cr-2Mo-1Ni. Hydrogen was implanted into the specimens by ion accelerator or chemical cathodic charging method, followed by electron irradiation in a HVEM at temperatures from room temperature to 773 K. Streaks in the electron diffraction patterns were observed only during electron irradiation at 623-723 K. From these results it is suggested that the occurrence of the streak pattern is due to the formation of radiation-induced complexes of Ni or Cr with hydrogen along <100> directions.

Application of the unified mask data format based on OASIS for VSB EB writers

NASA Astrophysics Data System (ADS)

Suzuki, Toshio; Hirumi, Junji; Suga, Osamu

2005-11-01

Mask data preparation (MDP) for modern mask manufacturing becomes a complex process because many kinds of EB data formats are used in mask makers and EB data files continue to become bigger by the application of RET. Therefore we developed a unified mask pattern data format named "OASIS.VSB1" and a job deck format named "MALY2" for Variable-Shaped-Beam (VSB) EB writers. OASIS.VSB is the mask pattern data format based on OASISTM 3 (Open Artwork System Interchange Standard) released as a successive format to GDSII by SEMI. We defined restrictions on OASIS for VSB EB writers to input OASIS.VSB data directly to VSB EB writers just like the native EB data. OASIS.VSB specification and MALY specification have been disclosed to the public and will become a SEMI standard in the near future. We started to promote the spread activities of OASIS.VSB and MALY. For practical use of OASIS.VSB and MALY, we are discussing the infrastructure system of MDP processing using OASIS.VSB and MALY with mask makers, VSB EB makers, and device makers. We are also discussing the tools for the infrastructure system with EDA vendors. The infrastructure system will enable TAT, the man-hour, and the cost in MDP to be reduced. In this paper, we propose the plan of the infrastructure system of MDP processing using OASIS.VSB and MALY as an application of OASIS.VSB and MALY.

Local control of globally competing patterns in coupled Swift-Hohenberg equations

NASA Astrophysics Data System (ADS)

Becker, Maximilian; Frenzel, Thomas; Niedermayer, Thomas; Reichelt, Sina; Mielke, Alexander; Bär, Markus

2018-04-01

We present analytical and numerical investigations of two anti-symmetrically coupled 1D Swift-Hohenberg equations (SHEs) with cubic nonlinearities. The SHE provides a generic formulation for pattern formation at a characteristic length scale. A linear stability analysis of the homogeneous state reveals a wave instability in addition to the usual Turing instability of uncoupled SHEs. We performed weakly nonlinear analysis in the vicinity of the codimension-two point of the Turing-wave instability, resulting in a set of coupled amplitude equations for the Turing pattern as well as left- and right-traveling waves. In particular, these complex Ginzburg-Landau-type equations predict two major things: there exists a parameter regime where multiple different patterns are stable with respect to each other and that the amplitudes of different patterns interact by local mutual suppression. In consequence, different patterns can coexist in distinct spatial regions, separated by localized interfaces. We identified specific mechanisms for controlling the position of these interfaces, which distinguish what kinds of patterns the interface connects and thus allow for global pattern selection. Extensive simulations of the original SHEs confirm our results.

Courtship display dynamics, iridescent structural color and nanostructural pattern formation in ocellated pheasants

NASA Astrophysics Data System (ADS)

Kane, Suzanne Amador; Dakin, Roslyn; Fang, Rui; Lu, Yabin

Peacocks court females by tilting a fan-like array of feathers decorated with multicolored eyespots (ocelli). Previous research has shown that half of the variation in peacock mating success can be attributed to eyespot iridescence. Several closely-related pheasant species perform similar, but less complex, courtship displays using ocellated feathers with less complex coloration, patterns and underlying nanostructures. This study explores the relationship between the dynamics of male courtship behavior and optical properties and nanostructure of each species' iridescent feather ornaments. In particular, we examined videos of courting males and of individual feathers to measure how the angles used during displays compared to those corresponding to optimal eyespot reflected intensity and iridescent contrast. Bidirectional reflectance spectroscopy was used to measure how the spectrum of reflected light depends on the characteristic angles used during displays, and hence how displays stimulate the four classes of cones found in the color vision systems of these birds. This work reveals a close correlation between the complexity of the angular dependence of iridescent feather reflectance properties and that of the motions used by males of each species.

Polygonal crack patterns by drying thin films under quasi-two-dimensional confinement

NASA Astrophysics Data System (ADS)

Ma, Xiaolei; Lowensohn, Janna; Burton, Justin

Cracks patterns such as T/Y junction cracks in dried mud are ubiquitous in nature. Although the conditions for cracking in solids is well-known, cracks in colloidal and granular systems are more complex. Here we report the formations of polygonal cracks by drying thin films of corn starch ( 10 μm in diameter) under quasi-2D confinement. We find there are two drying stages before the films are completely dried. Initially, a compaction front invades throughout the film. Then, a second drying stage ''percolates'' throughout the film with a characteristic branching pattern, leading to a dense packing of particles connected by liquid capillary bridges. Finally, polygonal cracks appear as the remaining liquid dries. The same drying kinetics occur for films with different thickness, h, except that fractal-like fracture patterns form in thin films, where the thickness is comparable to the particle size, while polygons form in thick films with many layers of particles. We also find that the average area of the polygons, A, in fully dried films scales with the thickness, A hβ , where β 1 . 5 , and the prefactor depends on the initial packing fraction of the suspension. This form is consistent with a simple energy balance criterion for crack formation.

Storm and tide influenced depositional architecture of the Pliocene-Pleistocene Chad Formation, Chad Basin (Bornu Sub-basin) NE Nigeria: A mixed fluvial, deltaic, shoreface and lacustrine complex

NASA Astrophysics Data System (ADS)

Shettima, Bukar; Kyari, Aji Maina; Aji, Mallam Musa; Adams, Fatimoh Dupe

2018-07-01

Lithofacies analyses of the upper part of the Chad Formation (Bama Ridge Complex) in the Bornu Sub-basin of the Chad Basin indicated four facies associations; fluvial, deltaic, shoreface and lacustrine sequences. The fluvial sequences are composed of fining upward cycles with successive occurrence of planar crossbedded sandstone facies displaying unimodal paleocurrent system and rare mudstone facies typical of braided river system. The deltaic succession consists of both fining and coarsening upwards cycles with the former depicting fluvial setting of an upper delta plain while the later suggestive of mouth-bar sequences. The setting displays a polymodal current system of fluvial, waves, storms and tides that were primarily induced by complex interactions of seiches and lunar tides. Similar current systems devoid of fluvial patterns were reflected in the coarsening upward packages of the shoreface sequences. Lacustrine succession composed of thick bioturbated mudstone facies generally defines the base of these coarsening upward profiles, giving a fluvio-lacustrine geomorphic relief where complex interaction developed the deltaic and shoreface facies along its shorelines. Clay mineral fractions of the formation are dominantly kaolinitic, indicating a predominantly humid tropical-subtropical climatic condition during their deposition. This climatic regime falls within the African humid period of the early-mid Holocene that led to the third lacustrine transgression of the Lake Mega-Chad, whereas the subordinate smectite mineralization points to aridification that characterizes most of the post humid period to recent.

Reproductive isolation and patterns of genetic differentiation in a cryptic butterfly species complex

PubMed Central

Dincâ, V; Wiklund, C; Lukhtanov, V A; Kodandaramaiah, U; Norén, K; Dapporto, L; Wahlberg, N; Vila, R; Friberg, M

2013-01-01

Molecular studies of natural populations are often designed to detect and categorize hidden layers of cryptic diversity, and an emerging pattern suggests that cryptic species are more common and more widely distributed than previously thought. However, these studies are often decoupled from ecological and behavioural studies of species divergence. Thus, the mechanisms by which the cryptic diversity is distributed and maintained across large spatial scales are often unknown. In 1988, it was discovered that the common Eurasian Wood White butterfly consisted of two species (Leptidea sinapis and Leptidea reali), and the pair became an emerging model for the study of speciation and chromosomal evolution. In 2011, the existence of a third cryptic species (Leptidea juvernica) was proposed. This unexpected discovery raises questions about the mechanisms preventing gene flow and about the potential existence of additional species hidden in the complex. Here, we compare patterns of genetic divergence across western Eurasia in an extensive data set of mitochondrial and nuclear DNA sequences with behavioural data on inter- and intraspecific reproductive isolation in courtship experiments. We show that three species exist in accordance with both the phylogenetic and biological species concepts and that additional hidden diversity is unlikely to occur in Europe. The Leptidea species are now the best studied cryptic complex of butterflies in Europe and a promising model system for understanding the formation of cryptic species and the roles of local processes, colonization patterns and heterospecific interactions for ecological and evolutionary divergence. PMID:23909947

Calcifying tissue regeneration via biomimetic materials chemistry

PubMed Central

Green, David W.; Goto, Tazuko K.; Kim, Kye-Seong; Jung, Han-Sung

2014-01-01

Materials chemistry is making a fundamental impact in regenerative sciences providing many platforms for tissue development. However, there is a surprising paucity of replacements that accurately mimic the structure and function of the structural fabric of tissues or promote faithful tissue reconstruction. Methodologies in biomimetic materials chemistry have shown promise in replicating morphologies, architectures and functional building blocks of acellular mineralized tissues dentine, enamel and bone or that can be used to fully regenerate them with integrated cell populations. Biomimetic materials chemistry encompasses the two processes of crystal formation and mineralization of crystals into inorganic formations on organic templates. This review will revisit the successes of biomimetics materials chemistry in regenerative medicine, including coccolithophore simulants able to promote in vivo bone formation. In-depth knowledge of biomineralization throughout evolution informs the biomimetic materials chemist of the most effective techniques for regenerative framework construction exemplified via exploitation of liquid crystals (LCs) and complex self-organizing media. Therefore, a new innovative direction would be to create chemical environments that perform reaction–diffusion exchanges as the basis for building complex biomimetic inorganic structures. This has evolved widely in biology, as have LCs, serving as self-organizing templates in pattern formation of structural biomaterials. For instance, a study is highlighted in which artificially fabricated chiral LCs, made from bacteriophages are transformed into a faithful copy of enamel. While chemical-based strategies are highly promising at creating new biomimetic structures there are limits to the degree of complexity that can be generated. Thus, there may be good reason to implement living or artificial cells in ‘morphosynthesis’ of complex inorganic constructs. In the future, cellular construction is probably key to instruct building of ultimate biomimetic hierarchies with a totality of functions. PMID:25320063

Nanostructure Formation by controlled dewetting on patterned substrates: A combined theoretical, modeling and experimental study.

PubMed

Lu, Liang-Xing; Wang, Ying-Min; Srinivasan, Bharathi Madurai; Asbahi, Mohamed; Yang, Joel K W; Zhang, Yong-Wei

2016-09-01

We perform systematic two-dimensional energetic analysis to study the stability of various nanostructures formed by dewetting solid films deposited on patterned substrates. Our analytical results show that by controlling system parameters such as the substrate surface pattern, film thickness and wetting angle, a variety of equilibrium nanostructures can be obtained. Phase diagrams are presented to show the complex relations between these system parameters and various nanostructure morphologies. We further carry out both phase field simulations and dewetting experiments to validate the analytically derived phase diagrams. Good agreements between the results from our energetic analyses and those from our phase field simulations and experiments verify our analysis. Hence, the phase diagrams presented here provide guidelines for using solid-state dewetting as a tool to achieve various nanostructures.

Navier-Stokes flow field analysis of compressible flow in a high pressure safety relief valve

NASA Technical Reports Server (NTRS)

Vu, Bruce; Wang, Ten-See; Shih, Ming-Hsin; Soni, Bharat

1993-01-01

The objective of this study is to investigate the complex three-dimensional flowfield of an oxygen safety pressure relieve valve during an incident, with a computational fluid dynamic (CFD) analysis. Specifically, the analysis will provide a flow pattern that would lead to the expansion of the eventual erosion pattern of the hardware, so as to combine it with other findings to piece together a most likely scenario for the investigation. The CFD model is a pressure based solver. An adaptive upwind difference scheme is employed for the spatial discretization, and a predictor, multiple corrector method is used for the velocity-pressure coupling. The computational result indicated vortices formation near the opening of the valve which matched the erosion pattern of the damaged hardware.

Genetic and cellular mechanisms of the formation of Esophageal Atresia and Tracheoesophageal Fistula

PubMed Central

Jacobs, Ian J.; Que, Jianwen

2015-01-01

Foregut separation involves dynamic changes in the activities of signaling pathways and transcription factors. Recent mouse genetic studies demonstrate that some of these pathways interact with each other to form a complex network, leading to a unique dorsal-ventral patterning in the early foregut. In this review we will discuss how this unique dorsal-ventral patterning is set prior to the foregut separation and how disruption of this patterning affects the separation process. We will further discuss the roles of downstream targets of these pathways in regulating separation at cellular and molecular levels. Understanding the mechanism of normal separation process will provide us insights into the pathobiology of a relatively common birth defect Esophageal Atresia (EA) with/without Tracheo-esophageal Fistula (TEF). PMID:23679023

Optical Pattern Formation in Cold Atoms: Explaining the Red-Blue Asymmetry

NASA Astrophysics Data System (ADS)

Schmittberger, Bonnie; Gauthier, Daniel

2013-05-01

The study of pattern formation in atomic systems has provided new insight into fundamental many-body physics and low-light-level nonlinear optics. Pattern formation in cold atoms in particular is of great interest in condensed matter physics and quantum information science because atoms undergo self-organization at ultralow input powers. We recently reported the first observation of pattern formation in cold atoms but found that our results were not accurately described by any existing theoretical model of pattern formation. Previous models describing pattern formation in cold atoms predict that pattern formation should occur using both red and blue-detuned pump beams, favoring a lower threshold for blue detunings. This disagrees with our recent work, in which we only observed pattern formation with red-detuned pump beams. Previous models also assume a two-level atom, which cannot account for the cooling processes that arise when beams counterpropagate through a cold atomic vapor. We describe a new model for pattern formation that accounts for Sisyphus cooling in multi-level atoms, which gives rise to a new nonlinearity via spatial organization of the atoms. This spatial organization causes a sharp red-blue detuning asymmetry, which agrees well with our experimental observations. We gratefully acknowledge the financial support of the NSF through Grant #PHY-1206040.

Growth ring formation in the starch granules of potato tubers.

PubMed

Pilling, Emma; Smith, Alison M

2003-05-01

Starch granules from higher plants contain alternating zones of semicrystalline and amorphous material known as growth rings. The regulation of growth ring formation is not understood. We provide several independent lines of evidence that growth ring formation in the starch granules of potato (Solanum tuberosum) tubers is not under diurnal control. Ring formation is not abolished by growth in constant conditions, and ring periodicity and appearance are relatively unaffected by a change from a 24-h to a 40-h photoperiod, and by alterations in substrate supply to the tuber that are known to affect the diurnal pattern of tuber starch synthesis. Some, but not all, of the features of ring formation are consistent with the involvement of a circadian rhythm. Such a rhythm might operate by changing the relative activities of starch-synthesizing enzymes: Growth ring formation is disrupted in tubers with reduced activity of a major isoform of starch synthase. We suggest that physical as well as biological mechanisms may contribute to the control of ring formation, and that a complex interplay of several factors may by involved.

Growth Ring Formation in the Starch Granules of Potato Tubers1

PubMed Central

Pilling, Emma; Smith, Alison M.

2003-01-01

Starch granules from higher plants contain alternating zones of semicrystalline and amorphous material known as growth rings. The regulation of growth ring formation is not understood. We provide several independent lines of evidence that growth ring formation in the starch granules of potato (Solanum tuberosum) tubers is not under diurnal control. Ring formation is not abolished by growth in constant conditions, and ring periodicity and appearance are relatively unaffected by a change from a 24-h to a 40-h photoperiod, and by alterations in substrate supply to the tuber that are known to affect the diurnal pattern of tuber starch synthesis. Some, but not all, of the features of ring formation are consistent with the involvement of a circadian rhythm. Such a rhythm might operate by changing the relative activities of starch-synthesizing enzymes: Growth ring formation is disrupted in tubers with reduced activity of a major isoform of starch synthase. We suggest that physical as well as biological mechanisms may contribute to the control of ring formation, and that a complex interplay of several factors may by involved. PMID:12746541

Development, Regeneration, and Evolution of Feathers

PubMed Central

Chen, Chih-Feng; Foley, John; Tang, Pin-Chi; Li, Ang; Jiang, Ting Xin; Wu, Ping; Widelitz, Randall B.; Chuong, Cheng Ming

2017-01-01

The feather is a complex ectodermal organ with hierarchical branching patterns. It provides functions in endothermy, communication, and flight. Studies of feather growth, cycling, and health are of fundamental importance to avian biology and poultry science. In addition, feathers are an excellent model for morphogenesis studies because of their accessibility, and their distinct patterns can be used to assay the roles of specific molecular pathways. Here we review the progress in aspects of development, regeneration, and evolution during the past three decades. We cover the development of feather buds in chicken embryos, regenerative cycling of feather follicle stem cells, formation of barb branching patterns, emergence of intrafeather pigmentation patterns, interplay of hormones and feather growth, and the genetic identification of several feather variants. The discovery of feathered dinosaurs redefines the relationship between feathers and birds. Inspiration from biomaterials and flight research further fuels biomimetic potential of feathers as a multidisciplinary research focal point. PMID:25387232

High throughput screening of ligand binding to macromolecules using high resolution powder diffraction

DOEpatents

Von Dreele, Robert B.; D'Amico, Kevin

2006-10-31

A process is provided for the high throughput screening of binding of ligands to macromolecules using high resolution powder diffraction data including producing a first sample slurry of a selected polycrystalline macromolecule material and a solvent, producing a second sample slurry of a selected polycrystalline macromolecule material, one or more ligands and the solvent, obtaining a high resolution powder diffraction pattern on each of said first sample slurry and the second sample slurry, and, comparing the high resolution powder diffraction pattern of the first sample slurry and the high resolution powder diffraction pattern of the second sample slurry whereby a difference in the high resolution powder diffraction patterns of the first sample slurry and the second sample slurry provides a positive indication for the formation of a complex between the selected polycrystalline macromolecule material and at least one of the one or more ligands.

In vivo analysis of Purkinje cell firing properties during postnatal mouse development

PubMed Central

Arancillo, Marife; White, Joshua J.; Lin, Tao; Stay, Trace L.

2014-01-01

Purkinje cell activity is essential for controlling motor behavior. During motor behavior Purkinje cells fire two types of action potentials: simple spikes that are generated intrinsically and complex spikes that are induced by climbing fiber inputs. Although the functions of these spikes are becoming clear, how they are established is still poorly understood. Here, we used in vivo electrophysiology approaches conducted in anesthetized and awake mice to record Purkinje cell activity starting from the second postnatal week of development through to adulthood. We found that the rate of complex spike firing increases sharply at 3 wk of age whereas the rate of simple spike firing gradually increases until 4 wk of age. We also found that compared with adult, the pattern of simple spike firing during development is more irregular as the cells tend to fire in bursts that are interrupted by long pauses. The regularity in simple spike firing only reached maturity at 4 wk of age. In contrast, the adult complex spike pattern was already evident by the second week of life, remaining consistent across all ages. Analyses of Purkinje cells in alert behaving mice suggested that the adult patterns are attained more than a week after the completion of key morphogenetic processes such as migration, lamination, and foliation. Purkinje cell activity is therefore dynamically sculpted throughout postnatal development, traversing several critical events that are required for circuit formation. Overall, we show that simple spike and complex spike firing develop with unique developmental trajectories. PMID:25355961

Gigantism in a Bacterium, Epulopiscium fishelsoni, Correlates with Complex Patterns in Arrangement, Quantity, and Segregation of DNA

PubMed Central

Bresler, V.; Montgomery, W. L.; Fishelson, L.; Pollak, P. E.

1998-01-01

Epulopiscium fishelsoni, gut symbiont of the brown surgeonfish (Acanthurus nigrofuscus) in the Red Sea, attains a larger size than any other eubacterium, varies 10- to 20-fold in length (and >2,000-fold in volume), and undergoes a complex daily life cycle. In early morning, nucleoids contain highly condensed DNA in elongate, chromosome-like structures which are physically separated from the general cytoplasm. Cell division involves production of two (rarely three) nucleoids within a cell, deposition of cell walls around expanded nucleoids, and emergence of daughter cells from the parent cell. Fluorescence measurements of DNA, RNA, and other cell components indicate the following. DNA quantity is proportional to cell volume over cell lengths of ∼30 μm to >500 μm. For cells of a given size, nucleoids of cells with two nucleoids (binucleoid) contain approximately equal amounts of DNA. And each nucleoid of a binucleoid cell contains one-half the DNA of the single nucleoid in a uninucleoid cell of the same size. The life cycle involves approximately equal subdivision of DNA among daughter cells, formation of apical caps of condensed DNA from previously decondensed and diffusely distributed DNA, and “pinching” of DNA near the middle of the cell in the absence of new wall formation. Mechanisms underlying these patterns remain unclear, but formation of daughter nucleoids and cells occurs both during diurnal periods of host feeding and bacterial cell growth and during nocturnal periods of host inactivity when mean bacterial cell size declines. PMID:9791108

Fluorine-substitution induced switching of dissociation patterns of C6H4*+ produced by photoelimination of MgF2 from the complexes of mg*+ (multifluorobenzene).

PubMed

Liu, Hai-Chuan; Zhang, Xin-Hao; Wu, Yun-Dong; Yang, Shihe

2005-03-07

Complexes of fluorinated benzenes (o-C6H4-nF2+n) and Mg*+ are subjected to ultraviolet photodissociation (260-340 nm), producing efficiently benzyne radical cations (C6H4-nFn*+) besides Mg*+ and MgF+. We show that the consecutive dissociation of C6H4-nFn*+ follows the [C4(+) + C2] pattern exclusively for n < or = 2 after the parent complexes absorb one or two photons. However, the dissociation pattern is switched to [C5(+) + C1] and [C1 + C5] for n > or = 3. In particular, upon two-photon absorption at 340 nm by the complexes of Mg*+ (C6HF5) (1) and Mg*+ (C6F6) (2), photoproducts of CF+, C5H+, and C5HF*+ from C6HF3*+ and CF+, C5F+, C5F2*+, and C5F3+ from C6F4*+ are detected, respectively. Theoretical calculations are used to explain the switching of the dissociation patterns induced by the fluorine substitutions. It was found that the formation of C5+ + C1 is energetically more favorable than that of C4(+) + C2 from C6HF3*+ and C6F4*+ and of C1(+) + C5. Except for C5H2F(+) + CF, all the channels of [C5(+) + C1] and [C1(+) + C5] are energetically less favorable than those of [C4(+) + C2] from C6H3F*+ and C6H2F2*+. In most cases, the calculated results agree well with the experimental observations.

Intrinsic membrane properties of pre-oromotor neurons in the intermediate zone of the medullary reticular formation.

PubMed

Venugopal, S; Boulant, J A; Chen, Z; Travers, J B

2010-06-16

Neurons in the lower brainstem that control consummatory behavior are widely distributed in the reticular formation (RF) of the pons and medulla. The intrinsic membrane properties of neurons within this distributed system shape complex excitatory and inhibitory inputs from both orosensory and central structures implicated in homeostatic control to produce coordinated oromotor patterns. The current study explored the intrinsic membrane properties of neurons in the intermediate subdivision of the medullary reticular formation (IRt). Neurons in the IRt receive input from the overlying (gustatory) nucleus of the solitary tract and project to the oromotor nuclei. Recent behavioral pharmacology studies as well as computational modeling suggest that inhibition in the IRt plays an important role in the transition from a taste-initiated oromotor pattern of ingestion to one of rejection. The present study explored the impact of hyperpolarization on membrane properties. In response to depolarization, neurons responded with either a tonic discharge, an irregular/burst pattern or were spike-adaptive. A hyperpolarizing pre-pulse modulated the excitability of most (82%) IRt neurons to subsequent depolarization. Instances of both increased (30%) and decreased (52%) excitability were observed. Currents induced by the hyperpolarization included an outward 4-aminopyridine (4-AP) sensitive K+ current that suppressed excitability and an inward cation current that increased excitability. These currents are also present in other subpopulations of RF neurons that influence the oromotor nuclei and we discuss how these currents could alter firing characteristics to impact pattern generation. 2010 IBRO. Published by Elsevier Ltd. All rights reserved.

The impact of transport processes on rare earth element patterns in marine authigenic and biogenic phosphates

NASA Astrophysics Data System (ADS)

Auer, Gerald; Reuter, Markus; Hauzenberger, Christoph A.; Piller, Werner E.

2017-04-01

Rare earth elements (REEs) are commonly used proxies to reconstruct water chemistry and oxygen saturation during the formation of authigenic and biogenic phosphates in marine environments. In the modern ocean REEs exhibit a distinct pattern with enrichment of heavy REEs and strong depletion in cerium (Ce). The wide range of REE enrichment patterns found in ancient marine phosphates lead to the proposition that water chemistry has been very different in the Earth's past. However, both early and late diagenesis are known to affect REE signatures in phosphates altering primary marine signals. Herein we present a dataset of REE signatures in 38 grain specific LA-ICP-MS measurements of isolated phosphate and carbonate grains in three discrete rock samples. The phosphates mainly consist of authigenic phosphates and phosphatized microfossils that formed in a microbially mediated micro-milieu. In addition, isolated biogenic and reworked phosphatic grains are also present. The phosphates are emplaced in bioclastic grain- to packstones deposited on a carbonate ramp setting in the central Mediterranean Sea during the middle Miocene Monterey event. The results reveal markedly different REE patterns (normalized to the Post Archean Australian Shale standard) in terms of total enrichment and pattern shape. Analyses of REE diagenesis proxies show that diagenetic alteration affected the samples only to a minor degree. Grain shape and REE patterns together indicate that authigenic, biogenic and reworked phosphates have distinct REE patterns irrespective of the sample. Our study shows that while REE patterns in phosphates do reflect water chemistry during authigenesis, they are often already heavily altered during reworking, a process, which can occur in geologically negligible timespans. REE patterns are therefore more likely to reflect complex enrichment processes after their formation. Similarities in the REE patterns of reworked and biogenic phosphate further suggest that the frequently observed hat-shaped pattern in biogenic phosphates can result from increased middle REE (Neodymium to Holmium) scavenging during taphonomic processes prior to final deposition. Cluster analysis coupled with sedimentological and previously published geochemical data (bulk carbon isotope and X-ray fluorescence spectrometry) allowed the characterization of REE patterns of phosphates in terms of their formation conditions and depositional history, such as the distinction of phosphates formed in situ from reworked and transported phosphate grains.

[Development of spatial orientation during pilot training].

PubMed

Ivanov, V V; Vorob'ev, O A; Snipkov, Iu Iu

1988-01-01

The problem of spatial orientation of pilots flying high-altitude aircraft is in the focus of present-day aviation medicine because of a growing number of accidents in the air. One of the productive lines of research is to study spatial orientation in terms of active formation and maintenance of its imagery in a complex environment. However investigators usually emphasize the role of visual (instrumental) information in the image construction, almost ignoring the sensorimotor component of spatial orientation. The theoretical analysis of the process of spatial orientation has facilitated the development of the concept assuming that the pattern of space perception changes with growing professional experience. The concept is based on an active approach to the essence, emergence, formation and variation in the pattern of sensory perception of space in man's consciousness. This concept asserts that as pilot's professional expertise increases, the pattern of spatial orientation becomes geocentric because a new system of spatial perception evolves which is a result of the development of a new (instrumental) type of motor activity in space. This finds expression in the fact that perception of spatial position inflight occurs when man has to resolve a new motor task--movement along a complex trajectory in the three-dimensional space onboard a flying vehicle. The meaningful structure of this problem which is to be implemented through controlling movements of the pilot acts as a factor that forms this new system of perception. All this underlies the arrangement of meaningful collection of instrumental data and detection of noninstrumental signals in the comprehensive perception of changes in the spatial position of a flying vehicle.

Secondary cell walls: biosynthesis, patterned deposition and transcriptional regulation.

PubMed

Zhong, Ruiqin; Ye, Zheng-Hua

2015-02-01

Secondary walls are mainly composed of cellulose, hemicelluloses (xylan and glucomannan) and lignin, and are deposited in some specialized cells, such as tracheary elements, fibers and other sclerenchymatous cells. Secondary walls provide strength to these cells, which lend mechanical support and protection to the plant body and, in the case of tracheary elements, enable them to function as conduits for transporting water. Formation of secondary walls is a complex process that requires the co-ordinated expression of secondary wall biosynthetic genes, biosynthesis and targeted secretion of secondary wall components, and patterned deposition and assembly of secondary walls. Here, we provide a comprehensive review of genes involved in secondary wall biosynthesis and deposition. Most of the genes involved in the biosynthesis of secondary wall components, including cellulose, xylan, glucomannan and lignin, have been identified and their co-ordinated activation has been shown to be mediated by a transcriptional network encompassing the secondary wall NAC and MYB master switches and their downstream transcription factors. It has been demonstrated that cortical microtubules and microtubule-associated proteins play important roles in the targeted secretion of cellulose synthase complexes, the oriented deposition of cellulose microfibrils and the patterned deposition of secondary walls. Further investigation of many secondary wall-associated genes with unknown functions will provide new insights into the mechanisms controlling the formation of secondary walls that constitute the bulk of plant biomass. © The Author 2014. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

The Policy Formation Process: A Conceptual Framework for Analysis. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Fuchs, E. F.

1972-01-01

A conceptual framework for analysis which is intended to assist both the policy analyst and the policy researcher in their empirical investigations into policy phenomena is developed. It is meant to facilitate understanding of the policy formation process by focusing attention on the basic forces shaping the main features of policy formation as a dynamic social-political-organizational process. The primary contribution of the framework lies in its capability to suggest useful ways of looking at policy formation reality. It provides the analyst and the researcher with a group of indicators which suggest where to look and what to look for when attempting to analyze and understand the mix of forces which energize, maintain, and direct the operation of strategic level policy systems. The framework also highlights interconnections, linkage, and relational patterns between and among important variables. The framework offers an integrated set of conceptual tools which facilitate understanding of and research on the complex and dynamic set of variables which interact in any major strategic level policy formation process.

Patterning with metal-oxide EUV photoresist: patterning capability, resist smoothing, trimming, and selective stripping

NASA Astrophysics Data System (ADS)

Mao, Ming; Lazzarino, Frederic; De Schepper, Peter; De Simone, Danilo; Piumi, Daniele; Luong, Vinh; Yamashita, Fumiko; Kocsis, Michael; Kumar, Kaushik

2017-03-01

Inpria metal-oxide photoresist (PR) serves as a thin spin-on patternable hard mask for EUV lithography. Compared to traditional organic photoresists, the ultrathin metal-oxide photoresist ( 12nm after development) effectively mitigates pattern collapse. Because of the high etch resistance of the metal-oxide resist, this may open up significant scope for more aggressive etches, new chemistries, and novel integration schemes. We have previously shown that metal-oxide PR can be successfully used to pattern the block layer for the imec 7-nm technology node[1] and advantageously replace a multiple patterning approach, which significantly reduces the process complexity and effectively decreases the cost. We also demonstrated the formation of 16nm half pitch 1:1 line/space with EUV single print[2], which corresponds to a metal 2 layer for the imec 7-nm technology node. In this paper, we investigate the feasibility of using Inpria's metal-oxide PR for 16nm line/space patterning. In meanwhile, we also explore the different etch process for LWR smoothing, resist trimming and resist stripping.

Adaptive Conditioning of Multiple-Point Geostatistical Facies Simulation to Flow Data with Facies Probability Maps

NASA Astrophysics Data System (ADS)

Khodabakhshi, M.; Jafarpour, B.

2013-12-01

Characterization of complex geologic patterns that create preferential flow paths in certain reservoir systems requires higher-order geostatistical modeling techniques. Multipoint statistics (MPS) provides a flexible grid-based approach for simulating such complex geologic patterns from a conceptual prior model known as a training image (TI). In this approach, a stationary TI that encodes the higher-order spatial statistics of the expected geologic patterns is used to represent the shape and connectivity of the underlying lithofacies. While MPS is quite powerful for describing complex geologic facies connectivity, the nonlinear and complex relation between the flow data and facies distribution makes flow data conditioning quite challenging. We propose an adaptive technique for conditioning facies simulation from a prior TI to nonlinear flow data. Non-adaptive strategies for conditioning facies simulation to flow data can involves many forward flow model solutions that can be computationally very demanding. To improve the conditioning efficiency, we develop an adaptive sampling approach through a data feedback mechanism based on the sampling history. In this approach, after a short period of sampling burn-in time where unconditional samples are generated and passed through an acceptance/rejection test, an ensemble of accepted samples is identified and used to generate a facies probability map. This facies probability map contains the common features of the accepted samples and provides conditioning information about facies occurrence in each grid block, which is used to guide the conditional facies simulation process. As the sampling progresses, the initial probability map is updated according to the collective information about the facies distribution in the chain of accepted samples to increase the acceptance rate and efficiency of the conditioning. This conditioning process can be viewed as an optimization approach where each new sample is proposed based on the sampling history to improve the data mismatch objective function. We extend the application of this adaptive conditioning approach to the case where multiple training images are proposed to describe the geologic scenario in a given formation. We discuss the advantages and limitations of the proposed adaptive conditioning scheme and use numerical experiments from fluvial channel formations to demonstrate its applicability and performance compared to non-adaptive conditioning techniques.

Wnt/β-catenin signalling regulates Sox17 expression and is essential for organizer and endoderm formation in the mouse.

PubMed

Engert, Silvia; Burtscher, Ingo; Liao, W Perry; Dulev, Stanimir; Schotta, Gunnar; Lickert, Heiko

2013-08-01

Several signalling cascades are implicated in the formation and patterning of the three principal germ layers, but their precise temporal-spatial mode of action in progenitor populations remains undefined. We have used conditional gene deletion of mouse β-catenin in Sox17-positive embryonic and extra-embryonic endoderm as well as vascular endothelial progenitors to address the function of canonical Wnt signalling in cell lineage formation and patterning. Conditional mutants fail to form anterior brain structures and exhibit posterior body axis truncations, whereas initial blood vessel formation appears normal. Tetraploid rescue experiments reveal that lack of β-catenin in the anterior visceral endoderm results in defects in head organizer formation. Sox17 lineage tracing in the definitive endoderm (DE) shows a cell-autonomous requirement for β-catenin in midgut and hindgut formation. Surprisingly, wild-type posterior visceral endoderm (PVE) in midgut- and hindgut-deficient tetraploid chimera rescues the posterior body axis truncation, indicating that the PVE is important for tail organizer formation. Upon loss of β-catenin in the visceral endoderm and DE lineages, but not in the vascular endothelial lineage, Sox17 expression is not maintained, suggesting downstream regulation by canonical Wnt signalling. Strikingly, Tcf4/β-catenin transactivation complexes accumulated on Sox17 cis-regulatory elements specifically upon endoderm induction in an embryonic stem cell differentiation system. Together, these results indicate that the Wnt/β-catenin signalling pathway regulates Sox17 expression for visceral endoderm pattering and DE formation and provide the first functional evidence that the PVE is necessary for gastrula organizer gene induction and posterior axis development.

Stress-driven buckling patterns in spheroidal core/shell structures.

PubMed

Yin, Jie; Cao, Zexian; Li, Chaorong; Sheinman, Izhak; Chen, Xi

2008-12-09

Many natural fruits and vegetables adopt an approximately spheroidal shape and are characterized by their distinct undulating topologies. We demonstrate that various global pattern features can be reproduced by anisotropic stress-driven buckles on spheroidal core/shell systems, which implies that the relevant mechanical forces might provide a template underpinning the topological conformation in some fruits and plants. Three dimensionless parameters, the ratio of effective size/thickness, the ratio of equatorial/polar radii, and the ratio of core/shell moduli, primarily govern the initiation and formation of the patterns. A distinct morphological feature occurs only when these parameters fall within certain ranges: In a prolate spheroid, reticular buckles take over longitudinal ridged patterns when one or more parameters become large. Our results demonstrate that some universal features of fruit/vegetable patterns (e.g., those observed in Korean melons, silk gourds, ribbed pumpkins, striped cavern tomatoes, and cantaloupes, etc.) may be related to the spontaneous buckling from mechanical perspectives, although the more complex biological or biochemical processes are involved at deep levels.

Mirror neurons, procedural learning, and the positive new experience: a developmental systems self psychology approach.

PubMed

Wolf, N S; Gales, M; Shane, E; Shane, M

2000-01-01

In summary, we are impressed with the existence of a mirror neuron system in the prefrontal cortex that serves as part of a complex neural network, including afferent and efferent connections to the limbic system, in particular the amygdala, in addition to the premotor and motor cortex. We think it is possible to arrive at an integration that postulates the mirror neuron system and its many types of associated multimodal neurons as contributing significantly to implicit procedural learning, a process that underlies a range of complex nonconscious, unconscious, preconscious and conscious cognitive activities, from playing musical instruments to character formation and traumatic configurations. This type of brain circuitry may establish an external coherence with developmental systems self psychology which implies that positive new experience is meliorative and that the intentional revival of old-old traumatic relational configurations might enhance maladaptive procedural patterns that would lead to the opposite of the intended beneficial change. When analysts revive traumatic transference patterns for the purpose of clarification and interpretation, they may fail to appreciate that such traumatic transference patterns make interpretation ineffective because, as we have stated above, the patient lacks self-reflection under such traumatic conditions. The continued plasticity and immediacy of the mirror neuron system can contribute to positive new experiences that promote the formation of new, adaptive, implicit-procedural patterns. Perhaps this broadened repertoire in the patient of ways of understanding interrelational events through the psychoanalytic process allows the less adaptive patterns ultimately to become vestigial and the newer, more adaptive patterns to emerge as dominant. Finally, as we have stated, we believe that the intentional transferential revival of trauma (i.e., the old-old relational configuration) may not contribute to therapeutic benefit. In contrast, the revival of trauma in the old-new configuration (i.e., in the presence of a helpful other who can reduce anxiety and foster eventual positive new experience) can be beneficial, as trauma research has demonstrated. This is the process that promotes new implicit-procedural learning, new-new relational configurations, and a richer understanding of the self narrative.

The Influence of Obliquity on Europan Cycloid Formation

NASA Technical Reports Server (NTRS)

Hurford, T. a.; Sarid, A. R.; Greenberg, R.; Bills, B. G.

2009-01-01

Tectonic patterns on Europa are influenced by tidal stress. An important well-organized component is associated with the orbital eccentricity, which produces a diurnally varying stress as Jupiter's apparent position in Europa's sky oscillates in longitude. Cycloidal lineaments seem to have formed as cracks propagated in this diurnally varying stress field. Maps of theoretical cycloid patterns capture many of the characteristics of the observed distribution on Europa. However, a few details of the observed cycloids distribution have not reproduced by previous models. Recently, it has been shown that Europa has a finite forced obliquity, so Jupiter's apparent positon in Europa's sky will also oscillate in latitude. We explore this new type of diurnal effect on cycloid formation. We find that stress from obliquity may be the key to explaining several characteristics of observed cycloids such as the shape of equator-crossing cycloids and the shift in the crack patterns in the Argadnel Regio region. All of those improvements of the fit between observaiton and theory seem to require Jupiter crossing Europa's equatorial plane 45 deg. to 180 deg after perijove passage. Suggestive of complex orbital dynamics that lock the direction of Europe's pericenter with the direction of the ascending node at the time these cracks were formed.

A Numerical Modeling Study of Mesodinium Bloom Formation and Retention in a River-Dominated Mesotidal Estuary

NASA Astrophysics Data System (ADS)

Spitz, Y. H.; Cervantes, B.

2016-02-01

The Columbia River estuary experiences extensive seasonal red-colored blooms caused by a mixotrophic ciliate of the genus Mesodinium. Although the blooms are non-toxic, they have a significant influence on the levels of nutrients, light and oxygen in the estuary. Mesodinium spp. displays very particular physiology that makes it one of few planktonic species able to thrive in a highly flushed system: a high growth rate due to its ability to photosynthesize using the photosynthetic organelles of its preys, and complex vertical migration patterns. Knowledge of the migration pattern is based on limited observations of Mesodinium behavior in culture and recent in-situ measurements collected in the Columbia River estuary. A more comprehensive understanding is needed of the mechanisms allowing Mesodinium spp. to be retained and experience rapid growth. To this end, we extended the finite element circulation model SELFE to include a 5-component behavioral model that simulates the relationships between nutrients, detritus, Mesodinium spp. and its cryptophyte prey. We then used the model to investigate various migration patterns and growth scenarios to determine their role in the formation and retention of the Mesodinium spp. bloom in the brackish water of the estuary.

Usefulness of charge-transfer complexation for the assessment of sympathomimetic drugs: Spectroscopic properties of drug ephedrine hydrochloride complexed with some π-acceptors

NASA Astrophysics Data System (ADS)

Refat, Moamen S.; Ibrahim, Omar B.; Saad, Hosam A.; Adam, Abdel Majid A.

2014-05-01

Recently, ephedrine (Eph) assessment in food products, pharmaceutical formulations, human fluids of athletes and detection of drug toxicity and abuse, has gained a growing interest. To provide basic data that can be used to assessment of Eph quantitatively based on charge-transfer (CT) complexation, the CT complexes of Eph with 7‧,8,8‧-tetracyanoquinodimethane (TCNQ), dichlorodicyanobenzoquinone (DDQ), 1,3-dinitrobenzene (DNB) or tetrabromothiophene (TBT) were synthesized and spectroscopically investigated. The newly synthesized complexes have been characterized via elemental analysis, IR, Raman, 1H NMR, and UV-visible spectroscopy. The formation constant (KCT), molar extinction coefficient (εCT) and other spectroscopic data have been determined using the Benesi-Hildebrand method and its modifications. The sharp, well-defined Bragg reflections at specific 2θ angles have been identified from the powder X-ray diffraction patterns. Thermal decomposition behavior of these complexes was also studied, and their kinetic thermodynamic parameters were calculated with Coats-Redfern and Horowitz-Metzger equations.

Re-membering the body: applications of computational neuroscience to the top-down control of regeneration of limbs and other complex organs.

PubMed

Pezzulo, G; Levin, M

2015-12-01

A major goal of regenerative medicine and bioengineering is the regeneration of complex organs, such as limbs, and the capability to create artificial constructs (so-called biobots) with defined morphologies and robust self-repair capabilities. Developmental biology presents remarkable examples of systems that self-assemble and regenerate complex structures toward their correct shape despite significant perturbations. A fundamental challenge is to translate progress in molecular genetics into control of large-scale organismal anatomy, and the field is still searching for an appropriate theoretical paradigm for facilitating control of pattern homeostasis. However, computational neuroscience provides many examples in which cell networks - brains - store memories (e.g., of geometric configurations, rules, and patterns) and coordinate their activity towards proximal and distant goals. In this Perspective, we propose that programming large-scale morphogenesis requires exploiting the information processing by which cellular structures work toward specific shapes. In non-neural cells, as in the brain, bioelectric signaling implements information processing, decision-making, and memory in regulating pattern and its remodeling. Thus, approaches used in computational neuroscience to understand goal-seeking neural systems offer a toolbox of techniques to model and control regenerative pattern formation. Here, we review recent data on developmental bioelectricity as a regulator of patterning, and propose that target morphology could be encoded within tissues as a kind of memory, using the same molecular mechanisms and algorithms so successfully exploited by the brain. We highlight the next steps of an unconventional research program, which may allow top-down control of growth and form for numerous applications in regenerative medicine and synthetic bioengineering.

Inner/Outer nuclear membrane fusion in nuclear pore assembly: biochemical demonstration and molecular analysis.

PubMed

Fichtman, Boris; Ramos, Corinne; Rasala, Beth; Harel, Amnon; Forbes, Douglass J

2010-12-01

Nuclear pore complexes (NPCs) are large proteinaceous channels embedded in double nuclear membranes, which carry out nucleocytoplasmic exchange. The mechanism of nuclear pore assembly involves a unique challenge, as it requires creation of a long-lived membrane-lined channel connecting the inner and outer nuclear membranes. This stabilized membrane channel has little evolutionary precedent. Here we mapped inner/outer nuclear membrane fusion in NPC assembly biochemically by using novel assembly intermediates and membrane fusion inhibitors. Incubation of a Xenopus in vitro nuclear assembly system at 14°C revealed an early pore intermediate where nucleoporin subunits POM121 and the Nup107-160 complex were organized in a punctate pattern on the inner nuclear membrane. With time, this intermediate progressed to diffusion channel formation and finally to complete nuclear pore assembly. Correct channel formation was blocked by the hemifusion inhibitor lysophosphatidylcholine (LPC), but not if a complementary-shaped lipid, oleic acid (OA), was simultaneously added, as determined with a novel fluorescent dextran-quenching assay. Importantly, recruitment of the bulk of FG nucleoporins, characteristic of mature nuclear pores, was not observed before diffusion channel formation and was prevented by LPC or OA, but not by LPC+OA. These results map the crucial inner/outer nuclear membrane fusion event of NPC assembly downstream of POM121/Nup107-160 complex interaction and upstream or at the time of FG nucleoporin recruitment.

Buckling-Induced Kirigami

NASA Astrophysics Data System (ADS)

Rafsanjani, Ahmad; Bertoldi, Katia

2017-02-01

We investigate the mechanical response of thin sheets perforated with a square array of mutually orthogonal cuts, which leaves a network of squares connected by small ligaments. Our combined analytical, experimental and numerical results indicate that under uniaxial tension the ligaments buckle out of plane, inducing the formation of 3D patterns whose morphology is controlled by the load direction. We also find that by largely stretching the buckled perforated sheets, plastic strains develop in the ligaments. This gives rise to the formation of kirigami sheets comprising periodic distribution of cuts and permanent folds. As such, the proposed buckling-induced pop-up strategy points to a simple route for manufacturing complex morphable structures out of flat perforated sheets.

Studies of the Permian Phosphoria Formation and related rocks, Great Basin-Rocky Mountain region

USGS Publications Warehouse

Wardlaw, Bruce R.

1979-01-01

PART A: The transgression of the Permian Retort Phosphatic Shale Member of the Phosphoria Formation is dated by the occurrence of diagnostic brachiopods. The complex pattern of this transgression reflects the paleogeography and indicates two initial basins of deposition: one in southwestern Montana and one in southeastern Idaho. PART B: A new formation is proposed for middle Permian rocks of a transitional facies positioned laterally between the Rex Chert Member of the Phosphoria Formation in northeastern Utah and southeastern Idaho and the Plympton Formation in northeastern Nevada and northwestern Utah. PART C: The relationships of the Permian Park City Group to the Phosphoria and Park City Formations are clarified by the stratigraphy of four sections in northwestern Utah, northeastern Nevada, and southern Idaho. PART D: Five biostratigraphic zones based on the distribution of brachiopods and conodonts are proposed for the Park City Group. They are: the Peniculauris ivesi-Neostreptognathodus prayi Zone, the Peniculauris bassi-Neostreptognathodus sulcoplicatus Zone, the Peniculauris bassi-Neostreptognathodus sp. C Zone, the Thamnosia depressa Zone, and the Yakovlevia. multistriata-Neogondolella bitteri Zone. They range in age from Leonardian to Wordian.

PNA binding to the non-template DNA strand interferes with transcription, suggesting a blockage mechanism mediated by R-loop formation.

PubMed

Belotserkovskii, Boris P; Hanawalt, Philip C

2015-11-01

Peptide Nucleic Acids (PNAs) are artificial DNA mimics with superior nucleic acid binding capabilities. T7 RNA polymerase (T7 RNAP) transcription upon encountering PNA bound to the non-template DNA strand was studied in vitro. A characteristic pattern of blockage signals was observed, extending downstream from the PNA binding site, similar to that produced by G-rich homopurine-homopyrimidine (hPu-hPy) sequences and likely caused by R-loop formation. Since blocked transcription complexes in association with stable R-loops may interfere with replication and in some cases trigger apoptosis, targeted R-loop formation might be employed to inactivate selected cells, such as those in tumors, based upon their unique complement of expressed genes. © 2014 The Authors. Molecular Carcinogenesis published by Wiley Periodicals, Inc.

Pixel-based OPC optimization based on conjugate gradients.

PubMed

Ma, Xu; Arce, Gonzalo R

2011-01-31

Optical proximity correction (OPC) methods are resolution enhancement techniques (RET) used extensively in the semiconductor industry to improve the resolution and pattern fidelity of optical lithography. In pixel-based OPC (PBOPC), the mask is divided into small pixels, each of which is modified during the optimization process. Two critical issues in PBOPC are the required computational complexity of the optimization process, and the manufacturability of the optimized mask. Most current OPC optimization methods apply the steepest descent (SD) algorithm to improve image fidelity augmented by regularization penalties to reduce the complexity of the mask. Although simple to implement, the SD algorithm converges slowly. The existing regularization penalties, however, fall short in meeting the mask rule check (MRC) requirements often used in semiconductor manufacturing. This paper focuses on developing OPC optimization algorithms based on the conjugate gradient (CG) method which exhibits much faster convergence than the SD algorithm. The imaging formation process is represented by the Fourier series expansion model which approximates the partially coherent system as a sum of coherent systems. In order to obtain more desirable manufacturability properties of the mask pattern, a MRC penalty is proposed to enlarge the linear size of the sub-resolution assistant features (SRAFs), as well as the distances between the SRAFs and the main body of the mask. Finally, a projection method is developed to further reduce the complexity of the optimized mask pattern.

Influence of the size and charge of gold nanoclusters on complexation with siRNA: a molecular dynamics simulation study.

PubMed

Mudedla, Sathish Kumar; Azhagiya Singam, Ettayapuram Ramaprasad; Balamurugan, Kanagasabai; Subramanian, Venkatesan

2015-11-11

The complexation of small interfering RNA (siRNA) with positively charged gold nanoclusters has been studied in the present investigation with the help of classical molecular dynamics and steered molecular dynamics simulations accompanied by free energy calculations. The results show that gold nanoclusters form a stable complex with siRNA. The wrapping of siRNA around the gold nanocluster depends on the size and charge on the surface of the gold cluster. The binding pattern of the gold nanocluster with siRNA is also influenced by the presence of another cluster. The interaction between the positively charged amines in the gold nanocluster and the negatively charged phosphate group in the siRNA is responsible for the formation of complexes. The binding free energy value increases with the size of the gold cluster and the number of positive charges present on the surface of the gold nanocluster. The results reveal that the binding energy of small gold nanoclusters increases in the presence of another gold nanocluster while the binding of large gold nanoclusters decreases due to the introduction of another gold nanocluster. Overall, the findings have clearly demonstrated the effect of size and charge of gold nanoclusters on their interaction pattern with siRNA.

Brassinosteroids control root epidermal cell fate via direct regulation of a MYB-bHLH-WD40 complex by GSK3-like kinases

PubMed Central

Cheng, Yinwei; Zhu, Wenjiao; Chen, Yuxiao; Ito, Shinsaku; Asami, Tadao; Wang, Xuelu

2014-01-01

In Arabidopsis, root hair and non-hair cell fates are determined by a MYB-bHLH-WD40 transcriptional complex and are regulated by many internal and environmental cues. Brassinosteroids play important roles in regulating root hair specification by unknown mechanisms. Here, we systematically examined root hair phenotypes in brassinosteroid-related mutants, and found that brassinosteroid signaling inhibits root hair formation through GSK3-like kinases or upstream components. We found that with enhanced brassinosteroid signaling, GL2, a cell fate marker for non-hair cells, is ectopically expressed in hair cells, while its expression in non-hair cells is suppressed when brassinosteroid signaling is reduced. Genetic analysis demonstrated that brassinosteroid-regulated root epidermal cell patterning is dependent on the WER-GL3/EGL3-TTG1 transcriptional complex. One of the GSK3-like kinases, BIN2, interacted with and phosphorylated EGL3, and EGL3s mutated at phosphorylation sites were retained in hair cell nuclei. BIN2 phosphorylated TTG1 to inhibit the activity of the WER-GL3/EGL3-TTG1 complex. Thus, our study provides insights into the mechanism of brassinosteroid regulation of root hair patterning. DOI: http://dx.doi.org/10.7554/eLife.02525.001 PMID:24771765

Multiscale structure in eco-evolutionary dynamics

NASA Astrophysics Data System (ADS)

Stacey, Blake C.

In a complex system, the individual components are neither so tightly coupled or correlated that they can all be treated as a single unit, nor so uncorrelated that they can be approximated as independent entities. Instead, patterns of interdependency lead to structure at multiple scales of organization. Evolution excels at producing such complex structures. In turn, the existence of these complex interrelationships within a biological system affects the evolutionary dynamics of that system. I present a mathematical formalism for multiscale structure, grounded in information theory, which makes these intuitions quantitative, and I show how dynamics defined in terms of population genetics or evolutionary game theory can lead to multiscale organization. For complex systems, "more is different," and I address this from several perspectives. Spatial host--consumer models demonstrate the importance of the structures which can arise due to dynamical pattern formation. Evolutionary game theory reveals the novel effects which can result from multiplayer games, nonlinear payoffs and ecological stochasticity. Replicator dynamics in an environment with mesoscale structure relates to generalized conditionalization rules in probability theory. The idea of natural selection "acting at multiple levels" has been mathematized in a variety of ways, not all of which are equivalent. We will face down the confusion, using the experience developed over the course of this thesis to clarify the situation.

Stellar Clusters in the NGC 6334 Star-Forming Complex

NASA Astrophysics Data System (ADS)

Feigelson, Eric D.; Martin, Amanda L.; McNeill, Collin J.; Broos, Patrick S.; Garmire, Gordon P.

2009-07-01

The full stellar population of NGC 6334, one of the most spectacular regions of massive star formation in the nearby Galaxy, has not been well sampled in past studies. We analyze here a mosaic of two Chandra X-ray Observatory images of the region using sensitive data analysis methods, giving a list of 1607 faint X-ray sources with arcsecond positions and approximate line-of-sight absorption. About 95% of these are expected to be cluster members, most lower mass pre-main-sequence stars. Extrapolating to low X-ray levels, the total stellar population is estimated to be 20,000-30,000 pre-main-sequence stars. The X-ray sources show a complicated spatial pattern with ~10 distinct star clusters. The heavily obscured clusters are mostly associated with previously known far-infrared sources and radio H II regions. The lightly obscured clusters are mostly newly identified in the X-ray images. Dozens of likely OB stars are found, both in clusters and dispersed throughout the region, suggesting that star formation in the complex has proceeded over millions of years. A number of extraordinarily heavily absorbed X-ray sources are associated with the active regions of star formation.

Morphology of Dbx1 respiratory neurons in the preBötzinger complex and reticular formation of neonatal mice.

PubMed

Akins, Victoria T; Weragalaarachchi, Krishanthi; Picardo, Maria Cristina D; Revill, Ann L; Del Negro, Christopher A

2017-08-01

The relationship between neuron morphology and function is a perennial issue in neuroscience. Information about synaptic integration, network connectivity, and the specific roles of neuronal subpopulations can be obtained through morphological analysis of key neurons within a microcircuit. Here we present morphologies of two classes of brainstem respiratory neurons. First, interneurons derived from Dbx1-expressing precursors (Dbx1 neurons) in the preBötzinger complex (preBötC) of the ventral medulla that generate the rhythm for inspiratory breathing movements. Second, Dbx1 neurons of the intermediate reticular formation that influence the motor pattern of pharyngeal and lingual movements during the inspiratory phase of the breathing cycle. We describe the image acquisition and subsequent digitization of morphologies of respiratory Dbx1 neurons from the preBötC and the intermediate reticular formation that were first recorded in vitro. These data can be analyzed comparatively to examine how morphology influences the roles of Dbx1 preBötC and Dbx1 reticular interneurons in respiration and can also be utilized to create morphologically accurate compartmental models for simulation and modeling of respiratory circuits.

Nanostructure Formation by controlled dewetting on patterned substrates: A combined theoretical, modeling and experimental study

PubMed Central

Lu, Liang-Xing; Wang, Ying-Min; Srinivasan, Bharathi Madurai; Asbahi, Mohamed; Yang, Joel K. W.; Zhang, Yong-Wei

2016-01-01

We perform systematic two-dimensional energetic analysis to study the stability of various nanostructures formed by dewetting solid films deposited on patterned substrates. Our analytical results show that by controlling system parameters such as the substrate surface pattern, film thickness and wetting angle, a variety of equilibrium nanostructures can be obtained. Phase diagrams are presented to show the complex relations between these system parameters and various nanostructure morphologies. We further carry out both phase field simulations and dewetting experiments to validate the analytically derived phase diagrams. Good agreements between the results from our energetic analyses and those from our phase field simulations and experiments verify our analysis. Hence, the phase diagrams presented here provide guidelines for using solid-state dewetting as a tool to achieve various nanostructures. PMID:27580943

What does the Sr-substituted 2.1 Å resolution crystal structure of photosystem II reveal about the water oxidation mechanism?

PubMed

Terrett, Richard; Petrie, Simon; Pace, Ron J; Stranger, Robert

2014-03-25

A density functional study of the Sr-substituted photosystem II water oxidising complex demonstrates that its recent X-ray crystal structure is consistent with a (Mn(III))4 oxidation state pattern, and with a Sr-bound hydroxide ion. The Sr-water-hydroxide interactions rationalize differences in the exchange rates of substrate water and kinetics of dioxygen bond formation relative to the Ca-containing structure.

Spongy-like porosity in peritidal carbonates: An interaction of cyclic sea-level oscillations, fresh water supply and sediment texture

NASA Astrophysics Data System (ADS)

Todaro, S.; Hollis, C.; Di Stefano, P.

2016-03-01

This paper focuses upon the analysis of a complex paleokarstic system recorded within uppermost Triassic peritidal cycles in northwestern Sicily. Besides documenting spectacular karstification at the Triassic/Jurassic boundary, it provides an example of stratabound 'spongy' or 'swiss-cheese' dissolution. On the base of field observations, microfacies analysis, transmitted-light and cathodoluminescence petrography and stable-isotope analyses we put forward an original model for the formation of this peculiar stratabound dissolution. It implies a complex interaction of several controlling factors at the interface between the marine and meteoric diagenetic realms during the relative cyclic oscillations of sea-level. The presence of a fresh water supply from an adjacent emerged area is the key for the periodic formation of a mixing water lens during the relative sea level lowstand that brought about the subaerial exposure of the platform. The resulting dissolution pattern in the subtidal unit of a specific cycle is strongly controlled by the textural features of the sediments. In the case of bioturbated wackestones the 'spongy' or 'swiss-cheese' pattern develops, while in mollusk-rich beds biomoldic porosity occurs. In well-sorted subtidal members, such as algal grainstones, the dissolution originates as randomly distributed vuggy porosity. During periodic flooding of the platform, a new subtidal unit is formed and the dissolution stops as fully marine phreatic conditions are re-established.

Simulation of the formation of nonequilibrium structures in magnetorheological fluids subject to an external magnetic field

NASA Astrophysics Data System (ADS)

Mohebi, M.; Jamasbi, N.; Liu, Jing

1996-11-01

We developed a computer model to understand the nonequilibrium structures induced in a magnetorheological (MR) fluid by rapidly applying an external magnetic field. MR fluids consist of particles suspended in a liquid where particles interact through dipole moments induced by the external magnetic field. We have simulated these induced structures in both directions, parallel and perpendicular to the field, in the limit of fastest response, by neglecting thermal motion and applying the field instantaneously. Our results show that the process of structure formation starts with particles forming chains aligned with the external field. The chains then coalesce to form columns and wall-like structures (``worms'' as viewed from the top). The complexity of this pattern is found to depend on the concentration of particles and the confinement of the cell in the direction of the external field. These results are consistent with experimental observations [G.A. Flores et al., in Proceedings of the Fifth International Conference on ER Fluids, MR Suspensions, and Associate Technology, University of Sheffield, Sheffield, 1995, edited by W. Bullough (World Scientific, Singapore, 1996), p. 140]. We have also used this model to study the interaction of two chains. The results of this study help in the understanding of the connection between the thickness of the sample and the increased complexity of the observed lateral pattern.

Structural bases for neurophysiological investigations of amygdaloid complex of the brain

NASA Astrophysics Data System (ADS)

Kalimullina, Liliya B.; Kalkamanov, Kh. A.; Akhmadeev, Azat V.; Zakharov, Vadim P.; Sharafullin, Ildus F.

2015-11-01

Amygdala (Am) as a part of limbic system of the brain defines such important functions as adaptive behavior of animals, formation of emotions and memory, regulation of endocrine and visceral functions. We worked out, with the help of mathematic modelling of the pattern recognition theory, principles for organization of neurophysiological and neuromorphological studies of Am nuclei, which take into account the existing heterogeneity of its formations and optimize, to a great extent, the protocol for carrying out of such investigations. The given scheme of studies of Am’s structural-functional organization at its highly-informative sections can be used as a guide for precise placement of electrodes’, cannulae’s and microsensors into particular Am nucleus in the brain with the registration not only the nucleus itself, but also its extensions. This information is also important for defining the number of slices covering specific Am nuclei which must be investigated to reveal the physiological role of a particular part of amygdaloid complex.

Continuous monitoring of the lunar or Martian subsurface using on-board pattern recognition and neural processing of Rover geophysical data

NASA Technical Reports Server (NTRS)

Mcgill, J. W.; Glass, C. E.; Sternberg, B. K.

1990-01-01

The ultimate goal is to create an extraterrestrial unmanned system for subsurface mapping and exploration. Neural networks are to be used to recognize anomalies in the profiles that correspond to potentially exploitable subsurface features. The ground penetrating radar (GPR) techniques are likewise identical. Hence, the preliminary research focus on GPR systems will be directly applicable to seismic systems once such systems can be designed for continuous operation. The original GPR profile may be very complex due to electrical behavior of the background, targets, and antennas, much as the seismic record is made complex by multiple reflections, ghosting, and ringing. Because the format of the GPR data is similar to the format of seismic data, seismic processing software may be applied to GPR data to help enhance the data. A neural network may then be trained to more accurately identify anomalies from the processed record than from the original record.

Self-organization principles of intracellular pattern formation.

PubMed

Halatek, J; Brauns, F; Frey, E

2018-05-26

Dynamic patterning of specific proteins is essential for the spatio-temporal regulation of many important intracellular processes in prokaryotes, eukaryotes and multicellular organisms. The emergence of patterns generated by interactions of diffusing proteins is a paradigmatic example for self-organization. In this article, we review quantitative models for intracellular Min protein patterns in Escherichia coli , Cdc42 polarization in Saccharomyces cerevisiae and the bipolar PAR protein patterns found in Caenorhabditis elegans By analysing the molecular processes driving these systems we derive a theoretical perspective on general principles underlying self-organized pattern formation. We argue that intracellular pattern formation is not captured by concepts such as 'activators', 'inhibitors' or 'substrate depletion'. Instead, intracellular pattern formation is based on the redistribution of proteins by cytosolic diffusion, and the cycling of proteins between distinct conformational states. Therefore, mass-conserving reaction-diffusion equations provide the most appropriate framework to study intracellular pattern formation. We conclude that directed transport, e.g. cytosolic diffusion along an actively maintained cytosolic gradient, is the key process underlying pattern formation. Thus the basic principle of self-organization is the establishment and maintenance of directed transport by intracellular protein dynamics.This article is part of the theme issue 'Self-organization in cell biology'. © 2018 The Authors.

A novel double patterning approach for 30nm dense holes

NASA Astrophysics Data System (ADS)

Hsu, Dennis Shu-Hao; Wang, Walter; Hsieh, Wei-Hsien; Huang, Chun-Yen; Wu, Wen-Bin; Shih, Chiang-Lin; Shih, Steven

2011-04-01

Double Patterning Technology (DPT) was commonly accepted as the major workhorse beyond water immersion lithography for sub-38nm half-pitch line patterning before the EUV production. For dense hole patterning, classical DPT employs self-aligned spacer deposition and uses the intersection of horizontal and vertical lines to define the desired hole patterns. However, the increase in manufacturing cost and process complexity is tremendous. Several innovative approaches have been proposed and experimented to address the manufacturing and technical challenges. A novel process of double patterned pillars combined image reverse will be proposed for the realization of low cost dense holes in 30nm node DRAM. The nature of pillar formation lithography provides much better optical contrast compared to the counterpart hole patterning with similar CD requirements. By the utilization of a reliable freezing process, double patterned pillars can be readily implemented. A novel image reverse process at the last stage defines the hole patterns with high fidelity. In this paper, several freezing processes for the construction of the double patterned pillars were tested and compared, and 30nm double patterning pillars were demonstrated successfully. A variety of different image reverse processes will be investigated and discussed for their pros and cons. An economic approach with the optimized lithography performance will be proposed for the application of 30nm DRAM node.

Bacterial Trapping in Porous Media Flows

NASA Astrophysics Data System (ADS)

Dehkharghani, Amin; Waisbord, Nicolas; Dunkel, Jörn; Guasto, Jeffrey

2016-11-01

Swimming bacteria inhabit heterogeneous, microstructured environments that are often characterized by complex, ambient flows. Understanding the physical mechanisms underlying cell transport in these systems is key to controlling important processes such as bioremediation in porous soils and infections in human tissues. We study the transport of swimming bacteria (Bacillus subtilis) in quasi-two-dimensional porous microfluidic channels with a range of periodic microstructures and flow strengths. Measured cell trajectories and the local cell number density reveal the formation of filamentous cell concentration patterns within the porous structures. The local cell densification is maximized at shear rates in the range 1-10 s-1, but widely varies with pore geometry and flow topology. Experimental observations are complemented by Langevin simulations to demonstrate that the filamentous patterns result from a coupling of bacterial motility to the complex flow fields via Jeffery orbits, which effectively 'trap' the bacteria on streamlines. The resulting microscopic heterogeneity observed here suppresses bacterial transport and likely has implications for both mixing and cell nutrient uptake in porous media flows. NSF CBET-1511340.

Integrative Mechanisms of Oriented Neuronal Migration in the Developing Brain

PubMed Central

Evsyukova, Irina; Plestant, Charlotte; Anton, E.S.

2014-01-01

The emergence of functional neuronal connectivity in the developing cerebral cortex depends on neuronal migration. This process enables appropriate positioning of neurons and the emergence of neuronal identity so that the correct patterns of functional synaptic connectivity between the right types and numbers of neurons can emerge. Delineating the complexities of neuronal migration is critical to our understanding of normal cerebral cortical formation and neurodevelopmental disorders resulting from neuronal migration defects. For the most part, the integrated cell biological basis of the complex behavior of oriented neuronal migration within the developing mammalian cerebral cortex remains an enigma. This review aims to analyze the integrative mechanisms that enable neurons to sense environmental guidance cues and translate them into oriented patterns of migration toward defined areas of the cerebral cortex. We discuss how signals emanating from different domains of neurons get integrated to control distinct aspects of migratory behavior and how different types of cortical neurons coordinate their migratory activities within the developing cerebral cortex to produce functionally critical laminar organization. PMID:23937349

Endogenous Bioelectric Signaling Networks: Exploiting Voltage Gradients for Control of Growth and Form.

PubMed

Levin, Michael; Pezzulo, Giovanni; Finkelstein, Joshua M

2017-06-21

Living systems exhibit remarkable abilities to self-assemble, regenerate, and remodel complex shapes. How cellular networks construct and repair specific anatomical outcomes is an open question at the heart of the next-generation science of bioengineering. Developmental bioelectricity is an exciting emerging discipline that exploits endogenous bioelectric signaling among many cell types to regulate pattern formation. We provide a brief overview of this field, review recent data in which bioelectricity is used to control patterning in a range of model systems, and describe the molecular tools being used to probe the role of bioelectrics in the dynamic control of complex anatomy. We suggest that quantitative strategies recently developed to infer semantic content and information processing from ionic activity in the brain might provide important clues to cracking the bioelectric code. Gaining control of the mechanisms by which large-scale shape is regulated in vivo will drive transformative advances in bioengineering, regenerative medicine, and synthetic morphology, and could be used to therapeutically address birth defects, traumatic injury, and cancer.

The effect of butterfly scales on flight efficiency and leading edge vortex formation

NASA Astrophysics Data System (ADS)

Lang, Amy; Wilroy, Jacob; Wahidi, Redha; Slegers, Nathan; Heilman, Micahel; Cranford, Jacob

2016-11-01

It is hypothesized that the scales on a butterfly wing lead to increased flight efficiency. Recent testing of live butterflies tracked their motion over 246 flights for 11 different specimens. Results show a 37.8 percent mean decrease in flight efficiency and a flapping amplitude reduction of 6.7 percent once the scales were removed. This change could be largely a result of how the leading edge vortex (LEV) interacts with the wing. To simplify this complex flow problem, an experiment was designed to focus on the alteration of 2-D vortex development with a variation in surface patterning. Specifically, the secondary vorticity generated by the LEV interacting at the patterned surface was studied, as well as the subsequent effect on the LEV's growth rate and peak circulation. For this experiment butterfly inspired grooves were created using additive manufacturing and were attached to a flat plate with a chordwise orientation, thus increasing plate surface area. The vortex generated by the grooved plate was then compared to a smooth case as the plate translated vertically through a tow tank at Re = 1500, 3000, and 6000. Using DPIV, the vortex formation was documented and a maximum vortex formation time of 4.22 was found based on the flat plate travel distance and chord length. Results indicate that the patterned surface slows down the growth of the vortex which corroborates the flight test results. Funding from NSF CBET Fluid Dynamcis is gratefully acknowledged.

Stability of spermine oxidase to thermal and chemical denaturation: comparison with bovine serum amine oxidase.

PubMed

Cervelli, Manuela; Leonetti, Alessia; Cervoni, Laura; Ohkubo, Shinji; Xhani, Marla; Stano, Pasquale; Federico, Rodolfo; Polticelli, Fabio; Mariottini, Paolo; Agostinelli, Enzo

2016-10-01

Spermine oxidase (SMOX) is a flavin-containing enzyme that specifically oxidizes spermine to produce spermidine, 3-aminopropanaldehyde and hydrogen peroxide. While no crystal structure is available for any mammalian SMOX, X-ray crystallography showed that the yeast Fms1 polyamine oxidase has a dimeric structure. Based on this scenario, we have investigated the quaternary structure of the SMOX protein by native gel electrophoresis, which revealed a composite gel band pattern, suggesting the formation of protein complexes. All high-order protein complexes are sensitive to reducing conditions, showing that disulfide bonds were responsible for protein complexes formation. The major gel band other than the SMOX monomer is the covalent SMOX homodimer, which was disassembled by increasing the reducing conditions, while being resistant to other denaturing conditions. Homodimeric and monomeric SMOXs are catalytically active, as revealed after gel staining for enzymatic activity. An engineered SMOX mutant deprived of all but two cysteine residues was prepared and characterized experimentally, resulting in a monomeric species. High-sensitivity differential scanning calorimetry of SMOX was compared with that of bovine serum amine oxidase, to analyse their thermal stability. Furthermore, enzymatic activity assays and fluorescence spectroscopy were used to gain insight into the unfolding process.

Nonlinear Fluid Migration Patterns in Fractured Reservoirs due to Stress-Pressure Coupling induced Changes in Reservoir Permeabilities

NASA Astrophysics Data System (ADS)

Annewandter, R.; Geiger, S.; Main, I. G.

2011-12-01

Sustainable storage of carbon dioxide (CO2) requires a thorough understanding of injection induced pressure build-up and its effects on the storage formation's integrity, since it determines the cap rock's sealing properties as well as the total storable amount of carbon dioxide. Fractures are abundant in the subsurface and difficult to detect due to their subseismic characteristic. If present in the cap during injection, they can be primary pathways for CO2 leakage. The North Sea is considered as Europe's most important carbon dioxide storage area. However, almost all of the potential storage formations have been exposed to post-glacial lithospheric flexure, possibly causing the generation of new fracture networks in the overburden whilst rebounding. Drawing upon, fast carbon dioxide uprise can be facilitated due to opening of fractures caused by changes in the stress field over time. The overall effective permeability, and hence possible leakage rates, of a fractured storage formation is highly sensitive to the fracture aperture which itself depends on the far field and in situ stress field. For this reason, our in-house general purpose reservoir simulator Complex System Modeling Platform (CSMP++) has been expanded, which is particularly designed to simulate multiphase flow on fractured porous media. It combines finite element (FE) and finite volume (FV) methods on mixed-dimensional hybrid-element meshes. The unstructured FE-FV based scheme allows us to model complex geological structures, such as fractures, at great detail. The simulator uses a compositional model for NaCl-H2O-CO2-systems for compressible fluids for computing thermophysical properties as a function of formation pressure and temperature. A fixed stress-split sequential procedure is being used to calculate coupled fluid flow and geomechanics. Numerical proof of concept studies will be presented showing the impact of fracture opening and closure on fluid migration patterns due to coupled stress-pressure induced changes in effective permeabilities.

Rocks, resolution, and the record at the terrestrial K/T boundary, eastern Montana and western North Dakota

NASA Technical Reports Server (NTRS)

Fastovsky, D. E.

1988-01-01

Reconstructions of mass extinction events are based upon faunal patterns, reconstructed from numerical and diversity data ultimately derived from rocks. It follows that geological complexity must not be subsumed in the desire to establish patterns. This is exemplified at the Terrestrial Cretaceous-Tertiary (K/T) boundary in eastern Montana and western North Dakota, where there are represented all of the major indicators of the terrestrial K/T transition: dinosaurian and non-dinosaurian vertebrate faunas, pollen, a megaflora, iridium, and shocked quartz. It is the patterns of these indicators that shape ideas about the terrestrial K/T transition. In eastern Montana and western North Dakota, the K/T transition is represented lithostratigraphically by the Cretaceous Hell Creek Formation, and the Tertiary Tullock Formation. Both of these are the result of aggrading, meandering, fluvial systems, a fact that has important consequences for interpretations of fossils they contain. Direct consequences of the fluvial depositional environments are: facies are lenticular, interfingering, and laterally discontinuous; the occurrence of fossils in the Hell Creek and Tullock formations is facies-dependent; and the K/T sequence in eastern Montana and western North Dakota is incomplete, as indicated by repetitive erosional contacts and soil successions. The significance for faunal patterns of lenticular facies, facies-dependent preservation, and incompleteness is discussed. A project attempting to reconstruct vertebrate evolution in a reproducible manner in Hell Creek-type sediments must be based upon a reliable scale of correlations, given the lenticular nature of the deposits, and a recognition of the fact that disparate facies are not comparable in terms of either numbers of preserved vertebrates or depositional rates.

A bifurcation giving birth to order in an impulsively driven complex system

NASA Astrophysics Data System (ADS)

Seshadri, Akshay; Sujith, R. I.

2016-08-01

Nonlinear oscillations lie at the heart of numerous complex systems. Impulsive forcing arises naturally in many scenarios, and we endeavour to study nonlinear oscillators subject to such forcing. We model these kicked oscillatory systems as a piecewise smooth dynamical system, whereby their dynamics can be investigated. We investigate the problem of pattern formation in a turbulent combustion system and apply this formalism with the aim of explaining the observed dynamics. We identify that the transition of this system from low amplitude chaotic oscillations to large amplitude periodic oscillations is the result of a discontinuity induced bifurcation. Further, we provide an explanation for the occurrence of intermittent oscillations in the system.

The QuakeSim Project: Numerical Simulations for Active Tectonic Processes

NASA Technical Reports Server (NTRS)

Donnellan, Andrea; Parker, Jay; Lyzenga, Greg; Granat, Robert; Fox, Geoffrey; Pierce, Marlon; Rundle, John; McLeod, Dennis; Grant, Lisa; Tullis, Terry

2004-01-01

In order to develop a solid earth science framework for understanding and studying of active tectonic and earthquake processes, this task develops simulation and analysis tools to study the physics of earthquakes using state-of-the art modeling, data manipulation, and pattern recognition technologies. We develop clearly defined accessible data formats and code protocols as inputs to the simulations. these are adapted to high-performance computers because the solid earth system is extremely complex and nonlinear resulting in computationally intensive problems with millions of unknowns. With these tools it will be possible to construct the more complex models and simulations necessary to develop hazard assessment systems critical for reducing future losses from major earthquakes.

A bifurcation giving birth to order in an impulsively driven complex system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Seshadri, Akshay, E-mail: akshayseshadri@gmail.com; Sujith, R. I., E-mail: sujith@iitm.ac.in

Nonlinear oscillations lie at the heart of numerous complex systems. Impulsive forcing arises naturally in many scenarios, and we endeavour to study nonlinear oscillators subject to such forcing. We model these kicked oscillatory systems as a piecewise smooth dynamical system, whereby their dynamics can be investigated. We investigate the problem of pattern formation in a turbulent combustion system and apply this formalism with the aim of explaining the observed dynamics. We identify that the transition of this system from low amplitude chaotic oscillations to large amplitude periodic oscillations is the result of a discontinuity induced bifurcation. Further, we provide anmore » explanation for the occurrence of intermittent oscillations in the system.« less

Pleistocene hydrology of North America: The role of ice sheets in reorganizing groundwater flow systems

NASA Astrophysics Data System (ADS)

Person, Mark; McIntosh, Jennifer; Bense, Victor; Remenda, V. H.

2007-09-01

While the geomorphic consequences of Pleistocene megafloods have been known for some time, it has been only in the past 2 decades that hydrogeologists and glaciologists alike have begun to appreciate the important impact that ice sheet-aquifer interactions have had in controlling subsurface flow patterns, recharge rates, and the distribution of fresh water in confined aquifer systems across North America. In this paper, we document the numerous lines of geochemical, isotopic, and geomechanical evidence of ice sheet hydrogeology across North America. We also review the mechanical, thermal, and hydrologic processes that control subsurface fluid migration beneath ice sheets. Finite element models of subsurface fluid flow, permafrost formation, and ice sheet loading are presented to investigate the coupled nature of transport processes during glaciation/deglaciation. These indicate that recharge rates as high as 10 times modern values occurred as the Laurentide Ice Sheet overran the margins of sedimentary basins. The effects of ice sheet loading and permafrost formation result in complex transient flow patterns within aquifers and confining units alike. Using geochemical and environmental isotopic data, we estimate that the volume of glacial meltwater emplaced at the margins of sedimentary basins overrun by the Laurentide Ice Sheet totals about 3.7 × 104 km3, which is about 0.2% of the volume of the Laurentide Ice Sheet. Subglacial infiltration estimates based on continental-scale hydrologic models are even higher (5-10% of meltwater generated). These studies in sum call into question the widely held notion that groundwater flow patterns within confined aquifer systems are controlled primarily by the water table configuration during the Pleistocene. Rather, groundwater flow patterns were likely much more complex and transient in nature than has previously been thought. Because Pleistocene recharge rates are believed to be highly variable, these studies have profound implications for water resource managers charged with determining sustainable pumping rates from confined aquifers that host ice sheet meltwater.

Sterols in spermatogenesis and sperm maturation

PubMed Central

Keber, Rok; Rozman, Damjana; Horvat, Simon

2013-01-01

Mammalian spermatogenesis is a complex developmental program in which a diploid progenitor germ cell transforms into highly specialized spermatozoa. One intriguing aspect of sperm production is the dynamic change in membrane lipid composition that occurs throughout spermatogenesis. Cholesterol content, as well as its intermediates, differs vastly between the male reproductive system and nongonadal tissues. Accumulation of cholesterol precursors such as testis meiosis-activating sterol and desmosterol is observed in testes and spermatozoa from several mammalian species. Moreover, cholesterogenic genes, especially meiosis-activating sterol-producing enzyme cytochrome P450 lanosterol 14α-demethylase, display stage-specific expression patterns during spermatogenesis. Discrepancies in gene expression patterns suggest a complex temporal and cell-type specific regulation of sterol compounds during spermatogenesis, which also involves dynamic interactions between germ and Sertoli cells. The functional importance of sterol compounds in sperm production is further supported by the modulation of sterol composition in spermatozoal membranes during epididymal transit and in the female reproductive tract, which is a prerequisite for successful fertilization. However, the exact role of sterols in male reproduction is unknown. This review discusses sterol dynamics in sperm maturation and describes recent methodological advances that will help to illuminate the complexity of sperm formation and function. PMID:23093550

The role of historical barriers in the diversification processes in open vegetation formations during the Miocene/Pliocene using an ancient rodent lineage as a model.

PubMed

Nascimento, Fabrícia F; Lazar, Ana; Menezes, Albert N; Durans, Andressa da Matta; Moreira, Jânio C; Salazar-Bravo, Jorge; D'Andrea, Paulo S; Bonvicino, Cibele R

2013-01-01

The Neotropics harbors a high diversity of species and several hypotheses have been proposed to account for this pattern. However, while species of forested domains are frequently studied, less is known of species from open vegetation formations occupying, altogether, a larger area than the Amazon Forest. Here we evaluate the role of historical barriers and the riverine hypothesis in the speciation patterns of small mammals by analyzing an ancient rodent lineage (Thrichomys, Hystricomorpha). Phylogenetic and biogeographic analyses were carried out with mitochondrial and nuclear DNA markers to analyze the evolutionary relationships between Thrichomys lineages occurring in dry domains along both banks of the Rio São Francisco. This river is one of the longest of South America whose course and water flow have been modified by inland tectonic activities and climate changes. Molecular data showed a higher number of lineages than previously described. The T. inermis species complex with 2n = 26, FN = 48 was observed in both banks of the river showing a paraphyletic arrangement, suggesting that river crossing had occurred, from east to west. A similar pattern was also observed for the T. apereoides complex. Thrichomys speciation occurred in Late Miocene when the river followed a different course. The current geographic distribution of Thrichomys species and their phylogenetic relationships suggested the existence of frequent past connections between both banks in the middle section of the Rio São Francisco. The extensive palaeodune region found in this area has been identified as a centre of endemism of several vertebrate species and is likely to be a center of Thrichomys diversification.

The Role of Historical Barriers in the Diversification Processes in Open Vegetation Formations during the Miocene/Pliocene Using an Ancient Rodent Lineage as a Model

PubMed Central

Nascimento, Fabrícia F.; Lazar, Ana; Menezes, Albert N.; Durans, Andressa da Matta; Moreira, Jânio C.; Salazar-Bravo, Jorge; D′Andrea, Paulo S.; Bonvicino, Cibele R.

2013-01-01

The Neotropics harbors a high diversity of species and several hypotheses have been proposed to account for this pattern. However, while species of forested domains are frequently studied, less is known of species from open vegetation formations occupying, altogether, a larger area than the Amazon Forest. Here we evaluate the role of historical barriers and the riverine hypothesis in the speciation patterns of small mammals by analyzing an ancient rodent lineage (Thrichomys, Hystricomorpha). Phylogenetic and biogeographic analyses were carried out with mitochondrial and nuclear DNA markers to analyze the evolutionary relationships between Thrichomys lineages occurring in dry domains along both banks of the Rio São Francisco. This river is one of the longest of South America whose course and water flow have been modified by inland tectonic activities and climate changes. Molecular data showed a higher number of lineages than previously described. The T. inermis species complex with 2n = 26, FN = 48 was observed in both banks of the river showing a paraphyletic arrangement, suggesting that river crossing had occurred, from east to west. A similar pattern was also observed for the T. apereoides complex. Thrichomys speciation occurred in Late Miocene when the river followed a different course. The current geographic distribution of Thrichomys species and their phylogenetic relationships suggested the existence of frequent past connections between both banks in the middle section of the Rio São Francisco. The extensive palaeodune region found in this area has been identified as a centre of endemism of several vertebrate species and is likely to be a center of Thrichomys diversification. PMID:24349576

Finger-like pattern formation in dilute surfactant pentaethylene glycol monododecyl ether solutions.

PubMed

Kubo, Yoshihide; Yokoyama, Yasuhiro; Tanaka, Shinpei

2013-04-07

We report here peculiar finger-like patterns observed during the phase separation process of dilute micellar pentaethylene glycol monododecyl ether solutions. The patterns were composed of parallel and periodic threads of micelle-rich domains. Prior to this pattern formation, the phase separation always started with the appearance of water-rich domains rimmed by the micelle-rich domains. It was found that these rims played a significant role in the pattern formation. We explain this pattern formation using a simple simulation model with disconnectable springs. The simulation results suggested that the spatially inhomogeneous elasticity or connectivity of a transient gel of worm-like micelles was responsible for the rim formation. The rims thus formed lead rim-induced nucleation, growth, and elongation of the domains owing to their small mobility and the elastic frustration around them. These rim-induced processes eventually produce the observed finger-like patterns.

Dnmts and Tet target memory-associated genes after appetitive olfactory training in honey bees

PubMed Central

Biergans, Stephanie D.; Giovanni Galizia, C.; Reinhard, Judith; Claudianos, Charles

2015-01-01

DNA methylation and demethylation are epigenetic mechanisms involved in memory formation. In honey bees DNA methyltransferase (Dnmt) function is necessary for long-term memory to be stimulus specific (i.e. to reduce generalization). So far, however, it remains elusive which genes are targeted and what the time-course of DNA methylation is during memory formation. Here, we analyse how DNA methylation affects memory retention, gene expression, and differential methylation in stimulus-specific olfactory long-term memory formation. Out of 30 memory-associated genes investigated here, 9 were upregulated following Dnmt inhibition in trained bees. These included Dnmt3 suggesting a negative feedback loop for DNA methylation. Within these genes also the DNA methylation pattern changed during the first 24 hours after training. Interestingly, this was accompanied by sequential activation of the DNA methylation machinery (i.e. Dnmts and Tet). In sum, memory formation involves a temporally complex epigenetic regulation of memory-associated genes that facilitates stimulus specific long-term memory in the honey bee. PMID:26531238

Bioconvective patterns, synchrony, and survival. [in light-limited growth model of motile algae culture

NASA Technical Reports Server (NTRS)

Noever, David A.

1990-01-01

With and without bioconvective pattern formation, a theoretical model predicts growth in light-limited cultures of motile algae. At the critical density for pattern formation, the resulting doubly exponential population curves show an inflection. Such growth corresponds quantitatively to experiments in mechanically unstirred cultures. This attaches survival value to synchronized pattern formation.

Direct laser interference patterning for decreased bacterial attachment

NASA Astrophysics Data System (ADS)

Guenther, Denise; Valle, Jaoine; Burgui, Saioa; Gil, Carmen; Solano, Cristina; Toledo-Arana, Alejandro; Helbig, Ralf; Werner, Carsten; Lasa, Inigo; Lasagni, Andrés. F.

2016-03-01

In the past 15 years, many efforts were made to create functionalized artificial surfaces showing special anti-bacterial and anti-biofouling properties. Thereby, the topography of medical relevant materials plays an important role. However, the targeted fabrication of promising surface structures like hole-, lamella- and pyramid-like patterns with feature sizes in the sub-micrometer range in a one-step process is still a challenge. Optical and e-beam lithography, molding and selfassembly layers show a great potential to design topographies for this purpose. At the same time, most of these techniques are based on sequential processes, require masks or molds and thus are very device relevant and time consuming. In this work, we present the Direct Laser Interference Patterning (DLIP) technology as a capable method for the fast, flexible and direct fabrication of periodic micrometer- and submicrometer structures. This method offers the possibility to equip large plain areas and curved devices with 1D, 2D and 3D patterns. Simple 1D (e.g. lines) and complex 3D (e.g. lamella, pillars) patterns with periodic distances from 0.5 μm to 5 μm were fabricated on polymeric materials (polyimide, polystyrene). Subsequently, we characterized the adhesion behavior of Staphylococcus epidermidis and S. aureus bacteria under in vitro and in vivo conditions. The results revealed that the topographies have a significant impact on bacteria adhesion. On the one side, one-dimensional line-like structures especially with dimensions of the bacteria enhanced microbe attachment. While on the other hand, complex three-dimensional patterns prevented biofilm formation even after implantation and contamination in living organisms.

From "seahorse" to "molecular Recording"

NASA Astrophysics Data System (ADS)

Gao, Hong-Jun

2002-08-01

We will first present unique dendritic "seahorse" patterns observed when we study structural features in functional C60-TCNQ complex thin films, and their formation mechanism. Then we report a new process for ultrahigh density, erasable data storage, based on the molecular electrical bistability of an organic charge transfer complex, 3-nitrobenzal malononitrile and 1,4-phenylenediamine (NBMN-pDA). Switched by a voltage pulse from a scanning tunneling microscope (STM), we demonstrate a data density exceeding 1013 bits/cm2. The experiment results and theoretical ab initio calculations show the writing and erasing mechanism to be a conductance transition of the organic compound due to a structural change from crystalline to noncrystalline. The ultimate bit density appears limited only by the size of the organic complex, less than 1 nm in our case, corresponding to 1014 bits/cm2.

A three-dimensional model for lubricant depletion under sliding condition on bit patterned media of hard disk drives

NASA Astrophysics Data System (ADS)

Wu, Lin

2018-05-01

In this paper, we model the depletion dynamics of the molecularly thin layer of lubricants on a bit patterned media disk of hard disk drives under a sliding air bearing head. The dominant physics and consequently, the lubricant depletion dynamics on a patterned disk are shown to be significantly different from the well-studied cases of a smooth disk. Our results indicate that the surface tension effect, which is negligible on a flat disk, apparently suppresses depletion by enforcing a bottleneck effect around the disk pattern peak regions to thwart the migration of lubricants. When the disjoining pressure is relatively small, it assists the depletion. But, when the disjoining pressure becomes dominant, the disjoining pressure resists depletion. Disk pattern orientation plays a critical role in the depletion process. The effect of disk pattern orientation on depletion originates from its complex interaction with other intermingled factors of external air shearing stress distribution and lubricant particle trajectory. Patterning a disk surface with nanostructures of high density, large height/pitch ratio, and particular orientation is demonstrated to be one efficient way to alleviate the formation of lubricant depletion tracks.

Patterning of supported lipid bilayers and proteins using material selective nitrodopamine-mPEG.

PubMed

Spycher, Philipp R; Hall, Heike; Vogel, Viola; Reimhult, Erik

2015-01-01

We present a generic patterning process by which biomolecules in a passivated background are patterned directly from physiological buffer to microfabricated surfaces without the need for further processing. First, nitrodopamine-mPEG is self-assembled to selectively render TiO2 patterns non-fouling to biomolecule adsorption on hydrophilic and adhesive glass surfaces. After the controlled TiO2 passivation, the biomolecules can be directly adsorbed from solution in a single step creating large scale micropatterned and highly homogeneous arrays of biomolecules with very high pattern definition. We demonstrate the formation of fluid supported lipid bilayers (SLBs) down to the single μm-level limited only by the photolithographic process. Non-specific adsorption of lipid vesicles to the TiO2 background was found to be almost completely suppressed. The SLB patterns can be further selectively functionalized with retained mobility, which we demonstrate through biotin-streptavidin coupling. We envision this single step patterning approach to be very beneficial for membrane-based biosensors and for pattering of cells on a passivated background with complex, sub-cellular geometries; in each application the adherent areas have a tunable mobility of interaction sites controlled by the fluidity of the membrane.

Non-Covalent Photo-Patterning of Gelatin Matrices Using Caged Collagen Mimetic Peptides

PubMed Central

Li, Yang; Hoa San, Boi; L. Kessler, Julian; Hwan Kim, Jin; Xu, Qingguo; Hanes, Justin; Yu, Seungju Michael

2015-01-01

Advancements in photolithography have enabled us to spatially encode biochemical cues in biocompatible platforms such as synthetic hydrogels. Conventional patterning works through photo-activated chemical reactions on inert polymer networks. However, these techniques cannot be directly applied to protein hydrogels without chemically altering the protein scaffolds. To this end, we developed a non-covalent photo-patterning strategy for gelatin (denatured collagen) hydrogels utilizing a caged collagen mimetic peptide (caged CMP) which binds to gelatin strands through UV activated, triple helix hybridization. Here we present 2D and 3D photo-patterning of gelatin hydrogels enabled by the caged CMPs as well as creation of concentration gradients of CMPs. We show that photo-patterning of PEG-conjugated caged CMPs can be used to spatially control cell adhesion on gelatin films. CMP’s specificity for binding to gelatin allows patterning of almost any synthetic or natural gelatin-containing matrix, such as zymograms, gelatin-methacrylate hydrogels, and even a corneal tissue. Since the CMP is a chemically and biologically inert peptide which is proven to be an ideal carrier for bioactive molecules, our patterning method provides a radically new tool for immobilizing drugs to natural tissues and for functionalizing scaffolds for complex tissue formation. PMID:25476588

The morphology of solar granulations and dark networks

NASA Astrophysics Data System (ADS)

Graves, J. Elon; Pierce, A. Keith

1986-08-01

Solar granules are classified into four groups based on shape and splitting by sharp rifts crossing them. Grains are classified as: single granules varying in size from 1/8 to 3 in., single granules embayed by a broad dark area or possessing a central darkening, single granules split by very narrow rifts which are significantly narrower than the intergranular lanes, and complexes of granules displaying a daisy pattern. The formation and growth of 'white-light dark networks' are also discussed

Geologically Controlled Isotope-Time Patterns Reveal Early Differentiation and Crust Formation Processes

NASA Astrophysics Data System (ADS)

Bennett, V. C.; Nutman, A. P.

2014-12-01

The mechanisms of continental crust production and evolution in the early Earth remain controversial, as are questions of the relative roles of early differentiation versus subsequent tectonic procssing in creating Earth's chemical signatures. Here we present geologic observations integrated with whole rock major, trace element and Sm-Nd isotopic signatures and combined with U-Pb and Lu-Hf isotopic compositions of zircon populations from the same rocks, from the most extensive early rock record comprising the 3.9 Ga to 3.6 Ga terranes of southwest Greenland. These data reveal repeated patterns of formation of juvenile TTG crust and associated mafic and ultramafic rocks in convergent margin settings followed by formation of more evolved granites [1]. Our new zircon Lu-Hf data from rare 3.6-3.7 Ga tonalites within the Itsaq Gneiss Complex, obtained from single component, non-migmatitic gneisses with simple zircon populations, limited within sample Hf isotopic variability and accurate U-Pb ages, now document extraction of juvenile tonalites from a near chondritic mantle source between 3.9 Ga and 3.6 Ga. The more evolved, granitic rocks in each area show slightly negative initial ɛHf in accord with crustal reworking of the older (3.8-3.9 Ga) gniesses. There is no evidence for Hadean material in the sources of the granitoids. The Hf isotope-time patterns are consistent with juvenile crust production from a mantle source that experienced only modest amounts of prior crustal extraction. They are distinct from those predicted by reprocessing of an enriched Hadean mafic crust, as has been proposed for this region [2] and for the source of the Hadean Jack Hills zircons [3]. The well-documented, time decreasing, positive 142Nd anomalies [e.g., 4] from these rocks are further evidence of crustal derivation from a convecting mantle source, rather than reworking of an enriched mafic lithosphere. The 143Nd isotopic -time patterns are more complex, reflecting the interplay between early Sm/Nd fractionation processes as required by the 142Nd data, juvenile crustal growth and in some cases geologic disturbance of the whole rock Sm-Nd system. [1] Nutman, et al, (2013) Amer. Jour. Sci. 313, 877-911. [2] Naeraa et al.. (2012) Nature 485, 627-631. [3] Kemp et al., (2010) EPSL 296, 45-56. [4] Bennett et al., (20070 Science 318, 1907.

Modeling propellant-based stimulation of a borehole with peridynamics

DOE PAGES

Panchadhara, Rohan; Gordon, Peter A.; Parks, Michael L.

2017-02-27

A non-local formulation of classical continuum mechanics theory known as peridynamics is used to study fracture initiation and growth from a wellbore penetrating the subsurface within the context of propellant-based stimulation. The principal objectives of this work are to analyze the influence of loading conditions on the resulting fracture pattern, to investigate the effect of in-situ stress anisotropy on fracture propagation, and to assess the suitability of peridynamics for modeling complex fracture formation. In peridynamics, the momentum equation from the classical theory of solid mechanics is replaced by a non-local analogue, which results in an integrodifferential conservation equation. A continuummore » material is discretized with a set of material points that interact with all other points within a specified distance. Interactions between points are governed by bonds that can deform and break depending on loading conditions. The accumulated breakage of bonds gives rise to a picture of complex growth of fractures that is seen as a key advantage in the peridynamic representation of discontinuities. It is shown that the loading rate significantly influences the number and ex- tent of fractures initiated from a borehole. Results show that low loading rates produce fewer but longer fractures, whereas high loading rates produce numerous shorter fractures around the borehole. The numerical method is able to predict fracture growth patterns over a wide range of loading and stress conditions. Our results also show that fracture growth is attenuated with increasing in-situ confining stress, and, in the case of confining stress anisotropy, fracture extensions are largest in the direction perpendicular to the minimum compressive stress. Since the results are in broad qualitative agreement with experimental and numerical studies found in the literature, suggesting that peridynamics can be a powerful tool in the study of complex fracture network formation.« less

Modeling propellant-based stimulation of a borehole with peridynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Panchadhara, Rohan; Gordon, Peter A.; Parks, Michael L.

A non-local formulation of classical continuum mechanics theory known as peridynamics is used to study fracture initiation and growth from a wellbore penetrating the subsurface within the context of propellant-based stimulation. The principal objectives of this work are to analyze the influence of loading conditions on the resulting fracture pattern, to investigate the effect of in-situ stress anisotropy on fracture propagation, and to assess the suitability of peridynamics for modeling complex fracture formation. In peridynamics, the momentum equation from the classical theory of solid mechanics is replaced by a non-local analogue, which results in an integrodifferential conservation equation. A continuummore » material is discretized with a set of material points that interact with all other points within a specified distance. Interactions between points are governed by bonds that can deform and break depending on loading conditions. The accumulated breakage of bonds gives rise to a picture of complex growth of fractures that is seen as a key advantage in the peridynamic representation of discontinuities. It is shown that the loading rate significantly influences the number and ex- tent of fractures initiated from a borehole. Results show that low loading rates produce fewer but longer fractures, whereas high loading rates produce numerous shorter fractures around the borehole. The numerical method is able to predict fracture growth patterns over a wide range of loading and stress conditions. Our results also show that fracture growth is attenuated with increasing in-situ confining stress, and, in the case of confining stress anisotropy, fracture extensions are largest in the direction perpendicular to the minimum compressive stress. Since the results are in broad qualitative agreement with experimental and numerical studies found in the literature, suggesting that peridynamics can be a powerful tool in the study of complex fracture network formation.« less

[Mechanisms of immune deposit formation in glomerulonephritis].

PubMed

Bussolati, B; Camussi, G

1996-03-01

Recent experimental studies allowed the identification of several mechanisms of immune deposit formation, which are able to reproduce the morphological and clinical pattern of human glomerulonephritis. Moreover, it was shown that most of the lesions considered, in the past, as due to circulating immune complexes (IC), are instead caused by the "in situ" formation of IC. As a result of these studies, the following schematic classification was proposed: 1) immune deposits formed by glomerular localization of IC primarily formed in the circulation; 2) immune deposits formed "in situ" by reaction of circulating antibodies with fixed structural antigens; 3) immune deposits formed "in situ" by antibodies reactive with movable structural antigens; 4) immune deposits formed "in situ" by antibodies reactive with sequestered antigens leaking out of tissues; 5) IC formed "in situ" by antibodies reactive with exogenous or non-glomerular endogenous antigens planted in the glomeruli; 6) ANCA-associated glomerular disease.

The influence of projectile ion induced chemistry on surface pattern formation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Karmakar, Prasanta, E-mail: prasantak@vecc.gov.in; Satpati, Biswarup

We report the critical role of projectile induced chemical inhomogeneity on surface nanostructure formation. Experimental inconsistency is common for low energy ion beam induced nanostructure formation in the presence of uncontrolled and complex contamination. To explore the precise role of contamination on such structure formation during low energy ion bombardment, a simple and clean experimental study is performed by selecting mono-element semiconductors as the target and chemically inert or reactive ion beams as the projectile as well as the source of controlled contamination. It is shown by Atomic Force Microscopy, Cross-sectional Transmission Electron Microscopy, and Electron Energy Loss Spectroscopy measurementsmore » that bombardment of nitrogen-like reactive ions on Silicon and Germanium surfaces forms a chemical compound at impact zones. Continuous bombardment of the same ions generates surface instability due to unequal sputtering and non-uniform re-arrangement of the elemental atom and compound. This instability leads to ripple formation during ion bombardment. For Argon-like chemically inert ion bombardment, the chemical inhomogeneity induced boost is absent; as a result, no ripples are observed in the same ion energy and fluence.« less

The Interaction Network Ontology-supported modeling and mining of complex interactions represented with multiple keywords in biomedical literature.

PubMed

Özgür, Arzucan; Hur, Junguk; He, Yongqun

2016-01-01

The Interaction Network Ontology (INO) logically represents biological interactions, pathways, and networks. INO has been demonstrated to be valuable in providing a set of structured ontological terms and associated keywords to support literature mining of gene-gene interactions from biomedical literature. However, previous work using INO focused on single keyword matching, while many interactions are represented with two or more interaction keywords used in combination. This paper reports our extension of INO to include combinatory patterns of two or more literature mining keywords co-existing in one sentence to represent specific INO interaction classes. Such keyword combinations and related INO interaction type information could be automatically obtained via SPARQL queries, formatted in Excel format, and used in an INO-supported SciMiner, an in-house literature mining program. We studied the gene interaction sentences from the commonly used benchmark Learning Logic in Language (LLL) dataset and one internally generated vaccine-related dataset to identify and analyze interaction types containing multiple keywords. Patterns obtained from the dependency parse trees of the sentences were used to identify the interaction keywords that are related to each other and collectively represent an interaction type. The INO ontology currently has 575 terms including 202 terms under the interaction branch. The relations between the INO interaction types and associated keywords are represented using the INO annotation relations: 'has literature mining keywords' and 'has keyword dependency pattern'. The keyword dependency patterns were generated via running the Stanford Parser to obtain dependency relation types. Out of the 107 interactions in the LLL dataset represented with two-keyword interaction types, 86 were identified by using the direct dependency relations. The LLL dataset contained 34 gene regulation interaction types, each of which associated with multiple keywords. A hierarchical display of these 34 interaction types and their ancestor terms in INO resulted in the identification of specific gene-gene interaction patterns from the LLL dataset. The phenomenon of having multi-keyword interaction types was also frequently observed in the vaccine dataset. By modeling and representing multiple textual keywords for interaction types, the extended INO enabled the identification of complex biological gene-gene interactions represented with multiple keywords.

Pattern formation in rotating Bénard convection

NASA Astrophysics Data System (ADS)

Fantz, M.; Friedrich, R.; Bestehorn, M.; Haken, H.

1992-12-01

Using an extension of the Swift-Hohenberg equation we study pattern formation in the Bénard experiment close to the onset of convection in the case of rotating cylindrical fluid containers. For small Taylor numbers we emphasize the existence of slowly rotating patterns and describe behaviour exhibiting defect motion. Finally, we study pattern formation close to the Küppers-Lortz instability. The instability is nucleated at defects and proceeds through front propagation into the bulk patterns.

Size-dependent diffusion promotes the emergence of spatiotemporal patterns

NASA Astrophysics Data System (ADS)

Zhang, Lai; Thygesen, Uffe Høgsbro; Banerjee, Malay

2014-07-01

Spatiotemporal patterns, indicating the spatiotemporal variability of individual abundance, are a pronounced scenario in ecological interactions. Most of the existing models for spatiotemporal patterns treat species as homogeneous groups of individuals with average characteristics by ignoring intraspecific physiological variations at the individual level. Here we explore the impacts of size variation within species resulting from individual ontogeny, on the emergence of spatiotemporal patterns in a fully size-structured population model. We found that size dependency of animal's diffusivity greatly promotes the formation of spatiotemporal patterns, by creating regular spatiotemporal patterns out of temporal chaos. We also found that size-dependent diffusion can substitute large-amplitude base harmonics with spatiotemporal patterns with lower amplitude oscillations but with enriched harmonics. Finally, we found that the single-generation cycle is more likely to drive spatiotemporal patterns compared to predator-prey cycles, meaning that the mechanism of Hopf bifurcation might be more common than hitherto appreciated since the former cycle is more widespread than the latter in case of interacting populations. Due to the ubiquity of individual ontogeny in natural ecosystems we conclude that diffusion variability within populations is a significant driving force for the emergence of spatiotemporal patterns. Our results offer a perspective on self-organized phenomena, and pave a way to understand such phenomena in systems organized as complex ecological networks.

Structure, form, and meaning in the mental lexicon: evidence from Arabic

PubMed Central

Boudelaa, Sami; Marslen-Wilson, William D.

2015-01-01

Does the organization of the mental lexicon reflect the combination of abstract underlying morphemic units or the concatenation of word-level phonological units? We address these fundamental issues in Arabic, a Semitic language where every surface form is potentially analyzable into abstract morphemic units – the word pattern and the root – and where this view contrasts with stem-based approaches, chiefly driven by linguistic considerations, in which neither roots nor word patterns play independent roles in word formation and lexical representation. Five cross-modal priming experiments examine the processing of morphologically complex forms in the three major subdivisions of the Arabic lexicon – deverbal nouns, verbs, and primitive nouns. The results demonstrate that root and word pattern morphemes function as abstract cognitive entities, operating independently of semantic factors and dissociable from possible phonological confounds, while stem-based approaches consistently fail to accommodate the basic psycholinguistic properties of the Arabic mental lexicon. PMID:26682237

Novel avulsion pattern of the left principal bronchus with involvement of the carina and caudal thoracic trachea in a cat.

PubMed

Schmierer, Philipp A; Schwarz, Andrea; Bass, Danielle A; Knell, Sebastian Christoph

2014-08-01

A 2-year-old, 4.5 kg, neutered male domestic shorthair cat was presented to the emergency service with dyspnoea, anorexia and apathetic behaviour. Thoracic radiographs showed typical signs for a thoracic trauma and a tracheal lesion in the region of the carina, consistent with pseudoairway formation. Computed tomography (CT) was performed in the conscious cat to avoid aggravation of air leakage associated with ventilation. The additional CT findings were consistent with a novel pattern of a traumatic avulsion of the left principal bronchus expanding into the carina and caudal thoracic trachea. Despite the complex avulsion pattern, successful treatment was achieved surgically by performing an end-to-end anastomosis via a fifth right intercostal lateral thoracotomy. The cat was ventilated with a feeding tube and jet ventilation throughout. The cat showed excellent recovery 6 months after surgery. © ISFM and AAFP 2013.

Spatiotemporal relationships among Late Pennsylvanian plant assemblages: Palynological evidence from the Markley Formation, West Texas, U.S.A.

PubMed

Looy, Cindy V; Hotton, Carol L

2014-12-01

The Pennsylvanian lowlands of western Pangea are best known for their diverse wetland floras of arborescent and herbaceous ferns, and arborescent horsetails and clubmosses. In apparent juxtaposition, a very different kind of flora, dominated by a xerophilous assemblage of conifers, taeniopterids and peltasperms, is occasionally glimpsed. Once believed to represent upland or extrabasinal floras from well-drained portions of the landscape, these dryland floras more recently have been interpreted as lowland assemblages growing during drier phases of glacial/interglacial cycles. Whether Pennsylvanian dryland and wetland floras were separated spatially or temporally remains an unsettled question, due in large part to taphonomic bias toward preservation of wetland plants. Previous paleobotanical and sedimentological analysis of the Markley Formation of latest Pennsylvanian (Gzhelian) age, from north central Texas, U.S.A, indicates close correlation between lithofacies and distinct dryland and wetland megaflora assemblages. Here we present a detailed analysis one of those localities, a section unusual in containing abundant palynomorphs, from the lower Markley Formation. Paleobotanical, palynological and lithological data from a section thought to represent a single interglacial/glacial phase are integrated and analyzed to create a complex picture of an evolving landscape. Megafloral data from throughout the Markley Formation show that conifer-dominated dryland floras occur exclusively in highly leached kaolinite beds, likely eroded from underlying soils, whereas a mosaic of wetland floras occupy histosols, ultisols, and fluvial overbank deposits. Palynological data largely conform to this pattern but reveal a more complex picture. An assemblage of mixed wetland and dryland palynofloral taxa is interpolated between a dryland assemblage and an overlying histosol containing wetland taxa. In this section, as well as elsewhere in the Markley Formation, kaolinite and overlying organic beds appear to have formed as a single genetic unit, with the kaolinite forming an impermeable aquiclude upon which a poorly drained wetland subsequently formed. Within a single inferred glacial/interglacial cycle, lithological data indicate significant fluctuations in water availability tracked by changes in palynofloral and megafloral taxa. Palynology reveals that elements of the dryland floras appear at low abundance even within wetland deposits. The combined data indicate a complex pattern of succession and suggest a mosaic of dryland and wetland plant communities in the Late Pennsylvanian. Our data alone cannot show whether dryland and wetland assemblages succeed one another temporally, or coexisted on the landscape. However, the combined evidence suggests relatively close spatial proximity within a fragmenting and increasingly arid environment.

Spatiotemporal relationships among Late Pennsylvanian plant assemblages: Palynological evidence from the Markley Formation, West Texas, U.S.A

PubMed Central

Looy, Cindy V.; Hotton, Carol L.

2014-01-01

The Pennsylvanian lowlands of western Pangea are best known for their diverse wetland floras of arborescent and herbaceous ferns, and arborescent horsetails and clubmosses. In apparent juxtaposition, a very different kind of flora, dominated by a xerophilous assemblage of conifers, taeniopterids and peltasperms, is occasionally glimpsed. Once believed to represent upland or extrabasinal floras from well-drained portions of the landscape, these dryland floras more recently have been interpreted as lowland assemblages growing during drier phases of glacial/interglacial cycles. Whether Pennsylvanian dryland and wetland floras were separated spatially or temporally remains an unsettled question, due in large part to taphonomic bias toward preservation of wetland plants. Previous paleobotanical and sedimentological analysis of the Markley Formation of latest Pennsylvanian (Gzhelian) age, from north central Texas, U.S.A, indicates close correlation between lithofacies and distinct dryland and wetland megaflora assemblages. Here we present a detailed analysis one of those localities, a section unusual in containing abundant palynomorphs, from the lower Markley Formation. Paleobotanical, palynological and lithological data from a section thought to represent a single interglacial/glacial phase are integrated and analyzed to create a complex picture of an evolving landscape. Megafloral data from throughout the Markley Formation show that conifer-dominated dryland floras occur exclusively in highly leached kaolinite beds, likely eroded from underlying soils, whereas a mosaic of wetland floras occupy histosols, ultisols, and fluvial overbank deposits. Palynological data largely conform to this pattern but reveal a more complex picture. An assemblage of mixed wetland and dryland palynofloral taxa is interpolated between a dryland assemblage and an overlying histosol containing wetland taxa. In this section, as well as elsewhere in the Markley Formation, kaolinite and overlying organic beds appear to have formed as a single genetic unit, with the kaolinite forming an impermeable aquiclude upon which a poorly drained wetland subsequently formed. Within a single inferred glacial/interglacial cycle, lithological data indicate significant fluctuations in water availability tracked by changes in palynofloral and megafloral taxa. Palynology reveals that elements of the dryland floras appear at low abundance even within wetland deposits. The combined data indicate a complex pattern of succession and suggest a mosaic of dryland and wetland plant communities in the Late Pennsylvanian. Our data alone cannot show whether dryland and wetland assemblages succeed one another temporally, or coexisted on the landscape. However, the combined evidence suggests relatively close spatial proximity within a fragmenting and increasingly arid environment. PMID:26028779

Environmental and genetic factors that contribute to Escherichia coli K-12 biofilm formation

PubMed Central

Prüß, Birgit M.; Verma, Karan; Samanta, Priyankar; Sule, Preeti; Kumar, Sunil; Wu, Jianfei; Christianson, David; Horne, Shelley M.; Stafslien, Shane J.; Wolfe, Alan J.; Denton, Anne

2010-01-01

Biofilms are communities of bacteria whose formation on surfaces requires a large portion of the bacteria’s transcriptional network. To identify environmental conditions and transcriptional regulators that contribute to sensing these conditions, we used a high-throughput approach to monitor biofilm biomass produced by an isogenic set of Escherichia coli K-12 strains grown under combinations of environmental conditions. Of the environmental combinationsd, growth in tryptic soy broth at 37°C supported the most biofilm production. To analyze the complex relationships between the diverse cell surface organelles, transcriptional regulators, and metabolic enzymes represented by the tested mutant set, we used a novel vector-item pattern-mining algorithm. The algorithm related biofilm amounts to the functional annotations of each mutated protein. The pattern with the best statistical significance was the gene ontology ‘pyruvate catabolic process,’ which is associated with enzymes of acetate metabolism. Phenotype microarray experiments illustrated that carbon sources that are metabolized to acetyl-coenzyme A, acetyl phosphate, and acetate are particularly supportive of biofilm formation. Scanning electron microscopy revealed structural differences between mutants that lack acetate metabolism enzymes and their parent and confirmed the quantitative differences. We conclude that acetate metabolism functions as a metabolic sensor, transmitting changes in environmental conditions to biofilm biomass and structure. PMID:20559621

Segmented cold cathode display panel

NASA Technical Reports Server (NTRS)

Payne, Leslie (Inventor)

1998-01-01

The present invention is a video display device that utilizes the novel concept of generating an electronically controlled pattern of electron emission at the output of a segmented photocathode. This pattern of electron emission is amplified via a channel plate. The result is that an intense electronic image can be accelerated toward a phosphor thus creating a bright video image. This novel arrangement allows for one to provide a full color flat video display capable of implementation in large formats. In an alternate arrangement, the present invention is provided without the channel plate and a porous conducting surface is provided instead. In this alternate arrangement, the brightness of the image is reduced but the cost of the overall device is significantly lowered because fabrication complexity is significantly decreased.

Controlling morphology in swelling-induced wrinkled surfaces

NASA Astrophysics Data System (ADS)

Breid, Derek Ronald

Wrinkles represent a pathway towards the spontaneous generation of ordered surface microstructure for applications in numerous fields. Examples of highly complex ordered wrinkle structures abound in Nature, but the ability to harness this potential for advanced material applications remains limited. This work focuses on understanding the relationship between the patterns on a wrinkled surface and the experimental conditions under which they form. Because wrinkles form in response to applied stresses, particular attention is given to the nature of the stresses in a wrinkling surface. The fundamental insight gained was then utilized to account for observed wrinkle formation phenomena within more complex geometric and kinetic settings. In order to carefully control and measure the applied stresses on a wrinkling film, a swelling-based system was developed using poly(dimethylsiloxane) (PDMS), surface-oxidized with a UV-ozone treatment. The swelling of the oxidized surface upon exposure to an ethanol vapor atmosphere was characterized using beam-bending experiments, allowing quantitative measurements of the applied stress. The wrinkle morphologies were characterized as a function of the overstress, defined as the ratio of the applied swelling stress to the critical buckling stress of the material. A transition in the dominant morphology of the wrinkled surfaces from dimple patterns to ridge patterns was observed at an overstress value of ˜2. The pattern dependence of wrinkles on the ratio of the principal stresses was examined by fabricating samples with a gradient prestress. When swollen, these samples exhibited a smooth morphological transition from non-equibiaxial to equibiaxial patterns, with prestrains as low as 2.5% exhibiting non-equibiaxial characteristics. This transition was seen both in samples with low and high overstresses. To explore the impact of these stress states in more complex geometries, wrinkling hemispherical surfaces with radii of curvature ranging from 50--1000 μm were fabricated using the same material system. Upon wrinkling, the hemispheres formed complex hierarchical assemblies reminiscent of naturally occurring structures. The curvature of a surface exhibited a correlation with its critical buckling stress, independent of other factors. This enables the surface curvature to be used as an independent control over the dimple-to-ridge transition which occurs as a function of overstress. As in the flat buckling surfaces, this transition was shown to occur at an overstress value of ˜2. Surface curvature was also shown to improve the observed hexagonal ordering of the dimple arrays, resulting in the formation of regular "golf ball" structures. Geometric effects in finite flat plates were also examined. Using circular masks during the oxidation process, plates with radii ranging from 0.4--8.6 mm were created. Upon wrinkling, a dimple-to-ridge transition was observed with increasing plate size, with the morphological switch occurring at a radius of ˜2 mm. This observed transition was not found to be due to the inherent mechanics of plates of different sizes, but instead to a reduction in the oxide conversion due to shadowing or stagnation caused by the masking process, which lowered the applied overstress. The shape of the finite plate was found to have little impact on the resulting wrinkle morphologies. Kinetic aspects of wrinkling were qualitatively characterized by observing the wrinkling process over the course of swelling. Wrinkling was observed to frontally propagate across the surface, and the ordering of the patterns which developed showed a qualitative correlation with the degree of uniformity in the advancing wrinkle front. Swelling with different solvents was found to lead to the formation of different patterns, based on the swelling kinetics of the UVO-treated PDMS upon exposure to each solvent.

The role of feedback mechanisms in the initial development of the constructed catchment Chicken Creek

NASA Astrophysics Data System (ADS)

Schaaf, Wolfgang; Hinz, Christoph; Gerwin, Werner; Zaplata, Markus; Hüttl, Reinhard F.

2015-04-01

Over a period of ten years, we investigated the initial development of the constructed catchment 'Chicken Creek', south of Cottbus, Germany (Gerwin et al., 2009). Since the boundary conditions and inner structures of the hillslope are well known and documented (Gerwin et al., 2011), the site offers unique possibilities to study the relevant processes of ecosystem development interacting with various structures and patterns. We observed considerable changes within the catchment (Elmer et al., 2013). Both internal and external factors could be identified as driving forces for the formation of structures and patterns in the artificial catchment. Initial structures formed by the construction process and initial substrate characteristics were decisive for the distribution and flow of water. External factors like episodic events triggered erosion and dissection during this initial phase, promoted by the low vegetation cover and the unconsolidated sandy substrate (Schaaf et al., 2013). With time, secondary structures and patterns evolved and became more and more important. Invading biota and vegetation succession initialized abiotic/biotic feedback mechanisms resulting in pattern and habitat formation, and generally in increased differentiation, heterogeneity and complexity that are typical characteristics of ecosystems (Schaaf et al., 2011). The processes and feedback mechanisms in the initial development of a new landscape may deviate in rates, intensity, and dominance from those known from mature ecosystems. It is therefore crucial to understand these early phases of ecosystem development and to disentangle the increasingly complex interactions between the evolving terrestrial and aquatic, biotic, and abiotic compartments of the system. Elmer M, Gerwin W, Schaaf W, Zaplata MK, Hohberg K, Nenov R, Bens O, Hüttl RF (2013): Dynamics of initial ecosystem development at the artificial catchment Chicken Creek, Lusatia, Germany. Environ Earth Sci 69, 491-505. Gerwin W, Schaaf W, Biemelt D, Fischer A, Winter S, Hüttl RF (2009): The artificial catchment "Chicken Creek" (Lusatia, Germany) - A landscape laboratory for interdisciplinary studies of initial ecosystem development, Ecol Eng 35, 1786-1796. Gerwin W, Schaaf W, Biemelt D, Winter S, Fischer A, Veste M, Hüttl RF (2011): Overview and first results of ecological monitoring at the artificial watershed Chicken Creek (Germany). Phys Chem Earth 36, 61-73. Schaaf W, Bens O, Fischer A, Gerke HH, Gerwin W, Grünewald U, Holländer HM, Kögel-Knabner I, Mutz M, Schloter M, Schulin R, Veste M, Winter S, Hüttl, RF (2011): Patterns and processes of initial terrestrial ecosystem development. J Plant Nutr Soil Sci 174, 229-239. Schaaf W, Elmer M, Fischer A, Gerwin W, Nenov R, Pretsch H, Seifert S, Winter S, Zaplata MK (2013): Monitoring the formation of structures and patterns during initial development of an artificial catchment. Environ Monit Assess 185, 5965-5986.

Large-Scale Patterns in a Minimal Cognitive Flocking Model: Incidental Leaders, Nematic Patterns, and Aggregates

NASA Astrophysics Data System (ADS)

Barberis, Lucas; Peruani, Fernando

2016-12-01

We study a minimal cognitive flocking model, which assumes that the moving entities navigate using the available instantaneous visual information exclusively. The model consists of active particles, with no memory, that interact by a short-ranged, position-based, attractive force, which acts inside a vision cone (VC), and lack velocity-velocity alignment. We show that this active system can exhibit—due to the VC that breaks Newton's third law—various complex, large-scale, self-organized patterns. Depending on parameter values, we observe the emergence of aggregates or millinglike patterns, the formation of moving—locally polar—files with particles at the front of these structures acting as effective leaders, and the self-organization of particles into macroscopic nematic structures leading to long-ranged nematic order. Combining simulations and nonlinear field equations, we show that position-based active models, as the one analyzed here, represent a new class of active systems fundamentally different from other active systems, including velocity-alignment-based flocking systems. The reported results are of prime importance in the study, interpretation, and modeling of collective motion patterns in living and nonliving active systems.

Large-Scale Patterns in a Minimal Cognitive Flocking Model: Incidental Leaders, Nematic Patterns, and Aggregates.

PubMed

Barberis, Lucas; Peruani, Fernando

2016-12-09

We study a minimal cognitive flocking model, which assumes that the moving entities navigate using the available instantaneous visual information exclusively. The model consists of active particles, with no memory, that interact by a short-ranged, position-based, attractive force, which acts inside a vision cone (VC), and lack velocity-velocity alignment. We show that this active system can exhibit-due to the VC that breaks Newton's third law-various complex, large-scale, self-organized patterns. Depending on parameter values, we observe the emergence of aggregates or millinglike patterns, the formation of moving-locally polar-files with particles at the front of these structures acting as effective leaders, and the self-organization of particles into macroscopic nematic structures leading to long-ranged nematic order. Combining simulations and nonlinear field equations, we show that position-based active models, as the one analyzed here, represent a new class of active systems fundamentally different from other active systems, including velocity-alignment-based flocking systems. The reported results are of prime importance in the study, interpretation, and modeling of collective motion patterns in living and nonliving active systems.

Automated numerical simulation of biological pattern formation based on visual feedback simulation framework

PubMed Central

Sun, Mingzhu; Xu, Hui; Zeng, Xingjuan; Zhao, Xin

2017-01-01

There are various fantastic biological phenomena in biological pattern formation. Mathematical modeling using reaction-diffusion partial differential equation systems is employed to study the mechanism of pattern formation. However, model parameter selection is both difficult and time consuming. In this paper, a visual feedback simulation framework is proposed to calculate the parameters of a mathematical model automatically based on the basic principle of feedback control. In the simulation framework, the simulation results are visualized, and the image features are extracted as the system feedback. Then, the unknown model parameters are obtained by comparing the image features of the simulation image and the target biological pattern. Considering two typical applications, the visual feedback simulation framework is applied to fulfill pattern formation simulations for vascular mesenchymal cells and lung development. In the simulation framework, the spot, stripe, labyrinthine patterns of vascular mesenchymal cells, the normal branching pattern and the branching pattern lacking side branching for lung branching are obtained in a finite number of iterations. The simulation results indicate that it is easy to achieve the simulation targets, especially when the simulation patterns are sensitive to the model parameters. Moreover, this simulation framework can expand to other types of biological pattern formation. PMID:28225811

Automated numerical simulation of biological pattern formation based on visual feedback simulation framework.

PubMed

Sun, Mingzhu; Xu, Hui; Zeng, Xingjuan; Zhao, Xin

2017-01-01

There are various fantastic biological phenomena in biological pattern formation. Mathematical modeling using reaction-diffusion partial differential equation systems is employed to study the mechanism of pattern formation. However, model parameter selection is both difficult and time consuming. In this paper, a visual feedback simulation framework is proposed to calculate the parameters of a mathematical model automatically based on the basic principle of feedback control. In the simulation framework, the simulation results are visualized, and the image features are extracted as the system feedback. Then, the unknown model parameters are obtained by comparing the image features of the simulation image and the target biological pattern. Considering two typical applications, the visual feedback simulation framework is applied to fulfill pattern formation simulations for vascular mesenchymal cells and lung development. In the simulation framework, the spot, stripe, labyrinthine patterns of vascular mesenchymal cells, the normal branching pattern and the branching pattern lacking side branching for lung branching are obtained in a finite number of iterations. The simulation results indicate that it is easy to achieve the simulation targets, especially when the simulation patterns are sensitive to the model parameters. Moreover, this simulation framework can expand to other types of biological pattern formation.

Electrical Field Guided Electrospray Deposition for Production of Gradient Particle Patterns.

PubMed

Yan, Wei-Cheng; Xie, Jingwei; Wang, Chi-Hwa

2018-06-06

Our previous work demonstrated the uniform particle pattern formation on the substrates using electrical field guided electrospray deposition. In this work, we reported for the first time the fabrication of gradient particle patterns on glass slides using an additional point, line, or bar electrode based on our previous electrospray deposition configuration. We also demonstrated that the polydimethylsiloxane (PDMS) coating could result in the formation of uniform particle patterns instead of gradient particle patterns on glass slides using the same experimental setup. Meanwhile, we investigated the effect of experimental configurations on the gradient particle pattern formation by computational simulation. The simulation results are in line with experimental observations. The formation of gradient particle patterns was ascribed to the gradient of electric field and the corresponding focusing effect. Cell patterns can be formed on the particle patterns deposited on PDMS-coated glass slides. The formed particle patterns hold great promise for high-throughput screening of biomaterial-cell interactions and sensing.

Concept Formation Skills in Long-Term Cochlear Implant Users

PubMed Central

Castellanos, Irina; Kronenberger, William G.; Beer, Jessica; Colson, Bethany G.; Henning, Shirley C.; Ditmars, Allison; Pisoni, David B.

2015-01-01

This study investigated if a period of auditory sensory deprivation followed by degraded auditory input and related language delays affects visual concept formation skills in long-term prelingually deaf cochlear implant (CI) users. We also examined if concept formation skills are mediated or moderated by other neurocognitive domains (i.e., language, working memory, and executive control). Relative to normally hearing (NH) peers, CI users displayed significantly poorer performance in several specific areas of concept formation, especially when multiple comparisons and relational concepts were components of the task. Differences in concept formation between CI users and NH peers were fully explained by differences in language and inhibition–concentration skills. Language skills were also found to be more strongly related to concept formation in CI users than in NH peers. The present findings suggest that complex relational concepts may be adversely affected by a period of early prelingual deafness followed by access to underspecified and degraded sound patterns and spoken language transmitted by a CI. Investigating a unique clinical population such as early-implanted prelingually deaf children with CIs can provide new insights into foundational brain–behavior relations and developmental processes. PMID:25583706

Dual role for the latent transforming growth factor-beta binding protein in storage of latent TGF-beta in the extracellular matrix and as a structural matrix protein

PubMed Central

1995-01-01

The role of the latent TGF-beta binding protein (LTBP) is unclear. In cultures of fetal rat calvarial cells, which form mineralized bonelike nodules, both LTBP and the TGF-beta 1 precursor localized to large fibrillar structures in the extracellular matrix. The appearance of these fibrillar structures preceded the appearance of type I collagen fibers. Plasmin treatment abolished the fibrillar staining pattern for LTBP and released a complex containing both LTBP and TGF-beta. Antibodies and antisense oligonucleotides against LTBP inhibited the formation of mineralized bonelike nodules in long-term fetal rat calvarial cultures. Immunohistochemistry of fetal and adult rat bone confirmed a fibrillar staining pattern for LTBP in vivo. These findings, together with the known homology of LTBP to the fibrillin family of proteins, suggest a novel function for LTBP, in addition to its role in matrix storage of latent TGF-beta, as a structural matrix protein that may play a role in bone formation. PMID:7593177

How We Choose One over Another: Predicting Trial-by-Trial Preference Decision

PubMed Central

Bhushan, Vidya; Saha, Goutam; Lindsen, Job; Shimojo, Shinsuke; Bhattacharya, Joydeep

2012-01-01

Preference formation is a complex problem as it is subjective, involves emotion, is led by implicit processes, and changes depending on the context even within the same individual. Thus, scientific attempts to predict preference are challenging, yet quite important for basic understanding of human decision making mechanisms, but prediction in a group-average sense has only a limited significance. In this study, we predicted preferential decisions on a trial by trial basis based on brain responses occurring before the individuals made their decisions explicit. Participants made a binary preference decision of approachability based on faces while their electrophysiological responses were recorded. An artificial neural network based pattern-classifier was used with time-frequency resolved patterns of a functional connectivity measure as features for the classifier. We were able to predict preference decisions with a mean accuracy of 74.3±2.79% at participant-independent level and of 91.4±3.8% at participant-dependent level. Further, we revealed a causal role of the first impression on final decision and demonstrated the temporal trajectory of preference decision formation. PMID:22912859

Exploiting lipopolysaccharide-induced deformation of lipid bilayers to modify membrane composition and generate two-dimensional geometric membrane array patterns

DOE PAGES

Adams, Peter G.; Swingle, Kirstie L.; Paxton, Walter F.; ...

2015-05-27

Supported lipid bilayers have proven effective as model membranes for investigating biophysical processes and in development of sensor and array technologies. The ability to modify lipid bilayers after their formation and in situ could greatly advance membrane technologies, but is difficult via current state-of-the-art technologies. Here we demonstrate a novel method that allows the controlled post-formation processing and modification of complex supported lipid bilayer arrangements, under aqueous conditions. We exploit the destabilization effect of lipopolysaccharide, an amphiphilic biomolecule, interacting with lipid bilayers to generate voids that can be backfilled to introduce desired membrane components. We further demonstrate that when usedmore » in combination with a single, traditional soft lithography process, it is possible to generate hierarchically-organized membrane domains and microscale 2-D array patterns of domains. Significantly, this technique can be used to repeatedly modify membranes allowing iterative control over membrane composition. This approach expands our toolkit for functional membrane design, with potential applications for enhanced materials templating, biosensing and investigating lipid-membrane processes.« less

Measurement of Strain Distributions in Mouse Femora with 3D-Digital Speckle Pattern Interferometry

PubMed Central

Yang, Lianxiang; Zhang, Ping; Liu, Sheng; Samala, Praveen R; Su, Min; Yokota, Hiroki

2007-01-01

Bone is a mechanosensitive tissue that adapts its mass, architecture and mechanical properties to external loading. Appropriate mechanical loads offer an effective means to stimulate bone remodeling and prevent bone loss. A role of in situ strain in bone is considered essential in enhancement of bone formation, and establishing a quantitative relationship between 3D strain distributions and a rate of local bone formation is important. Digital speckle pattern interferometry (DSPI) can achieve whole-field, non-contacting measurements of microscopic deformation for high-resolution determination of 3D strain distributions. However, the current system does not allow us to derive accurate strain distributions because of complex surface contours inherent to biological samples. Through development of a custom-made piezoelectric loading device as well as a new DSPI-based force calibration system, we built an advanced DSPI system and integrated local contour information to deformation data. Using a mouse femur in response to a knee loading modality as a model system, we determined 3D strain distributions and discussed effectiveness and limitations of the described system. PMID:18670581

Developmental evolutionary biology of the vertebrate ear: conserving mechanoelectric transduction and developmental pathways in diverging morphologies

NASA Technical Reports Server (NTRS)

Fritzsch, B.; Beisel, K. W.; Bermingham, N. A.

2000-01-01

This brief overview shows that a start has been made to molecularly dissect vertebrate ear development and its evolutionary conservation to the development of the insect hearing organ. However, neither the patterning process of the ear nor the patterning process of insect sensory organs is sufficiently known at the moment to provide more than a first glimpse. Moreover, hardly anything is known about otocyst development of the cephalopod molluscs, another triploblast lineage that evolved complex 'ears'. We hope that the apparent conserved functional and cellular components present in the ciliated sensory neurons/hair cells will also be found in the genes required for vertebrate ear and insect sensory organ morphogenesis (Fig. 3). Likewise, we expect that homologous pre-patterning genes will soon be identified for the non-sensory cell development, which is more than a blocking of neuronal development through the Delta/Notch signaling system. Generation of the apparently unique ear could thus represent a multiplication of non-sensory cells by asymmetric and symmetric divisions as well as modification of existing patterning process by implementing novel developmental modules. In the final analysis, the vertebrate ear may come about by increasing the level of gene interactions in an already existing and highly conserved interactive cascade of bHLH genes. Since this was apparently achieved in all three lineages of triploblasts independently (Fig. 3), we now need to understand how much of the morphogenetic cascades are equally conserved across phyla to generate complex ears. The existing mutations in humans and mice may be able to point the direction of future research to understand the development of specific cell types and morphologies in the formation of complex arthropod, cephalopod, and vertebrate 'ears'.

Semi-Targeted Analysis of Complex Matrices by ESI FT-ICR MS or How an Experimental Bias may be Used as an Analytical Tool.

PubMed

Hertzog, Jasmine; Carré, Vincent; Dufour, Anthony; Aubriet, Frédéric

2018-03-01

Ammonia is well suited to favor deprotonation process in electrospray ionization mass spectrometry (ESI-MS) to increase the formation of [M - H] - . Nevertheless, NH 3 may react with carbonyl compounds (aldehyde, ketone) and bias the composition description of the investigated sample. This is of significant importance in the study of complex mixture such as oil or bio-oil. To assess the ability of primary amines to form imines with carbonyl compounds during the ESI-MS process, two aldehydes (vanillin and cinnamaldehyde) and two ketones (butyrophenone and trihydroxyacetophenone) have been infused in an ESI source with ammonia and two different amines (aniline and 3-chloronaniline). The (+) ESI-MS analyses have demonstrated the formation of imine whatever the considered carbonyl compound and the used primary amine, the structure of which was extensively studied by tandem mass spectrometry. Thus, it has been established that the addition of ammonia, in the solution infused in an ESI source, may alter the composition description of a complex mixture and leads to misinterpretations due to the formation of imines. Nevertheless, this experimental bias can be used to identify the carbonyl compounds in a pyrolysis bio-oil. As we demonstrated, infusion of the bio-oil with 3-chloroaniline in ESI source leads to specifically derivatized carbonyl compounds. Thanks to their chlorine isotopic pattern and the high mass measurement accuracy, (+) ESI Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) unambiguously highlighted them from the numerous C x H y O z bio-oil components. These results offer a new perspective into the detailed molecular structure of complex mixtures such as bio-oils. Graphical Abstract ᅟ.

Semi-Targeted Analysis of Complex Matrices by ESI FT-ICR MS or How an Experimental Bias may be Used as an Analytical Tool

NASA Astrophysics Data System (ADS)

Hertzog, Jasmine; Carré, Vincent; Dufour, Anthony; Aubriet, Frédéric

2018-03-01

Ammonia is well suited to favor deprotonation process in electrospray ionization mass spectrometry (ESI-MS) to increase the formation of [M - H]-. Nevertheless, NH3 may react with carbonyl compounds (aldehyde, ketone) and bias the composition description of the investigated sample. This is of significant importance in the study of complex mixture such as oil or bio-oil. To assess the ability of primary amines to form imines with carbonyl compounds during the ESI-MS process, two aldehydes (vanillin and cinnamaldehyde) and two ketones (butyrophenone and trihydroxyacetophenone) have been infused in an ESI source with ammonia and two different amines (aniline and 3-chloronaniline). The (+) ESI-MS analyses have demonstrated the formation of imine whatever the considered carbonyl compound and the used primary amine, the structure of which was extensively studied by tandem mass spectrometry. Thus, it has been established that the addition of ammonia, in the solution infused in an ESI source, may alter the composition description of a complex mixture and leads to misinterpretations due to the formation of imines. Nevertheless, this experimental bias can be used to identify the carbonyl compounds in a pyrolysis bio-oil. As we demonstrated, infusion of the bio-oil with 3-chloroaniline in ESI source leads to specifically derivatized carbonyl compounds. Thanks to their chlorine isotopic pattern and the high mass measurement accuracy, (+) ESI Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) unambiguously highlighted them from the numerous CxHyOz bio-oil components. These results offer a new perspective into the detailed molecular structure of complex mixtures such as bio-oils. [Figure not available: see fulltext.

Physiologically Distributed Loading Patterns Drive the Formation of Zonally Organized Collagen Structures in Tissue-Engineered Meniscus.

PubMed

Puetzer, Jennifer L; Bonassar, Lawrence J

2016-07-01

The meniscus is a dense fibrocartilage tissue that withstands the complex loads of the knee via a unique organization of collagen fibers. Attempts to condition engineered menisci with compression or tensile loading alone have failed to reproduce complex structure on the microscale or anatomic scale. Here we show that axial loading of anatomically shaped tissue-engineered meniscus constructs produced spatial distributions of local strain similar to those seen in the meniscus when the knee is loaded at full extension. Such loading drove formation of tissue with large organized collagen fibers, levels of mechanical anisotropy, and compressive moduli that match native tissue. Loading accelerated the development of native-sized and aligned circumferential and radial collagen fibers. These loading patterns contained both tensile and compressive components that enhanced the major biochemical and functional properties of the meniscus, with loading significantly improved glycosaminoglycan (GAG) accumulation 200-250%, collagen accumulation 40-55%, equilibrium modulus 1000-1800%, and tensile moduli 500-1200% (radial and circumferential). Furthermore, this study demonstrates local changes in mechanical environment drive heterogeneous tissue development and organization within individual constructs, highlighting the importance of recapitulating native loading environments. Loaded menisci developed cartilage-like tissue with rounded cells, a dense collagen matrix, and increased GAG accumulation in the more compressively loaded horns, and fibrous collagen-rich tissue in the more tensile loaded outer 2/3, similar to native menisci. Loaded constructs reached a level of organization not seen in any previous engineered menisci and demonstrate great promise as meniscal replacements.

(Why) Does Evolution Favour Embryogenesis?

PubMed

Rensing, Stefan A

2016-07-01

Complex multicellular organisms typically possess life cycles in which zygotes (formed by gamete fusion) and meiosis occur. Canonical animal embryogenesis describes development from zygote to birth. It involves polarisation of the egg/zygote, asymmetric cell divisions, establishment of axes, symmetry breaking, formation of organs, and parental nutrition (at least in early stages). Similar developmental patterns have independently evolved in other eukaryotic lineages, including land plants and brown algae. The question arises whether embryo-like structures and associated developmental processes recurrently emerge because they are local optima of the evolutionary landscape. To understand which evolutionary principles govern complex multicellularity, we need to analyse why and how similar processes evolve convergently - von Baer's and Haeckel's phylotypic stage revisited in other phyla. Copyright © 2016 Elsevier Ltd. All rights reserved.

Patterning at the 10 nanometer length scale using a strongly segregating block copolymer thin film and vapor phase infiltration of inorganic precursors

DOE PAGES

Choi, Jonathan W.; Li, Zhaodong; Black, Charles T.; ...

2016-05-04

Here in this work, we demonstrate the use of self-assembled thin films of the cylinder-forming block copolymer poly(4-tert-butylstyrene-block-2-vinylpyridine) to pattern high density features at the 10 nm length scale. This material's large interaction parameter facilitates pattern formation in single-digit nanometer dimensions. This block copolymer's accessible order–disorder transition temperature allows thermal annealing to drive the assembly of ordered 2-vinylpyridine cylinders that can be selectively complexed with the organometallic precursor trimethylaluminum. This unique chemistry converts organic 2-vinylpyridine cylinders into alumina nanowires with diameters ranging from 8 to 11 nm, depending on the copolymer molecular weight. Graphoepitaxy of this block copolymer aligns andmore » registers sub-12 nm diameter nanowires to larger-scale rectangular, curved, and circular features patterned by optical lithography. The alumina nanowires function as a robust hard mask to withstand the conditions required for patterning the underlying silicon by plasma etching. Lastly, we conclude with a discussion of some of the challenges that arise with using block copolymers for patterning at sub-10 nm feature sizes.« less

Patterning at the 10 nanometer length scale using a strongly segregating block copolymer thin film and vapor phase infiltration of inorganic precursors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Choi, Jonathan W.; Li, Zhaodong; Black, Charles T.

Here in this work, we demonstrate the use of self-assembled thin films of the cylinder-forming block copolymer poly(4-tert-butylstyrene-block-2-vinylpyridine) to pattern high density features at the 10 nm length scale. This material's large interaction parameter facilitates pattern formation in single-digit nanometer dimensions. This block copolymer's accessible order–disorder transition temperature allows thermal annealing to drive the assembly of ordered 2-vinylpyridine cylinders that can be selectively complexed with the organometallic precursor trimethylaluminum. This unique chemistry converts organic 2-vinylpyridine cylinders into alumina nanowires with diameters ranging from 8 to 11 nm, depending on the copolymer molecular weight. Graphoepitaxy of this block copolymer aligns andmore » registers sub-12 nm diameter nanowires to larger-scale rectangular, curved, and circular features patterned by optical lithography. The alumina nanowires function as a robust hard mask to withstand the conditions required for patterning the underlying silicon by plasma etching. Lastly, we conclude with a discussion of some of the challenges that arise with using block copolymers for patterning at sub-10 nm feature sizes.« less

Cycle time reduction by Html report in mask checking flow

NASA Astrophysics Data System (ADS)

Chen, Jian-Cheng; Lu, Min-Ying; Fang, Xiang; Shen, Ming-Feng; Ma, Shou-Yuan; Yang, Chuen-Huei; Tsai, Joe; Lee, Rachel; Deng, Erwin; Lin, Ling-Chieh; Liao, Hung-Yueh; Tsai, Jenny; Bowhill, Amanda; Vu, Hien; Russell, Gordon

2017-07-01

The Mask Data Correctness Check (MDCC) is a reticle-level, multi-layer DRC-like check evolved from mask rule check (MRC). The MDCC uses extended job deck (EJB) to achieve mask composition and to perform a detailed check for positioning and integrity of each component of the reticle. Different design patterns on the mask will be mapped to different layers. Therefore, users may be able to review the whole reticle and check the interactions between different designs before the final mask pattern file is available. However, many types of MDCC check results, such as errors from overlapping patterns usually have very large and complex-shaped highlighted areas covering the boundary of the design. Users have to load the result OASIS file and overlap it to the original database that was assembled in MDCC process on a layout viewer, then search for the details of the check results. We introduce a quick result-reviewing method based on an html format report generated by Calibre® RVE. In the report generation process, we analyze and extract the essential part of result OASIS file to a result database (RDB) file by standard verification rule format (SVRF) commands. Calibre® RVE automatically loads the assembled reticle pattern and generates screen shots of these check results. All the processes are automatically triggered just after the MDCC process finishes. Users just have to open the html report to get the information they need: for example, check summary, captured images of results and their coordinates.

Waiting in the wings: what can we learn about gene co-option from the diversification of butterfly wing patterns?

PubMed

Jiggins, Chris D; Wallbank, Richard W R; Hanly, Joseph J

2017-02-05

A major challenge is to understand how conserved gene regulatory networks control the wonderful diversity of form that we see among animals and plants. Butterfly wing patterns are an excellent example of this diversity. Butterfly wings form as imaginal discs in the caterpillar and are constructed by a gene regulatory network, much of which is conserved across the holometabolous insects. Recent work in Heliconius butterflies takes advantage of genomic approaches and offers insights into how the diversification of wing patterns is overlaid onto this conserved network. WntA is a patterning morphogen that alters spatial information in the wing. Optix is a transcription factor that acts later in development to paint specific wing regions red. Both of these loci fit the paradigm of conserved protein-coding loci with diverse regulatory elements and developmental roles that have taken on novel derived functions in patterning wings. These discoveries offer insights into the 'Nymphalid Ground Plan', which offers a unifying hypothesis for pattern formation across nymphalid butterflies. These loci also represent 'hotspots' for morphological change that have been targeted repeatedly during evolution. Both convergent and divergent evolution of a great diversity of patterns is controlled by complex alleles at just a few genes. We suggest that evolutionary change has become focused on one or a few genetic loci for two reasons. First, pre-existing complex cis-regulatory loci that already interact with potentially relevant transcription factors are more likely to acquire novel functions in wing patterning. Second, the shape of wing regulatory networks may constrain evolutionary change to one or a few loci. Overall, genomic approaches that have identified wing patterning loci in these butterflies offer broad insight into how gene regulatory networks evolve to produce diversity.This article is part of the themed issue 'Evo-devo in the genomics era, and the origins of morphological diversity'. © 2016 The Author(s).

Waiting in the wings: what can we learn about gene co-option from the diversification of butterfly wing patterns?

PubMed Central

Wallbank, Richard W. R.; Hanly, Joseph J.

2017-01-01

A major challenge is to understand how conserved gene regulatory networks control the wonderful diversity of form that we see among animals and plants. Butterfly wing patterns are an excellent example of this diversity. Butterfly wings form as imaginal discs in the caterpillar and are constructed by a gene regulatory network, much of which is conserved across the holometabolous insects. Recent work in Heliconius butterflies takes advantage of genomic approaches and offers insights into how the diversification of wing patterns is overlaid onto this conserved network. WntA is a patterning morphogen that alters spatial information in the wing. Optix is a transcription factor that acts later in development to paint specific wing regions red. Both of these loci fit the paradigm of conserved protein-coding loci with diverse regulatory elements and developmental roles that have taken on novel derived functions in patterning wings. These discoveries offer insights into the ‘Nymphalid Ground Plan’, which offers a unifying hypothesis for pattern formation across nymphalid butterflies. These loci also represent ‘hotspots’ for morphological change that have been targeted repeatedly during evolution. Both convergent and divergent evolution of a great diversity of patterns is controlled by complex alleles at just a few genes. We suggest that evolutionary change has become focused on one or a few genetic loci for two reasons. First, pre-existing complex cis-regulatory loci that already interact with potentially relevant transcription factors are more likely to acquire novel functions in wing patterning. Second, the shape of wing regulatory networks may constrain evolutionary change to one or a few loci. Overall, genomic approaches that have identified wing patterning loci in these butterflies offer broad insight into how gene regulatory networks evolve to produce diversity. This article is part of the themed issue ‘Evo-devo in the genomics era, and the origins of morphological diversity’. PMID:27994126

Mathematical study on robust tissue pattern formation in growing epididymal tubule.

PubMed

Hirashima, Tsuyoshi

2016-10-21

Tissue pattern formation during development is a reproducible morphogenetic process organized by a series of kinetic cellular activities, leading to the building of functional and stable organs. Recent studies focusing on mechanical aspects have revealed physical mechanisms on how the cellular activities contribute to the formation of reproducible tissue patterns; however, the understanding for what factors achieve the reproducibility of such patterning and how it occurs is far from complete. Here, I focus on a tube pattern formation during murine epididymal development, and show that two factors influencing physical design for the patterning, the proliferative zone within the tubule and the viscosity of tissues surrounding to the tubule, control the reproducibility of epididymal tubule pattern, using a mathematical model based on experimental data. Extensive numerical simulation of the simple mathematical model revealed that a spatially localized proliferative zone within the tubule, observed in experiments, results in more reproducible tubule pattern. Moreover, I found that the viscosity of tissues surrounding to the tubule imposes a trade-off regarding pattern reproducibility and spatial accuracy relating to the region where the tubule pattern is formed. This indicates an existence of optimality in material properties of tissues for the robust patterning of epididymal tubule. The results obtained by numerical analysis based on experimental observations provide a general insight on how physical design realizes robust tissue pattern formation. Copyright © 2016 Elsevier Ltd. All rights reserved.

Dynamical Signatures of Living Systems

NASA Technical Reports Server (NTRS)

Zak, M.

1999-01-01

One of the main challenges in modeling living systems is to distinguish a random walk of physical origin (for instance, Brownian motions) from those of biological origin and that will constitute the starting point of the proposed approach. As conjectured, the biological random walk must be nonlinear. Indeed, any stochastic Markov process can be described by linear Fokker-Planck equation (or its discretized version), only that type of process has been observed in the inanimate world. However, all such processes always converge to a stable (ergodic or periodic) state, i.e., to the states of a lower complexity and high entropy. At the same time, the evolution of living systems directed toward a higher level of complexity if complexity is associated with a number of structural variations. The simplest way to mimic such a tendency is to incorporate a nonlinearity into the random walk; then the probability evolution will attain the features of diffusion equation: the formation and dissipation of shock waves initiated by small shallow wave disturbances. As a result, the evolution never "dies:" it produces new different configurations which are accompanied by an increase or decrease of entropy (the decrease takes place during formation of shock waves, the increase-during their dissipation). In other words, the evolution can be directed "against the second law of thermodynamics" by forming patterns outside of equilibrium in the probability space. Due to that, a specie is not locked up in a certain pattern of behavior: it still can perform a variety of motions, and only the statistics of these motions is constrained by this pattern. It should be emphasized that such a "twist" is based upon the concept of reflection, i.e., the existence of the self-image (adopted from psychology). The model consists of a generator of stochastic processes which represents the motor dynamics in the form of nonlinear random walks, and a simulator of the nonlinear version of the diffusion equation which represents the mental dynamics. It has been demonstrated that coupled mental-motor dynamics can simulate emerging self-organization, prey-predator games, collaboration and competition, "collective brain," etc.

Inkjet Deposition of Layer by Layer Assembled Films

PubMed Central

Andres, Christine M.; Kotov, Nicholas A.

2010-01-01

Layer-by-layer assembly (LBL) can create advanced composites with exceptional properties unavailable by other means, but the laborious deposition process and multiple dipping cycles hamper their utilization in microtechnologies and electronics. Multiple rinse steps provide both structural control and thermodynamic stability to LBL multilayers but they significantly limit their practical applications and contribute significantly to the processing time and waste. Here we demonstrate that by employing inkjet technology one can deliver the necessary quantities of LBL components required for film build-up without excess, eliminating the need for repetitive rinsing steps. This feature differentiates this approach from all other recognized LBL modalities. Using a model system of negatively charged gold nanoparticles and positively charged poly(diallyldimethylammonium) chloride, the material stability, nanoscale control over thickness and particle coverage offered by the inkjet LBL technique are shown to be equal or better than the multilayers made with traditional dipping cycles. The opportunity for fast deposition of complex metallic patterns using a simple inkjet printer was also shown. The additive nature of LBL deposition based on the formation of insoluble nanoparticle-polyelectrolyte complexes of various compositions provides an excellent opportunity for versatile, multi-component, and non-contact patterning for the simple production of stratified patterns that are much needed in advanced devices. PMID:20863114

The Kto-Skd complex can regulate ptc expression by interacting with Cubitus interruptus (Ci) in the Hedgehog signaling pathway.

PubMed

Mao, Feifei; Yang, Xiaofeng; Fu, Lin; Lv, Xiangdong; Zhang, Zhao; Wu, Wenqing; Yang, Siqi; Zhou, Zhaocai; Zhang, Lei; Zhao, Yun

2014-08-08

The hedgehog (Hh) signaling pathway plays a very important role in metazoan development by controlling pattern formation. Drosophila imaginal discs are subdivided into anterior and posterior compartments that derive from adjacent cell populations. The anterior/posterior (A/P) boundaries, which are critical to maintaining the position of organizers, are established by a complex mechanism involving Hh signaling. Here, we uncover the regulation of ptc in the Hh signaling pathway by two subunits of mediator complex, Kto and Skd, which can also regulate boundary location. Collectively, we provide further evidence that Kto-Skd affects the A/P-axial development of the whole wing disc. Kto can interact with Cubitus interruptus (Ci), bind to the Ci-binding region on ptc promoter, which are both regulated by Hh signals to down-regulate ptc expression. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Kinetics of thermolysis of lanthanum nitrate with hexamethylenetetramine: Crystal structure, TG-DSC, impact and friction sensitivity studies, Part-96

NASA Astrophysics Data System (ADS)

Nibha; Baranwal, B. P.; Singh, Gurdip; Singh, C. P.; Daniliuc, Constantin G.; Soni, P. K.; Nath, Yogeshwar

2014-11-01

The development of high energetic materials includes process ability and the ability to attain insensitive munitions (IM). This paper investigates the preparation of lanthanum metal nitrate complex of hexamethylenetetramine in water at room temperature. This complex of molecular formulae [La (NO3)2(H2O)6] (2HMTA) (NO3-) (H2O) was characterized by X-ray crystallography. Thermal decomposition was investigated using TG, TG-DSC and ignition delay measurements. Kinetic analysis of isothermal TG data has been investigated using model fitting methods as well as model free isoconversional methods. The sensitivity measurements towards mechanical destructive stimuli such as impact and friction were carried out and the complex was found to be insensitive. In order to identify the end product of thermolysis, X-ray diffraction patterns of end product was carried out which proves the formation of La2O3.

Selective detection of carbohydrates and their peptide conjugates by ESI-MS using synthetic quaternary ammonium salt derivatives of phenylboronic acids.

PubMed

Kijewska, Monika; Kuc, Adam; Kluczyk, Alicja; Waliczek, Mateusz; Man-Kupisinska, Aleksandra; Lukasiewicz, Jolanta; Stefanowicz, Piotr; Szewczuk, Zbigniew

2014-06-01

We present new tags based on the derivatives of phenylboronic acid and apply them for the selective detection of sugars and peptide-sugar conjugates in mass spectrometry. We investigated the binding of phenylboronic acid and its quaternary ammonium salt (QAS) derivatives to carbohydrates and peptide-derived Amadori products by HR-MS and MS/MS experiments. The formation of complexes between sugar or sugar-peptide conjugates and synthetic tags was confirmed on the basis of the unique isotopic distribution resulting from the presence of boron atom. Moreover, incorporation of a quaternary ammonium salt dramatically improved the efficiency of ionization in mass spectrometry. It was found that the formation of a complex with phenylboronic acid stabilizes the sugar moiety in glycated peptides, resulting in simplification of the fragmentation pattern of peptide-derived Amadori products. The obtained results suggest that derivatization of phenylboronic acid as QAS is a promising method for sensitive ESI-MS detection of carbohydrates and their conjugates formed by non-enzymatic glycation or glycosylation.

Selective Detection of Carbohydrates and Their Peptide Conjugates by ESI-MS Using Synthetic Quaternary Ammonium Salt Derivatives of Phenylboronic Acids

NASA Astrophysics Data System (ADS)

Kijewska, Monika; Kuc, Adam; Kluczyk, Alicja; Waliczek, Mateusz; Man-Kupisinska, Aleksandra; Lukasiewicz, Jolanta; Stefanowicz, Piotr; Szewczuk, Zbigniew

2014-06-01

We present new tags based on the derivatives of phenylboronic acid and apply them for the selective detection of sugars and peptide-sugar conjugates in mass spectrometry. We investigated the binding of phenylboronic acid and its quaternary ammonium salt (QAS) derivatives to carbohydrates and peptide-derived Amadori products by HR-MS and MS/MS experiments. The formation of complexes between sugar or sugar-peptide conjugates and synthetic tags was confirmed on the basis of the unique isotopic distribution resulting from the presence of boron atom. Moreover, incorporation of a quaternary ammonium salt dramatically improved the efficiency of ionization in mass spectrometry. It was found that the formation of a complex with phenylboronic acid stabilizes the sugar moiety in glycated peptides, resulting in simplification of the fragmentation pattern of peptide-derived Amadori products. The obtained results suggest that derivatization of phenylboronic acid as QAS is a promising method for sensitive ESI-MS detection of carbohydrates and their conjugates formed by non-enzymatic glycation or glycosylation.

Laboratory investigation of shale rock to identify fracture propagation in vertical direction to bedding

NASA Astrophysics Data System (ADS)

Peng, Tan; Yan, Jin; Bing, Hou; Yingcao, Zhou; Ruxin, Zhang; Zhi, Chang; Meng, Fan

2018-06-01

Affected by beddings and natural fractures, fracture geometry in the vertical plane is complex in shale formation, which differs from a simple fracture in homogeneous sandstone reservoirs. However, the propagation mechanism of a hydraulic fracture in the vertical plane has not been well understood. In this paper, a true tri-axial pressure machine was deployed for shale horizontal well fracturing simulation experiments of shale outcrops. The effects of multiple factors on hydraulic fracture vertical propagation were studied. The results revealed that hydraulic fracture initiation and propagation displayed four basic patterns in the vertical plane of laminated shale formation. A hydraulic fracture would cross the beddings under the high vertical stress difference between a vertical stress and horizontal minimum stress of 12 MPa, while a hydraulic fracture propagates along the beddings under a low vertical stress difference of 3 MPa. Four kinds of fracture geometry, including a single main fracture, a nonplanar fracture, a complex fracture, and a complex fracture network, were observed due to the combined effects of flow rate and viscosity. Due to the influence of binding strength (or cementing strength) on the fracture communication effects between a hydraulic fracture and the beddings, the opening region of the beddings takes the shape of an ellipse.

Identification of the altered pyrrole in the isomeric sulfmyoglobins: hyperfine shift patterns as indicators of ring saturation in ferric chlorins.

PubMed

Chatfield, M J; La Mar, G N; Smith, K M; Leung, H K; Pandey, R K

1988-03-08

Analysis of the 1H NMR hyperfine shift patterns of isomeric sulfmyoglobins is carried out in the met-aquo and met-cyano states to determine the site of saturation in each protein. The utility of the patterns for structure elucidation is established by specific deuterium labeling of the heme methyls of the terminal base product. On the basis of the known saturation of ring B in this isomer [Chatfield, M.J., La Mar, G.N., Lecomte, J.T.J., Balch, A.L., Smith, K.M., & Langry, K.C. (1986) J. Am. Chem. Soc. 108, 7108-7110], the methyl resonance of the saturated ring is found to have strongly attenuated contact shift. Thus, the heme methyl contact shift pattern is diagnostic for the saturated pyrrole in the high-spin state. This rationale is then applied to analyze the assigned NMR spectra of the initial and terminal acid sulfmyoglobin products, revealing that the same ring B is saturated in each isomer. In contrast, the heme methyl contact shift pattern in low-spin ferric complexes reveals that the methyls both on the affected pyrrole and on the trans pyrrole are influenced similarly on sulfmyoglobin formation, precluding the use of this methyl shift pattern as a unique indicator of the site of saturation. Identification of exchangeable proximal histidine resonances for met-aquo sulfmyoglobin complexes with shifts similar to that in native myoglobin dictates inconsequential axial alterations in the sulfmyoglobins, while location of downfield meso proton resonances analogous to those of the native protein demonstrates the retention of the coordinate water in the active site of met-sulfmyoglobin.

Large-Scale Constraint-Based Pattern Mining

ERIC Educational Resources Information Center

Zhu, Feida

2009-01-01

We studied the problem of constraint-based pattern mining for three different data formats, item-set, sequence and graph, and focused on mining patterns of large sizes. Colossal patterns in each data formats are studied to discover pruning properties that are useful for direct mining of these patterns. For item-set data, we observed robustness of…

Self-organization of spatial patterning in human embryonic stem cells

PubMed Central

Deglincerti, Alessia; Etoc, Fred; Ozair, M. Zeeshan; Brivanlou, Ali H.

2017-01-01

The developing embryo is a remarkable example of self-organization, where functional units are created in a complex spatio-temporal choreography. Recently, human embryonic stem cells (ESCs) have been used to recapitulate in vitro the self-organization programs that are executed in the embryo in vivo. This represents a unique opportunity to address self-organization in humans that is otherwise not addressable with current technologies. In this essay, we review the recent literature on self-organization of human ESCs, with a particular focus on two examples: formation of embryonic germ layers and neural rosettes. Intriguingly, both activation and elimination of TGFβ signaling can initiate self-organization, albeit with different molecular underpinnings. We discuss the mechanisms underlying the formation of these structures in vitro and explore future challenges in the field. PMID:26970615

GRAIL gravity observations of the transition from complex crater to peak-ring basin on the Moon: Implications for crustal structure and impact basin formation

NASA Astrophysics Data System (ADS)

Baker, David M. H.; Head, James W.; Phillips, Roger J.; Neumann, Gregory A.; Bierson, Carver J.; Smith, David E.; Zuber, Maria T.

2017-08-01

High-resolution gravity data from the Gravity Recovery and Interior Laboratory (GRAIL) mission provide the opportunity to analyze the detailed gravity and crustal structure of impact features in the morphological transition from complex craters to peak-ring basins on the Moon. We calculate average radial profiles of free-air anomalies and Bouguer anomalies for peak-ring basins, protobasins, and the largest complex craters. Complex craters and protobasins have free-air anomalies that are positively correlated with surface topography, unlike the prominent lunar mascons (positive free-air anomalies in areas of low elevation) associated with large basins. The Bouguer gravity anomaly profiles of complex craters are highly irregular, with central positive anomalies that are generally absent or not clearly tied to interior morphology. In contrast, gravity profiles for peak-ring basins (∼200 km to 580 km) are much more regular and are highly correlated with surface morphology. A central positive Bouguer anomaly is confined within the peak ring and a negative Bouguer anomaly annulus extends from the edge of the positive anomaly outward to about the rim crest. A number of degraded basins lacking interior peak rings have diameters and gravity patterns similar to those of well-preserved peak-ring basins. If these structures represent degraded peak-ring basins, the number of peak-ring basins on the Moon would increase by more than a factor of two to 34. The gravity anomalies within basins are interpreted to be due to uplift of the mantle confined within the peak ring and an annulus of thickened crust between the peak ring and rim crest. We hypothesize that mantle uplift is influenced by interaction between the transient cavity and the mantle. Further, mascon formation is generally disconnected from the number of basin rings formed and occurs over a wide range of basin sizes. These observations have important implications for models of basin and mascon formation on the Moon and other planetary bodies.

Pacopampa: Early evidence of violence at a ceremonial site in the northern Peruvian highlands.

PubMed

Nagaoka, Tomohito; Uzawa, Kazuhiro; Seki, Yuji; Morales Chocano, Daniel

2017-01-01

Pacopampa, a ceremonial complex in Peru's northern highlands, reveals early evidence of trauma in the Middle to Late Formative Period coinciding with the emergence of social stratification in the area. We examine the prevalence of trauma in human remains found at the site and present evidence of the circumstances surrounding the deaths of individuals who lived during the early stages of Andean civilization. The materials are the remains of 104 individuals (38 non-adult and 66 adult) from the Middle to Late Formative Periods. We explored trauma macroscopically and recorded patterns based on skeletons' locations, age at death, sex, social class, and chronology. We detected trauma in remains over the Middle to Late Formative Periods. While the prevalence of trauma was minimal in the Middle Formative Period, skeletons from the subsequent era exhibit more severe disturbances. However, all the skeletons show signs of healing and affected individuals experienced a low degree of trauma. Given the archaeological context (the remains were recovered from sites of ceremonial practices), as well as the equal distribution of trauma among both sexes and a lack of defensive architecture, it is plausible that rituals, rather than organized warfare or raids, caused most of the exhibited trauma. Pacopampa was home to a complex society founded on ritual activity in a ceremonial center: this is indicated by the presence of ritual violence in a society that built impressively large, ceremonial architecture and developed social stratification without any political control of surplus agricultural goods.

Pattern formation in the iodate-sulfite-thiosulfate reaction-diffusion system.

PubMed

Liu, Haimiao; Pojman, John A; Zhao, Yuemin; Pan, Changwei; Zheng, Juhua; Yuan, Ling; Horváth, Attila K; Gao, Qingyu

2012-01-07

Sodium polyacrylate-induced pH pattern formation and starch-induced iodine pattern formation were investigated in the iodate-sulfite-thiosulfate (IST) reaction in a one-side fed disc gel reactor (OSFR). As binding agents of the autocatalyst of hydrogen ions or iodide ions, different content of sodium polyacrylate or starch has induced various types of pattern formation. We observed pH pulses, striped patterns, mixed spots and stripes, and hexagonal spots upon increasing the content of sodium polyacrylate and observed iodine pulses, branched patterns, and labyrinthine patterns upon increasing the starch content in the system. Coexistence of a pH front and an iodine front was also studied in a batch IST reaction-diffusion system. Both pH and iodine front instabilities were observed in the presence of sodium polyacrylate, i.e., cellular fronts and transient Turing structures resulting from the decrease in diffusion coefficients of activators. The mechanism of multiple feedback may explain the different patterns in the IST reaction-diffusion system.

The response of plasma density to breaking inertial gravity wave in the lower regions of ionosphere

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tang, Wenbo, E-mail: Wenbo.Tang@asu.edu; Mahalov, Alex, E-mail: Alex.Mahalov@asu.edu

2014-04-15

We present a three-dimensional numerical study for the E and lower F region ionosphere coupled with the neutral atmosphere dynamics. This model is developed based on a previous ionospheric model that examines the transport patterns of plasma density given a prescribed neutral atmospheric flow. Inclusion of neutral dynamics in the model allows us to examine the charge-neutral interactions over the full evolution cycle of an inertial gravity wave when the background flow spins up from rest, saturates and eventually breaks. Using Lagrangian analyses, we show the mixing patterns of the ionospheric responses and the formation of ionospheric layers. The correspondingmore » plasma density in this flow develops complex wave structures and small-scale patches during the gravity wave breaking event.« less

Affinity communities in United Nations voting: Implications for democracy, cooperation, and conflict

NASA Astrophysics Data System (ADS)

Pauls, Scott D.; Cranmer, Skyler J.

2017-10-01

A network oriented examination of the co-voting network of the United Nations (UN) provides powerful insights into the international alignment of states, as well as normatively important processes such as democracy, defensive cooperation, and armed conflict. Here, we investigate the UN co-voting network using the tools of community detection and inductively identify "affinity communities" in which states articulate similar policy preferences through their voting patterns. Analysis of these communities reveals that there is more information contained in UN voting and co-voting patterns than has previously been thought. Affinity communities have complex relationships with some of the most normatively important international outcomes: they reflect transitions to democracy, have a feedback loop with the formation of defensive alliances, and actively help states avoid armed conflict.

Pattern formation and self-organization in plasmas interacting with surfaces

NASA Astrophysics Data System (ADS)

Trelles, Juan Pablo

2016-10-01

Pattern formation and self-organization are fascinating phenomena commonly observed in diverse types of biological, chemical and physical systems, including plasmas. These phenomena are often responsible for the occurrence of coherent structures found in nature, such as recirculation cells and spot arrangements; and their understanding and control can have important implications in technology, e.g. from determining the uniformity of plasma surface treatments to electrode erosion rates. This review comprises theoretical, computational and experimental investigations of the formation of spatiotemporal patterns that result from self-organization events due to the interaction of low-temperature plasmas in contact with confining or intervening surfaces, particularly electrodes. The basic definitions associated to pattern formation and self-organization are provided, as well as some of the characteristics of these phenomena within natural and technological contexts, especially those specific to plasmas. Phenomenological aspects of pattern formation include the competition between production/forcing and dissipation/transport processes, as well as nonequilibrium, stability, bifurcation and nonlinear interactions. The mathematical modeling of pattern formation in plasmas has encompassed from theoretical approaches and canonical models, such as reaction-diffusion systems, to drift-diffusion and nonequilibrium fluid flow models. The computational simulation of pattern formation phenomena imposes distinct challenges to numerical methods, such as high sensitivity to numerical approximations and the occurrence of multiple solutions. Representative experimental and numerical investigations of pattern formation and self-organization in diverse types of low-temperature electrical discharges (low and high pressure glow, dielectric barrier and arc discharges, etc) in contact with solid and liquid electrodes are reviewed. Notably, plasmas in contact with liquids, found in diverse emerging applications ranging from nanomaterial synthesis to medicine, show marked sensitivity to pattern formation and a broadened range of controlling parameters. The results related to the characteristics of the patterns, such as their geometric configuration and static or dynamic nature; as well as their controlling factors, including gas composition, driving voltage and current, electrode cooling, and imposed gas flow, are summarized and discussed. The article finalizes with an outlook of the research area, including theoretical, computational, and experimental needs to advance the field.

Ring-shaped stain patterns driven by solute reactive mesogens in liquid crystal solution

NASA Astrophysics Data System (ADS)

Cha, Tae Woon; Bulliard, Xavier; Choi, Sang Gun; Lee, Hyoung Sub; Kong, Hyang-Shik; Han, Sang Youn

2014-07-01

We report on the formation of ring-shaped stain patterns in a polymer-stabilized patterned vertical alignment mode liquid crystal display (LCD) during the cell filling process. Through the interpretation of the formation mechanism, an effective way to control its development is provided. Systematic trace of the reactive mesogens reveals that the formation of patterns is strongly related to the segregation of solute mesogens in the stain area. These undesirable patterns can be avoided or controlled by reducing the drop volume at each droplet using an inkjet printing technique, meaning that the printing technique could be a useful solution in display technology. For the formation of ring-shaped patterns, the dragging of reactive mesogens during the spreading of the liquid crystal solution plays a key role in the closed LCD cell.

Star Clusters in the Magellanic Clouds

NASA Astrophysics Data System (ADS)

Gallagher, J. S., III

2014-09-01

The Magellanic Clouds (MC) are prime locations for studies of star clusters covering a full range in age and mass. This contribution briefly reviews selected properties of Magellanic star clusters, by focusing first on young systems that show evidence for hierarchical star formation. The structures and chemical abundance patterns of older intermediate age star clusters in the Small Magellanic Cloud (SMC) are a second topic. These suggest a complex history has affected the chemical enrichment in the SMC and that low tidal stresses in the SMC foster star cluster survival.

High-Resolution Printing of 3D Structures Using an Electrohydrodynamic Inkjet with Multiple Functional Inks.

PubMed

An, Byeong Wan; Kim, Kukjoo; Lee, Heejoo; Kim, So-Yun; Shim, Yulhui; Lee, Dae-Young; Song, Jun Yeob; Park, Jang-Ung

2015-08-05

Electrohydrodynamic-inkjet-printed high-resolution complex 3D structures with multiple functional inks are demonstrated. Printed 3D structures can have a variety of fine patterns, such as vertical or helix-shaped pillars and straight or rounded walls, with high aspect ratios (greater than ≈50) and narrow diameters (≈0.7 μm). Furthermore, the formation of freestanding, bridge-like Ag wire structures on plastic substrates suggests substantial potentials as high-precision, flexible 3D interconnects. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Measuring helium bubble diameter distributions in tungsten with grazing incidence small angle x-ray scattering (GISAXS)

NASA Astrophysics Data System (ADS)

Thompson, M.; Kluth, P.; Doerner, R. P.; Kirby, N.; Riley, D.; Corr, C. S.

2016-02-01

Grazing incidence small angle x-ray scattering was performed on tungsten samples exposed to helium plasma in the MAGPIE and Pisces-A linear plasma devices to measure the size distributions of resulting helium nano-bubbles. Nano-bubbles were fitted assuming spheroidal particles and an exponential diameter distribution. These particles had mean diameters between 0.36 and 0.62 nm. Pisces-A exposed samples showed more complex patterns, which may suggest the formation of faceted nano-bubbles or nano-scale surface structures.

On the mechanochemical theory of biological pattern formation with application to vasculogenesis.

PubMed

Murray, James D

2003-02-01

We first describe the Murray-Oster mechanical theory of pattern formation, the biological basis of which is experimentally well documented. The model quantifies the interaction of cells and the extracellular matrix via the cell-generated forces. The model framework is described in quantitative detail. Vascular endothelial cells, when cultured on gelled basement membrane matrix, rapidly aggregate into clusters while deforming the matrix into a network of cord-like structures tessellating the planar culture. We apply the mechanical theory of pattern formation to this culture system and show that neither strain-biased anisotropic cell traction nor cell migration are necessary for pattern formation: isotropic, strain-stimulated cell traction is sufficient to form the observed patterns. Predictions from the model were confirmed experimentally.

Minimal perceptrons for memorizing complex patterns

NASA Astrophysics Data System (ADS)

Pastor, Marissa; Song, Juyong; Hoang, Danh-Tai; Jo, Junghyo

2016-11-01

Feedforward neural networks have been investigated to understand learning and memory, as well as applied to numerous practical problems in pattern classification. It is a rule of thumb that more complex tasks require larger networks. However, the design of optimal network architectures for specific tasks is still an unsolved fundamental problem. In this study, we consider three-layered neural networks for memorizing binary patterns. We developed a new complexity measure of binary patterns, and estimated the minimal network size for memorizing them as a function of their complexity. We formulated the minimal network size for regular, random, and complex patterns. In particular, the minimal size for complex patterns, which are neither ordered nor disordered, was predicted by measuring their Hamming distances from known ordered patterns. Our predictions agree with simulations based on the back-propagation algorithm.

Dune field pattern formation and recent transporting winds in the Olympia Undae Dune Field, north polar region of Mars

NASA Astrophysics Data System (ADS)

Ewing, Ryan C.; Peyret, Aymeric-Pierre B.; Kocurek, Gary; Bourke, Mary

2010-08-01

High-Resolution Imaging Science Experiment (HiRISE) imagery of the central Olympia Undae Dune Field in the north polar region of Mars shows a reticulate dune pattern consisting of two sets of nearly orthogonal dune crestlines, with apparent slipfaces on the primary crests, ubiquitous wind ripples, areas of coarse-grained wind ripples, and deflated interdune areas. Geomorphic evidence and dune field pattern analysis of dune crest length, spacing, defect density, and orientation indicates that the pattern is complex, representing two constructional generations of dunes. The oldest and best-organized generation forms the primary crestlines and is transverse to circumpolar easterly winds. Gross bed form-normal analysis of the younger pattern of crestlines indicates that it emerged with both circumpolar easterly winds and NE winds and is reworking the older pattern. Mapping of secondary flow fields over the dunes indicates that the most recent transporting winds were from the NE. The younger pattern appears to represent an influx of sediment to the dune field associated with the development of the Olympia Cavi reentrant, with NE katabatic winds channeling through the reentrant. A model of the pattern reformation based upon the reconstructed primary winds and resulting secondary flow fields shows that the development of the secondary pattern is controlled by the boundary condition of the older dune topography.

Soliton interactions and the formation of solitonic patterns

NASA Astrophysics Data System (ADS)

Sears, Suzanne M.

From the stripes of a zebra, to the spirals of cream in a hot cup of coffee, we are surrounded by patterns in the natural world. But why are there patterns? Why drives their formation? In this thesis we study some of the diverse ways patterns can arise due to the interactions between solitary waves in nonlinear systems, sometimes starting from nothing more than random noise. What follows is a set of three studies. In the first, we show how a nonlinear system that supports solitons can be driven to generate exact (regular) Cantor set fractals. As an example, we use numerical simulations to demonstrate the formation of Cantor set fractals by temporal optical solitons. This fractal formation occurs in a cascade of nonlinear optical fibers through the dynamical evolution of a single input soliton. In the second study, we investigate pattern formation initiated by modulation instability in nonlinear partially coherent wave fronts and show that anisotropic noise and/or anisotropic correlation statistics can lead to ordered patterns such as grids and stripes. For the final study, we demonstrate the spontaneous clustering of solitons in partially coherent wavefronts during the final stages of pattern formation initiated by modulation instability and noise. Experimental observations are in agreement with theoretical predictions and are confirmed using numerical simulations.

Interpreting Chromosome Aberration Spectra

NASA Technical Reports Server (NTRS)

Levy, Dan; Reeder, Christopher; Loucas, Bradford; Hlatky, Lynn; Chen, Allen; Cornforth, Michael; Sachs, Rainer

2007-01-01

Ionizing radiation can damage cells by breaking both strands of DNA in multiple locations, essentially cutting chromosomes into pieces. The cell has enzymatic mechanisms to repair such breaks; however, these mechanisms are imperfect and, in an exchange process, may produce a large-scale rearrangement of the genome, called a chromosome aberration. Chromosome aberrations are important in killing cells, during carcinogenesis, in characterizing repair/misrepair pathways, in retrospective radiation biodosimetry, and in a number of other ways. DNA staining techniques such as mFISH ( multicolor fluorescent in situ hybridization) provide a means for analyzing aberration spectra by examining observed final patterns. Unfortunately, an mFISH observed final pattern often does not uniquely determine the underlying exchange process. Further, resolution limitations in the painting protocol sometimes lead to apparently incomplete final patterns. We here describe an algorithm for systematically finding exchange processes consistent with any observed final pattern. This algorithm uses aberration multigraphs, a mathematical formalism that links the various aspects of aberration formation. By applying a measure to the space of consistent multigraphs, we will show how to generate model-specific distributions of aberration processes from mFISH experimental data. The approach is implemented by software freely available over the internet. As a sample application, we apply these algorithms to an aberration data set, obtaining a distribution of exchange cycle sizes, which serves to measure aberration complexity. Estimating complexity, in turn, helps indicate how damaging the aberrations are and may facilitate identification of radiation type in retrospective biodosimetry.

Very-Long-Chain Fatty Acids Are Involved in Polar Auxin Transport and Developmental Patterning in Arabidopsis[W

PubMed Central

Roudier, François; Gissot, Lionel; Beaudoin, Frédéric; Haslam, Richard; Michaelson, Louise; Marion, Jessica; Molino, Diana; Lima, Amparo; Bach, Liên; Morin, Halima; Tellier, Frédérique; Palauqui, Jean-Christophe; Bellec, Yannick; Renne, Charlotte; Miquel, Martine; DaCosta, Marco; Vignard, Julien; Rochat, Christine; Markham, Jonathan E.; Moreau, Patrick; Napier, Johnathan; Faure, Jean-Denis

2010-01-01

Very-long-chain fatty acids (VLCFAs) are essential for many aspects of plant development and necessary for the synthesis of seed storage triacylglycerols, epicuticular waxes, and sphingolipids. Identification of the acetyl-CoA carboxylase PASTICCINO3 and the 3-hydroxy acyl-CoA dehydratase PASTICCINO2 revealed that VLCFAs are important for cell proliferation and tissue patterning. Here, we show that the immunophilin PASTICCINO1 (PAS1) is also required for VLCFA synthesis. Impairment of PAS1 function results in reduction of VLCFA levels that particularly affects the composition of sphingolipids, known to be important for cell polarity in animals. Moreover, PAS1 associates with several enzymes of the VLCFA elongase complex in the endoplasmic reticulum. The pas1 mutants are deficient in lateral root formation and are characterized by an abnormal patterning of the embryo apex, which leads to defective cotyledon organogenesis. Our data indicate that in both tissues, defective organogenesis is associated with the mistargeting of the auxin efflux carrier PIN FORMED1 in specific cells, resulting in local alteration of polar auxin distribution. Furthermore, we show that exogenous VLCFAs rescue lateral root organogenesis and polar auxin distribution, indicating their direct involvement in these processes. Based on these data, we propose that PAS1 acts as a molecular scaffold for the fatty acid elongase complex in the endoplasmic reticulum and that the resulting VLCFAs are required for polar auxin transport and tissue patterning during plant development. PMID:20145257

A survey of cellulose microfibril patterns in dividing, expanding, and differentiating cells of Arabidopsis thaliana.

PubMed

Fujita, Miki; Wasteneys, Geoffrey O

2014-05-01

Cellulose microfibrils are critical for plant cell specialization and function. Recent advances in live cell imaging of fluorescently tagged cellulose synthases to track cellulose synthesis have greatly advanced our understanding of cellulose biosynthesis. Nevertheless, cellulose deposition patterns remain poorly described in many cell types, including those in the process of division or differentiation. In this study, we used field emission scanning electron microscopy analysis of cryo-planed tissues to determine the arrangement of cellulose microfibrils in various faces of cells undergoing cytokinesis or specialized development, including cell types in which cellulose cannot be imaged by conventional approaches. In dividing cells, we detected microfibrillar meshworks in the cell plates, consistent with the concentration at the cell plate of cellulose synthase complexes, as detected by fluorescently tagged CesA6. We also observed a loss of parallel cellulose microfibril orientation in walls of the mother cell during cytokinesis, which corresponded with the loss of fluorescently tagged cellulose synthase complexes from these surfaces. In recently formed guard cells, microfibrils were randomly organized and only formed a highly ordered circumferential pattern after pore formation. In pit fields, cellulose microfibrils were arranged in circular patterns around plasmodesmata. Microfibrils were random in most cotyledon cells except the epidermis and were parallel to the growth axis in trichomes. Deposition of cellulose microfibrils was spatially delineated in metaxylem and protoxylem cells of the inflorescence stem, supporting recent studies on microtubule exclusion mechanisms.

Interaction between Foxc1 and Fgf8 during Mammalian Jaw Patterning and in the Pathogenesis of Syngnathia

PubMed Central

Inman, Kimberly E.; Purcell, Patricia; Kume, Tsutomu; Trainor, Paul A.

2013-01-01

Syngnathia (bony fusion of the upper and lower jaw) is a rare human congenital condition, with fewer than sixty cases reported in the literature. Syngnathia typically presents as part of a complex syndrome comprising widespread oral and maxillofacial anomalies, but it can also occur in isolation. Most cartilage, bone, and connective tissue of the head and face is derived from neural crest cells. Hence, congenital craniofacial anomalies are often attributed to defects in neural crest cell formation, survival, migration, or differentiation. The etiology and pathogenesis of syngnathia however remains unknown. Here, we report that Foxc1 null embryos display bony syngnathia together with defects in maxillary and mandibular structures, and agenesis of the temporomandibular joint (TMJ). In the absence of Foxc1, neural crest cell derived osteogenic patterning is affected, as osteoblasts develop ectopically in the maxillary prominence and fuse with the dentary bone. Furthermore, we observed that the craniofacial musculature is also perturbed in Foxc1 null mice, which highlights the complex tissue interactions required for proper jaw development. We present evidence that Foxc1 and Fgf8 genetically interact and that Fgf8 dosage is associated with variation in the syngnathic phenotype. Together our data demonstrates that Foxc1 – Fgf8 signaling regulates mammalian jaw patterning and provides a mechanistic basis for the pathogenesis of syngnathia. Furthermore, our work provides a framework for understanding jaw patterning and the etiology of other congenital craniofacial anomalies, including temporomandibular joint agenesis. PMID:24385915

Enhancing multiple-point geostatistical modeling: 1. Graph theory and pattern adjustment

NASA Astrophysics Data System (ADS)

Tahmasebi, Pejman; Sahimi, Muhammad

2016-03-01

In recent years, higher-order geostatistical methods have been used for modeling of a wide variety of large-scale porous media, such as groundwater aquifers and oil reservoirs. Their popularity stems from their ability to account for qualitative data and the great flexibility that they offer for conditioning the models to hard (quantitative) data, which endow them with the capability for generating realistic realizations of porous formations with very complex channels, as well as features that are mainly a barrier to fluid flow. One group of such models consists of pattern-based methods that use a set of data points for generating stochastic realizations by which the large-scale structure and highly-connected features are reproduced accurately. The cross correlation-based simulation (CCSIM) algorithm, proposed previously by the authors, is a member of this group that has been shown to be capable of simulating multimillion cell models in a matter of a few CPU seconds. The method is, however, sensitive to pattern's specifications, such as boundaries and the number of replicates. In this paper the original CCSIM algorithm is reconsidered and two significant improvements are proposed for accurately reproducing large-scale patterns of heterogeneities in porous media. First, an effective boundary-correction method based on the graph theory is presented by which one identifies the optimal cutting path/surface for removing the patchiness and discontinuities in the realization of a porous medium. Next, a new pattern adjustment method is proposed that automatically transfers the features in a pattern to one that seamlessly matches the surrounding patterns. The original CCSIM algorithm is then combined with the two methods and is tested using various complex two- and three-dimensional examples. It should, however, be emphasized that the methods that we propose in this paper are applicable to other pattern-based geostatistical simulation methods.

Extensible Stylesheet Language Formatting Objects (XSL-FO): a tool to transform patient data into attractive clinical reports.

PubMed

Simonaitis, Linas; Belsito, Anne; Warvel, Jeff; Hui, Siu; McDonald, Clement J

2006-01-01

Clinicians at Wishard Hospital in Indianapolis print and carry clinical reports called "Pocket Rounds". This paper describes a new process we developed to improve these clinical reports. The heart of our new process is a World Wide Web Consortium standard: Extensible Stylesheet Language Formatting Objects (XSL-FO). Using XSL-FO stylesheets we generated Portable Document Format (PDF) and PostScript reports with complex formatting: columns, tables, borders, shading, indents, dividing lines. We observed patterns of clinical report printing during a eight month study period on three Medicine wards. Usage statistics indicated that clinicians accepted the new system enthusiastically: 78% of 26,418 reports were printed using the new system. We surveyed 67 clinical users. Respondents gave the new reports a rating of 4.2 (on a 5 point scale); they gave the old reports a rating of 3.4. The primary complaint was that it took longer to print the new reports. We believe that XSL-FO is a promising way to transform text data into functional and attractive clinical reports: relatively easy to implement and modify.

Argon ion beam induced surface pattern formation on Si

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hofsäss, H.; Bobes, O.; Zhang, K.

The development of self-organized surface patterns on Si due to noble gas ion irradiation has been studied extensively in the past. In particular, Ar ions are commonly used and the pattern formation was analyzed as function of ion incidence angle, ion fluence, and ion energies between 250 eV and 140 keV. Very few results exist for the energy regime between 1.5 keV and 10 keV and it appears that pattern formation is completely absent for these ion energies. In this work, we present experimental data on pattern formation for Ar ion irradiation between 1 keV and 10 keV and ion incidence angles between 50° and 75°.more » We confirm the absence of patterns at least for ion fluences up to 10{sup 18} ions/cm{sup 2}. Using the crater function formalism and Monte Carlo simulations, we calculate curvature coefficients of linear continuum models of pattern formation, taking into account contribution due to ion erosion and recoil redistribution. The calculations consider the recently introduced curvature dependence of the erosion crater function as well as the dynamic behavior of the thickness of the ion irradiated layer. Only when taking into account these additional contributions to the linear theory, our simulations clearly show that that pattern formation is strongly suppressed between about 1.5 keV and 10 keV, most pronounced at 3 keV. Furthermore, our simulations are now able to predict whether or not parallel oriented ripple patterns are formed, and in case of ripple formation the corresponding critical angles for the whole experimentally studied energies range between 250 eV and 140 keV.« less

Synthesis, spectroscopic, thermal and antimicrobial investigations of charge-transfer complexes formed from the drug procaine hydrochloride with quinol, picric acid and TCNQ

NASA Astrophysics Data System (ADS)

Adam, Abdel Majid A.

2012-12-01

Intermolecular charge-transfer or proton-transfer complexes between the drug procaine hydrochloride (PC-HCl) as a donor and quinol (QL), picric acid (PA) or 7,7',8,8'-tetracyanoquinodimethane (TCNQ) as a π-acceptor have been synthesized and spectroscopically studied in methanol at room temperature. Based on elemental analyses and photometric titrations, the stoichiometry of the complexes (donor:acceptor molar ratios) was determined to be 1:1 for all three complexes. The formation constant (KCT), molar extinction coefficient (ɛCT) and other spectroscopic data have been determined using the Benesi-Hildebrand method and its modifications. The newly synthesized CT complexes have been characterized via elemental analysis, IR, Raman, 1H NMR, and electronic absorption spectroscopy. The morphological features of these complexes were investigated using scanning electron microscopy (SEM), and the sharp, well-defined Bragg reflections at specific 2θ angles have been identified from the powder X-ray diffraction patterns. Thermogravimetric analyses (TGAs) and kinetic thermodynamic parameters were also used to investigate the thermal stability of the synthesized solid CT complexes. Finally, the CT complexes were screened for their antibacterial and antifungal activities against various bacterial and fungal strains, and only the complex obtained using picric acid exhibited moderate antibacterial activity against all of the tested strains.

Crowning: a novel Escherichia coli colonizing behaviour generating a self-organized corona

PubMed Central

2014-01-01

Background Encased in a matrix of extracellular polymeric substances (EPS) composed of flagella, adhesins, amyloid fibers (curli), and exopolysaccharides (cellulose, β-1,6-N-acetyl-D-glucosamine polymer-PGA-, colanic acid), the bacteria Escherichia coli is able to attach to and colonize different types of biotic and abiotic surfaces forming biofilms and colonies of intricate morphological architectures. Many of the biological aspects that underlie the generation and development of these E. coli’s formations are largely poorly understood. Results Here, we report the characterization of a novel E. coli sessile behaviour termed "crowning" due to the bacterial generation of a new 3-D architectural pattern: a corona. This bacterial pattern is formed by joining bush-like multilayered "coronal flares or spikes" arranged in a ring, which self-organize through the growth, self-clumping and massive self-aggregation of cells tightly interacting inside semisolid agar on plastic surfaces. Remarkably, the corona’s formation is developed independently of the adhesiveness of the major components of E. coli’s EPS matrix, the function of chemotaxis sensory system, type 1 pili and the biofilm master regulator CsgD, but its formation is suppressed by flagella-driven motility and glucose. Intriguingly, this glucose effect on the corona development is not mediated by the classical catabolic repression system, the cyclic AMP (cAMP)-cAMP receptor protein (CRP) complex. Thus, corona formation departs from the canonical regulatory transcriptional core that controls biofilm formation in E. coli. Conclusions With this novel "crowning" activity, E. coli expands its repertoire of colonizing collective behaviours to explore, invade and exploit environments whose critical viscosities impede flagella driven-motility. PMID:24568619

The role of hydroxo-bridged dinuclear species and the influence of "innocent" buffers in the reactivity of cis-[Co(III)(cyclen)(H₂O)₂]³⁺ and [Co(III)(tren)(H₂O)₂]³⁺ complexes with biologically relevant ligands at physiological pH.

PubMed

Basallote, Manuel G; Martínez, Manuel; Vázquez, Marta

2014-07-28

In view of the relevance of the reactivity of inert tetraamine Co(III) complexes having two substitutionally active cis positions capable of interact with biologically relevant ligands, the study of the reaction of cis-[Co(cyclen)(H2O)2](3+) and [Co(tren)(H2O)2](3+) with chlorides, inorganic phosphate and 5'-CMP (5'-cytidinemonophosphate) has been pursued at physiological pH. The results indicate that, in addition to the actuation of the expected labilising conjugate-base mechanism, the formation of mono and inert bis hydroxo-bridged species is relevant for understanding their speciation and reactivity. The reactivity pattern observed also indicates the key role played by the "innocent" buffers frequently used in most in vitro studies, which can make the results unreliable in many cases. The differences between the reactivity of inorganic and biologically relevant phosphates has also been found to be remarkable, with outer-sphere hydrogen bonding interactions being a dominant factor for the process. While for the inorganic phosphate substitution process the formation of μ-η(2)-OPO2O represents the termination of the reactivity monitored, for 5'-CMP only the formation of η(1)-OPO3 species is observed, which evolve with time to the final dead-end bis hydroxo-bridged complexes. The promoted hydrolysis of the 5'-CMP phosphate has not been observed in any of the processes studied.

Investigating the interaction of anticancer drug temsirolimus with human transferrin: Molecular docking and spectroscopic approach.

PubMed

Shamsi, Anas; Ahmed, Azaj; Khan, Mohd Shahnawaz; Husain, Fohad Mabood; Amani, Samreen; Bano, Bilqees

2018-05-16

In our present study, binding between an important anti renal cancer drug temsirolimus and human transferrin (hTF) was investigated employing spectroscopic and molecular docking approach. In the presence of temsirolimus, hyper chromaticity is observed in hTF in UV spectroscopy suggestive of complex formation between hTF and temsirolimus. Fluorescence spectroscopy revealed the occurrence of quenching in hTF in the presence of temsirolimus implying complex formation taking place between hTF and temsirolimus. Further, the mode of interaction between hTF and temsirolimus was revealed to be static by fluorescence quenching analysis at 3 different temperatures. Binding constant values obtained employing fluorescence spectroscopy depicts strong interaction between hTF and temsirolimus; temsirolimus binds to hTF at 298 K with a binding constant of .32 × 10 4  M -1 implying the strength of this interaction. The negative Gibbs free energy obtained through quenching experiments is evident of the fact that the binding is spontaneous. CD spectra of hTF also showed a downward shift in the presence of temsirolimus as compared with free hTF implying complex formation between hTF and temsirolimus. Molecular docking was performed with a view to find out which residues are key players in this interaction. The importance of our study stems from the fact it will provide an insight into binding pattern of commonly administered renal cancer drug with an important protein that plays a pivotal role in many physiological processes. Copyright © 2018 John Wiley & Sons, Ltd.

Probing the modulated formation of gold nanoparticles-beta-lactoglobulin corona complexes and their applications.

PubMed

Yang, Jiang; Wang, Bo; You, Youngsang; Chang, Woo-Jin; Tang, Ke; Wang, Yi-Cheng; Zhang, Wenzhao; Ding, Feng; Gunasekaran, Sundaram

2017-11-23

Understanding the interactions between proteins and nanoparticles (NPs) along with the underlying structural and dynamic information is of utmost importance to exploit nanotechnology for biomedical applications. Upon adsorption onto a NP surface, proteins form a well-organized layer, termed the corona, that dictates the identity of the NP-protein complex and governs its biological pathways. Given its high biological relevance, in-depth molecular investigations and applications of NPs-protein corona complexes are still scarce, especially since different proteins form unique corona patterns, making identification of the biomolecular motifs at the interface critical. In this work, we provide molecular insights and structural characterizations of the bio-nano interface of a popular food-based protein, namely bovine beta-lactoglobulin (β-LG), with gold nanoparticles (AuNPs) and report on our investigations of the formation of corona complexes by combined molecular simulations and complementary experiments. Two major binding sites in β-LG were identified as being driven by citrate-mediated electrostatic interactions, while the associated binding kinetics and conformational changes in the secondary structures were also characterized. More importantly, the superior stability of the corona led us to further explore its biomedical applications, such as in the smartphone-based point-of-care biosensing of Escherichia coli (E. coli) and in the computed tomography (CT) of the gastrointestinal (GI) tract through oral administration to probe GI tolerance and functions. Considering their biocompatibility, edible nature, and efficient excretion through defecation, AuNPs-β-LG corona complexes have shown promising perspectives for future in vitro and in vivo clinical settings.

Defects formation and spiral waves in a network of neurons in presence of electromagnetic induction.

PubMed

Rostami, Zahra; Jafari, Sajad

2018-04-01

Complex anatomical and physiological structure of an excitable tissue (e.g., cardiac tissue) in the body can represent different electrical activities through normal or abnormal behavior. Abnormalities of the excitable tissue coming from different biological reasons can lead to formation of some defects. Such defects can cause some successive waves that may end up to some additional reorganizing beating behaviors like spiral waves or target waves. In this study, formation of defects and the resulting emitted waves in an excitable tissue are investigated. We have considered a square array network of neurons with nearest-neighbor connections to describe the excitable tissue. Fundamentally, electrophysiological properties of ion currents in the body are responsible for exhibition of electrical spatiotemporal patterns. More precisely, fluctuation of accumulated ions inside and outside of cell causes variable electrical and magnetic field. Considering undeniable mutual effects of electrical field and magnetic field, we have proposed the new Hindmarsh-Rose (HR) neuronal model for the local dynamics of each individual neuron in the network. In this new neuronal model, the influence of magnetic flow on membrane potential is defined. This improved model holds more bifurcation parameters. Moreover, the dynamical behavior of the tissue is investigated in different states of quiescent, spiking, bursting and even chaotic state. The resulting spatiotemporal patterns are represented and the time series of some sampled neurons are displayed, as well.

Mixed copper-platinum complex formation could explain synergistic antiproliferative effect exhibited by binary mixtures of cisplatin and copper-1,10-phenanthroline compounds: An ESI-MS study.

PubMed

Pivetta, Tiziana; Lallai, Viola; Valletta, Elisa; Trudu, Federica; Isaia, Francesco; Perra, Daniela; Pinna, Elisabetta; Pani, Alessandra

2015-10-01

Cisplatin, cis-diammineplatinum(II) dichloride, is a metal complex used in clinical practice for the treatment of cancer. Despite its great efficacy, it causes adverse reactions and most patients develop a resistance to cisplatin. To overcome these issues, a multi-drug therapy was introduced as a modern approach to exploit the drug synergy. A synergistic effect had been previously found when testing binary combinations of cisplatin and three copper complexes in vitro, namely, Cu(phen)(OH2)2(OClO3)2, [Cu(phen)2(OH2)](ClO4)2 and [Cu(phen)2(H2dit)](ClO4)2,(phen=1,10-phenanthroline, H2dit=imidazolidine-2-thione), against the human acute T-lymphoblastic leukaemia cell line (CCRF-CEM). In this work [Cu(phen)2(OH2)](ClO4)2 was also tested in combination with cisplatin against cisplatin-resistant sublines of CCRF-CEM (CCRF-CEM-res) and ovarian (A2780-res) cancer cell lines. The tested combinations show a synergistic effect against both the types of resistant cells. The possibility that this effect was caused by the formation of new adducts was considered and mass spectra of solutions containing cisplatin and one of the three copper complexes at a time were measured using electrospray ionisation at atmospheric-pressure mass spectrometry (ESI-MS). A mixed complex was detected and its stoichiometry was assessed on the basis of the isotopic pattern and the results of tandem mass spectrometry experiments. The formed complex was found to be [Cu(phen)(OH)μ-(Cl)2Pt(NH3)(H2O)](+). Copyright © 2015 Elsevier Inc. All rights reserved.

Dewetting-mediated pattern formation in nanoparticle assemblies

NASA Astrophysics Data System (ADS)

Stannard, Andrew

2011-03-01

The deposition of nanoparticles from solution onto solid substrates is a diverse subfield of current nanoscience research. Complex physical and chemical processes underpin the self-assembly and self-organization of colloidal nanoparticles at two-phase (solid-liquid, liquid-air) interfaces and three-phase (solid-liquid-air) contact lines. This review discusses key recent advances made in the understanding of nonequilibrium dewetting processes of nanoparticle-containing solutions, detailing how such an apparently simple experimental system can give rise to such a strikingly varied palette of two-dimensional self-organized nanoparticle array morphologies. Patterns discussed include worm-like domains, cellular networks, microscale rings, and fractal-like fingering structures. There remain many unresolved issues regarding the role of the solvent dewetting dynamics in assembly processes of this type, with a significant focus on how dewetting can be coerced to produce nanoparticle arrays with desirable characteristics such as long-range order. In addition to these topics, methods developed to control nanofluid dewetting through routes such as confining the geometries of drying solutions, depositing onto pre-patterned heterogeneous substrates, and post-dewetting pattern evolution via local or global manipulation are covered.

Dewetting-mediated pattern formation in nanoparticle assemblies.

PubMed

Stannard, Andrew

2011-03-02

The deposition of nanoparticles from solution onto solid substrates is a diverse subfield of current nanoscience research. Complex physical and chemical processes underpin the self-assembly and self-organization of colloidal nanoparticles at two-phase (solid-liquid, liquid-air) interfaces and three-phase (solid-liquid-air) contact lines. This review discusses key recent advances made in the understanding of nonequilibrium dewetting processes of nanoparticle-containing solutions, detailing how such an apparently simple experimental system can give rise to such a strikingly varied palette of two-dimensional self-organized nanoparticle array morphologies. Patterns discussed include worm-like domains, cellular networks, microscale rings, and fractal-like fingering structures. There remain many unresolved issues regarding the role of the solvent dewetting dynamics in assembly processes of this type, with a significant focus on how dewetting can be coerced to produce nanoparticle arrays with desirable characteristics such as long-range order. In addition to these topics, methods developed to control nanofluid dewetting through routes such as confining the geometries of drying solutions, depositing onto pre-patterned heterogeneous substrates, and post-dewetting pattern evolution via local or global manipulation are covered.

Simulating Microbial Community Patterning Using Biocellion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kang, Seung-Hwa; Kahan, Simon H.; Momeni, Babak

2014-04-17

Mathematical modeling and computer simulation are important tools for understanding complex interactions between cells and their biotic and abiotic environment: similarities and differences between modeled and observed behavior provide the basis for hypothesis forma- tion. Momeni et al. [5] investigated pattern formation in communities of yeast strains engaging in different types of ecological interactions, comparing the predictions of mathematical modeling and simulation to actual patterns observed in wet-lab experiments. However, simu- lations of millions of cells in a three-dimensional community are ex- tremely time-consuming. One simulation run in MATLAB may take a week or longer, inhibiting exploration of the vastmore » space of parameter combinations and assumptions. Improving the speed, scale, and accu- racy of such simulations facilitates hypothesis formation and expedites discovery. Biocellion is a high performance software framework for ac- celerating discrete agent-based simulation of biological systems with millions to trillions of cells. Simulations of comparable scale and accu- racy to those taking a week of computer time using MATLAB require just hours using Biocellion on a multicore workstation. Biocellion fur- ther accelerates large scale, high resolution simulations using cluster computers by partitioning the work to run on multiple compute nodes. Biocellion targets computational biologists who have mathematical modeling backgrounds and basic C++ programming skills. This chap- ter describes the necessary steps to adapt the original Momeni et al.'s model to the Biocellion framework as a case study.« less

Mass fractionation of noble gases in synthetic methane hydrate: Implications for naturally occurring gas hydrate dissociation

USGS Publications Warehouse

Hunt, Andrew G.; Stern, Laura; Pohlman, John W.; Ruppel, Carolyn; Moscati, Richard J.; Landis, Gary P.

2013-01-01

As a consequence of contemporary or longer term (since 15 ka) climate warming, gas hydrates in some settings may presently be dissociating and releasing methane and other gases to the ocean-atmosphere system. A key challenge in assessing the impact of dissociating gas hydrates on global atmospheric methane is the lack of a technique able to distinguish between methane recently released from gas hydrates and methane emitted from leaky thermogenic reservoirs, shallow sediments (some newly thawed), coal beds, and other sources. Carbon and deuterium stable isotopic fractionation during methane formation provides a first-order constraint on the processes (microbial or thermogenic) of methane generation. However, because gas hydrate formation and dissociation do not cause significant isotopic fractionation, a stable isotope-based hydrate-source determination is not possible. Here, we investigate patterns of mass-dependent noble gas fractionation within the gas hydrate lattice to fingerprint methane released from gas hydrates. Starting with synthetic gas hydrate formed under laboratory conditions, we document complex noble gas fractionation patterns in the gases liberated during dissociation and explore the effects of aging and storage (e.g., in liquid nitrogen), as well as sampling and preservation procedures. The laboratory results confirm a unique noble gas fractionation pattern for gas hydrates, one that shows promise in evaluating modern natural gas seeps for a signature associated with gas hydrate dissociation.

Spatio-temporal dynamics induced by competing instabilities in two asymmetrically coupled nonlinear evolution equations.

PubMed

Schüler, D; Alonso, S; Torcini, A; Bär, M

2014-12-01

Pattern formation often occurs in spatially extended physical, biological, and chemical systems due to an instability of the homogeneous steady state. The type of the instability usually prescribes the resulting spatio-temporal patterns and their characteristic length scales. However, patterns resulting from the simultaneous occurrence of instabilities cannot be expected to be simple superposition of the patterns associated with the considered instabilities. To address this issue, we design two simple models composed by two asymmetrically coupled equations of non-conserved (Swift-Hohenberg equations) or conserved (Cahn-Hilliard equations) order parameters with different characteristic wave lengths. The patterns arising in these systems range from coexisting static patterns of different wavelengths to traveling waves. A linear stability analysis allows to derive a two parameter phase diagram for the studied models, in particular, revealing for the Swift-Hohenberg equations, a co-dimension two bifurcation point of Turing and wave instability and a region of coexistence of stationary and traveling patterns. The nonlinear dynamics of the coupled evolution equations is investigated by performing accurate numerical simulations. These reveal more complex patterns, ranging from traveling waves with embedded Turing patterns domains to spatio-temporal chaos, and a wide hysteretic region, where waves or Turing patterns coexist. For the coupled Cahn-Hilliard equations the presence of a weak coupling is sufficient to arrest the coarsening process and to lead to the emergence of purely periodic patterns. The final states are characterized by domains with a characteristic length, which diverges logarithmically with the coupling amplitude.

Voids and the Cosmic Web: cosmic depression & spatial complexity

NASA Astrophysics Data System (ADS)

van de Weygaert, Rien

2016-10-01

Voids form a prominent aspect of the Megaparsec distribution of galaxies and matter. Not only do theyrepresent a key constituent of the Cosmic Web, they also are one of the cleanest probesand measures of global cosmological parameters. The shape and evolution of voids are highly sensitive tothe nature of dark energy, while their substructure and galaxy population provides a direct key to thenature of dark matter. Also, the pristine environment of void interiors is an important testing groundfor our understanding of environmental influences on galaxy formation and evolution. In this paper, we reviewthe key aspects of the structure and dynamics ofvoids, with a particular focus on the hierarchical evolution of the void population. We demonstratehow the rich structural pattern of the Cosmic Web is related to the complex evolution and buildupof voids.

Spongiosa Primary Development: A Biochemical Hypothesis by Turing Patterns Formations

PubMed Central

López-Vaca, Oscar Rodrigo; Garzón-Alvarado, Diego Alexander

2012-01-01

We propose a biochemical model describing the formation of primary spongiosa architecture through a bioregulatory model by metalloproteinase 13 (MMP13) and vascular endothelial growth factor (VEGF). It is assumed that MMP13 regulates cartilage degradation and the VEGF allows vascularization and advances in the ossification front through the presence of osteoblasts. The coupling of this set of molecules is represented by reaction-diffusion equations with parameters in the Turing space, creating a stable spatiotemporal pattern that leads to the formation of the trabeculae present in the spongy tissue. Experimental evidence has shown that the MMP13 regulates VEGF formation, and it is assumed that VEGF negatively regulates MMP13 formation. Thus, the patterns obtained by ossification may represent the primary spongiosa formation during endochondral ossification. Moreover, for the numerical solution, we used the finite element method with the Newton-Raphson method to approximate partial differential nonlinear equations. Ossification patterns obtained may represent the primary spongiosa formation during endochondral ossification. PMID:23193429

Effects of Cross-axis Wind Jet Events on the Northern Red Sea Circulation

NASA Astrophysics Data System (ADS)

Menezes, V. V.; Bower, A. S.; Farrar, J. T.

2016-12-01

Despite its small size, the Red Sea has a complex circulation. There are boundary currents in both sides of the basin, a meridional overturning circulation, water mass formation in the northern part and an intense eddy activity. This complex pattern is driven by strong air-sea interactions. The Red Sea has one of the largest evaporation rates of the global oceans (2m/yr), an intricate and seasonally varying wind pattern. The winds blowing over the Northern Rea Sea (NRS, north of 20N) are predominantly southeastward along the main axis all year round; in the southern, they reverse seasonally due to the monsoonal regime. Although the winds are mostly along-axis in the NRS, several works have shown that sometimes during the boreal winter, the winds blow in a cross-axis direction. The westward winds from Saudi Arabia bring relatively cold dry air and dust from the desert, enhancing heat loss and evaporation off the Red Sea. These wind-jet events may contribute to increased eddy activity and are a trigger for water mass formation. Despite that, our knowledge about the cross-axis winds and their effect on NRS circulation is still incipient. In the present work we analyze 10-years of Quikscat scatterometer winds and altimetric sea surface height anomalies, together with 2-yrs of mooring data, to characterize the westward wind jet events and their impacts on the circulation. We show that the cross-axis winds are, indeed, an important component of the wind regime, explaining 11% of wind variability of the NRS (well-described by a 2nd EOF mode). The westward events occur predominantly in the winter, preferentially in January (about 15 events in 10-years) and have a mean duration of 4-5 days, with a maximum of 12 days (north of 22N). There are around 6 events per year, but in 2002-2003 and 2007-2008, twice more events were detected. The westward wind events are found to strongly modify the wind stress curl, causing a distinct positive/negative curl pattern along the main axis. This pattern enhances the eddy activity and impacts the NRS circulation.

Family Formation Processes: Assessing the Need for a New Nationally Representative Household Panel Survey in the United States

PubMed Central

Manning, Wendy D.

2015-01-01

The American family has undergone rapid transformation. Careful measurement attention to family formation is important because families are at the heart of numerous decisions, roles, and responsibilities with implications for understanding the well-being of families, adults and children. This paper considers whether there is a need for a new household panel study that addresses family formation. This paper consists of a review of the recent body of population-based, American surveys and finds a considerable gap in the ability to study the implications of families for the health and well-being of Americans. Earlier panel surveys used to assess family life anchored questions around marital events, but changes in family patterns require attention to a more diverse set of family forms. The paper concludes with recommendations for a multi-purpose panel study. The key challenge is to keep to pace with complexity and changes in American family life while at the same time maintaining a parsimonious set of survey questions. PMID:26612969

Involvement of Lipocalin-like CghA in Decalin-Forming Stereoselective Intramolecular [4+2] Cycloaddition

PubMed Central

Sato, Michio; Yagishita, Fumitoshi; Mino, Takashi; Uchiyama, Nahoko; Patel, Ashay; Chooi, Yit-Heng; Goda, Yukihiro; Xu, Wei; Noguchi, Hiroshi; Yamamoto, Tsuyoshi; Hotta, Kinya; Houk, Kendall N.; Tang, Yi

2016-01-01

Understanding enzymatic Diels—Alder (DA) reactions that can form complex natural product scaffold is of considerable interest. Sch 210972 1, a potential anti-HIV fungal natural product, contains a decalin core that is proposed to form via a DA reaction. We identified the gene cluster responsible for the biosynthesis of 1 and heterologously reconstituted the biosynthetic pathway in Aspergillus nidulans to characterize the enzymes involved. Most notably, deletion of cghA resulted in a loss of stereoselective decalin core formation, yielding both an endo 1 and a diastereomeric exo adducts of the proposed DA reaction. Complementation with cghA restored the sole formation of 1. Density functional theory computation of the proposed DA reaction provided a plausible explanation of the observed pattern of product formation. Based on our study, we propose that lipocalin-like CghA is responsible for the stereoselective intramolecular [4+2] cycloaddition that forms the decalin core of 1. PMID:26360642

Loss of Pancreas upon Activated Wnt Signaling Is Concomitant with Emergence of Gastrointestinal Identity

PubMed Central

Herrero-Martin, Griselda; Puri, Sapna; Taketo, Makoto Mark; Rojas, Anabel; Hebrok, Matthias; Cano, David A.

2016-01-01

Organ formation is achieved through the complex interplay between signaling pathways and transcriptional cascades. The canonical Wnt signaling pathway plays multiple roles during embryonic development including patterning, proliferation and differentiation in distinct tissues. Previous studies have established the importance of this pathway at multiple stages of pancreas formation as well as in postnatal organ function and homeostasis. In mice, gain-of-function experiments have demonstrated that activation of the canonical Wnt pathway results in pancreatic hypoplasia, a phenomenon whose underlying mechanisms remains to be elucidated. Here, we show that ectopic activation of epithelial canonical Wnt signaling causes aberrant induction of gastric and intestinal markers both in the pancreatic epithelium and mesenchyme, leading to the development of gut-like features. Furthermore, we provide evidence that β -catenin-induced impairment of pancreas formation depends on Hedgehog signaling. Together, our data emphasize the developmental plasticity of pancreatic progenitors and further underscore the key role of precise regulation of signaling pathways to maintain appropriate organ boundaries. PMID:27736991

Sensitivity analysis of geometrical parameters to study haemodynamics and thrombus formation in the left atrial appendage.

PubMed

García-Isla, Guadalupe; Olivares, Andy Luis; Silva, Etelvino; Nuñez-Garcia, Marta; Butakoff, Constantine; Sanchez-Quintana, Damian; G Morales, Hernán; Freixa, Xavier; Noailly, Jérôme; De Potter, Tom; Camara, Oscar

2018-05-08

The left atrial appendage (LAA) is a complex and heterogeneous protruding structure of the left atrium (LA). In atrial fibrillation patients, it is the location where 90% of the thrombi are formed. However, the role of the LAA in thrombus formation is not fully known yet. The main goal of this work is to perform a sensitivity analysis to identify the most relevant LA and LAA morphological parameters in atrial blood flow dynamics. Simulations were run on synthetic ellipsoidal left atria models where different parameters were individually studied: pulmonary veins and mitral valve dimensions; LAA shape; and LA volume. Our computational analysis confirmed the relation between large LAA ostia, low blood flow velocities and thrombus formation. Additionally, we found that pulmonary vein configuration exerted a critical influence on LAA blood flow patterns. These findings contribute to a better understanding of the LAA and to support clinical decisions for atrial fibrillation patients. Copyright © 2018 John Wiley & Sons, Ltd.

Modeling the formation of cell-matrix adhesions on a single 3D matrix fiber.

PubMed

Escribano, J; Sánchez, M T; García-Aznar, J M

2015-11-07

Cell-matrix adhesions are crucial in different biological processes like tissue morphogenesis, cell motility, and extracellular matrix remodeling. These interactions that link cell cytoskeleton and matrix fibers are built through protein clutches, generally known as adhesion complexes. The adhesion formation process has been deeply studied in two-dimensional (2D) cases; however, the knowledge is limited for three-dimensional (3D) cases. In this work, we simulate different local extracellular matrix properties in order to unravel the fundamental mechanisms that regulate the formation of cell-matrix adhesions in 3D. We aim to study the mechanical interaction of these biological structures through a three dimensional discrete approach, reproducing the transmission pattern force between the cytoskeleton and a single extracellular matrix fiber. This numerical model provides a discrete analysis of the proteins involved including spatial distribution, interaction between them, and study of the different phenomena, such as protein clutches unbinding or protein unfolding. Copyright © 2015 Elsevier Ltd. All rights reserved.

The Mysteries and Curiosities of Mars: A Tour of Unusual and Unexplained Terrains

NASA Astrophysics Data System (ADS)

Kerber, L.

2017-12-01

The large amount of data available from orbiting satellites around Mars has provided a wealth of information about the Martian surface and geological history. The published literature tends to focus on regions of Mars for which there are ready explanations; however, many regions of Mars remain mysterious. In this contribution, we present some of the strangest and least explained terrains on Mars: The Taffy Terrain: This complex terrain, consisting of swirling layers with variably sized bands, is present mostly at the bottom of Hellas Basin, but versions of it can also be found on the floor of Melas Chasma and in the Medusae Fossae Formation near Apollinaris Sulci. While little has been written about the taffy terrain, hypotheses include "glacial features" and salt domes. The taffy terrain bears some resemblance to submarine salt domes in the Gulf of Mexico, glacial deposits with mixed ash and ice in Iceland, or chalk formations in Egypt's White Desert. The Fishscale Terrain: At the northern edge of Lucus Planum, the friable Medusae Fossae Formation transitions into a chaos-like terrain with hundreds of mesas forming a pattern like the scales of a fish. While chaos terrains are mysterious in general, this morphologically fresh, near-equatorial chaos is especially unusual. Polygonal Ridges in Gordii Dorsum: Also a part of the Medusae Fossae Formation, the ridges in Gordii Dorsum represent a negative image of the fishscale terrain—a intricate lattice of slender black ridges. These are thought to form via the embayment of the fishscale terrain with lava and the subsequent erosion of the original mesas. Horseshoe Features: These geomorphological features look like inverted barchan dunes, but they are actually pits eroded into the surface of the Medusae Fossae Formation. Channels surrounding Elysium Mons: These channel systems are among the most complex on Mars, but they appear on a young Amazonian lava surface. The channels cut through topography, anastomose, and create streamlined islands. Strange flows around cones: Some rootless cones in Cerberus Palus have unusual flows coming out of them. Possible hypotheses include lava or mudflows. Sinus Meridiani: This region is host to arcuate ridge lattices, circular mesas with concentric patterns, and straight, subparallel ridges, similar to other ridges found near the South Pole.

Influence of depositional environment on diagenesis in St. Peter sandstone, Michigan basin

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lundgren, C.E. Jr.; Barnes, D.A.

1989-03-01

The Middle Ordovician St. Peter Sandstone in the Michigan basin was deposited in marine peritidal to storm-dominated, outer shelf depositional environments that evolved in a regionally significant transgressive pattern. The formation is bounded by carbonate and shaly clastic strata of the Prairie du Chien Group below and is transitional to condensed sequence clastics and carbonates of the Glenwood Formation above. Sedimentologic and petrographic analysis of conventional core from 25 wells suggests that reservoir quality in the formation is strongly dependent on a complex diagenetic history, especially the nature and subsequent dissolution of intergranular carbonate in the sandstone. Petrographic evidence indicatesmore » that porosity in the formation formed by dissolution of precursor dolomite of various origins and, locally, the formation of pore-filling authigenic clay (chlorite-illite). Authigenic clay is the incongruent dissolution product of dolomite, detrital K-feldspar, and, possibly, muscovite and results in diminished reservoir quality where abundant in the St. Peter Sandstone. Authigenic clay is volumetrically more significant in the upper portions of the formation and is associated with higher concentrations of detrital K-feldspar. Depositional facies controlled the distribution and types of intergranular carbonate (now dolomite) and detrital K-feldspar in the St. Peter Sandstone and hence reservoir quality; both components were more significant in storm-shelf sandstone facies.« less

Complexes and imagination.

PubMed

Kast, Verena

2014-11-01

Fantasies as imaginative activities are seen by Jung as expressions of psychic energy. In the various descriptions of active imagination the observation of the inner image and the dialogue with inner figures, if possible, are important. The model of symbol formation, as Jung describes it, can be experienced in doing active imagination. There is a correspondence between Jung's understanding of complexes and our imaginations: complexes develop a fantasy life. Complex episodes are narratives of difficult dysfunctional relationship episodes that have occurred repeatedly and are internalized with episodic memory. This means that the whole complex episode (the image for the child and the image for the aggressor, connected with emotions) is internalized and can get constellated in everyday relationship. Therefore inner dialogues do not necessarily qualify as active imaginations, often they are the expression of complex-episodes, very similar to fruitless soliloquies. If imaginations of this kind are repeated, new symbols and new possibilities of behaviour are not found. On the contrary, old patterns of behaviour and fantasies are perpetuated and become cemented. Imaginations of this kind need an intervention by the analyst. In clinical examples different kinds of imaginations are discussed. © 2014, The Society of Analytical Psychology.

A model complex of a possible intermediate in the mechanism of action of peptide deformylase: first example of an (N2S)zinc(II)-formate complex.

PubMed

Chang, S C; Sommer, R D; Rheingold, A L; Goldberg, D P

2001-11-21

The synthesis and crystallographic characterization of a new (N2S)zinc-alkyl complex and (N2S)zinc-formate complex is described; the bonding mode of the formate complex has implications for the mechanism of action of the enzyme peptide deformylase.

The influence of vegetation on the hydrodynamics and geomorphology of a tree island in Everglades National Park (Florida, United States)

USGS Publications Warehouse

Sullivan, Pamela L.; Engel, Victor C.; Ross, Michael S.; Price, René M.

2013-01-01

Transpiration-driven nutrient accumulation has been identified as a potential mechanism governing the creation and maintenance of wetland vegetation patterning. This process may contribute to the formation of nutrient-rich tree islands within the expansive oligotrophic marshes of the Everglades (Florida, United States). This study presents hydrogeochemical data indicating that tree root water uptake is a primary driver of groundwater ion accumulation across one of these islands. Sap flow, soil moisture, water level, water chemistry, and rainfall were measured to identify the relationships between climate, transpiration, and groundwater uptake by phreatophytes and to examine the effect this uptake has on groundwater chemistry and mineral formation in three woody plant communities of differing elevations. During the dry season, trees relied more on groundwater for transpiration, which led to a depressed water table and the advective movement of groundwater and dissolved ions, including phosphorus, from the surrounding marsh towards the centre of the island. Ion exclusion during root water uptake led to elevated concentrations of all major dissolved ions in the tree island groundwater compared with the adjacent marsh. Groundwater was predominately supersaturated with respect to aragonite and calcite in the lower-elevation woody communities, indicating the potential for soil formation. Elevated groundwater phosphorous concentrations detected in the highest-elevation woody community were associated with the leaching of inorganic sediments (i.e. hydroxyapatite) in the vadose zone. Understanding the complex feedback mechanisms regulating plant/groundwater/surface water interactions, nutrient dynamics, and potential soil formation is necessary to manage and restore patterned wetlands such as the Everglades.

Communicating with sentences: A multi-word naming game model

NASA Astrophysics Data System (ADS)

Lou, Yang; Chen, Guanrong; Hu, Jianwei

2018-01-01

Naming game simulates the process of naming an object by a single word, in which a population of communicating agents can reach global consensus asymptotically through iteratively pair-wise conversations. We propose an extension of the single-word model to a multi-word naming game (MWNG), simulating the case of describing a complex object by a sentence (multiple words). Words are defined in categories, and then organized as sentences by combining them from different categories. We refer to a formatted combination of several words as a pattern. In such an MWNG, through a pair-wise conversation, it requires the hearer to achieve consensus with the speaker with respect to both every single word in the sentence as well as the sentence pattern, so as to guarantee the correct meaning of the saying; otherwise, they fail reaching consensus in the interaction. We validate the model in three typical topologies as the underlying communication network, and employ both conventional and man-designed patterns in performing the MWNG.

Before the 'Big Chill': Patterns of plant-insect associations from the Neogene of Iceland

NASA Astrophysics Data System (ADS)

Wappler, Torsten; Grímsson, Friðgeir

2016-07-01

Iceland is the only known terrestrial place in the subarctic North Atlantic providing a fairly continuous sedimentary and plant fossil record over the past 15 million years. While the basic palaeobotanical framework of this pattern has been well established during the last decade, less attention has been paid to the abundant insect traces on fossil leaves/leaflets. Here, we assess the diversity and frequency of insect herbivory on 4349 fossil angiosperm leaves/leaflets from six plant-bearing sedimentary formations exposed at 18 localities. By combining analyses of environmental factors, species interactions, ecology, biogeography, and the geological history, our results demonstrate how patterns of herbivory have changed over time in relation to temperature fluctuations that profoundly influenced levels of insect-mediated damage diversity and frequency. In addition, higher structural complexity, particularly the establishment of species-rich herb layer communities seems to have positively influenced the structure of insect communities in early late Miocene palaeoforests of Iceland.

The morphogenetically active polymer, inorganic polyphosphate complexed with GdCl3, as an inducer of hydroxyapatite formation in vitro.

PubMed

Wang, Xiaohong; Huang, Jian; Wang, Kui; Neufurth, Meik; Schröder, Heinz C; Wang, Shunfeng; Müller, Werner E G

2016-02-15

Inorganic polyphosphate (polyP) is a physiological polymer composed of tens to hundreds of phosphate units linked together via phosphoanhydride bonds. Here we compared the biological activity of polyP (chain length of 40 phosphate units), complexed with Gd(3+) (polyP·Gd), with the one caused by polyP (as calcium salt) and by GdCl3 alone, regarding their potencies to induce hydroxyapatite (HA) formation in SaOS-2 cells in vitro. The three compounds, GdCl3, polyP and polyP·Gd were found to be non-toxic at concentrations up to at least 30μM. Selecting a low, 5μM, concentration it was found that polyP·Gd significantly induced HA formation, as determined by Alizarin Red S staining and by quantitative determinations using that dye. Under those conditions polyP·Gd and to a smaller extent also polyP or GdCl3 (5μM each) caused HA crystal formation arranged in a nest-like pattern. Exposure of cells to polyP·Gd resulted in a strong increase in alkaline phosphatase activity; this enzyme did not cause a distinct degradation of polyP but of polyP·Gd which was extensively hydrolyzed. The morphogenetic activity of gadolinium, in the form of polyP·Gd, is underscored by the finding that this polymer causes a strong upregulation of the genes encoding morphogenetic protein-2 (BMP2) as well as collagen type I. It is concluded that polyP·Gd is not an inert polymer but acts as a morphogenetically active polymer and induces HA formation in vitro. Copyright © 2015 Elsevier Inc. All rights reserved.

Edaphic fauna in a vegetation gradient in the Sete Cidades National Park.

PubMed

Nunes, L A P L; Araújo, A S F; Pessoa, M M C; Sousa, R S; Silva, J D C; Matos-Filho, C H A

2018-04-09

The vegetation physionomy and cover can show patterns of diversity and composition of the edaphic community, depending on the quantity and quality of litter in a specific habitat. The objective of this study was to evaluate the effect of the vegetation gradient formed by Graminoid Field (GRF), Cerrado Sensu Stricto (CSS), Cerradão (CRD) and Semideciduous Seasonal Forest (SSF) on density, diversity and composition of the edaphic fauna community in two seasons of the year, in the Sete Cidades National Park (Piauí state). For fauna sampling, a total of eight pitfall traps, distanced 10 m, were placed in each area in the central part of each system, where they remained for seven days. In the wet period, there was a tendency to increase the number of individuals as a function of the complexity of the vegetation formation, with the inverse occurring in the dry period. It was verified an environmental variation of the climatic factors temperature and humidity according to the vegetal formation, contributing to a heterogeneous distribution of the fauna. The GRF formation presented a significantly lower value of average richness only in the dry period. Regarding the variables of diversity and uniformity, they did not show drastic variations in relation to the vegetation gradient studied. The dominant groups in the vegetation gradient were Formicidae, Coleoptera, Aranae, Acari and Collembola, with reduction of the number of Coleoptera in the dry season. Principal component analysis (PCA) revealed greater differences in the composition of the communities between the vegetation formations for the rainy season. At this time, the formations SSF and CRD were associated to a greater diversity of invertebrates than CSS and GRF, demonstrating the influence of the vegetation complexity on the soil fauna community.

Effect of cerulenin on fatty acid composition and gene expression pattern of DHA-producing strain Colwellia psychrerythraea strain 34H.

PubMed

Wan, Xia; Peng, Yun-Feng; Zhou, Xue-Rong; Gong, Yang-Min; Huang, Feng-Hong; Moncalián, Gabriel

2016-02-06

Colwellia psychrerythraea 34H is a psychrophilic bacterium able to produce docosahexaenoic acid (DHA). Polyketide synthase pathway is assumed to be responsible for DHA production in marine bacteria. Five pfa genes from strain 34H were confirmed to be responsible for DHA formation by heterogeneous expression in Escherichia coli. The complexity of fatty acid profile of this strain was revealed by GC and GC-MS. Treatment of cells with cerulenin resulted in significantly reduced level of C16 monounsaturated fatty acid (C16:1(Δ9t), C16:1(Δ7)). In contrast, the amount of saturated fatty acids (C10:0, C12:0, C14:0), hydroxyl fatty acids (3-OH C10:0 and 3-OH C12:0), as well as C20:4ω3, C20:5ω3 and C22:6ω3 were increased. RNA sequencing (RNA-Seq) revealed the altered gene expression pattern when C. psychrerythraea cells were treated with cerulenin. Genes involved in polyketide synthase pathway and fatty acid biosynthesis pathway were not obviously affected by cerulenin treatment. In contrast, several genes involved in fatty acid degradation or β-oxidation pathway were dramatically reduced at the transcriptional level. Genes responsible for DHA formation in C. psychrerythraea was first cloned and characterized. We revealed the complexity of fatty acid profile in this DHA-producing strain. Cerulenin could substantially change the fatty acid composition by affecting the fatty acid degradation at transcriptional level. Acyl-CoA dehydrogenase gene family involved in the first step of β-oxidation pathway may be important to the selectivity of degraded fatty acids. In addition, inhibition of FabB protein by cerulenin may lead to the accumulation of malonyl-CoA, which is the substrate for DHA formation.

Fundamental structures of dynamic social networks.

PubMed

Sekara, Vedran; Stopczynski, Arkadiusz; Lehmann, Sune

2016-09-06

Social systems are in a constant state of flux, with dynamics spanning from minute-by-minute changes to patterns present on the timescale of years. Accurate models of social dynamics are important for understanding the spreading of influence or diseases, formation of friendships, and the productivity of teams. Although there has been much progress on understanding complex networks over the past decade, little is known about the regularities governing the microdynamics of social networks. Here, we explore the dynamic social network of a densely-connected population of ∼1,000 individuals and their interactions in the network of real-world person-to-person proximity measured via Bluetooth, as well as their telecommunication networks, online social media contacts, geolocation, and demographic data. These high-resolution data allow us to observe social groups directly, rendering community detection unnecessary. Starting from 5-min time slices, we uncover dynamic social structures expressed on multiple timescales. On the hourly timescale, we find that gatherings are fluid, with members coming and going, but organized via a stable core of individuals. Each core represents a social context. Cores exhibit a pattern of recurring meetings across weeks and months, each with varying degrees of regularity. Taken together, these findings provide a powerful simplification of the social network, where cores represent fundamental structures expressed with strong temporal and spatial regularity. Using this framework, we explore the complex interplay between social and geospatial behavior, documenting how the formation of cores is preceded by coordination behavior in the communication networks and demonstrating that social behavior can be predicted with high precision.

Fundamental structures of dynamic social networks

PubMed Central

Sekara, Vedran; Stopczynski, Arkadiusz; Lehmann, Sune

2016-01-01

Social systems are in a constant state of flux, with dynamics spanning from minute-by-minute changes to patterns present on the timescale of years. Accurate models of social dynamics are important for understanding the spreading of influence or diseases, formation of friendships, and the productivity of teams. Although there has been much progress on understanding complex networks over the past decade, little is known about the regularities governing the microdynamics of social networks. Here, we explore the dynamic social network of a densely-connected population of ∼1,000 individuals and their interactions in the network of real-world person-to-person proximity measured via Bluetooth, as well as their telecommunication networks, online social media contacts, geolocation, and demographic data. These high-resolution data allow us to observe social groups directly, rendering community detection unnecessary. Starting from 5-min time slices, we uncover dynamic social structures expressed on multiple timescales. On the hourly timescale, we find that gatherings are fluid, with members coming and going, but organized via a stable core of individuals. Each core represents a social context. Cores exhibit a pattern of recurring meetings across weeks and months, each with varying degrees of regularity. Taken together, these findings provide a powerful simplification of the social network, where cores represent fundamental structures expressed with strong temporal and spatial regularity. Using this framework, we explore the complex interplay between social and geospatial behavior, documenting how the formation of cores is preceded by coordination behavior in the communication networks and demonstrating that social behavior can be predicted with high precision. PMID:27555584

Effects of convection patterns on freckle formation of directionally solidified Nickel-based superalloy casting with abruptly varying cross-sections

NASA Astrophysics Data System (ADS)

Qin, Ling; Shen, Jun; Li, Qiudong; Shang, Zhao

2017-05-01

The effects of convection patterns on freckle formation of directionally solidified Nickel-based superalloy sample with abruptly varying cross-sections were investigated experimentally and numerically. The experimental results demonstrate that freckles were only observed at the bottom of larger cross-section. Numerical results indicate that this phenomenon should be attributed to the different convection patterns at front of solidification interface. As the withdrawal rate increased, the primary dendrites spacing has an obvious influence on freckle formation. A more in-depth investigation of the convection patterns can provide a better understanding of freckle formation and perhaps offer methods to minimize freckles in turbine blades.

Altered expression pattern of molecular factors involved in colonic smooth muscle functions: an immunohistochemical study in patients with diverticular disease.

PubMed

Mattii, Letizia; Ippolito, Chiara; Segnani, Cristina; Battolla, Barbara; Colucci, Rocchina; Dolfi, Amelio; Bassotti, Gabrio; Blandizzi, Corrado; Bernardini, Nunzia

2013-01-01

The pathogenesis of diverticular disease (DD) is thought to result from complex interactions among dietary habits, genetic factors and coexistence of other bowel abnormalities. These conditions lead to alterations in colonic pressure and motility, facilitating the formation of diverticula. Although electrophysiological studies on smooth muscle cells (SMCs) have investigated colonic motor dysfunctions, scarce attention has been paid to their molecular abnormalities, and data on SMCs in DD are lacking. Accordingly, the main purpose of this study was to evaluate the expression patterns of molecular factors involved in the contractile functions of SMCs in the tunica muscularis of colonic specimens from patients with DD. By means of immunohistochemistry and image analysis, we examined the expression of Cx26 and Cx43, which are prominent components of gap junctions in human colonic SMCs, as well as pS368-Cx43, PKCps, RhoA and αSMA, all known to regulate the functions of gap junctions and the contractile activity of SMCs. The immunohistochemical analysis revealed significant abnormalities in DD samples, concerning both the expression and distribution patterns of most of the investigated molecular factors. This study demonstrates, for the first time, that an altered pattern of factors involved in SMC contractility is present at level of the tunica muscularis of DD patients. Moreover, considering that our analysis was conducted on colonic tissues not directly affected by diverticular lesions or inflammatory reactions, it is conceivable that these molecular alterations may precede and predispose to the formation of diverticula, rather than being mere consequences of the disease.

Localization of caveolin-1 and c-src in mature and differentiating photoreceptors: raft proteins co-distribute with rhodopsin during development

PubMed Central

Berta, Ágnes I.; Boesze-Battaglia, Kathleen; Magyar, Attila; Szél, Ágoston; Kiss, Anna L.

2014-01-01

Numerous biochemical and morphological studies have provided insight into the distribution pattern of caveolin-1 and the presence of membrane rafts in the vertebrate retina. To date however, studies have not addressed the localization profile of raft specific proteins during development. Therefore the purpose of our studies was to follow the localization pattern of caveolin-1, phosphocaveolin-1 and c-src in the developing retina and compare it to that observed in adults. Specific antibodies were used to visualize the distribution of caveolin-1, c-src, a kinase phosphorylating caveolin-1, and phospho-caveolin-1. The labeling pattern of this scaffolded complex was compared to those of rhodopsin and rhodopsin kinase. Samples were analyzed at various time points during postnatal development and compared to adult retinas. The immunocytochemical studies were complemented with immunoblots and immunoprecipitation studies. In the mature retina caveolin-1 and c-src localized mainly to the cell body and IS of photoreceptors, with only very weakly labeled OS. In contrast, phospho-caveolin-1 was only detectable in the OS of photoreceptors. During development we followed the expression and distribution profile of these proteins in a temporal sequence with special attention to the period when OS formation is most robust. Double labeling immunocytochemistry and immunoprecipitation showed rhodopsin to colocalize and co-immunoprecipitate with caveolin-1 and c-src. Individual punctate structures between the outer limiting membrane and the outer plexiform layer were seen at P10 to be labeled by both rhodopsin and caveolin-1 as well as by rhodopsin and c-src, respectively. These studies suggest that membrane raft specific proteins are co-distributed during development, thereby pointing to a role for such complexes in OS formation. In addition, the presence of small punctate structures containing caveolin-1, c-src and rhodopsin raise the possibility that these proteins may transport together to OS during development and that caveolin-1 exists predominantly in a phosphorylated form in the OS. PMID:21938483

Formation of the acrosome complex in the bush cricket Gampsocleis gratiosa (Orthoptera: Tettigoniidae).

PubMed

Su, Cai Xia; Chen, Jie; Shi, Fu Ming; Guo, Ming Shen; Chang, Yan Lin

2017-07-01

The acrosome complex plays an indispensable role in the normal function of mature spermatozoa. However, the dynamic process of acrosome complex formation in insect remains poorly understood. Gampsocleis gratiosa Brunner von Wattenwyl possesses the typical characteristic of insect sperms, which is tractable in terms of size, and therefore was selected for the acrosome formation study in this report. The results show that acrosome formation can be divided into six phases: round, rotating, rhombic, cylindrical, transforming and mature phase, based on the morphological dynamics of acrosome complex and nucleus. In addition, the cytoskeleton plays a critical role in the process of acrosome formation. The results from this study indicate that: (1) glycoprotein is the major component of the acrosome proper; (2) the microfilament is one element of the acrosome complex, and may mediate the morphologic change of the acrosome complex; (3) the microtubules might also shape the nucleus and acrosome complex during the acrosome formation. Copyright © 2017 Elsevier Ltd. All rights reserved.

Biphasic regulation of the transcription factor ABORTED MICROSPORES (AMS) is essential for tapetum and pollen development in Arabidopsis.

PubMed

Ferguson, Alison C; Pearce, Simon; Band, Leah R; Yang, Caiyun; Ferjentsikova, Ivana; King, John; Yuan, Zheng; Zhang, Dabing; Wilson, Zoe A

2017-01-01

Viable pollen is essential for plant reproduction and crop yield. Its production requires coordinated expression at specific stages during anther development, involving early meiosis-associated events and late pollen wall formation. The ABORTED MICROSPORES (AMS) transcription factor is a master regulator of sporopollenin biosynthesis, secretion and pollen wall formation in Arabidopsis. Here we show that it has complex regulation and additional essential roles earlier in pollen formation. An inducible-AMS reporter was created for functional rescue, protein expression pattern analysis, and to distinguish between direct and indirect targets. Mathematical modelling was used to create regulatory networks based on wild-type RNA and protein expression. Dual activity of AMS was defined by biphasic protein expression in anther tapetal cells, with an initial peak around pollen meiosis and then later during pollen wall development. Direct AMS-regulated targets exhibit temporal regulation, indicating that additional factors are associated with their regulation. We demonstrate that AMS biphasic expression is essential for pollen development, and defines distinct functional activities during early and late pollen development. Mathematical modelling suggests that AMS may competitively form a protein complex with other tapetum-expressed transcription factors, and that biphasic regulation is due to repression of upstream regulators and promotion of AMS protein degradation. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

Computational model of cerebral blood flow redistribution during cortical spreading depression

NASA Astrophysics Data System (ADS)

Verisokin, Andrey Y.; Verveyko, Darya V.; Postnov, Dmitry E.

2016-04-01

In recent decades modelling studies on cortical spreading depression (CSD) and migraine waves successfully contributed to formation of modern view on these fundamental phenomena of brain physiology. However, due to the extreme complexity of object under study (brain cortex) and the diversity of involved physiological pathways, the development of new mathematical models of CSD is still a very relevant and challenging research problem. In our study we follow the functional modelling approach aimed to map the action of known physiological pathways to the specific nonlinear mechanisms that govern formation and evolution of CSD wave patterns. Specifically, we address the role of cerebral blood flow (CBF) redistribution that is caused by excessive neuronal activity by means of neurovascular coupling and mediates a spatial pattern of oxygen and glucose delivery. This in turn changes the local metabolic status of neural tissue. To build the model we simplify the web of known cell-to-cell interactions within a neurovascular unit by selecting the most relevant ones, such as local neuron-induced elevation of extracellular potassium concentration and biphasic response of arteriole radius. We propose the lumped description of distance-dependent hemodynamic coupling that fits the most recent experimental findings.

Slow-Theta-to-Gamma Phase–Amplitude Coupling in Human Hippocampus Supports the Formation of New Episodic Memories

PubMed Central

Lega, Bradley; Burke, John; Jacobs, Joshua; Kahana, Michael J.

2016-01-01

Phase–amplitude coupling (PAC) has been proposed as a neural mechanism for coordinating information processing across brain regions. Here we sought to characterize PAC in the human hippocampus, and in temporal and frontal cortices, during the formation of new episodic memories. Intracranial recordings taken as 56 neurosurgical patients studied and recalled lists of words revealed significant hippocampal PAC, with slow-theta activity (2.5–5 Hz) modulating gamma band activity (34–130 Hz). Furthermore, a significant number of hippocampal electrodes exhibited greater PAC during successful than unsuccessful encoding, with the gamma activity at these sites coupled to the trough of the slow-theta oscillation. These same conditions facilitate LTP in animal models, providing a possible mechanism of action for this effect in human memory. Uniquely in the hippocampus, phase preference during item encoding exhibited a biphasic pattern. Overall, our findings help translate between the patterns identified during basic memory tasks in animals and those present during complex human memory encoding. We discuss the unique properties of human hippocampal PAC and how our findings relate to influential theories of information processing based on theta–gamma interactions. PMID:25316340

The Meckel syndrome- associated protein MKS1 functionally interacts with components of the BBSome and IFT complexes to mediate ciliary trafficking and hedgehog signaling

PubMed Central

Barrington, Chloe L.; Katsanis, Nicholas

2017-01-01

The importance of primary cilia in human health is underscored by the link between ciliary dysfunction and a group of primarily recessive genetic disorders with overlapping clinical features, now known as ciliopathies. Many of the proteins encoded by ciliopathy-associated genes are components of a handful of multi-protein complexes important for the transport of cargo to the basal body and/or into the cilium. A key question is whether different complexes cooperate in cilia formation, and whether they participate in cilium assembly in conjunction with intraflagellar transport (IFT) proteins. To examine how ciliopathy protein complexes might function together, we have analyzed double mutants of an allele of the Meckel syndrome (MKS) complex protein MKS1 and the BBSome protein BBS4. We find that Mks1; Bbs4 double mutant mouse embryos exhibit exacerbated defects in Hedgehog (Hh) dependent patterning compared to either single mutant, and die by E14.5. Cells from double mutant embryos exhibit a defect in the trafficking of ARL13B, a ciliary membrane protein, resulting in disrupted ciliary structure and signaling. We also examined the relationship between the MKS complex and IFT proteins by analyzing double mutant between Mks1 and a hypomorphic allele of the IFTB component Ift172. Despite each single mutant surviving until around birth, Mks1; Ift172avc1 double mutants die at mid-gestation, and exhibit a dramatic failure of cilia formation. We also find that Mks1 interacts genetically with an allele of Dync2h1, the IFT retrograde motor. Thus, we have demonstrated that the MKS transition zone complex cooperates with the BBSome to mediate trafficking of specific trans-membrane receptors to the cilium. Moreover, the genetic interaction of Mks1 with components of IFT machinery suggests that the transition zone complex facilitates IFT to promote cilium assembly and structure. PMID:28291807

Self-Organization of Spatial Patterning in Human Embryonic Stem Cells.

PubMed

Deglincerti, Alessia; Etoc, Fred; Ozair, M Zeeshan; Brivanlou, Ali H

2016-01-01

The developing embryo is a remarkable example of self-organization, where functional units are created in a complex spatiotemporal choreography. Recently, human embryonic stem cells (ESCs) have been used to recapitulate in vitro the self-organization programs that are executed in the embryo in vivo. This represents an unique opportunity to address self-organization in humans that is otherwise not addressable with current technologies. In this chapter, we review the recent literature on self-organization of human ESCs, with a particular focus on two examples: formation of embryonic germ layers and neural rosettes. Intriguingly, both activation and elimination of TGFβ signaling can initiate self-organization, albeit with different molecular underpinnings. We discuss the mechanisms underlying the formation of these structures in vitro and explore future challenges in the field. © 2016 Elsevier Inc. All rights reserved.

Composite transform-convergent plate boundaries: description and discussion

USGS Publications Warehouse

Ryan, H.F.; Coleman, P.J.

1992-01-01

The leading edge of the overriding plate at an obliquely convergent boundary is commonly sliced by a system of strike-slip faults. This fault system is often structurally complex, and may show correspondingly uneven strain effects, with great vertical and translational shifts of the component blocks of the fault system. The stress pattern and strain effects vary along the length of the system and change through time. These margins are considered to be composite transform-convergent (CTC) plate boundaries. Examples are given of structures formed along three CTC boundaries: the Aleutian Ridge, the Solomon Islands, and the Philippines. The dynamism of the fault system along a CTC boundary can enhance vertical tectonism and basin formation. This concept provides a framework for the evaluation of petroleum resources related to basin formation, and mineral exploration related to igneous activity associated with transtensional processes. ?? 1992.

Forest Connectivity Regions of Canada Using Circuit Theory and Image Analysis

PubMed Central

Pelletier, David; Lapointe, Marc-Élie; Wulder, Michael A.; White, Joanne C.; Cardille, Jeffrey A.

2017-01-01

Ecological processes are increasingly well understood over smaller areas, yet information regarding interconnections and the hierarchical nature of ecosystems remains less studied and understood. Information on connectivity over large areas with high resolution source information provides for both local detail and regional context. The emerging capacity to apply circuit theory to create maps of omnidirectional connectivity provides an opportunity for improved and quantitative depictions of forest connectivity, supporting the formation and testing of hypotheses about the density of animal movement, ecosystem structure, and related links to natural and anthropogenic forces. In this research, our goal was to delineate regions where connectivity regimes are similar across the boreal region of Canada using new quantitative analyses for characterizing connectivity over large areas (e.g., millions of hectares). Utilizing the Earth Observation for Sustainable Development of forests (EOSD) circa 2000 Landsat-derived land-cover map, we created and analyzed a national-scale map of omnidirectional forest connectivity at 25m resolution over 10000 tiles of 625 km2 each, spanning the forested regions of Canada. Using image recognition software to detect corridors, pinch points, and barriers to movements at multiple spatial scales in each tile, we developed a simple measure of the structural complexity of connectivity patterns in omnidirectional connectivity maps. We then mapped the Circuitscape resistance distance measure and used it in conjunction with the complexity data to study connectivity characteristics in each forested ecozone. Ecozone boundaries masked substantial systematic patterns in connectivity characteristics that are uncovered using a new classification of connectivity patterns that revealed six clear groups of forest connectivity patterns found in Canada. The resulting maps allow exploration of omnidirectional forest connectivity patterns at full resolution while permitting quantitative analyses of connectivity over broad areas, informing modeling, planning and monitoring efforts. PMID:28146573

A reinvestigation of phylogeny and divergence times of the Ablepharus kitaibelii species complex (Sauria, Scincidae) based on mtDNA and nuDNA genes.

PubMed

Skourtanioti, Eirini; Kapli, Paschalia; Ilgaz, Çetin; Kumlutaş, Yusuf; Avcı, Aziz; Ahmadzadeh, Faraham; Crnobrnja-Isailović, Jelka; Gherghel, Iulian; Lymberakis, Petros; Poulakakis, Nikos

2016-10-01

Morphological and DNA data support that the East Mediterranean snake-eyed skink Ablepharus kitaibelii represents a species complex that includes four species A. kitaibelii, A. budaki, A. chernovi, and A. rueppellii, highlighting the need of its taxonomic reevaluation. Here, we used Bayesian and Maximum Likelihood methods to estimate the phylogenetic relationships of all members of the complex based on two mitochondrial (cyt b, 16S rRNA) and two nuclear markers (MC1R, and NKTR) and using Chalcides, Eumeces, and Eutropis as outgroups. The biogeographic history of the complex was also investigated through the application of several phylogeographic (BEAST) and biogeographic (BBM) analyses. Paleogeographic and paleoclimatic data were used to support the inferred phylogeographic patterns. The A. kitaibelli species complex exhibits high genetic diversity, revealing cases of hidden diversity and cases of non-monophyletic species such as A. kitaibelii and A. budaki. Our results indicate that A. pannonicus branches off first and a group that comprises specimens of A. kitaibelli and A. budaki from Kastelorizo Island group (southeast Greece) and southwest Turkey, respectively is differentiated from the rest A. kitaibelli and A. budaki populations and may represent a new species. The estimated divergence times place the origin of the complex in the Middle Miocene (∼16Mya) and the divergence of most currently recognized species in the Late Miocene. The inferred ancestral distribution suggests that the complex originated in Anatolia, supposing that several vicariance and dispersal events that are related with the formation of the Mid-Aegean Trench, the Anatolian Diagonal and the orogenesis of the mountain chains in southern and eastern Anatolia have led to current distribution pattern of A. kitaibelii species complex in the Balkans and Middle East. Copyright © 2016 Elsevier Inc. All rights reserved.

Global stability and pattern formation in a nonlocal diffusive Lotka-Volterra competition model

NASA Astrophysics Data System (ADS)

Ni, Wenjie; Shi, Junping; Wang, Mingxin

2018-06-01

A diffusive Lotka-Volterra competition model with nonlocal intraspecific and interspecific competition between species is formulated and analyzed. The nonlocal competition strength is assumed to be determined by a diffusion kernel function to model the movement pattern of the biological species. It is shown that when there is no nonlocal intraspecific competition, the dynamics properties of nonlocal diffusive competition problem are similar to those of classical diffusive Lotka-Volterra competition model regardless of the strength of nonlocal interspecific competition. Global stability of nonnegative constant equilibria are proved using Lyapunov or upper-lower solution methods. On the other hand, strong nonlocal intraspecific competition increases the system spatiotemporal dynamic complexity. For the weak competition case, the nonlocal diffusive competition model may possess nonconstant positive equilibria for some suitably large nonlocal intraspecific competition coefficients.

Rayleigh-Taylor instability in soft elastic layers

NASA Astrophysics Data System (ADS)

Riccobelli, D.; Ciarletta, P.

2017-04-01

This work investigates the morphological stability of a soft body composed of two heavy elastic layers attached to a rigid surface and subjected only to the bulk gravity force. Using theoretical and computational tools, we characterize the selection of different patterns as well as their nonlinear evolution, unveiling the interplay between elastic and geometric effects for their formation. Unlike similar gravity-induced shape transitions in fluids, such as the Rayleigh-Taylor instability, we prove that the nonlinear elastic effects saturate the dynamic instability of the bifurcated solutions, displaying a rich morphological diagram where both digitations and stable wrinkling can emerge. The results of this work provide important guidelines for the design of novel soft systems with tunable shapes, with several applications in engineering sciences. This article is part of the themed issue 'Patterning through instabilities in complex media: theory and applications.'

The significance of ACTH for the process of formation of complex heparin compounds in the blood during immobilization stress

NASA Technical Reports Server (NTRS)

Kudryashov, B. A.; Shapiro, F. B.; Lomovskaya, F. B.; Lyapina, L. A.

1979-01-01

Adrenocorticotropin (ACTH) was administered to rats at different times following adrenalectomy. Adrenocorticotropin caused a significant increase in the formation of heparin complexes even in the absence of stress factor. When ACTH secretion is blocked, immobilization stress is not accompanied by an increase in the process of complex formation. The effect of ACTH on the formation of heparin complexes was mediated through its stimulation of the adrenal cortex.

The role of phase separation for self-organized surface pattern formation by ion beam erosion and metal atom co-deposition

NASA Astrophysics Data System (ADS)

Hofsäss, H.; Zhang, K.; Pape, A.; Bobes, O.; Brötzmann, M.

2013-05-01

We investigate the ripple pattern formation on Si surfaces at room temperature during normal incidence ion beam erosion under simultaneous deposition of different metallic co-deposited surfactant atoms. The co-deposition of small amounts of metallic atoms, in particular Fe and Mo, is known to have a tremendous impact on the evolution of nanoscale surface patterns on Si. In previous work on ion erosion of Si during co-deposition of Fe atoms, we proposed that chemical interactions between Fe and Si atoms of the steady-state mixed Fe x Si surface layer formed during ion beam erosion is a dominant driving force for self-organized pattern formation. In particular, we provided experimental evidence for the formation of amorphous iron disilicide. To confirm and generalize such chemical effects on the pattern formation, in particular the tendency for phase separation, we have now irradiated Si surfaces with normal incidence 5 keV Xe ions under simultaneous gracing incidence co-deposition of Fe, Ni, Cu, Mo, W, Pt, and Au surfactant atoms. The selected metals in the two groups (Fe, Ni, Cu) and (W, Pt, Au) are very similar regarding their collision cascade behavior, but strongly differ regarding their tendency to silicide formation. We find pronounced ripple pattern formation only for those co deposited metals (Fe, Mo, Ni, W, and Pt), which are prone to the formation of mono and disilicides. In contrast, for Cu and Au co-deposition the surface remains very flat, even after irradiation at high ion fluence. Because of the very different behavior of Cu compared to Fe, Ni and Au compared to W, Pt, phase separation toward amorphous metal silicide phases is seen as the relevant process for the pattern formation on Si in the case of Fe, Mo, Ni, W, and Pt co-deposition.

Pacopampa: Early evidence of violence at a ceremonial site in the northern Peruvian highlands

PubMed Central

Uzawa, Kazuhiro; Seki, Yuji; Morales Chocano, Daniel

2017-01-01

Objectives Pacopampa, a ceremonial complex in Peru’s northern highlands, reveals early evidence of trauma in the Middle to Late Formative Period coinciding with the emergence of social stratification in the area. We examine the prevalence of trauma in human remains found at the site and present evidence of the circumstances surrounding the deaths of individuals who lived during the early stages of Andean civilization. Materials and methods The materials are the remains of 104 individuals (38 non-adult and 66 adult) from the Middle to Late Formative Periods. We explored trauma macroscopically and recorded patterns based on skeletons’ locations, age at death, sex, social class, and chronology. Results We detected trauma in remains over the Middle to Late Formative Periods. While the prevalence of trauma was minimal in the Middle Formative Period, skeletons from the subsequent era exhibit more severe disturbances. However, all the skeletons show signs of healing and affected individuals experienced a low degree of trauma. Discussion Given the archaeological context (the remains were recovered from sites of ceremonial practices), as well as the equal distribution of trauma among both sexes and a lack of defensive architecture, it is plausible that rituals, rather than organized warfare or raids, caused most of the exhibited trauma. Pacopampa was home to a complex society founded on ritual activity in a ceremonial center: this is indicated by the presence of ritual violence in a society that built impressively large, ceremonial architecture and developed social stratification without any political control of surplus agricultural goods. PMID:28957380

Photosynthesis-dependent formation of convoluted plasma membrane domains in Chara internodal cells is independent of chloroplast position.

PubMed

Foissner, Ilse; Sommer, Aniela; Hoeftberger, Margit

2015-07-01

The characean green alga Chara australis forms complex plasma membrane convolutions called charasomes when exposed to light. Charasomes are involved in local acidification of the surrounding medium which facilitates carbon uptake required for photosynthesis. They have hitherto been only described in the internodal cells and in close contact with the stationary chloroplasts. Here, we show that charasomes are not only present in the internodal cells of the main axis, side branches, and branchlets but that the plasma membranes of chloroplast-containing nodal cells, protonemata, and rhizoids are also able to invaginate into complex domains. Removal of chloroplasts by local irradiation with intense light revealed that charasomes can develop at chloroplast-free "windows" and that the resulting pH banding pattern is independent of chloroplast or window position. Charasomes were not detected along cell walls containing functional plasmodesmata. However, charasomes formed next to a smooth wound wall which was deposited onto the plasmodesmata-containing wall when the neighboring cell was damaged. In contrast, charasomes were rarely found at uneven, bulged wound walls which protrude into the streaming endoplasm and which were induced by ligation or puncturing. The results of this study show that charasome formation, although dependent on photosynthesis, does not require intimate contact with chloroplasts. Our data suggest further that the presence of plasmodesmata inhibits charasome formation and/or that exposure to the outer medium is a prerequisite for charasome formation. Finally, we hypothesize that the absence of charasomes at bulged wound walls is due to the disturbance of uniform laminar mass streaming.

Human Cytomegalovirus Nuclear Capsids Associate with the Core Nuclear Egress Complex and the Viral Protein Kinase pUL97

PubMed Central

Sonntag, Eric; Wagner, Sabrina; Strojan, Hanife; Wangen, Christina; Lenac Rovis, Tihana; Lisnic, Berislav; Jonjic, Stipan; Schlötzer-Schrehardt, Ursula; Marschall, Manfred

2018-01-01

The nuclear phase of herpesvirus replication is regulated through the formation of regulatory multi-component protein complexes. Viral genomic replication is followed by nuclear capsid assembly, DNA encapsidation and nuclear egress. The latter has been studied intensely pointing to the formation of a viral core nuclear egress complex (NEC) that recruits a multimeric assembly of viral and cellular factors for the reorganization of the nuclear envelope. To date, the mechanism of the association of human cytomegalovirus (HCMV) capsids with the NEC, which in turn initiates the specific steps of nuclear capsid budding, remains undefined. Here, we provide electron microscopy-based data demonstrating the association of both nuclear capsids and NEC proteins at nuclear lamina budding sites. Specifically, immunogold labelling of the core NEC constituent pUL53 and NEC-associated viral kinase pUL97 suggested an intranuclear NEC-capsid interaction. Staining patterns with phospho-specific lamin A/C antibodies are compatible with earlier postulates of targeted capsid egress at lamina-depleted areas. Important data were provided by co-immunoprecipitation and in vitro kinase analyses using lysates from HCMV-infected cells, nuclear fractions, or infectious virions. Data strongly suggest that nuclear capsids interact with pUL53 and pUL97. Combined, the findings support a refined concept of HCMV nuclear trafficking and NEC-capsid interaction. PMID:29342872

Phosphorus and carbon availability regulate structural composition and complexity of AM fungal mycelium.

PubMed

Olsson, Ola; Olsson, Pål Axel; Hammer, Edith C

2014-08-01

The regulation of the structural composition and complexity of the mycelium of arbuscular mycorrhizal (AM) fungi is not well understood due to their obligate biotrophic nature. The aim of this study was to investigate the structure of extraradical mycelium at high and low availability of carbon (C) to the roots and phosphorus (P) to the fungus. We used monoxenic cultures of the AM fungus Rhizophagus irregularis (formerly Glomus intraradices) with transformed carrot roots as the host in a cultivation system including a root-free compartment into which the extraradical mycelium could grow. We found that high C availability increased hyphal length and spore production and anastomosis formation within individual mycelia. High P availability increased the formation of branched absorbing structures and reduced spore production and the overall length of runner hyphae. The complexity of the mycelium, as indicated by its fractal dimensions, increased with both high C and P availability. The results indicate that low P availability induces a growth pattern that reflects foraging for both P and C. Low C availability to AM roots could still support the explorative development of the mycelium when P availability was low. These findings help us to better understand the development of AM fungi in ecosystems with high P input and/or when plants are subjected to shading, grazing or any management practice that reduces the photosynthetic ability of the plant.

Human Cytomegalovirus Nuclear Capsids Associate with the Core Nuclear Egress Complex and the Viral Protein Kinase pUL97.

PubMed

Milbradt, Jens; Sonntag, Eric; Wagner, Sabrina; Strojan, Hanife; Wangen, Christina; Lenac Rovis, Tihana; Lisnic, Berislav; Jonjic, Stipan; Sticht, Heinrich; Britt, William J; Schlötzer-Schrehardt, Ursula; Marschall, Manfred

2018-01-13

The nuclear phase of herpesvirus replication is regulated through the formation of regulatory multi-component protein complexes. Viral genomic replication is followed by nuclear capsid assembly, DNA encapsidation and nuclear egress. The latter has been studied intensely pointing to the formation of a viral core nuclear egress complex (NEC) that recruits a multimeric assembly of viral and cellular factors for the reorganization of the nuclear envelope. To date, the mechanism of the association of human cytomegalovirus (HCMV) capsids with the NEC, which in turn initiates the specific steps of nuclear capsid budding, remains undefined. Here, we provide electron microscopy-based data demonstrating the association of both nuclear capsids and NEC proteins at nuclear lamina budding sites. Specifically, immunogold labelling of the core NEC constituent pUL53 and NEC-associated viral kinase pUL97 suggested an intranuclear NEC-capsid interaction. Staining patterns with phospho-specific lamin A/C antibodies are compatible with earlier postulates of targeted capsid egress at lamina-depleted areas. Important data were provided by co-immunoprecipitation and in vitro kinase analyses using lysates from HCMV-infected cells, nuclear fractions, or infectious virions. Data strongly suggest that nuclear capsids interact with pUL53 and pUL97. Combined, the findings support a refined concept of HCMV nuclear trafficking and NEC-capsid interaction.

Competitive FRET-aptamer-based detection of methylphosphonic acid, a common nerve agent metabolite.

PubMed

Bruno, John G; Carrillo, Maria P; Phillips, Taylor; Vail, Neal K; Hanson, Douglas

2008-09-01

Competitive fluorescence resonance energy transfer (FRET)-aptamer-based assay formats are described for one-step detection of methylphosphonic acid (MPA; a metabolite of several organophosphorus (OP) nerve agents). AminoMPA was attached to tosyl-magnetic beads and used for DNA aptamer selection from which one dominant aptamer sequence emerged. Two different FRET approaches were attempted. In one approach, the complementary DNA sequence was used as a template for labeling the aptamer with Alexa Fluor 546 (AF 546)-14-dUTP by asymmetric PCR. Following 3-dimensional (3-D), molecular modeling of the aptamer-MPA complex, a series of three fluoresceinated aptamers labeled at positions 50, 51, and 52 in the putative optimal binding pocket were synthesized. In both FRET formats, aminoMPA was linked to Black Hole Quencher (BHQ-1 or BHQ-2)-succinimides and allowed to bind the fluorescein or AF 546-labeled MPA aptamer. Following gel filtration to purify the labeled MPA aptamer-BHQ-aminoMPA FRET complexes, the complexes were competed against various concentrations of unlabeled MPA, MPA derivatives, and unrelated compounds in titration and cross-reactivity studies. Both approaches yielded low microgram per milliliter detection limits for MPA with generally low levels of cross-reactivity for unrelated compounds. However, the data suggest a pattern of traits that may effect the direction (lights on or off) and intensity of the FRET.

Pattern formation and geometry of the manifold

NASA Astrophysics Data System (ADS)

Haji, Amir Hossein; Mahzoon, Mojtaba; Javadpour, Sirus

2011-03-01

The objective of the present work is to investigate how pattern formation in the Cahn-Hilliard system can be influenced by geometry of the manifold. This is in contrast to control methods in which the physical field is modified and the pattern formation of the original system changes in response to control inputs. The idea begins with the cylindrical manifold symmetry leading to circumferential rolls while the torus manifold can be used to produce and control helical rolls. The next step is to search for a weaker restriction on the geometry of the manifold in order to reduce its dimension. In particular a short amplitude sinusoidal modulation on a flat surface is studied. At the final step a sequential pattern formation is presented.

Microsolvation effect and hydrogen-bonding pattern of taurine-water TA-(H2O)n (n = 1-3) complexes.

PubMed

Dai, Yumei; Wang, Yuhua; Huang, Zhengguo; Wang, Hongke; Yu, Lei

2012-01-01

The microsolvation of taurine (TA) with one, two or three water molecules was investigated by a density functional theory (DFT) approach. Quantum theory of atoms in molecules (QTAIM) analyses were employed to elucidate the hydrogen bond (H-bond) interaction characteristics in TA-(H(2)O)(n) (n = 1-3) complexes. The results showed that the intramolecular H-bond formed between the hydroxyl and the N atom of TA are retained in most TA-(H(2)O)(n) (n = 1-3) complexes, and are strengthened via cooperative effects among multiple H-bonds from n = 1-3. A trend of proton transformation exists from the hydroxyl to the N atom, which finally results in the cleavage of the origin intramolecular H-bond and the formation of a new intramolecular H-bond between the amino and the O atom of TA. Therefore, the most stable TA-(H(2)O)(3) complex becomes a zwitterionic complex rather than a neutral type. A many-body interaction analysis showed that the major contributors to the binding energies for complexes are the two-body energies, while three-body energies and relaxation energies make significant contributions to the binding energies for some complexes, whereas the four-body energies are too small to be significant.

Envelope: interactive software for modeling and fitting complex isotope distributions.

PubMed

Sykes, Michael T; Williamson, James R

2008-10-20

An important aspect of proteomic mass spectrometry involves quantifying and interpreting the isotope distributions arising from mixtures of macromolecules with different isotope labeling patterns. These patterns can be quite complex, in particular with in vivo metabolic labeling experiments producing fractional atomic labeling or fractional residue labeling of peptides or other macromolecules. In general, it can be difficult to distinguish the contributions of species with different labeling patterns to an experimental spectrum and difficult to calculate a theoretical isotope distribution to fit such data. There is a need for interactive and user-friendly software that can calculate and fit the entire isotope distribution of a complex mixture while comparing these calculations with experimental data and extracting the contributions from the differently labeled species. Envelope has been developed to be user-friendly while still being as flexible and powerful as possible. Envelope can simultaneously calculate the isotope distributions for any number of different labeling patterns for a given peptide or oligonucleotide, while automatically summing these into a single overall isotope distribution. Envelope can handle fractional or complete atom or residue-based labeling, and the contribution from each different user-defined labeling pattern is clearly illustrated in the interactive display and is individually adjustable. At present, Envelope supports labeling with 2H, 13C, and 15N, and supports adjustments for baseline correction, an instrument accuracy offset in the m/z domain, and peak width. Furthermore, Envelope can display experimental data superimposed on calculated isotope distributions, and calculate a least-squares goodness of fit between the two. All of this information is displayed on the screen in a single graphical user interface. Envelope supports high-quality output of experimental and calculated distributions in PNG or PDF format. Beyond simply comparing calculated distributions to experimental data, Envelope is useful for planning or designing metabolic labeling experiments, by visualizing hypothetical isotope distributions in order to evaluate the feasibility of a labeling strategy. Envelope is also useful as a teaching tool, with its real-time display capabilities providing a straightforward way to illustrate the key variable factors that contribute to an observed isotope distribution. Envelope is a powerful tool for the interactive calculation and visualization of complex isotope distributions for comparison to experimental data. It is available under the GNU General Public License from http://williamson.scripps.edu/envelope/.

Gene Loss and Lineage-Specific Restriction-Modification Systems Associated with Niche Differentiation in the Campylobacter jejuni Sequence Type 403 Clonal Complex

PubMed Central

Morley, Laura; McNally, Alan; Paszkiewicz, Konrad; Corander, Jukka; Méric, Guillaume; Sheppard, Samuel K.; Blom, Jochen

2015-01-01

Campylobacter jejuni is a highly diverse species of bacteria commonly associated with infectious intestinal disease of humans and zoonotic carriage in poultry, cattle, pigs, and other animals. The species contains a large number of distinct clonal complexes that vary from host generalist lineages commonly found in poultry, livestock, and human disease cases to host-adapted specialized lineages primarily associated with livestock or poultry. Here, we present novel data on the ST403 clonal complex of C. jejuni, a lineage that has not been reported in avian hosts. Our data show that the lineage exhibits a distinctive pattern of intralineage recombination that is accompanied by the presence of lineage-specific restriction-modification systems. Furthermore, we show that the ST403 complex has undergone gene decay at a number of loci. Our data provide a putative link between the lack of association with avian hosts of C. jejuni ST403 and both gene gain and gene loss through nonsense mutations in coding sequences of genes, resulting in pseudogene formation. PMID:25795671

Dynamic pathway modeling of signal transduction networks: a domain-oriented approach.

PubMed

Conzelmann, Holger; Gilles, Ernst-Dieter

2008-01-01

Mathematical models of biological processes become more and more important in biology. The aim is a holistic understanding of how processes such as cellular communication, cell division, regulation, homeostasis, or adaptation work, how they are regulated, and how they react to perturbations. The great complexity of most of these processes necessitates the generation of mathematical models in order to address these questions. In this chapter we provide an introduction to basic principles of dynamic modeling and highlight both problems and chances of dynamic modeling in biology. The main focus will be on modeling of s transduction pathways, which requires the application of a special modeling approach. A common pattern, especially in eukaryotic signaling systems, is the formation of multi protein signaling complexes. Even for a small number of interacting proteins the number of distinguishable molecular species can be extremely high. This combinatorial complexity is due to the great number of distinct binding domains of many receptors and scaffold proteins involved in signal transduction. However, these problems can be overcome using a new domain-oriented modeling approach, which makes it possible to handle complex and branched signaling pathways.

Site-Specific Expression of Polycomb-Group Genes Encoding the HPC-HPH/PRC1 Complex in Clinically Defined Primary Nodal and Cutaneous Large B-Cell Lymphomas

PubMed Central

Raaphorst, Frank M.; Vermeer, Maarten; Fieret, Elly; Blokzijl, Tjasso; Dukers, Danny; Sewalt, Richard G.A.B.; Otte, Arie P.; Willemze, Rein; Meijer, Chris J.L.M.

2004-01-01

Polycomb-group (PcG) genes preserve cell identity by gene silencing, and contribute to regulation of lymphopoiesis and malignant transformation. We show that primary nodal large B-cell lymphomas (LBCLs), and secondary cutaneous deposits from such lymphomas, abnormally express the BMI-1, RING1, and HPH1 PcG genes in cycling neoplastic cells. By contrast, tumor cells in primary cutaneous LBCLs lacked BMI-1 expression, whereas RING1 was variably detected. Lack of BMI-1 expression was characteristic for primary cutaneous LBCLs, because other primary extranodal LBCLs originating from brain, testes, and stomach were BMI-1-positive. Expression of HPH1 was rarely detected in primary cutaneous LBCLs of the head or trunk and abundant in primary cutaneous LBCLs of the legs, which fits well with its earlier recognition as a distinct clinical pathological entity with different clinical behavior. We conclude that clinically defined subclasses of primary LBCLs display site-specific abnormal expression patterns of PcG genes of the HPC-HPH/PRC1 PcG complex. Some of these patterns (such as the expression profile of BMI-1) may be diagnostically relevant. We propose that distinct expression profiles of PcG genes results in abnormal formation of HPC-HPH/PRC1 PcG complexes, and that this contributes to lymphomagenesis and different clinical behavior of clinically defined LBCLs. PMID:14742259

Neon ion beam induced pattern formation on amorphous carbon surfaces

NASA Astrophysics Data System (ADS)

Bobes, Omar; Hofsäss, Hans; Zhang, Kun

2018-02-01

We investigate the ripple pattern formation on amorphous carbon surfaces at room temperature during low energy Ne ion irradiation as a function of the ion incidence angle. Monte Carlo simulations of the curvature coefficients applied to the Bradley-Harper and Cater-Vishnyakov models, including the recent extensions by Harrison-Bradley and Hofsäss predict that pattern formation on amorphous carbon thin films should be possible for low energy Ne ions from 250 eV up to 1500 eV. Moreover, simulations are able to explain the absence of pattern formation in certain cases. Our experimental results are compared with prediction using current linear theoretical models and applying the crater function formalism, as well as Monte Carlo simulations to calculate curvature coefficients using the SDTrimSP program. Calculations indicate that no patterns should be generated up to 45° incidence angle if the dynamic behavior of the thickness of the ion irradiated layer introduced by Hofsäss is taken into account, while pattern formation most pronounced from 50° for ion energy between 250 eV and 1500 eV, which are in good agreement with our experimental data.

Formation, Migration, and Reactivity of Au CO Complexes on Gold Surfaces

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Jun; McEntee, Monica; Tang, Wenjie

2016-01-12

Here, we report experimental as well as theoretical evidence that suggests Au CO complex formation upon the exposure of CO to active sites (step edges and threading dislocations) on a Au(111) surface. Room-temperature scanning tunneling microscopy (STM), X-ray photoelectron spectroscopy, transmission infrared spectroscopy, and density functional theory calculations point to Au CO complex formation and migration. Room-temperature STM of the Au(111) surface at CO pressures in the range from 10^ 8 to 10^ 4 Torr (dosage up to 10^6 langmuir) indicates Au atom extraction from dislocation sites of the herringbone reconstruction, mobile Au CO complex formation and diffusion, and Aumore » adatom cluster formation on both elbows and step edges on the Au surface. The formation and mobility of the Au CO complex result from the reduced Au Au bonding at elbows and step edges leading to stronger Au CO bonding and to the formation of a more positively charged CO (CO +) on Au. These studies indicate that the mobile Au CO complex is involved in the Au nanoparticle formation and reactivity, and that the positive charge on CO increases due to the stronger adsorption of CO at Au sites with lower coordination numbers.« less

Polariton Pattern Formation and Photon Statistics of the Associated Emission

NASA Astrophysics Data System (ADS)

Whittaker, C. E.; Dzurnak, B.; Egorov, O. A.; Buonaiuto, G.; Walker, P. M.; Cancellieri, E.; Whittaker, D. M.; Clarke, E.; Gavrilov, S. S.; Skolnick, M. S.; Krizhanovskii, D. N.

2017-07-01

We report on the formation of a diverse family of transverse spatial polygon patterns in a microcavity polariton fluid under coherent driving by a blue-detuned pump. Patterns emerge spontaneously as a result of energy-degenerate polariton-polariton scattering from the pump state to interfering high-order vortex and antivortex modes, breaking azimuthal symmetry. The interplay between a multimode parametric instability and intrinsic optical bistability leads to a sharp spike in the value of second-order coherence g(2 )(0 ) of the emitted light, which we attribute to the strongly superlinear kinetics of the underlying scattering processes driving the formation of patterns. We show numerically by means of a linear stability analysis how the growth of parametric instabilities in our system can lead to spontaneous symmetry breaking, predicting the formation and competition of different pattern states in good agreement with experimental observations.

Relationships between chromosome structure and chromosomal aberrations

NASA Astrophysics Data System (ADS)

Eidelman, Yuri; Andreev, Sergey

An interphase nucleus of human lymphocyte was simulated by the novel Monte Carlo tech-nique. The main features of interphase chromosome structure and packaging were taken into account: different levels of chromatin organisation; nonrandom localisation of chromosomes within a nucleus; chromosome loci dynamics. All chromosomes in a nucleus were modelled as polymer globules. A dynamic pattern of intra/interchromosomal contacts was simulated. The detailed information about chromosomal contacts, such as distribution of intrachromoso-mal contacts over the length of each chromosome and dependence of contact probability on genomic separation between chromosome loci, were calculated and compared to the new exper-imental data obtained by the Hi-C technique. Types and frequencies of simple and complex radiation-induced chromosomal exchange aberrations (CA) induced by X-rays were predicted with taking formation and decay of chromosomal contacts into account. Distance dependence of exchange formation probability was calculated directly. mFISH data for human lymphocytes were analysed. The calculated frequencies of simple CA agreed with the experimental data. Complex CA were underestimated despite the dense packaging of chromosome territories within a nucleus. Possible influence of chromosome-nucleus structural organisation on the frequency and spectrum of radiation-induced chromosome aberrations is discussed.

Identifying metabolic pathways for production of extracellular polymeric substances by the diatom Fragilariopsis cylindrus inhabiting sea ice.

PubMed

Aslam, Shazia N; Strauss, Jan; Thomas, David N; Mock, Thomas; Underwood, Graham J C

2018-05-01

Diatoms are significant primary producers in sea ice, an ephemeral habitat with steep vertical gradients of temperature and salinity characterizing the ice matrix environment. To cope with the variable and challenging conditions, sea ice diatoms produce polysaccharide-rich extracellular polymeric substances (EPS) that play important roles in adhesion, cell protection, ligand binding and as organic carbon sources. Significant differences in EPS concentrations and chemical composition corresponding to temperature and salinity gradients were present in sea ice from the Weddell Sea and Eastern Antarctic regions of the Southern Ocean. To reconstruct the first metabolic pathway for EPS production in diatoms, we exposed Fragilariopsis cylindrus, a key bi-polar diatom species, to simulated sea ice formation. Transcriptome profiling under varying conditions of EPS production identified a significant number of genes and divergent alleles. Their complex differential expression patterns under simulated sea ice formation was aligned with physiological and biochemical properties of the cells, and with field measurements of sea ice EPS characteristics. Thus, the molecular complexity of the EPS pathway suggests metabolic plasticity in F. cylindrus is required to cope with the challenging conditions of the highly variable and extreme sea ice habitat.

Utilization of oriented crystal growth for screening of aromatic carboxylic acids cocrystallization with urea

NASA Astrophysics Data System (ADS)

Przybyłek, Maciej; Ziółkowska, Dorota; Kobierski, Mirosław; Mroczyńska, Karina; Cysewski, Piotr

2016-01-01

The possibility of molecular complex formation in the solid state of urea with benzoic acid analogues was measured directly on the crystallite films deposited on the glass surface using powder X-ray diffractometry (PXRD). Obtained solid mixtures were also analyzed using Fourier transform infrared spectroscopy (FTIR). The simple droplet evaporation method was found to be efficient, robust, fast and cost-preserving approach for first stage cocrystal screening. Additionally, the application of orientation effect to cocrystal screening simplifies the analysis due to damping of majority of diffraction signals coming from coformers. During validation phase the proposed approach successfully reproduced both positive cases of cocrystallization (urea:salicylic acid and urea:4-hydroxy benzoic acid) as well as pairs of co-formers immiscible in the solid state (urea:benzoic acid and urea:acetylsalicylic acids). Based on validated approach new cocrystals of urea were identified in complexes with 3-hydroxybenzoic acid, 2,4-dihydroxybenzoic acid, 2,5-dihydroxybenzoic acid, 2,6-dihydroxybenzoic acid and 3,5-dihydroxybenzoic acid. In all cases formation of multicomponent crystal phase was confirmed by the appearance of new reflexes on the diffraction patterns and FTIR absorption band shifts of O-H and N-H groups.

The elementome of calcium-based urinary stones and its role in urolithiasis

PubMed Central

Ramaswamy, Krishna; Killilea, David W.; Kapahi, Pankaj; Kahn, Arnold J.; Chi, Thomas; Stoller, Marshall L.

2016-01-01

Urolithiasis affects around 10% of the US population with an increasing rate of prevalence, recurrence and penetrance. The causes for the formation of most urinary calculi remain poorly understood, but obtaining the chemical composition of these stones might help identify key aspects of this process and new targets for treatment. The majority of urinary stones are composed of calcium that is complexed in a crystalline matrix with organic and inorganic components. Surprisingly, mitigation of urolithiasis risk by altering calcium homeostasis has not been very effective. Thus, studies to identify other therapeutic stone-specific targets, using proteomics, metabolomics and microscopy techniques, have been conducted, revealing a high level of complexity. The data suggest that numerous metals other than calcium and many nonmetals are present within calculi at measurable levels and several have distinct distribution patterns. Manipulation of the levels of some of these elemental components of calcium-based stones has resulted in clinically beneficial changes in stone chemistry and rate of stone formation. The elementome—the full spectrum of elemental content—of calcium-based urinary calculi is emerging as a new concept in stone research that continues to provide important insights for improved understanding and prevention of urinary stone disease. PMID:26334088

Stochastic nonlinear dynamics pattern formation and growth models

PubMed Central

Yaroslavsky, Leonid P

2007-01-01

Stochastic evolutionary growth and pattern formation models are treated in a unified way in terms of algorithmic models of nonlinear dynamic systems with feedback built of a standard set of signal processing units. A number of concrete models is described and illustrated by numerous examples of artificially generated patterns that closely imitate wide variety of patterns found in the nature. PMID:17908341

Dynamic Pattern Formation in Electron-Beam-Induced Etching [Emergent formation of dynamic topographic patterns in electron beam induced etching

DOE PAGES

Martin, Aiden A.; Bahm, Alan; Bishop, James; ...

2015-12-15

Here, we report highly ordered topographic patterns that form on the surface of diamond, span multiple length scales, and have a symmetry controlled by the precursor gas species used in electron-beam-induced etching (EBIE). The pattern formation dynamics reveals an etch rate anisotropy and an electron energy transfer pathway that is overlooked by existing EBIE models. Therefore, we, modify established theory such that it explains our results and remains universally applicable to EBIE. Furthermore, the patterns can be exploited in controlled wetting, optical structuring, and other emerging applications that require nano- and microscale surface texturing of a wide band-gap material.

A novel host factor for integration of mycobacteriophage L5

PubMed Central

Pedulla, Marisa L.; Lee, Mong Hong; Lever, Dawn C.; Hatfull, Graham F.

1996-01-01

Bacterial integration host factors (IHFs) play central roles in the cellular processes of recombination, DNA replication, transcription, and bacterial pathogenesis. We describe here a novel mycobacterial IHF (mIHF) of Mycobacterium smegmatis and Mycobacterium tuberculosis that stimulates integration of mycobacteriophage L5. mIHF is the product of a single gene and is unrelated at the sequence level to other integration host factors. By itself, mIHF does not bind preferentially to attP DNA, although it significantly alters the pattern of integrase (Int) binding, promoting the formation of specific integrase–mIHF–attP intasome complexes. PMID:8986825

Peering Through a Martian Veil: ALHA84001 Sm-Nd Age Revisited

NASA Technical Reports Server (NTRS)

Nyquist, Laurence E.; Shih, Chi-Yu

2013-01-01

The ancient Martian orthopyroxenite ALH84001experienced a complex history of impact and aqueous alteration events. Here we summarize Sm-147-Nd-143 and Sm-146-Nd-142 analyses performed at JSC. Further, using REE data, we model the REE abundance pattern of the basaltic magma parental to ALH84001 cumulus orthopyroxene. We find the Sm-146-Nd-142 isotopic data to be consistent with isotopic evolution in material having the modeled Sm/Nd ratio from a time very close to the planet's formation to igneous crystallization of ALH84001 as inferred from the Sm-Nd studies.

Lamination cooling system formation method

DOEpatents

Rippel, Wally E [Altadena, CA; Kobayashi, Daryl M [Monrovia, CA

2012-06-19

An electric motor, transformer or inductor having a cooling system. A stack of laminations have apertures at least partially coincident with apertures of adjacent laminations. The apertures define straight or angled cooling-fluid passageways through the lamination stack. Gaps between the adjacent laminations are sealed by injecting a heat-cured sealant into the passageways, expelling excess sealant, and heat-curing the lamination stack. Manifold members adjoin opposite ends of the lamination stack, and each is configured with one or more cavities to act as a manifold to adjacent passageway ends. Complex manifold arrangements can create bidirectional flow in a variety of patterns.

Lamination cooling system formation method

DOEpatents

Rippel, Wally E [Altadena, CA; Kobayashi, Daryl M [Monrovia, CA

2009-05-12

An electric motor, transformer or inductor having a cooling system. A stack of laminations have apertures at least partially coincident with apertures of adjacent laminations. The apertures define straight or angled cooling-fluid passageways through the lamination stack. Gaps between the adjacent laminations are sealed by injecting a heat-cured sealant into the passageways, expelling excess sealant, and heat-curing the lamination stack. Manifold members adjoin opposite ends of the lamination stack, and each is configured with one or more cavities to act as a manifold to adjacent passageway ends. Complex manifold arrangements can create bidirectional flow in a variety of patterns.

Method for shallow junction formation

DOEpatents

Weiner, K.H.

1996-10-29

A doping sequence is disclosed that reduces the cost and complexity of forming source/drain regions in complementary metal oxide silicon (CMOS) integrated circuit technologies. The process combines the use of patterned excimer laser annealing, dopant-saturated spin-on glass, silicide contact structures and interference effects creates by thin dielectric layers to produce source and drain junctions that are ultrashallow in depth but exhibit low sheet and contact resistance. The process utilizes no photolithography and can be achieved without the use of expensive vacuum equipment. The process margins are wide, and yield loss due to contact of the ultrashallow dopants is eliminated. 8 figs.

Method for shallow junction formation

DOEpatents

Weiner, Kurt H.

1996-01-01

A doping sequence that reduces the cost and complexity of forming source/drain regions in complementary metal oxide silicon (CMOS) integrated circuit technologies. The process combines the use of patterned excimer laser annealing, dopant-saturated spin-on glass, silicide contact structures and interference effects creates by thin dielectric layers to produce source and drain junctions that are ultrashallow in depth but exhibit low sheet and contact resistance. The process utilizes no photolithography and can be achieved without the use of expensive vacuum equipment. The process margins are wide, and yield loss due to contact of the ultrashallow dopants is eliminated.

High-throughput preparation of complex multi-scale patterns from block copolymer/homopolymer blend films.

PubMed

Park, Hyungmin; Kim, Jae-Up; Park, Soojin

2012-02-21

A simple, straightforward process for fabricating multi-scale micro- and nanostructured patterns from polystyrene-block-poly(2-vinylpyridine) (PS-b-P2VP)/poly(methyl methacrylate) (PMMA) homopolymer in a preferential solvent for PS and PMMA is demonstrated. When the PS-b-P2VP/PMMA blend films were spin-coated onto a silicon wafer, PS-b-P2VP micellar arrays consisting of a PS corona and a P2VP core were formed, while the PMMA macrodomains were isolated, due to the macrophase separation caused by the incompatibility between block copolymer micelles and PMMA homopolymer during the spin-coating process. With an increase of PMMA composition, the size of PMMA macrodomains increased. Moreover, the P2VP blocks have a strong interaction with a native oxide of the surface of the silicon wafer, so that the P2VP wetting layer was first formed during spin-coating, and PS nanoclusters were observed on the PMMA macrodomains beneath. Whereas when a silicon surface was modified with a PS brush layer, the PS nanoclusters underlying PMMA domains were not formed. The multi-scale patterns prepared from copolymer micelle/homopolymer blend films are used as templates for the fabrication of gold nanoparticle arrays by incorporating the gold precursor into the P2VP chains. The combination of nanostructures prepared from block copolymer micellar arrays and macrostructures induced by incompatibility between the copolymer and the homopolymer leads to the formation of complex, multi-scale surface patterns by a simple casting process. This journal is © The Royal Society of Chemistry 2012

Attack Coverage in High-Level Men’s Volleyball: Organization on the Edge of Chaos?

PubMed Central

Laporta, Lorenzo; Nikolaidis, Pantelis; Thomas, Luke; Afonso, José

2015-01-01

Change is pervasive, but emerging patterns are occasionally detectable through analysis of systemic behaviors. Match analysis uses these patterns in order to reduce the degree of improvisation and to optimize the training process. However, it is possible that certain game phases elude systematic patterning. In this vein, our aim was to analyze the case of attack coverage in men’s volleyball, as we suspected it would elude systematic patterning and has received negligible attention in scientific research. We analyzed the occurrence of attack coverage in 4544 plays of the 2011 Volleyball World League. A Chi-square test with residual adjusted values was applied to explore significant associations between variables. A Monte Carlo correction was applied, as some cells had n<5. Effect sizes were determined using Cramer’s V. Overall, attack coverage occurred in 3.89% of ball possessions, and 23 distinct structures emerged. These structures lacked significant associations with the game complex, setting zone, and effect of attack coverage. Conversely, attack coverage structures showed significant associations with the attack zone and tempo, with very strong effect sizes (V=0.472 and V=0.521, respectively). As certain attack zones are deeply associated with attack tempo, it is apparent that quicker attack plays affect attack coverage structuring, promoting the formation of less complex structures. Ultimately, attack coverage structures seem to depend on momentary constraints, thereby rendering rigid systematization impracticable. Still, we contended that a principle-based approach might be suitable. This invites researchers to rethink how to interpret game regularities. PMID:26557208

Polycomb-Mediated Repression and Sonic Hedgehog Signaling Interact to Regulate Merkel Cell Specification during Skin Development

PubMed Central

Bar, Carmit; Tsai, Pai-Chi; Valdes, Victor J.; Cohen, Idan; Santoriello, Francis J.; Zhao, Dejian; Hsu, Ya-Chieh; Ezhkova, Elena

2016-01-01

An increasing amount of evidence indicates that developmental programs are tightly regulated by the complex interplay between signaling pathways, as well as transcriptional and epigenetic processes. Here, we have uncovered coordination between transcriptional and morphogen cues to specify Merkel cells, poorly understood skin cells that mediate light touch sensations. In murine dorsal skin, Merkel cells are part of touch domes, which are skin structures consisting of specialized keratinocytes, Merkel cells, and afferent neurons, and are located exclusively around primary hair follicles. We show that the developing primary hair follicle functions as a niche required for Merkel cell specification. We find that intraepidermal Sonic hedgehog (Shh) signaling, initiated by the production of Shh ligand in the developing hair follicles, is required for Merkel cell specification. The importance of Shh for Merkel cell formation is further reinforced by the fact that Shh overexpression in embryonic epidermal progenitors leads to ectopic Merkel cells. Interestingly, Shh signaling is common to primary, secondary, and tertiary hair follicles, raising the possibility that there are restrictive mechanisms that regulate Merkel cell specification exclusively around primary hair follicles. Indeed, we find that loss of Polycomb repressive complex 2 (PRC2) in the epidermis results in the formation of ectopic Merkel cells that are associated with all hair types. We show that PRC2 loss expands the field of epidermal cells competent to differentiate into Merkel cells through the upregulation of key Merkel-differentiation genes, which are known PRC2 targets. Importantly, PRC2-mediated repression of the Merkel cell differentiation program requires inductive Shh signaling to form mature Merkel cells. Our study exemplifies how the interplay between epigenetic and morphogen cues regulates the complex patterning and formation of the mammalian skin structures. PMID:27414999

Polycomb-Mediated Repression and Sonic Hedgehog Signaling Interact to Regulate Merkel Cell Specification during Skin Development.

PubMed

Perdigoto, Carolina N; Dauber, Katherine L; Bar, Carmit; Tsai, Pai-Chi; Valdes, Victor J; Cohen, Idan; Santoriello, Francis J; Zhao, Dejian; Zheng, Deyou; Hsu, Ya-Chieh; Ezhkova, Elena

2016-07-01

An increasing amount of evidence indicates that developmental programs are tightly regulated by the complex interplay between signaling pathways, as well as transcriptional and epigenetic processes. Here, we have uncovered coordination between transcriptional and morphogen cues to specify Merkel cells, poorly understood skin cells that mediate light touch sensations. In murine dorsal skin, Merkel cells are part of touch domes, which are skin structures consisting of specialized keratinocytes, Merkel cells, and afferent neurons, and are located exclusively around primary hair follicles. We show that the developing primary hair follicle functions as a niche required for Merkel cell specification. We find that intraepidermal Sonic hedgehog (Shh) signaling, initiated by the production of Shh ligand in the developing hair follicles, is required for Merkel cell specification. The importance of Shh for Merkel cell formation is further reinforced by the fact that Shh overexpression in embryonic epidermal progenitors leads to ectopic Merkel cells. Interestingly, Shh signaling is common to primary, secondary, and tertiary hair follicles, raising the possibility that there are restrictive mechanisms that regulate Merkel cell specification exclusively around primary hair follicles. Indeed, we find that loss of Polycomb repressive complex 2 (PRC2) in the epidermis results in the formation of ectopic Merkel cells that are associated with all hair types. We show that PRC2 loss expands the field of epidermal cells competent to differentiate into Merkel cells through the upregulation of key Merkel-differentiation genes, which are known PRC2 targets. Importantly, PRC2-mediated repression of the Merkel cell differentiation program requires inductive Shh signaling to form mature Merkel cells. Our study exemplifies how the interplay between epigenetic and morphogen cues regulates the complex patterning and formation of the mammalian skin structures.

Multi-scale Fracture Patterns Associated with a Complex Anticline Structure: Insights from Field Outcrop Analogues of the Jebel Hafit Pericline, Al Ain-UAE

NASA Astrophysics Data System (ADS)

Kokkalas, S.; Jones, R. R.; Long, J. J.; Zampos, M.; Wilkinson, M. W.; Gilment, S.

2017-12-01

The formation of folds and their associated fracture patterns plays an important role in controlling the migration and concentration of fluids within the upper crust. Prediction of fracture patterns from various fold shapes and kinematics still remains poorly understood in terms of spatial and temporal distribution of fracture sets. Thus, a more detailed field-based multi scale approach is required to better constrain 3D models of fold-fracture relationships, which are critical for reservoir characterization studies. In order to generate reservoir-scale fracture models representative fracture properties across a wider range of scales are needed. For this reason we applied modern geospatial technologies, including terrestrial LiDAR, photogrammetry and satellite images in the asymmetric, east verging, four-way closure Jebel Hafit anticline, in the eastern part of the United Arab Emirates. The excellent surface outcrops allowed the rapid acquisition of extensive areas of fracture data from both limbs and fold hinge area of the anticline, even from large areas of steep exposure that are practically inaccessible on foot. The digital outcrops provide longer 1D transects, and 2D or 3D surface datasets and give more robust data, particularly for fracture heights, lengths, spacing, clustering, termination and connectivity. The fracture patterns across the folded structure are more complex than those predicted from conceptual models and geomechanical fracture modeling. Mechanical layering, pre-existing structures and sedimentation during fold growth seem to exert a critical influence in the development of fracture systems within Jebel Hafit anticline and directly affect fracture orientations, spacing/intensity, segmentation and connectivity. Seismic and borehole data provide additional constraints on the sub-surface fold geometry and existence of large-scale thrusting in the core of the anticline. The complexity of the relationship between fold geometry and fracture intensity is presented and the implications for prediction of fracture networks in naturally fractured reservoirs are discussed.

Modeling and simulation of multiphase multicomponent multiphysics porous media flows in the context of chemical enhanced oil recovery

NASA Astrophysics Data System (ADS)

Dutta, Sourav; Daripa, Prabir; Fluids Team

2015-11-01

One of the most important methods of chemical enhanced oil recovery (EOR) involves the use of complex flooding schemes comprising of various layers of fluids mixed with suitable amounts of polymer or surfactant or both. The fluid flow is characterized by the spontaneous formation of complex viscous fingering patterns which is considered detrimental to oil recovery. Here we numerically study the physics of such EOR processes using a modern, hybrid method based on a combination of a discontinuous, multiscale finite element formulation and the method of characteristics. We investigate the effect of different types of heterogeneity on the fingering mechanism of these complex multiphase flows and determine the impact on oil recovery. We also study the effect of surfactants on the dynamics of the flow via reduction of capillary forces and increase in relative permeabilities. Supported by the grant NPRP 08-777-1-141 from the Qatar National Research Fund (a member of The Qatar Foundation).

Influence of dose rate on the induction of simple and complex chromosome exchanges by gamma rays.

PubMed

Loucas, Bradford D; Eberle, Richard; Bailey, Susan M; Cornforth, Michael N

2004-10-01

Single-color painting of whole chromosomes, or protocols in which only a few chromosomes are distinctively painted, will always fail to detect a proportion of complex exchanges because they frequently produce pseudosimple painting patterns that are indistinguishable from those produced by bona fide simple exchanges. When 24-color multi-fluor FISH (mFISH) was employed for the purpose of distinguishing (truly) simple from pseudosimple exchanges, it was confirmed that the acute low-LET radiation dose-response relationship for simple exchanges lacked significant upward curvature. This result has been interpreted to indicate that the formation of simple exchanges requires only one chromosome locus be damaged (e.g. broken) by radiation to initiate an exchange-not two, as classical cytogenetic theory maintains. Because a one-lesion mechanism implies single-track action, it follows that the production of simple exchanges should not be influenced by changes in dose rate. To examine this prediction, we irradiated noncycling primary human fibroblasts with graded doses of (137)Cs gamma rays at an acute dose rate of 1.10 Gy/min and compared, using mFISH, the yield of simple exchanges to that observed after exposure to the same radiation delivered at a chronic dose rate of 0.08 cGy/min. The shape of the dose response was found to be quasi-linear for both dose rates, but, counter to providing support for a one-lesion mechanism, the yield of simple aberrations was greatly reduced by protracted exposure. Although chronic doses were delivered at rates low enough to produce damage exclusively by single-track action, this did not altogether eliminate the formation of complex aberrations, an analysis of which leads to the conclusion that a single track of low-LET radiation is capable of inducing complex exchanges requiring up to four proximate breaks for their formation. For acute exposures, the ratio of simple reciprocal translocations to simple dicentrics was near unity.

Spatio-temporal dynamics induced by competing instabilities in two asymmetrically coupled nonlinear evolution equations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schüler, D.; Alonso, S.; Bär, M.

2014-12-15

Pattern formation often occurs in spatially extended physical, biological, and chemical systems due to an instability of the homogeneous steady state. The type of the instability usually prescribes the resulting spatio-temporal patterns and their characteristic length scales. However, patterns resulting from the simultaneous occurrence of instabilities cannot be expected to be simple superposition of the patterns associated with the considered instabilities. To address this issue, we design two simple models composed by two asymmetrically coupled equations of non-conserved (Swift-Hohenberg equations) or conserved (Cahn-Hilliard equations) order parameters with different characteristic wave lengths. The patterns arising in these systems range from coexistingmore » static patterns of different wavelengths to traveling waves. A linear stability analysis allows to derive a two parameter phase diagram for the studied models, in particular, revealing for the Swift-Hohenberg equations, a co-dimension two bifurcation point of Turing and wave instability and a region of coexistence of stationary and traveling patterns. The nonlinear dynamics of the coupled evolution equations is investigated by performing accurate numerical simulations. These reveal more complex patterns, ranging from traveling waves with embedded Turing patterns domains to spatio-temporal chaos, and a wide hysteretic region, where waves or Turing patterns coexist. For the coupled Cahn-Hilliard equations the presence of a weak coupling is sufficient to arrest the coarsening process and to lead to the emergence of purely periodic patterns. The final states are characterized by domains with a characteristic length, which diverges logarithmically with the coupling amplitude.« less

Dancing your moves away: How memory retrieval shapes complex motor action.

PubMed

Tempel, Tobias; Loran, Igor; Frings, Christian

2015-09-01

Human memory is subject to continuous change. Besides the accumulation of contents as a consequence of encoding new information, the accessing of memory influences later accessibility. The authors investigated how retrieval-related memory-shaping processes affect intentionally acquired complex motion patterns. Dance figures served as the material to be learned. The authors found that selectively retrieving a subset of dance moves facilitated later recall of the retrieved dance figures, whereas figures that were related to these but that did not receive selective practice suffered from forgetting. These opposing effects were shown in experiments with different designs involving either the learning of only 1 set of body movements or 2 sets of movements categorized into 2 dances. A 3rd experiment showed that selective restudy also entailed a recall benefit for restudied dance figures but did not induce forgetting for related nonrestudied dance figures. The results suggest that motor programs representing the motion patterns in a format closely corresponding to parameters of movement execution were affected. The reported experiments demonstrate how retrieval determines motor memory plasticity and emphasize the importance of separating restudy and retrieval practice when teaching people new movements. (c) 2015 APA, all rights reserved).

Extrinsic curvature, geometric optics, and lamellar order on curved substrates

NASA Astrophysics Data System (ADS)

Kamien, Randall D.; Nelson, David R.; Santangelo, Christian D.; Vitelli, Vincenzo

2009-11-01

When thermal energies are weak, two-dimensional lamellar structures confined on a curved substrate display complex patterns arising from the competition between layer bending and compression in the presence of geometric constraints. We present broad design principles to engineer the geometry of the underlying substrate so that a desired lamellar pattern can be obtained by self-assembly. Two distinct physical effects are identified as key factors that contribute to the interaction between the shape of the underlying surface and the resulting lamellar morphology. The first is a local ordering field for the direction of each individual layer, which tends to minimize its curvature with respect to the three-dimensional embedding. The second is a nonlocal effect controlled by the intrinsic geometry of the surface that forces the normals to the (nearly incompressible) layers to lie on geodesics, leading to caustic formation as in optics. As a result, different surface morphologies with predominantly positive or negative Gaussian curvature can act as converging or diverging lenses, respectively. By combining these ingredients, as one would with different optical elements, complex lamellar morphologies can be obtained. This smectic optometry enables the manipulation of lamellar configurations for the design of materials.

Discovering Network Structure Beyond Communities

NASA Astrophysics Data System (ADS)

Nishikawa, Takashi; Motter, Adilson E.

2011-11-01

To understand the formation, evolution, and function of complex systems, it is crucial to understand the internal organization of their interaction networks. Partly due to the impossibility of visualizing large complex networks, resolving network structure remains a challenging problem. Here we overcome this difficulty by combining the visual pattern recognition ability of humans with the high processing speed of computers to develop an exploratory method for discovering groups of nodes characterized by common network properties, including but not limited to communities of densely connected nodes. Without any prior information about the nature of the groups, the method simultaneously identifies the number of groups, the group assignment, and the properties that define these groups. The results of applying our method to real networks suggest the possibility that most group structures lurk undiscovered in the fast-growing inventory of social, biological, and technological networks of scientific interest.

Silver clusters encapsulated in C{sub 60}: A density functional study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dhiman, Shobhna; Kumar, Ranjan; Dharamvir, Keya

2015-08-28

We explore the possibility of formation of endohedral complexes of Ag{sub n} atoms (n=1-9) inside C{sub 60} molecule using density functional theory and molecular dynamics. The obtained results reveal that Ag{sub n} (n=8) atoms can form stable complexes with the C{sub 60} molecule. Encapsulation of large number of Ag{sub n} atoms (n>8) make C{sub 60} cage instable, showing distortion of cage. Binding energy/atom increases with the number of Ag atoms up to n=4, after that it increases. Ionization potential decreases till n=4 and then increases, electron affinity increases till n=4 and then shows oscillatory nature as a function of Agmore » atoms inside the cage. Homo –Lumo gap shows no systematic pattern. Our results agreed well with the data available.« less

Dynamics of localized structures in reaction-diffusion systems induced by delayed feedback

NASA Astrophysics Data System (ADS)

Gurevich, Svetlana V.

2013-05-01

We are interested in stability properties of a single localized structure in a three-component reaction-diffusion system subjected to the time-delayed feedback. We shall show that variation in the product of the delay time and the feedback strength leads to complex dynamical behavior of the system, including formation of target patterns, spontaneous motion, and spontaneous breathing as well as various complex structures, arising from combination of different oscillatory instabilities. In the case of spontaneous motion, we provide a bifurcation analysis of the delayed system and derive an order parameter equation for the position of the localized structure, explicitly describing its temporal evolution in the vicinity of the bifurcation point. This equation is a subject to a nonlinear delay differential equation, which can be transformed to the normal form of the pitchfork drift bifurcation.

How Escherichia coli lands and forms cell clusters on a surface: a new role of surface topography

PubMed Central

Gu, Huan; Chen, Aaron; Song, Xinran; Brasch, Megan E.; Henderson, James H.; Ren, Dacheng

2016-01-01

Bacterial response to surface topography during biofilm formation was studied using 5 μm tall line patterns of poly (dimethylsiloxane) (PDMS). Escherichia coli cells attached on top of protruding line patterns were found to align more perpendicularly to the orientation of line patterns when the pattern narrowed. Consistently, cell cluster formation per unit area on 5 μm wide line patterns was reduced by 14-fold compared to flat PDMS. Contrasting the reduced colony formation, cells attached on narrow patterns were longer and had higher transcriptional activities, suggesting that such unfavorable topography may present a stress to attached cells. Results of mutant studies indicate that flagellar motility is involved in the observed preference in cell orientation on narrow patterns, which was corroborated by the changes in cell rotation pattern before settling on different surface topographies. These findings led to a set of new design principles for creating antifouling topographies, which was validated using 10 μm tall hexagonal patterns. PMID:27412365

First report of charge-transfer induced heat-set hydrogel. Structural insights and remarkable properties

NASA Astrophysics Data System (ADS)

Bhattacharjee, Subham; Maiti, Bappa; Bhattacharya, Santanu

2016-05-01

The remarkable ability of a charge-transfer (CT) complex prepared from a pyrene-based donor (Py-D) and a naphthalenediimide-based acceptor (NDI-A) led to the formation of a deep-violet in color, transparent hydrogel at room temperature (RT-gel). Simultaneously, the RT-gel was diluted beyond its critical gelator concentration (CGC) to obtain a transparent sol. Very interestingly, the resultant sol, on heating above 70 °C, transformed into a heat-set gel instantaneously with a hitherto unknown CGC value. Detailed studies revealed the smaller globular aggregates of the RT-gels fuse to form giant globules upon heating, which, in turn, resulted in heat-set gelation through further aggregation. The thermoresponsive property of Py-D alone and 1 : 1 Py-D : NDI-A CT complex was investigated in detail which revealed the hydrophobic collapse of the oxyethylene chains of the CT complex upon heating was mainly responsible for heat-set gelation. Thixotropy, injectability, as well as stimuli responsiveness of the RT-gels were also addressed. In contrast, heat-set gel did not show thixotropic behavior. The X-ray diffraction (XRD) patterns of the xerogel depicted lamellar packing of the CT stacks in the gel phase. Single crystal XRD studies further evidenced the 1 : 1 mixed CT stack formation in the lamellae and also ruled out orthogonal hydrogen bonding possibilities among the hydrazide unit in the CT gel although such interaction was observed in a single crystal of NDI-A alone. In addition, a Ag+-ion triggered metallogelation of NDI-A and nematic liquid-crystalline property of Py-D were also observed.The remarkable ability of a charge-transfer (CT) complex prepared from a pyrene-based donor (Py-D) and a naphthalenediimide-based acceptor (NDI-A) led to the formation of a deep-violet in color, transparent hydrogel at room temperature (RT-gel). Simultaneously, the RT-gel was diluted beyond its critical gelator concentration (CGC) to obtain a transparent sol. Very interestingly, the resultant sol, on heating above 70 °C, transformed into a heat-set gel instantaneously with a hitherto unknown CGC value. Detailed studies revealed the smaller globular aggregates of the RT-gels fuse to form giant globules upon heating, which, in turn, resulted in heat-set gelation through further aggregation. The thermoresponsive property of Py-D alone and 1 : 1 Py-D : NDI-A CT complex was investigated in detail which revealed the hydrophobic collapse of the oxyethylene chains of the CT complex upon heating was mainly responsible for heat-set gelation. Thixotropy, injectability, as well as stimuli responsiveness of the RT-gels were also addressed. In contrast, heat-set gel did not show thixotropic behavior. The X-ray diffraction (XRD) patterns of the xerogel depicted lamellar packing of the CT stacks in the gel phase. Single crystal XRD studies further evidenced the 1 : 1 mixed CT stack formation in the lamellae and also ruled out orthogonal hydrogen bonding possibilities among the hydrazide unit in the CT gel although such interaction was observed in a single crystal of NDI-A alone. In addition, a Ag+-ion triggered metallogelation of NDI-A and nematic liquid-crystalline property of Py-D were also observed. Electronic supplementary information (ESI) available: General experimental section, synthesis and characterization, single crystal X-ray data including CIF files and additional experimental results. See DOI: 10.1039/c6nr01128d

Microbial bebop: creating music from complex dynamics in microbial ecology.

PubMed

Larsen, Peter; Gilbert, Jack

2013-01-01

In order for society to make effective policy decisions on complex and far-reaching subjects, such as appropriate responses to global climate change, scientists must effectively communicate complex results to the non-scientifically specialized public. However, there are few ways however to transform highly complicated scientific data into formats that are engaging to the general community. Taking inspiration from patterns observed in nature and from some of the principles of jazz bebop improvisation, we have generated Microbial Bebop, a method by which microbial environmental data are transformed into music. Microbial Bebop uses meter, pitch, duration, and harmony to highlight the relationships between multiple data types in complex biological datasets. We use a comprehensive microbial ecology, time course dataset collected at the L4 marine monitoring station in the Western English Channel as an example of microbial ecological data that can be transformed into music. Four compositions were generated (www.bio.anl.gov/MicrobialBebop.htm.) from L4 Station data using Microbial Bebop. Each composition, though deriving from the same dataset, is created to highlight different relationships between environmental conditions and microbial community structure. The approach presented here can be applied to a wide variety of complex biological datasets.

Encapsulation of CO2 into amorphous alpha-cyclodextrin powder at different moisture contents - Part 2: Characterization of complexed powders and determination of crystalline structure.

PubMed

Ho, Thao M; Howes, Tony; Jack, Kevin S; Bhandari, Bhesh R

2016-09-01

This study aims to characterize CO2-α-cyclodextrin (α-CD) inclusion complexes produced from amorphous α-CD powder at moisture contents (MC) close to or higher than the critical level of crystallization (e.g. 13, 15 and 17% MC on wet basis, w.b.) at 0.4 and 1.6MPa pressure for 72h. The results of (13)C NMR, SEM, DSC and X-ray analyses showed that these MC levels were high enough to induce crystallization of CO2-α-CD complexed powders during encapsulation, by which amount of CO2 encapsulated by amorphous α-CD powder was significantly increased. The formation of inclusion complexes were well confirmed by results of FTIR and (13)C NMR analyses through an appearance of a peak associated with CO2 on the FTIR (2334cm(-1)) and NMR (125.3ppm) spectra. Determination of crystal packing patterns of CO2-α-CD complexed powders showed that during crystallization, α-CD molecules were arranged in cage-type structure in which CO2 molecules were entrapped in isolated cavities. Copyright © 2016 Elsevier Ltd. All rights reserved.

3D Numerical Models of the Effect of Diking on the Faulting Pattern at Incipient Continental Rifts and Steady-State Spreading Centers

NASA Astrophysics Data System (ADS)

Tian, X.; Choi, E.; Buck, W. R.

2015-12-01

The offset of faults and related topographic relief varies hugely at both continental rifts and mid-ocean ridges (MORs). In some areas fault offset is measured in 10s of meters while in places marked by core complexes it is measured in 10s of kilometers. Variation in the magma supply is thought to control much of these differences. Magma supply is most usefully described by the ratio (M) between rates of lithospheric extension accommodated by magmatic dike intrusion and that occurring via faulting. 2D models with different values of M successfully explain much of the observed cross-sectional structure seen at rifts and ridges. However, magma supply varies along the axis of extension and the interactions between the tectonics and magmatism are inevitably three-dimensional. We investigate the consequences of this along-axis variation in diking in terms of faulting patterns and the associated structures using a 3D parallel geodynamic modeling code, SNAC. Many observed 3D structural features are reproduced: e.g., abyssal hill, oceanic core complex (OCC), inward fault jump, mass wasting, hourglass-shaped median valley, corrugation and mullion structure. An estimated average value of M = 0.65 is suggested as a boundary value for separating abyssal hills and OCCs formation. Previous inconsistency in the M range for OCC formation between 2D model results (M = 0.3˜0.5) and field observations (M < 0.3 or M > 0.5) is reconciled by the along-ridge coupling between different faulting regimes. We also propose asynchronous faulting-induced tensile failure as a new possibility for explaining corrugations seen on the surface of core complexes. For continental rifts, we will describe a suite of 2D and 3D model calculations with a range of initial lithospheric structures and values of M. In one set of the 2D models we limit the extensional tectonic force and show how this affects the maximum topographic relief produced across the rift. We are also interested in comparing models in which the value of M varies as the rift evolves with observations from real rifts and continental margins. Finally, we plan to show how the faulting pattern in 3D can depend on the distribution of dike opening rate along segments for incipient continental rifts.

Structural and functional features of formate hydrogen lyase, an enzyme of mixed-acid fermentation from Escherichia coli.

PubMed

Bagramyan, K; Trchounian, A

2003-11-01

Formate hydrogen lyase from Escherichia coli is a membrane-bound complex that oxidizes formic acid to carbon dioxide and molecular hydrogen. Under anaerobic growth conditions and fermentation of sugars (glucose), it exists in two forms. One form is constituted by formate dehydrogenase H and hydrogenase 3, and the other one is the same formate dehydrogenase and hydrogenase 4; the presence of small protein subunits, carriers of electrons, is also probable. Other proteins may also be involved in formation of the enzyme complex, which requires the presence of metal (nickel-cobalt). Its formation also depends on the external pH and the presence of formate. Activity of both forms requires F(0)F(1)-ATPase; this explains dependence of the complex functioning on proton-motive force. It is also possible that the formate hydrogen lyase complex will exhibit its own proton-translocating function.

Controlled evaporative self-assembly of confined microfluids: A route to complex ordered structures

NASA Astrophysics Data System (ADS)

Byun, Myunghwan

The evaporative self-assembly of nonvolatile solutes such as polymers, nanocrystals, and carbon nanotubes has been widely recognized as a non-lithographic means of producing a diverse range of intriguing complex structures. Due to the spatial variation of evaporative flux and possible convection, however, these non-equilibrium dissipative structures (e.g., fingering patterns and polygonal network structures) are often irregularly and stochastically organized. Yet for many applications in microelectronics, data storage devices, and biotechnology, it is highly desirable to achieve surface patterns having a well-controlled spatial arrangement. To date, only a few elegant studies have centered on precise control over the evaporation process to produce ordered structures. In a remarked comparison with conventional lithography techniques, surface patterning by controlled solvent evaporation is simple and cost-effective, offering a lithography- and external field-free means to organize nonvolatile materials into ordered microscopic structures over large surface areas. The ability to engineer an evaporative self-assembly process that yields a wide range of complex, self-organizing structures over large areas offers tremendous potential for applications in electronics, optoelectronics, and bio- or chemical sensors. We developed a facile, robust tool for evaporating polymer, nanoparticle, or DNA solutions in curve-on-flat geometries to create versatile, highly regular microstructures, including hierarchically structured polymer blend rings, conjugated polymer "snake-skins", block copolymer stripes, and punch-hole-like meshes, biomolecular microring arrays, etc. The mechanism of structure formation was elucidated both experimentally and theoretically. Our method further enhances current fabrication approaches to creating highly ordered structures in a simple and cost-effective manner, envisioning the potential to be tailored for use in photonics, optoelectronics, microfluidic devices, nanotechnology and biotechnology, etc.

The socio-genetics of a complex society: female gelada relatedness patterns mirror association patterns in a multilevel society.

PubMed

Snyder-Mackler, Noah; Alberts, Susan C; Bergman, Thore J

2014-12-01

Multilevel societies with fission-fusion dynamics--arguably the most complex animal societies--are defined by two or more nested levels of organization. The core of these societies are modular social units that regularly fission and fuse with one another. Despite convergent evolution in disparate taxa, we know strikingly little about how such societies form and how fitness benefits operate. Understanding the kinship structure of complex societies could inform us about the origins of the social structure as well as about the potential for individuals in these societies to accrue indirect fitness benefits. Here, we combined genetic and behavioural data on geladas (Theropithecus gelada), an Old World Monkey, to complete the most comprehensive socio-genetic analysis of a multilevel society to date. In geladas, individuals in the core social 'units', associate at different frequencies to form 'teams', 'bands' and, the largest aggregations, 'communities'. Units were composed of closely related females, and females remained with their close kin during permanent fissions of units. Interestingly, female-female relatedness also significantly predicted between-unit, between-team and between-band association patterns, while male-male relatedness did not. Thus, it is likely that the socio-genetic structure of gelada society results from females maintaining associations with their female relatives during successive unit fissions--possibly in an attempt to balance the direct and indirect fitness benefits of group living. Overall, the persistence of associations among related females across generations appears to drive the formation of higher levels of gelada society, suggesting that females seek kin for inclusive fitness benefits at multiple levels of gelada society. © 2014 John Wiley & Sons Ltd.

Spiraling patterns in evolutionary models inspired by bacterial games with cyclic dominance

NASA Astrophysics Data System (ADS)

Mobilia, Mauro

2015-03-01

Understanding the mechanisms allowing the maintenance of biodiversity is a central issue in biology. Evolutionary game theory, where the success of one species depends on what the others are doing, provides a promising framework to investigate this complex problem. Experiments on microbial populations have shown that cyclic local interactions promote species coexistence. In this context, rock-paper-scissors games - in which rock crushes scissors, scissors cut paper, and paper wraps rock - are often used to model the dynamics of populations in cyclic competition. After a brief survey of some inspiring experiments, I will discuss the subtle interplay between individuals' mobility and their local interactions in two-dimensional rock-paper-scissors systems. This leads to the loss of biodiversity above a certain mobility threshold, and to the formation of spiraling patterns below the critical mobility rate. I will then study a generic rock-paper-scissors metapopulation model formulated on a two-dimensional grid of patches. When these have a large carrying capacity, the model's dynamics is faithfully described in terms of the system's complex Ginzburg-Landau equation properly derived from a multiscale expansion. The properties of the ensuing complex Ginzburg-Landau equation are exploited to derive the system's phase diagram and to characterize the spatio-temporal properties of the spiraling patterns in each phase. This enables us to analyze the spiral waves stability, how these are influenced by linear and nonlinear diffusion, and to discuss phenomena such as far-field breakup. Presentation mainy based on joint work with B. Szczesny and A. M. Rucklidge. Fruitful earlier collaborations with E. Frey, Q. He, T. Reichenbach, and U. C. Täuber are also acknowledged. Work supported by the UK EPSRC (Grant No. EP/P505593/1).

Numerical simulation of magma chamber dynamics.

NASA Astrophysics Data System (ADS)

Longo, Antonella; Papale, Paolo; Montagna, Chiara Paola; Vassalli, Melissa; Giudice, Salvatore; Cassioli, Andrea

2010-05-01

Magma chambers are characterized by periodic arrivals of deep magma batches that give origin to complex patterns of magma convection and mixing, and modify the distribution of physical quantities inside the chamber. We simulate the transient, 2D, multi-component homogeneous dynamics in geometrically complex dyke+chamber systems, by means of GALES, a finite element parallel C++ code solving mass, momentum and energy equations for multi-component homogeneous gas-liquid (± crystals) mixtures in compressible-to-incompressible flow conditions. Code validation analysis includes several cases from the classical engineering literature, corresponding to a variety of subsonic to supersonic gas-liquid flow regimes (see http://www.pi.ingv.it/~longo/gales/gales.html). The model allows specification of the composition of the different magmas in the domain, in terms of ten major oxides plus the two volatile species H2O and CO2. Gas-liquid thermodynamics are modeled by using the compositional dependent, non-ideal model in Papale et al. (Chem.. Geol., 2006). Magma properties are defined in terms of local pressure, temperature, and composition including volatiles. Several applications are performed within domains characterized by the presence of one or more magma chambers and one or more dykes, with different geometries and characteristic size from hundreds of m to several km. In most simulations an initial compositional interface is placed at the top of a feeding dyke, or at larger depth, with the deeper magma having a lower density as a consequence of larger volatile content. The numerical results show complex patterns of magma refilling in the chamber, with alternating phases of magma ingression and magma sinking from the chamber into the feeding dyke. Intense mixing takes place in feeding dykes, so that the new magma entering the chamber is always a mixture of the deep and the initially resident magma. Buoyant plume rise occurs through the formation of complex convective patterns, giving origin to a density-stratified magma chamber.

Identifying gene coexpression networks underlying the dynamic regulation of wood-forming tissues in Populus under diverse environmental conditions.

PubMed

Zinkgraf, Matthew; Liu, Lijun; Groover, Andrew; Filkov, Vladimir

2017-06-01

Trees modify wood formation through integration of environmental and developmental signals in complex but poorly defined transcriptional networks, allowing trees to produce woody tissues appropriate to diverse environmental conditions. In order to identify relationships among genes expressed during wood formation, we integrated data from new and publically available datasets in Populus. These datasets were generated from woody tissue and include transcriptome profiling, transcription factor binding, DNA accessibility and genome-wide association mapping experiments. Coexpression modules were calculated, each of which contains genes showing similar expression patterns across experimental conditions, genotypes and treatments. Conserved gene coexpression modules (four modules totaling 8398 genes) were identified that were highly preserved across diverse environmental conditions and genetic backgrounds. Functional annotations as well as correlations with specific experimental treatments associated individual conserved modules with distinct biological processes underlying wood formation, such as cell-wall biosynthesis, meristem development and epigenetic pathways. Module genes were also enriched for DNase I hypersensitivity footprints and binding from four transcription factors associated with wood formation. The conserved modules are excellent candidates for modeling core developmental pathways common to wood formation in diverse environments and genotypes, and serve as testbeds for hypothesis generation and testing for future studies. No claim to original US government works. New Phytologist © 2017 New Phytologist Trust.

Numerical Simulation of the Global Star Formation Pattern in the LMC

NASA Astrophysics Data System (ADS)

Gardiner, L. T.; Turfus, C.

Dottori et al. (1996, ApJ 461, 742) have recently presented evidence for the idea that the observed distribution of young star clusters in the Large Magellanic Cloud (LMC) has resulted from the gravitational perturbation induced by a bar potential offset from the LMC disk center. We have constructed a dynamical model of the LMC to examine the effects of such an off-center perturbation on the global distribution of the gas and star formation activity. We have used a newly developed hybrid N-body/cellular automaton scheme for modeling star formation in galaxies which incorporates the dual mechanisms of gravitational instability and self-propagating star formation, combined with feedback of kinetic energy from star-forming regions into the interstellar medium. We find that a weak rotating bar perturbation, whose center is displaced by 0.6 kpc from the disk center, gives rise to an asymmetric spiral structure which mimics the chains of recent star formation observed in the LMC as well as delineating activity in the bar region. Large gas concentrations are produced where the spiral arms merge in the northern part of the galaxy, and such structures may have observed counterparts in giant star-forming complexes such as Constellation III in the NE part of the LMC.

Patterns of pair formation and mating in an ectoparasitic caligid copepod Lepeophtheirus salmonis (Krøyer 1837): implications for its sensory and mating biology

PubMed Central

Hull, M. Q.

1998-01-01

Non-invasive observations of single cohort and manipulated populations of the sealouse on laboratory-maintained salmon established the sequence of reproductive events and mating. Protandry occurs with adult male emergence synchronized with pre-adult II female emergence, the stage at which most pair formation and pre-copular guarding takes place. Male competence for pair formation and mating was achieved within 24 h of the final moult and pairing occurred according to the preference hierarchy, virgin adult females greater than pre-adult II females much greater than pre-adult I females. This hierarchy broke down when the adult male to unmated female ratio increased rapidly. Males mated successfully not only with newly moulted adult females, but also with older virgin females in which enlargement of the genital complex and premature extrusion of egg strings had occurred. Multiple mating by adult males was demonstrated and may be widespread. Significant inter-host transfer was also demonstrated. Adult males were more mobile than adult females and showed significantly more inter-host transfer. Ablation of the distal tip of the antennules significantly reduced the success of host-finding, pair formation and males' mating.

Complex chromatin condensation patterns and nuclear protein transitions during spermiogenesis: examples from mollusks.

PubMed

Chiva, M; Saperas, N; Ribes, E

2011-12-01

In this paper we review and analyze the chromatin condensation pattern during spermiogenesis in several species of mollusks. Previously, we had described the nuclear protein transitions during spermiogenesis in these species. The results of our study show two types of condensation pattern: simple patterns and complex patterns, with the following general characteristics: (a) When histones (always present in the early spermatid nucleus) are directly replaced by SNBP (sperm nuclear basic proteins) of the protamine type, the spermiogenic chromatin condensation pattern is simple. However, if the replacement is not direct but through intermediate proteins, the condensation pattern is complex. (b) The intermediate proteins found in mollusks are precursor molecules that are processed during spermiogenesis to the final protamine molecules. Some of these final protamines represent proteins with the highest basic amino acid content known to date, which results in the establishment of a very strong electrostatic interaction with DNA. (c) In some instances, the presence of complex patterns of chromatin condensation clearly correlates with the acquisition of specialized forms of the mature sperm nuclei. In contrast, simple condensation patterns always lead to rounded, oval or slightly cylindrical nuclei. (d) All known cases of complex spermiogenic chromatin condensation patterns are restricted to species with specialized sperm cells (introsperm). At the time of writing, we do not know of any report on complex condensation pattern in species with external fertilization and, therefore, with sperm cells of the primitive type (ect-aquasperm). (e) Some of the mollusk an spermiogenic chromatin condensation patterns of the complex type are very similar (almost identical) to those present in other groups of animals. Interestingly, the intermediate proteins involved in these cases can be very different.In this study, we discuss the biological significance of all these features and conclude that the appearance of precursor (intermediate) molecules facilitated the development of complex patterns of condensation and, as a consequence, a great diversity of forms in the sperm cell nuclei Copyright © 2011 Elsevier Ltd. All rights reserved.

Molecular interactions of orthologues of floral homeotic proteins from the gymnosperm Gnetum gnemon provide a clue to the evolutionary origin of 'floral quartets'.

PubMed

Wang, Yong-Qiang; Melzer, Rainer; Theissen, Günter

2010-10-01

Several lines of evidence suggest that the identity of floral organs in angiosperms is specified by multimeric transcription factor complexes composed of MADS-domain proteins. These bind to specific cis-regulatory elements ('CArG-boxes') of their target genes involving DNA-loop formation, thus constituting 'floral quartets'. Gymnosperms, angiosperms' closest relatives, contain orthologues of floral homeotic genes, but when and how the interactions constituting floral quartets were established during evolution has remained unknown. We have comprehensively studied the dimerization and DNA-binding of several classes of MADS-domain proteins from the gymnosperm Gnetum gnemon. Determination of protein-protein and protein-DNA interactions by yeast two-hybrid, in vitro pull-down and electrophoretic mobility shift assays revealed complex patterns of homo- and heterodimerization among orthologues of floral homeotic class B, class C and class E proteins and B(sister) proteins. Using DNase I footprint assays we demonstrate that both orthologues of class B with C proteins, and orthologues of class C proteins alone, but not orthologues of class B proteins alone can loop DNA in floral quartet-like complexes. This is in contrast to class B and class C proteins from angiosperms, which require other factors such as class E floral homeotic proteins to 'glue' them together in multimeric complexes. Our findings suggest that the evolutionary origin of floral quartet formation is based on the interaction of different DNA-bound homodimers, does not depend on class E proteins, and predates the origin of angiosperms. © 2010 The Authors. Journal compilation © 2010 Blackwell Publishing Ltd.

Development of functional ectopic compound eyes in scarabaeid beetles by knockdown of orthodenticle.

PubMed

Zattara, Eduardo E; Macagno, Anna L M; Busey, Hannah A; Moczek, Armin P

2017-11-07

Complex traits like limbs, brains, or eyes form through coordinated integration of diverse cell fates across developmental space and time, yet understanding how complexity and integration emerge from uniform, undifferentiated precursor tissues remains limited. Here, we use ectopic eye formation as a paradigm to investigate the emergence and integration of novel complex structures following massive ontogenetic perturbation. We show that down-regulation via RNAi of a single head patterning gene- orthodenticle -induces ectopic structures externally resembling compound eyes at the middorsal adult head of both basal and derived scarabaeid beetle species (Onthophagini and Oniticellini). Scanning electron microscopy documents ommatidial organization of these induced structures, while immunohistochemistry reveals the presence of rudimentary ommatidial lenses, crystalline cones, and associated neural-like tissue within them. Further, RNA-sequencing experiments show that after orthodenticle down-regulation, the transcriptional signature of the middorsal head-the location of ectopic eye induction-converges onto that of regular compound eyes, including up-regulation of several retina-specific genes. Finally, a light-aversion behavioral assay to assess functionality reveals that ectopic compound eyes can rescue the ability to respond to visual stimuli when wild-type eyes are surgically removed. Combined, our results show that knockdown of a single gene is sufficient for the middorsal head to acquire the competence to ectopically generate a functional compound eye-like structure. These findings highlight the buffering capacity of developmental systems, allowing massive genetic perturbations to be channeled toward orderly and functional developmental outcomes, and render ectopic eye formation a widely accessible paradigm to study the evolution of complex systems. Published under the PNAS license.

Rice No Pollen 1 (NP1) is required for anther cuticle formation and pollen exine patterning.

PubMed

Liu, Ze; Lin, Sen; Shi, Jianxin; Yu, Jing; Zhu, Lu; Yang, Xiujuan; Zhang, Dabing; Liang, Wanqi

2017-07-01

Angiosperm male reproductive organs (anthers and pollen grains) have complex and interesting morphological features, but mechanisms that underlie their patterning are poorly understood. Here we report the isolation and characterization of a male sterile mutant of No Pollen 1 (NP1) in rice (Oryza sativa). The np1-4 mutant exhibited smaller anthers with a smooth cuticle surface, abnormal Ubisch bodies, and aborted pollen grains covered with irregular exine. Wild-type exine has two continuous layers; but np1-4 exine showed a discontinuous structure with large granules of varying size. Chemical analysis revealed reduction in most of the cutin monomers in np1-4 anthers, and less cuticular wax. Map-based cloning suggested that NP1 encodes a putative glucose-methanol-choline oxidoreductase; and expression analyses found NP1 preferentially expressed in the tapetal layer from stage 8 to stage 10 of anther development. Additionally, the expression of several genes involved in biosynthesis and in the transport of lipid monomers of sporopollenin and cutin was decreased in np1-4 mutant anthers. Taken together, these observations suggest that NP1 is required for anther cuticle formation, and for patterning of Ubisch bodies and the exine. We propose that products of NP1 are likely important metabolites in the development of Ubisch bodies and pollen exine, necessary for polymerization, assembly, or both. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

Ultrasonic Nondestructive Evaluation Techniques Applied to the Quantitative Characterization of Textile Composite Materials

NASA Technical Reports Server (NTRS)

Miller, James G.

1997-01-01

In this Progress Report, we describe our further development of advanced ultrasonic nondestructive evaluation methods applied to the characterization of anisotropic materials. We present images obtained from experimental measurements of ultrasonic diffraction patterns transmitted through water only and transmitted through water and a thin woven composite. All images of diffraction patterns have been included on the accompanying CD-ROM in the JPEG format and Adobe TM Portable Document Format (PDF), in addition to the inclusion of hardcopies of the images contained in this report. In our previous semi-annual Progress Report (NAG 1-1848, December, 1996), we proposed a simple model to simulate the effect of a thin woven composite on an insonifying ultrasonic pressure field. This initial approach provided an avenue to begin development of a robust measurement method for nondestructive evaluation of anisotropic materials. In this Progress Report, we extend that work by performing experimental measurements on a single layer of a five-harness biaxial woven composite to investigate how a thin, yet architecturally complex, material interacts with the insonifying ultrasonic field. In Section 2 of this Progress Report we describe the experimental arrangement and methods for data acquisition of the ultrasonic diffraction patterns upon transmission through a thin woven composite. We also briefly describe the thin composite specimen investigated. Section 3 details the analysis of the experimental data followed by the experimental results in Section 4. Finally, a discussion of the observations and conclusions is found in Section 5.

Lineage diversification in a widespread species: roles for niche divergence and conservatism in the common kingsnake, Lampropeltis getula.

PubMed

Alexander Pyron, R; Burbrink, Frank T

2009-08-01

Niche conservatism and niche divergence are both important ecological mechanisms associated with promoting allopatric speciation across geographical barriers. However, the potential for variable responses in widely distributed organisms has not been fully investigated. For allopatric sister lineages, three patterns for the interaction of ecological niche preference and geographical barriers are possible: (i) niche conservatism at a physical barrier; (ii) niche divergence at a physical barrier; and (iii) niche divergence in the absence of a physical barrier. We test for the presence of these patterns in a transcontinentally distributed snake species, the common kingsnake (Lampropeltis getula), to determine the relative frequency of niche conservatism or divergence in a single species complex inhabiting multiple distinct ecoregions. We infer the phylogeographic structure of the kingsnake using a range-wide data set sampled for the mitochondrial gene cytochrome b. We use coalescent simulation methods to test for the presence of structured lineage formation vs. fragmentation of a widespread ancestor. Finally, we use statistical techniques for creating and evaluating ecological niche models to test for conservatism of ecological niche preferences. Significant geographical structure is present in the kingsnake, for which coalescent tests indicate structured population division. Surprisingly, we find evidence for all three patterns of conservatism and divergence. This suggests that ecological niche preferences may be labile on recent phylogenetic timescales, and that lineage formation in widespread species can result from an interaction between inertial tendencies of niche conservatism and natural selection on populations in ecologically divergent habitats.

C-Cbl reverses HER2-mediated tamoxifen resistance in human breast cancer cells.

PubMed

Li, Wei; Xu, Ling; Che, Xiaofang; Li, Haizhou; Zhang, Ye; Song, Na; Wen, Ti; Hou, Kezuo; Yang, Yi; Zhou, Lu; Xin, Xing; Xu, Lu; Zeng, Xue; Shi, Sha; Liu, Yunpeng; Qu, Xiujuan; Teng, Yuee

2018-05-02

Tamoxifen is a frontline therapy for estrogen receptor (ER)-positive breast cancer in premenopausal women. However, many patients develop resistance to tamoxifen, and the mechanism underlying tamoxifen resistance is not well understood. Here we examined whether ER-c-Src-HER2 complex formation is involved in tamoxifen resistance. MTT and colony formation assays were used to measure cell viability and proliferation. Western blot was used to detect protein expression and protein complex formations were detected by immunoprecipitation and immunofluorescence. SiRNA was used to examine the function of HER2 in of BT474 cells. An in vivo xenograft animal model was established to examine the role of c-Cbl in tumor growth. MTT and colony formation assay showed that BT474 cells are resistant to tamoxifen and T47D cells are sensitive to tamoxifen. Immunoprecipitation experiments revealed ER-c-Src-HER2 complex formation in BT474 cells but not in T47D cells. However, ER-c-Src-HER2 complex formation was detected after overexpressing HER2 in T47D cells and these cells were more resistant to tamoxifen. HER2 knockdown by siRNA in BT474 cells reduced ER-c-Src-HER2 complex formation and reversed tamoxifen resistance. ER-c-Src-HER2 complex formation was also disrupted and tamoxifen resistance was reversed in BT474 cells by the c-Src inhibitor PP2 and HER2 antibody trastuzumab. Nystatin, a lipid raft inhibitor, reduced ER-c-Src-HER2 complex formation and partially reversed tamoxifen resistance. ER-c-Src-HER2 complex formation was disrupted by overexpression of c-Cbl but not by the c-Cbl ubiquitin ligase mutant. In addition, c-Cbl could reverse tamoxifen resistance in BT474 cells, but the ubiquitin ligase mutant had no effect. The effect of c-Cbl was validated in BT474 tumor-bearing nude mice in vivo. Immunofluorescence also revealed ER-c-Src-HER2 complex formation was reduced in tumor tissues of nude mice with c-Cbl overexpression. Our results suggested that c-Cbl can reverse tamoxifen resistance in HER2-overexpressing breast cancer cells by inhibiting the formation of the ER-c-Src-HER2 complex.

How regularity representations of short sound patterns that are based on relative or absolute pitch information establish over time: An EEG study.

PubMed

Bader, Maria; Schröger, Erich; Grimm, Sabine

2017-01-01

The recognition of sound patterns in speech or music (e.g., a melody that is played in different keys) requires knowledge about pitch relations between successive sounds. We investigated the formation of regularity representations for sound patterns in an event-related potential (ERP) study. A pattern, which consisted of six concatenated 50 ms tone segments differing in fundamental frequency, was presented 1, 2, 3, 6, or 12 times and then replaced by another pattern by randomly changing the pitch of the tonal segments (roving standard paradigm). In an absolute repetition condition, patterns were repeated identically, whereas in a transposed condition, only the pitch relations of the tonal segments of the patterns were repeated, while the entire patterns were shifted up or down in pitch. During ERP measurement participants were not informed about the pattern repetition rule, but were instructed to discriminate rarely occurring targets of lower or higher sound intensity. EPRs for pattern changes (mismatch negativity, MMN; and P3a) and for pattern repetitions (repetition positivity, RP) revealed that the auditory system is able to rapidly extract regularities from unfamiliar complex sound patterns even when absolute pitch varies. Yet, enhanced RP and P3a amplitudes, and improved behavioral performance measured in a post-hoc test, in the absolute as compared with the transposed condition suggest that it is more difficult to encode patterns without absolute pitch information. This is explained by dissociable processing of standards and deviants as well as a back propagation mechanism to early sensory processing stages, which is effective after less repetitions of a standard stimulus for absolute pitch.

How regularity representations of short sound patterns that are based on relative or absolute pitch information establish over time: An EEG study

PubMed Central

Schröger, Erich; Grimm, Sabine

2017-01-01

The recognition of sound patterns in speech or music (e.g., a melody that is played in different keys) requires knowledge about pitch relations between successive sounds. We investigated the formation of regularity representations for sound patterns in an event-related potential (ERP) study. A pattern, which consisted of six concatenated 50 ms tone segments differing in fundamental frequency, was presented 1, 2, 3, 6, or 12 times and then replaced by another pattern by randomly changing the pitch of the tonal segments (roving standard paradigm). In an absolute repetition condition, patterns were repeated identically, whereas in a transposed condition, only the pitch relations of the tonal segments of the patterns were repeated, while the entire patterns were shifted up or down in pitch. During ERP measurement participants were not informed about the pattern repetition rule, but were instructed to discriminate rarely occurring targets of lower or higher sound intensity. EPRs for pattern changes (mismatch negativity, MMN; and P3a) and for pattern repetitions (repetition positivity, RP) revealed that the auditory system is able to rapidly extract regularities from unfamiliar complex sound patterns even when absolute pitch varies. Yet, enhanced RP and P3a amplitudes, and improved behavioral performance measured in a post-hoc test, in the absolute as compared with the transposed condition suggest that it is more difficult to encode patterns without absolute pitch information. This is explained by dissociable processing of standards and deviants as well as a back propagation mechanism to early sensory processing stages, which is effective after less repetitions of a standard stimulus for absolute pitch. PMID:28472146

Wnt signaling during tooth replacement in zebrafish (Danio rerio): pitfalls and perspectives

PubMed Central

Huysseune, Ann; Soenens, Mieke; Elderweirdt, Fien

2014-01-01

The canonical (β-catenin dependent) Wnt signaling pathway has emerged as a likely candidate for regulating tooth replacement in continuously renewing dentitions. So far, the involvement of canonical Wnt signaling has been experimentally demonstrated predominantly in amniotes. These studies tend to show stimulation of tooth formation by activation of the Wnt pathway, and inhibition of tooth formation when blocking the pathway. Here, we report a strong and dynamic expression of the soluble Wnt inhibitor dickkopf1 (dkk1) in developing zebrafish (Danio rerio) tooth germs, suggesting an active repression of Wnt signaling during morphogenesis and cytodifferentiation of a tooth, and derepression of Wnt signaling during start of replacement tooth formation. To further analyse the role of Wnt signaling, we used different gain-of-function approaches. These yielded disjunct results, yet none of them indicating enhanced tooth replacement. Thus, masterblind (mbl) mutants, defective in axin1, mimic overexpression of Wnt, but display a normally patterned dentition in which teeth are replaced at the appropriate times and positions. Activating the pathway with LiCl had variable outcomes, either resulting in the absence, or the delayed formation, of first-generation teeth, or yielding a regular dentition with normal replacement, but no supernumerary teeth or accelerated tooth replacement. The failure so far to influence tooth replacement in the zebrafish by perturbing Wnt signaling is discussed in the light of (i) potential technical pitfalls related to dose- or time-dependency, (ii) the complexity of the canonical Wnt pathway, and (iii) species-specific differences in the nature and activity of pathway components. Finally, we emphasize the importance of in-depth knowledge of the wild-type pattern for reliable interpretations. It is hoped that our analysis can be inspiring to critically assess and elucidate the role of Wnt signaling in tooth development in polyphyodonts. PMID:25339911

Integrated approaches to terminal Proterozoic stratigraphy: an example from the Olenek Uplift, northeastern Siberia

NASA Technical Reports Server (NTRS)

Knoll, A. H.; Grotzinger, J. P.; Kaufman, A. J.; Kolosov, P.

1995-01-01

In the Olenek Uplift of northeastern Siberia, the Khorbusuonka Group and overlying Kessyusa and Erkeket formations preserve a significant record of terminal Proterozoic and basal Cambrian Earth history. A composite section more than 350 m thick is reconstructed from numerous exposures along the Khorbusuonka River. The Khorbusuonka Group comprises three principal sedimentary sequences: peritidal dolomites of the Mastakh Formation, which are bounded above and below by red beds; the Khatyspyt and most of the overlying Turkut formations, which shallow upward from relatively deep-water carbonaceous micrites to cross-bedded dolomitic grainstones and stromatolites; and a thin upper Turkut sequence bounded by karst surfaces. The overlying Kessyusa Formation is bounded above and below by erosional surfaces and contains additional parasequence boundaries internally. Ediacaran metazoans, simple trace fossils, and vendotaenids occur in the Khatyspyt Formation; small shelly fossils, more complex trace fossils, and acritarchs all appear near the base of the Kessyusa Formation and diversify upward. The carbon-isotopic composition of carbonates varies stratigraphically in a pattern comparable to that determined for other terminal Proterozoic and basal Cambrian successions. In concert, litho-, bio-, and chemostratigraphic data indicate the importance of the Khorbusuonka Group in the global correlation of terminal Proterozoic sedimentary rocks. Stratigraphic data and a recently determined radiometric date on basal Kessyusa volcanic breccias further underscore the significance of the Olenek region in investigations of the Proterozoic-cambrian boundary.

Integrated approaches to terminal Proterozoic stratigraphy: an example from the Olenek Uplift, northeastern Siberia.

PubMed

Knoll, A H; Grotzinger, J P; Kaufman, A J; Kolosov, P

1995-01-01

In the Olenek Uplift of northeastern Siberia, the Khorbusuonka Group and overlying Kessyusa and Erkeket formations preserve a significant record of terminal Proterozoic and basal Cambrian Earth history. A composite section more than 350 m thick is reconstructed from numerous exposures along the Khorbusuonka River. The Khorbusuonka Group comprises three principal sedimentary sequences: peritidal dolomites of the Mastakh Formation, which are bounded above and below by red beds; the Khatyspyt and most of the overlying Turkut formations, which shallow upward from relatively deep-water carbonaceous micrites to cross-bedded dolomitic grainstones and stromatolites; and a thin upper Turkut sequence bounded by karst surfaces. The overlying Kessyusa Formation is bounded above and below by erosional surfaces and contains additional parasequence boundaries internally. Ediacaran metazoans, simple trace fossils, and vendotaenids occur in the Khatyspyt Formation; small shelly fossils, more complex trace fossils, and acritarchs all appear near the base of the Kessyusa Formation and diversify upward. The carbon-isotopic composition of carbonates varies stratigraphically in a pattern comparable to that determined for other terminal Proterozoic and basal Cambrian successions. In concert, litho-, bio-, and chemostratigraphic data indicate the importance of the Khorbusuonka Group in the global correlation of terminal Proterozoic sedimentary rocks. Stratigraphic data and a recently determined radiometric date on basal Kessyusa volcanic breccias further underscore the significance of the Olenek region in investigations of the Proterozoic-cambrian boundary.

Soilscapes in the dynamic tropical environments: The case of Sierra Madre del Sur

NASA Astrophysics Data System (ADS)

Krasilnikov, P. V.; García-Calderón, N. E.; Ibáñez-Huerta, A.; Bazán-Mateos, M.; Hernández-Santana, J. R.

2011-12-01

The paper gives an analysis of the pattern of soil cover of the Sierra Madre del Sur, one of the most complex physiographic regions of Mexico. It presents the results of the study of four latitudinal traverses across the region. We show that the distribution of soils in the Sierra Madre del Sur is associated with major climatic gradients, namely by vertical bioclimatic zonality in the mountains and by the effect of mountain shadow. Altitudinal distribution of soil-bioclimatic belts is complex due to non-uniform gradients of temperature and rainfall, and varies with the configuration of the mountain range. The distribution of soils is associated with the erosion and accumulation rates both on mountain slopes and in river valleys. The abundance of poorly developed soils in (semi)arid areas was ascribed to high erosion rate rather than to low pedogenetic potential. The formation of soil mosaic at a larger scale might be ascribed to the complex net of gully erosion and to the system of seismically triggered landslides of various ages. In the valleys, the distribution of soils depends upon the dynamics of sedimentation and erosion, which eventually exposes paleosols. Red-colored clayey sediments are remains of ancient weathering and pedogenesis. Their distribution is associated mainly with the intensity of recent slope processes. The soil cover pattern of the Sierra Madre del Sur cannot be explained by simplified schemes of bioclimatic zonality. The soil ranges can be explained by the distribution of climates, lithology, complex geological history of the region, and recent geomorphological processes.

GRAIL Gravity Observations of the Transition from Complex Crater to Peak-Ring Basin on the Moon: Implications for Crustal Structure and Impact Basin Formation

NASA Technical Reports Server (NTRS)

Baker, David M. H.; Head, James W.; Phillips, Roger J.; Neumann, Gregory A.; Bierson, Carver J.; Smith, David E.; Zuber, Maria T.

2017-01-01

High-resolution gravity data from the Gravity Recovery and Interior Laboratory (GRAIL) mission provide the opportunity to analyze the detailed gravity and crustal structure of impact features in the morphological transition from complex craters to peak-ring basins on the Moon. We calculate average radial profiles for free-air anomalies and Bouguer anomalies for peak-ring basins, proto-basins, and the largest complex craters. Complex craters and proto-basins have free-air anomalies that are positively correlated with surface topography, unlike the prominent lunar mascons (positive free-air anomalies in areas of low elevation) associated with large basins. The Bouguer gravity anomaly profiles of complex craters are highly irregular, with central positive anomalies that are generally absent or not clearly tied to interior morphology. In contrast, gravity profiles for peak-ring basins (approx. 200 km to 580 km) are much more regular and are highly correlated with surface morphology. A central positive Bouguer anomaly is confined within the peak ring and a negative Bouguer anomaly annulus extends from the edge of the positive anomaly outward to about the rim crest. A number of degraded basins lacking interior peak rings have diameters and gravity patterns similar to those of well-preserved peak-ring basins. If these structures represent degraded peak-ring basins, the number of peak-ring basins on the Moon would increase by more than a factor of two to 34. The gravity anomalies within basins are interpreted to be due to uplift of the mantle confined within the peak ring and an annulus of thickened crust between the peak ring and rim crest. We hypothesize that mantle uplift is influenced by interaction between the transient cavity and the mantle. Further, mascon formation is generally disconnected from the number of basin rings formed and occurs over a wide range of basin sizes. These observations have important implications for models of basin and mascon formation on the Moon and other planetary bodies.

Disruption of direct 3D telomere-TRF2 interaction through two molecularly disparate mechanisms is a hallmark of primary Hodgkin and Reed-Sternberg cells.

PubMed

Knecht, Hans; Johnson, Nathalie A; Haliotis, Tina; Lichtensztejn, Daniel; Mai, Sabine

2017-07-01

In classical Hodgkin's lymphoma (cHL), specific changes in the 3D telomere organization cause progression from mononuclear Hodgkin cells (H) to multinucleated Reed-Sternberg cells (RS). In a post-germinal center B-cell in vitro model, permanent latent membrane protein 1 (LMP1) expression, as observed in Epstein-Barr virus (EBV)-associated cHL, results in multinuclearity and complex chromosomal aberrations through downregulation of key element of the shelterin complex, the telomere repeat binding factor 2 (TRF2). Thus, we hypothesized that the three-dimensional (3D) telomere-TRF2 interaction was progressively disturbed during transition from H to RS cells. To this end, we developed and applied for the first time a combined quantitative 3D TRF2-telomere immune fluorescent in situ hybridization (3D TRF2/Telo-Q-FISH) technique to monolayers of primary H and RS cells, and adjacent benign internal control lymphocytes of lymph node biopsy suspensions from diagnostic lymph node biopsies of 14 patients with cHL. We show that H and RS cells are characterized by two distinct patterns of disruption of 3D telomere-TRF2 interaction. Disruption pattern A is defined by massive attrition of telomere signals and a considerable increase of TRF2 signals not associated with telomeres. This pattern is restricted to EBV-negative cHL. Disruption pattern B is defined by telomere de-protection due to an impressive loss of TRF2 signals, physically linked to telomeres. This pattern is typical of, but is not restricted to, LMP1+EBV-associated cHL. In the disruption pattern B group, so-called 'ghost' end-stage RS cells, void of both TRF2 and telomere signals, were identified, whether or not associated with EBV. Our findings demonstrate that two molecularly disparate mechanisms converge on the level of 3D telomere-TRF2 interaction in the formation of RS cells.

Positional information in axolotl and mouse limb extracellular matrix is mediated via heparan sulfate and fibroblast growth factor during limb regeneration in the axolotl (Ambystoma mexicanum).

PubMed

Phan, Anne Q; Lee, Jangwoo; Oei, Michelle; Flath, Craig; Hwe, Caitlyn; Mariano, Rachele; Vu, Tiffany; Shu, Cynthia; Dinh, Andrew; Simkin, Jennifer; Muneoka, Ken; Bryant, Susan V; Gardiner, David M

2015-08-01

Urodele amphibians are unique among adult vertebrates in their ability to regenerate complex body structures after traumatic injury. In salamander regeneration, the cells maintain a memory of their original position and use this positional information to recreate the missing pattern. We used an in vivo gain-of-function assay to determine whether components of the extracellular matrix (ECM) have positional information required to induce formation of new limb pattern during regeneration. We discovered that salamander limb ECM has a position-specific ability to either inhibit regeneration or induce de novo limb structure, and that this difference is dependent on heparan sulfates that are associated with differential expression of heparan sulfate sulfotransferases. We also discovered that an artificial ECM containing only heparan sulfate was sufficient to induce de novo limb pattern in salamander limb regeneration. Finally, ECM from mouse limbs is capable of inducing limb pattern in axolotl blastemas in a position-specific, developmental-stage-specific, and heparan sulfate-dependent manner. This study demonstrates a mechanism for positional information in regeneration and establishes a crucial functional link between salamander regeneration and mammals.

Positional information in axolotl and mouse limb extracellular matrix is mediated via heparan sulfate and fibroblast growth factor during limb regeneration in the axolotl (Ambystoma mexicanum)

PubMed Central

Phan, Anne Q.; Lee, Jangwoo; Oei, Michelle; Flath, Craig; Hwe, Caitlyn; Mariano, Rachele; Vu, Tiffany; Shu, Cynthia; Dinh, Andrew; Simkin, Jennifer; Muneoka, Ken; Bryant, Susan V.

2015-01-01

Abstract Urodele amphibians are unique among adult vertebrates in their ability to regenerate complex body structures after traumatic injury. In salamander regeneration, the cells maintain a memory of their original position and use this positional information to recreate the missing pattern. We used an in vivo gain‐of‐function assay to determine whether components of the extracellular matrix (ECM) have positional information required to induce formation of new limb pattern during regeneration. We discovered that salamander limb ECM has a position‐specific ability to either inhibit regeneration or induce de novo limb structure, and that this difference is dependent on heparan sulfates that are associated with differential expression of heparan sulfate sulfotransferases. We also discovered that an artificial ECM containing only heparan sulfate was sufficient to induce de novo limb pattern in salamander limb regeneration. Finally, ECM from mouse limbs is capable of inducing limb pattern in axolotl blastemas in a position‐specific, developmental‐stage‐specific, and heparan sulfate‐dependent manner. This study demonstrates a mechanism for positional information in regeneration and establishes a crucial functional link between salamander regeneration and mammals. PMID:27499874

Waves and patterning in developmental biology: vertebrate segmentation and feather bud formation as case studies

PubMed Central

Baker, Ruth E.; Schnell, Santiago; Maini, Philip K.

2014-01-01

In this article we will discuss the integration of developmental patterning mechanisms with waves of competency that control the ability of a homogeneous field of cells to react to pattern forming cues and generate spatially heterogeneous patterns. We base our discussion around two well known patterning events that take place in the early embryo: somitogenesis and feather bud formation. We outline mathematical models to describe each patterning mechanism, present the results of numerical simulations and discuss the validity of each model in relation to our example patterning processes. PMID:19557684

Determinants of postfire recovery and succession in mediterranean-climate shrublands of California

USGS Publications Warehouse

Keeley, J.E.; Fotheringham, C.J.; Baer-Keeley, M.

2005-01-01

Evergreen chaparral and semideciduous sage scrub shrublands were studied for five years after fires in order to evaluate hypothesized determinants of postfire recovery and succession. Residual species present in the immediate postfire environment dominated early succession. By the fifth year postfire, roughly half of the species were colonizers not present in the first year, but they comprised only 7-14% cover. Successional changes were evaluated in the context of four hypotheses: (1) event-dependent, (2) fire interval, (3) self-regulatory, and (4) environmental filter hypotheses. Characteristics specific to the fire event, for example, fire severity and annual fluctuations in precipitation, were important determinants of patterns of change in cover and density, supporting the "event-dependent" hypothesis. The "fire interval" hypothesis is also supported, primarily through the impact of short intervals on reproductive failure in obligate seeding shrubs and the impact of long intervals on fuel accumulation and resultant fire severity. Successional changes in woody cover were correlated with decreases in herb cover, indicating support for "self-regulatory" effects. Across this landscape there were strong "environmental filter" effects that resulted in complex patterns of postfire recovery and succession between coastal and interior associations of both vegetation types. Of relevance to fire managers is the finding that postfire recovery patterns are substantially slower in the interior sage scrub formations, and thus require different management strategies than coastal formations. Also, in sage scrub (but not chaparral), prefire stand age is positively correlated with fire severity, and negatively correlated with postfire cover. Differential responses to fire severity suggest that landscapes with combinations of high and low severity may lead to enhanced biodiversity. Predicting postfire management needs is complicated by the fact that vegetation recovery is significantly controlled by patterns of precipitation. ?? 2005 by the Ecological Society of America.

The effect of butterfly-scale inspired patterning on leading-edge vortex growth

NASA Astrophysics Data System (ADS)

Wilroy, Jacob Aaron

Leading edge vortices (LEVs) are important for generating thrust and lift in flapping flight, and the surface patterning (scales) on butterfly wings is hypothesized to play a role in the vortex formation of the LEV. To simplify this complex flow problem, an experiment was designed to focus on the alteration of 2-D vortex development with a variation in surface patterning. Specifically, the secondary vorticity generated by the LEV interacting at the patterned surface was studied, as well as the subsequent effect on the LEV's growth rate and peak circulation. For this experiment, rapid-prototyped grooves based on the scale geometry of the Monarch butterfly (Danaus plexippus) were created using additive manufacturing and were attached to a flat plate with a chordwise orientation, thus increasing plate surface area. The vortex generated by the grooved plate was then compared to a smooth plate case in an experiment where the plate translated vertically through a 2 x 3 x 5 cubic foot tow tank. The plate was impulsively started in quiescent water and flow fields at Rec = 1416, 2833, and 5667 are examined using Digital Particle Image Velocimetry (DPIV). The maximum vortex formation number is 2.8 and is based on the flat plate travel length and chord length. Flow fields from each case show the generation of a secondary vortex whose interaction with the shear layer and LEV caused different behaviors depending upon the surface type. The vortex development process varied for each Reynolds number and it was found that for the lowest Reynolds number case a significant difference does not exist between surface types, however, for the other two cases the grooves affected the secondary vortex's behavior and the LEV's ability to grow at a rate similar to the smooth plate case.

Formation of banded vegetation patterns resulted from interactions between sediment deposition and vegetation growth.

PubMed

Huang, Tousheng; Zhang, Huayong; Dai, Liming; Cong, Xuebing; Ma, Shengnan

2018-03-01

This research investigates the formation of banded vegetation patterns on hillslopes affected by interactions between sediment deposition and vegetation growth. The following two perspectives in the formation of these patterns are taken into consideration: (a) increased sediment deposition from plant interception, and (b) reduced plant biomass caused by sediment accumulation. A spatial model is proposed to describe how the interactions between sediment deposition and vegetation growth promote self-organization of banded vegetation patterns. Based on theoretical and numerical analyses of the proposed spatial model, vegetation bands can result from a Turing instability mechanism. The banded vegetation patterns obtained in this research resemble patterns reported in the literature. Moreover, measured by sediment dynamics, the variation of hillslope landform can be described. The model predicts how treads on hillslopes evolve with the banded patterns. Thus, we provide a quantitative interpretation for coevolution of vegetation patterns and landforms under effects of sediment redistribution. Copyright © 2018. Published by Elsevier Masson SAS.

Evaporation-induced patterns from droplets containing motile and nonmotile bacteria.

PubMed

Nellimoottil, Tittu Thomas; Rao, Pinjala Nagaraju; Ghosh, Siddhartha Sankar; Chattopadhyay, Arun

2007-08-14

In this letter, we report the observations of specific pattern formation from the evaporation of aqueous droplets containing motile and nonmotile bacteria. We found that when motile bacteria were present the droplet evaporated into disclike patterned deposits of bacteria. However, when the bacteria were made nonmotile by treatment with liquid nitrogen, the droplet evaporated into ringlike deposits. We also observed that bacteria with higher motility produced more uniformly deposited disclike patterns. Furthermore, we propose a model with numerical simulations to explain the mechanism of formation of these patterns. The model is based on the advective fluid flow from the center of the droplet toward the edge due to enhanced evaporation from the edge of the pinned droplet in comparison to that from the free surface. For the case of motile bacteria, we have added another velocity parameter toward the axis of the droplet and directed against the fluid flow in order to account for the disclike pattern formation. The numerical simulations match the experimental observations well. The present work, by qualitative and quantitative understanding of the evaporation of bacteria droplets, demonstrates that the inherent bacterial motility is primarily responsible for the formation of these differential patterns.

Complex of solonetzes and vertic chestnut soils in the manych-gudilo depression

NASA Astrophysics Data System (ADS)

Kovda, I. V.; Morgun, E. P.; Il'ina, L. P.

2013-01-01

Morphological, physicochemical, and isotopic properties of a two-member soil complex developed under dry steppe have been studied in the central part of the Manych Depression. The soils are formed on chocolate-colored clayey sediments, and have pronounced microrelief and the complex vegetation pattern. A specific feature of the studied soil complex is the inverse position of its components: vertic chestnut soil occupies the microhigh, while solonetz is in the microlow. The formation of such complexes is explained by the biological factor, i.e., by the destruction of the solonetzic horizon under the impact of vegetation and earth-burrowing animals with further transformation under steppe plants and dealkalinization of the soil in the microhighs. The manifestation of vertic features and shrink-swell process in soils of the complex developing in dry steppe are compared with those in the vertic soils of the Central Pre-Caucasus formed under more humid environment. It is supposed that slickensides in the investigated vertic chestnut soil are relict feature inherited from the former wetter stage of the soil development and are subjected to a gradual degradation at present. In the modern period, vertic processes are weak and cannot be distinctly diagnosed. However, their activation may take place upon an increase of precipitation or the rise in the groundwater level.

Dynamics of spiral patterns in gas discharge detected by optical method

NASA Astrophysics Data System (ADS)

Yang, Fan; Wang, Mingyi; Liu, Shuhua

2016-09-01

The dynamics behavior of spiral patterns is investigated in gas discharge using optical method. Rich kinks of spiral patterns are obtained and the formation and evolution process is investigated. The process of pattern formation is breakdown -> hexagon -> bee comb-like -> strip -> spiral -> chaos. Spiral pattern always formed after the strip pattern. It is found that the temperature of the water electrodes plays an important role in the spiral patterns formation. When it exceeds 20°C no spiral has been obtained. The discharge current waveform and the emission spectrum of the discharge have been measured when the filaments self-organized in spiral pattern. Electron excited temperature of forming spiral pattern is calculated using intensity ratio method. It is found that the electron excited temperature of spiral pattern increase as the power supply frequency increased. Relation between wavelength and discharge parameter has been measured. It shows that the wavelength of spiral pattern increases as the discharge gap increases, and decreases as the air ratio mixed in argon increases. Accompanying measurements proved that the wavelength is approximately linear to the square root of the spiral rotating period .This work has useful reference value for studying pattern dynamics.

Coordination properties of tridentate (N,O,O) heterocyclic alcohol (PDC) with Cu(II). Mixed ligand complex formation reactions of Cu(II) with PDC and some bio-relevant ligands.

PubMed

El-Sherif, Ahmed A; Shoukry, Mohamed M

2007-03-01

The formation equilibria of copper(II) complexes and the ternary complexes Cu(PDC)L (PDC=2,6-bis-(hydroxymethyl)-pyridine, HL=amino acid, amides or DNA constituents) have been investigated. Ternary complexes are formed by a simultaneous mechanism. The results showed the formation of Cu(PDC)L, Cu(PDC, H(-1))(L) and Cu(PDC, H(-2))(L) complexes. The concentration distribution of the complexes in solution is evaluated as a function of pH. The effect of dioxane as a solvent on the protonation constant of PDC and the formation constants of Cu(II) complexes are discussed. The thermodynamic parameters DeltaH degrees and DeltaS degrees calculated from the temperature dependence of the equilibrium constants are investigated.

Differential expression of neuroligin genes in the nervous system of zebrafish.

PubMed

Davey, Crystal; Tallafuss, Alexandra; Washbourne, Philip

2010-02-01

The establishment and maturation of appropriate synaptic connections is crucial in the development of neuronal circuits. Cellular adhesion is believed to play a central role in this process. Neuroligins are neuronal cell adhesion molecules that are hypothesized to act in the initial formation and maturation of synaptic connections. In order to establish the zebrafish as a model to investigate the in vivo role of Neuroligin proteins in nervous system development, we identified the zebrafish orthologs of neuroligin family members and characterized their expression. Zebrafish possess seven neuroligin genes. Synteny analysis and sequence comparisons show that NLGN2, NLGN3, and NLGN4X are duplicated in zebrafish, but NLGN1 has a single zebrafish ortholog. All seven zebrafish neuroligins are expressed in complex patterns in the developing nervous system and in the adult brain. The spatial and temporal expression patterns of these genes suggest that they occupy a role in nervous system development and maintenance.

Modification of surface properties of solids by femtosecond LIPSS writing: comparative studies on silicon and stainless steel

NASA Astrophysics Data System (ADS)

Varlamova, Olga; Hoefner, Kevin; Ratzke, Markus; Reif, Juergen; Sarker, Debasish

2017-12-01

We investigate the implication of modified surface morphology on wettability of stainless steel (AISI 304) and silicon (100) targets covered by laser-induced periodic surface structures (LIPSS) on extended areas (10 × 10 mm2). Using multiple pulses from a Ti: Sapphire laser (790 nm/100 fs/1 kHz) at a fluence in the range of 0.35-2.1 J/cm2 on a spot of 1.13 × 10- 4 cm2, we scanned the target under the spot to cover a large area. A systematical variation of the irradiation dose by changing the scanning speed and thus dwelling time per spot results in the formation of surface patterns ranging from very regular linear structures with a lateral period of about 500-600 nm to complex patterns of 3D microstructures with several-µm feature size, hierarchically covered by nano-ripples.

Changes in magnetic domain structure during twin boundary motion in single crystal Ni-Mn-Ga exhibiting magnetic shape memory effect

NASA Astrophysics Data System (ADS)

Kopecký, V.; Fekete, L.; Perevertov, O.; Heczko, O.

2016-05-01

The complexity of Ni-Mn-Ga single crystal originates from the interplay between ferromagnetic domain structure and ferroelastic twinned microstructure. Magnetic domain structure in the vicinity of single twin boundary was studied using magneto-optical indicator film and magnetic force microscopy technique. The single twin boundary of Type I was formed mechanically and an initial magnetization state in both variants were restored by local application of magnetic field (≈40 kA/m). The differently oriented variants exhibited either stripe or labyrinth magnetic domain pattern in agreement with the uniaxial magnetocrystalline anisotropy of the martensite. The twin boundary was then moved by compressive or tensile stress. The passage of the boundary resulted in the formation of granular or rake domains, respectively. Additionally, the specific magnetic domains pattern projected by twin boundary gradually vanished during twin boundary motion.

Functional signaling and gene regulatory networks between the oocyte and the surrounding cumulus cells.

PubMed

Biase, Fernando H; Kimble, Katelyn M

2018-05-10

The maturation and successful acquisition of developmental competence by an oocyte, the female gamete, during folliculogenesis is highly dependent on molecular interactions with somatic cells. Most of the cellular interactions identified, thus far, are modulated by growth factors, ions or metabolites. We hypothesized that this interaction is also modulated at the transcriptional level, which leads to the formation of gene regulatory networks between the oocyte and cumulus cells. We tested this hypothesis by analyzing transcriptome data from single oocytes and the surrounding cumulus cells collected from antral follicles employing an analytical framework to determine interdependencies at the transcript level. We overlapped our transcriptome data with putative protein-protein interactions and identified hundreds of ligand-receptor pairs that can transduce paracrine signaling between an oocyte and cumulus cells. We determined that 499 ligand-encoding genes expressed in oocytes and cumulus cells are functionally associated with transcription regulation (FDR < 0.05). Ligand-encoding genes with specific expression in oocytes or cumulus cells were enriched for biological functions that are likely associated with the coordinated formation of transzonal projections from cumulus cells that reach the oocyte's membrane. Thousands of gene pairs exhibit significant linear co-expression (absolute correlation > 0.85, FDR < 1.8 × 10 - 5 ) patterns between oocytes and cumulus cells. Hundreds of co-expressing genes showed clustering patterns associated with biological functions (FDR < 0.5) necessary for a coordinated function between the oocyte and cumulus cells during folliculogenesis (i.e. regulation of transcription, translation, apoptosis, cell differentiation and transport). Our analyses revealed a complex and functional gene regulatory circuit between the oocyte and surrounding cumulus cells. The regulatory profile of each cumulus-oocyte complex is likely associated with the oocytes' developmental potential to derive an embryo.

Positronium formation studies in solid molecular complexes: Triphenylphosphine oxide-triphenylmethanol

NASA Astrophysics Data System (ADS)

Oliveira, F. C.; Denadai, A. M. L.; Fulgêncio, F. H.; Magalhães, W. F.; Alcântara, A. F. C.; Windmöller, D.; Machado, J. C.

2012-06-01

Positronium formation in triphenylphosphine oxide (TPPO), triphenylmethanol (TPM), and systems [TPPO(1-X)ṡTPMX] has been studied. The low probability of positronium formation in complex [TPPO0.5ṡTPM0.5] was attributed to strong hydrogen bond and sixfold phenyl embrace interactions. These strong interactions in complex reduce the possibility of the n- and π-electrons to interact with positrons on the spur and consequently, the probability of positronium formation is lower. The τ3 parameter and free volume (correlated to τ3) were also sensitive to the formation of hydrogen bonds and sixfold phenyl embrace interactions within the complex. For physical mixture the positron annihilation parameters remained unchanged throughout the composition range.

A model to explain joint patterns found in ignimbrite deposits

NASA Astrophysics Data System (ADS)

Tibaldi, A.; Bonali, F. L.

2018-03-01

The study of fracture systems is of paramount importance for economic applications, such as CO2 storage in rock successions, geothermal and hydrocarbon exploration and exploitation, and also for a better knowledge of seismogenic fault formation. Understanding the origin of joints can be useful for tectonic studies and for a geotechnical characterisation of rock masses. Here, we illustrate a joint pattern discovered in ignimbrite deposits of South America, which can be confused with conjugate tectonic joint sets but which have another origin. The pattern is probably common, but recognisable only in plan view and before tectonic deformation obscures and overprints it. Key sites have been mostly studied by field surveys in Bolivia and Chile. The pattern is represented by hundreds-of-meters up to kilometre-long swarms of master joints, which show circular to semi-circular geometries and intersections that have "X" and "Y" patterns. Inside each swarm, joints are systematic, rectilinear or curvilinear in plan view, and as much as 900 m long. In section view, they are from sub-vertical to vertical and do not affect the underlying deposits. Joints with different orientation mostly interrupt each other, suggesting they have the same age. This joint architecture is here interpreted as resulting from differential contraction after emplacement of the ignimbrite deposit above a complex topography. The set of the joint pattern that has suitable orientation with respect to tectonic stresses may act to nucleate faults.

A Theoretical Model of Jigsaw-Puzzle Pattern Formation by Plant Leaf Epidermal Cells.

PubMed

Higaki, Takumi; Kutsuna, Natsumaro; Akita, Kae; Takigawa-Imamura, Hisako; Yoshimura, Kenji; Miura, Takashi

2016-04-01

Plant leaf epidermal cells exhibit a jigsaw puzzle-like pattern that is generated by interdigitation of the cell wall during leaf development. The contribution of two ROP GTPases, ROP2 and ROP6, to the cytoskeletal dynamics that regulate epidermal cell wall interdigitation has already been examined; however, how interactions between these molecules result in pattern formation remains to be elucidated. Here, we propose a simple interface equation model that incorporates both the cell wall remodeling activity of ROP GTPases and the diffusible signaling molecules by which they are regulated. This model successfully reproduces pattern formation observed in vivo, and explains the counterintuitive experimental results of decreased cellulose production and increased thickness. Our model also reproduces the dynamics of three-way cell wall junctions. Therefore, this model provides a possible mechanism for cell wall interdigitation formation in vivo.

Melanosome metabolism in the retinal pigmented epithelium of the opossum.

PubMed

Herman, K G; Steinberg, R H

1982-01-01

Melanosomal metabolism, including both formation and degradation of melanosomes, was studied in the retinal pigmented epithelium (RPE) of the adult opossum. The majority of the observations were made on a transitional zone between the tapetal and non-tapetal RPE, the region where melanosome metabolism was at its highest level. Formation of melanosomes, demonstrated ultrastructurally by the presence of stage-II and -III premelanosomes, was also examined autoradiographically following the incorporation of the melanin precursor, dihydroxyphenylalanine. The autoradiographic evidence indicated that many newly formed melanosomes were rapidly incorporated into complexes. Ultrastructural observations suggested that melanosome complexes were formed by at least two methods, via the fusion of melanosomes with phagosomes derived from outer segments of photoreceptors, or by the sequestration of melanosomes by cisternae. A central finding of this study, supported by both ultrastructural and histochemical data, is that there are specialized cellular regions that vary in melanosomal formation and lysosomal activity. Stage-II premelanosomes were observed only in the basal parts of the RPE cells, whereas stage-III and -IV melanosomes were found primarily in the apical RPE. Both ultrastructural and cytochemical observations indicated that degradation of melanosomes occurs only in the basal RPE. These findings are interpreted in terms of the expression of both tapetal and nontapetal characteristics in transitional cells. Finally, this study illustrates the role of lysosomal enzymes in shaping the pattern of pigmentation, and shows that the association of lysosomal activity with melanosomes depends on the functional state of the melanosome.

Ground-State Structure of the Proton-Bound Formate Dimer by Cold-Ion Infrared Action Spectroscopy.

PubMed

Thomas, Daniel; Marianski, Mateusz; Mucha, Eike; Meijer, Gerard; Johnson, Mark A; von Helden, Gert

2018-06-19

The proton-bound dicarboxylate motif, RCOO-·H+·-OOCR, is a prevalent chemical configuration found in many condensed phase systems. We study the archetypal proton-bound formate dimer, HCOO-·H+·-OOCH, utilizing cold-ion infrared action spectroscopy in the photon energy range of 400-1800 cm-1. The spectrum obtained at ~0.4 K utilizing action spectroscopy of ions captured in helium nanodroplets is compared to that measured at ~10 K by photodissociation of Ar-ion complexes. Similar band patterns are obtained by the two techniques that are consistent with calculations for a C2 symmetry structure with a proton shared equally between the two formate moieties. Isotopic substitution experiments point to the nominal parallel stretch of the bridging proton appearing as a sharp, dominant feature near 600 cm-1. Multidimensional anharmonic calculations, however, reveal that the bridging proton motion is strongly coupled to the flanking -COO- framework, an effect that is qualitatively in line with the expected change in -C=O bond rehybridization upon protonation. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Formation kinetics and mechanism of metastable vacancy-dioxygen complex in neutron irradiated Czochralski silicon

NASA Astrophysics Data System (ADS)

Dong, Peng; Wang, Rong; Yu, Xuegong; Chen, Lin; Ma, Xiangyang; Yang, Deren

2017-07-01

We have quantitatively investigated the formation kinetics of metastable vacancy-dioxygen (VO2) complex in a structure of [VO + Oi], where a VO complex is trapped in a next-neighbor position to an interstitial oxygen atom (Oi). It is found that the VO annihilation is accompanied by the generation of metastable [VO + Oi] complex during annealing in the temperature range of 220-250 °C. The activation energy for [VO + Oi] generation appears at around 0.48 eV, which is much lower than the counterpart of stable VO2 complex. This indicates that the formation of [VO + Oi] complex originates from the reaction between VO and Oi. The ab initio calculations show that the formation energy of [VO + Oi] complex is larger than that of VO2 complex, which means that [VO + Oi] complex is thermodynamically unfavorable as compared to VO2 complex. However, the binding energy of [VO + Oi] complex is positive, indicating that [VO + Oi] complex is stable against decomposition of VO and Oi in silicon. It is believed that [VO + Oi] complex serves as the intermediate for VO to VO2 conversion.

Hormone-Mediated Pattern Formation in Seedling of Plants: a Competitive Growth Dynamics Model

NASA Astrophysics Data System (ADS)

Kawaguchi, Satoshi; Mimura, Masayasu; Ohya, Tomoyuki; Oikawa, Noriko; Okabe, Hirotaka; Kai, Shoichi

2001-10-01

An ecologically relevant pattern formation process mediated by hormonal interactions among growing seedlings is modeled based on the experimental observations on the effects of indole acetic acid, which can act as an inhibitor and activator of root growth depending on its concentration. In the absence of any lateral root with constant hormone-sensitivity, the edge effect phenomenon is obtained depending on the secretion rate of hormone from the main root. Introduction of growth-stage-dependent hormone-sensitivity drastically amplifies the initial randomness, resulting in spatially irregular macroscopic patterns. When the lateral root growth is introduced, periodic patterns are obtained whose periodicity depends on the length of lateral roots. The growth-stage-dependent hormone-sensitivity and the lateral root growth are crucial for macroscopic periodic-pattern formation.

Self-organized surface ripple pattern formation by ion implantation

NASA Astrophysics Data System (ADS)

Hofsäss, Hans; Zhang, Kun; Bobes, Omar

2016-10-01

Ion induced ripple pattern formation on solid surfaces has been extensively studied in the past and the theories describing curvature dependent ion erosion as well as redistribution of recoil atoms have been very successful in explaining many features of the pattern formation. Since most experimental studies use noble gas ion irradiation, the incorporation of the ions into the films is usually neglected. In this work we show that the incorporation or implantation of non-volatile ions also leads to a curvature dependent term in the equation of motion of a surface height profile. The implantation of ions can be interpreted as a negative sputter yield; and therefore, the effect of ion implantation is opposite to the one of ion erosion. For angles up to about 50°, implantation of ions stabilizes the surface, whereas above 50°, ion implantation contributes to the destabilization of the surface. We present simulations of the curvature coefficients using the crater function formalism and we compare the simulation results to the experimental data on the ion induced pattern formation using non-volatile ions. We present several model cases, where the incorporation of ions is a crucial requirement for the pattern formation.

Pattern formation in a model for mountain pine beetle dispersal: linking model predictions to data.

PubMed

Strohm, S; Tyson, R C; Powell, J A

2013-10-01

Pattern formation occurs in a wide range of biological systems. This pattern formation can occur in mathematical models because of diffusion-driven instability or due to the interaction between reaction, diffusion, and chemotaxis. In this paper, we investigate the spatial pattern formation of attack clusters in a system for Mountain Pine Beetle. The pattern formation (aggregation) of the Mountain Pine Beetle in order to attack susceptible trees is crucial for their survival and reproduction. We use a reaction-diffusion equation with chemotaxis to model the interaction between Mountain Pine Beetle, Mountain Pine Beetle pheromones, and susceptible trees. Mathematical analysis is utilized to discover the spacing in-between beetle attacks on the susceptible landscape. The model predictions are verified by analysing aerial detection survey data of Mountain Pine Beetle Attack from the Sawtooth National Recreation Area. We find that the distance between Mountain Pine Beetle attack clusters predicted by our model closely corresponds to the observed attack data in the Sawtooth National Recreation Area. These results clarify the spatial mechanisms controlling the transition from incipient to epidemic populations and may lead to control measures which protect forests from Mountain Pine Beetle outbreak.

Is pigment patterning in fish skin determined by the Turing mechanism?

PubMed

Watanabe, Masakatsu; Kondo, Shigeru

2015-02-01

More than half a century ago, Alan Turing postulated that pigment patterns may arise from a mechanism that could be mathematically modeled based on the diffusion of two substances that interact with each other. Over the past 15 years, the molecular and genetic tools to verify this prediction have become available. Here, we review experimental studies aimed at identifying the mechanism underlying pigment pattern formation in zebrafish. Extensive molecular genetic studies in this model organism have revealed the interactions between the pigment cells that are responsible for the patterns. The mechanism discovered is substantially different from that predicted by the mathematical model, but it retains the property of 'local activation and long-range inhibition', a necessary condition for Turing pattern formation. Although some of the molecular details of pattern formation remain to be elucidated, current evidence confirms that the underlying mechanism is mathematically equivalent to the Turing mechanism. Copyright © 2014 Elsevier Ltd. All rights reserved.

From Patterns to Function in Living Systems: Dryland Ecosystems as a Case Study

NASA Astrophysics Data System (ADS)

Meron, Ehud

2018-03-01

Spatial patterns are ubiquitous in animate matter. Besides their intricate structure and beauty they generally play functional roles. The capacity of living systems to remain functional in changing environments is a question of utmost importance, but its intimate relationship to pattern formation is largely unexplored. Here, we address this relationship using dryland vegetation as a case study. Following a brief introduction to pattern-formation theory, we describe a mathematical model that captures several mechanisms of vegetation pattern formation and discuss ecological contexts that showcase different mechanisms. Using this model, we unravel the different vegetation patterns that keep dryland ecosystems viable along the rainfall gradient, identify multistability ranges where fronts separating domains of alternative stable states exist, and highlight the roles of front dynamics in mitigating or reversing desertification. The utility of satellite images in testing model predictions is discussed. An outlook on outstanding open problems concludes this paper.

Investigating the Interaction Pattern and Structural Elements of a Drug-Polymer Complex at the Molecular Level.

PubMed

Nie, Haichen; Mo, Huaping; Zhang, Mingtao; Song, Yang; Fang, Ke; Taylor, Lynne S; Li, Tonglei; Byrn, Stephen R

2015-07-06

Strong associations between drug and polymeric carriers are expected to contribute to higher drug loading capacities and better physical stability of amorphous solid dispersions. However, molecular details of the interaction patterns and underlying mechanisms are still unclear. In the present study, a series of amorphous solid dispersions of clofazimine (CLF), an antileprosy drug, were prepared with different polymers by applying the solvent evaporation method. When using hypromellose phthalate (HPMCP) as the carrier, the amorphous solid dispersion system exhibits not only superior drug loading capacity (63% w/w) but also color change due to strong drug-polymer association. In order to further explain these experimental observations, the interaction between CLF and HPMCP was investigated in a nonpolar volatile solvent system (chloroform) prior to forming the solid dispersion. We observed significant UV/vis and (1)H NMR spectral changes suggesting the protonation of CLF and formation of ion pairs between CLF and HPMCP in chloroform. Furthermore, nuclear Overhauser effect spectroscopy (NOESY) and diffusion order spectroscopy (DOSY) were employed to evaluate the strength of associations between drug and polymers, as well as the molecular mobility of CLF. Finally, by correlating the experimental values with quantum chemistry calculations, we demonstrate that the protonated CLF is binding to the carboxylate group of HPMCP as an ion pair and propose a possible structural model of the drug-polymer complex. Understanding the drug and carrier interaction patterns from a molecular perspective is critical for the rational design of new amorphous solid dispersions.

Bi-PROF

PubMed Central

Gries, Jasmin; Schumacher, Dirk; Arand, Julia; Lutsik, Pavlo; Markelova, Maria Rivera; Fichtner, Iduna; Walter, Jörn; Sers, Christine; Tierling, Sascha

2013-01-01

The use of next generation sequencing has expanded our view on whole mammalian methylome patterns. In particular, it provides a genome-wide insight of local DNA methylation diversity at single nucleotide level and enables the examination of single chromosome sequence sections at a sufficient statistical power. We describe a bisulfite-based sequence profiling pipeline, Bi-PROF, which is based on the 454 GS-FLX Titanium technology that allows to obtain up to one million sequence stretches at single base pair resolution without laborious subcloning. To illustrate the performance of the experimental workflow connected to a bioinformatics program pipeline (BiQ Analyzer HT) we present a test analysis set of 68 different epigenetic marker regions (amplicons) in five individual patient-derived xenograft tissue samples of colorectal cancer and one healthy colon epithelium sample as a control. After the 454 GS-FLX Titanium run, sequence read processing and sample decoding, the obtained alignments are quality controlled and statistically evaluated. Comprehensive methylation pattern interpretation (profiling) assessed by analyzing 102-104 sequence reads per amplicon allows an unprecedented deep view on pattern formation and methylation marker heterogeneity in tissues concerned by complex diseases like cancer. PMID:23803588

Anisotropic shear stress patterns predict the orientation of convergent tissue movements in the embryonic heart

PubMed Central

2017-01-01

Myocardial contractility and blood flow provide essential mechanical cues for the morphogenesis of the heart. In general, endothelial cells change their migratory behavior in response to shear stress patterns, according to flow directionality. Here, we assessed the impact of shear stress patterns and flow directionality on the behavior of endocardial cells, the specialized endothelial cells of the heart. At the early stages of zebrafish heart valve formation, we show that endocardial cells are converging to the valve-forming area and that this behavior depends upon mechanical forces. Quantitative live imaging and mathematical modeling allow us to correlate this tissue convergence with the underlying flow forces. We predict that tissue convergence is associated with the direction of the mean wall shear stress and of the gradient of harmonic phase-averaged shear stresses, which surprisingly do not match the overall direction of the flow. This contrasts with the usual role of flow directionality in vascular development and suggests that the full spatial and temporal complexity of the wall shear stress should be taken into account when studying endothelial cell responses to flow in vivo. PMID:29183943

Rotating stellar populations in the Fornax dSph galaxy

NASA Astrophysics Data System (ADS)

del Pino, Andrés; Aparicio, Antonio; Hidalgo, Sebastian L.; Łokas, Ewa L.

2017-03-01

We present a novel analysis of the internal kinematics of the Fornax dwarf spheroidal galaxy. Our results are based on the largest sample of spectroscopic data for Fornax stars presently available (>2500 stars), for which we have chemical and kinematic information. We introduce new software, BEACON, designed to detect chemo-kinematic patterns among stars of different stellar populations using their metallicity and velocity along the line of sight. Applying BEACON to Fornax, we have detected non-negligible rotation signals around main optical axes of the galaxy, characteristic for a triaxial system partially supported by rotation. The dominant rotation pattern is relatively strong (∼12 km s-1), but the galaxy also shows additional weaker albeit complex rotation patterns. Using the information available from the star formation history of Fornax, we have also derived the average age of the different chemo-kinematic components found by BEACON, which has allowed us to obtain its kinematic history. Our results point to a possible major merger suffered by Fornax at redshift z ∼ 1, in agreement with the previous works.

Field coupling-induced pattern formation in two-layer neuronal network

NASA Astrophysics Data System (ADS)

Qin, Huixin; Wang, Chunni; Cai, Ning; An, Xinlei; Alzahrani, Faris

2018-07-01

The exchange of charged ions across membrane can generate fluctuation of membrane potential and also complex effect of electromagnetic induction. Diversity in excitability of neurons induces different modes selection and dynamical responses to external stimuli. Based on a neuron model with electromagnetic induction, which is described by magnetic flux and memristor, a two-layer network is proposed to discuss the pattern control and wave propagation in the network. In each layer, gap junction coupling is applied to connect the neurons, while field coupling is considered between two layers of the network. The field coupling is approached by using coupling of magnetic flux, which is associated with distribution of electromagnetic field. It is found that appropriate intensity of field coupling can enhance wave propagation from one layer to another one, and beautiful spatial patterns are formed. The developed target wave in the second layer shows some difference from target wave triggered in the first layer of the network when two layers are considered by different excitabilities. The potential mechanism could be pacemaker-like driving from the first layer will be encoded by the second layer.

Impact of Motile Bacterial Suspensions on Viscous Fingering and Mixing

NASA Astrophysics Data System (ADS)

Chui, Jane; Auradou, Harold; de Anna, Pietro; Fahrner, Karen; Berg, Howard; Juanes, Ruben

2017-11-01

Viscous fingering is a hydrodynamic instability that occurs when a less viscous fluid displaces a more viscous one. Instead of progressing as a uniform front, the less viscous fluid forms fingers to create complex patterns. Understanding how these patterns and their associated gradients evolve over time is of critical importance in characterizing the mixing of two fluids, which in turn is important to applications such as enhanced oil recovery, bioremediation, and microfluidics. Here, we investigate the impact of replacing the less viscous fluid with an active suspension of motile bacteria. In this series of experiments, a suspension of motile Escherichia coli capable of collective swimming is injected into a microfluidic Hele-Shaw cell under viscous fingering conditions. Through videomicroscopy, we obtain high-resolution concentration fields to determine the evolution of the mixing zone (region with concentration gradients). We quantify the impact that active suspensions have on the formation of viscous fingering patterns and mixing efficiency between the two fluids, and-conversely-report details of the collective swimming behavior in the presence of a viscous-gradient front.

Manipulation of competing ferromagnetic and antiferromagnetic domains in exchange-biased nanostructures

DOE PAGES

Fraile Rodríguez, Arantxa; Basaran, Ali C.; Morales, Rafael; ...

2015-11-20

In this work, using photoemission electron microscopy combined with x-ray magnetic circular dichroism we show that a progressive spatial confinement of a ferromagnet (FM), either through thickness variation or laterally via patterning, actively controls the domains of uncompensated spins in the antiferromagnet (AF) in exchange-biased systems. Direct observations of the spin structure in both sides of the FM/AF interface in a model system, Ni/FeF 2, show that the spin structure is determined by the balance between the competing FM and AF magnetic energies. Coexistence of exchange bias domains, with opposite directions, can be established in Ni/FeF 2 bilayers for Nimore » thicknesses below 10 nm. Patterning the Ni/FeF 2 heterostructures with antidots destabilizes the FM state, enhancing the formation of opposite exchange bias domains below a critical antidot separation of the order of a few FeF 2 crystal domains. The results suggest that dimensional confinement of the FM may be used to manipulate the AF spin structure in spintronic devices and ultrahigh-density information storage media. Lastly, the underlying mechanism of the uncompensated AF domain formation in Ni/FeF 2 may be generic to other magnetic systems with complex noncollinear FM/AF spin structures.« less

Transcriptional Modulation of Genes Encoding Structural Characteristics of Differentiating Enterocytes During Development of a Polarized Epithelium In Vitro

PubMed Central

Halbleib, Jennifer M.; Sääf, Annika M.

2007-01-01

Although there is considerable evidence implicating posttranslational mechanisms in the development of epithelial cell polarity, little is known about the patterns of gene expression and transcriptional regulation during this process. We characterized the temporal program of gene expression during cell–cell adhesion–initiated polarization of human Caco-2 cells in tissue culture, which develop structural and functional polarity similar to that of enterocytes in vivo. A distinctive switch in gene expression patterns occurred upon formation of cell–cell contacts between neighboring cells. Expression of genes involved in cell proliferation was down-regulated concomitant with induction of genes necessary for functional specialization of polarized epithelial cells. Transcriptional up-regulation of these latter genes correlated with formation of important structural and functional features in enterocyte differentiation and establishment of structural and functional cell polarity; components of the apical microvilli were induced as the brush border formed during polarization; as barrier function was established, expression of tight junction transmembrane proteins peaked; transcripts encoding components of the apical, but not the basal-lateral trafficking machinery were increased during polarization. Coordinated expression of genes encoding components of functional cell structures were often observed indicating temporal control of expression and assembly of multiprotein complexes. PMID:17699590

Stabilization and activation of alpha-chymotrypsin in water-organic solvent systems by complex formation with oligoamines.

PubMed

Kudryashova, Elena V; Artemova, Tatiana M; Vinogradov, Alexei A; Gladilin, Alexander K; Mozhaev, Vadim V; Levashov, Andrey V

2003-04-01

Formation of enzyme-oligoamine complexes was suggested as an approach to obtain biocatalysts with enhanced resistance towards inactivation in water-organic media. Complex formation results in broadening (by 20-40% v/v ethanol) of the range of cosolvent concentrations where the enzyme retains its catalytic activity (stabilization effect). At moderate cosolvent concentrations (20-40% v/v) complex formation activates the enzyme (by 3-6 times). The magnitude of activation and stabilization effects increases with the number of possible electrostatic contacts between the protein surface and the molecules of oligoamines (OA). Circular dichroism spectra in the far-UV region show that complex formation stabilizes protein conformation and prevents aggregation in water-organic solvent mixtures. Two populations of the complexes with different thermodynamic stabilities were found in alpha-chymotrypsin (CT)-OA systems depending on the CT/OA ratio. The average dissociation constants and stoichiometries of both low- and high-affinity populations of the complexes were estimated. It appears that it is the low-affinity sites on the CT surface that are responsible for the activation effect.

Surface morphology of molybdenum silicide films upon low-energy ion beam sputtering.

PubMed

Gago, R; Jaafar, M; Palomares, F J

2018-07-04

The surface morphology of molybdenum silicide (Mo x Si 1-x ) films has been studied after low-energy Ar + ion beam sputtering (IBS) to explore eventual pattern formation on compound targets and, simultaneously, gather information about the mechanisms behind silicide-assisted nanopatterning of silicon surfaces by IBS. For this purpose, Mo x Si 1-x films with compositions below, equal and above the MoSi 2 stoichiometry (x  =  0.33) have been produced by magnetron sputtering, as assessed by Rutherford backscattering spectrometry (RBS). The surface morphology of silicon and silicide films before and after IBS has been imaged by atomic force microscopy (AFM), comprising conditions where typical nanodot or ripple patterns emerge on the former. In the case of irradiated Mo x Si 1-x surfaces, AFM shows a marked surface smoothing at normal incidence with and without additional Mo incorporation (the former results in nanodot patterns on Si). The morphological analysis also provides no evidence of ion-induced phase separation in irradiated Mo x Si 1-x . Contrary to silicon, Mo x Si 1-x surfaces also do not display ripple formation for (impurity free) oblique irradiations, except at grazing incidence conditions where parallel ripples emerge in a more evident fashion than in the Si counterpart. By means of RBS, irradiated Mo x Si 1-x films with 1 keV Ar + at normal incidence have also been used to measure experimentally the (absolute) sputtering yield and rate of Si and Mo x Si 1-x materials. The analysis reveals that, under the present working conditions, the erosion rate of silicides is larger than for silicon, supporting simulations from the TRIDYN code. This finding questions the shielding effect from silicide regions as roughening mechanism in metal-assisted nanopatterning of silicon. On the contrary, the results highlight the relevance of in situ silicide formation. Ripple formation on Mo x Si 1-x under grazing incidence is also attributed to the dominance of sputtering effects under this geometry. In conclusion, our work provides some insights into the complex morphological evolution of compound surfaces and solid experimental evidences regarding the mechanisms behind silicide-assisted nanopatterning.

Adaptive self-organization during growth of bacterial colonies

NASA Astrophysics Data System (ADS)

Ben-Jacob, Eshel; Shmueli, Haim; Shochet, Ofer; Tenenbaum, Adam

1992-09-01

We present a study of interfacial pattern formation during diffusion-limited growth of Bacillus subtilis. It is demonstrated that bacterial colonies can develop patterns similar to morphologies observed during diffusion-limited growth in non-living (azoic) systems such as solidification and electro-chemical deposition. The various growth morphologies, that is the global structure of the colony, are observed as we vary the growth conditions. These include fractal growth, dense-branching growth, compact growth, dendritic growth and chiral growth. The results demonstrate the action of a singular interplay between the micro-level (individual bacterium) and macro-level (the colony) in selecting the observed morphologies as is understood for non-living systems. Furthermore, the observed morphologies can be organized within a morphology diagram indicating the existence of a morphology selection principle similar to the one proposed for azoic systems. We propose a phase-field-like model (the phase being the bacterial concentration and the field being the nutrient concentration) to describe the growth. The bacteria-bacteria interaction is manifested as a phase dependent diffusion constant. Growth of a bacterial colony presents an inherent additional level of complexity compared to azoic systems, since the building blocks themselves are living systems. Thus, our studies also focus on the transition between morphologies. We have observed extended morphology transitions due to phenotypic changes of the bacteria, as well as bursts of new morphologies resulting from genotypic changes. In addition, we have observed extended and heritable transitions (mainly between dense branching growth and chiral growth) as well as phenotypic transitions that turn genotypic over time. We discuss the implications of our results in the context of the evolving picture of genome cybernetics. Diffusion limited growth of bacterial colonies combined with new understanding of pattern formation in azoic systems provide new tools for the study of adaptive self-organization and mutation in the presence of selective pressures. We include brief reviews of both the recent developments in the study of interfacial pattern formation in non-living systems and the current trends in the view of mutation dynamics.

A new mechanism for spatial pattern formation via lateral and protrusion-mediated lateral signalling

PubMed Central

Hunter, Ginger L.; Baum, Buzz

2016-01-01

Tissue organization and patterning are critical during development when genetically identical cells take on different fates. Lateral signalling plays an important role in this process by helping to generate self-organized spatial patterns in an otherwise uniform collection of cells. Recent data suggest that lateral signalling can be mediated both by junctional contacts between neighbouring cells and via cellular protrusions that allow non-neighbouring cells to interact with one another at a distance. However, it remains unclear precisely how signalling mediated by these distinct types of cell–cell contact can physically contribute to the generation of complex patterns without the assistance of diffusible morphogens or pre-patterns. To explore this question, in this work we develop a model of lateral signalling based on a single receptor/ligand pair as exemplified by Notch and Delta. We show that allowing the signalling kinetics to differ at junctional versus protrusion-mediated contacts, an assumption inspired by recent data which show that the cleavage of Notch in several systems requires both Delta binding and the application of mechanical force, permits individual cells to act to promote both lateral activation and lateral inhibition. Strikingly, under this model, in which Delta can sequester Notch, a variety of patterns resembling those typical of reaction–diffusion systems is observed, together with more unusual patterns that arise when we consider changes in signalling kinetics, and in the length and distribution of protrusions. Importantly, these patterns are self-organizing—so that local interactions drive tissue-scale patterning. Together, these data show that protrusions can, in principle, generate different types of patterns in addition to contributing to long-range signalling and to pattern refinement. PMID:27807273

LA-ICP-MS analysis of isolated phosphatic grains indicates selective rare earth element enrichment during reworking and transport processes

NASA Astrophysics Data System (ADS)

Auer, Gerald; Reuter, Markus; Hauzenberger, Christoph A.; Piller, Werner E.

2016-04-01

Rare earth elements (REE) are a commonly used proxy to reconstruct water chemistry and oxygen saturation during the formation history of authigenic and biogenic phosphates in marine environments. In the modern ocean REE exhibit a distinct pattern with enrichment of heavy REE and strong depletion in Cerium. Studies of ancient phosphates and carbonates, however, showed that this 'modern' pattern is only rarely present in the geological past. Consequently, the wide range of REE enrichment patterns found in ancient marine phosphates lead to the proposition that water chemistry had to have been radically different in the earth's past. A wealth of studies has already shown that both early and late diagenesis can strongly affect REE signatures in phosphates and severely alter primary marine signals. However, no previous research was conducted on how alteration processes occurring prior to final deposition affect marine phosphates. Herein we present a dataset of multiple LA-ICP-MS measurements of REE signatures in isolated phosphate and carbonate grains deposited in a carbonate ramp setting in the central Mediterranean Sea during the middle Miocene "Monterey event". The phosphates are represented by authigenic, biogenic and detrital grains emplaced in bioclastic grain- to packstones dominated by bryozoan and echinoderm fragments, as well as abundant benthic and planktic foraminifers. The results of 39 grain specific LA-ICP-MS measurements in three discrete rock samples reveals four markedly different REE patterns (normalized to the Post Archean Australian Shale standard) in terms of total enrichment and pattern shape. Analyses of REE diagenesis proxies show that diagenetic alteration affected the samples only to a minor degree. Considering grain shape and REE patterns together indicate that authigenic, detrital and biogenic phosphates have distinct REE patterns irrespective of the sample. Our results show that the observed REE patterns in phosphates only broadly reflect water chemistry under certain well constrained circumstances of primary authigenesis. Are these conditions not met, REE patterns are more likely to reflect complex enrichment processes that likely already started to occur during reworking over geologically relatively short time frames. Similarities in the REE patterns of clearly detrital and biogenic phosphate further suggest that the often observed 'hat-shaped' pattern in biogenic phosphates can easily result from increased middle REE (Neodymium to Holmium) scavenging during taphonomic processes prior to final deposition. Finally, cluster analysis coupled with sedimentological considerations proved a valuable tool for the characterization of REE patterns of phosphates in terms of their formation conditions and depositional history, such as the distinction of phosphates formed in situ from reworked and transported phosphate grains.

The Effects of Similarity on High-Level Visual Working Memory Processing.

PubMed

Yang, Li; Mo, Lei

2017-01-01

Similarity has been observed to have opposite effects on visual working memory (VWM) for complex images. How can these discrepant results be reconciled? To answer this question, we used a change-detection paradigm to test visual working memory performance for multiple real-world objects. We found that working memory for moderate similarity items was worse than that for either high or low similarity items. This pattern was unaffected by manipulations of stimulus type (faces vs. scenes), encoding duration (limited vs. self-paced), and presentation format (simultaneous vs. sequential). We also found that the similarity effects differed in strength in different categories (scenes vs. faces). These results suggest that complex real-world objects are represented using a centre-surround inhibition organization . These results support the category-specific cortical resource theory and further suggest that centre-surround inhibition organization may differ by category.

Communication: Enhanced chemical reactivity of graphene on a Ni(111) substrate

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ambrosetti, Alberto; Silvestrelli, Pier Luigi

2016-03-21

Due to the unique combination of structural, mechanical, and transport properties, graphene has emerged as an exceptional candidate for catalysis applications. The low chemical reactivity caused by sp{sup 2} hybridization and strongly delocalized π electrons, however, represents a main challenge for straightforward use of graphene in its pristine, free-standing form. Following recent experimental indications, we show that due to charge hybridization, a Ni(111) substrate can enhance the chemical reactivity of graphene, as exemplified by the interaction with the CO molecule. While CO only physisorbs on free-standing graphene, chemisorption of CO involving formation of ethylene dione complexes is predicted in Ni(111)-graphene.more » Higher chemical reactivity is also suggested in the case of oxidized graphene, opening the way to a simple and efficient control of graphene chemical properties, devoid of complex defect patterning or active metallic structures deposition.« less

Bioinformatics: perspectives for the future.

PubMed

Costa, Luciano da Fontoura

2004-12-30

I give here a very personal perspective of Bioinformatics and its future, starting by discussing the origin of the term (and area) of bioinformatics and proceeding by trying to foresee the development of related issues, including pattern recognition/data mining, the need to reintegrate biology, the potential of complex networks as a powerful and flexible framework for bioinformatics and the interplay between bio- and neuroinformatics. Human resource formation and market perspective are also addressed. Given the complexity and vastness of these issues and concepts, as well as the limited size of a scientific article and finite patience of the reader, these perspectives are surely incomplete and biased. However, it is expected that some of the questions and trends that are identified will motivate discussions during the IcoBiCoBi round table (with the same name as this article) and perhaps provide a more ample perspective among the participants of that conference and the readers of this text.

Evolutionary dynamics of group interactions on structured populations: a review

PubMed Central

Perc, Matjaž; Gómez-Gardeñes, Jesús; Szolnoki, Attila; Floría, Luis M.; Moreno, Yamir

2013-01-01

Interactions among living organisms, from bacteria colonies to human societies, are inherently more complex than interactions among particles and non-living matter. Group interactions are a particularly important and widespread class, representative of which is the public goods game. In addition, methods of statistical physics have proved valuable for studying pattern formation, equilibrium selection and self-organization in evolutionary games. Here, we review recent advances in the study of evolutionary dynamics of group interactions on top of structured populations, including lattices, complex networks and coevolutionary models. We also compare these results with those obtained on well-mixed populations. The review particularly highlights that the study of the dynamics of group interactions, like several other important equilibrium and non-equilibrium dynamical processes in biological, economical and social sciences, benefits from the synergy between statistical physics, network science and evolutionary game theory. PMID:23303223