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Sample records for m137 sim motility

  1. Cell Motility

    CERN Document Server

    Lenz, Peter

    2008-01-01

    Cell motility is a fascinating example of cell behavior which is fundamentally important to a number of biological and pathological processes. It is based on a complex self-organized mechano-chemical machine consisting of cytoskeletal filaments and molecular motors. In general, the cytoskeleton is responsible for the movement of the entire cell and for movements within the cell. The main challenge in the field of cell motility is to develop a complete physical description on how and why cells move. For this purpose new ways of modeling the properties of biological cells have to be found. This long term goal can only be achieved if new experimental techniques are developed to extract physical information from these living systems and if theoretical models are found which bridge the gap between molecular and mesoscopic length scales. Cell Motility gives an authoritative overview of the fundamental biological facts, theoretical models, and current experimental developments in this fascinating area.

  2. The SIM Time Network.

    Science.gov (United States)

    Lombardi, Michael A; Novick, Andrew N; Lopez R, J Mauricio; Jimenez, Francisco; de Carlos Lopez, Eduardo; Boulanger, Jean-Simon; Pelletier, Raymond; de Carvalho, Ricardo J; Solis, Raul; Sanchez, Harold; Quevedo, Carlos Andres; Pascoe, Gregory; Perez, Daniel; Bances, Eduardo; Trigo, Leonardo; Masi, Victor; Postigo, Henry; Questelles, Anthony; Gittens, Anselm

    2011-01-01

    The Sistema Interamericano de Metrologia (SIM) is a regional metrology organization (RMO) whose members are the national metrology institutes (NMIs) located in the 34 nations of the Organization of American States (OAS). The SIM/OAS region extends throughout North, Central, and South America and the Caribbean Islands. About half of the SIM NMIs maintain national standards of time and frequency and must participate in international comparisons in order to establish metrological traceability to the International System (SI) of units. The SIM time network (SIMTN) was developed as a practical, cost effective, and technically sound way to automate these comparisons. The SIMTN continuously compares the time standards of SIM NMIs and produces measurement results in near real-time by utilizing the Internet and the Global Positioning System (GPS). Fifteen SIM NMIs have joined the network as of December 2010. This paper provides a brief overview of SIM and a technical description of the SIMTN. It presents international comparison results and examines the measurement uncertainties. It also discusses the metrological benefits that the network provides to its participants.

  3. SIMS applications workshop. Proceedings

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-04-01

    The first ANSTO/AINSE SIMS Workshop drew together a mixture of Surface Analysis experts and Surface Analysis users with the concept that SIMS analysis has to be enfolded within the spectrum of surface analysis techniques and that the user should select the technique most applicable to the problem. With this concept in mind the program was structured as sessions on SIMS Facilities; Applications to Mineral Surfaces; Applications to Biological Systems, Applications to Surfaces as Semi- conductors, Catalysts and Surface Coatings; and Applications to Ceramics

  4. Progress in molecular SIMS

    Energy Technology Data Exchange (ETDEWEB)

    Borman, S.

    1987-04-15

    A review of sputtering and molecular ion emission is presented. New derivatization techniques have produced lower detection limits for molecular secondary ion mass spectrometry (SIMS). Spectra of representative organic compounds are presented.

  5. Learn About GI Motility

    Science.gov (United States)

    ... eNewsletter Sidebar × MOBILE MENU About Us Learn About GI Motility Digestive Tract Disorders of the Esophagus Disorders ... Pelvic Floor Motility Testing Personal Stories Contact About GI Motility Twitter Facebook YouTube Search Search ... About Us ...

  6. About GI Motility

    Science.gov (United States)

    ... eNewsletter Sidebar × MOBILE MENU About Us Learn About GI Motility Digestive Tract Disorders of the Esophagus Disorders ... Pelvic Floor Motility Testing Personal Stories Contact About GI Motility Twitter Facebook YouTube Search Search ... About Us ...

  7. Coloring GPenSIM

    OpenAIRE

    2008-01-01

    The object of this report is to present a solution on how to implement color functionality in GPenSIM. Current version of GPenSIM is based on Place/Transition nets (PT-nets). When creating systems with PT-nets there are some issues when modeling large real life systems. First of all PT-nets have no data concepts. This results in extremely large nets, because the data manipulation has to be represented in the net as places and transitions. The other issue concerns the hierarc...

  8. Social Impacts Module (SIM) Transition

    Science.gov (United States)

    2012-09-28

    the agent constructor in the Java source code. Agents are SimEntities, as defined by the SimKit Java Libraries. An agent perceives events and seeks...technical overview of these key SIM components. For an in depth understanding of SIM components, refer to the JavaDocs and Dr. Buss’s Manual on...volume of data generated5, a combination of manual and batch-file processing methods were used to organize the outputs into similar dataset

  9. BioFET-SIM

    DEFF Research Database (Denmark)

    Hediger, M. R.; Martinez, K. L.; Nygård, J.

    2013-01-01

    signals through its web-based interface www.biofetsim.org. The model also allows for predictions of the effects of changes in the experimental setup on the sensor signal. After an introduction to nanowire-based FET biosensors, this chapter reviews the theoretical basis of BioFET-SIM models describing both...... single and multiple charges on the analyte. Afterwards the usage of the interface and its relative command line version is briefly shown. Finally, possible applications of the BioFET-SIM model are presented. Among the possible uses of the interface, the effects on the predicted signal of pH, buffer ionic...... strength, analyte concentration, and analyte relative orientation on nanowire surface are illustrated. Wherever possible, a comparison to experimental data available in literature is given, displaying the potential of BioFETSIM for interpreting experimental results....

  10. Improvements in SIMS continue

    Energy Technology Data Exchange (ETDEWEB)

    Winograd, Nicholas [Department of Chemistry, Penn State University, University Park, PA 16802 (United States)]. E-mail: nxw@psu.edu; Postawa, Zbigniew [Smoluchowski Institute of Physics, Jagiellonian University, Cracow (Poland); Cheng, Juan [Department of Chemistry, Penn State University, University Park, PA 16802 (United States); Szakal, Christopher [Department of Chemistry, Penn State University, University Park, PA 16802 (United States); Kozole, Joseph [Department of Chemistry, Penn State University, University Park, PA 16802 (United States); Garrison, Barbara J. [Department of Chemistry, Penn State University, University Park, PA 16802 (United States)

    2006-07-30

    Cluster ion bombardment is at the forefront of current ToF-SIMS research, particularly when examining the feasibility of molecular depth profiling and three-dimensional imaging applications. It has become increasingly clear that secondary ion emission after cluster projectile impact results from a radically different sputtering mechanism than the linear collision cascades that dominate after atomic ion bombardment. The new physics involved with cluster ion impacts dramatically change the traditional approaches toward sample analysis with the SIMS technique. Several new ion bombardment properties have emerged from experimental and theoretical work involving cluster ions such as Au{sub 3} {sup +}, Bi{sub 3} {sup +}, SF{sub 5} {sup +}, and C{sub 60} {sup +}-all of which are commercially available ion sources. These new properties lead to new rules for traditional static SIMS experiments, provoking new methodologies, and introducing new applications-especially where high mass sensitivity and high-resolution imaging of organic and biological materials are necessary. This paper aims to elucidate recent experimental and theoretical work on these new cluster ion properties and offers insights into how these special properties can be used for future experiments and applications.

  11. SIM Configuration Evolution

    Science.gov (United States)

    Aaron, Kim M.

    2000-01-01

    The Space Interferometry Mission (SIM) is a space-based 10 m baseline Michelson interferometer. Planned for launch in 2005 aboard a Delta III launch vehicle, or equivalent, its primary objective is to measure the positions of stars and other celestial objects with an unprecedented accuracy of 4 micro arc seconds. With such an instrument, tremendous advancement can be expected in our understanding of stellar and galactic dynamics. Using triangulation from opposite sides of the orbit around the sun (i.e. by using parallax) one can measure the distance to any observable object in our galaxy. By directly measuring the orbital wobble of nearby stars, the mass and orbit of planets can be determined over a wide range of parameters. The distribution of velocity within nearby galaxies will be measurable. Observations of these and other objects will improve the calibration of distance estimators by more than an order of magnitude. This will permit a much better determination of the Hubble Constant as well as improving our overall understanding of the evolution of the universe. SIM has undergone several transformations, especially over the past year and a half since the start of Phase A. During this phase of a project, it is desirable to perform system-level trade studies, so the substantial evolution of the design that has occurred is quite appropriate. Part of the trade-off process has addressed two major underlying architectures: SIM Classic; and Son of SIM. The difference between these two architectures is related to the overall arrangement of the optical elements and the associated metrology system. Several different configurations have been developed for each architecture. Each configuration is the result of design choices that are influenced by many competing considerations. Some of the more important aspects will be discussed. The Space Interferometry Mission has some extremely challenging goals: millikelvin thermal stability, nanometer stabilization of optics

  12. SIM2 NERO

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    近期,SIM2推出了最新的NERO系列3D投影机,外壳涂层采用柔软的黑色塑料,造型典雅美观。NERO系列包括NERO 1、NERO 2、NERO HB和NERO 235四款型号。NERO 1是该系列产品的入门级型号,亮度为2000流明,具有PureMovie和PureMotion技术,支持HDMI 1.4版本;NERO 2在NERO 1基础上增加了sim2动态黑技术(加强方案)、极致色彩技术以及电动虹膜控制,对比度达30000:1;NERO HB具有更高的亮度,达3000流明;NERO 235具有新的WQXGA DMD芯片,分辨率为2560×1600像素,这样就可以在没有丢失像素、亮度及无需增加变形镜头的情况下,投射出2.35:1模式的影片。

  13. Cytoskeleton and Cell Motility

    CERN Document Server

    Risler, Thomas

    2011-01-01

    The present article is an invited contribution to the Encyclopedia of Complexity and System Science, Robert A. Meyers Ed., Springer New York (2009). It is a review of the biophysical mechanisms that underly cell motility. It mainly focuses on the eukaryotic cytoskeleton and cell-motility mechanisms. Bacterial motility as well as the composition of the prokaryotic cytoskeleton is only briefly mentioned. The article is organized as follows. In Section III, I first present an overview of the diversity of cellular motility mechanisms, which might at first glance be categorized into two different types of behaviors, namely "swimming" and "crawling". Intracellular transport, mitosis - or cell division - as well as other extensions of cell motility that rely on the same essential machinery are briefly sketched. In Section IV, I introduce the molecular machinery that underlies cell motility - the cytoskeleton - as well as its interactions with the external environment of the cell and its main regulatory pathways. Sec...

  14. NCAM regulates cell motility

    DEFF Research Database (Denmark)

    Prag, Søren; Lepekhin, Eugene A; Kolkova, Kateryna

    2002-01-01

    Cell migration is required during development of the nervous system. The regulatory mechanisms for this process, however, are poorly elucidated. We show here that expression of or exposure to the neural cell adhesion molecule (NCAM) strongly affected the motile behaviour of glioma cells...... independently of homophilic NCAM interactions. Expression of the transmembrane 140 kDa isoform of NCAM (NCAM-140) caused a significant reduction in cellular motility, probably through interference with factors regulating cellular attachment, as NCAM-140-expressing cells exhibited a decreased attachment...... to a fibronectin substratum compared with NCAM-negative cells. Ectopic expression of the cytoplasmic part of NCAM-140 also inhibited cell motility, presumably via the non-receptor tyrosine kinase p59(fyn) with which NCAM-140 interacts. Furthermore, we showed that the extracellular part of NCAM acted as a paracrine...

  15. Mechanotaxis and cell motility

    CERN Document Server

    Recho, Pierre; Truskinovsky, Lev

    2013-01-01

    We propose a mechanism of cell motility which is based on contraction and does not require protrusion. The contraction driven translocation of a cell is due to internal flow of the cytoskeleton generated by molecular motors. Each motor contributes to the stress field and simultaneously undergoes biased random motion in the direction of a higher value of this stress. In this way active cross-linkers use passive actin network as a medium through which they interact and self-organize. The model exhibits motility initiation pattern similar to the one observed in experiments on keratocytes.

  16. Sims, Christopher Albert (born 1942)

    NARCIS (Netherlands)

    Boumans, Marcel

    2015-01-01

    Christopher Sims is one of the leaders in time-series econometrics and empirical macroeconomics and is well known for introducing the VAR approach to econometrics and macroeconomic modelling. Sims’ main contribution to empirical macroeconomics was to show how macro-econometric modeling should be rev

  17. Sims, Christopher Albert (born 1942)

    NARCIS (Netherlands)

    Boumans, Marcel

    2015-01-01

    Christopher Sims is one of the leaders in time-series econometrics and empirical macroeconomics and is well known for introducing the VAR approach to econometrics and macroeconomic modelling. Sims’ main contribution to empirical macroeconomics was to show how macro-econometric modeling should be

  18. Sphincter of Oddi motility

    DEFF Research Database (Denmark)

    Funch-Jensen, P; Ebbehøj, N

    1996-01-01

    Gastroenterology. RESULTS: The SO is a zone with an elevated basal pressure with superimposed phasic contractions. It acts mainly as a resistor in the regulation of bile flow. Neurohormonal regulation influences the motility pattern. The contractions are under the control of slow waves. Clinical subgroups show...

  19. Sperm Motility in Flow

    Science.gov (United States)

    Guasto, Jeffrey; Juarez, Gabriel; Stocker, Roman

    2012-11-01

    A wide variety of plants and animals reproduce sexually by releasing motile sperm that seek out a conspecific egg, for example in the reproductive tract for mammals or in the water column for externally fertilizing organisms. Sperm are aided in their quest by chemical cues, but must also contend with hydrodynamic forces, resulting from laminar flows in reproductive tracts or turbulence in aquatic habitats. To understand how velocity gradients affect motility, we subjected swimming sperm to a range of highly-controlled straining flows using a cross-flow microfluidic device. The motion of the cell body and flagellum were captured through high-speed video microscopy. The effects of flow on swimming are twofold. For moderate velocity gradients, flow simply advects and reorients cells, quenching their ability to cross streamlines. For high velocity gradients, fluid stresses hinder the internal bending of the flagellum, directly inhibiting motility. The transition between the two regimes is governed by the Sperm number, which compares the external viscous stresses with the internal elastic stresses. Ultimately, unraveling the role of flow in sperm motility will lead to a better understanding of population dynamics among aquatic organisms and infertility problems in humans.

  20. Electrospray Droplet Impact/SIMS

    Science.gov (United States)

    Hiraoka, Kenzo

    A new type of cluster SIMS, named as electrospray droplet impact (EDI), has been developed in our laboratory. It was found that peptides deposited on the stainless steel substrate were ionized/desorbed without the accumulation of radiation products. The organic samples with film thickness thinner than 10 monolayers are desorbed/ionized with little damage underneath the surface. In general, rather strong negative ions as well as positive ions are generated. The mechanism for the ionization/desorption in EDI is much less complicated than those for MALDI and SIMS due to the fact that only very thin sample layers take part in the shock-wave excited selvedge and higher-order side reactions are largely suppressed.

  1. Fragmentation at and above surfaces in SIMS

    Science.gov (United States)

    Luxembourg, Stefan L.; Heeren, Ron M. A.

    2006-07-01

    Matrix-enhanced SIMS and metal-assisted SIMS are successfully employed to increase the organic ion yield in SIMS. In this study we compare kinetic energy distributions obtained for the SIMS, ME-SIMS and MetA-SIMS sputtering of molecular ions. In comparison to the SIMS kinetic energy distributions, those obtained for ME-SIMS display larger energy deficits, indicative of entrainment of analyte ions by matrix molecules or collisions taking place above the sample surface. In the case of MetA-SIMS high energy broadening of the distributions is observed, resulting from the high stopping power of the gold used. A selection of substituted benzylpyridinium salts is used to investigate the effect of internal energy reduction in ME-SIMS. Kinetic energy distributions were used to separate the daughter ions formed in the sample region from those resulting from unimolecular decay on nanosecond timescales, in the first tens of micrometers above the sample surface. The longer-timescale decay was monitored by changing the energy acceptance window of the mass spectrometer used. From the decay rate constants internal energies of the precursor ions decaying on nanosecond timescales were determined using RRKM theory. Within the framework of the precursor model the results indicate an extension of the collision cascade over a wider area than in SIMS.

  2. Motility of ureter

    Energy Technology Data Exchange (ETDEWEB)

    Schroth, H.J.; Steinstraesser, A.; Berberich, R.; Kloss, G.

    1985-01-01

    Motility of ureter. Changes of secretion-phase during sequential scintigraphy of the kidneys under the influence of Metamizol - a parameter to study the effect of Metamizol: The aim of the study is to get quantitative information about the effect of Metamizol (Novalgin) on the motility of the ureter. We compared the renal excretion of 99m-Tc-MDP (Tecebon) and the extent of flowing off towards gravity through the ureter with and without Metamizol. The effect of Metamizol is shown in comparing the final amplitudes of nephrograms recorded during sequential scintigraphy of the kidneys and comparing the integrals of these curves before and after injection of Metamizol. It can be demonstrated that the flow off towards gravity through the ureter is significantly diminished under Metamizol caused by its spasmolytic effect.

  3. Sequencing Information Management System (SIMS). Final report

    Energy Technology Data Exchange (ETDEWEB)

    Fields, C.

    1996-02-15

    A feasibility study to develop a requirements analysis and functional specification for a data management system for large-scale DNA sequencing laboratories resulted in a functional specification for a Sequencing Information Management System (SIMS). This document reports the results of this feasibility study, and includes a functional specification for a SIMS relational schema. The SIMS is an integrated information management system that supports data acquisition, management, analysis, and distribution for DNA sequencing laboratories. The SIMS provides ad hoc query access to information on the sequencing process and its results, and partially automates the transfer of data between laboratory instruments, analysis programs, technical personnel, and managers. The SIMS user interfaces are designed for use by laboratory technicians, laboratory managers, and scientists. The SIMS is designed to run in a heterogeneous, multiplatform environment in a client/server mode. The SIMS communicates with external computational and data resources via the internet.

  4. NCAM regulates cell motility.

    Science.gov (United States)

    Prag, Søren; Lepekhin, Eugene A; Kolkova, Kateryna; Hartmann-Petersen, Rasmus; Kawa, Anna; Walmod, Peter S; Belman, Vadym; Gallagher, Helen C; Berezin, Vladimir; Bock, Elisabeth; Pedersen, Nina

    2002-01-15

    Cell migration is required during development of the nervous system. The regulatory mechanisms for this process, however, are poorly elucidated. We show here that expression of or exposure to the neural cell adhesion molecule (NCAM) strongly affected the motile behaviour of glioma cells independently of homophilic NCAM interactions. Expression of the transmembrane 140 kDa isoform of NCAM (NCAM-140) caused a significant reduction in cellular motility, probably through interference with factors regulating cellular attachment, as NCAM-140-expressing cells exhibited a decreased attachment to a fibronectin substratum compared with NCAM-negative cells. Ectopic expression of the cytoplasmic part of NCAM-140 also inhibited cell motility, presumably via the non-receptor tyrosine kinase p59(fyn) with which NCAM-140 interacts. Furthermore, we showed that the extracellular part of NCAM acted as a paracrine inhibitor of NCAM-negative cell locomotion through a heterophilic interaction with a cell-surface receptor. As we showed that the two N-terminal immunoglobulin modules of NCAM, which are known to bind to heparin, were responsible for this inhibition, we presume that this receptor is a heparan sulfate proteoglycan. A model for the inhibitory effect of NCAM is proposed, which involves competition between NCAM and extracellular components for the binding to membrane-associated heparan sulfate proteoglycan.

  5. QCD at $\\Theta \\sim \\pi$

    CERN Document Server

    Smilga, A V

    1999-01-01

    Taking into account the quadratic in quark mass terms in the effective chiral lagrangian, we show that, at \\theta \\sim \\pi, the theory with 2 light quarks of equal mass involves two degenerate vacuum states separated by a barrier. For three flavors, the energy barrier between two vacua appears already in the leading order in mass. This corresponds to the first order phase transition at different vacua is calculated. In the immediate vicinity of the phase transition point, two minima of the potential still exist, but one of them becomes metastable. The probability of the false vacuum decay is estimated.

  6. SimProp v2r3

    CERN Document Server

    Aloisio, Roberto; di Matteo, Armando; Grillo, Aurelio; Petrera, Sergio; Salamida, Francesco

    2016-01-01

    We introduce the a version of SimProp, a Monte Carlo code for simulating the propagation of ultra-high energy cosmic rays in intergalactic space. This version, SimProp v2r3, allows the choice of many more models for the extragalactic background light spectrum and evolution and photodisintegration cross sections and branching ratios than previous versions of SimProp.

  7. Mechanics of motility initiation and motility arrest in crawling cells

    Science.gov (United States)

    Recho, Pierre; Putelat, Thibaut; Truskinovsky, Lev

    2015-11-01

    Motility initiation in crawling cells requires transformation of a symmetric state into a polarized state. In contrast, motility arrest is associated with re-symmetrization of the internal configuration of a cell. Experiments on keratocytes suggest that polarization is triggered by the increased contractility of motor proteins but the conditions of re-symmetrization remain unknown. In this paper we show that if adhesion with the extra-cellular substrate is sufficiently low, the progressive intensification of motor-induced contraction may be responsible for both transitions: from static (symmetric) to motile (polarized) at a lower contractility threshold and from motile (polarized) back to static (symmetric) at a higher contractility threshold. Our model of lamellipodial cell motility is based on a 1D projection of the complex intra-cellular dynamics on the direction of locomotion. In the interest of analytical transparency we also neglect active protrusion and view adhesion as passive. Despite the unavoidable oversimplifications associated with these assumptions, the model reproduces quantitatively the motility initiation pattern in fish keratocytes and reveals a crucial role played in cell motility by the nonlocal feedback between the mechanics and the transport of active agents. A prediction of the model that a crawling cell can stop and re-symmetrize when contractility increases sufficiently far beyond the motility initiation threshold still awaits experimental verification.

  8. Secondary Ion Mass Spectrometry SIMS XI

    Science.gov (United States)

    Gillen, G.; Lareau, R.; Bennett, J.; Stevie, F.

    2003-05-01

    This volume contains 252 contributions presented as plenary, invited and contributed poster and oral presentations at the 11th International Conference on Secondary Ion Mass Spectrometry (SIMS XI) held at the Hilton Hotel, Walt Disney World Village, Orlando, Florida, 7 12 September, 1997. The book covers a diverse range of research, reflecting the rapid growth in advanced semiconductor characterization, ultra shallow depth profiling, TOF-SIMS and the new areas in which SIMS techniques are being used, for example in biological sciences and organic surface characterization. Papers are presented under the following categories: Isotopic SIMS Biological SIMS Semiconductor Characterization Techniques and Applications Ultra Shallow Depth Profiling Depth Profiling Fundamental/Modelling and Diffusion Sputter-Induced Topography Fundamentals of Molecular Desorption Organic Materials Practical TOF-SIMS Polyatomic Primary Ions Materials/Surface Analysis Postionization Instrumentation Geological SIMS Imaging Fundamentals of Sputtering Ion Formation and Cluster Formation Quantitative Analysis Environmental/Particle Characterization Related Techniques These proceedings provide an invaluable source of reference for both newcomers to the field and experienced SIMS users.

  9. Motility initiation in active gels

    CERN Document Server

    Recho, Pierre; Truskinovsky, Lev

    2015-01-01

    Motility initiation in crawling cells requires a symmetry breaking mechanism which transforms a symmetric state into a polarized state. Experiments on keratocytes suggest that polarization is triggered by increased contractility of motor proteins. In this paper we argue that contraction can be responsible not only for the symmetry breaking transition but also for the incipient translocation of the segment of an active gel mimicking the crawling cell. Our model suggests that when the contractility increases sufficiently far beyond the motility initiation threshold, the cell can stop and re-symmetrizes. The proposed theory reproduces the motility initiation pattern in fish keratocytes and the behavior of keratocytes prior to cell division.

  10. Grafisk presentasjon av GPenSim-simulering

    OpenAIRE

    2009-01-01

    GPenSim er et verktøy for modellering og simulering av diskret hendelsesystemer (DES). GPenSim er integrert i Matlab-plattformen, og har dermed tilgang til innebygde Matlabfunksjoner som plot etc. I GPenSim blir Petri net-grafen definert i Petri netdefinisjonsfiler. Resultatet av en simulering blir vist i tekst. Oppgaven gikk ut på å utvikle et verktøy som skulle presentere både Petri net-grafen og simuleringsresultatet grafisk. En grafisk presentasjon viser tydeligere sammenhe...

  11. Surface motility of Myxococcus Xanthus

    Science.gov (United States)

    Gibiansky, Maxsim; Hu, William; Jin, Fan; Zhao, Kun; Shi, Wenyuan; Wong, Gerard

    2011-03-01

    We examine the surface motility of Myxococcus Xanthus, a bacterium species found in soil that exhibits a broad range of self-organizing behavior, including predatory ``swarms'' and survival-enhancing ``fruiting bodies.'' To quantify the effects of exopolysaccharides (EPS) on surface adhesion and motility, we use modified versions of particle tracking algorithms from colloid physics to analyze bacterial trajectories, and compare the wild type (WT) strain to EPS knockout and EPS overproducer strains. We find that EPS deficiency leads to an increase in the number of ``standing'' bacteria oriented normal to the surface, attached by one end with minimal motility. EPS overproduction, by contrast, suppresses this phenotype. A detailed investigation of the influence of EPS on Myxococcus social motility will be presented.

  12. Bacterial motility on abiotic surfaces

    OpenAIRE

    Gibiansky, Maxsim

    2013-01-01

    Bacterial biofilms are structured microbial communities which are widespread both in nature and in clinical settings. When organized into a biofilm, bacteria are extremely resistant to many forms of stress, including a greatly heightened antibiotic resistance. In the early stages of biofilm formation on an abiotic surface, many bacteria make use of their motility to explore the surface, finding areas of high nutrition or other bacteria to form microcolonies. They use motility appendages, incl...

  13. Elenoside increases intestinal motility

    Institute of Scientific and Technical Information of China (English)

    E Navarro; SJ Alonso; R Navarro; J Trujillo; E Jorge

    2006-01-01

    AIM: To study the effects of elenoside, an arylnaphthalene lignan from Justicia hyssopifolia, on gastrointestinal motility in vivo and in vitro in rats.METHODS: Routine in vivo experimental assessments were catharsis index, water percentage of boluses,intestinal transit, and codeine antagonism. The groups included were vehicle control (propylene glycol-ethanolplant oil-tween 80), elenoside (i.p. 25 and 50 mg/kg),cisapride (i.p. 10 mg/kg), and codeine phosphate (intragastric route, 50 mg/kg). In vitro approaches used isolated rat intestinal tissues (duodenum, jejunum, and ileum). The effects of elenoside at concentrations of 3.2× 10-4, 6.4 × 10-4 and 1.2 × 10-3 mol/L, and cisapride at 10-6 mol/L were investigated.RESULTS: Elenoside in vivo produced an increase in the catharsis index and water percentage of boluses and in the percentage of distance traveled by a suspension of activated charcoal. Codeine phosphate antagonized the effect of 25 mg/kg of elenoside. In vitro, elenoside in duodenum, jejunum and ileum produced an initial decrease in the contraction force followed by an increase.Elenoside resulted in decreased intestinal frequency in duodenum, jejunum, and ileum. The in vitro and in vivo effects of elenoside were similar to those produced by cisapride.CONCLUSION: Elenoside is a lignan with an action similar to that of purgative and prokinetics drugs.Elenoside, could be an alternative to cisapride in treatment of gastrointestinal diseases as well as a preventive therapy for the undesirable gastrointestinal effects produced by opioids used for mild to moderate pain.

  14. G-SIMS of crystallisable organics

    Energy Technology Data Exchange (ETDEWEB)

    Gilmore, I.S.; Seah, M.P

    2003-01-15

    In this study, the gentle SIMS (G-SIMS) concept has been applied to the crystallisable organic materials of Irganox 1010, caffeine, cholesterol, glucose, poly-L-lysine and bovine serum albumin. These are chosen to represent as wide a range of material types as possible. For each case, the G-SIMS spectra are considerably simpler than the static SIMS, enabling direct interpretation and identification. It is demonstrated that the amount of fragmentation in the mass spectrum may be controlled numerically and this information can be used to re-assemble the parent molecule. Wherever possible, the use of dual column ion beams is recommended to eliminate alignment requirements. Additionally, the total electron beam fluence should be kept below 6x10{sup 18} electrons/m{sup 2} to prevent electron damage.

  15. G-SIMS of crystallisable organics

    Science.gov (United States)

    Gilmore, I. S.; Seah, M. P.

    2003-01-01

    In this study, the gentle SIMS (G-SIMS) concept has been applied to the crystallisable organic materials of Irganox 1010, caffeine, cholesterol, glucose, poly- L-lysine and bovine serum albumin. These are chosen to represent as wide a range of material types as possible. For each case, the G-SIMS spectra are considerably simpler than the static SIMS, enabling direct interpretation and identification. It is demonstrated that the amount of fragmentation in the mass spectrum may be controlled numerically and this information can be used to re-assemble the parent molecule. Wherever possible, the use of dual column ion beams is recommended to eliminate alignment requirements. Additionally, the total electron beam fluence should be kept below 6×10 18 electrons/m 2 to prevent electron damage.

  16. Se i Sims vanno su Facebook…

    Directory of Open Access Journals (Sweden)

    Agata Meneghelli

    2012-03-01

    Full Text Available Subito dopo il lancio, la versione facebookiana di The Sims ha riscosso un enorme successo, ma a distanza di qualche mese si è registrato un significativo calo di interesse. L’articolo propone una possibile lettura di questo fenomeno, partendo da alcune caratteristiche della serie The Sims e mostrando come il gioco si sia modificato, sposandosi con le logiche 2.0 di Facebook, per diventare più social e in real time.

  17. Stochastic models of cell motility

    DEFF Research Database (Denmark)

    Gradinaru, Cristian

    2012-01-01

    Cell motility and migration are central to the development and maintenance of multicellular organisms, and errors during this process can lead to major diseases. Consequently, the mechanisms and phenomenology of cell motility are currently under intense study. In recent years, a new...... interdisciplinary field focusing on the study of biological processes at the nanoscale level, with a range of technological applications in medicine and biological research, has emerged. The work presented in this thesis is at the interface of cell biology, image processing, and stochastic modeling. The stochastic...... models introduced here are based on persistent random motion, which I apply to real-life studies of cell motility on flat and nanostructured surfaces. These models aim to predict the time-dependent position of cell centroids in a stochastic manner, and conversely determine directly from experimental...

  18. Motility of electric cable bacteria

    DEFF Research Database (Denmark)

    Bjerg, Jesper Tataru; Damgaard, Lars Riis; Holm, Simon Agner

    2016-01-01

    Cable bacteria are filamentous bacteria that electrically couple sulfide oxidation and oxygen reduction at centimeter distances, and observations in sediment environments have suggested that they are motile. By time-lapse microscopy, we found that cable bacteria used gliding motility on surfaces...... with a highly variable speed of 0.50.3 ms1 (meanstandard deviation) and time between reversals of 155108 s. They frequently moved forward in loops, and formation of twisted loops revealed helical rotation of the filaments. Cable bacteria responded to chemical gradients in their environment, and around the oxic......-anoxic interface, they curled and piled up, with straight parts connecting back to the source of sulfide. Thus, it appears that motility serves the cable bacteria in establishing and keeping optimal connections between their distant electron donor and acceptors in a dynamic sediment environment....

  19. Stellar and Galactic Astrophysics with SIM

    Science.gov (United States)

    Gould, A.

    2001-05-01

    SIM will revolutionize stellar and Galactic astrophysics by tackling new questions that could never previously be addressed and making order of magnitude improvements in key parameters. SIM will measure R0 and Theta0 to measurements of the Milky Way mass and rotation curve. It will probe the Galactic 3-D mass distribution by 2 independent methods. By calibrating the RR Lyrae MV-[Fe/H] relation as well as obtaining direct distances to clusters and halo field objects, SIM will precisely date halo and globular-cluster formation as a function of metallicity. SIM will obtain 1 measurements for 200 stars of all types ranging from brown dwarfs (BD) to O stars from a broad range of metallicities, including both binaries and single stars, and it will yield precision measurements of white dwarf (WD) and black hole (BH) remnants as well. SIM microlensing will take an unbiased census of all objects in the Galactic bulge, both dark (BD WD NS BH) and luminous, and will resolve the nature of the dark-halo (MACHO) candidates currently being detected toward the LMC.

  20. Motility of Electric Cable Bacteria

    OpenAIRE

    Bjerg, Jesper Tataru; Damgaard, Lars Riis; Holm, Simon Agner; Schramm, Andreas; Nielsen, Lars Peter

    2016-01-01

    Cable bacteria are filamentous bacteria that electrically couple sulfide oxidation and oxygen reduction at centimeter distances, and observations in sediment environments have suggested that they are motile. By time-lapse microscopy, we found that cable bacteria used gliding motility on surfaces with a highly variable speed of 0.5 ± 0.3 μm s−1 (mean ± standard deviation) and time between reversals of 155 ± 108 s. They frequently moved forward in loops, and formation of twisted loops revealed ...

  1. Social motility in african trypanosomes.

    Directory of Open Access Journals (Sweden)

    Michael Oberholzer

    2010-01-01

    Full Text Available African trypanosomes are devastating human and animal pathogens that cause significant human mortality and limit economic development in sub-Saharan Africa. Studies of trypanosome biology generally consider these protozoan parasites as individual cells in suspension cultures or in animal models of infection. Here we report that the procyclic form of the African trypanosome Trypanosoma brucei engages in social behavior when cultivated on semisolid agarose surfaces. This behavior is characterized by trypanosomes assembling into multicellular communities that engage in polarized migrations across the agarose surface and cooperate to divert their movements in response to external signals. These cooperative movements are flagellum-mediated, since they do not occur in trypanin knockdown parasites that lack normal flagellum motility. We term this behavior social motility based on features shared with social motility and other types of surface-induced social behavior in bacteria. Social motility represents a novel and unexpected aspect of trypanosome biology and offers new paradigms for considering host-parasite interactions.

  2. Barriers to bacterial motility on unsaturated surfaces

    DEFF Research Database (Denmark)

    Dechesne, Arnaud; Smets, Barth F.

    2013-01-01

    contributes to microbial spatial dynamics. In bacteria, active dispersal is enabled by a diversity of appendages and, in the case of swarming motility, by the secretion of surface active biomolecules. It is however unclear to which degree di_erent types of motility can take place in the soil pores, a habitat...... and their isogenic mutants unable to express various type of motility we aimed to quantify the physical limits of bacterial motility. Our results demonstrate how hydration controls bacterial motility under unsaturated conditions. They can form the base of improved biodegradation models that include microbial...

  3. Axoneme Structure from Motile Cilia.

    Science.gov (United States)

    Ishikawa, Takashi

    2017-01-03

    The axoneme is the main extracellular part of cilia and flagella in eukaryotes. It consists of a microtubule cytoskeleton, which normally comprises nine doublets. In motile cilia, dynein ATPase motor proteins generate sliding motions between adjacent microtubules, which are integrated into a well-orchestrated beating or rotational motion. In primary cilia, there are a number of sensory proteins functioning on membranes surrounding the axoneme. In both cases, as the study of proteomics has elucidated, hundreds of proteins exist in this compartmentalized biomolecular system. In this article, we review the recent progress of structural studies of the axoneme and its components using electron microscopy and X-ray crystallography, mainly focusing on motile cilia. Structural biology presents snapshots (but not live imaging) of dynamic structural change and gives insights into the force generation mechanism of dynein, ciliary bending mechanism, ciliogenesis, and evolution of the axoneme. Copyright © 2017 Cold Spring Harbor Laboratory Press; all rights reserved.

  4. Physical models of cell motility

    CERN Document Server

    2016-01-01

    This book surveys the most recent advances in physics-inspired cell movement models. This synergetic, cross-disciplinary effort to increase the fidelity of computational algorithms will lead to a better understanding of the complex biomechanics of cell movement, and stimulate progress in research on related active matter systems, from suspensions of bacteria and synthetic swimmers to cell tissues and cytoskeleton.Cell motility and collective motion are among the most important themes in biology and statistical physics of out-of-equilibrium systems, and crucial for morphogenesis, wound healing, and immune response in eukaryotic organisms. It is also relevant for the development of effective treatment strategies for diseases such as cancer, and for the design of bioactive surfaces for cell sorting and manipulation. Substrate-based cell motility is, however, a very complex process as regulatory pathways and physical force generation mechanisms are intertwined. To understand the interplay between adhesion, force ...

  5. Gender effects on esophageal motility

    Directory of Open Access Journals (Sweden)

    Dantas R.O.

    1998-01-01

    Full Text Available It has been suggested that there are no gender effects on esophageal motility. However, in previous studies the subjects did not perform multiple swallows and the quantitative features of esophageal contractions were not evaluated. In order to investigate the gender effects on esophageal motility we studied 40 healthy normal volunteers, 20 men aged 37 ± 15 years (mean ± SD, and 20 women aged 38 ± 14 years. We used the manometric method with an eight-lumen polyvinyl catheter and continuous perfusion. The upper and lower esophageal sphincter pressures were measured by the rapid pull-through method. With the catheter positioned with one lumen opening in the lower esophageal sphincter, and the others at 5, 10 and 15 cm above the sphincter, ten swallows of a 5-ml water bolus alternated with ten dry swallows were performed. Statistical analysis was done by the Student t-test and Mann-Whitney test. Gender differences (P<0.05 were observed for wet swallows in the duration of contractions 5 cm above the lower esophageal sphincter (men: 3.7 ± 0.2 s, women: 4.5 ± 0.3 s, mean ± SEM, and in the velocity of contractions from 15 to 10 cm above the lower esophageal sphincter (men: 4.7 ± 0.3 cm/s, women: 3.5 ± 0.2 cm/s. There was no difference (P>0.05 in sphincter pressure, duration and percentage of complete lower esophageal sphincter relaxation, amplitude of contractions, or in the number of failed, multipeaked and synchronous contractions. We conclude that gender may cause some differences in esophageal motility which, though of no clinical significance, should be taken into consideration when interpreting esophageal motility tests.

  6. Analysis of volatile nanoparticles emitted from diesel engine using TOF-SIMS and metal-assisted SIMS (MetA-SIMS)

    Science.gov (United States)

    Inoue, Masae; Murase, Atsushi; Yamamoto, Masami; Kubo, Shuichi

    2006-07-01

    Time-of-flight secondary ion mass spectrometry (TOF-SIMS) and metal-assisted SIMS (MetA-SIMS), which is TOF-SIMS analysis of metal-deposited sample surfaces, were applied to analyze small quantities of volatile nanoparticles emitted from a light-duty diesel engine under idling and deceleration conditions. We investigated nucleation materials, i.e., >C35 hydrocarbons, oxidation products, etc., which have lower volatility than the main components of volatile nanoparticles and control the formation of volatile nanoparticles. Oxygenated hydrocarbons were detected by TOF-SIMS in volatile nanoparticles under idling condition. Their relative intensities increased as particle diameter decreased. This resulted in the oxygenated hydrocarbons acting as nucleation materials for volatile nanoparticles under idling condition. High-molecular-weight hydrocarbons of greater than C35 were detected in volatile nanoparticles under deceleration condition by MetA-SIMS. It was concluded that the detected hydrocarbons originated in lubricants and acted as nucleation materials for volatile nanoparticles under deceleration condition. TOF-SIMS makes it possible to detect traces of low-volatility molecules due to its high-vacuum environment. MetA-SIMS is the only method of directly detecting high-molecular-weight hydrocarbons in small quantities of nanoparticles. TOF-SIMS and MetA-SIMS were proved to be useful tools for analyzing of the properties of volatile nanoparticles.

  7. 20-SIM code generation for PC/104 target

    NARCIS (Netherlands)

    Groothuis, Marcel

    2001-01-01

    From version 3.2, 20-Sim will contain a new tool, called C-code generation. With this tool it will be possible to generate C code from a 20-Sim model. This tool works on basis of templates. For each target, a target specific template has to be made. The goal of this project was to write a new 20-Sim

  8. SIMS analysis: Development and evaluation program summary

    Energy Technology Data Exchange (ETDEWEB)

    Groenewold, G.S.; Appelhans, A.D.; Ingram, J.C.; Delmore, J.E.; Dahl, D.A.

    1996-11-01

    This report provides an overview of the ``SIMS Analysis: Development and Evaluation Program``, which was executed at the Idaho National Engineering Laboratory from mid-FY-92 to the end of FY-96. It should be noted that prior to FY-1994 the name of the program was ``In-Situ SIMS Analysis``. This report will not go into exhaustive detail regarding program accomplishments, because this information is contained in annual reports which are referenced herein. In summary, the program resulted in the design and construction of an ion trap secondary ion mass spectrometer (IT-SIMS), which is capable of the rapid analysis of environmental samples for adsorbed surface contaminants. This instrument achieves efficient secondary ion desorption by use of a molecular, massive ReO{sub 4}{sup {minus}} primary ion particle. The instrument manages surface charge buildup using a self-discharging principle, which is compatible with the pulsed nature of the ion trap. The instrument can achieve high selectivity and sensitivity using its selective ion storage and MS/MS capability. The instrument was used for detection of tri-n-butyl phosphate, salt cake (tank cake) characterization, and toxic metal speciation studies (specifically mercury). Technology transfer was also an important component of this program. The approach that was taken toward technology transfer was that of component transfer. This resulted in transfer of data acquisition and instrument control software in FY-94, and ongoing efforts to transfer primary ion gun and detector technology to other manufacturers.

  9. The USNO SIM Grid Star Selection Program

    Science.gov (United States)

    Mason, B. D.; Corbin, T. E.; Hajian, A. R.; Hummel, C. A.; Rafferty, T. J.; Urban, S. E.; Zacharias, N.

    1999-09-01

    The United States Naval Observatory (USNO) is in the process of preparing an input catalog of SIM grid stars by utilizing existing databases, observing capabilities, and instrumental development. The SIM grid should be astrometrically stable at the 4 mu as level over the five year life of the program, therefore, double and multiple stars must be avoided. Stars in the apparent magnitude range 6.5 Navy Prototype Optical Interferometer and wide-field CCD work. In addition, a Fourier Transform Spectrometer (FTS), with a potential for sub-meter per second radial velocity determinations, is being developed to eliminate companions (both stellar and substellar). In total, 7,200 candidate stars, evenly distributed over the sky will be examined observationally. The combination of the four astrometric methods will remove double and multiple systems in the ~ 15 arcsec to ~ 1 milliarcsecond range with Delta m_v of 3.5 magnitudes, while the FTS is expected to detect companions with masses as low as Saturn in the range of 0.1 to 10 au. The first year of the program has thus far seen significant progress. The SIM grid candidate list has been prepared and speckle observations of these candidates have begun: in the northern hemisphere, by the USNO and the RIT/Yale group (Elliott Horch & Zoran Nikov, Rochester Institute of Technology and William van Altena, Yale).

  10. Does Hypothyroidism Affect Gastrointestinal Motility?

    Directory of Open Access Journals (Sweden)

    Olga Yaylali

    2009-01-01

    Full Text Available Background. Gastrointestinal motility and serum thyroid hormone levels are closely related. Our aim was to analyze whether there is a disorder in esophagogastric motor functions as a result of hypothyroidism. Materials and Methods. The study group included 30 females (mean age ± SE 45.17 ± 2.07 years with primary hypothyroidism and 10 healthy females (mean age ± SE 39.40 ± 3.95 years. All cases underwent esophagogastric endoscopy and scintigraphy. For esophageal scintigraphy, dynamic imaging of esophagus motility protocol, and for gastric emptying scintigraphy, anterior static gastric images were acquired. Results. The mean esophageal transit time (52.56 ± 4.07 sec for patients; 24.30 ± 5.88 sec for controls; P=.02 and gastric emptying time (49.06 ± 4.29 min for the hypothyroid group; 30.4 ± 4.74 min for the control group; P=.01 were markedly increased in cases of hypothyroidism. Conclusion. Hypothyroidism prominently reduces esophageal and gastric motor activity and can cause gastrointestinal dysfunction.

  11. Rim Sim: A Role-Play Simulation

    Science.gov (United States)

    Barrett, Robert C.; Frew, Suzanne L.; Howell, David G.; Karl, Herman A.; Rudin, Emily B.

    2003-01-01

    Rim Sim is a 6-hour, eight-party negotiation that focuses on creating a framework for the long-term disaster-recovery efforts. It involves a range of players from five countries affected by two natural disasters: a typhoon about a year ago and an earthquake about 6 months ago. The players are members of an International Disaster Working Group (IDWG) that has been created by an international commission. The IDWG has been charged with drawing up a framework for managing two issues: the reconstruction of regionally significant infrastructure and the design of a mechanism for allocating funding to each country for reconstruction of local infrastructure and ongoing humanitarian needs. The first issue will involve making choices among five options (two harbor options, two airport options, and one rail-line option), each of which will have three levels at which to rebuild. The second issue will involve five starting-point options. Participants are encouraged to invent other options for both issues. The goal of Rim Sim is to raise questions about traditional approaches to disaster-preparedness planning and reconstruction efforts in an international setting, in this case the Pacific Rim. Players must confront the reverberating effects of disasters and the problems of using science and technical information in decisionmaking, and are introduced to a consensus-building approach emphasizing face-to-face dialog and multinational cooperation in dealing with humanitarian concerns, as well as long-term efforts to reconstruct local and regional infrastructure. The Rim Sim simulation raises four key points: ripple effects of disasters, role of science, multiparty negotiation, and building personal relationships.

  12. 21 CFR 876.1725 - Gastrointestinal motility monitoring system.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Gastrointestinal motility monitoring system. 876... Gastrointestinal motility monitoring system. (a) Identification. A gastrointestinal motility monitoring system is a... esophageal motility monitor and tube, the gastrointestinal motility (electrical) system, and...

  13. Interest of silver and gold metallization for molecular SIMS and SIMS imaging

    Science.gov (United States)

    Delcorte, A.; Bertrand, P.

    2004-06-01

    The metallization procedure, recently proposed for signal improvement in organic secondary ion mass spectrometry (metal assisted-SIMS or MetA-SIMS), has been quantitatively evaluated for Irganox 1010 and polystyrene fragment and quasimolecular ions. In addition to gold, we investigate the effect of silver evaporation as a sample treatment prior to static SIMS analysis. Ion yields and yield enhancement factors are compared for Ag and Au-metallized molecular films, pristine coatings on silicon and sub-monolayers of the same molecules adsorbed on silver and gold. The results are sample-dependent but, as an example, the yield enhancement calculated for metallized polymer additive (Irganox 1010) films with respect to untreated coatings is larger than two orders of magnitude for the quasimolecular ion and a factor between 1 and 10 for characteristic fragments. The interest of the method for imaging SIMS applications is illustrated by the study of a non-uniform coating of polystyrene oligomers on a 100 μm polypropylene film.

  14. CoaSim Guile Manual — Using the Guile-based CoaSim Simulator

    DEFF Research Database (Denmark)

    Mailund, T

    2006-01-01

    CoaSim is a tool for simulating the coalescent process with recombination and geneconversion, under either constant population size or exponential population growth. It effectively constructs the ancestral recombination graph for a given number of chromosomes and uses this to simulate samples...

  15. Getting Started with CoaSim — An Introduction to the Simulator CoaSim

    DEFF Research Database (Denmark)

    Mailund, T

    2005-01-01

    CoaSim is a tool for simulating the coalescent process with recombination and geneconversion, under either constant population size or exponential population growth. It effectively constructs the ancestral recombination graph for a given number of chromosomes and uses this to simulate samples...

  16. CoaSim Guile Manual — Using the Guile-based CoaSim Simulator

    DEFF Research Database (Denmark)

    Mailund, T

    2006-01-01

    CoaSim is a tool for simulating the coalescent process with recombination and geneconversion, under either constant population size or exponential population growth. It effectively constructs the ancestral recombination graph for a given number of chromosomes and uses this to simulate samples of ...... of SNP and micro-satellite haplotypes or genotypes....

  17. Getting Started with CoaSim — An Introduction to the Simulator CoaSim

    DEFF Research Database (Denmark)

    Mailund, T

    2005-01-01

    CoaSim is a tool for simulating the coalescent process with recombination and geneconversion, under either constant population size or exponential population growth. It effectively constructs the ancestral recombination graph for a given number of chromosomes and uses this to simulate samples of ...... of SNP and micro-satellite haplotypes or genotypes....

  18. Gaslike model of social motility

    CERN Document Server

    Parravano, A; 10.1103/PhysRevE.78.026120

    2009-01-01

    We propose a model to represent the motility of social elements. The model is completely deterministic, possesses a small number of parameters, and exhibits a series of properties that are reminiscent of the behavior of comunities in social-ecological competition; these are: (i) similar individuals attract each other; (ii) individuals can form stable groups; (iii) a group of similar individuals breaks into subgroups if it reaches a critical size; (iv) interaction between groups can modify the distribution of the elements as a result of fusion, fission, or pursuit; (v) individuals can change their internal state by interaction with their neighbors. The simplicity of the model and its richness of emergent behaviors, such as, for example, pursuit between groups, make it a useful toy model to explore a diversity of situations by changing the rule by which the internal state of individuals is modified by the interactions with the environment.

  19. Experimental Results for SimFuels

    Energy Technology Data Exchange (ETDEWEB)

    Buck, Edgar C.; Casella, Andrew M.; Skomurski, Frances N.; MacFarlan, Paul J.; Soderquist, Chuck Z.; Wittman, Richard S.; Mcnamara, Bruce K.

    2012-08-22

    Assessing the performance of Spent (or Used) Nuclear Fuel (UNF) in geological repository requires quantification of time-dependent phenomena that may influence its behavior on a time-scale up to millions of years. A high-level waste repository environment will be a dynamic redox system because of the time-dependent generation of radiolytic oxidants and reductants and the corrosion of Fe-bearing canister materials. One major difference between used fuel and natural analogues, including unirradiated UO2, is the intense radiolytic field. The radiation emitted by used fuel can produce radiolysis products in the presence of water vapor or a thin-film of water that may increase the waste form degradation rate and change radionuclide behavior. To study UNF, we have been working on producing synthetic UO2 ceramics, or SimFuels that can be used in testing and which will contain specific radionuclides or non-radioactive analogs so that we can test the impact of radiolysis on fuel corrosion without using actual spent fuel. Although, testing actual UNF would be ideal for understanding the long term behavior of UNF, it requires the use of hot cells and is extremely expensive. In this report, we discuss, factors influencing the preparation of SimFuels and the requirements for dopants to mimic the behavior of UNF. We have developed a reliable procedure for producing large grain UO2 at moderate temperatures. This process will be applied to a series of different formulations.

  20. Active Gel Model of Amoeboid Cell Motility

    CERN Document Server

    Callan-Jones, A C

    2013-01-01

    We develop a model of amoeboid cell motility based on active gel theory. Modeling the motile apparatus of a eukaryotic cell as a confined layer of finite length of poroelastic active gel permeated by a solvent, we first show that, due to active stress and gel turnover, an initially static and homogeneous layer can undergo a contractile-type instability to a polarized moving state in which the rear is enriched in gel polymer. This agrees qualitatively with motile cells containing an actomyosin-rich uropod at their rear. We find that the gel layer settles into a steadily moving, inhomogeneous state at long times, sustained by a balance between contractility and filament turnover. In addition, our model predicts an optimal value of the gel-susbstrate adhesion leading to maximum layer speed, in agreement with cell motility assays. The model may be relevant to motility of cells translocating in complex, confining environments that can be mimicked experimentally by cell migration through microchannels.

  1. SimApp 1.8.x

    Energy Technology Data Exchange (ETDEWEB)

    2017-02-21

    System for converting DESIRE (Direct Executing Simulation in Real Time) simulation models to executable code models (C# / C++). These converted models are used as the basis for 2 products, one of which is the focus of this review: an engineering design interface for Fissile Solution Systems. ModelConverter.exe (C#) converts DESIRE model inputs to a C++ plug-in subclass. SimApp.exe (C# / C++) has a C++ dll that is a numerical integration engine that the Converted models plug into. The engineering design interface is a C# GUI that calls on the C++ dll to execute a particular converted model. The GUI allows the user to specify the length of a simulation, run the simulation, view data plots and data tables. Stability plots may also be produced and manipulated. The engineering design interface will be released as source code and executable; the model converter source is also intended for release.

  2. Tracking microbial interactions with NanoSIMS

    Energy Technology Data Exchange (ETDEWEB)

    Musat, Niculina; Musat, Florin; Weber, Peter Kilian; Pett-Ridge, Jennifer

    2016-10-01

    The combination of stable isotope probing (SIP), NanoSIMS imaging and microbe identification via fluorescence in situ hybridization (FISH) is often used to link identity to function at the cellular level in microbial communities. Many opportunities remain for nanoSIP to identify metabolic interactions and nutrient fluxes within syntrophic associations and obligate symbioses where exchanges can be extremely rapid. However, additional data, such as genomic potential, gene expression or other imaging modalities are often critical to deciphering the mechanisms underlying specific interactions, and researchers must keep sample preparation artefacts in mind. Here we focus on recent applications of nanoSIP, particularly where used to track exchanges of isotopically labelled molecules between organisms. We highlight metabolic interactions within syntrophic consortia, carbon/nitrogen fluxes between phototrophs and their heterotrophic partners, and symbiont–host nutrient sharing.

  3. Biochemical imaging of tissues by SIMS for biomedical applications

    Science.gov (United States)

    Lee, Tae Geol; Park, Ji-Won; Shon, Hyun Kyong; Moon, Dae Won; Choi, Won Woo; Li, Kapsok; Chung, Jin Ho

    2008-12-01

    With the development of optimal surface cleaning techniques by cluster ion beam sputtering, certain applications of SIMS for analyzing cells and tissues have been actively investigated. For this report, we collaborated with bio-medical scientists to study bio-SIMS analyses of skin and cancer tissues for biomedical diagnostics. We pay close attention to the setting up of a routine procedure for preparing tissue specimens and treating the surface before obtaining the bio-SIMS data. Bio-SIMS was used to study two biosystems, skin tissues for understanding the effects of photoaging and colon cancer tissues for insight into the development of new cancer diagnostics for cancer. Time-of-flight SIMS imaging measurements were taken after surface cleaning with cluster ion bombardment by Bi n or C 60 under varying conditions. The imaging capability of bio-SIMS with a spatial resolution of a few microns combined with principal component analysis reveal biologically meaningful information, but the lack of high molecular weight peaks even with cluster ion bombardment was a problem. This, among other problems, shows that discourse with biologists and medical doctors are critical to glean any meaningful information from SIMS mass spectrometric and imaging data. For SIMS to be accepted as a routine, daily analysis tool in biomedical laboratories, various practical sample handling methodology such as surface matrix treatment, including nano-metal particles and metal coating, in addition to cluster sputtering, should be studied.

  4. CQI reporting strategy for Multi-SIM UEs

    DEFF Research Database (Denmark)

    Buthler, Jakob Lindbjerg; Sørensen, Troels Bundgaard

    2016-01-01

    UEs which support simultaneous activity from Multiple Active Subscriber Identities (Multi-SIM) has gained popularity within the last years. Such UEs are forced to discard data on one of the SIMs when both try to access the Radio Frequency (RF) interface simultaneously, creating gaps in the data t...

  5. Design and development of a unified subscribers' SIM registration ...

    African Journals Online (AJOL)

    Journal Home > Vol 13, No 2 (2016) > ... The new system surpasses the existing one as it is able to register all SIM cards of the four (4) major ... It is recommended that SIM card availability/sales on the road side should be stopped or such SIM ...

  6. Chern-Simons theory in SIM(1) superspace

    Energy Technology Data Exchange (ETDEWEB)

    Vohanka, Jiri [Masaryk University, Department of Theoretical Physics and Astrophysics, Brno (Czech Republic); Faizal, Mir [University of Waterloo, Department of Physics and Astronomy, Waterloo, ON (Canada)

    2015-12-15

    In this paper,wewill analyze a three-dimensional supersymmetric Chern-Simons theory in SIM(1) superspace formalism. The breaking of the Lorentz symmetry down to the SIM(1) symmetry breaks half the supersymmetry of the Lorentz invariant theory. So, the supersymmetry of the Lorentz invariant Chern-Simons theory with N = 1 supersymmetry will break down to N = 1/2 supersymmetry, when the Lorentz symmetry is broken down to the SIM(1) symmetry. First, we will write the Chern-Simons action using SIM(1) projections ofN = 1 superfields. However, as the SIM(1) transformations of these projections are very complicated, we will define SIM(1) superfields which transform simply under SIM(1) transformations. We will then express the Chern-Simons action using these SIM(1) superfields. Furthermore, we will analyze the gauge symmetry of this Chern-Simons theory. This is the first time that a Chern-Simons theory with N = 1/2 supersymmetry will be constructed on a manifold without a boundary. (orig.)

  7. Chern–Simons theory in SIM(1) superspace

    Energy Technology Data Exchange (ETDEWEB)

    Vohánka, Jiří [Department of Theoretical Physics and Astrophysics, Masaryk University, Kotlářská 267/2, 611 37, Brno (Czech Republic); Faizal, Mir, E-mail: mirfaizalmir@gmail.com [Department of Physics and Astronomy, University of Waterloo, N2L 3G1, Waterloo, ON (Canada)

    2015-12-14

    In this paper, we will analyze a three-dimensional supersymmetric Chern–Simons theory in SIM(1) superspace formalism. The breaking of the Lorentz symmetry down to the SIM(1) symmetry breaks half the supersymmetry of the Lorentz invariant theory. So, the supersymmetry of the Lorentz invariant Chern–Simons theory with N=1 supersymmetry will break down to N=1/2 supersymmetry, when the Lorentz symmetry is broken down to the SIM(1) symmetry. First, we will write the Chern–Simons action using SIM(1) projections of N=1 superfields. However, as the SIM(1) transformations of these projections are very complicated, we will define SIM(1) superfields which transform simply under SIM(1) transformations. We will then express the Chern–Simons action using these SIM(1) superfields. Furthermore, we will analyze the gauge symmetry of this Chern–Simons theory. This is the first time that a Chern–Simons theory with N=1/2 supersymmetry will be constructed on a manifold without a boundary.

  8. Binding properties of SUMO-interacting motifs (SIMs) in yeast.

    Science.gov (United States)

    Jardin, Christophe; Horn, Anselm H C; Sticht, Heinrich

    2015-03-01

    Small ubiquitin-like modifier (SUMO) conjugation and interaction play an essential role in many cellular processes. A large number of yeast proteins is known to interact non-covalently with SUMO via short SUMO-interacting motifs (SIMs), but the structural details of this interaction are yet poorly characterized. In the present work, sequence analysis of a large dataset of 148 yeast SIMs revealed the existence of a hydrophobic core binding motif and a preference for acidic residues either within or adjacent to the core motif. Thus the sequence properties of yeast SIMs are highly similar to those described for human. Molecular dynamics simulations were performed to investigate the binding preferences for four representative SIM peptides differing in the number and distribution of acidic residues. Furthermore, the relative stability of two previously observed alternative binding orientations (parallel, antiparallel) was assessed. For all SIMs investigated, the antiparallel binding mode remained stable in the simulations and the SIMs were tightly bound via their hydrophobic core residues supplemented by polar interactions of the acidic residues. In contrary, the stability of the parallel binding mode is more dependent on the sequence features of the SIM motif like the number and position of acidic residues or the presence of additional adjacent interaction motifs. This information should be helpful to enhance the prediction of SIMs and their binding properties in different organisms to facilitate the reconstruction of the SUMO interactome.

  9. Playing with Sims as a space of one's own

    DEFF Research Database (Denmark)

    Iversen, Sara Mosberg

    2014-01-01

    , this article analyses the articulated experiences of playing The Sims 2 and The Sims 3 in relation to how the players perceive the activity’s function in their everyday lives. Seven emic categories are identified and discussed in the inductive analysis, namely “relaxation and dealing with stress,” “playing...

  10. Plankton motility patterns and encounter rates

    DEFF Research Database (Denmark)

    Visser, Andre; Kiørboe, Thomas

    2006-01-01

    measure of run length to reaction distance determines whether the underlying encounter is ballistic or diffusive. Since ballistic interactions are intrinsically more efficient than diffusive, we predict that organisms will display motility with long correlation run lengths compared to their reaction...... distances to their prey, but short compared to the reaction distances of their predators. We show motility data for planktonic organisms ranging from bacteria to copepods that support this prediction. We also present simple ballistic and diffusive motility models for estimating encounter rates, which lead...

  11. Deterministic patterns in cell motility

    Science.gov (United States)

    Lavi, Ido; Piel, Matthieu; Lennon-Duménil, Ana-Maria; Voituriez, Raphaël; Gov, Nir S.

    2016-12-01

    Cell migration paths are generally described as random walks, associated with both intrinsic and extrinsic noise. However, complex cell locomotion is not merely related to such fluctuations, but is often determined by the underlying machinery. Cell motility is driven mechanically by actin and myosin, two molecular components that generate contractile forces. Other cell functions make use of the same components and, therefore, will compete with the migratory apparatus. Here, we propose a physical model of such a competitive system, namely dendritic cells whose antigen capture function and migratory ability are coupled by myosin II. The model predicts that this coupling gives rise to a dynamic instability, whereby cells switch from persistent migration to unidirectional self-oscillation, through a Hopf bifurcation. Cells can then switch to periodic polarity reversals through a homoclinic bifurcation. These predicted dynamic regimes are characterized by robust features that we identify through in vitro trajectories of dendritic cells over long timescales and distances. We expect that competition for limited resources in other migrating cell types can lead to similar deterministic migration modes.

  12. Methanogens, Methane and Gastrointestinal Motility

    Science.gov (United States)

    Triantafyllou, Konstantinos; Chang, Christopher

    2014-01-01

    Anaerobic fermentation of the undigested polysaccharide fraction of carbohydrates produces hydrogen in the intestine which is the substrate for methane production by intestinal methanogens. Hydrogen and methane are excreted in the flatus and in breath giving the opportunity to indirectly measure their production using breath testing. Although methane is detected in 30%-50% of the healthy adult population worldwide, its production has been epidemiologically and clinically associated with constipation related diseases, like constipation predominant irritable bowel syndrome and chronic constipation. While a causative relation is not proven yet, there is strong evidence from animal studies that methane delays intestinal transit, possibly acting as a neuromuscular transmitter. This evidence is further supported by the universal finding that methane production (measured by breath test) is associated with delayed transit time in clinical studies. There is also preliminary evidence that antibiotic reduction of methanogens (as evidenced by reduced methane production) predicts the clinical response in terms of symptomatic improvement in patients with constipation predominant irritable bowel syndrome. However, we have not identified yet the mechanism of action of methane on intestinal motility, and since methane production does not account for all constipation associated cases, there is need for high quality clinical trials to examine methane as a biomarker for the diagnosis or as a biomarker that predicts antibiotic treatment response in patients with constipation related disorders. PMID:24466443

  13. Motility-Induced Phase Separation

    Science.gov (United States)

    Cates, Michael E.; Tailleur, Julien

    2015-03-01

    Self-propelled particles include both self-phoretic synthetic colloids and various microorganisms. By continually consuming energy, they bypass the laws of equilibrium thermodynamics. These laws enforce the Boltzmann distribution in thermal equilibrium: The steady state is then independent of kinetic parameters. In contrast, self-propelled particles tend to accumulate where they move more slowly. They may also slow down at high density for either biochemical or steric reasons. This creates positive feedback, which can lead to motility-induced phase separation (MIPS) between dense and dilute fluid phases. At leading order in gradients, a mapping relates variable-speed, self-propelled particles to passive particles with attractions. This deep link to equilibrium phase separation is confirmed by simulations but generally breaks down at higher order in gradients: New effects, with no equilibrium counterpart, then emerge. We give a selective overview of the fast-developing field of MIPS, focusing on theory and simulation but including a brief speculative survey of its experimental implications.

  14. Mammalian Sperm Motility: Observation and Theory

    KAUST Repository

    Gaffney, E.A.

    2011-01-21

    Mammalian spermatozoa motility is a subject of growing importance because of rising human infertility and the possibility of improving animal breeding. We highlight opportunities for fluid and continuum dynamics to provide novel insights concerning the mechanics of these specialized cells, especially during their remarkable journey to the egg. The biological structure of the motile sperm appendage, the flagellum, is described and placed in the context of the mechanics underlying the migration of mammalian sperm through the numerous environments of the female reproductive tract. This process demands certain specific changes to flagellar movement and motility for which further mechanical insight would be valuable, although this requires improved modeling capabilities, particularly to increase our understanding of sperm progression in vivo. We summarize current theoretical studies, highlighting the synergistic combination of imaging and theory in exploring sperm motility, and discuss the challenges for future observational and theoretical studies in understanding the underlying mechanics. © 2011 by Annual Reviews. All rights reserved.

  15. Fluoxetine causes decrease in intestinal motility

    Directory of Open Access Journals (Sweden)

    Ayesha Afzal

    2015-04-01

    Conclusion: Our study has indicated that fluoxetine on isolated ileal intestinal smooth muscle decrease the motility and this decrease in motility is possibly due to the inability of fluoxetine in vitro to enhance the serotonergic transmission and also because of the interaction of these agents with some of the other receptors, present in the intestinal smooth muscles. [Int J Basic Clin Pharmacol 2015; 4(2.000: 265-268

  16. Flagellar motility in eukaryotic human parasites.

    Science.gov (United States)

    Krüger, Timothy; Engstler, Markus

    2015-10-01

    A huge variety of protists rely on one or more motile flagella to either move themselves or move fluids and substances around them. Many of these flagellates have evolved a symbiotic or parasitic lifestyle. Several of the parasites have adapted to human hosts, and include agents of prevalent and serious diseases. These unicellular parasites have become specialised in colonising a wide range of biological niches within humans. They usually have diverse transmission cycles, and frequently manifest a variety of distinct morphological stages. The motility of the single or multiple flagella plays important but understudied roles in parasite transmission, host invasion, dispersal, survival, proliferation and pathology. In this review we provide an overview of the important human pathogens that possess a motile flagellum for at least part of their life cycle. We highlight recently published studies that aim to elucidate motility mechanisms, and their relevance for human disease. We then bring the physics of swimming at the microscale into context, emphasising the importance of interdisciplinary approaches for a full understanding of flagellate motility - especially in light of the parasites' microenvironments and population dynamics. Finally, we summarise some important technological aspects, describing challenges for the field and possibilities for motility analyses in the future.

  17. Characterizing motility dynamics in human RPE cells

    Science.gov (United States)

    Liu, Zhuolin; Kurokawa, Kazuhiro; Zhang, Furu; Miller, Donald T.

    2017-02-01

    Retinal pigment epithelium (RPE) cells are vital to health of the outer retina, however, are often compromised in ageing and ocular diseases that lead to blindness. Early manifestation of RPE disruption occurs at the cellular level, but while in vivo biomarkers at this scale hold considerable promise, RPE cells have proven extremely challenging to image in the living human eye. Recently we addressed this problem by using organelle motility as a novel contrast agent to enhance the RPE cell in conjunction with 3D resolution of adaptive optics-optical coherence tomography (AO-OCT) to section the RPE layer. In this study, we expand on the central novelty of our method - organelle motility - by characterizing the dynamics of the motility in individual RPE cells, important because of its direct link to RPE physiology. To do this, AO-OCT videos of the same retinal patch were acquired at approximately 1 min intervals or less, time stamped, and registered in 3D with sub-cellular accuracy. Motility was quantified by an exponential decay time constant, the time for motility to decorrelate the speckle field across an RPE cell. In two normal subjects, we found the decay time constant to be just 3 seconds, thus indicating rapid motility in normal RPE cells.

  18. Ghrelin family of peptides and gut motility.

    Science.gov (United States)

    Asakawa, Akihiro; Ataka, Koji; Fujino, Kazunori; Chen, Chih-Yen; Kato, Ikuo; Fujimiya, Mineko; Inui, Akio

    2011-04-01

    Acyl ghrelin, des-acyl ghrelin, and obestatin are three peptides isolated from the gastrointestinal tract and encoded by the same preproghrelin gene. Three ghrelin gene products participate in modulating appetite, adipogenesis, glucose metabolism, cell proliferation, immune, sleep, memory, anxiety, cognition, and stress. We have investigated the effects of ghrelin family of peptides on fed and fasted motor activities in the stomach and duodenum of freely moving conscious rats by manometric method. Intracerebroventricular (ICV) and intravenous (IV) administration of acyl ghrelin induced fasted motor activity in the duodenum in fed rats. ICV and IV administration of des-acyl ghrelin disrupted fasted motor activity in the antrum. Changes in gastric motility induced by IV administration of des-acyl ghrelin were antagonized by ICV administration of a corticotropin-releasing factor (CRF) 2 receptor antagonist. IV administration of obestatin decreased the percentage motor index in the antrum and prolonged the time taken to return to fasted motility in the duodenum in fed rats. ICV administration of CRF 1 and 2 receptor antagonists prevented the effects of obestatin on gastroduodenal motility. Ghrelin gene products regulate feeding-associated gastroduodenal motility. Stomach may regulate various functions including gastrointestinal motility via acyl ghrelin, des-acyl ghrelin and obestatin as an endocrine organ. Increasing knowledge of the effects of ghrelin family of peptides on gastrointestinal motility could lead to innovative new therapies for functional gastrointestinal disorders.

  19. How can BIM support Construction Safety Management? Development of SIM

    Directory of Open Access Journals (Sweden)

    Chan Isabelle Y S

    2016-01-01

    Full Text Available BIM is continuously changing the way construction can be approached, from design, scheduling, costing to facilities management. However, even though construction safety is a worldwide issue, and though previous, yet limited, studies have proven its great potential, BIM has not been extended to include automated construction safety management functions, i.e., hazard identification, assessment and control for construction works. In fact, as many as 71% of safety incidents can be prevented by safety considerations at design stage. Automation via BIM is the key to enhance effectiveness and efficiency of safety management, but development of Safety Information Modelling (SIM is the key pre-requisite. This paper aims to outline a research project for developing both information and technical requirements for SIM via questionnaire survey, focus group, and real case studies. The project results, to be validated by real projects, will act as solid platform for developing:- i Practical guidance to construction and safety professionals on the types of safety management a SIM can conduct, and the ways of utilizing the safety information in a SIM model [based on the systematic SIM information requirements (e.g., object identification, geometry attributes, safety rules]; and ii Overall guidance to software developers to develop appropriate SIM tools for different scenarios [based on the systematic SIM technical requirements (e.g., model information exchange, visualization, conflict analysis process for risk assessment, reliability].

  20. SIM PlanetQuest: Science with the Space Interferometry Mission

    Science.gov (United States)

    Unwin, Stephen (Editor); Turyshev, Slava (Editor)

    2004-01-01

    SIM - the Space Interferometry Mission - will perform precision optical astrometry on objects as faint as R magnitude 20. It will be the first space-based astrometric interferometer, operating in the optical band with a 10-m baseline. The Project is managed by the Jet Propulsion Laboratory, California Institute of Technology, in close collaboration with two industry partners, Lockheed Martin Missiles and Space, and TRW Inc., Space and Electronics Group. Launch of SIM is currently planned for 2009. In its wide-angle astrometric mode, SIM will yield 4 microarcsecond absolute position and parallax measurements. Astrometric planet searches will be done in a narrow-angle mode, with an accuracy of 4 microarcseconds or better in a single measurement. As a pointed rather than a survey instrument, SIM will maintain.its astrometric accuracy down to the faintest, magnitudes, opening up the opportunity for astrometry of active galactic nuclei to better than 10 pas. SIM will define a new astrometric reference frame, using a grid of approximately 1500 stars with positions accurate to 4 microarcseconds. The SIM Science Team comprises the Principal Investigators of ten Key Projects, and five Mission Scientists contributing their expertise to specific areas of the mission. Their science programs cover a wide range of topics in Galactic and extragalactic astronomy. They include: searches for low-mass planets - including analogs to our own solar system - tlie formation and dynamics of our Galaxy, calibration of the cosmic distance scale, and fundamental stellar astrophysics. All of the science observing on SIM is competitively awarded; the Science Team programs total about 40% of the total available, and the remainder will be assigned via future NASA competitions. This report is a compilation of science summaries by members of the Science Team, and it illustrates the wealth of scientific problems that microarcsecond-precision astrometry can contribute to. More information on SIM

  1. Port-O-Sim Object Simulation Application

    Science.gov (United States)

    Lanzi, Raymond J.

    2009-01-01

    Port-O-Sim is a software application that supports engineering modeling and simulation of launch-range systems and subsystems, as well as the vehicles that operate on them. It is flexible, distributed, object-oriented, and realtime. A scripting language is used to configure an array of simulation objects and link them together. The script is contained in a text file, but executed and controlled using a graphical user interface. A set of modules is defined, each with input variables, output variables, and settings. These engineering models can be either linked to each other or run as standalone. The settings can be modified during execution. Since 2001, this application has been used for pre-mission failure mode training for many Range Safety Scenarios. It contains range asset link analysis, develops look-angle data, supports sky-screen site selection, drives GPS (Global Positioning System) and IMU (Inertial Measurement Unit) simulators, and can support conceptual design efforts for multiple flight programs with its capacity for rapid six-degrees-of-freedom model development. Due to the assembly of various object types into one application, the application is applicable across a wide variety of launch range problem domains.

  2. Electrotechnical systems simulation with Simulink and SimPowerSystems

    CERN Document Server

    Perelmuter, Viktor

    2012-01-01

    Filling a gap in the literature, Electrotechnical Systems: Simulation with Simulink® and SimPowerSystems™ explains how to simulate complicated electrical systems more easily using SimPowerSystems™ blocks. It gives a comprehensive overview of the powerful SimPowerSystems toolbox and demonstrates how it can be used to create and investigate models of both classic and modern electrotechnical systems.Build from Circuit Elements and Blocks to System ModelsBuilding from simple to more complex topics, the book helps readers better understand the principles, features, and detailed functions of various

  3. Statistical physical models of cellular motility

    Science.gov (United States)

    Banigan, Edward J.

    Cellular motility is required for a wide range of biological behaviors and functions, and the topic poses a number of interesting physical questions. In this work, we construct and analyze models of various aspects of cellular motility using tools and ideas from statistical physics. We begin with a Brownian dynamics model for actin-polymerization-driven motility, which is responsible for cell crawling and "rocketing" motility of pathogens. Within this model, we explore the robustness of self-diffusiophoresis, which is a general mechanism of motility. Using this mechanism, an object such as a cell catalyzes a reaction that generates a steady-state concentration gradient that propels the object in a particular direction. We then apply these ideas to a model for depolymerization-driven motility during bacterial chromosome segregation. We find that depolymerization and protein-protein binding interactions alone are sufficient to robustly pull a chromosome, even against large loads. Next, we investigate how forces and kinetics interact during eukaryotic mitosis with a many-microtubule model. Microtubules exert forces on chromosomes, but since individual microtubules grow and shrink in a force-dependent way, these forces lead to bistable collective microtubule dynamics, which provides a mechanism for chromosome oscillations and microtubule-based tension sensing. Finally, we explore kinematic aspects of cell motility in the context of the immune system. We develop quantitative methods for analyzing cell migration statistics collected during imaging experiments. We find that during chronic infection in the brain, T cells run and pause stochastically, following the statistics of a generalized Levy walk. These statistics may contribute to immune function by mimicking an evolutionarily conserved efficient search strategy. Additionally, we find that naive T cells migrating in lymph nodes also obey non-Gaussian statistics. Altogether, our work demonstrates how physical

  4. Cellular Motility--Experiments on Contractile and Motile Mechanisms in the Slime Mould, Physarum Polycephalum

    Science.gov (United States)

    Holmes, R. P.; Stewart, P. R.

    1977-01-01

    Actin and myosin have now been demonstrated to be important constituents of many eukaryotic cells. Their role is primarily that of a contractile system underlying all aspects of cellular motility. Described here is a simple experimental system to demonstrate quantitatively aspects of motility and its regulation in a slime mold. (Author/MA)

  5. CQI reporting strategy for Multi-SIM UEs

    DEFF Research Database (Denmark)

    Buthler, Jakob Lindbjerg; Sørensen, Troels Bundgaard

    UEs which support simultaneous activity from Multiple Active Subscriber Identities (Multi-SIM) has gained popularity within the last years. Such UEs are forced to discard data on one of the SIMs when both try to access the Radio Frequency (RF) interface simultaneously, creating gaps in the data...... transfer. The discarded data due to Multi-SIM gaps, along with channel errors, significantly increase the probability of high latency data subframes. High latency increases the probability of data subframes being discarded. In this paper we present an algorithm with which it is possible to decrease...... the probability of discarded data subframes due to high latency. The algorithm takes advantage of the fact that the connections of each SIMs are unaligned and therefore gaps will only cover some timeslots partially. In such a case, it is possible to recover data using existing error correction coding...

  6. Competency based medical education in gastrointestinal motility.

    Science.gov (United States)

    Yadlapati, R; Keswani, R N; Pandolfino, J E

    2016-10-01

    Traditional apprenticeship-based medical education methods focusing on subjective evaluations and case-volume requirements do not reliably produce clinicians that provide high-quality care in unsupervised practice. Consequently, training approaches are shifting towards competency based medical education, which incorporates robust assessment methods and credible standards of physician proficiency. However, current gastroenterology and hepatology training in the US continues to utilize procedural volume and global impressions without standardized criteria as markers of competence. In particular, efforts to optimize competency based training in gastrointestinal (GI) motility are not underway, even though GI motility disorders account for nearly half of outpatient gastroenterology visits. These deficiencies compromise the quality of patient care. Thus, there is a great need and opportunity to shift our focus in GI motility training towards a competency based approach. First, we need to clarify the variable rates of learning for individual diagnostic tests. We must develop integrated systems that standardize training and monitor physician competency for GI motility diagnostics. Finally, as a profession and society, we must create certification processes to credential competent physicians. These advances are critical to optimizing the quality of GI motility diagnostics in practice.

  7. Motility modes of the parasite Trypanosoma brucei

    Science.gov (United States)

    Temel, Fatma Zeynep; Qu, Zijie; McAllaster, Michael; de Graffenried, Christopher; Breuer, Kenneth

    2015-11-01

    The parasitic single-celled protozoan Trypanosoma brucei causes African Sleeping Sickness, which is a fatal disease in humans and animals that threatens more than 60 million people in 36 African countries. Cell motility plays a critical role in the developmental phases and dissemination of the parasite. Unlike many other motile cells such as bacteria Escherichia coli or Caulobacter crescentus, the flagellum of T. brucei is attached along the length of its awl-like body, producing a unique mode of motility that is not fully understood or characterized. Here, we report on the motility of T. brucei, which swims using its single flagellum employing both rotating and undulating propulsion modes. We tracked cells in real-time in three dimensions using fluorescent microscopy. Data obtained from experiments using both short-term tracking within the field of view and long-term tracking using a tracking microscope were analyzed. Motility modes and swimming speed were analyzed as functions of cell size, rotation rate and undulation pattern. Research supported by NSF.

  8. Hydraulic Arm Modeling via Matlab SimHydraulics

    OpenAIRE

    Věchet, Stanislav; Krejsa, Jiří

    2009-01-01

    System modeling is a vital tool for cost reduction and design process speed up in most engineering fields. The paper is focused on modeling of hydraulic arm as a part of intelligent prosthesis project, in the form of 2DOF open kinematic chain. The arm model combines mechanical, hydraulic and electric subsystems and uses Matlab as modeling tool. SimMechanics Matlab extension is used for mechanical part modeling, SimHydraulics toolbox is used for modeling of hydraulic circuit used for actuating...

  9. Compositional analysis in the nano-regime:A SIMS perspective

    Institute of Scientific and Technical Information of China (English)

    Subhendu Sarkar; Purushottam Chakraborty

    2005-01-01

    A serious problem in secondary ion mass spectrometry (SIMS) analysis is its "matrix effect" that hinders the quantification of a certain species in a sample and consequently, appropriate corrective measures are taken to calibrate the secondary ion currents into respective concentrations for accurate compositional analysis. Use of "calibration standards" is necessary for this purpose. Detection of molecular MCsn+ ions (M-element to be analyzed, n=1, 2, 3,....) under Cs+ ion bombardment is a possible mean to minimize such matrix effect, enabling one to quantify without the need of calibration standards. Our recent studies on MCsn+ molecular ions aim towards the understanding of their formation mechanisms, which are important to know their effects on SIMS quantification.In-depth quantitative analysis is a major strength of SIMS for which 'depth resolution' is of significant relevance. The optimal choice of the impact parameters during SIMS analyses can play an effective role in obtaining data with ultra-high depth resolution. SIMS is possible at depth resolution in the nm or even sub-nm range, with quantifiable data obtained from the top monolayer onwards into the material. With optimized experimental conditions, like extremely low beam current (down to ~10 nA), and low bombarding energy (below 1 keV), ultra-high depth resolution SIMS has enabled interfacial composition analysis of ultra-thin films, quantum wells, heterostructures, etc. and complex low-dimensional structures with high precision and repeatability.

  10. Asyn-SimRank:An Asynchronous Large-Scale SimRank Algorithm%Asyn-SimRank:一种可异步执行的大规模 SimRank 算法

    Institute of Scientific and Technical Information of China (English)

    王春磊; 张岩峰; 鲍玉斌; 赵长宽; 于戈; 高立新

    2015-01-01

    SimRank 算法利用网络结构来评估网络中任意2点的相似性,它被广泛应用于社交网络和链接预测等诸多领域中.近年来,随着大数据技术的发展,SimRank 算法处理的数据不断增大,人们利用MapReduce 等分布式计算模型设计实现分布式的大规模 SimRank 算法来适应大数据处理的需求.但是,由于 SimRank 算法包含开销较大的迭代过程,每次迭代之后都需要一个全局同步,且每次迭代的计算复杂度高、通信量大,SimRank 算法不能在分布式环境下高效地实现.1)提出 Asyn‐SimRank 算法,该算法采用迭代‐累积的方式完成迭代计算,异步执行 SimRank 的核心迭代过程,避免了大规模分布式计算中的大量同步开销,同时有效降低计算量并减少通信开销;2)提出关键点优先调度计算,提升了 Asyn‐SimRank 算法的全局收敛速度;3)证明了 Asyn‐SimRank 算法的正确性和收敛性以及关键点优先调度计算的有效性;4)支持异步迭代的分布式框架 Maiter 上实现了 Asyn‐SimRank 算法.实验结果显示,相比较于 Hadoop ,Spark 上实现的 SimRank 算法和 Delta‐SimRank 算法,Asyn‐SimRank 算法大大提升了算法的计算效率,加速了算法收敛.%The SimRank algorithm , which exploits network structure to measure the similarity between node pairs ,has been widely used in many areas ,such as online social networks and link prediction .In recent years ,with the development of big data , the input data set of the SimRank algorithm is constantly increasing . People are utilizing distributed computing models , such as MapReduce ,to design large‐scale SimRank algorithm for solving the big data problems .However , since SimRank algorithm contains a high‐cost iterative process with synchronization barriers between iterations and the computational complexity is high in each iteration , the large‐scale Sim

  11. KEY COMPARISONS: Final report: SIM regional comparison of ac-dc voltage transfer difference (SIM.EM.K6a, SIM.EM-K9 and SIM.EM-K11)

    Science.gov (United States)

    Campos, Sara; Filipski, Piotr; Izquierdo, Daniel; Afonso, Edson; Landim, Régis P.; Di Lillo, Lucas; Lipe, Thomas

    2009-01-01

    Three comparisons of ac-dc voltage transfer difference held from January to December 2004 are reported. Six NMIs in the SIM region took part: NRC (Canada), NIST (United States of America), CENAM (Mexico), INTI (Argentina), UTE (Uruguay) and INMETRO (Brazil). The comparisons were proposed to assess the measurement capabilities in ac-dc voltage transfer difference of the NMIs in the SIM region. The test points were selected to link the results with the equivalent CCEM Key Comparisons, through three NMIs participating in both SIM and CCEM key comparisons. Additionally, a SIM.EM-Supplementary comparison was proposed, in support of the SIM NMIs' power/energy meter calibration capabilities. One technical protocol and one travelling standard were used, to economize on time and resources. The report shows the degree of equivalence in the SIM region and also the degree of equivalence with the corresponding CCEM reference value. The results of all participants support the values and uncertainties of the applicable CMC entries for ac-dc voltage transfer difference in the Key Comparison Database held at the BIPM. Main text. To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/. The final report has been peer-reviewed and approved for publication by the CCEM, according to the provisions of the CIPM Mutual Recognition Arrangement (MRA).

  12. A field guide to bacterial swarming motility.

    Science.gov (United States)

    Kearns, Daniel B

    2010-09-01

    How bacteria regulate, assemble and rotate flagella to swim in liquid media is reasonably well understood. Much less is known about how some bacteria use flagella to move over the tops of solid surfaces in a form of movement called swarming. The focus of bacteriology is changing from planktonic to surface environments, and so interest in swarming motility is on the rise. Here, I review the requirements that define swarming motility in diverse bacterial model systems, including an increase in the number of flagella per cell, the secretion of a surfactant to reduce surface tension and allow spreading, and movement in multicellular groups rather than as individuals.

  13. Evaluation of the airway of the SimMan full-scale patient simulator

    DEFF Research Database (Denmark)

    Hesselfeldt, R; Kristensen, M S; Rasmussen, L S

    2005-01-01

    SimMan is a full-scale patient simulator, capable of simulating normal and pathological airways. The performance of SimMan has never been critically evaluated.......SimMan is a full-scale patient simulator, capable of simulating normal and pathological airways. The performance of SimMan has never been critically evaluated....

  14. Depth profiling of fingerprint and ink signals by SIMS and MeV SIMS

    Energy Technology Data Exchange (ETDEWEB)

    Bailey, M.J., E-mail: m.bailey@surrey.ac.u [University of Surrey Ion Beam Centre, Surrey GU2 7XH (United Kingdom); Jones, B.N. [University of Surrey Ion Beam Centre, Surrey GU2 7XH (United Kingdom); Hinder, S.; Watts, J. [Surface Analysis Laboratory, University of Surrey, GU2 7XH (United Kingdom); Bleay, S. [Home Office Scientific Development Branch, St. Albans (United Kingdom); Webb, R.P. [University of Surrey Ion Beam Centre, Surrey GU2 7XH (United Kingdom)

    2010-06-15

    Police institutions currently have no analytical method of knowing whether a fingerprint was deposited before or after the document was written or printed. The suitability of using MeV secondary ion mass spectrometry (i.e. SIMS with an MeV ion beam) to determine the order in which a fingerprint and written text were deposited on paper was therefore investigated. A 10 MeV O{sup 4+} beam was used to generate secondary ions from the surface of the samples and to map the molecular fragments from doped fingerprints and inks on paper. The images obtained and the sputtering behaviour of the samples was found to be indicative of the sequence of ink and fingerprint deposits.

  15. Esophageal motility abnormalities in gastroesophageal reflux disease.

    Science.gov (United States)

    Martinucci, Irene; de Bortoli, Nicola; Giacchino, Maria; Bodini, Giorgia; Marabotto, Elisa; Marchi, Santino; Savarino, Vincenzo; Savarino, Edoardo

    2014-05-06

    Esophageal motility abnormalities are among the main factors implicated in the pathogenesis of gastroesophageal reflux disease. The recent introduction in clinical and research practice of novel esophageal testing has markedly improved our understanding of the mechanisms contributing to the development of gastroesophageal reflux disease, allowing a better management of patients with this disorder. In this context, the present article intends to provide an overview of the current literature about esophageal motility dysfunctions in patients with gastroesophageal reflux disease. Esophageal manometry, by recording intraluminal pressure, represents the gold standard to diagnose esophageal motility abnormalities. In particular, using novel techniques, such as high resolution manometry with or without concurrent intraluminal impedance monitoring, transient lower esophageal sphincter (LES) relaxations, hypotensive LES, ineffective esophageal peristalsis and bolus transit abnormalities have been better defined and strongly implicated in gastroesophageal reflux disease development. Overall, recent findings suggest that esophageal motility abnormalities are increasingly prevalent with increasing severity of reflux disease, from non-erosive reflux disease to erosive reflux disease and Barrett's esophagus. Characterizing esophageal dysmotility among different subgroups of patients with reflux disease may represent a fundamental approach to properly diagnose these patients and, thus, to set up the best therapeutic management. Currently, surgery represents the only reliable way to restore the esophagogastric junction integrity and to reduce transient LES relaxations that are considered to be the predominant mechanism by which gastric contents can enter the esophagus. On that ground, more in depth future studies assessing the pathogenetic role of dysmotility in patients with reflux disease are warranted.

  16. Flagellar Motility of Trypanosoma cruzi Epimastigotes

    Directory of Open Access Journals (Sweden)

    G. Ballesteros-Rodea

    2012-01-01

    Full Text Available The hemoflagellate Trypanosoma cruzi is the causative agent of American trypanosomiasis. Despite the importance of motility in the parasite life cycle, little is known about T. cruzi motility, and there is no quantitative description of its flagellar beating. Using video microscopy and quantitative vectorial analysis of epimastigote trajectories, we find a forward parasite motility defined by tip-to-base symmetrical flagellar beats. This motion is occasionally interrupted by base-to-tip highly asymmetric beats, which represent the ciliary beat of trypanosomatid flagella. The switch between flagellar and ciliary beating facilitates the parasite's reorientation, which produces a large variability of movement and trajectories that results in different distance ranges traveled by the cells. An analysis of the distance, speed, and rotational angle indicates that epimastigote movement is not completely random, and the phenomenon is highly dependent on the parasite behavior and is characterized by directed and tumbling parasite motion as well as their combination, resulting in the alternation of rectilinear and intricate motility paths.

  17. Directed Autonomic Flow : Functional Motility Fluidics

    NARCIS (Netherlands)

    Kuehn, Philipp T.; de Miranda, Barbara Santos; van Rijn, Patrick

    2015-01-01

    Unidirectional coherent motion of a self-moving droplet is achieved and combined in a functional motility fluidic chip for chemical reactions via a novel and straightforward approach. The droplet shows both increased movement speeds and displacement distances without any input of energy. Nanoparticl

  18. Esophageal motility disorders; Motilitaetsstoerungen des Oesophagus

    Energy Technology Data Exchange (ETDEWEB)

    Hannig, C.; Rummeny, E. [Klinikum rechts der Isar der Technischen Universitaet Muenchen, Institut fuer Roentgendiagnostik, Muenchen (Germany); Wuttge-Hannig, A. [Gemeinschaftspraxis fuer Radiologie, Nuklearmedizin und Strahlentherapie, Muenchen (Germany)

    2007-02-15

    For the better understanding of esophageal motility, the muscle texture and the distribution of skeletal and smooth muscle fibers in the esophagus are of crucial importance. Esophageal physiology will be shortly mentioned as far as necessary for a comprehensive understanding of peristaltic disturbances. Besides the pure depiction of morphologic criteria, a complete esophageal study has to include an analysis of the motility. New diagnostic tools with reduced radiation for dynamic imaging (digital fluoroscopy, videofluoroscopy) at 4-30 frames/s are available. Radiomanometry is a combination of a functional pressure measurement and a simultaneous dynamic morphologic analysis. Esophageal motility disorders are subdivided by radiologic and manometric criteria into primary, secondary, and nonclassifiable forms. Primary motility disorders of the esophagus are achalasia, diffuse esophageal spasm, nutcracker esophagus, and the hypertonic lower esophageal sphincter. The secondary motility disorders include pseudoachalasia, reflux-associated motility disorders, functionally caused impactions, Boerhaave's syndrome, Chagas' disease, scleroderma, and presbyesophagus. The nonclassificable motility disorders (NEMD) are a very heterogeneous collective. (orig.) [German] Zum Verstaendnis der Motilitaet des Oesophagus sind muskulaere Architektur und Verteilung der quergestreiften und glatten Muskelfasern von Bedeutung. Die Physiologie des Oesophagus wird in soweit kurz dargestellt, als sie fuer das Verstaendnis von peristaltischen Stoerungen notwendig ist. Neben der Erfassung rein morphologischer Kriterien ist bei der Untersuchung der Speiseroehre eine diagnostische Bewertung der Motilitaet erforderlich. Es stehen uns heute strahlungsarme dynamische Aufzeichnungsverfahren (digitale dynamische Aufzeichnung, Videofluoroskopie) mit Bildsequenzen von 4-30 Bildern/s zur Verfuegung. Die Kombination einer funktionellen Methode zur Darstellung der Morphologie und der

  19. An animated model of reticulorumen motility.

    Science.gov (United States)

    Gookin, Jody L; Foster, Derek M; Harvey, Alice M; McWhorter, Dan

    2009-01-01

    Understanding reticulorumen motility is important to the assessment of ruminant health and optimal production, and in the recognition, diagnosis, and treatment of disease. Accordingly, the teaching of reticulorumen motility is a staple of all veterinary curricula. This teaching has historically been based on written descriptions, line drawings, or pressure tracings obtained during contraction sequences. We developed an animated model of reticulorumen motility and hypothesized that veterinary students would prefer use of the model over traditional instructional methods. First-year veterinary students were randomly allocated to one of two online learning exercises: with the animated model (Group A) or with text and line drawings (Group B) depicting reticulorumen motility. Learning was assessed with a multiple-choice quiz and feedback on the learning alternatives was obtained by survey. Seventy-four students participated in the study, including 38/42 in Group A and 36/36 in Group B. Sixty-four out of 72 students (89%) responded that they would prefer use of the animated model if only one of the two learning methods was available. A majority of students agreed or strongly agreed that the animated model was easy to understand and improved their knowledge and appreciation of the importance of reticulorumen motility, and would recommend the model to other veterinary students. Interestingly, students in Group B achieved higher scores on examination than students in Group A. This could be speculatively attributed to the inclusion of an itemized list of contraction sequences in the text provided to Group B and failure of Group A students to read the text associated with the animations.

  20. Sperm motility under exposure of hydrogen dioxide

    Directory of Open Access Journals (Sweden)

    V. V. Evdokimov

    2015-01-01

    Full Text Available The paper contains research data on the effect of low concentrations of hydrogen dioxide on human sperm motility and specific enzyme activity of sperms of glyceraldehyde-3-phosphate dehydrogenase. It is shown that incubation of sperms with hydrogen dioxide in a low concentration leads to a change and motility in sperm and activity of sperm enzyme. Intensity of observed effect depended on the concentration of hydrogen dioxide: active mobility increased by 17–19 % and the total mobility – 11 %. Motility changes in sperms were accompanied by increased activity of glyceraldehyde-3-phosphate dehydrogenase by 24 %, in normozoospermia response was higher than in pathozoospermia and also depended on the concentration of hydrogen dioxide. The use of sperm analyzer enabled revealing changes in the diapason of different speeds of the active fraction of sperm, which have been observed in the first 15 min of incubation with hydrogen dioxide. A possible mechanism of action of the detected effect is discussed. Reactive oxygen species easily oxidize enzyme for glyceraldehyde-3-phosphate dehydrogenase of sperms, which leads to a loss of sperm motility, for example, in varicocele. Initially low enzyme activity in varicocele (pathozoospermia may be associated with the suppression of sperm antioxidant defense. Addition of low concentrations of hydrogen dioxide into sperm samples leads to an increase in the concentration of reduced glutathione in a cell. Increase of sperm motility in this case can serve as an indicator of normal operation of the cellular antioxidant defense system. Obtained experimental results provide a background for their introduction into clinical practice in the program of assisted reproductive technologies. 

  1. Sperm motility under exposure of hydrogen dioxide

    Directory of Open Access Journals (Sweden)

    V. V. Evdokimov

    2015-04-01

    Full Text Available The paper contains research data on the effect of low concentrations of hydrogen dioxide on human sperm motility and specific enzyme activity of sperms of glyceraldehyde-3-phosphate dehydrogenase. It is shown that incubation of sperms with hydrogen dioxide in a low concentration leads to a change and motility in sperm and activity of sperm enzyme. Intensity of observed effect depended on the concentration of hydrogen dioxide: active mobility increased by 17–19 % and the total mobility – 11 %. Motility changes in sperms were accompanied by increased activity of glyceraldehyde-3-phosphate dehydrogenase by 24 %, in normozoospermia response was higher than in pathozoospermia and also depended on the concentration of hydrogen dioxide. The use of sperm analyzer enabled revealing changes in the diapason of different speeds of the active fraction of sperm, which have been observed in the first 15 min of incubation with hydrogen dioxide. A possible mechanism of action of the detected effect is discussed. Reactive oxygen species easily oxidize enzyme for glyceraldehyde-3-phosphate dehydrogenase of sperms, which leads to a loss of sperm motility, for example, in varicocele. Initially low enzyme activity in varicocele (pathozoospermia may be associated with the suppression of sperm antioxidant defense. Addition of low concentrations of hydrogen dioxide into sperm samples leads to an increase in the concentration of reduced glutathione in a cell. Increase of sperm motility in this case can serve as an indicator of normal operation of the cellular antioxidant defense system. Obtained experimental results provide a background for their introduction into clinical practice in the program of assisted reproductive technologies. 

  2. Description of Chiral Doublets in $A\\sim130$ Nuclei and the Possible Chiral Doublets in $A\\sim100$ Nuclei

    CERN Document Server

    Peng, J; Zhang, S Q

    2003-01-01

    The chiral doublets for nuclei in $A\\sim100$ and $A\\sim130$ regions have been studied with the particle-rotor model. The experimental spectra of chiral partners bands for four N=75 isotones in $A\\sim130$ region have been well reproduced by the calculation with the configuration $\\pi h_{11/2}\\otimes\

  3. Effect of zinc treatment on intestinal motility in experimentally ...

    African Journals Online (AJOL)

    olayemitoyin

    meal and the mechanisms of action of zinc sulphate on motility were investigated. The effective ... The positive action of zinc in acute ..... of gastrointestinal motility by inhibiting acetylcholine ... activity in smooth muscle is initiated by a Ca2+-.

  4. SIMS: addressing the problem of heterogeneity in databases

    Science.gov (United States)

    Arens, Yigal

    1997-02-01

    The heterogeneity of remotely accessible databases -- with respect to contents, query language, semantics, organization, etc. -- presents serious obstacles to convenient querying. The SIMS (single interface to multiple sources) system addresses this global integration problem. It does so by defining a single language for describing the domain about which information is stored in the databases and using this language as the query language. Each database to which SIMS is to provide access is modeled using this language. The model describes a database's contents, organization, and other relevant features. SIMS uses these models, together with a planning system drawing on techniques from artificial intelligence, to decompose a given user's high-level query into a series of queries against the databases and other data manipulation steps. The retrieval plan is constructed so as to minimize data movement over the network and maximize parallelism to increase execution speed. SIMS can recover from network failures during plan execution by obtaining data from alternate sources, when possible. SIMS has been demonstrated in the domains of medical informatics and logistics, using real databases.

  5. NanoSIMS for Biological Applications: Current Practices and Analyses

    Energy Technology Data Exchange (ETDEWEB)

    Dunn, Jamie R.; Renslow, Ryan S.; Cliff, John B.; Anderton, Christopher R.

    2017-09-27

    Secondary ion mass spectrometry (SIMS) has become an increasingly utilized tool in biologically-relevant studies. Of these, high lateral resolution methodologies using the NanoSIMS 50/50L have been especially powerful within many biological fields over the past decade. Here, we provide a review of this technology, sample preparation and analysis considerations, examples of recent biological studies, data analysis, and current outlooks. Specifically, we offer an overview of SIMS and development of the NanoSIMS. We describe the major experimental factors that should be considered prior to NanoSIMS analysis and then provide information on best practices for data analysis and image generation, which includes an in-depth discussion of appropriate colormaps. Additionally, we provide an open-source method for data representation that allows simultaneous visualization of secondary electron and ion information within a single image. Finally, we present a perspective on the future of this technology and where we think it will have the greatest impact in near future.

  6. TOF SIMS characterization of SEI layer on battery electrodes

    Science.gov (United States)

    Veryovkin, I. V.; Tripa, C. E.; Zinovev, A. V.; Baryshev, S. V.; Li, Y.; Abraham, D. P.

    2014-08-01

    In the last decade, many studies applied surface analysis techniques (SEM, XPS and SIMS) to understand the formation of SEI layers on Li-ion battery electrodes. This work was meant as a comparative model study of the SEI layer formation, which combined in situ SEM imaging with TOF SIMS depth profiling of four samples of the same graphite electrode material, which was subjected to different charge-discharge cycling schemes in a Li-ion battery. Besides comparing compositions of sub-surface regions of these differently processed electrodes, we wanted to know whether these compositions depend on after-cycling sample preparation, in particular if a brief exposure of these samples to air would affect the compositions measured by TOF SIMS. We found that the exposure to air (1) increases secondary ion yield for all species, and (2) changes shapes of SIMS depth profiles for some key species. For selected samples, we also conducted a comparison between the conventional single beam TOF-SIMS depth profiling and a high resolution dual beam depth profiling and found that the former approach can detect the same features in depth profiles as the latter one. We interpreted this as an indication that the sample surface morphology (high roughness) could be a limiting factor in this SEI study, suggesting that specially designed model samples with smooth surfaces are a better choice for future studies.

  7. Colony Expansion of Socially Motile Myxococcus xanthus Cells Is Driven by Growth, Motility, and Exopolysaccharide Production.

    Science.gov (United States)

    Patra, Pintu; Kissoon, Kimberley; Cornejo, Isabel; Kaplan, Heidi B; Igoshin, Oleg A

    2016-06-01

    Myxococcus xanthus, a model organism for studies of multicellular behavior in bacteria, moves exclusively on solid surfaces using two distinct but coordinated motility mechanisms. One of these, social (S) motility is powered by the extension and retraction of type IV pili and requires the presence of exopolysaccharides (EPS) produced by neighboring cells. As a result, S motility requires close cell-to-cell proximity and isolated cells do not translocate. Previous studies measuring S motility by observing the colony expansion of cells deposited on agar have shown that the expansion rate increases with initial cell density, but the biophysical mechanisms involved remain largely unknown. To understand the dynamics of S motility-driven colony expansion, we developed a reaction-diffusion model describing the effects of cell density, EPS deposition and nutrient exposure on the expansion rate. Our results show that at steady state the population expands as a traveling wave with a speed determined by the interplay of cell motility and growth, a well-known characteristic of Fisher's equation. The model explains the density-dependence of the colony expansion by demonstrating the presence of a lag phase-a transient period of very slow expansion with a duration dependent on the initial cell density. We propose that at a low initial density, more time is required for the cells to accumulate enough EPS to activate S-motility resulting in a longer lag period. Furthermore, our model makes the novel prediction that following the lag phase the population expands at a constant rate independent of the cell density. These predictions were confirmed by S motility experiments capturing long-term expansion dynamics.

  8. BioFET-SIM Web Interface: Implementation and Two Applications

    CERN Document Server

    Hediger, Martin R; De Vico, Luca

    2012-01-01

    We present a web interface for the BioFET-SIM program. The web interface allows to conveniently setup calculations based on the BioFET-SIM multiple charges model. As an illustration, two case studies are presented. In the first case, a generic peptide with opposite charges on both ends is inverted in orientation on a semiconducting nanowire surface leading to a corresponding change in sign of the computed sensitivity of the device. In the second case, the binding of an antibody/antigen complex on the nanowire surface is studied in terms of orientation and analyte/nanowire surface distance. We demonstrate how the BioFET-SIM web interface can aid in the understanding of experimental data and postulate alternative ways of antibody/antigen orientation on the nanowire surface.

  9. SimClust - A Program to Simulate Star Clusters

    CERN Document Server

    Deveikis, V; Stonkute, R; Bridzius, A; Vansevicius, V

    2009-01-01

    We present a program tool, SimClust, designed for Monte-Carlo modeling of star clusters. It populates the available stellar isochrones with stars according to the initial mass function and distributes stars randomly following the analytical surface number density profile. The tool is aimed at simulating realistic images of extragalactic star clusters and can be used to: (i) optimize object detection algorithms, (ii) perform artificial cluster tests for the analysis of star cluster surveys, and (iii) assess the stochastic effects introduced into photometric and structural parameters of clusters due to random distribution of luminous stars and non-uniform interstellar extinction. By applying SimClust, we have demonstrated a significant influence of stochastic effects on the determined photometric and structural parameters of low-mass star clusters in the M31 galaxy disk. The source code and examples are available at the SimClust website: http://www.astro.ff.vu.lt/software/simclust/

  10. Intercalibration of FTIR and SIMS for Hydrogen Measurements in Garnets

    Science.gov (United States)

    Huang, Y.; Rossman, G.; Guan, Y.; Ma, C.

    2008-12-01

    The importance of understanding the hydrogen incorporated in nominally anhydrous minerals (NAMs) that influences their physical and chemical properties significantly is well accepted, however, quantitatively experimental constraints between hydrogen concentration and physical and chemical properties are only meaningful if hydrogen concentration can be accurately determined. Fourier Transform Infrared Spectroscopy (FTIR) may be the most powerful technique since it provides information about both bulk concentration and local bonding environments, while Secondary Ion Mass Spec-trometry (SIMS) has held promise as an ideal method for hydrogen analyses for its advantages of high spatial resolution and insensitivity to crystal orientation. Great efforts have been made to establish experimental standards for these two techniques since they have no rigorous self-calibration. We here present new Fourier Transform Infrared Spectroscopy (FTIR) and Secondary Ion Mass Spectrometry (SIMS) analyses of 1H in 11 natural garnets (grossular, spessartite and pyrope). This set of garnets extends to a wider range of H2O contents (~4 to 6790 wt. ppm H2O) than previous studies and can be more reliable if more garnets can be investigated. We routinely achieve a less than 5 ppm by weight H2O with high vacuum quality, the use of a Cs+ primary beam, and carefully prepared samples using a resin-free mounting technique (described in Aubaud C. et al., 2007. Intercalibration of FTIR and SIMS for hydrogen measurements in glasses and nominally anhydrous minerals. American Mineralogist, 92, 811-828). Although some scatter is observed, the straight line with a slope of 0.0722 defined by all garnets in a plot of (H)FTIR vs. (H+/Si+)SIMS* (SiO2)EMP suggests small matrix effects, while some previous efforts demonstrated the existence of such matrix effects. Discrepancies between FTIR and SIMS measurements can be partially distributed to the impurities, which have different hydrogen concentration as the

  11. Virus and Bacterial Cell Chemical Analysis by NanoSIMS

    Energy Technology Data Exchange (ETDEWEB)

    Weber, P; Holt, J

    2008-07-28

    In past work for the Department of Homeland Security, the LLNL NanoSIMS team has succeeded in extracting quantitative elemental composition at sub-micron resolution from bacterial spores using nanometer-scale secondary ion mass spectrometry (NanoSIMS). The purpose of this task is to test our NanoSIMS capabilities on viruses and bacterial cells. This initial work has proven successful. We imaged Tobacco Mosaic Virus (TMV) and Bacillus anthracis Sterne cells using scanning electron microscopy (SEM) and then analyzed those samples by NanoSIMS. We were able resolve individual viral particles ({approx}18 nm by 300 nm) in the SEM and extract correlated elemental composition in the NanoSIMS. The phosphorous/carbon ratio observed in TMV is comparable to that seen in bacterial spores (0.033), as was the chlorine/carbon ratio (0.11). TMV elemental composition is consistent from spot to spot, and TMV is readily distinguished from debris by NanoSIMS analysis. Bacterial cells were readily identified in the SEM and relocated in the NanoSIMS for elemental analysis. The Ba Sterne cells were observed to have a measurably lower phosphorous/carbon ratio (0.005), as compared to the spores produced in the same run (0.02). The chlorine/carbon ratio was approximately 2.5X larger in the cells (0.2) versus the spores (0.08), while the fluorine/carbon ratio was approximately 10X lower in the cells (0.008) than the spores (0.08). Silicon/carbon ratios for both cells and spores encompassed a comparable range. The initial data in this study suggest that high resolution analysis is useful because it allows the target agent to be analyzed separate from particulates and other debris. High resolution analysis would also be useful for trace sample analysis. The next step in this work is to determine the potential utility of elemental signatures in these kinds of samples. We recommend bulk analyses of media and agent samples to determine the range of media compositions in use, and to determine how

  12. Motility states in bidirectional cargo transport

    CERN Document Server

    Klein, Sarah; Santen, Ludger

    2015-01-01

    Intracellular cargos which are transported by molecular motors move stochastically along cytoskeleton filaments. In particular for bidirectionally transported cargos it is an open question whether the characteristics of their motion can result from pure stochastic fluctuations or whether some coordination of the motors is needed. The results of a mean-field model of cargo-motors dynamics, which was proposed by M\\"uller et al.[1] suggest the existence of high motility states which would result from a stochastic tug-of-war. Here we analyze a non-mean field extension of their model, that takes explicitly the position of each motor into account. We find that high motility states then disappear. We consider also a mutual motor-motor activation, as an explicit mechanism of motor coordination. We show that the results of the mean-field model are recovered only in case of a strong motor-motor activation in the limit of a high number of motors.

  13. Soft micromachines with programmable motility and morphology

    Science.gov (United States)

    Huang, Hen-Wei; Sakar, Mahmut Selman; Petruska, Andrew J.; Pané, Salvador; Nelson, Bradley J.

    2016-07-01

    Nature provides a wide range of inspiration for building mobile micromachines that can navigate through confined heterogenous environments and perform minimally invasive environmental and biomedical operations. For example, microstructures fabricated in the form of bacterial or eukaryotic flagella can act as artificial microswimmers. Due to limitations in their design and material properties, these simple micromachines lack multifunctionality, effective addressability and manoeuvrability in complex environments. Here we develop an origami-inspired rapid prototyping process for building self-folding, magnetically powered micromachines with complex body plans, reconfigurable shape and controllable motility. Selective reprogramming of the mechanical design and magnetic anisotropy of body parts dynamically modulates the swimming characteristics of the micromachines. We find that tail and body morphologies together determine swimming efficiency and, unlike for rigid swimmers, the choice of magnetic field can subtly change the motility of soft microswimmers.

  14. Automated measurement of cell motility and proliferation

    Directory of Open Access Journals (Sweden)

    Goff Julie

    2005-04-01

    Full Text Available Abstract Background Time-lapse microscopic imaging provides a powerful approach for following changes in cell phenotype over time. Visible responses of whole cells can yield insight into functional changes that underlie physiological processes in health and disease. For example, features of cell motility accompany molecular changes that are central to the immune response, to carcinogenesis and metastasis, to wound healing and tissue regeneration, and to the myriad developmental processes that generate an organism. Previously reported image processing methods for motility analysis required custom viewing devices and manual interactions that may introduce bias, that slow throughput, and that constrain the scope of experiments in terms of the number of treatment variables, time period of observation, replication and statistical options. Here we describe a fully automated system in which images are acquired 24/7 from 384 well plates and are automatically processed to yield high-content motility and morphological data. Results We have applied this technology to study the effects of different extracellular matrix compounds on human osteoblast-like cell lines to explore functional changes that may underlie processes involved in bone formation and maintenance. We show dose-response and kinetic data for induction of increased motility by laminin and collagen type I without significant effects on growth rate. Differential motility response was evident within 4 hours of plating cells; long-term responses differed depending upon cell type and surface coating. Average velocities were increased approximately 0.1 um/min by ten-fold increases in laminin coating concentration in some cases. Comparison with manual tracking demonstrated the accuracy of the automated method and highlighted the comparative imprecision of human tracking for analysis of cell motility data. Quality statistics are reported that associate with stage noise, interference by non

  15. Hydrodynamic Contributions to Amoeboid Cell Motility

    Science.gov (United States)

    Lewis, Owen; Guy, Robert

    2012-11-01

    Understanding the methods by which cells move is a fundamental problem in modern biology. Recent evidence has shown that the fluid dynamics of cytoplasm can play a vital role in cellular motility. The slime mold Physarum polycephalum provides an excellent model organism for the study of amoeboid motion. In this research, we use a simply analytic model in conjuction with computational experiments to investigate intracellular fluid flow in a simple model of Physarum. Of particlar interest are stresses generated by cytoplasmic flow which may be used to aid in cellular motility. In our numerical model, the Immersed Boundary Method is used to account for such stresses. We investigate the relationship between contraction waves, flow waves, adhesion, and locomotive forces in an attempt to characterize conditions necessary to generate directed motion.

  16. New advances in gastrointestinal motility research

    CERN Document Server

    Pullan, A; Farrugia, G

    2013-01-01

    Research into gastrointestinal motility has received renewed interest in part due to recent advances in the techniques for measuring the structure and function of gastrointestinal cells, tissue and organs. The integration of this wealth of data into biophysically based computation models can aid in interpretation of experimental and clinical measurements and the refinement of measurement techniques. The contents of this book span multiple scales - from cell, tissue, organ, to whole body and is divided into four broad sections covering: i) gastrointestinal cellular activity and tissue structure; (ii) techniques for measuring, analyzing and visualizing high-resolution extra-cellular recordings; (iii) methods for sensing gastroelectrical activity using non-invasive bio-electro-magnetic fields and for modulating the underlying gastric electrical activity, and finally; (iv) methods for assessing manometric and videographic motility patterns and the application of these data for predicting the flow and mixing behav...

  17. Endocytic reawakening of motility in jammed epithelia

    Science.gov (United States)

    Malinverno, Chiara; Corallino, Salvatore; Giavazzi, Fabio; Bergert, Martin; Li, Qingsen; Leoni, Marco; Disanza, Andrea; Frittoli, Emanuela; Oldani, Amanda; Martini, Emanuele; Lendenmann, Tobias; Deflorian, Gianluca; Beznoussenko, Galina V.; Poulikakos, Dimos; Ong, Kok Haur; Uroz, Marina; Trepat, Xavier; Parazzoli, Dario; Maiuri, Paolo; Yu, Weimiao; Ferrari, Aldo; Cerbino, Roberto; Scita, Giorgio

    2017-05-01

    Dynamics of epithelial monolayers has recently been interpreted in terms of a jamming or rigidity transition. How cells control such phase transitions is, however, unknown. Here we show that RAB5A, a key endocytic protein, is sufficient to induce large-scale, coordinated motility over tens of cells, and ballistic motion in otherwise kinetically arrested monolayers. This is linked to increased traction forces and to the extension of cell protrusions, which align with local velocity. Molecularly, impairing endocytosis, macropinocytosis or increasing fluid efflux abrogates RAB5A-induced collective motility. A simple model based on mechanical junctional tension and an active cell reorientation mechanism for the velocity of self-propelled cells identifies regimes of monolayer dynamics that explain endocytic reawakening of locomotion in terms of a combination of large-scale directed migration and local unjamming. These changes in multicellular dynamics enable collectives to migrate under physical constraints and may be exploited by tumours for interstitial dissemination.

  18. Electrical Signaling in Motile and Primary Cilia

    OpenAIRE

    Steven J Kleene; Van Houten, Judith L.

    2014-01-01

    Cilia are highly conserved for their structure and also for their sensory functions. They serve as antennae for extracellular information. Whether the cilia are motile or not, they respond to environmental mechanical and chemical stimuli and signal to the cell body. The information from extracellular stimuli is commonly converted to electrical signals through the repertoire of ion-conducting channels in the ciliary membrane resulting in changes in concentrations of ions, esp...

  19. Swimming Motility Reduces Deposition to Silica Surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Lu, Nanxi [Univ. of Illinois, Urbana-Champaign, IL (United States); Massoudieh, Arash [The Catholic Univ. of America, Washington, DC (United States); Liang, Xiaomeng [The Catholic Univ. of America, Washington, DC (United States); Hu, Dehong [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Kamai, Tamir [Agricultural Research Organization, Bet Dagan (Israel); Ginn, Timothy R. [Univ. of California, Davis, CA (United States); Zilles, Julie L. [Univ. of Illinois, Urbana-Champaign, IL (United States); Nguyen, Thanh H. [Univ. of Illinois, Urbana-Champaign, IL (United States)

    2015-01-01

    The role of swimming motility on bacterial transport and fate in porous media was evaluated. We present microscopic evidence showing that strong swimming motility reduces attachment of Azotobacter vinelandii cells to silica surfaces. Applying global and cluster statistical analyses to microscopic videos taken under non-flow conditions, wild type, flagellated A. vinelandii strain DJ showed strong swimming ability with an average speed of 13.1 μm/s, DJ77 showed impaired swimming averaged at 8.7 μm/s, and both the non-flagellated JZ52 and chemically treated DJ cells were non-motile. Quantitative analyses of trajectories observed at different distances above the collector of a radial stagnation point flow cell (RSPF) revealed that both swimming and non-swimming cells moved with the flow when at a distance of at least 20 μm from the collector surface. Near the surface, DJ cells showed both horizontal and vertical movement diverging them from reaching surfaces, while chemically treated DJ cells moved with the flow to reach surfaces, suggesting that strong swimming reduced attachment. In agreement with the RSPF results, the deposition rates obtained for two-dimensional multiple-collector micromodels were also lowest for DJ, while DJ77 and JZ52 showed similar values. Strong swimming specifically reduced deposition on the upstream surfaces of the micromodel collectors.

  20. Esophageal motility abnormalities in gastroesophageal reflux disease

    Institute of Scientific and Technical Information of China (English)

    Irene; Martinucci; Nicola; de; Bortoli; Maria; Giacchino; Giorgia; Bodini; Elisa; Marabotto; Santino; Marchi; Vincenzo; Savarino; Edoardo; Savarino

    2014-01-01

    Esophageal motility abnormalities are among the main factors implicated in the pathogenesis of gastroesophageal reflux disease. The recent introduction in clinical and research practice of novel esophageal testing has markedly improved our understanding of the mechanisms contributing to the development of gastroesophageal reflux disease, allowing a better management of patients with this disorder. In this context, the present article intends to provide an overview of the current literature about esophageal motility dysfunctions in patients with gastroesophageal reflux disease. Esophageal manometry, by recording intraluminal pressure, represents the gold standard to diagnose esophagealmotility abnormalities. In particular, using novel techniques, such as high resolution manometry with or without concurrent intraluminal impedance monitoring, transient lower esophageal sphincter (LES) relaxations, hypotensive LES, ineffective esophageal peristalsis and bolus transit abnormalities have been better defined and strongly implicated in gastroesophageal reflux disease development. Overall, recent findings suggest that esophageal motility abnormalities are increasingly prevalent with increasing severity of reflux disease, from nonerosive reflux disease to erosive reflux disease and Barrett’s esophagus. Characterizing esophageal dysmotility among different subgroups of patients with reflux disease may represent a fundamental approach to properly diagnose these patients and, thus, to set up the best therapeutic management. Currently, surgery represents the only reliable way to restore the esophagogastric junction integrity and to reduce transient LES relaxations that are considered to be the predominant mechanism by which gastric contents can enter the esophagus. On that ground, more in depth future studies assessing the pathogenetic role of dysmotility in patients with reflux disease are warranted.

  1. Effects of Seminal Plasma Relaxin on Human Sperm Motility

    Institute of Scientific and Technical Information of China (English)

    于宁妮; 陆欣; 徐胜; 冯京生; 吴明章

    1999-01-01

    To clarify the role of endogenous relaxin on sperm motility, relaxin in semen was neutraliged by anti-relaxin antibody in vitro.22 semen samples were collected from infertility clinic and tested with Hamilton-Thorn 2000 Motility Analyzer to detect spermmotility(%),progressive motility(%),path velocity (micro/sec) and velocity(0-4 grade) at the time of 0,15,30 and 60 min respectively.The results showed that sperm motility declined significantly after being incubated with anti-relaxin serum.Sperm progressive motility declined more obviously.This experiment revealed that endogenous relaxin could play an important role in the physiological process of maintaining sperm motility,especially progressive motility.

  2. Bacterial motility in the sea and its ecological implications

    DEFF Research Database (Denmark)

    Grossart, Hans-Peter; Riemann, Lasse; Azam, F.

    2001-01-01

    Motility could be an important adaptation of heterotrophic bacteria and archaea, and it may have ecological and biogeochemical implications. However, the limited observations so far show that only a small fraction (=10%) of bacteria is motile. We report a systematic 10 mo long field study off......, and heterotrophic nanoflagellates. However, it was positively related with particulate organic carbon throughout diel sampling on 24 to 26 September 1997. During a mesocosm diatom bloom % motile rose sharply as the bloom crashed, suggesting algal detritus may elicit motility. Enhanced % motile resulted in increased...... swimming. Our results show that a variable fraction of marine bacteria is able to respond to loci of organic matter, e.g. organic particles and algae, and that motility underlies dynamic patterns of ecological relationships (symbiosis, competition, parasitism) between bacteria and algae. Since motility may...

  3. TOF-SIMS studies of yttria-stabilised zirconia

    DEFF Research Database (Denmark)

    Hansen, Karin Vels; Norrman, Kion; Mogensen, Mogens Bjerg

    2006-01-01

    The surface of an as-polished and an as-sintered yttria-stabilised zirconia pellet was analysed with XPS and TOF-SIMS (depth profiling and imaging) in order to study the distribution of impurities. The polished sample was slightly contaminated with Na, K, Mg and Ca. The sintered sample showed...

  4. Trace element analysis in silicon by accelerator SIMS

    Energy Technology Data Exchange (ETDEWEB)

    Ender, R.M.; Suter, M. [Eidgenoessische Technische Hochschule, Zurich (Switzerland); Doebeli, M.; Synal, H.A. [Paul Scherrer Inst. (PSI), Villigen (Switzerland)

    1997-09-01

    The accelerator SIMS technique has been applied to Si samples implanted with different elements. It has been shown that concentrations of several trace elements can be analysed down to about 1 ppb in depth profiling mode. (author) 2 figs., 1 ref.

  5. ToF-SIMS PCA analysis of Myrtus communis L.

    Science.gov (United States)

    Piras, F. M.; Dettori, M. F.; Magnani, A.

    2009-06-01

    Nowadays there is a growing interest of researchers for the application of sophisticated analytical techniques in conjunction with statistical data analysis methods to the characterization of natural products to assure their authenticity and quality, and for the possibility of direct analysis of food to obtain maximum information. In this work, time-of-flight secondary ion mass spectrometry (ToF-SIMS) in conjunction with principal components analysis (PCA) are applied to study the chemical composition and variability of Sardinian myrtle ( Myrtus communis L.) through the analysis of both berries alcoholic extracts and berries epicarp. ToF-SIMS spectra of berries epicarp show that the epicuticular waxes consist mainly of carboxylic acids with chain length ranging from C20 to C30, or identical species formed from fragmentation of long-chain esters. PCA of ToF-SIMS data from myrtle berries epicarp distinguishes two groups characterized by a different surface concentration of triacontanoic acid. Variability in antocyanins, flavonols, α-tocopherol, and myrtucommulone contents is showed by ToF-SIMS PCA analysis of myrtle berries alcoholic extracts.

  6. 20-Sim ANSI-C code on a 8051 target

    NARCIS (Netherlands)

    Geerlings, Joël

    2001-01-01

    In the forth-coming version of 20-sim the option code-generation for targets will be available. After selection of a template, it’s filled in with model specific information. Then this adapted template can be compiled and linked such that it can be run on the target. Theo Lammerink designed around t

  7. Non primary standards SIM force comparison up to 10 kn

    Directory of Open Access Journals (Sweden)

    Claudia Santo

    2011-04-01

    Full Text Available This force comparison was performed among IDIC (Chile, LATU (Uruguay and CENAM (Mexico, national laboratories within the Interamerican Metrology System (SIM region. Each laboratory used its national standard for the established measuring range. The comparison started in August 2002 and finished in September 2004. This comparison is the second part of a SIM primary standards comparison carried out with the participation of INMETRO (Brazil, INTI (Argentina and SIC (Colombia, having CENAM as pilot laboratory, (SIM comparison number SIM 7.7. This comparison has an overlap with the force steps used in the CIPM Key Comparison CCM.F-K1.a and CCM.F-K1.b., force points 5 kN and 10 kN.The objective of the comparison was to estimate the level of agreement for the realization of the quantity force and the uncertainty associated to its measurement in the range up to 10 kN. Two transducers (load cells were used as transfer standards, to obtain its maximum accuracy, thecomparison range was selected from 4 kN to 10 kN (starting at 40% of the full load cells range. The results obtained by the participating laboratories were in agreement according to the analysis of comparability performed by the normalized error equation and the Youden plot techniques used.

  8. Physics of protein motility and motor proteins

    Science.gov (United States)

    Kolomeisky, Anatoly B.

    2013-09-01

    Motor proteins are enzymatic molecules that transform chemical energy into mechanical motion and work. They are critically important for supporting various cellular activities and functions. In the last 15 years significant progress in understanding the functioning of motor proteins has been achieved due to revolutionary breakthroughs in single-molecule experimental techniques and strong advances in theoretical modelling. However, microscopic mechanisms of protein motility are still not well explained, and the collective efforts of many scientists are needed in order to solve these complex problems. In this special section the reader will find the latest advances on the difficult road to mapping motor proteins dynamics in various systems. Recent experimental developments have allowed researchers to monitor and to influence the activity of single motor proteins with a high spatial and temporal resolution. It has stimulated significant theoretical efforts to understand the non-equilibrium nature of protein motility phenomena. The latest results from all these advances are presented and discussed in this special section. We would like to thank the scientists from all over the world who have reported their latest research results for this special section. We are also grateful to the staff and editors of Journal of Physics: Condensed Matter for their invaluable help in handling all the administrative and refereeing activities. The field of motor proteins and protein motility is fast moving, and we hope that this collection of articles will be a useful source of information in this highly interdisciplinary area. Physics of protein motility and motor proteins contents Physics of protein motility and motor proteinsAnatoly B Kolomeisky Identification of unique interactions between the flexible linker and the RecA-like domains of DEAD-box helicase Mss116 Yuan Zhang, Mirkó Palla, Andrew Sun and Jung-Chi Liao The load dependence of the physical properties of a molecular motor

  9. Development practices and lessons learned in developing SimPEG

    Science.gov (United States)

    Cockett, R.; Heagy, L. J.; Kang, S.; Rosenkjaer, G. K.

    2015-12-01

    Inverse modelling provides a mathematical framework for constructing a model of physical property distributions in the subsurface that are consistent with the data collected in geophysical surveys. The geosciences are increasingly moving towards the integration of geological, geophysical, and hydrological information to better characterize the subsurface. This integration must span disciplines and is not only challenging scientifically, but additionally the inconsistencies between conventions often makes implementations complicated, non­ reproducible, or inefficient. SimPEG is an open-source, multi-university effort aimed at providing a generalized framework for solving forward and inverse problems. SimPEG includes finite volume discretizations on structured and unstructured meshes, interfaces to standard numerical solver packages, convex optimization algorithms, model parameterizations, and visualization routines. The SimPEG package (http://simpeg.xyz) supports an ecosystem of forward and inverse modelling applications, including electromagnetics, vadose zone flow, seismic, and potential­ fields, that are all written with a common interface and toolbox. The goal of SimPEG is to support a community of researchers with well-tested, extensible tools, and encourage transparency and reproducibility both of the SimPEG software and the geoscientific research it is applied to. In this presentation, we will share some of the lessons we have learned in designing the modular infrastructure, testing and development practices of SimPEG. We will discuss our use of version control, extensive unit-testing, continuous integration, documentation, issue tracking, and resources that facilitate communication between existing team members and allows new researchers to get involved. These practices have enabled the use of SimPEG in research, industry, and education as well as the ability to support a growing number of dependent repositories and applications. We hope that sharing our

  10. AlphaSim: Software for Breeding Program Simulation.

    Science.gov (United States)

    Faux, Anne-Michelle; Gorjanc, Gregor; Gaynor, R Chris; Battagin, Mara; Edwards, Stefan M; Wilson, David L; Hearne, Sarah J; Gonen, Serap; Hickey, John M

    2016-11-01

    This paper describes AlphaSim, a software package for simulating plant and animal breeding programs. AlphaSim enables the simulation of multiple aspects of breeding programs with a high degree of flexibility. AlphaSim simulates breeding programs in a series of steps: (i) simulate haplotype sequences and pedigree; (ii) drop haplotypes into the base generation of the pedigree and select single-nucleotide polymorphism (SNP) and quantitative trait nucleotide (QTN); (iii) assign QTN effects, calculate genetic values, and simulate phenotypes; (iv) drop haplotypes into the burn-in generations; and (v) perform selection and simulate new generations. The program is flexible in terms of historical population structure and diversity, recent pedigree structure, trait architecture, and selection strategy. It integrates biotechnologies such as doubled-haploids (DHs) and gene editing and allows the user to simulate multiple traits and multiple environments, specify recombination hot spots and cold spots, specify gene jungles and deserts, perform genomic predictions, and apply optimal contribution selection. AlphaSim also includes restart functionalities, which increase its flexibility by allowing the simulation process to be paused so that the parameters can be changed or to import an externally created pedigree, trial design, or results of an analysis of previously simulated data. By combining the options, a user can simulate simple or complex breeding programs with several generations, variable population structures and variable breeding decisions over time. In conclusion, AlphaSim is a flexible and computationally efficient software package to simulate biotechnology enhanced breeding programs with the aim of performing rapid, low-cost, and objective in silico comparison of breeding technologies. Copyright © 2016 Crop Science Society of America.

  11. SORCE SIM Level 3 Solar Spectral Irradiance Daily Means V019

    Data.gov (United States)

    National Aeronautics and Space Administration — The SORCE SIM Solar Spectral Irradiance (SSI) data product SOR3SIMD is constructed using measurements from the SIM instruments, which are combined into merged daily...

  12. SORCE SIM Level 3 Solar Spectral Irradiance Daily Means V020

    Data.gov (United States)

    National Aeronautics and Space Administration — The SORCE SIM Solar Spectral Irradiance (SSI) data product SOR3SIMD is constructed using measurements from the SIM instruments, which are combined into merged daily...

  13. Effects of radiation upon gastrointestinal motility

    Institute of Scientific and Technical Information of China (English)

    Mary F Otterson

    2007-01-01

    Whether due to therapeutic or belligerent exposure, the gastrointestinal effects of irradiation produce symptoms dreaded by a majority of the population. Nausea, vomiting, diarrhea and abdominal cramping are hallmarks of the prodromal phase of radiation sickness, occurring hours to days following radiation exposure. The prodromal phase is distinct from acute radiation sickness in that the absorptive, secretory and anatomic changes associated with radiation damage are not easily identifiable. It is during this phase of radiation sickness that gastrointestinal motility significantly changes. In addition, there is evidence that motor activity of the gut contributes to some of the acute and chronic effects of radiation.

  14. Swimming and swarming motility properties of peanut-nodulating rhizobia.

    Science.gov (United States)

    Vicario, Julio C; Dardanelli, Marta S; Giordano, Walter

    2015-01-01

    Motility allows populations of bacteria to rapidly reach and colonize new microniches or microhabitats. The motility of rhizobia (symbiotic nitrogen-fixing bacteria that nodulate legume roots) is an important factor determining their competitive success. We evaluated the effects of temperature, incubation time, and seed exudates on swimming and swarming motility of five strains of Bradyrhizobium sp. (peanut-nodulating rhizobia). Swimming motility was increased by exudate exposure for all strains except native Pc34. In contrast, swarming motility was increased by exudate exposure for native 15A but unchanged for the other four strains. All five strains displayed the ability to differentiate into swarm cells. Morphological examination by scanning electron microscopy showed that the length of the swarm cells was variable, but generally greater than that of vegetative cells. Our findings suggest the importance of differential motility properties of peanut-nodulating rhizobial strains during agricultural inoculation and early steps of symbiotic interaction with the host.

  15. Aging and intestinal motility: a review of factors that affect intestinal motility in the aged.

    LENUS (Irish Health Repository)

    O'Mahony, Denis

    2012-02-03

    Normal aging is associated with significant changes in the function of most organs and tissues. In this regard, the gastrointestinal tract is no exception. The purpose of this review is to detail the important age-related changes in motor function of the various parts of the gastrointestinal tract and to highlight some of the important motility changes that may occur, either in relation to common age-related disorders, or as a result of certain drugs commonly prescribed in the aged. A major confounding factor in the interpretation of motor phenomena throughout the gastrointestinal tract in this age group is the frequent coexistence of neurological, endocrinological and other disease states, which may be independently associated with dysmotility. Overall, current data are insufficient to implicate normal aging as a cause of dysmotility in the elderly. Normal aging is associated with various changes in gastrointestinal motility, but the clinical significance of such changes remains unclear. More important is the impact of various age-related diseases on gastrointestinal motility in the elderly: for example, long-standing diabetes mellitus may reduce gastric emptying in up to 50% of patients; depression significantly prolongs whole-gut transit time; hypothyroidism may prolong oro-caecal transit time; and chronic renal failure is associated with impaired gastric emptying. In addition, various, frequently used drugs in the elderly cause disordered gastrointestinal motility. These drugs include anticholinergics, especially antidepressants with an anticholinergic effect, opioid analgesics and calcium antagonists.

  16. PACRG, a protein linked to ciliary motility, mediates cellular signaling.

    OpenAIRE

    Loucks, Catrina M.; Bialas, Nathan J.; Dekkers, Martijn; Walker, Denise S.; Grundy, Laura J.; Li, Chunmei; Inglis, P. Nick; Kida, Katarzyna; Schafer, William R; Blacque, Oliver E; Jansen, Gert; Michel R Leroux

    2016-01-01

    Cilia are microtubule-based organelles that project from nearly all mammalian cell types. Motile cilia generate fluid flow, whereas nonmotile (primary) cilia are required for sensory physiology and modulate various signal transduction pathways. Here we investigate the nonmotile ciliary signaling roles of parkin coregulated gene (PACRG), a protein linked to ciliary motility. PACRG is associated with the protofilament ribbon, a structure believed to dictate the regular arrangement of motility-a...

  17. PACRG, a protein linked to ciliary motility, mediates cellular signaling

    OpenAIRE

    Loucks, Catrina M.; Bialas, Nathan J.; Dekkers, Martijn P. J.; Walker, Denise S.; Grundy, Laura J.; Li, Chunmei; Inglis, P. Nick; Kida, Katarzyna; Schafer, William R; Blacque, Oliver E; Jansen, Gert; Michel R Leroux

    2016-01-01

    Cilia are microtubule-based organelles that project from nearly all mammalian cell types. Motile cilia generate fluid flow, whereas nonmotile (primary) cilia are required for sensory physiology and modulate various signal transduction pathways. Here we investigate the nonmotile ciliary signaling roles of parkin coregulated gene (PACRG), a protein linked to ciliary motility. PACRG is associated with the protofilament ribbon, a structure believed to dictate the regular arrangement of motility-a...

  18. High motility reduces grazing mortality of planktonic bacteria

    DEFF Research Database (Denmark)

    Matz, Carsten; Jurgens, K.

    2005-01-01

    We tested the impact of bacterial swimming speed on the survival of planktonic bacteria in the presence of protozoan grazers. Grazing experiments with three common bacterivorous nanoflagellates revealed low clearance rates for highly motile bacteria. High-resolution video microscopy demonstrated ......(3), >50 mum s(-1)) illustrated the combined protective action of small cell size and high motility. Our findings suggest that motility has an important adaptive function in the survival of planktonic bacteria during protozoan grazing....

  19. Paraventricular nucleus Sim1 neuron ablation mediated obesity is resistant to high fat diet.

    Directory of Open Access Journals (Sweden)

    Dong Xi

    Full Text Available Single minded 1 (SIM1 is a transcription factor involved in brain patterning and control of energy balance. In humans, haploinsufficiency of SIM1 causes early-onset obesity. Mice deficient in the homologous gene, SIM1, also exhibit early onset obesity and increased sensitivity to a high fat diet. SIM1 is expressed in several areas of the brain implicated in control of energy balance including the paraventricular nucleus (PVN, the supraoptic nucleus (SON, the medial amygdala and nucleus of the lateral olfactory tract. We have previously shown that mice with global Sim1 neuron ablation exhibit obesity with hyperphagia as the primary defect. The PVN has a critical role in feeding and in high-fat appetite, thus, we sought to determine the effect of Sim1 neuron ablation limited to the PVN. We achieved PVN-SIM1 limited ablation through stereotactic injection of diphtheria toxin into the PVN of Sim1Cre-iDTR mice. The specificity of this ablation was confirmed by immunohistochemistry and quantitative real time PCR of the PVN, supraoptic nucleus and the amygdala. Mice with PVN Sim1 neuron ablation, similar to mice with global Sim1 neuron ablation, exhibit early onset obesity with hyperphagia as the primary defect. However, PVN-Sim1 neuron ablated mice have a decreased response to fasting-induced hyperphagia. Consistent with this decrement, PVN-Sim1 neuron ablated mice have a decreased hyperphagic response to PVN injection of agouti-related peptide (AgRP. When PVN-Sim1 neuron ablated mice are placed on a high fat diet, surprisingly, their intake decreases and they actually lose weight. When allowed ad lib access to high fat diet and normal chow simultaneously, PVN-Sim1 neuron ablated mice exhibit overall decreased intake. That is, in PVN-Sim1 neuron ablated mice, access to fat suppresses overall appetite.

  20. Using ToF-SIMS to study industrial surface phenomena

    Science.gov (United States)

    Smentkowski, Vincent S.; Keenan, Michael R.; Arlinghaus, Henrik

    2016-10-01

    Time of flight secondary ion mass spectrometry (ToF-SIMS) is frequently used to analyze industrial samples since it offers high (ppb) detection sensitivity, very high surface specificity (analysis of the top 1-3 surface layers during a spectral/image acquisition), high mass resolution (allowing the analyst the ability to separate Cu from C5H3 for instance), the ability to detect hydrogen, high depth resolution for depth profile measurements, and detection of high-mass fragments associated with molecular species/additives. In this manuscript, we demonstrate the advantages of ToF-SIMS including the ability to measure trace quantities of unexpected species on the surfaces of devices, and the ability to extract high-mass resolution information from data sets which were collected at degraded mass resolution. The importance of applying unbiased multivariate statistical analysis (MVSA) to the complete set of measured data is also demonstrated.

  1. Type Ia supernova rate at $z \\sim 0.1$

    CERN Document Server

    Hardin, D P; Alard, C; Albert, J N; Amadon, A; Andersen, J; Ansari, R; Aubourg, E; Bareyre, P; Bauer, F; Beaulieu, J P; Blanc, G; Bouquet, A; Char, S; Charlot, X; Couchot, F; Coutures, C; Derue, F; Ferlet, R; Glicenstein, J F; Goldman, B; Gould, A; Graff, D; Gros, M H; Haïssinski, J; Hamilton, J C; Kat, J; Kim, A; Lasserre, T; Lesquoy, E; Loup, C; Magneville, C; Mansoux, B; Marquette, J B; Maurice, E; Milshtein, A I; Moniez, M; Palanque-Delabrouille, Nathalie; Perdereau, O; Prévôt, L; Regnault, N; Rich, J; Spiro, Michel; Vidal-Madjar, A; Vigroux, L; Zylberajch, S

    2000-01-01

    We present the EROS nearby supernova ($z \\sim 0.02 - 0.2$) search and the analysis of the first year of data (1997). A total of 80 square degrees were surveyed. Eight supernov{\\ae} were detected, four of which were spectroscopically identified as type Ia supernov{\\ae}. The search efficiency was determined with a Monte-Carlo simulation taking into account the efficiencies for both supernova detection and host galaxy identification. Assuming that for a given galaxy the supernova rate is proportional to the galactic luminosity, we compute a type Ia supernova explosion rate of: ${\\cal R} = 0.44 {}_{-0.21}^{+0.35} {}_{-0.07}^{+0.13} h^2: / 10^{10} \\lbsun / 100 {\\rm yrs}$ at an average redshift of $\\sim 0.1$ where the errors are respectively statistical and systematic (type misidentification included).

  2. Motility Evaluation in the Patient with Inflammatory Bowel Disease.

    Science.gov (United States)

    Abdalla, Sherine M; Kalra, Gorav; Moshiree, Baha

    2016-10-01

    Patients with inflammatory bowel disease (IBD) suffer frequently from functional bowel diseases (FBD) and motility disorders. Management of FBD and motility disorders in IBD combined with continued treatment of a patient's IBD symptoms will likely lead to better clinical outcomes and improve the patient's quality of life. The goals of this review were to summarize the most recent literature on motility disturbances in patients with IBD and to give a brief overview of the ranges of motility disturbances, from reflux disease to anorectal disorders, and discuss their diagnosis and specific management.

  3. Small intestine motility development in newborn mammals.

    Science.gov (United States)

    Woliński, Jarosław; Słupecka-Ziemilska, Monika; Boryczka, Maria; Grzesiak, Paulina; Kwiatkowski, Jakub; Kotarba, Grzegorz

    2016-01-01

    Since the beginning of the 20th century, researchers have been working to improve the understanding of gastrointestinal motility. The first major discovery was the observation of a migrating myoelectric complex that turned out to be a universal occurrence among vertebrates. Further inquires resulted in a detailed description of its development during different stages of ontogeny. Some time before that, a cornerstone had been laid for a breakthrough that would come years later. That cornerstone came in the form of interstitial cells of Cajal whose true role could not be discerned until the discovery of a CD117 receptor - their main marker. With the ability to precisely mark interstitial cells of Cajal, a wave of subsequent new experiments and observations connected them to the occurrence of slow waves and allowed an understanding of the mechanism responsible for their generation. Some of these findings suggested that Cajal cells might have a role in the development of several motility disorders thus opening an avenue of research that requires the usage of both traditional and advanced diagnostic methods.

  4. Mechanics and polarity in cell motility

    Science.gov (United States)

    Ambrosi, D.; Zanzottera, A.

    2016-09-01

    The motility of a fish keratocyte on a flat substrate exhibits two distinct regimes: the non-migrating and the migrating one. In both configurations the shape is fixed in time and, when the cell is moving, the velocity is constant in magnitude and direction. Transition from a stable configuration to the other one can be produced by a mechanical or chemotactic perturbation. In order to point out the mechanical nature of such a bistable behaviour, we focus on the actin dynamics inside the cell using a minimal mathematical model. While the protein diffusion, recruitment and segregation govern the polarization process, we show that the free actin mass balance, driven by diffusion, and the polymerized actin retrograde flow, regulated by the active stress, are sufficient ingredients to account for the motile bistability. The length and velocity of the cell are predicted on the basis of the parameters of the substrate and of the cell itself. The key physical ingredient of the theory is the exchange among actin phases at the edges of the cell, that plays a central role both in kinematics and in dynamics.

  5. Major regulatory mechanisms involved in sperm motility.

    Science.gov (United States)

    Pereira, Rute; Sá, Rosália; Barros, Alberto; Sousa, Mário

    2017-01-01

    The genetic bases and molecular mechanisms involved in the assembly and function of the flagellum components as well as in the regulation of the flagellar movement are not fully understood, especially in humans. There are several causes for sperm immotility, of which some can be avoided and corrected, whereas other are related to genetic defects and deserve full investigation to give a diagnosis to patients. This review was performed after an extensive literature search on the online databases PubMed, ScienceDirect, and Web of Science. Here, we review the involvement of regulatory pathways responsible for sperm motility, indicating possible causes for sperm immotility. These included the calcium pathway, the cAMP-dependent protein kinase pathway, the importance of kinases and phosphatases, the function of reactive oxygen species, and how the regulation of cell volume and osmolarity are also fundamental components. We then discuss main gene defects associated with specific morphological abnormalities. Finally, we slightly discuss some preventive and treatments approaches to avoid development of conditions that are associated with unspecified sperm immotility. We believe that in the near future, with the development of more powerful techniques, the genetic causes of sperm immotility and the regulatory mechanisms of sperm motility will be better understand, thus enabling to perform a full diagnosis and uncover new therapies.

  6. Epilepsy-induced motility of differentiated neurons.

    Science.gov (United States)

    Chai, Xuejun; Münzner, Gert; Zhao, Shanting; Tinnes, Stefanie; Kowalski, Janina; Häussler, Ute; Young, Christina; Haas, Carola A; Frotscher, Michael

    2014-08-01

    Neuronal ectopia, such as granule cell dispersion (GCD) in temporal lobe epilepsy (TLE), has been assumed to result from a migration defect during development. Indeed, recent studies reported that aberrant migration of neonatal-generated dentate granule cells (GCs) increased the risk to develop epilepsy later in life. On the contrary, in the present study, we show that fully differentiated GCs become motile following the induction of epileptiform activity, resulting in GCD. Hippocampal slice cultures from transgenic mice expressing green fluorescent protein in differentiated, but not in newly generated GCs, were incubated with the glutamate receptor agonist kainate (KA), which induced GC burst activity and GCD. Using real-time microscopy, we observed that KA-exposed, differentiated GCs translocated their cell bodies and changed their dendritic organization. As found in human TLE, KA application was associated with decreased expression of the extracellular matrix protein Reelin, particularly in hilar interneurons. Together these findings suggest that KA-induced motility of differentiated GCs contributes to the development of GCD and establish slice cultures as a model to study neuronal changes induced by epileptiform activity.

  7. Gastrointestinal motility and functional gastrointestinal diseases.

    Science.gov (United States)

    Kusano, Motoyasu; Hosaka, Hiroko; Kawada, Akiyo; Kuribayashi, Shiko; Shimoyama, Yasuyuki; Zai, Hiroaki; Kawamura, Osamu; Yamada, Masanobu

    2014-01-01

    Digestive tract motility patterns are closely related to the pathophysiology of functional gastrointestinal diseases (FGID), and these patterns differ markedly between the interdigestive period and the postprandial period. The characteristic motility pattern in the interdigestive period is so-called interdigestive migrating contraction (IMC). IMCs have a housekeeping role in the intestinal tract, and could also be related to FGID. IMCs arising from the stomach are called gastrointestinal IMCs (GI-IMC), while IMCs arising from the duodenum without associated gastric contractions are called intestinal IMCs (I-IMC). It is thought that I-IMCs are abnormal in FGID. Transport of food residue to the duodenum via gastric emptying is one of the most important postprandial functions of the stomach. In patients with functional dyspepsia (FD), abnormal gastric emptying is a possible mechanism of gastric dysfunction. Accordingly, delayed gastric emptying has attracted attention, with prokinetic agents and herbal medicines often being administered in Japan to accelerate gastric emptying in patients who have anorexia associated with dyspepsia. Recently, we found that addition of monosodium L-glutamate (MSG) to a high-calorie liquid diet rich in casein promoted gastric emptying in healthy men. Therefore, another potential method of improving delayed gastric emptying could be activation of chemosensors that stimulate the autonomic nervous system of the gastrointestinal tract, suggesting a role for MSG in the management of delayed gastric emptying in patients with FD.

  8. TOF-SIMS imaging of protein adsorption on dialysis membrane

    Science.gov (United States)

    Aoyagi, Satoka; Hayama, Msayo; Hasegawa, Urara; Sakai, Kiyotaka; Hoshi, Takahiro; Kudo, Masahiro

    2004-06-01

    Time-of-flight secondary ion mass spectrometry (TOF-SIMS) is capable of chemical imaging of proteins on insulated samples such as hollow-fiber dialysis membranes. Albumin loss and a lowering of diffusive permeability caused by protein adsorption on dialysis membranes should be reduced in order to enhance dialysis adequacy of the patients. Bovine serum albumin (BSA)-adsorbed hollow-fiber dialysis membranes were tested in the present study. TOF-SIMS images and spectra of both native membranes and BSA-adsorbed membranes were compared in order to identify secondary ions related to BSA and membranes. Peaks of secondary ions related to BSA and each membrane were selected by means of information theory, and they are characterized by principal component analysis (PCA). Chemical images of BSA adsorption on both native and treated membranes were obtained to find that BSA permeability and interaction between the membranes and BSA definitely depend on the properties of a membrane. TOF-SIMS imaging obtained with information theory is a powerful tool to estimate protein adsorption on the dialysis membranes.

  9. SIMS analysis: Development and evaluation 1995 summary report

    Energy Technology Data Exchange (ETDEWEB)

    Groenewold, G.S.; Appelhans, A.D.; Ingram, J.C.; Delmore, J.E.; Dahl, D.A.

    1995-10-01

    Secondary ion mass spectrometry (SIMS) was evaluated for characterizing Hg salts. It was found that sulfate and chloride species could be identified directly without sample preparation. Mercuric oxide could be identified by complexation with formic acid. Hg nitrates could be identified by complexation with cyclohexylamine (CHA). Laser desorption ion trap MS was evaluated for characterizing EDTA on environmental samples. No intact EDTA ions were observed, but a series of EDTA fragment ions were visible, particularly on basalt and soil. An ion trap SIMS was developed: a perrhenate ion gun was interfaced to a Teledyne ion trap spectrometer, and the entire device was mounted on a cart. The technology was demonstrated using a prototype ion trap SIMS instrument for detecting Hg{center_dot}CHA complexes formed from nitrate salts. Intensity of the ion gun was improved, and the surface damage of the particle was small, and ion gun technology transfer to Phi-Evans, Inc. is being considered. Two technology end users are at INEL`s Central Facilities Area 674 pond and acid pit of the Radioactive Waste Management Complex; target problem at both sites is the need for Hg speciation on soil samples.

  10. SimVascular: An Open Source Pipeline for Cardiovascular Simulation.

    Science.gov (United States)

    Updegrove, Adam; Wilson, Nathan M; Merkow, Jameson; Lan, Hongzhi; Marsden, Alison L; Shadden, Shawn C

    2017-03-01

    Patient-specific cardiovascular simulation has become a paradigm in cardiovascular research and is emerging as a powerful tool in basic, translational and clinical research. In this paper we discuss the recent development of a fully open-source SimVascular software package, which provides a complete pipeline from medical image data segmentation to patient-specific blood flow simulation and analysis. This package serves as a research tool for cardiovascular modeling and simulation, and has contributed to numerous advances in personalized medicine, surgical planning and medical device design. The SimVascular software has recently been refactored and expanded to enhance functionality, usability, efficiency and accuracy of image-based patient-specific modeling tools. Moreover, SimVascular previously required several licensed components that hindered new user adoption and code management and our recent developments have replaced these commercial components to create a fully open source pipeline. These developments foster advances in cardiovascular modeling research, increased collaboration, standardization of methods, and a growing developer community.

  11. SIM-Lite Mission Spectral Calibration Sensitivities and Refinements

    Science.gov (United States)

    Zhai, C.; An, X.; Goullioud, R.; Nemati, B.; Shao, M.; Shen, J.; Wehmeier, U.; Wang, X.; Weiler, M.; Werne, T.; Wu, J.

    2010-01-01

    SIM-Lite missions will perform astrometry at microarcsecond accuracy using star light interferometry. For typical baselines that are shorter than 10 meters, this requires to measure optical path difference (OPD) accurate to tens of picometers calling for highly accurate calibration. A major challenge is to calibrate the star spectral dependency in fringe measurements -- the spectral calibration. Previously, we have developed a spectral calibration and estimation scheme achieving picometer level accuracy. In this paper, we present the improvements regarding the application of this scheme from sensitivity studies. Data from the SIM Spectral Calibration Development Unit (SCDU) test facility shows that the fringe OPD is very sensitive to pointings of both beams from the two arms of the interferometer. This sensitivity coupled with a systematic pointing error provides a mechanism to explain the bias changes in 2007. Improving system alignment can effectively reduce this sensitivity and thus errors due to pointing errors. Modeling this sensitivity can lead to further improvement in data processing. We then investigate the sensitivity to a model parameter, the bandwidth used in the fringe model, which presents an interesting trade between systematic and random errors. Finally we show the mitigation of calibration errors due to system drifts by interpolating instrument calibrations. These improvements enable us to use SCDU data to demonstrate that SIM-Lite missions can meet the 1pm noise floor requirement for detecting earth-like exoplanets.

  12. Alternative Liquid Fuels Simulation Model (AltSim).

    Energy Technology Data Exchange (ETDEWEB)

    Williams, Ryan; Baker, Arnold Barry; Drennen, Thomas E.

    2009-12-01

    The Alternative Liquid Fuels Simulation Model (AltSim) is a high-level dynamic simulation model which calculates and compares the production and end use costs, greenhouse gas emissions, and energy balances of several alternative liquid transportation fuels. These fuels include: corn ethanol, cellulosic ethanol from various feedstocks (switchgrass, corn stover, forest residue, and farmed trees), biodiesel, and diesels derived from natural gas (gas to liquid, or GTL), coal (coal to liquid, or CTL), and coal with biomass (CBTL). AltSim allows for comprehensive sensitivity analyses on capital costs, operation and maintenance costs, renewable and fossil fuel feedstock costs, feedstock conversion ratio, financial assumptions, tax credits, CO{sub 2} taxes, and plant capacity factor. This paper summarizes the structure and methodology of AltSim, presents results, and provides a detailed sensitivity analysis. The Energy Independence and Security Act (EISA) of 2007 sets a goal for the increased use of biofuels in the U.S., ultimately reaching 36 billion gallons by 2022. AltSim's base case assumes EPA projected feedstock costs in 2022 (EPA, 2009). For the base case assumptions, AltSim estimates per gallon production costs for the five ethanol feedstocks (corn, switchgrass, corn stover, forest residue, and farmed trees) of $1.86, $2.32, $2.45, $1.52, and $1.91, respectively. The projected production cost of biodiesel is $1.81/gallon. The estimates for CTL without biomass range from $1.36 to $2.22. With biomass, the estimated costs increase, ranging from $2.19 per gallon for the CTL option with 8% biomass to $2.79 per gallon for the CTL option with 30% biomass and carbon capture and sequestration. AltSim compares the greenhouse gas emissions (GHG) associated with both the production and consumption of the various fuels. EISA allows fuels emitting 20% less greenhouse gases (GHG) than conventional gasoline and diesels to qualify as renewable fuels. This allows several of the

  13. Alternative Liquid Fuels Simulation Model (AltSim).

    Energy Technology Data Exchange (ETDEWEB)

    Williams, Ryan; Baker, Arnold Barry; Drennen, Thomas E.

    2009-12-01

    The Alternative Liquid Fuels Simulation Model (AltSim) is a high-level dynamic simulation model which calculates and compares the production and end use costs, greenhouse gas emissions, and energy balances of several alternative liquid transportation fuels. These fuels include: corn ethanol, cellulosic ethanol from various feedstocks (switchgrass, corn stover, forest residue, and farmed trees), biodiesel, and diesels derived from natural gas (gas to liquid, or GTL), coal (coal to liquid, or CTL), and coal with biomass (CBTL). AltSim allows for comprehensive sensitivity analyses on capital costs, operation and maintenance costs, renewable and fossil fuel feedstock costs, feedstock conversion ratio, financial assumptions, tax credits, CO{sub 2} taxes, and plant capacity factor. This paper summarizes the structure and methodology of AltSim, presents results, and provides a detailed sensitivity analysis. The Energy Independence and Security Act (EISA) of 2007 sets a goal for the increased use of biofuels in the U.S., ultimately reaching 36 billion gallons by 2022. AltSim's base case assumes EPA projected feedstock costs in 2022 (EPA, 2009). For the base case assumptions, AltSim estimates per gallon production costs for the five ethanol feedstocks (corn, switchgrass, corn stover, forest residue, and farmed trees) of $1.86, $2.32, $2.45, $1.52, and $1.91, respectively. The projected production cost of biodiesel is $1.81/gallon. The estimates for CTL without biomass range from $1.36 to $2.22. With biomass, the estimated costs increase, ranging from $2.19 per gallon for the CTL option with 8% biomass to $2.79 per gallon for the CTL option with 30% biomass and carbon capture and sequestration. AltSim compares the greenhouse gas emissions (GHG) associated with both the production and consumption of the various fuels. EISA allows fuels emitting 20% less greenhouse gases (GHG) than conventional gasoline and diesels to qualify as renewable fuels. This allows several of the

  14. Gene expression in Pseudomonas aeruginosa swarming motility

    Directory of Open Access Journals (Sweden)

    Déziel Eric

    2010-10-01

    Full Text Available Abstract Background The bacterium Pseudomonas aeruginosa is capable of three types of motilities: swimming, twitching and swarming. The latter is characterized by a fast and coordinated group movement over a semi-solid surface resulting from intercellular interactions and morphological differentiation. A striking feature of swarming motility is the complex fractal-like patterns displayed by migrating bacteria while they move away from their inoculation point. This type of group behaviour is still poorly understood and its characterization provides important information on bacterial structured communities such as biofilms. Using GeneChip® Affymetrix microarrays, we obtained the transcriptomic profiles of both bacterial populations located at the tip of migrating tendrils and swarm center of swarming colonies and compared these profiles to that of a bacterial control population grown on the same media but solidified to not allow swarming motility. Results Microarray raw data were corrected for background noise with the RMA algorithm and quantile normalized. Differentially expressed genes between the three conditions were selected using a threshold of 1.5 log2-fold, which gave a total of 378 selected genes (6.3% of the predicted open reading frames of strain PA14. Major shifts in gene expression patterns are observed in each growth conditions, highlighting the presence of distinct bacterial subpopulations within a swarming colony (tendril tips vs. swarm center. Unexpectedly, microarrays expression data reveal that a minority of genes are up-regulated in tendril tip populations. Among them, we found energy metabolism, ribosomal protein and transport of small molecules related genes. On the other hand, many well-known virulence factors genes were globally repressed in tendril tip cells. Swarm center cells are distinct and appear to be under oxidative and copper stress responses. Conclusions Results reported in this study show that, as opposed to

  15. Mechanics model for actin-based motility.

    Science.gov (United States)

    Lin, Yuan

    2009-02-01

    We present here a mechanics model for the force generation by actin polymerization. The possible adhesions between the actin filaments and the load surface, as well as the nucleation and capping of filament tips, are included in this model on top of the well-known elastic Brownian ratchet formulation. A closed form solution is provided from which the force-velocity relationship, summarizing the mechanics of polymerization, can be drawn. Model predictions on the velocity of moving beads driven by actin polymerization are consistent with experiment observations. This model also seems capable of explaining the enhanced actin-based motility of Listeria monocytogenes and beads by the presence of Vasodilator-stimulated phosphoprotein, as observed in recent experiments.

  16. A Biomechanical Model for Dictyostelium Motility

    CERN Document Server

    Buenemann, Mathias; Rappel, Wouter-Jan; Sander, Leonard M

    2009-01-01

    The crawling motion of Dictyostelium discoideum on substrata involves a number of coordinated events including cell contractions and cell protrusions. The mechanical forces exerted on the substratum during these contractions have recently been quantified using traction force experiments. Based on the results from these experiments, we present a biomechanical model of Dictyostelium discoideum motility with an emphasis on the adhesive properties of the cell-substratum contact. Our model assumes that the cell contracts at a constant rate and is bound to the substratum by adhesive bridges which are modeled as elastic springs. These bridges are established at a spatially uniform rate while detachment occurs at a spatially varying, load-dependent rate. Using Monte-Carlo simulations and assuming a rigid substratum, we find that the cell speed depends only weakly on the adhesive properties of the cell-substratum, in agreement with experimental data. Varying the parameters that control the adhesive and contractile pro...

  17. Pediatric Gastrointestinal Motility Disorders: Challenges and a Clinical Update

    OpenAIRE

    Chumpitazi, Bruno; Nurko, Samuel

    2008-01-01

    Pediatric gastrointestinal motility disorders are common and can range from relatively benign conditions such as functional constipation to more serious disorders such as achalasia, Hirschsprung disease, and intestinal pseudoobstruction. Performing and interpreting motility evaluations in children presents unique challenges and is complicated by a dearth of control information, underlying gastrointestinal developmental maturation, technical challenges (eg, catheter size limitations), and pati...

  18. Motility - Finding a Way to Mobility Attitude and Behavior

    DEFF Research Database (Denmark)

    Kjærulff, Aslak Aamot

    2011-01-01

    This paper presents the notion of motility as a way of understanding individual attitude and behavior in relation to mobility. Motility provides an elaborate understanding of the premises for individual mobility, and opens up for a conceptual analysis of mobility management policies....

  19. Bacterial motility in the sea and its ecological implications

    DEFF Research Database (Denmark)

    Grossart, Hans-Peter; Riemann, Lasse; Azam, F.

    2001-01-01

    colonization of living and dead algal cells by bacteria. Filtering seawater through a 1 µm filter reduced % motile, again suggesting the importance of particulate loci. Enrichment with dissolved organic nutrients enhanced % motile only after 6 h but it rapidly (=1 h) increased the time individual bacteria were...

  20. Thyroxin Is Useful to Improve Sperm Motility

    Directory of Open Access Journals (Sweden)

    Mendeluk Gabriela Ruth

    2016-07-01

    Full Text Available Background The aim of this study was to evaluate the non-genomic action of thyroxin on sperm kinetic and its probable use to improve sperm recovery after applying an en- richment method like “swim-up” in comparison with the available one, pentoxifylline. Materials and Methods This is an experimental study. A total of 50 patients were re- cruited, followed by infertility consultation. Conventional sperm assays were performed according to World Health Organization criteria-2010 (WHO-2010. A Computer Aided Semen Analysis System was employed to assess kinetic parameters and concentrations. Number of the motile sperm recovered after preparation technique was calculated. Results Addition of T4 (0.002 µg/ml to semen samples increased hypermotility at 20 minutes (control: 14.18 ± 5.1% vs. 17.66 ± 8.88%, P<0.03, data expressed as mean ± SD and remained unchanged after 40 minutes. Significant differences were found in the motile sperm recovered after swim-up (control: 8.93×106 ± 9.52× 06vs. 17.20×106 ± 21.16×106, P<0.03, achieving all of the tested samples a desirable threshold value for artificial insemination outcome, while adding pentoxifylline increased the number of recovered sperm after swim-up in 60% of the studied cases. No synergism between two treatments could be determined. Conclusion We propose a new physiological tool to artificially improve insemination. The discussion opens windows to investigate unknown pathways involved in sperm ca- pacitation and gives innovative arguments to better understand infertility mechanisms.

  1. Detection and genomic characterization of motility in Lactobacillus curvatus: confirmation of motility in a species outside the Lactobacillus salivarius clade.

    Science.gov (United States)

    Cousin, Fabien J; Lynch, Shónagh M; Harris, Hugh M B; McCann, Angela; Lynch, Denise B; Neville, B Anne; Irisawa, Tomohiro; Okada, Sanae; Endo, Akihito; O'Toole, Paul W

    2015-02-01

    Lactobacillus is the largest genus within the lactic acid bacteria (LAB), with almost 180 species currently identified. Motility has been reported for at least 13 Lactobacillus species, all belonging to the Lactobacillus salivarius clade. Motility in lactobacilli is poorly characterized. It probably confers competitive advantages, such as superior nutrient acquisition and niche colonization, but it could also play an important role in innate immune system activation through flagellin–Toll-like receptor 5 (TLR5) interaction. We now report strong evidence of motility in a species outside the L. salivarius clade, Lactobacillus curvatus (strain NRIC0822). The motility of L. curvatus NRIC 0822 was revealed by phase-contrast microscopy and soft-agar motility assays. Strain NRIC 0822 was motile at temperatures between 15 °C and 37 °C, with a range of different carbohydrates, and under varying atmospheric conditions. We sequenced the L. curvatus NRIC 0822 genome, which revealed that the motility genes are organized in a single operon and that the products are very similar (>98.5% amino acid similarity over >11,000 amino acids) to those encoded by the motility operon of Lactobacillus acidipiscis KCTC 13900 (shown for the first time to be motile also). Moreover, the presence of a large number of mobile genetic elements within and flanking the motility operon of L. curvatus suggests recent horizontal transfer between members of two distinct Lactobacillus clades: L. acidipiscis in the L. salivarius clade and L. curvatus inthe L. sakei clade. This study provides novel phenotypic, genetic, and phylogenetic insights into flagellum-mediated motility in lactobacilli.

  2. Bacterial signaling and motility: Sure bets

    Energy Technology Data Exchange (ETDEWEB)

    Zhulin, Igor B [University of Tennessee, Knoxville (UTK) & Oak Ridge National Laboratory (ORNL)

    2008-01-01

    The IX International Conference on Bacterial Locomotion and Signal Transduction (BLAST IX) was held from 14 to 19 January 2007 in Laughlin, NV, a town in the Mojave Desert on the Nevada-Arizona border near old Route 66 and along the banks of the Colorado River. This area is a home to rattlesnakes, sagebrush, abandoned gold mines, and compulsive gamblers. What better venue could scientists possibly dream of for a professional meeting? So there they were, about 190 scientists gathered in the Aquarius Casino Resort, the largest hotel and casino in Laughlin, discussing the latest advances in the field. Aside from a brief excursion to an abandoned gold mine and a dinner cruise on the Colorado River, the scientists focused on nothing but their data and hypotheses, in spirited arguments and rebuttals, and outlined their visions and future plans in a friendly and open environment. The BLAST IX program was dense, with nearly 50 talks and over 90 posters. For that reason, this meeting report will not attempt to be comprehensive; instead it will first provide general background information on the central topics of the meeting and then highlight only a few talks that were of special interest to us and hopefully to the wider scientific community. We will also attempt to articulate some of the future directions or perspectives to the best of our abilities. The best known and understood bacterial motility mechanism is swimming powered by flagella. The rotation of bacterial flagella drives this form of bacterial movement in an aqueous environment. A bacterial flagellum consists of a helical filament attached to the cell body through a complex structure known as the hook-basal body, which drives flagellar rotation. The essential components of the basal body are the MotA-MotB motor-stator proteins bound to the cytoplasmic membrane. These stator proteins interact with proteins that comprise the supramembrane and cytoplasmic rings, which are components of the motor imbedded in the

  3. CalSimHydro Tool - A Web-based interactive tool for the CalSim 3.0 Hydrology Prepropessor

    Science.gov (United States)

    Li, P.; Stough, T.; Vu, Q.; Granger, S. L.; Jones, D. J.; Ferreira, I.; Chen, Z.

    2011-12-01

    CalSimHydro, the CalSim 3.0 Hydrology Preprocessor, is an application designed to automate the various steps in the computation of hydrologic inputs for CalSim 3.0, a water resources planning model developed jointly by California State Department of Water Resources and United States Bureau of Reclamation, Mid-Pacific Region. CalSimHydro consists of a five-step FORTRAN based program that runs the individual models in succession passing information from one model to the next and aggregating data as required by each model. The final product of CalSimHydro is an updated CalSim 3.0 state variable (SV) DSS input file. CalSimHydro consists of (1) a Rainfall-Runoff Model to compute monthly infiltration, (2) a Soil moisture and demand calculator (IDC) that estimates surface runoff, deep percolation, and water demands for natural vegetation cover and various crops other than rice, (3) a Rice Water Use Model to compute the water demands, deep percolation, irrigation return flow, and runoff from precipitation for the rice fields, (4) a Refuge Water Use Model that simulates the ponding operations for managed wetlands, and (5) a Data Aggregation and Transfer Module to aggregate the outputs from the above modules and transfer them to the CalSim SV input file. In this presentation, we describe a web-based user interface for CalSimHydro using Google Earth Plug-In. The CalSimHydro tool allows users to - interact with geo-referenced layers of the Water Budget Areas (WBA) and Demand Units (DU) displayed over the Sacramento Valley, - view the input parameters of the hydrology preprocessor for a selected WBA or DU in a time series plot or a tabular form, - edit the values of the input parameters in the table or by downloading a spreadsheet of the selected parameter in a selected time range, - run the CalSimHydro modules in the backend server and notify the user when the job is done, - visualize the model output and compare it with a base run result, - download the output SV file to be

  4. THE EFFECT OF DEOXYNIVALENOL ON RABBIT SPERMATOZOA MOTILITY IN VITRO

    Directory of Open Access Journals (Sweden)

    Marína Medveďová

    2012-08-01

    Full Text Available In this in vitro study the effects of mycotoxin deoxynivalenol (DON on the motility parameters of rabbit spermatozoa were investigated. The spermatozoa motility was evaluated using CASA assay. Different concentrations of DON in the ejaculate was divided into four experimental group: 0 ng/mL, 10 ng/mL, 100 ng/mL and 1000 ng/mL. Significant differences have not been detected between control group and experimental groups after the detailed analysis of certain motility parameters – total motile spermatozoa (%, progressively motile spermatozoa (%, average path distance (DAP, µm, average path velocity (VAP, µm/s and amplitude of lateral head displacement (ALH, µm. Observed data suggested that further experiments are needed to be done because of a lack of the evidence toxinogenic effects of mycotoxin DON during its constant detection in feed and food.

  5. Motility of copepod nauplii and implications for food encounter

    DEFF Research Database (Denmark)

    Titelman, Josefin; Kiørboe, Thomas

    2003-01-01

    Velocity differences drive all encounter processes. Therefore, knowledge of both prey and predator motility are essential in order to understand feeding behavior and predict food acquisition rates. Here, we describe and quantify the motility behavior of young and old naupliar stages of 6 copepods...... of tracks, speeds, durations and frequencies of events as well as time budgets. Motility mode often changes drastically during naupliar ontogeny. Crudely, nauplii can be divided into those moving with a jump-sink type of motility of various frequencies (1 min(-1) to 3 s(-1)) and those swimming...... with a smoother glide of varying continuity. We apply observed time budgets and behavior-specific speeds in simple models to examine mechanisms of food encounter. The motility of all nauplii may account for clearance rates reported in the literature, but through different mechanisms. Smoothly swimming nauphi...

  6. Computational approaches to substrate-based cell motility

    Science.gov (United States)

    Ziebert, Falko; Aranson, Igor S.

    2016-07-01

    Substrate-based crawling motility of eukaryotic cells is essential for many biological functions, both in developing and mature organisms. Motility dysfunctions are involved in several life-threatening pathologies such as cancer and metastasis. Motile cells are also a natural realisation of active, self-propelled 'particles', a popular research topic in nonequilibrium physics. Finally, from the materials perspective, assemblies of motile cells and evolving tissues constitute a class of adaptive self-healing materials that respond to the topography, elasticity and surface chemistry of the environment and react to external stimuli. Although a comprehensive understanding of substrate-based cell motility remains elusive, progress has been achieved recently in its modelling on the whole-cell level. Here we survey the most recent advances in computational approaches to cell movement and demonstrate how these models improve our understanding of complex self-organised systems such as living cells.

  7. Evolutionary aspects of collective motility in pathogenic bacteria

    Science.gov (United States)

    Deforet, Maxime; Xavier, Joao

    Pseudomonas aeruginosa is a pathogenic bacteria that can use its single polar flagellum to swim through liquids. It can move collectively over semisolid surfaces, a behavior called swarming. It can also settle and form surface-attached communities called biofilms that protect them from antibiotics. The transition from single motility (swimming) to collective motility (swarming) is biologically relevant as it enables exploring environments that a single bacterium cannot explore on its own. It is also clinically relevant since swarming and biofilm formation are thought to be antagonistic. We investigate the mechanisms of bacterial collective motility using a multidisciplinary approach that combines mathematical modeling, quantitative experiments, and microbial genetics. We aim to identify how these mechanisms may evolve under the selective pressure of population expansion, and consequently reinforce or hinder collective motility. In particular, we clarify the role of growth rate and motility in invasive populations.

  8. SIMS: a hybrid method for rapid conformational analysis.

    Directory of Open Access Journals (Sweden)

    Bryant Gipson

    Full Text Available Proteins are at the root of many biological functions, often performing complex tasks as the result of large changes in their structure. Describing the exact details of these conformational changes, however, remains a central challenge for computational biology due the enormous computational requirements of the problem. This has engendered the development of a rich variety of useful methods designed to answer specific questions at different levels of spatial, temporal, and energetic resolution. These methods fall largely into two classes: physically accurate, but computationally demanding methods and fast, approximate methods. We introduce here a new hybrid modeling tool, the Structured Intuitive Move Selector (sims, designed to bridge the divide between these two classes, while allowing the benefits of both to be seamlessly integrated into a single framework. This is achieved by applying a modern motion planning algorithm, borrowed from the field of robotics, in tandem with a well-established protein modeling library. sims can combine precise energy calculations with approximate or specialized conformational sampling routines to produce rapid, yet accurate, analysis of the large-scale conformational variability of protein systems. Several key advancements are shown, including the abstract use of generically defined moves (conformational sampling methods and an expansive probabilistic conformational exploration. We present three example problems that sims is applied to and demonstrate a rapid solution for each. These include the automatic determination of "active" residues for the hinge-based system Cyanovirin-N, exploring conformational changes involving long-range coordinated motion between non-sequential residues in Ribose-Binding Protein, and the rapid discovery of a transient conformational state of Maltose-Binding Protein, previously only determined by Molecular Dynamics. For all cases we provide energetic validations using well

  9. CET exSim: mineral exploration experience via simulation

    Science.gov (United States)

    Wong, Jason C. 13Holden, Eun-Jung 1Kovesi, Peter 1McCuaig, T. Campbell 1Hronsky, Jon

    2013-08-01

    Undercover mineral exploration is a challenging task as it requires understanding of subsurface geology by relying heavily on remotely sensed (i.e. geophysical) data. Cost-effective exploration is essential in order to increase the chance of success using finite budgets. This requires effective decision-making in both the process of selecting the optimum data collection methods and in the process of achieving accuracy during subsequent interpretation. Traditionally, developing the skills, behaviour and practices of exploration decision-making requires many years of experience through working on exploration projects under various geological settings, commodities and levels of available resources. This implies long periods of sub-optimal exploration decision-making, before the necessary experience has been successfully obtained. To address this critical industry issue, our ongoing research focuses on the development of the unique and novel e-learning environment, exSim, which simulates exploration scenarios where users can test their strategies and learn the consequences of their choices. This simulator provides an engaging platform for self-learning and experimentation in exploration decision strategies, providing a means to build experience more effectively. The exSim environment also provides a unique platform on which numerous scenarios and situations (e.g. deposit styles) can be simulated, potentially allowing the user to become virtually familiarised with a broader scope of exploration practices. Harnessing the power of computer simulation, visualisation and an intuitive graphical user interface, the simulator provides a way to assess the user's exploration decisions and subsequent interpretations. In this paper, we present the prototype functionalities in exSim including: simulation of geophysical surveys, follow-up drill testing and interpretation assistive tools.

  10. StandsSIM-MD: a Management Driven forest SIMulator

    Energy Technology Data Exchange (ETDEWEB)

    Barreiro, S.; Rua, J.; Tomé, M.

    2016-07-01

    Aim of the study. The existing stand level forest simulators available in Portugal were not developed with the aim of including up-to-date model versions and were limited in terms of accounting for forest management. The simulators’ platform, sIMfLOR was recently created to implement different growth models with a common philosophy. The objective was developing one easily-updatable, user-friendly, forest management and climate change sensitive simulator capable of projecting growth for the main tree species in Portugal. Area of the study: Portugal. Material and methods: The new simulator was programmed in a modular form consisting of several modules. The growth module integrates different forest growth and yield models (empirical and process-based) for the main wood production tree species in Portugal (eucalypt, umbrella and maritime pines); whereas the management module drives the growth projections along the planning horizon according to a range of forest management approaches and climate (at present only available for eucalypt). Main results: The main result is the StandsSIM-MD Management Driven simulator that overcomes the limitations of the existing stand level simulators. It is a step forward when compared to the models currently available in the sIMfLOR platform covering more tree species, stand structures and stand compositions. It is focused on end-users and it is based on similar concepts regarding the generation of required inputs and generated outputs. Research highlights: Forest Management Driven simulations approach. Multiple Prescriptions-Per-Stand functionality. StandsSIM-MD can be used to support landowners decisions on stand forest management. StandsSIM-MD simulations at regional level can be combined with optimization routines. (Author)

  11. StandsSIM-MD: a Management Driven forest SIMulator

    Directory of Open Access Journals (Sweden)

    Susana Barreiro

    2016-07-01

    Full Text Available Aim of the study: The existing stand level forest simulators available in Portugal were not developed with the aim of including up-to-date model versions and were limited in terms of accounting for forest management. The simulators’ platform, sIMfLOR was recently created to implement different growth models with a common philosophy. The objective was developing one easily-updatable, user-friendly, forest management and climate change sensitive simulator capable of projecting growth for the main tree species in Portugal. Area of the study: Portugal. Material and methods: The new simulator was programmed in a modular form consisting of several modules. The growth module integrates different forest growth and yield models (empirical and process-based for the main wood production tree species in Portugal (eucalypt, umbrella and maritime pines; whereas the management module drives the growth projections along the planning horizon according to a range of forest management approaches and climate (at present only available for eucalypt. Main results: The main result is the StandsSIM-MD Management Driven simulator that overcomes the limitations of the existing stand level simulators. It is a step forward when compared to the models currently available in the sIMfLOR platform covering more tree species, stand structures and stand compositions. It is focused on end-users and it is based on similar concepts regarding the generation of required inputs and generated outputs. Research highlights: -          Forest Management Driven simulations approach -          Multiple Prescriptions-Per-Stand functionality -          StandsSIM-MD can be used to support landowners decisions on stand forest management -          StandsSIM-MD simulations at regional level can be combined with optimization routines Keywords: Forest simulator, Forest Management Approaches; StandsSIM-MD; forest management.

  12. The core competencies of James Marion Sims, MD.

    Science.gov (United States)

    Straughn, J Michael; Gandy, Roy E; Rodning, Charles B

    2012-07-01

    The concept of core competencies in graduate medical education was introduced by the Accreditation Council for Graduate Medical Education of the American Medical Association to semiquantitatively assess the professional performance of students, residents, practitioners, and faculty. Many aspects of the career of J. Marion Sims, MD, are exemplary of those core competencies: MEDICAL KNOWLEDGE: Author of the first American textbook related to gynecology. MEDICAL CARE: Innovator of the Sims' Vaginal Speculum, Sims' Position, Sims' Test, and vesico-/rectovaginal fistulorrhaphy; advocated abdominal exploration for penetrating wounds; performed the first cholecystostomy. PROFESSIONALISM: Served as President of the New York Academy of Medicine, the American Medical Association, and the American Gynecologic Society. INTERPERSONAL RELATIONSHIPS/COMMUNICATION: Cared for the indigent, hearthless, indentured, disenfranchised; served as consulting surgeon to the Empress Eugénie (France), the Duchess of Hamilton (Scotland), the Empress of Austria, and other royalty of the aristocratic Houses of Europe; accorded the National Order of the Legion of Honor. PRACTICE-BASED LEARNING: Introduction of silver wire sutures; adoption of the principles of asepsis/antisepsis; adoption of the principles of general anesthesia. SYSTEMS-BASED PRACTICE: Established the Woman's Hospital, New York City, New York, the predecessor of the Memorial Sloan-Kettering Center for the Treatment of Cancer and Allied Diseases; organized the Anglo-American Ambulance Corps under the patronage of Napoleon III. What led him to a life of clinical and humanitarian service? First, he was determined to succeed. His formal medical/surgical education was perhaps the best available to North Americans during that era. Second, he was courageous in experimentation and innovation, applying new developments in operative technique, asepsis/antisepsis, and general anesthesia. Third, his curiosity was not burdened by rigid

  13. SIM(1)-VSR Maxwell-Chern-Simons electrodynamics

    Science.gov (United States)

    Bufalo, R.

    2016-06-01

    In this paper we propose a very special relativity (VSR)-inspired generalization of the Maxwell-Chern-Simons (MCS) electrodynamics. This proposal is based upon the construction of a proper study of the SIM (1)-VSR gauge-symmetry. It is shown that the VSR nonlocal effects present a significant and healthy departure from the usual MCS theory. The classical dynamics is analysed in full detail, by studying the solution for the electric field and static energy for this configuration. Afterwards, the interaction energy between opposite charges is derived and we show that the VSR effects play an important part in obtaining a (novel) finite expression for the static potential.

  14. SIM$(1)$--VSR Maxwell-Chern-Simons electrodynamics

    CERN Document Server

    Bufalo, R

    2016-01-01

    In this paper we propose a very special relativity (VSR)-inspired generalization of the Maxwell-Chern-Simons (MCS) electrodynamics. This proposal is based upon the construction of a proper study of the SIM$(1)$--VSR gauge-symmetry. It is shown that the VSR nonlocal effects present a significant and health departure from the usual MCS theory. The classical dynamics is analysed in full detail, by studying the solution for the electric field and static energy for this configuration. Afterwards, the interaction energy between opposite charges are derived and we show that the VSR effects play an important part in obtaining a (novel) finite expression for the static potential.

  15. Astrometric imaging of crowded stellar fields with only two SIM pointings

    CERN Document Server

    Dalal, N; Dalal, Neal; Griest, Kim

    2001-01-01

    The Space Interferometry Mission (SIM) will observe sources in crowded fields. Recent work has shown that source crowding can induce significant positional errors in SIM's astrometric measurements, even for targets many magnitudes brighter than all other crowding sources. Here we investigate whether the spectral decomposition of the fringe pattern may be used to disentangle the overlapping fringes from multiple blended sources, effectively by performing synthesis imaging with two baselines. We find that spectrally dispersed fringes enable SIM to identify and localize a limited number of field sources quite robustly, thereby removing their effect from SIM astrometry and reducing astrometry errors to near photon noise levels. We simulate SIM measurements of the LMC, and show that (a) SIM astrometry will not be corrupted by blending and (b) extremely precise imaging of mildly crowded fields may be performed using only two orthogonal baseline orientations, allowing microarcsecond positional measurements. We lastl...

  16. Elemental and isotopic imaging of biological samples using NanoSIMS.

    Science.gov (United States)

    Kilburn, Matt R; Clode, Peta L

    2014-01-01

    With its low detection limits and the ability to analyze most of the elements in the periodic table, secondary ion mass spectrometry (SIMS) represents one of the most versatile in situ analytical techniques available, and recent developments have resulted in significant advantages for the use of imaging mass spectrometry in biological and biomedical research. Increases in spatial resolution and sensitivity allow detailed interrogation of samples at relevant scales and chemical concentrations. Advances in dynamic SIMS, specifically with the advent of NanoSIMS, now allow the tracking of stable isotopes within biological systems at subcellular length scales, while static SIMS combines subcellular imaging with molecular identification. In this chapter, we present an introduction to the SIMS technique, with particular reference to NanoSIMS, and discuss its application in biological and biomedical research.

  17. Coordination of glioblastoma cell motility by PKCι

    Directory of Open Access Journals (Sweden)

    Baldwin R Mitchell

    2010-09-01

    Full Text Available Abstract Background Glioblastoma is one of the deadliest forms of cancer, in part because of its highly invasive nature. The tumor suppressor PTEN is frequently mutated in glioblastoma and is known to contribute to the invasive phenotype. However the downstream events that promote invasion are not fully understood. PTEN loss leads to activation of the atypical protein kinase C, PKCι. We have previously shown that PKCι is required for glioblastoma cell invasion, primarily by enhancing cell motility. Here we have used time-lapse videomicroscopy to more precisely define the role of PKCι in glioblastoma. Results Glioblastoma cells in which PKCι was either depleted by shRNA or inhibited pharmacologically were unable to coordinate the formation of a single leading edge lamellipod. Instead, some cells generated multiple small, short-lived protrusions while others generated a diffuse leading edge that formed around the entire circumference of the cell. Confocal microscopy showed that this behavior was associated with altered behavior of the cytoskeletal protein Lgl, which is known to be inactivated by PKCι phosphorylation. Lgl in control cells localized to the lamellipod leading edge and did not associate with its binding partner non-muscle myosin II, consistent with it being in an inactive state. In PKCι-depleted cells, Lgl was concentrated at multiple sites at the periphery of the cell and remained in association with non-muscle myosin II. Videomicroscopy also identified a novel role for PKCι in the cell cycle. Cells in which PKCι was either depleted by shRNA or inhibited pharmacologically entered mitosis normally, but showed marked delays in completing mitosis. Conclusions PKCι promotes glioblastoma motility by coordinating the formation of a single leading edge lamellipod and has a role in remodeling the cytoskeleton at the lamellipod leading edge, promoting the dissociation of Lgl from non-muscle myosin II. In addition PKCι is required

  18. Pattern formation mechanisms in motility mutants of Myxococcus xanthus

    CERN Document Server

    Starruss, Joern; Jakovljevic, Vladimir; Sogaard-Andersen, Lotte; Deutsch, Andreas; Baer, Markus

    2016-01-01

    Formation of spatial patterns of cells is a recurring theme in biology and often depends on regulated cell motility. Motility of M. xanthus depends on two motility machineries: the S-engine and A-engine. Moving M. xanthus cells can organize into spreading colonies or spore-filled fruiting bodies depending on their nutritional status. To understand these two pattern formation processes and the contributions by the two motility machineries, as well as cell reversal, we analyze spatial self-organization in 3 strains: i) a mutant that moves unidirectionally without reversing by the A-motility system only, ii) a unidirectional mutant that is also equipped with the S-motility system, and iii) the wild-type that, in addition to the two motility systems, reverses its direction of movement. The mutant moving by the A-engine illustrates that collective motion in the form of large moving clusters can arise in gliding bacteria due to steric interactions of the rod-shaped cells, without the need of invoking any biochemica...

  19. SIMS and NanoSIMS analyses of Mesoproterozoic individual microfossils indicating continuous oxygen-producing photosynthesis in Proterozoic Ocean

    Science.gov (United States)

    Peng, X.; Guo, Z.; House, C. H.; Chen, S.; Ta, K.

    2015-12-01

    Well-preserved microfossils in the stromatolites from the Gaoyuzhuang Formation (~1500Ma), which is younger than the Gunflint Formation (~1880Ma) and older than the Bitter Springs Formation (~850Ma), may play key roles in systematizing information about the evolution of early life and environmental changes in the Proterozoic Ocean. Here, a combination of light microscopy (LM), scanning electron microscopy (SEM), focused ion beam (FIB), nano-scale secondary ion mass spectrometry (NanoSIMS) and secondary ion mass spectrometry (SIMS) were employed to characterize the morphology, elemental distributions and carbon isotope values of individual microfossils in the stromatolites from the Gaoyuahzuang Formation. Light microscopy analyses show that abundant filamentous and coccoid microfossils are exceptionally well preserved in chert. NanoSIMS analyses show that metabolically important elements such as 12C-, 13C-, 12C14N-, 32S-, and 34S- are concentrated in these microfossils and that the variations in the concentrations of these elements are similar, establishing the elemental distributions in incontestably biogenic microstructures. Carbon isotope (δ13C) values of individual microfossils range from -32.2‰ ± 0.9‰ to -23.3‰ ± 1.0‰ (weighted mean= -28.9‰ ± 0.1‰), consistent with carbon fixation via the Calvin cycle. The elevated δ13C values of the microfossils from Early-, Meso- to Late Proterozoic Era, possibly indicate decreasing CO2 and increasing O2 concentrations in the Proterozoic atmosphere. Our results, for the first time, provided the element distributions and cell specific carbon isotope values on convincing Mesoproterozoic cyanobacterial fossils, supporting continuous oxygen-producing photosynthesis in the Proterozoic Ocean.

  20. Exopolysaccharide-independent social motility of Myxococcus xanthus.

    Directory of Open Access Journals (Sweden)

    Wei Hu

    Full Text Available Social motility (S motility, the coordinated movement of large cell groups on agar surfaces, of Myxococcus xanthus requires type IV pili (TFP and exopolysaccharides (EPS. Previous models proposed that this behavior, which only occurred within cell groups, requires cycles of TFP extension and retraction triggered by the close interaction of TFP with EPS. However, the curious observation that M. xanthus can perform TFP-dependent motility at a single-cell level when placed onto polystyrene surfaces in a highly viscous medium containing 1% methylcellulose indicated that "S motility" is not limited to group movements. In an apparent further challenge of the previous findings for S motility, mutants defective in EPS production were found to perform TFP-dependent motility on polystyrene surface in methylcellulose-containing medium. By exploring the interactions between pilin and surface materials, we found that the binding of TFP onto polystyrene surfaces eliminated the requirement for EPS in EPS(- cells and thus enabled TFP-dependent motility on a single cell level. However, the presence of a general anchoring surface in a viscous environment could not substitute for the role of cell surface EPS in group movement. Furthermore, EPS was found to serve as a self-produced anchoring substrate that can be shed onto surfaces to enable cells to conduct TFP-dependent motility regardless of surface properties. These results suggested that in certain environments, such as in methylcellulose solution, the cells could bypass the need for EPS to anchor their TPF and conduct single-cell S motility to promote exploratory movement of colonies over new specific surfaces.

  1. Alternative Liquid Fuels Simulation Model (AltSim).

    Energy Technology Data Exchange (ETDEWEB)

    Baker, Arnold Barry; Williams, Ryan (Hobart and William Smith Colleges, Geneva, NY); Drennen, Thomas E.; Klotz, Richard (Hobart and William Smith Colleges, Geneva, NY)

    2007-10-01

    The Alternative Liquid Fuels Simulation Model (AltSim) is a high-level dynamic simulation model which calculates and compares the production costs, carbon dioxide emissions, and energy balances of several alternative liquid transportation fuels. These fuels include: corn ethanol, cellulosic ethanol, biodiesel, and diesels derived from natural gas (gas to liquid, or GTL) and coal (coal to liquid, or CTL). AltSim allows for comprehensive sensitivity analyses on capital costs, operation and maintenance costs, renewable and fossil fuel feedstock costs, feedstock conversion efficiency, financial assumptions, tax credits, CO{sub 2} taxes, and plant capacity factor. This paper summarizes the preliminary results from the model. For the base cases, CTL and cellulosic ethanol are the least cost fuel options, at $1.60 and $1.71 per gallon, respectively. Base case assumptions do not include tax or other credits. This compares to a $2.35/gallon production cost of gasoline at September, 2007 crude oil prices ($80.57/barrel). On an energy content basis, the CTL is the low cost alternative, at $12.90/MMBtu, compared to $22.47/MMBtu for cellulosic ethanol. In terms of carbon dioxide emissions, a typical vehicle fueled with cellulosic ethanol will release 0.48 tons CO{sub 2} per year, compared to 13.23 tons per year for coal to liquid.

  2. The influenza pandemic preparedness planning tool InfluSim

    Directory of Open Access Journals (Sweden)

    Duerr Hans-Peter

    2007-03-01

    Full Text Available Abstract Background Planning public health responses against pandemic influenza relies on predictive models by which the impact of different intervention strategies can be evaluated. Research has to date rather focused on producing predictions for certain localities or under specific conditions, than on designing a publicly available planning tool which can be applied by public health administrations. Here, we provide such a tool which is reproducible by an explicitly formulated structure and designed to operate with an optimal combination of the competing requirements of precision, realism and generality. Results InfluSim is a deterministic compartment model based on a system of over 1,000 differential equations which extend the classic SEIR model by clinical and demographic parameters relevant for pandemic preparedness planning. It allows for producing time courses and cumulative numbers of influenza cases, outpatient visits, applied antiviral treatment doses, hospitalizations, deaths and work days lost due to sickness, all of which may be associated with economic aspects. The software is programmed in Java, operates platform independent and can be executed on regular desktop computers. Conclusion InfluSim is an online available software http://www.influsim.info which efficiently assists public health planners in designing optimal interventions against pandemic influenza. It can reproduce the infection dynamics of pandemic influenza like complex computer simulations while offering at the same time reproducibility, higher computational performance and better operability.

  3. Training of basic laparoscopy skills on SimSurgery SEP.

    Science.gov (United States)

    Buzink, Sonja N; Goossens, Richard H M; De Ridder, Huib; Jakimowicz, Jack J

    2010-01-01

    The aim of this study was to assess the performance curve for novices training in bimanual tissue manipulation and angled laparoscope navigation, and compare those performances with the performances of experienced laparoscopic surgeons. The Camera Navigation task with a 30 degrees angled laparoscope and the Place Arrow task of the new SimSurgery SEP virtual reality simulator were used. Fourteen medical trainees (no laparoscopy experience) performed four training sessions within one week, including 15 repetitions of each task in total. The experienced participants (>50 procedures & familiar with angled laparoscope) performed each task twice. The performance on both tasks by the novices improved significantly over the training sessions. The experienced participants performed both tasks significantly better than the novices in repetition 3. After repetition 15, the performances of the novices on both tasks were of the same level as the performances of the experienced participants. By training on SimSurgery SEP, medical trainees can extensively improve their skills in navigation with 30 degrees angled laparoscope and bimanual tissue manipulation. Further research should focus on the transfer of skills acquired on the simulator to the clinical setting. Knowledge on proficiency thresholds and training end-points for pre-clinical criterion-based training of different laparoscopic tasks also needs to be extended.

  4. Multimodal image fusion with SIMS: Preprocessing with image registration.

    Science.gov (United States)

    Tarolli, Jay Gage; Bloom, Anna; Winograd, Nicholas

    2016-06-14

    In order to utilize complementary imaging techniques to supply higher resolution data for fusion with secondary ion mass spectrometry (SIMS) chemical images, there are a number of aspects that, if not given proper consideration, could produce results which are easy to misinterpret. One of the most critical aspects is that the two input images must be of the same exact analysis area. With the desire to explore new higher resolution data sources that exists outside of the mass spectrometer, this requirement becomes even more important. To ensure that two input images are of the same region, an implementation of the insight segmentation and registration toolkit (ITK) was developed to act as a preprocessing step before performing image fusion. This implementation of ITK allows for several degrees of movement between two input images to be accounted for, including translation, rotation, and scale transforms. First, the implementation was confirmed to accurately register two multimodal images by supplying a known transform. Once validated, two model systems, a copper mesh grid and a group of RAW 264.7 cells, were used to demonstrate the use of the ITK implementation to register a SIMS image with a microscopy image for the purpose of performing image fusion.

  5. Analysis of TOF-SIMS spectra from fullerene compounds

    Energy Technology Data Exchange (ETDEWEB)

    Kato, N. [Department of Materials and Life Science, Faculty of Science and Technology, Seikei University, 3-3-1, Kichijoji-Kitamachi, Musashino-shi, Tokyo 180-8633 (Japan)], E-mail: kato-nobuhiko@st.seikei.ac.jp; Yamashita, Y. [Department of Materials and Life Science, Faculty of Science and Technology, Seikei University, 3-3-1, Kichijoji-Kitamachi, Musashino-shi, Tokyo 180-8633 (Japan); Iida, S.; Sanada, N. [ULVAC-PHI, Inc., 370 Enzo, Chigasaki, Kanagawa 253-0084 (Japan); Kudo, M. [Department of Materials and Life Science, Faculty of Science and Technology, Seikei University, 3-3-1, Kichijoji-Kitamachi, Musashino-shi, Tokyo 180-8633 (Japan)

    2008-12-15

    We analyzed TOF-SIMS spectra obtained from three different size of fullerenes (C{sub 60}, C{sub 70} and C{sub 84}) by using Ga{sup +}, Au{sup +} and Au{sub 3}{sup +} primary ion beams and investigated the fragmentation patterns, the enhancement of secondary ion yields and the restraint of fragmentation by using cluster primary ion beams compared with monoatomic primary ion beams. In the TOS-SIMS spectra from C{sub 70} and C{sub 84}, it was found that a fragment ion, identified as C{sub 60}{sup +} (m/z = 720), showed a relatively high intensity compared with that of other fragment ions related to C{sub 2} depletion. It was also found that the Au{sub 3}{sup +} bombardment caused intensity enhancement of intact molecules (C{sub 60}{sup +}, C{sub 70}{sup +} and C{sub 84}{sup +}) and restrained the fragmentation due to C{sub 2} depletion.

  6. MetaSim: a sequencing simulator for genomics and metagenomics.

    Directory of Open Access Journals (Sweden)

    Daniel C Richter

    Full Text Available BACKGROUND: The new research field of metagenomics is providing exciting insights into various, previously unclassified ecological systems. Next-generation sequencing technologies are producing a rapid increase of environmental data in public databases. There is great need for specialized software solutions and statistical methods for dealing with complex metagenome data sets. METHODOLOGY/PRINCIPAL FINDINGS: To facilitate the development and improvement of metagenomic tools and the planning of metagenomic projects, we introduce a sequencing simulator called MetaSim. Our software can be used to generate collections of synthetic reads that reflect the diverse taxonomical composition of typical metagenome data sets. Based on a database of given genomes, the program allows the user to design a metagenome by specifying the number of genomes present at different levels of the NCBI taxonomy, and then to collect reads from the metagenome using a simulation of a number of different sequencing technologies. A population sampler optionally produces evolved sequences based on source genomes and a given evolutionary tree. CONCLUSIONS/SIGNIFICANCE: MetaSim allows the user to simulate individual read datasets that can be used as standardized test scenarios for planning sequencing projects or for benchmarking metagenomic software.

  7. Chemical Imaging of the Cell Membrane by NanoSIMS

    Energy Technology Data Exchange (ETDEWEB)

    Weber, P K; Kraft, M L; Frisz, J F; Carpenter, K J; Hutcheon, I D

    2010-02-23

    The existence of lipid microdomains and their role in cell membrane organization are currently topics of great interest and controversy. The cell membrane is composed of a lipid bilayer with embedded proteins that can flow along the two-dimensional surface defined by the membrane. Microdomains, known as lipid rafts, are believed to play a central role in organizing this fluid system, enabling the cell membrane to carry out essential cellular processes, including protein recruitment and signal transduction. Lipid rafts are also implicated in cell invasion by pathogens, as in the case of the HIV. Therefore, understanding the role of lipid rafts in cell membrane organization not only has broad scientific implications, but also has practical implications for medical therapies. One of the major limitations on lipid organization research has been the inability to directly analyze lipid composition without introducing artifacts and at the relevant length-scales of tens to hundreds of nanometers. Fluorescence microscopy is widely used due to its sensitivity and specificity to the labeled species, but only the labeled components can be observed, fluorophores can alter the behavior of the lipids they label, and the length scales relevant to imaging cell membrane domains are between that probed by fluorescence resonance energy transfer (FRET) imaging (<10 nm) and the diffraction limit of light. Topographical features can be imaged on this length scale by atomic force microscopy (AFM), but the chemical composition of the observed structures cannot be determined. Immuno-labeling can be used to study the distribution of membrane proteins at high resolution, but not lipid composition. We are using imaging mass spectrometry by secondary ion mass spectrometry (SIMS) in concert with other high resolution imaging methods to overcome these limitations. The experimental approach of this project is to combine molecule-specific stable isotope labeling with high-resolution SIMS using a

  8. Eye Motility Alterations in Retinitis Pigmentosa

    Directory of Open Access Journals (Sweden)

    Raffaele Migliorini

    2015-01-01

    Full Text Available Purpose. We evaluated a sample of individuals with retinitis pigmentosa (RP with the aim of assessing the presence or absence of ocular motility (OM disorders. Materials and Methods. We included 23 out of the 25 individuals from the sample (9 females and 14 males with an average visual acuity of 6/10. Results. The cover test about the vertical deviation in near distance showed an r/l in 3.45% and an l/r in 6.9%. The assessment of OM showed that 39.1% of the sample had a severe hyperfunction of the IO of the right eye and a severe hyperfunction (34.5% of the SO of the left eye; 21.8% had a moderate hypofunction of right SO with a moderate percentage of hypofunction of 17.5% for the SO of the left eye; 30.5%, however, showed a serious hypofunction of the SR of both eyes; 21.7% of the sample showed a hyperfunction in both eyes of the IR. Conclusion. This alteration, however, is not attributable to either a high refractive defect (medium-low myopia: −1 diopter ±3 SD or to a severely impaired binocular vision (visual acuity, motor fusion, and stereopsis are normal or within a range of values commonly accepted. Therefore, the disorders of OM lead to a genetic origin.

  9. Eye Motility Alterations in Retinitis Pigmentosa.

    Science.gov (United States)

    Migliorini, Raffaele; Comberiati, Anna Maria; Galeoto, Giovanni; Fratipietro, Manuela; Arrico, Loredana

    2015-01-01

    Purpose. We evaluated a sample of individuals with retinitis pigmentosa (RP) with the aim of assessing the presence or absence of ocular motility (OM) disorders. Materials and Methods. We included 23 out of the 25 individuals from the sample (9 females and 14 males) with an average visual acuity of 6/10. Results. The cover test about the vertical deviation in near distance showed an r/l in 3.45% and an l/r in 6.9%. The assessment of OM showed that 39.1% of the sample had a severe hyperfunction of the IO of the right eye and a severe hyperfunction (34.5%) of the SO of the left eye; 21.8% had a moderate hypofunction of right SO with a moderate percentage of hypofunction of 17.5% for the SO of the left eye; 30.5%, however, showed a serious hypofunction of the SR of both eyes; 21.7% of the sample showed a hyperfunction in both eyes of the IR. Conclusion. This alteration, however, is not attributable to either a high refractive defect (medium-low myopia: -1 diopter ±3 SD) or to a severely impaired binocular vision (visual acuity, motor fusion, and stereopsis are normal or within a range of values commonly accepted). Therefore, the disorders of OM lead to a genetic origin.

  10. Shear alters motility of Escherichia coli

    Science.gov (United States)

    Molaei, Mehdi; Jalali, Maryam; Sheng, Jian

    2013-11-01

    Understanding of locomotion of microorganisms in shear flows drew a wide range of interests in microbial related topics such as biological process including pathogenic infection and biophysical interactions like biofilm formation on engineering surfaces. We employed microfluidics and digital holography microscopy to study motility of E. coli in shear flows. We controlled the shear flow in three different shear rates: 0.28 s-1, 2.8 s-1, and 28 s-1 in a straight channel with the depth of 200 μm. Magnified holograms, recorded at 15 fps with a CCD camera over more than 20 minutes, are analyzed to obtain 3D swimming trajectories and subsequently used to extract shear responses of E.coli. Thousands of 3-D bacterial trajectories are tracked. The change of bacteria swimming characteristics including swimming velocity, reorientation, and dispersion coefficient are computed directly for individual trajectory and ensemble averaged over thousands of realizations. The results show that shear suppresses the bacterial dispersions in bulk but promote dispersions near the surface contrary to those in quiescent flow condition. Ongoing analyses are focusing to quantify effect of shear rates on tumbling frequency and reorientation of cell body, and its implication in locating the hydrodynamic mechanisms for shear enhanced angular scattering. NIH, NSF, GoMRI.

  11. Morfoanatomia de folhas e caules de Passiflora edulis Sims, Passifloraceae Leaf and stem morphoanatomy of Passiflora edulis Sims, Passifloraceae

    Directory of Open Access Journals (Sweden)

    Josseara Beraldo

    2010-05-01

    Full Text Available Passiflora edulis Sims, espécie vegetal empregada na medicina popular e amplamente cultivada no território nacional, tem suas folhas e seus caules, muitas vezes utilizados como adulterante de amostras comerciais da droga vegetal oficializada no país também conhecida como maracujá, Passiflora alata Curtis. Caracteres morfoanatômicos de folhas e de caules de P. edulis, foram descritos e documentados. Dentre os caracteres auxiliares na distinção entre a droga oficial e os órgãos aéreos de P. edulis podem-se destacar o contorno da lâmina foliar, a forma da nervura mediana em secção transversal, o número e a localização de nectários extraflorais e, o indumentoPassiflora edulis Sims, vegetal species employed in the Brazilian traditional medicine and broadly cultivated across its territory, has its leaves and stems often used as an adulterant for commercial samples of the crude drug Passiflora alata Curtis, officially known in Brazil as "maracujá". Morphoanatomic data from leaves and stems in P. edulis were described and documented. Amongst these characteristics, the shape of the foliar blade, the shape of the midrib in transverse section, the number and the location of the extrafloral nectaries and the indumentum are all emphasized.

  12. Surface motility and associated surfactant production in Agrobacterium vitis

    National Research Council Canada - National Science Library

    Süle, S; Cursino, L; Zheng, D; Hoch, H C; Burr, T J

    2009-01-01

    Agrobacterium vitis is the causal agent of crown gall of grapevine. Surface motility (swarming), an important mechanism for bacterial colonization of new environments and a previously unknown behaviour of Ag...

  13. Motility and peristaltic flow in maintaining microbiome populations

    Science.gov (United States)

    Mirbagheri, Seyed Amir; Fu, Henry C.

    2016-11-01

    Bacteria are an important component of the microbiome in the digestive tract, and must be able to maintain their population despite the fact that the contents of the intestines are constantly flowing towards evacuation. Many bacteria accomplish this by colonizing the surfaces of the intestines where flows diminish, but some species live in the lumen. We attempt to address whether swimming motility of these species plays an important role in maintaining bacterial population in the face of peristaltic pumping out of the intestine. Using a two-dimensional model of peristaltic flows induced by small-amplitude traveling waves we examine the Lagrangian trajectories of passive bacteria as well as motile bacteria, which are treated as Brownian particles undergoing enhanced diffusion due to the bacteria's run-and-tumble motility. We examine how the densities of growing populations of bacteria depend on the combination of motility and peristaltic flow.

  14. The Hydrogen Futures Simulation Model (H[2]Sim) technical description.

    Energy Technology Data Exchange (ETDEWEB)

    Jones, Scott A.; Kamery, William; Baker, Arnold Barry; Drennen, Thomas E.; Lutz, Andrew E.; Rosthal, Jennifer Elizabeth

    2004-10-01

    Hydrogen has the potential to become an integral part of our energy transportation and heat and power sectors in the coming decades and offers a possible solution to many of the problems associated with a heavy reliance on oil and other fossil fuels. The Hydrogen Futures Simulation Model (H2Sim) was developed to provide a high level, internally consistent, strategic tool for evaluating the economic and environmental trade offs of alternative hydrogen production, storage, transport and end use options in the year 2020. Based on the model's default assumptions, estimated hydrogen production costs range from 0.68 $/kg for coal gasification to as high as 5.64 $/kg for centralized electrolysis using solar PV. Coal gasification remains the least cost option if carbon capture and sequestration costs ($0.16/kg) are added. This result is fairly robust; for example, assumed coal prices would have to more than triple or the assumed capital cost would have to increase by more than 2.5 times for natural gas reformation to become the cheaper option. Alternatively, assumed natural gas prices would have to fall below $2/MBtu to compete with coal gasification. The electrolysis results are highly sensitive to electricity costs, but electrolysis only becomes cost competitive with other options when electricity drops below 1 cent/kWhr. Delivered 2020 hydrogen costs are likely to be double the estimated production costs due to the inherent difficulties associated with storing, transporting, and dispensing hydrogen due to its low volumetric density. H2Sim estimates distribution costs ranging from 1.37 $/kg (low distance, low production) to 3.23 $/kg (long distance, high production volumes, carbon sequestration). Distributed hydrogen production options, such as on site natural gas, would avoid some of these costs. H2Sim compares the expected 2020 per mile driving costs (fuel, capital, maintenance, license, and registration) of current technology internal combustion engine (ICE

  15. Cell motility as persistent random motion: Theories from experiments

    DEFF Research Database (Denmark)

    Selmeczi, D.; Mosler, S.; Hagedorn, P.H.

    2005-01-01

    Experimental time series for trajectories of motile cells may contain so much information that a systematic analysis will yield cell-type- specific motility models. Here we demonstrate how, using human keratinocytes and fibroblasts as examples. The two resulting models reflect the cells' different...... roles in the organism, it seems, and show that a cell has a memory of past velocities. They also suggest how to distinguish quantitatively between various surfaces' compatibility with the two cell types....

  16. Spontaneous motility of the pig oviduct in vitro.

    Science.gov (United States)

    Rodriguez-Martinez, H; Einarsson, S; Larsson, B; Akusu, M; Settergren, I

    1982-02-01

    The spontaneous motility of the pig oviductal isthmus and ampulla during the estrous cycle was recorded in vitro using an intraluminally located pressure microtransducer. A very high motility was recorded in the isthmic portion throughout the whole cycle, while the ampulla revealed an active pattern during the periovulatory period only. In proestrus the tubal pattern in both segments consisted of regular contractions of high frequency, increasing in amplitude when approaching estrus. During heat the motility changed abruptly, and was characterized by the presence of regular strong waves in the two tubal segments. This pattern might contribute to the transport of gametes to the fertilization site. After ovulation, during the time when ova are retained in the oviducts, the high preovulatory peaks disappeared. The isthmic pattern showed regular phasic contractions of high frequency and amplitude, while the ampullar motility was low. The ova are arrested at the level of the ampullar-isthmic junction (AIJ) during this period. During the short period when eggs are passing to the uterus, the ampullar motility remained low, while the isthmus showed a very active pattern with the presence of heavy contractions. This suggests the active participation of the isthmus in ovum descent. During the rest of the luteal phase, the ampulla maintained its stable low motility, while the isthmus showed an irregular although still active pattern characterized by heavy outbursts of increased activity superimposed on a consistent basal contractility.

  17. Upper gastrointestinal motility: prenatal development and problems in infancy.

    Science.gov (United States)

    Singendonk, Maartje M J; Rommel, Nathalie; Omari, Taher I; Benninga, Marc A; van Wijk, Michiel P

    2014-09-01

    Deglutition, or swallowing, refers to the process of propulsion of a food bolus from the mouth into the stomach and involves the highly coordinated interplay of swallowing and breathing. At 34 weeks gestational age most neonates are capable of successful oral feeding if born at this time; however, the maturation of respiration is still in progress at this stage. Infants can experience congenital and developmental pharyngeal and/or gastrointestinal motility disorders, which might manifest clinically as gastro-oesophageal reflux (GER) symptoms, feeding difficulties and/or refusal, choking episodes and airway changes secondary to micro or overt aspiration. These problems might lead to impaired nutritional intake and failure to thrive. These gastrointestinal motility disorders are mostly classified according to the phase of swallowing in which they occur, that is, the oral preparatory, oral, pharyngeal and oesophageal phases. GER is a common phenomenon in infancy and is referred to as GERD when it causes troublesome complications. GER is predominantly caused by transient relaxation of the lower oesophageal sphincter. In oesophageal atresia, oesophageal motility disorders develop in almost all patients after surgery; however, a congenital origin of disordered motility has also been proposed. This Review highlights the prenatal development of upper gastrointestinal motility and describes the most common motility disorders that occur in early infancy.

  18. Guaifenesin and increased sperm motility: a preliminary case report

    Directory of Open Access Journals (Sweden)

    Gary Means

    2010-12-01

    Full Text Available Gary Means1, Cristóbal S Berry-Cabán2, Kurt Hammermeuller11Department of Family Medicine, 2Department of Research, Womack Army Medical Center, Fort Bragg, NC, USABackground: A review of the literature and an extensive Medline search revealed that this is the first case report of the use of guaifenesin to increase sperm motility.Case: A 32-year-old male presented for an infertility evaluation. He reported an inability to conceive with his wife after 18 months of unprotected intercourse. A semen analysis was performed that included spermatozoa count, liquefaction, morphology, motility, viscosity and volume. Initial results of the semen analysis demonstrated low sperm count and motility. The provider offered treatment with guaifenesin 600 mg extended release tablets twice daily. Two months after guaifenesin therapy the semen analysis was repeated that demonstrated marked improvement in both total sperm count and motility.Conclusion: Evidence for the effectiveness of guaifenesin is almost entirely anecdotal. Given the mechanism of action of guaifenesin, it is not clear from this case why the patient demonstrated such a large improvement in both sperm count and motility. Additional studies of the effects of guaifenesin on male fertility could yield information of the medication's effect on men with normal or decreased total sperm counts.Keywords: sperm motility, guaifenesin, infertility, male pregnancy

  19. Role of Social Motility in Facilitating Collective Motion of Myxobacteria

    Science.gov (United States)

    Wu, Yilin; Chen, Nan; Rissler, Matthew; Jiang, Yi; Kaiser, Dale; Alber, Mark

    2007-03-01

    Social motility is a unique form of behavior exhibited by a wide range of bacteria, including most pathogens that cause plant and animal disease. It is operated by type IV pili that attach to other cells' surfaces and pull; the retracting force pulls the cell forward. Experiments have demonstrated that social motility is important for the collective motion of bacteria colonies, and it facilitates the colonization of pathogens in hosts. We use a cell-based model to study the role of social motility in swarming of bacteria colonies. Mycococcus xathus, a species of myxobacteria, is our model bacteria because it exhibits typical social motility and has been well studied. Our simulation results suggest that social motility has an effect on alignment of neighboring cells, resulting in a highly ordered collective motion. We also show that social motility can significantly improve the swarming efficiency of bacteria. We track GFP labeled Mycococcus xathus cell cultures and derive model parameters from the cell motion data. Our work may shed light on the infection process of many diseases.

  20. Migration of ions in cement paste as studied by SIMS

    Energy Technology Data Exchange (ETDEWEB)

    Prince, K.E.; Aldridge, L.P. [Australian Nuclear Science and Technology Organisation (ANSTO), Lucas Heights, NSW (Australia); Rougeron, P. [Electricite de France Direction des Etudes et Recherches, Les Renardiers (France)

    1998-06-01

    Cement is often used to condition and encapsulate low level radioactive waste before it is disposed of in a repository. Ground water can attack these waste-forms by transporting aggressive ions into the cement paste and by removing radioactive ions from the paste. The extent of the attack will be governed by the diffusion of the ions in the cement paste. In this study we examine the migration of aggressive carbonate ions and inactive Cs and Sr through cement pastes. The use of SIMS for establishing the penetration depths and diffusion profiles for Cs and Sr in cement will be explored. The penetration profiles of Cs and Sr in a non-zeolite cement paste were examined and compared to those of a paste made with zeolite. The effects of the non-homogeneous nature of the cement was most pronounced in the study of the zeolite rich cement; Cs being preferentially accumulated in the zeolite material. (authors). 4 refs., 2 figs.

  1. TOF-SIMS investigation of Streptomyces coelicolor, a mycelial bacterium

    Energy Technology Data Exchange (ETDEWEB)

    Vaidyanathan, Seetharaman [Surface Analytical Research Centre, Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess Street, Manchester M1 7DN (United Kingdom)], E-mail: S.Vaidyanathan@manchester.ac.uk; Fletcher, John S.; Lockyer, Nicholas P.; Vickerman, John C. [Surface Analytical Research Centre, Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess Street, Manchester M1 7DN (United Kingdom)

    2008-12-15

    Streptomyces coelicolor is a mycelial microorganism that produces several secondary metabolites, including antibiotics. The physiology of the organism has largely been investigated in liquid cultures due to ease of monitoring different physiological parameters and more homogeneous culture conditions. However, solid cultures reflect the natural physiology of the microorganism better, given that in its natural state it grows in the soil. Imaging mass spectrometry with TOF-SIMS and C{sub 60}{sup +} primary ion beams offers a potential route to studying chemical changes at the molecular level, both intracellular and extracellular that can help in understanding the natural physiology of the microorganism. Here, we report the application of the technique for studying the lateral distribution of the chemical species detected in a population, grown in both liquid and solid cultures. The capability of the technique for studying biological systems with minimal system intervention is demonstrated.

  2. Una mirada a los productos simétricos

    OpenAIRE

    2009-01-01

    La Teoría de Hiperespacios de Continuos es una línea de investigación en topología que apareció aproximadamente en la década de 1910 a 1920. En México se ha trabajado en esta área en los últimos 20 años. El hiperespacio conocido como el n-ésimo producto simétrico fue introducido por K. Borsuk y S. Ulam en 1931. En este artículo enfocamos nuestra atención a los modelos geométricos de dichos hiperespacios y algunas de sus propiedades más importantes.

  3. SIM-Lite: status of the engineering progress toward flight

    Science.gov (United States)

    Dekens, Frank G.; Bloemhof, Eric E.; Dubovitsky, Serge; Eldred, Daniel; Goullioud, Renaud; Jeganathan, Muthu; Nicaise, Fabien; Zhao, Feng

    2008-07-01

    We present an overview of the ongoing progress towards flight readiness of the SIM project. We summarize the engineering milestones that have been completed in the last two years, namely: the Brass-Board Internal and External Metrology Beam Launchers, the Brass-Board Metrology Source, and the Instrument Communication Hardware/Software Architecture Demonstration. We also show other progress such as: the life test of the bass-screw and PZT actuators, building the Metrology Fiducials and the Single Strut Test Article. We status the ongoing work on the Brass-Board Fast Steering Mirror and the Brass-Board Astrometric Beam Combiner. We end with a proposed path towards finishing the Brass-Board suite.

  4. Una mirada a los productos simétricos

    Directory of Open Access Journals (Sweden)

    Gloria Andablo-Reyes

    2009-01-01

    Full Text Available La Teoría de Hiperespacios de Continuos es una línea de investigación en topología que apareció aproximadamente en la década de 1910 a 1920. En México se ha trabajado en esta área en los últimos 20 años. El hiperespacio conocido como el n-ésimo producto simétrico fue introducido por K. Borsuk y S. Ulam en 1931. En este artículo enfocamos nuestra atención a los modelos geométricos de dichos hiperespacios y algunas de sus propiedades más importantes.

  5. TOF-SIMS investigation of Streptomyces coelicolor, a mycelial bacterium

    Science.gov (United States)

    Vaidyanathan, Seetharaman; Fletcher, John S.; Lockyer, Nicholas P.; Vickerman, John C.

    2008-12-01

    Streptomyces coelicolor is a mycelial microorganism that produces several secondary metabolites, including antibiotics. The physiology of the organism has largely been investigated in liquid cultures due to ease of monitoring different physiological parameters and more homogeneous culture conditions. However, solid cultures reflect the natural physiology of the microorganism better, given that in its natural state it grows in the soil. Imaging mass spectrometry with TOF-SIMS and C 60+ primary ion beams offers a potential route to studying chemical changes at the molecular level, both intracellular and extracellular that can help in understanding the natural physiology of the microorganism. Here, we report the application of the technique for studying the lateral distribution of the chemical species detected in a population, grown in both liquid and solid cultures. The capability of the technique for studying biological systems with minimal system intervention is demonstrated.

  6. Front- and back-end process characterization by SIMS to achieve electrically matched devices

    Science.gov (United States)

    Budri, Thanas; Kouzminov, Dimitry

    2004-06-01

    Application of SIMS metrology in high volume wafer manufacturing allows comparison of important physical characteristics of devices and can address changes in the process during early stages of process flow, thus improving production yields and cycles. In the current paper, we investigate the correlation between wafer-level SIMS characterization and electrical characteristics of devices in a wide spectrum of front- and back-end applications: high precision SIMS analysis for implanter recipe development and monitoring is a technique that has provided major contributions to achieve electrically matched devices. SIMS analysis is also used widely on gate material selection and characterization. As SiGe/SiGeC is taking precedence over III-V materials for rf applications due to processing simplicity, SIMS analytical technique provides major metrology support on process targeting and development. The SIMS analytical technique has earned its reputation and is wide used as metrology solution on front-end semiconductor processing. Fluorine SIMS analysis investigation in TiN, W and its relation with increased via resistance and voids on the nucleation is an example of SIMS analysis application for back-end process support.

  7. Cognitive Anatomy of Tutor Learning: Lessons Learned with SimStudent

    Science.gov (United States)

    Matsuda, Noboru; Yarzebinski, Evelyn; Keiser, Victoria; Raizada, Rohan; Cohen, William W.; Stylianides, Gabriel J.; Koedinger, Kenneth R.

    2013-01-01

    This article describes an advanced learning technology used to investigate hypotheses about learning by teaching. The proposed technology is an instance of a teachable agent, called SimStudent, that learns skills (e.g., for solving linear equations) from examples and from feedback on performance. SimStudent has been integrated into an online,…

  8. Understanding IEC standard wind turbine models using SimPowerSystems

    DEFF Research Database (Denmark)

    Das, Kaushik; Hansen, Anca Daniela; Sørensen, Poul Ejnar

    2016-01-01

    This article describes and exemplifies the IEC 61400-27 generic wind turbine models through an interactive multimedia learning environment - Matlab SimPowerSystems. The article aims help engineers with different backgrounds to get a better understanding of wind turbine dynamics and control...... by easily conducting different study simulations in the SimPowerSystems platform ....

  9. WTA President Sim Jae-Duck and His Party Visit China

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    <正>Sim Jae-Duck, president of the World Toilet Association (WTA), and his party visited Beijing, Shandong and Shanghai from May 19 to 23 at the invitation of the CPAFFC. Sim Jae-Duck is the founder of the WTA,

  10. Denitrification in the root zone using a simple empirical model SimDen

    DEFF Research Database (Denmark)

    Vinther, Finn Pilgaard

    2006-01-01

    Only by knowing soil type and amount of nitrogen applied, an estimate of the annual denitrification can be obtained with the simple empirical model SimDen.......Only by knowing soil type and amount of nitrogen applied, an estimate of the annual denitrification can be obtained with the simple empirical model SimDen....

  11. The Pedagogical Benefits of "SimCity" in Urban Geography Education

    Science.gov (United States)

    Kim, Minsung; Shin, Jungyeop

    2016-01-01

    This article investigated the pedagogical potential of the "SimCity" simulation game in an urban geography course. University students used "SimCity" to build their own cities and applied a wide range of theories to support their urban structures. Moreover, the students critically evaluated the logic and functioning of the…

  12. The role of the transcription factor SIM2 in prostate cancer.

    Directory of Open Access Journals (Sweden)

    Bin Lu

    Full Text Available BACKGROUND: Recent reports have suggested a possible involvement of Single-minded homolog 2 (SIM2 in human solid cancers, including prostate cancer. However, the exact role of SIM2 in cancer in general, and in prostate cancer in particular, remains largely unknown. This study was designed to elucidate the role of SIM2 in prostate cancer using a shRNA-based approach in the PC3 prostate cancer cell line. METHODS: Lentiviral shRNAs were used to inhibit SIM2 gene and protein levels in PC3 cells. Quantitative RT-PCR and branched DNA were performed to evaluate transcript expression. SIM2 protein expression level was measured by western blot. Profiling of gene expression spanning the whole genome, as well as polar metabolomics of several major metabolic pathways was performed to identify major pathway dysregulations. RESULTS: SIM2 gene and protein products were significantly downregulated by lenti-shRNA in PC3 cell line. This low expression of SIM2 affected gene expression profile, revealing significant changes in major signaling pathways, networks and functions. In addition, major metabolic pathways were affected. CONCLUSION: Taken together, our results suggest an involvement of SIM2 in key traits of prostate tumor cell biology and might underlie a contribution of this transcription factor to prostate cancer onset and progression.

  13. Transformation of Printed Course Materials into Self Instructional Materials (SIMs): Some Basic Issues.

    Science.gov (United States)

    Rausaria, R. R.; Bhushan, Bharat

    2001-01-01

    Discussion of the use of self-instructional materials (SIMs) in distance learning at Indira Gandhi National Open University (IGNOU) and State Open Universities (SOUs) in India. Focuses on the need for Correspondence Course Institutes in conventional Indian universities to transform printed course materials into SIMs. Discusses revision and…

  14. SimDelta global: Towards a standardised interactive model for water infrastructure development

    NARCIS (Netherlands)

    Rijcken, T.; Christopher, D.K.

    2013-01-01

    The research project ‘SimDelta’ builds on novel internet technology to support the development of the Rhine-Meuse delta water infrastructure. It has three goals: education, organisation of research and design studies, and stakeholder polling. A current question is how the SimDelta technology could b

  15. Functionality of novel black silicon based nanostructured surfaces studied by TOF SIMS

    DEFF Research Database (Denmark)

    Talian, Ivan; Aranyosiova, M.; Orinak, A.

    2010-01-01

    depends on Ag layer thickness and measured ion mode (negative, positive). The best SIMS signal enhancement was obtained at BS2 surface coated with 400 nm of Ag layer. SIMS fragmentation schemes were developed for a model analyte deposited onto a silver and gold surface. Significant differences in pre...

  16. OpenSimRoot: widening the scope and application of root architectural models.

    Science.gov (United States)

    Postma, Johannes A; Kuppe, Christian; Owen, Markus R; Mellor, Nathan; Griffiths, Marcus; Bennett, Malcolm J; Lynch, Jonathan P; Watt, Michelle

    2017-08-01

    OpenSimRoot is an open-source, functional-structural plant model and mathematical description of root growth and function. We describe OpenSimRoot and its functionality to broaden the benefits of root modeling to the plant science community. OpenSimRoot is an extended version of SimRoot, established to simulate root system architecture, nutrient acquisition and plant growth. OpenSimRoot has a plugin, modular infrastructure, coupling single plant and crop stands to soil nutrient and water transport models. It estimates the value of root traits for water and nutrient acquisition in environments and plant species. The flexible OpenSimRoot design allows upscaling from root anatomy to plant community to estimate the following: resource costs of developmental and anatomical traits; trait synergisms; and (interspecies) root competition. OpenSimRoot can model three-dimensional images from magnetic resonance imaging (MRI) and X-ray computed tomography (CT) of roots in soil. New modules include: soil water-dependent water uptake and xylem flow; tiller formation; evapotranspiration; simultaneous simulation of mobile solutes; mesh refinement; and root growth plasticity. OpenSimRoot integrates plant phenotypic data with environmental metadata to support experimental designs and to gain a mechanistic understanding at system scales. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

  17. Challenges of biological sample preparation for SIMS imaging of elements and molecules at subcellular resolution

    Energy Technology Data Exchange (ETDEWEB)

    Chandra, Subhash [Cornell SIMS Laboratory, Department of Earth and Atmospheric Sciences, Snee Hall, Cornell University, Ithaca, NY 14853 (United States)], E-mail: sc40@cornell.edu

    2008-12-15

    Secondary ion mass spectrometry (SIMS) based imaging techniques capable of subcellular resolution characterization of elements and molecules are becoming valuable tools in many areas of biology and medicine. Due to high vacuum requirements of SIMS, the live cells cannot be analyzed directly in the instrument. The sample preparation, therefore, plays a critical role in preserving the native chemical composition for SIMS analysis. This work focuses on the evaluation of frozen-hydrated and frozen freeze-dried sample preparations for SIMS studies of cultured cells with a CAMECA IMS-3f dynamic SIMS ion microscope instrument capable of producing SIMS images with a spatial resolution of 500 nm. The sandwich freeze-fracture method was used for fracturing the cells. The complimentary fracture planes in the plasma membrane were characterized by field-emission secondary electron microscopy (FESEM) in the frozen-hydrated state. The cells fractured at the dorsal surface were used for SIMS analysis. The frozen-hydrated SIMS analysis of individual cells under dynamic primary ion beam (O{sub 2}{sup +}) revealed local secondary ion signal enhancements correlated with the water image signals of {sup 19}(H{sub 3}O){sup +}. A preferential removal of water from the frozen cell matrix in the Z-axis was also observed. These complications render the frozen-hydrated sample type less desirable for subcellular dynamic SIMS studies. The freeze-drying of frozen-hydrated cells, either inside the instrument or externally in a freeze-drier, allowed SIMS imaging of subcellular chemical composition. Morphological evaluations of fractured freeze-dried cells with SEM and confocal laser scanning microscopy (CLSM) revealed well-preserved mitochondria, Golgi apparatus, and stress fibers. SIMS analysis of fractured freeze-dried cells revealed well-preserved chemical composition of even the most highly diffusible ions like K{sup +} and Na{sup +} in physiologically relevant concentrations. The high K

  18. Multi-dimensional TOF-SIMS analysis for effective profiling of disease-related ions from the tissue surface

    Science.gov (United States)

    Park, Ji-Won; Jeong, Hyobin; Kang, Byeongsoo; Kim, Su Jin; Park, Sang Yoon; Kang, Sokbom; Kim, Hark Kyun; Choi, Joon Sig; Hwang, Daehee; Lee, Tae Geol

    2015-06-01

    Time-of-flight secondary ion mass spectrometry (TOF-SIMS) emerges as a promising tool to identify the ions (small molecules) indicative of disease states from the surface of patient tissues. In TOF-SIMS analysis, an enhanced ionization of surface molecules is critical to increase the number of detected ions. Several methods have been developed to enhance ionization capability. However, how these methods improve identification of disease-related ions has not been systematically explored. Here, we present a multi-dimensional SIMS (MD-SIMS) that combines conventional TOF-SIMS and metal-assisted SIMS (MetA-SIMS). Using this approach, we analyzed cancer and adjacent normal tissues first by TOF-SIMS and subsequently by MetA-SIMS. In total, TOF- and MetA-SIMS detected 632 and 959 ions, respectively. Among them, 426 were commonly detected by both methods, while 206 and 533 were detected uniquely by TOF- and MetA-SIMS, respectively. Of the 426 commonly detected ions, 250 increased in their intensities by MetA-SIMS, whereas 176 decreased. The integrated analysis of the ions detected by the two methods resulted in an increased number of discriminatory ions leading to an enhanced separation between cancer and normal tissues. Therefore, the results show that MD-SIMS can be a useful approach to provide a comprehensive list of discriminatory ions indicative of disease states.

  19. Subcellular boron and fluorine distributions with SIMS ion microscopy in BNCT and cancer research

    Energy Technology Data Exchange (ETDEWEB)

    Subhash Chandra

    2008-05-30

    The development of a secondary ion mass spectrometry (SIMS) based technique of Ion Microscopy in boron neutron capture therapy (BNCT) was the main goal of this project, so that one can study the subcellular location of boron-10 atoms and their partitioning between the normal and cancerous tissue. This information is fundamental for the screening of boronated drugs appropriate for neutron capture therapy of cancer. Our studies at Cornell concentrated mainly on studies of glioblastoma multiforme (GBM). The early years of the grant were dedicated to the development of cryogenic methods and correlative microscopic approaches so that a reliable subcellular analysis of boron-10 atoms can be made with SIMS. In later years SIMS was applied to animal models and human tissues of GBM for studying the efficacy of potential boronated agents in BNCT. Under this grant the SIMS program at Cornell attained a new level of excellence and collaborative SIMS studies were published with leading BNCT researchers in the U.S.

  20. 访Sim 2出口部经理Sergio Cadin先生

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    Sim 2是意大利的投影机品牌,是1987年由意大利视丽(Seleco)电子集团分离出来的。Sim 2公司的投影机产品在世界上拥有良好的声誉,其特点是高品质与外观艺术的完美结合。对于Sim 2我国消费者知之较少,但对其前身视丽(Seleco)就不陌生了。为了多了解一些Sim 2的情况,本刊记者采访了Sim 2出口部经理Sergio Cadin。

  1. WEC-SIM Phase 1 Validation Testing -- Numerical Modeling of Experiments: Preprint

    Energy Technology Data Exchange (ETDEWEB)

    Ruehl, Kelley; Michelen, Carlos; Bosma, Bret; Yu, Yi-Hsiang

    2016-08-01

    The Wave Energy Converter Simulator (WEC-Sim) is an open-source code jointly developed by Sandia National Laboratories and the National Renewable Energy Laboratory. It is used to model wave energy converters subjected to operational and extreme waves. In order for the WEC-Sim code to be beneficial to the wave energy community, code verification and physical model validation is necessary. This paper describes numerical modeling of the wave tank testing for the 1:33-scale experimental testing of the floating oscillating surge wave energy converter. The comparison between WEC-Sim and the Phase 1 experimental data set serves as code validation. This paper is a follow-up to the WEC-Sim paper on experimental testing, and describes the WEC-Sim numerical simulations for the floating oscillating surge wave energy converter.

  2. WEC-Sim Phase 1 Validation Testing: Numerical Modeling of Experiments

    Energy Technology Data Exchange (ETDEWEB)

    Ruehl, Kelley; Michelen, Carlos; Bosma, Bret; Yu, Yi-Hsiang

    2016-06-24

    The Wave Energy Converter Simulator (WEC-Sim) is an open-source code jointly developed by Sandia National Laboratories and the National Renewable Energy Laboratory. It is used to model wave energy converters subjected to operational and extreme waves. In order for the WEC-Sim code to be beneficial to the wave energy community, code verification and physical model validation is necessary. This paper describes numerical modeling of the wave tank testing for the 1:33-scale experimental testing of the floating oscillating surge wave energy converter. The comparison between WEC-Sim and the Phase 1 experimental data set serves as code validation. This paper is a follow-up to the WEC-Sim paper on experimental testing, and describes the WEC-Sim numerical simulations for the floating oscillating surge wave energy converter.

  3. SIM regional comparison SIM.L-K4.2009 on the calibration of internal and external diameter standards

    Science.gov (United States)

    Doiron, Theodore; Pires Alves, J. A.; Gastaldi, Bruno R.; Navarrete, Guillermo

    2015-01-01

    The Inter-American Metrology System (SIM) has carried out a key comparison of diameter measurements. The artifacts studied were four ring gages and four plug gages. The measurand was a specified diameter of each gauge at 20 °C and corrected to zero force. This report presents results obtained by the individual participants and an analysis of the results and their uncertainties. The results are in good agreement with one another, well within the range expected based on the measurement uncertainties claimed by the participants. Main text. To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/. The final report has been peer-reviewed and approved for publication by the CCL, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).

  4. Computational and Modeling Strategies for Cell Motility

    Science.gov (United States)

    Wang, Qi; Yang, Xiaofeng; Adalsteinsson, David; Elston, Timothy C.; Jacobson, Ken; Kapustina, Maryna; Forest, M. Gregory

    A predictive simulation of the dynamics of a living cell remains a fundamental modeling and computational challenge. The challenge does not even make sense unless one specifies the level of detail and the phenomena of interest, whether the focus is on near-equilibrium or strongly nonequilibrium behavior, and on localized, subcellular, or global cell behavior. Therefore, choices have to be made clear at the outset, ranging from distinguishing between prokaryotic and eukaryotic cells, specificity within each of these types, whether the cell is "normal," whether one wants to model mitosis, blebs, migration, division, deformation due to confined flow as with red blood cells, and the level of microscopic detail for any of these processes. The review article by Hoffman and Crocker [48] is both an excellent overview of cell mechanics and an inspiration for our approach. One might be interested, for example, in duplicating the intricate experimental details reported in [43]: "actin polymerization periodically builds a mechanical link, the lamellipodium, connecting myosin motors with the initiation of adhesion sites, suggesting that the major functions driving motility are coordinated by a biomechanical process," or to duplicate experimental evidence of traveling waves in cells recovering from actin depolymerization [42, 35]. Modeling studies of lamellipodial structure, protrusion, and retraction behavior range from early mechanistic models [84] to more recent deterministic [112, 97] and stochastic [51] approaches with significant biochemical and structural detail. Recent microscopic-macroscopic models and algorithms for cell blebbing have been developed by Young and Mitran [116], which update cytoskeletal microstructure via statistical sampling techniques together with fluid variables. Alternatively, whole cell compartment models (without spatial details) of oscillations in spreading cells have been proposed [35, 92, 109] which show positive and negative feedback

  5. NanoSIMS analysis of Bacillus spores for forensics

    Energy Technology Data Exchange (ETDEWEB)

    Weber, P K; Davisson, M L; Velsko, S P

    2010-02-23

    The threat associated with the potential use of radiological, nuclear, chemical and biological materials in terrorist acts has resulted in new fields of forensic science requiring the application of state-of-the-science analytical techniques. Since the anthrax letter attacks in the United States in the fall of 2001, there has been increased interest in physical and chemical characterization of bacterial spores. While molecular methods are powerful tools for identifying genetic differences, other methods may be able to differentiate genetically identical samples based on physical and chemical properties, as well as provide complimentary information, such as methods of production and approximate date of production. Microanalysis has the potential to contribute significantly to microbial forensics. Bacillus spores are highly structured, consisting of a core, cortex, coat, and in some species, an exosporium. This structure provides a template for constraining elemental abundance differences at the nanometer scale. The primary controls on the distribution of major elements in spores are likely structural and physiological. For example, P and Ca are known to be abundant in the spore core because that is where P-rich nucleic acids and Cadipicolinic acid are located, respectively. Trace elements are known to bind to the spore coat but the controls on these elements are less well understood. Elemental distributions and abundances may be directly related to spore production, purification and stabilization methodologies, which are of particular interest for forensic investigation. To this end, we are developing a high-resolution secondary ion mass spectrometry method using a Cameca NanoSIMS 50 to study the distribution and abundance of trace elements in bacterial spores. In this presentation we will review and compare methods for preparing and analyzing samples, as well as review results on the distribution and abundance of elements in bacterial spores. We use NanoSIMS to

  6. Effects of surface passivation on gliding motility assays.

    Directory of Open Access Journals (Sweden)

    Andy Maloney

    Full Text Available In this study, we report differences in the observed gliding speed of microtubules dependent on the choice of bovine casein used as a surface passivator. We observed differences in both speed and support of microtubules in each of the assays. Whole casein, comprised of α(s1, α(s2, β, and κ casein, supported motility and averaged speeds of 966±7 nm/s. Alpha casein can be purchased as a combination of α(s1 and α(s2 and supported gliding motility and average speeds of 949±4 nm/s. Beta casein did not support motility very well and averaged speeds of 870±30 nm/s. Kappa casein supported motility very poorly and we were unable to obtain an average speed. Finally, we observed that mixing alpha, beta, and kappa casein with the proportions found in bovine whole casein supported motility and averaged speeds of 966±6 nm/s.

  7. Rac and Rho GTPases in cancer cell motility control

    Directory of Open Access Journals (Sweden)

    Parri Matteo

    2010-09-01

    Full Text Available Abstract Rho GTPases represent a family of small GTP-binding proteins involved in cell cytoskeleton organization, migration, transcription, and proliferation. A common theme of these processes is a dynamic reorganization of actin cytoskeleton which has now emerged as a major switch control mainly carried out by Rho and Rac GTPase subfamilies, playing an acknowledged role in adaptation of cell motility to the microenvironment. Cells exhibit three distinct modes of migration when invading the 3 D environment. Collective motility leads to movement of cohorts of cells which maintain the adherens junctions and move by photolytic degradation of matrix barriers. Single cell mesenchymal-type movement is characterized by an elongated cellular shape and again requires extracellular proteolysis and integrin engagement. In addition it depends on Rac1-mediated cell polarization and lamellipodia formation. Conversely, in amoeboid movement cells have a rounded morphology, the movement is independent from proteases but requires high Rho GTPase to drive elevated levels of actomyosin contractility. These two modes of cell movement are interconvertible and several moving cells, including tumor cells, show an high degree of plasticity in motility styles shifting ad hoc between mesenchymal or amoeboid movements. This review will focus on the role of Rac and Rho small GTPases in cell motility and in the complex relationship driving the reciprocal control between Rac and Rho granting for the opportunistic motile behaviour of aggressive cancer cells. In addition we analyse the role of these GTPases in cancer progression and metastatic dissemination.

  8. Guaifenesin and increased sperm motility: a preliminary case report.

    Science.gov (United States)

    Means, Gary; Berry-Cabán, Cristóbal S; Hammermeuller, Kurt

    2010-12-20

    A review of the literature and an extensive Medline search revealed that this is the first case report of the use of guaifenesin to increase sperm motility. A 32-year-old male presented for an infertility evaluation. He reported an inability to conceive with his wife after 18 months of unprotected intercourse. A semen analysis was performed that included spermatozoa count, liquefaction, morphology, motility, viscosity and volume. Initial results of the semen analysis demonstrated low sperm count and motility. The provider offered treatment with guaifenesin 600 mg extended release tablets twice daily. Two months after guaifenesin therapy the semen analysis was repeated that demonstrated marked improvement in both total sperm count and motility. Evidence for the effectiveness of guaifenesin is almost entirely anecdotal. Given the mechanism of action of guaifenesin, it is not clear from this case why the patient demonstrated such a large improvement in both sperm count and motility. Additional studies of the effects of guaifenesin on male fertility could yield information of the medication's effect on men with normal or decreased total sperm counts.

  9. PACRG, a protein linked to ciliary motility, mediates cellular signaling.

    Science.gov (United States)

    Loucks, Catrina M; Bialas, Nathan J; Dekkers, Martijn P J; Walker, Denise S; Grundy, Laura J; Li, Chunmei; Inglis, P Nick; Kida, Katarzyna; Schafer, William R; Blacque, Oliver E; Jansen, Gert; Leroux, Michel R

    2016-07-01

    Cilia are microtubule-based organelles that project from nearly all mammalian cell types. Motile cilia generate fluid flow, whereas nonmotile (primary) cilia are required for sensory physiology and modulate various signal transduction pathways. Here we investigate the nonmotile ciliary signaling roles of parkin coregulated gene (PACRG), a protein linked to ciliary motility. PACRG is associated with the protofilament ribbon, a structure believed to dictate the regular arrangement of motility-associated ciliary components. Roles for protofilament ribbon-associated proteins in nonmotile cilia and cellular signaling have not been investigated. We show that PACRG localizes to a small subset of nonmotile cilia in Caenorhabditis elegans, suggesting an evolutionary adaptation for mediating specific sensory/signaling functions. We find that it influences a learning behavior known as gustatory plasticity, in which it is functionally coupled to heterotrimeric G-protein signaling. We also demonstrate that PACRG promotes longevity in C. elegans by acting upstream of the lifespan-promoting FOXO transcription factor DAF-16 and likely upstream of insulin/IGF signaling. Our findings establish previously unrecognized sensory/signaling functions for PACRG and point to a role for this protein in promoting longevity. Furthermore, our work suggests additional ciliary motility-signaling connections, since EFHC1 (EF-hand containing 1), a potential PACRG interaction partner similarly associated with the protofilament ribbon and ciliary motility, also positively regulates lifespan.

  10. Bidirectional motility of the fission yeast kinesin-5, Cut7

    Energy Technology Data Exchange (ETDEWEB)

    Edamatsu, Masaki, E-mail: cedam@mail.ecc.u-tokyo.ac.jp

    2014-03-28

    Highlights: • Motile properties of Cut7 (fission yeast kinesin-5) were studied for the first time. • Half-length Cut7 moved toward plus-end direction of microtubule. • Full-length Cut7 moved toward minus-end direction of microtubule. • N- and C-terminal microtubule binding sites did not switch the motile direction. - Abstract: Kinesin-5 is a homotetrameric motor with its motor domain at the N-terminus. Kinesin-5 crosslinks microtubules and functions in separating spindle poles during mitosis. In this study, the motile properties of Cut7, fission yeast kinesin-5, were examined for the first time. In in vitro motility assays, full-length Cut7 moved toward minus-end of microtubules, but the N-terminal half of Cut7 moved toward the opposite direction. Furthermore, additional truncated constructs lacking the N-terminal or C-terminal regions, but still contained the motor domain, did not switch the motile direction. These indicated that Cut7 was a bidirectional motor, and microtubule binding regions at the N-terminus and C-terminus were not involved in its directionality.

  11. Geometry-Driven Polarity in Motile Amoeboid Cells.

    Directory of Open Access Journals (Sweden)

    Oliver Nagel

    Full Text Available Motile eukaryotic cells, such as leukocytes, cancer cells, and amoeba, typically move inside the narrow interstitial spacings of tissue or soil. While most of our knowledge of actin-driven eukaryotic motility was obtained from cells that move on planar open surfaces, recent work has demonstrated that confinement can lead to strongly altered motile behavior. Here, we report experimental evidence that motile amoeboid cells undergo a spontaneous symmetry breaking in confined interstitial spaces. Inside narrow channels, the cells switch to a highly persistent, unidirectional mode of motion, moving at a constant speed along the channel. They remain in contact with the two opposing channel side walls and alternate protrusions of their leading edge near each wall. Their actin cytoskeleton exhibits a characteristic arrangement that is dominated by dense, stationary actin foci at the side walls, in conjunction with less dense dynamic regions at the leading edge. Our experimental findings can be explained based on an excitable network model that accounts for the confinement-induced symmetry breaking and correctly recovers the spatio-temporal pattern of protrusions at the leading edge. Since motile cells typically live in the narrow interstitial spacings of tissue or soil, we expect that the geometry-driven polarity we report here plays an important role for movement of cells in their natural environment.

  12. Outflowing atomic and molecular gas at $z \\sim 0.67$ towards 1504+377

    CERN Document Server

    Kanekar, Nissim

    2007-01-01

    We report the detection of OH 1667 MHz and wide HI 21cm absorption at $z \\sim 0.67$ towards the red quasar 1504+377, with the Green Bank Telescope and the Giant Metrewave Radio Telescope. The HI 21cm absorption extends over a velocity range of $\\sim 600$ km/s blueward of the quasar redshift ($z=0.674$), with the new OH 1667 MHz absorption component at $\\sim -430$ \\kms, nearly coincident with earlier detections of mm-wave absorption at $z \\sim 0.6715$. The atomic and molecular absorption appear to arise from a fast gas outflow from the quasar, with a mass outflow rate ${\\dot M} \\sim 12 M_\\odot$ yr$^{-1}$ and a molecular hydrogen fraction $f_{\\rm H_2} \\equiv (N_{\\rm H_2}/N_{\\rm HI}) \\sim 0.2$. The radio structure of 1504+377 is consistent with the outflow arising due to a jet-cloud interaction, followed by rapid cooling of the cloud material. The observed ratio of HCO$^+$ to OH column densities is $\\sim 20$ times higher than typical values in Galactic and high-$z$ absorbers. This could arise due to small-scale ...

  13. Single cell motility and trail formation in populations of microglia

    Science.gov (United States)

    Lee, Kyoung Jin

    2009-03-01

    Microglia are a special type of glia cell in brain that has immune responses. They constitute about 20 % of the total glia population within the brain. Compared to other glia cells, microglia are very motile, constantly moving to destroy pathogens and to remove dead neurons. While doing so, they exhibit interesting body shapes, have cell-to-cell communications, and have chemotatic responses to each other. Interestingly, our recent in vitro studies show that their unusual motile behaviors can self-organize to form trails, similar to those in populations of ants. We have studied the changes in the physical properties of these trails by varying the cell population density and by changing the degree of spatial inhomogeneities (``pathogens''). Our experimental observations can be quite faithfully reproduced by a simple mathematical model involving many motile cells whose mechanical motion are driven by actin polymerization and depolymerization process within the individual cell body and by external chemical gradients.

  14. FUNCTIONAL IMPAIRMENTS OF GASTROINTESTINAL MOTILITY AND GASTROINTESTINAL TRACT MICROBIOTA

    Directory of Open Access Journals (Sweden)

    A.V. Malkoch

    2009-01-01

    Full Text Available Functional dysmotility is one of the most common evidence of pathology in gastrointestinal tract (GIT. GIT motility regulation is multilevel in nature at the level of central and peripheral nervous system, vegetative nervous system as well as locally directly in the intestinal tract. Gastrointestinal tract microbiota significantly contributes to the local regulation of motility both by forming fecal masses and secreting various metabolites, particularly short chain fatty acids whose composition and number depends on the nutritive factors of microbiota. For normal functioning and metabolism, saprophitic microbiota needs a significant number of undigestible carbohydrates, i.e. prebiotics. Prebiotics are an integral component of the complex therapy for functional impairments of gastrointestinal tract.Key words: gastrointestinal tract, motility, functional impairments, mictobiota, short chain fatty acids, prebiotics, lactulose.

  15. Gastrointestinal Motility Disorders and Their Clinical Implications in Cirrhosis

    Directory of Open Access Journals (Sweden)

    Eleni Theocharidou

    2017-01-01

    Full Text Available Gastrointestinal motility is impaired in a substantial proportion of patients with cirrhosis. Cirrhosis-related autonomic neuropathy, increased nitric oxide production, and gut hormonal changes have been implicated. Oesophageal dysmotility has been associated with increased frequency of abnormal gastro-oesophageal reflux. Impaired gastric emptying and accommodation may result in early satiety and may have an impact on the nutritional status of these patients. Small intestinal dysmotility might be implicated in small intestinal bacterial overgrowth and increased bacterial translocation. The latter has been implicated in the pathophysiology of hepatic encephalopathy and spontaneous bacterial peritonitis. Enhanced colonic motility is usually associated with the use of lactulose. Pharmacological interventions aiming to alter gastrointestinal motility in cirrhosis could potentially have a beneficial effect reducing the risk of hepatic decompensation and improving prognosis.

  16. Bacteria rolling: motilities of rosette colonies in Caulobacter crescentus

    Science.gov (United States)

    Zeng, Yu; Liu, Bin

    2016-11-01

    The aquatic bacterium Caulobacter crescentus has two life cycle stages with distinct motilities: freely swimming swarmer cells and immotile stalked cells. Here, we show a new type of movement performed by freely suspended rosettes, spontaneous aggregates of stalked cells aligned radially relative to each other. Reproductive rosette members generate predivisional daughter cells with flagella, inducing rotations of the rosette as a whole. Such rotations exhibit dynamic angular velocities and lead to intermittent linear movements along liquid-solid interfaces, resembling rolling movements. We reconstructed the translational and rotational dynamics of the rosette movements from high-speed filming and long-term tracking. A mechanical model was developed to explain the hydrodynamic mechanism underlying such motilities. Our study illustrated a nontrivial mechanism for clustered bacteria to achieve motilities and sheds light on the adaptive significance of the collective behaviors of microorganisms in complex fluid environments.

  17. Activation of Drosophila hemocyte motility by the ecdysone hormone

    Directory of Open Access Journals (Sweden)

    Christopher J. Sampson

    2013-11-01

    Drosophila hemocytes compose the cellular arm of the fly's innate immune system. Plasmatocytes, putative homologues to mammalian macrophages, represent ∼95% of the migratory hemocyte population in circulation and are responsible for the phagocytosis of bacteria and apoptotic tissues that arise during metamorphosis. It is not known as to how hemocytes become activated from a sessile state in response to such infectious and developmental cues, although the hormone ecdysone has been suggested as the signal that shifts hemocyte behaviour from quiescent to migratory at metamorphosis. Here, we corroborate this hypothesis by showing the activation of hemocyte motility by ecdysone. We induce motile behaviour in larval hemocytes by culturing them with 20-hydroxyecdysone ex vivo. Moreover, we also determine that motile cell behaviour requires the ecdysone receptor complex and leads to asymmetrical redistribution of both actin and tubulin cytoskeleton.

  18. Assessment of gastrointestinal motility using three different assays in vitro.

    Science.gov (United States)

    Pozzoli, Cristina; Poli, Enzo

    2010-11-01

    The protocols detailed in this unit are designed to assess the motor activity of different gastric and intestinal muscle preparations in vitro and the effects of drugs that modulate gastrointestinal motility. The preparations described are characterized by different contractile behaviors, consisting of spontaneous (duodenum), neurogenic (ileum), and drug-stimulated (fundus, ileum) motility; these reproduce motility patterns occurring in the gut wall in vivo. These protocols document the variety of factors that can influence the responses of isolated tissues and describe how such tissues can be used for testing substances that affect gut movements. These preparations allow evaluation of direct interactions with the processes that control contractile machinery, as well as indirect effects resulting from the modification of neurotransmitter release from myenteric neurons. These models can be exploited to assay novel compounds undergoing preclinical development or to evaluate the functional toxicity exerted by environmental or alimentary pollutants, like xenobiotics and naturally occurring toxins, as well as the mechanisms underlying these effects.

  19. TUTORIAL: An introduction to cell motility for the physical scientist

    Science.gov (United States)

    Fletcher, Daniel A.; Theriot, Julie A.

    2004-03-01

    Directed, purposeful movement is one of the qualities that we most closely associate with living organisms, and essentially all known forms of life on this planet exhibit some type of self-generated movement or motility. Even organisms that remain sessile most of the time, like flowering plants and trees, are quite busy at the cellular level, with large organelles, including chloroplasts, constantly racing around within cellular boundaries. Directed biological movement requires that the cell be able to convert its abundant stores of chemical energy into mechanical energy. Understanding how this mechanochemical energy transduction takes place and understanding how small biological forces generated at the molecular level are marshaled and organized for large-scale cellular or organismal movements are the focus of the field of cell motility. This tutorial, aimed at readers with a background in physical sciences, surveys the state of current knowledge and recent advances in modeling cell motility.

  20. Model for self-polarization and motility of keratocyte fragments

    KAUST Repository

    Ziebert, F.

    2011-10-19

    Computational modelling of cell motility on substrates is a formidable challenge; regulatory pathways are intertwined and forces that influence cell motion are not fully quantified. Additional challenges arise from the need to describe a moving deformable cell boundary. Here, we present a simple mathematical model coupling cell shape dynamics, treated by the phase-field approach, to a vector field describing the mean orientation (polarization) of the actin filament network. The model successfully reproduces the primary phenomenology of cell motility: discontinuous onset of motion, diversity of cell shapes and shape oscillations. The results are in qualitative agreement with recent experiments on motility of keratocyte cells and cell fragments. The asymmetry of the shapes is captured to a large extent in this simple model, which may prove useful for the interpretation of experiments.

  1. Active Hair-Bundle Motility by the Vertebrate Hair Cell

    Science.gov (United States)

    Tinevez, J.-Y.; Martin, P.; Jülicher, F.

    2009-02-01

    The hair bundle is both a mechano-sensory antenna and a force generator that might help the vertebrate hair cell from the inner ear to amplify its responsiveness to small stimuli. To study active hair-bundle motility, we combined calcium iontophoresis with mechanical stimulation of single hair bundles from the bullfrog's sacculus. A hair bundle could oscillate spontaneously, or be quiescent but display non-monotonic movements in response to abrupt force steps. Extracellular calcium changes or static biases to the bundle's position at rest could affect the kinetics of bundle motion and evoke transitions between the different classes of motility. The calcium-dependent location of a bundle's operating point within its nonlinear force-displacement relation controlled the type of movements observed. A unified theoretical description, in which mechanical activity stems from myosin-based adaptation and electro-mechanical feedback by Ca2+, could account for the fast and slow manifestations of active hair-bundle motility.

  2. Bioforensics: Characterization of biological weapons agents by NanoSIMS

    Energy Technology Data Exchange (ETDEWEB)

    Weber, P K; Ghosal, S; Leighton, T J; Wheeler, K E; Hutcheon, I D

    2007-02-26

    The anthrax attacks of Fall 2001 highlight the need to develop forensic methods based on multiple identifiers to determine the origin of biological weapons agents. Genetic typing methods (i.e., DNA and RNA-based) provide one attribution technology, but genetic information alone is not usually sufficient to determine the provenance of the material. Non-genetic identifiers, including elemental and isotopic signatures, provide complementary information that can be used to identify the means, geographic location and date of production. Under LDRD funding, we have successfully developed the techniques necessary to perform bioforensic characterization with the NanoSIMS at the individual spore level. We have developed methods for elemental and isotopic characterization at the single spore scale. We have developed methods for analyzing spore sections to map elemental abundance within spores. We have developed rapid focused ion beam (FIB) sectioning techniques for spores to preserve elemental and structural integrity. And we have developed a high-resolution depth profiling method to characterize the elemental distribution in individual spores without sectioning. We used these newly developed methods to study the controls on elemental abundances in spores, characterize the elemental distribution of in spores, and to study elemental uptake by spores. Our work under this LDRD project attracted FBI and DHS funding for applied purposes.

  3. Metrology Optical Power Budgeting in SIM Using Statistical Analysis Techniques

    Science.gov (United States)

    Kuan, Gary M

    2008-01-01

    The Space Interferometry Mission (SIM) is a space-based stellar interferometry instrument, consisting of up to three interferometers, which will be capable of micro-arc second resolution. Alignment knowledge of the three interferometer baselines requires a three-dimensional, 14-leg truss with each leg being monitored by an external metrology gauge. In addition, each of the three interferometers requires an internal metrology gauge to monitor the optical path length differences between the two sides. Both external and internal metrology gauges are interferometry based, operating at a wavelength of 1319 nanometers. Each gauge has fiber inputs delivering measurement and local oscillator (LO) power, split into probe-LO and reference-LO beam pairs. These beams experience power loss due to a variety of mechanisms including, but not restricted to, design efficiency, material attenuation, element misalignment, diffraction, and coupling efficiency. Since the attenuation due to these sources may degrade over time, an accounting of the range of expected attenuation is needed so an optical power margin can be book kept. A method of statistical optical power analysis and budgeting, based on a technique developed for deep space RF telecommunications, is described in this paper and provides a numerical confidence level for having sufficient optical power relative to mission metrology performance requirements.

  4. Enhancement of mouse sperm motility by trophinin-binding peptide

    Directory of Open Access Journals (Sweden)

    Park Seong

    2012-11-01

    Full Text Available Abstract Background Trophinin is an intrinsic membrane protein that forms a complex in the cytoplasm with bystin and tastin, linking it microtubule-associated motor dynein (ATPase in some cell types. Previously, we found that human sperm tails contain trophinin, bystin and tastin proteins, and that trophinin-binding GWRQ (glycine, tryptophan, arginine, glutamine peptide enhanced motility of human sperm. Methods Immunohistochemistry was employed to determine trophinin protein in mouse spermatozoa from wild type mouse, by using spermatozoa from trophinin null mutant mice as a negative control. Multivalent 8-branched GWRQ (glycine, tryptophan, arginine, glutamine peptide or GWRQ-MAPS, was chemically synthesized, purified by HPLC and its structure was confirmed by MALDI-TOF mass spectrometry. Effect of GWRQ-MAPS on mouse spermatozoa from wild type and trophinin null mutant was assessed by a computer-assisted semen analyzer (CASA. Results Anti-trophinin antibody stained the principal (central piece of the tail of wild type mouse sperm, whereas the antibody showed no staining on trophinin null sperm. Phage particles displaying GWRQ bound to the principal piece of sperm tail from wild type but not trophinin null mice. GWRQ-MAPS enhanced motility of spermatozoa from wild type but not trophinin null mice. CASA showed that GWRQ-MAPS enhanced both progressive motility and rapid motility in wild type mouse sperm. Conclusions Present study established the expression of trophinin in the mouse sperm tail and trophinin-dependent effect of GWRQ-MAPS on sperm motility. GWRQ causes a significant increase in sperm motility.

  5. Neural mechanism of acupuncture-modulated gastric motility

    Institute of Scientific and Technical Information of China (English)

    Yu-Qing Li; Bing Zhu; Pei-Jing Rong; Hui Ben; Yan-Hua Li

    2007-01-01

    AIM: To investigate the acupuncture-modulated gastric motility and its underlying neural mechanism.METHODS: Intragastric pressure and/or waves of gastric contraction in rats were recorded by intrapyloric balloon and changes of gastric motility induced by acupuncture stimulation were compared with the background activity before any stimulation. Gastrovagal or splanchnic-sympathetic nerves were recorded or cut respectively for investigating the involvement of autonomic nerve pathways. Spinalization experiment was also performed.RESULTS: Acupuncture-stimulation by exciting Aδ and/or C afferent fibers, could only modulate gastric motility.Acupuncture-stimulation on fore- and hind-limbs evoked a moderate gastric motility followed by increased vagus discharges with unchanged sympathetic activity, while the same stimulus to the acupoints in abdomen resulted in reversed effects on gastric motility and autonomic nervous activities. The inhibitory gastric response was completely abolished by splanchnic denervation, but the facilitative gastric response to stimulation of acupoints in limbs was not influenced, which was opposite to the effect when vagotomy was performed. The similar depressive effects were produced by the stimulation at the acupoints homo-segmental to the gastric innervation in the animals with or without spinalization. However, the facilitation induced by the stimulation at the acupoints heteto-segmental to the gastric innervation was not observed in the spinalized animals.CONCLUSION: Facilitative effects of stimulating hetero-segmental acupoints are involved in the intact preparation of vagal nerves and spinal cord, while the inhibitory response induced by stimulating homosegmental acupoints is involved in the intact preparation of sympathetic nerves. Only the acupuncture-stimulation with intensity over the threshold of Aδ and/or C afferent fibers can markedly modulate gastrointestinal motility.

  6. TOF SIMS Study on PAHs in Individual Particle from a Power Station

    Institute of Scientific and Technical Information of China (English)

    梁汉东; 于春海; 周强; 李艳芳

    2001-01-01

    The individual particles collected from a power station were analyzed by time of flight secondary ion mass spectrometry (TOF SIMS). The result indicates the presence of the polycyclic aromatic hydrocarbon (PAHs) as well as the oxygenated one. They might be derived from the incomplete combustion of coals. SIMS has proved to be a rapid method for the qualitative analysis of PAHs and OPAHs absorbed on the aerosol particles. New perspectives for better understanding the SIMS spectra obtained from complex mixture such as environmental samples have been opened.

  7. Motility mapping as evaluation tool for bowel motility: initial results on the development of an automated color-coding algorithm in cine MRI.

    Science.gov (United States)

    Hahnemann, Maria L; Nensa, Felix; Kinner, Sonja; Gerken, Guido; Lauenstein, Thomas C

    2015-02-01

    To develop and implement an automated algorithm for visualizing and quantifying bowel motility using cine magnetic resonance imaging (MRI). Four healthy volunteers as well as eight patients with suspected or diagnosed inflammatory bowel disease (IBD) underwent MR examinations on a 1.5T scanner. Coronal T2-weighted cine MR images were acquired in healthy volunteers without and with intravenous (i.v.) administration of butylscopolamine. In patients with IBD, cine MRI sequences were collected prior to standard bowel MRI. Bowel motility was assessed using an optical flow algorithm. The resulting motion vector magnitudes were presented as bowel motility maps. Motility changes after i.v. administration of butylscopolamine were measured in healthy volunteers. Inflamed bowel segments in patients were correlated with motility map findings. The acquisition of bowel motility maps was feasible in all subjects examined. In healthy volunteers butylscopolamine led to quantitatively measurable decrease in bowel motility (mean decrease of 59%; P = 0.171). In patients with IBD, visualization of bowel movement by color-coded motility mapping allowed for the detection of segments with abnormal bowel motility. Inflamed bowel segments could be identified by exhibiting a decreased motility. Our method is a feasible and promising approach for the assessment of bowel motility disorders. © 2014 Wiley Periodicals, Inc.

  8. G-SIMS-FPM: Molecular structure at surfaces—a combined positive and negative secondary ion study

    Science.gov (United States)

    Gilmore, I. S.; Green, F. M.; Seah, M. P.

    2006-07-01

    G-SIMS is an easy to use method that considerably simplifies complex static SIMS spectra. The G-SIMS peaks relate directly to the parent molecular structure and so provide a library independent method for direct interpretation and identification. For larger molecules (>100 u) the mass alone may be insufficient to identify the molecule unambiguously. A development of G-SIMS, G-SIMS-fragmentation pathway mapping (FPM), solves this problem. G-SIMS-FPM allows the molecular structure to be re-assembled by following fragmentation pathways as the G-SIMS surface plasma temperature is varied. In this study, we develop the inclusion of negative secondary ion fragmentation data to provide a more complete analysis. This approach is exampled with data for complex molecules of Irganox 1010 and folic acid.

  9. Investigation of the drying process of linseed oil using FTIR and ToF-SIMS

    Science.gov (United States)

    Grehk, T. M.; Berger, R.; Bexell, U.

    2008-03-01

    The drying process of linseed oil, oxidized at 80 oC, has been investigated with rheology measurements, Fourier transformation infrared spectroscopy (FTIR), and time of flight secondary ion mass spectrometry (ToF-SIMS). The drying process can be divided into three main steps: initiation, propagation and termination. ToF-SIMS spectra show that the oxidation is initiated at the linolenic (three double bonds) and linoleic fatty acids (two double bonds). ToF-SIMS spectra reveal peaks that can be assigned to ketones, alcohols and hydroperoxides. In this article it is shown that FTIR in combination with ToF-SIMS are well suited tools for investigations of various fatty acid components and reaction products of linseed oil.

  10. Structured illumination fluorescence microscopy with distorted excitations using a filtered blind-SIM algorithm.

    Science.gov (United States)

    Ayuk, R; Giovannini, H; Jost, A; Mudry, E; Girard, J; Mangeat, T; Sandeau, N; Heintzmann, R; Wicker, K; Belkebir, K; Sentenac, A

    2013-11-15

    Structured illumination microscopy (SIM) is a powerful technique for obtaining super-resolved fluorescence maps of samples, but it is very sensitive to aberrations or misalignments affecting the excitation patterns. Here, we present a reconstruction algorithm that is able to process SIM data even if the illuminations are strongly distorted. The approach is an extension of the recent blind-SIM technique, which reconstructs simultaneously the sample and the excitation patterns without a priori information on the latter. Our algorithm was checked on synthetic and experimental data using distorted and nondistorted illuminations. The reconstructions were similar to that obtained by up-to-date SIM methods when the illuminations were periodic and remained artifact-free when the illuminations were strongly distorted.

  11. SimCADO - an instrument data simulator package for MICADO at the E-ELT

    CERN Document Server

    Leschinski, Kieran; Köhler, Rainer; Mach, Michael; Zeilinger, Werner; Kleijn, Gijs Verdoes; Alves, Joao; Kausch, Wolfgang; Przybilla, Norbert

    2016-01-01

    MICADO will be the first-light wide-field imager for the European Extremely Large Telescope (E-ELT) and will provide difiraction limited imaging (7mas at 1.2mm) over a ~53 arcsecond field of view. In order to support various consortium activities we have developed a first version of SimCADO: an instrument simulator for MICADO. SimCADO uses the results of the detailed simulation efforts conducted for each of the separate consortium-internal work packages in order to generate a model of the optical path from source to detector readout. SimCADO is thus a tool to provide scientific context to both the science and instrument development teams who are ultimately responsible for the final design and future capabilities of the MICADO instrument. Here we present an overview of the inner workings of SimCADO and outline our plan for its further development.

  12. Rapid identification of phthalates in blood bags and food packaging using ToF-SIMS

    Science.gov (United States)

    Chen, Ching Yuan; Ghule, Anil Vithal; Chen, Wen Yin; Wang, Chiung Chi; Chiang, Yi Shin; Ling, Yong Chien

    2004-06-01

    ToF-SIMS with Ga + ion as primary source is used to analyze plasticizers like bis(2-ethylhexyl) phthalate (DEHP) from the inner surface of the blood bags and their migration into the blood. Food packing materials were also analyzed for the presence of DEHP. The simplicity of using ToF-SIMS with high mass resolution as an aid in the identification and analysis are discussed. The ToF-SIMS results, the fragmentation pattern, and the ratio of ions were comparable to those obtained from traditional GC-MS analysis. This indicates that ToF-SIMS could be a promising technique for direct detection of DEHP (and phthalates in general) in blood bags and food packaging polymeric materials.

  13. Kruger strict morphology and post-thaw progressive motility in cryopreserved human spermatozoa.

    Science.gov (United States)

    Lee, C-Y; Lee, C-T; Wu, C-H; Hsu, C-S; Hsu, M-I

    2012-05-01

    The purpose of this prospective study was to evaluate Kruger strict morphology and conventional semen analysis in predicting cryosurvival and the progressive motility recovery rate of frozen spermatozoa. Our study included 56 semen samples with >10 million spermatozoa per ejaculate. The main outcome measures were conventional semen analysis, strict morphology analysis by the Kruger method, cryosurvival rate and post-thaw sperm motility. A significant reduction in sperm motility after cryopreservation was demonstrated. The freeze-thawing process caused a 66% reduction in rapid progressive motile spermatozoa, a 45% reduction in slow progressive motile spermatozoa and a 2% reduction in nonprogressive motile spermatozoa. The cryosurvival and progressive motility recovery rates were not correlated with parameters of conventional semen analysis, such as sperm concentration, motility, WHO morphology and total motile count, but the progressive motility recovery rate was significantly correlated with the percentage of spermatozoa exhibiting Kruger normal morphology (P = 0.028). The recovery rate of rapidly progressive motility was profoundly decreased compared with slow progressive motility following the frozen-thaw procedure of semen. Kruger strict morphology assessment was a better predictor of the progressive motility recovery rate following the freezing-thaw procedure than parameters of conventional semen analysis.

  14. Synergistic Antimycobacterial Actions of Knowltonia vesicatoria (L.f Sims

    Directory of Open Access Journals (Sweden)

    Antoinette Labuschagné

    2012-01-01

    Full Text Available Euclea natalensis A.DC., Knowltonia vesicatoria (L.f Sims, and Pelargonium sidoides DC. are South African plants traditionally used to treat tuberculosis. Extracts from these plants were used in combination with isoniazid (INH to investigate the possibility of synergy with respect to antimycobacterial activity. The ethanol extract of K. vesicatoria was subjected to fractionation to identify the active compounds. The activity of the Knowltonia extract remained superior to the fractions with a minimum inhibitory concentration (MIC of 625.0 μg/mL against Mycobacterium smegmatis and an MIC of 50.00 μg/mL against M. tuberculosis. The K. vesicatoria extract was tested against two different drug-resistant strains of M. tuberculosis, which resulted in an MIC of 50.00 μg/mL on both strains. The combination of K. vesicatoria with INH exhibited the best synergistic antimycobacterial activity with a fractional inhibitory concentration index of 0.25 (a combined concentration of 6.28 μg/mL. A fifty percent inhibitory concentration of this combination against U937 cells was 121.0 μg/mL. Two compounds, stigmasta-5,23-dien-3-ol (1 and 5-(hydroxymethylfuran-2(5H-one (2, were isolated from K. vesicatoria as the first report of isolation for both compounds from this plant and the first report of antimycobacterial activity. Compound (1 was active against drug-sensitive M. tuberculosis with an MIC of 50.00 μg/mL.

  15. Phase 1 Validation Testing and Simulation for the WEC-Sim Open Source Code

    Science.gov (United States)

    Ruehl, K.; Michelen, C.; Gunawan, B.; Bosma, B.; Simmons, A.; Lomonaco, P.

    2015-12-01

    WEC-Sim is an open source code to model wave energy converters performance in operational waves, developed by Sandia and NREL and funded by the US DOE. The code is a time-domain modeling tool developed in MATLAB/SIMULINK using the multibody dynamics solver SimMechanics, and solves the WEC's governing equations of motion using the Cummins time-domain impulse response formulation in 6 degrees of freedom. The WEC-Sim code has undergone verification through code-to-code comparisons; however validation of the code has been limited to publicly available experimental data sets. While these data sets provide preliminary code validation, the experimental tests were not explicitly designed for code validation, and as a result are limited in their ability to validate the full functionality of the WEC-Sim code. Therefore, dedicated physical model tests for WEC-Sim validation have been performed. This presentation provides an overview of the WEC-Sim validation experimental wave tank tests performed at the Oregon State University's Directional Wave Basin at Hinsdale Wave Research Laboratory. Phase 1 of experimental testing was focused on device characterization and completed in Fall 2015. Phase 2 is focused on WEC performance and scheduled for Winter 2015/2016. These experimental tests were designed explicitly to validate the performance of WEC-Sim code, and its new feature additions. Upon completion, the WEC-Sim validation data set will be made publicly available to the wave energy community. For the physical model test, a controllable model of a floating wave energy converter has been designed and constructed. The instrumentation includes state-of-the-art devices to measure pressure fields, motions in 6 DOF, multi-axial load cells, torque transducers, position transducers, and encoders. The model also incorporates a fully programmable Power-Take-Off system which can be used to generate or absorb wave energy. Numerical simulations of the experiments using WEC-Sim will be

  16. TOF-SIMS analysis: Application to ultra-thin AWA film on magnetic head

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    F-containing polymer was coated on the magnetic head of hard disc drive (HDD) as theultra-thin (<20(?)) film of anti-wetting agent (AWA). A static TOF-SIMS method has been applied tomeasuring the thickness and coating uniformity of the ultra-thin film. TOF- SIMS is also used tostudy the micro-tribology and transfer of lubricant between the magnetic head and media interface.

  17. Gastrointestinal motility during cardiopulmonary bypass : A sonomicrometric study

    NARCIS (Netherlands)

    Gu, YJ; de Kroon, TL; Elstrodt, JM; Rakhorst, G

    2006-01-01

    Cardiopulmonary bypass (CPB) is known to impair the integrity of the gastrointestinal tract. However, little is known about the movement behavior of the gastrointestinal tract during CPB. This study was aimed to assess the gastrointestinal motility with sonomicrometry, a distance measurement using u

  18. Helical motion of the cell body enhances Caulobacter crescentus motility.

    Science.gov (United States)

    Liu, Bin; Gulino, Marco; Morse, Michael; Tang, Jay X; Powers, Thomas R; Breuer, Kenneth S

    2014-08-01

    We resolve the 3D trajectory and the orientation of individual cells for extended times, using a digital tracking technique combined with 3D reconstructions. We have used this technique to study the motility of the uniflagellated bacterium Caulobacter crescentus and have found that each cell displays two distinct modes of motility, depending on the sense of rotation of the flagellar motor. In the forward mode, when the flagellum pushes the cell, the cell body is tilted with respect to the direction of motion, and it precesses, tracing out a helical trajectory. In the reverse mode, when the flagellum pulls the cell, the precession is smaller and the cell has a lower translation distance per rotation period and thus a lower motility. Using resistive force theory, we show how the helical motion of the cell body generates thrust and can explain the direction-dependent changes in swimming motility. The source of the cell body precession is believed to be associated with the flexibility of the hook that connects the flagellum to the cell body.

  19. Effects of storage temperature and extension media on motility of ...

    African Journals Online (AJOL)

    ADEYEYE

    2016-07-26

    Jul 26, 2016 ... Keywords: Egg-yolk citrate, Goat-milk citrate, Motility, Semen extension, Spermatozoa. Received: ... In addition, it was acclimatized for the experiment two weeks ... spreader slide to a drop of a mixture of the stain and fresh ...

  20. Surfactin restores and enhances swarming motility under heavy metal stress.

    Science.gov (United States)

    Singh, Anil Kumar; Dhanjal, Soniya; Cameotra, Swaranjit Singh

    2014-04-01

    The present work reports the importance of lipopeptide biosurfactant on swarming motility of multi-metal resistant (MMR) bacterium under heavy metal stress. The MMR bacteria strain CM100B, identified as Bacillus cereus, was isolated from the coal mine sample. The strain was able to grow and reduce several metals namely Cd(2+), Co(2+), Cu(2+), Ni(2+), Mn(2+) and Pb(2+) ions which are common environmental pollutants. Presence of toxic heavy metal ions in the swarming medium significantly altered the motility of CM100B. Presence of Cd(2+) and Pb(2+) ions inhibited development of peritrichous flagella, thus inhibiting swarming motility. However, the addition of anionic biosurfactant surfactin restored (in case of Cd(2+) and Pb(2+) ions) or enhanced (in case of Co(2+), Cu(2+), Ni(2+) and Mn(2+)) the swarming ability of CM100B. Zeta potential studies for determining bacterial cell surface charge indicated that surfactin provided a suitable swarming environment to bacteria even under metal stress by chelating to cationic metal ions. Non-ionic surfactant Triton X-100 was unable to restore swarming under Cd(2+) and Pb(2+) ion stress. Thus, suggesting that surfactin can aid in motility not only by reducing the surface tension of swarming medium but also by binding to metal ions in the presence of metal ions stress.

  1. A computational model of gastro-intestinal motility

    Science.gov (United States)

    Wilson, K. F.; Goossens, D. J.

    2001-12-01

    A simulated neural network model of a section of enteric nervous system is presented. The network is a layered feed-forward network consisting of integrate and fire units. The network shows the basic form of intestinal motility; a descending wave of relaxation followed by a wave of contraction. It also shows interesting (but not biologically realistic) spontaneous behaviours when no stimulus is present.

  2. HES6 enhances the motility of alveolar rhabdomyosarcoma cells

    Energy Technology Data Exchange (ETDEWEB)

    Wickramasinghe, Caroline M [MRC Cancer Cell Unit, Hutchison-MRC Research centre, Addenbrooke' s Hospital Cambridge, CB2 0XZ (United Kingdom); MRC Laboratory of Molecular Biology, Addenbrooke' s Hospital Cambridge, CB2 0QH (United Kingdom); Domaschenz, Renae [MRC Cancer Cell Unit, Hutchison-MRC Research centre, Addenbrooke' s Hospital Cambridge, CB2 0XZ (United Kingdom); Gene Regulation and Chromatin Group, MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College, Hammersmith Campus, Du Cane Road, London W12 ONN (United Kingdom); Amagase, Yoko [MRC Cancer Cell Unit, Hutchison-MRC Research centre, Addenbrooke' s Hospital Cambridge, CB2 0XZ (United Kingdom); Department of Pathophysiology, Faculty of Pharmaceutical Sciences, Doshisha Women' s College of Liberal Arts, Kodo, Kyotanabe, Kyoto 610-0395 (Japan); Williamson, Daniel [Molecular Cytogenetics, The Institute of Cancer Research, Sutton SM2 5NG (United Kingdom); Northern Institute for Cancer Research, Paul O' Gorman Building, Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH (United Kingdom); Missiaglia, Edoardo; Shipley, Janet [Molecular Cytogenetics, The Institute of Cancer Research, Sutton SM2 5NG (United Kingdom); Murai, Kasumi [MRC Cancer Cell Unit, Hutchison-MRC Research centre, Addenbrooke' s Hospital Cambridge, CB2 0XZ (United Kingdom); Jones, Philip H, E-mail: phj20@cam.ac.uk [MRC Cancer Cell Unit, Hutchison-MRC Research centre, Addenbrooke' s Hospital Cambridge, CB2 0XZ (United Kingdom)

    2013-01-01

    Absract: HES6, a member of the hairy-enhancer-of-split family of transcription factors, plays multiple roles in myogenesis. It is a direct target of the myogenic transcription factor MyoD and has been shown to regulate the formation of the myotome in development, myoblast cell cycle exit and the organization of the actin cytoskeleton during terminal differentiation. Here we investigate the expression and function of HES6 in rhabdomyosarcoma, a soft tissue tumor which expresses myogenic genes but fails to differentiate into muscle. We show that HES6 is expressed at high levels in the subset of alveolar rhabdomyosarcomas expressing PAX/FOXO1 fusion genes (ARMSp). Knockdown of HES6 mRNA in the ARMSp cell line RH30 reduces proliferation and cell motility. This phenotype is rescued by expression of mouse Hes6 which is insensitive to HES6 siRNA. Furthermore, expression microarray analysis indicates that the HES6 knockdown is associated with a decrease in the levels of Transgelin, (TAGLN), a regulator of the actin cytoskeleton. Knockdown of TAGLN decreases cell motility, whilst TAGLN overexpression rescues the motility defect resulting from HES6 knockdown. These findings indicate HES6 contributes to the pathogenesis of ARMSp by enhancing both proliferation and cell motility.

  3. Spermometer: electrical characterization of single boar sperm motility

    NARCIS (Netherlands)

    Wagenaar, de Bjorn; Geijs, Daan J.; Boer, de Hans; Bomer, Johan G.; Olthuis, Wouter; Berg, van den Albert; Segerink, Loes I.

    2016-01-01

    Objective: To study single sperm boar motility using electrical impedance measurements in a microfluidic system. Design: Comparison of the optical data and electrical impedance data. Setting: Research laboratory at a university. Animal(s): Boar semen sample were used. Intervention(s): A micr

  4. Opiate Modulation of Gastrointestinal Motility and the Actions of Trimebutine

    Directory of Open Access Journals (Sweden)

    Stephen M Collins

    1991-01-01

    novel therapeutic approaches to the treatment of motility disorders, including postoperative ileus and pseudo-obstruction. Finally, the effect of the drug on the colon supports the use of trimcbutine in irritable bowel syndrome patients who have constipation due to colonic inertia.

  5. Social motility in African trypanosomes: fact or model?

    Science.gov (United States)

    Bastin, Philippe; Rotureau, Brice

    2015-02-01

    African trypanosomes grown on agarose plates exhibit behaviours akin to social motility. This phenomenon has not been observed in vivo so far but recently turned out to be instrumental in the definition of two specific stages of the parasite cycle and as a tool to probe for trypanosome sensing functions. Copyright © 2015 Elsevier Ltd. All rights reserved.

  6. Pili-driven surface motility of Myxococcus xanthus

    Science.gov (United States)

    Gibiansky, Maxsim; Hu, Wei; Zhao, Kun; Pan, Hongwei; Shi, Wenyuan; Dahmen, Karin; Wong, Gerard

    2012-02-01

    Myxococcus xanthus is a common, rod-shaped soil-dwelling bacterium with complex motility characteristics. In groups, M. xanthus bacteria can move via social ``S'' motility, in which the Type IV Pili (TFP) attach to secreted exopolysaccharides (EPS). We examine this motility mechanism using high-framerate video acquisition, taking data on individual bacteria at 400 frames per second; using particle tracking algorithms, we algorithmically reconstruct the bacterial trajectories. The motion of a single bacterium as it is pulled by its TFP through the EPS layer on the surface is not smooth, but instead displays distinct plateaus and slips, with a wide range of plateau and slip lengths. The distribution of slips exhibits power law scaling, consistent with a crackling noise model; crackling noise has previously been used to model nonbiological systems such as earthquake dynamics and Barkhausen noise. We show quantitative agreement between mean field friction models and observed bacterial dynamics. We demonstrate that the crackling noise behavior of M. xanthus is strongly dependent on the presence of EPS, but is unaffected by the chemotactic behavior of the bacterium; we also demonstrate velocity coupling between pairs of bacteria in the early stages of social motility.

  7. Bacterial growth and motility in sub-micron constrictions

    NARCIS (Netherlands)

    Männik, J.; Driessen, R.; Galajda, P.; Keymer, J.E.; Dekker, C.

    2009-01-01

    In many naturally occurring habitats, bacteria live in micrometer-size confined spaces. Although bacterial growth and motility in such constrictions is of great interest to fields as varied as soil microbiology, water purification, and biomedical research, quantitative studies of the effects of conf

  8. SIRT1 inhibits the mouse intestinal motility and epithelial proliferation

    Science.gov (United States)

    SIRT1 inhibits the mouse intestinal motility and epithelial proliferation. Sirtuin 1 (SIRT1), a NAD+-dependent histone deacetylase, is involved in a wide array of cellular processes, including glucose homeostasis, energy metabolism, proliferation and apoptosis, and immune response. However, it is un...

  9. Flagellar motility and structure in the hyperthermoacidophilic archaeon Sulfolobus solfataricus

    NARCIS (Netherlands)

    Szabo, Zalan; Sani, Musa; Groeneveld, Maarten; Zolghadr, Benham; Schelert, James; Albers, Sonja-Verena; Blum, Paul; Boekema, Egbert J.; Driessen, Arnold J. M.

    2007-01-01

    Flagellation in archaea is widespread and is involved in swimming motility. Here, we demonstrate that the structural flagellin gene from the crenarchaeaon Suffolobus soffiataricus is highly expressed in stationary-phase-grown cells and under unfavorable nutritional conditions. A mutant in a flagella

  10. Morphological characteristics of motile plants for dynamic motion

    Science.gov (United States)

    Song, Kahye; Yeom, Eunseop; Kim, Kiwoong; Lee, Sang Joon

    2014-11-01

    Most plants have been considered as non-motile organisms. However, plants move in response to environmental changes for survival. In addition, some species drive dynamic motions in a short period of time. Mimosa pudica is a plant that rapidly shrinks its body in response to external stimuli. It has specialized organs that are omnidirectionally activated due to morphological features. In addition, scales of pinecone open or close up depending on humidity for efficient seed release. A number of previous studies on the dynamic motion of plants have been investigated in a biochemical point of view. In this study, the morphological characteristics of those motile organs were investigated by using X-ray CT and micro-imaging techniques. The results show that the dynamic motions of motile plants are supported by structural features related with water transport. These studies would provide new insight for better understanding the moving mechanism of motile plant in morphological point of view. This research was financially supported by the Creative Research Initiative of the Ministry of Science, ICT and Future Planning (MSIP) and the National Research Foundation (NRF) of Korea (Grant Number: 2008-0061991).

  11. SimFlu: a simulation tool for predicting the variation pattern of influenza A virus.

    Science.gov (United States)

    Ahn, Insung; Kim, Ha-Yeon; Jung, Sunghoon; Lee, Ji-Hae; Son, Hyeon Seok

    2014-09-01

    Since the first pandemic outbreak of avian influenza A virus (H5N1 subtype) in 1997, the National Center for Biotechnology Information (NCBI) has provided a large number of influenza virus sequences with well-organized annotations. Using the time-series sequences of influenza A viruses, we developed a simulation tool for influenza virus, named SimFlu, to predict possible future variants of influenza viruses. SimFlu can create variants from a seed nucleotide sequence of influenza A virus using the codon variation parameters included in the SimFlu package. The SimFlu library provides pre-calculated codon variation parameters for the H1N1, H3N2, and H5N1 subtypes of influenza A virus isolated from 2000 to 2011, allowing the users to simulate their own nucleotide sequences by selecting their preferred parameter options. SimFlu supports three operating systems - Windows, Linux, and Mac OS X. SimFlu is publicly available at http://lcbb.snu.ac.kr/simflu. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

  12. Direct infusion-SIM as fast and robust method for absolute protein quantification in complex samples

    Directory of Open Access Journals (Sweden)

    Christina Looße

    2015-06-01

    Full Text Available Relative and absolute quantification of proteins in biological and clinical samples are common approaches in proteomics. Until now, targeted protein quantification is mainly performed using a combination of HPLC-based peptide separation and selected reaction monitoring on triple quadrupole mass spectrometers. Here, we show for the first time the potential of absolute quantification using a direct infusion strategy combined with single ion monitoring (SIM on a Q Exactive mass spectrometer. By using complex membrane fractions of Escherichia coli, we absolutely quantified the recombinant expressed heterologous human cytochrome P450 monooxygenase 3A4 (CYP3A4 comparing direct infusion-SIM with conventional HPLC-SIM. Direct-infusion SIM revealed only 14.7% (±4.1 (s.e.m. deviation on average, compared to HPLC-SIM and a decreased processing and analysis time of 4.5 min (that could be further decreased to 30 s for a single sample in contrast to 65 min by the LC–MS method. Summarized, our simplified workflow using direct infusion-SIM provides a fast and robust method for quantification of proteins in complex protein mixtures.

  13. Mass assembly and morphological transformations since $z\\sim3$ from CANDELS

    CERN Document Server

    Huertas-Company, M; Pérez-González, P G; Ashby, M L N; Barro, G; Conselice, C; Daddi, E; Dekel, A; Dimauro, P; Faber, S M; Grogin, N A; Kartaltepe, J S; Kocevski, D D; Koekemoer, A M; Koo, D C; Mei, S; Shankar, F

    2016-01-01

    [abridged] We quantify the evolution of the stellar mass functions of star-forming and quiescent galaxies as a function of morphology from $z\\sim 3$ to the present. Our sample consists of ~50,000 galaxies in the CANDELS fields ($\\sim880$ $arcmin^2$), which we divide into four main morphological types, i.e. pure bulge dominated systems, pure spiral disk dominated, intermediate 2-component bulge+disk systems and irregular disturbed galaxies. Our main results are: Star-formation: At $z\\sim 2$, 80\\% of the stellar mass density of star-forming galaxies is in irregular systems. However, by $z\\sim 0.5$, irregular objects only dominate at stellar masses below $10^9M\\odot$. A majority of the star-forming irregulars present at $z\\sim 2$ undergo a gradual transformation from disturbed to normal spiral disk morphologies by $z\\sim 1$ without significant interruption to their star-formation. Rejuvenation after a quenching event does not seem to be common except perhaps for the most massive objects. Quenching: We confirm th...

  14. The medical ethics of Dr J Marion Sims: a fresh look at the historical record.

    Science.gov (United States)

    Wall, L L

    2006-06-01

    Vesicovaginal fistula was a catastrophic complication of childbirth among 19th century American women. The first consistently successful operation for this condition was developed by Dr J Marion Sims, an Alabama surgeon who carried out a series of experimental operations on black slave women between 1845 and 1849. Numerous modern authors have attacked Sims's medical ethics, arguing that he manipulated the institution of slavery to perform ethically unacceptable human experiments on powerless, unconsenting women. This article reviews these allegations using primary historical source material and concludes that the charges that have been made against Sims are largely without merit. Sims's modern critics have discounted the enormous suffering experienced by fistula victims, have ignored the controversies that surrounded the introduction of anaesthesia into surgical practice in the middle of the 19th century, and have consistently misrepresented the historical record in their attacks on Sims. Although enslaved African American women certainly represented a "vulnerable population" in the 19th century American South, the evidence suggests that Sims's original patients were willing participants in his surgical attempts to cure their affliction-a condition for which no other viable therapy existed at that time.

  15. GLABROUS INFLORESCENCE STEMS regulates trichome branching by genetically interacting with SIM in Arabidopsis

    Institute of Scientific and Technical Information of China (English)

    Li-li SUN; Zhong-jing ZHOU; Li-jun AN; Yan AN; Yong-qin ZHAO; Xiao-fang MENG; Clare STEELE-KING

    2013-01-01

    Arabidopsis trichomes are large branched single cells that protrude from the epidermis.The first morphological indication of trichome development is an increase in nuclear content resulting from an initial cycle of endoreduplication.Our previous study has shown that the C2H2 zinc finger protein GLABROUS INFLORESCENCE STEMS (GIS) is required for trichome initiation in the inflorescence organ and for trichome branching in response to gibberellic acid signaling,although GIS gene does not play a direct role in regulating trichome cell division.Here,we describe a novel role of GIS,controlling trichome cell division indirectly by interacting genetically with a key endoreduplication regulator SIAMESE (SIM).Our molecular and genetic studies have shown that GIS might indireclty control cell division and trichome branching by acting downstream of SIM.A loss of function mutation of SIM signficantly reduced the expression of GIS.Futhermore,the overexpression of GIS rescued the trichome cluster cell phenotypes of sim mutant.The gain or loss of function of GIS had no significant effect on the expression of SIM.These results suggest that GIS may play an indirect role in regulating trichome cell division by genetically interacting with SIM.

  16. The sim operon facilitates the transport and metabolism of sucrose isomers in Lactobacillus casei ATCC 334.

    Science.gov (United States)

    Thompson, John; Jakubovics, Nicholas; Abraham, Bindu; Hess, Sonja; Pikis, Andreas

    2008-05-01

    Inspection of the genome sequence of Lactobacillus casei ATCC 334 revealed two operons that might dissimilate the five isomers of sucrose. To test this hypothesis, cells of L. casei ATCC 334 were grown in a defined medium supplemented with various sugars, including each of the five isomeric disaccharides. Extracts prepared from cells grown on the sucrose isomers contained high levels of two polypeptides with M(r)s of approximately 50,000 and approximately 17,500. Neither protein was present in cells grown on glucose, maltose or sucrose. Proteomic, enzymatic, and Western blot analyses identified the approximately 50-kDa protein as an NAD(+)- and metal ion-dependent phospho-alpha-glucosidase. The oligomeric enzyme was purified, and a catalytic mechanism is proposed. The smaller polypeptide represented an EIIA component of the phosphoenolpyruvate-dependent sugar phosphotransferase system. Phospho-alpha-glucosidase and EIIA are encoded by genes at the LSEI_0369 (simA) and LSEI_0374 (simF) loci, respectively, in a block of seven genes comprising the sucrose isomer metabolism (sim) operon. Northern blot analyses provided evidence that three mRNA transcripts were up-regulated during logarithmic growth of L. casei ATCC 334 on sucrose isomers. Internal simA and simF gene probes hybridized to approximately 1.5- and approximately 1.3-kb transcripts, respectively. A 6.8-kb mRNA transcript was detected by both probes, which was indicative of cotranscription of the entire sim operon.

  17. Sperm motility of externally fertilizing fish and amphibians.

    Science.gov (United States)

    Browne, R K; Kaurova, S A; Uteshev, V K; Shishova, N V; McGinnity, D; Figiel, C R; Mansour, N; Agney, D; Wu, M; Gakhova, E N; Dzyuba, B; Cosson, J

    2015-01-01

    We review the phylogeny, sperm competition, morphology, physiology, and fertilization environments of the sperm of externally fertilizing fish and amphibians. Increased sperm competition in both fish and anurans generally increases sperm numbers, sperm length, and energy reserves. The difference between the internal osmolarity and iconicity of sperm cells and those of the aquatic medium control the activation, longevity, and velocity of sperm motility. Hypo-osmolarity of the aquatic medium activates the motility of freshwater fish and amphibian sperm and hyperosmolarity activates the motility of marine fish sperm. The average longevity of the motility of marine fish sperm (~550 seconds) was significantly (P fish sperm (~150 seconds), with the longevities of both marine and freshwater fish being significantly (P fish (140 μm/s) or freshwater fish (135 μm/s) sperm. The longevity of the sperm of giant salamanders (Cryptobranchoidea) of approximately 600 seconds was greater than that of freshwater fish sperm but much lower than anuran sperm. Our research and information from the literature showed that higher osmolarities promote greater longevity in anuran sperm, and some freshwater fish sperm, and that anuran and cryptobranchid sperm maintained membrane integrity long after the cessation of motility, demonstrating a preferential sharing of energy reserves toward the maintenance of membrane integrity. The maintenance of the membrane integrity of anuran sperm in fresh water for up to 6 hours showed an extremely high osmotic tolerance relative to fish sperm. The very high longevity and osmotic tolerance of anuran sperm and high longevity of cryptobranchid sperm, relative to those of freshwater fish, may reflect the complex fertilization history of amphibian sperm in general and anurans reversion from internal to external fertilization. Our findings provide a greater understanding of the reproductive biology of externally fertilizing fish and amphibians, and a

  18. Analyzing Neutrophil Morphology, Mechanics, and Motility in Sepsis : Options and Challenges for Novel Bedside Technologies

    NARCIS (Netherlands)

    Zonneveld, Rens; Molema, Grietje; Plötz, Frans B

    Objective: Alterations in neutrophil morphology (size, shape, and composition), mechanics (deformability), and motility (chemotaxis and migration) have been observed during sepsis. We combine summarizing features of neutrophil morphology, mechanics, and motility that change during sepsis with an

  19. Control of exoenzyme production, motility and cell differentiation in Serratia liquefaciens

    DEFF Research Database (Denmark)

    Givskov, Michael Christian; Eberl, Leo; Molin, Søren

    1997-01-01

    Serratia liquefaciens secretes a broad spectrum of hydrolytic enzymes to the surrounding medium and possesses the ability to differentiate into specialized swarmer cells capable of rapid surface motility. Control of exoenzyme production and swarming motility is governed by similar regulatory...

  20. Chemical abrasion-SIMS (CA-SIMS) U-Pb dating of zircon from the late Eocene Caetano caldera, Nevada

    Science.gov (United States)

    Watts, Kathryn E.; Coble, Matthew A.; Vazquez, Jorge A.; Henry, Christopher D.; Colgan, Joseph P.; John, David A.

    2016-01-01

    Zircon geochronology is a critical tool for establishing geologic ages and time scales of processes in the Earth's crust. However, for zircons compromised by open system behavior, achieving robust dates can be difficult. Chemical abrasion (CA) is a routine step prior to thermal ionization mass spectrometry (TIMS) dating of zircon to remove radiation-damaged parts of grains that may have experienced open system behavior and loss of radiogenic Pb. While this technique has been shown to improve the accuracy and precision of TIMS dating, its application to high-spatial resolution dating methods, such as secondary ion mass spectrometry (SIMS), is relatively uncommon. In our efforts to U-Pb date zircons from the late Eocene Caetano caldera by SIMS (SHRIMP-RG: sensitive high resolution ion microprobe, reverse geometry), some grains yielded anomalously young U-Pb ages that implicated Pb-loss and motivated us to investigate with a comparative CA and non-CA dating study. We present CA and non-CA 206Pb/238U ages and trace elements determined by SHRIMP-RG for zircons from three Caetano samples (Caetano Tuff, Redrock Canyon porphyry, and a silicic ring-fracture intrusion) and for R33 and TEMORA-2 reference zircons. We find that non-CA Caetano zircons have weighted mean or bimodal U-Pb ages that are 2–4% younger than CA zircons for the same samples. CA Caetano zircons have mean U-Pb ages that are 0.4–0.6 Myr older than the 40Ar/39Ar sanidine eruption age (34.00 ± 0.03 Ma; error-weighted mean, 2σ), whereas non-CA zircons have ages that are 0.7–1.3 Myr younger. U-Pb ages do not correlate with U (~ 100–800 ppm), Th (~ 50–300 ppm) or any other measured zircon trace elements (Y, Hf, REE), and CA and non-CA Caetano zircons define identical trace element ranges. No statistically significant difference in U-Pb age is observed for CA versus non-CA R33 or TEMORA-2 zircons. Optical profiler measurements of ion microprobe pits demonstrate consistent depths of ~ 1.6

  1. [Cerebral paragonimiasis and Bo Sung Sim's hemispherectomy in Korea in 1950s-1960s].

    Science.gov (United States)

    Park, Jiyoung; Miyagawa, Takuya; Hong, Jeonghwa; Kim, Ockjoo

    2011-06-30

    This paper deals with cerebral paragonimiasis and cerebral hemispherectomy conducted as a treatment of cerebral paragonimiasis by Bo Sung Sim in Korea in 1950s-1960s. He demonstrated that cerebral hemispherectomy could be used for unilateral diffuse cerebral paragonimiasis. Sim learned cerebral hemispherectomy from Dr. L. A. French. at the University of Minnesota from 1955 to 1957 in America. The authors argues that Bo Sung Sim's introduction of cerebral hemispherectomy to Korea was not a simple application of an advanced medical technology, but a complicated and active process in that Sim used the technique to intervene intractable complications from cerebral paragonimiasis such as generalized convulsions, spastic hemiplegia and mental deterioration. Bo Sung Sim, one of the neurosurgeons of the first generation in Korea, was trained in neurology, neuropathology, neuroradiology and animal experiments as well as in neurosurgery at the University of Minnesota. After returning to Korea, Sim faced parasitic diseases, one of the most serious public health problems at that time, which were far different from what he learned in America. As a neurosurgeon, Sim tackled with parasitic diseases of the central nervous system with various diagnostics and therapeutics. In 1950s, more than one million populations suffered from pulmonary paragonimiasis acquired by eating raw crabs or by feeding juice of crushed crayfish for the treatment of measles in Korea. About 26.6 percent of people with paragonimiasis had cerebral paragonimiasis. Before bithionol therapy was introduced in 1962, neurosurgery was the only available treatment to control increased intracranial pressures, intractable epilepsy, paralysis and mental deterioration. Between 1958 to 1962, Bo Sung Sim operated on 24 patients of cerebral paragonimiasis. In two of them, he performed cerebral hemispherectomy to control intractable convulsions when he found diffuse cerebral paragonimiasis and cerebral atrophy at the

  2. Multivariate analysis of TOF-SIMS spectra from self-assembled monolayers

    Science.gov (United States)

    Graham, Daniel Jay

    Recently the concept of engineered biomaterial surfaces has started a revolution in the biomaterials community. These biomaterial surfaces are designed using knowledge from cell biology to produce a healing response that will integrate the biomaterials into the body. These surfaces will require specific, complex chemistries that will elicit the desired responses. Such complex surfaces will require an equally detailed surface characterization method. Due to its molecular specificity and high sensitivity, TOF-SIMS appears to be an ideal method for this challenge. Nevertheless TOF-SIMS spectra are complex and difficult to interpret. This complexity results from the shear number of peaks within the spectra, the inter-related nature of the peaks, and lack of fundamental understanding of TOF-SIMS fragmentation mechanisms. This work approaches addressing these problems through use of multivariate analysis. Multivariate analysis enables detailed spectral interpretation and provides insight into fragmentation mechanisms by extracting the salient information from within the complex spectral data set. Multivariate spectral interpretation was explored using a series of self-assembled monolayers that varied in surface order, surface functionality, formation method, and chain length. A multivariate SAM ratio was developed that correlates with thermodynamic properties of the surface. This ratio is the first to demonstrate a direct relationship between TOF-SIMS data and surface thermodynamic parameters. A model for TOF-SIMS fragmentation of SAMs was created and explored using multivariate analysis of a thiol containing a hydroxyl end group. This model explains the emission of fragments from the surface over a time course experiment. This is the first use of multivariate analysis with TOF-SIMS data to provide mechanistic information about the TOF-SIMS process. This methodology provides a technique for studying TOF-SIMS fragmentation using actual data without the need for molecular

  3. SIM_EXPLORE: Software for Directed Exploration of Complex Systems

    Science.gov (United States)

    Burl, Michael; Wang, Esther; Enke, Brian; Merline, William J.

    2013-01-01

    Physics-based numerical simulation codes are widely used in science and engineering to model complex systems that would be infeasible to study otherwise. While such codes may provide the highest- fidelity representation of system behavior, they are often so slow to run that insight into the system is limited. Trying to understand the effects of inputs on outputs by conducting an exhaustive grid-based sweep over the input parameter space is simply too time-consuming. An alternative approach called "directed exploration" has been developed to harvest information from numerical simulators more efficiently. The basic idea is to employ active learning and supervised machine learning to choose cleverly at each step which simulation trials to run next based on the results of previous trials. SIM_EXPLORE is a new computer program that uses directed exploration to explore efficiently complex systems represented by numerical simulations. The software sequentially identifies and runs simulation trials that it believes will be most informative given the results of previous trials. The results of new trials are incorporated into the software's model of the system behavior. The updated model is then used to pick the next round of new trials. This process, implemented as a closed-loop system wrapped around existing simulation code, provides a means to improve the speed and efficiency with which a set of simulations can yield scientifically useful results. The software focuses on the case in which the feedback from the simulation trials is binary-valued, i.e., the learner is only informed of the success or failure of the simulation trial to produce a desired output. The software offers a number of choices for the supervised learning algorithm (the method used to model the system behavior given the results so far) and a number of choices for the active learning strategy (the method used to choose which new simulation trials to run given the current behavior model). The software

  4. Cluster SIMS and the Temperature Dependence of Molecular Depth Profiles

    Science.gov (United States)

    Mao, Dan; Wucher, Andreas; Brenes, Daniel A; Lu, Caiyan; Winograd, Nicholas

    2012-01-01

    The quality of molecular depth profiles created by erosion of organic materials by cluster ion beams exhibits a strong dependence upon temperature. To elucidate the fundamental nature of this dependence, we employ the Irganox 3114/1010 organic delta layer reference material as a model system. This delta-layer system is interrogated using a 40 keV C60+ primary ion beam. Parameters associated with the depth profile such as depth resolution, uniformity of sputtering yield and topography are evaluated between 90 K and 300 K using a unique wedge-crater beveling strategy that allows these parameters to be determined as a function of erosion depth from atomic force microscope measurements. The results show that the erosion rate calibration performed using the known Δ-layer depth in connection with the fluence needed to reach the peak of the corresponding SIMS signal response is misleading. Moreover, we show that the degradation of depth resolution is linked to a decrease of the average erosion rate and the buildup of surface topography in a thermally activated manner. This underlying process starts to influence the depth profile above a threshold temperature between 210 and 250 K for the system studied here. Below that threshold, the process is inhibited and steady-state conditions are reached with constant erosion rate, depth resolution and molecular secondary ion signals from both the matrix and the Δ-layers. In particular, the results indicate that further reduction of the temperature below 90 K does not lead to further improvement of the depth profile. Above the threshold, the process becomes stronger at higher temperature, leading to an immediate decrease of the molecular secondary ion signals. This signal decay is most pronounced for the highest m/z ions but is less for the smaller m/z ions, indicating a shift toward small fragments by accumulation of chemical damage. The erosion rate decay and surface roughness buildup, on the other hand, exhibit a rather sudden

  5. Beating the numbers through strategic intervention materials (SIMs): Innovative science teaching for large classes

    Science.gov (United States)

    Alboruto, Venus M.

    2017-05-01

    The study aimed to find out the effectiveness of using Strategic Intervention Materials (SIMs) as an innovative teaching practice in managing large Grade Eight Science classes to raise the performance of the students in terms of science process skills development and mastery of science concepts. Utilizing experimental research design with two groups of participants, which were purposefully chosen, it was obtained that there existed a significant difference in the performance of the experimental and control groups based on actual class observation and written tests on science process skills with a p-value of 0.0360 in favor of the experimental class. Further, results of written pre-test and post-test on science concepts showed that the experimental group with the mean of 24.325 (SD =3.82) performed better than the control group with the mean of 20.58 (SD =4.94), with a registered p-value of 0.00039. Therefore, the use of SIMs significantly contributed to the mastery of science concepts and the development of science process skills. Based on the findings, the following recommendations are offered: 1. that grade eight science teachers should use or adopt the SIMs used in this study to improve their students' performance; 2. training-workshop on developing SIMs must be conducted to help teachers develop SIMs to be used in their classes; 3. school administrators must allocate funds for the development and reproduction of SIMs to be used by the students in their school; and 4. every division should have a repository of SIMs for easy access of the teachers in the entire division.

  6. A platform for dynamic simulation and control of movement based on OpenSim and MATLAB.

    Science.gov (United States)

    Mansouri, Misagh; Reinbolt, Jeffrey A

    2012-05-11

    Numerical simulations play an important role in solving complex engineering problems and have the potential to revolutionize medical decision making and treatment strategies. In this paper, we combine the rapid model-based design, control systems and powerful numerical method strengths of MATLAB/Simulink with the simulation and human movement dynamics strengths of OpenSim by developing a new interface between the two software tools. OpenSim is integrated with Simulink using the MATLAB S-function mechanism, and the interface is demonstrated using both open-loop and closed-loop control systems. While the open-loop system uses MATLAB/Simulink to separately reproduce the OpenSim Forward Dynamics Tool, the closed-loop system adds the unique feature of feedback control to OpenSim, which is necessary for most human movement simulations. An arm model example was successfully used in both open-loop and closed-loop cases. For the open-loop case, the simulation reproduced results from the OpenSim Forward Dynamics Tool with root mean square (RMS) differences of 0.03° for the shoulder elevation angle and 0.06° for the elbow flexion angle. MATLAB's variable step-size integrator reduced the time required to generate the forward dynamic simulation from 7.1s (OpenSim) to 2.9s (MATLAB). For the closed-loop case, a proportional-integral-derivative controller was used to successfully balance a pole on model's hand despite random force disturbances on the pole. The new interface presented here not only integrates the OpenSim and MATLAB/Simulink software tools, but also will allow neuroscientists, physiologists, biomechanists, and physical therapists to adapt and generate new solutions as treatments for musculoskeletal conditions. Copyright © 2012 Elsevier Ltd. All rights reserved.

  7. Le tecnologie mobili dell’apprendimento permanente, il progetto MOTILL

    Directory of Open Access Journals (Sweden)

    Marco Arrigo

    2013-03-01

    Full Text Available In questo articolo vengono presentati alcuni dei risultati del progetto MOTILL. MOTILL, ovvero «Le Tecnologie Mobili nell’apprendimento permanente: buone pratiche», è un progetto finanziato dalla Comunità Europea, nell’ambito del National Lifelong Learning Strategies (NLLS. Il progetto, durato un anno e terminato a Marzo 2010, si è focalizzato sull’uso delle tecnologie mobili in contesti di lifelong learning (LLL. L’articolo sarà dedicato a una breve introduzione del progetto, dei suoi obiettivi e delle azioni portate avanti, e a un rapido riassunto dei principali risultati ottenuti, i quali sono stati resi disponibili online alla comunità scientifica e diffusi ai policy makers impegnati nei programmi di apprendimento permanente.

  8. Dopaminergic and beta-adrenergic effects on gastric antral motility

    DEFF Research Database (Denmark)

    Bech, K; Hovendal, C P; Gottrup, F

    1984-01-01

    of bethanechol or pentagastrin inducing motor activity patterns as in the phase III of the MMC and the digestive state respectively. The stimulated antral motility was dose-dependently inhibited by dopamine. The effect was significantly blocked by specifically acting dopaminergic blockers, while alpha- and beta......-adrenergic blockers were without any significant effects. Dose-response experiments with bethanechol and dopamine showed inhibition of a non-competitive type. Isoprenaline was used alone and in conjunction with selective blockade of beta 1- and beta 2-receptors during infusion of bethanechol which induces a pattern...... similar to phase III in the migrating myoelectric complex. The stimulated antral motility was dose-dependently inhibited by isoprenaline. The effect could be significantly blocked by propranolol (beta 1 + beta 2-adrenoceptor blocker) and by using in conjunction the beta 1-adrenoceptor blocker practolol...

  9. Curvature-guided motility of microalgae in geometric confinement

    CERN Document Server

    Ostapenko, Tanya; Böddeker, Thomas; Kreis, Christian; Cammann, Jan; Mazza, Marco G; Bäumchen, Oliver

    2016-01-01

    Microorganisms often live in microhabitats that consist of a liquid phase and a plethora of typically curved interfaces. The ways in which motile cells possessing propulsive appendages sense and interact with the physical nature of their environment remains unclear today. For pusher-type microswimmers with rear-mounted flagella, such as bacteria and spermatozoa, cell trapping at a wall was attributed to contrasting microscopic mechanisms, namely hydrodynamic and contact interactions. Here, we demonstrate that, in confined spaces, the geometry of the habitat controls the motility of microalgae that propel themselves by the beating of two anterior flagella. Brownian dynamics simulations and analytical theory both quantitatively match the experimental data and capture a characteristic curvature scaling observed in the experiments. This curvature-guided navigation of the microalgae originates from only two essential ingredients: excluded volume resulting in predominantly ballistic swimming in confinement and the ...

  10. Gastrointestinal transit times and motility in patients with cystic fibrosis

    DEFF Research Database (Denmark)

    Hedsund, Caroline; Gregersen, Tine; Jønsson, Iben;

    2012-01-01

    OBJECTIVE: Patients with cystic fibrosis (CF) often suffer from gastrointestinal (GI) dysfunction including obstructive symptoms, malabsorption and pain, but the underlying pathophysiology remains obscure. AIM: To compare GI motility and transit times in CF patients and healthy controls. MATERIAL...... AND METHODS: Ten CF patients (five women, median age 23) with pancreatic insufficiency were studied. Total gastrointestinal transit time (GITT) and segmental colonic transit times (SCTT) were assessed by radiopaque markers. Gastric emptying and small intestinal transit were evaluated using the magnet......-based motility tracking system (MTS-1). With each method patients were compared with 16 healthy controls. RESULTS: Basic contraction frequencies of the stomach and small intestine were normal, but the pill reached the cecum after 7 h in only 20% of CF patients while in 88% of controls (p = 0.001). Paradoxically...

  11. Physical models of collective cell motility: from cell to tissue

    Science.gov (United States)

    Camley, B. A.; Rappel, W.-J.

    2017-03-01

    In this article, we review physics-based models of collective cell motility. We discuss a range of techniques at different scales, ranging from models that represent cells as simple self-propelled particles to phase field models that can represent a cell’s shape and dynamics in great detail. We also extensively review the ways in which cells within a tissue choose their direction, the statistics of cell motion, and some simple examples of how cell–cell signaling can interact with collective cell motility. This review also covers in more detail selected recent works on collective cell motion of small numbers of cells on micropatterns, in wound healing, and the chemotaxis of clusters of cells.

  12. Persistence-driven durotaxis: Generic, directed motility in rigidity gradients

    CERN Document Server

    Novikova, Elizaveta A; Discher, Dennis E; Storm, Cornelis

    2015-01-01

    Cells move differently on substrates with different elasticities. In particular, the persistence time of their motion is higher on stiffer substrates. We show that this behavior will result in a net transport of cells directed up a soft-to-stiff gradient. Using simple random walk models with controlled persistence and stochastic simulations, we characterize this propensity to move in terms of the durotactic index measured in experiments. A one-dimensional model captures the essential features of this motion and highlights the competition between diffusive spreading and linear, wavelike propagation. Since the directed motion is rooted in a non-directional change in the behavior of individual cells, the motility is a kinesis rather than a taxis. Persistence-driven durokinesis is generic and may be of use in the design of instructive environments for cells and other motile, mechanosensitive objects.

  13. Microbial Morphology and Motility as Biosignatures for Outer Planet Missions

    Science.gov (United States)

    Nadeau, Jay; Lindensmith, Chris; Deming, Jody W.; Fernandez, Vicente I.; Stocker, Roman

    2016-10-01

    Meaningful motion is an unambiguous biosignature, but because life in the Solar System is most likely to be microbial, the question is whether such motion may be detected effectively on the micrometer scale. Recent results on microbial motility in various Earth environments have provided insight into the physics and biology that determine whether and how microorganisms as small as bacteria and archaea swim, under which conditions, and at which speeds. These discoveries have not yet been reviewed in an astrobiological context. This paper discusses these findings in the context of Earth analog environments and environments expected to be encountered in the outer Solar System, particularly the jovian and saturnian moons. We also review the imaging technologies capable of recording motility of submicrometer-sized organisms and discuss how an instrument would interface with several types of sample-collection strategies.

  14. Particle-based simulations of self-motile suspensions

    CERN Document Server

    Hinz, Denis F; Kim, Tae-Yeon; Fried, Eliot

    2013-01-01

    A simple model for simulating flows of active suspensions is investigated. The approach is based on dissipative particle dynamics. While the model is potentially applicable to a wide range of self-propelled particle systems, the specific class of self-motile bacterial suspensions is considered as a modeling scenario. To mimic the rod-like geometry of a bacterium, two dissipative particle dynamics particles are connected by a stiff harmonic spring to form an aggregate dissipative particle dynamics molecule. Bacterial motility is modeled through a constant self-propulsion force applied along the axis of each such aggregate molecule. The model accounts for hydrodynamic interactions between self-propelled agents through the pairwise dissipative interactions conventional to dissipative particle dynamics. Numerical simulations are performed using a customized version of the open-source LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) software package. Detailed studies of the influence of agent con...

  15. Motility contrast imaging of live porcine cumulus-oocyte complexes

    Science.gov (United States)

    An, Ran; Turek, John; Machaty, Zoltan; Nolte, David

    2013-02-01

    Freshly-harvested porcine oocytes are invested with cumulus granulosa cells in cumulus-oocyte complexes (COCs). The cumulus cell layer is usually too thick to image the living oocyte under a conventional microscope. Therefore, it is difficult to assess the oocyte viability. The low success rate of implantation is the main problem for in vitro fertilization. In this paper, we demonstrate our dynamic imaging technique called motility contrast imaging (MCI) that provides a non-invasive way to monitor the COCs before and after maturation. MCI shows a change of intracellular activity during oocyte maturation, and a measures dynamic contrast between the cumulus granulosa shell and the oocytes. MCI also shows difference in the spectral response between oocytes that were graded into quality classes. MCI is based on shortcoherence digital holography. It uses intracellular motility as the endogenous imaging contrast of living tissue. MCI presents a new approach for cumulus-oocyte complex assessment.

  16. Voltage- and calcium-dependent motility of saccular hair bundles

    Science.gov (United States)

    Quiñones, Patricia M.; Meenderink, Sebastiaan W. F.; Bozovic, Dolores

    2015-12-01

    Active bundle motility, which is hypothesized to supply feedback for mechanical amplification of signals, is thought to enhance sensitivity and sharpen tuning in vestibular and auditory organs. To study active hair bundle motility, we combined high-speed camera recordings of bullfrog sacculi, which were mounted in a two-compartment chamber, and voltage-clamp of the hair cell membrane potential. Using this paradigm, we measured three types of bundle motions: 1) spontaneous oscillations which can be analyzed to measure the physiological operating range of the transduction channel; 2) a sustained quasi-static movement of the bundle that depends on membrane potential; and 3) a fast, transient and asymmetric movement that resets the bundle position and depends on changes in the membrane potential. These data support a role for both calcium and voltage in the transduction-channel function.

  17. Motility-driven glass and jamming transitions in biological tissues

    CERN Document Server

    Bi, Dapeng; Marchetti, M Cristina; Manning, M Lisa

    2015-01-01

    Cell motion inside dense tissues governs many biological processes, including embryonic development and cancer metastasis, and recent experiments suggest that these tissues exhibit collective glassy behavior. To make quantitative predictions about glass transitions in tissues, we study a self-propelled Voronoi (SPV) model that simultaneously captures polarized cell motility and multi-body cell-cell interactions in a confluent tissue, where there are no gaps between cells. We demonstrate that the model exhibits a jamming transition from a solid-like state to a fluid-like state that is controlled by three parameters: the single-cell motile speed, the persistence time of single-cell tracks, and a target shape index that characterizes the competition between cell-cell adhesion and cortical tension. In contrast to traditional particulate glasses, we are able to identify an experimentally accessible structural order parameter that specifies the entire jamming surface as a function of model parameters. We demonstrat...

  18. Hydration-controlled bacterial motility and dispersal on surfaces

    DEFF Research Database (Denmark)

    Dechesne, Arnaud; Wang, G.; Gulez, Gamze

    2010-01-01

    hydrated habitats, where water dynamics result in fragmented aquatic habitats connected by micrometric films, is debated. Here, we quantify the spatial dynamics of Pseudomonas putida KT2440 and its nonflagellated isogenic mutant as affected by the hydration status of a rough porous surface using......Flagellar motility, a mode of active motion shared by many prokaryotic species, is recognized as a key mechanism enabling population dispersal and resource acquisition in microbial communities living in marine, freshwater, and other liquid-replete habitats. By contrast, its role in variably...... an experimental system that mimics aquatic habitats found in unsaturated soils. The flagellar motility of the model soil bacterium decreased sharply within a small range of water potential (0 to −2 kPa) and nearly ceased in liquid films of effective thickness smaller than 1.5 μm. However, bacteria could rapidly...

  19. Motility precedes egress of malaria parasites from oocysts

    Science.gov (United States)

    Klug, Dennis; Frischknecht, Friedrich

    2017-01-01

    Malaria is transmitted when an infected Anopheles mosquito deposits Plasmodium sporozoites in the skin during a bite. Sporozoites are formed within oocysts at the mosquito midgut wall and are released into the hemolymph, from where they invade the salivary glands and are subsequently transmitted to the vertebrate host. We found that a thrombospondin-repeat containing sporozoite-specific protein named thrombospondin-releated protein 1 (TRP1) is important for oocyst egress and salivary gland invasion, and hence for the transmission of malaria. We imaged the release of sporozoites from oocysts in situ, which was preceded by active motility. Parasites lacking TRP1 failed to migrate within oocysts and did not egress, suggesting that TRP1 is a vital component of the events that precede intra-oocyst motility and subsequently sporozoite egress and salivary gland invasion. DOI: http://dx.doi.org/10.7554/eLife.19157.001 PMID:28115054

  20. Benchmarking Exercises To Validate The Updated ELLWF GoldSim Slit Trench Model

    Energy Technology Data Exchange (ETDEWEB)

    Taylor, G. A.; Hiergesell, R. A.

    2013-11-12

    The Savannah River National Laboratory (SRNL) results of the 2008 Performance Assessment (PA) (WSRC, 2008) sensitivity/uncertainty analyses conducted for the trenches located in the EArea LowLevel Waste Facility (ELLWF) were subject to review by the United States Department of Energy (U.S. DOE) Low-Level Waste Disposal Facility Federal Review Group (LFRG) (LFRG, 2008). LFRG comments were generally approving of the use of probabilistic modeling in GoldSim to support the quantitative sensitivity analysis. A recommendation was made, however, that the probabilistic models be revised and updated to bolster their defensibility. SRS committed to addressing those comments and, in response, contracted with Neptune and Company to rewrite the three GoldSim models. The initial portion of this work, development of Slit Trench (ST), Engineered Trench (ET) and Components-in-Grout (CIG) trench GoldSim models, has been completed. The work described in this report utilizes these revised models to test and evaluate the results against the 2008 PORFLOW model results. This was accomplished by first performing a rigorous code-to-code comparison of the PORFLOW and GoldSim codes and then performing a deterministic comparison of the two-dimensional (2D) unsaturated zone and three-dimensional (3D) saturated zone PORFLOW Slit Trench models against results from the one-dimensional (1D) GoldSim Slit Trench model. The results of the code-to-code comparison indicate that when the mechanisms of radioactive decay, partitioning of contaminants between solid and fluid, implementation of specific boundary conditions and the imposition of solubility controls were all tested using identical flow fields, that GoldSim and PORFLOW produce nearly identical results. It is also noted that GoldSim has an advantage over PORFLOW in that it simulates all radionuclides simultaneously - thus avoiding a potential problem as demonstrated in the Case Study (see Section 2.6). Hence, it was concluded that the follow

  1. Developing integrated TOF-SIMS/MALDI IMS system in studying biological systems

    Science.gov (United States)

    Wu, Ligang

    Using imaging mass spectrometry (IMS) techniques (including TOF-SIMS and MALDI IMS) to study biological systems is a relatively new concept and quickly gained popularity in recent years. Imaging mass spectrometry is a discovery technology that utilizes a focused ion beam or laser beam to desorb ions from sample surface. By detecting the desorbed ions, the chemical distributions and biological changes of a sample surface can be analyzed. These techniques offer a new analytical imaging approach to investigate biological processes at the cellular and tissue level. In this research, a novel integrated TOF-SIMS/MALDI IMS system as well as IMS based biological-sample-preparation techniques and data-reduction methods are developed. We then demonstrate the power of these techniques in studying different biological systems, including monosaccharides isomers, human breast cancer cell lines, mouse embryo tissues and mouse kidney sections. Using TOF-SIMS and statistical analysis methods, seven monosaccharide isomers are fully differentiated by analyzing their characteristic spectral pattern. In addition, a deep understanding of the fragmentation pathway of these isomers under ion bombardment is gained. In an application of TOF-SIMS to the differentiation of three human breast cancer cell lines, MCF-7, T47D, and MDA-MB-231, we show that principal component analysis (PCA) data reduction of TOF-SIMS spectra can differentiate cellular compartments (cytosol, nuclear and particulate) within the cell types, as well as homogenates from among the three cell lines. In a tissue-specific application, we extend the analytical capabilities of TOF-SIMS and PCA by imaging and differentiating Formalin-fixed paraffin-embedded (FFPE) mouse embryo tissues. We demonstrate reproducible differentiation of six tissue types based on the remaining small molecules after paraffin-embedding and the fragments of the cellular proteins. In a unique study of fresh frozen mouse kidney tissues, both TOF-SIMS

  2. Stathmin activity influences sarcoma cell shape, motility, and metastatic potential.

    OpenAIRE

    Belletti, B; Nicoloso, M S; Schiappacassi, M; Berton, S; Lovat, F.; Wolf, K.; Canzonieri, V; D'Andrea, S.; Zucchetto, A; Friedl, P.H.A.; Colombatti, A; Baldassarre, G.

    2008-01-01

    The balanced activity of microtubule-stabilizing and -destabilizing proteins determines the extent of microtubule dynamics, which is implicated in many cellular processes, including adhesion, migration, and morphology. Among the destabilizing proteins, stathmin is overexpressed in different human malignancies and has been recently linked to the regulation of cell motility. The observation that stathmin was overexpressed in human recurrent and metastatic sarcomas prompted us to investigate sta...

  3. Discrimination of motile bacteria from filamentous fungi using dynamic speckle

    Science.gov (United States)

    Murialdo, Silvia E.; Passoni, Lucía I.; Guzman, Marcelo N.; Sendra, G. Hernán; Rabal, Héctor; Trivi, Marcelo; Gonzalez, J. Froilán

    2012-05-01

    We present a dynamic laser speckle method to easily discriminate filamentous fungi from motile bacteria in soft surfaces, such as agar plate. The method allows the detection and discrimination between fungi and bacteria faster than with conventional techniques. The new procedure could be straightforwardly extended to different micro-organisms, as well as applied to biological and biomedical research, infected tissues analysis, and hospital water and wastewaters studies.

  4. Non-motile tetraploid spermatozoa of Misgurnus loach hybrids

    OpenAIRE

    Zhao, Yan; Fujimoto, Takafumi; Psenicka, Martin; Saito, Taiju; Arai, Katsutoshi

    2016-01-01

    We have compared various properties of spermatozoa from the wild diploid male pond loach Misgurnus anguillicaudatus to those from the interspecific male hybrid of the cross between a female M. anguillicaudatus and a male mud loach M. mizolepis. Our results show that spermatozoa from this interspecific hybrid had poor motility, low viability, abnormal morphology, a larger volume of mitochondrial mass per cell and higher ATP content of spermatozoa with tetraploid DNA content, and they were pres...

  5. Effect of preoperative suggestion on postoperative gastrointestinal motility.

    OpenAIRE

    Disbrow, E A; Bennett, H L; Owings, J T

    1993-01-01

    Autonomic behavior is subject to direct suggestion. We found that patients undergoing major operations benefit more from instruction than from information and reassurance. We compared the return of intestinal function after intra-abdominal operations in 2 groups of patients: the suggestion group received specific instructions for the early return of gastrointestinal motility, and the control group received an equal-length interview offering reassurance and nonspecific instructions. The sugges...

  6. Effect of mepacrine on gastric motility in the rat.

    Science.gov (United States)

    Minker, E; Matejka, Z

    1979-01-01

    Mepacrine given orally to rats inhibits gastric motility; its blocking effect is comparable to that of chloroquine, papaverine, and drotaverine, but less expressed than that of bencyclane. Similarly as the delayed gastric emptying induced by chloroquine, the effect of mepacrine is antagonized by acetyl-beta-methylcholine in a dose-related fashion, while that of papaverine, drotaverine, and bencyclane remains unchanged after treatment with the cholinomimetic drug.

  7. The Semen pH Affects Sperm Motility and Capacitation.

    Science.gov (United States)

    Zhou, Ji; Chen, Li; Li, Jie; Li, Hongjun; Hong, Zhiwei; Xie, Min; Chen, Shengrong; Yao, Bing

    2015-01-01

    As the chemical environment of semen can have a profound effect on sperm quality, we examined the effect of pH on the motility, viability and capacitation of human sperm. The sperm in this study was collected from healthy males to avoid interference from other factors. The spermatozoa cultured in sperm nutrition solution at pH 5.2, 6.2, 7.2 and 8.2 were analyzed for sperm total motility, progressive motility (PR), hypo-osmotic swelling (HOS) rate, and sperm penetration. Our results showed that these parameters were similar in pH 7.2 and 8.2 sperm nutrition solutions, but decreased in pH 5.2 and 6.2 solutions. The HOS rate exhibited positive correlation with the sperm total motility and PR. In addition, the sperm Na(+)/K(+)-ATPase activity at different pHs was measured, and the enzyme activity was significantly lower in pH 5.2 and 6.2 media, comparing with that in pH 8.2 and pH 7.2 solutions. Using flow cytometry (FCM) and laser confocal scanning microscopy (LCSM) analysis, the intracellular Ca2(+ )concentrations of sperm cultured in sperm capacitation solution at pH 5.2, 6.2, 7.2 and 8.2 were determined. Compared with that at pH 7.2, the mean fluorescence intensity of sperm in pH 5.2 and 6.2 media decreased significantly, while that of pH 8.2 group showed no difference. Our results suggested that the declined Na(+)/K(+)-ATPase activity at acidic pHs result in decreased sperm movement and capacitation, which could be one of the mechanisms of male infertility.

  8. SimAlba: a Spatial Microsimulation approach to the analysis of health inequalities

    Directory of Open Access Journals (Sweden)

    Malcolm Campbell

    2016-10-01

    Full Text Available This paper presents applied geographical research based on a Spatial Microsimulation model, SimAlba aimed at estimating geographically sensitive health variables in Scotland. SimAlba has been developed in order to answer a variety of 'what-if' policy questions pertaining to health policy in Scotland. Using the SimAlba model, it is possible to simulate the distributions of previously unknown variables at the small area level such as; smoking, alcohol consumption, mental well-being and obesity. The SimAlba microdataset has been created by combining Scottish Health Survey (SHS and Census data using a deterministic reweighting Spatial Microsimulation algorithm developed for this purpose. The paper presents SimAlba outputs for Scotland’s largest city, Glasgow and examines the spatial distribution of the simulated variables for small geographical areas in Glasgow as well as the effects on individuals of different policy scenario outcomes. In simulating previously unknown spatial data a wealth of new perspectives can be examined and explored. This paper explores a small set of those potential avenues of research and shows the power of spatial microsimulation modelling in an urban context.

  9. SimAlba: A Spatial Microsimulation Approach to the Analysis of Health Inequalities.

    Science.gov (United States)

    Campbell, Malcolm; Ballas, Dimitris

    2016-01-01

    This paper presents applied geographical research based on a spatial microsimulation model, SimAlba, aimed at estimating geographically sensitive health variables in Scotland. SimAlba has been developed in order to answer a variety of "what-if" policy questions pertaining to health policy in Scotland. Using the SimAlba model, it is possible to simulate the distributions of previously unknown variables at the small area level such as smoking, alcohol consumption, mental well-being, and obesity. The SimAlba microdataset has been created by combining Scottish Health Survey and Census data using a deterministic reweighting spatial microsimulation algorithm developed for this purpose. The paper presents SimAlba outputs for Scotland's largest city, Glasgow, and examines the spatial distribution of the simulated variables for small geographical areas in Glasgow as well as the effects on individuals of different policy scenario outcomes. In simulating previously unknown spatial data, a wealth of new perspectives can be examined and explored. This paper explores a small set of those potential avenues of research and shows the power of spatial microsimulation modeling in an urban context.

  10. Graphene Oxide as a Novel Evenly Continuous Phase Matrix for TOF-SIMS

    Science.gov (United States)

    Cai, Lesi; Sheng, Linfeng; Xia, Mengchan; Li, Zhanping; Zhang, Sichun; Zhang, Xinrong; Chen, Hongyuan

    2016-12-01

    Using matrix to enhance the molecular ion signals for biomolecule identification without loss of spatial resolution caused by matrix crystallization is a great challenge for the application of TOF-SIMS in real-world biological research. In this report, graphene oxide (GO) was used as a matrix for TOF-SIMS to improve the secondary ion yields of intact molecular ions ([M + H]+). Identifying and distinguishing the molecular ions of lipids (m/z >700) therefore became straightforward. The spatial resolution of TOF-SIMS imaging could also be improved as GO can form a homogeneous layer of matrix instead of crystalline domain, which prevents high spatial resolution in TOF-SIMS imaging. Lipid mapping in presence of GO revealed the delicate morphology and distribution of single vesicles with a diameter of 800 nm. On GO matrix, the vesicles with similar shape but different chemical composition could be distinguished using molecular ions. This novel matrix holds potentials in such applications as the analysis and imaging of complex biological samples by TOF-SIMS.

  11. XCluSim: a visual analytics tool for interactively comparing multiple clustering results of bioinformatics data

    Science.gov (United States)

    2015-01-01

    Background Though cluster analysis has become a routine analytic task for bioinformatics research, it is still arduous for researchers to assess the quality of a clustering result. To select the best clustering method and its parameters for a dataset, researchers have to run multiple clustering algorithms and compare them. However, such a comparison task with multiple clustering results is cognitively demanding and laborious. Results In this paper, we present XCluSim, a visual analytics tool that enables users to interactively compare multiple clustering results based on the Visual Information Seeking Mantra. We build a taxonomy for categorizing existing techniques of clustering results visualization in terms of the Gestalt principles of grouping. Using the taxonomy, we choose the most appropriate interactive visualizations for presenting individual clustering results from different types of clustering algorithms. The efficacy of XCluSim is shown through case studies with a bioinformatician. Conclusions Compared to other relevant tools, XCluSim enables users to compare multiple clustering results in a more scalable manner. Moreover, XCluSim supports diverse clustering algorithms and dedicated visualizations and interactions for different types of clustering results, allowing more effective exploration of details on demand. Through case studies with a bioinformatics researcher, we received positive feedback on the functionalities of XCluSim, including its ability to help identify stably clustered items across multiple clustering results. PMID:26328893

  12. SimArray: a user-friendly and user-configurable microarray design tool

    Directory of Open Access Journals (Sweden)

    Meadows Lisa A

    2006-03-01

    Full Text Available Abstract Background Microarrays were first developed to assess gene expression but are now also used to map protein-binding sites and to assess allelic variation between individuals. Regardless of the intended application, efficient production and appropriate array design are key determinants of experimental success. Inefficient production can make larger-scale studies prohibitively expensive, whereas poor array design makes normalisation and data analysis problematic. Results We have developed a user-friendly tool, SimArray, which generates a randomised spot layout, computes a maximum meta-grid area, and estimates the print time, in response to user-specified design decisions. Selected parameters include: the number of probes to be printed; the microtitre plate format; the printing pin configuration, and the achievable spot density. SimArray is compatible with all current robotic spotters that employ 96-, 384- or 1536-well microtitre plates, and can be configured to reflect most production environments. Print time and maximum meta-grid area estimates facilitate evaluation of each array design for its suitability. Randomisation of the spot layout facilitates correction of systematic biases by normalisation. Conclusion SimArray is intended to help both established researchers and those new to the microarray field to develop microarray designs with randomised spot layouts that are compatible with their specific production environment. SimArray is an open-source program and is available from http://www.flychip.org.uk/SimArray/.

  13. High Gas Surface Densities yet Low UV Attenuation in z $\\sim$ 1 Disc Galaxies

    CERN Document Server

    Nordon, Raanan

    2016-01-01

    The gas in galaxies is both the fuel for star formation and a medium that attenuates the light of the young stars. We study the relations between UV attenuation, spectral slope, star formation rates, and molecular gas surface densities in a sample of 28 z$\\sim$1 and a reference sample of 32 z$\\sim$0 galaxies that are detected in CO, far-infrared, and rest frame UV. The samples are dominated by disc-like galaxies close to the main SFR--mass relation. We find that the location of the z$\\sim$1 galaxies on the IRX-$\\beta$ plane is correlated with their gas-depletion time-scale $\\tau_{dep}$ and can predict $\\tau_{dep}$ with a standard deviation of 0.16 dex. We use IRX-$\\beta$ to estimate the mean total gas column densities at the locations of star formation in the galaxies, and compare them to the mean molecular gas surface densities as measured from CO. We confirm previous results regarding high $N_H/A_V$ in z$\\sim$1 galaxies. We estimate an increase in the gas filling factor by a factor of 4--6 from z$\\sim$0 to ...

  14. Exploring the progenitors of brightest cluster galaxies at $z\\sim 2$

    CERN Document Server

    Zhao, Dongyao; Aragón-Salamanca, Alfonso; Almaini, Omar; Hartley, William G; Lani, Caterina; Mortlock, Alice; Old, Lyndsay

    2016-01-01

    We present a new method for tracing the evolution of BCGs from $z\\sim 2$ to $z\\sim 0$. We conclude on the basis of semi-analytical models that the best method to select BCG progenitors at $z\\sim 2$ is a hybrid environmental density and stellar mass ranking approach. Ultimately we are able to retrieve 45\\% of BCG progenitors. We apply this method on the CANDELS UDS data to construct a progenitor sample at high redshift. We furthermore populate the comparisons in local universe by using SDSS data with statistically likely contamination to ensure a fair comparison between high and low redshifts. Using these samples we demonstrate that the BCG sizes have grown by a factor of $\\sim 3.2$ since $z\\sim 2$, and BCG progenitors are mainly late-type galaxies, exhibiting less concentrated profiles than their early-type local counterparts. We find that BCG progenitors have more disturbed morphologies. In contrast, local BCGs have much smoother profiles. Moreover, we find that the stellar masses of BCGs have grown by a fac...

  15. SimRNAweb: a web server for RNA 3D structure modeling with optional restraints.

    Science.gov (United States)

    Magnus, Marcin; Boniecki, Michał J; Dawson, Wayne; Bujnicki, Janusz M

    2016-07-08

    RNA function in many biological processes depends on the formation of three-dimensional (3D) structures. However, RNA structure is difficult to determine experimentally, which has prompted the development of predictive computational methods. Here, we introduce a user-friendly online interface for modeling RNA 3D structures using SimRNA, a method that uses a coarse-grained representation of RNA molecules, utilizes the Monte Carlo method to sample the conformational space, and relies on a statistical potential to describe the interactions in the folding process. SimRNAweb makes SimRNA accessible to users who do not normally use high performance computational facilities or are unfamiliar with using the command line tools. The simplest input consists of an RNA sequence to fold RNA de novo. Alternatively, a user can provide a 3D structure in the PDB format, for instance a preliminary model built with some other technique, to jump-start the modeling close to the expected final outcome. The user can optionally provide secondary structure and distance restraints, and can freeze a part of the starting 3D structure. SimRNAweb can be used to model single RNA sequences and RNA-RNA complexes (up to 52 chains). The webserver is available at http://genesilico.pl/SimRNAweb.

  16. Investigation of the cosmetic ingredient distribution in the stratum corneum using NanoSIMS imaging

    Energy Technology Data Exchange (ETDEWEB)

    Tanji, N. [Kao Corporation, 1334 Minato, Wakayama-shi, Wakayama, 640-8580 (Japan)], E-mail: tanji.noriyuki@kao.co.jp; Okamoto, M. [Kao Corporation, 1334 Minato, Wakayama-shi, Wakayama, 640-8580 (Japan); Katayama, Y.; Hosokawa, M. [Kao Corporation, 2-1-3 Bunka, Sumida-ku, Tokyo, 131-8501 (Japan); Takahata, N.; Sano, Y. [Ocean Research Institute, University of Tokyo, 1-15-1 Minamidai, Nakano-ku, Tokyo 164-8639 (Japan)

    2008-12-15

    In order to understand the mechanisms of action of cosmetic ingredients, it is important to establish the distribution of the component agents within the epidermis of the skin. To date, time-of-flight secondary ion mass spectrometry (TOF-SIMS) has been used to detect cosmetic ingredients in the skin. However, it is technically difficult to investigate the distribution of the agents in the stratum corneum using TOF-SIMS. Therefore, an analytical method with higher spatial resolution is required. In this study, we investigated an imaging analysis technique based on NanoSIMS to detect cosmetic ingredients in the skin. Pig skin was used as a model for human skin. The sample was treated with a cosmetic formulation containing {sup 15}N-labelled pseudo-ceramide (SLE). The sample was frozen with liquid nitrogen and cross-sections were cut using a cryomicrotome. As a result, the fine layer structure of the corneocytes was clearly observed by using NanoSIMS. Our studies indicate that SLE penetrates into the stratum corneum via an intercellular route. We conclude that application of NanoSIMS analysis can contribute to a better understanding of the function of cosmetic ingredients in the skin.

  17. Elemental imaging at the nanoscale: NanoSIMS and complementary techniques for element localisation in plants.

    Science.gov (United States)

    Moore, Katie L; Lombi, Enzo; Zhao, Fang-Jie; Grovenor, Chris R M

    2012-04-01

    The ability to locate and quantify elemental distributions in plants is crucial to understanding plant metabolisms, the mechanisms of uptake and transport of minerals and how plants cope with toxic elements or elemental deficiencies. High-resolution secondary ion mass spectrometry (SIMS) is emerging as an important technique for the analysis of biological material at the subcellular scale. This article reviews recent work using the CAMECA NanoSIMS to determine elemental distributions in plants. The NanoSIMS is able to map elemental distributions at high resolution, down to 50 nm, and can detect very low concentrations (milligrams per kilogram) for some elements. It is also capable of mapping almost all elements in the periodic table (from hydrogen to uranium) and can distinguish between stable isotopes, which allows the design of tracer experiments. In this review, particular focus is placed upon studying the same or similar specimens with both the NanoSIMS and a wide range of complementary techniques, showing how the advantages of each technique can be combined to provide a fuller data set to address complex scientific questions. Techniques covered include optical microscopy, synchrotron techniques, including X-ray fluorescence and X-ray absorption spectroscopy, transmission electron microscopy, electron probe microanalysis, particle-induced X-ray emission and inductively coupled plasma mass spectrometry. Some of the challenges associated with sample preparation of plant material for SIMS analysis, the artefacts and limitations of the technique and future trends are also discussed.

  18. Emergence of coherent motion in aggregates of motile coupled maps

    Energy Technology Data Exchange (ETDEWEB)

    Garcia Cantu Ros, A., E-mail: anselmo@pik-potsdam.de [Potsdam Institute for Climate Impact Research, 14412 Potsdam (Germany); Interdisciplinary Center for Nonlinear Phenomena and Complex Systems (CENOLI), Service de Physique des Systemes Complexes et Mecanique Statistique, Universite Libre de Bruxelles, 1050 Brussels (Belgium); Antonopoulos, Ch.G., E-mail: cantonop@ulb.ac.be [Interdisciplinary Center for Nonlinear Phenomena and Complex Systems (CENOLI), Service de Physique des Systemes Complexes et Mecanique Statistique, Universite Libre de Bruxelles, 1050 Brussels (Belgium); Basios, V., E-mail: vbasios@ulb.ac.be [Interdisciplinary Center for Nonlinear Phenomena and Complex Systems (CENOLI), Service de Physique des Systemes Complexes et Mecanique Statistique, Universite Libre de Bruxelles, 1050 Brussels (Belgium)

    2011-08-15

    Highlights: > A minimal model of motile particles with adjustable intrinsic steering is presented. > Collective motion emerges due to self-adaptation of each particle's intrinsic state. > Adaptation is achieved by a map which behavior ranges from periodic to chaotic. > Higher cohesion occurs in a balanced combination of ordered and chaotic motion. > Exhibits an abrupt change in degree of coherence as a function of particle density. - Abstract: In this paper we study the emergence of coherence in collective motion described by a system of interacting motiles endowed with an inner, adaptative, steering mechanism. By means of a nonlinear parametric coupling, the system elements are able to swing along the route to chaos. Thereby, each motile can display different types of behavior, i.e. from ordered to fully erratic motion, accordingly with its surrounding conditions. The appearance of patterns of collective motion is shown to be related to the emergence of interparticle synchronization and the degree of coherence of motion is quantified by means of a graph representation. The effects related to the density of particles and to interparticle distances are explored. It is shown that the higher degrees of coherence and group cohesion are attained when the system elements display a combination of ordered and chaotic behaviors, which emerges from a collective self-organization process.

  19. Actin-based motility propelled by molecular motors

    Science.gov (United States)

    Upadyayula, Sai Pramod; Rangarajan, Murali

    2012-09-01

    Actin-based motility of Listeria monocytogenes propelled by filament end-tracking molecular motors has been simulated. Such systems may act as potential nanoscale actuators and shuttles useful in sorting and sensing biomolecules. Filaments are modeled as three-dimensional elastic springs distributed on one end of the capsule and persistently attached to the motile bacterial surface through an end-tracking motor complex. Filament distribution is random, and monomer concentration decreases linearly as a function of position on the bacterial surface. Filament growth rate increases with monomer concentration but decreases with the extent of compression. The growing filaments exert push-pull forces on the bacterial surface. In addition to forces, torques arise due to two factors—distribution of motors on the bacterial surface, and coupling of torsion upon growth due to the right-handed helicity of F-actin—causing the motile object to undergo simultaneous translation and rotation. The trajectory of the bacterium is simulated by performing a force and torque balance on the bacterium. All simulations use a fixed value of torsion. Simulations show strong alignment of the filaments and the long axis of the bacterium along the direction of motion. In the absence of torsion, the bacterial surface essentially moves along the direction of the long axis. When a small amount of the torsion is applied to the bacterial surface, the bacterium is seen to move in right-handed helical trajectories, consistent with experimental observations.

  20. Tektin 3 is required for progressive sperm motility in mice

    Science.gov (United States)

    Roy, Angshumoy; Lin, Yi-Nan; Agno, Julio E.; DeMayo, Francesco J.; Matzuk, Martin M.

    2008-01-01

    Tektins are evolutionarily-conserved flagellar (and ciliary) filamentous proteins present in the axoneme and peri-axonemal structures in diverse metazoan species. We have previously shown that tektin 3 (TEKT3) and tektin 4 (TEKT4) are male germ cell-enriched proteins, and that TEKT4 is essential for coordinated and progressive sperm motility in mice. Here we report that male mice null for TEKT3 produce sperm with reduced motility (47.2% motility) and forward progression, and increased flagellar structural bending defects. Male TEKT3-null mice however maintain normal fertility in two different genetic backgrounds tested, in contrast to TEKT4-null mice. Furthermore, male mice null for both TEKT3 and TEKT4 show subfertility on a mixed B6;129 genetic background, significantly different from either single knockouts, suggesting partial non-redundant roles for these two proteins in sperm physiology. Our results suggest that tektins are potential candidate genes for non-syndromic asthenozoospermia in humans. PMID:18951373

  1. EFFECTS OF METHYLNALTREXONE ON GUINEA PIG GASTROINTESTINAL MOTILITY

    Science.gov (United States)

    Anselmi, Laura; Huynh, Jennifer; Vegezzi, Gaia; Sternini, Catia

    2013-01-01

    The purpose of the present study was to compare the effects of methylnaltrexone (MNTX), a peripherally acting μ opioid receptor (μOR) antagonist, on gastrointestinal (GI) motility in naïve vs. opiate-chronically treated guinea pigs in vitro and in vivo. We have used the electrically stimulated muscle twitch contractions of longitudinal muscle-myenteric plexus (LMMP) preparations and total GI transit as measure of GI motility. In LMMP preparations of naïve guinea pigs, MNTX (1–30 μM) induced a significant, dose-response reduction of morphine-induced inhibition of electrically stimulated muscle twitch contractions, with an IC50 of 9.4 10−8M. By contrast, MNTX abolished the inhibitory effect of acute morphine at any concentration tested (1–30 μM) in the guinea pigs chronically treated with opiates. In vivo, MNTX (10–50 mg s.c.) did not affect GI transit in naïve guinea pigs when administered acutely or for 5 consecutive days, but reversed the GI transit delay induced by chronic morphine treatment. These findings show that MNTX is effective in reversing opiate-induced inhibition of GI motility acting at peripheral μORs, but does not exert a pharmacologic effect on GI transit in the absence of opiate stimulation. PMID:23361094

  2. Impact of external factors on sperm motility of Sepiella maindroni

    Institute of Scientific and Technical Information of China (English)

    WANG Jia; JIANG Xiamin; FENG Xiandong

    2011-01-01

    Sperm motility is important in reproductive biology. To understand the physiological ecology characteristics of sperm of Sepiella maindroni, we studied the activation rate, active time, and lifespan of sperm to evaluate the influence of external factors, including temperature, salinity, pH, glucose, NaC1, KC1, MgCl2, CaCl2, EDTA-2Na and artificial seawater on sperm motility. The results show that the appropriate activation and motility condition for sperm were: temperature 20-30掳C (optimum 25掳C), salinity 10.6-30.6 (optimum 15.9) and pH 8.0-8.6 (optimum 8.0-8.4). Sperm activity varied in different concentrations of glucose, NaCl, K.C1, MgCl2 and CaCl2. None of the selected concentrations of EDTA-2Na solution could activate the sperm. The activation rate in artificial seawater devoid of Ca+2, Mg+2 or HCO-3 was low. The results should help further studies on the preservation and activation of squid sperm.

  3. Reduced Protein Synthesis Fidelity Inhibits Flagellar Biosynthesis and Motility.

    Science.gov (United States)

    Fan, Yongqiang; Evans, Christopher R; Ling, Jiqiang

    2016-07-29

    Accurate translation of the genetic information from DNA to protein is maintained by multiple quality control steps from bacteria to mammals. Genetic and environmental alterations have been shown to compromise translational quality control and reduce fidelity during protein synthesis. The physiological impact of increased translational errors is not fully understood. While generally considered harmful, translational errors have recently been shown to benefit cells under certain stress conditions. In this work, we describe a novel regulatory pathway in which reduced translational fidelity downregulates expression of flagellar genes and suppresses bacterial motility. Electron microscopy imaging shows that the error-prone Escherichia coli strain lacks mature flagella. Further genetic analyses reveal that translational errors upregulate expression of a small RNA DsrA through enhancing its transcription, and deleting DsrA from the error-prone strain restores motility. DsrA regulates expression of H-NS and RpoS, both of which regulate flagellar genes. We demonstrate that an increased level of DsrA in the error-prone strain suppresses motility through the H-NS pathway. Our work suggests that bacteria are capable of switching on and off the flagellar system by altering translational fidelity, which may serve as a previously unknown mechanism to improve fitness in response to environmental cues.

  4. Effect of pre-freezing conditions on the progressive motility recovery rate of human frozen spermatozoa.

    Science.gov (United States)

    Zhang, X; Zhou, Y; Xia, W; Wu, H; Yao, K; Liu, H; Xiong, C

    2012-10-01

    We evaluated the effects of sperm concentration, progressive motility, sperm morphology, duration of abstinence and collection season on the progressive motility recovery rate of human frozen spermatozoa to identify characteristics that predict the progressive motility recovery rate of human frozen spermatozoa and improve the protocol for sperm collecting in sperm banks. A total of 14 190 semen samples donated at Zhejiang human sperm bank of China between September 2006 and June 2011 were collected from 1624 donors. Semen was evaluated according to WHO standard procedures for sperm concentration. Progressive motility, sperm morphology, ejaculate collection season and abstinence time were recorded. After freezing and thawing, the progressive motility was assessed. Results showed that sperm concentration, progressive motility and normal morphology were significantly associated with the progressive motility recovery rate of human frozen spermatozoa. In addition, the abstinence time and collection season also significantly affected progressive motility recovery rate. Our results indicated that sperm concentration, progressive motility and normal morphology could be valuable in predicting the progressive motility recovery rate of human frozen spermatozoa. As such, progressive motility recovery may be improved by donating semen when abstinent for 3-5 days and during seasons other than summer.

  5. Relaxation of Spin Polarized $^3$He in Mixtures of $^3$He and $^4$He at $\\sim$330 mK

    CERN Document Server

    Ye, Q; Zheng, W; Dutta, D; Dubose, F; Golub, R; Huffman, P; Swank, C; Korobkina, E; 10.1103/PhysRevA.80.023403

    2009-01-01

    We report the measurements of depolarization probabilities of polarized $^3$He in a rectangular acrylic cell with a deuterated tetraphenyl butadiene-doped deuterated polystyrene coating filled with superfluid $^4$He at $\\sim$330 mk with a magnetic holding field of $\\sim$7.3 G. We achieve a wall depolarization probability of $\\sim1.0\\times10^{-7}$. Such a surface will find application in a new experiment searching for the neutron electric dipole moment and other applications.

  6. Surface-motility induction, attraction and hitchhiking between bacterial species promote dispersal on solid surfaces.

    Science.gov (United States)

    Hagai, Efrat; Dvora, Reut; Havkin-Blank, Tal; Zelinger, Einat; Porat, Ziv; Schulz, Stefan; Helman, Yael

    2014-05-01

    The ability to move on solid surfaces provides ecological advantages for bacteria, yet many bacterial species lack this trait. We found that Xanthomonas spp. overcome this limitation by making use of proficient motile bacteria in their vicinity. Using X. perforans and Paenibacillus vortex as models, we show that X. perforans induces surface motility, attracts proficient motile bacteria and 'rides' them for dispersal. In addition, X. perforans was able to restore surface motility of strains that lost this mode of motility under multiple growth cycles in the lab. The described interaction occurred both on agar plates and tomato leaves and was observed between several xanthomonads and motile bacterial species. Thus, suggesting that this motility induction and hitchhiking strategy might be widespread and ecologically important. This study provides an example as to how bacteria can rely on the abilities of their neighboring species for their own benefit, signifying the importance of a communal organization for fitness.

  7. Sperm motility-initiating substance in newt egg-jelly induces differential initiation of sperm motility based on sperm intracellular calcium levels.

    Science.gov (United States)

    Watanabe, Akihiko; Takayama-Watanabe, Eriko; Vines, Carol A; Cherr, Gary N

    2011-01-01

    Sperm motility-initiating substance (SMIS), a novel motility inducer from newt egg-jelly, is activated by the release from associated jelly substances at the beginning of internal fertilization and affects female-stored sperm. We examined motility initiation kinetics of newt sperm in response to SMIS by monitoring the changes of sperm intracellular calcium ([Ca²(+)](i)). In quiescent non-motile sperm loaded with the Ca²(+) indicator Fluo-4, intracellular free Ca²(+) was observed around mitochondria using confocal scanning laser microscopy. A slight increase in [Ca²(+)](i) occurred simultaneously and transiently at motility initiation in sperm treated with either heated jelly extract (hJE) containing activated SMIS, or a low osmotic solution, which naturally initiates motility in externally-fertilizing amphibians and can initiate motility in urodele sperm. When the increase of [Ca²(+)](i) at motility-initiation was monitored using spectrofluorometry, large increases in [Ca²(+)](i) occurred immediately in the low osmotic solution and within 1.5 min in the hJE. In the intact jelly extract (no heating), small increases of [Ca²(+)](i) irregularly occurred from around 1 min and for about 4 min, during which motility was differentially initiated among sperm. These results indicate that the SMIS induces differential initiation of sperm motility depending on the activational states of the SMIS and its overall activity. The motility initiation in the jelly extract was delayed in sperm whose intracellular Ca²(+) had been chelated with BAPTA-AM. The relative levels of [Ca²(+)](i) were variable with a mean of 414 ± 256 nmol/L among resting sperm, suggesting that the level of [Ca²(+)](i) in the resting sperm modulates the responsiveness to the SMIS.

  8. Execution of the SimSET Monte Carlo PET/SPECT simulator in the condor distributed computing environment.

    Science.gov (United States)

    Baum, Karl G; Helguera, María

    2007-11-01

    SimSET is a package for simulation of emission tomography data sets. Condor is a popular distributed computing environment. Simple C/C++ applications and shell scripts are presented which allow the execution of SimSET on the Condor environment. This is accomplished without any modification to SimSET by executing multiple instances and using its combinebin utility. This enables research facilities without dedicated parallel computing systems to utilize the idle cycles of desktop workstations to greatly reduce the run times of their SimSET simulations. The necessary steps to implement this approach in other environments are presented along with sample results.

  9. Characterization of pro-inflammatory flagellin proteins produced by Lactobacillus ruminis and related motile Lactobacilli.

    Directory of Open Access Journals (Sweden)

    B Anne Neville

    Full Text Available Lactobacillus ruminis is one of at least twelve motile but poorly characterized species found in the genus Lactobacillus. Of these, only L. ruminis has been isolated from mammals, and this species may be considered as an autochthonous member of the gastrointestinal microbiota of humans, pigs and cows. Nine L. ruminis strains were investigated here to elucidate the biochemistry and genetics of Lactobacillus motility. Six strains isolated from humans were non-motile while three bovine isolates were motile. A complete set of flagellum biogenesis genes was annotated in the sequenced genomes of two strains, ATCC25644 (human isolate and ATCC27782 (bovine isolate, but only the latter strain produced flagella. Comparison of the L. ruminis and L. mali DSM20444(T motility loci showed that their genetic content and gene-order were broadly similar, although the L. mali motility locus was interrupted by an 11.8 Kb region encoding rhamnose utilization genes that is absent from the L. ruminis motility locus. Phylogenetic analysis of 39 motile bacteria indicated that Lactobacillus motility genes were most closely related to those of motile carnobacteria and enterococci. Transcriptome analysis revealed that motility genes were transcribed at a significantly higher level in motile L. ruminis ATCC27782 than in non-motile ATCC25644. Flagellin proteins were isolated from L. ruminis ATCC27782 and from three other Lactobacillus species, while recombinant flagellin of aflagellate L. ruminis ATCC25644 was expressed and purified from E. coli. These native and recombinant Lactobacillus flagellins, and also flagellate L. ruminis cells, triggered interleukin-8 production in cultured human intestinal epithelial cells in a manner suppressed by short interfering RNA directed against Toll-Like Receptor 5. This study provides genetic, transcriptomic, phylogenetic and immunological insights into the trait of flagellum-mediated motility in the lactobacilli.

  10. ROBO-SIM: a simulator for minimally invasive neurosurgery using an active manipulator.

    Science.gov (United States)

    Radetzky, A; Rudolph, M; Starkie, S; Davies, B; Auer, L M

    2000-01-01

    This application report describes the software system ROBO-SIM, which is a planning and simulation tool for minimally invasive neurosurgery. Using actual patient's datasets, ROBO-SIM includes all planning steps necessary. These are; defining the trepanation point for entry into the skull and the target point within the depth of the brain, checking the surgical track, performing virtual trepanations (virtual craniotomy), and defining sanctioned volumes for use with an intra-operative active manipulator. With the additional simulation part, neurosurgeons are able to simulate whole surgical interventions directly on the patient's anatomy using the same instruments as for the real operation. First tests with ROBO-SIM are performed on actual patient's datasets with ventricular tumours.

  11. PowderSim: Lagrangian Discrete and Mesh-Free Continuum Simulation Code for Cohesive Soils

    Science.gov (United States)

    Johnson, Scott; Walton, Otis; Settgast, Randolph

    2013-01-01

    PowderSim is a calculation tool that combines a discrete-element method (DEM) module, including calibrated interparticle-interaction relationships, with a mesh-free, continuum, SPH (smoothed-particle hydrodynamics) based module that utilizes enhanced, calibrated, constitutive models capable of mimicking both large deformations and the flow behavior of regolith simulants and lunar regolith under conditions anticipated during in situ resource utilization (ISRU) operations. The major innovation introduced in PowderSim is to use a mesh-free method (SPH-based) with a calibrated and slightly modified critical-state soil mechanics constitutive model to extend the ability of the simulation tool to also address full-scale engineering systems in the continuum sense. The PowderSim software maintains the ability to address particle-scale problems, like size segregation, in selected regions with a traditional DEM module, which has improved contact physics and electrostatic interaction models.

  12. Tracing the evolution of massive galaxies up to z \\sim 3

    CERN Document Server

    Longhetti, M; Fontana, A; Giallongo, E; Nonino, M; Saracco, P; Vanzella, E

    2003-01-01

    A census of massive galaxies at redshift increasingly higher than $z\\sim$1 may provide strong constraints on the history of mass assembly and of star formation. Here we report on the analysis of three galaxies selected in the Hubble Deep Field South on the basis of their unusually red near-IR color J-K$\\ge$3. These objects result to be massive (M$_{star}\\sim 10^{11}$M$_{\\odot}$) galaxies at redshift 2.5$5) at 1$$4) on the basis of which we identified 4 massive evolved galaxies at 1.5$sim$3 which evolves passively in time down to $z=0$.

  13. Comparison of low-temperature oxides on polycrystalline InP by AES, SIMS and XPS

    Science.gov (United States)

    Kazmerski, L. L.; Ireland, P. J.; Sheldon, P.; Chu, T. L.; Chu, S. S.; Lin, C. L.

    1980-10-01

    Oxides and their interfaces with polycrystalline InP are examined using complementary high-resolution AES, SIMS and XPS. The oxides, grown by low-temperature dry and wet processes, are compared for composition and phase content. SIMS and AES depth-composition data are used to compare the uniformity of the oxide layers and the composition of the interfacial region. Confirmation of impurity accumulation at the oxide-InP interfaces is presented, including buildup of elemental P and InP dopant, S. Other impurities associated with the growth of the wet oxide are found to be localized at the interface. Some evidence of impurity accumulation at grain boundaries at the wet oxide-polycrystalline InP interface is provided by SIMS and EBIC.

  14. The Northwest Frontier: Spectroscopy of N sim Z Nuclei Below Mass 100

    Science.gov (United States)

    Wadsworth, R.; Nara Singh, B. S.; Steer, A. N.; Jenkins, D. G.; Bentley, M. A.; Brock, T.; Davies, P.; Glover, R.; Pattabiraman, N. S.; Scholey, C.; Grahn, T.; Greenlees, P. T.; Jones, P.; Jakobsson, U.; Julin, R.; Juutinen, S.; Ketelhut, S.; Leino, M.; Nyman, M.; Perua, P.; Pakarinen, J.; Rahkila, P.; Ruotslainen, P.; Sorri, J.; Uusitalo, J.; Lister, C. J.; Butler, P. A.; Dimmock, M.; Joss, D. T.; Thomson, J.; Rinta-Antila, S.; Cederwall, B.; Hadinia, B.; Sandzelius, M.; Atac, A.; Betterman, L.; Blazhev, A.; Braun, N.; Finke, F.; Geibel, K.; Ilie, G.; Iwasaki, H.; Jolie, J.; Reiter, P.; Scholl, C.; Warr, N.; Boutachkov, P.; Caceres, L.; Domingo, C.; Engert, T.; Farinon, F.; Gerl, J.; Goel, N.; Gorska, M.; Grawe, H.; Kurz, N.; Kojuharov, I.; Pietri, S.; Nociforo, C.; Prochazka, A.; Wollersheim, H.-J.; Eppinger, K.; Faestermann, T.; Hinke, C.; Hoischen, R.; Kruecken, R.; Gottardo, A.; Liu, Z.; Woods, P.; Grebosz, J.; Merchant, E.; Nyberg, J.; Soderstrom, P.-A.; Podolyak, Z.; Regan, P.; Steer, S.; Pfutzner, M.; Rudolph, D.

    2009-03-01

    The spectroscopy and structure of excited states of N sim Z nuclei in the mass 70-100 region has been investigated using two techniques. In the A sim 70-80 region fusion evaporation reactions coupled with the recoil- beta -tagging method have been employed at Jyvaskyla to study low-lying states in odd-odd N = Z nuclei. Results from these and other data for known odd-odd nuclei above mass 60 will be discussed. In the heavier mass 90 region a fragmentation experiment has been performed using the RISING/FRS setup at GSI. This experiment was primarily aimed at searching for spin gap isomers in nuclei around A sim 96. The objectives of the latter experiment will be discussed.

  15. Implementation of DSP Based Cost Effective Inverter Fed Induction Motor Drive with VisSim

    Science.gov (United States)

    Mohanty, Nalin K.; Muthu, Ranganath

    2012-03-01

    The implementation of a Digital Signal Processor (DSP) based high-performance cost effective fed Induction Motor drive with VisSim/Embedded Controls Developer (ECD) is presented in this paper. In the experimental work VisSim/ECD software automatically converts the in built block diagram to C code and compiles, links, and downloads the code to DSP processor TMS320F2812. The DSP processor generates the required PWM to a cost effective ie four switch 3-phase (FSTPI) inverter. The power circuit of FSTPI fed drive system consists of an IGBT based FSTPI bridge inverter module feeding to a 5 hp three-phase squirrel cage induction motor. In this work the speed of induction motor output is shown by the GUI of VisSim/ECD and SPWM pulses, line voltages and line current output curves are shown using digital storage oscilloscope to demonstrate the feasibility of the system.

  16. Imaging and differentiation of mouse embryo tissues by ToF-SIMS

    Energy Technology Data Exchange (ETDEWEB)

    Wu, L; Lu, X; Kulp, K; Knize, M; Berman, E; Nelson, E; Felton, J; Wu, K J

    2006-06-16

    Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) equipped with a gold ion gun was used to image mouse embryos and differentiate tissue types (brain, spinal cord, skull, rib, heart and liver). Embryos were paraffin-embedded and then de-paraffinized. The robustness and repeatability of the method was determined by analyzing nine tissue slices from three different embryos over a period of several weeks. Using Principal Component Analysis (PCA) to reduce the spectral data generated by ToF-SIMS, histopathologically identified tissue types of the mouse embryos can be differentiated based on the characteristic differences in their mass spectra. These results demonstrate the ability of ToF-SIMS to determine subtle chemical differences even in fixed histological specimens.

  17. SimWall: a practical user-friendly stereo tiled display wall system

    Institute of Scientific and Technical Information of China (English)

    XIE Li-jun; ZHENG Yao; YANG Ting-jun; GAO Wen-xuan; PAN Ning-he

    2007-01-01

    Sim Wall is a user-friendly, stereo tiled display wall system composed of 18 commodity projectors operated by a Linux graphics cluster. Collaborating together, these projectors work as a single logical display capable of giving a high-resolution show,large-scale, and passive stereo scene. In order to avoid tedious system setup and maintenance, software-based automatic geometry and photometric calibration are used. The software calibration is integrated to the system seamlessly by an on-card transform method and is transparent to users. To end-users, Sim Wall works just as a common PC, but provides super computing, rendering and displaying ability. In addition, Sim Wall has stereoscopic function that gives users a semi-immersive experience in polarized passive way. This paper presents system architecture, implementation, and other technical issues such as hardware constraints,projectors alignment, geometry and photometric calibration, implementation of passive stereo, and development of overall software environment.

  18. Comparative assessment of bone pose estimation using Point Cluster Technique and OpenSim.

    Science.gov (United States)

    Lathrop, Rebecca L; Chaudhari, Ajit M W; Siston, Robert A

    2011-11-01

    Estimating the position of the bones from optical motion capture data is a challenge associated with human movement analysis. Bone pose estimation techniques such as the Point Cluster Technique (PCT) and simulations of movement through software packages such as OpenSim are used to minimize soft tissue artifact and estimate skeletal position; however, using different methods for analysis may produce differing kinematic results which could lead to differences in clinical interpretation such as a misclassification of normal or pathological gait. This study evaluated the differences present in knee joint kinematics as a result of calculating joint angles using various techniques. We calculated knee joint kinematics from experimental gait data using the standard PCT, the least squares approach in OpenSim applied to experimental marker data, and the least squares approach in OpenSim applied to the results of the PCT algorithm. Maximum and resultant RMS differences in knee angles were calculated between all techniques. We observed differences in flexion/extension, varus/valgus, and internal/external rotation angles between all approaches. The largest differences were between the PCT results and all results calculated using OpenSim. The RMS differences averaged nearly 5° for flexion/extension angles with maximum differences exceeding 15°. Average RMS differences were relatively small (techniques appeared to be a constant offset between the PCT and all OpenSim results, which may be due to differences in the definition of anatomical reference frames, scaling of musculoskeletal models, and/or placement of virtual markers within OpenSim. Different methods for data analysis can produce largely different kinematic results, which could lead to the misclassification of normal or pathological gait. Improved techniques to allow non-uniform scaling of generic models to more accurately reflect subject-specific bone geometries and anatomical reference frames may reduce differences

  19. Study and optimisation of SIMS performed with He{sup +} and Ne{sup +} bombardment

    Energy Technology Data Exchange (ETDEWEB)

    Pillatsch, L.; Vanhove, N.; Dowsett, D. [Department “Science and Analysis of Materials” (SAM), Centre de Recherche Public – Gabriel Lippmann, 41 rue du Brill, L-4422 Belvaux (Luxembourg); Sijbrandij, S.; Notte, J. [Carl Zeiss Microscopy LLC, One Corporation Way, Peabody, MA 01960 (United States); Wirtz, T., E-mail: wirtz@lippmann.lu [Department “Science and Analysis of Materials” (SAM), Centre de Recherche Public – Gabriel Lippmann, 41 rue du Brill, L-4422 Belvaux (Luxembourg)

    2013-10-01

    The combination of the high-brightness He{sup +}/Ne{sup +} atomic level ion source with the detection capabilities of secondary ion mass spectrometry (SIMS) opens up the prospect of obtaining chemical information with high lateral resolution and high sensitivity on the Zeiss ORION helium ion microscope (HIM). A feasibility study with He{sup +} and Ne{sup +} ion bombardment is presented in order to determine the performance of SIMS analyses using the HIM. Therefore, the sputtering yields, useful yields and detection limits obtained for metallic (Al, Ni and W) as well as semiconductor samples (Si, Ge, GaAs and InP) were investigated. All the experiments were performed on a Cameca IMS4f SIMS instrument which was equipped with a caesium evaporator and oxygen flooding system. For most of the elements, useful yields in the range of 10{sup −4} to 3 × 10{sup −2} were measured with either O{sub 2} or Cs flooding. SIMS experiments performed directly on the ORION with a prototype secondary ion extraction and detection system lead to results that are consistent with those obtained on the IMS4f. Taking into account the obtained useful yields and the analytical conditions, such as the ion current and typical dwell time on the ORION HIM, detection limits in the at% range and better can be obtained during SIMS imaging at 10 nm lateral resolution with Ne{sup +} bombardment and down to the ppm level when a lateral resolution of 100 nm is chosen. Performing SIMS on the HIM with a good detection limit while maintaining an excellent lateral resolution (<50 nm) is therefore very promising.

  20. CystiSim – An Agent-Based Model for Taenia solium Transmission and Control

    Science.gov (United States)

    Gabriël, Sarah; Dorny, Pierre; Speybroeck, Niko; Magnussen, Pascal; Torgerson, Paul; Johansen, Maria Vang

    2016-01-01

    Taenia solium taeniosis/cysticercosis was declared eradicable by the International Task Force for Disease Eradication in 1993, but remains a neglected zoonosis. To assist in the attempt to regionally eliminate this parasite, we developed cystiSim, an agent-based model for T. solium transmission and control. The model was developed in R and available as an R package (http://cran.r-project.org/package=cystiSim). cystiSim was adapted to an observed setting using field data from Tanzania, but adaptable to other settings if necessary. The model description adheres to the Overview, Design concepts, and Details (ODD) protocol and consists of two entities—pigs and humans. Pigs acquire cysticercosis through the environment or by direct contact with a tapeworm carrier's faeces. Humans acquire taeniosis from slaughtered pigs proportional to their infection intensity. The model allows for evaluation of three interventions measures or combinations hereof: treatment of humans, treatment of pigs, and pig vaccination, and allows for customary coverage and efficacy settings. cystiSim is the first agent-based transmission model for T. solium and suggests that control using a strategy consisting of an intervention only targeting the porcine host is possible, but that coverage and efficacy must be high if elimination is the ultimate goal. Good coverage of the intervention is important, but can be compensated for by including an additional intervention targeting the human host. cystiSim shows that the scenarios combining interventions in both hosts, mass drug administration to humans, and vaccination and treatment of pigs, have a high probability of success if coverage of 75% can be maintained over at least a four year period. In comparison with an existing mathematical model for T. solium transmission, cystiSim also includes parasite maturation, host immunity, and environmental contamination. Adding these biological parameters to the model resulted in new insights in the potential

  1. The role of public policies in reducing smoking: the Minnesota SimSmoke tobacco policy model.

    Science.gov (United States)

    Levy, David T; Boyle, Raymond G; Abrams, David B

    2012-11-01

    Following the landmark lawsuit and settlement with the tobacco industry, Minnesota pursued the implementation of stricter tobacco control policies, including tax increases, mass media campaigns, smokefree air laws, and cessation treatment policies. Modeling is used to examine policy effects on smoking prevalence and smoking-attributable deaths. To estimate the effect of tobacco control policies in Minnesota on smoking prevalence and smoking-attributable deaths using the SimSmoke simulation model. Minnesota data starting in 1993 are applied to SimSmoke, a simulation model used to examine the effect of tobacco control policies over time on smoking initiation and cessation. Upon validating the model against smoking prevalence, SimSmoke is used to distinguish the effect of policies implemented since 1993 on smoking prevalence. Using standard attribution methods, SimSmoke also estimates deaths averted as a result of the policies. SimSmoke predicts smoking prevalence accurately between 1993 and 2011. Since 1993, a relative reduction in smoking rates of 29% by 2011 and of 41% by 2041 can be attributed to tobacco control policies, mainly tax increases, smokefree air laws, media campaigns, and cessation treatment programs. Moreover, 48,000 smoking-attributable deaths will be averted by 2041. Minnesota SimSmoke demonstrates that tobacco control policies, especially taxes, have substantially reduced smoking prevalence and smoking-attributable deaths. Taxes, smokefree air laws, mass media, cessation treatment policies, and youth-access enforcement contributed to the decline in prevalence and deaths averted, with the strongest component being taxes. With stronger policies, for example, increasing cigarette taxes to $4.00 per pack, Minnesota's smoking rate could be reduced by another 13%, and 7200 deaths could be averted by 2041. Copyright © 2012 American Journal of Preventive Medicine. Published by Elsevier Inc. All rights reserved.

  2. CystiSim - An Agent-Based Model for Taenia solium Transmission and Control.

    Science.gov (United States)

    Braae, Uffe Christian; Devleesschauwer, Brecht; Gabriël, Sarah; Dorny, Pierre; Speybroeck, Niko; Magnussen, Pascal; Torgerson, Paul; Johansen, Maria Vang

    2016-12-01

    Taenia solium taeniosis/cysticercosis was declared eradicable by the International Task Force for Disease Eradication in 1993, but remains a neglected zoonosis. To assist in the attempt to regionally eliminate this parasite, we developed cystiSim, an agent-based model for T. solium transmission and control. The model was developed in R and available as an R package (http://cran.r-project.org/package=cystiSim). cystiSim was adapted to an observed setting using field data from Tanzania, but adaptable to other settings if necessary. The model description adheres to the Overview, Design concepts, and Details (ODD) protocol and consists of two entities-pigs and humans. Pigs acquire cysticercosis through the environment or by direct contact with a tapeworm carrier's faeces. Humans acquire taeniosis from slaughtered pigs proportional to their infection intensity. The model allows for evaluation of three interventions measures or combinations hereof: treatment of humans, treatment of pigs, and pig vaccination, and allows for customary coverage and efficacy settings. cystiSim is the first agent-based transmission model for T. solium and suggests that control using a strategy consisting of an intervention only targeting the porcine host is possible, but that coverage and efficacy must be high if elimination is the ultimate goal. Good coverage of the intervention is important, but can be compensated for by including an additional intervention targeting the human host. cystiSim shows that the scenarios combining interventions in both hosts, mass drug administration to humans, and vaccination and treatment of pigs, have a high probability of success if coverage of 75% can be maintained over at least a four year period. In comparison with an existing mathematical model for T. solium transmission, cystiSim also includes parasite maturation, host immunity, and environmental contamination. Adding these biological parameters to the model resulted in new insights in the potential

  3. 基于SimMechanics的仿人机器人运动学仿真%Kinematics Simulation of Humanoid Robot Based on SimMechanics

    Institute of Scientific and Technical Information of China (English)

    江乐果; 朱华炳

    2014-01-01

    The SimMechanics of Matlab toolbox is used to build the simulation model of humanoid robot mechanism. According to the model diagram,the humanoid robot dynamic walking process was observed intuitively,and the angular acceleration of robot body center of gravity and torque variation map of hip joint were solved. A planner five-bar mechanism motion model simulating to the instan-taneous state of humanoid robot was established,based on Kane method to solve the dynamic equation of the mechanism. The SimMe-chanics simulation tools are applied in the mechanism analysis,which provides a convenient and simple method for the mechanical sys-tem simulation.%利用Matlab/SimMechanics机构仿真工具建立了仿人机器人机构的仿真模型,并由模型图直观地观察仿人机器人的动态步行过程,求出了机器人躯体重心的角加速度和髋关节的扭矩变化图。建立了仿人机器人的瞬时状态的平面五杆机构运动模型,根据Kane法求解出了机构的动力学方程。在机构分析中应用SimMechanics仿真工具,为机械系统的仿真提供一种十分简便的方法。

  4. Surface Characterization of Polymer Blends by XPS and ToF-SIMS

    Directory of Open Access Journals (Sweden)

    Chi Ming Chan

    2016-08-01

    Full Text Available The surface properties of polymer blends are important for many industrial applications. The physical and chemical properties at the surface of polymer blends can be drastically different from those in the bulk due to the surface segregation of the low surface energy component. X-ray photoelectron spectroscopy (XPS and time-of-flight secondary mass spectrometry (ToF-SIMS have been widely used to characterize surface and bulk properties. This review provides a brief introduction to the principles of XPS and ToF-SIMS and their application to the study of the surface physical and chemical properties of polymer blends.

  5. A ToF-SIMS study of linseed oil bonded to mercapto silane treated aluminium

    Science.gov (United States)

    Bexell, U.; Olsson, M.; Sundell, P.-E.; Johansson, M.; Carlsson, P.; Hellsing, M.

    2004-06-01

    ToF-SIMS has been used to analyse an aluminium surface treated with a vegetable oil using a mercapto silane as a coupling agent between the aluminium substrate and the vegetable oil. The coupling between the vegetable oil and the mercapto silane was obtained through a photoinduced thiol-ene reaction using UV-radiation. The ToF-SIMS results show that the desired thiol-ene reaction has taken place between the unsaturated parts of the vegetable oil and the thiol groups of the mercapto silane via the thiol-ene reaction forming a surface film.

  6. CoaSim: A Flexible Environment for Simulating Genetic Data under Coalescent Models

    DEFF Research Database (Denmark)

    Mailund; Schierup, Mikkel Heide; Pedersen, Christian Nørgaard Storm

    2005-01-01

    get insight into these. Results We have created the CoaSim application as a flexible environment for Monte various types of genetic data under equilibrium and non-equilibrium coalescent variety of applications. Interaction with the tool is through the Guile version scripting language. Scheme scripts...... for many standard and advanced applications these can easily be modified by the user for a much wider range of applications. interface with less functionality and flexibility is also included. It is primarily exploratory and educational tool. Conclusions CoaSim is a powerful tool because of its flexibility...

  7. CulSim: A simulator of emergence and resilience of cultural diversity

    Science.gov (United States)

    Ulloa, Roberto

    CulSim is an agent-based computer simulation software that allows further exploration of influential and recent models of emergence of cultural groups grounded in sociological theories. CulSim provides a collection of tools to analyze resilience of cultural diversity when events affect agents, institutions or global parameters of the simulations; upon combination, events can be used to approximate historical circumstances. The software provides a graphical and text-based user interface, and so makes this agent-based modeling methodology accessible to a variety of users from different research fields.

  8. High-resolution imaging of complex crack chemistry in reactor steels by NanoSIMS

    Energy Technology Data Exchange (ETDEWEB)

    Lozano-Perez, S. [Department of Materials, University of Oxford, Parks Road, OX1 3PH Oxford (United Kingdom)], E-mail: Sergio.lozano-perez@materials.ox.ac.uk; Kilburn, M.R. [Department of Materials, University of Oxford, Parks Road, OX1 3PH Oxford (United Kingdom); Centre for Microscopy and Microanalysis, University of Western Australia, 35 Stirling Hwy, Crawley 6009 WA (Australia); Yamada, T.; Terachi, T. [Institute of Nuclear Safety Systems Inc, 64 Sata, Mikata-gun, Fukui 919-1205 (Japan); English, C.A. [Nexia Solutions, Harwell Business Centre, Didcot, Oxon OX11 0RA (United Kingdom); Grovenor, C.R.M. [Department of Materials, University of Oxford, Parks Road, OX1 3PH Oxford (United Kingdom)

    2008-02-29

    High-resolution analysis using a Cameca NanoSIMS 50 has been used to map the oxide chemistry in intergranular cracks in stainless steels. The technique has proven ideal for this type of sample, as it is able to discern between the different oxide layers and clarify the role of minor segregants such as boron and sulphur. Results are compared with analysis of the same sample by scanning auger microscopy and its interpretation discussed. The short time required to prepare and examine multiple regions present the NanoSIMS as an optimum tool for corrosion characterization.

  9. Taking the Measure of the Universe : Precision Astrometry with SIM PlanetQuest

    Science.gov (United States)

    Unwin, Stephen C.; Shao, Michael; Tanner, Angelle M.; Allen, Ronald J.; Beichman, Charles A.; Boboltz, David; Catanzarite, Joseph H.; Chaboyer, Brian C.; Ciardi, David R.; Edberg, Stephen J.; Fey, Alan L.; Fischer, Debra A.; Gelino, Christopher R.; Gould, Andrew P.; Grillmair, Carl; Henry, Todd J.; Johnston, Kathryn V.; Johnston, Kenneth J.; Jones, Dayton L.; Kulkarni, Shrinivas R.; Law, Nicholas M.; Majewski, Steven R.; Makarov, Valeri V.; Marcy, Geoffrey W.; Meier, David L.

    2008-01-01

    Precision astrometry at microarcsecond accuracy has application to a wide range of astrophysical problems. This paper is a study of the science questions that can be addressed using an instrument with flexible scheduling that delivers parallaxes at about 4 microarcsec (microns)as) on targets as faint as V = 20, and differential accuracy of 0.6 (microns)as on bright targets. The science topics are drawn primarily from the Team Key Projects, selected in 2000, for the Space Interferometry Mission PlanetQuest (SIM PlanetQuest). We use the capabilities of this mission to illustrate the importance of the next level of astrometric precision in modern astrophysics. SIM PlanetQuest is currently in the detailed design phase, having completed in 2005 all of the enabling technologies needed for the flight instrument. It will be the first space-based long baseline Michelson interferometer designed for precision astrometry. SIM will contribute strongly to many astronomical fields including stellar and galactic astrophysics, planetary systems around nearby stars, and the study of quasar and AGN nuclei. Using differential astrometry SIM will search for planets with masses as small as an Earth orbiting in the 'habitable zone' around the nearest stars, and could discover many dozen if Earth-like planets are common. It will characterize the multiple-planet systems that are now known to exist, and it will be able to search for terrestrial planets around all of the candidate target stars in the Terrestrial Planet Finder and Darwin mission lists. It will be capable of detecting planets around young stars, thereby providing insights into how planetary systems are born and how they evolve with time. Precision astrometry allows the measurement of accurate dynamical masses for stars in binary systems. SIM will observe significant numbers of very high- and low-mass stars, providing stellar masses to 1%, the accuracy needed to challenge physical models. Using precision proper motion

  10. Effects of Environment Factors on Initiation of Sperm Motility in Sea Cucumber Apostichopusjaponicus (Selenka)

    Institute of Scientific and Technical Information of China (English)

    YU Li; SHAO Mingyu; BAO Zhenmin; HU Jingjie; ZHANG Zhifeng

    2011-01-01

    Sperm of sea cucumber Apostichopus japonicus (Selenka) were quiescent in electrolyte NaCI solution and artificial seawater (ASW) and nonelectrolyte glucose and mannitol solutions when the osmolality was less than 200 mOsm kg-1 The sperm started to be motile as a result of increased osmolality, indicating an osmolality-dependent initiation of sperm motility in sea cucumber. After a brief incubation in hypotonic NaCI and glucose solutions with osmolalities of 200 and 400 mOsm kg-1, sperm lost partial motile ability. Sperm became immobilized when pH was 6.0 in NaCI, glucose and mannitol solutions, suggesting that an H+ release is involved in sperm activation. The decreased pH had no effect on the percentage of motile sperm in ASW, whereas it delayed the time period to reach the maximum motility (motilitymax). Extracellular Ca2+ in electrolyte solutions was not essential for motility stimulation but shortened the time of reaching motilitymax,. When Ca2+ was mixed in nonelectrolyte solutions the sperm motility was completely suppressed. The K+ channel blocker, quinine, suppressed the sperm motility in electrolyte solution, showing a possible involvement of K+ transport in the process. High K+ concentration did not affect the sperm motility in NsC1 solution, but decreased it in ASW and almost entirely suppressed it in nonelectrolyte solutions. The different effects of pH and K+ in ASW and NaCI solution indicate that external ions may also regulate sperm motility.

  11. The complex interplay among bacterial motility and virulence factors in different Escherichia coli infections.

    Science.gov (United States)

    Kao, C Y; Lin, W H; Tseng, C C; Wu, A B; Wang, M C; Wu, J J

    2014-12-01

    Motility mediated by the flagella of Escherichia coli is important for the bacteria to move toward host cells. Here, we present the relationship among bacterial motility, virulence factors, antimicrobial susceptibility, and types of infection. A total of 231 clinical E. coli isolates from different infections were collected and analyzed. Higher-motility strains (motility diameter ≥6.6 mm) were more common in spontaneous bacterial peritonitis (SBP) (SBP 59 %, colonization 32 %, urinary tract infection 16 %, urosepsis 34 %, and biliary tract infection 29 %; p coli strains with lower motility. E. coli isolates with higher and lower motility were in different phylogenetic groups (p = 0.018), with a lower prevalence of A and B1 subgroups in higher-motility strains. Also, the patterns of virulence factors and antibiotic susceptibility of E. coli isolates derived from various infections were significantly different. This study demonstrates that the prevalence of higher-motility strains was greater in E. coli isolates from SBP compared to other types of infection. Various types of E. coli infection were associated with differences in bacterial motility, virulence factors, and antibiotic susceptibility. More bacterial virulence factors may be necessary for the development of extraintestinal infections caused by E. coli isolates with lower motility.

  12. [On the significance of Solcoseryl on fertility. 1. The effect of Solcoseryl on sperm motility in vitro].

    Science.gov (United States)

    Mattheus, A; Heise, H; Hofmann, R

    1980-01-01

    The effect of different Solcoseryl (Solco, Basel, Switzerland) concentrations on the motility of human sperm were tested on 37 ejaculates taken from two subject groups. Altogether 111 motility studies were performed using the eosine vitality test. In view of the considerable variations associated with motility tests, Solcoseryl appeared to have no effect on sperm motility in the majority of cases in group 1. The observed improvement in motility (20%) was countered by still greater motility losses (27%). The results, obtained by studies on selected asthenospermia (group 2) are different, however: the 26% increase in motility was opposed to a motility loss of only 17%. A Solcoseryl concentration of 50% was found to have the best effects on motility. A general rise in sperm motility by means of Solcoseryl cannot be considered, although tests would appear advisable in isolated instances. Solcoseryl may be a valuable protective resuspension agent for insemination purposes.

  13. Characterization of plasma-functionalized surfaces by means of Tof-SIMS and multivariate analysis methods; Charakterisierung von plasmafunktionalisierten Oberflaechen mittels ToF-SIMS und multivariaten Analysemethoden

    Energy Technology Data Exchange (ETDEWEB)

    Gradowski, M. von

    2006-11-13

    The basic principles and opportunities of surface characterisation of selected functionalised samples via ToF-SIMS (time-of-flight secondary ion mass spectrometry) are presented. One major focus of the project was the investigation of non-cohesive surface layers which could exhibit either domain like structure or well defined single functionalised surfaces. By means of ToF-SIMS with the ability of displaying the lateral distribution of surface fragments information on the structure and surface density of specific fragments on the investigated film can be obtained. The combination of the ToF-SIMS experiment with a multivariate algorithm (partial least squares, PLS) provides an interesting opportunity to quantitatively determine surface properties such as elemental and molecular concentrations. Due to the fact that the ToF-SIMS spectrum consist of a huge amount of intensities, a single one-dimensional correlation (e.g. CF{sub 3} fragment intensity <-{yields} CF{sub 3} concentration) would disregard the rest of the spectral information. The large number of fragment intensities in the spectrum is representative for the chemical structure of the analysed surface. Therefore, it is crucial to consider this total information for the quantification of surface properties (element concentration, water contact angle etc.). Furthermore, this method allows the determination of surface properties with a lateral resolution of a few microns only. This can be used for chemically structured surfaces which for many applications show micrometer sized surface structures. Finally, a successful application of the multivariate models is presented for samples from the biological and medical area. Human fibroblasts and pancreas cells have been cultivated on plasma functionalised surfaces in order to study the influence of the functionalisation on the cell growth. The samples have been covered by TEM grids with meshes in the {mu}m range before the plasma treatment to generate structured

  14. Extending the molecular clutch beyond actin-based cell motility

    Science.gov (United States)

    Havrylenko, Svitlana; Mezanges, Xavier; Batchelder, Ellen; Plastino, Julie

    2014-10-01

    Many cell movements occur via polymerization of the actin cytoskeleton beneath the plasma membrane at the front of the cell, forming a protrusion called a lamellipodium, while myosin contraction squeezes forward the back of the cell. In what is known as the ‘molecular clutch’ description of cell motility, forward movement results from the engagement of the acto-myosin motor with cell-matrix adhesions, thus transmitting force to the substrate and producing movement. However during cell translocation, clutch engagement is not perfect, and as a result, the cytoskeleton slips with respect to the substrate, undergoing backward (retrograde) flow in the direction of the cell body. Retrograde flow is therefore inversely proportional to cell speed and depends on adhesion and acto-myosin dynamics. Here we asked whether the molecular clutch was a general mechanism by measuring motility and retrograde flow for the Caenorhabditis elegans sperm cell in different adhesive conditions. These cells move by adhering to the substrate and emitting a dynamic lamellipodium, but the sperm cell does not contain an acto-myosin cytoskeleton. Instead the lamellipodium is formed by the assembly of major sperm protein, which has no biochemical or structural similarity to actin. We find that these cells display the same molecular clutch characteristics as acto-myosin containing cells. We further show that retrograde flow is produced both by cytoskeletal assembly and contractility in these cells. Overall this study shows that the molecular clutch hypothesis of how polymerization is transduced into motility via adhesions is a general description of cell movement regardless of the composition of the cytoskeleton.

  15. Small doses of melatonin increase intestinal motility in rats.

    Science.gov (United States)

    Drago, Filippo; Macauda, Silvia; Salehi, Soudabeh

    2002-09-01

    Since melatonin receptors are present in the intestines, the possibility that this hormone may affect intestinal motility has been studied in the rat. Sprague-Dawley male rats were given a carmine cochineal powder meal and were injected intraperitoneally with 1, 10, 100, or 1000 microg/kg melatonin. Sixty minutes after treatment, intestinal transit was found to be faster in animals treated with small doses of melatonin (1 or 10 microg/kg) than in saline-injected controls. This effect, however, appear to be clearly reversed with 100 or 1000 microg/kg melatonin. In fact, these doses of the hormone reduced intestinal transit in rats. The nonselective melatonin receptor antagonist, luzindole (administered intraperitoneally in a dose of 0.25 mg/kg, 15 min prior to melatonin injection) totally prevented the accelerating effect of melatonin (10 microg/kg) on intestinal transit. Luzindole per se failed to affect gut motility. Injection of the reversible acetylcholinesterase inhibitor and cholinergic agent, neostigmine, accelerated intestinal transit but failed to influence melatonin effect on this parameter. In contrast, intraperitoneal injection of the muscarinic receptor antagonist atropine delayed intestinal transit per se but did not reduce the stimulating effect of melatonin on this parameter. Intestinal myoelectrical recording revealed that intestinal myoelectrical activity was increased by intraperitoneal injection of melatonin (10 microg/kg). Administration of luzindole totally prevented melatonin-induced increase of intestinal myoelectrical activity. These results indicate that melatonin may affect intestinal motility in rats when administered in small doses. This effect might be mediated by melatonin receptors in the intestines, although the involvement of central receptors for the hormone is also possible.

  16. SirA orthologs affect both motility and virulence.

    Science.gov (United States)

    Goodier, R I; Ahmer, B M

    2001-04-01

    The sirA gene of Salmonella enterica serovar Typhimurium encodes a two-component response regulator of the FixJ family that has a positive regulatory influence on the expression of type III secretion genes involved with epithelial cell invasion and the elicitation of bovine gastroenteritis. SirA orthologs in Pseudomonas, Vibrio, and Erwinia control the expression of distinct virulence genes in these genera, but an evolutionarily conserved target of SirA regulation has never been identified. In this study we tested the hypothesis that sirA may be an ancient member of the flagellar regulon. We examined the effect of a sirA mutation on transcriptional fusions to flagellar promoters (flhD, fliE, fliF, flgA, flgB, fliC, fliD, motA, and fliA) while using fusions to the virulence gene sopB as a positive control. SirA had only small regulatory effects on all fusions in liquid medium (less than fivefold). However, in various types of motility agar plates, sirA was able to activate a sopB fusion by up to 63-fold while repressing flagellar fusions by values exceeding 100-fold. Mutations in the sirA orthologs of Escherichia coli, Vibrio cholerae, Pseudomonas fluorescens, and Pseudomonas aeruginosa result in defects in either motility or motility gene regulation, suggesting that control of flagellar regulons may be an evolutionarily conserved function of sirA orthologs. The implications for our understanding of virulence gene regulation in the gamma Proteobacteria are discussed.

  17. Influence of electromagnetic SHF-waves on motility of tubifex

    Directory of Open Access Journals (Sweden)

    I. K. Smolyarenko

    2005-02-01

    Full Text Available We investigated influence of electromagnetic superhigh frequency (SHF waves (10 hHz on mechanical parameters of motility of bunch tubifex (1300 - 1500 units at a different load and sequence of its mechanical stimulation. Is shown, that after a пот-thermal waveirradiation (1 MVt/sm2 latency and forward front of mechanograms is increased on 5 - 10 %, amplitude and duration of the answers simultaneously decreases. The maximal mass, which can lift single unit tubifex is decreased. The capacity of single unit is reduced on the average about 80 %. The authors make conclusion about temporary negative influence SHF-waves on simple biological systems.

  18. Guaifenesin and increased sperm motility: a preliminary case report

    OpenAIRE

    Gary Means; Cristóbal S Berry-Cabán; Kurt Hammermeuller

    2010-01-01

    Gary Means1, Cristóbal S Berry-Cabán2, Kurt Hammermeuller11Department of Family Medicine, 2Department of Research, Womack Army Medical Center, Fort Bragg, NC, USABackground: A review of the literature and an extensive Medline search revealed that this is the first case report of the use of guaifenesin to increase sperm motility.Case: A 32-year-old male presented for an infertility evaluation. He reported an inability to conceive with his wife after 18 months of unprotect...

  19. Cancer cell motility: lessons from migration in confined spaces

    Science.gov (United States)

    Paul, Colin D.; Mistriotis, Panagiotis; Konstantopoulos, Konstantinos

    2017-01-01

    Time-lapse, deep-tissue imaging made possible by advances in intravital microscopy has demonstrated the importance of tumour cell migration through confining tracks in vivo. These tracks may either be endogenous features of tissues or be created by tumour or tumour-associated cells. Importantly, migration mechanisms through confining microenvironments are not predicted by 2D migration assays. Engineered in vitro models have been used to delineate the mechanisms of cell motility through confining spaces encountered in vivo. Understanding cancer cell locomotion through physiologically relevant confining tracks could be useful in developing therapeutic strategies to combat metastasis. PMID:27909339

  20. Transient state model of actin-based motility

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    We developed a transient model for actin-based motility.Diffusion of actin monomers was included in the formulation and its influence on the speed of actin-driven cargos was examined in detail.Our results clearly demonstrated how actin polymerization accelerates cargos that are initially stationary,as well as how steady-state is eventually reached.We also found that,due to polymerization and diffusion,actin monomer concentration near the load surface can be significantly lower than that in the rest of th...

  1. Motility of small nematodes in wet granular media

    CERN Document Server

    Juarez, G; Sznitman, J; Arratia, P E

    2010-01-01

    The motility behavior of the \\textit{Caenorhabditis elegans} is investigated in wet granular medium as a function of area density ($\\phi$) and dispersity. Surprisingly, the locomotion speed increases in granular media compared to free swimming. The surrounding structure of the medium leads to enhanced undulatory propulsion due to its ability to sustain a finite shear stress and convert lateral force into forward motion. For $\\phi > 0.55$, the nematode is observed to change its gate from swimming to crawling in polydisperse media \\textit{only}. This highlights the subtle difference in local structure between media.

  2. Digital radiography in the evaluation of oesophageal motility disorders

    Energy Technology Data Exchange (ETDEWEB)

    Aly, Yehia A

    2000-07-01

    AIMS: To develop a simple technique for examination of the oesophagus by digital radiography and to assess its role in the evaluation of motility disorders of the oesophagus. MATERIALS AND METHODS: Forty-nine patients and 44 control subjects underwent manometry and digital examination of the oesophagus. The digital study consisted of two parts: firstly examination of the pharynx and cervical oesophagus using 15 ml of fluid barium in anterio-posterior (AP) and lateral views, with image acquisition of four frames/s for 2 s. Secondly, examination of the thoracic oesophagus and oesophagogastric junction using 25 ml of barium in two prone oblique and one supine AP series, with image acquisition of one frame/s for 20 s. Oesophageal transit time (OTT) was measured in each case. Abnormal or non-peristaltic contractions were described regarding their morphology, time of visualization and length. The presence or absence of hiatal hernia, reflux or any associated organic lesions was noted. RESULTS: Digital radiography diagnosed 14 cases of achalasia and 28 cases of non-specific oesophageal motility disorder (NOMD). Normal OTT was 11.95 {+-} 1.304 s. The OTT was prolonged (16 s or more) in all patients except five; four of these were cases of NOMD. Abnormal contractions were classified into circular and longitudinal types. The circular non-obliterating type was commoner. Achalasia was diagnosed in all cases, as failure of relaxation of the inferior oesophageal sphincter was always present and easily depicted by digital radiography. Abnormal contractions in the body of the oesophagus were elicited in 57% of cases of achalasia. The sensitivity of digital radiography in detecting oesophageal motility disorders was 85.7% based on the presence of abnormal contractions and 91.6% by eliciting a prolonged OTT. CONCLUSIONS: Examination of the oesophagus by digital radiography is simple, non-invasive, reproducible, rapid and without discomfort to patients. It allows the diagnosis of

  3. A Mach-Zender Holographic Microscope for Quantifying Bacterial Motility

    Science.gov (United States)

    Niraula, B.; Nadeau, J. L.; Serabyn, E.; Wallace, J. K.; Liewer, K.; Kuhn, J.; Graff, E.; Lindensmith, C.

    2014-12-01

    New microscopic techniques have revolutionized cell biology over the past two decades. However, there are still biological processes whose details elude us, especially those involving motility: e.g. feeding behavior of microorganisms in the ocean, or migration of cancer cells to form metastases. Imaging prokaryotes, which range in size from several hundred nm to a few microns, is especially challenging. An emerging technique to address these issues is Digital Holographic Microscopy (DHM). DHM is an imaging technique that uses the interference of light to record and reproduce three-dimensional magnified images of objects. This approach has several advantages over ordinary brightfield microscopy for fieldwork: a larger depth of field, hands-off operation, robustness regarding environmental conditions, and large sampling volumes with quantitative 3D records of motility behavior. Despite these promising features, real-time DHM was thought to be impractical for technological and computational reasons until recently, and there has so far been very limited application of DHM to biology. Most existing instruments are limited in performance by their particular (e.g. in-line, lens-less, phase-shifting) approach to holography. These limitations can be mitigated with an off-axis dual-path configuration. Here we describe the design and implementation of a design for a Mach-Zehnder-type holographic microscope with diffraction-limited lateral resolution, with intended applications in environmental microbiology. We have achieved sub-micron resolution and three-dimensional tracking of prokaryotic and eukaryotic test strains designed to represent different modes and speeds of microbial motility. Prokaryotes are Escherichia coli, Vibrio alginolyticus, and Bacillus subtilis. Each shows a characteristic motility pattern, as we illustrate in holographic videos in sample chambers 0.6 mm in depth. The ability to establish gradients of attractants with bacterial taxis towards the

  4. Molecular depth profiling of organic photovoltaic heterojunction layers by ToF-SIMS: comparative evaluation of three sputtering beams

    NARCIS (Netherlands)

    Mouhib, T.; Poleunis, C.; Wehbe, N.; Michels, J.J.; Galagan, Y.; Houssiau, L.; Bertrand, P.; Delcorte, A.

    2013-01-01

    With the recent developments in secondary ion mass spectrometry (SIMS), it is now possible to obtain molecular depth profiles and 3D molecular images of organic thin films, i.e. SIMS depth profiles where the molecular information of the mass spectrum is retained through the sputtering of the sample.

  5. Cryopreservation of human spermatozoa. III. The effect of cryoprotectants on motility.

    Science.gov (United States)

    Critser, J K; Huse-Benda, A R; Aaker, D V; Arneson, B W; Ball, G D

    1988-08-01

    A series of experiments was conducted to examine potential toxic effects of cryoprotectants on motility of human spermatozoa. The data indicated that exposure of spermatozoa to cryoprotectant medium for as little as 15 minutes at room temperature caused a reduction in motility. This reduction in motility was caused by glycerol. Lowering glycerol concentrations from 7.5% to 5.0% improved sperm motility at 24 hours post-thaw. Sperm motility was not affected by either slow or abrupt cooling rates above -5 degrees C. Motility was greater in cryopreserved sperm at 24 hours post-thaw when glycerol was added at -5 degrees C rather than at room temperature. These data suggest that avoiding glycerol toxicity either by reducing the concentration used or by adding glycerol at a lower temperature, or both, may improve human sperm cryosurvival rates.

  6. Influences of dibutyryl cyclic adenosine monophosphate and forskolin on human sperm motility in vitro

    Institute of Scientific and Technical Information of China (English)

    Ji-HongLIU; YangLI; Zheng-GuoCAO; Zhang-QunYE

    2003-01-01

    Aim: To study the influences of dibutyryl cyclic adenosine monophosphate (dbcAMP) and forskolin on human sperm motility in vitro. Methods: Semen samples, aseptically obtained by masturbation and prepared by swim-up technique from 20 fertile men, were incubated with different concenlrations of dbcAMP and forskolin at 37℃. Measurements were carried out after l0 min, 20 min, 30 min and 60 min incubation. Motility parameters were estimated by using an automatic analyzing system. Results: Treatment with dbcAMP or forskolin resulted in a significant increase in sperm motility and progressive motility. The larger the concenlrations of dbcAMP or forskolin,the greater the effect appeared. The straight linear velocity and curvilinear velocity were not affected by both agents.Conclusion: dbcAMP and forskolin increase the motility and progressive motility of human sperm in vitro. ( Asian J Androl 2003 Jun; 5: 113-115)

  7. SimSketch: multiagent simulations based on learner-created sketches for early science education

    NARCIS (Netherlands)

    Bollen, L.; Joolingen, van W.R.

    2013-01-01

    This paper presents an approach to create simulations of science phenomena based on sketches. SimSketch, an integrated drawing and modeling tool, allows students to create sketches and apply behaviors to elements of their drawing. A multiagent simulation engine interprets and executes the model, thu

  8. The narrative structure of the unconsciousness in The Story of Sim Cheong.

    Science.gov (United States)

    Yoon, In Sun

    2014-01-01

    The narrative structure of The Story of Sim Cheong^1 exists on two levels: the narrative structure of the surface and the narrative structure of the unconscious ness in my terminology. The former is deduced from the content of the work corresponding to the concept of objective physical reality, and the other to the concept of psychic reality according to Freud. I see that the heroine Cheong was in an incestuous love relationship with her blind father nicknamed Sim Bongsa - Sim being his family name, Bongsa meaning the blind person - at the unconscious level. Their relationship became an incestuous symbiosis in which they are indispensable to each other. However, there is a break-up of their intimate relationship between father and daughter due to her abandonment by her father. This abandonment results in turn by her abandoning him; there is a mutual abandonment between the father and the daughter. A psychoanalytic study leads us to discover the narrative structure of the unconsciousness of The Story of Sim Cheong: being abandoned by her father and abandoning him from the perspective of the daughter.

  9. Rosmarinic acid content in antidiabetic aqueous extract from ocimum canum sims in Ghana

    Science.gov (United States)

    Rosmarinic acid (RA) is an important polyphenol that is found in a variety of herbs including Ocimum canum sims (locally called eme or akokobesa in Ghana). Aqueous extracts from the leaves of O. canum are used as an antidiabetic herbal medicine in Ghana. Analytical TLC was used to examine the compos...

  10. Rosmarinic acid content in antidiabetic aqueous extract of Ocimum canum Sims grown in Ghana

    Science.gov (United States)

    Rosmarinic acid (RA) is an important polyphenol that is found in a variety of herbs including Ocimum canum sims (locally called eme or akokobesa in Ghana). Aqueous extracts from the leaves of O.canum are used as an antidiabetic herbal medicine in Ghana. Interestingly, rosmarinic acid content and p...

  11. Hanford Soil Inventory Model (SIM) Rev. 1 Software Documentation – Requirements, Design, and Limitations

    Energy Technology Data Exchange (ETDEWEB)

    Simpson, Brett C.; Corbin, Rob A.; Anderson, Michael J.; Kincaid, Charles T.

    2006-09-25

    The objective of this document is to support the simulation results reported by Corbin et al. (2005) by documenting the requirements, conceptual model, simulation methodology, testing, and quality assurance associated with the Hanford Soil Inventory Model (SIM). There is no conventional software life-cycle documentation associated with the Hanford SIM because of the research and development nature of the project. Because of the extensive use of commercial- off-the-shelf software products, there was little actual software development as part of this application. This document is meant to provide historical context and technical support of Corbin et al. (2005), which is a significant revision and update to an earlier product Simpson et al. (2001). The SIM application computed waste discharges composed of 75 analytes at 377 waste sites (liquid disposal, unplanned releases, and tank farm leaks) over an operational period of approximately 50 years. The development and application of SIM was an effort to develop a probabilistic approach to estimate comprehensive, mass balanced-based contaminant inventories for the Hanford Site post-closure setting. A computer model capable of calculating inventories and the associated uncertainties as a function of time was identified to address the needs of the Remediation and Closure Science (RCS) Project.

  12. Why is SIMS underused in chemical and biological analysis? Challenges and opportunities.

    Science.gov (United States)

    Walker, Amy V

    2008-12-01

    Improvements have led to many developments in SIMS, including better 2D MS imaging, the ability to perform molecular depth profiling, and the development of 3D MS imaging. (To listen to a podcast about this feature, please go to the Analytical Chemistry website at pubs.acs.org/ac.).

  13. ToF-SIMS of tissues: "lessons learned" from mice and women.

    Science.gov (United States)

    Gamble, Lara J; Graham, Daniel J; Bluestein, Blake; Whitehead, Nicholas P; Hockenbery, David; Morrish, Fionnuala; Porter, Peggy

    2015-03-13

    The ability to image cells and tissues with chemical and molecular specificity could greatly expand our understanding of biological processes. The subcellular resolution mass spectral imaging capability of time of flight secondary ion mass spectrometry (ToF-SIMS) has the potential to acquire chemically detailed images. However, the complexities of biological systems combined with the sensitivity of ToF-SIMS require careful planning of experimental methods. Tissue sample preparation methods of formalin fixation followed by paraffin embedding (FFPE) and OCT embedding are compared. Results show that the FFPE can potentially be used as a tissue sample preparation protocol for ToF-SIMS analysis if a cluster ion pre-sputter is used prior to analysis and if nonlipid related tissue features are the features of interest. In contrast, embedding tissue in OCT minimizes contamination and maintains lipid signals. Various data acquisition methodologies and analysis options are discussed and compared using mouse breast and diaphragm muscle tissue. Methodologies for acquiring ToF-SIMS 2D images are highlighted along with applications of multivariate analysis to better identify specific features in a tissue sections when compared to H&E images of serial sections. Identification of tissue features is necessary for researchers to visualize a molecular map that correlates with specific biological features or functions. Finally, lessons learned from sample preparation, data acquisition, and data analysis methods developed using mouse models are applied to a preliminary analysis of human breast tumor tissue sections.

  14. Simulation Study (SimStudy): A Simulation Tool for Engineers and Mission Planners

    Science.gov (United States)

    2013-09-01

    meters of 0.065-inch Zylon Cable Tension Droop 8 The data tables input into the towed target input file for SimStudy are based on the towlines that...are most commonly used for each particular tow. For instance, the TIX-4 is most often towed with 5,000 feet of 0.050-inch diameter Zylon , while the

  15. SimLandScape, a sketching tool for collaborative spatial planning

    NARCIS (Netherlands)

    Ligtenberg, A.; Vries, de E.A.; Vreenegoor, R.; Bulens, J.D.

    2011-01-01

    Interactive spatial planning requires the development of planning support systems (PSSs) that are specifically tailored to support the exchange of ideas and visions during the planning process. This article presents SimLandScape, a client-server-based PSS designed to combine sketching and geographic

  16. No Selling the Genie Lamp: A Game Literacy Practice in "The Sims"

    Science.gov (United States)

    Hayes, Elisabeth R.; Gee, James Paul

    2010-01-01

    Drawing on the New Literacy Studies, the authors argue that game literacy takes multiple forms and is embedded in different practices associated with particular games and gaming communities. They examine one specific game literacy practice that involves players of "The Sims" creating challenges for other players, and they identify how playing and…

  17. VO2sim 0.1: Using Simulation to Understand Measurement Error in Indirect Calorimetry

    Science.gov (United States)

    2015-08-01

    Calorimetry by Matthew S Tenan Approved for public release; distribution is unlimited. NOTICES Disclaimers...Simulation to Understand Measurement Error in Indirect Calorimetry by Matthew S Tenan Human Research and Engineering Directorate, ARL...VO2sim 0.1: Using Simulation to Understand Measurement Error in Indirect Calorimetry 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT

  18. Continuos y el producto simétrico suspensión

    Directory of Open Access Journals (Sweden)

    Franco Barragán

    2012-01-01

    Full Text Available En este artículo presentamos una breve introducción a la teoría de los continuos y sus hiperespacios. Nos enfocamos en algunos modelos geométricos del producto simétrico suspensión de un continuo y mostramos resultados acerca de conexidad local y arcoconexidad de este espacio.

  19. ToF-SIMS study of polycrystalline uranium after exposure to deuterium

    Energy Technology Data Exchange (ETDEWEB)

    Morrall, P; Price, D; Nelson, A; Siekhaus, W; Nelson, E; Wu, K J; Stratman, M; McLean, B

    2006-01-19

    Time-of-flight secondary ion mass spectrometry (ToF-SIMS) is employed to examine specific features observed on a polycrystalline depleted uranium sample after exposure to high purity D{sub 2} gas. The ToF-SIMS investigation, being the first of its kind on uranium, investigates a site where the deuterated form of uranium hydride (UD{sub 3}) is clearly observed to have broken through the thin, air-formed oxide. Density functional theory calculations have been performed, which confirm the stability of, and also assign structural geometries to, the various uranium containing fragments observed with SIMS. An inclusion site was also investigated using ToF-SIMS, and these data suggest that the edges of such inclusions exhibit increased D ion, and hence H ion, diffusion when compared to the surrounding surface oxide. These results offer support to the previously published hypotheses that inclusion sites on uranium surfaces exhibit an increased probability to form hydride sites under H{sub 2} exposure.

  20. I’d like to have a house like that : Female players of The Sims

    NARCIS (Netherlands)

    M. Vosmeer (Mirjam); J. Jansz (Jeroen); E.A. van Zoonen (Liesbet)

    2015-01-01

    textabstractAbstract This qualitative interview study explores the practices of adult female gamers who play the videogame The Sims, focusing on the motivations they have for playing and how playing a video game might influence their digital competence. We address the wider context of leisure and

  1. ActivitySim: large-scale agent based activity generation for infrastructure simulation

    Energy Technology Data Exchange (ETDEWEB)

    Gali, Emmanuel [Los Alamos National Laboratory; Eidenbenz, Stephan [Los Alamos National Laboratory; Mniszewski, Sue [Los Alamos National Laboratory; Cuellar, Leticia [Los Alamos National Laboratory; Teuscher, Christof [PORTLAND STATE UNIV

    2008-01-01

    The United States' Department of Homeland Security aims to model, simulate, and analyze critical infrastructure and their interdependencies across multiple sectors such as electric power, telecommunications, water distribution, transportation, etc. We introduce ActivitySim, an activity simulator for a population of millions of individual agents each characterized by a set of demographic attributes that is based on US census data. ActivitySim generates daily schedules for each agent that consists of a sequence of activities, such as sleeping, shopping, working etc., each being scheduled at a geographic location, such as businesses or private residences that is appropriate for the activity type and for the personal situation of the agent. ActivitySim has been developed as part of a larger effort to understand the interdependencies among national infrastructure networks and their demand profiles that emerge from the different activities of individuals in baseline scenarios as well as emergency scenarios, such as hurricane evacuations. We present the scalable software engineering principles underlying ActivitySim, the socia-technical modeling paradigms that drive the activity generation, and proof-of-principle results for a scenario in the Twin Cities, MN area of 2.6 M agents.

  2. TOF-SIMS characterization of impurity enrichment and redistribution in solid oxide electrolysis cells during operation

    DEFF Research Database (Denmark)

    Kiebach, Wolff-Ragnar; Norrman, Kion; Chatzichristodoulou, Christodoulos

    2014-01-01

    TOF-SIMS analyses of state-of-the-art high temperature solid oxide electrolysis cells before and after testing under different operating conditions were performed. The investigated cells consist of an yttria stabilized zirconia (YSZ) electrolyte, a La1-xSrxMnO3-δ composite anode and a Ni-YSZ cerm...

  3. SimConcept: a hybrid approach for simplifying composite named entities in biomedical text.

    Science.gov (United States)

    Wei, Chih-Hsuan; Leaman, Robert; Lu, Zhiyong

    2015-07-01

    One particular challenge in biomedical named entity recognition (NER) and normalization is the identification and resolution of composite named entities, where a single span refers to more than one concept (e.g., BRCA1/2). Previous NER and normalization studies have either ignored composite mentions, used simple ad hoc rules, or only handled coordination ellipsis, making a robust approach for handling multitype composite mentions greatly needed. To this end, we propose a hybrid method integrating a machine-learning model with a pattern identification strategy to identify the individual components of each composite mention. Our method, which we have named SimConcept, is the first to systematically handle many types of composite mentions. The technique achieves high performance in identifying and resolving composite mentions for three key biological entities: genes (90.42% in F-measure), diseases (86.47% in F-measure), and chemicals (86.05% in F-measure). Furthermore, our results show that using our SimConcept method can subsequently improve the performance of gene and disease concept recognition and normalization. SimConcept is available for download at: http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/SimConcept/.

  4. In situ molecular imaging of hydrated biofilm in a microfluidic reactor by ToF-SIMS

    Energy Technology Data Exchange (ETDEWEB)

    Hua, Xin; Yu, Xiao-Ying; Wang, Zhaoying; Yang, Li; Liu, Bingwen; Zhu, Zihua; Tucker, Abigail E.; Chrisler, William B.; Hill, Eric A.; Thevuthasan, Suntharampillai; Lin, Yuehe; Liu, Songqin; Marshall, Matthew J.

    2014-02-26

    The first results of using a novel single channel microfluidic reactor to enable Shewanella biofilm growth and in situ characterization using time-of-flight secondary ion mass spectrometry (ToF-SIMS) in the hydrated environment are presented. The new microfluidic interface allows direct probing of the liquid surface using ToF-SIMS, a vacuum surface technique. The detection window is an aperture of 2 m in diameter on a thin silicon nitride (SiN) membrane and it allows direct detection of the liquid surface. Surface tension of the liquid flowing inside the microchannel holds the liquid within the aperture. ToF-SIMS depth profiling was used to drill through the SiN membrane and the biofilm grown on the substrate. In situ 2D imaging of the biofilm in hydrated state was acquired, providing spatial distribution of the chemical compounds in the biofilm system. This data was compared with a medium filled microfluidic reactor devoid of biofilm and dried biofilm samples deposited on clean silicon wafers. Principle Component Analysis (PCA) was used to investigate these observations. Our results show that imaging biofilms in the hydrated environment using ToF-SIMS is possible using the unique microfluidic reactor. Moreover, characteristic biofilm fatty acids fragments were observed in the hydrated biofilm grown in the microfluidic channel, illustrating the advantage of imaging biofilm in its native environment.

  5. Cyclic Voltammetry Simulations with DigiSim Software: An Upper-Level Undergraduate Experiment

    Science.gov (United States)

    Messersmith, Stephania J.

    2014-01-01

    An upper-division undergraduate chemistry experiment is described which utilizes DigiSim software to simulate cyclic voltammetry (CV). Four mechanisms were studied: a reversible electron transfer with no subsequent or proceeding chemical reactions, a reversible electron transfer followed by a reversible chemical reaction, a reversible chemical…

  6. Trace Element Determination in Presolar Grains with the NRL SIMS-SSAMS

    Science.gov (United States)

    Groopman, E. E.; Fahey, A. J.; Grabowski, K. S.

    2016-08-01

    With the NRL SIMS-SSAMS we measured trace element abundances down to a few ppb completely free of molecular isobars. We accurately measured 56Fe+ in the presence of Si2+, where 56Fe+ was only 10 ppm of the molecule signal.

  7. SimFuse: A Novel Fusion Simulator for RNA Sequencing (RNA-Seq Data

    Directory of Open Access Journals (Sweden)

    Yuxiang Tan

    2015-01-01

    Full Text Available The performance evaluation of fusion detection algorithms from high-throughput sequencing data crucially relies on the availability of data with known positive and negative cases of gene rearrangements. The use of simulated data circumvents some shortcomings of real data by generation of an unlimited number of true and false positive events, and the consequent robust estimation of accuracy measures, such as precision and recall. Although a few simulated fusion datasets from RNA Sequencing (RNA-Seq are available, they are of limited sample size. This makes it difficult to systematically evaluate the performance of RNA-Seq based fusion-detection algorithms. Here, we present SimFuse to address this problem. SimFuse utilizes real sequencing data as the fusions’ background to closely approximate the distribution of reads from a real sequencing library and uses a reference genome as the template from which to simulate fusions’ supporting reads. To assess the supporting read-specific performance, SimFuse generates multiple datasets with various numbers of fusion supporting reads. Compared to an extant simulated dataset, SimFuse gives users control over the supporting read features and the sample size of the simulated library, based on which the performance metrics needed for the validation and comparison of alternative fusion-detection algorithms can be rigorously estimated.

  8. CPU SIM: A Computer Simulator for Use in an Introductory Computer Organization-Architecture Class.

    Science.gov (United States)

    Skrein, Dale

    1994-01-01

    CPU SIM, an interactive low-level computer simulation package that runs on the Macintosh computer, is described. The program is designed for instructional use in the first or second year of undergraduate computer science, to teach various features of typical computer organization through hands-on exercises. (MSE)

  9. SIM parameter-based security for mobile e-commerce settings

    Directory of Open Access Journals (Sweden)

    Francisco Orlando Martínez Pabón

    2010-04-01

    Full Text Available Security requirements are more demanding in the e-commerce domain. However, mobile e -commerce settings not only insist on security requirements, they also require balance between security levels and hardware and usability device ability. These features require designing models having simple authentication and authorisation scheme which also ensures information integrity for each e -transaction. The Mobile and Wireless Applications’ Development Interest Group W@Pcolombia thus developed the P3SIM platform so that mobile applications might include SIM parameter-based security features. The P3SIM platform’s framework and compilation and simulation settings combines the advantages of identification provided by the SIM module with the security features provided by SATSA and Java Card APIs for Java ME environments, one of the most-used platforms for mobile application development. Developing an m-commerce-based prototype not only shows the platform’s ability to operate in secure environments, it also shows its ability to comply with environmental security requirements.

  10. The Sim-SEQ Project: Comparison of Selected Flow Models for the S-3 Site

    Energy Technology Data Exchange (ETDEWEB)

    Mukhopadhyay, Sumit; Doughty, Christine A.; Bacon, Diana H.; Li, Jun; Wei, Lingli; Yamamoto, Hajime; Gasda, Sarah E.; Hosseini, Seyyed; Nicot, Jean-Philippe; Birkholzer, Jens

    2015-05-23

    Sim-SEQ is an international initiative on model comparison for geologic carbon sequestration, with an objective to understand and, if possible, quantify model uncertainties. Model comparison efforts in Sim-SEQ are at present focusing on one specific field test site, hereafter referred to as the Sim-SEQ Study site (or S-3 site). Within Sim-SEQ, different modeling teams are developing conceptual models of CO2 injection at the S-3 site. In this paper, we select five flow models of the S-3 site and provide a qualitative comparison of their attributes and predictions. These models are based on five different simulators or modeling approaches: TOUGH2/EOS7C, STOMP-CO2e, MoReS, TOUGH2-MP/ECO2N, and VESA. In addition to model-to-model comparison, we perform a limited model-to-data comparison, and illustrate how model choices impact model predictions. We conclude the paper by making recommendations for model refinement that are likely to result in less uncertainty in model predictions.

  11. MI-Sim: A MATLAB package for the numerical analysis of microbial ecological interactions.

    Science.gov (United States)

    Wade, Matthew J; Oakley, Jordan; Harbisher, Sophie; Parker, Nicholas G; Dolfing, Jan

    2017-01-01

    Food-webs and other classes of ecological network motifs, are a means of describing feeding relationships between consumers and producers in an ecosystem. They have application across scales where they differ only in the underlying characteristics of the organisms and substrates describing the system. Mathematical modelling, using mechanistic approaches to describe the dynamic behaviour and properties of the system through sets of ordinary differential equations, has been used extensively in ecology. Models allow simulation of the dynamics of the various motifs and their numerical analysis provides a greater understanding of the interplay between the system components and their intrinsic properties. We have developed the MI-Sim software for use with MATLAB to allow a rigorous and rapid numerical analysis of several common ecological motifs. MI-Sim contains a series of the most commonly used motifs such as cooperation, competition and predation. It does not require detailed knowledge of mathematical analytical techniques and is offered as a single graphical user interface containing all input and output options. The tools available in the current version of MI-Sim include model simulation, steady-state existence and stability analysis, and basin of attraction analysis. The software includes seven ecological interaction motifs and seven growth function models. Unlike other system analysis tools, MI-Sim is designed as a simple and user-friendly tool specific to ecological population type models, allowing for rapid assessment of their dynamical and behavioural properties.

  12. PhyloSim - Monte Carlo simulation of sequence evolution in the R statistical computing environment

    Directory of Open Access Journals (Sweden)

    Massingham Tim

    2011-04-01

    Full Text Available Abstract Background The Monte Carlo simulation of sequence evolution is routinely used to assess the performance of phylogenetic inference methods and sequence alignment algorithms. Progress in the field of molecular evolution fuels the need for more realistic and hence more complex simulations, adapted to particular situations, yet current software makes unreasonable assumptions such as homogeneous substitution dynamics or a uniform distribution of indels across the simulated sequences. This calls for an extensible simulation framework written in a high-level functional language, offering new functionality and making it easy to incorporate further complexity. Results PhyloSim is an extensible framework for the Monte Carlo simulation of sequence evolution, written in R, using the Gillespie algorithm to integrate the actions of many concurrent processes such as substitutions, insertions and deletions. Uniquely among sequence simulation tools, PhyloSim can simulate arbitrarily complex patterns of rate variation and multiple indel processes, and allows for the incorporation of selective constraints on indel events. User-defined complex patterns of mutation and selection can be easily integrated into simulations, allowing PhyloSim to be adapted to specific needs. Conclusions Close integration with R and the wide range of features implemented offer unmatched flexibility, making it possible to simulate sequence evolution under a wide range of realistic settings. We believe that PhyloSim will be useful to future studies involving simulated alignments.

  13. Cyclic Voltammetry Simulations with DigiSim Software: An Upper-Level Undergraduate Experiment

    Science.gov (United States)

    Messersmith, Stephania J.

    2014-01-01

    An upper-division undergraduate chemistry experiment is described which utilizes DigiSim software to simulate cyclic voltammetry (CV). Four mechanisms were studied: a reversible electron transfer with no subsequent or proceeding chemical reactions, a reversible electron transfer followed by a reversible chemical reaction, a reversible chemical…

  14. Development of an Open Source Image-Based Flow Modeling Software - SimVascular

    Science.gov (United States)

    Updegrove, Adam; Merkow, Jameson; Schiavazzi, Daniele; Wilson, Nathan; Marsden, Alison; Shadden, Shawn

    2014-11-01

    SimVascular (www.simvascular.org) is currently the only comprehensive software package that provides a complete pipeline from medical image data segmentation to patient specific blood flow simulation. This software and its derivatives have been used in hundreds of conference abstracts and peer-reviewed journal articles, as well as the foundation of medical startups. SimVascular was initially released in August 2007, yet major challenges and deterrents for new adopters were the requirement of licensing three expensive commercial libraries utilized by the software, a complicated build process, and a lack of documentation, support and organized maintenance. In the past year, the SimVascular team has made significant progress to integrate open source alternatives for the linear solver, solid modeling, and mesh generation commercial libraries required by the original public release. In addition, the build system, available distributions, and graphical user interface have been significantly enhanced. Finally, the software has been updated to enable users to directly run simulations using models and boundary condition values, included in the Vascular Model Repository (vascularmodel.org). In this presentation we will briefly overview the capabilities of the new SimVascular 2.0 release. National Science Foundation.

  15. NanoSIMS analysis of arsenic and selenium in cereal grain

    Energy Technology Data Exchange (ETDEWEB)

    Moore, Katie L.; Schröder, Markus; Lombi, Enzo; Zhao, Fang-Jie; McGrath, Steve P.; Hawkesford, Malcolm J.; Shewry, Peter R.; Grovenor, Chris R.M. (Rothamsted); (UCopenhagen); (Oxford)

    2012-09-05

    Cereals are an important source of selenium (Se) to humans and many people have inadequate intakes of this essential trace element. Conversely, arsenic (As) is toxic and may accumulate in rice grain at levels that pose a health risk. Knowledge of the localization of selenium and arsenic within the cereal grain will aid understanding of their deposition patterns and the impact of processes such as milling. High-resolution secondary ion mass spectrometry (NanoSIMS) was used to determine the localization of Se in wheat (Triticum aestivum) and As in rice (Oryza sativa). Combined synchrotron X-ray fluorescence (S-XRF) and NanoSIMS analysis utilized the strengths of both techniques. Selenium was concentrated in the protein surrounding the starch granules in the starchy endosperm cells and more homogeneously distributed in the aleurone cells but with Se-rich hotspots. Arsenic was concentrated in the subaleurone endosperm cells in association with the protein matrix rather than in the aleurone cells. NanoSIMS indicated that the high intensity of As identified in the S-XRF image was localized in micron-sized hotspots near the ovular vascular trace and nucellar projection. This is the first study showing subcellular localization in grain samples containing parts per million concentrations of Se and As. There is good quantitative agreement between NanoSIMS and S-XRF.

  16. Making It Real: Sim-School[C] a Backdrop for Contextualizing Teacher Preparation

    Science.gov (United States)

    Foley, Jean Ann; McAllister, Gretchen

    2005-01-01

    Researchers and teacher educators have called for contextualizing the learning of pedagogy and content within the complex context of schools. This account provides an overview of a web-based simulation called Sim-School[C] that provides a realistic framework for students to contextualize curricular decisions, differentiate instruction and reflect…

  17. Role of p-induced population of medium mass(A $\\sim$ 150) neutron rich nuclei

    CERN Document Server

    Banerjee, D; Bhattacharjee, T; Guin, R; Das, S K; Das, P; Pandit, Deepak; Mukherjee, A; Chowdhury, A; Bhattacharya, Soumik; Gupta, S Das; Bhattacharyya, S; Mukhopadhyay, P; Banerjee, S R

    2014-01-01

    Excitation functions were measured by stacked-foil activation technique for the $^{150}$Nd(p, xpyn) reaction using 97.65$%$ enriched $^{150}$Nd target. Measurement up to $\\sim$50$%$ above barrier and down to 18$%$ below the barrier was performed using proton beam energy (E$_p$) of 7 - 15 MeV from VECC Cyclotron. The yield of suitable $\\gamma$ rays emitted following the decay of relevant evaporation residues was determined using a 50$%$ High Purity Germanium (HPGe) detector.(p,n) cross section was found to follow the expected trend with a maximum value of 63.7(4.9)mb at E$_p$ $\\sim$ 8.6 MeV. (p,2n) cross section gradually increased with E$_p$ and had maximum contribution to the total reaction cross section after E$_p$ $\\sim$ 9.0 MeV. (p, p$^{\\prime}$n) reaction channel also showed a reasonable yield with a threshold of E$_p$ $\\sim$ 12.0 MeV. The experimental data were corroborated with statistical model calculations using different codes, viz., CASCADE, ALICE/91 and EMPIRE3.1. All the calculations using a suit...

  18. SIM PlanetQuest: The TOM-3 (Thermo-Optical-Mechanical) Siderostat Mirror Test

    Science.gov (United States)

    Phillips, Charles J.

    2006-01-01

    This slide presentation reviews the Space Interferometry Mission (SIM) PlanetQuest mission. It describes the mission, shows diagrams of the instrument, the collector bays, the Siderostat mirrors, the COL bay thermal environment, the TOM-3 replicating COL Bay Environment, the thermal hardware for the SID heater control, and the results of the test are shown

  19. Glutamate mediates the function of melanocortin receptor 4 on sim1 neurons in body weight regulation

    Science.gov (United States)

    The melanocortin receptor 4 (MC4R) is a well-established mediator of body weight homeostasis. However, the neurotransmitter(s) that mediate MC4R function remain largely unknown; as a result, little is known about the second-order neurons of the MC4R neural pathway. Single-minded 1 (Sim1)-expressing ...

  20. Si1- x Ge x /Si Interface Profiles Measured to Sub-Nanometer Precision Using uleSIMS Energy Sequencing

    Science.gov (United States)

    Morris, R. J. H.; Hase, T. P. A.; Sanchez, A. M.; Rowlands, G.

    2016-10-01

    The utility of energy sequencing for extracting an accurate matrix level interface profile using ultra-low energy SIMS (uleSIMS) is reported. Normally incident O2 + over an energy range of 0.25-2.5 keV were used to probe the interface between Si0.73Ge0.27/Si, which was also studied using high angle annular dark field scanning transmission electron microscopy (HAADF-STEM). All the SIMS profiles were linearized by taking the well understood matrix effects on ion yield and erosion rate into account. A method based on simultaneous fitting of the SIMS profiles measured at different energies is presented, which allows the intrinsic sample profile to be determined to sub-nanometer precision. Excellent agreement was found between the directly imaged HAADF-STEM interface and that derived from SIMS.

  1. Esophageal motility impairment in Plummer-Vinson syndrome. Correction by iron treatment.

    Science.gov (United States)

    Dantas, R O; Villanova, M G

    1993-05-01

    We report the case of a 41-year-old woman with Plummer-Vinson syndrome and an esophageal motility disorder. She complained of dysphagia and odynophagia and had cheilitis, glossitis, and hypochromic anemia. An esophageal motility study showed low amplitude of contraction and high intrabolus pressure in the esophageal body. After iron replacement, the patient was free from symptoms, and a new motility study showed increased amplitude of contraction and decreased intrabolus pressure.

  2. Sperm motility initiation by egg jelly of the anuran, Discoglossus pictus may be mediated by sperm motility-initiating substance of the internally-fertilizing newt, Cynops pyrrhogaster.

    Science.gov (United States)

    Takayama-Watanabe, Eriko; Campanella, Chiara; Kubo, Hideo; Watanabe, Akihiko

    2012-11-01

    The egg jelly of Discoglossus pictus contains sperm motility-activating activity, the molecular basis of which has not been studied. Discoglossus pictus sperm initiated motility immediately after immersion in egg-jelly extract, as well as after immersion in hyposmotic solution, which initiates sperm motility in the external fertilization of anuran amphibians. Sequential treatment of the D. pictus sperm with these two solutions revealed the predominant effect of hyposmolality in initiation of motility. The motility initiation induced by jelly extract was suppressed by a monoclonal antibody (mAb) that is specific for the 34 kDa sperm motility-initiating substance (SMIS) in the egg jelly of the newt, Cynops pyrrhogaster. Immunoblotting using the anti-SMIS mAb revealed several antigenic proteins that included major ones with sizes of 18- and 34-kDa in D. pictus jelly extract. Scanning electron microscopic observation revealed that granules of jelly matrix, in which SMIS localizes and which have a critical role in the internal fertilization of C. pyrrhogaster, were not observed near the surface of the D. pictus egg jelly. These results suggest that sperm motility-activating activity in egg jelly of D. pictus may be mediated by SMIS homologous proteins that act through a mechanism that is partially different from that of C. pyrrhogaster.

  3. Cannabinoid type 1 (CB1) receptors on Sim1-expressing neurons regulate energy expenditure in male mice.

    Science.gov (United States)

    Cardinal, Pierre; Bellocchio, Luigi; Guzmán-Quevedo, Omar; André, Caroline; Clark, Samantha; Elie, Melissa; Leste-Lasserre, Thierry; Gonzales, Delphine; Cannich, Astrid; Marsicano, Giovanni; Cota, Daniela

    2015-02-01

    The paraventricular nucleus of the hypothalamus (PVN) regulates energy balance by modulating not only food intake, but also energy expenditure (EE) and brown adipose tissue thermogenesis. To test the hypothesis that cannabinoid type 1 (CB1) receptor in PVN neurons might control these processes, we used the Cre/loxP system to delete CB1 from single-minded 1 (Sim1) neurons, which account for the majority of PVN neurons. On standard chow, mice lacking CB1 receptor in Sim1 neurons (Sim1-CB1-knockout [KO]) had food intake, body weight, adiposity, glucose metabolism, and EE comparable with wild-type (WT) (Sim1-CB1-WT) littermates. However, maintenance on a high-fat diet revealed a gene-by-diet interaction whereby Sim1-CB1-KO mice had decreased adiposity, improved insulin sensitivity, and increased EE, whereas feeding behavior was similar to Sim1-CB1-WT mice. Additionally, high-fat diet-fed Sim1-CB1-KO mice had increased mRNA expression of the β3-adrenergic receptor, as well as of uncoupling protein-1, cytochrome-c oxidase subunit IV and mitochondrial transcription factor A in the brown adipose tissue, all molecular changes suggestive of increased thermogenesis. Pharmacological studies using β-blockers suggested that modulation of β-adrenergic transmission play an important role in determining EE changes observed in Sim1-CB1-KO. Finally, chemical sympathectomy abolished the obesity-resistant phenotype of Sim1-CB1-KO mice. Altogether, these findings reveal a diet-dependent dissociation in the CB1 receptor control of food intake and EE, likely mediated by the PVN, where CB1 receptors on Sim1-positive neurons do not impact food intake but hinder EE during dietary environmental challenges that promote body weight gain.

  4. Intrashell δ13C SIMS measurements in the cultured planktic foraminifer Orbulina universa

    Science.gov (United States)

    Vetter, L.; Kozdon, R.; Valley, J. W.; Mora, C. I.; Spero, H. J.

    2013-12-01

    In this study, we present experimental data from the planktic foraminifer Orbulina universa cultured in laboratory experiments. We demonstrate that the δ13C of calcite precipitated in 13C-labeled seawater for 24 h can be resolved and accurately measured using Secondary Ion Mass Spectrometry (SIMS). Specimens maintained at 20°C were transferred from ambient seawater (δ13CDIC = +1.3‰) into 13C-enriched seawater with δ13CDIC = +51.5‰ and elevated [Ba] for 24 h. Specimens were then transferred into ambient seawater with elevated [87Sr] for 6-9 h of calcification, followed by a transfer back into unlabeled ambient seawater until gametogenesis. This technique produced O. universa shells with calcite layers of distinct geochemical signatures. We quantify the spatial positions of trace element labels in the shells using laser ablation ICP-MS depth profiling. Using fragments from the same shells, we quantify intrashell δ13Ccalcite using SIMS with a 6 or 8 μm spot (×1.1‰ (2 SD)). Measured δ13Ccalcite values in ambient O. universa shell layers are within 2‰ of predicted δ13Ccalcite values. In 13C-labeled bands of calcite, 6 μm SIMS spot measurements are within 2‰ of predicted δ13Ccalcite values, whereas 8 μm SIMS spots yield values that are intermediate between predicted values for ambient and spiked calcite. The spatial agreement between trace element and carbon isotope data suggest that δ13C, Ba, and Sr tracers are incorporated synchronously into shell calcite, within the resolution of the two analytical techniques. These results demonstrate the ability of SIMS δ13C measurements to resolve 6 μm features in foraminifer shell calcite, and highlight the potential of this technique for addressing questions about foraminifer ecology, biomineralization, and paleoceanography.

  5. SIMS measurements of intrashell δ13C in the cultured planktic foraminifer Orbulina universa

    Science.gov (United States)

    Vetter, Lael; Kozdon, Reinhard; Valley, John W.; Mora, Claudia I.; Spero, Howard J.

    2014-08-01

    In this study, we present experimental results from the planktic foraminifer Orbulina universa, cultured in the laboratory. We demonstrate that the δ13C of shell calcite precipitated in 13C-labeled seawater for 24 h can be resolved and accurately measured using Secondary Ion Mass Spectrometry (SIMS). Specimens maintained at 20 °C were transferred from ambient seawater (δ13CDIC = +1.3‰) into seawater with δ13CDIC = +51.5‰ and enriched [Ba2+] for 24 h. Specimens were then transferred into ambient seawater with elevated [87Sr] for 6-9 h of calcification, followed by a transfer back into unlabeled ambient seawater until gametogenesis. This technique produced O. universa shells with calcite layers of distinct geochemical signatures. We quantify the spatial positions of trace element labels in the shells using laser ablation ICP-MS depth profiling. Using fragments from the same shells, we quantify intrashell δ13Ccalcite using SIMS with a 6 or 8 μm spot (2 SD range ±0.5‰ to 1.7‰). Measured δ13Ccalcite values in O. universa shell layers precipitated in ambient seawater are within 2‰ of predicted δ13Ccalcite values. In 13C-labeled bands of calcite, 6 μm SIMS spot measurements are within 2‰ of predicted δ13Ccalcite values, whereas 8 μm SIMS spots yield intermediate, mixed values. The spatial agreement between trace element and carbon isotope data suggests that 13C and cation tracers are synchronously incorporated into shell calcite. These results demonstrate the ability of SIMS δ13C measurements to resolve ∼10 μm features in foraminifer shell calcite using a 6 μm spot, and highlight the potential of this technique for addressing questions about ecology, biomineralization, and paleoceanography.

  6. The impact of detergents on the tissue decellularization process: A ToF-SIMS study.

    Science.gov (United States)

    White, Lisa J; Taylor, Adam J; Faulk, Denver M; Keane, Timothy J; Saldin, Lindsey T; Reing, Janet E; Swinehart, Ilea T; Turner, Neill J; Ratner, Buddy D; Badylak, Stephen F

    2017-03-01

    Biologic scaffolds are derived from mammalian tissues, which must be decellularized to remove cellular antigens that would otherwise incite an adverse immune response. Although widely used clinically, the optimum balance between cell removal and the disruption of matrix architecture and surface ligand landscape remains a considerable challenge. Here we describe the use of time of flight secondary ion mass spectroscopy (ToF-SIMS) to provide sensitive, molecular specific, localized analysis of detergent decellularized biologic scaffolds. We detected residual detergent fragments, specifically from Triton X-100, sodium deoxycholate and sodium dodecyl sulphate (SDS) in decellularized scaffolds; increased SDS concentrations from 0.1% to 1.0% increased both the intensity of SDS fragments and adverse cell outcomes. We also identified cellular remnants, by detecting phosphate and phosphocholine ions in PAA and CHAPS decellularized scaffolds. The present study demonstrates ToF-SIMS is not only a powerful tool for characterization of biologic scaffold surface molecular functionality, but also enables sensitive assessment of decellularization efficacy. We report here on the use of a highly sensitive analytical technique, time of flight secondary ion mass spectroscopy (ToF-SIMS) to characterize detergent decellularized scaffolds. ToF-SIMS detected cellular remnants and residual detergent fragments; increased intensity of the detergent fragments correlated with adverse cell matrix interactions. This study demonstrates the importance of maintaining a balance between cell removal and detergent disruption of matrix architecture and matrix surface ligand landscape. This study also demonstrates the power of ToF-SIMS for the characterization of decellularized scaffolds and capability for assessment of decellularization efficacy. Future use of biologic scaffolds in clinical tissue reconstruction will benefit from the fundamental results described in this work. Copyright © 2016 Acta

  7. Image segmentation for uranium isotopic analysis by SIMS: Combined adaptive thresholding and marker controlled watershed approach

    Energy Technology Data Exchange (ETDEWEB)

    Willingham, David G.; Naes, Benjamin E.; Heasler, Patrick G.; Zimmer, Mindy M.; Barrett, Christopher A.; Addleman, Raymond S.

    2016-05-31

    A novel approach to particle identification and particle isotope ratio determination has been developed for nuclear safeguard applications. This particle search approach combines an adaptive thresholding algorithm and marker-controlled watershed segmentation (MCWS) transform, which improves the secondary ion mass spectrometry (SIMS) isotopic analysis of uranium containing particle populations for nuclear safeguards applications. The Niblack assisted MCWS approach (a.k.a. SEEKER) developed for this work has improved the identification of isotopically unique uranium particles under conditions that have historically presented significant challenges for SIMS image data processing techniques. Particles obtained from five NIST uranium certified reference materials (CRM U129A, U015, U150, U500 and U850) were successfully identified in regions of SIMS image data 1) where a high variability in image intensity existed, 2) where particles were touching or were in close proximity to one another and/or 3) where the magnitude of ion signal for a given region was count limited. Analysis of the isotopic distributions of uranium containing particles identified by SEEKER showed four distinct, accurately identified 235U enrichment distributions, corresponding to the NIST certified 235U/238U isotope ratios for CRM U129A/U015 (not statistically differentiated), U150, U500 and U850. Additionally, comparison of the minor uranium isotope (234U, 235U and 236U) atom percent values verified that, even in the absence of high precision isotope ratio measurements, SEEKER could be used to segment isotopically unique uranium particles from SIMS image data. Although demonstrated specifically for SIMS analysis of uranium containing particles for nuclear safeguards, SEEKER has application in addressing a broad set of image processing challenges.

  8. High resolution isotopic analysis of U-bearing particles via fusion of SIMS and EDS images

    Energy Technology Data Exchange (ETDEWEB)

    Tarolli, Jay G.; Naes, Benjamin E.; Garcia, Benjamin J.; Fischer, Ashley E.; Willingham, David

    2016-01-01

    Image fusion of secondary ion mass spectrometry (SIMS) images and X-ray elemental maps from energy-dispersive spectroscopy (EDS) was performed to facilitate the isolation and re-analysis of isotopically unique U-bearing particles where the highest precision SIMS measurements are required. Image registration, image fusion and particle micromanipulation were performed on a subset of SIMS images obtained from a large area pre-screen of a particle distribution from a sample containing several certified reference materials (CRM) U129A, U015, U150, U500 and U850, as well as a standard reference material (SRM) 8704 (Buffalo River Sediment) to simulate particles collected on swipes during routine inspections of declared uranium enrichment facilities by the International Atomic Energy Agency (IAEA). In total, fourteen particles, ranging in size from 5 – 15 µm, were isolated and re-analyzed by SIMS in multi-collector mode identifying nine particles of CRM U129A, one of U150, one of U500 and three of U850. These identifications were made within a few percent errors from the National Institute of Standards and Technology (NIST) certified atom percent values for 234U, 235U and 238U for the corresponding CRMs. This work represents the first use of image fusion to enhance the accuracy and precision of isotope ratio measurements for isotopically unique U-bearing particles for nuclear safeguards applications. Implementation of image fusion is essential for the identification of particles of interests that fall below the spatial resolution of the SIMS images.

  9. Potential contribution of SIM2 and ETS2 functional polymorphisms in Down syndrome associated malignancies

    Directory of Open Access Journals (Sweden)

    Chatterjee Arpita

    2013-01-01

    Full Text Available Abstract Background Proper expression and functioning of transcription factors (TFs are essential for regulation of different traits and thus could be crucial for the development of complex diseases. Subjects with Down syndrome (DS have a higher incidence of acute lymphoblastic leukemia (ALL while solid tumors, like breast cancer (BC and oral cancer (OC, show rare incidences. Triplication of the human chromosome 21 in DS is associated with altered genetic dosage of different TFs. V-ets erythroblastosis virus E26 oncogene homolog 2 (ETS2 and Single Minded 2 (SIM2 are two such TFs that regulate several downstream genes involved in developmental and neurological pathways. Here we studied functional genetic polymorphisms (fSNP in ETS2 and SIM2 encoding genes in a group of patients and control subjects to better understand association of these variants with DS phenotypes. Methods We employed an in silico approach to identify potential target pathways of ETS2 and SIM2. fSNPs in genes encoding for these two TFs were identified using available databases. Selected sites were genotyped in individuals with DS, their parents, ALL, BC, OC as well as ethnically matched control individuals. We further analyzed these data by population-based statistical methods. Results Allelic/genotypic association analysis showed significant (P  Conclusions We infer from the present investigation that the difference in frequencies of fSNPs and their independent as well as interactive effects may be the cause for altered expression of SIM2 and ETS2 in DS and malignant groups, which affects different downstream biological pathways. Thus, altered expression of SIM2 and ETS2 could be one of the reasons for variable occurrence of different malignant conditions in DS.

  10. Thermodynamics of the motility-induced phase separation

    Science.gov (United States)

    Solon, Alexandre; Stenhammar, Joachim; Cates, Michael; Tailleur, Julien

    Self-propelled particles are known to accumulate in regions of space where their velocity is lowered. In addition, if their velocity diminishes when the local density increases (for example due to crowding effects), a positive feedback loop leads to the now well-established motility-induced phase separation (MIPS) between a dense immotile phase and a dilute motile phase. Understanding the phase equilibrium of MIPS is still a matter of debate. Although, depending on the models used to study the transition, a chemical potential or a pressure can be defined, these quantities do not play their usual thermodynamic role. In particular, the usual common tangent or equal-area constructions fail in these systems. Indeed, we will show that describing the phase equilibrium of MIPS necessitates generalized thermodynamics that include non-equilibrium contributions. This approach allows us to predict correctly the phase diagram of MIPS and to gain insight into the thermodynamics of active systems. It also sheds light on the (in)equivalence of statistical ensembles for these systems, paving the way for more efficient computational studies.

  11. Tegaserod (HTF 919) stimulates gut motility in normal horses.

    Science.gov (United States)

    Lippold, B S; Hildebrand, J; Straub, R

    2004-11-01

    It has been shown that the selective 5-HT4 receptor agonist tegaserod induces an increase in frequency and amplitude of contractions in isolated muscle preparations of equine ileum and pelvic flexure. To investigate the effects of tegaserod on gut motility and transit of spheres in normal horses. Six mature Freiberger horses were kept under standardised conditions. Effects of tegaserod (0.02 mg/kg bwt i.v. b.i.d. for 2 days) or vehicle on intestinal transit of barium-filled spheres, defaecation and gut sounds were studied in a cross-over design. Spheres were given via stomach tube prior to the first dosing of tegaserod or vehicle. Faeces were collected every 3 h and spheres eliminated were identified radiologically in the faeces. Tegaserod significantly accelerated the gastrointestinal (GI) transit time of spheres and increased the frequency of defaecation and scores of gut sounds compared to vehicle. The compound was well tolerated; no effects on behaviour, body temperature, heart rate, respiratory rate and clinical laboratory data were observed. Tegaserod efficaciously stimulated motility and accelerate GI transit in healthy horses. Tegaserod may offer therapeutic potential in horses suffering from impaction or paralytic ileus.

  12. Fascin promotes the motility and invasiveness of pancreatic cancer cells

    Institute of Scientific and Technical Information of China (English)

    Yan-Feng Xu; Shuang-Ni Yu; Zhao-Hui Lu; Jian-Ping Liu; Jie Chen

    2011-01-01

    AIM: To explore the role of actin-bundling protein, fascin during the progression of pancreatic cancer. METHODS: The plasmid expressing human fascin-1 was stably transfected into the pancreatic cancer cell line MIA PaCa-2. The proliferation, cell cycle, motility, scattering, invasiveness and organization of the actin filament system in fascin-transfected MIA PaCa-2 cells and control non-transfected cells were determined. RESULTS: Heterogeneous overexpression of fascin markedly enhanced the motility, scattering, and invasiveness of MIA PaCa-2 cells. However, overexpression of fascin had minimal effect on MIA PaCa-2 cell proliferation and cell cycle. In addition, cell morphology and organization of the actin filament system were distinctly altered in fascin overexpressed cells. When transplanted into BALB/c-nu mice, fascin-transfected pancreatic cancer cells developed solid tumors at a slightly slower rate, but these tumors displayed more aggressive behavior in comparison with control tumors. CONCLUSION: Fascin promotes pancreatic cancer cell migration, invasion and scattering, thus contributes to the aggressive behavior of pancreatic cancer cells.

  13. Molecular mechanism of fluoroquinolones modulation on corneal fibroblast motility.

    Science.gov (United States)

    Chen, Tsan-Chi; Tsai, Tzu-Yun; Chang, Shu-Wen

    2016-04-01

    Topical fluoroquinolones are widely used to prevent ocular infections after ophthalmic surgery. However, they have been shown to affect the corneal cell motility, whose mechanism remains indefinite. The purpose of this study was to investigate how fluoroquinolones affect corneal stromal cell motility. Human corneal fibroblasts (HCFs) were incubated in ciprofloxacin (CIP), levofloxacin (LEV), or moxifloxacin (MOX) at 0, 10, 50, and 100 μg/ml for up to 3 days. Effect of CIP, LEV, or MOX on HCF migration was monitored using migration assay. HCF viability was determined by WST-1 assay. Expression of focal adhesion kinase (FAK), paxillin (PXN), and their phosphorylated forms were analyzed by immunoblotting. Binding affinity between FAK and PXN was determined by co-immunoprecipitation. Our results revealed that CIP and MOX, but not LEV, noticeably retarded HCF migration. HCF proliferation was significantly reduced by CIP (38.2%), LEV (29.5%), and MOX (21.3%), respectively (p = 0.002). CIP and MOX suppressed the phosphorylation of PXN at tyrosines (10.2 ± 4.3%, p MOX diminished the binding affinity between FAK and PXN (8.2 ± 1.8%, p MOX, but not LEV, might delay corneal fibroblast migration via interfering with recruitment of PXN to focal adhesions and dephosphorylation of PXN at the tyrosines.

  14. Modulation of Chlamydomonas reinhardtii flagellar motility by redox poise

    Science.gov (United States)

    Wakabayashi, Ken-ichi; King, Stephen M.

    2006-01-01

    Redox-based regulatory systems are essential for many cellular activities. Chlamydomonas reinhardtii exhibits alterations in motile behavior in response to different light conditions (photokinesis). We hypothesized that photokinesis is signaled by variations in cytoplasmic redox poise resulting from changes in chloroplast activity. We found that this effect requires photosystem I, which generates reduced NADPH. We also observed that photokinetic changes in beat frequency and duration of the photophobic response could be obtained by altering oxidative/reductive stress. Analysis of reactivated cell models revealed that this redox poise effect is mediated through the outer dynein arms (ODAs). Although the global redox state of the thioredoxin-related ODA light chains LC3 and LC5 and the redox-sensitive Ca2+-binding subunit of the docking complex DC3 did not change upon light/dark transitions, we did observe significant alterations in their interactions with other flagellar components via mixed disulfides. These data indicate that redox poise directly affects ODAs and suggest that it may act in the control of flagellar motility. PMID:16754958

  15. Trajectories of Listeria-type motility in two dimensions

    Science.gov (United States)

    Wen, Fu-Lai; Leung, Kwan-tai; Chen, Hsuan-Yi

    2012-12-01

    Force generated by actin polymerization is essential in cell motility and the locomotion of organelles or bacteria such as Listeria monocytogenes. Both in vivo and in vitro experiments on actin-based motility have observed geometrical trajectories including straight lines, circles, S-shaped curves, and translating figure eights. This paper reports a phenomenological model of an actin-propelled disk in two dimensions that generates geometrical trajectories. Our model shows that when the evolutions of actin density and force per filament on the disk are strongly coupled to the disk self-rotation, it is possible for a straight trajectory to lose its stability. When the instability is due to a pitchfork bifurcation, the resulting trajectory is a circle; a straight trajectory can also lose stability through a Hopf bifurcation, and the resulting trajectory is an S-shaped curve. We also show that a half-coated disk, which mimics the distribution of functionalized proteins in Listeria, also undergoes similar symmetry-breaking bifurcations when the straight trajectory loses stability. For both a fully coated disk and a half-coated disk, when the trajectory is an S-shaped curve, the angular frequency of the disk self-rotation is different from that of the disk trajectory. However, for circular trajectories, these angular frequencies are different for a fully coated disk but the same for a half-coated disk.

  16. Studies on the ovarian motility of small laboratory rodents.

    Science.gov (United States)

    Gimeno, M F; Gimeno, A L

    1975-01-01

    Guinea pig ovaries were isolated and immersed in Krebs-Ringer bicarbonate solution, gassed with carbogen and added with glucose as the substrate. The experiments were carried out at 37 degrees C and the preparations were subjected to a basal tension of 500 mg. The spontaneous motility (contractile tension and frequency) of guinea pig ovaries obtained in late proestrus was significantly greater than that of the estrus or early proestrus. The influence of oxytocin on ovarian motility was significantly more marked in late proestrus than in estrus or early proestrus. Both the spontaneous and induced mortility of guinea pig ovaries are augmented in the immediate prevoulatory moment. In isolated rat ovaries, the isometric contractile tension and the frequency of contractions increased as the estral cycle progressed. During late proestrus, left ovaries had a contractile activity of greater intensity and frequency than the right ones, whereas during early proestrus the magnitudes were comparable. Oxytocin elicited greater responses in left than right ovaries of the late proestrus, the effect becoming similar in estrus and early proestrus. Rat ovaries obtained immediately before ovulation are specifically sensitized to the influence of oxytocin and not to other smooth muscle stimulants.

  17. We do, therefore we think: time, motility, and consciousness.

    Science.gov (United States)

    Goodrich, Barbara Gwenn

    2010-01-01

    This article is a philosopher's expanded review of two recent books on neurophysiology: Rodolfo Llinás's I of the Vortex and György Buszáki's Rhythms of the Brain. Researchers such as these are converging on a view of consciousness as originating in motility and as inherently temporal due to the brainwave oscillations that underlay it. Most current discussions of consciousness include implicit philosophical presuppositions inherited from the canon of Plato, Aristotle, Descartes, and Kant, e.g. that consciousness is self-reflective, passive, and timeless. Because of this, Llinás's and Buszáki's insights may not be fully appreciated. Western philosophy, however, also includes what might be described as a counter-tradition--and one that is more compatible with empirical biological science than the usual canon. Heraclitus, Spinoza, Schopenhauer, Nietzsche, and especially the 20th century French philosopher and psychologist, Merleau-Ponty, all anticipated aspects of Llinás's and Buszáki's approaches. Their alternative conceptual vocabularies are useful for strengthening Llinás's and Buszáki's approaches, sketching out a notion of consciousness emerging from motility, and generating new hypotheses for neurophysiological research.

  18. Collective cell motility promotes chemotactic prowess and resistance to chemorepulsion.

    Science.gov (United States)

    Malet-Engra, Gema; Yu, Weimiao; Oldani, Amanda; Rey-Barroso, Javier; Gov, Nir S; Scita, Giorgio; Dupré, Loïc

    2015-01-19

    Collective cell migration is a widespread biological phenomenon, whereby groups of highly coordinated, adherent cells move in a polarized fashion. This migration mode is a hallmark of tissue morphogenesis during development and repair and of solid tumor dissemination. In addition to circulating as solitary cells, lymphoid malignancies can assemble into tissues as multicellular aggregates. Whether malignant lymphocytes are capable of coordinating their motility in the context of chemokine gradients is, however, unknown. Here, we show that, upon exposure to CCL19 or CXCL12 gradients, malignant B and T lymphocytes assemble into clusters that migrate directionally and display a wider chemotactic sensitivity than individual cells. Physical modeling recapitulates cluster motility statistics and shows that intracluster cell cohesion results in noise reduction and enhanced directionality. Quantitative image analysis reveals that cluster migration runs are periodically interrupted by transitory rotation and random phases that favor leader cell turnover. Additionally, internalization of CCR7 in leader cells is accompanied by protrusion retraction, loss of polarity, and the ensuing replacement by new leader cells. These mechanisms ensure sustained forward migration and resistance to chemorepulsion, a behavior of individual cells exposed to steep CCL19 gradients that depends on CCR7 endocytosis. Thus, coordinated cluster dynamics confer distinct chemotactic properties, highlighting unexpected features of lymphoid cell migration.

  19. Membrane tension and cytoskeleton organization in cell motility

    Science.gov (United States)

    Sens, Pierre; Plastino, Julie

    2015-07-01

    Cell membrane shape changes are important for many aspects of normal biological function, such as tissue development, wound healing and cell division and motility. Various disease states are associated with deregulation of how cells move and change shape, including notably tumor initiation and cancer cell metastasis. Cell motility is powered, in large part, by the controlled assembly and disassembly of the actin cytoskeleton. Much of this dynamic happens in close proximity to the plasma membrane due to the fact that actin assembly factors are membrane-bound, and thus actin filaments are generally oriented such that their growth occurs against or near the membrane. For a long time, the membrane was viewed as a relatively passive scaffold for signaling. However, results from the last five years show that this is not the whole picture, and that the dynamics of the actin cytoskeleton are intimately linked to the mechanics of the cell membrane. In this review, we summarize recent findings concerning the role of plasma membrane mechanics in cell cytoskeleton dynamics and architecture, showing that the cell membrane is not just an envelope or a barrier for actin assembly, but is a master regulator controlling cytoskeleton dynamics and cell polarity.

  20. Particle-based simulations of self-motile suspensions

    Science.gov (United States)

    Hinz, Denis F.; Panchenko, Alexander; Kim, Tae-Yeon; Fried, Eliot

    2015-11-01

    A simple model for simulating flows of active suspensions is investigated. The approach is based on dissipative particle dynamics. While the model is potentially applicable to a wide range of self-propelled particle systems, the specific class of self-motile bacterial suspensions is considered as a modeling scenario. To mimic the rod-like geometry of a bacterium, two dissipative particle dynamics particles are connected by a stiff harmonic spring to form an aggregate dissipative particle dynamics molecule. Bacterial motility is modeled through a constant self-propulsion force applied along the axis of each such aggregate molecule. The model accounts for hydrodynamic interactions between self-propelled agents through the pairwise dissipative interactions conventional to dissipative particle dynamics. Numerical simulations are performed using a customized version of the open-source software package LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) software package. Detailed studies of the influence of agent concentration, pairwise dissipative interactions, and Stokes friction on the statistics of the system are provided. The simulations are used to explore the influence of hydrodynamic interactions in active suspensions. For high agent concentrations in combination with dominating pairwise dissipative forces, strongly correlated motion patterns and a fluid-like spectral distributions of kinetic energy are found. In contrast, systems dominated by Stokes friction exhibit weaker spatial correlations of the velocity field. These results indicate that hydrodynamic interactions may play an important role in the formation of spatially extended structures in active suspensions.

  1. Motility-Driven Glass and Jamming Transitions in Biological Tissues

    Science.gov (United States)

    Bi, Dapeng; Yang, Xingbo; Marchetti, M. Cristina; Manning, M. Lisa

    2016-04-01

    Cell motion inside dense tissues governs many biological processes, including embryonic development and cancer metastasis, and recent experiments suggest that these tissues exhibit collective glassy behavior. To make quantitative predictions about glass transitions in tissues, we study a self-propelled Voronoi model that simultaneously captures polarized cell motility and multibody cell-cell interactions in a confluent tissue, where there are no gaps between cells. We demonstrate that the model exhibits a jamming transition from a solidlike state to a fluidlike state that is controlled by three parameters: the single-cell motile speed, the persistence time of single-cell tracks, and a target shape index that characterizes the competition between cell-cell adhesion and cortical tension. In contrast to traditional particulate glasses, we are able to identify an experimentally accessible structural order parameter that specifies the entire jamming surface as a function of model parameters. We demonstrate that a continuum soft glassy rheology model precisely captures this transition in the limit of small persistence times and explain how it fails in the limit of large persistence times. These results provide a framework for understanding the collective solid-to-liquid transitions that have been observed in embryonic development and cancer progression, which may be associated with epithelial-to-mesenchymal transition in these tissues.

  2. The influence of electric field and confinement on cell motility.

    Science.gov (United States)

    Huang, Yu-Ja; Samorajski, Justin; Kreimer, Rachel; Searson, Peter C

    2013-01-01

    The ability of cells to sense and respond to endogenous electric fields is important in processes such as wound healing, development, and nerve regeneration. In cell culture, many epithelial and endothelial cell types respond to an electric field of magnitude similar to endogenous electric fields by moving preferentially either parallel or antiparallel to the field vector, a process known as galvanotaxis. Here we report on the influence of dc electric field and confinement on the motility of fibroblast cells using a chip-based platform. From analysis of cell paths we show that the influence of electric field on motility is much more complex than simply imposing a directional bias towards the cathode or anode. The cell velocity, directedness, as well as the parallel and perpendicular components of the segments along the cell path are dependent on the magnitude of the electric field. Forces in the directions perpendicular and parallel to the electric field are in competition with one another in a voltage-dependent manner, which ultimately govern the trajectories of the cells in the presence of an electric field. To further investigate the effects of cell reorientation in the presence of a field, cells are confined within microchannels to physically prohibit the alignment seen in 2D environment. Interestingly, we found that confinement results in an increase in cell velocity both in the absence and presence of an electric field compared to migration in 2D.

  3. Acidosis Promotes Metastasis Formation by Enhancing Tumor Cell Motility.

    Science.gov (United States)

    Riemann, A; Schneider, B; Gündel, D; Stock, C; Gekle, M; Thews, O

    2016-01-01

    The tumor microenvironment is characterized by hypoxia, acidosis as well as other metabolic and biochemical alterations. Its role in cancer progression is increasingly appreciated especially on invasive capacity and the formation of metastasis. The effect of acidosis on metastasis formation of two rat carcinoma cell lines was studied in the animal model. In order to analyze the pH dependency of different steps of metastasis formation, invasiveness, cell adhesion and migration of AT-1 prostate cancer cells as well as possible underlying cell signaling pathways were studied in vitro. Acidosis significantly increased the formation of lung metastases of both tumor cell lines in vivo. In vitro, extracellular acidosis neither enhanced invasiveness nor affected cell adhesion to a plastic or to an endothelial layer. However, cellular motility was markedly elevated at pH 6.6 and this effect was sustained even when extracellular pH was switched back to pH 7.4. When analyzing the underlying mechanism, a prominent role of ROS in the induction of migration was observed. Signaling through the MAP kinases ERK1/2 and p38 as well as Src family kinases was not involved. Thus, cancer cells in an acidic microenvironment can acquire enhanced motility, which is sustained even if the tumor cells leave their acidic microenvironment e.g. by entering the blood stream. This increase depended on elevated ROS production and may contribute to the augmented formation of metastases of acidosis-primed tumor cells in vivo.

  4. Realizing the Physics of Motile Cilia Synchronization with Driven Colloids

    Science.gov (United States)

    Bruot, Nicolas; Cicuta, Pietro

    2016-03-01

    Cilia and flagella in biological systems often show large scale cooperative behaviors such as the synchronization of their beats in "metachronal waves." These are beautiful examples of emergent dynamics in biology, and are essential for life, allowing diverse processes from the motility of eukaryotic microorganisms, to nutrient transport and clearance of pathogens from mammalian airways. How these collective states arise is not fully understood, but it is clear that individual cilia interact mechanically, and that a strong and long-ranged component of the coupling is mediated by the viscous fluid. We review here the work by ourselves and others aimed at understanding the behavior of hydrodynamically coupled systems, and particularly a set of results that have been obtained both experimentally and theoretically by studying actively driven colloidal systems. In these controlled scenarios, it is possible to selectively test aspects of living motile cilia, such as the geometrical arrangement, the effects of the driving profile and the distance to no-slip boundaries. We outline and give examples of how it is possible to link model systems to observations on living systems, which can be made on microorganisms, on cell cultures or on tissue sections. This area of research has clear clinical application in the long term, as severe pathologies are associated with compromised cilia function in humans.

  5. Is ineffective esophageal motility associated with gastropharyngeal reflux disease?

    Institute of Scientific and Technical Information of China (English)

    Kyung Yup Kim; Gwang Ha Kim; Dong Uk Kim; Soo Geun Wang; Byung Joo Lee; Jin Choon Lee; Do Youn Park; Geun Am Song

    2008-01-01

    AIM: To evaluate the association between IEM and gastropharyngeal reflux disease (GPRD) in patients who underwent ambulatory 24-h dual-probe pH monitoring for the evaluation of supraesophageal symptoms.METHODS: A total of 632 patients who underwent endoscopy, esophageal manometry and ambulatory 24-h dual-pH monitoring due to supraesophageal symptoms (e.g. globus, hoarseness, or cough) were enrolled. Of them, we selected the patients who had normal esophageal motility and IEM. The endoscopy and ambulatory pH monitoring findings were compared between the two groups.RESULTS: A total of 264 patients with normal esophageal motility and 195 patients with the diagnosis of IEM were included in this study. There was no difference in the frequency of reflux esophagitis and hiatal hernia between the two groups. All the variables showing gastroesophageal reflux and gastropharyngeal reflux were not different between the two groups. The frequency of GERD and GPRD, as defined by ambulatory pH monitoring, was not different between the two groups.CONCLUSION: There was no association between IEM and GPRD as well as between IEM and GERD. IEM alone cannot be considered as a definitive marker for reflux disease.

  6. Changes in the molecular ion yield and fragmentation of peptides under various primary ions in ToF-SIMS and matrix-enhanced ToF-SIMS.

    Science.gov (United States)

    Körsgen, Martin; Tyler, Bonnie J; Pelster, Andreas; Lipinsky, Dieter; Dreisewerd, Klaus; Arlinghaus, Heinrich F

    2016-06-01

    Time of flight secondary ion mass spectrometry (ToF-SIMS) is a powerful technique for the nanoanalysis of biological samples, but improvements in sensitivity are needed in order to detect large biomolecules, such as peptides, on the individual cell level at physiological concentrations. Two promising options to improve the sensitivity of SIMS to large peptides are the use of cluster primary ions to increase desorption of intact molecules or the use of matrix-assisted laser desorption/ionization (MALDI) matrices to increase the ionization probability. In this paper, the authors have combined these two approaches in order to improve understanding of the interaction between ionization and fragmentation processes. The peptides bradykinin and melittin were prepared as neat monolayers on silicon, in a Dextran-40 matrix and in two common MALDI matrices, 2,5-dihydroxybenzoic acid (DHB) and α-cyano-4-hydroxy cinnamic acid (HCCA). ToF-SIMS spectra of these samples were collected using a range of small Bi cluster primary ions and large Ar cluster primary ions. The trends observed in the molecular ion yield and the [M+H](+)/C4H8N(+) ratio with primary ion cluster size were sample system dependent. The molecular ion yield of the bradykinin was maximized by using 30 keV Bi3 (+) primary ions in a DHB matrix but in the HCCA matrix, the maximum molecular ion yield was obtained by using 30 keV Bi7 (+) primary ions. In contrast, the molecular ion yield for melittin in both matrices was greatest using 20 keV Ar2000 (+) primary ions. Improvements in the molecular ion yield were only loosely correlated with a decrease in small fragment ions. The data indicate a complex interplay between desorption processes and ion formation processes which mean that the optimal analytical conditions depend on both the target analyte and the matrix.

  7. In silico reconstitution of actin-based symmetry breaking and motility.

    Directory of Open Access Journals (Sweden)

    Mark J Dayel

    2009-09-01

    Full Text Available Eukaryotic cells assemble viscoelastic networks of crosslinked actin filaments to control their shape, mechanical properties, and motility. One important class of actin network is nucleated by the Arp2/3 complex and drives both membrane protrusion at the leading edge of motile cells and intracellular motility of pathogens such as Listeria monocytogenes. These networks can be reconstituted in vitro from purified components to drive the motility of spherical micron-sized beads. An Elastic Gel model has been successful in explaining how these networks break symmetry, but how they produce directed motile force has been less clear. We have combined numerical simulations with in vitro experiments to reconstitute the behavior of these motile actin networks in silico using an Accumulative Particle-Spring (APS model that builds on the Elastic Gel model, and demonstrates simple intuitive mechanisms for both symmetry breaking and sustained motility. The APS model explains observed transitions between smooth and pulsatile motion as well as subtle variations in network architecture caused by differences in geometry and conditions. Our findings also explain sideways symmetry breaking and motility of elongated beads, and show that elastic recoil, though important for symmetry breaking and pulsatile motion, is not necessary for smooth directional motility. The APS model demonstrates how a small number of viscoelastic network parameters and construction rules suffice to recapture the complex behavior of motile actin networks. The fact that the model not only mirrors our in vitro observations, but also makes novel predictions that we confirm by experiment, suggests that the model captures much of the essence of actin-based motility in this system.

  8. Different computer-assisted sperm analysis (CASA) systems highly influence sperm motility parameters.

    Science.gov (United States)

    Boryshpolets, S; Kowalski, R K; Dietrich, G J; Dzyuba, B; Ciereszko, A

    2013-10-15

    In this study, we examined different computer-assisted sperm analysis (CASA) systems (CRISMAS, Hobson Sperm Tracker, and Image J CASA) on the exact same video recordings to evaluate the differences in sperm motility parameters related to the specific CASA used. To cover a wide range of sperm motility parameters, we chose 12-second video recordings at 25 and 50 Hz frame rates after sperm motility activation using three taxonomically distinct fish species (sterlet: Acipenser ruthenus L.; common carp: Cyprinus carpio L.; and rainbow trout: Oncorhynchus mykiss Walbaum) that are characterized by essential differences in sperm behavior during motility. Systematically higher values of velocity and beat cross frequency (BCF) were observed in video recordings obtained at 50 Hz frame frequency compared with 25 Hz for all three systems. Motility parameters were affected by the CASA and species used for analyses. Image J and CRISMAS calculated higher curvilinear velocity (VCL) values for rainbow trout and common carp at 25 Hz frequency compared with the Hobson Sperm Tracker, whereas at 50 Hz, a significant difference was observed only for rainbow trout sperm recordings. No significant difference was observed between the CASA systems for sterlet sperm motility at 25 and 50 Hz. Additional analysis of 1-second segments taken at three time points (1, 6, and 12 seconds of the recording) revealed a dramatic decrease in common carp and rainbow trout sperm speed. The motility parameters of sterlet spermatozoa did not change significantly during the 12-second motility period and should be considered as a suitable model for longer motility analyses. Our results indicated that the CASA used can affect motility results even when the same motility recordings are used. These results could be critically altered by the recording quality, time of analysis, and frame rate of camera, and could result in erroneous conclusions. Copyright © 2013 Elsevier Inc. All rights reserved.

  9. Characterization of Novel Factors Involved in Swimming and Swarming Motility in Salmonella enterica Serovar Typhimurium.

    Directory of Open Access Journals (Sweden)

    Julia Andrea Deditius

    Full Text Available Salmonella enterica utilizes flagellar motility to swim through liquid environments and on surfaces. The biosynthesis of the flagellum is regulated on various levels, including transcriptional and posttranscriptional mechanisms. Here, we investigated the motility phenotype of 24 selected single gene deletions that were previously described to display swimming and swarming motility effects. Mutations in flgE, fliH, ydiV, rfaG, yjcC, STM1267 and STM3363 showed an altered motility phenotype. Deletions of flgE and fliH displayed a non-motile phenotype in both swimming and swarming motility assays as expected. The deletions of STM1267, STM3363, ydiV, rfaG and yjcC were further analyzed in detail for flagellar and fimbrial gene expression and filament formation. A ΔydiV mutant showed increased swimming motility, but a decrease in swarming motility, which coincided with derepression of curli fimbriae. A deletion of yjcC, encoding for an EAL domain-containing protein, increased swimming motility independent on flagellar gene expression. A ΔSTM1267 mutant displayed a hypermotile phenotype on swarm agar plates and was found to have increased numbers of flagella. In contrast, a knockout of STM3363 did also display an increase in swarming motility, but did not alter flagella numbers. Finally, a deletion of the LPS biosynthesis-related protein RfaG reduced swimming and swarming motility, associated with a decrease in transcription from flagellar class II and class III promoters and a lack of flagellar filaments.

  10. HSA21 Single-Minded 2 (Sim2 Binding Sites Co-Localize with Super-Enhancers and Pioneer Transcription Factors in Pluripotent Mouse ES Cells.

    Directory of Open Access Journals (Sweden)

    Audrey Letourneau

    Full Text Available The HSA21 encoded Single-minded 2 (SIM2 transcription factor has key neurological functions and is a good candidate to be involved in the cognitive impairment of Down syndrome. We aimed to explore the functional capacity of SIM2 by mapping its DNA binding sites in mouse embryonic stem cells. ChIP-sequencing revealed 1229 high-confidence SIM2-binding sites. Analysis of the SIM2 target genes confirmed the importance of SIM2 in developmental and neuronal processes and indicated that SIM2 may be a master transcription regulator. Indeed, SIM2 DNA binding sites share sequence specificity and overlapping domains of occupancy with master transcription factors such as SOX2, OCT4 (Pou5f1, NANOG or KLF4. The association between SIM2 and these pioneer factors is supported by co-immunoprecipitation of SIM2 with SOX2, OCT4, NANOG or KLF4. Furthermore, the binding of SIM2 marks a particular sub-category of enhancers known as super-enhancers. These regions are characterized by typical DNA modifications and Mediator co-occupancy (MED1 and MED12. Altogether, we provide evidence that SIM2 binds a specific set of enhancer elements thus explaining how SIM2 can regulate its gene network in neuronal features.

  11. Effect of enterokinetic prucalopride on intestinal motility in fast rats

    Institute of Scientific and Technical Information of China (English)

    Hui-Bin Qi; Jin-Yan Luo; Xin Liu

    2003-01-01

    AIM: To evaluate the effects of prucalopride on intestinal prokinetic activity in fast rats and to provide experimental basis for clinical treatrnent of gastrointestinal motility diseases.METHODS: Gastrointestinal propulsion rate was measured by the migration rate of activated charcoal, which reflexes gastrointestinal motility function. 120 Spraque-Dawley rats were randomly divided into four groups and received an intravenous injection of physiological saline (served as control), prucalopdde 1 mg/kg, prucalopride 2 mg/kg and cisapride 1 mg/kg,respectively. The gastrointestinal propulsion rate was measured 1, 2 or 4 hours after intravenous injection of the drugs.RESULTS: Significant accelerations of gastrointestinal propulsion rate in prucalopride 1 mg/kg and 2 mg/kg groups were found compared with control group at 2 and 4 hours (83.2%±5.5%, 81.7%±8.5% vs70.5%±9.2%, P<0.01;91.2%±2.2%, 91.3%±3.9% vs86.8%±2.6%, P<0.01).The gastrointestinal propulsion rates at 1, 2 or 4 hours were faster in prucalopride 1 mg/kg and 2 mg/kg groups than in cisapride group (84.0%±11.7%, 77.1%±11.9% vs 66.3%±13.6%, P<0.01, P<0.05; 83.2%±5.5%, 81.7%±8.5% vs75.4%±5.9 %, P<0.01, P<0.05; 91.2%±2.2%,91.3%±3.9% vs 88.6%±3.5%,P<0.05, P<0.05). No difference of gastrointestinal propulsion rate was found between prucalopride 1 mg/kg group and prucalopride 2 mg/kg group (P>0.05).CONCLUSION: Prucalopride accelerates intestinal motility in fast rats, and has no dose dependent effect.

  12. Isophote Shapes of Early-Type Galaxies in Massive Clusters at $z\\sim1$ and 0

    CERN Document Server

    Mitsuda, Kazuma; Morokuma, Tomoki; Suzuki, Nao; Yasuda, Naoki; Perlmutter, Saul; Aldering, Greg; Meyers, Joshua

    2016-01-01

    We compare the isophote shape parameter $a_{4}$ of early-type galaxies (ETGs) between $z\\sim1$ and 0 as a proxy for dynamics to investigate the epoch at which the dynamical properties of ETGs are established, using cluster ETG samples with stellar masses of $\\log(M_{*}/M_{\\odot})\\geq10.5$ which have spectroscopic redshifts. We have 130 ETGs from the Hubble Space Telescope Cluster Supernova Survey for $z\\sim1$ and 355 ETGs from the Sloan Digital Sky Survey for $z\\sim0$. We have developed an isophote shape analysis method which can be used for high-redshift galaxies and has been carefully compared with published results. We have applied the same method for both the $z\\sim1$ and $0$ samples. We find similar dependence of the $a_{4}$ parameter on the mass and size at $z\\sim1$ and 0; the main population of ETGs changes from disky to boxy at a critical stellar mass of $\\log(M_{*}/M_{\\odot})\\sim11.5$ with the massive end dominated by boxy. The disky ETG fraction decreases with increasing stellar mass both at $z\\sim1...

  13. ArchSim: A System-Level Parallel Simulation Platform for the Architecture Design of High Performance Computer

    Institute of Scientific and Technical Information of China (English)

    Yong-Qin Huang; Hong-Liang Li; Xiang-Hui Xie; Lei Qian; Zi-Yu Hao; Feng Guo; Kun Zhang

    2009-01-01

    High performance computer(HPC)is a complex huge system,of which the architecture design meets increasing difficulties and risks.Traditional methods,such as theoretical analysis,component-level simulation and sequential simulation,are not applicable to system-level simulations of HPC systems.Eyen the parallel simulation using large-scale parallel machines also have many difficulties in scalability,reliability,generality,as well as efficiency.According to the current needs of HPC architecture design,this paper proposes a system-level parallel simulation platform:ArchSim.We first introduce the architecture of ArchSim simulation platform which is composed of a global server(GS),local server agents(LSA)and entities.Secondly,we emphasize some key techniques of ArchSim,including the synchronization protocol,the communication mechanism and the distributed checkpointing/restart mechanism.We then make a synthesized test of some main performance indices of ArchSim with the phold benchmark and analyze the extra overhead generated by ArchSim.Finally,based on ArchSim.we construct a parallel event-driven interconnection network simulator and a system-level simulator for a small scale HPC system with 256 processors.The results of the performance test and HPC system simulations demonstrate that ArchSim can achieve high speedup ratio and high scalability on parallel host machine and support system-level simulations for the architecture design of HPC systems.

  14. Development and validation of SIMS: an instrument for measuring quality of life of adults with sickle cell disease.

    Science.gov (United States)

    Adams-Graves, Patricia; Lamar, Kimberly; Johnson, Cage; Corley, Pat

    2008-07-01

    In recent years, there has been a growing interest in the assessment of quality of life (QOL) issues, particularly in chronic debilitating conditions. Several instruments have been developed, tested, and validated in the general population and in other chronic diseases; however, few studies have examined QOL issues in adults with sickle cell disease (SCD). We developed Sickle Cell Impact Measurement Scale (SIMS), an instrument for measuring the QOL of adults with SCD. The 142-item multi-dimensional SIMS questionnaire was developed using 4 validated instruments and additional questions based upon recommendations of patient focus groups. The SIMS was self-administered to 106 SCD and 45 rheumatoid arthritis (RA) patients over 4 sites. SIMS was evaluated on measures of both internal consistency and construct validity. Item reduction was performed based on results of factor analysis. The SIMS achieved good internal consistency, with a Cronbach's alpha coefficient reported of 0.86, and distinguished between patients with SCD and RA. Overall, QOL did not differ significantly among SCD and RA patients. However, SCD patients scored higher in both physical and social domains, which was expected and reflected the differences in the pathophysiology of each disease. The SIMS is a reliable, valid, and responsive questionnaire, which functions well as a discriminative instrument for the measure of health-related QOL (HRQOL) of adults with SCD. The SIMS is currently being administered to adults with SCD across several centers for further validation to become a disease-specific, global QOL instrument.

  15. Spatially resolved quantification of organic matter in synthetic organo-mineral associations by NanoSIMS

    Science.gov (United States)

    Schurig, Christian; Schrank, Thomas; Müller, Carsten W.; Pohl, Lydia; Höschen, Carmen; Totsche, Kai-Uwe; Kögel-Knabner, Ingrid

    2016-04-01

    Soil structure is resulting from soil forming processes at the molecular scale, but has feedbacks on soil functions on macroscopic or even global scales. In this framework, soil organic matter (SOM) is of special importance as a gluing agent for soil structure, besides being a carbon sink. Conventional bulk-scale analyses allows for quantification and for a characterisation of the chemical bonding types of OM. However, all information of the spatial distribution of OM on the relevant scale of few nano- to micrometres is lost during this kind of analyses. While nano-scale secondary ion mass-spectroscopy (NanoSIMS) delivers qualitative data on the spatial distribution of SOM at the nano-scale, receiving quantitative data from this method remains challenging due to matrix and charging effects. In order to overcome this problem, the aim of this study was to develop scaling factors between conventional bulk-scale methods and NanoSIMS. For developing these factors, dissolved organic matter (DOM) was extracted from organic material, which was sampled from a podzol. Subsequently, model minerals, such as boehmite and illite, were loaded with defined amounts of this DOM by means of sorption experiments. After the end of the experiments the liquid and solid phases were divided by means of centrifugation and the solid phase was subjected to freeze drying. Carbon and nitrogen content of the solid and liquid phases were measured via C/N and TOC analyses, respectively. The measured data was fitted with Freundlich-type adsorption isotherms. Samples for NanoSIMS analyses were distributed onto silicon wafers as individual particles. The following elements were analysed: C, N, O, Si, S and Al. Spatially resolved analysis of the NanoSIMS data yielded a increased detection of SOM on the minerals in higher concentration steps. Linear relationships with high correlation and low deviation were found when comparing the spatially resolved NanoSIMS data with the bulk scale methods. The

  16. Motion Simulation of 3-DOF Parallel Robot Based on SimMechanics%基于SimMechanics的三自由度并联机器人仿真

    Institute of Scientific and Technical Information of China (English)

    李志斌; 董旭明; 钟德永

    2012-01-01

    Delta型机器人是一种三自由度纯平动并联机构,介绍了应用Simulink的SimMechanics模块集对Delta平台进行仿真研究的方法.运用SimMechanics模块对并联机器人进行建模,并根据机构的几何特性建立运动学逆解求取模块,给出动平台规划运动轨迹,通过运动学逆解求取模块生成机构驱动轴输入运动信号,对机构模型进行运动仿真.仿真结果表明,所建立的机械模型和逆解求取模块以及轨迹跟踪都符合实际系统特性,仿真方法高效、实用.

  17. Multilayer analysis using SIMS: interpretation of profiles at interfaces. Analyse de couches ou multicouches par SIMS : interpretation du profil aux interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Aucouturier, M. (CNRS, Labs. de Meudon-Bellevue, 92 Meudon (France)); Grattepain, C. (CNRS, Labs. de Meudon-Bellevue, 92 Meudon (France)); Tromson-Carli, A. (CNRS, Labs. de Meudon-Bellevue, 92 Meudon (France)); Barbe, M. (CNRS, Labs. de Meudon-Bellevue, 92 Meudon (France)); Cohen-Solal, G. (CNRS, Labs. de Meudon-Bellevue, 92 Meudon (France)); Marfaing, Y. (CNRS, Labs. de Meudon-Bellevue, 92 Meudon (France)); Chevrier, F. (CNRS, Labs. de Meudon-Bellevue, 92 Meudon (France)); Gall, H. le (CNRS, Labs. de Meudon-Bellevue, 92 Meudon (France)); Imhoff, D. (CNRS, Labs. de Meudon-Bellevue, 92 Meudon (France))

    1993-11-01

    Secondary ion mass spectrometry (SIMS) is a well adapted analytical method for the chemical characterization of concentration profiles in layered or multilayered materials, particularly concerning the more or less abrupt interfaces bounding those layers. It is known that the fiability and accuracy of the interface characterization may be affected by methodological factors, which alter the depth resolution such as: macroscopical or microscopical initial roughness of the substrate and/or of the layers, ion-induced roughening, effects of differential sputtering of the various elements, transitory stage of the primary ion beam implantation, ion beam induced accelerated diffusion, balistic mixing or segregation; etc.. This communication describes several examples of SIMS analysis performed on metal multilayers (Co/Cu) and on epitaxial semiconductor layers (CdTe/GaAs), focussing the interest on the particular analytical problems raised by the initial roughness and the ion induced roughening effect. The interpretation of the measured profiles, the influence of analytical parameters (such as the nature of the primary ion beam, sputtering conditions, detected ion species), and the limitations of profilometry roughness measurements, are discussed. Solutions are proposed in order to improve the depth resolution of interface characterization, including a tentative modelization of roughness effects. (orig.).

  18. 基于SIM900A儿童防丢器终端设计%Design of Children Anti-loss Device Terminal Based on SIM900A

    Institute of Scientific and Technical Information of China (English)

    贺婷

    2015-01-01

    Aiming at the single function of children anti-loss device in the market, a smart children anti-loss device is designed to meet with people's needs. The terminal contains the main control STM32F103C, the peripheral part and the SIM900A module. The main function is to realize station location and send the location information to the main control terminal or call the main con-trol terminal when the terminal identifies the AT command sending by the main control terminal.%针对市面儿童防丢器功能单一的情况,设计一款智能儿童防丢器满足人们需求。儿童防丢器的终端包含主控STM32F103C及外设部分和SIM900A模块。主要实现当终端识别主控端发送的AT指令信息,执行基站定位并将位置信息发送给主控端或拨打主控端电话等相关功能。

  19. Persistence-Driven Durotaxis: Generic, Directed Motility in Rigidity Gradients

    Science.gov (United States)

    Novikova, Elizaveta A.; Raab, Matthew; Discher, Dennis E.; Storm, Cornelis

    2017-02-01

    Cells move differently on substrates with different rigidities: the persistence time of their motion is higher on stiffer substrates. We show that this behavior—in and of itself—results in a net flux of cells directed up a soft-to-stiff gradient. Using simple random walk models with varying persistence and stochastic simulations, we characterize the propensity to move in terms of the durotactic index also measured in experiments. A one-dimensional model captures the essential features and highlights the competition between diffusive spreading and linear, wavelike propagation. Persistence-driven durokinesis is generic and may be of use in the design of instructive environments for cells and other motile, mechanosensitive objects.

  20. Motility of magnetotactic bacteria/MTB to Geomagnetic fields

    Science.gov (United States)

    Hidajatullah-Maksoed, Fatahillah

    2016-03-01

    Bacteria with motility directed by a local geomagnetic fields have been observed in marine sediments'' discussed by R. Blakemore, 1975. Magnetotactic bacteria/MTB discovered in 1963 by Salvatore Bellini. For ``off-axis electron holography in the transmission electron microscope was used to correlates the physical & magnetic microstructure of magnetite nanocrystals in magnetotactic bacteria'' sought ``single-domain magnetite in hemopelagic sediments'' from JF Stolz. Otherwise, for potential source of bioproducts- product meant from result to multiplier -of magnetotactic bacteria[ACV Araujo, et.al, 2014 ] of marine drugs retrieved the `measurement of cellular chemotaxis with ECIS/Taxis, from KM Pietrosimone, 2012, whereas after ``earth magnetic field role on small living models'' are other interpretation of ``taxis'' as a movement of a cell instead usual ``tax'' for yew's taxus cuspidate, hired car & taxes in financial realms. Acknowledgements to HE. Mr. H. TUK SETYOHADI, Jl. Sriwijaya Raya 3, South-Jakarta, INDONESIA.

  1. Peroral Endoscopic Myotomy for Treating Achalasia and Esophageal Motility Disorders.

    Science.gov (United States)

    Youn, Young Hoon; Minami, Hitomi; Chiu, Philip Wai Yan; Park, Hyojin

    2016-01-31

    Peroral endoscopic myotomy (POEM) is the application of esophageal myotomy to the concept of natural orifice transluminal surgery (NOTES) by utilizing a submucosal tunneling method. Since the first case of POEM was performed for treating achalasia in Japan in 2008, this procedure is being more widely used by many skillful endosopists all over the world. Currently, POEM is a spotlighted, emerging treatment option for achalasia, and the indications for POEM are expanding to include long-standing, sigmoid shaped esophagus in achalasia, even previously failed endoscopic treatment or surgical myotomy, and other spastic esophageal motility disorders. Accumulating data about POEM demonstrate excellent short-term outcomes with minimal risk of major adverse events, and some existing long-term data show the efficacy of POEM to be long lasting. In this review article, we review the technical details and clinical outcomes of POEM, and discuss some considerations of POEM in special situations.

  2. Bacillus subtilis Hfq: A role in chemotaxis and motility

    Indian Academy of Sciences (India)

    CHANDRAKANT B JAGTAP; PRADEEP KUMAR; K KRISHNAMURTHY RAO

    2016-09-01

    Hfq is a global post-transcriptional regulator that modulates the translation and stability of target mRNAs and therebyregulates pleiotropic functions, such as growth, stress, virulence and motility, in many Gram-negative bacteria.However, comparatively little is known about the regulation and function(s) of Hfq in Gram-positive bacteria.Recently, in Bacillus subtilis, a role for Hfq in stationary phase survival has been suggested, although the possibilityof Hfq having an additional role(s) cannot be ruled out. In this study we show that an ortholog of Hfq in B. subtilis isregulated by the stress sigma factor, σB, in addition to the stationary phase sigma factor, σH. We further demonstratethat Hfq positively regulates the expression of flagellum and chemotaxis genes (fla/che) that control chemotaxis andmotility, thus assigning a new function for Hfq in B. subtilis.

  3. Curved trajectories of actin-based motility in two dimensions

    Science.gov (United States)

    Wen, Fu-Lai; Leung, Kwan-tai; Chen, Hsuan-Yi

    2012-05-01

    Recent experiments have reported fascinating geometrical trajectories for actin-based motility of bacteria Listeria monocytogenes and functionalized beads. To understand the physical mechanism for these trajectories, we constructed a phenomenological model to study the motion of an actin-propelled disk in two dimensions. In our model, the force and actin density on the surface of the disk are influenced by the translation and rotation of the disk, which in turn is induced by the asymmetric distributions of those densities. We show that this feedback can destabilize a straight trajectory, leading to circular, S-shape and other geometrical trajectories observed in the experiments through bifurcations in the distributions of the force and actin density. The relation between our model and the models for self-propelled deformable particles is emphasized and discussed.

  4. Membrane tension feedback on shape and motility of eukaryotic cells

    Science.gov (United States)

    Winkler, Benjamin; Aranson, Igor S.; Ziebert, Falko

    2016-04-01

    In the framework of a phase field model of a single cell crawling on a substrate, we investigate how the properties of the cell membrane affect the shape and motility of the cell. Since the membrane influences the cell dynamics on multiple levels and provides a nontrivial feedback, we consider the following fundamental interactions: (i) the reduction of the actin polymerization rate by membrane tension; (ii) area conservation of the cell's two-dimensional cross-section vs. conservation of the circumference (i.e. membrane inextensibility); and (iii) the contribution from the membrane's bending energy to the shape and integrity of the cell. As in experiments, we investigate two pertinent observables - the cell's velocity and its aspect ratio. We find that the most important effect is the feedback of membrane tension on the actin polymerization. Bending rigidity has only minor effects, visible mostly in dynamic reshaping events, as exemplified by collisions of the cell with an obstacle.

  5. Accumulation of motile elongated micro-organisms in turbulence

    Science.gov (United States)

    Zhan, Caijuan; Sardina, Gaetano; Lushi, Enkeleida; Brandt, Luca

    2014-01-01

    We study the effect of turbulence on marine life by performing numerical simulations of motile microorganisms, modelled as prolate spheroids, in isotropic homogeneous turbulence. We show that the clustering and patchiness observed in laminar flows, linear shear and vortex flows, are significantly reduced in a three-dimensional turbulent flow mainly because of the complex topology; elongated micro-orgamisms show some level of clustering in the case of swimmers without any preferential alignment whereas spherical swimmers remain uniformly distributed. Micro-organisms with one preferential swimming direction (e.g. gyrotaxis) still show significant clustering if spherical in shape, whereas prolate swimmers remain more uniformly distributed. Due to their large sensitivity to the local shear, these elongated swimmers react slower to the action of vorticity and gravity and therefore do not have time to accumulate in a turbulent flow. These results show how purely hydrodynamic effects can alter the ecology of microorganisms that can vary their shape and their preferential orientation.

  6. Endoplasmic motility spectral characteristics in plasmodium of Physarum polycephalum

    Science.gov (United States)

    Avsievich, T. I.; Ghaleb, K. E. S.; Frolov, S. V.; Proskurin, S. G.

    2015-03-01

    Spectral Fourier analysis of experimentally acquired velocity time dependencies, V(t), of shuttle endoplasmic motility in an isolated strand of plasmodium of slime mold Physarum Polycephalum has been realized. V(t) registration was performed in normal conditions and after the treatment by respiration inhibitors, which lead to a complete cessation of endoplasmic motion in the strand. Spectral analysis of the velocity time dependences of the endoplasm allows obtaining two distinct harmonic components in the spectra. Their ratio appeared to be constant in all cases, ν2/ν1=1.97±0.17. After the inhibitors are washed out respiratory system becomes normal, gradually restoring the activity of both harmonic oscillatory sources with time. Simulated velocity time dependences correspond to experimental data with good accuracy.

  7. [Radiotelemetric studies of uterine motility in cows with acute endometritis].

    Science.gov (United States)

    Kostov, I

    1980-01-01

    Thirty two cows with postpartum complication were radiotelemetrically studied to register uterine motility. The results were compared with those of the control group of 42 cows with normal calving and no complications. Enhanced uterine reactivity to oxytocin and other agents was established in all cows with complications in the postpartum period. It is manifested in the spring also by intensified motor activity of the uterus. Motor activity of the uterus is hardly registered during to summer months in cows with normal peurperium and complications following day 2 of calving. No essential difference was found in estradiol-17 beta content in the blood plasma of both groups of cows. Body temperature rises in cows with postpartum complications.

  8. LBP based detection of intestinal motility in WCE images

    Science.gov (United States)

    Gallo, Giovanni; Granata, Eliana

    2011-03-01

    In this research study, a system to support medical analysis of intestinal contractions by processing WCE images is presented. Small intestine contractions are among the motility patterns which reveal many gastrointestinal disorders, such as functional dyspepsia, paralytic ileus, irritable bowel syndrome, bacterial overgrowth. The images have been obtained using the Wireless Capsule Endoscopy (WCE) technique, a patented, video colorimaging disposable capsule. Manual annotation of contractions is an elaborating task, since the recording device of the capsule stores about 50,000 images and contractions might represent only the 1% of the whole video. In this paper we propose the use of Local Binary Pattern (LBP) combined with the powerful textons statistics to find the frames of the video related to contractions. We achieve a sensitivity of about 80% and a specificity of about 99%. The achieved high detection accuracy of the proposed system has provided thus an indication that such intelligent schemes could be used as a supplementary diagnostic tool in endoscopy.

  9. Determination of motility forces on isolated chromosomes with laser tweezers.

    Science.gov (United States)

    Khatibzadeh, Nima; Stilgoe, Alexander B; Bui, Ann A M; Rocha, Yesenia; Cruz, Gladys M; Loke, Vince; Shi, Linda Z; Nieminen, Timo A; Rubinsztein-Dunlop, Halina; Berns, Michael W

    2014-10-31

    Quantitative determination of the motility forces of chromosomes during cell division is fundamental to understanding a process that is universal among eukaryotic organisms. Using an optical tweezers system, isolated mammalian chromosomes were held in a 1064 nm laser trap. The minimum force required to move a single chromosome was determined to be ≈ 0.8-5 pN. The maximum transverse trapping efficiency of the isolated chromosomes was calculated as ≈ 0.01-0.02. These results confirm theoretical force calculations of ≈ 0.1-12 pN to move a chromosome on the mitotic or meiotic spindle. The verification of these results was carried out by calibration of the optical tweezers when trapping microspheres with a diameter of 4.5-15 µm in media with 1-7 cP viscosity. The results of the chromosome and microsphere trapping experiments agree with optical models developed to simulate trapping of cylindrical and spherical specimens.

  10. Effect of sennosides on colon motility in cats.

    Science.gov (United States)

    Wienbeck, M; Kortenhaus, E; Wallenfels, M; Karaus, M

    1988-01-01

    The actions of sennosides on colonic motility are incompletely understood. We therefore studied the effects of sennosides A + B on colonic myoelectric activity and transit of a radio-opaque meal in 7 conscious cats. Intraduodenal application of sennosides (2 mg/kg body weight) accelerated the half colon transit time from 60 +/- 10 (SEM) to 43 +/- 7 min. At the same time the ratio of long-spike bursts to short-spike bursts was changed from 0.22 to 10.1. Loperamide, an antidiarrheal agent, had the opposite effect. The overall spike activity was not altered by sennosides, but increased by loperamide. It is concluded that the propulsive action of sennosides in the colon is reflected by myoelectric patterns and not by the total number of spikes.

  11. Motility of a model bristle-bot: A theoretical analysis

    Science.gov (United States)

    Cicconofri, Giancarlo; DeSimone, Antonio

    2015-11-01

    Bristle-bots are legged robots that can be easily made out of a toothbrush head and a small vibrating engine. Despite their simple appearance, the mechanism enabling them to propel themselves by exploiting friction with the substrate is far from trivial. Numerical experiments on a model bristle-bot have been able to reproduce such a mechanism revealing, in addition, the ability to switch direction of motion by varying the vibration frequency. This paper provides a detailed account of these phenomena through a fully analytical treatment of the model. The equations of motion are solved through an expansion in terms of a properly chosen small parameter. The convergence of the expansion is rigorously proven. In addition, the analysis delivers formulas for the average velocity of the robot and for the frequency at which the direction switch takes place. A quantitative description of the mechanism for the friction modulation underlying the motility of the bristle-bot is also provided.

  12. Effect of short abstinence time on sperm motility parameters

    DEFF Research Database (Denmark)

    Alipour, Hiva; Dardmeh, Fereshteh; Van Der Horst, Gerhard

    2015-01-01

    Semen preparation medium have an important role in assisted reproduction techniques and their composition influences sperm binding and motility. Some studies have assessed the influence of pH on sperm kinetics. However, no study to date has assessed the effect of environmental pH on subtle...... differences in the details of the sperm movement (kinematics) of human sperm provided by computerized sperm analysis systems. This study was designed to assess the effect of two different media pH levels on kinematic parameters of the human sperm. Samples were prepared using the 40%/80% Pureception (Sage, USA......) density gradient and resuspended in customized sperm culture media with pH levels of 7.9 and 8.3 (Origio, Denmark). Kinematic parameters of the sperm in both groups were analyzed using the Sperm Class Analyzer (Microptic S.L., Spain) at 0, 6 and 24 hours following the addition of media. Results...

  13. Accumulation of motile elongated micro-organisms in turbulence

    CERN Document Server

    Zhan, Caijuan; Lushi, Enkeleida; Brandt, Luca

    2013-01-01

    We study the effect of turbulence on marine life by performing numerical simulations of motile microorganisms, modelled as prolate spheroids, in isotropic homogeneous turbulence. We show that the clustering and patchiness observed in laminar flows, linear shear and vortex flows, are significantly reduced in a three-dimensional turbulent flow mainly because of the complex topology; elongated micro-orgamisms show some level of clustering in the case of swimmers without any preferential alignment whereas spherical swimmers remain uniformly distributed. Micro-organisms with one preferential swimming direction (e.g. gyrotaxis) still show significant clustering if spherical in shape, whereas prolate swimmers remain more uniformly distributed. Due to their large sensitivity to the local shear, these elongated swimmers react slower to the action of vorticity and gravity and therefore do not have time to accumulate in a turbulent flow. These results show how purely hydrodynamic effects can alter the ecology of microor...

  14. Functional Magnetic Resonance in the Evaluation of Oesophageal Motility Disorders

    Directory of Open Access Journals (Sweden)

    Francesco Covotta

    2011-01-01

    Our aim is to assess the role of fMRI as a technique to assess morphological and functional parameters of the esophagus in patients with esophageal motor disorders and in healthy controls. Subsequently, we assessed the diagnostic efficiency of fMRI in comparison to videofluoroscopic and manometric findings in the investigation of patients with esophageal motor disorders. Considering that fMRI was shown to offer valuable information on bolus transit and on the caliber of the esophagus, variations of these two parameters in the different types of esophageal motor alterations have been assessed. fMRI, compared to manometry and videofluoroscopy, showed that a deranged or absent peristalsis is significantly associated with slower transit time and with increased esophageal diameter. Although further studies are needed, fMRI represents a promising noninvasive technique for the integrated functional and morphological evaluation of esophageal motility disorders.

  15. Automated cell tracking tools for quantitative motility studies

    Science.gov (United States)

    Zimmer, Christophe; Zhang, Bo; Blazquez, Samantha; Labruyère, Elisabeth; Frischknecht, Freddy; Ménard, Robert; Guillén, Nancy; Olivo-Marin, Jean-Christophe

    2005-03-01

    Optical microscopy in 2 or 3 dimensions allows extensive observations of the motility and morphology of living cells, in culture or in tissue. This leads to an exploding accumulation of imaging data and shifts the bottleneck from data acquisition to data analysis. Manual image analysis is often either impossible or exceedingly time-consuming and subject to uncontrollable user bias and errors. Computerized methods promise to ensure fast, accurate and reproducible processing, but the basic image analysis functions available in standard commercial software are generally not adapted to the complexity of biological images. For this reason, we develop methods based on active contours, a powerful and flexible technique to segment and track objects, that has become very popular in computer vision research. Here, we describe the main benefits and limitations of active contours for our application, and our efforts to adapt and improve these methods for the analysis of cellular dynamics.

  16. Impedance planimetric description of normal rectoanal motility in humans

    DEFF Research Database (Denmark)

    Andersen, Inge S; Michelsen, Hanne B; Krogh, Klaus

    2007-01-01

    studied during one-hour fasting and one hour after a meal. Rectal cross-sectional areas were determined at five levels each 2 cm apart, as well as rectal and anal pressure. RESULTS: A number of rectoanal motility patterns were observed. A total of 25 episodes with very localized cyclic rectal contractions...... detected at only one of five channels were observed lasting two to four minutes with a median frequency of three per minute (range, 2-6). A total of 44 episodes of cyclic rectal contractions propagating over two or more channels were detected lasting 2 to 36 minutes. Most were associated with contractions...... of the anal canal. A significant increase in rectal contractile activity was observed after the meal (P

  17. Hydrogen Sulfide and/or Ammonia Reduces Spermatozoa Motility through AMPK/AKT Related Pathways

    Science.gov (United States)

    Zhao, Yong; Zhang, Wei-Dong; Liu, Xin-Qi; Zhang, Peng-Fei; Hao, Ya-Nan; Li, Lan; Chen, Liang; Shen, Wei; Tang, Xiang-Fang; Min, Ling-Jiang; Meng, Qing-Shi; Wang, Shu-Kun; Yi, Bao; Zhang, Hong-Fu

    2016-11-01

    A number of emerging studies suggest that air pollutants such as hydrogen sulfide (H2S) and ammonia (NH3) may cause a decline in spermatozoa motility. The impact and underlying mechanisms are currently unknown. Boar spermatozoa (in vitro) and peripubertal male mice (in vivo) were exposed to H2S and/or NH3 to evaluate the impact on spermatozoa motility. Na2S and/or NH4Cl reduced the motility of boar spermatozoa in vitro. Na2S and/or NH4Cl disrupted multiple signaling pathways including decreasing Na+/K+ ATPase activity and protein kinase B (AKT) levels, activating Adenosine 5‧-monophosphate (AMP)-activated protein kinase (AMPK) and phosphatase and tensin homolog deleted on chromosome ten (PTEN), and increasing reactive oxygen species (ROS) to diminish boar spermatozoa motility. The increase in ROS might have activated PTEN, which in turn diminished AKT activation. The ATP deficiency (indicated by reduction in Na+/K+ ATPase activity), transforming growth factor (TGFβ) activated kinase-1 (TAK1) activation, and AKT deactivation stimulated AMPK, which caused a decline in boar spermatozoa motility. Simultaneously, the deactivation of AKT might play some role in the reduction of boar spermatozoa motility. Furthermore, Na2S and/or NH4Cl declined the motility of mouse spermatozoa without affecting mouse body weight gain in vivo. Findings of the present study suggest that H2S and/or NH3 are adversely associated with spermatozoa motility.

  18. Relationship between Porcine Sperm Motility and Sperm Enzymatic Activity using Paper-based Devices

    Science.gov (United States)

    Matsuura, Koji; Huang, Han-Wei; Chen, Ming-Cheng; Chen, Yu; Cheng, Chao-Min

    2017-04-01

    Mammalian sperm motility has traditionally been analyzed to determine fertility using computer-assisted semen analysis (CASA) systems. To develop low-cost and robust male fertility diagnostics, we created a paper-based MTT assay and used it to estimate motile sperm concentration. When porcine sperm motility was inhibited using sperm enzyme inhibitors for sperm enzymes related to mitochondrial activity and glycolysis, we simultaneously recorded sperm motility and enzymatic reactivity using a portable motility analysis system (iSperm) and a paper-based MTT assay, respectively. When using our paper-based MTT-assay, we calculated the area mean value signal intensity (AMV) to evaluate enzymatic reactivity. Both sperm motility and AMV decreased following treatment with iodoacetamide (IODO) and 3-bromopyruvic acid (3BP), both of which are inhibitors of glycolytic enzymes including glyceraldehyde-3-phosphate dehydrogenase (GAPDH). We found a correlation between recorded motility using iSperm and AMV from our paper-based assay (P Based on this inhibitor study, sperm motility can be estimated using our paper-based MTT-assay.

  19. Regulation of gastroduodenal motility: acyl ghrelin, des-acyl ghrelin and obestatin and hypothalamic peptides.

    Science.gov (United States)

    Fujimiya, Mineko; Ataka, Koji; Asakawa, Akihiro; Chen, Chih-Yen; Kato, Ikuo; Inui, Akio

    2012-01-01

    Real-time measurements for gut motility in conscious rats or mice combined with intracerebroventricular or intravenous injection of peptide agonists or antagonists allow us to understand the regulatory mechanism of gastrointestinal motility. Neuropeptide Y (NPY) in the arcuate nucleus in the hypothalamus stimulates the fasted motility in the duodenum, while urocortin in the paraventricular nucleus inhibits fed and fasted motility in the antrum and duodenum. Acyl ghrelin exerts stimulatory effects on the motility of the antrum and duodenum in both the fed and fasted state of animals. NPY Y2 and Y4 receptors in the brain may mediate the action of acyl ghrelin, and vagal afferent pathways might be involved in this mechanism. Des-acyl ghrelin exerts inhibitory effects on the motility of the antrum but not on the motility of the duodenum in the fasted state of animals. CRF type 2 receptor in the brain may mediate the action of des-acyl ghrelin, and vagal afferent pathways might not be involved in this mechanism. Obestatin exerts inhibitory effects on the motility of the antrum and duodenum in the fed state but not in the fasted state of animals. CRF type 1 and type 2 receptors in the brain may mediate the action of obestatin, and vagal afferent pathways might be partially involved in this mechanism.

  20. Effect of dopamine on bethanechol-stimulated gastric antral motility in dogs with gastric fistula

    DEFF Research Database (Denmark)

    Bech, K; Hovendal, C P

    1982-01-01

    The purpose of the present study was to evaluate the effect of dopamine on gastric antral motility in conscious dogs with gastric fistula, using intraluminal strain-gauge transducers. Infusion of bethanechol increased the motility with regard to both frequency and strength. Dopamine, an endogenous...

  1. Effect of isoprenaline on bethanechol-stimulated gastric antral motility in dogs with gastric fistula

    DEFF Research Database (Denmark)

    Bech, K; Hovendal, C P

    1982-01-01

    The purpose of the present study was to evaluate the effect of isoprenaline on gastric antral motility in conscious dogs with gastric fistula, using intraluminal strain-gauge transducers. Infusion of bethanechol increased the motility for both frequency and strength. Isoprenaline, a beta 1...

  2. Effect of honey consumption on intestinal motility in male albino rats

    African Journals Online (AJOL)

    olayemitoyin

    Summary: This study investigated the effects of honey on intestinal motility and transit using twenty (20) male ... sections of the ileum (2-3cm) were mounted on organ bath instrument for motility experiment with varying concentrations ... fructose, glucose, erlose, melezitose) , amino acids, .... was measured using a meter rule.

  3. FabSim: facilitating computational research through automation on large-scale and distributed e-infrastructures

    CERN Document Server

    Groen, Derek; Suter, James; Hetherington, James; Zasada, Stefan; Coveney, Peter

    2015-01-01

    We present FabSim, a toolkit developed to simplify a range of computational tasks for researchers in diverse disciplines. FabSim is flexible, adaptable, and allows users to perform a wide range of tasks with ease. It also provides a systematic way to automate the use of resourcess, including HPC and distributed resources, and to make tasks easier to repeat by recording contextual information. To demonstrate this, we present three use cases where FabSim has enhanced our research productivity. These include simulating cerebrovascular bloodflow, modelling clay-polymer nanocomposites across multiple scales, and calculating ligand-protein binding affinities.

  4. Enhancement of flagellated bacterial motility in polymer solutions

    Science.gov (United States)

    Zhang, Wenyu; Sha, Sha; Pelcovits, Robert; Tang, Jay

    2015-11-01

    Measurements of the swimming speed of many species of flagellated bacteria in polymer solutions have shown that with the addition of high molecular weight polymers, the speed initially increases as a function of the kinematic viscosity. It peaks at around 1.5-2 cP with typically 10-30% higher values than in cell media without added polymers (~ 1 cP). Past the peak, the average speed gradually decreases as the solution becomes more viscous. Swimming motility persists until solution viscosity reaches 5-10 cP. Models have been proposed to account for this behavior, and the magnitude of the peak becomes a crucial test of theoretical predictions. The status of the field is complicated in light of a recent report (Martinez et al., PNAS, 2014), stressing that low-molecular weight impurities account for the peaked speed-viscosity curves in some cases. We measured the swimming speed of a uni-flagellated bacterium, caulobacter crescentus, in solutions of a number of polymers of several different sizes. Our findings confirm the peaked speed-viscosity curve, only as the molecular weight of the flexible polymers used surpassed ~ 50,000 da. The threshold molecular weight required to augment swimming speed varies somewhat with the polymer species, but it generally corresponds to radius of gyration over tens of nanometers. This general feature is consistent with the model of Powers et al. (Physics of Fluid, 2009), predicting that nonlinear viscoelasticity of the fluid enhances swimming motility. Work Supported by the NSF Fluid Physics Program (Award number CBET 1438033).

  5. Role of extracellular cations in cell motility, polarity, and chemotaxis

    Directory of Open Access Journals (Sweden)

    Soll D

    2011-04-01

    Full Text Available David R Soll1, Deborah Wessels1, Daniel F Lusche1, Spencer Kuhl1, Amanda Scherer1, Shawna Grimm1,21Monoclonal Antibody Research Institute, Developmental Studies, Hybridoma Bank, Department of Biology, University of Iowa, Iowa City; 2Mercy Medical Center, Surgical Residency Program, Des Moines, Iowa, USAAbstract: The concentration of cations in the aqueous environment of free living organisms and cells within the human body influence motility, shape, and chemotaxis. The role of extracellular cations is usually perceived to be the source for intracellular cations in the process of homeostasis. The role of surface molecules that interact with extracellular cations is believed to be that of channels, transporters, and exchangers. However, the role of Ca2+ as a signal and chemoattractant and the discovery of the Ca2+ receptor have demonstrated that extracellular cations can function as signals at the cell surface, and the plasma membrane molecules they interact with can function as bona fide receptors that activate coupled signal transduction pathways, associated molecules in the plasma membrane, or the cytoskeleton. With this perspective in mind, we have reviewed the cationic composition of aqueous environments of free living cells and cells that move in multicellular organisms, most notably humans, the range of molecules interacting with cations at the cell surface, the concept of a cell surface cation receptor, and the roles extracellular cations and plasma membrane proteins that interact with them play in the regulation of motility, shape, and chemotaxis. Hopefully, the perspective of this review will increase awareness of the roles extracellular cations play and the possibility that many of the plasma membrane proteins that interact with them could also play roles as receptors.Keywords: extracellular cations, chemotaxis, transporters, calcium, receptors

  6. SIMS characterization of segregation in InAs/GaAs heterostructures

    Energy Technology Data Exchange (ETDEWEB)

    Gallardo, S. [Electrical Engineer Department, Centro de Investigacion y de Estudios Avanzados del IPN, Apartado postal 14470, Mexico, D.F. (Mexico); Kudriatsev, Y. [Electrical Engineer Department, Centro de Investigacion y de Estudios Avanzados del IPN, Apartado postal 14470, Mexico, D.F. (Mexico)], E-mail: yuriyk@cinvestav.mx; Villegas, A.; Ramirez, G.; Asomoza, R. [Electrical Engineer Department, Centro de Investigacion y de Estudios Avanzados del IPN, Apartado postal 14470, Mexico, D.F. (Mexico); Cruz-Hernandez, E.; Rojas-Ramirez, J.S.; Lopez-Lopez, M. [Physics Department, Centro de Investigacion y de Estudios Avanzados del IPN, Apartado postal 14470, Mexico, D.F. (Mexico)

    2008-12-15

    We performed a detailed study of in situ indium segregation in InAs/GaAs heterostructures during conventional MBE growth process. A set of heterostructures grown under different substrate temperatures was tested. We used in the study a recently developed equation for SIMS's Depth Resolution Function (DRF), which included Recoil Implantation, Cascade Mixing and Sputtering Induced Roughness phenomena (RMR model). Segregation process was included in this DRF as an exponentially increasing function. Then we found from experimental SIMS depth profiles segregation parameters for different growth temperatures and the energy activation for the segregation process. It was found equal to 0.27 eV that is close to values published in literature. A segregation free regime of the growth process was developed experimentally.

  7. Formation of oxides and segregation of mobile atoms during SIMS profiling of Si with oxygen ions

    Energy Technology Data Exchange (ETDEWEB)

    Petravic, M.; Williams, J.S.; Svensson, B.G.; Conway, M. [Australian National Univ., Canberra, ACT (Australia). Research School of Physical Sciences

    1993-12-31

    An oxygen beam is commonly used in secondary ion mass spectroscopy (SIMS) analysis to enhance the ionization probability for positive secondary ions. It has been observed, however, that this technique produces in some cases a great degradation of depth resolution. The most pronounced effects have been found for impurities in silicon under oxygen bombardment at angles of incidence smaller than {approx} 30 deg from the surface normal. A new approach is described which involved broadening of SIMS profiles for some mobile atoms, such as Cu, Ni and Au, implanted into silicon. The anomalously large broadening is explained in terms of segregation at a SiO{sub 2}/Si interface formed during bombardment with oxygen at impact angles less than 30 deg. 2 refs., 1 tab., 4 figs.

  8. SIMS ion microscopy as a novel, practical tool for subcellular chemical imaging in cancer research

    Energy Technology Data Exchange (ETDEWEB)

    Chandra, S

    2003-01-15

    The development of cryogenic sample preparations, subcellular image quantification schemes, and correlative confocal laser scanning microscopy and ion microscopy have made dynamic SIMS a versatile tool in biology and medicine. For example, ion microscopy can provide much needed, novel information on calcium influx and intracellular calcium stores at organelle resolution in normal and transformed cells in order to better understand the altered calcium signaling in malignant cells. 3-D SIMS imaging of cells revealed dynamic gradients of calcium in cells undergoing mitosis and cytokinesis. Studies of subcellular localization of anticancer drugs is another area of research where ion microscopy can provide novel observations in many types of cancers. Ion microscopy is already an essential tool in boron neutron capture therapy (BNCT) of brain cancer as it can be used to quantitatively image the subcellular location of boron in cells and tissues. This information is critically needed for testing the efficacy of boronated agents and for calculations of radiation dosimetry.

  9. La construcción de personajes en el videojuego SIMS 2

    Directory of Open Access Journals (Sweden)

    Mª Luisa García Guardia

    2012-04-01

    Full Text Available El artículo recoge el análisis del videojuego Sims2 como un universo simbólico en el que se establecen relaciones de género entre los personajes. Para ello, se aborda el papel del usuario como “inter-autor” en la construcción de los personaje, en la medida en que realiza una inmersión para conocer el mundo recreado de los Sims y  juega a crear un mundo perfecto. Un personaje plano y sin personalidad, reflejo del sujeto moderno tremendamente estereotipado: ideología utilitarista, individualización, fragmentación, diferenciación con respecto a la autoridad, competitividad; apariencia y consumismo.

  10. Analysis of multilayer film using RBS/channeling, sputtering/RBS and SIMS

    CERN Document Server

    Zhao Guo Qing; Zhou Zhu Ying; Jiang Lei; Song Ling Gen; Yang Yu

    2002-01-01

    RBS/Channeling, Sputtering/RBS and SIMS analysis have been performed on the MBE-grown Si/Ge sub x Si sub 1 sub - sub x multilayer. The thickness, atomic ratio and crystalline perfectness of the epitaxial layer are determined by 2 MeV sup 4 He sup + RBS/Channeling analysis. By sputter etching of the sample with low energy Ar sup + ions, the thickness of epitaxial layer is reduced. Then RBS analysis of 2 MeV sup 4 He sup + ions on the etched sample yields information about the deeper layers, the interface of the multilayer samples and the concerned phenomena induced by sputter etching. The periodical structure of Si/Ge sub x Si sub 1 sub - sub x multilayer samples is clearly identified by the SIMS analysis before and after sputter etching

  11. MixSim : An R Package for Simulating Data to Study Performance of Clustering Algorithms

    Directory of Open Access Journals (Sweden)

    Volodymyr Melnykov

    2012-11-01

    Full Text Available The R package MixSim is a new tool that allows simulating mixtures of Gaussian distributions with different levels of overlap between mixture components. Pairwise overlap, defined as a sum of two misclassification probabilities, measures the degree of interaction between components and can be readily employed to control the clustering complexity of datasets simulated from mixtures. These datasets can then be used for systematic performance investigation of clustering and finite mixture modeling algorithms. Among other capabilities of MixSim, there are computing the exact overlap for Gaussian mixtures, simulating Gaussian and non-Gaussian data, simulating outliers and noise variables, calculating various measures of agreement between two partitionings, and constructing parallel distribution plots for the graphical display of finite mixture models. All features of the package are illustrated in great detail. The utility of the package is highlighted through a small comparison study of several popular clustering algorithms.

  12. AlgaeSim: a model for integrated algal biofuel production and wastewater treatment.

    Science.gov (United States)

    Drexler, Ivy L C; Joustra, Caryssa; Prieto, Ana; Bair, Robert; Yeh, Daniel H

    2014-02-01

    AlgaeSim, a dynamic multiple-systems (C, N, P) mass balance model, was developed to explore the potential for algae biomass production from wastewater by coupling two photobioreactors into the main treatment train at a municipal wastewater resource recovery facility (WRRF) in Tampa, Florida. The scoping model examined the synergy between algae cultivation and wastewater treatment through algal growth and substrate removal kinetics, as well as through macroeconomic analyses of biomass conversion to bioproducts. Sensitivity analyses showed that biomass production is strongly dependent on Monod variables and harvesting regime, with sensitivity changing with growth phase. Profitability was sensitive to processing costs and market prices of products. Under scenarios based on current market conditions and typical algae production, AlgaeSim shows that a WRRF can potentially generate significant profit if algae are processed for biodiesel, biogas, or fertilizer. Wastewater resource recovery facilities could similarly save on operating costs resulting from the reduction in aeration (for nitrification) and chemicals (for denitrification).

  13. An investigation of the oxidation behaviour of zirconium alloys using isotopic tracers and high resolution SIMS

    Energy Technology Data Exchange (ETDEWEB)

    Yardley, Sean S., E-mail: sean.yardley@materials.ox.ac.uk [Department of Materials, Oxford University, Parks Road, Oxford OX1 3PH (United Kingdom); Moore, Katie L. [Department of Materials, Oxford University, Parks Road, Oxford OX1 3PH (United Kingdom); Ni, Na [Department of Materials, Imperial College London, Exhibition Road, London SW7 2AZ (United Kingdom); Wei, Jang Fei; Lyon, Stuart; Preuss, Michael [School of Materials, University of Manchester, Materials Performance Centre, Manchester, Lancashire M13 9PL (United Kingdom); Lozano-Perez, Sergio; Grovenor, Chris R.M. [Department of Materials, Oxford University, Parks Road, Oxford OX1 3PH (United Kingdom)

    2013-11-15

    Highlights: •Zr alloys were oxidised for various times in an autoclave to simulate PWR conditions. •Isotopic tracers {sup 18}O and {sup 2}H were added to reveal active oxidation sites by NanoSIMS analysis. •Hydrides were present in all samples, even those with short oxidation times. •Porosity mediated transitions between corrosion regimes occur at critical oxide thicknesses. -- Abstract: High resolution secondary ion mass spectrometry (SIMS) analysis has been used to study the oxidation mechanisms when commercial low tin ZIRLO™ and Zircaloy 4 materials are exposed to corroding environments containing both {sup 18}O and {sup 2}H isotopes. Clear evidence has been shown for different characteristic distributions of {sup 18}O before and after the kinetic transitions, and this behaviour has been correlated with the development of porosity in the oxide which allows the corroding medium to penetrate locally to the metal/oxide interface.

  14. A shielded SIMS in CEA: a new tool for the low abundant isotopes characterization

    Energy Technology Data Exchange (ETDEWEB)

    Desgranges, L.; Pasquet, B

    2004-07-01

    In the framework of studies on long term behaviour of nuclear fuel, the inventory of some isotopes with a low abundance is necessary (iodine 129 or carbon 14 for example). Up to now little attention was paid to these isotopes in the nuclear fuel because they have nearly no influence on the nuclear fuel behavior in irradiation conditions, despite their interest for waste studies. Recently a shielded SIMS was installed in the LECA-STAR facility which enables the detection of some isotopes up to the ppb. Its capabilities were tested with iodine and carbon in irradiated nuclear fuel. It is demonstrated that these elements can have different chemical forms and non homogeneous distribution within the UO{sub 2} ceramics. These results can provide a more realistic description of the behaviour of these elements. The SIMS characterization can be applied on numerous low abundant radio-nuclide and different solid materials. (authors)

  15. SimTrack: A compact c++ code for particle orbit and spin tracking in accelerators

    Science.gov (United States)

    Luo, Yun

    2015-11-01

    SimTrack is a compact c++ code of 6-d symplectic element-by-element particle tracking in accelerators originally designed for head-on beam-beam compensation simulation studies in the Relativistic Heavy Ion Collider (RHIC) at Brookhaven National Laboratory. It provides a 6-d symplectic orbit tracking with the 4th order symplectic integration for magnet elements and the 6-d symplectic synchro-beam map for beam-beam interaction. Since its inception in 2009, SimTrack has been intensively used for dynamic aperture calculations with beam-beam interaction for RHIC. Recently, proton spin tracking and electron energy loss due to synchrotron radiation were added. In this paper, I will present the code architecture, physics models, and some selected examples of its applications to RHIC and a future electron-ion collider design eRHIC.

  16. Análisis de un cifrador simétrico

    Directory of Open Access Journals (Sweden)

    Alfonso Manuel Mancilla Herrera

    2002-01-01

    Full Text Available Matt Blaze, un sobresaliente investigador de los laboratorios AT&T y con mucha experiencia en el campo de la criptografía, realizó una propuesta sobre un cifrador de clave simétrica basado en un subproblema NP-completo. El autor describe una primitiva de seguridad sencilla y eficiente que tiene como base las redes Feistel. Además, propone dos criptosistemas de clave simétrica que usan dicha primitiva: Turtle y Hare. El propósito fundamental de este artículo fue estudiar la propuesta de los cifradores Turtle y Hare. Nos apoyamos en la implementación expuesta por el autor con algunas modificaciones que realizamos, para el trabajo con archivos

  17. SimTrack: A compact c++ library for particle orbit and spin tracking in accelerators

    Energy Technology Data Exchange (ETDEWEB)

    Luo, Yun [Brookhaven National Laboratory (BNL), Upton, NY (United States)

    2015-06-24

    SimTrack is a compact c++ library of 6-d symplectic element-by-element particle tracking in accelerators originally designed for head-on beam-beam compensation simulation studies in the Relativistic Heavy Ion Collider (RHIC) at Brookhaven National Laboratory. It provides a 6-d symplectic orbit tracking with the 4th order symplectic integration for magnet elements and the 6-d symplectic synchro-beam map for beam-beam interaction. Since its inception in 2009, SimTrack has been intensively used for dynamic aperture calculations with beam-beam interaction for RHIC. Recently, proton spin tracking and electron energy loss due to synchrotron radiation were added. In this article, I will present the code architecture, physics models, and some selected examples of its applications to RHIC and a future electron-ion collider design eRHIC.

  18. Effects of uncertainties in simulations of extragalactic UHECR propagation, using CRPropa and SimProp

    CERN Document Server

    Batista, Rafael Alves; di Matteo, Armando; van Vliet, Arjen; Walz, David

    2015-01-01

    The results of simulations of the extragalactic propagation of ultra-high energy cosmic rays (UHECRs) have intrinsic uncertainties due to poorly known physical quantities and approximations used in the codes. We quantify the uncertainties in the simulated UHECR spectrum and composition due to different models for the extragalactic background light (EBL), different photodisintegration setups, approximations concerning photopion production and the use of different simulation codes. We discuss the results for several representative source scenarios with proton, nitrogen or iron at injection. For this purpose we used SimProp and CRPropa, two publicly available codes for Monte Carlo simulations of UHECR propagation. CRPropa is a detailed and extensive simulation code, while SimProp aims to achieve acceptable results using a simpler code. We show that especially the choices for the EBL model and the photodisintegration setup can have a considerable impact on the simulated UHECR spectrum and composition.

  19. Chemical differences between sapwood and heartwood of Chamaecyparis obtusa detected by ToF-SIMS

    Science.gov (United States)

    Saito, K.; Mitsutani, T.; Imai, T.; Matsushita, Y.; Yamamoto, A.; Fukushima, K.

    2008-12-01

    Time-of-flight secondary ion mass spectrometry (ToF-SIMS) was used to investigate the distribution of elements, Na, Mg, Al, K, and Ca, and lignin, in the contiguous growth rings including the sapwood/heartwood boundary in Hinoki cypress ( Chamaecyparis obtusa). Lignin was distributed almost uniformly from sapwood to heartwood. The concentrations of most of the elements showed a drastic increase or decrease in the transition zone between sapwood and heartwood. The ToF-SIMS mapping analysis showed that most of the elements predominantly localized in the ray parenchyma cells in the inner transition zone and heartwood, while the elements showed no localization and distributed almost uniformly in the outer transition zone near sapwood. The result suggests that the ray parenchyma cells play a role in behaviors of elements during the transition from sapwood to heartwood.

  20. Zircon SIMS ages and chemical compositions from Northern Dabie Terrain: Its implication for pyroxenite genesis

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    We present the results of a detailed micro-scale investigation of zircons from pyroxenites, Daoshicong Northern Dabie using a combination of SIMS and ICPMS. The SIMS measurements gave ages of 134-159 Ma. Its average of (144.5±6.2) Ma is interpreted as the best estimate of the pyroxenite intrusion. The crystallization of zircons continued for quite a long time and underwent slow cooling. The py-roxenites are products of post-collision magmatism. The REE pattern is HREE-enriched, and its HREE concentra-tions fall between the magmatic and metamorphic range of gneissic zircons from the Dabie area, which indicate the involvement of crust material in its mantle source.

  1. 'I can do the child no good': Dr Sims and the enslaved infants of Montgomery, Alabama.

    Science.gov (United States)

    Kenny, Stephen C

    2007-08-01

    This article examines the influence of slavery and race on medical education, practice and research in the American South. Drawing on the published autobiography, case-histories, and correspondence of American slave surgeon and 'pioneer' gynaecologist, James Marion Sims, the contribution highlights a lesser known episode from his early career, namely his surgical treatment of enslaved infants suffering from trismus nascentium (neonatal tetanus). Sims became a highly prestigious figure in his later medical career, but the foundations of his success relied on the use of slave bodies and enslaved patients. These were typically distinctive features of the life of an ambitious medical professional in the slave South, where the profession profited from the institution of slavery, and human experimentation and medical research were advanced specifically through the exploitation of the region's enslaved population.

  2. Distinguishing Monosaccharide Stereo- and Structural Isomers with ToF-SIMS and Multivariate Statistical Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Berman, E F; Kulp, K S; Knize, M G; Wu, L; Nelson, E J; Nelson, D O; Wu, K J

    2006-05-04

    Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) is utilized to examine the mass spectra and fragmentation patterns of seven isomeric monosaccharides. Multivariate statistical analysis techniques, including principal component analysis (PCA), allow discrimination of the extremely similar mass spectra of stereoisomers. Furthermore, PCA identifies those fragment peaks which vary significantly between spectra. Heavy isotope studies confirm that these peaks are indeed sugar fragments, allow identification of the fragments, and provide clues to the fragmentation pathways. Excellent reproducibility is shown by multiple experiments performed over time and on separate samples. This study demonstrates the combined selectivity and discrimination power of ToF-SIMS and PCA, and suggests new applications of the technique including differentiation of subtle chemical changes in biological samples that may provide insights into cellular processes, disease progress, and disease diagnosis.

  3. Modeling Multi-Wavelength Stellar Astrometry. I. SIM Lite Observations of Interacting Binaries

    CERN Document Server

    Coughlin, Jeffrey L; Harrison, Thomas E; Hoard, D W; Ciardi, David R; Benedict, G Fritz; Howell, Steve B; McArthur, Barbara E; Wachter, Stefanie

    2010-01-01

    Interacting binaries consist of a secondary star which fills or is very close to filling its Roche lobe, resulting in accretion onto the primary star, which is often, but not always, a compact object. In many cases, the primary star, secondary star, and the accretion disk can all be significant sources of luminosity. SIM Lite will only measure the photocenter of an astrometric target, and thus determining the true astrometric orbits of such systems will be difficult. We have modified the Eclipsing Light Curve code (Orosz & Hauschildt 2000) to allow us to model the flux-weighted reflex motions of interacting binaries, in a code we call REFLUX. This code gives us sufficient flexibility to investigate nearly every configuration of interacting binary. We find that SIM Lite will be able to determine astrometric orbits for all sufficiently bright interacting binaries where the primary or secondary star dominates the luminosity. For systems where there are multiple components that comprise the spectrum in the op...

  4. Oxygen bleed-in during SIMS depth profiling: curse or blessing?

    Science.gov (United States)

    Zalm, P. C.; Vriezema, C. J.

    1992-02-01

    Oxygen flooding of the target during SIMS depth profiling finds widespread application foranumber of reasons. Among others it enhances the (positive) secondary ionization efficiency, helps in suppressing bombardment-induced surface topography development and reduces the transition time to steady-state erosion conditions. These attractive properties are offset by a number of artefacts that may be introduced by O 2 inlet. A summary of vices and virtues, largely based on existing knowledge, is presented. Then one of the few open questions is addressed, namely to what extent O 2 bleed-in ffects depth resolution. This is examined in some detail by studying ultrashallow dopant profiles of B, P, Ga or Sb in Si by SIMS with and without O 2 leak.

  5. Teoría de gravitación no simétrica

    Directory of Open Access Journals (Sweden)

    Germán Rojas

    2008-01-01

    Full Text Available Se efectúa la revisión de la Teoría de gravitación no simétrica desarrollada por el profesor John Moffat, como una alternativa que permite solucionar problemas de la Relatividad General al describir la estructura del universo a gran escala. Algunos aspectos relacionados con el carácter físico y geométrico de las estructuras de campo espacio-temporal no simétricas, son discutidos. También, el problema de explicar la expansión acelerada del universo, y algunos inconvenientes teóricos relacionados con energía y materia oscura, son tratados.

  6. The toxic effect of opioid analgesics on human sperm motility in vitro.

    Science.gov (United States)

    Xu, Bo; Wang, Zhi-Ping; Wang, Yan-Juan; Lu, Pei-Hua; Wang, Li-Jun; Wang, Xiao-Hai

    2013-04-01

    Opioid analgesics are the most common therapeutic analgesic for acute pain. In this study, the toxicological and pharmacological features of a group of opioid analgesics were characterized by the motility of human sperm. Aliquots of sperm were incubated with various concentrations of opioid analgesics in vitro. Computer-assisted sperm analysis was used to assess sperm motility at 15 minutes, 2 hours, and 4 hours after drug addition to the medium. Butorphanol and dezocine showed marked reduction of motility after incubation with sperm for 15 minutes. Butorphanol was more effective than dezocine in immobilizing sperm. Other opioids studied, such as fentanyl, alfentanil, and sufentanil, showed only partial inhibitory activity. Based on the data reported herein, we have found that butorphanol and dezocine exert a sperm-immobilizing effect. However, fentanyl, alfentanil, and sufentanil exhibit only partial inhibition of sperm motility. Given the increasing use of opioids and their potential effect on sperm motility, these findings are greatly relevant to male reproductive health.

  7. Live from under the lens: exploring microbial motility with dynamic imaging and microfluidics.

    Science.gov (United States)

    Son, Kwangmin; Brumley, Douglas R; Stocker, Roman

    2015-12-01

    Motility is one of the most dynamic features of the microbial world. The ability to swim or crawl frequently governs how microorganisms interact with their physical and chemical environments, and underpins a myriad of microbial processes. The ability to resolve temporal dynamics through time-lapse video microscopy and the precise control of the physicochemical microenvironment afforded by microfluidics offer powerful new opportunities to study the many motility adaptations of microorganisms and thereby further our understanding of their ecology. In this Review, we outline recent insights into the motility strategies of microorganisms brought about by these techniques, including the hydrodynamic signature of microorganisms, their locomotion mechanics, chemotaxis, their motility near and on surfaces, swimming in moving fluids and motility in dense microbial suspensions.

  8. User Guide for GoldSim Model to Calculate PA/CA Doses and Limits

    Energy Technology Data Exchange (ETDEWEB)

    Smith, F. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL)

    2016-10-31

    A model to calculate doses for solid waste disposal at the Savannah River Site (SRS) and corresponding disposal limits has been developed using the GoldSim commercial software. The model implements the dose calculations documented in SRNL-STI-2015-00056, Rev. 0 “Dose Calculation Methodology and Data for Solid Waste Performance Assessment (PA) and Composite Analysis (CA) at the Savannah River Site”.

  9. Pemanfaatan Ekstrak Etanol Kulit Buah Markisa Ungu (Passiflora edulis Sims) Menjadi Pewarna Lipstik

    OpenAIRE

    Monalisa S

    2016-01-01

    Background: Lipstick is a cosmetic preparation used for coloring the lips by artistic touch in improving the esthetic of the facial make-up. Lip color crayons form is better known by the name lipstick from made of oil, wax, fats and dyestuffs. Purple passion fruit plant (Passiflora edulis Sims) has attractive colors that is red purplish comes from anthocyanin, which is derived flavonoid compounds. Anthocyanins have a variety of benefits such as natural dyes so that can become alternative in c...

  10. Characterization of mineral-associated organic matter: a combined approach of AFM and NanoSIMS

    Science.gov (United States)

    Pohl, Lydia; Schurig, Christian; Eusterhues, Karin; Mueller, Carsten W.; Höschen, Carmen; Totsche, Kai-Uwe; Kögel-Knabner, Ingrid

    2016-04-01

    The heterogeneous spatial distribution and amount of organic matter (OM) in soils, especially at the micro- or submicron-scale, has major consequences for the soil microstructure and for the accessibility of OM to decomposing microbial communities. Processes occurring at the microscale control soil properties and processes at larger scales, such as macro-aggregation and carbon turnover. Since OM acts as substrate and most important driver for biogeochemical processes, particular attention should be paid to its spatial interaction with soil minerals. In contrast to bulk analysis, Nanoscale Secondary Ion Mass Spectrometry (NanoSIMS) offers the possibility to examine the composition and spatial distribution of OM within the intact organo-mineral matrix. Nevertheless, the yield of secondary electrons is influenced by the individual topography of the analysed particles, which aggravated the quantitative interpretation of the data. A combination of NanoSIMS and Atomic Force Microscopy (AFM), enabled us to visualize and quantify the topographical features of individual particles and correct the NanoSIMS data for this effect. We performed adsorption experiments with water-soluble soil OM in 6 concentration steps, which was extracted from forest floor layer of a Podzol, and adsorbed to illite. Upon the end of the sorption experiments the liquid phase and the solid phase were separated and the carbon content was analysed with TOC- and C/N-measurement, respectively. For the spatially resolved analyses, the samples were applied as thin layers onto silicon wafers and individual particles were chosen by means of the AFM. Subsequently, the identical particles were analysed with NanoSIMS to investigate the distribution of C, N, O, Si, P and Al. The recorded data were analysed for differences in elemental distribution between the different concentration steps. Additionally, we performed a correlation of the detectable counts with the topography of the particle within one

  11. SIM Editor复制编辑手机个人资料

    Institute of Scientific and Technical Information of China (English)

    李波勇; 曾水有; 谭赞良

    2004-01-01

    SIME ditor软件是与“一卡多号”SIM卡号码复制软件SIM Scanner一并同时安装的,其主要作用是复制SIM卡的电话簿、短消息和进行待机图案与铃声的编辑写入,此外还具有一定的SIM卡密码管理功能:

  12. Subcellular SIMS imaging of isotopically labeled amino acids in cryogenically prepared cells

    Energy Technology Data Exchange (ETDEWEB)

    Chandra, Subhash

    2004-06-15

    Ion microscopy is a potentially powerful technique for localization of isotopically labeled molecules. In this study, L-arginine and phenylalanine amino acids labeled with stable isotopes {sup 13}C and {sup 15}N were localized in cultured cells with the ion microscope at 500 nm spatial resolution. Cells were exposed to the labeled amino acids and cryogenically prepared. SIMS analyses were made in fractured freeze-dried cells. A dynamic distribution was observed from labeled arginine-treated LLC-PK{sub 1} kidney cells at mass 28 ({sup 13}C{sup 15}N) in negative secondaries, revealing cell-to-cell heterogeneity and preferential accumulation of the amino acid (or its metabolite) in the nucleus and nucleolus of some cells. The smaller nucleolus inside the nucleus was clearly resolved in SIMS images and confirmed by correlative light microscopy. The distribution of labeled phenylalanine contrasted with arginine as it was rather homogeneously distributed in T98G human glioblastoma cells. Images of {sup 39}K, {sup 23}Na and {sup 40}Ca were also recorded to confirm the reliability of sample preparation and authenticity of the observed amino acid distributions. These observations indicate that SIMS techniques can provide a valuable technology for subcellular localization of nitrogen-containing molecules in proteomics since nitrogen does not have a radionuclide tracer isotope. Amino acids labeled with stable isotopes can be used as tracers for studying their transport and metabolism in distinct subcellular compartments with SIMS. Further studies of phenylalanine uptake in human glioblastoma cells may have special significance in boron neutron capture therapy (BNCT) as a boron analogue of phenylalanine, boronophenylalanine is a clinically approved compound for the treatment of brain tumors.

  13. Subcellular SIMS imaging of isotopically labeled amino acids in cryogenically prepared cells

    Science.gov (United States)

    Chandra, Subhash

    2004-06-01

    Ion microscopy is a potentially powerful technique for localization of isotopically labeled molecules. In this study, L-arginine and phenylalanine amino acids labeled with stable isotopes 13C and 15N were localized in cultured cells with the ion microscope at 500 nm spatial resolution. Cells were exposed to the labeled amino acids and cryogenically prepared. SIMS analyses were made in fractured freeze-dried cells. A dynamic distribution was observed from labeled arginine-treated LLC-PK 1 kidney cells at mass 28 ( 13C15N) in negative secondaries, revealing cell-to-cell heterogeneity and preferential accumulation of the amino acid (or its metabolite) in the nucleus and nucleolus of some cells. The smaller nucleolus inside the nucleus was clearly resolved in SIMS images and confirmed by correlative light microscopy. The distribution of labeled phenylalanine contrasted with arginine as it was rather homogeneously distributed in T98G human glioblastoma cells. Images of 39K, 23Na and 40Ca were also recorded to confirm the reliability of sample preparation and authenticity of the observed amino acid distributions. These observations indicate that SIMS techniques can provide a valuable technology for subcellular localization of nitrogen-containing molecules in proteomics since nitrogen does not have a radionuclide tracer isotope. Amino acids labeled with stable isotopes can be used as tracers for studying their transport and metabolism in distinct subcellular compartments with SIMS. Further studies of phenylalanine uptake in human glioblastoma cells may have special significance in boron neutron capture therapy (BNCT) as a boron analogue of phenylalanine, boronophenylalanine is a clinically approved compound for the treatment of brain tumors.

  14. VN-Sim: A Way to Keep Core Concepts in a Crowded Computing Curriculum

    Directory of Open Access Journals (Sweden)

    R. Raymond Lang

    2012-02-01

    Full Text Available Contemporary computer science curricula must accommodate a broad array of developments important to the field. Tough choices have to be made between introducing newer topics and retaining fundamentals that ground the discipline as a whole. All too frequently, understanding of low level coding and its relation to basic hardware is sacrificed to make room for newer material. VN-Sim, a von Neumann machine simulator, provides a mechanism for streamlined coverage of low level coding and hardware topics.

  15. Using NanoSIMS to map trace elements in stainless steels from nuclear reactors

    Energy Technology Data Exchange (ETDEWEB)

    Lozano-Perez, S. [Department of Materials, University of Oxford, Parks Road, OX1 3PH Oxford (United Kingdom)], E-mail: Sergio.lozano-perez@materials.ox.ac.uk; Schroeder, M. [Department of Materials, University of Oxford, Parks Road, OX1 3PH Oxford (United Kingdom); Yamada, T.; Terachi, T. [Institute of Nuclear Safety Systems Inc., 64 Sata, Mikata-gun, Fukui 919-1205 (Japan); English, C.A. [Nexia Solutions, Harwell Business Centre, Didcot, Oxon, OX11 0RA (United Kingdom); Grovenor, C.R.M. [Department of Materials, University of Oxford, Parks Road, OX1 3PH Oxford (United Kingdom)

    2008-12-15

    A Cameca NanoSIMS 50 has been used to map trace elements in stainless steels from nuclear reactors. The results prove that it is an ideal technique to map elements in small concentrations such as boron, sulphur or phosphorous which remain inaccessible to conventional microanalysis techniques. Especially remarkable is the ability to map boron, revealing segregation to grain boundaries or to carbides in sensitized samples.

  16. Convenciones en juegos puros de coordinación simétrica 2 x 2

    OpenAIRE

    Mora Jhon James

    2009-01-01

    Este ensayo analiza la formación de convenciones en juegos de coordinación simétrica 2 × 2. En particular, el análisis se restringe a juegos con iguales niveles de seguridad y se discute que tanto puede explicar la teoría de juegos la formación de convenciones.

  17. Assimilation of ASCAT near-surface soil moisture into the SIM hydrological model over France

    Directory of Open Access Journals (Sweden)

    C. Draper

    2011-12-01

    Full Text Available This study examines whether the assimilation of remotely sensed near-surface soil moisture observations might benefit an operational hydrological model, specifically Météo-France's SAFRAN-ISBA-MODCOU (SIM model. Soil moisture data derived from ASCAT backscatter observations are assimilated into SIM using a Simplified Extended Kalman Filter (SEKF over 3.5 years. The benefit of the assimilation is tested by comparison to a delayed cut-off version of SIM, in which the land surface is forced with more accurate atmospheric analyses, due to the availability of additional atmospheric observations after the near-real time data cut-off. However, comparing the near-real time and delayed cut-off SIM models revealed that the main difference between them is a dry bias in the near-real time precipitation forcing, which resulted in a dry bias in the root-zone soil moisture and associated surface moisture flux forecasts. While assimilating the ASCAT data did reduce the root-zone soil moisture dry bias (by nearly 50%, this was more likely due to a bias within the SEKF, than due to the assimilation having accurately responded to the precipitation errors. Several improvements to the assimilation are identified to address this, and a bias-aware strategy is suggested for explicitly correcting the model bias. However, in this experiment the moisture added by the SEKF was quickly lost from the model surface due to the enhanced surface fluxes (particularly drainage induced by the wetter soil moisture states. Consequently, by the end of each winter, during which frozen conditions prevent the ASCAT data from being assimilated, the model land surface had returned to its original (dry-biased climate. This highlights that it would be more effective to address the precipitation bias directly, than to correct it by constraining the model soil moisture through data assimilation.

  18. SimUVEx v2 : a numeric tool to predict anatomical solar ultraviolet exposure

    OpenAIRE

    2016-01-01

    Solar ultraviolet (UV) radiation has a dual effect on human health: low UV doses promote the photosynthesis of vitamin D and regulate calcium and phosphorus metabolism, while an excessive UV exposure is the main cause of skin cancer, along with eye diseases and premature skin ageing. The link between UV radiation levels and UV exposure is not fully understood since exposure data are limited and individual anatomical variations in UV doses are significant. SimUVEx is a numeric simulation tool ...

  19. Molecular imaging of alkaloids in khat (Catha edulis) leaves with MeV-SIMS

    Science.gov (United States)

    Jenčič, Boštjan; Jeromel, Luka; Ogrinc Potočnik, Nina; Vogel-Mikuš, Katarina; Vavpetič, Primož; Rupnik, Zdravko; Bučar, Klemen; Vencelj, Matjaž; Kelemen, Mitja; Matsuo, Jiro; Kusakari, Masakazu; Siketić, Zdravko; Al-Jalali, Muhammad A.; Shaltout, Abdallah; Pelicon, Primož

    2017-08-01

    Imaging Mass Spectroscopy (IMS) is a unique research tool providing localization and identification of a wide range of biomolecules as essential data to understand biochemical processes in living organisms. Secondary Ion Mass Spectrometry with high-energy heavy ions (MeV-SIMS) is emerging as a promising IMS technique for chemical imaging of biological tissue. We measured the molecular mass spatial distributions in leaves of khat (Catha edulis). Khat is a natural drug plant, native to eastern Africa and the Arabian Peninsula. In these countries, fresh leaves are being chewed by significant part of population. It was reported that 80% of the adult population in Yemen chew the khat leaves. The main stimulating effects of khat are induced by a monoamine alkaloid called cathinone. During leaf ageing, cathinone is further metabolised to cathine and norephedrine. Earlier studies identified the alkaloids in khat, however little is known on their spatial distribution, reflecting the biosynthesis and accumulation in the tissue. Chemical mapping of alkaloids on cross-sections of khat leaves by MeV-SIMS was done at JSI by a pulsed 5.8 MeV 35Cl6+ beam, focused to a diameter of 15 μm, using a linear time-of-flight (TOF) spectrometer with a mass resolution of 500. In addition, measurements of MeV-SIMS mass spectra were performed at Kyoto University by a continuous broad beam of 6 MeV 63Cu4+ ions at an orthogonal TOF spectrometer with a high mass resolution of 11,000. Sections of leaves were analysed and mass spectra obtained at both MeV-SIMS setups were compared. Tissue-level distributions of detected alkaloids are presented and discussed.

  20. SuReSim: simulating localization microscopy experiments from ground truth models.

    Science.gov (United States)

    Venkataramani, Varun; Herrmannsdörfer, Frank; Heilemann, Mike; Kuner, Thomas

    2016-04-01

    Super-resolution fluorescence microscopy has become a widely used tool in many areas of research. However, designing and validating super-resolution experiments to address a research question in a technically feasible and scientifically rigorous manner remains a fundamental challenge. We developed SuReSim, a software tool that simulates localization data of arbitrary three-dimensional structures represented by ground truth models, allowing users to systematically explore how changing experimental parameters can affect potential imaging outcomes.