WorldWideScience

Sample records for dynamic studies biological

  1. Nonlinear dynamics in biological systems

    CERN Document Server

    Carballido-Landeira, Jorge

    2016-01-01

    This book presents recent research results relating to applications of nonlinear dynamics, focusing specifically on four topics of wide interest: heart dynamics, DNA/RNA, cell mobility, and proteins. The book derives from the First BCAM Workshop on Nonlinear Dynamics in Biological Systems, held in June 2014 at the Basque Center of Applied Mathematics (BCAM). At this international meeting, researchers from different but complementary backgrounds, including molecular dynamics, physical chemistry, bio-informatics and biophysics, presented their most recent results and discussed the future direction of their studies using theoretical, mathematical modeling and experimental approaches. Such was the level of interest stimulated that the decision was taken to produce this publication, with the organizers of the event acting as editors. All of the contributing authors are researchers working on diverse biological problems that can be approached using nonlinear dynamics. The book will appeal especially to applied math...

  2. Dynamical systems in population biology

    CERN Document Server

    Zhao, Xiao-Qiang

    2017-01-01

    This research monograph provides an introduction to the theory of nonautonomous semiflows with applications to population dynamics. It develops dynamical system approaches to various evolutionary equations such as difference, ordinary, functional, and partial differential equations, and pays more attention to periodic and almost periodic phenomena. The presentation includes persistence theory, monotone dynamics, periodic and almost periodic semiflows, basic reproduction ratios, traveling waves, and global analysis of prototypical population models in ecology and epidemiology. Research mathematicians working with nonlinear dynamics, particularly those interested in applications to biology, will find this book useful. It may also be used as a textbook or as supplementary reading for a graduate special topics course on the theory and applications of dynamical systems. Dr. Xiao-Qiang Zhao is a University Research Professor at Memorial University of Newfoundland, Canada. His main research interests involve applied...

  3. Quantum Dynamics in Biological Systems

    Science.gov (United States)

    Shim, Sangwoo

    In the first part of this dissertation, recent efforts to understand quantum mechanical effects in biological systems are discussed. Especially, long-lived quantum coherences observed during the electronic energy transfer process in the Fenna-Matthews-Olson complex at physiological condition are studied extensively using theories of open quantum systems. In addition to the usual master equation based approaches, the effect of the protein structure is investigated in atomistic detail through the combined application of quantum chemistry and molecular dynamics simulations. To evaluate the thermalized reduced density matrix, a path-integral Monte Carlo method with a novel importance sampling approach is developed for excitons coupled to an arbitrary phonon bath at a finite temperature. In the second part of the thesis, simulations of molecular systems and applications to vibrational spectra are discussed. First, the quantum dynamics of a molecule is simulated by combining semiclassical initial value representation and density funcitonal theory with analytic derivatives. A computationally-tractable approximation to the sum-of-states formalism of Raman spectra is subsequently discussed.

  4. Life at extreme conditions: neutron scattering studies of biological molecules suggest that evolution selected dynamics

    International Nuclear Information System (INIS)

    Zaccai, Joseph Giuseppe

    2008-01-01

    The short review concentrates on recent work performed at the neutrons in biology laboratories of the Institut Laue Langevin and Institut de Biologie Structurale in Grenoble. Extremophile organisms have been discovered that require extreme conditions of temperature, pressure or solvent environment for survival. The existence of such organisms poses a significant challenge in understanding the physical chemistry of their proteins, in view of the great sensitivity of protein structure and stability to the aqueous environment and to external conditions in general. Results of neutron scattering measurements on the dynamics of proteins from extremophile organisms, in vitro as well as in vivo, indicated remarkably how adaptation to extreme conditions involves forces and fluctuation amplitudes that have been selected specifically, suggesting that evolutionary macromolecular selection proceeded via dynamics. The experiments were performed on a halophilic protein, and membrane adapted to high salt, a thermophilic enzyme adapted to high temperature and its mesophilic (adapted to 37 degC) homologue; and in vivo for psychrophilic, mesophilic, thermophilic and hyperthermophilic bacteria, adapted respectively to temperatures of 4 degC, 37 degC, 75 degC and 85 degC. Further work demonstrated the existence of a water component of exceptionally low mobility in an extreme halophile from the Dead Sea, which is not present in mesophile bacterial cells. (author)

  5. Synthesis of C-di-saccharidic compounds by radical cyclisation. Study of biological, structural and dynamic properties

    International Nuclear Information System (INIS)

    Rubinstenn, Gilles

    1996-01-01

    The synthesis of carbohydrate mimics and particularly of C-disaccharides, molecules in which the inter-glycosidic oxygen atom has been replaced by a methylene group, has become, this past two decades, an important challenge in organic chemistry. In the first chapter we present the synthesis of C-disaccharides from the neutral series by a silaketal tethering. The key step of this C-glycosylation is a radical macro-cyclisation. This strategy is applied to the synthesis of two analogues of natural, biologically active, products, the lactose and the Lewis x tri-saccharide. The biological activity of this mimetics is then evaluated. A new tethering strategy, based on the use of phosphorus III compounds, is applied, in the second chapter, to the building of C-disaccharides of the 2'-amino 2'- deoxy series. The third chapter deals with the structural and dynamics study of the C-glycosides prepared in chapter 1 by Nuclear Magnetic Resonance. A new methodology, studying the dipolar relaxation along an effective field, generated through an off-resonance RF field, allowed the precise measurement of longitudinal and transverse cross-relaxation rates. Structural and dynamics parameter thus derived are used as restraints for molecular modeling. The results of this study are then compared to those of the biological tests. (author) [fr

  6. BETAview: a digital {beta}-imaging system for dynamic studies of biological phenomena

    Energy Technology Data Exchange (ETDEWEB)

    Bertolucci, E.; Conti, M.; Mettivier, G.; Montesi, M.C. E-mail: montesi@na.infn.it; Russo, P

    2002-02-01

    We present a digital autoradiography (DAR) system, named BETAview, based on semiconductor pixel detectors and a single particle counting chip, for quantitative analysis of {beta}-emitting radioactive tracers in biological samples. The system is able to perform a real time monitoring of time-dependent biological phenomena. BETAview could be equipped either with GaAs or with Si semiconductor pixellated detectors. In this paper, we describe the results obtained with an assembly based on a Si detector, 300 {mu}m thick, segmented into 64x64 170 {mu}m size square pixels. The detector is bump-bonded to the low threshold, single particle counting chip named Medipix1, developed by a CERN-based European collaboration. The sensitive area is about 1 cm{sup 2}. Studies of background noise and detection efficiency have been performed. Moreover, time-resolved cellular uptake studies with radiolabelled molecules have been monitored. Specifically, we have followed in vivo and in real time, the [{sup 14}C]L-leucine amino acid uptake by eggs of Octopus vulgaris confirming the preliminary results of a previous paper. This opens the field of biomolecular kynetic studies with this new class of semiconductor DAR systems, whose evolution (using the Medipix2 chip, 256x256 pixels, 55 {mu}m pixel size) is soon to come.

  7. BETAview: a digital β-imaging system for dynamic studies of biological phenomena

    International Nuclear Information System (INIS)

    Bertolucci, E.; Conti, M.; Mettivier, G.; Montesi, M.C.; Russo, P.

    2002-01-01

    We present a digital autoradiography (DAR) system, named BETAview, based on semiconductor pixel detectors and a single particle counting chip, for quantitative analysis of β-emitting radioactive tracers in biological samples. The system is able to perform a real time monitoring of time-dependent biological phenomena. BETAview could be equipped either with GaAs or with Si semiconductor pixellated detectors. In this paper, we describe the results obtained with an assembly based on a Si detector, 300 μm thick, segmented into 64x64 170 μm size square pixels. The detector is bump-bonded to the low threshold, single particle counting chip named Medipix1, developed by a CERN-based European collaboration. The sensitive area is about 1 cm 2 . Studies of background noise and detection efficiency have been performed. Moreover, time-resolved cellular uptake studies with radiolabelled molecules have been monitored. Specifically, we have followed in vivo and in real time, the [ 14 C]L-leucine amino acid uptake by eggs of Octopus vulgaris confirming the preliminary results of a previous paper. This opens the field of biomolecular kynetic studies with this new class of semiconductor DAR systems, whose evolution (using the Medipix2 chip, 256x256 pixels, 55 μm pixel size) is soon to come

  8. Interferometric scattering (iSCAT) microscopy: studies of biological membrane dynamics

    Science.gov (United States)

    Reina, Francesco; Galiani, Silvia; Shrestha, Dilip; Sezgin, Erdinc; Lagerholm, B. Christoffer; Cole, Daniel; Kukura, Philipp; Eggeling, Christian

    2018-02-01

    The study of the organization and dynamics of molecules in model and cellular membranes is an important topic in contemporary biophysics. Imaging and single particle tracking in this particular field, however, proves particularly demanding, as it requires simultaneously high spatio-temporal resolution and high signal-to-noise ratios. A remedy to this challenge might be Interferometric Scattering (iSCAT) microscopy, due to its fast sampling rates, label-free imaging capabilities and, most importantly, tuneable signal level output. Here we report our recent advances in the imaging and molecular tracking on phase-separated model membrane systems and live-cell membranes using this technique.

  9. Zebrafish as a visual and dynamic model to study the transport of nanosized drug delivery systems across the biological barriers.

    Science.gov (United States)

    Li, Ye; Miao, Xiaoqing; Chen, Tongkai; Yi, Xiang; Wang, Ruibing; Zhao, Haitao; Lee, Simon Ming-Yuen; Wang, Xueqing; Zheng, Ying

    2017-08-01

    With the wide application of nanotechnology to drug delivery systems, a simple, dynamic and visual in vivo model for high-throughput screening of novel formulations with fluorescence markers across biological barriers is desperately needed. In vitro cell culture models have been widely used, although they are far from a complimentary in vivo system. Mammalian animal models are common predictive models to study transport, but they are costly and time consuming. Zebrafish (Danio rerio), a small vertebrate model, have the potential to be developed as an "intermediate" model for quick evaluations. Based on our previously established coumarin 6 nanocrystals (C6-NCs), which have two different sizes, the present study investigates the transportation of C6-NCs across four biological barriers, including the chorion, blood brain barrier (BBB), blood retinal barrier (BRB) and gastrointestinal (GI) barrier, using zebrafish embryos and larvae as in vivo models. The biodistribution and elimination of C6 from different organs were quantified in adult zebrafish. The results showed that compared to 200nm C6-NCs, 70nm C6-NCs showed better permeability across these biological barriers. A FRET study suggested that intact C6-NCs together with the free dissolved form of C6 were absorbed into the larval zebrafish. More C6 was accumulated in different organs after incubation with small sized NCs via lipid raft-mediated endocytosis in adult zebrafish, which is consistent with the findings from in vitro cell monolayers and the zebrafish larvae model. C6-NCs could be gradually eliminated in each organ over time. This study demonstrated the successful application of zebrafish as a simple and dynamic model to simultaneously assess the transport of nanosized drug delivery systems across several biological barriers and biodistribution in different organs, especially in the brain, which could be used for central nervous system (CNS) drug and delivery system screening. Copyright © 2017 Elsevier B

  10. A microfluidic flow-cell for the study of the ultrafast dynamics of biological systems

    Energy Technology Data Exchange (ETDEWEB)

    Chauvet, Adrien, E-mail: adrien.chauvet@epfl.ch; Chergui, Majed [Ecole Polytechnique Fédérale de Lausanne (EPFL), Laboratoire de Spectroscopie Ultrarapide, ISIC, Faculté des Sciences de Base, Station 6, 1015 Lausanne (Switzerland); Tibiletti, Tania; Caffarri, Stefano [Aix Marseille Université, CNRS, CEA, UMR 7265 Biologie Végétale et Microbiologie Environnementales, 13009 Marseille (France)

    2014-10-01

    The study of biochemical dynamics by ultrafast spectroscopic methods is often restricted by the limited amount of liquid sample available, while the high repetition rate of light sources can induce photodamage. In order to overcome these limitations, we designed a high flux, sub-ml, capillary flow-cell. While the 0.1 mm thin window of the 0.5 mm cross-section capillary ensures an optimal temporal resolution and a steady beam deviation, the cell-pump generates flows up to ~0.35 ml/s that are suitable to pump laser repetition rates up to ~14 kHz, assuming a focal spot-diameter of 100 μm. In addition, a decantation chamber efficiently removes bubbles and allows, via septum, for the addition of chemicals while preserving the closed atmosphere. The minimal useable amount of sample is ~250 μl.

  11. Molecular dynamics modeling the synthetic and biological polymers interactions pre-studied via docking

    Science.gov (United States)

    Tsvetkov, Vladimir B.; Serbin, Alexander V.

    2014-06-01

    In previous works we reported the design, synthesis and in vitro evaluations of synthetic anionic polymers modified by alicyclic pendant groups (hydrophobic anchors), as a novel class of inhibitors of the human immunodeficiency virus type 1 ( HIV-1) entry into human cells. Recently, these synthetic polymers interactions with key mediator of HIV-1 entry-fusion, the tri-helix core of the first heptad repeat regions [ HR1]3 of viral envelope protein gp41, were pre-studied via docking in terms of newly formulated algorithm for stepwise approximation from fragments of polymeric backbone and side-group models toward real polymeric chains. In the present article the docking results were verified under molecular dynamics ( MD) modeling. In contrast with limited capabilities of the docking, the MD allowed of using much more large models of the polymeric ligands, considering flexibility of both ligand and target simultaneously. Among the synthesized polymers the dinorbornen anchors containing alternating copolymers of maleic acid were selected as the most representative ligands (possessing the top anti-HIV activity in vitro in correlation with the highest binding energy in the docking). To verify the probability of binding of the polymers with the [HR1]3 in the sites defined via docking, various starting positions of polymer chains were tried. The MD simulations confirmed the main docking-predicted priority for binding sites, and possibilities for axial and belting modes of the ligands-target interactions. Some newly MD-discovered aspects of the ligand's backbone and anchor units dynamic cooperation in binding the viral target clarify mechanisms of the synthetic polymers anti-HIV activity and drug resistance prevention.

  12. Application of Wavelet-Based Tools to Study the Dynamics of Biological Processes

    DEFF Research Database (Denmark)

    Pavlov, A. N.; Makarov, V. A.; Mosekilde, Erik

    2006-01-01

    The article makes use of three different examples (sensory information processing in the rat trigeminal complex, intracellular interaction in snail neurons and multimodal dynamics in nephron autoregulation) to demonstrate how modern approaches to time-series analysis based on the wavelet-transfor...

  13. Molecular dynamics simulation studies of transmembrane transport of chemical components in Chinese herbs and the function of platycodin D in a biological membrane

    Directory of Open Access Journals (Sweden)

    Shufang Yang

    2017-04-01

    Conclusion: The Martini force field was successfully applied to the study of the interaction between herbal compounds and a biological membrane. By combining the dynamics equilibrium morphology, the distribution of drugs inside and outside the biomembrane, and the interaction sites of drugs on the DPPC bilayer, factors influencing transmembrane transport of drugs were elucidated and the function of platycodin D in a biological membrane was reproduced.

  14. Study of biological compartments

    International Nuclear Information System (INIS)

    Rocha, A.F.G. da

    1976-01-01

    The several types of biological compartments are studied such as monocompartmental system, one-compartment balanced system irreversible fluxes, two closed compartment system, three compartment systems, catenary systems and mammilary systems [pt

  15. Aquatic biology studies

    International Nuclear Information System (INIS)

    Anon.

    1976-01-01

    Aquatic biology studies focused on studying the hydrothermal effects of Par Pond reservoir on periphyton, plankton, zooplankton, macrophytes, human pathogens, and microbial activity; the variability between the artificial streams of the Flowing Streams Laboratory and Upper Three Runs Creek; and the bacterial production of methane in Savannah River Plant aquatic systems

  16. Green Algae as Model Organisms for Biological Fluid Dynamics

    Science.gov (United States)

    Goldstein, Raymond E.

    2015-01-01

    In the past decade, the volvocine green algae, spanning from the unicellular Chlamydomonas to multicellular Volvox, have emerged as model organisms for a number of problems in biological fluid dynamics. These include flagellar propulsion, nutrient uptake by swimming organisms, hydrodynamic interactions mediated by walls, collective dynamics and transport within suspensions of microswimmers, the mechanism of phototaxis, and the stochastic dynamics of flagellar synchronization. Green algae are well suited to the study of such problems because of their range of sizes (from 10 μm to several millimeters), their geometric regularity, the ease with which they can be cultured, and the availability of many mutants that allow for connections between molecular details and organism-level behavior. This review summarizes these recent developments and highlights promising future directions in the study of biological fluid dynamics, especially in the context of evolutionary biology, that can take advantage of these remarkable organisms.

  17. Neutron scattering studies of the dynamics of biological systems as a function of hydration, temperature and pressure

    International Nuclear Information System (INIS)

    Trapp, Marcus

    2010-01-01

    Incoherent elastic and quasi-elastic neutron scattering were used to measure membrane and protein dynamics in the nano- to picosecond time and Angstrom length scale. The hydration dependent dynamics of DMPC model membranes was studied using elastic and quasi-elastic neutron scattering. The elastic experiments showed a clear shift of the temperature of the main phase transition to higher temperatures with decreasing hydration level. The performed quasi-elastic measurements demonstrated nicely the influence, hydration has on the diffusive motions of the head lipid groups. Different models are necessary to fit the Q-dependence of the elastic incoherent structure factor and show therefore the reduced mobility as a result of reduced water content. In addition to temperature, pressure as a second thermodynamic variable was used to explore dynamics of DMPC membranes. The ordering introduced by applying pressure has similar effect to decreased hydration, therefore both approaches are complementary. Covering three orders of magnitude in observation time, the dynamics of native AChE and its complexed counterpart in presence of Huperzin A was investigated in the range from 1 ns to 100 ps. The mean square displacements obtained from the elastic data allowed the determination of activation energies and gave evidence that a hierarchy of motions contributes to the enzymatic activity. Diffusion constants and residence times were extracted from the quasi-elastic broadening. (author) [fr

  18. AC Calorimetric Design for Dynamic of Biological Materials

    OpenAIRE

    Shigeo Imaizumi

    2006-01-01

    We developed a new AC calorimeter for the measurement of dynamic specific heat capacity in liquids, including aqueous suspensions of biological materials. This method has several advantages. The first is that a high-resolution measurement of heat capacity, inmillidegrees, can be performed as a function of temperature, even with a very small sample. Therefore, AC calorimeter is a powerful tool to study critical behavior a tphase transition in biological materials. The second advantage is that ...

  19. Applying differential dynamic logic to reconfigurable biological networks.

    Science.gov (United States)

    Figueiredo, Daniel; Martins, Manuel A; Chaves, Madalena

    2017-09-01

    Qualitative and quantitative modeling frameworks are widely used for analysis of biological regulatory networks, the former giving a preliminary overview of the system's global dynamics and the latter providing more detailed solutions. Another approach is to model biological regulatory networks as hybrid systems, i.e., systems which can display both continuous and discrete dynamic behaviors. Actually, the development of synthetic biology has shown that this is a suitable way to think about biological systems, which can often be constructed as networks with discrete controllers, and present hybrid behaviors. In this paper we discuss this approach as a special case of the reconfigurability paradigm, well studied in Computer Science (CS). In CS there are well developed computational tools to reason about hybrid systems. We argue that it is worth applying such tools in a biological context. One interesting tool is differential dynamic logic (dL), which has recently been developed by Platzer and applied to many case-studies. In this paper we discuss some simple examples of biological regulatory networks to illustrate how dL can be used as an alternative, or also as a complement to methods already used. Copyright © 2017 Elsevier Inc. All rights reserved.

  20. Activating and inhibiting connections in biological network dynamics

    Directory of Open Access Journals (Sweden)

    Knight Rob

    2008-12-01

    Full Text Available Abstract Background Many studies of biochemical networks have analyzed network topology. Such work has suggested that specific types of network wiring may increase network robustness and therefore confer a selective advantage. However, knowledge of network topology does not allow one to predict network dynamical behavior – for example, whether deleting a protein from a signaling network would maintain the network's dynamical behavior, or induce oscillations or chaos. Results Here we report that the balance between activating and inhibiting connections is important in determining whether network dynamics reach steady state or oscillate. We use a simple dynamical model of a network of interacting genes or proteins. Using the model, we study random networks, networks selected for robust dynamics, and examples of biological network topologies. The fraction of activating connections influences whether the network dynamics reach steady state or oscillate. Conclusion The activating fraction may predispose a network to oscillate or reach steady state, and neutral evolution or selection of this parameter may affect the behavior of biological networks. This principle may unify the dynamics of a wide range of cellular networks. Reviewers Reviewed by Sergei Maslov, Eugene Koonin, and Yu (Brandon Xia (nominated by Mark Gerstein. For the full reviews, please go to the Reviewers' comments section.

  1. Modeling biological pathway dynamics with timed automata.

    Science.gov (United States)

    Schivo, Stefano; Scholma, Jetse; Wanders, Brend; Urquidi Camacho, Ricardo A; van der Vet, Paul E; Karperien, Marcel; Langerak, Rom; van de Pol, Jaco; Post, Janine N

    2014-05-01

    Living cells are constantly subjected to a plethora of environmental stimuli that require integration into an appropriate cellular response. This integration takes place through signal transduction events that form tightly interconnected networks. The understanding of these networks requires capturing their dynamics through computational support and models. ANIMO (analysis of Networks with Interactive Modeling) is a tool that enables the construction and exploration of executable models of biological networks, helping to derive hypotheses and to plan wet-lab experiments. The tool is based on the formalism of Timed Automata, which can be analyzed via the UPPAAL model checker. Thanks to Timed Automata, we can provide a formal semantics for the domain-specific language used to represent signaling networks. This enforces precision and uniformity in the definition of signaling pathways, contributing to the integration of isolated signaling events into complex network models. We propose an approach to discretization of reaction kinetics that allows us to efficiently use UPPAAL as the computational engine to explore the dynamic behavior of the network of interest. A user-friendly interface hides the use of Timed Automata from the user, while keeping the expressive power intact. Abstraction to single-parameter kinetics speeds up construction of models that remain faithful enough to provide meaningful insight. The resulting dynamic behavior of the network components is displayed graphically, allowing for an intuitive and interactive modeling experience.

  2. Organization of excitable dynamics in hierarchical biological networks.

    Directory of Open Access Journals (Sweden)

    Mark Müller-Linow

    Full Text Available This study investigates the contributions of network topology features to the dynamic behavior of hierarchically organized excitable networks. Representatives of different types of hierarchical networks as well as two biological neural networks are explored with a three-state model of node activation for systematically varying levels of random background network stimulation. The results demonstrate that two principal topological aspects of hierarchical networks, node centrality and network modularity, correlate with the network activity patterns at different levels of spontaneous network activation. The approach also shows that the dynamic behavior of the cerebral cortical systems network in the cat is dominated by the network's modular organization, while the activation behavior of the cellular neuronal network of Caenorhabditis elegans is strongly influenced by hub nodes. These findings indicate the interaction of multiple topological features and dynamic states in the function of complex biological networks.

  3. Dynamic models in research and management of biological invasions.

    Science.gov (United States)

    Buchadas, Ana; Vaz, Ana Sofia; Honrado, João P; Alagador, Diogo; Bastos, Rita; Cabral, João A; Santos, Mário; Vicente, Joana R

    2017-07-01

    Invasive species are increasing in number, extent and impact worldwide. Effective invasion management has thus become a core socio-ecological challenge. To tackle this challenge, integrating spatial-temporal dynamics of invasion processes with modelling approaches is a promising approach. The inclusion of dynamic processes in such modelling frameworks (i.e. dynamic or hybrid models, here defined as models that integrate both dynamic and static approaches) adds an explicit temporal dimension to the study and management of invasions, enabling the prediction of invasions and optimisation of multi-scale management and governance. However, the extent to which dynamic approaches have been used for that purpose is under-investigated. Based on a literature review, we examined the extent to which dynamic modelling has been used to address invasions worldwide. We then evaluated how the use of dynamic modelling has evolved through time in the scope of invasive species management. The results suggest that modelling, in particular dynamic modelling, has been increasingly applied to biological invasions, especially to support management decisions at local scales. Also, the combination of dynamic and static modelling approaches (hybrid models with a spatially explicit output) can be especially effective, not only to support management at early invasion stages (from prevention to early detection), but also to improve the monitoring of invasion processes and impact assessment. Further development and testing of such hybrid models may well be regarded as a priority for future research aiming to improve the management of invasions across scales. Copyright © 2017 Elsevier Ltd. All rights reserved.

  4. Chaotic population dynamics and biology of the top-predator

    International Nuclear Information System (INIS)

    Rai, Vikas; Upadhyay, Ranjit Kumar

    2004-01-01

    We study how the dynamics of a food chain depends on the biology of the top-predator. We consider two model food chains with specialist and generalist top-predators. Both types of food chains display same type of chaotic behavior, short-term recurrent chaos; but the generating mechanisms are drastically different. Food chains with specialist top-predators are dictated by exogenous stochastic factors. On the contrary, the dynamics of those with the generalist top-predator is governed by deterministic changes in system parameters. The study also suggests that robust chaos would be a rarity

  5. Biological Dynamics Markup Language (BDML): an open format for representing quantitative biological dynamics data.

    Science.gov (United States)

    Kyoda, Koji; Tohsato, Yukako; Ho, Kenneth H L; Onami, Shuichi

    2015-04-01

    Recent progress in live-cell imaging and modeling techniques has resulted in generation of a large amount of quantitative data (from experimental measurements and computer simulations) on spatiotemporal dynamics of biological objects such as molecules, cells and organisms. Although many research groups have independently dedicated their efforts to developing software tools for visualizing and analyzing these data, these tools are often not compatible with each other because of different data formats. We developed an open unified format, Biological Dynamics Markup Language (BDML; current version: 0.2), which provides a basic framework for representing quantitative biological dynamics data for objects ranging from molecules to cells to organisms. BDML is based on Extensible Markup Language (XML). Its advantages are machine and human readability and extensibility. BDML will improve the efficiency of development and evaluation of software tools for data visualization and analysis. A specification and a schema file for BDML are freely available online at http://ssbd.qbic.riken.jp/bdml/. Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

  6. The collective biology of the gene: Towards genetic dynamics engineering

    International Nuclear Information System (INIS)

    Chela-Flores, J.

    1985-11-01

    Chromatin dynamics is studied in terms of coupled vibrations (phonon pairing); this is shown to lead to a collective variable Δ, interpreted as a gene inhibition factor, which behaves as a biological switch turned off, not only by enzymatic action or metabolic energy, but also by means of an external probe:irradiation. We discuss the inactivation of the X chromosome and puffing. The relevance of being able to modulate Δ is emphasized, since it is equivalent to controlling chromatin dynamics without interfering with chromatin structure, unlike in the usual recombinant DNA techniques. (author)

  7. Mammalian synthetic biology for studying the cell.

    Science.gov (United States)

    Mathur, Melina; Xiang, Joy S; Smolke, Christina D

    2017-01-02

    Synthetic biology is advancing the design of genetic devices that enable the study of cellular and molecular biology in mammalian cells. These genetic devices use diverse regulatory mechanisms to both examine cellular processes and achieve precise and dynamic control of cellular phenotype. Synthetic biology tools provide novel functionality to complement the examination of natural cell systems, including engineered molecules with specific activities and model systems that mimic complex regulatory processes. Continued development of quantitative standards and computational tools will expand capacities to probe cellular mechanisms with genetic devices to achieve a more comprehensive understanding of the cell. In this study, we review synthetic biology tools that are being applied to effectively investigate diverse cellular processes, regulatory networks, and multicellular interactions. We also discuss current challenges and future developments in the field that may transform the types of investigation possible in cell biology. © 2017 Mathur et al.

  8. Dynamics of mathematical models in biology bringing mathematics to life

    CERN Document Server

    Zazzu, Valeria; Guarracino, Mario

    2016-01-01

    This volume focuses on contributions from both the mathematics and life science community surrounding the concepts of time and dynamicity of nature, two significant elements which are often overlooked in modeling process to avoid exponential computations. The book is divided into three distinct parts: dynamics of genomes and genetic variation, dynamics of motifs, and dynamics of biological networks. Chapters included in dynamics of genomes and genetic variation analyze the molecular mechanisms and evolutionary processes that shape the structure and function of genomes and those that govern genome dynamics. The dynamics of motifs portion of the volume provides an overview of current methods for motif searching in DNA, RNA and proteins, a key process to discover emergent properties of cells, tissues, and organisms. The part devoted to the dynamics of biological networks covers networks aptly discusses networks in complex biological functions and activities that interpret processes in cells. Moreover, chapters i...

  9. Structural Identifiability of Dynamic Systems Biology Models.

    Science.gov (United States)

    Villaverde, Alejandro F; Barreiro, Antonio; Papachristodoulou, Antonis

    2016-10-01

    A powerful way of gaining insight into biological systems is by creating a nonlinear differential equation model, which usually contains many unknown parameters. Such a model is called structurally identifiable if it is possible to determine the values of its parameters from measurements of the model outputs. Structural identifiability is a prerequisite for parameter estimation, and should be assessed before exploiting a model. However, this analysis is seldom performed due to the high computational cost involved in the necessary symbolic calculations, which quickly becomes prohibitive as the problem size increases. In this paper we show how to analyse the structural identifiability of a very general class of nonlinear models by extending methods originally developed for studying observability. We present results about models whose identifiability had not been previously determined, report unidentifiabilities that had not been found before, and show how to modify those unidentifiable models to make them identifiable. This method helps prevent problems caused by lack of identifiability analysis, which can compromise the success of tasks such as experiment design, parameter estimation, and model-based optimization. The procedure is called STRIKE-GOLDD (STRuctural Identifiability taKen as Extended-Generalized Observability with Lie Derivatives and Decomposition), and it is implemented in a MATLAB toolbox which is available as open source software. The broad applicability of this approach facilitates the analysis of the increasingly complex models used in systems biology and other areas.

  10. Network Reconstruction of Dynamic Biological Systems

    OpenAIRE

    Asadi, Behrang

    2013-01-01

    Inference of network topology from experimental data is a central endeavor in biology, since knowledge of the underlying signaling mechanisms a requirement for understanding biological phenomena. As one of the most important tools in bioinformatics area, development of methods to reconstruct biological networks has attracted remarkable attention in the current decade. Integration of different data types can lead to remarkable improvements in our ability to identify the connectivity of differe...

  11. Feedback dynamics and cell function: Why systems biology is called Systems Biology.

    Science.gov (United States)

    Wolkenhauer, Olaf; Mesarovic, Mihajlo

    2005-05-01

    A new paradigm, like Systems Biology, should challenge the way research has been conducted previously. This Opinion article aims to present Systems Biology, not as the application of engineering principles to biology but as a merger of systems- and control theory with molecular- and cell biology. In our view, the central dogma of Systems Biology is that it is system dynamics that gives rise to the functioning and function of cells. The concepts of feedback regulation and control of pathways and the coordination of cell function are emphasized as an important area of Systems Biology research. The hurdles and risks for this area are discussed from the perspective of dynamic pathway modelling. Most of all, the aim of this article is to promote mathematical modelling and simulation as a part of molecular- and cell biology. Systems Biology is a success if it is widely accepted that there is nothing more practical than a good theory.

  12. Dynamic Biological Functioning Important for Simulating and Stabilizing Ocean Biogeochemistry

    Science.gov (United States)

    Buchanan, P. J.; Matear, R. J.; Chase, Z.; Phipps, S. J.; Bindoff, N. L.

    2018-04-01

    The biogeochemistry of the ocean exerts a strong influence on the climate by modulating atmospheric greenhouse gases. In turn, ocean biogeochemistry depends on numerous physical and biological processes that change over space and time. Accurately simulating these processes is fundamental for accurately simulating the ocean's role within the climate. However, our simulation of these processes is often simplistic, despite a growing understanding of underlying biological dynamics. Here we explore how new parameterizations of biological processes affect simulated biogeochemical properties in a global ocean model. We combine 6 different physical realizations with 6 different biogeochemical parameterizations (36 unique ocean states). The biogeochemical parameterizations, all previously published, aim to more accurately represent the response of ocean biology to changing physical conditions. We make three major findings. First, oxygen, carbon, alkalinity, and phosphate fields are more sensitive to changes in the ocean's physical state. Only nitrate is more sensitive to changes in biological processes, and we suggest that assessment protocols for ocean biogeochemical models formally include the marine nitrogen cycle to assess their performance. Second, we show that dynamic variations in the production, remineralization, and stoichiometry of organic matter in response to changing environmental conditions benefit the simulation of ocean biogeochemistry. Third, dynamic biological functioning reduces the sensitivity of biogeochemical properties to physical change. Carbon and nitrogen inventories were 50% and 20% less sensitive to physical changes, respectively, in simulations that incorporated dynamic biological functioning. These results highlight the importance of a dynamic biology for ocean properties and climate.

  13. Biological study in schizophrenia

    International Nuclear Information System (INIS)

    Kasai, Kiyoto; Yoshikawa, Akane; Natsubori, Takanobu; Koike, Shinsuke; Nagai, Tatsuya; Araki, Tsuyoshi; Nishimura, Yukika; Iwamoto, Kazuya

    2012-01-01

    Schizophrenia is associated with enormous morbidity, mortality, personal disability, and social cost. Although considerable research on schizophrenia has been performed, the etiology of this disease has not been fully elucidated. In recent years, imaging and genetic technologies have been developed dramatically. Disturbances in glutamate and gamma-aminobutyric acid (GABA)ergic neurotransmission may underlie the pathophysiology of schizophrenia. We attempted an integrative review, of studies pertaining to recent advances of schizophrenia research with a focus on neuroimaging and genetic studies. Additionally, we present the preliminary findings of the clinical research in our outpatient unit, specialized for early intervention, at the University of Tokyo Hospital. (author)

  14. Separating intrinsic from extrinsic fluctuations in dynamic biological systems.

    Science.gov (United States)

    Hilfinger, Andreas; Paulsson, Johan

    2011-07-19

    From molecules in cells to organisms in ecosystems, biological populations fluctuate due to the intrinsic randomness of individual events and the extrinsic influence of changing environments. The combined effect is often too complex for effective analysis, and many studies therefore make simplifying assumptions, for example ignoring either intrinsic or extrinsic effects to reduce the number of model assumptions. Here we mathematically demonstrate how two identical and independent reporters embedded in a shared fluctuating environment can be used to identify intrinsic and extrinsic noise terms, but also how these contributions are qualitatively and quantitatively different from what has been previously reported. Furthermore, we show for which classes of biological systems the noise contributions identified by dual-reporter methods correspond to the noise contributions predicted by correct stochastic models of either intrinsic or extrinsic mechanisms. We find that for broad classes of systems, the extrinsic noise from the dual-reporter method can be rigorously analyzed using models that ignore intrinsic stochasticity. In contrast, the intrinsic noise can be rigorously analyzed using models that ignore extrinsic stochasticity only under very special conditions that rarely hold in biology. Testing whether the conditions are met is rarely possible and the dual-reporter method may thus produce flawed conclusions about the properties of the system, particularly about the intrinsic noise. Our results contribute toward establishing a rigorous framework to analyze dynamically fluctuating biological systems.

  15. Biological Sampling Variability Study

    Energy Technology Data Exchange (ETDEWEB)

    Amidan, Brett G. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Hutchison, Janine R. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2016-11-08

    There are many sources of variability that exist in the sample collection and analysis process. This paper addresses many, but not all, sources of variability. The main focus of this paper was to better understand and estimate variability due to differences between samplers. Variability between days was also studied, as well as random variability within each sampler. Experiments were performed using multiple surface materials (ceramic and stainless steel), multiple contaminant concentrations (10 spores and 100 spores), and with and without the presence of interfering material. All testing was done with sponge sticks using 10-inch by 10-inch coupons. Bacillus atrophaeus was used as the BA surrogate. Spores were deposited using wet deposition. Grime was coated on the coupons which were planned to include the interfering material (Section 3.3). Samples were prepared and analyzed at PNNL using CDC protocol (Section 3.4) and then cultured and counted. Five samplers were trained so that samples were taken using the same protocol. Each sampler randomly sampled eight coupons each day, four coupons with 10 spores deposited and four coupons with 100 spores deposited. Each day consisted of one material being tested. The clean samples (no interfering materials) were run first, followed by the dirty samples (coated with interfering material). There was a significant difference in recovery efficiency between the coupons with 10 spores deposited (mean of 48.9%) and those with 100 spores deposited (mean of 59.8%). There was no general significant difference between the clean and dirty (containing interfering material) coupons or between the two surface materials; however, there was a significant interaction between concentration amount and presence of interfering material. The recovery efficiency was close to the same for coupons with 10 spores deposited, but for the coupons with 100 spores deposited, the recovery efficiency for the dirty samples was significantly larger (65

  16. Towards a Population Dynamics Theory for Evolutionary Computing: Learning from Biological Population Dynamics in Nature

    Science.gov (United States)

    Ma, Zhanshan (Sam)

    In evolutionary computing (EC), population size is one of the critical parameters that a researcher has to deal with. Hence, it was no surprise that the pioneers of EC, such as De Jong (1975) and Holland (1975), had already studied the population sizing from the very beginning of EC. What is perhaps surprising is that more than three decades later, we still largely depend on the experience or ad-hoc trial-and-error approach to set the population size. For example, in a recent monograph, Eiben and Smith (2003) indicated: "In almost all EC applications, the population size is constant and does not change during the evolutionary search." Despite enormous research on this issue in recent years, we still lack a well accepted theory for population sizing. In this paper, I propose to develop a population dynamics theory forEC with the inspiration from the population dynamics theory of biological populations in nature. Essentially, the EC population is considered as a dynamic system over time (generations) and space (search space or fitness landscape), similar to the spatial and temporal dynamics of biological populations in nature. With this conceptual mapping, I propose to 'transplant' the biological population dynamics theory to EC via three steps: (i) experimentally test the feasibility—whether or not emulating natural population dynamics improves the EC performance; (ii) comparatively study the underlying mechanisms—why there are improvements, primarily via statistical modeling analysis; (iii) conduct theoretical analysis with theoretical models such as percolation theory and extended evolutionary game theory that are generally applicable to both EC and natural populations. This article is a summary of a series of studies we have performed to achieve the general goal [27][30]-[32]. In the following, I start with an extremely brief introduction on the theory and models of natural population dynamics (Sections 1 & 2). In Sections 4 to 6, I briefly discuss three

  17. Dynamic Open Inquiry Performances of High-School Biology Students

    Science.gov (United States)

    Zion, Michal; Sadeh, Irit

    2010-01-01

    In examining open inquiry projects among high-school biology students, we found dynamic inquiry performances expressed in two criteria: "changes occurring during inquiry" and "procedural understanding". Characterizing performances in a dynamic open inquiry project can shed light on both the procedural and epistemological…

  18. Scaling for Dynamical Systems in Biology.

    Science.gov (United States)

    Ledder, Glenn

    2017-11-01

    Asymptotic methods can greatly simplify the analysis of all but the simplest mathematical models and should therefore be commonplace in such biological areas as ecology and epidemiology. One essential difficulty that limits their use is that they can only be applied to a suitably scaled dimensionless version of the original dimensional model. Many books discuss nondimensionalization, but with little attention given to the problem of choosing the right scales and dimensionless parameters. In this paper, we illustrate the value of using asymptotics on a properly scaled dimensionless model, develop a set of guidelines that can be used to make good scaling choices, and offer advice for teaching these topics in differential equations or mathematical biology courses.

  19. Dynamic programming algorithms for biological sequence comparison.

    Science.gov (United States)

    Pearson, W R; Miller, W

    1992-01-01

    Efficient dynamic programming algorithms are available for a broad class of protein and DNA sequence comparison problems. These algorithms require computer time proportional to the product of the lengths of the two sequences being compared [O(N2)] but require memory space proportional only to the sum of these lengths [O(N)]. Although the requirement for O(N2) time limits use of the algorithms to the largest computers when searching protein and DNA sequence databases, many other applications of these algorithms, such as calculation of distances for evolutionary trees and comparison of a new sequence to a library of sequence profiles, are well within the capabilities of desktop computers. In particular, the results of library searches with rapid searching programs, such as FASTA or BLAST, should be confirmed by performing a rigorous optimal alignment. Whereas rapid methods do not overlook significant sequence similarities, FASTA limits the number of gaps that can be inserted into an alignment, so that a rigorous alignment may extend the alignment substantially in some cases. BLAST does not allow gaps in the local regions that it reports; a calculation that allows gaps is very likely to extend the alignment substantially. Although a Monte Carlo evaluation of the statistical significance of a similarity score with a rigorous algorithm is much slower than the heuristic approach used by the RDF2 program, the dynamic programming approach should take less than 1 hr on a 386-based PC or desktop Unix workstation. For descriptive purposes, we have limited our discussion to methods for calculating similarity scores and distances that use gap penalties of the form g = rk. Nevertheless, programs for the more general case (g = q+rk) are readily available. Versions of these programs that run either on Unix workstations, IBM-PC class computers, or the Macintosh can be obtained from either of the authors.

  20. Applications of dynamical systems in biology and medicine

    CERN Document Server

    Radunskaya, Ami

    2015-01-01

    This volume highlights problems from a range of biological and medical applications that can be interpreted as questions about system behavior or control.  Topics include drug resistance in cancer and malaria, biological fluid dynamics, auto-regulation in the kidney, anti-coagulation therapy, evolutionary diversification and photo-transduction.  Mathematical techniques used to describe and investigate these biological and medical problems include ordinary, partial and stochastic differentiation equations, hybrid discrete-continuous approaches, as well as 2 and 3D numerical simulation. .

  1. Quantum and classical dynamics in biologically inspired systems

    International Nuclear Information System (INIS)

    Guerreschi, G.

    2012-01-01

    Quantum biology is an emerging field in which traditional believes and paradigms are under examination. Typically, quantum effects are witnessed inside quantum optics or atomic physics laboratories in systems which are kept under control and isolated from any noise source by means of very advanced technology. Biological systems exhibit opposite characteristics: They are usually constituted of macromolecules continuously exposed to a warm and wet environment, well beyond our control; but at the same time, they operate far away from equilibrium. Recently, the experimental observation of excitonic coherence in photosynthetic complexes has con firmed that, in non-equilibrium scenarios, quantum phenomena can survive even in presence of a noisy environment. The challenge faced by the ongoing research is twofold: On one side, considering biological molecules as effective nanomachines, one has to address questions of principle regarding their design and functioning; on the other side, one has to investigate real systems which are experimentally accessible and identify such features in these concrete scenarios. The present thesis contributes to both of these aspects. In Part I, we demonstrate how entanglement can be persistently generated even under unfavorable environmental conditions. The physical mechanism is modeled after the idea of conformational changes, and it relies on the interplay of classical oscillations of large structures with the quantum dynamics of a few interacting degrees of freedom. In a similar context, we show that the transfer of an excitation through a linear chain of sites can be enhanced when the inter-site distances oscillate periodically. This enhancement is present even in comparison with the static con figuration which is optimal in the classical case and, therefore, it constitutes a clear signature of the underlying quantum dynamics. In Part II of this thesis, we study the radical pair mechanism from the perspective of quantum control and

  2. The biology and dynamics of mammalian cortical granules

    Directory of Open Access Journals (Sweden)

    Liu Min

    2011-11-01

    Full Text Available Abstract Cortical granules are membrane bound organelles located in the cortex of unfertilized oocytes. Following fertilization, cortical granules undergo exocytosis to release their contents into the perivitelline space. This secretory process, which is calcium dependent and SNARE protein-mediated pathway, is known as the cortical reaction. After exocytosis, the released cortical granule proteins are responsible for blocking polyspermy by modifying the oocytes' extracellular matrices, such as the zona pellucida in mammals. Mammalian cortical granules range in size from 0.2 um to 0.6 um in diameter and different from most other regulatory secretory organelles in that they are not renewed once released. These granules are only synthesized in female germ cells and transform an egg upon sperm entry; therefore, this unique cellular structure has inherent interest for our understanding of the biology of fertilization. Cortical granules are long thought to be static and awaiting in the cortex of unfertilized oocytes to be stimulated undergoing exocytosis upon gamete fusion. Not till recently, the dynamic nature of cortical granules is appreciated and understood. The latest studies of mammalian cortical granules document that this organelle is not only biochemically heterogeneous, but also displays complex distribution during oocyte development. Interestingly, some cortical granules undergo exocytosis prior to fertilization; and a number of granule components function beyond the time of fertilization in regulating embryonic cleavage and preimplantation development, demonstrating their functional significance in fertilization as well as early embryonic development. The following review will present studies that investigate the biology of cortical granules and will also discuss new findings that uncover the dynamic aspect of this organelle in mammals.

  3. Soil and terrestrial biology studies

    International Nuclear Information System (INIS)

    Anon.

    1976-01-01

    Soil and terrestrial biology studies focused on developing an understanding of the uptake of gaseous substances from the atmosphere by plants, biodegradation of oil, and the movement of Pu in the terrestrial ecosystems of the southeastern United States. Mathematical models were developed for SO 2 and tritium uptake from the atmosphere by plants; the uptake of tritium by soil microorganisms was measured; and the relationships among the Pu content of soil, plants, and animals of the Savannah River Plant area were studied. Preliminary results are reported for studies on the biodegradation of waste oil on soil surfaces

  4. Quantum Processes and Dynamic Networks in Physical and Biological Systems.

    Science.gov (United States)

    Dudziak, Martin Joseph

    Quantum theory since its earliest formulations in the Copenhagen Interpretation has been difficult to integrate with general relativity and with classical Newtonian physics. There has been traditionally a regard for quantum phenomena as being a limiting case for a natural order that is fundamentally classical except for microscopic extrema where quantum mechanics must be applied, more as a mathematical reconciliation rather than as a description and explanation. Macroscopic sciences including the study of biological neural networks, cellular energy transports and the broad field of non-linear and chaotic systems point to a quantum dimension extending across all scales of measurement and encompassing all of Nature as a fundamentally quantum universe. Theory and observation lead to a number of hypotheses all of which point to dynamic, evolving networks of fundamental or elementary processes as the underlying logico-physical structure (manifestation) in Nature and a strongly quantized dimension to macroscalar processes such as are found in biological, ecological and social systems. The fundamental thesis advanced and presented herein is that quantum phenomena may be the direct consequence of a universe built not from objects and substance but from interacting, interdependent processes collectively operating as sets and networks, giving rise to systems that on microcosmic or macroscopic scales function wholistically and organically, exhibiting non-locality and other non -classical phenomena. The argument is made that such effects as non-locality are not aberrations or departures from the norm but ordinary consequences of the process-network dynamics of Nature. Quantum processes are taken to be the fundamental action-events within Nature; rather than being the exception quantum theory is the rule. The argument is also presented that the study of quantum physics could benefit from the study of selective higher-scale complex systems, such as neural processes in the brain

  5. Receptor studies in biological psychiatry

    International Nuclear Information System (INIS)

    Fujiwara, Yutaka

    1992-01-01

    Recent advances in the pharmacological treatment of endogenous psychosis have led to the development of biological studies in psychiatry. Studies on neurotransmitter receptors were reviewed in order to apply positron-emission tomograph (PET) for biological psychiatry. The dopamine (DA) hypothesis for schizophrenia was advanced on the basis of the observed effects of neuroleptics and methamphetamine, and DA(D 2 ) receptor supersensitivity measured by PET and receptor binding in the schizophrenic brain. The clinical potencies of neuroleptics for schizophrenia were correlated with their abilities to inhibit the D 2 receptor, and not other receptors. The σ receptor was expected to be a site of antipsychotic action. However, the potency of drugs action on it was not correlated with clinical efficacy. Haloperidol binds with high affinity to the σ receptor, which may mediate acute dystonia, an extrapyramidal side effect of neuroleptics. Behavioral and neurochemical changes induced by methamphetamine treatment were studied as an animal model of schizophrenia, and both a decrease of D 2 receptor density and an increase of DA release were detected. The monoamine hypothesis for manic-depressive psychosis was advanced on the basis of the effect of reserpine, monoamine oxidase inhibitor and antidepressants. 3 H-clonidine binding sites were increased in platelet membranes of depressive patients, 3 H-imipramine binding sites were decreased. The GABA A receptor is the target site for the action of anxiolytics and antiepileptics such as benzodiazepines and barbiturates. Recent developments in molecular biology techniques have revealed the structure of receptor proteins, which are classified into two receptor families, the G-protein coupled type (D 2 ) and the ion-channel type (GABA A ). (J.P.N.)

  6. Breeding biology and the evolution of dynamic sexual dichromatism in frogs.

    Science.gov (United States)

    Bell, R C; Webster, G N; Whiting, M J

    2017-12-01

    Dynamic sexual dichromatism is a temporary colour change between the sexes and has evolved independently in a wide range of anurans, many of which are explosive breeders wherein males physically compete for access to females. Behavioural studies in a few species indicate that dynamic dichromatism functions as a visual signal in large breeding aggregations; however, the prevalence of this trait and the social and environmental factors underlying its expression are poorly understood. We compiled a database of 178 anurans with dynamic dichromatism that include representatives from 15 families and subfamilies. Dynamic dichromatism is common in two of the three subfamilies of hylid treefrogs. Phylogenetic comparative analyses of 355 hylid species (of which 95 display dynamic dichromatism) reveal high transition rates between dynamic dichromatism, ontogenetic (permanent) dichromatism and monochromatism reflecting the high evolutionary lability of this trait. Correlated evolution in hylids between dynamic dichromatism and forming large breeding aggregations indicates that the evolution of large breeding aggregations precedes the evolution of dynamic dichromatism. Multivariate phylogenetic logistic regression recovers the interaction between biogeographic distribution and forming breeding aggregations as a significant predictor of dynamic dichromatism in hylids. Accounting for macroecological differences between temperate and tropical regions, such as seasonality and the availability of breeding sites, may improve our understanding of ecological contexts in which dynamic dichromatism is likely to arise in tropical lineages and why it is retained in some temperate species and lost in others. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

  7. Self-Organized Biological Dynamics and Nonlinear Control

    Science.gov (United States)

    Walleczek, Jan

    2006-04-01

    The frontiers and challenges of biodynamics research Jan Walleczek; Part I. Nonlinear Dynamics in Biology and Response to Stimuli: 1. External signals and internal oscillation dynamics - principal aspects and response of stimulated rhythmic processes Friedemann Kaiser; 2. Nonlinear dynamics in biochemical and biophysical systems: from enzyme kinetics to epilepsy Raima Larter, Robert Worth and Brent Speelman; 3. Fractal mechanisms in neural control: human heartbeat and gait dynamics in health and disease Chung-Kang Peng, Jeffrey M. Hausdorff and Ary L. Goldberger; 4. Self-organising dynamics in human coordination and perception Mingzhou Ding, Yanqing Chen, J. A. Scott Kelso and Betty Tuller; 5. Signal processing in biochemical reaction networks Adam P. Arkin; Part II. Nonlinear Sensitivity of Biological Systems to Electromagnetic Stimuli: 6. Electrical signal detection and noise in systems with long-range coherence Paul C. Gailey; 7. Oscillatory signals in migrating neutrophils: effects of time-varying chemical and electrical fields Howard R. Petty; 8. Enzyme kinetics and nonlinear biochemical amplification in response to static and oscillating magnetic fields Jan Walleczek and Clemens F. Eichwald; 9. Magnetic field sensitivity in the hippocampus Stefan Engström, Suzanne Bawin and W. Ross Adey; Part III. Stochastic Noise-Induced Dynamics and Transport in Biological Systems: 10. Stochastic resonance: looking forward Frank Moss; 11. Stochastic resonance and small-amplitude signal transduction in voltage-gated ion channels Sergey M. Bezrukov and Igor Vodyanoy; 12. Ratchets, rectifiers and demons: the constructive role of noise in free energy and signal transduction R. Dean Astumian; 13. Cellular transduction of periodic and stochastic energy signals by electroconformational coupling Tian Y. Tsong; Part IV. Nonlinear Control of Biological and Other Excitable Systems: 14. Controlling chaos in dynamical systems Kenneth Showalter; 15. Electromagnetic fields and biological

  8. Modeling dynamics of biological and chemical components of aquatic ecosystems

    International Nuclear Information System (INIS)

    Lassiter, R.R.

    1975-05-01

    To provide capability to model aquatic ecosystems or their subsystems as needed for particular research goals, a modeling strategy was developed. Submodels of several processes common to aquatic ecosystems were developed or adapted from previously existing ones. Included are submodels for photosynthesis as a function of light and depth, biological growth rates as a function of temperature, dynamic chemical equilibrium, feeding and growth, and various types of losses to biological populations. These submodels may be used as modules in the construction of models of subsystems or ecosystems. A preliminary model for the nitrogen cycle subsystem was developed using the modeling strategy and applicable submodels. (U.S.)

  9. Dynamically analyzing cell interactions in biological environments using multiagent social learning framework.

    Science.gov (United States)

    Zhang, Chengwei; Li, Xiaohong; Li, Shuxin; Feng, Zhiyong

    2017-09-20

    Biological environment is uncertain and its dynamic is similar to the multiagent environment, thus the research results of the multiagent system area can provide valuable insights to the understanding of biology and are of great significance for the study of biology. Learning in a multiagent environment is highly dynamic since the environment is not stationary anymore and each agent's behavior changes adaptively in response to other coexisting learners, and vice versa. The dynamics becomes more unpredictable when we move from fixed-agent interaction environments to multiagent social learning framework. Analytical understanding of the underlying dynamics is important and challenging. In this work, we present a social learning framework with homogeneous learners (e.g., Policy Hill Climbing (PHC) learners), and model the behavior of players in the social learning framework as a hybrid dynamical system. By analyzing the dynamical system, we obtain some conditions about convergence or non-convergence. We experimentally verify the predictive power of our model using a number of representative games. Experimental results confirm the theoretical analysis. Under multiagent social learning framework, we modeled the behavior of agent in biologic environment, and theoretically analyzed the dynamics of the model. We present some sufficient conditions about convergence or non-convergence and prove them theoretically. It can be used to predict the convergence of the system.

  10. Dissipative particle dynamics simulations for biological tissues: rheology and competition

    International Nuclear Information System (INIS)

    Basan, Markus; Prost, Jacques; Joanny, Jean-François; Elgeti, Jens

    2011-01-01

    In this work, we model biological tissues using a simple, mechanistic simulation based on dissipative particle dynamics. We investigate the continuum behavior of the simulated tissue and determine its dependence on the properties of the individual cell. Cells in our simulation adhere to each other, expand in volume, divide after reaching a specific size checkpoint and undergo apoptosis at a constant rate, leading to a steady-state homeostatic pressure in the tissue. We measure the dependence of the homeostatic state on the microscopic parameters of our model and show that homeostatic pressure, rather than the unconfined rate of cell division, determines the outcome of tissue competitions. Simulated cell aggregates are cohesive and round up due to the effect of tissue surface tension, which we measure for different tissues. Furthermore, mixtures of different cells unmix according to their adhesive properties. Using a variety of shear and creep simulations, we study tissue rheology by measuring yield stresses, shear viscosities, complex viscosities as well as the loss tangents as a function of model parameters. We find that cell division and apoptosis lead to a vanishing yield stress and fluid-like tissues. The effects of different adhesion strengths and levels of noise on the rheology of the tissue are also measured. In addition, we find that the level of cell division and apoptosis drives the diffusion of cells in the tissue. Finally, we present a method for measuring the compressibility of the tissue and its response to external stress via cell division and apoptosis

  11. Structural Studies of Biological Solids Using NMR

    Science.gov (United States)

    Ramamoorthy, Ayyalusamy

    2011-03-01

    High-resolution structure and dynamics of biological molecules are important in understanding their function. While studies have been successful in solving the structures of water-soluble biomolecules, it has been proven difficult to determine the structures of membrane proteins and fibril systems. Recent studies have shown that solid-state NMR is a promising technique and could be highly valuable in studying such non-crystalline and non-soluble biosystems. I will present strategies to study the structures of such challenging systems and also about the applications of solid-state NMR to study the modes of membrane-peptide interactions for a better assessment of the prospects of antimicrobial peptides as substitutes to antibiotics in the control of human disease. Our studies on the mechanism of membrane disruption by LL-37 (a human antimicrobial peptide), analogs of the naturally occurring antimicrobial peptide magainin2 extracted from the skin of the African frog Xenopus Laevis, and pardaxin will be presented. Solid-state NMR experiments were used to determine the secondary structure, dynamics and topology of these peptides in lipid bilayers. Similarities and difference in the cell-lysing mechanism, and their dependence on the membrane composition, of these peptides will be discussed. Atomic-level resolution NMR structures of amyloidogenic proteins revealing the misfolding pathway and early intermediates that play key roles in amyloid toxicity will also be presented.

  12. Studies on biological macromolecules by neutron inelastic scattering

    International Nuclear Information System (INIS)

    Fujiwara, Satoru; Nakagawa, Hiroshi

    2013-01-01

    Neutron inelastic scattering techniques, including quasielastic and elastic incoherent neutron scattering, provide unique tools to directly measure the protein dynamics at a picosecond time scale. Since the protein dynamics at this time scale is indispensable to the protein functions, elucidation of the protein dynamics is indispensable for ultimate understanding of the protein functions. There are two complementary directions of the protein dynamics studies: one is to explore the physical basis of the protein dynamics using 'model' proteins, and the other is more biology-oriented. Examples of the studies on the protein dynamics with neutron inelastic scattering are described. The examples of the studies in the former direction include the studies on the dynamical transitions of the proteins, the relationship between the protein dynamics and the hydration water dynamics, and combined analysis of the protein dynamics with molecular dynamics simulation. The examples of the studies in the latter direction include the elastic incoherent and quasielastic neutrons scattering studies of actin. Future prospects of the studies on the protein dynamics with neutron scattering are briefly described. (author)

  13. Bayesian integration of position and orientation cues in perception of biological and non-biological dynamic forms

    Directory of Open Access Journals (Sweden)

    Steven Matthew Thurman

    2014-02-01

    Full Text Available Visual form analysis is fundamental to shape perception and likely plays a central role in perception of more complex dynamic shapes, such as moving objects or biological motion. Two primary form-based cues serve to represent the overall shape of an object: the spatial position and the orientation of locations along the boundary of the object. However, it is unclear how the visual system integrates these two sources of information in dynamic form analysis, and in particular how the brain resolves ambiguities due to sensory uncertainty and/or cue conflict. In the current study, we created animations of sparsely-sampled dynamic objects (human walkers or rotating squares comprised of oriented Gabor patches in which orientation could either coincide or conflict with information provided by position cues. When the cues were incongruent, we found a characteristic trade-off between position and orientation information whereby position cues increasingly dominated perception as the relative uncertainty of orientation increased and vice versa. Furthermore, we found no evidence for differences in the visual processing of biological and non-biological objects, casting doubt on the claim that biological motion may be specialized in the human brain, at least in specific terms of form analysis. To explain these behavioral results quantitatively, we adopt a probabilistic template-matching model that uses Bayesian inference within local modules to estimate object shape separately from either spatial position or orientation signals. The outputs of the two modules are integrated with weights that reflect individual estimates of subjective cue reliability, and integrated over time to produce a decision about the perceived dynamics of the input data. Results of this model provided a close fit to the behavioral data, suggesting a mechanism in the human visual system that approximates rational Bayesian inference to integrate position and orientation signals in dynamic

  14. Studies in Chemical Dynamics

    International Nuclear Information System (INIS)

    Rabitz, Herschel; Ho, Tak-San

    2003-01-01

    This final report draws together the research carried from February, 1986 through January, 2003 concerning a series of topics in chemical dynamics. The specific areas of study include molecular collisions, chemical kinetics, data inversion to extract potential energy surfaces, and model reduction of complex kinetic systems

  15. Dynamical 'in situ' observation of biological samples using variable pressure scanning electron microscope

    International Nuclear Information System (INIS)

    Nedela, V

    2008-01-01

    Possibilities of 'in-situ' observation of non-conductive biological samples free of charging artefacts in dynamically changed surrounding conditions are the topic of this work. The observed biological sample, the tongue of a rat, was placed on a cooled Peltier stage. We studied the visibility of topographical structure depending on transition between liquid and gas state of water in the specimen chamber of VP SEM.

  16. Information-theoretic analysis of the dynamics of an executable biological model.

    Directory of Open Access Journals (Sweden)

    Avital Sadot

    Full Text Available To facilitate analysis and understanding of biological systems, large-scale data are often integrated into models using a variety of mathematical and computational approaches. Such models describe the dynamics of the biological system and can be used to study the changes in the state of the system over time. For many model classes, such as discrete or continuous dynamical systems, there exist appropriate frameworks and tools for analyzing system dynamics. However, the heterogeneous information that encodes and bridges molecular and cellular dynamics, inherent to fine-grained molecular simulation models, presents significant challenges to the study of system dynamics. In this paper, we present an algorithmic information theory based approach for the analysis and interpretation of the dynamics of such executable models of biological systems. We apply a normalized compression distance (NCD analysis to the state representations of a model that simulates the immune decision making and immune cell behavior. We show that this analysis successfully captures the essential information in the dynamics of the system, which results from a variety of events including proliferation, differentiation, or perturbations such as gene knock-outs. We demonstrate that this approach can be used for the analysis of executable models, regardless of the modeling framework, and for making experimentally quantifiable predictions.

  17. Molecular dynamics modeling the synthetic and biological polymers interactions pre-studied via docking: anchors modified polyanions interference with the HIV-1 fusion mediator.

    Science.gov (United States)

    Tsvetkov, Vladimir B; Serbin, Alexander V

    2014-06-01

    In previous works we reported the design, synthesis and in vitro evaluations of synthetic anionic polymers modified by alicyclic pendant groups (hydrophobic anchors), as a novel class of inhibitors of the human immunodeficiency virus type 1 (HIV-1) entry into human cells. Recently, these synthetic polymers interactions with key mediator of HIV-1 entry-fusion, the tri-helix core of the first heptad repeat regions [HR1]3 of viral envelope protein gp41, were pre-studied via docking in terms of newly formulated algorithm for stepwise approximation from fragments of polymeric backbone and side-group models toward real polymeric chains. In the present article the docking results were verified under molecular dynamics (MD) modeling. In contrast with limited capabilities of the docking, the MD allowed of using much more large models of the polymeric ligands, considering flexibility of both ligand and target simultaneously. Among the synthesized polymers the dinorbornen anchors containing alternating copolymers of maleic acid were selected as the most representative ligands (possessing the top anti-HIV activity in vitro in correlation with the highest binding energy in the docking). To verify the probability of binding of the polymers with the [HR1]3 in the sites defined via docking, various starting positions of polymer chains were tried. The MD simulations confirmed the main docking-predicted priority for binding sites, and possibilities for axial and belting modes of the ligands-target interactions. Some newly MD-discovered aspects of the ligand's backbone and anchor units dynamic cooperation in binding the viral target clarify mechanisms of the synthetic polymers anti-HIV activity and drug resistance prevention.

  18. Structural biology by NMR: structure, dynamics, and interactions.

    Directory of Open Access Journals (Sweden)

    Phineus R L Markwick

    2008-09-01

    Full Text Available The function of bio-macromolecules is determined by both their 3D structure and conformational dynamics. These molecules are inherently flexible systems displaying a broad range of dynamics on time-scales from picoseconds to seconds. Nuclear Magnetic Resonance (NMR spectroscopy has emerged as the method of choice for studying both protein structure and dynamics in solution. Typically, NMR experiments are sensitive both to structural features and to dynamics, and hence the measured data contain information on both. Despite major progress in both experimental approaches and computational methods, obtaining a consistent view of structure and dynamics from experimental NMR data remains a challenge. Molecular dynamics simulations have emerged as an indispensable tool in the analysis of NMR data.

  19. Mass spectrometry in structural biology and biophysics architecture, dynamics, and interaction of biomolecules

    CERN Document Server

    Kaltashov, Igor A; Desiderio, Dominic M; Nibbering, Nico M

    2012-01-01

    The definitive guide to mass spectrometry techniques in biology and biophysics The use of mass spectrometry (MS) to study the architecture and dynamics of proteins is increasingly common within the biophysical community, and Mass Spectrometry in Structural Biology and Biophysics: Architecture, Dynamics, and Interaction of Biomolecules, Second Edition provides readers with detailed, systematic coverage of the current state of the art. Offering an unrivalled overview of modern MS-based armamentarium that can be used to solve the most challenging problems in biophysics, structural biol

  20. Female juvenile murderers: Biological and psychological dynamics leading to homicide.

    Science.gov (United States)

    Heide, Kathleen M; Solomon, Eldra P

    2009-01-01

    The increasing involvement of girls under 18 in violent crime has been a matter of growing concern in the United States in recent years. This article reviews the arrests of female juveniles for violent crime and then focuses specifically on their involvement in homicide. Arrests of girls for murder, unlike arrests for assault, have not risen over the last 30 years, suggesting that the dynamics that propel female juveniles to engage in lethal violence differ from those contributing to assaultive behavior by this same group. A review of the literature indicates that theories as to why female adolescents kill do not take into account recent scientific findings on brain development and the biological effects of early trauma in explaining serious violent behavior by girls. Three cases, evaluated by the authors, involving female adolescents charged with murder or attempted murder, are presented. The authors focus on the biological and psychological dynamics that help explain their violent behavior. They discuss the effects of insecure attachment and child maltreatment, and trace a critical pathway between these early experiences and future risk of violent behavior. The dynamics of child maltreatment in fostering rage and violence are discussed thereafter in terms of offender accountability. The article concludes with a discussion of treatment and recommendations for future research.

  1. River, delta and coastal morphological response accounting for biological dynamics

    Directory of Open Access Journals (Sweden)

    W. Goldsmith

    2015-03-01

    Full Text Available Management and construction can increase resilience in the face of climate change, and benefits can be enhanced through integration of biogenic materials including shells and vegetation. Rivers and coastal landforms are dynamic systems that respond to intentional and unintended manipulation of critical factors, often with unforeseen and/or undesirable resulting effects. River management strategies have impacts that include deltas and coastal areas which are increasingly vulnerable to climate change with reference to sea level rise and storm intensity. Whereas conventional assessment and analysis of rivers and coasts has relied on modelling of hydrology, hydraulics and sediment transport, incorporating additional biological factors can offer more comprehensive, beneficial and realistic alternatives. Suitable modelling tools can provide improved decision support. The question has been whether current models can effectively address biological responses with suitable reliability and efficiency. Since morphodynamic evolution exhibits its effects on a large timescale, the choice of mathematical model is not trivial and depends upon the availability of data, as well as the spatial extent, timelines and computation effort desired. The ultimate goal of the work is to set up a conveniently simplified river morphodynamic model, coupled with a biological dynamics plant population model able to predict the long-term evolution of large alluvial river systems managed through bioengineering. This paper presents the first step of the work related to the application of the model accounting for stationary vegetation condition. Sensitivity analysis has been performed on the main hydraulic, sedimentology, and biological parameters. The model has been applied to significant river training in Europe, Asia and North America, and comparative analysis has been used to validate analytical solutions. Data gaps and further areas for investigation are identified.

  2. River, delta and coastal morphological response accounting for biological dynamics

    Science.gov (United States)

    Goldsmith, W.; Bernardi, D.; Schippa, L.

    2015-03-01

    Management and construction can increase resilience in the face of climate change, and benefits can be enhanced through integration of biogenic materials including shells and vegetation. Rivers and coastal landforms are dynamic systems that respond to intentional and unintended manipulation of critical factors, often with unforeseen and/or undesirable resulting effects. River management strategies have impacts that include deltas and coastal areas which are increasingly vulnerable to climate change with reference to sea level rise and storm intensity. Whereas conventional assessment and analysis of rivers and coasts has relied on modelling of hydrology, hydraulics and sediment transport, incorporating additional biological factors can offer more comprehensive, beneficial and realistic alternatives. Suitable modelling tools can provide improved decision support. The question has been whether current models can effectively address biological responses with suitable reliability and efficiency. Since morphodynamic evolution exhibits its effects on a large timescale, the choice of mathematical model is not trivial and depends upon the availability of data, as well as the spatial extent, timelines and computation effort desired. The ultimate goal of the work is to set up a conveniently simplified river morphodynamic model, coupled with a biological dynamics plant population model able to predict the long-term evolution of large alluvial river systems managed through bioengineering. This paper presents the first step of the work related to the application of the model accounting for stationary vegetation condition. Sensitivity analysis has been performed on the main hydraulic, sedimentology, and biological parameters. The model has been applied to significant river training in Europe, Asia and North America, and comparative analysis has been used to validate analytical solutions. Data gaps and further areas for investigation are identified.

  3. Compartmental study of biological systems

    International Nuclear Information System (INIS)

    Moretti, J.L.

    1975-01-01

    The compartmental analysis of biological system is dealt with on several chapters devoted successively to: terminology; a mathematical and symbolic account of a system at equilibrium; different compartment systems; analysis of the experimental results. For this it is pointed out that the application of compartmental systems to biological phenomena is not always without danger. Sometimes the compartmental system established in a reference subject fails to conform in the patient. The compartments can divide into two or join together, completely changing the aspect of the system so that parameters calculated with the old model become entirely false. The conclusion is that the setting up of a compartmental system to represent a biological phenomenon is a tricky undertaking and the results must be constantly criticized and questioned [fr

  4. Dynamic light scattering with applications to chemistry, biology, and physics

    CERN Document Server

    Berne, Bruce J

    2000-01-01

    Lasers play an increasingly important role in a variety of detection techniques, making inelastic light scattering a tool of growing value in the investigation of dynamic and structural problems in chemistry, biology, and physics. Until the initial publication of this work, however, no monograph treated the principles behind current developments in the field.This volume presents a comprehensive introduction to the principles underlying laser light scattering, focusing on the time dependence of fluctuations in fluid systems; it also serves as an introduction to the theory of time correlation f

  5. Appendix U: benthic biological studies

    International Nuclear Information System (INIS)

    Hessler, R.R.

    1981-01-01

    Characterization of the biology and standing crop of the benthic organisms is divided into two major categories: (1) those organisms (sessile or with limited mobility) that live on or within the sediment (infauna); and (2) highly mobile organisms that have contact (if only occasionally) with the sediment (benthopelagic organisms). At this time our studies of benthopelagic organisms are restricted to amphipods. The amphipods trapped at MPG-I (30 to 31 0 N, 159 0 W) in 1978 have been sorted to species and compared with those trapped at Climax II (28 0 N, 155 to 156 0 W) in 1977. The species composition is the same at both stations and the numerical representation of the various species appears to be equivalent. Instar categories based on morphological and size criteria have been determined for Eurythenes gryllus. Comparison of the size range of the instar categories, morphological characters and female to male ratio show no detectable differences in E. gryllus from the two areas. Individuals of one of the smaller species of amphipods (Paralicella caperesca) were trapped at 710 m above the sediment, demonstrating that although the primary range of this species is 0-1 m off the bottom, it is capable of wide bathymetric movements. Males mature at a much smaller size (7 cm vs 11.5 cm) than females. Females appear to breed only once while males seem to be reproductively mature for several instars. After attaining maturity, male growth decreases to almost half the previous rate, and the time interval between molts appears to increase substantially. Females approximate a linear growth rate throughout their instar stages. The data are insufficient to determine if a decrease in growth rate occurs at the molt to maturity (female 14). The apparent difference in the time to maturity for males and females results in a high number of mature males present in the population to fertilize relatively few females

  6. Biology as population dynamics: heuristics for transmission risk.

    Science.gov (United States)

    Keebler, Daniel; Walwyn, David; Welte, Alex

    2013-02-01

    Population-type models, accounting for phenomena such as population lifetimes, mixing patterns, recruitment patterns, genetic evolution and environmental conditions, can be usefully applied to the biology of HIV infection and viral replication. A simple dynamic model can explore the effect of a vaccine-like stimulus on the mortality and infectiousness, which formally looks like fertility, of invading virions; the mortality of freshly infected cells; and the availability of target cells, all of which impact on the probability of infection. Variations on this model could capture the importance of the timing and duration of different key events in viral transmission, and hence be applied to questions of mucosal immunology. The dynamical insights and assumptions of such models are compatible with the continuum of between- and within-individual risks in sexual violence and may be helpful in making sense of the sparse data available on the association between HIV transmission and sexual violence. © 2012 John Wiley & Sons A/S.

  7. Tritium biological effects and perspective of the biological study

    International Nuclear Information System (INIS)

    Komatsu, Kenshi

    1998-01-01

    Since tritium is an emitter of weak β-rays (5.7keV) and is able to bind to DNA, i.e., the most important genome component, the biological effects should be expected to be more profound than that of X-rays and γ-rays. When carcinogenesis, genetical effects and the detriments for fetus and embryo were used as a biological endpoint, most of tritium RBE (relative biological effectiveness) ranged from 1 to 2. The tritium risk in man could be calculated from these RBEs and γ-ray risk for human exposure, which are obtained mainly from the data on Atomic Bomb survivors. However, the exposure modality from environmental tritium should be a chronic irradiation with ultra low dose rate or a fractionated irradiation. We must estimate the tritium effect in man based on biological experiments alone, due to lack of such epidemiological data. Low dose rate experiment should be always accompanied by the statistical problem of data, since their biological effects are fairy low, and they should involve a possible repair system, such as adaptive response (or hormesis effect) and 'Kada effect' observed in bacteria. Here we discuss future works for the tritium assessment in man, such as (1) developing a high radiation sensitive assay system with rodent hybrid cells containing a single human chromosome and also (2) study on mammal DNA repair at molecular levels using a radiosensitive hereditary disease, Nijmegen Breakage Syndrome. (author)

  8. Photonic engineering for biological study

    Science.gov (United States)

    Wu, Fei

    My dissertation focuses on designing and developing prototypes of optical tools in the laboratory that can facilitate practical medical therapies. More specifically, this dissertation examines two novel biophotonic techniques: (1) a frequency multiplexed confocal microscope with the potential to provide rational therapy of congestive heart failure (CHF), and (2) the "optical comb" with the potential to improve results of retina reattachment surgery and accelerate post surgical recovery. Next, I will discuss the background, design and initial experimental results of each study individually. Part I: The Frequency Multiplexed Confocal Microscope. To overcome the limitations of existing confocal microscope technology, this dissertation proposes a non-scanning, real-time, high resolution technique (a multi-point frequency multiplexed confocal microscope) to measure 3-D intracellular calcium ion concentration in a living cardiac myocyte. This method can be also applied to measure the intracellular sodium ion concentration, or other ions in which high quantum-yield fluorescent probes are available. The novelty of the proposed research lies in the introduction of carrier frequency multiplexing techniques which can differentiate fluorescence emitted at different spatial locations in cardiac myocyte by their modulated frequency. It therefore opens the possibility to visualize the transient dynamics of intracellular dynamics at multiple locations in cells simultaneously, which will shine a new light on our understanding of CHF. The procedure for frequency multiplexing proposed is described below. Multiple incident laser beams are focused onto different locations in an isolated rat cardiac myocyte with each beam modulated at a different carrier frequency. The fluorescence emission at each location therefore bears the same modulated frequency as the stimulation laser beam. Each fluorescence signal is sent to the photo multiplier tube (PMT) after being spatially filtered by a

  9. Nuclear biological studies in France

    International Nuclear Information System (INIS)

    Coursaget, J.

    1961-01-01

    On the occasion of a colloquium on radiobiological research programmes, a number of documents dealing with French accomplishments and projects in this field were collected together. We felt that it would be useful to assemble these papers in one report; although they are brief and leave gaps to be filled in, they provide certain data, give an overall view of the situation, and can also suggest a rough plan for the general policy to adopt in the field of 'nuclear' biological research; i.e. research based on the nuclear tracer method or devoted to the action of ionising radiations. (author) [fr

  10. Protein electron transfer: is biology (thermo)dynamic?

    International Nuclear Information System (INIS)

    Matyushov, Dmitry V

    2015-01-01

    Simple physical mechanisms are behind the flow of energy in all forms of life. Energy comes to living systems through electrons occupying high-energy states, either from food (respiratory chains) or from light (photosynthesis). This energy is transformed into the cross-membrane proton-motive force that eventually drives all biochemistry of the cell. Life’s ability to transfer electrons over large distances with nearly zero loss of free energy is puzzling and has not been accomplished in synthetic systems. The focus of this review is on how this energetic efficiency is realized. General physical mechanisms and interactions that allow proteins to fold into compact water-soluble structures are also responsible for a rugged landscape of energy states and a broad distribution of relaxation times. Specific to a protein as a fluctuating thermal bath is the protein-water interface, which is heterogeneous both dynamically and structurally. The spectrum of interfacial fluctuations is a consequence of protein’s elastic flexibility combined with a high density of surface charges polarizing water dipoles into surface nanodomains. Electrostatics is critical to the protein function and the relevant questions are: (i) What is the spectrum of interfacial electrostatic fluctuations? (ii) Does the interfacial biological water produce electrostatic signatures specific to proteins? (iii) How is protein-mediated chemistry affected by electrostatics? These questions connect the fluctuation spectrum to the dynamical control of chemical reactivity, i.e. the dependence of the activation free energy of the reaction on the dynamics of the bath. Ergodicity is often broken in protein-driven reactions and thermodynamic free energies become irrelevant. Continuous ergodicity breaking in a dense spectrum of relaxation times requires using dynamically restricted ensembles to calculate statistical averages. When applied to the calculation of the rates, this formalism leads to the nonergodic

  11. Parallel computing and molecular dynamics of biological membranes

    International Nuclear Information System (INIS)

    La Penna, G.; Letardi, S.; Minicozzi, V.; Morante, S.; Rossi, G.C.; Salina, G.

    1998-01-01

    In this talk I discuss the general question of the portability of molecular dynamics codes for diffusive systems on parallel computers of the APE family. The intrinsic single precision of the today available platforms does not seem to affect the numerical accuracy of the simulations, while the absence of integer addressing from CPU to individual nodes puts strong constraints on possible programming strategies. Liquids can be satisfactorily simulated using the ''systolic'' method. For more complex systems, like the biological ones at which we are ultimately interested in, the ''domain decomposition'' approach is best suited to beat the quadratic growth of the inter-molecular computational time with the number of atoms of the system. The promising perspectives of using this strategy for extensive simulations of lipid bilayers are briefly reviewed. (orig.)

  12. OFFl Models: Novel Schema for Dynamical Modeling of Biological Systems.

    Science.gov (United States)

    Ogbunugafor, C Brandon; Robinson, Sean P

    2016-01-01

    Flow diagrams are a common tool used to help build and interpret models of dynamical systems, often in biological contexts such as consumer-resource models and similar compartmental models. Typically, their usage is intuitive and informal. Here, we present a formalized version of flow diagrams as a kind of weighted directed graph which follow a strict grammar, which translate into a system of ordinary differential equations (ODEs) by a single unambiguous rule, and which have an equivalent representation as a relational database. (We abbreviate this schema of "ODEs and formalized flow diagrams" as OFFL.) Drawing a diagram within this strict grammar encourages a mental discipline on the part of the modeler in which all dynamical processes of a system are thought of as interactions between dynamical species that draw parcels from one or more source species and deposit them into target species according to a set of transformation rules. From these rules, the net rate of change for each species can be derived. The modeling schema can therefore be understood as both an epistemic and practical heuristic for modeling, serving both as an organizational framework for the model building process and as a mechanism for deriving ODEs. All steps of the schema beyond the initial scientific (intuitive, creative) abstraction of natural observations into model variables are algorithmic and easily carried out by a computer, thus enabling the future development of a dedicated software implementation. Such tools would empower the modeler to consider significantly more complex models than practical limitations might have otherwise proscribed, since the modeling framework itself manages that complexity on the modeler's behalf. In this report, we describe the chief motivations for OFFL, carefully outline its implementation, and utilize a range of classic examples from ecology and epidemiology to showcase its features.

  13. OFFl Models: Novel Schema for Dynamical Modeling of Biological Systems.

    Directory of Open Access Journals (Sweden)

    C Brandon Ogbunugafor

    Full Text Available Flow diagrams are a common tool used to help build and interpret models of dynamical systems, often in biological contexts such as consumer-resource models and similar compartmental models. Typically, their usage is intuitive and informal. Here, we present a formalized version of flow diagrams as a kind of weighted directed graph which follow a strict grammar, which translate into a system of ordinary differential equations (ODEs by a single unambiguous rule, and which have an equivalent representation as a relational database. (We abbreviate this schema of "ODEs and formalized flow diagrams" as OFFL. Drawing a diagram within this strict grammar encourages a mental discipline on the part of the modeler in which all dynamical processes of a system are thought of as interactions between dynamical species that draw parcels from one or more source species and deposit them into target species according to a set of transformation rules. From these rules, the net rate of change for each species can be derived. The modeling schema can therefore be understood as both an epistemic and practical heuristic for modeling, serving both as an organizational framework for the model building process and as a mechanism for deriving ODEs. All steps of the schema beyond the initial scientific (intuitive, creative abstraction of natural observations into model variables are algorithmic and easily carried out by a computer, thus enabling the future development of a dedicated software implementation. Such tools would empower the modeler to consider significantly more complex models than practical limitations might have otherwise proscribed, since the modeling framework itself manages that complexity on the modeler's behalf. In this report, we describe the chief motivations for OFFL, carefully outline its implementation, and utilize a range of classic examples from ecology and epidemiology to showcase its features.

  14. Biological Indicators in Studies of Earthquake Precursors

    Science.gov (United States)

    Sidorin, A. Ya.; Deshcherevskii, A. V.

    2012-04-01

    Time series of data on variations in the electric activity (EA) of four species of weakly electric fish Gnathonemus leopoldianus and moving activity (MA) of two cat-fishes Hoplosternum thoracatum and two groups of Columbian cockroaches Blaberus craniifer were analyzed. The observations were carried out in the Garm region of Tajikistan within the frameworks of the experiments aimed at searching for earthquake precursors. An automatic recording system continuously recorded EA and DA over a period of several years. Hourly means EA and MA values were processed. Approximately 100 different parameters were calculated on the basis of six initial EA and MA time series, which characterize different variations in the EA and DA structure: amplitude of the signal and fluctuations of activity, parameters of diurnal rhythms, correlated changes in the activity of various biological indicators, and others. A detailed analysis of the statistical structure of the total array of parametric time series obtained in the experiment showed that the behavior of all animals shows a strong temporal variability. All calculated parameters are unstable and subject to frequent changes. A comparison of the data obtained with seismicity allow us to make the following conclusions: (1) The structure of variations in the studied parameters is represented by flicker noise or even a more complex process with permanent changes in its characteristics. Significant statistics are required to prove the cause-and-effect relationship of the specific features of such time series with seismicity. (2) The calculation of the reconstruction statistics in the EA and MA series structure demonstrated an increase in their frequency in the last hours or a few days before the earthquake if the hypocenter distance is comparable to the source size. Sufficiently dramatic anomalies in the behavior of catfishes and cockroaches (changes in the amplitude of activity variation, distortions of diurnal rhythms, increase in the

  15. Dynamic respiration index as a descriptor of the biological stability of organic wastes.

    Science.gov (United States)

    Adani, Fabrizio; Confalonieri, Roberto; Tambone, Fulvia

    2004-01-01

    Analytical methods applicable to different organic wastes are needed to establish the extent to which readily biodegradable organic matter has decomposed (i.e., biological stability). The objective of this study was to test a new respirometric method for biological stability determination of organic wastes. Dynamic respiration index (DRI) measurements were performed on 16 organic wastes of different origin, composition, and biological stability degree to validate the test method and result expression, and to propose biological stability limits. In addition, theoretical DRI trends were obtained by using a mathematical model. Each test lasted 96 h in a 148-L-capacity respirometer apparatus, and DRI was monitored every hour. The biological stability was expressed as both single and cumulative DRI values. Results obtained indicated that DRI described biological stability in relation to waste typology and age well, revealing lower-stability waste characterized by a well-pronounced DRI profile (a marked peak was evident) that became practically flat for samples with higher biological stability. Fitting indices showed good model prediction compared with the experimental data, indicating that the method was able to reproduce the aerobic process, providing a reliable indication of the biological stability. The DRI can therefore be proposed as a useful method to measure the biological stability of organic wastes, and DRI values, calculated as a mean of 24 h of the highest microbial activity, of 1000 and 500 mg O(2) kg(-1) volatile solids (VS) h(-1) are proposed to indicate medium (e.g., fresh compost) and high (e.g., mature compost) biological stabilities, respectively.

  16. Biological-clinical study of radiosensitivity and chemosensitivity of squamous cell carcinoma of the mouth. Growth and regression rates, dynamic histology, and cell kinetics

    International Nuclear Information System (INIS)

    Friedman, M.; Nervi, C.

    1974-01-01

    Effects of combined methotrexate and radiotherapy were studied in 22 patients with advanced squamous cell cancer of the upper air passages. Studies included clinical growth rate of tumor volume prior to treatment, cell kinetics before treatment, electron microscope studies of serial biopsies, response of tumor to methotrexate and radiation, and time and rate of recurrences. Case histories are described for four different types of tumors and results are discussed. (U.S.)

  17. A logic-based dynamic modeling approach to explicate the evolution of the central dogma of molecular biology.

    Science.gov (United States)

    Jafari, Mohieddin; Ansari-Pour, Naser; Azimzadeh, Sadegh; Mirzaie, Mehdi

    It is nearly half a century past the age of the introduction of the Central Dogma (CD) of molecular biology. This biological axiom has been developed and currently appears to be all the more complex. In this study, we modified CD by adding further species to the CD information flow and mathematically expressed CD within a dynamic framework by using Boolean network based on its present-day and 1965 editions. We show that the enhancement of the Dogma not only now entails a higher level of complexity, but it also shows a higher level of robustness, thus far more consistent with the nature of biological systems. Using this mathematical modeling approach, we put forward a logic-based expression of our conceptual view of molecular biology. Finally, we show that such biological concepts can be converted into dynamic mathematical models using a logic-based approach and thus may be useful as a framework for improving static conceptual models in biology.

  18. Overshoot in biological systems modelled by Markov chains: a non-equilibrium dynamic phenomenon.

    Science.gov (United States)

    Jia, Chen; Qian, Minping; Jiang, Daquan

    2014-08-01

    A number of biological systems can be modelled by Markov chains. Recently, there has been an increasing concern about when biological systems modelled by Markov chains will perform a dynamic phenomenon called overshoot. In this study, the authors found that the steady-state behaviour of the system will have a great effect on the occurrence of overshoot. They showed that overshoot in general cannot occur in systems that will finally approach an equilibrium steady state. They further classified overshoot into two types, named as simple overshoot and oscillating overshoot. They showed that except for extreme cases, oscillating overshoot will occur if the system is far from equilibrium. All these results clearly show that overshoot is a non-equilibrium dynamic phenomenon with energy consumption. In addition, the main result in this study is validated with real experimental data.

  19. Use of proton-enhanced, natural abundance /sup 13/C NMR to study the molecular dynamics of model and biological membranes

    Energy Technology Data Exchange (ETDEWEB)

    Cornell, B A [Commonwealth Scientific and Industrial Research Organization, North Ryde (Australia). Div. of Food Research; Keniry, M [Sydney Univ. (Australia). Dept. of Physical Chemistry; Hiller, R G [Macquarie Univ., North Ryde (Australia). School of Biological Sciences; Smith, R [La Trobe Univ., Bundoora (Australia). Dept. of Biochemistry

    1980-06-16

    Proton-enhanced NMR of the natural abundance /sup 13/C nuclei is used to study the lipid mobility in dispersions containing cholesterol, the polypeptide gramicidin A, and in membrane proparations derived from spinach chloroplasts and bovine brain myelin.

  20. Quantum mechanical simulation methods for studying biological systems

    International Nuclear Information System (INIS)

    Bicout, D.; Field, M.

    1996-01-01

    Most known biological mechanisms can be explained using fundamental laws of physics and chemistry and a full understanding of biological processes requires a multidisciplinary approach in which all the tools of biology, chemistry and physics are employed. An area of research becoming increasingly important is the theoretical study of biological macromolecules where numerical experimentation plays a double role of establishing a link between theoretical models and predictions and allowing a quantitative comparison between experiments and models. This workshop brought researchers working on different aspects of the development and application of quantum mechanical simulation together, assessed the state-of-the-art in the field and highlighted directions for future research. Fourteen lectures (theoretical courses and specialized seminars) deal with following themes: 1) quantum mechanical calculations of large systems, 2) ab initio molecular dynamics where the calculation of the wavefunction and hence the energy and forces on the atoms for a system at a single nuclear configuration are combined with classical molecular dynamics algorithms in order to perform simulations which use a quantum mechanical potential energy surface, 3) quantum dynamical simulations, electron and proton transfer processes in proteins and in solutions and finally, 4) free seminars that helped to enlarge the scope of the workshop. (N.T.)

  1. Dynamical systems an introduction with applications in economics and biology

    CERN Document Server

    Tu, Pierre N V

    1994-01-01

    The favourable reception of the first edition and the encouragement received from many readers have prompted the author to bring out this new edition. This provides the opportunity for correcting a number of errors, typographical and others, contained in the first edition and making further improvements. This second edition has a new chapter on simplifying Dynamical Systems covering Poincare map, Floquet theory, Centre Manifold Theorems, normal forms of dynamical systems, elimination of passive coordinates and Liapunov-Schmidt reduction theory. It would provide a gradual transition to the study of Bifurcation, Chaos and Catastrophe in Chapter 10. Apart from this, most others - in fact all except the first three and last chapters - have been revised and enlarged to bring in some new materials, elaborate some others, especially those sections which many readers felt were rather too concise in the first edition, by providing more explana­ tion, examples and applications. Chapter 11 provides some good examples o...

  2. Studying Dynamics in Business Networks

    DEFF Research Database (Denmark)

    Andersen, Poul Houman; Anderson, Helen; Havila, Virpi

    1998-01-01

    This paper develops a theory on network dynamics using the concepts of role and position from sociological theory. Moreover, the theory is further tested using case studies from Denmark and Finland......This paper develops a theory on network dynamics using the concepts of role and position from sociological theory. Moreover, the theory is further tested using case studies from Denmark and Finland...

  3. Studying cell biology in the skin.

    Science.gov (United States)

    Morrow, Angel; Lechler, Terry

    2015-11-15

    Advances in cell biology have often been driven by studies in diverse organisms and cell types. Although there are technical reasons for why different cell types are used, there are also important physiological reasons. For example, ultrastructural studies of vesicle transport were aided by the use of professional secretory cell types. The use of tissues/primary cells has the advantage not only of using cells that are adapted to the use of certain cell biological machinery, but also of highlighting the physiological roles of this machinery. Here we discuss advantages of the skin as a model system. We discuss both advances in cell biology that used the skin as a driving force and future prospects for use of the skin to understand basic cell biology. A unique combination of characteristics and tools makes the skin a useful in vivo model system for many cell biologists. © 2015 Morrow and Lechler. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

  4. Spectroscopic, thermal and biological studies of coordination

    Indian Academy of Sciences (India)

    Spectroscopic, thermal and biological studies of coordination compounds of sulfasalazine drug: Mn(II), Hg(II), Cr(III), ZrO(II), VO(II) and Y(III) transition metal ... The thermal decomposition of the complexes as well as thermodynamic parameters ( *}, *, * and *) were estimated using Coats–Redfern and ...

  5. Study of biological effect of radiation

    International Nuclear Information System (INIS)

    Li Guisheng

    1992-01-01

    The some progress on the study of biological effect for protract exposure to low dose rate radiation is reported, and it is indicated that the potential risk of this exposure for the human health and the importance of the routine monitoring of radiation dose for various nuclear installations. The potential exposure to the low dose rate radiation would attract people's extra attention

  6. Dynamical compensation and structural identifiability of biological models: Analysis, implications, and reconciliation.

    Science.gov (United States)

    Villaverde, Alejandro F; Banga, Julio R

    2017-11-01

    The concept of dynamical compensation has been recently introduced to describe the ability of a biological system to keep its output dynamics unchanged in the face of varying parameters. However, the original definition of dynamical compensation amounts to lack of structural identifiability. This is relevant if model parameters need to be estimated, as is often the case in biological modelling. Care should we taken when using an unidentifiable model to extract biological insight: the estimated values of structurally unidentifiable parameters are meaningless, and model predictions about unmeasured state variables can be wrong. Taking this into account, we explore alternative definitions of dynamical compensation that do not necessarily imply structural unidentifiability. Accordingly, we show different ways in which a model can be made identifiable while exhibiting dynamical compensation. Our analyses enable the use of the new concept of dynamical compensation in the context of parameter identification, and reconcile it with the desirable property of structural identifiability.

  7. Integrating fluid dynamic and biologic effects on staphylococci bacteria biofilms

    Science.gov (United States)

    Sherman, Erica; Endres, Jennifer; Bayles, Kenneth; Wei, Timothy

    2017-11-01

    Staphylococcus aureus bacteria are able to form biofilms and distinctive tower structures that facilitate their ability to tolerate treatment and to spread within the human body. The formation of towers, which break off, get carried downstream and serve to initiate biofilms in other parts of the body are of particular interest here. In previous work on biofilm growth and evolution in steady, laminar microchannel flows, it has been established that tower formation occurs around a very limited range of applied shear stresses centered on 0.6 dynes/cm2. Quantifying cell density characteristics as a function of time during biofilm formation reveals indicators of tower development hours before towers actually form and become visible. The next step in this research is to explore biological factors that might explain why this specific shear is so important. Additional studies with mutants, e.g. ica-A, that have been tied to tower formation have been conducted. The shear dependence of these mutants and their correlation to the behavior of wild type S. aureus is examined.

  8. Studies in chemical dynamics

    International Nuclear Information System (INIS)

    Kuppermann, A.

    1978-01-01

    Progress made in the following studies is reported: low-energy electron scattering; variable-angle photoelectron spectroscopy; laser photochemistry and spectroscopy; and collisions in crossed molecular beams

  9. Robust and efficient parameter estimation in dynamic models of biological systems.

    Science.gov (United States)

    Gábor, Attila; Banga, Julio R

    2015-10-29

    Dynamic modelling provides a systematic framework to understand function in biological systems. Parameter estimation in nonlinear dynamic models remains a very challenging inverse problem due to its nonconvexity and ill-conditioning. Associated issues like overfitting and local solutions are usually not properly addressed in the systems biology literature despite their importance. Here we present a method for robust and efficient parameter estimation which uses two main strategies to surmount the aforementioned difficulties: (i) efficient global optimization to deal with nonconvexity, and (ii) proper regularization methods to handle ill-conditioning. In the case of regularization, we present a detailed critical comparison of methods and guidelines for properly tuning them. Further, we show how regularized estimations ensure the best trade-offs between bias and variance, reducing overfitting, and allowing the incorporation of prior knowledge in a systematic way. We illustrate the performance of the presented method with seven case studies of different nature and increasing complexity, considering several scenarios of data availability, measurement noise and prior knowledge. We show how our method ensures improved estimations with faster and more stable convergence. We also show how the calibrated models are more generalizable. Finally, we give a set of simple guidelines to apply this strategy to a wide variety of calibration problems. Here we provide a parameter estimation strategy which combines efficient global optimization with a regularization scheme. This method is able to calibrate dynamic models in an efficient and robust way, effectively fighting overfitting and allowing the incorporation of prior information.

  10. Study of estuarine dynamics

    International Nuclear Information System (INIS)

    Genders, S.

    1979-01-01

    A case study of a shallow, well mixed fjord illustrates the use of radioactive and an activable tracer. An instantaneous injection of the rare earth lanthanum was used as an activable tracer to determine residence-time and internal recirculation in the fjord system. An instantaneous injection of bromine-82 was used to investigate tae bypass of water from a harbour area through a power plant cooling water system to a partly enclosed basin of the fjord. Instantaneous releases of bromine-82 were further used for short time studies of the primary spread and transport of river water discharged to the inner section of the fjord system. (Author) [pt

  11. Biological Membrane Ion Channels Dynamics, Structure, and Applications

    CERN Document Server

    Chung, Shin-Ho; Krishnamurthy, Vikram

    2007-01-01

    Ion channels are biological nanotubes that are formed by membrane proteins. Because ion channels regulate all electrical activities in living cells, understanding their mechanisms at a molecular level is a fundamental problem in biology. This book deals with recent breakthroughs in ion-channel research that have been brought about by the combined effort of experimental biophysicists and computational physicists, who together are beginning to unravel the story of these exquisitely designed biomolecules. With chapters by leading experts, the book is aimed at researchers in nanodevices and biosensors, as well as advanced undergraduate and graduate students in biology and the physical sciences. Key Features Presents the latest information on the molecular mechanisms of ion permeation through membrane ion channels Uses schematic diagrams to illustrate important concepts in biophysics Written by leading researchers in the area of ion channel investigations

  12. Biological Studies of Posttraumatic Stress Disorder

    Science.gov (United States)

    Pitman, Roger K.; Rasmusson, Ann M.; Koenen, Karestan C.; Shin, Lisa M.; Orr, Scott P.; Gilbertson, Mark W.; Milad, Mohammed R.; Liberzon, Israel

    2016-01-01

    Preface Posttraumatic stress disorder (PTSD) is the only major mental disorder for which a cause is considered to be known, viz., an event that involves threat to the physical integrity of oneself or others and induces a response of intense fear, helplessness, or horror. Although PTSD is still largely regarded as a psychological phenomenon, over the past three decades the growth of the biological PTSD literature has been explosive, and thousands of references now exist. Ultimately, the impact of an environmental event, such as a psychological trauma, must be understood at organic, cellular, and molecular levels. The present review attempts to present the current state of this understanding, based upon psychophysiological, structural and functional neuroimaging, endocrinological, genetic, and molecular biological studies in humans and in animal models. PMID:23047775

  13. Improving the Timed Automata Approach to Biological Pathway Dynamics

    NARCIS (Netherlands)

    Langerak, R.; Pol, Jaco van de; Post, Janine N.; Schivo, Stefano; Aceto, Luca; Bacci, Giorgio; Bacci, Giovanni; Ingólfsdóttir, Anna; Legay, Axel; Mardare, Radu

    2017-01-01

    Biological systems such as regulatory or gene networks can be seen as a particular type of distributed systems, and for this reason they can be modeled within the Timed Automata paradigm, which was developed in the computer science context. However, tools designed to model distributed systems often

  14. Modelling the crop: from system dynamics to systems biology

    NARCIS (Netherlands)

    Yin, X.; Struik, P.C.

    2010-01-01

    There is strong interplant competition in a crop stand for various limiting resources, resulting in complex compensation and regulation mechanisms along the developmental cascade of the whole crop. Despite decades-long use of principles in system dynamics (e.g. feedback control), current crop models

  15. Function of dynamic models in systems biology: linking structure to behaviour.

    Science.gov (United States)

    Knüpfer, Christian; Beckstein, Clemens

    2013-10-08

    Dynamic models in Systems Biology are used in computational simulation experiments for addressing biological questions. The complexity of the modelled biological systems and the growing number and size of the models calls for computer support for modelling and simulation in Systems Biology. This computer support has to be based on formal representations of relevant knowledge fragments. In this paper we describe different functional aspects of dynamic models. This description is conceptually embedded in our "meaning facets" framework which systematises the interpretation of dynamic models in structural, functional and behavioural facets. Here we focus on how function links the structure and the behaviour of a model. Models play a specific role (teleological function) in the scientific process of finding explanations for dynamic phenomena. In order to fulfil this role a model has to be used in simulation experiments (pragmatical function). A simulation experiment always refers to a specific situation and a state of the model and the modelled system (conditional function). We claim that the function of dynamic models refers to both the simulation experiment executed by software (intrinsic function) and the biological experiment which produces the phenomena under investigation (extrinsic function). We use the presented conceptual framework for the function of dynamic models to review formal accounts for functional aspects of models in Systems Biology, such as checklists, ontologies, and formal languages. Furthermore, we identify missing formal accounts for some of the functional aspects. In order to fill one of these gaps we propose an ontology for the teleological function of models. We have thoroughly analysed the role and use of models in Systems Biology. The resulting conceptual framework for the function of models is an important first step towards a comprehensive formal representation of the functional knowledge involved in the modelling and simulation process

  16. How input fluctuations reshape the dynamics of a biological switching system

    Science.gov (United States)

    Hu, Bo; Kessler, David A.; Rappel, Wouter-Jan; Levine, Herbert

    2012-12-01

    An important task in quantitative biology is to understand the role of stochasticity in biochemical regulation. Here, as an extension of our recent work [Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.107.148101 107, 148101 (2011)], we study how input fluctuations affect the stochastic dynamics of a simple biological switch. In our model, the on transition rate of the switch is directly regulated by a noisy input signal, which is described as a non-negative mean-reverting diffusion process. This continuous process can be a good approximation of the discrete birth-death process and is much more analytically tractable. Within this setup, we apply the Feynman-Kac theorem to investigate the statistical features of the output switching dynamics. Consistent with our previous findings, the input noise is found to effectively suppress the input-dependent transitions. We show analytically that this effect becomes significant when the input signal fluctuates greatly in amplitude and reverts slowly to its mean.

  17. Disentangling physical and biological drivers of phytoplankton dynamics in a coastal system.

    Science.gov (United States)

    Cianelli, Daniela; D'Alelio, Domenico; Uttieri, Marco; Sarno, Diana; Zingone, Adriana; Zambianchi, Enrico; d'Alcalà, Maurizio Ribera

    2017-11-20

    This proof-of-concept study integrates the surface currents measured by high-frequency coastal radars with plankton time-series data collected at a fixed sampling point from the Mediterranean Sea (MareChiara Long Term Ecological Research site in the Gulf of Naples) to characterize the spatial origin of phytoplankton assemblages and to scrutinize the processes ruling their dynamics. The phytoplankton community generally originated from the coastal waters whereby species succession was mainly regulated by biological factors (life-cycle processes, species-specific physiological performances and inter-specific interactions). Physical factors, e.g. the alternation between coastal and offshore waters and the horizontal mixing, were also important drivers of phytoplankton dynamics promoting diversity maintenance by i) advecting species from offshore and ii) diluting the resident coastal community so as to dampen resource stripping by dominant species and thereby increase the numerical importance of rarer species. Our observations highlight the resilience of coastal communities, which may favour their persistence over time and the prevalence of successional events over small time and space scales. Although coastal systems may act differently from one another, our findings provide a conceptual framework to address physical-biological interactions occurring in coastal basins, which can be generalised to other areas.

  18. Theoretical studies of combustion dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Bowman, J.M. [Emory Univ., Atlanta, GA (United States)

    1993-12-01

    The basic objectives of this research program are to develop and apply theoretical techniques to fundamental dynamical processes of importance in gas-phase combustion. There are two major areas currently supported by this grant. One is reactive scattering of diatom-diatom systems, and the other is the dynamics of complex formation and decay based on L{sup 2} methods. In all of these studies, the authors focus on systems that are of interest experimentally, and for which potential energy surfaces based, at least in part, on ab initio calculations are available.

  19. Stochastic dynamics for two biological species and ecological niches

    Science.gov (United States)

    Ruziska, Flávia M.; Arashiro, Everaldo; Tomé, Tânia

    2018-01-01

    We consider an ecological system in which two species interact with two niches. To this end we introduce a stochastic model with four states. Our analysis is founded in three approaches: Monte Carlo simulations of the model on a square lattice, mean-field approximation, and birth and death master equation. From this last approach we obtain a description in terms of Langevin equations which show in an explicit way the role of noise in population biology. We focus mainly on the description of time oscillations of the species population and the alternating dominance between them. The model treated here may provide insights on these properties.

  20. Dynamics of problem setting and framing in citizen discussions on synthetic biology.

    Science.gov (United States)

    Betten, Afke Wieke; Broerse, Jacqueline E W; Kupper, Frank

    2018-04-01

    Synthetic biology is an emerging scientific field where engineers and biologists design and build biological systems for various applications. Developing synthetic biology responsibly in the public interest necessitates a meaningful societal dialogue. In this article, we argue that facilitating such a dialogue requires an understanding of how people make sense of synthetic biology. We performed qualitative research to unravel the underlying dynamics of problem setting and framing in citizen discussions on synthetic biology. We found that most people are not inherently for or against synthetic biology as a technology or development in itself, but that their perspectives are framed by core values about our relationships with science and technology and that sensemaking is much dependent on the context and general feelings of (dis)content. Given that there are many assumptions focused on a more binary idea of the public's view, we emphasize the need for frame awareness and understanding in a meaningful dialogue.

  1. Biological vs. physical mixing effects on benthic food web dynamics.

    Directory of Open Access Journals (Sweden)

    Ulrike Braeckman

    Full Text Available Biological particle mixing (bioturbation and solute transfer (bio-irrigation contribute extensively to ecosystem functioning in sediments where physical mixing is low. Macrobenthos transports oxygen and organic matter deeper into the sediment, thereby likely providing favourable niches to lower trophic levels (i.e., smaller benthic animals such as meiofauna and bacteria and thus stimulating mineralisation. Whether this biological transport facilitates fresh organic matter assimilation by the metazoan lower part of the food web through niche establishment (i.e., ecosystem engineering or rather deprives them from food sources, is so far unclear. We investigated the effects of the ecosystem engineers Lanice conchilega (bio-irrigator and Abra alba (bioturbator compared to abiotic physical mixing events on survival and food uptake of nematodes after a simulated phytoplankton bloom. The (13C labelled diatom Skeletonema costatum was added to 4 treatments: (1 microcosms containing the bioturbator, (2 microcosms containing the bio-irrigator, (3 control microcosms and (4 microcosms with abiotic manual surface mixing. Nematode survival and subsurface peaks in nematode density profiles were most pronounced in the bio-irrigator treatment. However, nematode specific uptake (Δδ(13C of the added diatoms was highest in the physical mixing treatment, where macrobenthos was absent and the diatom (13C was homogenised. Overall, nematodes fed preferentially on bulk sedimentary organic material rather than the added diatoms. The total C budget (µg C m(-2, which included TO(13C remaining in the sediment, respiration, nematode and macrobenthic uptake, highlighted the limited assimilation by the metazoan benthos and the major role of bacterial respiration. In summary, bioturbation and especially bio-irrigation facilitated the lower trophic levels mainly over the long-term through niche establishment. Since the freshly added diatoms represented only a limited food

  2. Spectroscopic study of biologically active glasses

    Science.gov (United States)

    Szumera, M.; Wacławska, I.; Mozgawa, W.; Sitarz, M.

    2005-06-01

    It is known that the chemical activity phenomenon is characteristic for some inorganic glasses and they are able to participate in biological processes of living organisms (plants, animals and human bodies). An example here is the selective removal of silicate-phosphate glass components under the influence of biological solutions, which has been applied in designing glasses acting as ecological fertilizers of controlled release rate of the nutrients for plants. The structure of model silicate-phosphate glasses containing the different amounts of the glass network formers, i.e. Ca 2+ and Mg 2+, as a binding components were studied. These elements besides other are indispensable of the normal growth of plants. In order to establish the function and position occupied by the particular components in the glass structure, the glasses were examined by FTIR spectroscopy (with spectra decomposition) and XRD methods. It has been found that the increasing amount of MgO in the structure of silicate-phosphate glasses causes the formation of domains the structure of which changes systematically from a structure of the cristobalite type to a structure corresponding to forsterite type. Whilst the increasing content of CaO in the structure of silicate-phosphate glasses causes the formation of domains the structure of which changes from a structure typical for cristobalite through one similar to the structure of calcium orthophosphate, to a structure corresponding to calcium silicates. The changing character of domains structure is the reason of different chemical activity of glasses.

  3. Proteomics in studying cancer stem cell biology.

    Science.gov (United States)

    Kranenburg, Onno; Emmink, Benjamin L; Knol, Jaco; van Houdt, Winan J; Rinkes, Inne H M Borel; Jimenez, Connie R

    2012-06-01

    Normal multipotent tissue stem cells (SCs) are the driving force behind tissue turnover and repair. The cancer stem cell theory holds that tumors also contain stem-like cells that drive tumor growth and metastasis formation. However, very little is known about the regulation of SC maintenance pathways in cancer and how these are affected by cancer-specific genetic alterations and by treatment. Proteomics is emerging as a powerful tool to identify the signaling complexes and pathways that control multi- and pluri-potency and SC differentiation. Here, the authors review the novel insights that these studies have provided and present a comprehensive strategy for the use of proteomics in studying cancer SC biology.

  4. A logic-based dynamic modeling approach to explicate the evolution of the central dogma of molecular biology.

    Directory of Open Access Journals (Sweden)

    Mohieddin Jafari

    Full Text Available It is nearly half a century past the age of the introduction of the Central Dogma (CD of molecular biology. This biological axiom has been developed and currently appears to be all the more complex. In this study, we modified CD by adding further species to the CD information flow and mathematically expressed CD within a dynamic framework by using Boolean network based on its present-day and 1965 editions. We show that the enhancement of the Dogma not only now entails a higher level of complexity, but it also shows a higher level of robustness, thus far more consistent with the nature of biological systems. Using this mathematical modeling approach, we put forward a logic-based expression of our conceptual view of molecular biology. Finally, we show that such biological concepts can be converted into dynamic mathematical models using a logic-based approach and thus may be useful as a framework for improving static conceptual models in biology.

  5. 6,7-dimethoxy-coumarin as a probe of hydration dynamics in biologically relevant systems

    Science.gov (United States)

    Ghose, Avisek; Amaro, Mariana; Kovaricek, Petr; Hof, Martin; Sykora, Jan

    2018-04-01

    Coumarin derivatives are well known fluorescence reporters for investigating biological systems due to their strong micro-environment sensitivity. Despite having wide range of environment sensitive fluorescence probes, the potential of 6,7-dimethoxy-coumarin has not been studied extensively so far. With a perspective of its use in protein studies, namely using the unnatural amino acid technology or as a substrate for hydrolase enzymes, we study acetyloxymethyl-6,7-dimethoxycoumarin (Ac-DMC). We investigate the photophysics and hydration dynamics of this dye in aerosol-OT (AOT) reverse micelles at various water contents using the time dependent fluorescence shift (TDFS) method. The TDFS response in AOT reverse micelles from water/surfactant ratio of 0 to 20 confirms its sensitivity towards the hydration and mobility of its microenvironment. Moreover, we show that the fluorophore can be efficiently quenched by halide ions. Hence, we conclude that the 6,7-dimethoxy-methylcoumarin fluorophore is useful for studying hydration parameters in biologically relevant systems.

  6. X-ray lasers for structural and dynamic biology

    International Nuclear Information System (INIS)

    Spence, J C H; Weierstall, U; Chapman, H N

    2012-01-01

    Research opportunities and techniques are reviewed for the application of hard x-ray pulsed free-electron lasers (XFEL) to structural biology. These include the imaging of protein nanocrystals, single particles such as viruses, pump–probe experiments for time-resolved nanocrystallography, and snapshot wide-angle x-ray scattering (WAXS) from molecules in solution. The use of femtosecond exposure times, rather than freezing of samples, as a means of minimizing radiation damage is shown to open up new opportunities for the molecular imaging of biochemical reactions at room temperature in solution. This is possible using a ‘diffract-and-destroy’ mode in which the incident pulse terminates before radiation damage begins. Methods for delivering hundreds of hydrated bioparticles per second (in random orientations) to a pulsed x-ray beam are described. New data analysis approaches are outlined for the correlated fluctuations in fast WAXS, for protein nanocrystals just a few molecules on a side, and for the continuous x-ray scattering from a single virus. Methods for determining the orientation of a molecule from its diffraction pattern are reviewed. Methods for the preparation of protein nanocrystals are also reviewed. New opportunities for solving the phase problem for XFEL data are outlined. A summary of the latest results is given, which now extend to atomic resolution for nanocrystals. Possibilities for time-resolved chemistry using fast WAXS (solution scattering) from mixtures is reviewed, toward the general goal of making molecular movies of biochemical processes. (key issues reviews)

  7. Advanced models of neural networks nonlinear dynamics and stochasticity in biological neurons

    CERN Document Server

    Rigatos, Gerasimos G

    2015-01-01

    This book provides a complete study on neural structures exhibiting nonlinear and stochastic dynamics, elaborating on neural dynamics by introducing advanced models of neural networks. It overviews the main findings in the modelling of neural dynamics in terms of electrical circuits and examines their stability properties with the use of dynamical systems theory. It is suitable for researchers and postgraduate students engaged with neural networks and dynamical systems theory.

  8. Novel nuclear magnetic resonance techniques for studying biological molecules

    International Nuclear Information System (INIS)

    Laws, David D.

    2000-01-01

    Over the fifty-five year history of Nuclear Magnetic Resonance (NMR), considerable progress has been made in the development of techniques for studying the structure, function, and dynamics of biological molecules. The majority of this research has involved the development of multi-dimensional NMR experiments for studying molecules in solution, although in recent years a number of groups have begun to explore NMR methods for studying biological systems in the solid-state. Despite this new effort, a need still exists for the development of techniques that improve sensitivity, maximize information, and take advantage of all the NMR interactions available in biological molecules. In this dissertation, a variety of novel NMR techniques for studying biomolecules are discussed. A method for determining backbone (φ/ψ) dihedral angles by comparing experimentally determined 13 C a , chemical-shift anisotropies with theoretical calculations is presented, along with a brief description of the theory behind chemical-shift computation in proteins and peptides. The utility of the Spin-Polarization Induced Nuclear Overhauser Effect (SPINOE) to selectively enhance NMR signals in solution is examined in a variety of systems, as are methods for extracting structural information from cross-relaxation rates that can be measured in SPINOE experiments. Techniques for the production of supercritical and liquid laser-polarized xenon are discussed, as well as the prospects for using optically pumped xenon as a polarizing solvent. In addition, a detailed study of the structure of PrP 89-143 is presented. PrP 89-143 is a 54 residue fragment of the prion proteins which, upon mutation and aggregation, can induce prion diseases in transgenic mice. Whereas the structure of the wild-type PrP 89-143 is a generally unstructured mixture of α-helical and β-sheet conformers in the solid state, the aggregates formed from the PrP 89-143 mutants appear to be mostly β-sheet.

  9. A spatial-dynamic value transfer model of economic losses from a biological invasion

    Science.gov (United States)

    Thomas P. Holmes; Andrew M. Liebhold; Kent F. Kovacs; Betsy. Von Holle

    2010-01-01

    Rigorous assessments of the economic impacts of introduced species at broad spatial scales are required to provide credible information to policy makers. We propose that economic models of aggregate damages induced by biological invasions need to link microeconomic analyses of site-specific economic damages with spatial-dynamic models of value change associated with...

  10. Pseudorandom numbers: evolutionary models in image processing, biology, and nonlinear dynamic systems

    Science.gov (United States)

    Yaroslavsky, Leonid P.

    1996-11-01

    We show that one can treat pseudo-random generators, evolutionary models of texture images, iterative local adaptive filters for image restoration and enhancement and growth models in biology and material sciences in a unified way as special cases of dynamic systems with a nonlinear feedback.

  11. Molecular dynamics study of silver

    International Nuclear Information System (INIS)

    Akhter, J.I.; Yaldram, K.; Ahmad, W.; Khan, M.K.; Rehman, T.S.

    1995-03-01

    We present results of molecular dynamics study using the embedded atom potential to examine the equilibrium bulk properties of Ag. We calculate the total energy and the lattice parameters as a function of temperature. From these we determine the specific heat and linear coefficient of thermal expansion. The comparison with experimental results of these two quantities is found to be excellent. We have also calculated the mean square displacement of the atoms in the three directions. As expected because of symmetry the displacements in the three directions are comparable and increase with increasing temperature. (author) 5 figs

  12. Pharmacovigilance of biologicals : dynamics in post-approval safety learning

    NARCIS (Netherlands)

    Vermeer, N.S.

    2015-01-01

    Regulatory decisions to allow new drugs on the market by definition have to accept a certain level of uncertainty about the full benefit-risk balance. Pre-approval studies typically provide information on a limited number of patients over a relative short follow-up period, and handle strict

  13. Developmental biology and the study of malformations.

    Science.gov (United States)

    Hughes, A F

    1976-05-01

    Experimental work on abnormal conditions of incubation in the chick has been undertaken to acquire a scientific approach to malformations. More precise experiments on causing abnormalities had a common origin with experimental embryology. Progress in experimental teratology during the last 50 years is reviewed in a commentary on the 4 principles formulated by Stockard in 1921. The results of cytogenetical studies in man and in other organisms have led to the tracing of some relationships between them. Present knowledge concerning malformations of the neural tube, originating either experimentally, spontaneously, or phenotypically, has been presented and the teratological implications of some recent theories on the expression of the genotype are discussed in particular reference to problems of hormones as teratogens, the implication of carbohydrate metabolism, and teratogenesis. It is speculated that teratogenesis is possibly related to cationic balance in early development and that 1 factor retarding progress in the understanding of malformations is the tendency toward the development of teratology in an adequately close relationship with other branches of cell biology.

  14. Using chemistry and microfluidics to understand the spatial dynamics of complex biological networks.

    Science.gov (United States)

    Kastrup, Christian J; Runyon, Matthew K; Lucchetta, Elena M; Price, Jessica M; Ismagilov, Rustem F

    2008-04-01

    Understanding the spatial dynamics of biochemical networks is both fundamentally important for understanding life at the systems level and also has practical implications for medicine, engineering, biology, and chemistry. Studies at the level of individual reactions provide essential information about the function, interactions, and localization of individual molecular species and reactions in a network. However, analyzing the spatial dynamics of complex biochemical networks at this level is difficult. Biochemical networks are nonequilibrium systems containing dozens to hundreds of reactions with nonlinear and time-dependent interactions, and these interactions are influenced by diffusion, flow, and the relative values of state-dependent kinetic parameters. To achieve an overall understanding of the spatial dynamics of a network and the global mechanisms that drive its function, networks must be analyzed as a whole, where all of the components and influential parameters of a network are simultaneously considered. Here, we describe chemical concepts and microfluidic tools developed for network-level investigations of the spatial dynamics of these networks. Modular approaches can be used to simplify these networks by separating them into modules, and simple experimental or computational models can be created by replacing each module with a single reaction. Microfluidics can be used to implement these models as well as to analyze and perturb the complex network itself with spatial control on the micrometer scale. We also describe the application of these network-level approaches to elucidate the mechanisms governing the spatial dynamics of two networkshemostasis (blood clotting) and early patterning of the Drosophila embryo. To investigate the dynamics of the complex network of hemostasis, we simplified the network by using a modular mechanism and created a chemical model based on this mechanism by using microfluidics. Then, we used the mechanism and the model to

  15. Quantitative analysis of dynamic association in live biological fluorescent samples.

    Directory of Open Access Journals (Sweden)

    Pekka Ruusuvuori

    Full Text Available Determining vesicle localization and association in live microscopy may be challenging due to non-simultaneous imaging of rapidly moving objects with two excitation channels. Besides errors due to movement of objects, imaging may also introduce shifting between the image channels, and traditional colocalization methods cannot handle such situations. Our approach to quantifying the association between tagged proteins is to use an object-based method where the exact match of object locations is not assumed. Point-pattern matching provides a measure of correspondence between two point-sets under various changes between the sets. Thus, it can be used for robust quantitative analysis of vesicle association between image channels. Results for a large set of synthetic images shows that the novel association method based on point-pattern matching demonstrates robust capability to detect association of closely located vesicles in live cell-microscopy where traditional colocalization methods fail to produce results. In addition, the method outperforms compared Iterated Closest Points registration method. Results for fixed and live experimental data shows the association method to perform comparably to traditional methods in colocalization studies for fixed cells and to perform favorably in association studies for live cells.

  16. High-speed AFM for Studying Dynamic Biomolecular Processes

    Science.gov (United States)

    Ando, Toshio

    2008-03-01

    Biological molecules show their vital activities only in aqueous solutions. It had been one of dreams in biological sciences to directly observe biological macromolecules (protein, DNA) at work under a physiological condition because such observation is straightforward to understanding their dynamic behaviors and functional mechanisms. Optical microscopy has no sufficient spatial resolution and electron microscopy is not applicable to in-liquid samples. Atomic force microscopy (AFM) can visualize molecules in liquids at high resolution but its imaging rate was too low to capture dynamic biological processes. This slow imaging rate is because AFM employs mechanical probes (cantilevers) and mechanical scanners to detect the sample height at each pixel. It is quite difficult to quickly move a mechanical device of macroscopic size with sub-nanometer accuracy without producing unwanted vibrations. It is also difficult to maintain the delicate contact between a probe tip and fragile samples. Two key techniques are required to realize high-speed AFM for biological research; fast feedback control to maintain a weak tip-sample interaction force and a technique to suppress mechanical vibrations of the scanner. Various efforts have been carried out in the past decade to materialize high-speed AFM. The current high-speed AFM can capture images on video at 30-60 frames/s for a scan range of 250nm and 100 scan lines, without significantly disturbing week biomolecular interaction. Our recent studies demonstrated that this new microscope can reveal biomolecular processes such as myosin V walking along actin tracks and association/dissociation dynamics of chaperonin GroEL-GroES that occurs in a negatively cooperative manner. The capacity of nanometer-scale visualization of dynamic processes in liquids will innovate on biological research. In addition, it will open a new way to study dynamic chemical/physical processes of various phenomena that occur at the liquid-solid interfaces.

  17. Structure and dynamics of photosynthetic proteins studied by neutron scattering and molecular dynamic simulation

    International Nuclear Information System (INIS)

    Dellerue, Serge

    2000-01-01

    Understand the structure-dynamics-function relation in the case of proteins is essential. But few experimental techniques allow to have access to knowledge of fast internal movements of biological macromolecules. With the neutron scattering method, it has been possible to study the reorientation dynamics of side chains and of polypeptide skeleton for two proteins in terms of water or detergent and of temperature. With the use of the molecular dynamics method, essential for completing and interpreting the experimental data, it has been possible to assess the different contributions of the whole structure of proteins to the overall dynamics. It has been shown that the polypeptide skeleton presents an energy relaxation comparable to those of the side chains. Moreover, it has been explained that the protein dynamics can only be understood in terms of relaxation time distribution. (author) [fr

  18. Ultrafast relaxation dynamics of a biologically relevant probe dansyl at the micellar surface.

    Science.gov (United States)

    Sarkar, Rupa; Ghosh, Manoranjan; Pal, Samir Kumar

    2005-02-01

    We report picosecond-resolved measurement of the fluorescence of a well-known biologically relevant probe, dansyl chromophore at the surface of a cationic micelle (cetyltrimethylammonium bromide, CTAB). The dansyl chromophore has environmentally sensitive fluorescence quantum yields and emission maxima, along with large Stokes shift. In order to study the solvation dynamics of the micellar environment, we measured the fluorescence of dansyl chromophore attached to the micellar surface. The fluorescence transients were observed to decay (with time constant approximately 350 ps) in the blue end and rise with similar timescale in the red end, indicative of solvation dynamics of the environment. The solvation correlation function is measured to decay with time constant 338 ps, which is much slower than that of ordinary bulk water. Time-resolved anisotropy of the dansyl chromophore shows a bi-exponential decay with time constants 413 ps (23%) and 1.3 ns (77%), which is considerably slower than that in free solvents revealing the rigidity of the dansyl-micelle complex. Time-resolved area-normalized emission spectroscopic (TRANES) analysis of the time dependent emission spectra of the dansyl chromophore in the micellar environment shows an isoemissive point at 21066 cm-1. This indicates the fluorescence of the chromophore contains emission from two kinds of excited states namely locally excited state (prior to charge transfer) and charge transfer state. The nature of the solvation dynamics in the micellar environments is therefore explored from the time-resolved anisotropy measurement coupled with the TRANES analysis of the fluorescence transients. The time scale of the solvation is important for the mechanism of molecular recognition.

  19. Postgraduate studies in radiation biology in Europe

    International Nuclear Information System (INIS)

    Trott, K.R.; Lohmann, P.H.M.; Zeeland, A.A. van; Natarajan, A.T.; Schibilla, H.; Chadwick, K.; Kellerer, A.M.; Steinhaeusler, F.

    1998-01-01

    The present system of radiobiological research in universities and research centres is no longer able to train radiobiologists who have a comprehensive understanding of the entire field of radiation biology including both 'classical' and molecular radiation biology. However, such experts are needed in view of the role radiation protection plays in our societies. No single institution in Europe could now run a 1-year, full-time course which covers all aspects of the radiobiological basis of radiation protection. Therefore, a cooperative action of several universities from different EU member states has been developed and is described herein. (orig.)

  20. Study of biocompatible and biological materials

    CERN Document Server

    Pecheva, Emilia

    2017-01-01

    The book gives an overview on biomineralization, biological, biocompatible and biomimetic materials. It reveals the use of biomaterials alone or in composites, how their performance can be improved by tailoring their surface properties by external factors and how standard surface modification techniques can be applied in the area of biomaterials to beneficially influence their growth on surfaces.

  1. 15N in biological nitrogen fixation studies

    International Nuclear Information System (INIS)

    Faust, H.

    1986-05-01

    A bibliography with 298 references on the use of the stable nitrogen isotope 15 N in the research on the biological fixation of dinitrogen is presented. The literature pertaining to this bibliography covers the period from 1975 to the middle of 1985. (author)

  2. Dynamic optimization of distributed biological systems using robust and efficient numerical techniques.

    Science.gov (United States)

    Vilas, Carlos; Balsa-Canto, Eva; García, Maria-Sonia G; Banga, Julio R; Alonso, Antonio A

    2012-07-02

    Systems biology allows the analysis of biological systems behavior under different conditions through in silico experimentation. The possibility of perturbing biological systems in different manners calls for the design of perturbations to achieve particular goals. Examples would include, the design of a chemical stimulation to maximize the amplitude of a given cellular signal or to achieve a desired pattern in pattern formation systems, etc. Such design problems can be mathematically formulated as dynamic optimization problems which are particularly challenging when the system is described by partial differential equations.This work addresses the numerical solution of such dynamic optimization problems for spatially distributed biological systems. The usual nonlinear and large scale nature of the mathematical models related to this class of systems and the presence of constraints on the optimization problems, impose a number of difficulties, such as the presence of suboptimal solutions, which call for robust and efficient numerical techniques. Here, the use of a control vector parameterization approach combined with efficient and robust hybrid global optimization methods and a reduced order model methodology is proposed. The capabilities of this strategy are illustrated considering the solution of a two challenging problems: bacterial chemotaxis and the FitzHugh-Nagumo model. In the process of chemotaxis the objective was to efficiently compute the time-varying optimal concentration of chemotractant in one of the spatial boundaries in order to achieve predefined cell distribution profiles. Results are in agreement with those previously published in the literature. The FitzHugh-Nagumo problem is also efficiently solved and it illustrates very well how dynamic optimization may be used to force a system to evolve from an undesired to a desired pattern with a reduced number of actuators. The presented methodology can be used for the efficient dynamic optimization of

  3. Carbon Nanomaterials in Biological Studies and Biomedicine.

    Science.gov (United States)

    Teradal, Nagappa L; Jelinek, Raz

    2017-09-01

    The "carbon nano-world" has made over the past few decades huge contributions in diverse scientific disciplines and technological advances. While dramatic advances have been widely publicized in using carbon nanomaterials such as fullerenes, carbon nanotubes, and graphene in materials sciences, nano-electronics, and photonics, their contributions to biology and biomedicine have been noteworthy as well. This Review focuses on the use of carbon nanotubes (CNTs), graphene, and carbon quantum dots [encompassing graphene quantum dots (GQDs) and carbon dots (C-dots)] in biologically oriented materials and applications. Examples of these remarkable nanomaterials in bio-sensing, cell- and tissue-imaging, regenerative medicine, and other applications are presented and discussed, emphasizing the significance of their unique properties and their future potential. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Integrating atomistic molecular dynamics simulations, experiments and network analysis to study protein dynamics: strength in unity

    Directory of Open Access Journals (Sweden)

    Elena ePapaleo

    2015-05-01

    Full Text Available In the last years, we have been observing remarkable improvements in the field of protein dynamics. Indeed, we can now study protein dynamics in atomistic details over several timescales with a rich portfolio of experimental and computational techniques. On one side, this provides us with the possibility to validate simulation methods and physical models against a broad range of experimental observables. On the other side, it also allows a complementary and comprehensive view on protein structure and dynamics. What is needed now is a better understanding of the link between the dynamic properties that we observe and the functional properties of these important cellular machines. To make progresses in this direction, we need to improve the physical models used to describe proteins and solvent in molecular dynamics, as well as to strengthen the integration of experiments and simulations to overcome their own limitations. Moreover, now that we have the means to study protein dynamics in great details, we need new tools to understand the information embedded in the protein ensembles and in their dynamic signature. With this aim in mind, we should enrich the current tools for analysis of biomolecular simulations with attention to the effects that can be propagated over long distances and are often associated to important biological functions. In this context, approaches inspired by network analysis can make an important contribution to the analysis of molecular dynamics simulations.

  5. Dynamical "in situ" observation of biological samples using variable pressure scanning electron microscope

    Czech Academy of Sciences Publication Activity Database

    Neděla, Vilém

    2008-01-01

    Roč. 126, - (2008), 012046:1-4 ISSN 1742-6588. [Electron Microscopy and Analysis Group Conference 2007 (EMAG 2007). Glasgow, 03.09.2007-07.09.2007] R&D Projects: GA ČR(CZ) GA102/05/0886; GA AV ČR KJB200650602 Institutional research plan: CEZ:AV0Z20650511 Keywords : biological sample * VP-SEM * dynamical experiments Subject RIV: JA - Electronics ; Optoelectronics, Electrical Engineering

  6. Biological Motion Preference in Humans at Birth: Role of Dynamic and Configural Properties

    Science.gov (United States)

    Bardi, Lara; Regolin, Lucia; Simion, Francesca

    2011-01-01

    The present study addresses the hypothesis that detection of biological motion is an intrinsic capacity of the visual system guided by a non-species-specific predisposition for the pattern of vertebrate movement and investigates the role of global vs. local information in biological motion detection. Two-day-old babies exposed to a biological…

  7. General method to find the attractors of discrete dynamic models of biological systems

    Science.gov (United States)

    Gan, Xiao; Albert, Réka

    2018-04-01

    Analyzing the long-term behaviors (attractors) of dynamic models of biological networks can provide valuable insight. We propose a general method that can find the attractors of multilevel discrete dynamical systems by extending a method that finds the attractors of a Boolean network model. The previous method is based on finding stable motifs, subgraphs whose nodes' states can stabilize on their own. We extend the framework from binary states to any finite discrete levels by creating a virtual node for each level of a multilevel node, and describing each virtual node with a quasi-Boolean function. We then create an expanded representation of the multilevel network, find multilevel stable motifs and oscillating motifs, and identify attractors by successive network reduction. In this way, we find both fixed point attractors and complex attractors. We implemented an algorithm, which we test and validate on representative synthetic networks and on published multilevel models of biological networks. Despite its primary motivation to analyze biological networks, our motif-based method is general and can be applied to any finite discrete dynamical system.

  8. General method to find the attractors of discrete dynamic models of biological systems.

    Science.gov (United States)

    Gan, Xiao; Albert, Réka

    2018-04-01

    Analyzing the long-term behaviors (attractors) of dynamic models of biological networks can provide valuable insight. We propose a general method that can find the attractors of multilevel discrete dynamical systems by extending a method that finds the attractors of a Boolean network model. The previous method is based on finding stable motifs, subgraphs whose nodes' states can stabilize on their own. We extend the framework from binary states to any finite discrete levels by creating a virtual node for each level of a multilevel node, and describing each virtual node with a quasi-Boolean function. We then create an expanded representation of the multilevel network, find multilevel stable motifs and oscillating motifs, and identify attractors by successive network reduction. In this way, we find both fixed point attractors and complex attractors. We implemented an algorithm, which we test and validate on representative synthetic networks and on published multilevel models of biological networks. Despite its primary motivation to analyze biological networks, our motif-based method is general and can be applied to any finite discrete dynamical system.

  9. Novel nuclear magnetic resonance techniques for studying biological molecules

    Energy Technology Data Exchange (ETDEWEB)

    Laws, David Douglas [Univ. of California, Berkeley, CA (United States)

    2000-06-01

    Over the fifty-five year history of Nuclear Magnetic Resonance (NMR), considerable progress has been made in the development of techniques for studying the structure, function, and dynamics of biological molecules. The majority of this research has involved the development of multi-dimensional NMR experiments for studying molecules in solution, although in recent years a number of groups have begun to explore NMR methods for studying biological systems in the solid-state. Despite this new effort, a need still exists for the development of techniques that improve sensitivity, maximize information, and take advantage of all the NMR interactions available in biological molecules. In this dissertation, a variety of novel NMR techniques for studying biomolecules are discussed. A method for determining backbone (Φ/Ψ) dihedral angles by comparing experimentally determined 13Ca, chemical-shift anisotropies with theoretical calculations is presented, along with a brief description of the theory behind chemical-shift computation in proteins and peptides. The utility of the Spin-Polarization Induced Nuclear Overhauser Effect (SPINOE) to selectively enhance NMR signals in solution is examined in a variety of systems, as are methods for extracting structural information from cross-relaxation rates that can be measured in SPINOE experiments. Techniques for the production of supercritical and liquid laser-polarized xenon are discussed, as well as the prospects for using optically pumped xenon as a polarizing solvent. In addition, a detailed study of the structure of PrP 89-143 is presented. PrP 89-143 is a 54 residue fragment of the prion proteins which, upon mutation and aggregation, can induce prion diseases in transgenic mice. Whereas the structure of the wild-type PrP 89-143 is a generally unstructured mixture of α-helical and β-sheet conformers in the solid state, the aggregates formed from the PrP 89-143 mutants appear to be mostly β-sheet.

  10. Studies in Chaotic adiabatic dynamics

    International Nuclear Information System (INIS)

    Jarzynski, C.

    1994-01-01

    Chaotic adiabatic dynamics refers to the study of systems exhibiting chaotic evolution under slowly time-dependent equations of motion. In this dissertation the author restricts his attention to Hamiltonian chaotic adiabatic systems. The results presented are organized around a central theme, namely, that the energies of such systems evolve diffusively. He begins with a general analysis, in which he motivates and derives a Fokker-Planck equation governing this process of energy diffusion. He applies this equation to study the open-quotes goodnessclose quotes of an adiabatic invariant associated with chaotic motion. This formalism is then applied to two specific examples. The first is that of a gas of noninteracting point particles inside a hard container that deforms slowly with time. Both the two- and three-dimensional cases are considered. The results are discussed in the context of the Wall Formula for one-body dissipation in nuclear physics, and it is shown that such a gas approaches, asymptotically with time, an exponential velocity distribution. The second example involves the Fermi mechanism for the acceleration of cosmic rays. Explicit evolution equations are obtained for the distribution of cosmic ray energies within this model, and the steady-state energy distribution that arises when this equation is modified to account for the injection and removal of cosmic rays is discussed. Finally, the author re-examines the multiple-time-scale approach as applied to the study of phase space evolution under a chaotic adiabatic Hamiltonian. This leads to a more rigorous derivation of the above-mentioned Fokker-Planck equation, and also to a new term which has relevance to the problem of chaotic adiabatic reaction forces (the forces acting on slow, heavy degrees of freedom due to their coupling to light, fast chaotic degrees)

  11. Computerised modelling for developmental biology : an exploration with case studies

    NARCIS (Netherlands)

    Bertens, Laura M.F.

    2012-01-01

    Many studies in developmental biology rely on the construction and analysis of models. This research presents a broad view of modelling approaches for developmental biology, with a focus on computational methods. An overview of modelling techniques is given, followed by several case studies. Using

  12. Chemical and biological activity in open flows: A dynamical system approach

    International Nuclear Information System (INIS)

    Tel, Tamas; Moura, Alessandro de; Grebogi, Celso; Karolyi, Gyoergy

    2005-01-01

    Chemical and biological processes often take place in fluid flows. Many of them, like environmental or microfluidical ones, generate filamentary patterns which have a fractal structure, due to the presence of chaos in the underlying advection dynamics. In such cases, hydrodynamical stirring strongly couples to the reactivity of the advected species: the outcome of the reaction is then typically different from that of the same reaction taking place in a well-mixed environment. Here we review recent progress in this field, which became possible due to the application of methods taken from dynamical system theory. We place special emphasis on the derivation of effective rate equations which contain singular terms expressing the fact that the reaction takes place on a moving fractal catalyst, on the unstable foliation of the reaction free advection dynamics

  13. Evolutionary game theory for physical and biological scientists. I. Training and validating population dynamics equations.

    Science.gov (United States)

    Liao, David; Tlsty, Thea D

    2014-08-06

    Failure to understand evolutionary dynamics has been hypothesized as limiting our ability to control biological systems. An increasing awareness of similarities between macroscopic ecosystems and cellular tissues has inspired optimism that game theory will provide insights into the progression and control of cancer. To realize this potential, the ability to compare game theoretic models and experimental measurements of population dynamics should be broadly disseminated. In this tutorial, we present an analysis method that can be used to train parameters in game theoretic dynamics equations, used to validate the resulting equations, and used to make predictions to challenge these equations and to design treatment strategies. The data analysis techniques in this tutorial are adapted from the analysis of reaction kinetics using the method of initial rates taught in undergraduate general chemistry courses. Reliance on computer programming is avoided to encourage the adoption of these methods as routine bench activities.

  14. Negotiating the dynamics of uncomfortable knowledge: The case of dual use and synthetic biology

    Science.gov (United States)

    Marris, Claire; Jefferson, Catherine; Lentzos, Filippa

    2014-01-01

    Institutions need to ignore some knowledge in order to function. This is “uncomfortable knowledge” because it undermines the ability of those institutions to pursue their goals (Rayner, 2012). We identify three bodies of knowledge that are relevant to understandings of the dual use threat posed by synthetic biology but are excluded from related policy discussions. We demonstrate how these “unknown knowns” constitute uncomfortable knowledge because they disrupt the simplified worldview that underpins contemporary discourse on the potential misuse of synthetic biology by malign actors. We describe how these inconvenient truths have been systematically ignored and argue that this is because they are perceived as a threat by organisations involved in the promotion of synthetic biology as well as by those involved in managing biosecurity risks. This has led to a situation where concerns about the biosecurity threat posed by synthetic biology are not only exaggerated, but are, more importantly, misplaced. This, in turn, means that related policies are misdirected and unlikely to have much impact. We focus on the dynamics of discussions about synthetic biology and dual use to demonstrate how the same “knowns” that are denied or dismissed as “unknown knowns” in certain circumstances are sometimes mobilised as “known knowns” by the same category of actors in a different context, when this serves to sustain the goals of the individuals and institutions involved. Based on our own experience, we argue that negotiating the dynamics of uncomfortable knowledge is a difficult, but necessary, component of meaningful transdisciplinary collaborations. PMID:25484910

  15. On the structural affinity of macromolecules with different biological properties: Molecular dynamics simulations of a series of TEM-1 mutants

    Energy Technology Data Exchange (ETDEWEB)

    Giampaolo, Alessia Di [Dipartimento di Scienze Fisiche e Chimiche, Universita’ degli Studi di l’Aquila, Via Vetoio snc, 67100 Coppito (AQ) (Italy); Mazza, Fernando [Department of Health Sciences, Univ. of L’Aquila, 67010 L’Aquila (Italy); Daidone, Isabella [Dipartimento di Scienze Fisiche e Chimiche, Universita’ degli Studi di l’Aquila, Via Vetoio snc, 67100 Coppito (AQ) (Italy); Amicosante, Gianfranco; Perilli, Mariagrazia [Dipartimento di Scienze Cliniche Applicate e Biotecnologiche, Università degli Studi di l’Aquila, Via Vetoio snc, 67100 Coppito (AQ) (Italy); Aschi, Massimiliano, E-mail: massimiliano.aschi@univaq.it [Dipartimento di Scienze Fisiche e Chimiche, Universita’ degli Studi di l’Aquila, Via Vetoio snc, 67100 Coppito (AQ) (Italy)

    2013-07-12

    Highlights: •We have performed molecular dynamics simulations of TEM-1 mutants. •Mutations effects on the mechanical properties are considered. •Mutants do not significantly alter the average enzymes structure. •Mutants produce sharp alterations in enzyme conformational repertoire. •Mutants also produce changes in the active site volume. -- Abstract: Molecular Dynamics simulations have been carried out in order to provide a molecular rationalization of the biological and thermodynamic differences observed for a class of TEM β-lactamases. In particular we have considered the TEM-1(wt), the single point mutants TEM-40 and TEM-19 representative of IRT and ESBL classes respectively, and TEM-1 mutant M182T, TEM-32 and TEM-20 which differ from the first three for the additional of M182T mutation. Results indicate that most of the thermodynamic, and probably biological behaviour of these systems arise from subtle effects which, starting from the alterations of the local interactions, produce drastic modifications of the conformational space spanned by the enzymes. The present study suggests that systems showing essentially the same secondary and tertiary structure may differentiate their chemical–biological activity essentially (and probably exclusively) on the basis of the thermal fluctuations occurring in their physiological environment.

  16. On the structural affinity of macromolecules with different biological properties: Molecular dynamics simulations of a series of TEM-1 mutants

    International Nuclear Information System (INIS)

    Giampaolo, Alessia Di; Mazza, Fernando; Daidone, Isabella; Amicosante, Gianfranco; Perilli, Mariagrazia; Aschi, Massimiliano

    2013-01-01

    Highlights: •We have performed molecular dynamics simulations of TEM-1 mutants. •Mutations effects on the mechanical properties are considered. •Mutants do not significantly alter the average enzymes structure. •Mutants produce sharp alterations in enzyme conformational repertoire. •Mutants also produce changes in the active site volume. -- Abstract: Molecular Dynamics simulations have been carried out in order to provide a molecular rationalization of the biological and thermodynamic differences observed for a class of TEM β-lactamases. In particular we have considered the TEM-1(wt), the single point mutants TEM-40 and TEM-19 representative of IRT and ESBL classes respectively, and TEM-1 mutant M182T, TEM-32 and TEM-20 which differ from the first three for the additional of M182T mutation. Results indicate that most of the thermodynamic, and probably biological behaviour of these systems arise from subtle effects which, starting from the alterations of the local interactions, produce drastic modifications of the conformational space spanned by the enzymes. The present study suggests that systems showing essentially the same secondary and tertiary structure may differentiate their chemical–biological activity essentially (and probably exclusively) on the basis of the thermal fluctuations occurring in their physiological environment

  17. Revisit of Machine Learning Supported Biological and Biomedical Studies.

    Science.gov (United States)

    Yu, Xiang-Tian; Wang, Lu; Zeng, Tao

    2018-01-01

    Generally, machine learning includes many in silico methods to transform the principles underlying natural phenomenon to human understanding information, which aim to save human labor, to assist human judge, and to create human knowledge. It should have wide application potential in biological and biomedical studies, especially in the era of big biological data. To look through the application of machine learning along with biological development, this review provides wide cases to introduce the selection of machine learning methods in different practice scenarios involved in the whole biological and biomedical study cycle and further discusses the machine learning strategies for analyzing omics data in some cutting-edge biological studies. Finally, the notes on new challenges for machine learning due to small-sample high-dimension are summarized from the key points of sample unbalance, white box, and causality.

  18. Dynamical study of liquid aluminium

    International Nuclear Information System (INIS)

    Dubey, G.S.; Chaturvedi, D.K.

    1979-09-01

    Recent molecular dynamics data of Ebbsjoe et al. in liquid aluminium have been analysed through the memory function formalism. Two forms of the memory functions which have correct asymptotic limit at large wavenumbers but accounts for interatomic correlations in a different manner are considered. The results for ω 2 s(q, ω) obtained from both models are compared with experimental data. (author)

  19. Dynamic neuronal ensembles: Issues in representing structure change in object-oriented, biologically-based brain models

    Energy Technology Data Exchange (ETDEWEB)

    Vahie, S.; Zeigler, B.P.; Cho, H. [Univ. of Arizona, Tucson, AZ (United States)

    1996-12-31

    This paper describes the structure of dynamic neuronal ensembles (DNEs). DNEs represent a new paradigm for learning, based on biological neural networks that use variable structures. We present a computational neural element that demonstrates biological neuron functionality such as neurotransmitter feedback absolute refractory period and multiple output potentials. More specifically, we will develop a network of neural elements that have the ability to dynamically strengthen, weaken, add and remove interconnections. We demonstrate that the DNE is capable of performing dynamic modifications to neuron connections and exhibiting biological neuron functionality. In addition to its applications for learning, DNEs provide an excellent environment for testing and analysis of biological neural systems. An example of habituation and hyper-sensitization in biological systems, using a neural circuit from a snail is presented and discussed. This paper provides an insight into the DNE paradigm using models developed and simulated in DEVS.

  20. A systems biology approach to study systemic inflammation.

    Science.gov (United States)

    Chen, Bor-Sen; Wu, Chia-Chou

    2014-01-01

    Systemic inflammation needs a precise control on the sequence and magnitude of occurring events. The high throughput data on the host-pathogen interactions gives us an opportunity to have a glimpse on the systemic inflammation. In this article, a dynamic Candida albicans-zebrafish interactive infectious network is built as an example to demonstrate how systems biology approach can be used to study systematic inflammation. In particular, based on microarray data of C. albicans and zebrafish during infection, the hyphal growth, zebrafish, and host-pathogen intercellular PPI networks were combined to form an integrated infectious PPI network that helps us understand the systematic mechanisms underlying the pathogenicity of C. albicans and the immune response of the host. The signaling pathways for morphogenesis and hyphal growth of C. albicans were 2 significant interactions found in the intercellular PPI network. Two cellular networks were also developed corresponding to the different infection stages (adhesion and invasion), and then compared with each other to identify proteins to gain more insight into the pathogenic role of hyphal development in the C. albicans infection process. Important defense-related proteins in zebrafish were predicted using the same approach. This integrated network consisting of intercellular invasion and cellular defense processes during infection can improve medical therapies and facilitate development of new antifungal drugs.

  1. Quantum Information Biology: From Theory of Open Quantum Systems to Adaptive Dynamics

    Science.gov (United States)

    Asano, Masanari; Basieva, Irina; Khrennikov, Andrei; Ohya, Masanori; Tanaka, Yoshiharu; Yamato, Ichiro

    This chapter reviews quantum(-like) information biology (QIB). Here biology is treated widely as even covering cognition and its derivatives: psychology and decision making, sociology, and behavioral economics and finances. QIB provides an integrative description of information processing by bio-systems at all scales of life: from proteins and cells to cognition, ecological and social systems. Mathematically QIB is based on the theory of adaptive quantum systems (which covers also open quantum systems). Ideologically QIB is based on the quantum-like (QL) paradigm: complex bio-systems process information in accordance with the laws of quantum information and probability. This paradigm is supported by plenty of statistical bio-data collected at all bio-scales. QIB re ects the two fundamental principles: a) adaptivity; and, b) openness (bio-systems are fundamentally open). In addition, quantum adaptive dynamics provides the most generally possible mathematical representation of these principles.

  2. Biological oscillations for learning walking coordination: dynamic recurrent neural network functionally models physiological central pattern generator.

    Science.gov (United States)

    Hoellinger, Thomas; Petieau, Mathieu; Duvinage, Matthieu; Castermans, Thierry; Seetharaman, Karthik; Cebolla, Ana-Maria; Bengoetxea, Ana; Ivanenko, Yuri; Dan, Bernard; Cheron, Guy

    2013-01-01

    The existence of dedicated neuronal modules such as those organized in the cerebral cortex, thalamus, basal ganglia, cerebellum, or spinal cord raises the question of how these functional modules are coordinated for appropriate motor behavior. Study of human locomotion offers an interesting field for addressing this central question. The coordination of the elevation of the 3 leg segments under a planar covariation rule (Borghese et al., 1996) was recently modeled (Barliya et al., 2009) by phase-adjusted simple oscillators shedding new light on the understanding of the central pattern generator (CPG) processing relevant oscillation signals. We describe the use of a dynamic recurrent neural network (DRNN) mimicking the natural oscillatory behavior of human locomotion for reproducing the planar covariation rule in both legs at different walking speeds. Neural network learning was based on sinusoid signals integrating frequency and amplitude features of the first three harmonics of the sagittal elevation angles of the thigh, shank, and foot of each lower limb. We verified the biological plausibility of the neural networks. Best results were obtained with oscillations extracted from the first three harmonics in comparison to oscillations outside the harmonic frequency peaks. Physiological replication steadily increased with the number of neuronal units from 1 to 80, where similarity index reached 0.99. Analysis of synaptic weighting showed that the proportion of inhibitory connections consistently increased with the number of neuronal units in the DRNN. This emerging property in the artificial neural networks resonates with recent advances in neurophysiology of inhibitory neurons that are involved in central nervous system oscillatory activities. The main message of this study is that this type of DRNN may offer a useful model of physiological central pattern generator for gaining insights in basic research and developing clinical applications.

  3. Application of Solution NMR Spectroscopy to Study Protein Dynamics

    Directory of Open Access Journals (Sweden)

    Christoph Göbl

    2012-03-01

    Full Text Available Recent advances in spectroscopic methods allow the identification of minute fluctuations in a protein structure. These dynamic properties have been identified as keys to some biological processes. The consequences of this structural flexibility can be far‑reaching and they add a new dimension to the structure-function relationship of biomolecules. Nuclear Magnetic Resonance (NMR spectroscopy allows the study of structure as well as dynamics of biomolecules in a very broad range of timescales at atomic level. A number of new NMR methods have been developed recently to allow the measurements of time scales and spatial fluctuations, which in turn provide the thermodynamics associated with the biological processes. Since NMR parameters reflect ensemble measurements, structural ensemble approaches in analyzing NMR data have also been developed. These new methods in some instances can even highlight previously hidden conformational features of the biomolecules. In this review we describe several solution NMR methods to study protein dynamics and discuss their impact on important biological processes.

  4. A submesoscale coherent vortex in the Ligurian Sea: From dynamical barriers to biological implications

    Science.gov (United States)

    Bosse, Anthony; Testor, Pierre; Mayot, Nicolas; Prieur, Louis; D'Ortenzio, Fabrizio; Mortier, Laurent; Le Goff, Hervé; Gourcuff, Claire; Coppola, Laurent; Lavigne, Héloïse; Raimbault, Patrick

    2017-08-01

    In June 2013, a glider equipped with oxygen and fluorescence sensors has been used to extensively sample an anticyclonic Submesoscale Coherent Vortex (SCV) in the Ligurian Sea (NW Mediterranean Sea). Those measurements are complemented by full-depth CTD casts (T, S, and oxygen) and water samples documenting nutrients and phytoplankton pigments within the SCV and outside. The SCV has a very homogeneous core of oxygenated waters between 300 and 1200 m formed 4.5 months earlier during the winter deep convection event. It has a strong dynamical signature with peak velocities at 700 m depth of 13.9 cm s-1 in cyclogeostrophic balance. The eddy has a small radius of 6.2 km corresponding to high Rossby number of -0.45. The vorticity at the eddy center reaches -0.8f. Cross-stream isopycnic diffusion of tracers between the eddy core and the surroundings is found to be very limited due to dynamical barriers set by the SCV associated with a diffusivity coefficient of about 0.2 m2 s-1. The deep core is nutrients-depleted with concentrations of nitrate, phosphate, and silicate, 13-18% lower than the rich surrounding waters. However, the nutriclines are shifted of about 20-50 m toward the surface thus increasing the nutrients availability for phytoplankton. Chlorophyll-a concentrations at the deep chlorophyll maximum are subsequently about twice bigger as compared to outside. Pigments further reveal the predominance of nanophytoplankton inside the eddy and an enhancement of the primary productivity. This study demonstrates the important impact of postconvective SCVs on nutrients distribution and phytoplankton community, as well as on the subsequent primary production and carbon sequestration.Plain Language SummaryDue to harsh meteorological conditions in winter, a few places of the world's ocean experience an intense cooling of their surface waters that start to sink in a process called oceanic deep convection. It is crucial for the functioning of the ocean, but also the marine

  5. Biological - Elwha River Dam Removal Study

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This study examines the ecosystem response of the Elwha River to the removal of the Elwha River dams. We will measure the following attributes of ecosystem response:...

  6. Theoretical studies of combustion dynamics

    International Nuclear Information System (INIS)

    Bowman, J.M.

    1986-01-01

    The reactions of O( 3 P)+H 2 , D 2 , and HD are the focus of this research. Their approximate three-dimensional quantum calculations of the rate constant for both the ground and first excited vibrational states of the above reactions were completed last year. Comparisons of the calculated rate constants, isotope effects and branching ratios have been made with available experimental work and also with the variational transition state theory calculations. The main conclusion of that paper is that tunneling plays a major role in the reaction dynamics at room temperature and below

  7. Phytoplankton biomass dynamics and environmental variables around the Rocas Atoll Biological Reserve, South Atlantic

    Directory of Open Access Journals (Sweden)

    Marina Cavalcanti Jales

    2015-12-01

    Full Text Available Abstract The Rocas Atoll Biological Reserve is located in the Atlantic Ocean, at 3º 51' S and 33º 49' W. It lies 143 nautical miles from the City of Natal, Rio Grande do Norte (Brazil. The purpose of this study was to analyze the hydrology, water masses, currents and chlorophyll a content to determine the dynamics of phytoplankton biomass around the Rocas Atoll. Samples were collected in July 2010 in the area around the Atoll, using the Research Vessel Cruzeiro do Sul of the Brazilian Navy. Two transects were established according to the surface currents, one of which at the southeast of the Atoll (SE and the other at norwest (NW. Three collection points were determined on each of these transects. Samples were collected at different depths (surface and DCM - Deep Chlorophyll Maximum and different times (day and night. According to PCA (Principal Component Analysis, the nutrients analyzed, DIN (dissolved inorganic nitrogen, DIP (dissolved inorganic phosphorus and silicate, were inversely correlated with temperature and dissolved oxygen. Most environmental variables showed a significant increase due to the turbulence on the Northwest transect. There was an increase in the concentration of chlorophyll a and nutrients when the temperature and oxygen in the mixed layer was reduced due to the influence of the SACW (South Atlantic Central Water. Despite the increase observed in some variables such as nutrient salts and chlorophyll a, the temperature in the mixed layer attained a mean value of 23.23 ºC due to the predominance of Tropical Water. The increase of the phytoplankton biomass on the NW transect was, therefore, caused by the "island effect" and not by upwelling.

  8. Population dynamics of bacteria involved in enhanced biological phosphorus removal in Danish wastewater treatment plants.

    Science.gov (United States)

    Mielczarek, Artur Tomasz; Nguyen, Hien Thi Thu; Nielsen, Jeppe Lund; Nielsen, Per Halkjær

    2013-03-15

    The enhanced biological phosphorus removal (EBPR) process is increasingly popular as a sustainable method for removal of phosphorus (P) from wastewater. This study consisted of a comprehensive three-year investigation of the identity and population dynamics of polyphosphate-accumulating organisms (PAOs) and glycogen-accumulating organisms (GAOs) in 28 Danish municipal wastewater treatment plants with nutrient removal. Fluorescence in situ hybridization was applied to quantify ten probe-defined populations of PAO and GAO that in total constituted a large fraction (30% on average) of the entire microbial community targeted by the EUBmix probes. Two PAO genera, Accumulibacter and Tetrasphaera, were very abundant in all EBPR plants (average of 3.7% and 27% of all bacteria, respectively), and their abundance was relatively stable in the Danish full-scale plants without clear temporal variations. GAOs were occasionally present in some plants (Competibacter in 11 plants, Defluviicoccus in 6 plants) and were consistent in only a few plants. This shows that these were not core species in the EBPR communities. The total GAO abundance was always lower than that of Accumulibacter. In plants without EBPR design, the abundance of PAO and GAO was significantly lower. Competibacter correlated in general with high fraction of industrial wastewater. In specific plants Accumulibacter correlated with high C/P ratio of the wastewater and Tetrasphaera with high organic loading. Interestingly, the relative microbial composition of the PAO/GAO species was unique to each plant over time, which gives a characteristic plant-specific "fingerprint". Copyright © 2012 Elsevier Ltd. All rights reserved.

  9. Biological Studies on a Live Volcano.

    Science.gov (United States)

    Zipko, Stephen J.

    1992-01-01

    Describes scientific research on an Earthwatch expedition to study Arenal, one of the world's most active volcanoes, in north central Costa Rica. The purpose of the two-week project was to monitor and understand the past and ongoing development of a small, geologically young, highly active stratovolcano in a tropical, high-rainfall environment.…

  10. Nuclear magnetic resonance studies of biological systems

    International Nuclear Information System (INIS)

    Antypas, W.G. Jr.

    1988-01-01

    The difference between intracellular and extracellular proton relaxation rates provides the basis for the determination of the mean hemoglobin concentration (MHC) in red blood cells. The observed water T 1 relaxation data from red blood cell samples under various conditions were fit to the complete equation for the time-dependent decay of magnetization for a two-compartment system including chemical exchange. The MHC for each sample was calculated from the hematocrit and the intracellular water fraction as determined by NMR. The binding of the phosphorylcholine (PC) analogue, 2-(trimethylphosphonio)-ethylphosphate (phosphoryl-phosphocholine, PPC) to the PC binding myeloma proteins TEPC-15, McPC 603, and MOPC 167 was studied by 31 P NMR

  11. Decay correction methods in dynamic PET studies

    International Nuclear Information System (INIS)

    Chen, K.; Reiman, E.; Lawson, M.

    1995-01-01

    In order to reconstruct positron emission tomography (PET) images in quantitative dynamic studies, the data must be corrected for radioactive decay. One of the two commonly used methods ignores physiological processes including blood flow that occur at the same time as radioactive decay; the other makes incorrect use of time-accumulated PET counts. In simulated dynamic PET studies using 11 C-acetate and 18 F-fluorodeoxyglucose (FDG), these methods are shown to result in biased estimates of the time-activity curve (TAC) and model parameters. New methods described in this article provide significantly improved parameter estimates in dynamic PET studies

  12. Ruminant Metabolic Systems Biology: Reconstruction and Integration of Transcriptome Dynamics Underlying Functional Responses of Tissues to Nutrition and Physiological Statea

    Science.gov (United States)

    Bionaz, Massimo; Loor, Juan J.

    2012-01-01

    High-throughput ‘omics’ data analysis via bioinformatics is one key component of the systems biology approach. The systems approach is particularly well-suited for the study of the interactions between nutrition and physiological state with tissue metabolism and functions during key life stages of organisms such as the transition from pregnancy to lactation in mammals, ie, the peripartal period. In modern dairy cows with an unprecedented genetic potential for milk synthesis, the nature of the physiologic and metabolic adaptations during the peripartal period is multifaceted and involves key tissues such as liver, adipose, and mammary. In order to understand such adaptation, we have reviewed several works performed in our and other labs. In addition, we have used a novel bioinformatics approach, Dynamic Impact Approach (DIA), in combination with partly previously published data to help interpret longitudinal biological adaptations of bovine liver, adipose, and mammary tissue to lactation using transcriptomics datasets. Use of DIA with transcriptomic data from those tissues during normal physiological adaptations and in animals fed different levels of energy prepartum allowed visualization and integration of most-impacted metabolic pathways around the time of parturition. The DIA is a suitable tool for applying the integrative systems biology approach. The ultimate goal is to visualize the complexity of the systems at study and uncover key molecular players involved in the tissue’s adaptations to physiological state or nutrition. PMID:22807626

  13. Study of phosphors determination in biological samples

    International Nuclear Information System (INIS)

    Oliveira, Rosangela Magda de.

    1994-01-01

    In this paper, phosphors determination by neutron activation analysis in milk and bone samples was studied employing both instrumental and radiochemical separation methods. The analysis with radiochemistry separation consisted of the simultaneous irradiation of the samples and standards during 30 minutes, dissolution of the samples, hold back carrier, addition precipitation of phosphorus with ammonium phosphomolibdate (A.M.P.) and phosphorus-32 by counting by using Geiger-Mueller detector. The instrumental analysis consisted of the simultaneous irradiation of the samples and standards during 30 minutes, transfer of the samples into a counting planchet and measurement of the beta radiation emitted by phosphorus-32, after a suitable decay period. After the phosphorus analysis methods were established they were applied to both commercial milk and animal bone samples, and data obtained in the instrumental and radiochemical separation methods for each sample, were compared between themselves. In this work, it became possible to obtain analysis methods for phosphorus that can be applied independently of the sample quantity available, and the phosphorus content in the samples or interference that can be present in them. (author). 51 refs., 7 figs., 4 tabs

  14. Host-parasitoid dynamics and the success of biological control when parasitoids are prone to allee effects.

    Directory of Open Access Journals (Sweden)

    Anaïs Bompard

    Full Text Available In sexual organisms, low population density can result in mating failures and subsequently yields a low population growth rate and high chance of extinction. For species that are in tight interaction, as in host-parasitoid systems, population dynamics are primarily constrained by demographic interdependences, so that mating failures may have much more intricate consequences. Our main objective is to study the demographic consequences of parasitoid mating failures at low density and its consequences on the success of biological control. For this, we developed a deterministic host-parasitoid model with a mate-finding Allee effect, allowing to tackle interactions between the Allee effect and key determinants of host-parasitoid demography such as the distribution of parasitoid attacks and host competition. Our study shows that parasitoid mating failures at low density result in an extinction threshold and increase the domain of parasitoid deterministic extinction. When proned to mate finding difficulties, parasitoids with cyclic dynamics or low searching efficiency go extinct; parasitoids with high searching efficiency may either persist or go extinct, depending on host intraspecific competition. We show that parasitoids suitable as biocontrol agents for their ability to reduce host populations are particularly likely to suffer from mate-finding Allee effects. This study highlights novel perspectives for understanding of the dynamics observed in natural host-parasitoid systems and improving the success of parasitoid introductions.

  15. Biologic targets identified from dynamic 18FDG-PET and implications for image-guided therapy

    International Nuclear Information System (INIS)

    Rusten, Espen; Malinen, Eirik; Roedal, Jan; Bruland, Oeyvind S.

    2013-01-01

    Purpose: The outcome of biologic image-guided radiotherapy depends on the definition of the biologic target. The purpose of the current work was to extract hyper perfused and hypermetabolic regions from dynamic positron emission tomography (D-PET) images, to dose escalate either region and to discuss implications of such image guided strategies. Methods: Eleven patients with soft tissue sarcomas were investigated with D-PET. The images were analyzed using a two-compartment model producing parametric maps of perfusion and metabolic rate. The two image series were segmented and exported to a treatment planning system, and biological target volumes BTV per and BTV met (perfusion and metabolism, respectively) were generated. Dice's similarity coefficient was used to compare the two biologic targets. Intensity-modulated radiation therapy (IMRT) plans were generated for a dose painting by contours regime, where planning target volume (PTV) was planned to 60 Gy and BTV to 70 Gy. Thus, two separate plans were created for each patient with dose escalation of either BTV per or BTV met . Results: BTV per was somewhat smaller than BTV met (209 ±170 cm 3 against 243 ±143 cm 3 , respectively; population-based mean and s.d.). Dice's coefficient depended on the applied margin, and was 0.72 ±0.10 for a margin of 10 mm. Boosting BTV per resulted in mean dose of 69 ±1.0 Gy to this region, while BTV met received 67 ±3.2 Gy. Boosting BTV met gave smaller dose differences between the respective non-boost DVHs (such as D 98 ). Conclusions: Dose escalation of one of the BTVs results in a partial dose escalation of the other BTV as well. If tumor aggressiveness is equally pronounced in hyper perfused and hypermetabolic regions, this should be taken into account in the treatment planning

  16. A consensus approach for estimating the predictive accuracy of dynamic models in biology.

    Science.gov (United States)

    Villaverde, Alejandro F; Bongard, Sophia; Mauch, Klaus; Müller, Dirk; Balsa-Canto, Eva; Schmid, Joachim; Banga, Julio R

    2015-04-01

    Mathematical models that predict the complex dynamic behaviour of cellular networks are fundamental in systems biology, and provide an important basis for biomedical and biotechnological applications. However, obtaining reliable predictions from large-scale dynamic models is commonly a challenging task due to lack of identifiability. The present work addresses this challenge by presenting a methodology for obtaining high-confidence predictions from dynamic models using time-series data. First, to preserve the complex behaviour of the network while reducing the number of estimated parameters, model parameters are combined in sets of meta-parameters, which are obtained from correlations between biochemical reaction rates and between concentrations of the chemical species. Next, an ensemble of models with different parameterizations is constructed and calibrated. Finally, the ensemble is used for assessing the reliability of model predictions by defining a measure of convergence of model outputs (consensus) that is used as an indicator of confidence. We report results of computational tests carried out on a metabolic model of Chinese Hamster Ovary (CHO) cells, which are used for recombinant protein production. Using noisy simulated data, we find that the aggregated ensemble predictions are on average more accurate than the predictions of individual ensemble models. Furthermore, ensemble predictions with high consensus are statistically more accurate than ensemble predictions with large variance. The procedure provides quantitative estimates of the confidence in model predictions and enables the analysis of sufficiently complex networks as required for practical applications. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  17. Perspective: Differential dynamic microscopy extracts multi-scale activity in complex fluids and biological systems

    Science.gov (United States)

    Cerbino, Roberto; Cicuta, Pietro

    2017-09-01

    Differential dynamic microscopy (DDM) is a technique that exploits optical microscopy to obtain local, multi-scale quantitative information about dynamic samples, in most cases without user intervention. It is proving extremely useful in understanding dynamics in liquid suspensions, soft materials, cells, and tissues. In DDM, image sequences are analyzed via a combination of image differences and spatial Fourier transforms to obtain information equivalent to that obtained by means of light scattering techniques. Compared to light scattering, DDM offers obvious advantages, principally (a) simplicity of the setup; (b) possibility of removing static contributions along the optical path; (c) power of simultaneous different microscopy contrast mechanisms; and (d) flexibility of choosing an analysis region, analogous to a scattering volume. For many questions, DDM has also advantages compared to segmentation/tracking approaches and to correlation techniques like particle image velocimetry. The very straightforward DDM approach, originally demonstrated with bright field microscopy of aqueous colloids, has lately been used to probe a variety of other complex fluids and biological systems with many different imaging methods, including dark-field, differential interference contrast, wide-field, light-sheet, and confocal microscopy. The number of adopting groups is rapidly increasing and so are the applications. Here, we briefly recall the working principles of DDM, we highlight its advantages and limitations, we outline recent experimental breakthroughs, and we provide a perspective on future challenges and directions. DDM can become a standard primary tool in every laboratory equipped with a microscope, at the very least as a first bias-free automated evaluation of the dynamics in a system.

  18. Structures in dynamics finite dimensional deterministic studies

    CERN Document Server

    Broer, HW; van Strien, SJ; Takens, F

    1991-01-01

    The study of non-linear dynamical systems nowadays is an intricate mixture of analysis, geometry, algebra and measure theory and this book takes all aspects into account. Presenting the contents of its authors' graduate courses in non-linear dynamical systems, this volume aims at researchers who wish to be acquainted with the more theoretical and fundamental subjects in non-linear dynamics and is designed to link the popular literature with research papers and monographs. All of the subjects covered in this book are extensively dealt with and presented in a pedagogic

  19. Novel recurrent neural network for modelling biological networks: oscillatory p53 interaction dynamics.

    Science.gov (United States)

    Ling, Hong; Samarasinghe, Sandhya; Kulasiri, Don

    2013-12-01

    Understanding the control of cellular networks consisting of gene and protein interactions and their emergent properties is a central activity of Systems Biology research. For this, continuous, discrete, hybrid, and stochastic methods have been proposed. Currently, the most common approach to modelling accurate temporal dynamics of networks is ordinary differential equations (ODE). However, critical limitations of ODE models are difficulty in kinetic parameter estimation and numerical solution of a large number of equations, making them more suited to smaller systems. In this article, we introduce a novel recurrent artificial neural network (RNN) that addresses above limitations and produces a continuous model that easily estimates parameters from data, can handle a large number of molecular interactions and quantifies temporal dynamics and emergent systems properties. This RNN is based on a system of ODEs representing molecular interactions in a signalling network. Each neuron represents concentration change of one molecule represented by an ODE. Weights of the RNN correspond to kinetic parameters in the system and can be adjusted incrementally during network training. The method is applied to the p53-Mdm2 oscillation system - a crucial component of the DNA damage response pathways activated by a damage signal. Simulation results indicate that the proposed RNN can successfully represent the behaviour of the p53-Mdm2 oscillation system and solve the parameter estimation problem with high accuracy. Furthermore, we presented a modified form of the RNN that estimates parameters and captures systems dynamics from sparse data collected over relatively large time steps. We also investigate the robustness of the p53-Mdm2 system using the trained RNN under various levels of parameter perturbation to gain a greater understanding of the control of the p53-Mdm2 system. Its outcomes on robustness are consistent with the current biological knowledge of this system. As more

  20. Students’ learning activities while studying biological process diagrams

    NARCIS (Netherlands)

    Kragten, M.; Admiraal, W.; Rijlaarsdam, G.

    2015-01-01

    Process diagrams describe how a system functions (e.g. photosynthesis) and are an important type of representation in Biology education. In the present study, we examined students’ learning activities while studying process diagrams, related to their resulting comprehension of these diagrams. Each

  1. Dynamic cell culture system: a new cell cultivation instrument for biological experiments in space

    Science.gov (United States)

    Gmunder, F. K.; Nordau, C. G.; Tschopp, A.; Huber, B.; Cogoli, A.

    1988-01-01

    The prototype of a miniaturized cell cultivation instrument for animal cell culture experiments aboard Spacelab is presented (Dynamic cell culture system: DCCS). The cell chamber is completely filled and has a working volume of 200 microliters. Medium exchange is achieved with a self-powered osmotic pump (flowrate 1 microliter h-1). The reservoir volume of culture medium is 230 microliters. The system is neither mechanically stirred nor equipped with sensors. Hamster kidney (Hak) cells growing on Cytodex 3 microcarriers were used to test the biological performance of the DCCS. Growth characteristics in the DCCS, as judged by maximal cell density, glucose consumption, lactic acid secretion and pH, were similar to those in cell culture tubes.

  2. Development and performance evaluation of a dynamic phantom for biological dosimetry of moving targets

    Science.gov (United States)

    Gemmel, A.; Bert, C.; Saito, N.; von Neubeck, C.; Iancu, G.; K-Weyrather, W.; Durante, M.; Rietzel, E.

    2010-06-01

    A dynamic phantom has been developed to allow for measurement of 3D cell survival distributions and the corresponding distributions of the RBE-weighted dose (RBED) in the presence of motion. The phantom consists of two 96-microwell plates holding Chinese hamster ovary cells inside a container filled with culture medium and is placed on a movable stage. Basic biological properties of the phantom were investigated without irradiation and after irradiation with a carbon ion beam, using both a stationary (reference) exposure and exposure during motion of the phantom perpendicular to the beam with beam tracking. There was no statistically significant difference between plating efficiency measured in the microwells with and without motion (0.75) and values reported in the literature. Mean differences between measured and calculated cell survival for these two irradiation modes were within ±5% of the target dose of 6 Gy (RBE).

  3. Development and performance evaluation of a dynamic phantom for biological dosimetry of moving targets

    Energy Technology Data Exchange (ETDEWEB)

    Gemmel, A; Bert, C; Saito, N; Von Neubeck, C; Iancu, G; K-Weyrather, W; Durante, M; Rietzel, E, E-mail: alexander.ag.gemmel@siemens.co [GSI Helmholtzzentrum fuer Schwerionenforschung, Planckstr 1, 64291 Darmstadt (Germany)

    2010-06-07

    A dynamic phantom has been developed to allow for measurement of 3D cell survival distributions and the corresponding distributions of the RBE-weighted dose (RBED) in the presence of motion. The phantom consists of two 96-microwell plates holding Chinese hamster ovary cells inside a container filled with culture medium and is placed on a movable stage. Basic biological properties of the phantom were investigated without irradiation and after irradiation with a carbon ion beam, using both a stationary (reference) exposure and exposure during motion of the phantom perpendicular to the beam with beam tracking. There was no statistically significant difference between plating efficiency measured in the microwells with and without motion (0.75) and values reported in the literature. Mean differences between measured and calculated cell survival for these two irradiation modes were within {+-}5% of the target dose of 6 Gy (RBE).

  4. Effects of dynamic operating conditions on nitrification in biological rapid sand filters for drinking water treatment

    DEFF Research Database (Denmark)

    Lee, Carson Odell; Boe-Hansen, Rasmus; Musovic, Sanin

    2014-01-01

    Biological rapid sand filters are often used to remove ammonium from groundwater for drinking water supply. They often operate under dynamic substrate and hydraulic loading conditions, which can lead to increased levels of ammonium and nitrite in the effluent. To determine the maximum nitrification...... operating conditions. The ammonium removal rate of the filter was determined by the ammonium loading rate, but was independent of both the flow and influent ammonium concentration individually. Ammonia-oxidizing bacteria and archaea were almost equally abundant in the filter. Both ammonium removal...... rates and safe operating windows of rapid sand filters, a pilot scale rapid sand filter was used to test short-term increased ammonium loads, set by varying either influent ammonium concentrations or hydraulic loading rates. Ammonium and iron (flock) removal were consistent between the pilot...

  5. Dynamics of Intracellular Polymers in Enhanced Biological Phosphorus Removal Processes under Different Organic Carbon Concentrations

    Directory of Open Access Journals (Sweden)

    Lizhen Xing

    2013-01-01

    Full Text Available Enhanced biological phosphorus removal (EBPR may deteriorate or fail during low organic carbon loading periods. Polyphosphate accumulating organisms (PAOs in EBPR were acclimated under both high and low organic carbon conditions, and then dynamics of polymers in typical cycles, anaerobic conditions with excess organic carbons, and endogenous respiration conditions were examined. After long-term acclimation, it was found that organic loading rates did not affect the yield of PAOs and the applied low organic carbon concentrations were advantageous for the enrichment of PAOs. A low influent organic carbon concentration induced a high production of extracellular carbohydrate. During both anaerobic and aerobic endogenous respirations, when glycogen decreased to around 80 ± 10 mg C per gram of volatile suspended solids, PAOs began to utilize polyphosphate significantly. Regressed by the first-order reaction model, glycogen possessed the highest degradation rate and then was followed by polyphosphate, while biomass decay had the lowest degradation rate.

  6. Biological sulphide removal from anaerobically treated domestic sewage: reactor performance and microbial community dynamics.

    Science.gov (United States)

    Garcia, Graziella Patrício Pereira; Diniz, Renata Côrtes Oliveira; Bicalho, Sarah Kinaip; Franco, Vitor Araujo de Souza; Gontijo, Eider Max de Oliveira; Toscano, Rodrigo Argolo; Canhestro, Kenia Oliveira; Santos, Merly Rita Dos; Carmo, Ana Luiza Rodrigues Dias; Lobato, Livia Cristina S; Brandt, Emanuel Manfred F; Chernicharo, Carlos A L; Calabria de Araujo, Juliana

    2015-01-01

    We developed a biological sulphide oxidation system and evaluated two reactors (shaped similar to the settler compartment of an up-flow anaerobic sludge blanket [UASB] reactor) with different support materials for biomass retention: polypropylene rings and polyurethane foam. The start-up reaction was achieved using microorganisms naturally occurring on the open surface of UASB reactors treating domestic wastewater. Sulphide removal efficiencies of 65% and 90% were achieved with hydraulic retention times (HRTs) of 24 and 12 h, respectively, in both reactors. However, a higher amount of elemental sulphur was formed and accumulated in the biomass from reactor 1 (20 mg S(0) g(-1) VTS) than in that from reactor 2 (2.9 mg S(0) g(-1) VTS) with an HRT of 24 h. Denaturing gradient gel electrophoresis (DGGE) results revealed that the the pink and green biomass that developed in both reactors comprised a diverse bacterial community and had sequences related to phototrophic green and purple-sulphur bacteria such as Chlorobium sp., Chloronema giganteum, and Chromatiaceae. DGGE band patterns also demonstrated that bacterial community was dynamic over time within the same reactor and that different support materials selected for distinct bacterial communities. Taken together, these results indicated that sulphide concentrations of 1-6 mg L(-1) could be efficiently removed from the effluent of a pilot-scale UASB reactor in two sulphide biological oxidation reactors at HRTs of 12 and 24 h, showing the potential for sulphur recovery from anaerobically treated domestic wastewater.

  7. Center of cancer systems biology second annual workshop--tumor metronomics: timing and dose level dynamics.

    Science.gov (United States)

    Hahnfeldt, Philip; Hlatky, Lynn; Klement, Giannoula Lakka

    2013-05-15

    Metronomic chemotherapy, the delivery of doses in a low, regular manner so as to avoid toxic side effects, was introduced over 12 years ago in the face of substantial clinical and preclinical evidence supporting its tumor-suppressive capability. It constituted a marked departure from the classic maximum-tolerated dose (MTD) strategy, which, given its goal of rapid eradication, uses dosing sufficiently intense to require rest periods between cycles to limit toxicity. Even so, upfront tumor eradication is frequently not achieved with MTD, whereupon a de facto goal of longer-term tumor control is often pursued. As metronomic dosing has shown tumor control capability, even for cancers that have become resistant to the same drug delivered under MTD, the question arises whether it may be a preferable alternative dosing approach from the outset. To date, however, our knowledge of the coupled dynamics underlying metronomic dosing is neither sufficiently well developed nor widely enough disseminated to establish its actual potential. Meeting organizers thus felt the time was right, armed with new quantitative approaches, to call a workshop on "Tumor Metronomics: Timing and Dose Level Dynamics" to explore prospects for gaining a deeper, systems-level appreciation of the metronomics concept. The workshop proved to be a forum in which experts from the clinical, biologic, mathematical, and computational realms could work together to clarify the principles and underpinnings of metronomics. Among other things, the need for significant shifts in thinking regarding endpoints to be used as clinical standards of therapeutic progress was recognized. ©2013 AACR.

  8. Influence of attapulgite addition on the biological performance and microbial communities of submerged dynamic membrane bioreactor

    Directory of Open Access Journals (Sweden)

    Wensong Duan

    2017-12-01

    Full Text Available A submerged dynamic membrane bioreactor (sDMBR was developed to test the influence of attapulgite (AT addition on the treatment performances and the microbial community structure and function. The batch experimental results displayed the highest UV254 and dissolved organic carbon (DOC removal efficiencies with 5% AT/mixed liquid suspended solids addition dosage. The continuous sDMBR results showed that the removal efficiencies of chemical oxygen demand, NH4+-N, total nitrogen and total phosphorus significantly increased in the AT added sDMBR. Excitation emission matrix analysis demonstrated that the protein-like peaks and fulvic acid-like peaks were significantly decreased in both in the mixed liquid and the effluent of the AT added reactor. The obligate anaerobes were observed in the sDMBR with AT addition, such as Bacteroidetes and Gamma proteobacterium in the dynamic membrane, which played an important role in the process of sludge granulation. Bacterial community richness significantly increased after AT addition with predominated phyla of Proteobacteria and Bacteroidetes. Similarly, species abundance significantly increased in the AT added sDMBR. Further investigations with cluster proved that AT was a favorite biological carrier for the microbial ecology, which enriched microbial abundance and community diversity of the sDMBR.

  9. Multimegawatt dynamic NEP PMAD study

    International Nuclear Information System (INIS)

    Metcalf, K.J.

    1993-01-01

    The National Aeronautics and Space Administration Lewis Research Center (NASA LeRC) is developing a Fortran--based model of a complete nuclear electric propulsion (NEP) vehicle to be used for piloted or cargo missions to the Moon or Mars. The proposed vehicle will use either a Brayton or K-Rankine power conversion cycle, and either ion or magnetoplasmadynamic (MPD) thrusters. In support of this effort, Rocketdyne evaluated various power management and distribution (PMAD) approaches and selected a low-frequency design that is based on the direct use of the alternator voltage and frequency for power transmission. This approach was compared with dc and high-frequency ac designs, and selected on the basis of mass, efficiency, and qualitative assessments of power quality, reliability and development costs. This low-frequency architecture will be used as the reference in future NEP PMAD studies and for the subsequent Fortran model development

  10. Biological soil crusts across disturbance–recovery scenarios: effect of grazing regime on community dynamics.

    Science.gov (United States)

    Concostrina-Zubiri, L; Huber-Sannwald, E; Martínez, I; Flores Flores, J L; Reyes-Agüero, J A; Escude, A; Belnap, J

    Grazing represents one of the most common disturbances in drylands worldwide, affecting both ecosystem structure and functioning. Despite the efforts to understand the nature and magnitude of grazing effects on ecosystem components and processes, contrasting results continue to arise. This is particularly remarkable for the biological soil crust (BSC) communities (i.e., cyanobacteria, lichens, and bryophytes), which play an important role in soil dynamics. Here we evaluated simultaneously the effect of grazing impact on BSC communities (resistance) and recovery after livestock exclusion (resilience) in a semiarid grassland of Central Mexico. In particular, we examined BSC species distribution, species richness, taxonomical group cover (i.e., cyanobacteria, lichen, bryophyte), and composition along a disturbance gradient with different grazing regimes (low, medium, high impact) and along a recovery gradient with differently aged livestock exclosures (short-, medium-, long-term exclusion). Differences in grazing impact and time of recovery from grazing both resulted in slight changes in species richness; however, there were pronounced shifts in species composition and group cover. We found we could distinguish four highly diverse and dynamic BSC species groups: (1) species with high resistance and resilience to grazing, (2) species with high resistance but low resilience, (3) species with low resistance but high resilience, and (4) species with low resistance and resilience. While disturbance resulted in a novel diversity configuration, which may profoundly affect ecosystem functioning, we observed that 10 years of disturbance removal did not lead to the ecosystem structure found after 27 years of recovery. These findings are an important contribution to our understanding of BCS dynamics from a species and community perspective placed in a land use change context.

  11. Biological soil crusts across disturbance-recovery scenarios: effect of grazing regime on community dynamics

    Science.gov (United States)

    Concostrina-Zubiri, L.; Huber-Sannwald, E.; Martínez, I.; Flores Flores, J. L.; Reyes-Agüero, J. A.; Escudero, A.; Belnap, Jayne

    2014-01-01

    Grazing represents one of the most common disturbances in drylands worldwide, affecting both ecosystem structure and functioning. Despite the efforts to understand the nature and magnitude of grazing effects on ecosystem components and processes, contrasting results continue to arise. This is particularly remarkable for the biological soil crust (BSC) communities (i.e., cyanobacteria, lichens, and bryophytes), which play an important role in soil dynamics. Here we evaluated simultaneously the effect of grazing impact on BSC communities (resistance) and recovery after livestock exclusion (resilience) in a semiarid grassland of Central Mexico. In particular, we examined BSC species distribution, species richness, taxonomical group cover (i.e., cyanobacteria, lichen, bryophyte), and composition along a disturbance gradient with different grazing regimes (low, medium, high impact) and along a recovery gradient with differently aged livestock exclosures (short-, medium-, long-term exclusion). Differences in grazing impact and time of recovery from grazing both resulted in slight changes in species richness; however, there were pronounced shifts in species composition and group cover. We found we could distinguish four highly diverse and dynamic BSC species groups: (1) species with high resistance and resilience to grazing, (2) species with high resistance but low resilience, (3) species with low resistance but high resilience, and (4) species with low resistance and resilience. While disturbance resulted in a novel diversity configuration, which may profoundly affect ecosystem functioning, we observed that 10 years of disturbance removal did not lead to the ecosystem structure found after 27 years of recovery. These findings are an important contribution to our understanding of BCS dynamics from a species and community perspective placed in a land use change context.

  12. [Application of network biology on study of traditional Chinese medicine].

    Science.gov (United States)

    Tian, Sai-Sai; Yang, Jian; Zhao, Jing; Zhang, Wei-Dong

    2018-01-01

    With the completion of the human genome project, people have gradually recognized that the functions of the biological system are fulfilled through network-type interaction between genes, proteins and small molecules, while complex diseases are caused by the imbalance of biological processes due to a number of gene expression disorders. These have contributed to the rise of the concept of the "multi-target" drug discovery. Treatment and diagnosis of traditional Chinese medicine are based on holism and syndrome differentiation. At the molecular level, traditional Chinese medicine is characterized by multi-component and multi-target prescriptions, which is expected to provide a reference for the development of multi-target drugs. This paper reviews the application of network biology in traditional Chinese medicine in six aspects, in expectation to provide a reference to the modernized study of traditional Chinese medicine. Copyright© by the Chinese Pharmaceutical Association.

  13. Dynamics on and of complex networks applications to biology, computer science, and the social sciences

    CERN Document Server

    Ganguly, Niloy; Mukherjee, Animesh

    2009-01-01

    This self-contained book systematically explores the statistical dynamics on and of complex networks having relevance across a large number of scientific disciplines. The theories related to complex networks are increasingly being used by researchers for their usefulness in harnessing the most difficult problems of a particular discipline. The book is a collection of surveys and cutting-edge research contributions exploring the interdisciplinary relationship of dynamics on and of complex networks. Towards this goal, the work is thematically organized into three main sections: Part I studies th

  14. Comparative study of biological activity of glutathione, sodium ...

    African Journals Online (AJOL)

    Glutathione (GSH) and sodium tungstate (Na2WO4) are important pharmacological agents. They provide protection to cells against cytotoxic agents and thus reduce their cytotoxicity. It was of interest to study the biological activity of these two pharmacological active agents. Different strains of bacteria were used and the ...

  15. Synthesis, biological evaluation and molecular docking studies of ...

    African Journals Online (AJOL)

    Synthesis, biological evaluation and molecular docking studies of Mannich bases derived from 1, 3, 4-oxadiazole- 2-thiones as potential urease inhibitors. ... Mannich bases (5-17) were subjected to in silico screening as urease inhibitors, using crystal structure of urease (Protein Data Bank ID: 5FSE) as a model enzyme.

  16. Biological, Histological and Ultra-Structural Studies of Female Mullet ...

    African Journals Online (AJOL)

    Biological, Histological and Ultra-Structural Studies of Female Mullet, Mugil cephalus , Ovaries Collected from Different Habitats during Annual Reproductive Cycle. ... 35 and 52 cm, respectively; whereas, the total number of ripe ova in brackish water fish ranged from 0.57±0.14 to 3.81±0.59 x106 for the same length groups.

  17. Moessbauer spectroscopic studies of magnetically ordered biological materials

    International Nuclear Information System (INIS)

    Dickson, D.P.E.

    1987-01-01

    This paper discusses recent work showing the application of Moessbauer spectroscopy to the study of the properties of the magnetically ordered materials which occur in a variety of biological systems. These materials display a diversity of behaviour which provides good examples of the various possibilities which can arise with iron-containing particles of different compositions and sizes. (orig.)

  18. Epistemological Syncretism in a Biology Classroom: A Case Study

    Science.gov (United States)

    Bennett, William D.; Park, Soonhye

    2011-01-01

    In teaching science, the beliefs of teachers may come into conflict and inhibit the implementation of reformed teaching practice. An experienced biology teacher, Mr. Hobbs, was found to have two different sets of epistemological beliefs while his classroom practice was predominantly teacher-centered. A case study was then performed in order to…

  19. Studies on bacterial flora and biological control agent of Cydia ...

    African Journals Online (AJOL)

    In the present study, in order to find a more effective and safe biological control agent against Cydia pomonella, we investigated the bacterial flora and tested them for insecticidal effects on this insect. According to morphological, physiological and biochemical tests, bacterial flora were identified as Proteus rettgeri (Cp1), ...

  20. Vitamin D biology and heart failure : Clinical and experimental studies

    NARCIS (Netherlands)

    Meems, Laura

    2015-01-01

    In the last decade, vitamin D biology has been studied more extensively than ever before.. The use of vitamin D supplements is common, and so is determination of plasma vitamin D status. Besides its role in bone homeostasis, vitamin D is thought to be an important player in the development and

  1. Researchers study decontamination of chemical, biological warfare agents

    OpenAIRE

    Trulove, Susan

    2007-01-01

    The U.S. Army Research Office has awarded Virginia Tech a $680,000 grant over two years to build an instrument that can be used to study the chemistry of gases that will decompose both chemical and biological warfare agents on surfaces.

  2. 2nd International Symposium "Atomic Cluster Collisions : Structure and Dynamics from the Nuclear to the Biological Scale"

    CERN Document Server

    Solov'yov, Andrey; ISACC 2007; Latest advances in atomic cluster collisions

    2008-01-01

    This book presents a 'snapshot' of the most recent and significant advances in the field of cluster physics. It is a comprehensive review based on contributions by the participants of the 2nd International Symposium on Atomic Cluster Collisions (ISACC 2007) held in July 19-23, 2007 at GSI, Darmstadt, Germany. The purpose of the Symposium is to promote the growth and exchange of scientific information on the structure and properties of nuclear, atomic, molecular, biological and complex cluster systems studied by means of photonic, electronic, heavy particle and atomic collisions. Particular attention is devoted to dynamic phenomena, many-body effects taking place in cluster systems of a different nature - these include problems of fusion and fission, fragmentation, collective electron excitations, phase transitions, etc.Both the experimental and theoretical aspects of cluster physics, uniquely placed between nuclear physics on the one hand and atomic, molecular and solid state physics on the other, are discuss...

  3. Biological sensing and control of emission dynamics of quantum dot bioconjugates using arrays of long metallic nanorods.

    Science.gov (United States)

    Sadeghi, Seyed M; Gutha, Rithvik R; Wing, Waylin J; Sharp, Christina; Capps, Lucas; Mao, Chuanbin

    2017-01-01

    We study biological sensing using plasmonic and photonic-plasmonic resonances of arrays of ultralong metallic nanorods and analyze the impact of these resonances on emission dynamics of quantum dot bioconjugates. We demonstrate that the LSPRs and plasmonic lattice modes of such array can be used to detect a single self-assembled monolayer of alkanethiol at the visible (550 nm) and near infrared (770 nm) range with well resolved shifts. We study adsorption of streptavidin-quantum dot conjugates to this monolayer, demonstrating that formation of nearly two dimensional arrays of quantum dots with limited emission blinking can lead to extra well-defined wavelength shifts in these modes. Using spectrally-resolved lifetime measurements we study the emission dynamics of such quantum dot bioconjugates within their monodispersed size distribution. We show that, despite their close vicinity to the nanorods, the rate of energy transfer from these quantum dots to nanorods is rather weak, while the plasmon field enhancement can be strong. Our results reveal that the nanorods present a strongly wavelength or size-dependent non-radiative decay channel to the quantum dot bioconjugates.

  4. Correlative and dynamic imaging of the hatching biology of Schistosoma japonicum from eggs prepared by high pressure freezing.

    Directory of Open Access Journals (Sweden)

    Malcolm K Jones

    Full Text Available BACKGROUND: Schistosome eggs must traverse tissues of the intestine or bladder to escape the human host and further the life cycle. Escape from host tissues is facilitated by secretion of immuno-reactive molecules by eggs and the formation of an intense strong granulomatous response by the host which acts to exclude the egg into gut or bladder lumens. Schistosome eggs hatch on contact with freshwater, but the mechanisms of activation and hatching are poorly understood. In view of the lack of knowledge of the behaviour of egg hatching in schistosomes, we undertook a detailed dynamic and correlative study of the hatching biology of Schistosoma japonicum. METHODOLOGY/PRINCIPAL FINDINGS: Hatching eggs of S. japonicum were studied using correlative light and electron microscopy (EM. The hatching behaviour was recorded by video microscopy. EM preparative methods incorporating high pressure freezing and cryo-substitution were used to investigate ultrastructural features of the miracidium and extra-embryonic envelopes in pre-activated and activated eggs, and immediately after eggshell rupture. Lectin cytochemistry was performed on egg tissues to investigate subcellular location of specific carbohydrate groups. CONCLUSIONS/SIGNIFICANCE: The hatching of S. japonicum eggs is a striking phenomenon, whereby the larva is liberated explosively while still encapsulated within its sub-shell envelopes. The major alterations that occur in the egg during activation are scission of the outer envelope-eggshell boundary, autolysis of the cellular inner envelope, and likely hydration of abundant complex and simple polysaccharides in the lacunal space between the miracidial larva and surrounding envelopes. These observations on hatching provide insight into the dynamic activity of the eggs and the biology of schistosomes within the host.

  5. Molecular dynamics studies of superionic conductors

    International Nuclear Information System (INIS)

    Rahman, A.; Vashishta, P.

    1983-01-01

    Structural and dynamical properties of superionic conductors AgI and CuI are studied using molecular dynamics (MD) techniques. The model of these superionic conductors is based on the use of effective pair potentials. To determine the constants in these potentials, cohesive energy and bulk modulus are used as input: in addition one uses notions of ionic size based on the known crystal structure. Salient features of the MD technique are outlined. Methods of treating long range Coulomb forces are discussed in detail. This includes the manner of doing Ewald sum for MD cells of arbitrary shape. Features that can be incorporated to expedite the MD calculations are also discussed. A novel MD technique which allows for a dynamically controlled variation of the shape and size of the MD cell is described briefly. The development of this novel technique has made it possible to study structural phase transitions in superionic conductors. 68 references, 17 figures, 2 tables

  6. Computer processing of dynamic scintigraphic studies

    International Nuclear Information System (INIS)

    Ullmann, V.

    1985-01-01

    The methods are discussed of the computer processing of dynamic scintigraphic studies which were developed, studied or implemented by the authors within research task no. 30-02-03 in nuclear medicine within the five year plan 1981 to 85. This was mainly the method of computer processing radionuclide angiography, phase radioventriculography, regional lung ventilation, dynamic sequential scintigraphy of kidneys and radionuclide uroflowmetry. The problems are discussed of the automatic definition of fields of interest, the methodology of absolute volumes of the heart chamber in radionuclide cardiology, the design and uses are described of the multipurpose dynamic phantom of heart activity for radionuclide angiocardiography and ventriculography developed within the said research task. All methods are documented with many figures showing typical clinical (normal and pathological) and phantom measurements. (V.U.)

  7. Biological soil crusts exhibit a dynamic response to seasonal rain and release from grazing with implications for soil stability

    Science.gov (United States)

    Jimenez, Aguilar A.; Huber-Sannwald, E.; Belnap, J.; Smart, D.R.; Arredondo, Moreno J.T.

    2009-01-01

    In Northern Mexico, long-term grazing has substantially degraded semiarid landscapes. In semiarid systems, ecological and hydrological processes are strongly coupled by patchy plant distribution and biological soil crust (BSC) cover in plant-free interspaces. In this study, we asked: 1) how responsive are BSC cover/composition to a drying/wetting cycle and two-year grazing removal, and 2) what are the implications for soil erosion? We characterized BSC morphotypes and their influence on soil stability under grazed/non-grazed conditions during a dry and wet season. Light- and dark-colored cyanobacteria were dominant at the plant tussock and community level. Cover changes in these two groups differed after a rainy season and in response to grazing removal. Lichens with continuous thalli were more vulnerable to grazing than those with semi-continuous/discontinuous thalli after the dry season. Microsites around tussocks facilitated BSC colonization compared to interspaces. Lichen and cyanobacteria morphotypes differentially enhanced resistance to soil erosion; consequently, surface soil stability depends on the spatial distribution of BSC morphotypes, suggesting soil stability may be as dynamic as changes in the type of BSC cover. Longer-term spatially detailed studies are necessary to elicit spatiotemporal dynamics of BSC communities and their functional role in biotically and abiotically variable environments. ?? 2009 Elsevier Ltd.

  8. Studying chemical reactions in biological systems with MBN Explorer

    DEFF Research Database (Denmark)

    Sushko, Gennady B.; Solov'yov, Ilia A.; Verkhovtsev, Alexey V.

    2016-01-01

    The concept of molecular mechanics force field has been widely accepted nowadays for studying various processes in biomolecular systems. In this paper, we suggest a modification for the standard CHARMM force field that permits simulations of systems with dynamically changing molecular topologies....... The implementation of the modified force field was carried out in the popular program MBN Explorer, and, to support the development, we provide several illustrative case studies where dynamical topology is necessary. In particular, it is shown that the modified molecular mechanics force field can be applied...

  9. Study of the effects of radon in three biological systems

    International Nuclear Information System (INIS)

    Tavera, L.; Balcazar, M.; Lopez, A.; Brena, M.; Rosa, M.E. De la; Villalobos P, R.

    2002-01-01

    The radon and its decay products are responsible of the 3/4 parts of the exposure of the persons to the environmental radiation. The discovery at the end of XIX Century of the illnesses, mainly of cancer, which appeared in the presence of radon, lead to an accelerated growing of the radon studies: monitoring, dosimetry, effects on the persons, etc. Several epidemiological studies of radon in miners and population in general have been realized; advancing in the knowledge about the concentration-lung cancer risk relationship, but with discrepancies in the results depending on the concentration levels. Therefor, studies which consuming time, efforts and money go on doing. The research of the radon effects in biological systems different to human, allows to realize studies in less time, in controlled conditions and generally at lower cost, generating information about the alpha radiation effects in the cellular field. Therefor it was decided to study the response of three biological systems exposed to radon: an unicellular bacteria Escherichia Coli which was exposed directly to alpha particles from an electrodeposited source for determining the sensitivity limit of the chose technique. A plant, Tradescantia, for studying the cytogenetic effect of the system exposed to controlled concentrations of radon. An insect, Drosophila Melanogaster, for studying the genetic effects and the accumulated effects in several generations exposed to radon. In this work the experimental settlements are presented for the expositions of the systems and the biological results commenting the importance of these. (Author)

  10. Photo fragmentation dynamics of small argon clusters and biological molecular: new tools by trapping and vectorial correlation

    International Nuclear Information System (INIS)

    Lepere, V.

    2006-09-01

    The present work concerns the building up of a complex set-up whose aim being the investigation of the photo fragmentation of ionised clusters and biological molecules. This new tool is based on the association of several techniques. Two ion sources are available: clusters produced in a supersonic beam are ionised by 70 eV electrons while ions of biological interest are produced in an 'electro-spray'. Ro-vibrational cooling is achieved in a 'Zajfman' electrostatic ion trap. The lifetime of ions can also be measured using the trap. Two types of lasers are used to excite the ionised species: the femtosecond laser available at the ELYSE facilities and a nanosecond laser. Both lasers have a repetition rate of 1 kHz. The neutral and ionised fragments are detected in coincidence using a sophisticated detection system allowing time and localisation of the various fragments to be determined. With such a tool, I was able to investigate in details the fragmentation dynamics of ionised clusters and bio-molecules. The first experiments deal with the measurement of the lifetime of the Ar 2+ dimer II(1/2)u metastable state. The relative population of this state was also determined. The Ar 2+ and Ar 3+ photo-fragmentation was then studied and electronic transitions responsible for their dissociation identified. The detailed analysis of our data allowed to distinguish the various fragmentation mechanisms. Finally, a preliminary investigation of the protonated tryptamine fragmentation is presented. (author)

  11. A Non-Homogeneous Dynamic Bayesian Network with Sequentially Coupled Interaction Parameters for Applications in Systems and Synthetic Biology

    NARCIS (Netherlands)

    Grzegorczyk, Marco; Husmeier, Dirk

    2012-01-01

    An important and challenging problem in systems biology is the inference of gene regulatory networks from short non-stationary time series of transcriptional profiles. A popular approach that has been widely applied to this end is based on dynamic Bayesian networks (DBNs), although traditional

  12. Contributions to the Study of Dynamic Absorbers, a Case Study

    Directory of Open Access Journals (Sweden)

    Monica Balcau

    2012-01-01

    Full Text Available Dynamic absorbers are used to reduce torsional vibrations. This paper studies the effect of a dynamic absorber attached to a mechanical system formed of three reduced masses which are acted on by one, two or three order x harmonics of a disruptive force.

  13. Studies on digoxin derivatives in different biological media by radioimmunoassay

    International Nuclear Information System (INIS)

    Barmasch, Martha; Perez, L.N.; Altschuler, Noe.

    1978-05-01

    The fundamental aim of this study was to develop a methodology to be applied to pharmacological studies, directed to demonstrate the passage of digitalic compounds through the blood-brain barrier. This study was a comparative one between β methyl digoxin (βMD) and digitoxin (Dt). A methodology of radioimmunoassay was developed for different biological media: serum (S), plasma (P) and cerebro spinal fluid (CSF). In addition, the immunochemical behaviour (affinity, displacement, etc.) of βMD was studied when reacted with digoxin (D) and digoxin-antisera, supplied by the commercial kits utilized in these studies. (author) [es

  14. Remote Sensing Dynamic Monitoring of Biological Invasive Species Based on Adaptive PCNN and Improved C-V Model

    Directory of Open Access Journals (Sweden)

    PENG Gang

    2014-12-01

    Full Text Available Biological species invasion problem bring serious damage to the ecosystem, and have become one of the six major enviromental problems that affect the future economic development, also have become one of the hot topic in domestic and foreign scholars. Remote sensing technology has been successfully used in the investigation of coastal zone resources, dynamic monitoring of the resources and environment, and other fields. It will cite a new remote sensing image change detection algorithm based on adaptive pulse coupled neural network (PCNN and improved C-V model, for remote sensing dynamic monitoring of biological species invasion. The experimental results show that the algorithm is effective in the test results of biological species invasions.

  15. A study of the HEB longitudinal dynamics

    International Nuclear Information System (INIS)

    Larson, D.J.

    1993-12-01

    A study of the High Energy Booster (HEB) longitudinal dynamics is presented. Full derivations of ramp dependent longitudinal variables are given. The formulas assume that the input magnetic field and beam longitudinal emittance are known as a function of time, and that either the rf voltage or the rf bucket area are known as a function of time. Once these three inputs are specified, the formulas can be used to calculate values for all other longitudinal dynamics variables. The formulas have been incorporated into a single computer code named ELVIRA: Evaluation of Longitudinal Variables in Relativistic Accelerators. The ELVIRA code is documented here in detail. The ELVIRA code is used under two initial longitudinal emittance assumptions to plot ramp functions for the longitudinal dynamics design of the HEB as of May 5, 1992

  16. Study on dynamic performance of SOFC

    Science.gov (United States)

    Zhan, Haiyang; Liang, Qianchao; Wen, Qiang; Zhu, Runkai

    2017-05-01

    In order to solve the problem of real-time matching of load and fuel cell power, it is urgent to study the dynamic response process of SOFC in the case of load mutation. The mathematical model of SOFC is constructed, and its performance is simulated. The model consider the influence factors such as polarization effect, ohmic loss. It also takes the diffusion effect, thermal effect, energy exchange, mass conservation, momentum conservation. One dimensional dynamic mathematical model of SOFC is constructed by using distributed lumped parameter method. The simulation results show that the I-V characteristic curves are in good agreement with the experimental data, and the accuracy of the model is verified. The voltage response curve, power response curve and the efficiency curve are obtained by this way. It lays a solid foundation for the research of dynamic performance and optimal control in power generation system of high power fuel cell stack.

  17. A Molecular Dynamics Study of the Structural and Dynamical Properties of Putative Arsenic Substituted Lipid Bilayers

    Directory of Open Access Journals (Sweden)

    Ratna Juwita

    2013-04-01

    Full Text Available Cell membranes are composed mainly of phospholipids which are in turn, composed of five major chemical elements: carbon, hydrogen, nitrogen, oxygen, and phosphorus. Recent studies have suggested the possibility of sustaining life if the phosphorus is substituted by arsenic. Although this issue is still controversial, it is of interest to investigate the properties of arsenated-lipid bilayers to evaluate this possibility. In this study, we simulated arsenated-lipid, 1-palmitoyl-2-oleoyl-sn-glycero-3-arsenocholine (POAC, lipid bilayers using all-atom molecular dynamics to understand basic structural and dynamical properties, in particular, the differences from analogous 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, (POPC lipid bilayers. Our simulations showed that POAC lipid bilayers have distinct structural and dynamical properties from those of native POPC lipid bilayers. Relative to POPC lipid bilayers, POAC lipid bilayers have a more compact structure with smaller lateral areas and greater order. The compact structure of POAC lipid bilayers is due to the fact that more inter-lipid salt bridges are formed with arsenate-choline compared to the phosphate-choline of POPC lipid bilayers. These inter-lipid salt bridges bind POAC lipids together and also slow down the head group rotation and lateral diffusion of POAC lipids. Thus, it would be anticipated that POAC and POPC lipid bilayers would have different biological implications.

  18. Improving Satellite Compatible Microdevices to Study Biology in Space

    Science.gov (United States)

    Kalkus, Trevor; Snyder, Jessica; Paulino-Lima, Ivan; Rothschild, Lynn

    2017-01-01

    sense for biochemicals. (3) Developing a modular, semi-autonomous microfluidic device that can be easily adapted for a variety of common biological experiments. This versatility will allow for quicker and cheaper experimentation. These improvements to satellite experiment platforms have the potential to radically increase the return from NASA's biological and field studies with reduced development time, mass, and cost with increased robustness data and interpretation.

  19. Radiolabelled substrates for studying biological effects of trace contaminants

    International Nuclear Information System (INIS)

    1975-01-01

    A programme of coordinated isotopic tracer-aided investigations of the biological side-effects of foreign chemical residues in food and agriculture, initiated in 1973, was reviewed. The current status of representative investigations from the point of view of techniques and priorities was assessed. Such investigations involved radioactive substrates for studying DNA injury and its repair; 14 C-labelled acetylcholine as substrate for measuring enzyme inhibition due to the presence of, or exposure to, anticholinesteratic contaminants; radioactive substrates as indication of side-effects in non-target organisms and of their comparative susceptibilities; radioactive substrates as indicators of persistence or biodegradability of trace contaminants of soil or water; and labelled pools for studying the biological side-effects of trace contaminants. Priorities were identified

  20. Modeling systems-level dynamics: Understanding without mechanistic explanation in integrative systems biology.

    Science.gov (United States)

    MacLeod, Miles; Nersessian, Nancy J

    2015-02-01

    In this paper we draw upon rich ethnographic data of two systems biology labs to explore the roles of explanation and understanding in large-scale systems modeling. We illustrate practices that depart from the goal of dynamic mechanistic explanation for the sake of more limited modeling goals. These processes use abstract mathematical formulations of bio-molecular interactions and data fitting techniques which we call top-down abstraction to trade away accurate mechanistic accounts of large-scale systems for specific information about aspects of those systems. We characterize these practices as pragmatic responses to the constraints many modelers of large-scale systems face, which in turn generate more limited pragmatic non-mechanistic forms of understanding of systems. These forms aim at knowledge of how to predict system responses in order to manipulate and control some aspects of them. We propose that this analysis of understanding provides a way to interpret what many systems biologists are aiming for in practice when they talk about the objective of a "systems-level understanding." Copyright © 2014 Elsevier Ltd. All rights reserved.

  1. The Dominance Behavioral System and Psychopathology: Evidence from Self-Report, Observational, and Biological Studies

    Science.gov (United States)

    Johnson, Sheri L.; Leedom, Liane J.; Muhtadie, Luma

    2012-01-01

    The dominance behavioral system (DBS) can be conceptualized as a biologically-based system which guides dominance motivation, dominant and subordinate behavior, and responsivity to perceptions of power and subordination. A growing body of research suggests that problems with the DBS are evident across a broad range of psychopathologies. We begin by describing psychological, social, and biological correlates of the dominance behavioral system (DBS). Extensive research suggests that externalizing disorders, mania-proneness, and narcissistic traits are related to heightened dominance motivation and behaviors. Mania and narcissistic traits also appear related to inflated self-perceptions of power. Anxiety and depression are related to subordination and submissiveness, as well as a desire to avoid subordination. Models of the DBS have received support from research with humans and animals; from self-report, observational, and biological methods; and using naturalistic and experimental paradigms. Limitations of available research include the relative lack of longitudinal studies using multiple measures of the DBS and the absence of relevant studies using diagnosed samples to study narcissistic personality disorder and bipolar disorder. We provide suggestions for future research on the DBS and psychopathology, including investigations of whether the DBS can be used to differentiate specific disorder outcomes; the need for more sophisticated biological research; and the value of longitudinal dynamical research. Implications of using the DBS as a tool in clinical assessment and treatment are discussed. PMID:22506751

  2. Application of magnetic resonance imaging and spectroscopy in studying the biological effects of manufactured nanoparticles

    International Nuclear Information System (INIS)

    Lei Hao; Wei Li; Liu Maili

    2006-01-01

    With the rapid development of nanoscience and nanotechnology in recent years, growing research interest and efforts have been directed to study the biological effects of manufactured nanoparticles and substances alike. Despite the fact that significant progress has been made, this is still largely an uncharted field. Any advances in this field would certainly require thorough multi-disciplinary collaboration, in which the expertise and tools in nanoscience/nanotechnoloogy, physics, chemistry and biomedicine have to be combined. Due to their wide range of applications in physics, chemistry and biomedicine, magnetic resonance (MR) imaging and spectroscopy are among the most important and powerful research tools currently in use, mainly because these techniques can be used in situ and noninvasively to acquire dynamic and real-time information in various samples ranging from protein solution to the human brain. In this paper, the application of MR imaging and spectroscopy in studying the biological effects of manufactured nanoparticles is discussed. It is expected that these techniques will play important roles in 1) detecting the presence of nanoparticles in biological tissues and in vivo, 2) studying the interactions between the nanoparticles and biomolecules and 3) investigating the metabonomic aspect of the biological effects of nanoparticles. (authors)

  3. A Molecular Dynamics Study of Lunasin | Singh | South African ...

    African Journals Online (AJOL)

    A Molecular Dynamics Study of Lunasin. ... profile of lunasin,using classical molecular dynamics (MD) simulations at the time scale of 300 ns. ... Keywords: Lunasin, molecular dynamics, amber, CLASICO, α-helix, β-turn, PTRAJ, RGD, RMSD ...

  4. Molecular Dynamics Studies of Nanofluidic Devices

    DEFF Research Database (Denmark)

    Zambrano Rodriguez, Harvey Alexander

    of such devices. Computational nanofluidics complements experimental studies by providing detailed spatial and temporal information of the nanosystem. In this thesis, we conduct molecular dynamics simulations to study basic nanoscale devices. We focus our studies on the understanding of transport mechanism...... to drive fluids and solids at the nanoscale. Specifically, we present the results of three different research projects. Throughout the first part of this thesis, we include a comprenhensive introduction to computational nanofluidics and to molecular simulations, and describe the molecular dynamics...... in opposite direction to the imposed thermal gradient also we measure higher velocities as higher thermal gradients are imposed. Secondly, we present an atomistic analysis of a molecular linear motor fabricated of coaxial carbon nanotubes and powered by thermal gradients. The MD simulation results indicate...

  5. Study of β-NMR for Liquid Biological Samples

    CERN Document Server

    Beattie, Caitlin

    2017-01-01

    β-NMR is an exotic form of NMR spectroscopy that allows for the characterization of matter based on the anisotropic β-decay of radioactive probe nuclei. This has been shown to be an effective spectroscopic technique for many different compounds, but its use for liquid biological samples is relatively unexplored. The work at the VITO line of ISOLDE seeks to employ this technique to study such samples. Currently, preparations are being made for an experiment to characterize DNA G-quadruplexes and their interactions with stabilizing cations. More specifically, the work in which I engaged as a summer student focused on the experiment’s liquid handling system and the stability of the relevant biological samples under vacuum.

  6. Biological dosimetry of X-rays by micronuclei study

    International Nuclear Information System (INIS)

    Gomez, E.; Silva, A.; Navlet, J.

    1991-01-01

    Biological dosimetry consists of estimating absorbed doses for people exposed to radiation by mean biological methods. Several indicators used are based in hematological, biochemical an cytogenetics data, although nowadays without doubt, the cytogenetic method is considered to be the most reliable, in this case, the study of micronuclei in peripheral blood lymphocytes cytokinetic blocked can be related to absorbed dose through an experimental calibration curve. An experimental dose-response curve, using micronuclei assay for X-rays at 250 kVp, 43,79 rads/min and temperature 37 degree celsius has been produced. Experimental data is fitted to model Y=c+ α D+β D 2 where. Y is the number micronuclei per cell and D the dose. the curve is compared with those produced elsewhere

  7. Biological Dosimetry of X-rays by micronuclei study

    International Nuclear Information System (INIS)

    Gomez, E.; Silva, A.; Navlet, J.

    1991-01-01

    Biological dosimetry consists of estimating absorbed doses for people exposed to radiation by mean biological methods. Several indicators used are based in haematological, biochemical an cytogenetics data, although nowadays without doubt, the cytogenetic method is considered to be the most reliable, in this case, the study of micronuclei in peripheral blood lymphocytes citokinetics blocked can be related to absorbed dose through an experimental calibration curve. An experimental dose-response curve, using micronuclei assay for X-rays at 250 kVp, 43,79 rads/min and temperature 37 degree centigree has been produced. Experimental data is fitted to model Y=C+ αD+BD''2 where Y is the number of micronuclei per cell and D the dose. The curve is compared with those produced elsewhere. (Author) 24 refs

  8. Study of nanoscale structural biology using advanced particle beam microscopy

    Science.gov (United States)

    Boseman, Adam J.

    This work investigates developmental and structural biology at the nanoscale using current advancements in particle beam microscopy. Typically the examination of micro- and nanoscale features is performed using scanning electron microscopy (SEM), but in order to decrease surface charging, and increase resolution, an obscuring conductive layer is applied to the sample surface. As magnification increases, this layer begins to limit the ability to identify nanoscale surface structures. A new technology, Helium Ion Microscopy (HIM), is used to examine uncoated surface structures on the cuticle of wild type and mutant fruit flies. Corneal nanostructures observed with HIM are further investigated by FIB/SEM to provide detailed three dimensional information about internal events occurring during early structural development. These techniques are also used to reconstruct a mosquito germarium in order to characterize unknown events in early oogenesis. Findings from these studies, and many more like them, will soon unravel many of the mysteries surrounding the world of developmental biology.

  9. An overview of surface radiance and biology studies in FIFE

    Science.gov (United States)

    Blad, B. L.; Schimel, D. S.

    1992-01-01

    The use of satellite data to study and to understand energy and mass exchanges between the land surface and the atmosphere requires information about various biological processes and how various reflected or emitted spectral radiances are influenced by or manifested in these processes. To obtain such information, studies were conducted by the First ISLSCP Field Experiment (FIFE) surface radiances and biology (SRB) group using surface, near-surface, helicopter, and aircraft measurements. The two primary objectives of this group were to relate radiative fluxes to biophysical parameters and physiological processes and to assess how various management treatments affect important biological processes. This overview paper summarizes the results obtained by various SRB teams working in nine different areas: (1) measurements of bidirectional reflectance and estimation of hemispherical albedo; (2) evaluation of spatial and seasonal variability reflectance and vegetation indices; (3) determination of surface and radiational factors and their effects on vegetation indices and photosynthetically active radiation relationships; (4) use of surface temperatures to estimate sensible heat flux; (5) controls over photosynthesis and respiration at small scales; (6) soil surface CO2 fluxes and grassland carbon budget; (7) landscape variations in controls over gas exchange and energy partitioning; (8) radiometric response of prairie to management and topography; and (9) determination of nitrogen gas exchanges in a tallgrass prairie.

  10. Biological effective dose studies in carcinoma of uterine cervix

    International Nuclear Information System (INIS)

    Yadav, Poonam; Ramasubramanian, V.

    2008-01-01

    Cancer of cervix is the second most common cancer worldwide among women. Several treatments related protocols of radiotherapy have been followed over few decades in its treatment for evaluating the response. These physical doses varying on the basics of fractionation size, dose rate and total dose needed to be indicated as biological effective dose (BED) to rationalize these treatments. The curative potential of radiation therapy in the management of carcinoma of the cervix is greatly enhanced by the use of intracavitary brachytherapy. Successful brachytherapy requires the high radiation dose to be delivered to the tumor where as minimum radiation dose reach to surrounding normal tissue. Present study is aimed to evaluate biologically effective dose in patients receiving high dose-rate brachytherapy plus external beam radiotherapy based on tumor cell proliferation values in cancer of the cervix patients. The study includes 30 patients' data as a retrospective analysis. In addition determine extent of a dose-response relationship existing between the biological effective dose at Point A and the bladder and rectum and the clinical outcomes

  11. An overview of surface radiance and biology studies in FIFE

    Science.gov (United States)

    Blad, B. L.; Schimel, D. S.

    1992-11-01

    The use of satellite data to study and to understand energy and mass exchanges between the land surface and the atmosphere requires information about various biological processes and how various reflected or emitted spectral radiances are influenced by or manifested in these processes. To obtain such information, studies were conducted by the First ISLSCP Field Experiment (FIFE) surface radiances and biology (SRB) group using surface, near-surface, helicopter, and aircraft measurements. The two primary objectives of this group were to relate radiative fluxes to biophysical parameters and physiological processes and to assess how various management treatments affect important biological processes. This overview paper summarizes the results obtained by various SRB teams working in nine different areas: (1) measurement of bidirectional reflectance and estimation of hemispherical albedo; (2) evaluation of spatial and seasonal variability of spectral reflectance and vegetation indices; (3) determination of surface and radiational factors and their effects on vegetation indices and PAR relationships; (4) use of surface temperatures to estimate sensible heat flux; (5) controls over photosynthesis and respiration at small scales; (6) soil surface CO2 fluxes and grassland carbon budget; (7) landscape variations in controls over gas exchange and energy partitioning; (8) radiometric response of prairie to management and topography; and (9) determination of nitrogen gas exchanges in a tallgrass prairie.

  12. Nanomaterials under extreme environments: A study of structural and dynamic properties using reactive molecular dynamics simulations

    Science.gov (United States)

    Shekhar, Adarsh

    nanoporous silica are different from that of bulk water, and insight into the properties of confined water is important for our understanding of many geological and biological processes. Nanoporous silica has a wide range of technological applications because it is easy to tune the size of pores and their morphologies and to functionalize pore surfaces with a variety of molecular moieties. Nanoporous silica is used in catalysis, chromatography, anticorrosion coatings, desalination membranes, and as drug delivery vehicles. We use reactive molecular dynamics to study the structure and dynamics of nanoconfined water between 100 and 300 K

  13. Biological methanation of hydrogen within biogas plants: A model-based feasibility study

    International Nuclear Information System (INIS)

    Bensmann, A.; Hanke-Rauschenbach, R.; Heyer, R.; Kohrs, F.; Benndorf, D.; Reichl, U.; Sundmacher, K.

    2014-01-01

    Highlights: • Simulation study about direct methanation of hydrogen within biogas plants. • In stationary operation two limitations, namely biological and transfer limit. • Biological limit at 4m H2 3 /m CO2 3 due to stoichiometry. • Dynamic behaviour shows three qualitatively different step responses. • A simple control scheme to meet the output quality was developed. - Abstract: One option to utilize excess electric energy is its conversion to hydrogen and the subsequent methanation. An alternative to the classical chemical Sabatier process is the biological methanation (methanogenesis) within biogas plants. In conventional biogas plants methane and carbon dioxide is produced. The latter can be directly converted to methane by feeding hydrogen into the reactor, since hydrogenotrophic bacteria are present. In the present contribution, a comprehensive simulation study with respect to stationary operating conditions and disturbances is presented. It reveals two qualitative different limitations, namely a biological limit (appr. at 4m H2 3 /m CO2 3 corresponds to 4.2m H2,STP 3 /m liq 3 /d) as well as a transfer limit. A parameter region for a safe operation was defined. The temporary operation with stationary unfeasible conditions was analysed and thereby three qualitatively different disturbances can be distinguished. In one of these the operation for several days is possible. On the basis of these results, a controller was proposed and tested that meets the demands on the conversion of hydrogen and also prevents the washout of the microbial community due to hydrogen overload

  14. DMPD: Lysophospholipid receptors: signaling and biology. [Dynamic Macrophage Pathway CSML Database

    Lifescience Database Archive (English)

    Full Text Available 15189145 Lysophospholipid receptors: signaling and biology. Ishii I, Fukushima N, Y...e X, Chun J. Annu Rev Biochem. 2004;73:321-54. (.png) (.svg) (.html) (.csml) Show Lysophospholipid receptors...: signaling and biology. PubmedID 15189145 Title Lysophospholipid receptors: signaling and biology. Authors

  15. Dynamic MRI study for breast tumors

    International Nuclear Information System (INIS)

    Seki, Tsuneaki

    1990-01-01

    Application of MRI for diagnosis of breast tumors was retrospectively examined in 103 consecutive cases. Contrast enhancement, mostly by dynamic study, was performed in 83 cases using Gd-DTPA and 0.5 T superconductive apparatus. Results were compared to those of mammography and sonography. On dynamic study, carcinoma showed abrupt rise of signal intensity with clear-cut peak formation in early phase, while benign fibroadenoma showed slow rise of signal intensity and prolonged enhancement without peak formation. In 12 of 33 carcinomas (33%), peripheral ring enhancement was noted reflecting vascular stroma of histologic sections. All fibroadenomas showed homogenous enhancement without peripheral ring. In MRI, sensitivity, specificity, and accuracy were 86%, 96%, 91%. In mammography 82%, 95%, 87% and in ultrasonography 91%, 95%, 93%. Although MRI should not be regarded as routine diagnostic procedure because of expense and limited availability, it may afford useful additional information when standard mammographic findings are not conclusive. (author)

  16. Granulometry use for the study of dynamics speckles patterns

    International Nuclear Information System (INIS)

    Mavilioa, Adriana; Fernandez, Margarita; Trivi, Marcelo; Rabal, Hector; Arizaga, Ricardo

    2009-01-01

    Dynamic speckle patterns are generated by laser light scattering on surfaces that exhibit some kind of activity, due to physical or biological processes that take place in the illuminated object. The characterization of this dynamic process is carried out by studying the texture changes of auxiliary images: temporal history of the speckle pattern (THSP) obtained from this speckles patterns. The drying process of water borne paint is studied through a method based on mathematical morphology applied to the THSP image processing. It is based on obtaining the granulometry of these images and their characteristic granulometric spectrum. From the granulometric size distribution of each THSP image four parameters are obtained: mean length, standard deviation, asymmetry and kurtosis. These parameters are found to be suitable as texture features. The Mahalanobis distance is calculated between the texture features of the THSP images representative of the temporary stages of the drying process and the features of the final stage or pattern texture. The behavior of the distance function describes satisfactorily the drying process of the water borne paint. Finally, these results are compared with the obtained by other methods. Compared with others, the granulometric method reported in this work distinguished by its simplicity and easy implementation and can be used to characterize the evolution of any process recorded through dynamic speckles. (Author)

  17. Experimental studies of nonlinear beam dynamics

    International Nuclear Information System (INIS)

    Caussyn, D.D.; Ball, M.; Brabson, B.; Collins, J.; Curtis, S.A.; Derenchuck, V.; DuPlantis, D.; East, G.; Ellison, M.; Ellison, T.; Friesel, D.; Hamilton, B.; Jones, W.P.; Lamble, W.; Lee, S.Y.; Li, D.; Minty, M.G.; Sloan, T.; Xu, G.; Chao, A.W.; Ng, K.Y.; Tepikian, S.

    1992-01-01

    The nonlinear beam dynamics of transverse betatron oscillations were studied experimentally at the Indiana University Cyclotron Facility cooler ring. Motion in one dimension was measured for betatron tunes near the third, fourth, fifth, and seventh integer resonances. This motion is described by coupling between the transverse modes of motion and nonlinear field errors. The Hamiltonian for nonlinear particle motion near the third- and fourth-integer-resonance conditions has been deduced

  18. Nonlinear longitudinal dynamics studies at the ALS

    International Nuclear Information System (INIS)

    Byrd, J.M.; Cheng, W.-H.; De Santis, S.; Li, D.; Stupakov, G.; Zimmermann, F.

    1999-01-01

    We present a summary of results for a variety of studies of nonlinear longitudinal dynamics in the Advanced Light Source, an electron storage ring. These include observation of decoherence at injection, decay of an injected beam, forced synchrotron oscillations and diffusion from one bunch to the next. All of the measurements were made using a dual-scan streak camera which allowed the real-time observation of the longitudinal distribution of the electron beam

  19. Biological studies of the U.S. subseabed disposal program

    International Nuclear Information System (INIS)

    Gomez, L.S.; Marietta, M.G.; Hessler, R.R.; Smith, K.L. Jr.; Talbert, D.M.; Yayanos, A.A.; Jackson, D.W.

    1980-01-01

    The Subseabed Disposal Program (SDP) of the U.S. is assessing the feasibility of emplacing high level radioactive wastes (HLW) within deep-sea sediments and is developing the means for assessing the feasibility of the disposal practices of other nations. This paper discusses the role and status of biological research in the SDP. Studies of the disposal methods and of the conceived barriers (canister, waste form and sediment) suggest that biological knowledge will be principally needed to address the impact of accidental releases of radionuclides. Current experimental work is focusing on the deep-sea ecosystem to determine: (1) the structure of benthic communities, including their microbial component; (2) the faunal composition of deep midwater nekton; (3) the biology of deep-sea amphipods; (4) benthic community metabolism; (5) the rates of bacterial processes; (6) the metabolism of deep-sea animals, and (7) the radiation sensitivity of deep-sea organisms. A multi-compartment model is being developed to assess quantitatively, the impact (on the environment and on man) of releases of radionuclides into the sea

  20. Theoretical studies of chemical reaction dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Schatz, G.C. [Argonne National Laboratory, IL (United States)

    1993-12-01

    This collaborative program with the Theoretical Chemistry Group at Argonne involves theoretical studies of gas phase chemical reactions and related energy transfer and photodissociation processes. Many of the reactions studied are of direct relevance to combustion; others are selected they provide important examples of special dynamical processes, or are of relevance to experimental measurements. Both classical trajectory and quantum reactive scattering methods are used for these studies, and the types of information determined range from thermal rate constants to state to state differential cross sections.

  1. Life at extreme conditions: Neutron scattering studies of biological

    Indian Academy of Sciences (India)

    Extremophile bacteria; molecular adaptation; halophile; water dynamics; protein dynamics. ... Results of neutron scattering measurements on the dynamics of proteins ... The experiments were performed on a halophilic protein, and membrane ...

  2. Coalescent models for developmental biology and the spatio-temporal dynamics of growing tissues.

    Science.gov (United States)

    Smadbeck, Patrick; Stumpf, Michael P H

    2016-04-01

    Development is a process that needs to be tightly coordinated in both space and time. Cell tracking and lineage tracing have become important experimental techniques in developmental biology and allow us to map the fate of cells and their progeny. A generic feature of developing and homeostatic tissues that these analyses have revealed is that relatively few cells give rise to the bulk of the cells in a tissue; the lineages of most cells come to an end quickly. Computational and theoretical biologists/physicists have, in response, developed a range of modelling approaches, most notably agent-based modelling. These models seem to capture features observed in experiments, but can also become computationally expensive. Here, we develop complementary genealogical models of tissue development that trace the ancestry of cells in a tissue back to their most recent common ancestors. We show that with both bounded and unbounded growth simple, but universal scaling relationships allow us to connect coalescent theory with the fractal growth models extensively used in developmental biology. Using our genealogical perspective, it is possible to study bulk statistical properties of the processes that give rise to tissues of cells, without the need for large-scale simulations. © 2016 The Authors.

  3. Solar dynamic power system definition study

    Science.gov (United States)

    Wallin, Wayne E.; Friefeld, Jerry M.

    1988-01-01

    The solar dynamic power system design and analysis study compared Brayton, alkali-metal Rankine, and free-piston Stirling cycles with silicon planar and GaAs concentrator photovoltaic power systems for application to missions beyond the Phase 2 Space Station level of technology for all power systems. Conceptual designs for Brayton and Stirling power systems were developed for 35 kWe and 7 kWe power levels. All power systems were designed for 7-year end-of-life conditions in low Earth orbit. LiF was selected for thermal energy storage for the solar dynamic systems. Results indicate that the Stirling cycle systems have the highest performance (lowest weight and area) followed by the Brayton cycle, with photovoltaic systems considerably lower in performance. For example, based on the performance assumptions used, the planar silicon power system weight was 55 to 75 percent higher than for the Stirling system. A technology program was developed to address areas wherein significant performance improvements could be realized relative to the current state-of-the-art as represented by Space Station. In addition, a preliminary evaluation of hardenability potential found that solar dynamic systems can be hardened beyond the hardness inherent in the conceptual designs of this study.

  4. Functionalised isocoumarins as antifungal compounds: Synthesis and biological studies.

    Science.gov (United States)

    Simic, Milena; Paunovic, Nikola; Boric, Ivan; Randjelovic, Jelena; Vojnovic, Sandra; Nikodinovic-Runic, Jasmina; Pekmezovic, Marina; Savic, Vladimir

    2016-01-01

    A series of novel 3-substituted isocoumarins was prepared via Pd-catalysed coupling processes and screened in vitro for antifungal activity against Candida species. The study revealed antifungal potential of isocoumarins possessing the azole substituents, which, in some cases, showed biological properties equal to those of clinically used voriconazole. Selected compounds were also screened against voriconazole resistant Candida krusei 6258 and a clinical isolate Candida parapsilosis CA-27. Although the activity against these targets needs to be improved further, the results emphasise additional potential of this new class of antifungal compounds. Copyright © 2015 Elsevier Ltd. All rights reserved.

  5. Studies of the reproductive biology of deep-sea megabenthos

    International Nuclear Information System (INIS)

    Tyler, P.A.

    1987-07-01

    The final report describes the general biology and ecology of the 15 holothurians, 3 asteroids, 2 zoanthids and 1 crustacea species studied in Reports I-XIII, the sampling methods used and the station data. A summary of the histological, histochemical and biochemical results for the species examined is given. The data suggest that the reproductive processes in the deep-sea species examined are highly unlikely to be part of a pathway for the transfer of radionuclides from the deep-sea back to man. (author)

  6. A Friendly-Biological Reactor SIMulator (BioReSIM for studying biological processes in wastewater treatment processes

    Directory of Open Access Journals (Sweden)

    Raul Molina

    2014-12-01

    Full Text Available Biological processes for wastewater treatments are inherently dynamic systems because of the large variations in the influent wastewater flow rate, concentration composition and the adaptive behavior of the involved microorganisms. Moreover, the sludge retention time (SRT is a critical factor to understand the bioreactor performances when changes in the influent or in the operation conditions take place. Since SRT are usually in the range of 10-30 days, the performance of biological reactors needs a long time to be monitored in a regular laboratory demonstration, limiting the knowledge that can be obtained in the experimental lab practice. In order to overcome this lack, mathematical models and computer simulations are useful tools to describe biochemical processes and predict the overall performance of bioreactors under different working operation conditions and variations of the inlet wastewater composition. The mathematical solution of the model could be difficult as numerous biochemical processes can be considered. Additionally, biological reactors description (mass balance, etc. needs models represented by partial or/and ordinary differential equations associated to algebraic expressions, that require complex computational codes to obtain the numerical solutions. Different kind of software for mathematical modeling can be used, from large degree of freedom simulators capable of free models definition (as AQUASIM, to closed predefined model structure programs (as BIOWIN. The first ones usually require long learning curves, whereas the second ones could be excessively rigid for specific wastewater treatment systems. As alternative, we present Biological Reactor SIMulator (BioReSIM, a MATLAB code for the simulation of sequencing batch reactors (SBR and rotating biological contactors (RBC as biological systems of suspended and attached biomass for wastewater treatment, respectively. This BioReSIM allows the evaluation of simple and complex

  7. Dynamic isotope studies in liver disease

    Energy Technology Data Exchange (ETDEWEB)

    Weits, J

    1978-01-01

    Much information in the field of liver research has been gained by dynamic isotope studies. Clinically, these studies can help to settle selection criteria for different types of surgical shunt, which relieve the complications of portal hypertension. By performing splenoportoscintigraphy, splenic and portal vein thrombosis can be easily and safely excluded. So-called hypoxaemia of cirrhosis can most easily be diagnosed. Suprahepatic caval vein obstruction in a patient with cryptogenic liver disease is easily excluded by a radionuclide cavogram after injection of pertechnetate into a foot vein.

  8. Biological Detection System Technologies Technology and Industrial Base Study. A Primer on Biological Detection Technologies

    National Research Council Canada - National Science Library

    2001-01-01

    .... and Canadian military personnel. In light of these concerns both defense departments have increased efforts to develop and field biological agent detection systems to help protect their military forces and fixed assets...

  9. Molecular biology in studies of oceanic primary production

    International Nuclear Information System (INIS)

    LaRoche, J.; Falkowski, P.G.; Geider, R.

    1992-01-01

    Remote sensing and the use of moored in situ instrumentation has greatly improved our ability to measure phytoplankton chlorophyll and photosynthesis on global scales with high temporal resolution. However, the interpretation of these measurements and their significance with respect to the biogeochemical cycling of carbon relies on their relationship with physiological and biochemical processes in phytoplankton. For example, the use of satellite images of surface chlorophyll to estimate primary production is often based on the functional relationship between photosynthesis and irradiance. A variety of environmental factors such as light, temperature, nutrient availability affect the photosynthesis/irradiance (P vs I) relationship in phytoplankton. We present three examples showing how molecular biology can be used to provide basic insight into the factors controlling primary productivity at three different levels of complexity: 1. Studies of light intensity regulation in unicellular alga show how molecular biology can help understand the processing of environmental cues leading to the regulation of photosynthetic gene expression. 2. Probing of the photosynthetic apparatus using molecular techniques can be used to test existing mechanistic models derived from the interpretation of physiological and biophysical measurements. 3. Exploratory work on the expression of specific proteins during nutrient-limited growth of phytoplankton may lead to the identification and production of molecular probes for field studies

  10. Biological Studies with Laser-Polarized ^129Xe

    Science.gov (United States)

    Tseng, C. H.; Oteiza, E. R.; Wong, G. A.; Walsworth, R. L.; Albert, M. S.; Nascimben, L.; Peled, S.; Sakai, K.; Jolesz, F. A.

    1996-05-01

    We have studied several biological systems using laser-polarized ^129Xe. In certain tissues magnetic resonance imaging (MRI) using inhaled laser-polarized noble gases may provide images superior to those from conventional proton MRI. High resolution laser-polarized ^3He images of air spaces in the human lung were recently obtained by the Princeton/Duke group. However, ^3He is not very soluble in tissue. Therefore, we are using laser polarized ^129Xe (tissue-soluble), with the long term goal of biomedical functional imaging. We have investigated multi-echo and multi-excitation magnetic resonance detection schemes to exploit the highly non-thermal ^129Xe magnetization produced by the laser polarization technique. We have inhalated live rats with laser-polarized ^129Xe gas and measured three distinct ^129Xe tissue resonances that last 20 to 40 sec. As a demonstration, we obtained a laser polarized ^129Xe image of the human oral cavity. Currently we are measuring the polarization lifetime of ^129Xe dissolved in human blood, the biological transporting medium. These studies and other recent developments will be reported.

  11. Metabolism of labeled parathyroid hormone. V. Collected biological studies

    Energy Technology Data Exchange (ETDEWEB)

    Neuman, W F; Neuman, M W; Lane, K; Miller, L; Sammon, P J

    1975-01-01

    Biologically active /sup 125/I-labeled parathyroid hormone (/sup 125/I-PTH) was used in a series of studies in dogs and chickens designed to confirm and augment earlier studies in rats. As in rats, a three exponential equation was required to describe disappearance of /sup 125/I-PTH from the blood in the dog. The first two ''half-lives'' (1.8 and 7 min) accounted for the bulk of the dose. Also as in rats, deposition of apparently intact hormone took place rapidly in kidney, liver and bone in both the dog and the chicken. Degradation occurred very rapidly in all three target organs. Three labeled hormones of different biological activities were compared in the rat. Inactive, oxidized hormone was rejected by the liver but showed markedly increased deposition in kidney and the higher the purity of the hormone the higher was its uptake by liver. Exploration of a wide range of dosages revealed few effects on distribution (smaller depositon in liver and kidney at highest dosages, 65 ..mu..g/rat). Fresh sera did not degrade hormone rapidly or extensively. There was no deposition of hormone in intestinal mucosa, marrow, and red cells. Nephrectomy increased deposition in liver and bone. Finally, the perfused liver was capable of extensive degradation of the hormone.

  12. Diffusion-advection within dynamic biological gaps driven by structural motion

    Science.gov (United States)

    Asaro, Robert J.; Zhu, Qiang; Lin, Kuanpo

    2018-04-01

    To study the significance of advection in the transport of solutes, or particles, within thin biological gaps (channels), we examine theoretically the process driven by stochastic fluid flow caused by random thermal structural motion, and we compare it with transport via diffusion. The model geometry chosen resembles the synaptic cleft; this choice is motivated by the cleft's readily modeled structure, which allows for well-defined mechanical and physical features that control the advection process. Our analysis defines a Péclet-like number, AD, that quantifies the ratio of time scales of advection versus diffusion. Another parameter, AM, is also defined by the analysis that quantifies the full potential extent of advection in the absence of diffusion. These parameters provide a clear and compact description of the interplay among the well-defined structural, geometric, and physical properties vis-a ̀-vis the advection versus diffusion process. For example, it is found that AD˜1 /R2 , where R is the cleft diameter and hence diffusion distance. This curious, and perhaps unexpected, result follows from the dependence of structural motion that drives fluid flow on R . AM, on the other hand, is directly related (essentially proportional to) the energetic input into structural motion, and thereby to fluid flow, as well as to the mechanical stiffness of the cleftlike structure. Our model analysis thus provides unambiguous insight into the prospect of competition of advection versus diffusion within biological gaplike structures. The importance of the random, versus a regular, nature of structural motion and of the resulting transient nature of advection under random motion is made clear in our analysis. Further, by quantifying the effects of geometric and physical properties on the competition between advection and diffusion, our results clearly demonstrate the important role that metabolic energy (ATP) plays in this competitive process.

  13. Molecular dynamics studies of actinide nitrides

    International Nuclear Information System (INIS)

    Kurosaki, Ken; Uno, Masayoshi; Yamanaka, Shinsuke; Minato, Kazuo

    2004-01-01

    The molecular dynamics (MD) calculation was performed for actinide nitrides (UN, NpN, and PuN) in the temperature range from 300 to 2800 K to evaluate the physical properties viz., the lattice parameter, thermal expansion coefficient, compressibility, and heat capacity. The Morse-type potential function added to the Busing-Ida type potential was employed for the ionic interactions. The interatomic potential parameters were determined by fitting to the experimental data of the lattice parameter. The usefulness and applicability of the MD method to evaluate the physical properties of actinide nitrides were studied. (author)

  14. The emerging molecular biology toolbox for the study of long noncoding RNA biology.

    Science.gov (United States)

    Fok, Ezio T; Scholefield, Janine; Fanucchi, Stephanie; Mhlanga, Musa M

    2017-10-01

    Long noncoding RNAs (lncRNAs) have been implicated in many biological processes. However, due to the unique nature of lncRNAs and the consequential difficulties associated with their characterization, there is a growing disparity between the rate at which lncRNAs are being discovered and the assignment of biological function to these transcripts. Here we present a molecular biology toolbox equipped to help dissect aspects of lncRNA biology and reveal functionality. We outline an approach that begins with a broad survey of genome-wide, high-throughput datasets to identify potential lncRNA candidates and then narrow the focus on specific methods that are well suited to interrogate the transcripts of interest more closely. This involves the use of imaging-based strategies to validate these candidates and observe the behaviors of these transcripts at single molecule resolution in individual cells. We also describe the use of gene editing tools and interactome capture techniques to interrogate functionality and infer mechanism, respectively. With the emergence of lncRNAs as important molecules in healthy and diseased cellular function, it remains crucial to deepen our understanding of their biology.

  15. Phytochemicals and biological studies of plants from the genus Balanophora

    Directory of Open Access Journals (Sweden)

    Wang Xiaohong

    2012-08-01

    Full Text Available Abstract This review focus on the phytochemical progress and biological studies of plants from the genus Balanophora (Balanophoraceae over the past few decades, in which most plants growth in tropical and subtropical regions of Asia and Oceania, and nearly 20 species ranged in southwest China. These dioeciously parasitic plants are normally growing on the roots of the evergreen broadleaf trees, especially in the family of Leguminosae, Ericaceae, Urticaceae, and Fagaceae. The plants are mainly used for clearing away heat and toxic, neutralizing the effect of alcoholic drinks, and as a tonic for the treatment of hemorrhoids, stomachache and hemoptysis. And it has been used widely throughtout local area by Chinese people. Cinnamic acid derivative tannins, possessing a phenylacrylic acid derivative (e. g. caffeoyl, coumaroyl, feruloyl or cinnamoyl, which connected to the C(1 position of a glucosyl unit by O-glycosidic bond, are the characteristic components in genus Balanophora. In addition, several galloyl, caffeoyl and hexahydroxydiphenoyl esters of dihydrochalcone glucosides are found in B. tobiracola, B. harlandii, and B. papuana. Other compounds like phenylpropanoids, flavonoids, terpenoids and sterols are also existed. And their biological activities, such as radical scavenging activities, HIV inhibiting effects, and hypoglycemic effects are highlighted in the review.

  16. Dynamic speckle interferometry of microscopic processes in solid state and thin biological objects

    Science.gov (United States)

    Vladimirov, A. P.

    2015-08-01

    Modernized theory of dynamic speckle interferometry is considered. It is shown that the time-average radiation intensity has the parameters characterizing the wave phase changes. It also brings forward an expression for time autocorrelation function of the radiation intensity. It is shown that with the vanishing averaging time value the formulas transform to the prior expressions. The results of experiments with high-cycle material fatigue and cell metabolism analysis conducted using the time-averaging technique are discussed. Good reproducibility of the results is demonstrated. It is specified that the upgraded technique allows analyzing accumulation of fatigue damage, detecting the crack start moment and determining its growth velocity with uninterrupted cyclic load. It is also demonstrated that in the experiments with a cell monolayer the technique allows studying metabolism change both in an individual cell and in a group of cells.

  17. Combined application of dynamic light scattering imaging and fluorescence intravital microscopy in vascular biology

    International Nuclear Information System (INIS)

    Kalchenko, V; Harmelin, A; Ziv, K; Addadi, Y; Madar-Balakirski, N; Neeman, M; Meglinski, I

    2010-01-01

    The dynamic light scattering imaging (DLSI) system combined with the conventional fluorescence intravital microscope (FIM) has been applied for the examination of blood and lymph vessels in the mouse ear in vivo. While the CCD camera can be shared by both techniques the combined application of DLSI and FIM allows rapid switching between the modalities. In current study temporal speckles fluctuations are used for rendering blood vessels structure and monitoring blood perfusion with the higher spatial resolution, whereas FIM provides the images of lymphatic vessels. The results clearly demonstrate that combined application of DLSI and FIM approaches provides synchronic in vivo images of blood and lymph vessels with higher contrast and specificity. The use of this new dual-modal diagnostic system is particularly important and has a great potential to significantly expand the capabilities of vascular diagnostics providing synchronic in vivo images of blood and lymph vessels

  18. In vitro and in vivo approaches to study osteocyte biology.

    Science.gov (United States)

    Kalajzic, Ivo; Matthews, Brya G; Torreggiani, Elena; Harris, Marie A; Divieti Pajevic, Paola; Harris, Stephen E

    2013-06-01

    Osteocytes, the most abundant cell population of the bone lineage, have been a major focus in the bone research field in recent years. This population of cells that resides within mineralized matrix is now thought to be the mechanosensory cell in bone and plays major roles in the regulation of bone formation and resorption. Studies of osteocytes had been impaired by their location, resulting in numerous attempts to isolate primary osteocytes and to generate cell lines representative of the osteocytic phenotype. Progress has been achieved in recent years by utilizing in vivo genetic technology and generation of osteocyte directed transgenic and gene deficiency mouse models. We will provide an overview of the current in vitro and in vivo models utilized to study osteocyte biology. We discuss generation of osteocyte-like cell lines and isolation of primary osteocytes and summarize studies that have utilized these cellular models to understand the functional role of osteocytes. Approaches that attempt to selectively identify and isolate osteocytes using fluorescent protein reporters driven by regulatory elements of genes that are highly expressed in osteocytes will be discussed. In addition, recent in vivo studies utilizing overexpression or conditional deletion of various genes using dentin matrix protein (Dmp1) directed Cre recombinase are outlined. In conclusion, evaluation of the benefits and deficiencies of currently used cell lines/genetic models in understanding osteocyte biology underlines the current progress in this field. The future efforts will be directed towards developing novel in vitro and in vivo models that would additionally facilitate in understanding the multiple roles of osteocytes. Copyright © 2012 Elsevier Inc. All rights reserved.

  19. Utilization and viability of biologically-inspired algorithms in a dynamic multiagent camera surveillance system

    Science.gov (United States)

    Mundhenk, Terrell N.; Dhavale, Nitin; Marmol, Salvador; Calleja, Elizabeth; Navalpakkam, Vidhya; Bellman, Kirstie; Landauer, Chris; Arbib, Michael A.; Itti, Laurent

    2003-10-01

    In view of the growing complexity of computational tasks and their design, we propose that certain interactive systems may be better designed by utilizing computational strategies based on the study of the human brain. Compared with current engineering paradigms, brain theory offers the promise of improved self-organization and adaptation to the current environment, freeing the programmer from having to address those issues in a procedural manner when designing and implementing large-scale complex systems. To advance this hypothesis, we discus a multi-agent surveillance system where 12 agent CPUs each with its own camera, compete and cooperate to monitor a large room. To cope with the overload of image data streaming from 12 cameras, we take inspiration from the primate"s visual system, which allows the animal to operate a real-time selection of the few most conspicuous locations in visual input. This is accomplished by having each camera agent utilize the bottom-up, saliency-based visual attention algorithm of Itti and Koch (Vision Research 2000;40(10-12):1489-1506) to scan the scene for objects of interest. Real time operation is achieved using a distributed version that runs on a 16-CPU Beowulf cluster composed of the agent computers. The algorithm guides cameras to track and monitor salient objects based on maps of color, orientation, intensity, and motion. To spread camera view points or create cooperation in monitoring highly salient targets, camera agents bias each other by increasing or decreasing the weight of different feature vectors in other cameras, using mechanisms similar to excitation and suppression that have been documented in electrophysiology, psychophysics and imaging studies of low-level visual processing. In addition, if cameras need to compete for computing resources, allocation of computational time is weighed based upon the history of each camera. A camera agent that has a history of seeing more salient targets is more likely to obtain

  20. Study Finds Association between Biological Marker and Susceptibility to the Common Cold

    Science.gov (United States)

    ... W X Y Z Study Finds Association Between Biological Marker and Susceptibility to the Common Cold Share: © ... a cold caused by a particular rhinovirus. The biological marker identified in the study was the length ...

  1. Systems biology studies of Aspergilli - from sequence to science

    DEFF Research Database (Denmark)

    Andersen, Mikael Rørdam

    2008-01-01

    sequenced Aspergilli are a known human pathogen (Aspergillus fumigatus), a model organism for cellular mechanisms (Aspergillus nidulans) and two industrial workhorses (Aspergillus niger and Aspergillus oryzae). In the presented work, new analytical and computational tools have been designed and a systems......-evolved and not as a haphazardly compiled list of parts. This has been made possible by the socalled genomic revolution — the sequencing of the genomic DNA of a rapidly increasing number of organisms — and the “omic” tecniques following in the wake of the genome projects: metabolomic, proteomic, and transcriptomic to mention...... a few. The recent publication of the genome sequences of several filamentous fungi of the Aspergillus species (Aspergilli), has, along with the accumulation of years of reductionist studies, been a catalyst for the application of systems biology to this interesting group of fungi. Among the genome...

  2. Visual Literacy in Preservice Teachers: a Case Study in Biology

    Science.gov (United States)

    Ruiz-Gallardo, José Reyes; García Fernández, Beatriz; Mateos Jiménez, Antonio

    2017-07-01

    In this study, we explore the competence of preservice teachers (n = 161) in labelling and creating new cross-sectional human diagrams, based on anatomy knowledge depicted in longitudinal sections. Using educational standards to assess visual literacy and ad hoc open questions, results indicate limited skills for both tasks. However, their competence is particularly poor creating diagrams, where shortcomings were observed not only in visual literacy but in content knowledge. We discuss the misconceptions detected during these assessments. Visual literacy training should be strengthened for these students, as it is a skill that is especially important for future teachers to use in learning, assessing, and reflecting on content in science education. This is particularly important in preservice teachers since they should be fluent in the use of visual teaching tools in teaching anatomy and other content in the biology curriculum.

  3. Biochemical studies on certain biologically active nitrogenous compounds

    International Nuclear Information System (INIS)

    Abdel kader, S.M.; El Sayed, M.M.; El Malt, E.A.; Shaker, E.S.; Abdel Aziz, H.G.

    2010-01-01

    Certain biologically active nitrogenous compounds such as alkaloids are widely distributed in many wild and medicinal plants such as peganum harmala L. (Phycophyllaceae). However, less literature cited on the natural compounds was extracted from the aerial parts of this plant; therefore this study was conducted on harmal leaves using several solvents. Data indicated that methanol extract was the inhibitoriest effect against some pathogenic bacteria, particularly Streptococcus pyogenus. Chromatographic separation illustrated that presence of four compounds; the most active one was the third compound (3). Elementary analysis (C, H, N) revealed that the primary chemical structure of the active antibacterial compound (C3) was: C17 H21 N3 O7 S with molecular weight 411. Spectroscopic analysis proved that coninical structure was = 1- thioformyl, 8?- D glucoperanoside- Bis- 2, 3 dihydroisopyridino pyrrol. This new compound is represented as a noval ?- carboline alkaloid compound

  4. Study of biological fluids by nuclear magnetic resonance spectroscopy

    International Nuclear Information System (INIS)

    Kriat, M.; Vion-Dury, J.; Confort-Gouny, S.; Sciaky, M.; Cozzone, P.J.

    1991-01-01

    The use of nuclear magnetic resonance (NMR) spectroscopy in the study of biofluids is rapidly developing and might soon constitute a new major medical application of this technique which benefits from technological and methodological progress such as higher magnetic fields, new probe design, solvent suppression sequences and advanced data processing routines. In this overview, the clinical and pharmacological impact of this new approach is examined, with emphasis on the NMR spectroscopy of plasma, cerebrospinal fluid and urine. Applications to pharmacokinetics and toxicology are illustrated. Interestingly, a number of biochemical components of fluids which are not usually assayed by conventional biochemical methods are readily detected by NMR spectroscopy which is clearly a new competitive entrant among the techniques used in clinical biology. Its ease-of-use, cost effectiveness and high informational content might turn it into a major diagnostic tool in the years to come [fr

  5. A dynamic approach to dependability studies

    International Nuclear Information System (INIS)

    Labeau, P.E.

    2008-01-01

    Dependability studies have now become an important part of the performance management of industrial plants. These last decades, several methods have been proposed and widely used for the analysis of systems of components subject to degradation and failure. These methods are based either on Boolean representations (for example, event trees/fault trees), or on discrete-state models (Markovian reliability, Petri nets, Bayesian networks...). However, the underlying, inherently continuous, physical processes have scarcely been accounted for, at least in an integrated fashion, in dependability studies. This paper first describes, through simple cases, the limitations of discrete approaches and the need of hybrid, discrete-continuous methods. It then summarizes the main concepts of dynamic reliability. Finally, some possible application domains are presented, as well as challenges that still need to be tackled to favour the diffusion of this approach among industrial circles. (author)

  6. Studies on influence of biological factors on concentration of radionuclides

    International Nuclear Information System (INIS)

    Anon.

    1974-01-01

    Biological factors influencing the concentration of radionuclides were studied from the points of uptake through digestive tract, food as pathways, and metabolic activities. The uptake of radionuclides by marine fishes through digestive tract was determined by whole body counter. 137 Cs, 65 Zn, 131 I, 54 Mn, 60 Co, 85 Sr, and 144 Ce were used as tracers and was given with solid feed. The feed given was excreated 24 to 48 hours later in small of middle sized fishes, and 20 to 48 hours later in large sized fishes. The uptake rate of 137 Cs and 65 Zn was high absorption of 20 to 80 per cent, that of 131 I, 60 Co and 54 Mn was not remarkable, and that of 85 Sr and 144 Ce was low absorption. The biological concentration of 137 Cs through pathways of food. In fishes taking up radionuclides through contaminated food, concentration factor increased in accordance with contamination level. In addition, radionuclides with small uptake but delayed excretion and those with high concentration rate could be the factors to decide the concentration factors of marine organisms. In order to study the relationship between metabolic activities and concentration, the uptake of one-year old fishes and adult fishes, and fishes fed and those non-fed were compared. One-year fishes took up large amount of 85 Sr during short period, however, concentration by metabolism in adult fishes was slow. Comparing feeding group and non-feeding group, the former showed 85 Sr concentration factor of 1.5 to 2 times that of the later, and the later showed 137 Cs concentration factor of 2 to 4 times that of the former. However, both uptake and excretion were rapid suggesting that taking food activated the metabolism of substances. (Kanao, N.)

  7. Contribution to the study of dynamic recrystallization

    International Nuclear Information System (INIS)

    Guillope, Michel

    1981-01-01

    An experimental and theoretical work on dynamic recrystallization is presented. The experimental study, sustained by creep deformation of NaCl single crystals, has shown that the structural evolution can occur in two distinct ways: rotation recrystallization, which consists in a progressive sub-boundary misorientation increase; migration recrystallization, which consists in the 'catastrophic' growth of some grains. Although rotation recrystallization is to be observed for all experimental used conditions, migration recrystallization occurs only in a well defined domain of the temperature-applied stress-impurity concentration space. The proposed interpretation emphasizes the generality of the observed behaviours: the sharp boundary of the migration recrystallization domain expresses the existence of a 'catastrophic' transition from a low velocity regime (boundaries migrate charged with segregate impurities) to a high velocity regime (boundaries migrate free from impurities). Owing to the importance of grain boundary migration in dynamic recrystallization, a detailed analysis of possible migration mechanisms is presented: we show how migration induced by applied stress or recrystallization force can be explained. Finally, an original kinetic model of grain growth is developed which throws a new insight in the abnormal grain growth process and, by analogy, in the migration recrystallization phenomenon. (author) [fr

  8. Molecular beam studies of reaction dynamics

    International Nuclear Information System (INIS)

    Lee, Yuan T.

    1991-03-01

    The major thrust of this research project is to elucidate detailed dynamics of simple elementary reactions that are theoretically important and to unravel the mechanism of complex chemical reactions or photochemical processes that play important roles in many macroscopic processes. Molecular beams of reactants are used to study individual reactive encounters between molecules or to monitor photodissociation events in a collision-free environment. Most of the information is derived from measurement of the product fragment energy, angular, and state distributions. Recent activities are centered on the mechanisms of elementary chemical reactions involving oxygen atoms with unsaturated hydrocarbons, the dynamics of endothermic substitution reactions, the dependence of the chemical reactivity of electronically excited atoms on the alignment of excited orbitals, the primary photochemical processes of polyatomic molecules, intramolecular energy transfer of chemically activated and locally excited molecules, the energetics of free radicals that are important to combustion processes, the infrared-absorption spectra of carbonium ions and hydrated hydronium ions, and bond-selective photodissociation through electric excitation

  9. Ultrasonic Study of Dislocation Dynamics in Lithium -

    Science.gov (United States)

    Han, Myeong-Deok

    1987-09-01

    Experimental studies of dislocation dynamics in LiF single crystals, using ultrasonic techniques combined with dynamic loading, were performed to investigate the time evolution of the plastic deformation process under a short stress pulse at room temperature, and the temperature dependence of the dislocation damping mechanism in the temperature range 25 - 300(DEGREES)K. From the former, the time dependence of the ultrasonic attenuation was understood as resulting from dislocation multiplication followed by the evolution of mobile dislocations to immobile ones under large stress. From the latter, the temperature dependence of the ultrasonic attenuation was interpreted as due to the motion of the dislocation loops overcoming the periodic Peierls potential barrier in a manner analogous to the motion of a thermalized sine-Gordon chain under a small stress. The Peierls stress obtained from the experimental results by application of Seeger's relaxation model with exponential dislocation length distribution was 4.26MPa, which is consistent with the lowest stress for the linear relation between the dislocation velocity and stress observed by Flinn and Tinder.

  10. Experimental study of vapor bubble dynamics

    International Nuclear Information System (INIS)

    Pasquini, Maria-Elena

    2015-01-01

    The object of this thesis is an experimental study of vapor bubble dynamics in sub-cooled nucleate boiling. The test section is locally heated by focusing a laser beam: heat fluxes from 1 e4 to 1.5 e6 W/m 2 and water temperature between 100 and 88 C have been considered. Three boiling regimes have been observed. Under saturated conditions and with low heat fluxes a developed nucleate boiling regime has been observed. Under higher sub-cooling and still with low heat fluxes an equilibrium regime has been observed in which the liquid flowrate evaporating at the bubble base is compensated by the vapor condensing flowrate at bubble top. A third regime have been observed at high heat fluxes for all water conditions: it is characterized by the formation of a large dry spot on the heated surface that keeps the nucleation site dry after bubble detachment. The condensation phase starts after bubble detachment. Bubble equivalent radius at detachment varies between 1 and 2.5 mm. Bubble properties have been measured and non-dimensional groups have been used to characterize bubble dynamics. Capillary waves have been observed on the bubble surface thanks to high-speed images acquisition. Two main phenomena have been proposed to explain capillary waves effects on bubble condensation: increasing of the phases interface area and decreasing of vapor bubble translation velocity, because of the increased drag force on the deformed bubble. (author) [fr

  11. Molecular beam studies of reaction dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Y.T. [Lawrence Berkeley Laboratory, CA (United States)

    1993-12-01

    The major thrust of this research project is to elucidate detailed dynamics of simple elementary reactions that are theoretically important and to unravel the mechanism of complex chemical reactions or photochemical processes that play important roles in many macroscopic processes. Molecular beams of reactants are used to study individual reactive encounters between molecules or to monitor photodissociation events in a collision-free environment. Most of the information is derived from measurement of the product fragment energy, angular, and state distributions. Recent activities are centered on the mechanisms of elementary chemical reactions involving oxygen atoms with unsaturated hydrocarbons, the dynamics of endothermic substitution reactions, the dependence of the chemical reactivity of electronically excited atoms on the alignment of excited orbitals, the primary photochemical processes of polyatomic molecules, intramolecular energy transfer of chemically activated and locally excited molecules, the energetics of free radicals that are important to combustion processes, the infrared-absorption spectra of carbonium ions and hydrated hydronium ions, and bond-selective photodissociation through electric excitation.

  12. Quantifying biologically and physically induced flow and tracer dynamics in permeable sediments

    Directory of Open Access Journals (Sweden)

    F. J. R. Meysman

    2007-08-01

    Full Text Available Insight in the biogeochemistry and ecology of sandy sediments crucially depends on a quantitative description of pore water flow and the associated transport of various solutes and particles. We show that widely different problems can be modelled by the same flow and tracer equations. The principal difference between model applications concerns the geometry of the sediment-water interface and the pressure conditions that are specified along this boundary. We illustrate this commonality with four different case studies. These include biologically and physically induced pore water flows, as well as simplified laboratory set-ups versus more complex field-like conditions: [1] lugworm bio-irrigation in laboratory set-up, [2] interaction of bio-irrigation and groundwater seepage on a tidal flat, [3] pore water flow induced by rotational stirring in benthic chambers, and [4] pore water flow induced by unidirectional flow over a ripple sequence. The same two example simulations are performed in all four cases: (a the time-dependent spreading of an inert tracer in the pore water, and (b the computation of the steady-state distribution of oxygen in the sediment. Overall, our model comparison indicates that model development for sandy sediments is promising, but within an early stage. Clear challenges remain in terms of model development, model validation, and model implementation.

  13. Biological Activity and Phytochemical Study of Scutellaria platystegia.

    Science.gov (United States)

    Madani Mousavi, Seyedeh Neda; Delazar, Abbas; Nazemiyeh, Hossein; Khodaie, Laleh

    2015-01-01

    This study aimed to determine biological activity and phytochemical study of Scutellaria platystegia (family Labiatae). Methanolic (MeOH) extract of aerial parts of S. platystegia and SPE fractions of methanolic extract (specially 20% and 40% methanolic fractions), growing in East-Azarbaijan province of Iran were found to have radical scavenging activity by DPPH (2, 2-diphenyl -1- pycryl hydrazyl) assay. Dichloromethane (DCM) extract of this plant exhibited animalarial activity by cell free method providing IC50 at 1.1876 mg/mL. Crude extracts did not exhibit any toxicity assessed by brine shrimp lethality assay. Phytochemical study of methanolic extract by using reverse phase HPLC method and NMR instrument for isolation and identification of pure compounds respectively, yielded 2-(4- hydroxy phenyl) ethyl-O-β-D- glucopyranoside from 10% and apigenin 7-O-glucoside, verbascoside and martynoside from 40% SPE fraction. Occurance of verbascoside and martynoside as biochemical markers appeared to be widespread in this genus. Antioxidant and antimalarial activity of MeOH and DCM extracts, respectively, as well as no general toxicity of them could provide a basis for further in-vitro and in-vivo studies and clinical trials to develop new therapeutical alternatives.

  14. Estudo comparativo das características fluidodinâmicas de próteses valvulares biológicas de pericárdio bovino de perfil alto e baixo Comparative study of fluid dynamic characteristics in high and low biological prosthetic heart valves from bovine pericardium

    Directory of Open Access Journals (Sweden)

    Aron J. P Andrade

    1989-12-01

    Full Text Available O comportamento fluidodinâmico e a vida útil média de uma prótese valvular cardíaca são características muito importantes na escolha do modelo de prótese a ser implantada em um determinado paciente. Por esse motivo, foi realizado um estudo comparativo entre as válvulas biológicas de perfil alto e baixo, para se verificarem possíveis alterações na vida média, gradiente de pressão e refluxo, causadas pela diminuição do perfil dessas próteses. Com o auxílio de um duplicador de pulso, foram analisadas cinco próteses de perfil alto e cinco de perfil baixo, todas tamanho 29, fabricadas no Instituto Dante Pazzanese de Cardiologia (IDPC. Mantendo-se a freqüência de batimentos em 100 bpm e a diferença de pressão em 1000 mmHg, verificou-se que a vida útil média da válvula de perfil baixo permaneceu equivalente à de perfil alto. Em outro equipamento, denominado simulador cardíaco, as próteses foram submetidas a condições semelhantes às condições fisiológicas de funcionamento para uma freqüência cardíaca de 75 bpm. Os resultados mostraram que o volume de retorno necessário para fechamento (refluxo, nas válvulas de perfil baixo, é menor do que nas de perfil alto. Isso traz um melhor aproveitamento do efeito de bombeamento do coração. As perdas de carga das válvulas foram comparadas através dos gradientes máximos de pressão visibilizados com a sobreposição dos sinais de pressão. Observou-se que as válvulas de perfil baixo oferecem menos resistência ao fluxo; assim, quando são implantadas, possibilitam uma passagem mais livre e desobstruída do sangue.The fluid dynamic performance and lifetime of a prosthetic heart valve are one of the most important characteristics to determine the choice of what prosthesis must be applied to a patient. Because of this, two different biological prosthetic heart valves profiles (one high profile and other low profile were studied, to verify possible alterations of working

  15. Summary of diamino pyrazoles derived and study their biological activities

    International Nuclear Information System (INIS)

    Hagui, Marwa

    2016-01-01

    The work involves the synthesis of new heterocyclic structures diamino pyrazoles derivatives that are present in many natural products and products of pharmacological and therapeutic interests and study their biological activities. In order to develop a radiotracer interest and use in diagnostic nuclear medicine, we are interested to synthesis a pyrazole derivative with the precursor [Re(CO)5Br] and studying the antibacterial and antifungal activity of 3.5-diamino pyrazole and even thioamide complex rhenium. The objectives of our workout: 1/ Synthesis of molecules 3,5-diamino pyrazole and thioamide. 2/ Synthesis of 3,5-diamino pyrazole-rhenium complex. 3/ The in vitro study: Bacteriological Tests (Study of antibacterial and antifungal activity of 3,5-diamino pyrazole and thioamide). The first part of this work concerns the chemical synthesis of molecules such as: thioamide, Amp z1 Ampz2 and then we had synthesized the complex 3,5-diamino pyrazole-rhenium. Similarly we determined the physicochemical characteristics of the compounds synthesized by CLHP, CCM and RMN ( 1 H, 13 C). The second part is devoted to the study in vitro of biological activities of the synthesized molecules and complex 3,5 diaminopyrazole-rhenium with concentration 1 mg/mL and 2 mg/mL. The results allow us to say that the thioamide and Ampz2 have antibacterial activity against S. enterica and Ampz2 has low activity against S. aureus and P. aeruginossa. Other pyrazole derivatives have no significant antibacterial and antifungal activity. The results also show that the synthesized compounds of concentration 2 mg/mL in relation to the inhibition zones of amoxicillin and DMSO: 1/ Escherichia coli, there is antibacterial activity for thioamide, and the Amp z1-Re Ampz2 compound. 2/ Staphylococcus aureus, the complex Ampz 1-Re and the thioamide have significant antibacterial activity. 3/ Salmonella, we observe that the thioamide molecules, Ampz2 and Amp z1-Re have significant antibacterial activity

  16. Microbiome studies in the biological control of plant pathogens

    Science.gov (United States)

    Biological control of plant pathogens, although it has been a successful alternative that has allowed to select microorganisms for the generation of bioproducts and to understand multiple biological mechanisms, cannot be considered as a strategy defined only from the selection of a range of cultiva...

  17. Studying of ion implantation effect on the biology in China

    International Nuclear Information System (INIS)

    Yu Zengliang

    1993-04-01

    Since low energy ion effect on the biology was observed, the ion implantation as a new mutagenic source has been widely used in improving crops and modifying microbes in China. The basic phenomenon of ion implantation effect on the biology and analytical results are reported, and the examples of its application and its further development are shown

  18. Molecular dynamic simulation study of molten cesium

    Directory of Open Access Journals (Sweden)

    Yeganegi Saeid

    2017-01-01

    Full Text Available Molecular dynamics simulations were performed to study thermodynamics and structural properties of expanded caesium fluid. Internal pressure, radial distribution functions (RDFs, coordination numbers and diffusion coefficients have been calculated at temperature range 700–1600 K and pressure range 100–800 bar. We used the internal pressure to predict the metal–non-metal transition occurrence region. RDFs were calculated at wide ranges of temperature and pressure. The coordination numbers decrease and positions of the first peak of RDFs slightly increase as the temperature increases and pressure decreases. The calculated self-diffusion coefficients at various temperatures and pressures show no distinct boundary between Cs metallic fluid and its expanded fluid where it continuously increases with temperature.

  19. Non Linear Beam Dynamics Studies at SPEAR

    International Nuclear Information System (INIS)

    Terebilo, A.; Pellegrini, C.; Cornacchia, M.; Corbett, J.; Martin, D.

    2011-01-01

    The frequency map analysis of a Hamiltonian system recently introduced to accelerators physics in combination with turn-by-turn phase space measurements opens new experimental opportunities for studying non linear dynamic in storage rings. In this paper we report on the experimental program at SPEAR having the goal of measuring the frequency map of the machine. In this paper we discuss the accuracy of the instantaneous tune extraction from experimental data and demonstrate the possibility of the frequency map measurement. The instantaneous tune extraction technique can be applied to experimental tracking data with reasonable accuracy. Frequency map can be experimentally determined using the existing turn-by-turn phase space measurement techniques and NAFF instantaneous tune extraction.

  20. Theoretical study of fission dynamics with muons

    International Nuclear Information System (INIS)

    Oberacker, V.E.; Umar, A.S.; Bottcher, C.; Strayer, M.R.; Maruhn, J.A.; Frankfurt Univ.

    1992-01-01

    Following muon capture by actinide atoms, some of the inner shell muonic transitions proceed by inverse internal conversion, i.e. the excitation energy of the muonic atom is transferred to the nucleus. In particular, the muonic E2:(3d→1s) transition energy is close to the peak of the isoscalar giant quadrupole resonance in actinide nuclei which exhibits a large fission width. Prompt fission in the presence of a bound muon allows us to study the dynamics of large-amplitude collective motion. We solve the time-dependent Dirac equation for the muonic spinor wave function in the Coulomb field of the fissioning nucleus on a 3-dimensional lattice and demonstrate that the muon attachment probability to the light fission fragment is a measure of the nuclear energy dissipation between the outer fission barrier and the scission point

  1. Radionuclide renal dynamic and function study

    International Nuclear Information System (INIS)

    Guan Liang

    1991-01-01

    The radionuclide dynamic and function study, glomerular filtration rate (GFR) and effective renal plasma flow (ERPF) were reported in 14 cases of renal and ureteral calculi patients before and after extracorporeal shock wave lithotripsy (ESWL). In 12 cases with normal renal blood flow, within 3 months after ESWL, the GFR of shock and non-shock side decreased with different extent, while the individual ERPF had little change. In 5 cases followed up 1 year after ESWL, the individual GFR and ERPF were normal. In 2 cases of severe renal function insufficiency, there was no improvement in renal function in shock side, after 5 months and 1 year, the renal function was still at low level. Thereby it is considered that ESWL is not suitable for the renal calculi patients with severe renal function insufficiency

  2. Integrating atomistic molecular dynamics simulations, experiments, and network analysis to study protein dynamics

    DEFF Research Database (Denmark)

    Papaleo, Elena

    2015-01-01

    that we observe and the functional properties of these important cellular machines. To make progresses in this direction, we need to improve the physical models used to describe proteins and solvent in molecular dynamics, as well as to strengthen the integration of experiments and simulations to overcome...... with the possibility to validate simulation methods and physical models against a broad range of experimental observables. On the other side, it also allows a complementary and comprehensive view on protein structure and dynamics. What is needed now is a better understanding of the link between the dynamic properties...... simulations with attention to the effects that can be propagated over long distances and are often associated to important biological functions. In this context, approaches inspired by network analysis can make an important contribution to the analysis of molecular dynamics simulations....

  3. Studies on the biological oxidation - The oxidation of ascorbic acid (vitamin C) in biological fluids

    OpenAIRE

    Guzmán Barrón, E. S.; Guzmán Barrón, Alberto; Klemperer, Friedrich

    2014-01-01

    Biological fluids can be divided according to their behavior toward ascorbic acid into two groups: those having an inhibitory mechanism that protects the ascorbic acid oxidation, and those lacking this mechanism. Animal fluids and some of vegetable origin (those containing dosables amounts of ascorbic acid) corresponding to the first group. Ascorbic acid is protected from oxidation in the fluids by the action of copper catalyst. Fluids from plants (those that contain very little ascorbic acid...

  4. Recommendations for designing and conducting veterinary clinical pathology biologic variation studies

    DEFF Research Database (Denmark)

    Freeman, Kathleen P; Baral, Randolph M; Dhand, Navneet K

    2017-01-01

    The recent creation of a veterinary clinical pathology biologic variation website has highlighted the need to provide recommendations for future studies of biologic variation in animals in order to help standardize and improve the quality of published information and to facilitate review......). These recommendations provide a valuable resource for clinicians, laboratorians, and researchers interested in conducting studies of biologic variation and in determining the quality of studies of biologic variation in veterinary laboratory testing....

  5. Microbial Community and Biochemical Dynamics of Biological Soil Crusts across a Gradient of Surface Coverage in the Central Mojave Desert.

    Science.gov (United States)

    Mogul, Rakesh; Vaishampayan, Parag; Bashir, Mina; McKay, Chris P; Schubert, Keith; Bornaccorsi, Rosalba; Gomez, Ernesto; Tharayil, Sneha; Payton, Geoffrey; Capra, Juliana; Andaya, Jessica; Bacon, Leonard; Bargoma, Emily; Black, David; Boos, Katie; Brant, Michaela; Chabot, Michael; Chau, Danny; Cisneros, Jessica; Chu, Geoff; Curnutt, Jane; DiMizio, Jessica; Engelbrecht, Christian; Gott, Caroline; Harnoto, Raechel; Hovanesian, Ruben; Johnson, Shane; Lavergne, Britne; Martinez, Gabriel; Mans, Paul; Morales, Ernesto; Oei, Alex; Peplow, Gary; Piaget, Ryan; Ponce, Nicole; Renteria, Eduardo; Rodriguez, Veronica; Rodriguez, Joseph; Santander, Monica; Sarmiento, Khamille; Scheppelmann, Allison; Schroter, Gavin; Sexton, Devan; Stephenson, Jenin; Symer, Kristin; Russo-Tait, Tatiane; Weigel, Bill; Wilhelm, Mary B

    2017-01-01

    In this study, we expand upon the biogeography of biological soil crusts (BSCs) and provide molecular insights into the microbial community and biochemical dynamics along the vertical BSC column structure, and across a transect of increasing BSC surface coverage in the central Mojave Desert, CA, United States. Next generation sequencing reveals a bacterial community profile that is distinct among BSCs in the southwestern United States. Distribution of major phyla in the BSC topsoils included Cyanobacteria (33 ± 8%), Proteobacteria (26 ± 6%), and Chloroflexi (12 ± 4%), with Phormidium being the numerically dominant genus. Furthermore, BSC subsurfaces contained Proteobacteria (23 ± 5%), Actinobacteria (20 ± 5%), and Chloroflexi (18 ± 3%), with an unidentified genus from Chloroflexi (AKIW781, order) being numerically dominant. Across the transect, changes in distribution at the phylum ( p < 0.0439) and genus ( p < 0.006) levels, including multiple biochemical and geochemical trends ( p < 0.05), positively correlated with increasing BSC surface coverage. This included increases in (a) Chloroflexi abundance, (b) abundance and diversity of Cyanobacteria, (b) OTU-level diversity in the topsoil, (c) OTU-level differentiation between the topsoil and subsurface, (d) intracellular ATP abundances and catalase activities, and (e) enrichments in clay, silt, and varying elements, including S, Mn, Co, As, and Pb, in the BSC topsoils. In sum, these studies suggest that BSCs from regions of differing surface coverage represent early successional stages, which exhibit increasing bacterial diversity, metabolic activities, and capacity to restructure the soil. Further, these trends suggest that BSC successional maturation and colonization across the transect are inhibited by metals/metalloids such as B, Ca, Ti, Mn, Co, Ni, Mo, and Pb.

  6. Microbial Community and Biochemical Dynamics of Biological Soil Crusts across a Gradient of Surface Coverage in the Central Mojave Desert

    Directory of Open Access Journals (Sweden)

    Rakesh Mogul

    2017-10-01

    Full Text Available In this study, we expand upon the biogeography of biological soil crusts (BSCs and provide molecular insights into the microbial community and biochemical dynamics along the vertical BSC column structure, and across a transect of increasing BSC surface coverage in the central Mojave Desert, CA, United States. Next generation sequencing reveals a bacterial community profile that is distinct among BSCs in the southwestern United States. Distribution of major phyla in the BSC topsoils included Cyanobacteria (33 ± 8%, Proteobacteria (26 ± 6%, and Chloroflexi (12 ± 4%, with Phormidium being the numerically dominant genus. Furthermore, BSC subsurfaces contained Proteobacteria (23 ± 5%, Actinobacteria (20 ± 5%, and Chloroflexi (18 ± 3%, with an unidentified genus from Chloroflexi (AKIW781, order being numerically dominant. Across the transect, changes in distribution at the phylum (p < 0.0439 and genus (p < 0.006 levels, including multiple biochemical and geochemical trends (p < 0.05, positively correlated with increasing BSC surface coverage. This included increases in (a Chloroflexi abundance, (b abundance and diversity of Cyanobacteria, (b OTU-level diversity in the topsoil, (c OTU-level differentiation between the topsoil and subsurface, (d intracellular ATP abundances and catalase activities, and (e enrichments in clay, silt, and varying elements, including S, Mn, Co, As, and Pb, in the BSC topsoils. In sum, these studies suggest that BSCs from regions of differing surface coverage represent early successional stages, which exhibit increasing bacterial diversity, metabolic activities, and capacity to restructure the soil. Further, these trends suggest that BSC successional maturation and colonization across the transect are inhibited by metals/metalloids such as B, Ca, Ti, Mn, Co, Ni, Mo, and Pb.

  7. Structural dynamics and aerodynamics measurements of biologically inspired flexible flapping wings

    International Nuclear Information System (INIS)

    Wu, P; Stanford, B K; Ifju, P G; Saellstroem, E; Ukeiley, L

    2011-01-01

    Flapping wing flight as seen in hummingbirds and insects poses an interesting unsteady aerodynamic problem: coupling of wing kinematics, structural dynamics and aerodynamics. There have been numerous studies on the kinematics and aerodynamics in both experimental and computational cases with both natural and artificial wings. These studies tend to ignore wing flexibility; however, observation in nature affirms that passive wing deformation is predominant and may be crucial to the aerodynamic performance. This paper presents a multidisciplinary experimental endeavor in correlating a flapping micro air vehicle wing's aeroelasticity and thrust production, by quantifying and comparing overall thrust, structural deformation and airflow of six pairs of hummingbird-shaped membrane wings of different properties. The results show that for a specific spatial distribution of flexibility, there is an effective frequency range in thrust production. The wing deformation at the thrust-productive frequencies indicates the importance of flexibility: both bending and twisting motion can interact with aerodynamic loads to enhance wing performance under certain conditions, such as the deformation phase and amplitude. By measuring structural deformations under the same aerodynamic conditions, beneficial effects of passive wing deformation can be observed from the visualized airflow and averaged thrust. The measurements and their presentation enable observation and understanding of the required structural properties for a thrust effective flapping wing. The intended passive responses of the different wings follow a particular pattern in correlation to their aerodynamic performance. Consequently, both the experimental technique and data analysis method can lead to further studies to determine the design principles for micro air vehicle flapping wings.

  8. Structural dynamics and aerodynamics measurements of biologically inspired flexible flapping wings

    Energy Technology Data Exchange (ETDEWEB)

    Wu, P; Stanford, B K; Ifju, P G [Department of Mechanical and Aerospace Engineering, MAE-A 231, University of Florida, Gainesville, FL 32611 (United States); Saellstroem, E; Ukeiley, L, E-mail: diccidwp@ufl.edu [Department of Mechanical and Aerospace Engineering, University of Florida, Shalimar, FL 32579 (United States)

    2011-03-15

    Flapping wing flight as seen in hummingbirds and insects poses an interesting unsteady aerodynamic problem: coupling of wing kinematics, structural dynamics and aerodynamics. There have been numerous studies on the kinematics and aerodynamics in both experimental and computational cases with both natural and artificial wings. These studies tend to ignore wing flexibility; however, observation in nature affirms that passive wing deformation is predominant and may be crucial to the aerodynamic performance. This paper presents a multidisciplinary experimental endeavor in correlating a flapping micro air vehicle wing's aeroelasticity and thrust production, by quantifying and comparing overall thrust, structural deformation and airflow of six pairs of hummingbird-shaped membrane wings of different properties. The results show that for a specific spatial distribution of flexibility, there is an effective frequency range in thrust production. The wing deformation at the thrust-productive frequencies indicates the importance of flexibility: both bending and twisting motion can interact with aerodynamic loads to enhance wing performance under certain conditions, such as the deformation phase and amplitude. By measuring structural deformations under the same aerodynamic conditions, beneficial effects of passive wing deformation can be observed from the visualized airflow and averaged thrust. The measurements and their presentation enable observation and understanding of the required structural properties for a thrust effective flapping wing. The intended passive responses of the different wings follow a particular pattern in correlation to their aerodynamic performance. Consequently, both the experimental technique and data analysis method can lead to further studies to determine the design principles for micro air vehicle flapping wings.

  9. Determination of the dynamical behaviour of biological materials during impact using a pendulum device

    Science.gov (United States)

    Van Zeebroeck, M.; Tijskens, E.; Van Liedekerke, P.; Deli, V.; De Baerdemaeker, J.; Ramon, H.

    2003-09-01

    A pendulum device has been developed to measure contact force, displacement and displacement rate of an impactor during its impact on the sample. Displacement, classically measured by double integration of an accelerometer, was determined in an alternative way using a more accurate incremental optical encoder. The parameters of the Kuwabara-Kono contact force model for impact of spheres have been estimated using an optimization method, taking the experimentally measured displacement, displacement rate and contact force into account. The accuracy of the method was verified using a rubber ball. Contact force parameters for the Kuwabara-Kono model have been estimated with success for three biological materials, i.e., apples, tomatoes and potatoes. The variability in the parameter estimations for the biological materials was quite high and can be explained by geometric differences (radius of curvature) and by biological variation of mechanical tissue properties.

  10. Observation of dehydration dynamics in biological tissues with terahertz digital holography [Invited].

    Science.gov (United States)

    Guo, Lihan; Wang, Xinke; Han, Peng; Sun, Wenfeng; Feng, Shengfei; Ye, Jiasheng; Zhang, Yan

    2017-05-01

    A terahertz (THz) digital holographic imaging system is utilized to investigate natural dehydration processes in three types of biological tissues, including cattle, mutton, and pork. An image reconstruction algorithm is applied to remove the diffraction influence of THz waves and further improve clarity of THz images. From THz images of different biological specimens, distinctive water content as well as dehydration features of adipose and muscle tissues are precisely distinguished. By analyzing THz absorption spectra of these samples, temporal evolution characteristics of the absorbances for adipose and muscle tissues are described and compared in detail. Discrepancies between water retention ability of different animal tissues are also discussed. The imaging technique provides a valuable measurement platform for biological sensing.

  11. A novel comprehensive learning artificial bee colony optimizer for dynamic optimization biological problems

    Directory of Open Access Journals (Sweden)

    Weixing Su

    2017-03-01

    Full Text Available There are many dynamic optimization problems in the real world, whose convergence and searching ability is cautiously desired, obviously different from static optimization cases. This requires an optimization algorithm adaptively seek the changing optima over dynamic environments, instead of only finding the global optimal solution in the static environment. This paper proposes a novel comprehensive learning artificial bee colony optimizer (CLABC for optimization in dynamic environments problems, which employs a pool of optimal foraging strategies to balance the exploration and exploitation tradeoff. The main motive of CLABC is to enrich artificial bee foraging behaviors in the ABC model by combining Powell’s pattern search method, life-cycle, and crossover-based social learning strategy. The proposed CLABC is a more bee-colony-realistic model that the bee can reproduce and die dynamically throughout the foraging process and population size varies as the algorithm runs. The experiments for evaluating CLABC are conducted on the dynamic moving peak benchmarks. Furthermore, the proposed algorithm is applied to a real-world application of dynamic RFID network optimization. Statistical analysis of all these cases highlights the significant performance improvement due to the beneficial combination and demonstrates the performance superiority of the proposed algorithm.

  12. A novel comprehensive learning artificial bee colony optimizer for dynamic optimization biological problems.

    Science.gov (United States)

    Su, Weixing; Chen, Hanning; Liu, Fang; Lin, Na; Jing, Shikai; Liang, Xiaodan; Liu, Wei

    2017-03-01

    There are many dynamic optimization problems in the real world, whose convergence and searching ability is cautiously desired, obviously different from static optimization cases. This requires an optimization algorithm adaptively seek the changing optima over dynamic environments, instead of only finding the global optimal solution in the static environment. This paper proposes a novel comprehensive learning artificial bee colony optimizer (CLABC) for optimization in dynamic environments problems, which employs a pool of optimal foraging strategies to balance the exploration and exploitation tradeoff. The main motive of CLABC is to enrich artificial bee foraging behaviors in the ABC model by combining Powell's pattern search method, life-cycle, and crossover-based social learning strategy. The proposed CLABC is a more bee-colony-realistic model that the bee can reproduce and die dynamically throughout the foraging process and population size varies as the algorithm runs. The experiments for evaluating CLABC are conducted on the dynamic moving peak benchmarks. Furthermore, the proposed algorithm is applied to a real-world application of dynamic RFID network optimization. Statistical analysis of all these cases highlights the significant performance improvement due to the beneficial combination and demonstrates the performance superiority of the proposed algorithm.

  13. Molecular beam studies of adsorption dynamics

    International Nuclear Information System (INIS)

    Arumainayagam, C.R.; McMaster, M.C.; Madix, R.J.

    1991-01-01

    We have investigated the trapping dynamics of C 1 -C 3 alkanes and Xe on Pt(111) using supersonic molecular beams and a direct technique to measure trapping probabilities. We have extended a one-dimensional model based on classical mechanics to include trapping and have found semiquantitative agreement with experimental results for the dependence of the initial trapping probability on incident translational energy at normal incidence. Our measurements of the initial trapping probability as a function of incident translational energy at normal incidence are in agreement with previous mean translational energy measurements for Xe and CH 4 desorbing near the surface normal, in accordance with detailed balance. However, the angular dependence of the initial trapping probability shows deviations from normal energy scaling, demonstrating the importance of parallel momentum in the trapping process and the inadequacy of one-dimensional models. The dependence of the initial trapping probability of Xe on incident translational energy and angle is quite well fit by three-dimensional stochastic classical trajectory calculations utilizing a Morse potential. Angular distributions of the scattered molecules indicate that the trapping probability is not a sensitive function of surface temperature. The trapping probability increases with surface coverage in quantitative agreement with a modified Kisliuk model which incorporates enhanced trapping onto the monolayer. We have also used the direct technique to study trapping onto a saturated monolayer state to investigate the dynamics of extrinsic precursor adsorption and find that the initial trapping probability onto the monolayer is higher than on the clean surface. The initial trapping probability onto the monolayer scales with total energy, indicating a highly corrugated interaction potential

  14. Biological and Docking Studies of Sulfonamide Derivatives of 4-Aminophenazone

    International Nuclear Information System (INIS)

    Akhtar, M.S.; Ismail, A.; Murtaza, S.; Shamim, S.; Tahir, M.N.; Usman Ali Rana, U.A.

    2016-01-01

    Sulfonamide derivatives of 4-aminophenazone (4APZ) were synthesized and accordingly characterized by spectroscopic techniques. These newly synthesized compounds were examined for their biological activities such as enzyme inhibition, analgesic, antibacterial, antioxidant and DNA interaction. A direct correlation between enzyme inhibition activity and concentration of the compounds was observed both by experimental and molecular docking studies. Analgesic activity of the compounds was investigated by formalin-induced paw licking (FIPL), acetic acid-induced writhing (AIW) and heat conduction methods in mice. Membrane stabilization effect was determined by hypotonicity-induced hemolysis. Bacterial strains, S. aureus, S. epidermidis, B. subtilis, E. coli, P. aeruginosa, S. mutans and A. odontolyticus were used for investigating the antibacterial potential of the compounds. Antioxidant potential was investigated by Ferric Reducing Antioxidant Power assay (FRAP) and DPPH free radical scavenging method. DNA interaction studies of the synthesized compounds showed weak interaction. Hyperchromic effect was observed along the series and large positive K values were obtained for most of the compounds. (author)

  15. Synthesis of potentially bioactive compounds and tools for biological studies

    International Nuclear Information System (INIS)

    Cappa, F.

    2014-01-01

    NMR spectroscopy is one of the most versatile tools for studying structural parameters of organic and bioorganic compounds. It became a highly suitable method to achieve spectra simplification of macromolecules in combination with isotope labeling techniques. This technique is used to study protein structures, folding properties and mechanisms of chemical and biochemical reactions. Proteins typically feature a high molecular mass showing a high number of spin systems, being responsible for increasingly difficult to interpret NMR spectra, which is why it is essential to introduce 13 C- and 15 N- isotopes to obtain reasonable signal intensities. The development of a new synthetic route towards 13 C-isotope labeled Phenylalanine or precursors thereof, starting from inexpensive and easily accessible labeled starting materials, is the main purpose of this work. Label sources such as [ 13 C]-acetic acid, [ 13 C]-formaldehyde, [ 13 C]-allyl alcohol and [ 13 C]-glycine will be used. The synthetic pathway will be carried out in a way where the position-selective incorporation of labeled isotopes can be performed. This important feature of the synthesis may open access towards newly designed NMR-experiments. Key steps for the tested route are ring closing metatheses as well as indium mediated reactions. The second part of this work focuses on the field of sugar chemistry, in particular on the family of deoxy sugars, components of many natural products, found in different plants, fungi and bacteria. Deoxy sugars also participate in a wide range of biological processes. Special focus is given to 3-deoxy sugars and the research of a versatile and flexible synthetic route for their preparation starting from the easily accessible D-glyceraldehyde. These sugars are found on Gram-negative bacteria where they are a key component of the lipopolysaccharides, or where they can take place in the biosynthesis of aromatic amino acids in bacteria and plants. Being able to perform this

  16. Systems-Dynamic Analysis for Neighborhood Study

    Science.gov (United States)

    Systems-dynamic analysis (or system dynamics (SD)) helps planners identify interrelated impacts of transportation and land-use policies on neighborhood-scale economic outcomes for households and businesses, among other applications. This form of analysis can show benefits and tr...

  17. The emerging molecular biology toolbox for the study of long noncoding RNA biology

    CSIR Research Space (South Africa)

    Fok, Ezio T

    2017-10-01

    Full Text Available cellular function, it remains crucial to deepen our understanding of their biology. First draft submitted: 4 May 2017; Accepted for publication: 4 July 2017; Published online: 6 September 2017 Keywords: CRISPR/Cas9 • epigenetic regulation • functional... efficient in the nucleus and preferably effective at the site of transcription. The use of targeted nucleases such as CRISPR/Cas9 for such purposes is possible, however, their application has to be carefully considered. Mutations to the sequence are usually...

  18. The Implementation of Research-based Learning on Biology Seminar Course in Biology Education Study Program of FKIP UMRAH

    Science.gov (United States)

    Amelia, T.

    2018-04-01

    Biology Seminar is a course in Biology Education Study Program of Faculty of Teacher Training and Education University of Maritim Raja Ali Haji (FKIP UMRAH) that requires students to have the ability to apply scientific attitudes, perform scientific writing and undertake scientific publications on a small scale. One of the learning strategies that can drive the achievement of learning outcomes in this course is Research-Based Learning. Research-Based Learning principles are considered in accordance with learning outcomes in Biology Seminar courses and generally in accordance with the purpose of higher education. On this basis, this article which is derived from a qualitative research aims at describing Research-based Learning on Biology Seminar course. Based on a case study research, it was known that Research-Based Learning on Biology Seminar courses is applied through: designing learning activities around contemporary research issues; teaching research methods, techniques and skills explicitly within program; drawing on personal research in designing and teaching courses; building small-scale research activities into undergraduate assignment; and infusing teaching with the values of researchers.

  19. Dynamics of a microbial biofilm in a rotating biological contactor for ...

    African Journals Online (AJOL)

    Wastewater from wine-related industries is characterised by high variability in COD and pH. Disposal of these effluents with little or no treatment could lead to heavy financial penalties or pollution of soil and water resources. A pilot-scale rotating biological contactor (RBC) was evaluated for the treatment of winery effluent, ...

  20. Study of the biology of Trichogramma chilonis Ishii (Hymenoptera ...

    African Journals Online (AJOL)

    user1

    oviposit in eggs of Plutella xylostella L. In the no-choice test, parasitism in eggs of H. ... KEYWORDS: Trichogramma chilonis, Maruca vitrata, biology, Plutella xylostella ..... synthetic sex pheromone of P. xylostella (Reddy et al., 2002), it did not.

  1. Biology as a Study of Man and Society

    Science.gov (United States)

    Hurd, Paul DeHart

    1971-01-01

    Biology ought to be taught within the context of human culture; "man" can be the "type animal." Consideration should be given to questions of race, population, food resources, environmental quality, intelligence, genetic engineering, and organ transplants. (AL)

  2. Systems biology approaches to the study of cardiovascular drugs

    NARCIS (Netherlands)

    Nikolsky, Y.; Kleemann, R.

    2010-01-01

    Atherogenic lipids and chronic inflammation drive the development of cardiovascular disorders such as atherosclerosis. Many cardiovascular drugs target the liver which is involved in the formation of lipid and inflammatory risk factors. With robust systems biology tools and comprehensive

  3. A descriptive study of biological and psychosocial factors associated ...

    African Journals Online (AJOL)

    2017-08-31

    Aug 31, 2017 ... Obesity has long been a major health concern among adults, but its increasing prevalence rates ... The association between the BMIs of the biological parents and their ... with different kinds of food, consumption of fatty foods.

  4. Experimental study of the biological properties of 188Re-Hepama-1 biologic superparamagnetic nanoparticles

    International Nuclear Information System (INIS)

    Feng Yanlin; Tan Jiaju; Sun Jing; Wen Guanghua; Wu Xiaolian; Liang Sheng; Xia Jiaoyun

    2007-01-01

    Objective: To investigate a new biologic-superparamagnetic nanoparticles's characteristics of immunological activity, biological distributing in vivo, targeting and inhibiting tumor effect. Methods: The experimental group 188 Re-Hepama-l-superparamagnetic nanoparticles, and control groups, including 188 ReO 4 - , 188 Re-Hepama-1, and 188 Re-superparamagnetic nanoparticles, were set up. The distributions were measured after injection 4 h and 24 h by caudal vein of Kuming mice. The magnetic targeting experiments in vivo were clone with and without magnetic field in liver after injection in New Zealand rabbit. The inhibiting tumor effect on hepatic cancer cell lines SMMC-7721 of the above four 188 Re labeled products were measured by mono nuclear cell direct cytotoxicity assay method. Results: After injection 4 h and 24 h by vein, the liver taking was highest in group 188 Re-Hepama-l-superparamagnetic nanoparticles. The radiative activity in liver in magnetism zoo was higher than in non magnetism zoo in 188 Re- Hepama-1-superparamagnetic nanoparticles after applying magnetic field in left lobe of liver, and the ratio of in magnetism zoo to non magnetism zoo was 1.87. And the half effective inhibition radioactive concentrations (IC 50 ) in 188 Re-Hepama-l-superparamagnetic nanoparticles was one forth of 188 ReO 4 - . Conclusion: 188 Re- Hepama-l-superparamagnetic nanoparticles showed its fine stability in intro, good immunological activity and significant liver target. (authors)

  5. Biological studies on Brazilian plants used in wound healing.

    Science.gov (United States)

    Schmidt, C; Fronza, M; Goettert, M; Geller, F; Luik, S; Flores, E M M; Bittencourt, C F; Zanetti, G D; Heinzmann, B M; Laufer, S; Merfort, I

    2009-04-21

    n-Hexanic and ethanolic extracts from twelve plants (Brugmansia suaveolens Brecht. et Presl., Eupatorium laevigatum Lam., Galinsoga parviflora Cav., Iresine herbstii Hook., Kalanchöe tubiflora Hamet-Ahti, Petiveria alliacea L., Pluchea sagittalis (Lam.) Cabrera, Piper regnellii DC., Schinus molle L., Sedum dendroideum Moç et Sessé ex DC., Waltheria douradinha St. Hill., Xanthium cavanillesii Schouw.) used in traditional South Brazilian medicine as wound healing agents were investigated in various biological assays, targeting different aspects in this complex process. The extracts were investigated on NF-kappaB DNA binding, p38alpha MAPK, TNF-alpha release, direct elastase inhibition and its release as well as on caspase-3. Fibroblasts migration to and proliferation into the wounded monolayers were evaluated in the scratch assay, the agar diffusion test for antibacterial and the MTT assay for cytotoxic effects. The hydrophilic extracts from Galinsoga parviflora, Petiveria alliacea, Schinus molle, Waltheria douradinha and Xanthium cavanillesii as well as the lipophilic extract of Waltheria douradinha turned out to be the most active ones. These results increase our knowledge on the wound healing effects of the investigated medicinal plants. Further studies are necessary to find out the effective secondary metabolites responsible for the observed effects.

  6. Imaging Primary Lung Cancers in Mice to Study Radiation Biology

    International Nuclear Information System (INIS)

    Kirsch, David G.; Grimm, Jan; Guimaraes, Alexander R.; Wojtkiewicz, Gregory R.; Perez, Bradford A.; Santiago, Philip M.; Anthony, Nikolas K.; Forbes, Thomas; Doppke, Karen

    2010-01-01

    Purpose: To image a genetically engineered mouse model of non-small-cell lung cancer with micro-computed tomography (micro-CT) to measure tumor response to radiation therapy. Methods and Materials: The Cre-loxP system was used to generate primary lung cancers in mice with mutation in K-ras alone or in combination with p53 mutation. Mice were serially imaged by micro-CT, and tumor volumes were determined. A comparison of tumor volume by micro-CT and tumor histology was performed. Tumor response to radiation therapy (15.5 Gy) was assessed with micro-CT. Results: The tumor volume measured with free-breathing micro-CT scans was greater than the volume calculated by histology. Nevertheless, this imaging approach demonstrated that lung cancers with mutant p53 grew more rapidly than lung tumors with wild-type p53 and also showed that radiation therapy increased the doubling time of p53 mutant lung cancers fivefold. Conclusions: Micro-CT is an effective tool to noninvasively measure the growth of primary lung cancers in genetically engineered mice and assess tumor response to radiation therapy. This imaging approach will be useful to study the radiation biology of lung cancer.

  7. Studies on the reproductive biology of downy brome (Bromus tectorum)

    International Nuclear Information System (INIS)

    Richardson, J.M.

    1986-01-01

    The ability of downy brome to successfully infest crop lands is partially due to its prolific nature. To better understand its reproductive biology, studies investigating (1) effects of temperature and photoperiod on flowering, (2) prevention of downy brome seed information with herbicides, and (3) effects of drought on reproduction, were conducted. Seedling vernalization was more effective than seed vernalization in promoting downy brome flowering. Vernalizing imbibed downy brome caryopses at 3 C for 0 to 30 days did not induce rapid flowering. Downy brome seedlings were exposed to six photoperiod/temperature treatments. After transfer to long days, plants from the short da/3 C treatment flowered within 30 days. DPX-Y6202 and fluazifop-butyl were tested for their ability to prevent seed formation in downy brome. Fluazifop-butyl prevented seed formation over a wider range of application rates and growth stages than did DPX-Y6202. Seed production was prevented most readily by herbicide applications made early in the reproductive cycle. Translocation of radiolabel was greater with 14 C-fluazifop-butyl than with 14 C-DPX-Y6202, particularly into developing spikelets. Microautoradiographic techniques were used to identify mechanisms involved in the prevention of downy brome seed formation by these herbicides. Tissue localization of both herbicides was similar. The highest concentration of radiolabel was found in developing pollen grains, suggesting that the herbicides prevented seed formation by interrupting pollen development or function. Water stress reduced apparent photosynthesis and increased diffusive resistance of flag leaves

  8. A canonical correlation analysis-based dynamic bayesian network prior to infer gene regulatory networks from multiple types of biological data.

    Science.gov (United States)

    Baur, Brittany; Bozdag, Serdar

    2015-04-01

    One of the challenging and important computational problems in systems biology is to infer gene regulatory networks (GRNs) of biological systems. Several methods that exploit gene expression data have been developed to tackle this problem. In this study, we propose the use of copy number and DNA methylation data to infer GRNs. We developed an algorithm that scores regulatory interactions between genes based on canonical correlation analysis. In this algorithm, copy number or DNA methylation variables are treated as potential regulator variables, and expression variables are treated as potential target variables. We first validated that the canonical correlation analysis method is able to infer true interactions in high accuracy. We showed that the use of DNA methylation or copy number datasets leads to improved inference over steady-state expression. Our results also showed that epigenetic and structural information could be used to infer directionality of regulatory interactions. Additional improvements in GRN inference can be gleaned from incorporating the result in an informative prior in a dynamic Bayesian algorithm. This is the first study that incorporates copy number and DNA methylation into an informative prior in dynamic Bayesian framework. By closely examining top-scoring interactions with different sources of epigenetic or structural information, we also identified potential novel regulatory interactions.

  9. Respectful Modeling: Addressing Uncertainty in Dynamic System Models for Molecular Biology.

    Science.gov (United States)

    Tsigkinopoulou, Areti; Baker, Syed Murtuza; Breitling, Rainer

    2017-06-01

    Although there is still some skepticism in the biological community regarding the value and significance of quantitative computational modeling, important steps are continually being taken to enhance its accessibility and predictive power. We view these developments as essential components of an emerging 'respectful modeling' framework which has two key aims: (i) respecting the models themselves and facilitating the reproduction and update of modeling results by other scientists, and (ii) respecting the predictions of the models and rigorously quantifying the confidence associated with the modeling results. This respectful attitude will guide the design of higher-quality models and facilitate the use of models in modern applications such as engineering and manipulating microbial metabolism by synthetic biology. Copyright © 2016 Elsevier Ltd. All rights reserved.

  10. Intermolecular dynamics studied by paramagnetic tagging

    Energy Technology Data Exchange (ETDEWEB)

    Xu Xingfu; Keizers, Peter H. J. [Leiden University, Institute of Chemistry (Netherlands); Reinle, Wolfgang; Hannemann, Frank; Bernhardt, Rita [Universitaet des Saarlandes, Naturwissenschaftlich-Technische Fakultaet III, Institut fuer Biochemie (Germany); Ubbink, Marcellus [Leiden University, Institute of Chemistry (Netherlands)], E-mail: m.ubbink@chem.leidenuniv.nl

    2009-04-15

    Yeast cytochrome c and bovine adrenodoxin form a dynamic electron transfer complex, which is a pure encounter complex. It is demonstrated that the dynamic nature of the interaction can readily be probed by using a rigid lanthanide tag attached to cytochrome c. The tag, Caged Lanthanide NMR Probe 5, induces pseudocontact shifts and residual dipolar couplings and does not perturb the binding interface. Due to the dynamics in the complex, residual dipolar couplings in adrenodoxin are very small. Simulation shows that cytochrome c needs to sample a large part of the surface of adrenodoxin to explain the small degree of alignment observed for adrenodoxin. The applied method provides a simple and straightforward way to observe dynamics in protein complexes or domain-domain mobility without the need for external alignment media.

  11. Intermolecular dynamics studied by paramagnetic tagging

    International Nuclear Information System (INIS)

    Xu Xingfu; Keizers, Peter H. J.; Reinle, Wolfgang; Hannemann, Frank; Bernhardt, Rita; Ubbink, Marcellus

    2009-01-01

    Yeast cytochrome c and bovine adrenodoxin form a dynamic electron transfer complex, which is a pure encounter complex. It is demonstrated that the dynamic nature of the interaction can readily be probed by using a rigid lanthanide tag attached to cytochrome c. The tag, Caged Lanthanide NMR Probe 5, induces pseudocontact shifts and residual dipolar couplings and does not perturb the binding interface. Due to the dynamics in the complex, residual dipolar couplings in adrenodoxin are very small. Simulation shows that cytochrome c needs to sample a large part of the surface of adrenodoxin to explain the small degree of alignment observed for adrenodoxin. The applied method provides a simple and straightforward way to observe dynamics in protein complexes or domain-domain mobility without the need for external alignment media

  12. NMR spectroscopic studies of membrane-bound biological systems

    International Nuclear Information System (INIS)

    Hohlweg, W.

    2013-01-01

    In the course of this thesis, biological NMR spectroscopy was employed in studying membrane-bound peptides and proteins, for which structural information is still comparatively hard to obtain. Initial work focused on various model peptides bound to membrane-mimicking micelles, studying the protonation state of arginine in a membrane environment. Strong evidence for a cation-π complex was found in TM7, a peptide which forms the seventh transmembrane helix of subunit a of the vacuolar-type H+-ATPase (V-ATPase). V-ATPase is a physiologically highly relevant proton pump, which is present in intracellular membranes of all eukaryotic organisms, as well as the plasma membrane of several specialized cells. Loss of functional V-ATPase is associated with human diseases such as osteopetrosis, distal renal tubular acidosis or the spreading of cancer. V-ATPase is considered a potential drug target in the treatment of osteoporosis and cancer, or in the development of novel contraceptives. Results from NMR solution structure determination, NMR titration experiments, paramagnetic relaxation enhancement experiments and tryptophan fluorescence spectroscopy confirm the existence of a buried cation-? complex formed between arginine residue R735, which is essential for proton transport, and neighbouring tryptophan and tyrosine residues. In vivo experiments in the yeast Saccharomyces cerevisiae using selective growth tests and fluorescence microscopy showed that formation of the cation-π complex is essential for V-ATPase function. Deletion of both aromatic residues, as well as only the one tryptophan residue leads to growth defects and inability to maintain vacuolar pH homeostasis. These findings shine new light on the still elusive mechanism of proton transport in V-ATPase, and show that arginine R735 may be directly involved in proton transfer across the membrane. (author) [de

  13. Large, dynamic, multi-protein complexes: a challenge for structural biology

    Czech Academy of Sciences Publication Activity Database

    Rozycki, B.; Bouřa, Evžen

    2014-01-01

    Roč. 26, č. 46 (2014), 463103/1-463103/11 ISSN 0953-8984 R&D Projects: GA MŠk LO1302 EU Projects: European Commission(XE) 333916 - STARPI4K Institutional support: RVO:61388963 Keywords : protein structure * multi-protein complexes * hybrid methods of structural biology Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.346, year: 2014

  14. Dynamic Analysis of a Phytoplankton-Fish Model with Biological and Artificial Control

    OpenAIRE

    Wang, Yapei; Zhao, Min; Pan, Xinhong; Dai, Chuanjun

    2014-01-01

    We investigate a nonlinear model of the interaction between phytoplankton and fish, which uses a pair of semicontinuous systems with biological and artificial control. First, the existence of an order-1 periodic solution to the system is analyzed using a Poincaré map and a geometric method. The stability conditions of the order-1 periodic solution are obtained by a theoretical mathematical analysis. Furthermore, based on previous analysis, we investigate the bifurcation in the order-1 periodi...

  15. Molecular dynamics studies of superionic conductors

    International Nuclear Information System (INIS)

    Rahman, A.

    1979-01-01

    Over the last fifteen years computer modeling of liquids and solids has become a useful method of understanding the structural and dynamical correlations in these systems. Some characteristics of the method are presented with an example from work on homogeneous nucleation in monoatomic liquids; the interaction potential determines the structure: a Lennard--Jones system nucleates a close packed structure while an alkali metal potential nucleates a bcc packing. In the study of ionic systems like CaF 2 the Coulomb interaction together with the short range repulsion is enough to produce a satisfactory model for the motion of F - ions in CaF 2 at approx. 1600 0 K. Analysis of this motion shows that F - ions reside at their fluorite sites for about 6 x 10 -12 s and that the diffusion is mainly due to F - jumps in the 100 direction. The motion can be analyzed in terms of the generation and annihilation of anti-Frenkel pairs. The temperature dependence of the F - diffusion constant at two different densities has also been calculated. The computer model does not correspond with experiment in this regard

  16. Prolactin secretion: the impact of dynamic studies

    International Nuclear Information System (INIS)

    L'Hermite, M.; Degueldre, M.; Caufriez, A.; Delvoye, P.; Robyn, C.

    1975-01-01

    Human prolactin blood levels were determined by radioimmunoassay in basal condition and in response to various inhibiting and/or stimulating agents (levodopa, water overload, insulinic hypoglycaemia, synthetic TRH, sulpiride) in cases of disturbed hypothalamo-pituitary axis (failure to lactate, prolactin-secreting pituitary adenomas, acromegaly, other pituitary tumours, clinical panhypopituitarism). A blunted prolactin response to suckling was evidenced in 2 post-partum women who were unable to breast feed. Hyperprolactinaemia, whether related to the existence of a prolactin-producing adenoma or not was associated with the disappearance of the normal circadian pattern of prolactin secretion and with a blunted relative response to TRH; the latter phenomenon occurred also in acromegaly regardless of the basal prolactinaemia, and during the last trimester of pregnancy. Water overload was unsuccessful to suppress prolactin during the last trimester of pregnancy while the acute administration of levodopa was quite effective in about half of the patients with pituitary tumour. Therefore none of the dynamic tests presently studied allowed to attribute a hyperprolactinaemia to a pituitary tumour rather than to a functional disturbance. On the contrary, stimulation tests can help to locate the level of a defect in cases of hypopituitarism [fr

  17. Dynamic Modeling Using MCSim and R (SOT 2016 Biological Modeling Webinar Series)

    Science.gov (United States)

    MCSim is a stand-alone software package for simulating and analyzing dynamic models, with a focus on Bayesian analysis using Markov Chain Monte Carlo. While it is an extremely powerful package, it is somewhat inflexible, and offers only a limited range of analysis options, with n...

  18. Carbon dynamics modelization and biological community sensitivity to temperature in an oligotrophic freshwater Antarctic lake

    DEFF Research Database (Denmark)

    Antonio Villaescusa, Juan; Jorgensen, Sven Erik; Rochera, Carlos

    2016-01-01

    food web. This preliminary model aims to describe part of the carbon dynamics, especially for bacterioplankton and associated factors, in this maritime Antarctic lake highly affected by temperature increase linked to regional warming. To describe the system, the effects of the variation of different...

  19. Static and dynamic light scattering by red blood cells: A numerical study.

    Science.gov (United States)

    Mauer, Johannes; Peltomäki, Matti; Poblete, Simón; Gompper, Gerhard; Fedosov, Dmitry A

    2017-01-01

    Light scattering is a well-established experimental technique, which gains more and more popularity in the biological field because it offers the means for non-invasive imaging and detection. However, the interpretation of light-scattering signals remains challenging due to the complexity of most biological systems. Here, we investigate static and dynamic scattering properties of red blood cells (RBCs) using two mesoscopic hydrodynamics simulation methods-multi-particle collision dynamics and dissipative particle dynamics. Light scattering is studied for various membrane shear elasticities, bending rigidities, and RBC shapes (e.g., biconcave and stomatocyte). Simulation results from the two simulation methods show good agreement, and demonstrate that the static light scattering of a diffusing RBC is not very sensitive to the changes in membrane properties and moderate alterations in cell shapes. We also compute dynamic light scattering of a diffusing RBC, from which dynamic properties of RBCs such as diffusion coefficients can be accessed. In contrast to static light scattering, the dynamic measurements can be employed to differentiate between the biconcave and stomatocytic RBC shapes and generally allow the differentiation based on the membrane properties. Our simulation results can be used for better understanding of light scattering by RBCs and the development of new non-invasive methods for blood-flow monitoring.

  20. Thermal transpiration: A molecular dynamics study

    Energy Technology Data Exchange (ETDEWEB)

    T, Joe Francis [Computational Nanotechnology Laboratory, School of Nano Science and Technology, National Institute of Technology Calicut, Kozhikode (India); Sathian, Sarith P. [Department of Applied Mechanics, Indian Institute of Technology Madras, Chennai (India)

    2014-12-09

    Thermal transpiration is a phenomenon where fluid molecules move from the cold end towards the hot end of a channel under the influence of longitudinal temperature gradient alone. Although the phenomenon of thermal transpiration is observed at rarefied gas conditions in macro systems, the phenomenon can occur at atmospheric pressure if the characteristic dimensions of the channel is less than 100 nm. The flow through these nanosized channels is characterized by the free molecular flow regimes and continuum theory is inadequate to describe the flow. Thus a non-continuum method like molecular dynamics (MD) is necessary to study such phenomenon. In the present work, MD simulations were carried out to investigate the occurance of thermal transpiration in copper and platinum nanochannels at atmospheric pressure conditions. The mean pressure of argon gas confined inside the nano channels was maintained around 1 bar. The channel height is maintained at 2nm. The argon atoms interact with each other and with the wall atoms through the Lennard-Jones potential. The wall atoms are modelled using an EAM potential. Further, separate simulations were carried out where a Harmonic potential is used for the atom-atom interaction in the platinum channel. A thermally insulating wall was introduced between the low and high temperature regions and those wall atoms interact with fluid atoms through a repulsive potential. A reduced cut off radius were used to achieve this. Thermal creep is induced by applying a temperature gradient along the channel wall. It was found that flow developed in the direction of the increasing temperature gradient of the wall. An increase in the volumetric flux was observed as the length of the cold and the hot regions of the wall were increased. The effect of temperature gradient and the wall-fluid interaction strength on the flow parameters have been studied to understand the phenomenon better.

  1. Effects of N-glycosylation on protein conformation and dynamics: Protein Data Bank analysis and molecular dynamics simulation study.

    Science.gov (United States)

    Lee, Hui Sun; Qi, Yifei; Im, Wonpil

    2015-03-09

    N-linked glycosylation is one of the most important, chemically complex, and ubiquitous post-translational modifications in all eukaryotes. The N-glycans that are covalently linked to proteins are involved in numerous biological processes. There is considerable interest in developments of general approaches to predict the structural consequences of site-specific glycosylation and to understand how these effects can be exploited in protein design with advantageous properties. In this study, the impacts of N-glycans on protein structure and dynamics are systematically investigated using an integrated computational approach of the Protein Data Bank structure analysis and atomistic molecular dynamics simulations of glycosylated and deglycosylated proteins. Our study reveals that N-glycosylation does not induce significant changes in protein structure, but decreases protein dynamics, likely leading to an increase in protein stability. Overall, these results suggest not only a common role of glycosylation in proteins, but also a need for certain proteins to be properly glycosylated to gain their intrinsic dynamic properties.

  2. Adsorption properties of biologically active derivatives of quaternary ammonium surfactants and their mixtures at aqueous/air interface II. Dynamics of adsorption, micelles dissociation and cytotoxicity of QDLS.

    Science.gov (United States)

    Rojewska, Monika; Prochaska, Krystyna; Olejnik, Anna; Rychlik, Joanna

    2014-07-01

    The main aim of our study was analysis of adsorption dynamics of mixtures containing quaternary derivatives of lysosomotropic substance (QDLS). Two types of equimolar mixtures were considered: the ones containing two derivatives of lysosomotropic substances (DMALM-12 and DMGM-12) as well as the catanionic mixtures i.e. the systems containing QDLS and DBSNa. Dynamic surface tension measurements of surfactant mixtures were made. The results suggested that the diffusivity of the mixed system could be treated as the average value of rates of diffusion of individual components, micelles and ion pairs, which are present in the mixtures studied. Moreover, an attempt was made to explain the influence of the presence of micelles in the mixtures on their adsorption dynamics. The compounds examined show interesting biological properties which can be useful, especially for drug delivery in medical treatment. In vitro cytotoxic activities of the mixtures studied towards human cancer cells were evaluated. Most of the mixtures showed a high antiproliferative potential, especially the ones containing DMALM-12. Each cancer cell line used demonstrated different sensitivity to the same dose of the mixtures tested. Copyright © 2014 Elsevier B.V. All rights reserved.

  3. International biological engagement programs facilitate Newcastle disease epidemiological studies

    Directory of Open Access Journals (Sweden)

    Patti J. Miller

    2015-10-01

    Full Text Available Infections of poultry species with virulent strains of Newcastle disease virus (NDV cause Newcastle disease (ND, one of the most economically significant and devastating diseases for poultry producers worldwide. Biological engagement programs (BEP between the Southeast Poultry Research Laboratory (SEPRL of the United States Department of Agriculture and laboratories from Russia, Pakistan, Ukraine, Kazakhstan and Indonesia collectively have produced a better understanding of the genetic diversity and evolution of the viruses responsible for ND, which is crucial for the control of the disease. The data from Kazakhstan, Russia and Ukraine identified possible migratory routes for birds that may carry both virulent NDV (vNDV and NDV of low virulence into Europe. In addition, related NDV strains were isolated from wild birds in Ukraine and Nigeria, and from birds in continental USA, Alaska, Russia, and Japan, identifying wild birds as a possible mechanism of intercontinental spread of NDV of low virulence. More recently, the detection of new sub-genotypes of vNDV suggests that a new, fifth, panzootic of ND has already originated in Southeast Asia, extended to the Middle East, and is now entering into Eastern Europe. Despite expected challenges when multiple independent laboratories interact, many scientists from the collaborating countries have successfully been trained by SEPRL on molecular diagnostics, best laboratory practices, and critical biosecurity protocols, providing our partners the capacity to further train other employees and to identify locally the viruses that cause this OIE listed disease. These and other collaborations with partners in Mexico, Bulgaria, Israel, and Tanzania have allowed SEPRL scientists to engage in field studies, to elucidate more aspects of ND epidemiology in endemic countries, and to understand the challenges that the scientists and field veterinarians in these countries face on a daily basis. Finally, new viral

  4. International Biological Engagement Programs Facilitate Newcastle Disease Epidemiological Studies

    Science.gov (United States)

    Miller, Patti J.; Dimitrov, Kiril M.; Williams-Coplin, Dawn; Peterson, Melanie P.; Pantin-Jackwood, Mary J.; Swayne, David E.; Suarez, David L.; Afonso, Claudio L.

    2015-01-01

    Infections of poultry species with virulent strains of Newcastle disease virus (NDV) cause Newcastle disease (ND), one of the most economically significant and devastating diseases for poultry producers worldwide. Biological engagement programs between the Southeast Poultry Research Laboratory (SEPRL) of the United States Department of Agriculture and laboratories from Russia, Pakistan, Ukraine, Kazakhstan, and Indonesia collectively have produced a better understanding of the genetic diversity and evolution of the viruses responsible for ND, which is crucial for the control of the disease. The data from Kazakhstan, Russia, and Ukraine identified possible migratory routes for birds that may carry both virulent NDV (vNDV) and NDV of low virulence into Europe. In addition, related NDV strains were isolated from wild birds in Ukraine and Nigeria, and from birds in continental USA, Alaska, Russia, and Japan, identifying wild birds as a possible mechanism of intercontinental spread of NDV of low virulence. More recently, the detection of new sub-genotypes of vNDV suggests that a new, fifth, panzootic of ND has already originated in Southeast Asia, extended to the Middle East, and is now entering into Eastern Europe. Despite expected challenges when multiple independent laboratories interact, many scientists from the collaborating countries have successfully been trained by SEPRL on molecular diagnostics, best laboratory practices, and critical biosecurity protocols, providing our partners the capacity to further train other employes and to identify locally the viruses that cause this OIE listed disease. These and other collaborations with partners in Mexico, Bulgaria, Israel, and Tanzania have allowed SEPRL scientists to engage in field studies, to elucidate more aspects of ND epidemiology in endemic countries, and to understand the challenges that the scientists and field veterinarians in these countries face on a daily basis. Finally, new viral characterization tools

  5. Studies on floral biology of passion fruit (passiflora spp.)

    International Nuclear Information System (INIS)

    Kishore, K.; Pathak, K.A.; Shukla, R.; Bharali, R.

    2010-01-01

    Floral biology of purple, yellow, giant and Passiflora foetida was studied at the ICAR Research Complex, Mizoram Centre, Kolasib, Mizoram, India during 2005-07. Purple, giant and P. foetida had major bloom during March-April, July-August and September-October. While major bloom in yellow was mainly during May-June and September-October. Purple, giant and P. foetida had the maximum duration of bloom of 42.4, 22.5 and 32.6 days, respectively during March-April with the maximum duration of effective bloom of 12.5 8.6 and 10.4 days in purple, giant and P. foetida, respectively. Yellow had the maximum duration of bloom for 28.4 days and effective bloom of 10.5 days during May-June. Most of the flowers of purple (54.5%) and giant (58.5%) opened between 6-7 hrs, while the maximum per cent of anthesis in yellow (70%) took place between 12-13 hrs. Pollen dehiscence and pollination in purple and giant mainly occurred between 7-8 hrs, while 13-14 hrs was the major period of pollen dehiscence and pollination in yellow. The earliest anthesis (5-6 hrs), anther dehiscence (6-7 hrs) and pollination (6-7 hrs) were recorded in P. foetida. The maximum stigma receptivity was recorded on the day of anthesis in all the passion fruits. Completely curved style was more common in all passion fruits that gave the maximum fruit set. The maximum number of bees observed between 7-8 hrs in purple and giant and between 13-14 hrs in yellow. The most common pollinating bee in purple, giant and yellow was Apis mellifera, while A. cerena was in P. foetida. (author)

  6. International Biological Engagement Programs Facilitate Newcastle Disease Epidemiological Studies.

    Science.gov (United States)

    Miller, Patti J; Dimitrov, Kiril M; Williams-Coplin, Dawn; Peterson, Melanie P; Pantin-Jackwood, Mary J; Swayne, David E; Suarez, David L; Afonso, Claudio L

    2015-01-01

    Infections of poultry species with virulent strains of Newcastle disease virus (NDV) cause Newcastle disease (ND), one of the most economically significant and devastating diseases for poultry producers worldwide. Biological engagement programs between the Southeast Poultry Research Laboratory (SEPRL) of the United States Department of Agriculture and laboratories from Russia, Pakistan, Ukraine, Kazakhstan, and Indonesia collectively have produced a better understanding of the genetic diversity and evolution of the viruses responsible for ND, which is crucial for the control of the disease. The data from Kazakhstan, Russia, and Ukraine identified possible migratory routes for birds that may carry both virulent NDV (vNDV) and NDV of low virulence into Europe. In addition, related NDV strains were isolated from wild birds in Ukraine and Nigeria, and from birds in continental USA, Alaska, Russia, and Japan, identifying wild birds as a possible mechanism of intercontinental spread of NDV of low virulence. More recently, the detection of new sub-genotypes of vNDV suggests that a new, fifth, panzootic of ND has already originated in Southeast Asia, extended to the Middle East, and is now entering into Eastern Europe. Despite expected challenges when multiple independent laboratories interact, many scientists from the collaborating countries have successfully been trained by SEPRL on molecular diagnostics, best laboratory practices, and critical biosecurity protocols, providing our partners the capacity to further train other employes and to identify locally the viruses that cause this OIE listed disease. These and other collaborations with partners in Mexico, Bulgaria, Israel, and Tanzania have allowed SEPRL scientists to engage in field studies, to elucidate more aspects of ND epidemiology in endemic countries, and to understand the challenges that the scientists and field veterinarians in these countries face on a daily basis. Finally, new viral characterization tools

  7. Yeast as a Model System to Study Tau Biology

    Directory of Open Access Journals (Sweden)

    Ann De Vos

    2011-01-01

    Full Text Available Hyperphosphorylated and aggregated human protein tau constitutes a hallmark of a multitude of neurodegenerative diseases called tauopathies, exemplified by Alzheimer's disease. In spite of an enormous amount of research performed on tau biology, several crucial questions concerning the mechanisms of tau toxicity remain unanswered. In this paper we will highlight some of the processes involved in tau biology and pathology, focusing on tau phosphorylation and the interplay with oxidative stress. In addition, we will introduce the development of a human tau-expressing yeast model, and discuss some crucial results obtained in this model, highlighting its potential in the elucidation of cellular processes leading to tau toxicity.

  8. Trimethylamine-N-oxide: its hydration structure, surface activity, and biological function, viewed by vibrational spectroscopy and molecular dynamics simulations.

    Science.gov (United States)

    Ohto, Tatsuhiko; Hunger, Johannes; Backus, Ellen H G; Mizukami, Wataru; Bonn, Mischa; Nagata, Yuki

    2017-03-08

    The osmolyte molecule trimethylamine-N-oxide (TMAO) stabilizes the structure of proteins. As functional proteins are generally found in aqueous solutions, an important aspect of this stabilization is the interaction of TMAO with water. Here, we review, using vibrational spectroscopy and molecular dynamics simulations, recent studies on the structure and dynamics of TMAO with its surrounding water molecules. This article ends with an outlook on the open questions on TMAO-protein and TMAO-urea interactions in aqueous environments.

  9. Future Directions of Nonlinear Dynamics in PhysicaL and Biological Systems,

    Science.gov (United States)

    1992-01-01

    the Comision Interministerial de Ciencia y Tecnologia (Spain) under Grant No. TIC 73/89. REFERENCES [1] Yu.S. Kivshar, Zhang Fei, and L. Vizquez, Phys...DYNAMICS Controlling Chaos in Hamiltonian Systems ........................... 129 Y .-C. Lai, M. Ding, and C. Grebogi Deterministic Disorder in Two...all Oi satisfy the following linear differential equations for n = 1 2,..- 8 ,0- , = a n ’ ( 5 ) where xi = x, X2 = Y , x3 = t, Here we note that the

  10. Boom-bust dynamics in biological invasions: towards an improved application of the concept

    Czech Academy of Sciences Publication Activity Database

    Strayer, D.L.; D'Antonio, C. M.; Essl, F.; Fowler, M. S.; Geist, J.; Hilt, S.; Jaric, I.; Jöhnk, K.; Jones, C. G.; Lambin, X.; Latzka, A. W.; Pergl, Jan; Pyšek, Petr; Robertson, P.; von Schmalensee, M.; Stefansson, R. A.; Wright, J.; Jeschke, J.M.

    2017-01-01

    Roč. 20, č. 10 (2017), s. 1337-1350 ISSN 1461-023X R&D Projects: GA ČR GA17-19025S; GA ČR GB14-36079G Grant - others:AV ČR(CZ) AP1002 Program:Akademická prémie - Praemium Academiae Institutional support: RVO:67985939 Keywords : invasions * population dynamics * alien species Subject RIV: EH - Ecology, Behaviour OBOR OECD: Ecology Impact factor: 9.449, year: 2016

  11. Dynamics and thermodynamics in hierarchically organized systems applications in physics, biology and economics

    CERN Document Server

    Auger, P

    2013-01-01

    One of the most fundamental and efficient ways of conceptualizing complex systems is to organize them hierarchically. A hierarchically organized system is represented by a network of interconnected subsystems, each of which has its own network of subsystems, and so on, until some elementary subsystems are reached that are not further decomposed. This original and important book proposes a general mathematical theory of a hierarchical system and shows how it can be applied to very different topics such as physics (Hamiltonian systems), biology (coupling the molecular and the cellular levels), e

  12. From systems biology to dynamical neuropharmacology: proposal for a new methodology.

    Science.gov (United States)

    Erdi, P; Kiss, T; Tóth, J; Ujfalussy, B; Zalányi, L

    2006-07-01

    The concepts and methods of systems biology are extended to neuropharmacology in order to test and design drugs for the treatment of neurological and psychiatric disorders. Computational modelling by integrating compartmental neural modelling techniques and detailed kinetic descriptions of pharmacological modulation of transmitter-receptor interaction is offered as a method to test the electrophysiological and behavioural effects of putative drugs. Even more, an inverse method is suggested as a method for controlling a neural system to realise a prescribed temporal pattern. In particular, as an application of the proposed new methodology, a computational platform is offered to analyse the generation and pharmacological modulation of theta rhythm related to anxiety.

  13. Studies on the fisheries and biology of Oreochromis urolepsis ...

    African Journals Online (AJOL)

    The fisheries and some aspects of the biology of Oreochromis urolepsis of the Mtera Reservoir (Tanzania) were examined in August 2002. It was observed that there was no proper management of the reservoir\\'s fisheries. Beach seine fishing dominated the fishery. Nearly all the O. urolepsis caught by this type of gear were ...

  14. Deep learning: Using machine learning to study biological vision

    OpenAIRE

    Majaj, Najib; Pelli, Denis

    2017-01-01

    Today most vision-science presentations mention machine learning. Many neuroscientists use machine learning to decode neural responses. Many perception scientists try to understand recognition by living organisms. To them, machine learning offers a reference of attainable performance based on learned stimuli. This brief overview of the use of machine learning in biological vision touches on its strengths, weaknesses, milestones, controversies, and current directions.

  15. Mössbauer study of some biological iron complexes

    Indian Academy of Sciences (India)

    Abstract. Some biological complexes containing iron are investigated experimentally at room temperature using the Mössbauer resonance. The complexes show quadrupole doublet and Kramer's degeneracy is found to exist. The electric field gradient, difference in s-electron densities and quadrupole coupling constant ...

  16. Dynamics of proteins and of their hydration layer studied by neutron scattering and additional biophysical methods

    International Nuclear Information System (INIS)

    Gallat, Francois-Xavier

    2011-01-01

    This thesis work focused on the dynamics of proteins, surrounded by their hydration layer, a water shell around the protein vital for its biological function. Each of these components is accompanied by a specific dynamics which union reforms the complex energy landscape of the system. The joint implementation of selective deuteration, incoherent neutron scattering and tera-hertz spectroscopy allowed to explore the dynamics of proteins and that of the hydration shell. The influence of the folding state of protein on its dynamics has been studied by elastic neutron scattering. Globular proteins were less dynamic than its intrinsically disordered analogues. Themselves appear to be stiffer than non-physiological unfolded proteins. The oligomerization state and the consequences on the dynamics were investigated. Aggregates of a globular protein proved to be more flexible than the soluble form. In contrast, aggregates of a disordered protein showed lower average dynamics compared to the soluble form. These observations demonstrate the wide range of dynamics among the proteome. Incoherent neutron scattering experiences on the hydration layer of globular and disordered proteins have yielded information on the nature of water motion around these proteins. The measurements revealed the presence of translational motions concomitant with the onset of the transition dynamics of hydration layers, at 220 K. Measurements have also shown a stronger coupling between a disordered protein and its hydration water, compared to a globular protein and its hydration shell. The nature of the hydration layer and its influence on its dynamics has been explored with the use of polymers that mimic the water behavior and that act as a source of flexibility for the protein. Eventually, the dynamics of methyl groups involved in the dynamical changes observed at 150 and 220 K, was investigated. (author) [fr

  17. Final report for NIF chamber dynamics studies

    International Nuclear Information System (INIS)

    Burnham, A; Peterson, P F; Scott, J M

    1998-01-01

    The National Ignition Facility (NIF), a 1.8 MJ, 192 laser beam facility, will have anticipated fusion yields of up to 20 MJ from D-T pellets encased in a gold hohlraum target. The energy emitted from the target in the form of x rays, neutrons, target debris kinetic energy, and target shrapnel will be contained in a 5 m. radius spherical target chamber. various diagnostics will be stationed around the target at varying distances from the target. During each shot, the target will emit x rays that will vaporize nearby target facing surfaces including those of the diagnostics, the target positioner, and other chamber structures. This ablated vapor will be transported throughout the chamber, and will eventually condense and deposit on surfaces in the chamber, including the final optics debris shields. The research at the University of California at Berkeley relates primarily to the NIF chamber dynamics. The key design issues are the ablation of the chamber structures, transport of the vapor through the chamber and the condensation or deposition processes of those vaporized materials. An understanding of these processes is essential in developing a concept for protecting the fina optics debris shields from an excessive coating (> 10 A) of target debris and ablated material, thereby prolonging their lifetime between change-outs. At Berkeley, we have studied the physical issues of the ablation process and the effects of varying materials, the condensation process of the vaporized material, and design schemes that can lower the threat posed to the debris shields by these processes. The work or portions of the work completed this year have been published in several papers and a dissertation [l-5

  18. Raman spectroscopic study of reaction dynamics

    Science.gov (United States)

    MacPhail, R. A.

    1990-12-01

    The Raman spectra of reacting molecules in liquids can yield information about various aspects of the reaction dynamics. The author discusses the analysis of Raman spectra for three prototypical unimolecular reactions, the rotational isomerization of n-butane and 1,2-difluoroethane, and the barrierless exchange of axial and equatorial hydrogens in cyclopentane via pseudorotation. In the first two cases the spectra are sensitive to torsional oscillations of the gauche conformer, and yield estimates of the torsional solvent friction. In the case of cyclopentane, the spectra can be used to discriminate between different stochastic models of the pseudorotation dynamics, and to determine the relevant friction coefficients.

  19. Inference problems in structural biology

    DEFF Research Database (Denmark)

    Olsson, Simon

    The structure and dynamics of biological molecules are essential for their function. Consequently, a wealth of experimental techniques have been developed to study these features. However, while experiments yield detailed information about geometrical features of molecules, this information is of...

  20. Utility rate equations of group population dynamics in biological and social systems.

    Directory of Open Access Journals (Sweden)

    Vyacheslav I Yukalov

    Full Text Available We present a novel system of equations to describe the evolution of self-organized structured societies (biological or human composed of several trait groups. The suggested approach is based on the combination of ideas employed in the theory of biological populations, system theory, and utility theory. The evolution equations are defined as utility rate equations, whose parameters are characterized by the utility of each group with respect to the society as a whole and by the mutual utilities of groups with respect to each other. We analyze in detail the cases of two groups (cooperators and defectors and of three groups (cooperators, defectors, and regulators and find that, in a self-organized society, neither defectors nor regulators can overpass the maximal fractions of about [Formula: see text] each. This is in agreement with the data for bee and ant colonies. The classification of societies by their distance from equilibrium is proposed. We apply the formalism to rank the countries according to the introduced metric quantifying their relative stability, which depends on the cost of defectors and regulators as well as their respective population fractions. We find a remarkable concordance with more standard economic ranking based, for instance, on GDP per capita.

  1. Unleashing elastic energy: dynamics of energy release in rubber bands and impulsive biological systems

    Science.gov (United States)

    Ilton, Mark; Cox, Suzanne; Egelmeers, Thijs; Patek, S. N.; Crosby, Alfred J.

    Impulsive biological systems - which include mantis shrimp, trap-jaw ants, and venus fly traps - can reach high speeds by using elastic elements to store and rapidly release energy. The material behavior and shape changes critical to achieving rapid energy release in these systems are largely unknown due to limitations of materials testing instruments operating at high speed and large displacement. In this work, we perform fundamental, proof-of-concept measurements on the tensile retraction of elastomers. Using high speed imaging, the kinematics of retraction are measured for elastomers with varying mechanical properties and geometry. Based on the kinematics, the rate of energy dissipation in the material is determined as a function of strain and strain-rate, along with a scaling relation which describes the dependence of maximum velocity on material properties. Understanding this scaling relation along with the material failure limits of the elastomer allows the prediction of material properties required for optimal performance. We demonstrate this concept experimentally by optimizing for maximum velocity in our synthetic model system, and achieve retraction velocities that exceed those in biological impulsive systems. This model system provides a foundation for future work connecting continuum performance to molecular architecture in impulsive systems.

  2. Biological and physical induced oxygen dynamics in melting sea ice of the Fram Strait

    DEFF Research Database (Denmark)

    Glud, Ronnie; Rysgaard, Søren; Turner, Gavin

    2014-01-01

    correlation (EC) measurements on the underside of the ice revealed a light-dependent O2 exchange rate. However, the integrated signal resolved a net O2 uptake of 7.70 mmol m−2 d−1. The net O2 exchange was therefore dominated by the production of O2-depleted meltwater rather than biological activity. The EC......We investigated the production, consumption, and exchange of O2 in melting sea ice to assess the biological- and physical-induced O2 turnover. The underside of the ice was covered with 5–20 cm3 large, buoyant algal aggregates. Their gross primary production amounted to 0.49 mmol C m−2 d−1, which...... was 4.5 times higher than the primary production of sea ice–encrusted microalgae (0.11 mmol C m−2 d−1). The phototrophic biomass of the aggregates (2.94 mg chlorophyll a m−2) was six times higher than that encountered in the sea ice itself. Taxono-specific investigations strongly suggest...

  3. The relative contributions of biological and abiotic processes to carbon dynamics in subarctic sea ice

    DEFF Research Database (Denmark)

    Søgaard, Dorte Haubjerg; Thomas, David; Rysgaard, Søren

    2013-01-01

    Knowledge on the relative effects of biological activity and precipitation/dissolution of calcium carbonate (CaCO3) in influencing the air-ice CO2 exchange in sea-ice-covered season is currently lacking. Furthermore, the spatial and temporal occurrence of CaCO3 and other biogeochemical parameters...... in sea ice are still not well described. Here we investigated autotrophic and heterotrophic activity as well as the precipitation/dissolution of CaCO3 in subarctic sea ice in South West Greenland. Integrated over the entire ice season (71 days), the sea ice was net autotrophic with a net carbon fixation...... and CaCO3 precipitation. The net biological production could only explain 4 % of this sea-ice-driven CO2 uptake. Abiotic processes contributed to an air-sea CO2 uptake of 1.5 mmol m(-2) sea ice day(-1), and dissolution of CaCO3 increased the air-sea CO2 uptake by 36 % compared to a theoretical estimate...

  4. Utility Rate Equations of Group Population Dynamics in Biological and Social Systems

    Science.gov (United States)

    Yukalov, Vyacheslav I.; Yukalova, Elizaveta P.; Sornette, Didier

    2013-01-01

    We present a novel system of equations to describe the evolution of self-organized structured societies (biological or human) composed of several trait groups. The suggested approach is based on the combination of ideas employed in the theory of biological populations, system theory, and utility theory. The evolution equations are defined as utility rate equations, whose parameters are characterized by the utility of each group with respect to the society as a whole and by the mutual utilities of groups with respect to each other. We analyze in detail the cases of two groups (cooperators and defectors) and of three groups (cooperators, defectors, and regulators) and find that, in a self-organized society, neither defectors nor regulators can overpass the maximal fractions of about each. This is in agreement with the data for bee and ant colonies. The classification of societies by their distance from equilibrium is proposed. We apply the formalism to rank the countries according to the introduced metric quantifying their relative stability, which depends on the cost of defectors and regulators as well as their respective population fractions. We find a remarkable concordance with more standard economic ranking based, for instance, on GDP per capita. PMID:24386163

  5. Ethnographic Observational Study of the Biologic Initiation Conversation Between Rheumatologists and Biologic-Naive Rheumatoid Arthritis Patients.

    Science.gov (United States)

    Kottak, Nicholas; Tesser, John; Leibowitz, Evan; Rosenberg, Melissa; Parenti, Dennis; DeHoratius, Raphael

    2018-01-30

    This ethnographic market research study investigated the biologic initiation conversation between rheumatologists and biologic-naive patients with rheumatoid arthritis to assess how therapy options, particularly mode of administration, were discussed. Consenting rheumatologists (n = 16) and patients (n = 48) were videotaped during medical visits and interviewed by a trained ethnographer. The content, structure, and timing of conversations regarding biologic initiation were analyzed. The mean duration of physician-patient visits was approximately 15 minutes; biologic therapies were discussed for a mean of 5.6 minutes. Subcutaneous (SC) and intravenous (IV) therapy options were mentioned in 45 and 35 visits, respectively, out of a total of 48 visits. All patients had some familiarity with SC administration, but nearly half of patients (22 of 48) were unfamiliar with IV therapy going into the visit. IV administration was not defined or described by rheumatologists in 77% of visits (27 of 35) mentioning IV therapy. Thus, 19 of 22 patients who were initially unfamiliar with IV therapy remained unfamiliar after the visit. Disparities in physician-patient perceptions were revealed, as all rheumatologists (16 of 16) believed IV therapy would be less convenient than SC therapy for patients, while 46% of patients (22 of 48) felt this way. In post-visit interviews, some patients seemed confused and overwhelmed, particularly when presented with many treatment choices in a visit. Some patients stated they would benefit from visual aids or summary sheets of key points. This study revealed significant educational opportunities to improve the biologic initiation conversation and indicated a disparity between patients' and rheumatologists' perception of IV therapy. © 2018 The Authors. Arthritis Care & Research published by Wiley Periodicals, Inc. on behalf of American College of Rheumatology.

  6. Rotational coherence spectroscopy at FLASH. Toward dynamic studies in nanosuperfluids

    Energy Technology Data Exchange (ETDEWEB)

    Kickermann, Andreas

    2013-07-15

    The field of molecular physics, which is focusing on molecular motion in the transition states of physical, chemical, and biological changes, is a wide-spread research area. It strives to reveal the structural and functional properties of molecules, the chemical bonds between atoms and the time evolution. Many processes occurring in nature upon electronic excitation proceed on the ultrafast femtosecond timescale and can be triggered by modern ultrashort femtosecond-laser sources under laboratory conditions. In the present thesis pump-probe studies were performed to follow molecular motion using ultrashort light pulses in the nanometer wavelength range provided by an XUV freeelectron laser (FEL). In detail, alignment of molecular species in space under field-free conditions was investigated. In the specific case of rotational wave packets in molecules the rotational dynamics shows characteristic temporal features, which contain a wealth of information on molecular structure and give insight into molecular coupling mechanisms, i.e. rotational constants and transition frequencies. Within this thesis, Rotational Coherence Spectroscopy (RCS) reveals wave-packet motion observed by subsequent Coulomb explosion of Raman excited carbon monoxide, which results in a time-dependent asymmetry of spatial fragmentation patterns. With the method presented here, the time resolution to elucidate the fast dynamics of strong couplings can be pushed toward a single rotational period even for the fastest rotors. This is due to large pump-probe delays with small subpicosecond step size. This kind of spectroscopy can also be expanded to molecular species, which are not accessible by other powerful spectroscopic methods, such as Fourier-transform microwave spectroscopy (FTMW). Furthermore, it allows to measure weak molecular couplings on a long timescale (large pump-probe delays), e.g. couplings of molecules in a solution or molecules dissolved in quantum fluids. This is valuable to

  7. Rotational coherence spectroscopy at FLASH. Toward dynamic studies in nanosuperfluids

    International Nuclear Information System (INIS)

    Kickermann, Andreas

    2013-07-01

    The field of molecular physics, which is focusing on molecular motion in the transition states of physical, chemical, and biological changes, is a wide-spread research area. It strives to reveal the structural and functional properties of molecules, the chemical bonds between atoms and the time evolution. Many processes occurring in nature upon electronic excitation proceed on the ultrafast femtosecond timescale and can be triggered by modern ultrashort femtosecond-laser sources under laboratory conditions. In the present thesis pump-probe studies were performed to follow molecular motion using ultrashort light pulses in the nanometer wavelength range provided by an XUV freeelectron laser (FEL). In detail, alignment of molecular species in space under field-free conditions was investigated. In the specific case of rotational wave packets in molecules the rotational dynamics shows characteristic temporal features, which contain a wealth of information on molecular structure and give insight into molecular coupling mechanisms, i.e. rotational constants and transition frequencies. Within this thesis, Rotational Coherence Spectroscopy (RCS) reveals wave-packet motion observed by subsequent Coulomb explosion of Raman excited carbon monoxide, which results in a time-dependent asymmetry of spatial fragmentation patterns. With the method presented here, the time resolution to elucidate the fast dynamics of strong couplings can be pushed toward a single rotational period even for the fastest rotors. This is due to large pump-probe delays with small subpicosecond step size. This kind of spectroscopy can also be expanded to molecular species, which are not accessible by other powerful spectroscopic methods, such as Fourier-transform microwave spectroscopy (FTMW). Furthermore, it allows to measure weak molecular couplings on a long timescale (large pump-probe delays), e.g. couplings of molecules in a solution or molecules dissolved in quantum fluids. This is valuable to

  8. Dynamic Aperture Studies for SPEAR 3

    International Nuclear Information System (INIS)

    Nosochkov, Yuri

    1999-01-01

    The SSRL is investigating an accelerator upgrade project to replace the present 130 nm.rad FODO lattice with an 18 nm.rad double bend achromat lattice: SPEAR 3. In this paper, we review the methods used to maximize the SPEAR 3 dynamic aperture including optimization of linear optics, betatron tune, chromaticity and coupling correction, and effects of machine errors and insertion devices

  9. Excess water dynamics in hydrotalcite: QENS study

    Indian Academy of Sciences (India)

    dynamics of excess water in hydrotalcite sample with varied content of excess water are reported. Translational motion of excess water can be best described by random transla- tional jump diffusion model. The observed increase in translational diffusivity with increase in the amount of excess water is attributed to the ...

  10. Dynamic impact indentation of hydrated biological tissues and tissue surrogate gels

    Science.gov (United States)

    Ilke Kalcioglu, Z.; Qu, Meng; Strawhecker, Kenneth E.; Shazly, Tarek; Edelman, Elazer; VanLandingham, Mark R.; Smith, James F.; Van Vliet, Krystyn J.

    2011-03-01

    For both materials engineering research and applied biomedicine, a growing need exists to quantify mechanical behaviour of tissues under defined hydration and loading conditions. In particular, characterisation under dynamic contact-loading conditions can enable quantitative predictions of deformation due to high rate 'impact' events typical of industrial accidents and ballistic insults. The impact indentation responses were examined of both hydrated tissues and candidate tissue surrogate materials. The goals of this work were to determine the mechanical response of fully hydrated soft tissues under defined dynamic loading conditions, and to identify design principles by which synthetic, air-stable polymers could mimic those responses. Soft tissues from two organs (liver and heart), a commercially available tissue surrogate gel (Perma-Gel™) and three styrenic block copolymer gels were investigated. Impact indentation enabled quantification of resistance to penetration and energy dissipative constants under the rates and energy densities of interest for tissue surrogate applications. These analyses indicated that the energy dissipation capacity under dynamic impact increased with increasing diblock concentration in the styrenic gels. Under the impact rates employed (2 mm/s to 20 mm/s, corresponding to approximate strain energy densities from 0.4 kJ/m3 to 20 kJ/m3), the energy dissipation capacities of fully hydrated soft tissues were ultimately well matched by a 50/50 triblock/diblock composition that is stable in ambient environments. More generally, the methodologies detailed here facilitate further optimisation of impact energy dissipation capacity of polymer-based tissue surrogate materials, either in air or in fluids.

  11. Catalytic performances of chemically immobilized urease under static and dynamic conditions: A comparative study

    OpenAIRE

    Yürekli, Yılmaz; Alsoy Altınkaya, Sacide

    2011-01-01

    Immobilized urease has been used for direct removal of urea from aqueous solution and as biological sensing material in the preparation of urea biosensors. The former application is carried out under dynamic condition using ultrafiltration membrane either in tubular form or in flat sheet, while the latter is used in static condition. In this study, the performance of chemically immobilized urease on poly(acrylonitrile-co-sodium methallyl sulfonate) ultrafiltration membrane was determined unde...

  12. Remote sensing of the biological dynamics of large-scale salt evaporation ponds

    Science.gov (United States)

    Richardson, Laurie L.; Bachoon, Dave; Ingram-Willey, Vebbra; Chow, Colin C.; Weinstock, Kenneth

    1992-01-01

    Optical properties of salt evaporation ponds associated with Exportadora de Sal, a salt production company in Baja California Sur, Mexico, were analyzed using a combination of spectroradiometer and extracted pigment data, and Landsat-5 Thematic Mapper imagery. The optical characteristics of each pond are determined by the biota, which consists of dense populations of algae and photosynthetic bacteria containing a wide variety of photosynthetic and photoprotective pigments. Analysis has shown that spectral and image data can differentiate between taxonomic groups of the microbiota, detect changes in population distributions, and reveal large-scale seasonal dynamics.

  13. Biological control and invading freshwater snails. A case study.

    Science.gov (United States)

    Pointier, J P; Augustin, D

    1999-12-01

    Introductions of four species of freshwater snails occurred between 1972 and 1996 onto Guadeloupe Island. Two of them, Melanoides tuberculata and Marisa cornuarietis, were subsequently used as biological control agents against Biomphalaria glabrata, the snail intermediate host of intestinal schistosomiasis. In 1996, a general survey was carried out in 134 sites which had already been investigated in 1972. The total number of mollusc species had increased from 19 to 21. Site numbers housing B. glabrata and two other species had strongly declined. This decline may be mainly attributed to a competitive displacement by M. tuberculata and M. cornuarietis as illustrated by several biological control programmes. There were no changes in the remainder of the malacological fauna.

  14. Biological dynamic lighting in an office building; Biologisch dynamische verlichting in een kantoorgebouw

    Energy Technology Data Exchange (ETDEWEB)

    Visser, R. [Professional Lighting Designers' Association PLDA, Guetersloh (Germany)

    2011-12-15

    The aim of so-called biodynamic lighting systems is to influence human biological rhythms such that productivity, alertness, wellbeing and health are improved. In the office building of Grontmij in Amersfoort, Netherlands, experiments were carried out with biodynamic lighting systems. [Dutch] In de afgelopen jaren hebben verschillende fabrikanten biologisch dynamische verlichtingssystemen op de markt gebracht. Uitgangspunt voor dergelijke systemen is om biologische ritmen van de mens zodanig te beinvloeden dat productiviteit, alertheid, welbevinden en ook de gezondheid in meer of mindere mate verbeteren. Om ervaring in de kantooromgeving op te doen, is een aantal van deze systemen op diverse locaties in het gebouw van de Grontmij in Amersfoort aangebracht. Vervolgens is onderzoek gedaan naar de toepassingsmogelijkheden en eigenschappen ervan in de praktijk.

  15. Study on biological dosimetry of premature chromosome condensation technique

    International Nuclear Information System (INIS)

    Jiang Bo

    2005-01-01

    The premature chromosome condensation technique has been applied for biological dosimetry purpose. Premature chromo-some condensation was induced by incubating unstimulated human peripheral blood lymphocytes in the presence of okadaic acid or calyculin A (a phosphatase inhibitor) which eliminated the need for fusion with mitotic cells. It is now possible to examine the early damage induced by radiation. It is simple, exact when it combines with fluorecence in situ hybridization. (authors)

  16. Studies on marine toxins: chemical and biological aspects

    International Nuclear Information System (INIS)

    Stonik, Valentin A; Stonik, Inna V

    2010-01-01

    The structures and mechanisms of biological action of the best known representatives of the main groups of marine toxins are presented. It is shown that many compounds have complex chemical structures and possess extremely high toxicities. Characteristic features of isolation, structure determination and syntheses of these compounds using the achievement of modern organic chemistry are discussed. The methods of identification and quantitative analysis of marine toxins are briefly reviewed.

  17. Recent advances in applying mass spectrometry and systems biology to determine brain dynamics.

    Science.gov (United States)

    Scifo, Enzo; Calza, Giulio; Fuhrmann, Martin; Soliymani, Rabah; Baumann, Marc; Lalowski, Maciej

    2017-06-01

    Neurological disorders encompass various pathologies which disrupt normal brain physiology and function. Poor understanding of their underlying molecular mechanisms and their societal burden argues for the necessity of novel prevention strategies, early diagnostic techniques and alternative treatment options to reduce the scale of their expected increase. Areas covered: This review scrutinizes mass spectrometry based approaches used to investigate brain dynamics in various conditions, including neurodegenerative and neuropsychiatric disorders. Different proteomics workflows for isolation/enrichment of specific cell populations or brain regions, sample processing; mass spectrometry technologies, for differential proteome quantitation, analysis of post-translational modifications and imaging approaches in the brain are critically deliberated. Future directions, including analysis of cellular sub-compartments, targeted MS platforms (selected/parallel reaction monitoring) and use of mass cytometry are also discussed. Expert commentary: Here, we summarize and evaluate current mass spectrometry based approaches for determining brain dynamics in health and diseases states, with a focus on neurological disorders. Furthermore, we provide insight on current trends and new MS technologies with potential to improve this analysis.

  18. Studying protein assembly with reversible Brownian dynamics of patchy particles

    International Nuclear Information System (INIS)

    Klein, Heinrich C. R.; Schwarz, Ulrich S.

    2014-01-01

    Assembly of protein complexes like virus shells, the centriole, the nuclear pore complex, or the actin cytoskeleton is strongly determined by their spatial structure. Moreover, it is becoming increasingly clear that the reversible nature of protein assembly is also an essential element for their biological function. Here we introduce a computational approach for the Brownian dynamics of patchy particles with anisotropic assemblies and fully reversible reactions. Different particles stochastically associate and dissociate with microscopic reaction rates depending on their relative spatial positions. The translational and rotational diffusive properties of all protein complexes are evaluated on-the-fly. Because we focus on reversible assembly, we introduce a scheme which ensures detailed balance for patchy particles. We then show how the macroscopic rates follow from the microscopic ones. As an instructive example, we study the assembly of a pentameric ring structure, for which we find excellent agreement between simulation results and a macroscopic kinetic description without any adjustable parameters. This demonstrates that our approach correctly accounts for both the diffusive and reactive processes involved in protein assembly

  19. Studying protein assembly with reversible Brownian dynamics of patchy particles

    Energy Technology Data Exchange (ETDEWEB)

    Klein, Heinrich C. R. [Institute for Theoretical Physics, Heidelberg University, 69120 Heidelberg (Germany); Schwarz, Ulrich S., E-mail: ulrich.schwarz@bioquant.uni-heidelberg.de [Institute for Theoretical Physics, Heidelberg University, 69120 Heidelberg (Germany); BioQuant, Heidelberg University, 69120 Heidelberg (Germany)

    2014-05-14

    Assembly of protein complexes like virus shells, the centriole, the nuclear pore complex, or the actin cytoskeleton is strongly determined by their spatial structure. Moreover, it is becoming increasingly clear that the reversible nature of protein assembly is also an essential element for their biological function. Here we introduce a computational approach for the Brownian dynamics of patchy particles with anisotropic assemblies and fully reversible reactions. Different particles stochastically associate and dissociate with microscopic reaction rates depending on their relative spatial positions. The translational and rotational diffusive properties of all protein complexes are evaluated on-the-fly. Because we focus on reversible assembly, we introduce a scheme which ensures detailed balance for patchy particles. We then show how the macroscopic rates follow from the microscopic ones. As an instructive example, we study the assembly of a pentameric ring structure, for which we find excellent agreement between simulation results and a macroscopic kinetic description without any adjustable parameters. This demonstrates that our approach correctly accounts for both the diffusive and reactive processes involved in protein assembly.

  20. Biological and analytical studies of peritoneal dialysis solutions

    Directory of Open Access Journals (Sweden)

    N. Hudz

    2018-04-01

    Full Text Available The purpose of our work was to conduct biological and analytical studies of the peritoneal dialysis (PD solutions containing glucose and sodium lactate and establish correlations between cell viability of the Vero cell line and values of analytical indexes of the tested solutions. The results of this study confirm the cytotoxicity of the PD solutions even compared with the isotonic solution of sodium chloride, which may be due to the low pH of the solutions, presence of glucose degradation products (GDPs and high osmolarity of the solutions, and unphysiological concentrations of glucose and sodium lactate. However, it is not yet known what factors or their combination and to what extent cause the cytotoxicity of PD solutions. In the neutral red (NR test the weak, almost middle (r = -0.496 and 0.498, respectively and unexpected correlations were found between reduced viability of monkey kidney cells and increased pH of the PD solutions and between increased cell viability and increased absorbance at 228 nm of the tested PD solutions. These two correlations can be explained by a strong correlation (r = -0.948 between a decrease in pH and an increase in the solution absorbance at 228 nm. The opposite effect was observed in the MTT test. The weak, but expected correlations (r = 0.32 and -0.202, respectively were found between increased cell viability and increased pH in the PD solutions and between decreased cell viability and increased absorbance at 228 nm of the tested PD solutions. The middle and weak correlations (r = 0.56 and 0.29, respectively were detected between increased cell viability and increased lactate concentration in the NR test and MTT test. The data of these correlations can be partially explained by the fact that a correlation with a coefficient r = -0.34 was found between decreased pH in the solutions and increased lactate concentration. The very weak correlations (0.138 and 0.196, respectively were found between increased cell

  1. Analysis of spatiotemporal metabolomic dynamics for sensitively monitoring biological alterations in cisplatin-induced acute kidney injury.

    Science.gov (United States)

    Irie, Miho; Hayakawa, Eisuke; Fujimura, Yoshinori; Honda, Youhei; Setoyama, Daiki; Wariishi, Hiroyuki; Hyodo, Fuminori; Miura, Daisuke

    2018-01-29

    Clinical application of the major anticancer drug, cisplatin, is limited by severe side effects, especially acute kidney injury (AKI) caused by nephrotoxicity. The detailed metabolic mechanism is still largely unknown. Here, we used an integrated technique combining mass spectrometry imaging (MSI) and liquid chromatography-mass spectrometry (LC-MS) to visualize the diverse spatiotemporal metabolic dynamics in the mouse kidney after cisplatin dosing. Biological responses to cisplatin was more sensitively detected within 24 h as a metabolic alteration, which is much earlier than possible with the conventional clinical chemistry method of blood urea nitrogen (BUN) measurement. Region-specific changes (e.g., medulla and cortex) in metabolites related to DNA damage and energy generation were observed over the 72-h exposure period. Therefore, this metabolomics approach may become a novel strategy for elucidating early renal responses to cisplatin, prior to the detection of kidney damage evaluated by conventional method. Copyright © 2018. Published by Elsevier Inc.

  2. Dynamic Aperture Studies for SPEAR 3

    International Nuclear Information System (INIS)

    Corbett, William

    1998-01-01

    The Stanford Synchrotron Radiation Laboratory is investigating an accelerator upgrade project that would replace the present 130 nm rad FODO lattice with an 18 nm rad double bend achromat (DBA) lattice: SPEAR 3. The low emittance design yields a high brightness beam, but the stronger focusing in the DBA lattice increases chromaticity and beam sensitivity to machine errors. To ensure efficient injection and long Touschek lifetime, an optimization of the design lattice and dynamic aperture has been performed. In this paper, we review the methods used to maximize the SPEAR 3 dynamic aperture including necessary optics modifications, choice of tune and phase advance, optimization of sextupole and coupling correction, and modeling effects of machine errors, wigglers and lattice periodicity

  3. Dynamic aperture studies for SPEAR 3

    International Nuclear Information System (INIS)

    Nosochkov, Y.; Corbett, J.

    1999-01-01

    The Stanford Synchrotron Radiation Laboratory is investigating an accelerator upgrade project that would replace the present 130 nm·rad FODO lattice with an 18 nm·rad double bend achromat (DBA) lattice: SPEAR 3. The low emittance design yields a high brightness beam, but the stronger focusing in the DBA lattice increases chromaticity and beam sensitivity to machine errors. To ensure efficient injection and long Touschek lifetime, an optimization of the design lattice and dynamic aperture has been performed. In this paper, we review the methods used to maximize the SPEAR 3 dynamic aperture including necessary optics modifications, choice of tune and phase advance, optimization of sextupole and coupling correction, and modeling effects of machine errors, wigglers and lattice periodicity

  4. Sensitivity case study in dynamic reliability

    International Nuclear Information System (INIS)

    Kopustinskas, V.

    2001-01-01

    Recent trends in the risk assessments of the complex industrial plants show increased interest in dynamical models arising from the coupling of the probabilistic and deterministic approaches. Conventionally used static system models, represented by the fault/event trees can not reflect dynamic behaviour of the system and complex interaction between the process variables, components and human actions. The nature of the most complex industrial systems, like nuclear power plants (NPP) suggests that Markov type stochastic differential equations (SDEs) consisting of jump and drift components can be successfully used to represent and analyze the phenomena. This paper discuss possible applications of the SDEs in reliability problems. In particular, Accident Localization System (ALS) of the Ignalina NPP was analyzed as a benchmark for further investigations in this area. (author)

  5. Novel tendencies in developing small-angle neutron scattering methods for studying the structure of biological macromolecules

    International Nuclear Information System (INIS)

    Serdyuk, I.

    1995-01-01

    In recent 20 years thermal neutron scattering has been acknowledged an important instrument for structural studies in molecular biology. The methods of neutron diffraction of high resolution, which are not discussed in this paper, have already permitted to obtain a detailed representation of the course of proteolytic reactions and have arisen a number of new problems connected with the localization of water molecules and the H-D exchange. The methods of low resolution widely used due to a relative simplicity of the experiment have been successfully applied for both solving structural problems per se and investigating the changes in the structure when macromolecules perform their biological functions. The most promising are novel experimental approaches: the triple isotopic substitution method and the method of spin dynamic polarization. These methods ensure solving structural problems at a higher resolution than the dimensions of the macromolecules studied. Installation of new experimental instruments makes neutron measurements more accessible, and development of direct methods for interpretation of experimental data using the apparatus of spherical harmonics opens new possibilities for small-angle neutron scattering making it a necessary element for interpretation of diffraction data of monocrystals of intricate biological macromolecules. The paper presents a brief account of the tendencies in theoretical development and practical use of small-angle scattering for studying biological macromolecules. Special attention is given to the studies carried out in the Laboratory of Neutron Physics on a unique pulse IBR-2 reactor. (author) 14 refs

  6. Application of iterative reconstruction in dynamic studies

    International Nuclear Information System (INIS)

    Meikle, S.R.

    1998-01-01

    Full text: The conventional approach to analysing dynamic tomographic data (SPECT or PET) is to reconstruct projections corresponding to each time interval separately and then fit a suitable tracer kinetic model to the dynamic sequence (method 1 ) . This approach assumes that the tracer distribution remains static during any given time interval and, for practical reasons, filtered back-projection (FBP) is the preferred reconstruction algorithm. However, alternative approaches exist which lend themselves to iterative algorithms, such as EM. One approach is to fit the model directly to the projection data, followed by EM reconstruction of the parameter estimates (method 2). This requires that the tracer model can be expressed as a linear function of the unknown model parameters. A third alternative is to incorporate the tracer model into the reconstruction algorithm (method 3). Such an extension was described during the early development of the EM algorithm, referred to as the EM parametric image reconstruction algorithm (EM-PIRA). We have investigated these various strategies for analysing dynamic data and their relative pros and cons. Tracer modelling was performed using a general model, referred to as spectral analysis, which makes no restriction on the number of physiological compartments and satisfies the linearity requirement of method 2. A kinetic software phantom was created and used to test the convergence and noise properties of the different approaches. In summary, method 2 is the most practical as it reduces the number of reconstructions by at least an order of magnitude and provides improved signal-to-noise ratios compared with method 1. EM-PIRA allows greater flexibility in the choice of parametric images and appears to have a regularising effect on convergence. Methods 2 and 3 are also better suited to dynamic scanning with a rotating camera, as they can potentially account for changes in tracer distribution between projections

  7. Exploring Pedagogical Content Knowledge of Biology Graduate Teaching Assistants through Their Participation in Lesson Study

    Science.gov (United States)

    Lampley, Sandra A.; Gardner, Grant E.; Barlow, Angela T.

    2018-01-01

    Graduate teaching assistants (GTAs) are responsible for teaching the majority of biology undergraduate laboratory sections, although many feel underprepared to do so. This study explored the impact of biology GTA participation in a professional development model known as lesson study. Using a case study methodology with multiple qualitative data…

  8. 4D measurements of biological and synthetic structures using a dynamic interferometer

    Science.gov (United States)

    Toto-Arellano, Noel-Ivan

    2017-12-01

    Considering the deficiency of time elapsed for phase-stepping interferometric techniques and the need of developing non-contact and on-line measurement with high accuracy, a single-shot phase-shifting triple-interferometer (PSTI) is developed for analysis of characteristics of transparent structures and optical path difference (OPD) measurements. In the proposed PSTI, coupled three interferometers which generate four interference patterns, and a polarizer array is used as phase shifters to produce four spatially separated interferograms with π/2-phase shifts, which are recorded in a single capture by a camera. The configuration of the PSTI allows dynamic measurements (4D measurements) and does not require vibration isolation. We have applied the developed system to examine the size and OPD of cells, and the slope of thin films

  9. Dynamic simulation and modeling of the motion modes produced during the 3D controlled manipulation of biological micro/nanoparticles based on the AFM.

    Science.gov (United States)

    Saraee, Mahdieh B; Korayem, Moharam H

    2015-08-07

    Determining the motion modes and the exact position of a particle displaced during the manipulation process is of special importance. This issue becomes even more important when the studied particles are biological micro/nanoparticles and the goals of manipulation are the transfer of these particles within body cells, repair of cancerous cells and the delivery of medication to damaged cells. However, due to the delicate nature of biological nanoparticles and their higher vulnerability, by obtaining the necessary force of manipulation for the considered motion mode, we can prevent the sample from interlocking with or sticking to the substrate because of applying a weak force or avoid damaging the sample due to the exertion of excessive force. In this paper, the dynamic behaviors and the motion modes of biological micro/nanoparticles such as DNA, yeast, platelet and bacteria due to the 3D manipulation effect have been investigated. Since the above nanoparticles generally have a cylindrical shape, the cylindrical contact models have been employed in an attempt to more precisely model the forces exerted on the nanoparticle during the manipulation process. Also, this investigation has performed a comprehensive modeling and simulation of all the possible motion modes in 3D manipulation by taking into account the eccentricity of the applied load on the biological nanoparticle. The obtained results indicate that unlike the macroscopic scale, the sliding of nanoparticle on substrate in nano-scale takes place sooner than the other motion modes and that the spinning about the vertical and transverse axes and the rolling of nanoparticle occur later than the other motion modes. The simulation results also indicate that the applied force necessary for the onset of nanoparticle movement and the resulting motion mode depend on the size and aspect ratio of the nanoparticle. Copyright © 2015 Elsevier Ltd. All rights reserved.

  10. Increasing biological diversity in a dynamic vegetation model and consequences for simulated response to climate change

    Science.gov (United States)

    Keribin, R. M.; Friend, A. D.; Purves, D.; Smith, M. J.

    2013-12-01

    Vegetation, from tropical rainforests to the tundra, is the basis of the world food chain but is also a key component of the Earth system, with biophysical and biogeochemical impacts on the global climate, and Dynamic Global Vegetation Models (DGVMs) are an important integrative tool for understanding its responses to climate change. DGVMs up to now have treated only a small number of plant types representing broad divisions in vegetation worldwide (e.g. trees and grasses, broadleaf and needleleaf, deciduousness), but these categories ignore most of the variation that exists between plant species and between individuals within a species. Research in community ecology makes it clear however that these variations can affect large-scale ecosystem properties such as productivity and resilience to environmental changes. The current challenge is for DGVMs to account for fine-grained variations between plants and a few such models are being developed using newly-available plant trait databases such as the TRY database and insights from community ecology such as habitat filtering. Hybrid is an individual-based DGVM, first published in 1993, that models plant physiology in a mechanistic way. We modified Hybrid 8, the latest version of the model which uses surface physics taken from the GISS ModelE GCM, to include a mechanistic gap-model component with individual-based variation in tree wood density. This key plant trait is known to be strongly correlated with a trade-off between growth and mortality in the majority of forests worldwide, which allows for otherwise-similar individuals to have different life-history strategies. We investigate how the inclusion of continuous variation in wood density into the model affects the ecosystem's transient dynamics under climate change.

  11. Dynamic cyanobacterial response to hydration and dehydration in a desert biological soil crust.

    Science.gov (United States)

    Rajeev, Lara; da Rocha, Ulisses Nunes; Klitgord, Niels; Luning, Eric G; Fortney, Julian; Axen, Seth D; Shih, Patrick M; Bouskill, Nicholas J; Bowen, Benjamin P; Kerfeld, Cheryl A; Garcia-Pichel, Ferran; Brodie, Eoin L; Northen, Trent R; Mukhopadhyay, Aindrila

    2013-11-01

    Biological soil crusts (BSCs) cover extensive portions of the earth's deserts. In order to survive desiccation cycles and utilize short periods of activity during infrequent precipitation, crust microorganisms must rely on the unique capabilities of vegetative cells to enter a dormant state and be poised for rapid resuscitation upon wetting. To elucidate the key events involved in the exit from dormancy, we performed a wetting experiment of a BSC and followed the response of the dominant cyanobacterium, Microcoleus vaginatus, in situ using a whole-genome transcriptional time course that included two diel cycles. Immediate, but transient, induction of DNA repair and regulatory genes signaled the hydration event. Recovery of photosynthesis occurred within 1 h, accompanied by upregulation of anabolic pathways. Onset of desiccation was characterized by the induction of genes for oxidative and photo-oxidative stress responses, osmotic stress response and the synthesis of C and N storage polymers. Early expression of genes for the production of exopolysaccharides, additional storage molecules and genes for membrane unsaturation occurred before drying and hints at preparedness for desiccation. We also observed signatures of preparation for future precipitation, notably the expression of genes for anaplerotic reactions in drying crusts, and the stable maintenance of mRNA through dormancy. These data shed light on possible synchronization between this cyanobacterium and its environment, and provides key mechanistic insights into its metabolism in situ that may be used to predict its response to climate, and or, land-use driven perturbations.

  12. A non-homogeneous dynamic Bayesian network with sequentially coupled interaction parameters for applications in systems and synthetic biology.

    Science.gov (United States)

    Grzegorczyk, Marco; Husmeier, Dirk

    2012-07-12

    An important and challenging problem in systems biology is the inference of gene regulatory networks from short non-stationary time series of transcriptional profiles. A popular approach that has been widely applied to this end is based on dynamic Bayesian networks (DBNs), although traditional homogeneous DBNs fail to model the non-stationarity and time-varying nature of the gene regulatory processes. Various authors have therefore recently proposed combining DBNs with multiple changepoint processes to obtain time varying dynamic Bayesian networks (TV-DBNs). However, TV-DBNs are not without problems. Gene expression time series are typically short, which leaves the model over-flexible, leading to over-fitting or inflated inference uncertainty. In the present paper, we introduce a Bayesian regularization scheme that addresses this difficulty. Our approach is based on the rationale that changes in gene regulatory processes appear gradually during an organism's life cycle or in response to a changing environment, and we have integrated this notion in the prior distribution of the TV-DBN parameters. We have extensively tested our regularized TV-DBN model on synthetic data, in which we have simulated short non-homogeneous time series produced from a system subject to gradual change. We have then applied our method to real-world gene expression time series, measured during the life cycle of Drosophila melanogaster, under artificially generated constant light condition in Arabidopsis thaliana, and from a synthetically designed strain of Saccharomyces cerevisiae exposed to a changing environment.

  13. Visualization in simulation tools: requirements and a tool specification to support the teaching of dynamic biological processes.

    Science.gov (United States)

    Jørgensen, Katarina M; Haddow, Pauline C

    2011-08-01

    Simulation tools are playing an increasingly important role behind advances in the field of systems biology. However, the current generation of biological science students has either little or no experience with such tools. As such, this educational glitch is limiting both the potential use of such tools as well as the potential for tighter cooperation between the designers and users. Although some simulation tool producers encourage their use in teaching, little attempt has hitherto been made to analyze and discuss their suitability as an educational tool for noncomputing science students. In general, today's simulation tools assume that the user has a stronger mathematical and computing background than that which is found in most biological science curricula, thus making the introduction of such tools a considerable pedagogical challenge. This paper provides an evaluation of the pedagogical attributes of existing simulation tools for cell signal transduction based on Cognitive Load theory. Further, design recommendations for an improved educational simulation tool are provided. The study is based on simulation tools for cell signal transduction. However, the discussions are relevant to a broader biological simulation tool set.

  14. Understanding of photosynthesis among students of biology and non-biology programmes of study

    OpenAIRE

    Lekan, Erika

    2016-01-01

    Photosynthesis is one of the most important processes on Earth, thus knowing at least its basic principles is essential. In Slovenia, the students become acquainted with these principles in the fifth form of elementary school. Due to the complexity of the photosynthesis process, the students hold misconceptions about it since the very beginning of the learning process. Due to several factors and reasons, these misconceptions persist throughout the secondary school and university studies. ...

  15. Atomic Force Microscopy Application in Biological Research: A Review Study

    Directory of Open Access Journals (Sweden)

    Surena Vahabi

    2013-06-01

    Full Text Available Atomic force microscopy (AFM is a three-dimensional topographic technique with a high atomic resolution to measure surface roughness. AFM is a kind of scanning probe microscope, and its near-field technique is based on the interaction between a sharp tip and the atoms of the sample surface. There are several methods and many ways to modify the tip of the AFM to investigate surface properties, including measuring friction, adhesion forces and viscoelastic properties as well as determining the Young modulus and imaging magnetic or electrostatic properties. The AFM technique can analyze any kind of samples such as polymers, adsorbed molecules, films or fibers, and powders in the air whether in a controlled atmosphere or in a liquid medium. In the past decade, the AFM has emerged as a powerful tool to obtain the nanostructural details and biomechanical properties of biological samples, including biomolecules and cells. The AFM applications, techniques, and -in particular- its ability to measure forces, are not still familiar to most clinicians. This paper reviews the literature on the main principles of the AFM modality and highlights the advantages of this technique in biology, medicine, and- especially- dentistry. This literature review was performed through E-resources, including Science Direct, PubMed, Blackwell Synergy, Embase, Elsevier, and Scholar Google for the references published between 1985 and 2010.

  16. Models to Study NK Cell Biology and Possible Clinical Application.

    Science.gov (United States)

    Zamora, Anthony E; Grossenbacher, Steven K; Aguilar, Ethan G; Murphy, William J

    2015-08-03

    Natural killer (NK) cells are large granular lymphocytes of the innate immune system, responsible for direct targeting and killing of both virally infected and transformed cells. NK cells rapidly recognize and respond to abnormal cells in the absence of prior sensitization due to their wide array of germline-encoded inhibitory and activating receptors, which differs from the receptor diversity found in B and T lymphocytes that is due to the use of recombination-activation gene (RAG) enzymes. Although NK cells have traditionally been described as natural killers that provide a first line of defense prior to the induction of adaptive immunity, a more complex view of NK cells is beginning to emerge, indicating they may also function in various immunoregulatory roles and have the capacity to shape adaptive immune responses. With the growing appreciation for the diverse functions of NK cells, and recent technological advancements that allow for a more in-depth understanding of NK cell biology, we can now begin to explore new ways to manipulate NK cells to increase their clinical utility. In this overview unit, we introduce the reader to various aspects of NK cell biology by reviewing topics ranging from NK cell diversity and function, mouse models, and the roles of NK cells in health and disease, to potential clinical applications. © 2015 by John Wiley & Sons, Inc. Copyright © 2015 John Wiley & Sons, Inc.

  17. Studies on the Promotion of Biological Application by Radiation

    International Nuclear Information System (INIS)

    No, Y. C.; Kuk, I. H.; Song, H. S.

    2006-03-01

    Radiation Technology (RT) has been widely used in most of all fields of industries, medical, bioresources, food and agriculture, public hygiene, and environment. Therefore, its application has been also researched in various parts. For industrialization of the developed technology, not only the application technology will be developed, but the accurate dosimetry and improvement of the services of irradiation practice should be performed as soon as possible. Evaluation of effects and reaction mechanism of biological materials by irradiation was performed in this year in the long term research planning. The researches and experiments were well performed and the good results were obtained. The results may be donated in the progress of radiation biology and the new establishment on the application of RT. Also, one of the results was the evaluation of the structural changes of biomolecules and its application in the fields of food and biotechnology industries. Advanced Radiation Technology Institute (ARTI) will be well settled down and promotion of research activity of newly established institute by the fundamental support of KAERI. And, ARTI can get the goal where the vision of the hub of RT in Asia/Pacific region by 2020

  18. A dynamical study on extrasolar comets

    Science.gov (United States)

    Loibnegger, B.; Dvorak, R.

    2017-09-01

    Since the detection of absorption features in spectra of beta Pictoris varying on short time scales it is known that comets exist in other stellar systems. We investigate the dynamics of comets in two differently build systems (HD 10180 and HIP 14810). The outcomes of the scattering process, as there are collisions with the planets, captures and ejections from the systems are analysed statistically. Collisions and close encounters with the planets are investigated in more detail in order to conclude about transport of water and organic material. We will also investigate the possibility of detection of comets in other planetary systems.

  19. Thinking about Digestive System in Early Childhood: A Comparative Study about Biological Knowledge

    Science.gov (United States)

    AHI, Berat

    2017-01-01

    The current study aims to explore how children explain the concepts of biology and how biological knowledge develops across ages by focusing on the structure and functions of the digestive system. The study was conducted with 60 children. The data were collected through the interviews conducted within a think-aloud protocol. The interview data…

  20. A molecular dynamics simulation study of chloroform

    Science.gov (United States)

    Tironi, Ilario G.; van Gunsteren, Wilfred F.

    Three different chloroform models have been investigated using molecular dynamics computer simulation. The thermodynamic, structural and dynamic properties of the various models were investigated in detail. In particular, the potential energies, diffusion coefficients and rotational correlation times obtained for each model are compared with experiment. It is found that the theory of rotational Brownian motion fails in describing the rotational diffusion of chloroform. The force field of Dietz and Heinzinger was found to give good overall agreement with experiment. An extended investigation of this chloroform model has been performed. Values are reported for the isothermal compressibility, the thermal expansion coefficient and the constant volume heat capacity. The values agree well with experiment. The static and frequency dependent dielectric permittivity were computed from a 1·2 ns simulation conducted under reaction field boundary conditions. Considering the fact that the model is rigid with fixed partial charges, the static dielectric constant and Debye relaxation time compare well with experiment. From the same simulation the shear viscosity was computed using the off-diagonal elements of the pressure tensor, both via an Einstein type relation and via a Green-Kubo equation. The calculated viscosities show good agreement with experimental values. The excess Helmholtz energy is calculated using the thermodynamic integration technique and simulations of 50 and 80 ps. The value obtained for the excess Helmholtz energy matches the theoretical value within a few per cent.

  1. Dimensionless study on dynamics of pressure controlled mechanical ventilation system

    International Nuclear Information System (INIS)

    Shi, Yan; Niu, Jinglong; Cai, Maolin; Xu, Weiqing

    2015-01-01

    Dynamics of mechanical ventilation system can be referred in pulmonary diagnostics and treatments. In this paper, to conveniently grasp the essential characteristics of mechanical ventilation system, a dimensionless model of mechanical ventilation system is presented. For the validation of the mathematical model, a prototype mechanical ventilation system of a lung simulator is proposed. Through the simulation and experimental studies on the dimensionless dynamics of the mechanical ventilation system, firstly, the mathematical model is proved to be authentic and reliable. Secondly, the dimensionless dynamics of the mechanical ventilation system are obtained. Last, the influences of key parameters on the dimensionless dynamics of the mechanical ventilation system are illustrated. The study provides a novel method to study the dynamic of mechanical ventilation system, which can be referred in the respiratory diagnostics and treatment.

  2. Dimensionless study on dynamics of pressure controlled mechanical ventilation system

    Energy Technology Data Exchange (ETDEWEB)

    Shi, Yan; Niu, Jinglong; Cai, Maolin; Xu, Weiqing [Beihang University, Beijing (Korea, Republic of)

    2015-02-15

    Dynamics of mechanical ventilation system can be referred in pulmonary diagnostics and treatments. In this paper, to conveniently grasp the essential characteristics of mechanical ventilation system, a dimensionless model of mechanical ventilation system is presented. For the validation of the mathematical model, a prototype mechanical ventilation system of a lung simulator is proposed. Through the simulation and experimental studies on the dimensionless dynamics of the mechanical ventilation system, firstly, the mathematical model is proved to be authentic and reliable. Secondly, the dimensionless dynamics of the mechanical ventilation system are obtained. Last, the influences of key parameters on the dimensionless dynamics of the mechanical ventilation system are illustrated. The study provides a novel method to study the dynamic of mechanical ventilation system, which can be referred in the respiratory diagnostics and treatment.

  3. Biological signatures of dynamic river networks from a coupled landscape evolution and neutral community model

    Science.gov (United States)

    Stokes, M.; Perron, J. T.

    2017-12-01

    Freshwater systems host exceptionally species-rich communities whose spatial structure is dictated by the topology of the river networks they inhabit. Over geologic time, river networks are dynamic; drainage basins shrink and grow, and river capture establishes new connections between previously separated regions. It has been hypothesized that these changes in river network structure influence the evolution of life by exchanging and isolating species, perhaps boosting biodiversity in the process. However, no general model exists to predict the evolutionary consequences of landscape change. We couple a neutral community model of freshwater organisms to a landscape evolution model in which the river network undergoes drainage divide migration and repeated river capture. Neutral community models are macro-ecological models that include stochastic speciation and dispersal to produce realistic patterns of biodiversity. We explore the consequences of three modes of speciation - point mutation, time-protracted, and vicariant (geographic) speciation - by tracking patterns of diversity in time and comparing the final result to an equilibrium solution of the neutral model on the final landscape. Under point mutation, a simple model of stochastic and instantaneous speciation, the results are identical to the equilibrium solution and indicate the dominance of the species-area relationship in forming patterns of diversity. The number of species in a basin is proportional to its area, and regional species richness reaches its maximum when drainage area is evenly distributed among sub-basins. Time-protracted speciation is also modeled as a stochastic process, but in order to produce more realistic rates of diversification, speciation is not assumed to be instantaneous. Rather, each new species must persist for a certain amount of time before it is considered to be established. When vicariance (geographic speciation) is included, there is a transient signature of increased

  4. Model for the dynamic study of AC contactors

    Energy Technology Data Exchange (ETDEWEB)

    Corcoles, F.; Pedra, J.; Garrido, J.P.; Baza, R. [Dep. d' Eng. Electrica ETSEIB. UPC, Barcelona (Spain)

    2000-08-01

    This paper proposes a model for the dynamic analysis of AC contactors. The calculation algorithm and implementation are discussed. The proposed model can be used to study the influence of the design parameters and the supply in their dynamic behaviour. The high calculation speed of the implemented algorithm allows extensive ranges of parameter variations to be analysed. (orig.)

  5. Autonomy and Fear of Synthetic Biology: How Can Patients' Autonomy Be Enhanced in the Field of Synthetic Biology? A Qualitative Study with Stable Patients.

    Science.gov (United States)

    Rakic, Milenko; Wienand, Isabelle; Shaw, David; Nast, Rebecca; Elger, Bernice S

    2017-04-01

    We analyzed stable patients' views regarding synthetic biology in general, the medical application of synthetic biology, and their potential participation in trials of synthetic biology in particular. The aim of the study was to find out whether patients' views and preferences change after receiving more detailed information about synthetic biology and its clinical applications. The qualitative study was carried out with a purposive sample of 36 stable patients, who suffered from diabetes or gout. Interviews were transcribed verbatim, translated and fully anonymized. Thematic analysis was applied in order to examine stable patients' attitudes towards synthetic biology, its medical application, and their participation in trials. When patients were asked about synthetic biology in general, most of them were anxious that something uncontrollable could be created. After a concrete example of possible future treatment options, patients started to see synthetic biology in a more positive way. Our study constitutes an important first empirical insight into stable patients' views on synthetic biology and into the kind of fears triggered by the term "synthetic biology." Our results show that clear and concrete information can change patients' initial negative feelings towards synthetic biology. Information should thus be transmitted with great accuracy and transparency in order to reduce irrational fears of patients and to minimize the risk that researchers present facts too positively for the purposes of persuading patients to participate in clinical trials. Potential participants need to be adequately informed in order to be able to autonomously decide whether to participate in human subject research involving synthetic biology.

  6. Dynamics of forest ecosystems regenerated on burned and harvested areas in mountain regions of Siberia: characteristics of biological diversity, structure and productivity

    Directory of Open Access Journals (Sweden)

    I. M. Danilin

    2016-12-01

    Full Text Available Complex estimation of forest ecosystems dynamics based on detailing characteristics of structure, growth and productivity of the stands and describing general geographical and biological management options for preserving their biodiversity and sustaining stability are discussed in the paper by describing examples of tree stands restored on burned and logged areas in mountain regions of Siberia. On vast areas in Siberia, characterized as sub-boreal, subarid and with a strongly continental climate, forests grow on seasonally frozen soils and in many cases are surrounded by vast steppe and forest-steppe areas and uplands. Developing criteria for sustainability of mountain forest ecosystems is necessary for forest resource management and conservation. It is therefore important to obtain complex biometric characteristics on forest stands and landscapes and to thoroughly study their structure, biological diversity and productivity. Morphometric methods, Weibull simulation and allometric equations were used to determine the dimensional hierarchies of coenopopulation individuals. Structure and productivity of the aboveground stand components were also studied.

  7. Studies of the reproductive biology of deep sea megabenthos

    International Nuclear Information System (INIS)

    Tyler, P.A.; Muirhead, A.

    1986-06-01

    Specimens of six species of aspidochirota from depths between 1245 and 2315m in the N.E. Atlantic have been examined and their reproductive biology determined. Two species Paelopatides grisea and Benthothuria funebris produce the large eggs typical of direct development. Mesothuria lactea and M. verrilli have an intermediate egg size of c. 400μm whilst Bathyplotes natans has an egg size of c. 280μm, which may be indicative of indirect development. The last species Paroriza pallens is an hermaphrodite producing an egg of c. 250μm. With the exception of Bathyplotes natans, which appears to show periodic reproduction if not seasonal, the species show no evidence of reproductive seasonality. (author)

  8. Biological response to radiation. Studies of model organism, C. elegans, with micro-ion beam

    International Nuclear Information System (INIS)

    Higashitani, Atsushi

    2006-01-01

    Described are mainly author's studies on radiation response and its biological significance in a nematode, C. elegans, particularly focusing its germ cells. The model organism is bisexual and the mature one is suitable to observe the development, differentiation and concomitant chromosome dynamics of male and female germ cells, and accordingly, the responses occurring in those cells at different stages post irradiation of the whole worm. Authors have shown in the organism irradiated by 100 Gy X-ray that pachytene cells in meiosis have high radio-resistance due to their increased expression of enzymes related with homologous recombination. They have also presented the apoptotic cascade in germ cells triggered by radiation by comparison of wild type and ab1-1-gene-deleted worms. Micro-beam of 12 C 5+ ion in Takasaki Ion Accelerators for Advanced Radiation Application (TIARA) has been used to irradiate the body parts of the worm to study the bystander effects, which has revealed that germ cells are shielded from the effect in the worm. It is thought important to use the micro-beam, with which the irradiation area can be precisely controllable, for studying the bystander effect in a body of higher animals like a mouse as well as in worm somatic cells. (T.I.)

  9. Dynamical study of symmetries: breaking and restauration

    International Nuclear Information System (INIS)

    Schuck, P.

    1986-09-01

    First symmetry breaking (spontaneous) is explained and the physical implication discussed for infinite systems. The relation with phase transitions is indicated. Then the specific aspects of symmetry breaking in finite systems is treated and illustrated in detail for the case of translational invariance with the help of an oversimplified but exactly solvable model. The method of projection (restauration of symmetry) is explained for the static case and also applied to the model. Symmetry breaking in the dynamical case and for instance the notion of a soft mode responsible for the symmetry breaking is discussed in the case of superfluidity and another exactly solvable model is introduced. The Goldstone mode is treated in detail. Some remarks on analogies with the breaking of chiral symmetry are made. Some recent developments in the theory of symmetry restauration are briefly outlined [fr

  10. Systems approaches to study root architecture dynamics

    Directory of Open Access Journals (Sweden)

    Candela eCuesta

    2013-12-01

    Full Text Available The plant root system is essential for providing anchorage to the soil, supplying minerals and water, and synthesizing metabolites. It is a dynamic organ modulated by external cues such as environmental signals, water and nutrients availability, salinity and others. Lateral roots are initiated from the primary root post-embryonically, after which they progress through discrete developmental stages which can be independently controlled, providing a high level of plasticity during root system formation.Within this review, main contributions are presented, from the classical forward genetic screens to the more recent high-throughput approaches, combined with computer model predictions, dissecting how lateral roots and thereby root system architecture is established and developed.

  11. Recommendations for designing and conducting veterinary clinical pathology biologic variation studies.

    Science.gov (United States)

    Freeman, Kathleen P; Baral, Randolph M; Dhand, Navneet K; Nielsen, Søren Saxmose; Jensen, Asger L

    2017-06-01

    The recent creation of a veterinary clinical pathology biologic variation website has highlighted the need to provide recommendations for future studies of biologic variation in animals in order to help standardize and improve the quality of published information and to facilitate review and selection of publications as standard references. The following recommendations are provided in the format and order commonly found in veterinary publications. A checklist is provided to aid in planning, implementing, and evaluating veterinary studies on biologic variation (Appendix S1). These recommendations provide a valuable resource for clinicians, laboratorians, and researchers interested in conducting studies of biologic variation and in determining the quality of studies of biologic variation in veterinary laboratory testing. © 2017 American Society for Veterinary Clinical Pathology.

  12. Short spatio-temporal variations in the population dynamics and biology of the deep-water rose shrimp Parapenaeus longirostris (Decapoda: Crustacea in the western Mediterranean

    Directory of Open Access Journals (Sweden)

    Beatriz Guijarro

    2009-03-01

    Full Text Available The deep-water rose shrimp Parapenaeus longirostris is a demersal decapod crustacean that is commercially exploited by trawl fleets. The present work compares its population dynamics, biology and condition in two locations (southern and north-western Mallorca in the Balearic Islands, western Mediterranean, separated by a distance of 120 km with different environmental conditions and explores the relationships between the species and certain environmental factors. Six multidisciplinary bimonthly surveys were carried out during 2003 and 2004 in these two locations (between 150 and 750 m depth in order to collect data on the demersal species with bottom trawl, the hydrography (temperature and salinity with CTD casts, and trophic resources (zooplankton in the water column and suprabenthos with Bongo net and Macer-GIROQ sledge respectively and sediments with a Shipeck dredge. The trawl fleets from both locations were monitored by monthly on board sampling and daily landings obtained from sales bills. Additional data was obtained from other trawl surveys. Temporal differences were detected both annually, with a decreasing trend over the last years in species abundance, and seasonally, in the biological indexes analysed. Bathymetric differences were also found in abundance, mean length, sex-ratio and condition of females. There were clear differences between the two locations studied, with higher abundance, condition and mean length and a lower length at first maturity for females in the north-western location. Trophic conditions could act as a link between geo-physical and biological changes. These short spatio-temporal differences could be due to the higher productivity found at this location, with higher density of preferred prey for the studied species together with adequate seafloor topography, sediment composition and hydrographical characteristics.

  13. Study of a spur gear dynamic behavior in transient regime

    Science.gov (United States)

    Khabou, M. T.; Bouchaala, N.; Chaari, F.; Fakhfakh, T.; Haddar, M.

    2011-11-01

    In this paper the dynamic behavior of a single stage spur gear reducer in transient regime is studied. Dynamic response of the single stage spur gear reducer is investigated at different rotating velocities. First, gear excitation is induced by the motor torque and load variation in addition to the fluctuation of meshing stiffness due to the variation of input rotational speed. Then, the dynamic response is computed using the Newmark method. After that, a parameter study is made on spur gear powered in the first place by an electric motor and in the second place by four strokes four cylinders diesel engine. Dynamic responses come to confirm a significant influence of the transient regime on the dynamic behavior of a gear set, particularly in the case of engine acyclism condition.

  14. Gas-Phase Molecular Dynamics: Theoretical Studies In Spectroscopy and Chemical Dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Yu H. G.; Muckerman, J.T.

    2012-05-29

    The main goal of this program is the development and application of computational methods for studying chemical reaction dynamics and molecular spectroscopy in the gas phase. We are interested in developing rigorous quantum dynamics algorithms for small polyatomic systems and in implementing approximate approaches for complex ones. Particular focus is on the dynamics and kinetics of chemical reactions and on the rovibrational spectra of species involved in combustion processes. This research also explores the potential energy surfaces of these systems of interest using state-of-the-art quantum chemistry methods, and extends them to understand some important properties of materials in condensed phases and interstellar medium as well as in combustion environments.

  15. Gas-Phase Molecular Dynamics: Theoretical Studies in Spectroscopy and Chemical Dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Yu, H.G.; Muckerman, J.T.

    2010-06-01

    The goal of this program is the development and application of computational methods for studying chemical reaction dynamics and molecular spectroscopy in the gas phase. We are interested in developing rigorous quantum dynamics algorithms for small polyatomic systems and in implementing approximate approaches for complex ones. Particular focus is on the dynamics and kinetics of chemical reactions and on the rovibrational spectra of species involved in combustion processes. This research also explores the potential energy surfaces of these systems of interest using state-of-the-art quantum chemistry methods.

  16. NATO Advanced Study Institute on Chaotic Dynamics : Theory and Practice

    CERN Document Server

    1992-01-01

    Many conferences, meetings, workshops, summer schools and symposia on nonlinear dynamical systems are being organized these days, dealing with a great variety of topics and themes -classical and quantum, theoretical and experimental. Some focus on integrability, or discuss the mathematical foundations of chaos. Others explore the beauty of fractals, or examine endless possibilities of applications to problems of physics, chemistry, biology and other sciences. A new scientific discipline has thus emerged, with its own distinct philosophical viewpoint and an impressive arsenal of new methods and techniques, which may be called Chaotic Dynamics. Perhaps its most outstanding achievement so far has been to shed new light on many long­ standing issues involving complicated, irregular or "chaotic" nonlinear phenomena. The concepts of randomness, complexity and unpredictability have been critically re-examined and the fundamental importance of scaling, self-similarity and sensitive dependence on parameters a...

  17. Dynamics of biopolymers on nanomaterials studied by quasielastic neutron scattering and MD simulations

    Science.gov (United States)

    Dhindsa, Gurpreet K.

    Neutron scattering has been proved to be a powerful tool to study the dynamics of biological systems under various conditions. This thesis intends to utilize neutron scattering techniques, combining with MD simulations, to develop fundamental understanding of several biologically interesting systems. Our systems include a drug delivery system containing Nanodiamonds with nucleic acid (RNA), and two specific model proteins, beta-Casein and Inorganic Pyrophosphatase (IPPase). RNA and nanodiamond (ND) both are suitable for drug-delivery applications in nano-biotechnology. The architecturally flexible RNA with catalytic functionality forms nanocomposites that can treat life-threatening diseases. The non-toxic ND has excellent mechanical and optical properties and functionalizable high surface area, and thus actively considered for biomedical applications. In this thesis, we utilized two tools, quasielastic neutron scattering (QENS) and Molecular Dynamics Simulations to probe the effect of ND on RNA dynamics. Our work provides fundamental understanding of how hydrated RNA motions are affected in the RNA-ND nanocomposites. From the experimental and Molecular Dynamics Simulation (MD), we found that hydrated RNA motion is faster on ND surface than a freestanding one. MD Simulation results showed that the failure of Stokes Einstein relation results the presence of dynamic heterogeneities in the biomacromolecules. Radial pair distribution function from MD Simulation confirmed that the hydrophilic nature of ND attracts more water than RNA results the de-confinement of RNA on ND. Therefore, RNA exhibits faster motion in the presence of ND than freestanding RNA. In the second project, we studied the dynamics of a natively disordered protein beta-Casein which lacks secondary structures. In this study, the temperature and hydration effects on the dynamics of beta-Casein are explored by Quasielastic Neutron Scattering (QENS). We investigated the mean square displacement (MSD) of

  18. Biologically based neural circuit modelling for the study of fear learning and extinction

    Science.gov (United States)

    Nair, Satish S.; Paré, Denis; Vicentic, Aleksandra

    2016-11-01

    The neuronal systems that promote protective defensive behaviours have been studied extensively using Pavlovian conditioning. In this paradigm, an initially neutral-conditioned stimulus is paired with an aversive unconditioned stimulus leading the subjects to display behavioural signs of fear. Decades of research into the neural bases of this simple behavioural paradigm uncovered that the amygdala, a complex structure comprised of several interconnected nuclei, is an essential part of the neural circuits required for the acquisition, consolidation and expression of fear memory. However, emerging evidence from the confluence of electrophysiological, tract tracing, imaging, molecular, optogenetic and chemogenetic methodologies, reveals that fear learning is mediated by multiple connections between several amygdala nuclei and their distributed targets, dynamical changes in plasticity in local circuit elements as well as neuromodulatory mechanisms that promote synaptic plasticity. To uncover these complex relations and analyse multi-modal data sets acquired from these studies, we argue that biologically realistic computational modelling, in conjunction with experiments, offers an opportunity to advance our understanding of the neural circuit mechanisms of fear learning and to address how their dysfunction may lead to maladaptive fear responses in mental disorders.

  19. A Comparative Study of Biologically Inspired Walking Gaits through Waypoint Navigation

    Directory of Open Access Journals (Sweden)

    Umar Asif

    2011-01-01

    Full Text Available This paper investigates the locomotion of a walking robot by delivering a comparative study of three different biologically inspired walking gaits, namely: tripod, ripple, and wave, in terms of ground slippage they experience while walking. The objective of this study is to identify the gait model which experiences the minimum slippage while walking on a ground with a specific coefficient of friction. To accomplish this feat, the robot is steered over a reference path using a waypoint navigation algorithm, and the divergence of the robot from the reference path is investigated in terms of slip errors. Experiments are conducted through closed-loop simulations using an open dynamics engine which emphasizes the fact that due to uneven and unsymmetrical distribution of payload in tripod and ripple gait models, the robot experiences comparatively larger drift in these gaits than when using the wave gait model in which the distribution of payload is even and symmetrical on both sides of the robot body. The paper investigates this phenomenon on the basis of force distribution of supporting legs in each gait model.

  20. Deterministic global optimization algorithm based on outer approximation for the parameter estimation of nonlinear dynamic biological systems.

    Science.gov (United States)

    Miró, Anton; Pozo, Carlos; Guillén-Gosálbez, Gonzalo; Egea, Jose A; Jiménez, Laureano

    2012-05-10

    The estimation of parameter values for mathematical models of biological systems is an optimization problem that is particularly challenging due to the nonlinearities involved. One major difficulty is the existence of multiple minima in which standard optimization methods may fall during the search. Deterministic global optimization methods overcome this limitation, ensuring convergence to the global optimum within a desired tolerance. Global optimization techniques are usually classified into stochastic and deterministic. The former typically lead to lower CPU times but offer no guarantee of convergence to the global minimum in a finite number of iterations. In contrast, deterministic methods provide solutions of a given quality (i.e., optimality gap), but tend to lead to large computational burdens. This work presents a deterministic outer approximation-based algorithm for the global optimization of dynamic problems arising in the parameter estimation of models of biological systems. Our approach, which offers a theoretical guarantee of convergence to global minimum, is based on reformulating the set of ordinary differential equations into an equivalent set of algebraic equations through the use of orthogonal collocation methods, giving rise to a nonconvex nonlinear programming (NLP) problem. This nonconvex NLP is decomposed into two hierarchical levels: a master mixed-integer linear programming problem (MILP) that provides a rigorous lower bound on the optimal solution, and a reduced-space slave NLP that yields an upper bound. The algorithm iterates between these two levels until a termination criterion is satisfied. The capabilities of our approach were tested in two benchmark problems, in which the performance of our algorithm was compared with that of the commercial global optimization package BARON. The proposed strategy produced near optimal solutions (i.e., within a desired tolerance) in a fraction of the CPU time required by BARON.

  1. Laser-induced damage in biological tissue: Role of complex and dynamic optical properties of the medium

    Science.gov (United States)

    Ahmed, Elharith M.

    Since its invention in the early 1960's, the laser has been used as a tool for surgical, therapeutic, and diagnostic purposes. To achieve maximum effectiveness with the greatest margin of safety it is important to understand the mechanisms of light propagation through tissue and how that light affects living cells. Lasers with novel output characteristics for medical and military applications are too often implemented prior to proper evaluation with respect to tissue optical properties and human safety. Therefore, advances in computational models that describe light propagation and the cellular responses to laser exposure, without the use of animal models, are of considerable interest. Here, a physics-based laser-tissue interaction model was developed to predict the spatial and temporal temperature and pressure rise during laser exposure to biological tissues. Our new model also takes into account the dynamic nature of tissue optical properties and their impact on the induced temperature and pressure profiles. The laser-induced retinal damage is attributed to the formation of microbubbles formed around melanosomes in the retinal pigment epithelium (RPE) and the damage mechanism is assumed to be photo-thermal. Selective absorption by melanin creates these bubbles that expand and collapse around melanosomes, destroying cell membranes and killing cells. The Finite Element (FE) approach taken provides suitable ground for modeling localized pigment absorption which leads to a non-uniform temperature distribution within pigmented cells following laser pulse exposure. These hot-spots are sources for localized thermo-elastic stresses which lead to rapid localized expansions that manifest themselves as microbubbles and lead to microcavitations. Model predictions for the interaction of lasers at wavelengths of 193, 694, 532, 590, 1314, 1540, 2000, and 2940 nm with biological tissues were generated and comparisons were made with available experimental data for the retina

  2. Applied Bayesian statistical studies in biology and medicine

    CERN Document Server

    D’Amore, G; Scalfari, F

    2004-01-01

    It was written on another occasion· that "It is apparent that the scientific culture, if one means production of scientific papers, is growing exponentially, and chaotically, in almost every field of investigation". The biomedical sciences sensu lato and mathematical statistics are no exceptions. One might say then, and with good reason, that another collection of bio­ statistical papers would only add to the overflow and cause even more confusion. Nevertheless, this book may be greeted with some interest if we state that most of the papers in it are the result of a collaboration between biologists and statisticians, and partly the product of the Summer School th "Statistical Inference in Human Biology" which reaches its 10 edition in 2003 (information about the School can be obtained at the Web site http://www2. stat. unibo. itleventilSito%20scuolalindex. htm). is common experience - and not only This is rather important. Indeed, it in Italy - that encounters between statisticians and researchers are spora...

  3. Preliminary Study of Greywater Treatment through Rotating Biological Contactor

    Directory of Open Access Journals (Sweden)

    Ashfaq Ahmed Pathan

    2011-07-01

    Full Text Available The characteristics of the greywater vary from country to country and it depends upon the cultural and social behavior of the respective country. There was a considerable need to characterize and recycle the greywater. In this regard greywater was separated from the black water and analyzed for various physiochemical parameters. Among various greywater recycling treatment technologies, RBC (Rotating Biological Contactor is more effective treatment technique in reducing COD (Chemical Oxygen Demand and organic matters from the greywater. But this technology was not applied and tested in Pakistan. There was extensive need to investigate the RBC technology for greywater recycling at small scale before applying at mass scale. To treat the greywater, a single-stage RBC simulator was designed and developed at laboratory scale. An electric motor equipped with gear box to control the rotations of the disks was mounted on the tank. The simulator was run at the rate of 1.7 rpm. The disc area of the RBC was immersed about 40% in the greywater. Water samples were collected at each HRT (Hydraulic Retention Time and analyzed for the parameters such as pH, conductivity, TDS (Total Dissolved Solids, salinity, BOD5 (Biochemical Oxygen Demand, COD and suspended solids by using standard methods. The results are encouraging with percentage removal of BOD5 and COD being 53 and 60% respectively.

  4. Extraction, characterization and biological studies of phytochemicals from Mammea suriga

    Directory of Open Access Journals (Sweden)

    Mahesha M. Poojary

    2015-06-01

    Full Text Available The present work involves extraction of phytochemicals from the root bark of a well-known Indian traditional medicinal plant, viz. Mammea suriga, with various solvents and evaluation of their in vitro antimicrobial and antioxidant activities using standard methods. The phytochemical analysis indicates the presence of some interesting secondary metabolites like flavonoids, cardiac glycosides, alkaloids, saponins and tannins in the extracts. Also, the solvent extracts displayed promising antimicrobial activity against Staphylococcus aureus, Bacillus subtilis and Cryptococcus neoformans with inhibition zone in a range of 20–33 mm. Further, results of their antioxidant screening revealed that aqueous extract (with IC50 values of 111.51±1.03 and 31.05±0.92 μg/mL in total reducing power assay and DPHH radical scavenging assay, respectively and ethanolic extract (with IC50 values of 128.00±1.01 and 33.25±0.89 μg/mL in total reducing power assay and DPHH radical scavenging assay, respectively were better antioxidants than standard ascorbic acid. Interestingly, FT-IR analysis of each extract established the presence of various biologically active functional groups in it. Keywords: Mammea suriga, Phytochemical analysis, Antimicrobial activity, Antioxidant assay, FT-IR analysis

  5. An ESR study on biological dosimeters: Human hair

    International Nuclear Information System (INIS)

    Colak, Seyda; Ozbey, Turan

    2011-01-01

    In the present work, characteristic features of the radicals found in untreated, gamma and UV-irradiated and mechanical damaged human hair samples were investigated by ESR spectroscopy. Heights of the resonance peaks measured with respect to the spectrum base line were used to monitor microwave power, dose-response, storage time and temperature dependent kinetic features of the radical species contributing to the formation of recorded experimental ESR spectra. Peak heights and g-values (2.0037-2.0052) determined from recorded spectra of hair were color dependent with ΔHpp-0.47 mT. The act of cutting hair samples gene rates sulfur centered radicals which are found in the a-keratin structure of hair. The variations of the peak heights with temperature were related with the water content found in the hair samples. In the 6-1100 Gy dose range, a linear + quadratic dose-response curve was recorded for hair and the mean radiation yield (G mean ) was calculated to be 0.4. The gamma radiation induced radicals were stable for a several hours at room temperature storage conditions. Based on these findings it was concluded that human hair samples could be used as biological/personnel dosimeters and that ESR spectroscopy could be successfully used as a potential technique for monitoring its dosimetric behaviours.

  6. Scanning Ion Conductance Microscopy for Studying Biological Samples

    Directory of Open Access Journals (Sweden)

    Irmgard D. Dietzel

    2012-11-01

    Full Text Available Scanning ion conductance microscopy (SICM is a scanning probe technique that utilizes the increase in access resistance that occurs if an electrolyte filled glass micro-pipette is approached towards a poorly conducting surface. Since an increase in resistance can be monitored before the physical contact between scanning probe tip and sample, this technique is particularly useful to investigate the topography of delicate samples such as living cells. SICM has shown its potential in various applications such as high resolution and long-time imaging of living cells or the determination of local changes in cellular volume. Furthermore, SICM has been combined with various techniques such as fluorescence microscopy or patch clamping to reveal localized information about proteins or protein functions. This review details the various advantages and pitfalls of SICM and provides an overview of the recent developments and applications of SICM in biological imaging. Furthermore, we show that in principle, a combination of SICM and ion selective micro-electrodes enables one to monitor the local ion activity surrounding a living cell.

  7. Radiochemistry - Applications in the study of radical mechanisms of biological interest

    International Nuclear Information System (INIS)

    Foos, Jacques

    1982-01-01

    In biology, oxygen reducing processes give rise to the formation of intermediate radicals. One of the major breakthroughs of radiation chemistry of aqueous solutions is the identification of these compounds. The author describes the techniques used to study the reaction of these radicals (of radiolytic origin) with biological molecules [fr

  8. Investigating Lebanese Grade Seven Biology Teachers Mathematical Knowledge and Skills: A Case Study

    Science.gov (United States)

    Raad, Nawal Abou; Chatila, Hanadi

    2016-01-01

    This paper investigates Lebanese grade 7 biology teachers' mathematical knowledge and skills, by exploring how they explain a visual representation in an activity depending on the mathematical concept "Function". Twenty Lebanese in-service biology teachers participated in the study, and were interviewed about their explanation for the…

  9. Water Quality Monitoring: An Environmental Studies Unit for Biology 20/30. Teacher's Guide.

    Science.gov (United States)

    Alberta Environment, Edmonton. Environmental Education Resources Branch.

    The objective of this environmental studies unit is to establish a water quality monitoring project for high school students in Alberta while simultaneously providing a unit which meets the objectives of the Biology 20 program (and which may also be used in Biology 10 and 30). Through this project, students assist in the collection,…

  10. Water Quality Monitoring: An Environmental Studies Unit for Biology 20/30. Student Manual.

    Science.gov (United States)

    Alberta Environment, Edmonton. Environmental Education Resources Branch.

    The objective of this environmental studies unit is to establish a water quality monitoring project for high school students in Alberta while simultaneously providing a unit which meets the objectives of the Biology 20 program (and which may also be used in Biology 10 and 30). Through this project, students assist in the collection,…

  11. A new methodology for studying nanoparticle interactions in biological systems: Dispersing titania in biocompatible media using chemical stabilisers

    Science.gov (United States)

    Ramirez-Garcia, Sonia; Chen, Lan; Morris, Michael A.; Dawson, Kenneth A.

    2011-11-01

    We report here a highly successful and original protocol for the dispersion of nanoparticles in biocompatible fluids for in vitro and in vivo studies of the nanoparticle-biology interaction. Titania is chosen as a suitable model as it is one of the priority materials listed by the OECD and small particles of the anatase structure are extensively used as e.g. photocatalysts in solar cells. Consequently, its delivery into the environment and its interaction with biological organisms is unavoidable. Therefore, its biological effect needs to be understood. In this work, we prepared stable nanoparticle dispersions of anatase aggregates using citrate stabilisations between 45 and 55 nm at concentrations of up to 10 mg mL-1. The optimum pH for this type of suspension was 7, resulting in ζ-potentials of approximately -50 mV. The stabilised aggregates were the subject of dialysis to produce stable dispersions without the chemical stabiliser, thus allowing studies in the absence of potentially toxic chemicals. Different sizing techniques such as Dynamic Light Scattering (DLS), Nanoparticle Tracking Analysis (NTA) and Differential Centrifuge Sedimentation (DCS) were used to characterise the different suspensions. The results obtained with each of these techniques are compared and a critical analysis of the suitability of each technique is given.We report here a highly successful and original protocol for the dispersion of nanoparticles in biocompatible fluids for in vitro and in vivo studies of the nanoparticle-biology interaction. Titania is chosen as a suitable model as it is one of the priority materials listed by the OECD and small particles of the anatase structure are extensively used as e.g. photocatalysts in solar cells. Consequently, its delivery into the environment and its interaction with biological organisms is unavoidable. Therefore, its biological effect needs to be understood. In this work, we prepared stable nanoparticle dispersions of anatase aggregates

  12. Molecular dynamics studies of displacement cascades

    International Nuclear Information System (INIS)

    Averback, R.S.; Hsieh, Horngming; Diaz de la Rubia, T.

    1990-02-01

    Molecular-dynamics simulations of cascades in Cu and Ni with primary-knock-on energies up to 5 keV and lattice temperatures in the range 0 K--700 K are described. Interatomic forces were represented by either the Gibson II (Cu) or Johnson-Erginsoy (Ni) potentials in most of this work, although some simulations using ''Embedded Atom Method'' potentials, e.g., for threshold events in Ni 3 Al, are also presented. The results indicate that the primary state of damage produced by displacement cascades is controlled by two phenomena, replacement collision sequences during the collisional phase of the cascade and local melting during the thermal spike. As expected, the collisional phase is rather similar in Cu and Ni, however, the thermal spike is of longer duration and has a more pronounced influence in Cu than Ni. When the ambient temperature of the lattice is increased, the melt zones are observed to both increase in size and cool more slowly. This has the effect of reducing defect production and enhancing atomic mixing and disordering. The implications of these results for defect production, cascade collapse, atomic disordering will be discussed. 34 refs., 7 figs., 2 tabs

  13. Biological Response to the Dynamic Spectral-Polarized Underwater Light Field

    Science.gov (United States)

    2013-09-30

    by studying a homogeneous turbid medium. The diffuse reflection is produced by incoherent multiple scattering and is solved through radiative...polarization manipulation experiments revealed that polarization reflectance in Atlantic needlefish is controlled at the periphery (Fig 28). 6 19...with camouflage researchers on isopod and kelp crab camouflage against algae and seagrasses at several different west coast universities (Dierssen

  14. Dynamical study of a polydisperse hard-sphere system

    KAUST Repository

    Nogawa, Tomoaki; Ito, Nobuyasu; Watanabe, Hiroshi

    2010-01-01

    We study the interplay between the fluid-crystal transition and the glass transition of elastic sphere system with polydispersity using nonequilibrium molecular dynamics simulations. It is found that the end point of the crystal-fluid transition

  15. New sources and instrumentation for neutrons in biology

    DEFF Research Database (Denmark)

    Teixeira, S. C. M.; Zaccai, G.; Ankner, J.

    2008-01-01

    Neutron radiation offers significant advantages for the study of biological molecular structure and dynamics. A broad and significant effort towards instrumental and methodological development to facilitate biology experiments at neutron sources worldwide is reviewed.......Neutron radiation offers significant advantages for the study of biological molecular structure and dynamics. A broad and significant effort towards instrumental and methodological development to facilitate biology experiments at neutron sources worldwide is reviewed....

  16. Concentration dynamics in lakes and reservoirs. Studies using radioactive tracers

    International Nuclear Information System (INIS)

    Gilath, Ch.

    1983-01-01

    The use of radioactive tracers for the investigation of concentration dynamics of inert soluble matter in lakes and reservoirs is reviewed. Shallow and deep stratified lakes are considered. The mechanism of mixing in lakes, flow pattern and input - output response are discussed. The methodology of the use of radioactive tracers for concentration dynamic studies is described. Examples of various investigations are reviewed. The dynamics of shallow lakes can be found and expressed in terms of transfer functions, axial dispersion models, residence time distributions and sometimes only semiquantitative information about the flow pattern. The dynamics of deep, stratified lakes is more complex and difficult to investigate with tracers. Flow pattern, horizontal and vertical eddy diffusivities, mass transfer between the hypolimnion and epilimnion are tools used for describing this dynamics. (author)

  17. Study on dynamic lifting characteristics of control rod drive mechanism

    International Nuclear Information System (INIS)

    Shen Xiaoyao

    2012-01-01

    Based on the equations of the electric circuit and the magnetic circuit and analysis of the dynamic lifting process for the control rod drive mechanism (CRDM), coupled magnetic-electric-mechanical equations both for the static status and the dynamic status are derived. The analytical method is utilized to obtain the current and the time when the lift starts. The numerical simulation method of dynamic analysis recommended by ASME Code is utilized to simulate the dynamic lifting process of CRDM, and the dynamic features of the system with different design gaps are studied. Conclusions are drawn as: (1) the lifting-start time increases with the design gap, and the time for the lifting process is longer with larger gaps; (2) the lifting velocity increases with time; (3) the lifting acceleration increases with time, and with smaller gaps, the impact acceleration is larger. (author)

  18. Tomography studies of biological cells on polymer scaffolds

    International Nuclear Information System (INIS)

    Thurner, P; Mueller, B; Sennhauser, U; Hubbell, J; Mueller, R

    2004-01-01

    Advances in cell biology and tissue engineering rely heavily on performing 2D cell culture experiments. Analysis of these is conventionally done with 2D imaging techniques such as light (LM) or electron microscopy (SEM), since they are readily available. Cells, however, might act significantly differently when cultured in 2D or 3D environments. In order to analyse cells in a 3D arrangement, new imaging techniques are necessary not only in order to visualize the periphery of the cell culture in reflection mode but also to perform qualitative and quantitative investigations of the inner parts. Synchrotron radiation micro-computed tomography (SRμCT) using hard x-rays was shown to be a promising tool that can be used for 3D cell culture visualization. SRμCT allows not only visualization of cell cultures in their native 3D environment but also use of the volumetric nature of this imaging procedure to evaluate the cells quantitatively. In our approach, cells were seeded on polymer yarns, stained and measured with SRμCT in absorption and in differential absorption contrast mode. A new segmentation procedure was developed and the measured volumetric data were quantitatively assessed. Quantification parameters included total cell volume, total yarn volume, cell volume density, which is the ratio of cell to yarn volume, and the radial cell mass distribution. The applied variation of the staining parameter of gold enhancement incubation time was shown to have significant influence on the cell volume density. Differential absorption contrast mode was found to provide similar but no additional information on the investigated sample. Using novel approaches of hierarchical volumetric imaging allows closure of the gap between imaging of whole organs and single cells and might be expanded to even higher resolutions, offering investigation of the cell machinery in closer detail

  19. Synthesis, characterization and biological studies of copper oxide nanostructures

    Science.gov (United States)

    Jillani, Saquf; Jelani, Mohsan; Hassan, Najam Ul; Ahmad, Shahbaz; Hafeez, Muhammad

    2018-04-01

    The development of synthetic methods has been broadly accepted as an area of fundamental importance to the understanding and application of nanoscale materials. It allows the individual to modulate basic parameters such as morphology, particle size, size distributions, and composition. Several methods have been developed to synthesize CuO nanostructures with diverse morphologies, sizes, and dimensions using different chemical and physical based approaches. In this work, CuO nanostructures have been synthesized by aqueous precipitation method and simple chemical deposition method. The characterization of these products has been carried out by the x-ray Diffraction (XRD), Scanning Electron Microscope (SEM), Fourier Transform Infrared (FTIR) and UV–vis spectroscopy. Biological activity such as antibacterial nature of synthesized CuO is also explored. XRD peaks analysis revealed the monoclinic crystalline phase of copper oxide nanostructures. While the rod-like and particle-like morphologies have been observed in SEM results. FTIR spectra have confirmed the formation of CuO nanoparticles by exhibiting its characteristic peaks corresponding to 494 cm‑1 and 604 cm‑1. The energy band gap of the as-prepared CuO nanostructures determined from UV–vis spectra is found to be 2.18 eV and 2.0 eV for precipitation and chemically deposited samples respectively. The antibacterial activity results described that the synthesized CuO nanoparticles showed better activity against Staphylococcus aureus. The investigated results suggested the synthesis of highly stable CuO nanoparticles with significant antibacterial activities.

  20. Investigating the Effect of Biological Crusts on Some Biological Properties of Soil (Case Study: Qare Qir Rangelands of Golestan Province

    Directory of Open Access Journals (Sweden)

    J. Kakeh

    2016-09-01

    Full Text Available Introduction: Physical and biological soil crusts are the principal types of soil crusts. Physical and biological soil crusts are distributed in arid, semi-arid and sub-humid regions which constitute over 40% of the earth terrestrial surface. Biological soil crusts (BSCs result from an intimate association between soil particles and cyanobacteria, algae, fungi, lichens and mosses in different proportions which live on the surface, or in the immediately uppermost millimeters of soil. Some of the functions that BSCs influences include: water absorption and retention, nutrient retention, Carbon and nitrogen fixation, biological activate and hydrologic Status. BSCs are important from the ecological view point and their effects on the environment, especially in rangeland, and desert ecosystems and this caused which researchers have a special attention to this component of the ecosystems more than before. Materials and Methods: This study carried out in the Qara Qir rangelands of Golestan province, northeast of Iran (37º15′ - 37º23′ N &54º33′ -54º39′ E, to investigate the effects of BSCs on some of soil biological properties. Four sites including with and without BSCs cover were selected. Soil biological properties such as microbial populations, soil respiration, microbial biomass carbon and nitrogen, as well as, other effective properties such asorganic carbon percent, total nitrogen, electrical conductivity, and available water content were measured in depths of 0-5 and 5-15 cm of soil with four replications. The gathered data were analyzed by nested plot, and the mean values were compared by Duncan test. Results and Discussion: The results showed that organic carbon and water content were higher at the surface under BSCs, followed by 5-15 cm soils under BSCs. Both soil depths of uncrusted soils showed substantially lower organic carbon and water content than the BSC-covered soils. Total nitrogen was far higher in BSC-encrusted surface

  1. An Analytical Study of Prostate-Specific Antigen Dynamics.

    Science.gov (United States)

    Esteban, Ernesto P; Deliz, Giovanni; Rivera-Rodriguez, Jaileen; Laureano, Stephanie M

    2016-01-01

    The purpose of this research is to carry out a quantitative study of prostate-specific antigen dynamics for patients with prostatic diseases, such as benign prostatic hyperplasia (BPH) and localized prostate cancer (LPC). The proposed PSA mathematical model was implemented using clinical data of 218 Japanese patients with histological proven BPH and 147 Japanese patients with LPC (stages T2a and T2b). For prostatic diseases (BPH and LPC) a nonlinear equation was obtained and solved in a close form to predict PSA progression with patients' age. The general solution describes PSA dynamics for patients with both diseases LPC and BPH. Particular solutions allow studying PSA dynamics for patients with BPH or LPC. Analytical solutions have been obtained and solved in a close form to develop nomograms for a better understanding of PSA dynamics in patients with BPH and LPC. This study may be useful to improve the diagnostic and prognosis of prostatic diseases.

  2. Usefulness and biological background of dynamic contrast-enhanced MR images in patients with primary breast cancer

    International Nuclear Information System (INIS)

    Yamamoto, Yutaka; Kurebayashi, Junichi; Sonoo, Hiroshi

    2002-01-01

    Dynamic contrast-enhanced MR images were obtained between September 1998 and May 2000 from 44 primary breast cancer patients who were scheduled to undergo breast-conserving surgery. The MR images and clinico-pathological findings were analyzed to investigate the risk factors for histologically positive margins and histologically positive lymph node metastases. We elucidated the relationship between MR images and the biological background of breast cancer. The following interesting findings were made from these analyses. An irregular shape and unclear border of the tumor mass and the coexistence of daughter nodule(s) were significant risk factors for positive-surgical margins; an irregularly shaped tumor mass and spiculated tumor mass were significant risk factors for positive lymph node metastases; breast tumors with a strand-like appearance had a significantly lower histological grade; breast tumors with high contrast enhancement ratios had a significantly higher nuclear grade and progesterone receptor negativity; and breast tumors showing a ring-like enhancement expressed a low level of VEGF. These findings suggest that preoperative MR images of primary breast cancer provide not only useful information on the extent of breast tumors and the possibility of lymph node metastasis but also on the malignant potency and hormone responsiveness of breast tumors. (author)

  3. Current Comparative Table (CCT) automates customized searches of dynamic biological databases.

    Science.gov (United States)

    Landsteiner, Benjamin R; Olson, Michael R; Rutherford, Robert

    2005-07-01

    The Current Comparative Table (CCT) software program enables working biologists to automate customized bioinformatics searches, typically of remote sequence or HMM (hidden Markov model) databases. CCT currently supports BLAST, hmmpfam and other programs useful for gene and ortholog identification. The software is web based, has a BioPerl core and can be used remotely via a browser or locally on Mac OS X or Linux machines. CCT is particularly useful to scientists who study large sets of molecules in today's evolving information landscape because it color-codes all result files by age and highlights even tiny changes in sequence or annotation. By empowering non-bioinformaticians to automate custom searches and examine current results in context at a glance, CCT allows a remote database submission in the evening to influence the next morning's bench experiment. A demonstration of CCT is available at http://orb.public.stolaf.edu/CCTdemo and the open source software is freely available from http://sourceforge.net/projects/orb-cct.

  4. Backtracing neutron analysis in the fusion-fission dynamics study

    International Nuclear Information System (INIS)

    Brennand, E. de Goes; Hanappe, F.; Stuttge, L.

    2001-01-01

    A new method for the analysis of multi parametric experimental data is used in the study of the dynamics of the fission process for the compound system 126 Ba. We apply this method to obtain the correlation between thermal energy related to the neutron total multiplicity and the correlation between pre-scission neutron and pos-scission neutron multiplicities. The results obtained are interpreted into the framework of a dynamical model. From this interpretation we have access to the following information: the friction intensity which drives the dynamical evolution of the system; the initial deformation of the compound system; the barrier evolution with temperature and angular momentum, and fission times. (author)

  5. A New Theoretical Approach to Single-Molecule Fluorescence Optical Studies of RNA Dynamics

    International Nuclear Information System (INIS)

    Zhao Xinghai; Shan Guangcun; Bao Shuying

    2011-01-01

    Single-molecule fluorescence spectroscopy in condensed phases has many important chemical and biological applications. The single-molecule fluorescence measurements contain information about conformational dynamics on a vast range of time scales. Based on the data analysis protocols methodology proposed by X. Sunney Xie, the theoretical study here mainly focuses on the single-molecule studies of single RNA with interconversions among different conformational states, to with a single FRET pair attached. We obtain analytical expressions for fluorescence lifetime correlation functions that relate changes in fluorescence lifetime to the distance-dependent FRET mechanism within the context of the Smoluchowski diffusion model. The present work establishes useful guideline for the single-molecule studies of biomolecules to reveal the complicated folding dynamics of single RNA molecules at nanometer scale.

  6. Temperature dependent dynamics of DegP-trimer: A molecular dynamics study

    Directory of Open Access Journals (Sweden)

    Nivedita Rai

    2015-01-01

    Full Text Available DegP is a heat shock protein from high temperature requirement protease A family, which reacts to the environmental stress conditions in an ATP independent way. The objective of the present analysis emerged from the temperature dependent functional diversity of DegP between chaperonic and protease activities at temperatures below and above 28 °C, respectively. DegP is a multimeric protein and the minimal functional unit, DegP-trimer, is of great importance in understanding the DegP pathway. The structural aspects of DegP-trimer with respect to temperature variation have been studied using molecular dynamics simulations (for 100 ns and principal component analysis to highlight the temperature dependent dynamics facilitating its functional diversity. The DegP-trimer revealed a pronounced dynamics at both 280 and 320 K, when compared to the dynamics observed at 300 K. The LA loop is identified as the highly flexible region during dynamics and at extreme temperatures, the residues 46–80 of LA loop express a flip towards right (at 280 and left ( at 320 K with respect to the fixed β-sheet connecting the LA loop of protease for which Phe46 acts as one of the key residues. Such dynamics of LA loop facilitates inter-monomeric interaction with the PDZ1 domain of the neighbouring monomer and explains its active participation when DegP exists as trimer. Hence, the LA loop mediated dynamics of DegP-trimer is expected to provide further insight into the temperature dependent dynamics of DegP towards the understanding of its assembly and functional diversity in the presence of substrate.

  7. NASA plan for international crustal dynamics studies

    Science.gov (United States)

    1979-01-01

    The international activities being planned as part of the NASA geodynamics program are described. Methods of studying the Earth's crustal movements and deformation characteristics are discussed. The significance of the eventual formalations of earthquake predictions methods is also discussed.

  8. Study Reveals Brain Biology behind Self-Control

    Science.gov (United States)

    Sparks, Sarah D.

    2011-01-01

    A new neuroscience twist on a classic psychology study offers some clues to what makes one student able to buckle down for hours of homework before a test while his classmates party. The study published in the September 2011 edition of "Proceedings of the National Academy of Science," suggests environmental cues may "hijack" the brain's mechanisms…

  9. Nonlinear dynamics in ecosystem response to climatic change: Case studies and policy implications

    Science.gov (United States)

    Burkett, Virginia R.; Wilcox, Douglas A.; Stottlemyer, Robert; Barrow, Wylie; Fagre, Dan; Baron, Jill S.; Price, Jeff; Nielsen, Jennifer L.; Allen, Craig D.; Peterson, David L.; Ruggerone, Greg; Doyle, Thomas

    2005-01-01

    Many biological, hydrological, and geological processes are interactively linked in ecosystems. These ecological phenomena normally vary within bounded ranges, but rapid, nonlinear changes to markedly different conditions can be triggered by even small differences if threshold values are exceeded. Intrinsic and extrinsic ecological thresholds can lead to effects that cascade among systems, precluding accurate modeling and prediction of system response to climate change. Ten case studies from North America illustrate how changes in climate can lead to rapid, threshold-type responses within ecological communities; the case studies also highlight the role of human activities that alter the rate or direction of system response to climate change. Understanding and anticipating nonlinear dynamics are important aspects of adaptation planning since responses of biological resources to changes in the physical climate system are not necessarily proportional and sometimes, as in the case of complex ecological systems, inherently nonlinear.

  10. Neutron scattering and diffraction instrument for structural study on biology in Japan

    Energy Technology Data Exchange (ETDEWEB)

    Niimura, Nobuo [Japan Atomic Energy Research Inst., Ibaraki-ken (Japan)

    1994-12-31

    Neutron scattering and diffraction instruments in Japan which can be used for structural studies in biology are briefly introduced. Main specifications and general layouts of the instruments are shown.

  11. Technological Development of High-Performance MALDI Mass Spectrometry Imaging for the Study of Metabolic Biology

    Energy Technology Data Exchange (ETDEWEB)

    Feenstra, Adam D. [Iowa State Univ., Ames, IA (United States)

    2016-12-17

    This thesis represents efforts made in technological developments for the study of metabolic biology in plants, specifically maize, using matrix-assisted laser desorption/ ionization-mass spectrometry imaging.

  12. Study on Human-structure Dynamic Interaction in Civil Engineering

    Science.gov (United States)

    Gao, Feng; Cao, Li Lin; Li, Xing Hua

    2018-06-01

    The research of human-structure dynamic interaction are reviewed. Firstly, the influence of the crowd load on structural dynamic characteristics is introduced and the advantages and disadvantages of different crowd load models are analyzed. Then, discussing the influence of structural vibration on the human-induced load, especially the influence of different stiffness structures on the crowd load. Finally, questions about human-structure interaction that require further study are presented.

  13. Dynamic scintigraphic studies after oesophageal reconstruction

    International Nuclear Information System (INIS)

    Maliska, C.M.; Maliska, C.; Pinto, E.; Castro, L.; Fonseca, L.B.E; Miranda, M.

    1997-01-01

    Full text: We have studied the oesophageal transit and gastric emptying in the monitoring of the effect of oesophageal reconstruction surgery. Oncologic patients were evaluated after oesophageal reconstruction surgery with gastric (14 patients) or colonic (5 patients) tube and they were compared with 15 healthy volunteers, using scintigraphic method with liquid food (S-colloid-Tc99m). In the oesophageal transit studies there were no significant statistical differences among the three groups, when we have just considered to two superior (of the three) segments, as oesophagus, showing that the distal neo-tube works just like the stomach of normal volunteers

  14. Structural Biology Fact Sheet

    Science.gov (United States)

    ... NIGMS NIGMS Home > Science Education > Structural Biology Structural Biology Tagline (Optional) Middle/Main Content Area PDF Version (688 KB) Other Fact Sheets What is structural biology? Structural biology is the study of how biological ...

  15. Biological, histological and ultra-structural studies of female mullet ...

    African Journals Online (AJOL)

    Aghomotsegin

    2015-07-29

    Jul 29, 2015 ... INTRODUCTION. Mugilids are widely distributed ... were fixed in 10% formal saline solution until used for histological studies. The gonadosomatic .... cephalus (October and November), in general all the ovaries of ripe marine ...

  16. Biological characteristics as a part of pollution monitoring studies

    Digital Repository Service at National Institute of Oceanography (India)

    Nair, V.R.; Govindan, K.

    Ecosystem modifications can be considered as an integral part of any pollution monitoring studies and in such cases community structure/diversity is of prime importance. Considering this advantage of aquatic life, pelagic and benthic communities...

  17. Northeast Cooperative Research Study Fleet (SF) Program Biological Sampling Data

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Northeast Cooperative Research Study Fleet (SF) Program partners with a subset of commercial fishermen to collect high quality, high resolution, haul by haul...

  18. Small-scale laser based electron accelerators for biology and medicine: a comparative study of the biological effectiveness

    Science.gov (United States)

    Labate, Luca; Andreassi, Maria Grazia; Baffigi, Federica; Basta, Giuseppina; Bizzarri, Ranieri; Borghini, Andrea; Candiano, Giuliana C.; Casarino, Carlo; Cresci, Monica; Di Martino, Fabio; Fulgentini, Lorenzo; Ghetti, Francesco; Gilardi, Maria Carla; Giulietti, Antonio; Köster, Petra; Lenci, Francesco; Levato, Tadzio; Oishi, Yuji; Russo, Giorgio; Sgarbossa, Antonella; Traino, Claudio; Gizzi, Leonida A.

    2013-05-01

    Laser-driven electron accelerators based on the Laser Wakefield Acceleration process has entered a mature phase to be considered as alternative devices to conventional radiofrequency linear accelerators used in medical applications. Before entering the medical practice, however, deep studies of the radiobiological effects of such short bunches as the ones produced by laser-driven accelerators have to be performed. Here we report on the setup, characterization and first test of a small-scale laser accelerator for radiobiology experiments. A brief description of the experimental setup will be given at first, followed by an overview of the electron bunch characterization, in particular in terms of dose delivered to the samples. Finally, the first results from the irradiation of biological samples will be briefly discussed.

  19. Physicochemical and biological study of a renal scintigraphy agent: the DMSA - 99mTc complex

    International Nuclear Information System (INIS)

    Laroche, Dominique

    1979-01-01

    This research thesis deals with the study of the dimercaptosuccinic acid (DMSA) marked with 99m Tc, a recently developed scintigraphy agent used for the kidney isotopic exploration. The author notably studied the relationships between the physicochemical properties of solutions of dimercaptosuccinic acid marked with 99m Tc and the biological distribution of 99m Tc in order to reach a better understanding of the biological mechanism which results in technetium fixation to the kidney

  20. A Trade Study of Two Membrane-Aerated Biological Water Processors

    Science.gov (United States)

    Allada, Ram; Lange, Kevin; Vega. Leticia; Roberts, Michael S.; Jackson, Andrew; Anderson, Molly; Pickering, Karen

    2011-01-01

    Biologically based systems are under evaluation as primary water processors for next generation life support systems due to their low power requirements and their inherent regenerative nature. This paper will summarize the results of two recent studies involving membrane aerated biological water processors and present results of a trade study comparing the two systems with regards to waste stream composition, nutrient loading and system design. Results of optimal configurations will be presented.

  1. Oscillation and stability of delay models in biology

    CERN Document Server

    Agarwal, Ravi P; Saker, Samir H

    2014-01-01

    Environmental variation plays an important role in many biological and ecological dynamical systems. This monograph focuses on the study of oscillation and the stability of delay models occurring in biology. The book presents recent research results on the qualitative behavior of mathematical models under different physical and environmental conditions, covering dynamics including the distribution and consumption of food. Researchers in the fields of mathematical modeling, mathematical biology, and population dynamics will be particularly interested in this material.

  2. Fundamental study of dynamic ECT by dual detector gammacamera system

    International Nuclear Information System (INIS)

    Kakegawa, M.; Matsui, S.; Maeda, H.; Takeda, K.; Nakagawa, T.

    1982-01-01

    The improvement of image quality of reconstructed image by the simple pre-processing of projections is studied. Using the improved algorithm and dual detector gammacamera system, the possibility of dynamic ECT is studied. As shown in clinical examples, renal flow study using Tc-99m-DTPA, dynamic ECT imaging is possible with measuring time of 1 or 2 minutes. By this method cortex and medulla are separately imaged and each function can be analyzed more precisely. Using high sensitive collimator it will be possible to take ECT images every 30 sec. with little resolution loss quantitative three dimensional time activity analysis is under study

  3. Clinical application of cerebral dynamic perfusion studies

    International Nuclear Information System (INIS)

    DeLand, F.H.

    1975-01-01

    Radionuclide cerebral perfusion studies are assuming a far greater importance in the detection and differential diagnosis of cerebral lesions. Perfusion studies not only contribute to the differential diagnosis of lesions but in certain cases are the preferred methods by which more accurate clinical interpretations can be made. The characteristic blood flow of arterio-venous malformations readily differentiates this lesion from neoplasms. The decreased perfusion or absent perfusion observed in cerebral infarctions is diagnostic without concurrent evidence from static images. Changes in rates and direction of blood flow contribute fundamental information to the status of stenosis and vascular occlusion and, in addition, offer valuable information on the competency and routes of collateral circulation. The degree of cerebral perfusion after cerebral vascular accidents appears to be directly related to patient recovery, particularly muscular function. Cerebral perfusion adds a new parameter in the diagnosis of subdural haematomas and concussion and in the differentiation of obscuring radioactivity from superficial trauma. Although pictorial displays of perfusion blood flow will offer information in most cerebral vascular problems, the addition of computer analysis better defines temporal relationships of regional blood flow, quantitative changes in flow and the detection of the more subtle increases or decreases in cerebral blood flow. The status of radionuclide cerebral perfusion studies has taken on an importance making it the primary modality for the diagnosis of cerebral lesions. (author)

  4. The Chemistry and Flow Dynamics of Molecular Biological Tools Used to Confirm In Situ Bioremediation of Benzene, TBA, and MTBE

    Science.gov (United States)

    North, K. P.; Mackay, D. M.; Scow, K. M.

    2010-12-01

    In situ bioremediation has typically been confirmed by collecting sediment and groundwater samples to directly demonstrate a degradation process in a laboratory microcosm. However, recent advances in molecular biological tools present options for demonstrating degradation processes with field-based tools that are less time-consuming. We have been investigating the capability of some of these molecular biological tools to evaluate in situ biodegradation of tert-butyl alcohol (TBA), methyl tert-butyl ether (MTBE), and benzene at two field sites in California. At both sites, we have deployed Bio-Traps® (“traps”), made of Bio-Sep® beads in slotted PVC pipe, which provide ideal environments for microbial colonization. Stable Isotope Probing can be accomplished by sorbing the13C-labeled organic contaminant of concern onto Bio-Sep® beads (“baiting”); incorporation of 13C into the biomass collected by the trap would indicate that the microbial community was capable of degrading the labeled compound. In addition, we examined the chemistry and flow dynamics of these traps and present those results here. We performed a field experiment and a lab experiment to, in part, define the rate that different baits leached off various traps. At a TBA- and MTBE-contaminated site at Vandenberg AFB, Lompoc, CA, the TBA-dominant plume was effectively treated by recirculation/oxygenation of groundwater, decreasing TBA and MTBE concentrations to detection limits along predicted flowpaths created by two pairs of recirculation wells. We used the generated aerobic treatment zone to deploy traps baited with 13C-labeled MTBE or TBA in a novel, ex situ experimental setup. The groundwater flow extracted from the aerobic treatment zone was split through several chambers, each containing a trap and monitoring of influent and effluent. The chamber effluent was measured throughout a six-week deployment and analyzed for both TBA and MTBE; the majority of mass leached from the baited traps did

  5. Dynamic Processes in Biology, Chemistry, and Materials Science: Opportunities for UltraFast Transmission Electron Microscopy - Workshop Summary Report

    Energy Technology Data Exchange (ETDEWEB)

    Kabius, Bernd C.; Browning, Nigel D.; Thevuthasan, Suntharampillai; Diehl, Barbara L.; Stach, Eric A.

    2012-07-25

    This report summarizes a 2011 workshop that addressed the potential role of rapid, time-resolved electron microscopy measurements in accelerating the solution of important scientific and technical problems. A series of U.S. Department of Energy (DOE) and National Academy of Science workshops have highlighted the critical role advanced research tools play in addressing scientific challenges relevant to biology, sustainable energy, and technologies that will fuel economic development without degrading our environment. Among the specific capability needs for advancing science and technology are tools that extract more detailed information in realistic environments (in situ or operando) at extreme conditions (pressure and temperature) and as a function of time (dynamic and time-dependent). One of the DOE workshops, Future Science Needs and Opportunities for Electron Scattering: Next Generation Instrumentation and Beyond, specifically addressed the importance of electron-based characterization methods for a wide range of energy-relevant Grand Scientific Challenges. Boosted by the electron optical advancement in the last decade, a diversity of in situ capabilities already is available in many laboratories. The obvious remaining major capability gap in electron microscopy is in the ability to make these direct in situ observations over a broad spectrum of fast (µs) to ultrafast (picosecond [ps] and faster) temporal regimes. In an effort to address current capability gaps, EMSL, the Environmental Molecular Sciences Laboratory, organized an Ultrafast Electron Microscopy Workshop, held June 14-15, 2011, with the primary goal to identify the scientific needs that could be met by creating a facility capable of a strongly improved time resolution with integrated in situ capabilities. The workshop brought together more than 40 leading scientists involved in applying and/or advancing electron microscopy to address important scientific problems of relevance to DOE’s research

  6. Biological studies on albino rats fed with Sorghum bicolor starch ...

    African Journals Online (AJOL)

    STORAGESEVER

    2008-06-17

    Jun 17, 2008 ... ghum and millets. It consists of amylopectin, a branched- chain polymer of glucose, and amylose, a straight-chain .... diamine tetracetic acid (EDTA) tubes for hematological studies. .... cially for people with diabetes such foods are known to ... consists of oligosaccharides, vitamins, essential amino acids ...

  7. NATO Advanced Study Institute on Advances in Chemical Reaction Dynamics

    CERN Document Server

    Capellos, Christos

    1986-01-01

    This book contains the formal lectures and contributed papers presented at the NATO Advanced Study Institute on. the Advances in Chemical Reaction Dynamics. The meeting convened at the city of Iraklion, Crete, Greece on 25 August 1985 and continued to 7 September 1985. The material presented describes the fundamental and recent advances in experimental and theoretical aspects of, reaction dynamics. A large section is devoted to electronically excited states, ionic species, and free radicals, relevant to chemical sys­ tems. In addition recent advances in gas phase polymerization, formation of clusters, and energy release processes in energetic materials were presented. Selected papers deal with topics such as the dynamics of electric field effects in low polar solutions, high electric field perturbations and relaxation of dipole equilibria, correlation in picosecond/laser pulse scattering, and applications to fast reaction dynamics. Picosecond transient Raman spectroscopy which has been used for the elucidati...

  8. Studies on the biological effects of deuteriated organic compounds

    International Nuclear Information System (INIS)

    Dinh-Nguyen, Nguyen; Vincent, J.

    1976-01-01

    The antifungal activity of some perdeuterated fatty acids with a normal chain of 11 to 18 carbon atoms was investigated on common dermatophytes Epidermophyton floccosum, Microsporum canis, Trichophyton mentagrophytes and T. rubrum under in vitro conditions. A perdeuterated compound is one in which most of the hydrogen atoms in the molecule are replaced by deuterium. These studies were performed by the dilution technique with respiratory measurements. Perdeuteration of of some fatty acids increases their inhibitory effect on the dermatophyte growth. Perdeuterated n-hendecanoic acid proved to be the most active of the substances tested. Possible mechanisms behind the enhanced antifungal activity due to the perdeuteration of fatty acids are discussed. The present study investigates the antifungal properties of some perdeuterated fatty acids on dermatophytes in vitro

  9. Study of Biological Pigments by Single Specimen Derivative Spectrophotometry

    Science.gov (United States)

    Goldstein, Jack M.

    1970-01-01

    The single specimen derivative (SSD) method provides an absolute absorption spectrum of a substance in the absence of a suitable reference. Both a reference and a measuring monochromatic beam pass through a single sample, and the specimen itself acts as its own reference. The two monochromatic beams maintain a fixed wavelength difference upon scanning, and the difference in absorbance of the two beams is determined. Thus, the resulting spectrum represents the first derivative of the conventional type absorption spectrum. Tissues and cell fractions have been examined at room and liquid N2 temperature and chromophoric molecules such as the mitochondrial cytochromes and blood pigments have been detectable in low concentrations. In the case of isolated cellular components, the observed effects of substrates and inhibitors confirm similar studies by conventional spectrophotometry. The extension of the SSD concept to the microscopic level has permitted the study of the tissue compartmentalization and function of cytochromes and other pigments within layered tissue. PMID:4392452

  10. Study on biologically active substances in irradiated apple juice

    International Nuclear Information System (INIS)

    Tencheva, S.

    1975-01-01

    The radiochemical changes proceeding by irradiation of foodstuffs rich in carbohydrates are studied. For the purpose pure solutions of D-glucose, D-fructose and sucrose and fresh apple juice, irradiated with 0,5 and 1,0 Mrad are investigated. Changes set in UV-spectra of the irradiated foodstuffs, the specific reaction of malonic dialdehyde formation with 2-thiobarbituric acid and the formation of carbonyl compounds reacting with 2,4-dinitro phenylhydrazine are studied. Results show that in the irradiated sample solutions of sugars and apple juice two peaks are formed. The malonic dialdehyde formation depends on the dose of irradiation applied. The newly formed carbonyl compounds both in the sample solutions and in the juice are 8 to 9 in number. (author)

  11. Synthesis labeling and biological studies of 16-131I

    International Nuclear Information System (INIS)

    Sato, M.K.

    1988-01-01

    The increasing interest in obtaining radiopharmaceuticals for metabolic imaging of heart muscle led us to prepare 16-IODINE HEXADECANOIC ACID by tosilation of the corresponding hydroxy acid, following iodination with NaI and finally, introducing radioiodine (Na 131 I) by isotopic exchange reaction. The reaction products were identified by determination of melting point, elementary and spectroscopic analysis such as infra-red absortion and magnetic nuclear resonance. The radiopharmaceutical after radiochemical and other specific control procedures for injetable such as sterility and apyrogenicity, was firstly utilized in dogs: preferencial uptake by the heart, as well as by the liver was confirmed. Then, studies in patients with or without heart diseases were performed. The biodistribution of 16- 131 I-HEXADECANOIC ACID was carried out in Wistar rats. The scintigraphic images in animals and in humans demonstrated that 16- 131 -HEXADECANOIC ACID is suitable for studying viable areas as well as energetic exchange of heart muscle. (author) [pt

  12. Biological study of a tritiated luminous paint (1962)

    International Nuclear Information System (INIS)

    Remy, J.; Meunier, J.; Aeberhardt, A.

    1962-01-01

    A powdered mixture of zinc sulphide and a tritiated polyester has been administered to rats by means of the oesophageal probe. The distribution of tritium in the organ, and its elimination, have been studied. It appears that from 75 to 80 per cent of the polyester has undergone sufficient degradation in the intestinal medium to be absorbed by the digestive mucous membrane and to be subjected to metabolic reactions. (authors) [fr

  13. Biological and Theoretical Studies of Adaptive Networks: The Conditioned Response.

    Science.gov (United States)

    1992-06-30

    suggest experimental tests and provide direction for physiological studies. 14 SU~la TIPO ~IS- NIJUMS Of PAGIS 17. @1d-ftA ITY CLASSIPtCATICON...mancte suditioned inhibition of the rabbit’s nictitating membrane response, CI tasks require the active suppression of CRs in the Bull . Psychon. Soc., 20... Bull ., 84 (1977) encephalon and mesencephalon26. 690-711. Several lines of evidence suggest that the septal and 8 Evans,J.A.C. and Thornton, E.W

  14. In vitro biological models in order to study BNCT

    International Nuclear Information System (INIS)

    Dagrosa, Maria A.; Kreimann, Erica L.; Schwint, Amanda E.; Juvenal, Guillermo J.; Pisarev, Mario A.; Farias, Silvia S.; Garavaglia, Ricardo N.; Batistoni, Daniel A.

    1999-01-01

    Undifferentiated thyroid carcinoma (UTC) lacks an effective treatment. Boron neutron capture therapy (BNCT) is based on the selective uptake of 10 B-boronated compounds by some tumours, followed by irradiation with an appropriate neutron beam. The radioactive boron originated ( 11 B) decays releasing 7 Li, gamma rays and alpha particles, and these latter will destroy the tumour. In order to explore the possibility of applying BNCT to UTC we have studied the biodistribution of BPA. In vitro studies: the uptake of p- 10 borophenylalanine (BPA) by the UTC cell line ARO, primary cultures of normal bovine thyroid cells (BT) and human follicular adenoma (FA) thyroid was studied. No difference in BPA uptake was observed between proliferating and quiescent ARO cells. The uptake by quiescent ARO, BT and FA showed that the ARO/BT and ARO/FA ratios were 4 and 5, respectively (p< 0.001). The present experimental results open the possibility of applying BNCT for the treatment of UTC. (author)

  15. Microscopic study on dynamic barrier in fusion reactions

    International Nuclear Information System (INIS)

    Wu Xizhen; Tian Junlong; Zhao Kai; Li Zhuxia; Wang Ning

    2004-01-01

    The authors briefly review the fusion process of very heavy nuclear systems and some theoretical models. The authors propose a microscopic transport dynamic model, i.e. the Improved Quantum Molecular Dynamic model, for describing fusion reactions of heavy systems, in which the dynamical behavior of the fusion barrier in heavy fusion systems has been studied firstly. The authors find that with the incident energy decreasing the lowest dynamic barrier is obtained which approaches to the adiabatic static barrier and with increase of the incident energy the dynamic barrier goes up to the diabatic static barrier. The authors also indicate that how the dynamical fusion barrier is correlated with the development of the configuration of fusion partners along the fusion path. Associating the single-particle potentials obtained at different stages of fusion with the Two Center Shell Model, authors can study the time evolution of the single particle states of fusion system in configuration space of single particle orbits along the fusion path. (author)

  16. Studies of Beam Dynamics in Cooler Rings

    International Nuclear Information System (INIS)

    Dietrich, J.; Stein, J.; Meshkov, I.; Sidorin, A.; Smirnov, A.

    2006-01-01

    This report describes the numerical simulation of the crystalline proton beam formation in COSY using BETACOOL code. The study includes the description of experimental results at NAP-M storage ring where the large reduction of the momentum spread was observed for first time. The present simulation shows that this behavior of proton beam can not be explained as ordered state of protons. The numerical simulation of crystalline proton beams was done for COSY parameters. The number of protons when the ordering state can be observed is limited by value 106 particles and momentum spread less then 10-6. Experimental results for the attempt to achieve of ordered state of proton beam for COSY is presented. This work is supported by RFBR grant no. 05-02-16320 and INTAS grant no. 03-54-5584

  17. RF quadrupole beam dynamics design studies

    International Nuclear Information System (INIS)

    Crandall, K.R.; Stokes, R.H.; Wangler, T.P.

    1979-01-01

    The radio-frequency quadrupole (RFQ) linear accelerator structure is expected to permit considerable flexibility in achieving linac design objectives at low velocities. Calculational studies show that the RFQ can accept a high-current, low-velocity, dc beam, bunch it with high efficiency, and accelerate it to a velocity suitable for injection into a drift-tube linac. Although it is relatively easy to generate a satisfactory design for an RFQ linac for low beam currents, the space-charge effects produced by high currents dominate the design criteria. Methods have been developed to generate solutions that make suitable compromises between the effects of emittance growth, transmission efficiency, and overall structure length. Results are given for a test RFQ linac operating at 425 MHz

  18. Biological Technologies for Life Beyond Low Earth Orbit (BT4LBLEO): Study Introductions and Synopsis

    Science.gov (United States)

    Hines, John W.

    2011-01-01

    The study will address the following mission concerns: -Extended human presence in the environments of deep space as well as the Moon and Mars will require a solid biological understanding of the integrated effects of diminished gravity, enhanced radiation, and transit- and destination-specific variables from the sub-cellular to the whole organism level. -Biological and associated technologies for biological and robotic precursor missions to realize future objectives for space colonization. -Surfaces, gravity levels, radiation environments, and atmospheres of these nearest neighbors are radically different in chemical and geological make-up from those on our home planet, and all of these contributory effects must be considered.

  19. Bacteriophage-based synthetic biology for the study of infectious diseases

    Science.gov (United States)

    Lu, Timothy K.

    2014-01-01

    Since their discovery, bacteriophages have contributed enormously to our understanding of molecular biology as model systems. Furthermore, bacteriophages have provided many tools that have advanced the fields of genetic engineering and synthetic biology. Here, we discuss bacteriophage-based technologies and their application to the study of infectious diseases. New strategies for engineering genomes have the potential to accelerate the design of novel phages as therapies, diagnostics, and tools. Though almost a century has elapsed since their discovery, bacteriophages continue to have a major impact on modern biological sciences, especially with the growth of multidrug-resistant bacteria and interest in the microbiome. PMID:24997401

  20. Biological study of some labeled C16 fatty acids

    Energy Technology Data Exchange (ETDEWEB)

    Riche, F.; Mathieu, J.P.; Busquet, G.; Vidal, M.; Comet, M.; Pernin, C. (C.H.R.U. de Grenoble, 38 - La Tronche (France)); Godart, J.; Benabed, A. (Institut des Sciences Nucleaires, 38 - Grenoble (France)); Bardy, A. (C.E.A.-ORIS, 91 - Gif-sur-Yvette (France))

    1983-01-01

    The evolution of myocardial, blood, liver and kidney activity is studied in mice after I.V. injection of some labelled C16 fatty acids. With ..omega.. iodo fatty acids, the presence or absence of a double bond and the character Z or E have no influence on the tissue activity. The presence of a triple bond decreases the fixation, modifies the intramyocardial metabolism of the fatty acid and accelerates the rate of decrease of myocardial activity. ..omega.. bromo fatty acid have the same maximal fixation as ..omega.. iodo fatty acid but a more rapid decrease of myocardial activity. ..cap alpha.. iodo fatty acid has a very low myocardial fixation.

  1. Biological study of some labeled C16 fatty acids

    International Nuclear Information System (INIS)

    Riche, F.; Mathieu, J.P.; Busquet, G.; Vidal, M.; Comet, M.; Pernin, C.; Godart, J.; Benabed, A.; Bardy, A.

    1983-01-01

    The evolution of myocardial, blood, liver and kidney activity is studied in mice after I.V. injection of some labelled C16 fatty acids. With ω iodo fatty acids, the presence or absence of a double bond and the character Z or E have no influence on the tissue activity. The presence of a triple bond decreases the fixation, modifies the intramyocardial metabolism of the fatty acid and accelerates the rate of decrease of myocardial activity. ω bromo fatty acid have the same maximal fixation as ω iodo fatty acid but a more rapid decrease of myocardial activity. α iodo fatty acid has a very low myocardial fixation [fr

  2. Study on biological and environmental factors for azoospermia

    Directory of Open Access Journals (Sweden)

    Spas Dzhoglov

    2016-09-01

    Full Text Available The absence of sperm in the seminal fluid is known as azoospermia. This medical condition is in a direct association with male's infertility. A complete medical history, physical examination, tests of selected hormones and tests for male fertility (including sperm analysis are used for the diagnosis of azoospermia. The number of 1314 men, with fertility problems, at age between 20 and 67 years, were included in this investigation. The data obtained in the study showed that azoospermia occurred in 5.25% of the group studied. The Klinefelter syndrome was cytogenetically diagnosed in 2.9% of the male individuals. There was found that 44.3% of males with azoospermia have been smokers, 7.1% of them – addicted to drugs, 17.1% have taken different medicaments, 4.35% – have had radiation therapy, 4.35% have had a diagnosis "varicocele". The volume of the ejaculate was less than 2 ml in 37.68% of the men and more than 7 ml in 2.89% of them.

  3. Preparation and biological studies of 68Ga-DOTA-alendronate

    Directory of Open Access Journals (Sweden)

    Ashraf Fakhari

    2016-07-01

    Full Text Available Objective(s: In line with previous research on the development of conjugated bisphosphonate ligands as new bone-avid agents, in this study, DOTA conjugated alendronate (DOTA-ALN was synthesized and evaluated after labeling with gallium-68 (68Ga.Methods: DOTA-ALN was synthesized and characterized, followed by 68Ga-DOTA-ALN preparation, using DOTA-ALN and 68GaCl3 (pH: 4-5 at 92-95°C for 10 min. Stability tests, hydroxyapatite assay, partition coefficient calculation,biodistribution studies, and imaging were performed on the developed agent in normal rats.Results: The complex was prepared with high radiochemical purity (>99% as depicted by radio thin-layer chromatography; specific activity: 310-320GBq/mmol after solid phase purification and was stabilized for up to 90 min with a logP value of -2.91. Maximum ligand binding (65% was observed in the presence of 50 mg of hydroxyapatite; a major portion of the activity was excreted through the kidneys. With the exception of excretory organs, gastrointestinal tract organs, including the liver, intestine, and colon, showed significant uptake; however, the bone uptake was low (

  4. Tensile strength of biological fibrin sealants: a comparative study.

    Science.gov (United States)

    Lacaze, Laurence; Le Dem, Nicolas; Bubenheim, Michael; Tsilividis, Basile; Mezghani, Julien; Schwartz, Lilian; Francois, Arnaud; Ertaud, Jean Yves; Bagot d'Arc, Maurice; Scotté, Michel

    2012-08-01

    Fibrin sealants are commonly used in liver surgery, although their effectiveness in routine clinical practice remains controversial. Individual sealant characteristics are based on hemostatic effects and adhesion properties that can be experimentally measured using the 'rat skin test' or the 'pig skin test'. This study used a more relevant and realistic experimental canine model to compare the differences in the adhesive properties of four fibrin sealants in hepatectomy: Tisseel/Tissucol, Tachosil, Quixil, and Beriplast. A partial hepatectomy was performed in beagle dogs under general anesthesia to obtain liver cross-sections. Fibrin sealants were allocated to dog livers using a Youden square design. The tensile strength measurement was performed using a traction system to measure the rupture stress point of a small wooden cylinder bonded to the liver cross-section. Significantly greater adhesion properties were observed with Tisseel/Tissucol compared with Quixil or Beriplast (P = 0.002 and 0.001, respectively). Similarly, Tachosil demonstrated significantly greater adhesive properties compared with Beriplast (P = 0.009) or Quixil (P = 0.014). No significant differences were observed between Tisseel/Tissucol and Tachosil or between Beriplast and Quixil. The results of this comparative study demonstrate that different fibrin sealants exhibit different adhesive properties. Tisseel/Tissucol and Tachosil provided greatest adhesion to liver cross-section in our canine model of hepatectomy. These results may enable the optimal choice of fibrin sealants for this procedure in clinical practice. Copyright © 2012 Elsevier Inc. All rights reserved.

  5. The applications of microdosimetry in radiation biology study

    International Nuclear Information System (INIS)

    Kim, Eunhee

    2002-01-01

    To understand the mechanisms by which the ionizing radiation causes these damages, the spatial patterns of interaction and energy deposition by radiations should be explained in cellular level. All the descriptions of the physical process of radiation interaction and energy transfer in cellular or microscopic scale constitute the field of microdosimetry. The underlying motivations of microdosimetry study range from the efficient control of the radiation protection measures to the improvement of the diagnostic and therapeutic effectiveness in medical applications of radiation. The major quantity in the conventional radiation dosimetry or the macroscopic dosimetry is the 'absorbed dose' defined as the mean value of the possible energy depositions per unit mass of the target. With the microscopic targets such as cells and subcellular organelles, the average quantity can not represent the radiation actions on the targets any more because of the inhomogeneous and stochastic nature in radiation interaction with matter. The essence of microdosimetry is to study the fluctuation of energy deposition in a microscopic volume and its deviation from the mean value attributed to the inherent randomness of radiation interactions with matter

  6. Preparation and Biological Study of (68)Ga-DOTA-alendronate.

    Science.gov (United States)

    Fakhari, Ashraf; Jalilian, Amir R; Johari-Daha, Fariba; Shafiee-Ardestani, Mehdi; Khalaj, Ali

    2016-01-01

    In line with previous research on the development of conjugated bisphosphonate ligands as new bone-avid agents, in this study, DOTA-conjugated alendronate (DOTA-ALN) was synthesized and evaluated after labeling with gallium-68 ((68)Ga). DOTA-ALN was synthesized and characterized, followed by (68)Ga-DOTA-ALN preparation, using DOTA-ALN and (68)GaCl3 (pH: 4-5) at 92-95° C for 10 min. Stability tests, hydroxyapatite assay, partition coefficient calculation, biodistribution studies, and imaging were performed on the developed agent in normal rats. The complex was prepared with high radiochemical purity (>99% as depicted by radio thin-layer chromatography; specific activity: 310-320 GBq/mmol) after solid phase purification and was stabilized for up to 90 min with a log P value of -2.91. Maximum ligand binding (65%) was observed in the presence of 50 mg of hydroxyapatite; a major portion of the activity was excreted through the kidneys. With the exception of excretory organs, gastrointestinal tract organs, including the liver, intestine, and colon, showed significant uptake; however, the bone uptake was low (<1%) at 30 min after the injection. The data were also confirmed by sequential imaging at 30-90 min following the intravenous injection. The high solubility and anionic properties of the complex led to major renal excretion and low hydroxyapatite uptake; therefore, the complex failed to demonstrate bone imaging behaviors.

  7. Structural, dynamical, and electronic properties of amorphous silicon: An ab initio molecular dynamics study

    Energy Technology Data Exchange (ETDEWEB)

    Car, R.; Parrinello, M.

    1988-01-18

    An amorphous silicon structure is obtained with a computer simulation based on a new molecular-dynamics technique in which the interatomic potential is derived from a parameter-free quantum mechanical method. Our results for the atomic structure, the phonon spectrum, and the electronic properties are in excellent agreement with experiment. In addition we study details of the microscopic dynamics which are not directly accessible to experiment. We find in particular that structural defects are associated with weak bonds. These may give rise to low-frequency vibrational modes.

  8. Molecular dynamics studies of the dynamics of supercooled Lennard-Jones liquids

    International Nuclear Information System (INIS)

    De Leeuw, S.W.; Brakkee, M.J.D.

    1990-01-01

    Results are presented of molecular dynamics experiments, in which the Lennard-Jones liquid is cooled isobarically into the metastable temperature region below the freezing temperature. The variation of the density-density and transverse current correlation functions with temperature is studied. We observed a power-law behaviour for the temperature dependence of dynamical properties (viscosity and coefficienty of self-diffusion) with an exponent in good agreement with prediction of mode coupling theories and recent experimental results. (author). 23 refs, 5 figs

  9. Protein Dynamics in Organic Media at Varying Water Activity Studied by Molecular Dynamics Simulation

    DEFF Research Database (Denmark)

    Wedberg, Nils Hejle Rasmus Ingemar; Abildskov, Jens; Peters, Günther H.J.

    2012-01-01

    In nonaqueous enzymology, control of enzyme hydration is commonly approached by fixing the thermodynamic water activity of the medium. In this work, we present a strategy for evaluating the water activity in molecular dynamics simulations of proteins in water/organic solvent mixtures. The method...... relies on determining the water content of the bulk phase and uses a combination of Kirkwood−Buff theory and free energy calculations to determine corresponding activity coefficients. We apply the method in a molecular dynamics study of Candida antarctica lipase B in pure water and the organic solvents...

  10. On finding and using identifiable parameter combinations in nonlinear dynamic systems biology models and COMBOS: a novel web implementation.

    Science.gov (United States)

    Meshkat, Nicolette; Kuo, Christine Er-zhen; DiStefano, Joseph

    2014-01-01

    Parameter identifiability problems can plague biomodelers when they reach the quantification stage of development, even for relatively simple models. Structural identifiability (SI) is the primary question, usually understood as knowing which of P unknown biomodel parameters p1,…, pi,…, pP are-and which are not-quantifiable in principle from particular input-output (I-O) biodata. It is not widely appreciated that the same database also can provide quantitative information about the structurally unidentifiable (not quantifiable) subset, in the form of explicit algebraic relationships among unidentifiable pi. Importantly, this is a first step toward finding what else is needed to quantify particular unidentifiable parameters of interest from new I-O experiments. We further develop, implement and exemplify novel algorithms that address and solve the SI problem for a practical class of ordinary differential equation (ODE) systems biology models, as a user-friendly and universally-accessible web application (app)-COMBOS. Users provide the structural ODE and output measurement models in one of two standard forms to a remote server via their web browser. COMBOS provides a list of uniquely and non-uniquely SI model parameters, and-importantly-the combinations of parameters not individually SI. If non-uniquely SI, it also provides the maximum number of different solutions, with important practical implications. The behind-the-scenes symbolic differential algebra algorithms are based on computing Gröbner bases of model attributes established after some algebraic transformations, using the computer-algebra system Maxima. COMBOS was developed for facile instructional and research use as well as modeling. We use it in the classroom to illustrate SI analysis; and have simplified complex models of tumor suppressor p53 and hormone regulation, based on explicit computation of parameter combinations. It's illustrated and validated here for models of moderate complexity, with

  11. Preliminary experiments on dynamic biology of micro-organisms to avoid any specific full-blown syndrome on humans

    Science.gov (United States)

    Meer, Sneer

    2002-06-01

    The aim of this paper is to apply an efficient system to detect, identify and quicken suppression of any dangerous micro-organism which threatens the health of the human body in any form. It is well known that some specimens of this kind of possess a specific energy related to their speed of division, toxin emissions and high-powered interaction with human and animal cells which have the capacity to provide certain deadly full-blown syndromes. Many problems relating to the above-mentioned properties have not been clarified to date, and it is vital to find a rapid and valid reply as soon as possible. Inter-disciplinary sciences directed us to start some experiments to solve such problems, considering that the human body is dotted with a multiple interactive system of energy release, a fact which can explain the source of the micro-organism's energy also, for their necessity to manifest their deadly pathology. From practical preliminary experiments with some micro-mechanical systems using light-microscopy, connected to video TV Recorder System, one obtains optical enlarged TV images of certain processes which indicated the right way towards our crucial target; ie: the preparation of safe vaccines and safe medicines. This will constitute a basic system to a void deadly manifestations of dangerous micro-organisms and/or even regular infections on earth and in space, a system which will probably be applied at the ISS Space Station and other future actions in space in long and very long flights. We look forward to applying this system of dynamic biology towards preparation of a real and valid vaccine(s) against HIV virus on AIDS diseases.

  12. STUDY ON HEAT DYNAMIC LOADING OF RUBBER

    Directory of Open Access Journals (Sweden)

    T. I. Igumenova

    2015-01-01

    Full Text Available A number of studies on heat buildup in tire rubber surface scan method samples using a thermal imaging camera. Investigated the exothermic chemical reaction mechanical destruction rubber when loading designs permanent cyclic stretching with deformation of the working zone 50%. Percentage of deformation of the working zone was chosen on the basis of the actual data on the stretch-compression zone "Rusk" tires, which is the maximum level difference of deformation during run-in. Experiment plan provided for periodic relaxation samples of at least 72 hours for more accurate simulation of operation process of structural products. Created and processed data on temperature changes in samples for bar and line profile for rubber compounds with the introduction of nanomodifiers (fulleren technical carbon in comparison with the control sample without him. The data obtained reflect the nature of heat depending on the composition of the compound. Identified common patterns of thermal nature of physico-chemical process mechanical destruction rubbers. For rubber with nanomodifikatorom there has been an increase in the temperature interval reaction from a minimum to a maximum 2 degrees that is also linked to the rise in the average temperature of the reaction on the histogram also at 2-3 degrees of deformation under the same conditions and the level of cyclic loading. However, the temperature in the control sample that is associated with the beginning of the formation of hardened rubber structures, economies of Mallinz-Petrikeev, occurs with delay twice compared with modified Fullerenes. Measurement of physic-mechanical indicators selected in the course of testing of samples showed the beginning of formation of structure with increased strength of samples in the sample temperature zone that corresponds to the thermal effect of èndotermičeskomu recombination reactions of macromolecules.

  13. Studies of Fundamental Particle Dynamics in Microgravity

    Science.gov (United States)

    Rangel, Roger; Trolinger, James D.; Coimbra, Carlos F. M.; Witherow, William; Rogers, Jan; Rose, M. Franklin (Technical Monitor)

    2001-01-01

    This work summarizes theoretical and experimental concepts used to design the flight experiment mission for SHIVA - Spaceflight Holography Investigation in a Virtual Apparatus. SHIVA is a NASA project that exploits a unique, holography-based, diagnostics tool to understand the behavior of small particles subjected to transient accelerations. The flight experiments are designed for testing model equations, measuring g, g-jitter, and other microgravity phenomena. Data collection will also include experiments lying outside of the realm of existing theory. The regime under scrutiny is the low Reynolds number, Stokes regime or creeping flow, which covers particles and bubbles moving at very low velocity. The equations describing this important regime have been under development and investigation for over 100 years and yet a complete analytical solution of the general equation had remained elusive yielding only approximations and numerical solutions. In the course of the ongoing NASA NRA, the first analytical solution of the general equation was produced by members of the investigator team using the mathematics of fractional derivatives. This opened the way to an even more insightful and important investigation of the phenomena in microgravity. Recent results include interacting particles, particle-wall interactions, bubbles, and Reynolds numbers larger than unity. The Space Station provides an ideal environment for SHIVA. Limited ground experiments have already confirmed some aspects of the theory. In general the space environment is required for the overall experiment, especially for cases containing very heavy particles, very light particles, bubbles, collections of particles and for characterization of the space environment and its effect on particle experiments. Lightweight particles and bubbles typically rise too fast in a gravitational field and heavy particles sink too fast. In a microgravity environment, heavy and light particles can be studied side-by-side for

  14. Understanding the biological concept "bird": A kindergarten case study

    Science.gov (United States)

    Buchholz, Dilek

    The purpose of this qualitative, multiple case study of 14 students in a metropolitan public school in the Deep South was to find out, during a period of three months, what these kindergarten-aged children knew about birds, whether this knowledge represented current scientific thought, if such science instruction meaningfully affected their prior knowledge, and if so, what the factors during instruction that seemed to influence their understanding of the concept of bird were. The research was conducted in three phases; preinstruction interviews, instruction, and postinstruction interviews. The theoretical framework for this research was based on the Human Constructivism theory of learning (Mintzes, Wandersee and Novak, 1997). Instructional materials consisted of carefully chosen books (both fiction and non-fiction), guest speakers, field trips, a live bird in the classroom, students' observation journals, teacher-made classification and sorting activities, and picture-based concept maps. The findings suggest that young children's knowledge of birds was limited chiefly to birds' anatomical and morphological characteristics, with repeated references being made by the children to human characteristics. There was a positive, significant difference in young children's pre- and postinstruction scientific knowledge of birds. Although performance varied from child to child after instruction, most children were able to identify some common birds by name. Just one child resisted conceptual change. Kindergarten children's basic knowledge of bird behavior was limited to flight and eating. Although the children had more conceptual knowledge at the end, understanding still appeared to be shallow. The children did develop their skill in observing markedly. It also became evident that these kindergarten children needed more (a) experience in asking questions, (b) practice in techniques of visual representation, and (c) language development in order to be able to explain what they

  15. Biological Actions of Artemisinin: Insights from Medicinal Chemistry Studies

    Directory of Open Access Journals (Sweden)

    Jian Li

    2010-03-01

    Full Text Available Artemisinins have become essential antimalarial drugs for increasingly widespread drug-resistant malaria strains. Although tremendous efforts have been devoted to decipher how this class of molecules works, their exact antimalarial mechanism is still an enigma. Several hypotheses have been proposed to explain their actions, including alkylation of heme by carbon-centered free radicals, interference with proteins such as the sarcoplasmic/endoplasmic calcium ATPase (SERCA, as well as damaging of normal mitochondrial functions. Besides artemisinins, other endoperoxides with various backbones have also been synthesized, some of which showed comparable or even higher antimalarial effects. It is noteworthy that among these artemisinin derivatives, some enantiomers displayed similar in vitro malaria killing efficacy. In this article, the proposed mechanisms of action of artemisinins are reviewed in light of medicinal chemistry findings characterized by efficacy-structure studies, with the hope of gaining more insight into how these potent drugs work.

  16. Molecular biological study on genetic stability of the genome

    International Nuclear Information System (INIS)

    Hori, Tada-aki; Takahashi, Ei-ichi; Tsuji, Hideo; Tsuji, Satsuki

    1989-01-01

    A population cytogenetic study has been performed in 1022 healthy subjects and 547 cancer patients to determine baseline frequencies of autosomal rate fragile sites. Out of 17 rare autosomal fragile sites defined in HBM9 (1985), the following six were detected: fra(2)(q11), fra(10)(q25), fra(11)(q13), fra(11)(q23), fra(16)(q22) and fra(17)(q12). Other three new fragile sites were also detected: fra(8)(q24.1), fra(11)(q15.1) and fra(16)(p12.1). They were all distamycin A-inducible and located at the junctions of G/R-bands. The incidence of these autosomal fragile sites was 5% in both healthy subjects and cancer patients. Distamycin A-induced fragile sites may play a role in the etiology of leukemia, myeloproliferative disorders, and gynecological tumors. The present study also examined the mechanism of fragile X expression associated with fragile X syndrome in thymidine-prototrophic and auxotrophic human-mouse somatic cell hybrids. In these hybrid cells, both low and high thymidylate stresses were found to be effective in inducing fragile X expression, even in a hybrid clone that retained a fragile X chromosome as the only human chromosome. An addition of deoxycytidine completely abolished the effect of high thymidylate stress achieved by excess amounts of thymidine. It is concluded that the expression is an intrinsic property of the fragile X mutation resulting from chromosomal change in a special class of replicons with polypurine/polypyrimidine DNA sequence. (Namekawa, K)

  17. Population dynamics and reproductive biology of Barilius bendelisis (Cyprinidae: Cypriniformes) from river Gaula of Central Indian Himalaya.

    Science.gov (United States)

    Saxena, Neha; Patiyal, Rabindar Singh; Dube, Kiran; Tiwari, Virendra K

    2016-09-01

    The Indian hill trout cyprinid, Barilius bendelisis is a member of family Cyprinidae that dwells in shallow, cold, and clear water. In this study, growth parameters and reproductive biology of Indian hill trout, Barilius bendelisis from river Gaula, Central Himalaya region, India, were studied. The length-frequency data were grouped sex wise and were analyzed to determine the growth and mortality parameters using the computer software programme, FAO-ICLARM Stock Assessment Tool (FISAT II). Altogether, 501 individuals were collected from river Gaula (November 2013-October 2014) and were preserved in formalin for further analysis. The results showed that the female outnumbered the male population. The minimum GSI of females was observed in the month of October (4.93 ± 0.26) and for males in the month of June and July (0.093 ± 0.12), whereas, the maximum value was in the month of April for both females (13.47 ± 0.52) and males (1.21 ± 0.12). Fluctuation in GSI values had a bimodal pattern showing two peaks during March-May and August-September in both the sexes, indicating the common spawning period of fish. The slope of regression showed the negative allometric growth for both males and females (b= 2.65 for male and b= 2.5 for female). A significant relationship between length and weight was observed in the present study (p < 0.05). The ELEFAN-I estimated L∞ and K of the von Bertalanffy growth factor for males (17.33 cm and 0.310 per year), females (17.33 cm and 0.3 per year) and pooled sexes (17.33 cm and 0.240 per year). The results indicated that Barilius bendelisis is a small sized fish having negative allometric growth that spawns twice a year. Thus, the present study on biological traits represents the baseline information for effective production, conservation and restoration planning.

  18. Biological and biochemical studies on irradiated potato tubers

    International Nuclear Information System (INIS)

    Salem, E.A.F.M

    2008-01-01

    The present investigation aimed to study and overcome two important diseases which attacks potato plant, using some chemical and physical treatments. The first disease was pre harvest brown rot caused by ralstonia solanacearum and the second was post harvest dry rot caused by fusarium oxysporum. The results are summarized as follows: firstly brown rot : 1- Foliar treatment of salicylic acid or calcium chloride on potato plants leads to increasing in plant height and number of potato tubers, since salicylic acid give the highest value of plant height and also calcium chloride give the highest number of potato tubers. Also, this treatment leads to insignificant decreasing in number of potato tubers infected by brown rot. 2- The bacteria ralstonia solanacearum isolated from infected tubers obtained from the project of brown rot, Ministry of agriculture, Egypt, added with irrigate water to the pots this bacteria could infect healthy potato plant and the symptoms of brown rot observed on tubers also pathogenicity test was carried out using seedling of tomato cultivar Gs plants and wilting of tomato plant observed after 10-15 days from injection with R.solanacearum. 3- Concerning D 10 -value determined from the relation between dose rate of gamma ray (k-rad) and log count of bacterial number it was found that the D 10 -value for R.solanacearum was 0.25 kGy

  19. Biological and psychosocial effects of space travel: A case study

    Science.gov (United States)

    Hsia, Robert Edward Tien Ming

    This dissertation interviewed a single astronaut to explore psychosocial issues relevant to long-duration space travel and how these issues relate to the astronaut's training. It examined the psychological impact of isolation, crew interaction, and the experience of microgravity with the goal of increasing understanding of how to foster crew survivability and positive small group interactions in space (Santy, 1994). It also focused on how to develop possible treatments for crews when they transition back to Earth from the extreme environment of space missions. The astronaut's responses agreed with the literature and the predictions for long-duration space missions except the participant reported no temporary or permanent cognitive or memory deficits due to microgravity exposure. The dissertation identified five frequently endorsed themes including communication, environmental stressors, personal strengths, un-researched problems, and other. The agreement found between the literature and astronaut's responses offer a strong foundation of questions and data that needs to be further studied before conducting research in space or long-duration space missions.

  20. Acetyl analogs of combretastatin A-4: synthesis and biological studies.

    Science.gov (United States)

    Babu, Balaji; Lee, Megan; Lee, Lauren; Strobel, Raymond; Brockway, Olivia; Nickols, Alexis; Sjoholm, Robert; Tzou, Samuel; Chavda, Sameer; Desta, Dereje; Fraley, Gregory; Siegfried, Adam; Pennington, William; Hartley, Rachel M; Westbrook, Cara; Mooberry, Susan L; Kiakos, Konstantinos; Hartley, John A; Lee, Moses

    2011-04-01

    The combretastatins have received significant attention because of their simple chemical structures, excellent antitumor efficacy and novel antivascular mechanisms of action. Herein, we report the synthesis of 20 novel acetyl analogs of CA-4 (1), synthesized from 3,4,5-trimethoxyphenylacetone that comprises the A ring of CA-4 with different aromatic aldehydes as the B ring. Molecular modeling studies indicate that these new compounds possess a 'twisted' conformation similar to CA-4. The new analogs effectively inhibit the growth of human and murine cancer cells. The most potent compounds 6k, 6s and 6t, have IC(50) values in the sub-μM range. Analog 6t has an IC(50) of 182 nM in MDA-MB-435 cells and has advantages over earlier analogs due to its enhanced water solubility (456 μM). This compound initiates microtubule depolymerization with an EC(50) value of 1.8 μM in A-10 cells. In a murine L1210 syngeneic tumor model 6t had antitumor activity and no apparent toxicity. Copyright © 2011 Elsevier Ltd. All rights reserved.

  1. Toxin studies using an integrated biophysical and structural biology approach.

    Energy Technology Data Exchange (ETDEWEB)

    Last, Julie A.; Schroeder, Anne E.; Slade, Andrea Lynn; Sasaki, Darryl Yoshio; Yip, Christopher M. (University of Toronto, Toronto, Ontario, Canada); Schoeniger, Joseph S. (Sandia National Laboratories, Livermore, CA)

    2005-03-01

    Clostridial neurotoxins, such as botulinum and tetanus, are generally thought to invade neural cells through a process of high affinity binding mediated by gangliosides, internalization via endosome formation, and subsequent membrane penetration of the catalytic domain activated by a pH drop in the endosome. This surface recognition and internalization process is still not well understood with regard to what specific membrane features the toxins target, the intermolecular interactions between bound toxins, and the molecular conformational changes that occur as a result of pH lowering. In an effort to elucidate the mechanism of tetanus toxin binding and permeation through the membrane a simple yet representative model was developed that consisted of the ganglioside G{sub tlb} incorporated in a bilayer of cholesterol and DPPC (dipalmitoylphosphatidyl choline). The bilayers were stable over time yet sensitive towards the binding and activity of whole toxin. A liposome leakage study at constant pH as well as with a pH gradient, to mimic the processes of the endosome, was used to elucidate the effect of pH on the toxin's membrane binding and permeation capability. Topographic imaging of the membrane surface, via in situ tapping mode AFM, provided nanoscale characterization of the toxin's binding location and pore formation activity.

  2. Application of single photon ECT for dynamic study

    International Nuclear Information System (INIS)

    Mukai, T.; Ishii, Y.; Tamaki, N.

    1982-01-01

    Feasibility of dynamic study in a form of ECT using a rotating gamma camera was evaluated. Since it takes longer one around time sampling, application for the dynamic study is limited under following conditions; 1) physiological gated process, 2) slow clearance process, 3) physiological steady state process. The gated study was applicated for heart pumping action synchronized with ECG. The ECG gated heart ECT either of blood pool or myocardium was useful to reveal a subtle wall motion abnormalities in a tomographic plane, even when a planar imaging failed to reveal it. As for slow dynamic process of tracer, an excretion process of hepatobiliary agent, was subjected to be analyzed in order to calculate clearance rate at each pixel. As for steady state process, an ECT of regional celebral blood flow (rCBF) was investigated during continuous infusion into intracarotid artery. All of these technique were proved to have a clinical feasibility and to potentiate usefulness of the single photon ECT (SPECT)

  3. Synthesis, structural, spectroscopic and biological studies of Schiff base complexes

    Science.gov (United States)

    Diab, M. A.; El-Sonbati, A. Z.; Shoair, A. F.; Eldesoky, A. M.; El-Far, N. M.

    2017-08-01

    Schiff base ligand 4-((pyridin-2- yl)methyleneamino)-1,2-dihydro-2,3-dimethyl-1-phenylpyrazol-5-one (PDMP) and its complexes were prepared and characterized on the basis of elemental analysis, IR, mass spectra and thermogravimetric analysis. All results confirm that the complexes have 1:1 (M: PMDP) stoichiometric formula [M(PMDP)Cl2H2O ] (M = Cu(II), Co(II), Ni(II) and Mn(II)), [Cd(PMDP)Cl2] and the ligand behaves as a bi/tridentate forming five-membered chelating ring towards the metal ions, bonding through azomethine nitrogen/exocyclic carbonyl oxygen, azomethine pyridine nitrogen and exocyclic carbonyl oxygen. The shift in the band positions of the groups involved in coordination has been utilized to estimate the metal-nitrogen and/or oxygen bond lengths. The complexes of Co(II), Ni(II) and Cu(II) are paramagnetic and the magnetic as well as spectral data suggest octahedral geometry, whereas the Cd(II) complex is tetrahedral. The XRD studies show that both the ligand and its metal complexes (1 and 3) show polycrystalline with crystal structure. Molecular docking was used to predict the binding between PMDP ligand and the receptors. The corrosion inhibition of mild steel in 2 M HCl solution by PDMP was explored utilizing potentiodynamic polarization, electrochemical impedance spectroscopy (EIS) and (EFM) electrochemical frequency modulation method. Potentiodynamic polarization demonstrated that PDMP compound is mixed-type inhibitor. EIS spectra exhibit one capacitive loop and confirm the protective ability. The percentage of inhibition efficiency was found to increase with increasing the inhibitor concentration.

  4. Cholera dynamics with Bacteriophage infection: A mathematical study

    International Nuclear Information System (INIS)

    Misra, A.K.; Gupta, Alok; Venturino, Ezio

    2016-01-01

    Highlights: • A mathematical model for the biological control of cholera has been proposed. • The feasibility and stability of all the equilibria have been investigated. • The ODE model is found to exhibit Hopf-bifurcation. • Conditions of global asymptotic stability have been obtained. • The impact of important parameters on cholera spread has been shown. - Abstract: Mathematical modeling of waterborne diseases, such as cholera, including a biological control using Bacteriophage viruses in the aquatic reservoirs is of great relevance in epidemiology. In this paper, our aim is twofold: at first, to understand the cholera dynamics in the region around a water body; secondly, to understand how the spread of Bacteriophage infection in the cholera bacterium V. cholerae controls the disease in the human population. For this purpose, we modify the model proposed by Codeço, for the spread of cholera infection in human population and the one proposed by Beretta and Kuang, for the spread of Bacteriophage infection in the bacteria population [1, 2]. We first discuss the feasibility and local asymptotic stability of all the possible equilibria of the proposed model. Further, in the numerical investigation, we have found that the parameter ϕ, called the phage adsorption rate, plays an important role. There is a critical value, ϕ c , at which the model possess Hopf-bifurcation. For lower values than ϕ c , the equilibrium E * is unstable and periodic solutions are observed, while above ϕ c , the equilibrium E * is locally asymptotically stable, and further shown to be also globally asymptotically stable. We investigate the effect of the various parameters on the dynamics of the infected humans by means of numerical simulations.

  5. Study of beam dynamics at cooler synchrotron TARN-II

    International Nuclear Information System (INIS)

    Watanabe, S.; Katayama, T.; Watanabe, T.; Yoshizawa, M.; Tomizawa, M.; Chida, K.; Arakaki, Y.; Noda, K.; Kanazawa, M.

    1992-08-01

    Several kinds of beam diagnostic instruments, have been developed at cooler-synchrotron TARN-II. These are intended to study beam dynamics at low beam current of several microamperes and then have high sensitivity of good S/N ratio. In addition, the acceleration system, especially low level RF system, has been improved to attain the maximum beam energy. With the successful performance of these instrumentations, the study of beam dynamics are presently being carried out. For example, the synchrotron acceleration of the light ions was achieved up to 220 MeV/u without any beam loss. (author)

  6. Study of dynamics of level of physical preparedness of students.

    Directory of Open Access Journals (Sweden)

    Коvalenko Y.A.

    2010-12-01

    Full Text Available The dynamics of level of physical preparedness of students is studied in the article. A tendency is marked to the decline of level of physical preparedness of students of 1-3 courses. Methodical recommendations are presented on the improvement of the system of organization of physical education of students of the Zaporizhzhya national university. The dynamics of indexes of physical preparedness of students 1, 2, 3 courses of different years of teaching is studied. Principal reasons of decline of level of physical preparedness of students are certain. There are recommendations the department of physical education in relation to physical preparedness of students.

  7. Artificial biomembrane morphology: a dissipative particle dynamics study.

    Science.gov (United States)

    Becton, Matthew; Averett, Rodney; Wang, Xianqiao

    2017-09-18

    Artificial membranes mimicking biological structures are rapidly breaking new ground in the areas of medicine and soft-matter physics. In this endeavor, we use dissipative particle dynamics simulation to investigate the morphology and behavior of lipid-based biomembranes under conditions of varied lipid density and self-interaction. Our results show that a less-than-normal initial lipid density does not create the traditional membrane; but instead results in the formation of a 'net', or at very low densities, a series of disparate 'clumps' similar to the micelles formed by lipids in nature. When the initial lipid density is high, a membrane forms, but due to the large number of lipids, the naturally formed membrane would be larger than the simulation box, leading to 'rippling' behavior as the excess repulsive force of the membrane interior overcomes the bending energy of the membrane. Once the density reaches a certain point however, 'bubbles' appear inside the membrane, reducing the rippling behavior and eventually generating a relatively flat, but thick, structure with micelles of water inside the membrane itself. Our simulations also demonstrate that the interaction parameter between individual lipids plays a significant role in the formation and behavior of lipid membrane assemblies, creating similar structures as the initial lipid density distribution. This work provides a comprehensive approach to the intricacies of lipid membranes, and offers a guideline to design biological or polymeric membranes through self-assembly processes as well as develop novel cellular manipulation and destruction techniques.

  8. Design and validation of a dynamic cell-culture system for bone biology research and exogenous tissue-engineering applications.

    Science.gov (United States)

    Allori, Alexander C; Davidson, Edward H; Reformat, Derek D; Sailon, Alexander M; Freeman, James; Vaughan, Adam; Wootton, David; Clark, Elizabeth; Ricci, John L; Warren, Stephen M

    2016-10-01

    Bone lacunocanalicular fluid flow ensures chemotransportation and provides a mechanical stimulus to cells. Traditional static cell-culture methods are ill-suited to study the intricacies of bone biology because they ignore the three-dimensionality of meaningful cellular networks and the lacunocanalicular system; furthermore, reliance on diffusion alone for nutrient supply and waste product removal effectively limits scaffolds to 2-3 mm thickness. In this project, a flow-perfusion system was custom-designed to overcome these limitations: eight adaptable chambers housed cylindrical cell-seeded scaffolds measuring 12 or 24 mm in diameter and 1-10 mm in thickness. The porous scaffolds were manufactured using a three-dimensional (3D) periodic microprinting process and were composed of hydroxyapatite/tricalcium phosphate with variable thicknesses, strut sizes, pore sizes and structural configurations. A multi-channel peristaltic pump drew medium from parallel reservoirs and perfused it through each scaffold at a programmable rate. Hermetically sealed valves permitted sampling or replacement of medium. A gas-permeable membrane allowed for gas exchange. Tubing was selected to withstand continuous perfusion for > 2 months without leakage. Computational modelling was performed to assess the adequacy of oxygen supply and the range of fluid shear stress in the bioreactor-scaffold system, using 12 × 6 mm scaffolds, and these models suggested scaffold design modifications that improved oxygen delivery while enhancing physiological shear stress. This system may prove useful in studying complex 3D bone biology and in developing strategies for engineering thick 3D bone constructs. Copyright © 2013 John Wiley & Sons, Ltd. Copyright © 2013 John Wiley & Sons, Ltd.

  9. Dynamics of polymers in a good solvent - a molecular dynamics study using the Connection Machine

    International Nuclear Information System (INIS)

    Shannon, S.R.; Choy, T.C.

    1996-01-01

    In recent times the use of molecular dynamics simulations has become an important tool in modelling and understanding the dynamics of interacting many-body systems. With recent advances in computing power it is now feasible to perform modelling of systems which contain a large number of interacting particles, and thus to simulate the behaviour of real systems reasonably. Our earlier discoveries of anomalous corrections to scaling behaviour of the Edward's polymer were applied to study the dynamical behaviour of two dimensional polymer systems - either a single chain immersed in a fluid, a pure polymer melt, or with any concentration of polymers in the fluid. By choosing a suitable interaction potential between the fluid particles and the monomers, we are able to study the experimentally observable time dependent structure factor of polymers in a good solvent. Simulations were performed using the Connection Machine CM5 supercomputer at the Australian National University which due to its fast multi- processor nearest neighbour communications facility, enables us to easily model large systems of at least 3000 fluid plus monomer particles. Our study is based on a finite difference solution of Newton's equations of motion i.e. the Verlet algorithm, and the results are used to test current theories of polymer dynamics, which were based primarily on the earlier models proposed by Rouse (1953) and Zimm (1956). In particular dynamical scaling predictions is scrutinised to examine the effects due to the anomalous corrections-to-scaling behaviour found in an earlier work using finite-size scaling analysis of Monte-Carlo data and now understood via a new perturbation concept

  10. Feasibility study for a recirculating linac-based facility for femtosecond dynamics

    CERN Document Server

    Corlett, J N; Barry, W; Byrd, J M; De Santis, S; Doolittle, L; Fawley, W; Green, M A; Hartman, N; Heimann, P A; Kairan, D; Kujawski, E; Li, D; Lidia, S M; Luft, P; McClure, R; Parmigiani, F; Petroff, Y; Pirkl, Werner; Placidi, Massimo; Ratti, A; Reavill, D; Reichel, I; Rimmer, R A; Robinson, K E; Sannibale, F; Schönlein, R W; Staples, J; Tanabe, J; Truchlikova, D; Wan, W; Wang, S; Wells, R; Wolski, A; Zholents, A

    2002-01-01

    LBNL is pursuing design studies and the scientific program for a facility of the production of x-ray pulses with ultra-short time duration, for application in dynamical studies of processes in physics, biology, and chemistry. The proposed x-ray facility has the short x-ray pulse length (approx 60 fs FWHM) necessary to study very fast dynamics, high flux (up to approximately 10E11 photons/sec/0.1 percentBW) to study weakly scattering systems, and tuneability over 1-12 keV photon energy. The hard x-ray photon production section of the machine accommodates seven 2-m long undulators. Design studies for longer wavelength sources, using high-gain harmonic generation, are in progress. The x-ray pulse repetition rate of 10 kHz is matched to studies of dynamical processes (initiated by ultra-short laser pulses) that typically have a long recovery time or are not generally cyclic or reversible and need time to allow relaxation, replacement, or flow of the sample. The technique for producing ultra-short x-ray pulses use...

  11. Role of quantitative and dynamic radioactive studies in renal testing

    International Nuclear Information System (INIS)

    Raynaud, C.

    1977-01-01

    Many dynamic and quantitative radioactive tests are at present used in studying renal function. Whether involving dynamic morphological tests such as sequential images, dynamic quantitative tests such as the renogram or quantitative static tests such as radioactive clearances, their effective and original contribution is rather unimportant. Only one provides original data, the Hg renal uptake test but it is generally avoided due to the radiation dose absorbed by the kidney in children. A study of the causes of this lack of effectiveness leads to the observation that such tests are not well adapted to the needs of kidneys specialists. They are for the most part based on replacing a 'cold' indicator by radioactive indicator and the advantages anticipated from using radionuclide are not evident. In fact, they are often cancelled by the shortcomings of external detection. For the future, it seems indispensable to abandon some traditional concepts which lead us to consider that the only exploitable renal function is represented by excretion. The kidney has other functions; one of the most interesting seems to be the function of uptake of heavy metals and toxic substances, a study of which is only possible using radionuclides. A new generation of radioactive tests based on a study of uptake and also on a study of other renal functions may provide dynamic or quantitative data which physician urgently need

  12. Femtosecond photodissociation dynamics of I studied by ion imaging

    DEFF Research Database (Denmark)

    Larsen, J.J.; Bjerre, N.; Mørkbak, N.J.

    1998-01-01

    on imaging is employed to analyze the fragments from timed Coulomb explosion studies of femtosecond (fs) molecular dynamics. The technique provides high detection efficiency and direct recording of the two-dimensional velocity of all ionized fragments. We illustrate the approach by studying...... agreement with quantum mechanical wave packet simulations. We discuss the perspectives for extending the studies to photochemical reactions of small polyatomic molecules...

  13. Dynamical study of a laser with a saturable absorber

    Energy Technology Data Exchange (ETDEWEB)

    Dignowity, D; RamIrez, R [Centro de Investigaciones en Optica, Loma del Bosque 115, Col. Lomas del Campestre, 37150, Leon, Guanajuato (Mexico)

    2005-01-01

    The study of a laser including a saturable absorber is presented. The non-linear system describing the complex dynamics of the laser is presented. The laser is shown to operate in several regimes depending on the parameters used. It is also shown how the control of the laser is possible depending on the operating regime parameters.

  14. A MOLECULAR-DYNAMICS STUDY OF LECITHIN MONOLAYERS

    NARCIS (Netherlands)

    AHLSTROM, P; BERENDSEN, HJC

    1993-01-01

    Two monolayers of didecanoyllecithin at the air-water interface have been studied using molecular dynamics simulations. The model system consisted of two monolayers of 42 lecithin molecules each separated by a roughly 4 nm thick slab of SPC water. The area per lecithin molecule was 0.78 nm(2)

  15. System Dynamic Modelling for a Balanced Scorecard: A Case Study

    DEFF Research Database (Denmark)

    Nielsen, Steen; Nielsen, Erland Hejn

    Purpose - The purpose of this research is to make an analytical model of the BSC foundation by using a dynamic simulation approach for a 'hypothetical case' model, based on only part of an actual case study of BSC. Design/methodology/approach - The model includes five perspectives and a number...

  16. Asymptotic study of a magneto-hydro-dynamic system

    International Nuclear Information System (INIS)

    Benameur, J.; Ibrahim, S.; Majdoub, M.

    2003-01-01

    In this paper, we study the convergence of solutions of a Magneto-Hydro-Dynamic system. On the torus T 3 , the proof is based on Schochet's methods, whereas in the case of the whole space R 3 , we use Strichartz's type estimates. (author)

  17. Spectroscopic studies of dynamically compacted monoclinic ZrO2

    NARCIS (Netherlands)

    Maczka, M.; Lutz, E.T.G.; Verbeek, H.J.; Oskam, K.; Meijerink, A.; Hanuza, J.; Stuivinga, M.E.C.

    1999-01-01

    The properties of dynamically compacted monoclinic zirconia have been studied by X-ray powder diffraction, IR, Raman, EPR and luminescence spectroscopy. Compaction introduces a large number of defects into the sample, which leads to a broadening of the X-ray lines, and IR and Raman bands. Besides,

  18. Charge-Transfer Complexes Studied by Dynamic Force Spectroscopy

    Directory of Open Access Journals (Sweden)

    Jurriaan Huskens

    2013-03-01

    Full Text Available In this paper, the strength and kinetics of two charge-transfer complexes, naphthol-methylviologen and pyrene-methylviologen, are studied using dynamic force spectroscopy. The dissociation rates indicate an enhanced stability of the pyrene-methylviologen complex, which agrees with its higher thermodynamic stability compared to naphthol-methylviologen complex.

  19. Body dynamics and hydrodynamics of swimming larvae: a computational study

    NARCIS (Netherlands)

    Li, G.; Müller, U.K.; Leeuwen, van J.L.; Liu, H.

    2012-01-01

    To understand the mechanics of fish swimming, we need to know the forces exerted by the fluid and how these forces affect the motion of the fish. To this end, we developed a 3-D computational approach that integrates hydrodynamics and body dynamics. This study quantifies the flow around a swimming

  20. Planning Intervention Using Dynamic Assessments: A Case Study

    Science.gov (United States)

    Hasson, Natalie; Dodd, Barbara

    2014-01-01

    Dynamic assessments (DA) of language have been shown to be a useful addition to the battery of tests used to diagnose language impairments in children, and to evaluate their skills. The current article explores the value of the information gained from a DA in planning intervention for a child with language impairment. A single case study was used…

  1. Molecular dynamics study on the relaxation properties of bilayered ...

    Indian Academy of Sciences (India)

    2017-08-31

    Aug 31, 2017 ... Abstract. The influence of defects on the relaxation properties of bilayered graphene (BLG) has been studied by molecular dynamics simulation in nanometre sizes. Type and position of defects were taken into account in the calculated model. The results show that great changes begin to occur in the ...

  2. Asymptotic study of a magneto-hydro-dynamic system

    Energy Technology Data Exchange (ETDEWEB)

    Benameur, J [Institut Preparatoire aux Etudes d' Ingenieurs de Monastir (Tunisia); Ibrahim, S [Faculte des Sciences de Bizerte, Departement de Mathematiques, Bizerte (TN); [Abdus Salam International Centre for Theoretical Physics, Trieste (Italy)]. E-mail: slim.ibrahim@fsb.rnu.tn; Majdoub, M [Faculte des Sciences de Tunis, Departement de Mathematiques, Tunis (Tunisia)

    2003-01-01

    In this paper, we study the convergence of solutions of a Magneto-Hydro-Dynamic system. On the torus T{sup 3}, the proof is based on Schochet's methods, whereas in the case of the whole space R{sup 3}, we use Strichartz's type estimates. (author)

  3. Adsorption dynamics and equilibrium studies of Zn (II) onto chitosan

    Indian Academy of Sciences (India)

    Unknown

    Adsorption dynamics and equilibrium studies of Zn (II) onto chitosan. G KARTHIKEYAN*, K ANBALAGAN and N MUTHULAKSHMI ANDAL. Department of Chemistry, Gandhigram Rural Institute – Deemed University, Gandhigram 624 302, India e-mail: drg_karthikeyan@rediffmail.com. MS received 3 June 2003; revised 12 ...

  4. Fission dynamics as brought out in cold fragmentation studies

    International Nuclear Information System (INIS)

    Signarbieux, G.

    1986-10-01

    Fission dynamics problem has been addressed since the beginning. This paper is specifically concerned by ''even-odd effects '' in fragment distribution. These effects are reinterpreted, some complementary thoughts on double ionization chamber are given together with a study of fission dymanics at low energy [fr

  5. Recoil generated radiotracers in studies of molecular dynamics

    International Nuclear Information System (INIS)

    Spicer, L.D.

    1981-01-01

    This chapter summarizes many of the contributions that the recoil technique of generating excited radiotracer atoms in the presence of a thermal environment is making to the field of chemical dynamics. Specific topics discussed critically include characterization of the generation and behavior of excited molecules including fragmentation kinetics and energy transfer, measurement of thermal and hot kinetic parameters, and studies of reaction mechanisms and stereochemistry as a function of reaction energy. Distinctive features that provide unique approaches to dynamical problems are evaluated in detail and the complementarity with more conventional techniques is addressed. Prospects for future applications are also presented

  6. A Study Assessing the Potential of Negative Effects in Interdisciplinary Math–Biology Instruction

    Science.gov (United States)

    Madlung, Andreas; Bremer, Martina; Himelblau, Edward; Tullis, Alexa

    2011-01-01

    There is increasing enthusiasm for teaching approaches that combine mathematics and biology. The call for integrating more quantitative work in biology education has led to new teaching tools that improve quantitative skills. Little is known, however, about whether increasing interdisciplinary work can lead to adverse effects, such as the development of broader but shallower skills or the possibility that math anxiety causes some students to disengage in the classroom, or, paradoxically, to focus so much on the mathematics that they lose sight of its application for the biological concepts in the center of the unit at hand. We have developed and assessed an integrative learning module and found disciplinary learning gains to be equally strong in first-year students who actively engaged in embedded quantitative calculations as in those students who were merely presented with quantitative data in the context of interpreting biological and biostatistical results. When presented to advanced biology students, our quantitative learning tool increased test performance significantly. We conclude from our study that the addition of mathematical calculations to the first year and advanced biology curricula did not hinder overall student learning, and may increase disciplinary learning and data interpretation skills in advanced students. PMID:21364099

  7. A study of dynamic filtration; Um estudo sobre filtracao dinamica

    Energy Technology Data Exchange (ETDEWEB)

    Girao, Joaquim Helder S [PETROBRAS, Natal, RN (Brazil). Distrito de Perfuracao da Bacia Potiguar. Div. de Tecnicas de Perfuracao

    1990-12-31

    The problems that cause cost increase such as: formation damage and borehole swelling or caving lead us to study the filtration of the liquid part of formation drilling fluid. With the aim of comparing static and dynamic filtration rates, we developed a modest dynamic filtration equipment, consisting of a modified API filter, connected to reservoir by means of a positive injection pump. We carried out various tests, and the results were set in charts and tables. Through these, it is possible to notice how the static and dynamic filtration curves come apart for a same pressure value. We also evaluated the effects of circulation speed, starch concentration and counter pressure. This paper does not include calculations or mathematical models accounting for filtrate invasion radii, but it demonstrates, for example, that cleaning circulation will cause lower filtration rates at lower flows. (author) 5 refs., 11 figs., 14 tabs.

  8. A study of dynamic filtration; Um estudo sobre filtracao dinamica

    Energy Technology Data Exchange (ETDEWEB)

    Girao, Joaquim Helder S. [PETROBRAS, Natal, RN (Brazil). Distrito de Perfuracao da Bacia Potiguar. Div. de Tecnicas de Perfuracao

    1989-12-31

    The problems that cause cost increase such as: formation damage and borehole swelling or caving lead us to study the filtration of the liquid part of formation drilling fluid. With the aim of comparing static and dynamic filtration rates, we developed a modest dynamic filtration equipment, consisting of a modified API filter, connected to reservoir by means of a positive injection pump. We carried out various tests, and the results were set in charts and tables. Through these, it is possible to notice how the static and dynamic filtration curves come apart for a same pressure value. We also evaluated the effects of circulation speed, starch concentration and counter pressure. This paper does not include calculations or mathematical models accounting for filtrate invasion radii, but it demonstrates, for example, that cleaning circulation will cause lower filtration rates at lower flows. (author) 5 refs., 11 figs., 14 tabs.

  9. Molecular dynamics study of atomic displacements in disordered solid alloys

    Science.gov (United States)

    Puzyrev, Yevgeniy S.

    The effects of atomic displacements on the energetics of alloys plays important role in the determining the properties of alloys. We studied the atomic displacements in disordered solid alloys using molecular dynamics and Monte-Carlo methods. The diffuse scattering of pure materials, copper, gold, nickel, and palladium was calculated. The experimental data for pure Cu was obtained from diffuse scattering intensity of synchrotron x-ray radiation. The comparison showed the advantages of molecular dynamics method for calculating the atomic displacements in solid alloys. The individual nearest neighbor separations were calculated for Cu 50Au50 alloy and compared to the result of XAFS experiment. The molecular dynamics method provided theoretical predictions of nearest neighbor pair separations in other binary alloys, Cu-Pd and Cu-Al for wide range of the concentrations. We also experimentally recovered the diffuse scattering maps for the Cu47.3Au52.7 and Cu85.2Al14.8 alloy.

  10. Study on dynamic behavior analysis of towed line array sensor

    Directory of Open Access Journals (Sweden)

    Hyun Kyoung Shin

    2012-03-01

    Full Text Available A set of equations of motion is derived for vibratory motions of an underwater cable connected to a moving vehicle at one end and with drogues at the other end. From the static analysis, cable configurations are obtained for different vehicle speeds and towing pretensions are determined by fluid resistance of drogues. Also the dynamic analysis is required to predict its vibratory motion. Nonlinear fluid drag forces greatly influence the dynamic tension. In this study, a numerical analysis program was developed to find out the characteristic of cable behaviour. The motion is described in terms of space and time coordinates based on Chebyshev polynomial expansions. For the spatial integration the collocation method is employed and the Newmark method is applied for the time integration. Dynamic tensions, displacements, velocities, accelerations were predicted in the time domain while natural frequencies and transfer functions were obtained in the frequency domain.

  11. Dynamic study on digital cineangiography of acute digestive tract hemorrhage

    International Nuclear Information System (INIS)

    Yu Jianming; Feng Gansheng; Zeng Jun; Xu Caiyuan

    2000-01-01

    Objective: To study dynamically acute gastrointestinal tract hemorrhage with digital cine angiography. Methods: Fifty patients with acute gastrointestinal tract hemorrhage were performed with digital cineangiography and observed dynamically during arterial, capillary and venous phases. Results: Among 50 cases, there were positive results in 44 ones including gastrointestinal hemorrhage in 14, biliary hemorrhage in 2, splenic arterial bleeding in 3, left gastric arterial bleeding in 4, right gastroepiploic arterial bleeding in 5, SMA bleeding in 7 and IMA bleeding in 9.17 cases underwent a permanent embolization through artery and 11 with temporary embolization as well as 9 with infusion of hemostatic agent via artery. Conclusions: Serial digital cineangiogram can dynamically show acute digestive tract hemorrhage within different phase. It is helpful to detect the location and cause of hemorrhage

  12. Dimension reduction for stochastic dynamical systems forced onto a manifold by large drift: a constructive approach with examples from theoretical biology

    International Nuclear Information System (INIS)

    Parsons, Todd L; Rogers, Tim

    2017-01-01

    Systems composed of large numbers of interacting agents often admit an effective coarse-grained description in terms of a multidimensional stochastic dynamical system, driven by small-amplitude intrinsic noise. In applications to biological, ecological, chemical and social dynamics it is common for these models to posses quantities that are approximately conserved on short timescales, in which case system trajectories are observed to remain close to some lower-dimensional subspace. Here, we derive explicit and general formulae for a reduced-dimension description of such processes that is exact in the limit of small noise and well-separated slow and fast dynamics. The Michaelis–Menten law of enzyme-catalysed reactions, and the link between the Lotka–Volterra and Wright–Fisher processes are explored as a simple worked examples. Extensions of the method are presented for infinite dimensional systems and processes coupled to non-Gaussian noise sources. (paper)

  13. Dimension reduction for stochastic dynamical systems forced onto a manifold by large drift: a constructive approach with examples from theoretical biology

    Science.gov (United States)

    Parsons, Todd L.; Rogers, Tim

    2017-10-01

    Systems composed of large numbers of interacting agents often admit an effective coarse-grained description in terms of a multidimensional stochastic dynamical system, driven by small-amplitude intrinsic noise. In applications to biological, ecological, chemical and social dynamics it is common for these models to posses quantities that are approximately conserved on short timescales, in which case system trajectories are observed to remain close to some lower-dimensional subspace. Here, we derive explicit and general formulae for a reduced-dimension description of such processes that is exact in the limit of small noise and well-separated slow and fast dynamics. The Michaelis-Menten law of enzyme-catalysed reactions, and the link between the Lotka-Volterra and Wright-Fisher processes are explored as a simple worked examples. Extensions of the method are presented for infinite dimensional systems and processes coupled to non-Gaussian noise sources.

  14. Environmental biology

    International Nuclear Information System (INIS)

    Tschumi, P.A.

    1981-01-01

    Environmental biology illustrates the functioning of ecosystems and the dynamics of populations with many examples from limnology and terrestrial ecology. On this basis, present environmental problems are analyzed. The present environmental crisis is seen as a result of the failure to observe ecological laws. (orig.) [de

  15. Correlativity study on MRI morphologic features, pathology, and molecular biology of breast cancer

    International Nuclear Information System (INIS)

    Chen Rong; Gong Shuigen; Zhang Weiguo; Chen Jinhua; He Shuangwu; Liu Baohua; Li Zengpeng

    2004-01-01

    Objective: To investigate the correlation among MRI morphologic features, pathology, and molecular biology of breast cancer. Methods: MR scanning was performed in 78 patients with breast cancer before operation and MRI morphologic features of breast cancer were analyzed. The mastectomy specimens of the breast neoplasm were stained with immunohistochemistry, and the expression of estrogen receptor (ER), progesterone receptor (PR), C-erbB-2, p53, and the distribution of microvessel density (MVD) was measured. The pathologic results were compared with MRI features. Results: Among the 80 breast cancers, ER positive expression was positively correlated with the spiculate margin of breast cancer (P 0.05). Among the 41 breast cancers with dynamic MR scans, there was positive correlation between the spatial distribution of contrast agent and MVD (P<0.01). Conclusion: There exists some correlation among MRI morphologic features, pathology, and molecular biology factors in breast cancer to certain extent. The biologic behavior and prognosis of the breast cancer can be assessed according to MRI features

  16. Review of Russian language studies on radionuclide behaviour in agricultural animals: biological half-lives

    International Nuclear Information System (INIS)

    Fesenko, S.; Isamov, N.; Barnett, C.L.; Beresford, N.A.; Howard, B.J.; Sanzharova, N.; Fesenko, E.

    2015-01-01

    Extensive studies on transfer of radionuclides to animals were carried out in the USSR from the 1950s. Few of these studies were published in the international refereed literature or taken into account in international reviews. This paper continues a series of reviews of Russian language literature on radionuclide transfer to animals, providing information on biological half-lives of radionuclides in various animal tissues. The data are compared, where possible, with those reported in other countries. The data are normally quantified using a single or double exponential accounting for different proportions of the loss. For some products, such as milk, biological half-lives tend to be rapid at 1–3 d for most radionuclides and largely described by a single exponential. However, for other animal products biological half-lives can vary widely as they are influenced by many factors such as the age and size of the animal. Experimental protocols, such as the duration of the study, radionuclide administration and/or sample collection protocol also influence the value of biological half-lives estimated. - Highlights: • The data on biological half-lives from Russian language literature were reviewed. • Radionuclides with the shortest half-lives in animals are those which accumulate in soft tissues. • Short term behaviour is affected by the form in which radionuclides are administered. • There is a tendency for more rapid radionuclide turnover in younger animals

  17. Application of Raman Microspectroscopic and Raman imaging techniques for cell biological studies

    NARCIS (Netherlands)

    Puppels, G.J.; Puppels, G.J.; Bakker schut, T.C.; Bakker Schut, T.C.; Sijtsema, N.M.; Grond, M.; Grond, M.; Maraboeuf, F.; de Grauw, C.J.; de Grauw, C.J.; Figdor, Carl; Greve, Jan

    1995-01-01

    Raman spectroscopy is being used to study biological molecules for some three decades now. Thanks to continuing advances in instrumentation more and more applications have become feasible in which molecules are studied in situ, and this has enabled Raman spectroscopy to enter the realms of

  18. Development and Application of Raman Microspectroscopic and Raman Imaging Techniques for Cell Biological Studies

    NARCIS (Netherlands)

    PUPPELS, G J; SCHUT, T C B; SIJTSEMA, N M; GROND, M; MARABOEUF, F; DEGRAUW, C G; FIGDOR, C G; GREVE, J

    1995-01-01

    Raman spectroscopy is being used to study biological molecules for some three decades now. Thanks to continuing advances in instrumentation more and more applications have become feasible in which molecules are studied in situ, and this has enabled Raman spectroscopy to enter the realms of

  19. Predicting in vivo effect levels for repeat-dose systemic toxicity using chemical, biological, kinetic and study covariates.

    Science.gov (United States)

    Truong, Lisa; Ouedraogo, Gladys; Pham, LyLy; Clouzeau, Jacques; Loisel-Joubert, Sophie; Blanchet, Delphine; Noçairi, Hicham; Setzer, Woodrow; Judson, Richard; Grulke, Chris; Mansouri, Kamel; Martin, Matthew

    2018-02-01

    In an effort to address a major challenge in chemical safety assessment, alternative approaches for characterizing systemic effect levels, a predictive model was developed. Systemic effect levels were curated from ToxRefDB, HESS-DB and COSMOS-DB from numerous study types totaling 4379 in vivo studies for 1247 chemicals. Observed systemic effects in mammalian models are a complex function of chemical dynamics, kinetics, and inter- and intra-individual variability. To address this complex problem, systemic effect levels were modeled at the study-level by leveraging study covariates (e.g., study type, strain, administration route) in addition to multiple descriptor sets, including chemical (ToxPrint, PaDEL, and Physchem), biological (ToxCast), and kinetic descriptors. Using random forest modeling with cross-validation and external validation procedures, study-level covariates alone accounted for approximately 15% of the variance reducing the root mean squared error (RMSE) from 0.96 log 10 to 0.85 log 10  mg/kg/day, providing a baseline performance metric (lower expectation of model performance). A consensus model developed using a combination of study-level covariates, chemical, biological, and kinetic descriptors explained a total of 43% of the variance with an RMSE of 0.69 log 10  mg/kg/day. A benchmark model (upper expectation of model performance) was also developed with an RMSE of 0.5 log 10  mg/kg/day by incorporating study-level covariates and the mean effect level per chemical. To achieve a representative chemical-level prediction, the minimum study-level predicted and observed effect level per chemical were compared reducing the RMSE from 1.0 to 0.73 log 10  mg/kg/day, equivalent to 87% of predictions falling within an order-of-magnitude of the observed value. Although biological descriptors did not improve model performance, the final model was enriched for biological descriptors that indicated xenobiotic metabolism gene expression, oxidative stress, and

  20. Fast "Feast/Famine" Cycles for Studying Microbial Physiology Under Dynamic Conditions: A Case Study with Saccharomyces cerevisiae.

    Science.gov (United States)

    Suarez-Mendez, Camilo A; Sousa, Andre; Heijnen, Joseph J; Wahl, Aljoscha

    2014-05-15

    Microorganisms are constantly exposed to rapidly changing conditions, under natural as well as industrial production scale environments, especially due to large-scale substrate mixing limitations. In this work, we present an experimental approach based on a dynamic feast/famine regime (400 s) that leads to repetitive cycles with moderate changes in substrate availability in an aerobic glucose cultivation of Saccharomyces cerevisiae. After a few cycles, the feast/famine produced a stable and repetitive pattern with a reproducible metabolic response in time, thus providing a robust platform for studying the microorganism's physiology under dynamic conditions. We found that the biomass yield was slightly reduced (-5%) under the feast/famine regime, while the averaged substrate and oxygen consumption as well as the carbon dioxide production rates were comparable. The dynamic response of the intracellular metabolites showed specific differences in comparison to other dynamic experiments (especially stimulus-response experiments, SRE). Remarkably, the frequently reported ATP paradox observed in single pulse experiments was not present during the repetitive perturbations applied here. We found that intracellular dynamic accumulations led to an uncoupling of the substrate uptake rate (up to 9-fold change at 20 s.) Moreover, the dynamic profiles of the intracellular metabolites obtained with the feast/famine suggest the presence of regulatory mechanisms that resulted in a delayed response. With the feast famine setup many cellular states can be measured at high frequency given the feature of reproducible cycles. The feast/famine regime is thus a versatile platform for systems biology approaches, which can help us to identify and investigate metabolite regulations under realistic conditions (e.g., large-scale bioreactors or natural environments).