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Sample records for dimensionless numbers expressed

  1. Dimensionless Numbers Expressed in Terms of Common CVD Process Parameters

    NASA Technical Reports Server (NTRS)

    Kuczmarski, Maria A.

    1999-01-01

    A variety of dimensionless numbers related to momentum and heat transfer are useful in Chemical Vapor Deposition (CVD) analysis. These numbers are not traditionally calculated by directly using reactor operating parameters, such as temperature and pressure. In this paper, these numbers have been expressed in a form that explicitly shows their dependence upon the carrier gas, reactor geometry, and reactor operation conditions. These expressions were derived for both monatomic and diatomic gases using estimation techniques for viscosity, thermal conductivity, and heat capacity. Values calculated from these expressions compared well to previously published values. These expressions provide a relatively quick method for predicting changes in the flow patterns resulting from changes in the reactor operating conditions.

  2. Dimensionless numbers in additive manufacturing

    NASA Astrophysics Data System (ADS)

    Mukherjee, T.; Manvatkar, V.; De, A.; DebRoy, T.

    2017-02-01

    The effects of many process variables and alloy properties on the structure and properties of additively manufactured parts are examined using four dimensionless numbers. The structure and properties of components made from 316 Stainless steel, Ti-6Al-4V, and Inconel 718 powders for various dimensionless heat inputs, Peclet numbers, Marangoni numbers, and Fourier numbers are studied. Temperature fields, cooling rates, solidification parameters, lack of fusion defects, and thermal strains are examined using a well-tested three-dimensional transient heat transfer and fluid flow model. The results show that lack of fusion defects in the fabricated parts can be minimized by strengthening interlayer bonding using high values of dimensionless heat input. The formation of harmful intermetallics such as laves phases in Inconel 718 can be suppressed using low heat input that results in a small molten pool, a steep temperature gradient, and a fast cooling rate. Improved interlayer bonding can be achieved at high Marangoni numbers, which results in vigorous circulation of liquid metal, larger pool dimensions, and greater depth of penetration. A high Fourier number ensures rapid cooling, low thermal distortion, and a high ratio of temperature gradient to the solidification growth rate with a greater tendency of plane front solidification.

  3. Dirac cosmology. [large dimensionless numbers relation to universe age

    NASA Technical Reports Server (NTRS)

    Canuto, V.; Lodenquai, J.

    1977-01-01

    The large numbers hypothesis (LNH) linking the magnitude of large dimensionless ratios in physics (on the order of 10 to the 40th power) to cosmic time is examined. The LNH is checked against evidence on 3K background radiation of the universe and the (log N, log S)-relation for radio galaxies. Earlier criticisms of LNH by Gamow and Teller are examined, and alternative hypotheses put forth by Dicke and Carter (1974) are discussed. The discussion covers: continuous (additive or multiplicative) creation of matter, the Einstein metric and the atomic metric, and general cosmological and local astronomical implications of LNH. LNH is also viewed in relation to solar evolution and pulsar physics.

  4. Dirac cosmology. [large dimensionless numbers relation to universe age

    NASA Technical Reports Server (NTRS)

    Canuto, V.; Lodenquai, J.

    1977-01-01

    The large numbers hypothesis (LNH) linking the magnitude of large dimensionless ratios in physics (on the order of 10 to the 40th power) to cosmic time is examined. The LNH is checked against evidence on 3K background radiation of the universe and the (log N, log S)-relation for radio galaxies. Earlier criticisms of LNH by Gamow and Teller are examined, and alternative hypotheses put forth by Dicke and Carter (1974) are discussed. The discussion covers: continuous (additive or multiplicative) creation of matter, the Einstein metric and the atomic metric, and general cosmological and local astronomical implications of LNH. LNH is also viewed in relation to solar evolution and pulsar physics.

  5. Reynolds-number dependence of the dimensionless dissipation rate in homogeneous magnetohydrodynamic turbulence

    NASA Astrophysics Data System (ADS)

    Linkmann, Moritz; Berera, Arjun; Goldstraw, Erin E.

    2017-01-01

    This paper examines the behavior of the dimensionless dissipation rate Cɛ for stationary and nonstationary magnetohydrodynamic (MHD) turbulence in the presence of external forces. By combining with previous studies for freely decaying MHD turbulence, we obtain here both the most general model equation for Cɛ applicable to homogeneous MHD turbulence and a comprehensive numerical study of the Reynolds number dependence of the dimensionless total energy dissipation rate at unity magnetic Prandtl number. We carry out a series of medium to high resolution direct numerical simulations of mechanically forced stationary MHD turbulence in order to verify the predictions of the model equation for the stationary case. Furthermore, questions of nonuniversality are discussed in terms of the effect of external forces as well as the level of cross- and magnetic helicity. The measured values of the asymptote Cɛ ,∞ lie between 0.193 ≤Cɛ ,∞≤0.268 for free decay, where the value depends on the initial level of cross- and magnetic helicities. In the stationary case we measure Cɛ ,∞=0.223 .

  6. Reynolds-number dependence of the dimensionless dissipation rate in homogeneous magnetohydrodynamic turbulence.

    PubMed

    Linkmann, Moritz; Berera, Arjun; Goldstraw, Erin E

    2017-01-01

    This paper examines the behavior of the dimensionless dissipation rate C_{ɛ} for stationary and nonstationary magnetohydrodynamic (MHD) turbulence in the presence of external forces. By combining with previous studies for freely decaying MHD turbulence, we obtain here both the most general model equation for C_{ɛ} applicable to homogeneous MHD turbulence and a comprehensive numerical study of the Reynolds number dependence of the dimensionless total energy dissipation rate at unity magnetic Prandtl number. We carry out a series of medium to high resolution direct numerical simulations of mechanically forced stationary MHD turbulence in order to verify the predictions of the model equation for the stationary case. Furthermore, questions of nonuniversality are discussed in terms of the effect of external forces as well as the level of cross- and magnetic helicity. The measured values of the asymptote C_{ɛ,∞} lie between 0.193≤C_{ɛ,∞}≤0.268 for free decay, where the value depends on the initial level of cross- and magnetic helicities. In the stationary case we measure C_{ɛ,∞}=0.223.

  7. Measurement of bladder compliance can be standardized by a dimensionless number: clinical perspective.

    PubMed

    Wahl, Edward F; Lerman, Steven E; Lahdes-Vasama, Tuija T; Churchill, Bernard M

    2004-10-01

    To devise a new, practical and more accurate method for measuring bladder compliance, and to show that traditional estimates of compliance are impractical. Childhood bladder capacity varies greatly with age while detrusor pressure in a normal bladder does not. Consequently, traditional bladder compliance (DeltaV/DeltaP) increases with age, i.e. maturation. Therefore we devised a standard method that includes normal values of pressures and volumes to calculate and report bladder compliance in children, and that also applies to adults. A dimensionless number (NWahl(-1)) was computed for standardizing bladder compliance, comparing the normalized capacity to normalized pressure by the ratio (DeltaV/V(cap,NL))/(DeltaP/P(cap,NL)), where DeltaP is the pressure at bladder capacity, DeltaV the volume at bladder capacity, V(cap,NL) the volume at mean expected bladder capacity and P(cap,NL) the pressure at mean expected bladder capacity. V(cap,NL) is obtained from nomograms of published data. The bladder compliance of patients undergoing urodynamic testing was calculated using NWahl(-1) and the traditional equation (DeltaV/DeltaP). NWahl(-1) provided a more accurate diagnosis and therefore was of more practical use. Bladder compliance depends on patient age, sex and size; the new estimate used to standardize bladder compliance is based on these factors and is a dimensionless number. This may help when comparing patients and assessing outcomes.

  8. A dimensionless number describing the effects of recharge and geometry on discharge from simple karstic aquifers

    NASA Astrophysics Data System (ADS)

    Covington, M. D.; Wicks, C. M.; Saar, M. O.

    2009-11-01

    The responses of karstic aquifers to storms are often used to obtain information about aquifer geometry. In general, spring hydrographs are a function of both system geometry and recharge. However, the majority of prior work on storm pulses through karst has not studied the effect of recharge on spring hydrographs. To examine the relative importance of geometry and recharge, we break karstic aquifers into elements according to the manner of their response to transient flow and demonstrate that each element has a characteristic response timescale. These fundamental elements are full pipes, open channels, reservoir/constrictions, and the porous matrix. Taking the ratio of the element timescale with the recharge timescale produces a dimensionless number, γ, that is used to characterize aquifer response to a storm event. Using sets of simulations run with randomly selected element parameters, we demonstrate that each element type has a critical value of γ below which the shape of the spring hydrograph is dominated by the shape of the recharge hydrograph and above which the spring hydrograph is significantly modified by the system geometry. This allows separation of particular element/storm pairs into recharge-dominated and geometry-dominated regimes. While most real karstic aquifers are complex combinations of these elements, we draw examples from several karst systems that can be represented by single elements. These examples demonstrate that for real karstic aquifers full pipe and open channel elements are generally in the recharge-dominated regime, whereas reservoir/constriction elements can fall in either the recharge- or geometry-dominated regimes.

  9. Dimensionless number is central to stress relaxation and expansive growth of the cell wall.

    PubMed

    Ortega, Joseph K E

    2017-06-07

    Experiments demonstrate that both plastic and elastic deformation of the cell wall are necessary for wall stress relaxation and expansive growth of walled cells. A biophysical equation (Augmented Growth Equation) was previously shown to accurately model the experimentally observed wall stress relaxation and expansive growth rate. Here, dimensional analysis is used to obtain a dimensionless Augmented Growth Equation with dimensionless coefficients (groups of variables, or Π parameters). It is shown that a single Π parameter controls the wall stress relaxation rate. The Π parameter represents the ratio of plastic and elastic deformation rates, and provides an explicit relationship between expansive growth rate and the wall's mechanical properties. Values for Π are calculated for plant, algal, and fungal cells from previously reported experimental results. It is found that the Π values for each cell species are large and very different from each other. Expansive growth rates are calculated using the calculated Π values and are compared to those measured for plant and fungal cells during different growth conditions, after treatment with IAA, and in different developmental stages. The comparison shows good agreement and supports the claim that the Π parameter is central to expansive growth rate of walled cells.

  10. Asymmetry during a horizontal annular flow in a micro-channel: optical measurements and effect of dimensionless numbers

    NASA Astrophysics Data System (ADS)

    Capo, C.; Layssac, T.; Lips, S.; Mauro, A. W.; Revellin, R.

    2017-01-01

    New applications of HFC refrigerants in organic Rankine cycles at high saturation temperatures and the wider use of CO2 for air-conditioning have pushed research to the characterization of two-phase heat transfer at medium/high reduced pressures and have pointed out the effect of these operating conditions on asymmetric distribution of refrigerant around tube perimeter and its indirect effect on heat transfer. Currently there is a lack of data about asymmetric distribution of liquid film at the wall, especially for refrigerants and micro-channels. In order to have a physical evidence of this asymmetry also for micro-channels and approach to a relationship between this phenomenon and dimensionless parameters, new data are here presented. The asymmetric annular flow of the refrigerant R245fa inside a horizontal, round 2.95 mm inner diameter channel is studied with pictures captured by a high speed video camera. The experimental results here presented were obtained at saturation temperatures equal to 20 °C and 40 °C at low mass velocities (50, 100 and 200 kg m-2s-1) to asymmetric distribution, enriching the database presented in previous studies. The new dimensionless parameter, eccentricity, has been related to the dimensionless groups: Froude and Bond numbers, and Martinelli parameter, showing the mutual correlation among them.

  11. Dimensionless cosmology

    NASA Astrophysics Data System (ADS)

    Narimani, Ali; Moss, Adam; Scott, Douglas

    2012-10-01

    Although it is well known that any consideration of the variations of fundamental constants should be restricted to their dimensionless combinations, the literature on variations of the gravitational constant G is entirely dimensionfull. To illustrate applications of this to cosmology, we explicitly give a dimensionless version of the parameters of the standard cosmological model, and describe the physics of both Big Bang Nucleosynthesis and recombination in a dimensionless manner. Rigorously determining how to talk about the model in a way which avoids physical dimensions is a requirement for proceeding with a calculation to constrain time-varying fundamental constants. The issue that appears to have been missed in many studies is that in cosmology the strength of gravity is bound up in the cosmological equations, and the epoch at which we live is a crucial part of the model. We argue that it is useful to consider the hypothetical situation of communicating with another civilization (with entirely different units), comparing only dimensionless constants, in order to decide if we live in a Universe governed by precisely the same physical laws. In this thought experiment, we would also have to compare epochs, which can be defined by giving the value of any one of the evolving cosmological parameters. By setting things up carefully in this way one can avoid inconsistent results when considering variable constants, caused by effectively fixing more than one parameter today. We show examples of this effect by considering microwave background anisotropies, being careful to maintain dimensionlessness throughout. We present Fisher matrix calculations to estimate how well the fine structure constants for electromagnetism and gravity can be determined with future microwave background experiments. We highlight how one can be misled by simply adding G to the usual cosmological parameter set.

  12. Scaling up adsorption media reactors for copper removal with the aid of dimensionless numbers.

    PubMed

    Chang, Ni-Bin; Houmann, Cameron; Wanielista, Martin

    2016-02-01

    Adsorption media may be used to sorb copper in an aquatic environment for pollution control. Effective design of adsorption media reactors is highly dependent on selection of the hydraulic residence time when scaling up a pilot-scale reactor to a field-scale reactor. This paper seeks to improve scaling-up technique of the reactor design process through the use of the Damköhler and Péclet numbers via a dimensional analysis. A new scaling-up theory is developed in this study through a joint consideration of the Damköhler and Péclet numbers for a constant media particle size such that a balance between transport control and reaction control can be harmonized. A series of column breakthrough tests at varying hydraulic residence times revealed a clear peak adsorption capacity at a Damköhler number of 2.74. The Péclet numbers for the column breakthrough tests indicated that mechanical dispersion is an important effect that requires further consideration in the scaling-up process. However, perfect similitude of the Damköhler number cannot be maintained for a constant media particle size, and relaxation of hydrodynamic similitude through variation of the Péclet number must occur.

  13. Flow paths and chemical reactivity of CO2 in carbonates using Mercury-Intrusion Capillary Pressure data and dimensionless numbers

    NASA Astrophysics Data System (ADS)

    Vialle, S.; Dvorkin, J. P.; Mavko, G. M.

    2012-12-01

    Experiments performed earlier by Vialle and Vanorio (2011) [1] have showed that the injection of CO2-rich water (pH=3.2) in various calcite limestones lead to heterogeneous dissolution of the pore structure, inducing secondary porosity and changing the rock stiffness. The presence of oil in the pore space affects the magnitude of these changes by lowering the reactive surface area. We present here a semi-quantitative analysis at the mesoscale to investigate how different initial pore microgeometries and heterogeneities in pore microgeometry affect the fluid-rock interactions. In particular, we aim at quantitatively explaining (1) why, in clean samples, higher-porosity micrite with rounded grains appears to be more affected by dissolution than tight micrite and spar cement and (2) why, for the same number of pore volumes of fluid injected, the magnitude of the changes in porosity (and subsequently elastic properties) differs among the studied rock samples. Rock microgeometry is studied by classical rock-physics methods, He-pycnometry and Mercury-Intrusion Capillary Pressure (MICP) tests, as well as by Scanning Electron Microscopy (SEM) imaging. Experiments were performed on subsamples (~0.5cm3) extracted from core plugs (~12cm3): two Fontainebleau sandstones, to serve as benchmarks, and two calcite carbonates from two different geological formations. In order to relate pore microgeometry to flow paths and chemical reactivity of CO2 in carbonate rocks, we chose to work at a scale that lies between the pore scale and the core scale. The method consists of physically subdividing the core plugs under examination into subsets based on the pore-throat sizes; these subsets correspond to three types of microstructure: "macropores", "microporous rounded micrite", and "spar cement"/"tight micrite". The dimensionless Péclet (Pe) and Damkhöler (Da) numbers, defined as the ratio between the advection rate and the diffusion rate, and as the ratio between the reaction rate and

  14. Advanced control of liquid water region in diffusion media of polymer electrolyte fuel cells through a dimensionless number

    SciTech Connect

    Wang, Yun; Chen, Ken S.

    2016-03-21

    In the present study, a three-dimension (3-D) model of polymer electrolyte fuel cells (PEFCs) is employed to investigate the complex, non-isothermal, two-phase flow in the gas diffusion layer (GDL). Phase change in gas flow channels is explained, and a simplified approach accounting for phase change is incorporated into the fuel cell model. It is found that the liquid water contours in the GDL are similar along flow channels when the channels are subject to two-phase flow. Here, analysis is performed on a dimensionless parameter Da0 introduced in our previous paper and the parameter is further evaluated in a realistic fuel cell. We found that the GDL's liquid water (or liquid-free) region is determined by the Da0 number which lumps several parameters, including the thermal conductivity and operating temperature. By adjusting these factors, a liquid-free GDL zone can be created even though the channel stream is two-phase flow. Such a liquid-free zone is adjacent to the two-phase region, benefiting local water management, namely avoiding both severe flooding and dryness.

  15. Advanced control of liquid water region in diffusion media of polymer electrolyte fuel cells through a dimensionless number

    DOE PAGES

    Wang, Yun; Chen, Ken S.

    2016-03-21

    In the present study, a three-dimension (3-D) model of polymer electrolyte fuel cells (PEFCs) is employed to investigate the complex, non-isothermal, two-phase flow in the gas diffusion layer (GDL). Phase change in gas flow channels is explained, and a simplified approach accounting for phase change is incorporated into the fuel cell model. It is found that the liquid water contours in the GDL are similar along flow channels when the channels are subject to two-phase flow. Here, analysis is performed on a dimensionless parameter Da0 introduced in our previous paper and the parameter is further evaluated in a realistic fuelmore » cell. We found that the GDL's liquid water (or liquid-free) region is determined by the Da0 number which lumps several parameters, including the thermal conductivity and operating temperature. By adjusting these factors, a liquid-free GDL zone can be created even though the channel stream is two-phase flow. Such a liquid-free zone is adjacent to the two-phase region, benefiting local water management, namely avoiding both severe flooding and dryness.« less

  16. Advanced control of liquid water region in diffusion media of polymer electrolyte fuel cells through a dimensionless number

    NASA Astrophysics Data System (ADS)

    Wang, Yun; Chen, Ken S.

    2016-05-01

    In the present work, a three-dimension (3-D) model of polymer electrolyte fuel cells (PEFCs) is employed to investigate the complex, non-isothermal, two-phase flow in the gas diffusion layer (GDL). Phase change in gas flow channels is explained, and a simplified approach accounting for phase change is incorporated into the fuel cell model. It is found that the liquid water contours in the GDL are similar along flow channels when the channels are subject to two-phase flow. Analysis is performed on a dimensionless parameter Da0 introduced in our previous paper [Y. Wang and K. S. Chen, Chemical Engineering Science 66 (2011) 3557-3567] and the parameter is further evaluated in a realistic fuel cell. We found that the GDL's liquid water (or liquid-free) region is determined by the Da0 number which lumps several parameters, including the thermal conductivity and operating temperature. By adjusting these factors, a liquid-free GDL zone can be created even though the channel stream is two-phase flow. Such a liquid-free zone is adjacent to the two-phase region, benefiting local water management, namely avoiding both severe flooding and dryness.

  17. Dimensionless numbers and correlating equations for the analysis of the membrane-gas diffusion electrode assembly in polymer electrolyte fuel cells

    NASA Astrophysics Data System (ADS)

    Gyenge, E. L.

    The Quraishi-Fahidy method [Can. J. Chem. Eng. 59 (1981) 563] was employed to derive characteristic dimensionless numbers for the membrane-electrolyte, cathode catalyst layer and gas diffuser, respectively, based on the model presented by Bernardi and Verbrugge for polymer electrolyte fuel cells [AIChE J. 37 (1991) 1151]. Monomial correlations among dimensionless numbers were developed and tested against experimental and mathematical modeling results. Dimensionless numbers comparing the bulk and surface-convective ionic conductivities, the electric and viscous forces and the current density and the fixed surface charges, were employed to describe the membrane ohmic drop and its non-linear dependence on current density due to membrane dehydration. The analysis of the catalyst layer yielded electrode kinetic equivalents of the second Damköhler number and Thiele modulus, influencing the penetration depth of the oxygen reduction front based on the pseudohomogeneous film model. The correlating equations for the catalyst layer could describe in a general analytical form, all the possible electrode polarization scenarios such as electrode kinetic control coupled or not with ionic and/or oxygen mass transport limitation. For the gas diffusion-backing layer correlations are presented in terms of the Nusselt number for mass transfer in electrochemical systems. The dimensionless number-based correlating equations for the membrane electrode assembly (MEA) could provide a practical approach to quantify single-cell polarization results obtained under a variety of experimental conditions and to implement them in models of the fuel cell stack.

  18. An empirical/theoretical model with dimensionless numbers to predict the performance of electrodialysis systems on the basis of operating conditions.

    PubMed

    Karimi, Leila; Ghassemi, Abbas

    2016-07-01

    Among the different technologies developed for desalination, the electrodialysis/electrodialysis reversal (ED/EDR) process is one of the most promising for treating brackish water with low salinity when there is high risk of scaling. Multiple researchers have investigated ED/EDR to optimize the process, determine the effects of operating parameters, and develop theoretical/empirical models. Previously published empirical/theoretical models have evaluated the effect of the hydraulic conditions of the ED/EDR on the limiting current density using dimensionless numbers. The reason for previous studies' emphasis on limiting current density is twofold: 1) to maximize ion removal, most ED/EDR systems are operated close to limiting current conditions if there is not a scaling potential in the concentrate chamber due to a high concentration of less-soluble salts; and 2) for modeling the ED/EDR system with dimensionless numbers, it is more accurate and convenient to use limiting current density, where the boundary layer's characteristics are known at constant electrical conditions. To improve knowledge of ED/EDR systems, ED/EDR models should be also developed for the Ohmic region, where operation reduces energy consumption, facilitates targeted ion removal, and prolongs membrane life compared to limiting current conditions. In this paper, theoretical/empirical models were developed for ED/EDR performance in a wide range of operating conditions. The presented ion removal and selectivity models were developed for the removal of monovalent ions and divalent ions utilizing the dominant dimensionless numbers obtained from laboratory scale electrodialysis experiments. At any system scale, these models can predict ED/EDR performance in terms of monovalent and divalent ion removal.

  19. General expression for laminar forced and natural convection heat transfer from isothermal flat plates for all Prandtl numbers

    NASA Astrophysics Data System (ADS)

    Yovanovich, M. M.

    1993-07-01

    It is presently shown that the correlation equations for forced and natural convection-involving bloundary-layer flows, over isothermal flat plates, collapse into a simple expression directly relating the dimensionless wall-temperature excess to a novel Prandtl number function. This function is demonstrated to be applicable for the full, zero-to-infinity Prandtl number range. This formulation allows forced and natural convection heat-transfer results to appear on the same graph, as dimensionless temperature excess vs Prandtl number functions.

  20. Dimensionless thermodynamics: a new paradigm for liquid state properties.

    PubMed

    Sanchez, Isaac C

    2014-08-07

    Equations of state in the van der Waals genre suggest that saturated liquids should adhere to the following corresponding states principle (CSP): saturated liquids at the same reduced density (ρR = ρ/ρc) have comparable dimensionless thermodynamic properties. This CSP is shown to be applicable to a variety of thermodynamic properties that include entropy of vaporization, cohesive energy density, thermal expansion coefficient, isothermal compressibility, thermal pressure coefficient, compressibility factor, temperature coefficient of the vapor pressure, heat capacity difference, and surface tension. For two classes of liquids, all properties rendered dimensionless by the proper choice of scaling variables superpose to form "master curves" that illustrate the CSP. Using scaled particle theory, an improved van der Waals model is developed whose results are compared with existing experimental thermodynamic data in dimensionless form. Properly expressing thermodynamic properties in dimensionless form acts to consolidate and harmonize liquid state properties.

  1. Revealing a quantum feature of dimensionless uncertainty in linear and quadratic potentials by changing potential intervals

    NASA Astrophysics Data System (ADS)

    Kheiri, R.

    2016-09-01

    As an undergraduate exercise, in an article (2012 Am. J. Phys. 80 780-14), quantum and classical uncertainties for dimensionless variables of position and momentum were evaluated in three potentials: infinite well, bouncing ball, and harmonic oscillator. While original quantum uncertainty products depend on {{\\hslash }} and the number of states (n), a dimensionless approach makes the comparison between quantum uncertainty and classical dispersion possible by excluding {{\\hslash }}. But the question is whether the uncertainty still remains dependent on quantum number n. In the above-mentioned article, there lies this contrast; on the one hand, the dimensionless quantum uncertainty of the potential box approaches classical dispersion only in the limit of large quantum numbers (n\\to ∞ )—consistent with the correspondence principle. On the other hand, similar evaluations for bouncing ball and harmonic oscillator potentials are equal to their classical counterparts independent of n. This equality may hide the quantum feature of low energy levels. In the current study, we change the potential intervals in order to make them symmetric for the linear potential and non-symmetric for the quadratic potential. As a result, it is shown in this paper that the dimensionless quantum uncertainty of these potentials in the new potential intervals is expressed in terms of quantum number n. In other words, the uncertainty requires the correspondence principle in order to approach the classical limit. Therefore, it can be concluded that the dimensionless analysis, as a useful pedagogical method, does not take away the quantum feature of the n-dependence of quantum uncertainty in general. Moreover, our numerical calculations include the higher powers of the position for the potentials.

  2. The excitation and propagation of dimensionless magnetostatic waves and oscillations in rectangular YIG rods

    NASA Astrophysics Data System (ADS)

    Zhurilenko, B. E.

    1983-04-01

    The spectrum of bulk magnetostatic waves (BMW) and oscillations (BMO) is studied in a rectangular YIG rod during excitation by different antenna systems. Theoretical and experimental results show that, besides the modes whose wave numbers depend on the specimen size, it is possible to excite BMW and BMO modes with various wave field structures. Dependencies and expressions are obtained for these dimensionless modes and oscillations which describe the structure of the wave field both inside and outside the specimen.

  3. Critical Dimensionless Shields Values for Bankfull Flow

    NASA Astrophysics Data System (ADS)

    Bunte, K.; Abt, S. R.; Swingle, K. W.

    2009-12-01

    The critical dimensionless shear stress τ*c (depicted in the Shields curve as a function of the Reynolds particle number Rep) quantifies the slope - flow depth product at which particles from a relatively well-sorted bed with a mean particle size Dm visually start to move. Contrary to many applications of the Shields curve, τ*c was not designed to predict the bed particle size becoming mobile at bankfull flow. This study sketches a bankfull and a critical bankfull Shields-type curve needed to predict the bankfull mobile particle size. Most studies on bedmaterial entrainment are performed in streams that are wadeable at low flow, but exceed wadeability around bankfull flow. Within the bounds of these stream dimensions, the study drafts a relationship of τ*bf versus Rep (bankfull Shields curve) for a sequence of stream types (in sensu Montgomery and Buffington 1997) ranging from steep cobble headwater streams to plane-bed and pool-riffle gravel-beds to low gradient valley streams with sand and silt beds. Probable values of stream gradient, bed D50 size, and a (roughness corrected) hydraulic radius can be assigned to each stream type. The resulting bankfull curve takes values of τ*bf near 10 for silt and 1 for sand-bedded streams, drops to around 0.05 - 0.02 for mobile gravel-bed streams and then increases towards 0.1 and 0.2 for the steepest streams. Transforming τ*bf into the critical bankfull curve τ*cbf from which to predict the bankfull entrainable particle size requires information on the bedload particle size that becomes mobile at bankfull flow. To estimate τ*cbf over a variety of coarse gravel- and cobble-bed mountain streams, the authors used flow competence curves measured with bedload traps at 10 sites. Bedload traps have a 0.3 m by 0.2 m opening, and 1-1.6 m long trailing net with a 4 mm mesh; mounting traps onto ground plates anchored to the stream bottom permits 1-hr sampling times; 4 to 6 traps are typically installed across the stream width

  4. Dimensionless Equation of State to Predict Microemulsion Phase Behavior.

    PubMed

    Ghosh, Soumyadeep; Johns, Russell T

    2016-09-06

    Prediction of microemulsion phase behavior for changing state variables is critical to formulation design of surfactant-oil-brine (SOB) systems. SOB systems find applications in various chemical and petroleum processes, including enhanced oil recovery. A dimensional equation-of-state (EoS) was recently presented by Ghosh and Johns1 that relied on estimation of the surfactant tail length and surface area. We give an algorithm for flash calculations for estimation of three-phase Winsor regions that is more robust, simpler, and noniterative by making the equations dimensionless so that estimates of tail length and surface area are no longer needed. We predict phase behavior as a function temperature, pressure, volume, salinity, oil type, oil-water ratio, and surfactant/alcohol concentration. The dimensionless EoS is based on coupling the HLD-NAC (Hydrophilic Lipophilic Difference-Net Average Curvature) equations with new relationships between optimum salinity and solubility. An updated HLD expression that includes pressure is also used to complete the state description. A significant advantage of the dimensionless form of the EoS over the dimensional version is that salinity scans are tuned based only on one parameter, the interfacial volume ratio. Further, stability conditions are developed in a simplified way to predict whether an overall compositions lies within the single, two-, or three-phase regions. Important new microemulsion relationships are also found, the most important of which is that optimum solubilization ratio is equal to the harmonic mean of the oil and water solubilization ratios in the type III region. Thus, only one experimental measurement is needed in the three-phase zone to estimate the optimum solubilization ratio, a result which can aid experimental design and improve estimates of optimum from noisy data. Predictions with changing state variables are illustrated by comparison to experimental data using standard diagrams including a new type

  5. Comment on ‘Dimensionless units in the SI’

    NASA Astrophysics Data System (ADS)

    Leonard, B. P.

    2015-08-01

    In their paper, Mohr and Phillips demonstrate that the SI’s representation of ‘plane angle’ as dimensionless rather than as an independent dimensional quantity continues to create confusion. The authors also address perceived problems in terminology regarding numbers of items, such as discrete events or particles. However, their general philosophy of equating the dimensionlessnumber of items’ to ‘(number of items)  ×  (item name)’ leads to false conclusions, such as that the hertz is equal to 2π radians per second, and therefore not a coherent SI unit. In attempting to specify kinds of entities, the authors introduce descriptive labels into their supposed ‘units,’ resulting in confusion between number of entities and amount of substance. And, in discussing the mole and related fundamental constants, they incorrectly portray the Avogadro constant as a conversion factor, identically equal to 1, thereby corrupting the relationships between the Boltzmann constant and the universal gas constant, and between the elementary charge and the Faraday constant. In my comment, I explain and correct these and related errors.

  6. Characteristics of heat transfer with different dimensionless distance in an enclosure

    NASA Astrophysics Data System (ADS)

    Wei, Yi-Kun; Dou, Hua-Shu; Yang, Hui

    2016-10-01

    In this paper, the influence of different dimensionless distance on heat transfer characteristics in a rectangular enclosure is studied using lattice Boltzmann method (LBM). It is shown that the relation between the Rayleigh number (Ra) and the Nusselt number (Nu) using LBM is in promising agreement with that of the previous experimental data by Corvaro and Paroncini [Appl. Therm. Eng. 28 (2007) 25]. It is found that the characteristic of heat transport is closely related to the dimensionless distance of heat source. Special attention is paid to investigate the relation between Ra and Nu. Some relations between Ra and Nu for different dimensionless distance are approximately established in natural convection. It is further found that the heat transport is enhanced with the increase of dimensionless distance.

  7. Dimensionless Parameter Scaling of Diesel Engine Combustion

    NASA Astrophysics Data System (ADS)

    Dowling, David R.; Filipi, Zoran

    1996-11-01

    Combustion in a modern heavy-duty Diesel engine with direct radial fuel injection typically takes place in a short nearly-cylindrical volume at a rate determined by turbulent mixing. Simple dimensionless-parameter scaling laws for turbulent gas-phase mixing and heat transfer have been shown to be effective for a variety of (oxidizer) flow and (fuel) injection conditions within a cylindrical geometry (Edwards et al., AIChE J., Vol. 31, 516 [1985].) (Breidenthal et al., JFM, Vol. 219, 531 [1990].) (Dowling et al., AIAA J. Thermophys. & HT, Vol. 4, 504 [1990].). These studies were driven by chemical laser applications emphasizing long cylinders and sidewall injection. The current investigation seeks to determine the applicability of dimensionless parameter scaling to the instantaneous in-cylinder fuel burning rate in a multi-cylinder Diesel engine typical of Class VIII trucks. Comparisons are made between scaled and unscaled fuel burning rate, as inferred from time-resolved in-cylinder pressure measurements, across the test engine's normal operating range. This research is supported by the US Army Tank-Automotive Research, Development, and Engineering Center.

  8. Stagnation region gas film cooling: Effects of dimensionless coolant temperature

    NASA Technical Reports Server (NTRS)

    Bonnice, M. A.; Lecuyer, M. R.

    1983-01-01

    An experimental investigation was conducted to mode the film cooling performance for a turbine vane leading edge using the stagnation region of a cylinder in cross flow. Experiments were conducted with a single row of spanwise angled (25 deg) coolant holes for a range of the coolant blowing ratio and dimensionless coolant temperature with free stream-to-wall temperature ratio approximately 1.7 and Re sub D = 90000. the cylindrical test surface was instrumented with miniature heat flux gages and wall thermocouples to determine the percentage reduction in the Stanton number as a function of the distance downstream from injection (x/d sub 0) and the location between adjacent holes (z/S). Data from local heat flux measurements are presented for injection from a single row located at 5 deg, 22.9 deg, 40.8 deg, from stagnation using a hole spacing ratio of S/d = 5. The film coolant was injected with T sub c T sub w with a dimensionless coolant temperature in the range 1.18 or equal to theta sub c or equal to 1.56. The data for local Stanton Number Reduction (SNR) showed a significant increase in SNR as theta sub c was increased above 1.0.

  9. Similarity Theory and Dimensionless Numbers in Heat Transfer

    ERIC Educational Resources Information Center

    Marin, E.; Calderon, A.; Delgado-Vasallo, O.

    2009-01-01

    We present basic concepts underlying the so-called similarity theory that in our opinion should be explained in basic undergraduate general physics courses when dealing with heat transport problems, in particular with those involving natural or free convection. A simple example is described that can be useful in showing a criterion for neglecting…

  10. Similarity Theory and Dimensionless Numbers in Heat Transfer

    ERIC Educational Resources Information Center

    Marin, E.; Calderon, A.; Delgado-Vasallo, O.

    2009-01-01

    We present basic concepts underlying the so-called similarity theory that in our opinion should be explained in basic undergraduate general physics courses when dealing with heat transport problems, in particular with those involving natural or free convection. A simple example is described that can be useful in showing a criterion for neglecting…

  11. Dimensionless embedding for nonlinear time series analysis

    NASA Astrophysics Data System (ADS)

    Hirata, Yoshito; Aihara, Kazuyuki

    2017-09-01

    Recently, infinite-dimensional delay coordinates (InDDeCs) have been proposed for predicting high-dimensional dynamics instead of conventional delay coordinates. Although InDDeCs can realize faster computation and more accurate short-term prediction, it is still not well-known whether InDDeCs can be used in other applications of nonlinear time series analysis in which reconstruction is needed for the underlying dynamics from a scalar time series generated from a dynamical system. Here, we give theoretical support for justifying the use of InDDeCs and provide numerical examples to show that InDDeCs can be used for various applications for obtaining the recurrence plots, correlation dimensions, and maximal Lyapunov exponents, as well as testing directional couplings and extracting slow-driving forces. We demonstrate performance of the InDDeCs using the weather data. Thus, InDDeCs can eventually realize "dimensionless embedding" while we enjoy faster and more reliable computations.

  12. Dimensionless parameters for lidar performance characterization

    NASA Astrophysics Data System (ADS)

    Comerón, Adolfo; Agishev, Ravil R.

    2014-10-01

    A set of three dimensionless parameters is proposed to characterize lidar systems. Two of them are based on an asymptotic approximation of the output signal-to-noise ratio as a function of the input optical power reaching the photoreceiver when there is no background radiation. Of these, one is defined as the ratio between the input signal power level coming from a reference range in a reference atmosphere (reference power level) and the input power level that would produce a reference output signal-to-noise ratio if the photoreceiver operated always in signal-shot noise limited regime. The other is defined as the ratio between the reference power level and the input power level for which the signal-induced shot noise power equals the receiver noise power. A third parameter, defined as the ratio between the background optical power at the photoreceiver input and the reference power level, quantifies the effect of background radiation. With these three parameters a good approximation to the output signal-to-noise ratio of the lidar can be calculated as a function of the power reduction with respect to the power reaching the photodetector in the reference situation. These parameters can also be used to compare and rank the performance of different systems.

  13. Dimensionless erosion laws for cohesive sediment

    USGS Publications Warehouse

    Walder, Joseph S.

    2016-01-01

    A method of achieving a dimensionless collapse of erosion-rate data for cohesive sediments is proposed and shown to work well for data collected in flume-erosion tests on mixtures of sand and mud (silt plus clay sized particles) for a wide range of mud fraction. The data collapse corresponds to a dimensional erosion law of the form E∼(τ−τc)m">E∼(τ−τc)mE∼(τ−τc)m, where E">EE is erosion rate, τ">ττ is shear stress, τc">τcτc is the threshold shear stress for erosion to occur, and m≈7/4">m≈7/4m≈7/4. This result contrasts with the commonly assumed linear erosion law E=kd(τ−τc)">E=kd(τ−τc)E=kd(τ−τc), where kd">kdkd is a measure of how easily sediment is eroded. The data collapse prompts a re-examination of the way that results of the hole-erosion test (HET) and jet-erosion test (JET) are customarily analyzed, and also calls into question the meaningfulness not only of proposed empirical relationships between kd">kdkd and τc">τcτc, but also of the erodibility parameter kd">kdkd itself. Fuller comparison of flume-erosion data with hole-erosion and jet-erosion data will require revised analyses of the HET and JET that drop the assumption m=1">m=1m=1 and, in the case of the JET, certain simplifying assumptions about the mechanics of jet scour.

  14. Determination of Dimensionless Attenuation Coefficient in Shaped Resonators

    NASA Technical Reports Server (NTRS)

    Daniels, C.; Steinetz, B.; Finkbeiner, J.; Raman, G.; Li, X.

    2003-01-01

    The value of dimensionless attenuation coefficient is an important factor when numerically predicting high-amplitude acoustic waves in shaped resonators. Both the magnitude of the pressure waveform and the quality factor rely heavily on this dimensionless parameter. Previous authors have stated the values used, but have not completely explained their methods. This work fully describes the methodology used to determine this important parameter. Over a range of frequencies encompassing the fundamental resonance, the pressure waves were experimentally measured at each end of the shaped resonators. At the corresponding dimensionless acceleration, the numerical code modeled the acoustic waveforms generated in the resonator using various dimensionless attenuation coefficients. The dimensionless attenuation coefficient that most closely matched the pressure amplitudes and quality factors of the experimental and numerical results was determined to be the value to be used in subsequent studies.

  15. A dimensionless parameter model for arc welding processes

    SciTech Connect

    Fuerschbach, P.W.

    1994-12-31

    A dimensionless parameter model previously developed for C0{sub 2} laser beam welding has been shown to be applicable to GTAW and PAW autogenous arc welding processes. The model facilitates estimates of weld size, power, and speed based on knowledge of the material`s thermal properties. The dimensionless parameters can also be used to estimate the melting efficiency, which eases development of weld schedules with lower heat input to the weldment. The mathematical relationship between the dimensionless parameters in the model has been shown to be dependent on the heat flow geometry in the weldment.

  16. A dimensionless parameter for classifying hemodynamics in intracranial

    NASA Astrophysics Data System (ADS)

    Asgharzadeh, Hafez; Borazjani, Iman

    2015-11-01

    Rupture of an intracranial aneurysm (IA) is a disease with high rates of mortality. Given the risk associated with the aneurysm surgery, quantifying the likelihood of aneurysm rupture is essential. There are many risk factors that could be implicated in the rupture of an aneurysm. However, the most important factors correlated to the IA rupture are hemodynamic factors such as wall shear stress (WSS) and oscillatory shear index (OSI) which are affected by the IA flows. Here, we carry out three-dimensional high resolution simulations on representative IA models with simple geometries to test a dimensionless number (first proposed by Le et al., ASME J Biomech Eng, 2010), denoted as An number, to classify the flow mode. An number is defined as the ratio of the time takes the parent artery flow transports across the IA neck to the time required for vortex ring formation. Based on the definition, the flow mode is vortex if An>1 and it is cavity if An<1. We show that the specific definition of Le et al. works for sidewall but needs to be modified for bifurcation aneurysms. In addition, we show that this classification works on three-dimensional geometries reconstructed from three-dimensional rotational angiography of human subjects. Furthermore, we verify the correlation of IA flow mode and WSS/OSI on the human subject IA. This work was supported partly by the NIH grant R03EB014860, and the computational resources were partly provided by CCR at UB. We thank Prof. Hui Meng and Dr. Jianping Xiang for providing us the database of aneurysms and helpful discussions.

  17. Exact expressions for ensemble functionals from particle number dependence.

    PubMed

    Joubert, Daniel P

    2012-05-07

    Some properties of exact ensemble density functionals can be determined by examining the particle number dependence of ground state ensemble density matrices for systems where the integer ground state energies satisfy a convexity condition. The results include the observation that the integral of the product of the functional derivative and Fukui function of functionals that can be expressed as the trace of an operator is particle number independent for particle numbers between successive integers and the integral itself is equal to the difference between functionals evaluated at successive integer particle numbers. Expressions that must be satisfied by 2nd and higher order functional derivatives are formulated and equations that must be satisfied point by point in space are derived. Using the analytic Hooke's atom model, it is shown that commonly used correlation functional approximations do not bear any resemblance to a spatially dependent expression derived from the exact second order functional derivative of the correlation functional. It is also shown that two expressions for the mutual Coulomb energy are not equal when approximate exchange and correlation functionals are used.

  18. Cross-Evaluation of Laboratory Permeability Tests by Dimensionless Analysis

    NASA Astrophysics Data System (ADS)

    Takeda, M.; Zhang, M.; Hiratsuka, T.

    2007-12-01

    Accurate estimations of transport parameters of engineered and natural barrier materials are indispensable for assessments of the safety of geological disposal of hazardous wastes including radioactive nuclear waste. In such projects, it is essential that the barrier materials be capable of retarding the migration of contaminants. When groundwater flow is dominant, the evaluation of hydraulic parameters, particularly the permeability and specific storage, is of fundamental importance in the safety assessment. The permeability and specific storage of synthetic and geological materials are measured using permeability tests; however, conventional test methods are routinely applied to barrier materials with relatively low-permeabilities with little knowledge about their applicabilities. In order to provide a theoretical basis for designing laboratory permeability tests, the applicabilites of currently available test methods were examined and cross-evaluated with emphases on the experimental time and the parameter sensitivity using a numerical approach. To allow for a general discussion, a series of examinations were conducted based on a dimensionless analysis using dimensionless parameters representing the hydraulic properties and dimensions of the specimen and the other experimental conditions. In the dimensionless-time scale, the experimental time and the parameter sensitivity of the individual test methods can be simulated and compared by varying a few dimensionless parameters representing the experimental conditions. From a series of examinations, it was found that the experimental time and the parameter sensitivity of the individual test methods can be ascertained and compared using a few dimensionless parameters. This research project has been conducted under the research contract with the Japan Nuclear Energy Safety Organization (JNES).

  19. Potential problem with mean dimensionless hydrographs at ungaged sites

    USGS Publications Warehouse

    Wahl, Kenneth L.; Rankl, James G.

    1993-01-01

    A flood hydrograph for an ungaged stream site can be estimated from a mean dimensionless hydrograph and estimates of instantaneous peak discharge (Q) and total storm runoff volume (V). However, the time base of the resulting flood hydrograph can be inversely related to the magnitude of the peak discharge if estimates of runoff volume were defined using ordinary least-squares regression relations of the form V=f(Q). Such an inverse relation is not hydrologically consistent. The problem can be solved in several ways. Redefining the relation between V and Q using an alternative model that preserves the variance in V generally will produce exponents for Q that are near 1. The resulting estimated flood-hydrograph volumes will nearly match the original volumes near the mean of the logarithms of V and Q, but will differ as volumes and peak discharges depart from the mean values. The difference will depend on how much the original exponent of Q differed from 1. Another solution is to simply hold T???, the multiplier needed to expand the time base of a mean dimensionless hydrograph into the time base of an estimated flood hydrograph, constant. That solution is a questionable approach if basins vary either in size, shape, or slope. A third solution is to define T??? as a function of time to peak, Tp. Flood volume then depends only on Q, Tp, and the dimensionless hydrograph, thereby removing the need to define a relation for estimating volume.

  20. A dimensionless model of impact piezoelectric energy harvesting with dissipation

    NASA Astrophysics Data System (ADS)

    Fu, Xinlei; Liao, Wei-Hsin

    2016-04-01

    Impact excitation is common in the environment. Impact piezoelectric energy harvesting could realize frequency up-conversion. However, the dissipation mechanism in impact piezoelectric energy harvesting has not been investigated so far. There is no comprehensive model to be able to analyze the impact piezoelectric energy harvesting thoroughly. This paper is aimed to develop a generalized model that considers dissipation mechanism of impact piezoelectric energy harvesting. In this electromechanical model, Hertzian contact theory and impact dissipation mechanism are identified as constitutive mechanisms. The impact force is compared and the energy distribution is analyzed so that input energy corresponds to impact dissipated energy, structural damping dissipated energy and harvested electrical energy. We then nondimensionalize the developed model and define five dimensionless parameters with attributed physical meanings, including dimensionless parameters of impact dissipation, mass ratio, structural damping, electromechanical coupling, and electrical load. We conclude it is more accurate to consider impact dissipation mechanism to predict impact force and harvested energy. The guideline for improving harvested energy based on parametric studies of dimensionless model is to increase mass ratio, to minimize structural damping, to maximize electromechanical coupling, to use optimal load resistance for impedance matching, and to choose proper impact velocity .

  1. Steady flows in an oscillating deformable container: Effect of the dimensionless frequency

    NASA Astrophysics Data System (ADS)

    Kozlov, V. G.; Kozlov, N. V.; Schipitsyn, V. D.

    2017-09-01

    This research involves an experimental study of steady streaming of a fluid excited in an oscillating cylindrical container with an elastically deformable boundary. The influence of the vibration parameters and fluid properties on the structure and intensity of flows in the container is studied. The dependence of the structure and intensity of the flows on the governing parameters, the Froude number, and the dimensionless frequency, which determines the ratio between the cavity size and the Stokes boundary layer, is investigated. It is shown that steady streaming is generated within a region of high dimensionless frequencies, which does not depend on frequency and is fully determined by the dimensionless amplitude. It is discovered that steady flows change qualitatively in a region of intermediate and low frequencies where the thickness of the dynamic boundary layers is comparable to the cavity size. In a region of low frequencies, the direction of steady flow is opposite to that in a region of high frequencies and the flow intensity decreases with frequency. The discovered dependencies have a similar nature and shed light on flows in oscillating containers, including droplets with a saturated interface.

  2. How the Number of Alleles Influences Gene Expression

    NASA Astrophysics Data System (ADS)

    Hat, Beata; Paszek, Pawel; Kimmel, Marek; Piechor, Kazimierz; Lipniacki, Tomasz

    2007-07-01

    The higher organisms, eukaryotes, are diploid and most of their genes have two homological copies (alleles). However, the number of alleles in a cell is not constant. In the S phase of the cell cycle all the genome is duplicated and then in the G2 phase and mitosis, which together last for several hours, most of the genes have four copies instead of two. Cancer development is, in many cases, associated with a change in allele number. Several genetic diseases are caused by haploinsufficiency: Lack of one of the alleles or its improper functioning. In the paper we consider the stochastic expression of a gene having a variable number of copies. We applied our previously developed method in which the reaction channels are split into slow (connected with change of gene state) and fast (connected with mRNA/protein synthesis/decay), the later being approximated by deterministic reaction rate equations. As a result we represent gene expression as a piecewise deterministic time-continuous Markov process, which is further related with a system of partial differential hyperbolic equations for probability density functions (pdfs) of protein distribution. The stationary pdfs are calculated analytically for haploidal gene or numerically for diploidal and tetraploidal ones. We distinguished nine classes of simultaneous activation of haploid, diploid and tetraploid genes. This allows for analysis of potential consequences of gene duplication or allele loss. We show that when gene activity is autoregulated by a positive feedback, the change in number of gene alleles may have dramatic consequences for its regulation and may not be compensated by the change of efficiency of mRNA synthesis per allele.

  3. Experimental investigation and dimensionless analysis of forming of rectangular plates subjected to hydrodynamic loading

    NASA Astrophysics Data System (ADS)

    Babaei, H.; Mirzababaie Mostofi, T.; Alitavoli, M.; Saeidinejad, A.

    2017-01-01

    This paper describes an experimental setup consisting of a drop hammer and a shock tube filled with a liquid, where a shock wave is formed, and results of experiments performed with fully clamped rectangular plates subjected to an impact load of the water shock wave. The results are presented in terms of the central deflection of the plates as a function of the kinetic energy of the drop hammer. The singular value decomposition method is used in conjunction with dimensionless numbers to obtain analytical dependences of the central deflection of the plates on the impact load parameters.

  4. Dimensionless parameters, scaling laws, and the implications for ETG

    SciTech Connect

    Castle, G.G.

    1995-04-20

    ETG will be useful in resolving several physical issues relevant to Spherical Tokamak Reactor concepts. First, it will provide a test of whether transport is Bohm or gyro-Bohm in nature. The second point is that ETG will operate in a completely different range of {rho}* space from other high performance machines, opening up a previously inaccessible region of parameter space. ETG is also a (very) high-{beta} machine. It would be the only device that would have all of its parameters except {rho}* similar to those of a Spherical tokamak Reactor. If it turns out that the transport scales definitively as either Bohm or gyro-Bohm, then extrapolation to reactor conditions with significantly lower values of {rho}* would become more credible. It is also shown that in general one cannot obtain a power law relation in the dimensionless variables for the confinement tim from a power law fit to the engineering variables. It is shown, however, that if T{sub i}/T{sub e} and n{sub i}/n{sub e} are constant or if a modified definition of certain dimensionless variables is adopted, then such a power law conversion is possible.

  5. Methodology of dimensionless multiplicative decomposition for atmospheric lidar evaluation

    NASA Astrophysics Data System (ADS)

    Agishev, Ravil; Gross, Barry; Comeron, Adolfo

    2006-09-01

    In the present paper, we show application examples of united generalized methodology for atmospheric lidar assessment, which uses the dimensionless-parameterization as a core component. It is based on a series of our previous works where the problem of universal parameterization over many lidar technologies were described and analyzed from different points of view. A methodology of spatial-angular filtering efficiency was used for comparison of different receiving system designs on the criterion of stability against background radiation. The dimensionless parameterization concept applied to photodetectors of remote sensing instruments allowed predicting the lidar receiver performance in presence of sky background. The approach can be widely used to evaluate a broad range of lidar system capabilities for a variety of lidar remote sensing applications, as well as to serve as a basis for selection of appropriate lidar system parameters for a specific application. Such a methodology provides generalized, uniform and objective approach for the evaluation of a broad range of lidar types and systems (aerosol, Raman, DIAL), operating on different targets (backscatter or topographic) and under intense sky background conditions, and can be used within the lidar community to compare different lidar instruments.

  6. Estimating Mass of Inflatable Aerodynamic Decelerators Using Dimensionless Parameters

    NASA Technical Reports Server (NTRS)

    Samareh, Jamshid A.

    2011-01-01

    This paper describes a technique for estimating mass for inflatable aerodynamic decelerators. The technique uses dimensional analysis to identify a set of dimensionless parameters for inflation pressure, mass of inflation gas, and mass of flexible material. The dimensionless parameters enable scaling of an inflatable concept with geometry parameters (e.g., diameter), environmental conditions (e.g., dynamic pressure), inflation gas properties (e.g., molecular mass), and mass growth allowance. This technique is applicable for attached (e.g., tension cone, hypercone, and stacked toroid) and trailing inflatable aerodynamic decelerators. The technique uses simple engineering approximations that were developed by NASA in the 1960s and 1970s, as well as some recent important developments. The NASA Mars Entry and Descent Landing System Analysis (EDL-SA) project used this technique to estimate the masses of the inflatable concepts that were used in the analysis. The EDL-SA results compared well with two independent sets of high-fidelity finite element analyses.

  7. Development and evaluation of a dimensionless mechanistic pan coating model for the prediction of coated tablet appearance.

    PubMed

    Niblett, Daniel; Porter, Stuart; Reynolds, Gavin; Morgan, Tomos; Greenamoyer, Jennifer; Hach, Ronald; Sido, Stephanie; Karan, Kapish; Gabbott, Ian

    2017-08-07

    A mathematical, mechanistic tablet film-coating model has been developed for pharmaceutical pan coating systems based on the mechanisms of atomisation, tablet bed movement and droplet drying with the main purpose of predicting tablet appearance quality. Two dimensionless quantities were used to characterise the product properties and operating parameters: the dimensionless Spray Flux (relating to area coverage of the spray droplets) and the Niblett Number (relating to the time available for drying of coating droplets). The Niblett Number is the ratio between the time a droplet needs to dry under given thermodynamic conditions and the time available for the droplet while on the surface of the tablet bed. The time available for drying on the tablet bed surface is critical for appearance quality. These two dimensionless quantities were used to select process parameters for a set of 22 coating experiments, performed over a wide range of multivariate process parameters. The dimensionless Regime Map created can be used to visualise the effect of interacting process parameters on overall tablet appearance quality and defects such as picking and logo bridging. Copyright © 2017 Elsevier B.V. All rights reserved.

  8. Dimensionless size scaling of intrinsic rotation in DIII-D

    SciTech Connect

    deGrassie, John S.; Solomon, Wayne M.; Rice, J. E.; Noterdaeme, J. -M.

    2016-08-01

    A dimensionless empirical scaling for intrinsic toroidal rotation is given; MANρ*, where MA is the toroidal velocity divided by the Alfvén velocity, βN the usual normalized β value, and ρ* is the ion gyroradius divided by the minor radius. This scaling describes well experimental data from DIII-D, and also some published data from C-Mod and JET. The velocity used in this scaling is in an outer location in minor radius, outside of the interior core and inside of the large gradient edge region in H-mode conditions. Furthermore, this scaling establishes the basic magnitude of the intrinsic toroidal rotation and its relation to the rich variety of rotation profiles that can be realized for intrinsic conditions is discussed.

  9. Dimensionless size scaling of intrinsic rotation in DIII-D

    DOE PAGES

    deGrassie, John S.; Solomon, Wayne M.; Rice, J. E.; ...

    2016-08-01

    A dimensionless empirical scaling for intrinsic toroidal rotation is given; MA ~βNρ*, where MA is the toroidal velocity divided by the Alfvén velocity, βN the usual normalized β value, and ρ* is the ion gyroradius divided by the minor radius. This scaling describes well experimental data from DIII-D, and also some published data from C-Mod and JET. The velocity used in this scaling is in an outer location in minor radius, outside of the interior core and inside of the large gradient edge region in H-mode conditions. Furthermore, this scaling establishes the basic magnitude of the intrinsic toroidal rotation andmore » its relation to the rich variety of rotation profiles that can be realized for intrinsic conditions is discussed.« less

  10. Dimensionless Analysis and Numerical Modeling of Rebalancing Phenomena During Levitation

    NASA Astrophysics Data System (ADS)

    Gao, Lei; Shi, Zhe; Li, Donghui; McLean, Alexander; Chattopadhyay, Kinnor

    2016-06-01

    Electromagnetic levitation (EML) has proved to be a powerful tool for research activities in areas pertaining to materials physics and engineering. The customized EML setups in various fields, ranging from solidification to nanomaterial manufacturing, require the designing of stable levitation systems. Since the elevated droplet is opaque, the most effective way to research on EML is mathematical modeling. In the present study, a 3D model was built to investigate the rebalancing phenomenon causing instabilities during droplet melting. A mathematical model modified based on Hooke's law (spring) was proposed to describe the levitation system. This was combined with dimensionless analysis to investigate the generation of levitation forces as it will significantly affect the behavior of the spring model.

  11. Bacterial expression system with tightly regulated gene expression and plasmid copy number.

    PubMed

    Bowers, Lisa M; Lapoint, Kathleen; Anthony, Larry; Pluciennik, Anna; Filutowicz, Marcin

    2004-09-29

    A new Escherichia coli host/vector system has been engineered to allow tight and uniform modulation of gene expression and gamma origin (ori) plasmid copy number. Regulation of gamma ori plasmid copy number is achieved through arabinose-inducible expression of the necessary Rep protein, pi, whose gene was integrated into the chromosome of the host strain under control of the P(BAD) promoter. gamma ori replication can be uniformly modulated over 100-fold by changing the concentration of l-arabinose in the growth medium. This strain avoids the problem of all-or-nothing induction of P(BAD) because it is deficient in both arabinose uptake and degradation genes. Arabinose enters the cell by a mutant LacY transporter, LacYA177C, which is expressed from the host chromosome. Although this strain could be compatible with any gamma ori plasmid, we describe the utility of a gamma ori expression vector that allows especially tight regulation of gene expression. With this host/vector system, it is possible to independently modulate gene expression and gene dosage, facilitating the cloning and overproduction of toxic gene products. We describe the successful use of this system for cloning a highly potent toxin, Colicin E3, in the absence of its cognate immunity protein. This system could be useful for cloning genes encoding other potent toxins, screening libraries for potential toxins, and maintaining any gamma ori vector at precise copy levels in a cell.

  12. Dimensionless ratios: Characteristics of quantum liquids and their phase transitions

    NASA Astrophysics Data System (ADS)

    Yu, Yi-Cong; Chen, Yang-Yang; Lin, Hai-Qing; Römer, Rudolf A.; Guan, Xi-Wen

    2016-11-01

    Dimensionless ratios of physical properties can characterize low-temperature phases in a wide variety of materials. As such, the Wilson ratio (WR), the Kadowaki-Woods ratio, and the Wiedemann-Franz law capture essential features of Fermi liquids in metals, heavy fermions, etc. Here we prove that the phases of many-body interacting multicomponent quantum liquids in one dimension (1D) can be described by WRs based on the compressibility, susceptibility, and specific heat associated with each component. These WRs arise due to additivity rules within subsystems reminiscent of the rules for multiresistor networks in series and parallel—a novel and useful characteristic of multicomponent Tomonaga-Luttinger liquids (TLL) independent of microscopic details of the systems. Using experimentally realized multispecies cold atomic gases as examples, we prove that the Wilson ratios uniquely identify phases of TLL, while providing universal scaling relations at the boundaries between phases. Their values within a phase are solely determined by the stiffnesses and sound velocities of subsystems and identify the internal degrees of freedom of said phase such as its spin degeneracy. This finding can be directly applied to a wide range of 1D many-body systems and reveals deep physical insights into recent experimental measurements of the universal thermodynamics in ultracold atoms and spins.

  13. Experimental constraints on transport from dimensionless parameter scaling studies

    SciTech Connect

    Petty, C.C.; Luce, T.C.; Baker, D.R.

    1998-02-01

    The scalings of heat transport with safety factor (q), normalized collisionality (v), plasma beta ({beta}), and relative gyroradius ({rho}*) have been measured on the DIII-D tokamak. The measured {rho}* {beta} and v scalings of heat transport indicate that E x B transport from drive wave turbulence is a plausible basis for anomalous transport. For high confinement (H) mode plasmas where the safety factor was varied at fixed magnetic shear, the effective (or one-fluid) thermal diffusivity was found to scale like {chi}{sub eff} {proportional_to} q{sup 2.3{+-}0.64}, with the ion and electron fluids having the same q scaling to within the experimental errors except near the plasma edge. The scaling of the thermal confinement time with safety factor was in good agreement with this local transport dependence, {tau}{sub th} {proportional_to} q{sup {minus}2.42{+-}0.31}; however, when the magnetic shear was allowed to vary to keep q{sub 0} fixed during the (edge) safety factor scan, a weaker global dependence was observed, {tau}{sub th} {proportional_to} q{sub 95}{sup {minus}1.43{+-}0.23}. This weaker dependence was mainly due to the change in the local value of q between the two types of scans. The combined {rho}*, {beta}, v and q scalings of heat transport for H-mode plasmas on DIII-D reproduce the empirical confinement scaling using physical (dimensionless) parameters with the exception of weaker power degradation.

  14. Unravelling abiotic and biotic controls on the seasonal water balance using data-driven dimensionless diagnostics

    NASA Astrophysics Data System (ADS)

    Seibert, Simon Paul; Jackisch, Conrad; Ehret, Uwe; Pfister, Laurent; Zehe, Erwin

    2017-06-01

    The baffling diversity of runoff generation processes, alongside our sketchy understanding of how physiographic characteristics control fundamental hydrological functions of water collection, storage, and release, continue to pose major research challenges in catchment hydrology. Here, we propose innovative data-driven diagnostic signatures for overcoming the prevailing status quo in catchment inter-comparison. More specifically, we present dimensionless double mass curves (dDMC) which allow inference of information on runoff generation and the water balance at the seasonal and annual timescales. By separating the vegetation and winter periods, dDMC furthermore provide information on the role of biotic and abiotic controls in seasonal runoff formation. A key aspect we address in this paper is the derivation of dimensionless expressions of fluxes which ensure the comparability of the signatures in space and time. We achieve this by using the limiting factors of a hydrological process as a scaling reference. We show that different references result in different diagnostics. As such we define two kinds of dDMC which allow us to derive seasonal runoff coefficients and to characterize dimensionless streamflow release as a function of the potential renewal rate of the soil storage. We expect these signatures for storage controlled seasonal runoff formation to remain invariant, as long as the ratios of release over supply and supply over storage capacity develop similarly in different catchments. We test the proposed methods by applying them to an operational data set comprising 22 catchments (12-166 km2) from different environments in southern Germany and hydrometeorological data from 4 hydrological years. The diagnostics are used to compare the sites and to reveal the dominant controls on runoff formation. The key findings are that dDMC are meaningful signatures for catchment runoff formation at the seasonal to annual scale and that the type of scaling strongly

  15. Application of symbolic regression to the derivation of scaling laws for tokamak energy confinement time in terms of dimensionless quantities

    NASA Astrophysics Data System (ADS)

    Murari, A.; Peluso, E.; Lungaroni, M.; Gelfusa, M.; Gaudio, P.

    2016-02-01

    In many scientific applications, it is important to investigate how certain properties scale with the parameters of the systems. The experimental studies of scalings have traditionally been addressed with log regression, which limits the results to power laws and to theoretical and not data-driven dimensionless quantities. This has also been the case in nuclear fusion, in which the scaling of the energy confinement time is a crucial aspect in understanding the physics of transport and in the design of future devices. Traditionally two main assumptions are at the basis of the most widely accepted empirical scaling laws for the confinement time: (a) the dimensionless variables used are the ones derived from the symmetries of the Vlasov equation; (b) the final scalings have the mathematical form of power laws. In this paper, it is shown how symbolic regression (SR), implemented with genetic programming (GP) techniques, can be used to test these hypotheses. Neither assumption is confirmed by the available data of the multi-machine International Tokamak Physics Activity (ITPA) of validated tokamak discharges. The statistically soundest expressions are not power laws and cannot be formulated in terms of the traditional dimensionless quantities. The consequences of the data-driven scaling laws obtained are both practical and theoretical: the confinement time for the ITER can be significantly shorter than foreseen by power laws and different dimensionless variables should be considered for theoretical investigations. On the other hand, higher quality databases should be built to reduce the uncertainties in the extrapolations. It is also worth emphasising that the proposed methodology is fully general and therefore can be applied to any field of science.

  16. Acoustic characterization and prediction of the cut-off dimensionless frequency of an elastic tube by neural networks.

    PubMed

    Dariouchy, Abdelilah; Aassif, El Houcein; Décultot, Dominique; Maze, Gérard

    2007-05-01

    A neural network is developed to predict cut-off dimensionless frequencies of the antisymmetric circumferential waves (Ai) propagating around an elastic circular cylindrical shell of different radius ratio b/a (a, outer radius; b, inner radius). The useful data to train and test the performances of the model are determinated from calculated trajectories of natural modes of resonances or extracted from time-frequency representations of Wigner-Ville of the acoustic backscattered time signal obtained from a computation. In this work, the studied tubes are made of aluminum or stainless steel. The material density, the radius ratio b/a, the index i of the antisymmetric waves, and the propagation velocities in the tube, are selected like relevant entries of the model of neural network. During the development of the network, several configurations are evaluated. The optimal model selected is a network with two hidden layers. This model is able to predict the cut-off dimensionless frequencies with a mean relative error (MRE) of about 1%, a mean absolute error (MAE) of 3.10(-3) k1a, and a standard error (SE) of 10(-3) k1a (k1a is the dimensionless frequency, k is the wave number in water).

  17. A hemodynamic-based dimensionless parameter for predicting rupture of intracranial aneurysms

    NASA Astrophysics Data System (ADS)

    Asgharzadeh, Hafez; Varble, Nicole; Meng, Hui; Borazjani, Iman

    2016-11-01

    Rupture of an intracranial aneurysm (IA) is a disease with high rates of mortality. Given the risk associated with the aneurysm surgery, quantifying the likelihood of aneurysm rupture is essential. There are many risk factors that could be implicated in the rupture of an aneurysm. However, the hemodynamic factors are believed to be the most influential ones. Here, we carry out three-dimensional high resolution simulations on human subjects IAs to test a dimensionless number, denoted as An number, to classify the flow mode. An number is defined as the ratio of the time takes the parent artery flow transports through the expansion region to the time required for vortex formation. Furthermore, we investigate the correlation of IA flow mode and WSS/OSI on the human subject IAs. Finally, we test if An number can distinguish ruptured from unruptured IAs on a database containing 204 human subjects IAs. This work was supported by National Institute Of Health (NIH) Grant R03EB014860 and the Center of Computational Research (CCR) of University at Buffalo.

  18. Linear (in oscillation dimensionless amplitude) interaction between the modes of a nonspherical charged drop in an external electrostatic field

    NASA Astrophysics Data System (ADS)

    Shiryaeva, S. O.; Petrushov, N. A.; Grigor'ev, A. I.

    2016-01-01

    The stability of a heavily charged drop in a weak uniform electrostatic field (in which the equilibrium shape of the drop can be represented by a prolate spheroid) is calculated in the fourth order of smallness in the eccentricity of the spheroidal drop and in the first order of smallness in the drop oscillation dimensionless amplitude. It is found that as the order of approximation in eccentricity grows, so does the number of modes interacting with the initially excited mode. In the given order of smallness, the preferred (initially excited) mode is shown to interact with the nearest eight modes. The drop becomes unstable if such is the second mode.

  19. Simple approach to predict APD/PMT lidar detector performance under sky background using dimensionless parametrization

    NASA Astrophysics Data System (ADS)

    Agishev, Ravil; Gross, Barry; Moshary, Fred; Gilerson, Alexander; Ahmed, Samir

    2006-08-01

    In this paper, we developed a simple approach to predict the APD/PMT (avalanche photodiode/photomultiplier) lidar detector performance in the presence of residual skylight background. By normalizing all relevant photodetector noise sources to the quantum noise, we obtain quantitative expressions for the degradation of the signal-to-noise ratio (SNR), the increasing threshold sensitivity of and decreasing lidar operation range. To apply the formalism to any lidar photodetectors operating in the ultra violet, visible and near-infrared spectral regions and to perform a comparative analysis of PMT and APD capabilities as the best photodetectors for ultra-violet (UV), visible (Vis) and near infra-red (NIR) lidar, we utilize a set of spectral characteristics that are built from an envelope of individual PMT and APD component responses. On this basis, the general analysis of system performance under intense background conditions is developed, and practical recommendations on detector use for each spectral region are given. The dimensionless formalism and the generalized detector spectral models used allows our analysis to be applied to nearly any lidar receiver operating over very different signal/background situations.

  20. A new dimensionless index for evaluating cell stiffness-based deformability in microchannel.

    PubMed

    Tsai, Chia-Hung Dylan; Sakuma, Shinya; Arai, Fumihito; Kaneko, Makoto

    2014-04-01

    This paper proposes a new index for evaluating the stiffness-based deformability of a cell using a microchannel. In conventional approaches, the transit time of a cell through a microchannel is often utilized for the evaluation of cell deformability. However, such time includes both the information of cell stiffness and viscosity. In this paper, we eliminate the effect from cell viscosity, and focus on the cell stiffness only. We find that the velocity of a cell varies when it enters a channel, and eventually reaches to equilibrium where the velocity becomes constant. The constant velocity is defined as the equilibrium velocity of the cell, and it is utilized to define the observability of stiffness-based deformability. The necessary and sufficient numbers of sensing points for evaluating stiffness-based deformability are discussed. Through the dimensional analysis on the microchannel system, three dimensionless parameters determining stiffness-based deformability are derived, and a new index is introduced based on these parameters. The experimental study is conducted on the red blood cells from a healthy subject and a diabetes patient. With the proposed index, we showed that the experimental data can be nicely arranged.

  1. Identification of candidate growth promoting genes in ovarian cancer through integrated copy number and expression analysis.

    PubMed

    Ramakrishna, Manasa; Williams, Louise H; Boyle, Samantha E; Bearfoot, Jennifer L; Sridhar, Anita; Speed, Terence P; Gorringe, Kylie L; Campbell, Ian G

    2010-04-08

    Ovarian cancer is a disease characterised by complex genomic rearrangements but the majority of the genes that are the target of these alterations remain unidentified. Cataloguing these target genes will provide useful insights into the disease etiology and may provide an opportunity to develop novel diagnostic and therapeutic interventions. High resolution genome wide copy number and matching expression data from 68 primary epithelial ovarian carcinomas of various histotypes was integrated to identify genes in regions of most frequent amplification with the strongest correlation with expression and copy number. Regions on chromosomes 3, 7, 8, and 20 were most frequently increased in copy number (> 40% of samples). Within these regions, 703/1370 (51%) unique gene expression probesets were differentially expressed when samples with gain were compared to samples without gain. 30% of these differentially expressed probesets also showed a strong positive correlation (r > or =0.6) between expression and copy number. We also identified 21 regions of high amplitude copy number gain, in which 32 known protein coding genes showed a strong positive correlation between expression and copy number. Overall, our data validates previously known ovarian cancer genes, such as ERBB2, and also identified novel potential drivers such as MYNN, PUF60 and TPX2.

  2. Identification of Candidate Growth Promoting Genes in Ovarian Cancer through Integrated Copy Number and Expression Analysis

    PubMed Central

    Ramakrishna, Manasa; Williams, Louise H.; Boyle, Samantha E.; Bearfoot, Jennifer L.; Sridhar, Anita; Speed, Terence P.; Gorringe, Kylie L.; Campbell, Ian G.

    2010-01-01

    Ovarian cancer is a disease characterised by complex genomic rearrangements but the majority of the genes that are the target of these alterations remain unidentified. Cataloguing these target genes will provide useful insights into the disease etiology and may provide an opportunity to develop novel diagnostic and therapeutic interventions. High resolution genome wide copy number and matching expression data from 68 primary epithelial ovarian carcinomas of various histotypes was integrated to identify genes in regions of most frequent amplification with the strongest correlation with expression and copy number. Regions on chromosomes 3, 7, 8, and 20 were most frequently increased in copy number (>40% of samples). Within these regions, 703/1370 (51%) unique gene expression probesets were differentially expressed when samples with gain were compared to samples without gain. 30% of these differentially expressed probesets also showed a strong positive correlation (r≥0.6) between expression and copy number. We also identified 21 regions of high amplitude copy number gain, in which 32 known protein coding genes showed a strong positive correlation between expression and copy number. Overall, our data validates previously known ovarian cancer genes, such as ERBB2, and also identified novel potential drivers such as MYNN, PUF60 and TPX2. PMID:20386695

  3. Gene Expression Correlates with the Number of Herpes Viral Genomes Initiating Infection in Single Cells

    PubMed Central

    Cohen, Efrat M.

    2016-01-01

    Viral gene expression varies significantly among genetically identical cells. The sources of these variations are not well understood and have been suggested to involve both deterministic host differences and stochastic viral host interactions. For herpesviruses, only a limited number of incoming viral genomes initiate expression and replication in each infected cell. To elucidate the effect of this limited number of productively infecting genomes on viral gene expression in single cells, we constructed a set of fluorescence-expressing genetically tagged herpes recombinants. The number of different barcodes originating from a single cell is a good representative of the number of incoming viral genomes replicating (NOIVGR) in that cell. We identified a positive correlation between the NOIVGR and viral gene expression, as measured by the fluorescent protein expressed from the viral genome. This correlation was identified in three distinct cell-types, although the average NOIVGR per cell differed among these cell-types. Among clonal single cells, high housekeeping gene expression levels are not supportive of high viral gene expression, suggesting specific host determinants effecting viral infection. We developed a model to predict NOIVGR from cellular parameters, which supports the notion that viral gene expression is tightly linked to the NOIVGR in single-cells. Our results support the hypothesis that the stochastic nature of viral infection and host cell determinants contribute together to the variability observed among infected cells. PMID:27923068

  4. Gene Expression Correlates with the Number of Herpes Viral Genomes Initiating Infection in Single Cells.

    PubMed

    Cohen, Efrat M; Kobiler, Oren

    2016-12-01

    Viral gene expression varies significantly among genetically identical cells. The sources of these variations are not well understood and have been suggested to involve both deterministic host differences and stochastic viral host interactions. For herpesviruses, only a limited number of incoming viral genomes initiate expression and replication in each infected cell. To elucidate the effect of this limited number of productively infecting genomes on viral gene expression in single cells, we constructed a set of fluorescence-expressing genetically tagged herpes recombinants. The number of different barcodes originating from a single cell is a good representative of the number of incoming viral genomes replicating (NOIVGR) in that cell. We identified a positive correlation between the NOIVGR and viral gene expression, as measured by the fluorescent protein expressed from the viral genome. This correlation was identified in three distinct cell-types, although the average NOIVGR per cell differed among these cell-types. Among clonal single cells, high housekeeping gene expression levels are not supportive of high viral gene expression, suggesting specific host determinants effecting viral infection. We developed a model to predict NOIVGR from cellular parameters, which supports the notion that viral gene expression is tightly linked to the NOIVGR in single-cells. Our results support the hypothesis that the stochastic nature of viral infection and host cell determinants contribute together to the variability observed among infected cells.

  5. Extensive genome heterogeneity leads to preferential allele expression and copy number-dependent expression in cultivated potato.

    PubMed

    Pham, Gina M; Newton, Linsey; Wiegert-Rininger, Krystle; Vaillancourt, Brieanne; Douches, David S; Buell, C Robin

    2017-09-04

    Relative to homozygous diploids, the presence of multiple homologs or homeologs in polyploids affords greater tolerance to mutations that can impact genome evolution. In this study, we describe sequence and structural variation in the genomes of six accessions of cultivated potato (Solanum tuberosum L.), a vegetatively propagated autotetraploid, and their impact on the transcriptome. Sequence diversity was high with a mean SNP rate of approximately 1 per 50 bases suggestive of high levels of allelic diversity. Additive gene expression was observed in leaves (3,605 genes) and tubers (6,156 genes) that contrasted the preferential allele expression of between 2,180 and 3,502 and 3,367 and 5,270 genes in the leaf and tuber transcriptome, respectively. Preferential allele expression was significantly associated with evolutionarily conserved genes suggesting selection of specific alleles of genes responsible for biological processes common to angiosperms during the breeding selection process. Copy number variation was rampant with between 16,098 and 18,921 genes in each cultivar exhibiting duplication or deletion. Copy number variable genes tended to be evolutionarily recent, lowly expressed, and enriched in genes that show increased expression in response to biotic and abiotic stress treatments suggestive of a role in adaptation. Gene copy number impacts on gene expression were detected with 528 genes having correlations between copy number and gene expression. Collectively, these data suggest that in addition to allelic variation of coding sequence, the heterogenous nature of the tetraploid potato genome contributes to a highly dynamic transcriptome impacted by allele preferential and copy number-dependent expression effects. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  6. qPCR for quantification of transgene expression and determination of transgene copy number.

    PubMed

    Fletcher, Stephen J

    2014-01-01

    Quantitative real-time PCR (qPCR) is a mature technology that can be used to accurately quantify the number of copies of a target nucleic acid in a sample. Here, we describe a method for using this technology to determine the copy number of a transgene stably integrated into a plant's genome and to ascertain the level of transgene expression.

  7. Prediction of Microporosity in Complex Thin-Wall Castings with the Dimensionless Niyama Criterion

    PubMed Central

    Kang, Maodong; Gao, Haiyan; Wang, Jun; Ling, Lishibao; Sun, Baode

    2013-01-01

    The dimensionless Niyama criterion was used to predict the formation of microporosity in nickel-based superalloy casting, which extended the model application from a simple plate casting to complex thin-wall superalloy casting. The physical characteristics of the superalloy were calculated by JMatPro software. The relation between the volume percentage of microporosity and the dimensionless Niyama values were constructed. Quantitative metallographic measurements of the microporosity of the practical thin-wall casting were carried out. The prediction agreed well with the experiment in general, except for some thick-wall sites in the casting. PMID:28809243

  8. Prediction of Shrinkage Pore Volume Fraction Using a Dimensionless Niyama Criterion

    NASA Astrophysics Data System (ADS)

    Carlson, Kent D.; Beckermann, Christoph

    2009-01-01

    A method is presented to use a dimensionless form of the well-known Niyama criterion to directly predict the amount of shrinkage porosity that forms during solidification of metal alloy castings. The main advancement offered by this method is that it avoids the need to know the threshold Niyama value below which shrinkage porosity forms; such threshold values are generally unknown and alloy dependent. The dimensionless criterion accounts for both the local thermal conditions (as in the original Niyama criterion) and the properties and solidification characteristics of the alloy. Once a dimensionless Niyama criterion value is obtained from casting simulation results, the corresponding shrinkage pore volume fraction can be determined knowing only the solid fraction-temperature curve and the total solidification shrinkage of the alloy. Curves providing the shrinkage pore volume percentage as a function of the dimensionless Niyama criterion are given for WCB steel, aluminum alloy A356, and magnesium alloy AZ91D. The present method is used in a general-purpose casting simulation software package to predict shrinkage porosity in three-dimensional (3-D) castings. Comparisons between simulated and experimental shrinkage porosity results for a WCB steel plate casting demonstrate that this method can reasonably predict shrinkage. Additional simulations for magnesium alloy AZ91D illustrate that this method is applicable to a wide variety of alloys and casting conditions.

  9. Relationship between mitochondrial DNA Copy Number and SIRT1 Expression in Porcine Oocytes

    PubMed Central

    Sato, Daichi; Itami, Nobuhiko; Tasaki, Hidetaka; Takeo, Shun; Kuwayama, Takehito; Iwata, Hisataka

    2014-01-01

    The present study assessed the effect of resveratrol on the expression of SIRT1 and mitochondrial quality and quantity in porcine oocytes. Supplementing the maturation medium with 20 µM resveratrol increased the expression of SIRT1, and enhanced mitochondrial functions, as observed from the increased ATP content and mitochondrial membrane potential. Addition of resveratrol also improved the ability of oocytes to develop into the blastocyst stage following activation. The effects of resveratrol on mitochondrial number were examined by comparing the mitochondrial DNA copy number (Mt number) between group of oocytes collected from the same donor gilt ovaries. Supplementing the maturation medium with only resveratrol did not affect the Mt number in the oocytes. However, supplementing the maturation medium with 10 µM MG132, a proteasome inhibitor, significantly increased the amount of ubiquitinated proteins and Mt number by 12 and 14%, respectively. In addition, when resveratrol was added to the medium containing MG132, the Mt number increased significantly by 39%, this effect was diminished by the addition of the SIRT1 inhibitor EX527. Furthermore, supplementing the medium with MG132 and EX527 did not affect Mt number. The mean SIRT1 expression in 20 oocytes was significantly and positively correlated with the Mt number in oocytes collected from the same donor. This study suggests that the expression of SIRT1 is associated with the Mt number in oocytes. In addition, activation of SIRT1 by resveratrol enhances the biosynthesis and degradation of mitochondria in oocytes, thereby replenishing and improving mitochondrial function and the developmental ability of oocytes. PMID:24747689

  10. Somatic Copy Number Alterations at Oncogenic Loci Show Diverse Correlations with Gene Expression

    NASA Astrophysics Data System (ADS)

    Roszik, Jason; Wu, Chang-Jiun; Siroy, Alan E.; Lazar, Alexander J.; Davies, Michael A.; Woodman, Scott E.; Kwong, Lawrence N.

    2016-01-01

    Somatic copy number alterations (SCNAs) affecting oncogenic drivers have a firmly established role in promoting cancer. However, no agreed-upon standard exists for calling locus-specific amplifications and deletions in each patient sample. Here, we report the correlative analysis of copy number amplitude and length with gene expression across 6,109 samples from The Cancer Genome Atlas (TCGA) dataset across 16 cancer types. Using specificity, sensitivity, and precision-based scores, we assigned optimized amplitude and length cutoffs for nine recurrent SCNAs affecting known oncogenic drivers, using mRNA expression as a functional readout. These cutoffs captured the majority of SCNA-driven, highly-expression-altered samples. The majority of oncogenes required only amplitude cutoffs, as high amplitude samples were almost invariably focal; however, CDKN2A and PTEN uniquely required both amplitude and length cutoffs as primary predictors. For PTEN, these extended to downstream AKT activation. In contrast, SCNA genes located peri-telomerically or in fragile sites showed poor expression-copy number correlations. Overall, our analyses identify optimized amplitude and length cutoffs as efficient predictors of gene expression changes for specific oncogenic SCNAs, yet warn against one-size-fits-all interpretations across all loci. Our results have implications for cancer data analyses and the clinic, where copy number and mutation data are increasingly used to personalize cancer therapy.

  11. Somatic Copy Number Alterations at Oncogenic Loci Show Diverse Correlations with Gene Expression

    PubMed Central

    Roszik, Jason; Wu, Chang-Jiun; Siroy, Alan E.; Lazar, Alexander J.; Davies, Michael A; Woodman, Scott E; Kwong, Lawrence N

    2016-01-01

    Somatic copy number alterations (SCNAs) affecting oncogenic drivers have a firmly established role in promoting cancer. However, no agreed-upon standard exists for calling locus-specific amplifications and deletions in each patient sample. Here, we report the correlative analysis of copy number amplitude and length with gene expression across 6,109 samples from The Cancer Genome Atlas (TCGA) dataset across 16 cancer types. Using specificity, sensitivity, and precision-based scores, we assigned optimized amplitude and length cutoffs for nine recurrent SCNAs affecting known oncogenic drivers, using mRNA expression as a functional readout. These cutoffs captured the majority of SCNA-driven, highly-expression-altered samples. The majority of oncogenes required only amplitude cutoffs, as high amplitude samples were almost invariably focal; however, CDKN2A and PTEN uniquely required both amplitude and length cutoffs as primary predictors. For PTEN, these extended to downstream AKT activation. In contrast, SCNA genes located peri-telomerically or in fragile sites showed poor expression-copy number correlations. Overall, our analyses identify optimized amplitude and length cutoffs as efficient predictors of gene expression changes for specific oncogenic SCNAs, yet warn against one-size-fits-all interpretations across all loci. Our results have implications for cancer data analyses and the clinic, where copy number and mutation data are increasingly used to personalize cancer therapy. PMID:26787600

  12. A HIERARCHICAL BAYESIAN MODEL FOR INFERENCE OF COPY NUMBER VARIANTS AND THEIR ASSOCIATION TO GENE EXPRESSION

    PubMed Central

    Cassese, Alberto; Guindani, Michele; Tadesse, Mahlet G.; Falciani, Francesco; Vannucci, Marina

    2014-01-01

    A number of statistical models have been successfully developed for the analysis of high-throughput data from a single source, but few methods are available for integrating data from different sources. Here we focus on integrating gene expression levels with comparative genomic hybridization (CGH) array measurements collected on the same subjects. We specify a measurement error model that relates the gene expression levels to latent copy number states which, in turn, are related to the observed surrogate CGH measurements via a hidden Markov model. We employ selection priors that exploit the dependencies across adjacent copy number states and investigate MCMC stochastic search techniques for posterior inference. Our approach results in a unified modeling framework for simultaneously inferring copy number variants (CNV) and identifying their significant associations with mRNA transcripts abundance. We show performance on simulated data and illustrate an application to data from a genomic study on human cancer cell lines. PMID:24834139

  13. Three distinct cell populations express extracellular matrix proteins and increase in number during skeletal muscle fibrosis.

    PubMed

    Chapman, Mark A; Mukund, Kavitha; Subramaniam, Shankar; Brenner, David; Lieber, Richard L

    2017-02-01

    Tissue extracellular matrix (ECM) provides structural support and creates unique environments for resident cells (Bateman JF, Boot-Handford RP, Lamandé SR. Nat Rev Genet 10: 173-183, 2009; Kjaer M. Physiol Rev 84: 649-98, 2004). However, the identities of cells responsible for creating specific ECM components have not been determined. In striated muscle, the identity of these cells becomes important in disease when ECM changes result in fibrosis and subsequent increased tissue stiffness and dysfunction. Here we describe a novel approach to isolate and identify cells that maintain the ECM in both healthy and fibrotic muscle. Using a collagen I reporter mouse, we show that there are three distinct cell populations that express collagen I in both healthy and fibrotic skeletal muscle. Interestingly, the number of collagen I-expressing cells in all three cell populations increases proportionally in fibrotic muscle, indicating that all cell types participate in the fibrosis process. Furthermore, while some profibrotic ECM and ECM-associated genes are significantly upregulated in fibrotic muscle, the fibrillar collagen gene expression profile is not qualitatively altered. This suggests that muscle fibrosis in this model results from an increased number of collagen I-expressing cells and not the initiation of a specific fibrotic collagen gene expression program. Finally, in fibrotic muscle, we show that these collagen I-expressing cell populations differentially express distinct ECM proteins-fibroblasts express the fibrillar components of ECM, fibro/adipogenic progenitors cells differentially express basal laminar proteins, and skeletal muscle progenitor cells differentially express genes important for the satellite cell.

  14. High-resolution analysis of copy number alterations and associated expression changes in ovarian tumors

    PubMed Central

    Haverty, Peter M; Hon, Lawrence S; Kaminker, Joshua S; Chant, John; Zhang, Zemin

    2009-01-01

    Background DNA copy number alterations are frequently observed in ovarian cancer, but it remains a challenge to identify the most relevant alterations and the specific causal genes in those regions. Methods We obtained high-resolution 500K SNP array data for 52 ovarian tumors and identified the most statistically significant minimal genomic regions with the most prevalent and highest-level copy number alterations (recurrent CNAs). Within a region of recurrent CNA, comparison of expression levels in tumors with a given CNA to tumors lacking that CNA and to whole normal ovary samples was used to select genes with CNA-specific expression patterns. A public expression array data set of laser capture micro-dissected (LCM) non-malignant fallopian tube epithelia and LCM ovarian serous adenocarcinoma was used to evaluate the effect of cell-type mixture biases. Results Fourteen recurrent deletions were detected on chromosomes 4, 6, 9, 12, 13, 15, 16, 17, 18, 22 and most prevalently on X and 8. Copy number and expression data suggest several apoptosis mediators as candidate drivers of the 8p deletions. Sixteen recurrent gains were identified on chromosomes 1, 2, 3, 5, 8, 10, 12, 15, 17, 19, and 20, with the most prevalent gains localized to 8q and 3q. Within the 8q amplicon, PVT1, but not MYC, was strongly over-expressed relative to tumors lacking this CNA and showed over-expression relative to normal ovary. Likewise, the cell polarity regulators PRKCI and ECT2 were identified as putative drivers of two distinct amplicons on 3q. Co-occurrence analyses suggested potential synergistic or antagonistic relationships between recurrent CNAs. Genes within regions of recurrent CNA showed an enrichment of Cancer Census genes, particularly when filtered for CNA-specific expression. Conclusion These analyses provide detailed views of ovarian cancer genomic changes and highlight the benefits of using multiple reference sample types for the evaluation of CNA-specific expression changes

  15. Common Spatial Organization of Number and Emotional Expression: A Mental Magnitude Line

    ERIC Educational Resources Information Center

    Holmes, Kevin J.; Lourenco, Stella F.

    2011-01-01

    Converging behavioral and neural evidence suggests that numerical representations are mentally organized in left-to-right orientation. Here we show that this format of spatial organization extends to emotional expression. In Experiment 1, right-side responses became increasingly faster as number (represented by Arabic numerals) or happiness…

  16. Common Spatial Organization of Number and Emotional Expression: A Mental Magnitude Line

    ERIC Educational Resources Information Center

    Holmes, Kevin J.; Lourenco, Stella F.

    2011-01-01

    Converging behavioral and neural evidence suggests that numerical representations are mentally organized in left-to-right orientation. Here we show that this format of spatial organization extends to emotional expression. In Experiment 1, right-side responses became increasingly faster as number (represented by Arabic numerals) or happiness…

  17. Effect of passage number on cellular response DNA-damaging agents: cell survival and gene expression

    SciTech Connect

    Chang-Liu, Chin-Mei; Wolschak, G.E.

    1996-03-01

    The effect of different passage numbers on plating efficiency, doubling time, cell growth, and radiation sensitivity was assessed in Syrian hamster embryo (SHE) cells. Changes in gene expression after UV or {gamma}-ray irradiation at different passage numbers were also examined. The SHE cells were maintained in culture medium for up to 64 passages. Cells were exposed to {sup 60}Co {gamma} rays or 254-m UV radiation. Differential display of cDNAs and Northern blots were used for the study of gene expression. With increasing passage number, SHE cells demonstrated decreased doubling time, increased plating efficiency, and a decreased yield in the number of cells per plate. Between passages 41 and 48 a ``crisis`` period was evident during which time cell growth in high serum (20%) was no longer optimal, and serum concentrations were reduced (to 10%) to maintain cell growth. Sensitivity to ionizing radiation was no different between early- and intermediate-passage cells. However, after UV exposure at low passages (passage 3), confluent cells were more sensitive to the killing effects of UV than were log-phase cells. At intermediate passages (passages 43, 48), confluent cells were slightly more radioresistant- than were log-phase cells. By passage 64, however, both confluent and log-phase cells showed similar patterns of UV sensitivity. Expression of {gamma}-actin, PCNA, and p53 transcripts did not change following UV exposure. p53 mRNA was induced following {gamma}-ray exposure of the intermediate (passage 45) epithelial cells. Differential display, however, revealed changes in expression of several transcripts following exposure to ionizing and ultraviolet radiations. The observed differences in radiation sensitivity associated with increasing passage number may be influenced by radiation-induced gene expression. We are conducting experiments to identify these genes.

  18. Integration of DNA Copy Number Alterations and Transcriptional Expression Analysis in Human Gastric Cancer

    PubMed Central

    Coral, Ho; Yuen, Siu Tsan; Chu, Kent Man; Law, Simon; Zhang, Lianhai; Ji, Jiafu; Leung, Suet Yi; Chen, Xin

    2012-01-01

    Background Genomic instability with frequent DNA copy number alterations is one of the key hallmarks of carcinogenesis. The chromosomal regions with frequent DNA copy number gain and loss in human gastric cancer are still poorly defined. It remains unknown how the DNA copy number variations contributes to the changes of gene expression profiles, especially on the global level. Principal Findings We analyzed DNA copy number alterations in 64 human gastric cancer samples and 8 gastric cancer cell lines using bacterial artificial chromosome (BAC) arrays based comparative genomic hybridization (aCGH). Statistical analysis was applied to correlate previously published gene expression data obtained from cDNA microarrays with corresponding DNA copy number variation data to identify candidate oncogenes and tumor suppressor genes. We found that gastric cancer samples showed recurrent DNA copy number variations, including gains at 5p, 8q, 20p, 20q, and losses at 4q, 9p, 18q, 21q. The most frequent regions of amplification were 20q12 (7/72), 20q12–20q13.1 (12/72), 20q13.1–20q13.2 (11/72) and 20q13.2–20q13.3 (6/72). The most frequent deleted region was 9p21 (8/72). Correlating gene expression array data with aCGH identified 321 candidate oncogenes, which were overexpressed and showed frequent DNA copy number gains; and 12 candidate tumor suppressor genes which were down-regulated and showed frequent DNA copy number losses in human gastric cancers. Three networks of significantly expressed genes in gastric cancer samples were identified by ingenuity pathway analysis. Conclusions This study provides insight into DNA copy number variations and their contribution to altered gene expression profiles during human gastric cancer development. It provides novel candidate driver oncogenes or tumor suppressor genes for human gastric cancer, useful pathway maps for the future understanding of the molecular pathogenesis of this malignancy, and the construction of new therapeutic

  19. Glutathione S-transferase Copy Number Variation Alters Lung Gene Expression

    PubMed Central

    Butler, Marcus W.; Hackett, Neil R; Salit, Jacqueline; Strulovici-Barel, Yael; Omberg, Larsson; Mezey, Jason; Crystal, Ronald G.

    2011-01-01

    Summary Background The glutathione S-transferase (GST) enzymes catalyze the conjugation of xenobiotics to glutathione. Based on reports that inherited copy number variations (CNV) modulate some GST gene expression levels, and that the small airway epithelium (SAE) and alveolar macrophages (AM) are involved early in the pathogenesis of smoking-induced lung disease, we asked: do germline CNVs modulate GST expression levels in SAE and AM? Methods Microarrays were used to survey GST gene expression in SAE and AM obtained by bronchoscopy from current smokers and nonsmokers, and to determine CNV genotypes. Results Twenty six % of subjects were null for both GSTM1 alleles, with reduced GSTM1 mRNA levels seen in both SAE and AM. Thirty % of subjects had homozygous deletions of GSTT1 with reduced mRNA levels in both tissues. Interestingly, GSTT2B, exhibited homozygous deletion in blood in 27% of subjects and was not expressed in SAE in the remainder of subjects but was expressed in AM of heterozygotes and wild type subjects, proportionate to genotype. Conclusions These data show a germline CNV-mediated linear relationship of genotype to expression level suggesting minimal compensation of gene expression levels in heterozygotes consistent with GST polymorphisms playing a role in the risk of smoking-associated xenobiotic-induced lung disease. PMID:21349909

  20. Copy Number Deletion Has Little Impact on Gene Expression Levels in Racehorses

    PubMed Central

    Park, Kyung-Do; Kim, Hyeongmin; Hwang, Jae Yeon; Lee, Chang-Kyu; Do, Kyoung-Tag; Kim, Heui-Soo; Yang, Young-Mok; Kwon, Young-jun; Kim, Jaemin; Kim, Hyeon Jeong; Song, Ki-Duk; Oh, Jae-Don; Kim, Heebal; Cho, Byung-Wook; Cho, Seoae; Lee, Hak-Kyo

    2014-01-01

    Copy number variations (CNVs), important genetic factors for study of human diseases, may have as large of an effect on phenotype as do single nucleotide polymorphisms. Indeed, it is widely accepted that CNVs are associated with differential disease susceptibility. However, the relationships between CNVs and gene expression have not been characterized in the horse. In this study, we investigated the effects of copy number deletion in the blood and muscle transcriptomes of Thoroughbred racing horses. We identified a total of 1,246 CNVs of deletion polymorphisms using DNA re-sequencing data from 18 Thoroughbred racing horses. To discover the tendencies between CNV status and gene expression levels, we extracted CNVs of four Thoroughbred racing horses of which RNA sequencing was available. We found that 252 pairs of CNVs and genes were associated in the four horse samples. We did not observe a clear and consistent relationship between the deletion status of CNVs and gene expression levels before and after exercise in blood and muscle. However, we found some pairs of CNVs and associated genes that indicated relationships with gene expression levels: a positive relationship with genes responsible for membrane structure or cytoskeleton and a negative relationship with genes involved in disease. This study will lead to conceptual advances in understanding the relationship between CNVs and global gene expression in the horse. PMID:25178379

  1. Explicit analytical expression for the condition number of polynomials in power form

    NASA Astrophysics Data System (ADS)

    Rack, Heinz-Joachim

    2017-07-01

    In his influential papers [1-3] W. Gautschi has defined and reshaped the condition number κ∞ of polynomials Pn of degree ≤ n which are represented in power form on a zero-symmetric interval [-ω, ω]. Basically, κ∞ is expressed as the product of two operator norms: an explicit factor times an implicit one (the l∞-norm of the coefficient vector of the n-th Chebyshev polynomial of the first kind relative to [-ω, ω]). We provide a new proof, economize the second factor and express it by an explicit analytical formula.

  2. On dimensionless parameters for generalization pressure head and flow rate characteristics of centrifugal disk pumps

    NASA Astrophysics Data System (ADS)

    Naumov, I. E.; Prikhodko, Yu. M.; Chekhov, V. P.; Fomichev, V. P.

    2012-03-01

    Experimental study was performed for operation of a centrifugal disk pump at atmospheric air pressure. The dimensionless parameters were developed for generalization of experimental data on flow rate and head of the pump. The method for calculation of a pumping curve and throttling characteristic was offered through use of semiemperical generalization formulas. The method ensures a good accuracy in calculations, which is proved by comparison of calculation and experimental data for the pump tested.

  3. A triangular model of dimensionless runoff producing rainfall hyetographs in Texas

    USGS Publications Warehouse

    Asquith, W.H.; Bumgarner, J.R.; Fahlquist, L.S.

    2003-01-01

    A synthetic triangular hyetograph for a large data base of Texas rainfall and runoff is needed. A hyetograph represents the temporal distribution of rainfall intensity at a point or over a watershed during a storm. Synthetic hyetographs are estimates of the expected time distribution for a design storm and principally are used in small watershed hydraulic structure design. A data base of more than 1,600 observed cumulative hyetographs that produced runoff from 91 small watersheds (generally less than about 50 km2) was used to provide statistical parameters for a simple triangular shaped hyetograph model. The model provides an estimate of the average hyetograph in dimensionless form for storm durations of 0 to 24 hours and 24 to 72 hours. As a result of this study, the authors concluded that the expected dimensionless cumulative hyetographs of 0 to 12 hour and 12 to 24 hour durations were sufficiently similar to be combined with minimal information loss. The analysis also suggests that dimensionless cumulative hyetographs are independent of the frequency level or return period of total storm depth and thus are readily used for many design applications. The two triangular hyetographs presented are intended to enhance small watershed design practice in applicable parts of Texas.

  4. iGC-an integrated analysis package of gene expression and copy number alteration.

    PubMed

    Lai, Yi-Pin; Wang, Liang-Bo; Wang, Wei-An; Lai, Liang-Chuan; Tsai, Mong-Hsun; Lu, Tzu-Pin; Chuang, Eric Y

    2017-01-14

    With the advancement in high-throughput technologies, researchers can simultaneously investigate gene expression and copy number alteration (CNA) data from individual patients at a lower cost. Traditional analysis methods analyze each type of data individually and integrate their results using Venn diagrams. Challenges arise, however, when the results are irreproducible and inconsistent across multiple platforms. To address these issues, one possible approach is to concurrently analyze both gene expression profiling and CNAs in the same individual. We have developed an open-source R/Bioconductor package (iGC). Multiple input formats are supported and users can define their own criteria for identifying differentially expressed genes driven by CNAs. The analysis of two real microarray datasets demonstrated that the CNA-driven genes identified by the iGC package showed significantly higher Pearson correlation coefficients with their gene expression levels and copy numbers than those genes located in a genomic region with CNA. Compared with the Venn diagram approach, the iGC package showed better performance. The iGC package is effective and useful for identifying CNA-driven genes. By simultaneously considering both comparative genomic and transcriptomic data, it can provide better understanding of biological and medical questions. The iGC package's source code and manual are freely available at https://www.bioconductor.org/packages/release/bioc/html/iGC.html .

  5. Expression, tandem repeat copy number variation and stability of four macrosatellite arrays in the human genome.

    PubMed

    Tremblay, Deanna C; Alexander, Graham; Moseley, Shawn; Chadwick, Brian P

    2010-11-15

    Macrosatellites are some of the largest variable number tandem repeats in the human genome, but what role these unusual sequences perform is unknown. Their importance to human health is clearly demonstrated by the 4q35 macrosatellite D4Z4 that is associated with the onset of the muscle degenerative disease facioscapulohumeral muscular dystrophy. Nevertheless, many other macrosatellite arrays in the human genome remain poorly characterized. Here we describe the organization, tandem repeat copy number variation, transmission stability and expression of four macrosatellite arrays in the human genome: the TAF11-Like array located on chromosomes 5p15.1, the SST1 arrays on 4q28.3 and 19q13.12, the PRR20 array located on chromosome 13q21.1, and the ZAV array at 9q32. All are polymorphic macrosatellite arrays that at least for TAF11-Like and SST1 show evidence of meiotic instability. With the exception of the SST1 array that is ubiquitously expressed, all are expressed at high levels in the testis and to a lesser extent in the brain. Our results extend the number of characterized macrosatellite arrays in the human genome and provide the foundation for formulation of hypotheses to begin assessing their functional role in the human genome.

  6. Expression, tandem repeat copy number variation and stability of four macrosatellite arrays in the human genome

    PubMed Central

    2010-01-01

    Background Macrosatellites are some of the largest variable number tandem repeats in the human genome, but what role these unusual sequences perform is unknown. Their importance to human health is clearly demonstrated by the 4q35 macrosatellite D4Z4 that is associated with the onset of the muscle degenerative disease facioscapulohumeral muscular dystrophy. Nevertheless, many other macrosatellite arrays in the human genome remain poorly characterized. Results Here we describe the organization, tandem repeat copy number variation, transmission stability and expression of four macrosatellite arrays in the human genome: the TAF11-Like array located on chromosomes 5p15.1, the SST1 arrays on 4q28.3 and 19q13.12, the PRR20 array located on chromosome 13q21.1, and the ZAV array at 9q32. All are polymorphic macrosatellite arrays that at least for TAF11-Like and SST1 show evidence of meiotic instability. With the exception of the SST1 array that is ubiquitously expressed, all are expressed at high levels in the testis and to a lesser extent in the brain. Conclusions Our results extend the number of characterized macrosatellite arrays in the human genome and provide the foundation for formulation of hypotheses to begin assessing their functional role in the human genome. PMID:21078170

  7. An optimised direct lysis method for gene expression studies on low cell numbers.

    PubMed

    Le, Anh Viet-Phuong; Huang, Dexing; Blick, Tony; Thompson, Erik W; Dobrovic, Alexander

    2015-08-05

    There is increasing interest in gene expression analysis of either single cells or limited numbers of cells. One such application is the analysis of harvested circulating tumour cells (CTCs), which are often present in very low numbers. A highly efficient protocol for RNA extraction, which involves a minimal number of steps to avoid RNA loss, is essential for low input cell numbers. We compared several lysis solutions that enable reverse transcription (RT) to be performed directly on the cell lysate, offering a simple rapid approach to minimise RNA loss for RT. The lysis solutions were assessed by reverse transcription quantitative polymerase chain reaction (RT-qPCR) in low cell numbers isolated from four breast cancer cell lines. We found that a lysis solution containing both the non-ionic detergent (IGEPAL CA-630, chemically equivalent to Nonidet P-40 or NP-40) and bovine serum albumin (BSA) gave the best RT-qPCR yield. This direct lysis to reverse transcription protocol outperformed a column-based extraction method using a commercial kit. This study demonstrates a simple, reliable, time- and cost-effective method that can be widely used in any situation where RNA needs to be prepared from low to very low cell numbers.

  8. From DNA Copy Number to Gene Expression: Local aberrations, Trisomies and Monosomies

    NASA Astrophysics Data System (ADS)

    Shay, Tal

    The goal of my PhD research was to study the effect of DNA copy number changes on gene expression. DNA copy number aberrations may be local, encompassing several genes, or on the level of an entire chromosome, such as trisomy and monosomy. The main dataset I studied was of Glioblastoma, obtained in the framework of a collaboration, but I worked also with public datasets of cancer and Down's Syndrome. The molecular basis of expression changes in Glioblastoma. Glioblastoma is the most common and aggressive type of primary brain tumors in adults. In collaboration with Prof. Hegi (CHUV, Switzerland), we analyzed a rich Glioblastoma dataset including clinical information, DNA copy number (array CGH) and expression profiles. We explored the correlation between DNA copy number and gene expression at the level of chromosomal arms and local genomic aberrations. We detected known amplification and over expression of oncogenes, as well as deletion and down-regulation of tumor suppressor genes. We exploited that information to map alterations of pathways that are known to be disrupted in Glioblastoma, and tried to characterize samples that have no known alteration in any of the studied pathways. Identifying local DNA aberrations of biological significance. Many types of tumors exhibit chromosomal losses or gains and local amplifications and deletions. A region that is aberrant in many tumors, or whose copy number change is stronger, is more likely to be clinically relevant, and not just a by-product of genetic instability. We developed a novel method that defines and prioritizes aberrations by formalizing these intuitions. The method scores each aberration by the fraction of patients harboring it, its length and its amplitude, and assesses the significance of the score by comparing it to a null distribution obtained by permutations. This approach detects genetic locations that are significantly aberrant, generating a 'genomic aberration profile' for each sample. The 'genomic

  9. ALK gene copy number gain and immunohistochemical expression status using three antibodies in neuroblastoma.

    PubMed

    Kim, Eun Kyung; Kim, Sewha

    2016-03-17

    Anaplastic lymphoma kinase (ALK) gene aberrations-such as mutations, amplifications, and copy number gains-represent a major genetic predisposition to neuroblastoma (NB). This study aimed to evaluate the correlation between ALK gene copy number status, ALK protein expression, and clinicopathological parameters. We retrospectively retrieved 30 cases of poorly differentiated NB and constructed tissue microarrays (TMAs). ALK copy number changes were assessed by fluorescence in situ hybridization (FISH) assays, and ALK immunohistochemistry (IHC) testing was performed using three different antibodies (ALK1, D5F3, and 5A4 clones). ALK amplification and copy number gain were observed in 10% (3/30) and 53.3% (16/30) of the cohort, respectively. There were positive correlations between ALK copy number and IHC positive rate in ALK1 and 5A4 antibodies (p= < 0.001 and 0.019, respectively). ALK1, D5F3, and 5A4 antibodies equally showed 100% sensitivity in detecting ALK amplification. However, the sensitivity for detecting copy number gain differed among the three antibodies, with 75% sensitivity in D5F3 and 0% sensitivity in ALK1. ALK-amplified NBs were correlated with synchronous MYCN amplification and chromosome 1p deletion. ALK IHC positivity was frequently observed in INSS stage IV and high-risk group patients. In conclusion, this study identified that an increase in the ALK copy number is a frequent genetic alteration in poorly differentiated NB. ALK-amplified NBs showed consistent ALK IHC positivity with all kinds of antibodies. In contrast, the detection performance of ALK copy number gain was antibody dependent, with the D5F3 antibody showing the best sensitivity.

  10. ALK Gene Copy Number Gain and Immunohistochemical Expression Status Using Three Antibodies in Neuroblastoma.

    PubMed

    Kim, Eun Kyung; Kim, Sewha

    2017-01-01

    Anaplastic lymphoma kinase ( ALK) gene aberrations-such as mutations, amplifications, and copy number gains-represent a major genetic predisposition to neuroblastoma (NB). This study aimed to evaluate the correlation between ALK gene copy number status, ALK protein expression, and clinicopathological parameters. We retrospectively retrieved 30 cases of poorly differentiated NB and constructed tissue microarrays (TMAs). ALK copy number changes were assessed by fluorescence in situ hybridization (FISH) assays, and ALK immunohistochemistry (IHC) testing was performed using three different antibodies (ALK1, D5F3, and 5A4 clones). ALK amplification and copy number gain were observed in 10% (3/30) and 53.3% (16/30) of the cohort, respectively. There were positive correlations between ALK copy number and IHC-positive rate in ALK1 and 5A4 antibodies ( P < 0.001 and P = 0.019, respectively). ALK1, D5F3, and 5A4 antibodies equally showed 100% sensitivity in detecting ALK amplification. However, the sensitivity for detecting copy number gain differed among the three antibodies, with 75% sensitivity in D5F3 and 0% sensitivity in ALK1. ALK-amplified NBs were correlated with synchronous MYCN amplification and chromosome 1p deletion. ALK IHC positivity was frequently observed in INSS stage IV and high-risk group patients. In conclusion, this study identified that an increase in the ALK copy number is a frequent genetic alteration in poorly differentiated NB. ALK-amplified NBs showed consistent ALK IHC positivity with all kinds of antibodies. In contrast, the detection performance of ALK copy number gain was antibody dependent, with the D5F3 antibody showing the best sensitivity.

  11. Generation of Large Numbers of Antigen-Expressing Human Dendritic Cells Using CD14-ML Technology

    PubMed Central

    Imamura, Yuya; Haruta, Miwa; Tomita, Yusuke; Matsumura, Keiko; Ikeda, Tokunori; Yuno, Akira; Hirayama, Masatoshi; Nakayama, Hideki; Mizuta, Hiroshi; Nishimura, Yasuharu; Senju, Satoru

    2016-01-01

    We previously reported a method to expand human monocytes through lentivirus-mediated introduction of cMYC and BMI1, and we named the monocyte-derived proliferating cells, CD14-ML. CD14-ML differentiated into functional DC (CD14-ML-DC) upon addition of IL-4, resulting in the generation of a large number of DC. One drawback of this method was the extensive donor-dependent variation in proliferation efficiency. In the current study, we found that introduction of BCL2 or LYL1 along with cMYC and BMI1 was beneficial. Using the improved method, we obtained CD14-ML from all samples, regardless of whether the donors were healthy individuals or cancer patients. In vitro stimulation of peripheral blood T cells with CD14-ML-DC that were loaded with cancer antigen-derived peptides led to the establishment of CD4+ and CD8+ T cell lines that recognized the peptides. Since CD14-ML was propagated for more than 1 month, we could readily conduct genetic modification experiments. To generate CD14-ML-DC that expressed antigenic proteins, we introduced lentiviral antigen-expression vectors and subjected the cells to 2 weeks of culture for drug-selection and expansion. The resulting antigen-expressing CD14-ML-DC successfully induced CD8+ T cell lines that were reactive to CMVpp65 or MART1/MelanA, suggesting an application in vaccination therapy. Thus, this improved method enables the generation of a sufficient number of DC for vaccination therapy from a small amount of peripheral blood from cancer patients. Information on T cell epitopes is not necessary in vaccination with cancer antigen-expressing CD14-ML-DC; therefore, all patients, irrespective of HLA type, will benefit from anti-cancer therapy based on this technology. PMID:27050553

  12. Generation of Large Numbers of Antigen-Expressing Human Dendritic Cells Using CD14-ML Technology.

    PubMed

    Imamura, Yuya; Haruta, Miwa; Tomita, Yusuke; Matsumura, Keiko; Ikeda, Tokunori; Yuno, Akira; Hirayama, Masatoshi; Nakayama, Hideki; Mizuta, Hiroshi; Nishimura, Yasuharu; Senju, Satoru

    2016-01-01

    We previously reported a method to expand human monocytes through lentivirus-mediated introduction of cMYC and BMI1, and we named the monocyte-derived proliferating cells, CD14-ML. CD14-ML differentiated into functional DC (CD14-ML-DC) upon addition of IL-4, resulting in the generation of a large number of DC. One drawback of this method was the extensive donor-dependent variation in proliferation efficiency. In the current study, we found that introduction of BCL2 or LYL1 along with cMYC and BMI1 was beneficial. Using the improved method, we obtained CD14-ML from all samples, regardless of whether the donors were healthy individuals or cancer patients. In vitro stimulation of peripheral blood T cells with CD14-ML-DC that were loaded with cancer antigen-derived peptides led to the establishment of CD4+ and CD8+ T cell lines that recognized the peptides. Since CD14-ML was propagated for more than 1 month, we could readily conduct genetic modification experiments. To generate CD14-ML-DC that expressed antigenic proteins, we introduced lentiviral antigen-expression vectors and subjected the cells to 2 weeks of culture for drug-selection and expansion. The resulting antigen-expressing CD14-ML-DC successfully induced CD8+ T cell lines that were reactive to CMVpp65 or MART1/MelanA, suggesting an application in vaccination therapy. Thus, this improved method enables the generation of a sufficient number of DC for vaccination therapy from a small amount of peripheral blood from cancer patients. Information on T cell epitopes is not necessary in vaccination with cancer antigen-expressing CD14-ML-DC; therefore, all patients, irrespective of HLA type, will benefit from anti-cancer therapy based on this technology.

  13. Assessment of contractility in intact ventricular cardiomyocytes using the dimensionless 'Frank-Starling Gain' index.

    PubMed

    Bollensdorff, Christian; Lookin, Oleg; Kohl, Peter

    2011-07-01

    This paper briefly recapitulates the Frank-Starling law of the heart, reviews approaches to establishing diastolic and systolic force-length behaviour in intact isolated cardiomyocytes, and introduces a dimensionless index called 'Frank-Starling Gain', calculated as the ratio of slopes of end-systolic and end-diastolic force-length relations. The benefits and limitations of this index are illustrated on the example of regional differences in Guinea pig intact ventricular cardiomyocyte mechanics. Potential applicability of the Frank-Starling Gain for the comparison of cell contractility changes upon stretch will be discussed in the context of intra- and inter-individual variability of cardiomyocyte properties.

  14. Long-term Ovariectomy Decreases Serotonin Neuron Number and Gene Expression in Free Ranging Macaques

    PubMed Central

    Bethea, Cynthia L.; Smith, Arik W.; Centeno, Maria Luisa; Reddy, Arubala P.

    2011-01-01

    The serotonin system responds to the ovarian steroid steroids, estradiol (E) and progesterone (P), in women and female animal models. In macaques, ovarian steroid administration to ovariectomized (Ovx) individuals improves serotonin neural function through actions on pivotal serotonin-related genes and proteins, such as TPH2 (tryptophan hydroxylase 2), SERT (serotonin reuptake transporter) and the 5HT1A autoreceptor. In addition, ovarian steroid administration reduces gene and protein expression in the caspase-independent pathway and reduces DNA fragmentation in serotonin neurons. This study examines the hypothesis that long-term ovariectomy will lead to a loss of serotonin neurons and compromised gene expression in serotonin neurons. Female Japanese macaques were ovariectomized or tubal-ligated (n=5/group) at 3 years of age and returned to their natal troop. After 3 years, the animals were collected, administered a fenfluramine challenge to determine global serotonin availability and then euthanized. Fev, TPH2, SERT and 5HT1A expression were examined with digoxigenin in situ hybridization (dig-ISH) and quantitative image analysis. Cell number, positive pixel area and average pixel density were determined. In the Ovx group, Fev, TPH2, SERT and 5HT1A showed a significant decease in average and total cell number and positive pixel area. The reduction in Fev-positive neurons suggests that there were fewer serotonin neurons in Ovx animals compared to ovary-intact animals. Compared to ovary-intact animals, SERT also showed a decrease in positive-pixel density. The decrease in TPH2 in the Ovx animals was consistent with earlier results in 5-month Ovx animals, but it may be due to the decrease in cell number rather than a decrease in expression on an individual cell basis. The decrease in SERT and 5HT1A in long-term Ovx differed from previous studies in short-term Ovx. In summary, long-term ovarian steroid loss resulted in fewer serotonin neurons and overall lower Fev

  15. Inference of plasmid-copy-number mean and noise from single-cell gene expression data

    NASA Astrophysics Data System (ADS)

    Ghozzi, Stéphane; Wong Ng, Jérôme; Chatenay, Didier; Robert, Jérôme

    2010-11-01

    Plasmids are extrachromosomal DNA molecules which code for their own replication. We previously reported a setup using genes coding for fluorescent proteins of two colors that allowed us, using a simple model, to extract the plasmid-copy-number noise in a monoclonal population of bacteria [J. Wong Ng , Phys. Rev. E 81, 011909 (2010)10.1103/PhysRevE.81.011909]. Here we present a detailed calculation relating this noise to the measured levels of fluorescence, taking into account all sources of fluorescence fluctuations: not only the fluctuation of gene expression as in the simple model but also the growth and division of bacteria, the nonuniform distribution of their ages, the random partition of proteins at divisions, and the replication and partition of plasmids and chromosome. We show how to use the chromosome as a reference, which helps extracting the plasmid-copy-number noise in a self-consistent manner.

  16. Entropy-based cluster validation and estimation of the number of clusters in gene expression data.

    PubMed

    Novoselova, Natalia; Tom, Igor

    2012-10-01

    Many external and internal validity measures have been proposed in order to estimate the number of clusters in gene expression data but as a rule they do not consider the analysis of the stability of the groupings produced by a clustering algorithm. Based on the approach assessing the predictive power or stability of a partitioning, we propose the new measure of cluster validation and the selection procedure to determine the suitable number of clusters. The validity measure is based on the estimation of the "clearness" of the consensus matrix, which is the result of a resampling clustering scheme or consensus clustering. According to the proposed selection procedure the stable clustering result is determined with the reference to the validity measure for the null hypothesis encoding for the absence of clusters. The final number of clusters is selected by analyzing the distance between the validity plots for initial and permutated data sets. We applied the selection procedure to estimate the clustering results on several datasets. As a result the proposed procedure produced an accurate and robust estimate of the number of clusters, which are in agreement with the biological knowledge and gold standards of cluster quality.

  17. Human obesity reduces the number of hepatic leptin receptor (ob-R) expressing NK cells.

    PubMed

    Lautenbach, Anne; Breitmeier, Dirk; Kuhlmann, Susanne; Nave, Heike

    2011-01-01

    In the industrialized world, obesity is an increasing socioeconomic health problem. Obese subjects have a higher risk of developing several types of cancer. NK cells are an integral component of the innate immune system, able to destruct tumor cells. The adipokine leptin plays a crucial role in the development of obesity and its related diseases. Peripheral leptin signaling is modulated by the liver. The aim of this study was to evaluate the number of hepatic NK cells (CD56+) and the number of leptin-receptor positive (Ob-R+) cells in the livers of five normal-weight and five obese humans. Livers were removed during autopsy and accurately defined sections were stained immunohistochemically and CD56+, Ob-R+, and double-positive cells were quantified. Results revealed a dramatic reduction of NK cells and Ob-R-expressing NK cells in the livers of obese individuals. The present study demonstrates, for the first time, body-weight-dependent numbers of hepatic NK cells. This supports the hypothesis of obesity-associated alterations of immune cell numbers in different human organs.

  18. Dimensionless analysis of valveless pumping in a thick-wall elastic tube: Application to the tubular embryonic heart.

    PubMed

    Kozlovsky, Pavel; Rosenfeld, Moshe; Jaffa, Ariel J; Elad, David

    2015-06-25

    The physical mechanism that drives blood flow in the valveless tubular embryonic heart is still debatable whether it is peristaltic flow or valveless dynamic suction. Previous studies of valveless pumping were concerned with either the role of the excitation parameters or the mechanisms that generate the unidirectional outflow. In this study, a dimensionless one-dimensional (1D) analysis of the valveless pumping due to local excitation at an asymmetric longitudinal location was performed for non-uniform thick-wall elastic tubes, including tubes with local bulging and tapering. A general tube law that accounts for wall thicknesses was implemented for describing the physically realistic dynamics of the tube and the two-step MacCormack algorithm was utilized for the numerical analysis. A comprehensive analysis was conducted to explore the affecting roles of the system (e.g., tube geometry) and the working (e.g., Strouhal number and flow friction parameter) parameters on the net outflow of the pump. The maximal positive net outflow in all the tested cases always occurred when the natural Strouhal number was about π. Flow reversals were observed only for relatively low friction parameters. A local bulging at the site of excitation and thick walls contributed to larger outflows, while tube tapering reduced the net outflow.

  19. Integrative analysis of gene expression and copy number alterations using canonical correlation analysis

    PubMed Central

    2010-01-01

    Background With the rapid development of new genetic measurement methods, several types of genetic alterations can be quantified in a high-throughput manner. While the initial focus has been on investigating each data set separately, there is an increasing interest in studying the correlation structure between two or more data sets. Multivariate methods based on Canonical Correlation Analysis (CCA) have been proposed for integrating paired genetic data sets. The high dimensionality of microarray data imposes computational difficulties, which have been addressed for instance by studying the covariance structure of the data, or by reducing the number of variables prior to applying the CCA. In this work, we propose a new method for analyzing high-dimensional paired genetic data sets, which mainly emphasizes the correlation structure and still permits efficient application to very large data sets. The method is implemented by translating a regularized CCA to its dual form, where the computational complexity depends mainly on the number of samples instead of the number of variables. The optimal regularization parameters are chosen by cross-validation. We apply the regularized dual CCA, as well as a classical CCA preceded by a dimension-reducing Principal Components Analysis (PCA), to a paired data set of gene expression changes and copy number alterations in leukemia. Results Using the correlation-maximizing methods, regularized dual CCA and PCA+CCA, we show that without pre-selection of known disease-relevant genes, and without using information about clinical class membership, an exploratory analysis singles out two patient groups, corresponding to well-known leukemia subtypes. Furthermore, the variables showing the highest relevance to the extracted features agree with previous biological knowledge concerning copy number alterations and gene expression changes in these subtypes. Finally, the correlation-maximizing methods are shown to yield results which are more

  20. Development of small high-copy-number plasmid vectors for gene expression in Caulobacter crescentus.

    PubMed

    Umelo-Njaka, E; Nomellini, J F; Yim, H; Smit, J

    2001-07-01

    Caulobacter crescentus is a bacterium with a distinctive life cycle and so it is studied as a cell development model. In addition, we have adapted this bacterium for recombinant protein production and display based on the crystalline surface protein (S)-layer and its C-terminal secretion signal. We report here the development of small, high-copy-number plasmid vectors and methods for producing an obligate expression host. The vectors are based on a narrow-host-range colE1-replicon-based plasmid commonly used in Escherichia coli, to which was added the replication origin of the IncQ plasmid RSF1010. C. crescentus strains were modified to enable plasmid replication by introduction of the RSF1010 repBAC genes at the recA locus. The small (4.0-4.5 kb) plasmids were in high copy numbers in both C. crescentus and E. coli and amenable to rapid methods for plasmid isolation and DNA sequencing. The method for introducing repBAC is suitable for other C. crescentus strains or any bacterium with an adequately homologous recA gene. Application of the vector for protein expression, based on the type I secretion system of the S-layer protein, when compared to constructs in broad-host-range plasmids, resulted in reduced time and steps required from clone construction to recombinant protein recovery and increased protein yield.

  1. Dimensionless, Scale Invariant, Edge Weight Metric for the Study of Complex Structural Networks.

    PubMed

    Colon-Perez, Luis M; Spindler, Caitlin; Goicochea, Shelby; Triplett, William; Parekh, Mansi; Montie, Eric; Carney, Paul R; Price, Catherine; Mareci, Thomas H

    2015-01-01

    High spatial and angular resolution diffusion weighted imaging (DWI) with network analysis provides a unique framework for the study of brain structure in vivo. DWI-derived brain connectivity patterns are best characterized with graph theory using an edge weight to quantify the strength of white matter connections between gray matter nodes. Here a dimensionless, scale-invariant edge weight is introduced to measure node connectivity. This edge weight metric provides reasonable and consistent values over any size scale (e.g. rodents to humans) used to quantify the strength of connection. Firstly, simulations were used to assess the effects of tractography seed point density and random errors in the estimated fiber orientations; with sufficient signal-to-noise ratio (SNR), edge weight estimates improve as the seed density increases. Secondly to evaluate the application of the edge weight in the human brain, ten repeated measures of DWI in the same healthy human subject were analyzed. Mean edge weight values within the cingulum and corpus callosum were consistent and showed low variability. Thirdly, using excised rat brains to study the effects of spatial resolution, the weight of edges connecting major structures in the temporal lobe were used to characterize connectivity in this local network. The results indicate that with adequate resolution and SNR, connections between network nodes are characterized well by this edge weight metric. Therefore this new dimensionless, scale-invariant edge weight metric provides a robust measure of network connectivity that can be applied in any size regime.

  2. Dimensionless factors for an alternating-current non-thermal arc plasma

    NASA Astrophysics Data System (ADS)

    Zhang, Si-Yuan; Li, Xiao-Song; Liu, Jin-Bao; Liu, Jing-Lin; Li, He-Ping; Zhu, Ai-Min

    2016-12-01

    A gliding arc discharge, as a source of warm plasma combining advantages of both thermal and cold plasmas, would have promising application prospects in the fields of fuel conversion, combustion enhancement, material synthesis, surface modifications, pollution control, etc. In order to gain insight into the features of an alternating-current gliding arc discharge plasma, three dimensionless factors, i.e., the extinction span (ψ), current lag (δ), and heating lag (χ) factors are proposed in this letter based on the measured waveforms of the discharge voltage and current in an AC gliding arc discharge plasma. The influences of the driving frequency of the power supply (f) on these three dimensionless parameters are investigated experimentally with the explanations on the physical meanings of these factors. The experimental results show that a higher value of f would lead to the lower values of ψ and δ, as well as a higher value of χ. These experimental phenomena indicate a lower threshold ignition voltage of the discharges, a lower current-growth inertia of the gliding arcs and a larger relative thermal inertia of the plasmas with increase the driving frequency of the power supply in the operating parameter range studied in this letter.

  3. A Numerical Investigation to Identify Dimensionless Parameters for Dual-Rotor Horizontal Axis Wind Turbines

    NASA Astrophysics Data System (ADS)

    Slew, K. Lee; Miller, M.; Matida, E.

    2016-09-01

    A numerical study was carried out to identify non-dimensional parameters for dual-rotor horizontal axis wind turbines (DRWTs). Based on some important DRWT parameters such as the rotor speeds, rotor diameters and the distance between the rotors, three dimensionless parameters were derived from the Buckingham Pi theorem. Hypothetical DRWT models were created using geometrically-scaled National Renewable Energy Laboratory (NREL) Phase VI rotor geometry and operating conditions in order to confirm the validity of these parameters. The performance of each turbine was simulated using DR_HAWT, an inhouse prediction tool for single and dual-rotor wind turbines created by the current authors. The variation in normalized output power as a function of the dimensionless parameters suggests that an improved performance of DRWTs can be obtained at lower diameter and gap ratios. The NREL Phase VI rotor equipped with a 5 m geometrically-scaled upwind rotor can generate about 88% of the combined power output of two equivalent single-rotors. In addition, the effect of having an auxiliary upwind rotor reduces the angle of attack along the inboard section of the downwind blade.

  4. Dimensionless, Scale Invariant, Edge Weight Metric for the Study of Complex Structural Networks

    PubMed Central

    Colon-Perez, Luis M.; Spindler, Caitlin; Goicochea, Shelby; Triplett, William; Parekh, Mansi; Montie, Eric; Carney, Paul R.; Price, Catherine; Mareci, Thomas H.

    2015-01-01

    High spatial and angular resolution diffusion weighted imaging (DWI) with network analysis provides a unique framework for the study of brain structure in vivo. DWI-derived brain connectivity patterns are best characterized with graph theory using an edge weight to quantify the strength of white matter connections between gray matter nodes. Here a dimensionless, scale-invariant edge weight is introduced to measure node connectivity. This edge weight metric provides reasonable and consistent values over any size scale (e.g. rodents to humans) used to quantify the strength of connection. Firstly, simulations were used to assess the effects of tractography seed point density and random errors in the estimated fiber orientations; with sufficient signal-to-noise ratio (SNR), edge weight estimates improve as the seed density increases. Secondly to evaluate the application of the edge weight in the human brain, ten repeated measures of DWI in the same healthy human subject were analyzed. Mean edge weight values within the cingulum and corpus callosum were consistent and showed low variability. Thirdly, using excised rat brains to study the effects of spatial resolution, the weight of edges connecting major structures in the temporal lobe were used to characterize connectivity in this local network. The results indicate that with adequate resolution and SNR, connections between network nodes are characterized well by this edge weight metric. Therefore this new dimensionless, scale-invariant edge weight metric provides a robust measure of network connectivity that can be applied in any size regime. PMID:26173147

  5. Characteristic thermal constant and dimensionless heating rate. The links to optimum heating rate in GC

    PubMed

    Blumberg; Klee

    2000-09-01

    An initial step in the quest of deriving a generalized approach to optimization of a temperature program in gas chromatography is presented. Central to this is the introduction of a dimensionless heating rate, r. As a first step to defining r, a characteristic thermal constant, thetachar, defined as thetachar = -dT/dk at k = 1, where T and k are, respectively, column temperature and solute retention factor, is introduced and evaluated for our own experimental data and for thermodynamic data from the literature. It was determined that, for silicone stationary phases with a phase ratio of 250, thetachar ranged from about 23 degrees C for low molecular weight hydrocarbons such as dimethylpropane to about 45 degrees C for high molecular weight pesticides such as mirex. It was also found that, for a particular solute and a stationary phase type, a 2 orders of magnitude increase in the film thickness caused only about a 2-fold increase in the characteristic thermal constant. Using thetachar as a fundamental temperature unit in GC and void time as a fundamental time unit, a dimensionless heating rate is introduced and its potential utility for the evaluation of the separation-speed tradeoffs in a temperature-programmed GC is demonstrated.

  6. Comparative analysis of animal growth: a primate continuum revealed by a new dimensionless growth rate coefficient.

    PubMed

    Vinicius, Lucio; Mumby, Hannah S

    2013-05-01

    The comparative analysis of animal growth still awaits full integration into life-history studies, partially due to the difficulty of defining a comparable measure of growth rate across species. Using growth data from 50 primate species, we introduce a modified "general growth model" and a dimensionless growth rate coefficient β that controls for size scaling and phylogenetic effects in the distribution of growth rates. Our results contradict the prevailing idea that slow growth characterizes primates as a group: the observed range of β values shows that not all primates grow slowly, with galago species exhibiting growth rates similar or above the mammalian average, while other strepsirrhines and most New World monkeys show limited reduction in growth rates. Low growth rate characterizes apes and some papionines. Phylogenetic regressions reveal associations between β and life-history variables, providing tests for theories of primate growth evolution. We also show that primate slow growth is an exclusively postnatal phenomenon. Our study exemplifies how the dimensionless approach promotes the integration of growth rate data into comparative life-history analysis, and demonstrates its potential applicability to other cases of adaptive diversification of animal growth patterns.

  7. Multi-objective optimization and design for free piston Stirling engines based on the dimensionless power

    NASA Astrophysics Data System (ADS)

    Mou, Jian; Hong, Guotong

    2017-02-01

    In this paper, the dimensionless power is used to optimize the free piston Stirling engines (FPSE). The dimensionless power is defined as a ratio of the heat power loss and the output work. The heat power losses include the losses of expansion space, heater, regenerator, cooler and the compression space and every kind of the heat loss calculated by empirical formula. The output work is calculated by the adiabatic model. The results show that 82.66% of the losses come from the expansion space and 54.59% heat losses of expansion space come from the shuttle loss. At different pressure the optimum bore-stroke ratio, heat source temperature, phase angle and the frequency have different values, the optimum phase angles increase with the increase of pressure, but optimum frequencies drop with the increase of pressure. However, no matter what the heat source temperature, initial pressure and frequency are, the optimum ratios of piston stroke and displacer stroke all about 0.8. The three-dimensional diagram is used to analyse Stirling engine. From the three-dimensional diagram the optimum phase angle, frequency and heat source temperature can be acquired at the same time. This study offers some guides for the design and optimization of FPSEs.

  8. Coelomocyte numbers and expression of HSP70 in wounded sea stars during hypoxia.

    PubMed

    Holm, Kristina; Hernroth, Bodil; Thorndyke, Michael

    2008-11-01

    Hypoxia, mainly caused by eutrophication, is a common and growing problem on marine soft bottoms. Echinoderms are known for their ability to regenerate tissue after wounding but hypoxia has a negative influence on regeneration and also on reproduction in echinoderms. We have investigated the cellular and molecular responses to wounding stress and hypoxia in the sea star Asterias rubens by using the total coelomocyte count (TCC) and the expression of heat shock proteins (HSPs). As early as 1 h after wounding, sea stars under hypoxic conditions show significantly increased TCC and, after 6 h, cell numbers increase approximately two-fold. After a 3-h hypoxia exposure of wounded animals, Western blot analysis reveals highly elevated coelomocyte cytoplasmic HSP70 expression. Non-wounded sea stars exposed to hypoxia and wounded animals kept in normoxia show enhanced HSP70 expression only after 24 h. Immunocytochemical analysis has not demonstrated any translocation of HSP70 from the cytoplasm to the nucleus. We conclude that both wounding and hypoxia elicit a stress response in sea stars and that the combined stress produces synergistic effects that may inhibit the initial processes of wound healing and regeneration.

  9. EGFR expression and copy number changes in low T-stage oral squamous cell carcinomas.

    PubMed

    Rössle, Matthias; Weber, Claudia S; Züllig, Lena; Graf, Nicole; Jochum, Wolfram; Stöckli, Sandro J; Moch, Holger; Huber, Gerhard F

    2013-08-01

    EGFR-directed therapies are used to treat patients with advanced head and neck squamous cell carcinoma (SCC). As it is still unclear whether or not EGFR amplification represents an early or late event in head and neck SCC progression, we aimed to determine the frequency of abnormalities of EGFR protein and gene copy numbers in early oral SCC. A tissue microarray of cancer tissue from 120 patients with pT1/2 oral SCC was constructed. We investigated EGFR protein expression by immunohistochemistry. EGFR gene copy enumeration was performed using fluorescence in-situ hybridization (FISH) and the novel automated silver in-situ hybridization (SISH) technology. Of early oral SCC, 19.3% showed high, 57.1% moderate and 23.6% low EGFR expression. EGFR amplification/polysomy was identified in 8% and 9% of cases by FISH and SISH, respectively. EGFR-SISH had a high concordance with EGFR-FISH (kappa value = 1.0), and both methods showed high conformity with EGFR immunohistochemistry (P = 0.001 and P = 0.006, respectively). No correlation was found of EGFR protein expression or gene amplification status with pT or pN stage. Only a small subgroup of early oral SCC is characterized by EGFR amplification, which can be identified reliably using EGFR-SISH technology. This finding suggests that EGFR gene amplification mostly occurs in advanced stages of oral SCC. © 2013 John Wiley & Sons Ltd.

  10. Integrated analysis of copy number variation and genome-wide expression profiling in colorectal cancer tissues.

    PubMed

    Ali Hassan, Nur Zarina; Mokhtar, Norfilza Mohd; Kok Sin, Teow; Mohamed Rose, Isa; Sagap, Ismail; Harun, Roslan; Jamal, Rahman

    2014-01-01

    Integrative analyses of multiple genomic datasets for selected samples can provide better insight into the overall data and can enhance our knowledge of cancer. The objective of this study was to elucidate the association between copy number variation (CNV) and gene expression in colorectal cancer (CRC) samples and their corresponding non-cancerous tissues. Sixty-four paired CRC samples from the same patients were subjected to CNV profiling using the Illumina HumanOmni1-Quad assay, and validation was performed using multiplex ligation probe amplification method. Genome-wide expression profiling was performed on 15 paired samples from the same group of patients using the Affymetrix Human Gene 1.0 ST array. Significant genes obtained from both array results were then overlapped. To identify molecular pathways, the data were mapped to the KEGG database. Whole genome CNV analysis that compared primary tumor and non-cancerous epithelium revealed gains in 1638 genes and losses in 36 genes. Significant gains were mostly found in chromosome 20 at position 20q12 with a frequency of 45.31% in tumor samples. Examples of genes that were associated at this cytoband were PTPRT, EMILIN3 and CHD6. The highest number of losses was detected at chromosome 8, position 8p23.2 with 17.19% occurrence in all tumor samples. Among the genes found at this cytoband were CSMD1 and DLC1. Genome-wide expression profiling showed 709 genes to be up-regulated and 699 genes to be down-regulated in CRC compared to non-cancerous samples. Integration of these two datasets identified 56 overlapping genes, which were located in chromosomes 8, 20 and 22. MLPA confirmed that the CRC samples had the highest gains in chromosome 20 compared to the reference samples. Interpretation of the CNV data in the context of the transcriptome via integrative analyses may provide more in-depth knowledge of the genomic landscape of CRC.

  11. Effects of reduced chloroplast gene copy number on chloroplast gene expression in maize.

    PubMed

    Udy, Dylan B; Belcher, Susan; Williams-Carrier, Rosalind; Gualberto, José M; Barkan, Alice

    2012-11-01

    Chloroplasts and other members of the plastid organelle family contain a small genome of bacterial ancestry. Young chloroplasts contain hundreds of genome copies, but the functional significance of this high genome copy number has been unclear. We describe molecular phenotypes associated with mutations in a nuclear gene in maize (Zea mays), white2 (w2), encoding a predicted organellar DNA polymerase. Weak and strong mutant alleles cause a moderate (approximately 5-fold) and severe (approximately 100-fold) decrease in plastid DNA copy number, respectively, as assayed by quantitative PCR and Southern-blot hybridization of leaf DNA. Both alleles condition a decrease in most chloroplast RNAs, with the magnitude of the RNA deficiencies roughly paralleling that of the DNA deficiency. However, some RNAs are more sensitive to a decrease in genome copy number than others. The rpoB messenger RNA (mRNA) exhibited a unique response, accumulating to dramatically elevated levels in response to a moderate reduction in plastid DNA. Subunits of photosynthetic enzyme complexes were reduced more severely than were plastid mRNAs, possibly because of impaired translation resulting from limiting ribosomal RNA, transfer RNA, and ribosomal protein mRNA. These results indicate that chloroplast genome copy number is a limiting factor for the expression of a subset of chloroplast genes in maize. Whereas in Arabidopsis (Arabidopsis thaliana) a pair of orthologous genes function redundantly to catalyze DNA replication in both mitochondria and chloroplasts, the w2 gene is responsible for virtually all chloroplast DNA replication in maize. Mitochondrial DNA copy number was reduced approximately 2-fold in mutants harboring strong w2 alleles, suggesting that w2 also contributes to mitochondrial DNA replication.

  12. MYC, FBXW7 and TP53 copy number variation and expression in Gastric Cancer

    PubMed Central

    2013-01-01

    Background MYC deregulation is a common event in gastric carcinogenesis, usually as a consequence of gene amplification, chromosomal translocations, or posttranslational mechanisms. FBXW7 is a p53-controlled tumor-suppressor that plays a role in the regulation of cell cycle exit and reentry via MYC degradation. Methods We evaluated MYC, FBXW7, and TP53 copy number, mRNA levels, and protein expression in gastric cancer and paired non-neoplastic specimens from 33 patients and also in gastric adenocarcinoma cell lines. We also determined the invasion potential of the gastric cancer cell lines. Results MYC amplification was observed in 51.5% of gastric tumor samples. Deletion of one copy of FBXW7 and TP53 was observed in 45.5% and 21.2% of gastric tumors, respectively. MYC mRNA expression was significantly higher in tumors than in non-neoplastic samples. FBXW7 and TP53 mRNA expression was markedly lower in tumors than in paired non-neoplastic specimens. Moreover, deregulated MYC and FBXW7 mRNA expression was associated with the presence of lymph node metastasis and tumor stage III-IV. Additionally, MYC immunostaining was more frequently observed in intestinal-type than diffuse-type gastric cancers and was associated with MYC mRNA expression. In vitro studies showed that increased MYC and reduced FBXW7 expression is associated with a more invasive phenotype in gastric cancer cell lines. This result encouraged us to investigate the activity of the gelatinases MMP-2 and MMP-9 in both cell lines. Both gelatinases are synthesized predominantly by stromal cells rather than cancer cells, and it has been proposed that both contribute to cancer progression. We observed a significant increase in MMP-9 activity in ACP02 compared with ACP03 cells. These results confirmed that ACP02 cells have greater invasion capability than ACP03 cells. Conclusion In conclusion, FBXW7 and MYC mRNA may play a role in aggressive biologic behavior of gastric cancer cells and may be a useful

  13. The absence of numbers to express the amount may affect delay discounting with humans.

    PubMed

    Reyes-Huerta, Hugo E; Dos Santos, Cristiano V

    2016-09-01

    Human delay discounting is usually studied with experimental protocols that use symbols to express delay and amount. In order to further understand discounting, we evaluated whether the absence of numbers to represent reward amounts affects discount rate in general, and whether the magnitude effect is generalized to nonsymbolic situations in particular. In Experiment 1, human participants were exposed to a delay-discounting task in which rewards were presented using dots to represent monetary rewards (nonsymbolic); under this condition the magnitude effect did not occur. Nevertheless, the magnitude effect was observed when equivalent reward amounts were presented using numbers (symbolic). Moreover, in estimation tasks, magnitude increments produced underestimation of large amounts. In Experiment 2, participants were exposed only to the nonsymbolic discounting task and were required to estimate reward amounts in each trial. Consistent with Experiment 1, the absence of numbers representing reward amounts produced similar discount rates of small and large rewards. These results suggest that value of nonsymbolic rewards is a nonlinear function of amount and that value attribution depends on perceived difference between the immediate and the delayed nonsymbolic rewards.

  14. Absolute SILAC-Compatible Expression Strain Allows Sumo-2 Copy Number Determination in Clinical Samples

    PubMed Central

    2011-01-01

    Quantitative mass spectrometry-based proteomics is a vital tool in modern life science research. In contrast to the popularity of approaches for relative protein quantitation, the widespread use of absolute quantitation has been hampered by inefficient and expensive production of labeled protein standards. To optimize production of isotopically labeled standards, we genetically modified a commonly employed protein expression Escherichia coli strain, BL21 (DE3), to construct an auxotroph for arginine and lysine. This bacterial strain allows low-cost, high-level expression of fully labeled proteins with no conversion of labeled arginine to proline. In combination with a fluorescence-based quantitation of standards and nontargeted LC–MS/MS analysis of unfractionated total cell lysates, this strain was used to determine the copy number of a post-translational modifier, small ubiquitin-like modifier (SUMO-2), in HeLa, human sperm, and chronic lymphocytic leukemia cells. By streamlining and improving the generation of labeled standards, this production system increases the breadth of absolute quantitation by mass spectrometry and will facilitate a far wider uptake of this important technique than previously possible. PMID:21830832

  15. Host Genetic Variants and Gene Expression Patterns Associated with Epstein-Barr Virus Copy Number in Lymphoblastoid Cell Lines

    PubMed Central

    Houldcroft, Charlotte J.; Petrova, Velislava; Liu, Jimmy Z.; Frampton, Dan; Anderson, Carl A.; Gall, Astrid; Kellam, Paul

    2014-01-01

    Lymphoblastoid cell lines (LCLs) are commonly used in molecular genetics, supplying DNA for the HapMap and 1000 Genomes Projects, used to test chemotherapeutic agents, and informing the basis of a number of population genetics studies of gene expression. The process of transforming human B cells into LCLs requires the presence of Epstein-Barr virus (EBV), a double-stranded DNA virus which through B-cell immortalisation maintains an episomal virus genome in every cell of an LCL at variable copy numbers. Previous studies have reported that EBV alters host-gene expression and EBV copy number may be under host genetic control. We performed a genome-wide association study of EBV genome copy number in LCLs and found the phenotype to be highly heritable, although no individual SNPs achieved a significant association with EBV copy number. The expression of two host genes (CXCL16 and AGL) was positively correlated and expression of ADARB2 was negatively correlated with EBV copy number in a genotype-independent manner. This study shows an association between EBV copy number and the gene expression profile of LCLs, and suggests that EBV copy number should be considered as a covariate in future studies of host gene expression in LCLs. PMID:25290448

  16. Mode tuning of a simplified string instrument using time-dimensionless state-derivative control

    NASA Astrophysics Data System (ADS)

    Benacchio, Simon; Chomette, Baptiste; Mamou-Mani, Adrien; Finel, Victor

    2015-01-01

    In recent years, there has been a growing interest in smart structures, particularly in the field of musical acoustics. Control methods, initially developed to reduce vibration and damage, can be a good way to shift modal parameters of a structure in order to modify its dynamic response. This study focuses on smart musical instruments and aims to modify their radiated sound. This is achieved by controlling the modal parameters of the soundboard of a simplified string instrument. A method combining a pole placement algorithm and a time-dimensionless state-derivative control is used and quickly compared to a usual state control method. Then the effect of the mode tuning on the coupling between the string and the soundboard is experimentally studied. Controlling two vibration modes of the soundboard, its acoustic response and the damping of the third partial of the sound are modified. Finally these effects are listened in the radiated sound.

  17. Escape from the Zero-Voltage State in Hysteretic Dc-Squids with Different Dimensionless Inductance

    NASA Astrophysics Data System (ADS)

    Castellano, M. G.; Intelisano, A.; Leoni, R.; Milanese, N.; Torrioli, G.; Cosmelli, C.; Carelli, P.; Chiarello, F.

    We studied the escape process from the zero-voltage state to the running state in hysteretic dc-SQUIDs made with trilayer Nb-AlOx-Nb junctions. We analyze the experimental results, according to the thermal activation model, for devices having similar parameters except for the dimensionless inductance βL, which however is always very small. The interest in hysteretic dc-SQUIDs is in the possibility of using them to perform non-invasive measurements of the flux states in rf-SQUIDs: this achievement would be very important both in tests of macroscopic quantum properties of SQUIDs and in measurements on a class of quantum bits that has been recently proposed, based on magnetic flux states in SQUIDs.

  18. Number of X-chromosome genes influences social behavior and vasopressin gene expression in mice.

    PubMed

    Cox, Kimberly H; Quinnies, Kayla M; Eschendroeder, Alex; Didrick, Paula M; Eugster, Erica A; Rissman, Emilie F

    2015-01-01

    Sex differences in behavior are widespread and often caused by hormonal differences between the sexes. In addition to hormones, the composition and numbers of the sex chromosomes also affect a variety of sex differences. In humans, X-chromosome genes are implicated in neurobehavioral disorders (i.e. fragile-X, autism). To investigate the role of X-chromosome genes in social behavior, we used a mouse model that has atypical sex chromosome configurations resembling Turner (45, XO) and Klinefelter syndromes (47, XXY). We examined a number of behaviors in juvenile mice. Mice with only one copy of most X-chromosome genes, regardless of gonadal sex, were less social in dyadic interaction and social preference tasks. In the elevated plus maze, mice with one X-chromosome spent less time in the distal ends of the open arms as compared to mice with two copies of X-chromosome genes. Using qRTPCR, we noted that amygdala from female mice with one X-chromosome had higher expression levels of vasopressin (Avp) as compared to mice in the other groups. Finally, in plasma from girls with Turner syndrome we detected reduced vasopressin (AVP) concentrations as compared to control patients. These novel findings link sex chromosome genes with social behavior via concentrations of AVP in brain, adding to our understanding of sex differences in neurobehavioral disorders.

  19. Laboratory longitudinal diffusion tests: 1. Dimensionless formulations and validity of simplified solutions.

    PubMed

    Takeda, M; Nakajima, H; Zhang, M; Hiratsuka, T

    2008-04-28

    To obtain reliable diffusion parameters for diffusion testing, multiple experiments should not only be cross-checked but the internal consistency of each experiment should also be verified. In the through- and in-diffusion tests with solution reservoirs, test interpretation of different phases often makes use of simplified analytical solutions. This study explores the feasibility of steady, quasi-steady, equilibrium and transient-state analyses using simplified analytical solutions with respect to (i) valid conditions for each analytical solution, (ii) potential error, and (iii) experimental time. For increased generality, a series of numerical analyses are performed using unified dimensionless parameters and the results are all related to dimensionless reservoir volume (DRV) which includes only the sorptive parameter as an unknown. This means the above factors can be investigated on the basis of the sorption properties of the testing material and/or tracer. The main findings are that steady, quasi-steady and equilibrium-state analyses are applicable when the tracer is not highly sorptive. However, quasi-steady and equilibrium-state analyses become inefficient or impractical compared to steady state analysis when the tracer is non-sorbing and material porosity is significantly low. Systematic and comprehensive reformulation of analytical models enables the comparison of experimental times between different test methods. The applicability and potential error of each test interpretation can also be studied. These can be applied in designing, performing, and interpreting diffusion experiments by deducing DRV from the available information for the target material and tracer, combined with the results of this study.

  20. A Double-Layered Mixture Model for the Joint Analysis of DNA Copy Number and Gene Expression Data

    PubMed Central

    Choi, Hyungwon; Qin, Zhaohui S.

    2010-01-01

    Abstract Copy number aberration is a common form of genomic instability in cancer. Gene expression is closely tied to cytogenetic events by the central dogma of molecular biology, and serves as a mediator of copy number changes in disease phenotypes. Accordingly, it is of interest to develop proper statistical methods for jointly analyzing copy number and gene expression data. This work describes a novel Bayesian inferential approach for a double-layered mixture model (DLMM) which directly models the stochastic nature of copy number data and identifies abnormally expressed genes due to aberrant copy number. Simulation studies were conducted to illustrate the robustness of DLMM under various settings of copy number aberration frequency, confounding effects, and signal-to-noise ratio in gene expression data. Analysis of a real breast cancer data shows that DLMM is able to identify expression changes specifically attributable to copy number aberration in tumors and that a sample-specific index built based on the selected genes is correlated with relevant clinical information. PMID:20170400

  1. Genes and small RNA transcripts exhibit dosage-dependent expression pattern in maize copy-number alterations

    USDA-ARS?s Scientific Manuscript database

    Copy-number alterations are widespread in animal and plant genomes, but their immediate impact on gene expression is still unclear. In animals, copy-number alterations usually exhibit dosage effects, except for sex chromosomes that tend to be dosage compensated. In plants, genes within small duplica...

  2. Cloning of intronic sequence within DsRed2 increased the number of cells expressing red fluorescent protein.

    PubMed

    Pisal, Rishikaysh V; Hrebikova, Hana; Chvatalova, Jana; Soukup, Tomas; Stanislav, Filip; Mokry, Jaroslav

    2017-08-24

    Cloning of artificial intronic sequence within the open reading frame (ORF) of DsRed2 gene. Splice prediction software was used to analyze DsRed2 sequence to find an ideal site for cloning artificial intronic sequence. Intron was cloned within DsRed2 using cyclic ligation assembly. Flow cytometry was used to quantify the number of cells expressing red fluorescence. Sequencing data confirmed precise cloning of intron at the desired position using cyclic ligation assembly. Successful expression of red fluorescence after cloning of intron confirmed successful intron recognition and splicing by host cell line. Cloning of intron increased the number of cells expressing red fluorescent protein. Cloning of intronic sequence within DsRed2 has helped to increase the number of cells expressing red fluorescence by approximately four percent.

  3. Histone Deacetylase Inhibitors Reduce the Number of Herpes Simplex Virus-1 Genomes Initiating Expression in Individual Cells

    PubMed Central

    Shapira, Lev; Ralph, Maya; Tomer, Enosh; Cohen, Shai; Kobiler, Oren

    2016-01-01

    Although many viral particles can enter a single cell, the number of viral genomes per cell that establish infection is limited. However, mechanisms underlying this restriction were not explored in depth. For herpesviruses, one of the possible mechanisms suggested is chromatinization and silencing of the incoming genomes. To test this hypothesis, we followed infection with three herpes simplex virus 1 (HSV-1) fluorescence expressing recombinants in the presence or absence of histone deacetylases inhibitors (HDACi’s). Unexpectedly, a lower number of viral genomes initiated expression in the presence of these inhibitors. This phenomenon was observed using several HDACi: Trichostatin A (TSA), Suberohydroxamic Acid, Valporic Acid, and Suberoylanilide Hydroxamic Acid. We found that HDACi presence did not change the progeny outcome from the infected cells but did alter the kinetic of the gene expression from the viral genomes. Different cell types (HFF, Vero, and U2OS), which vary in their capability to activate intrinsic and innate immunity, show a cell specific basal average number of viral genomes establishing infection. Importantly, in all cell types, treatment with TSA reduced the number of viral genomes. ND10 nuclear bodies are known to interact with the incoming herpes genomes and repress viral replication. The viral immediate early protein, ICP0, is known to disassemble the ND10 bodies and to induce degradation of some of the host proteins in these domains. HDACi treated cells expressed higher levels of some of the host ND10 proteins (promyelocytic leukemia and ATRX), which may explain the lower number of viral genomes initiating expression per cell. Corroborating this hypothesis, infection with three HSV-1 recombinants carrying a deletion in the gene coding for ICP0, show a reduction in the number of genomes being expressed in U2OS cells. We suggest that alterations in the levels of host proteins involved in intrinsic antiviral defense may result in

  4. On hydrologic similarity: A dimensionless flood frequency model using a generalized geomorphologic unit hydrograph and partial area runoff generation

    NASA Technical Reports Server (NTRS)

    Sivapalan, Murugesu; Wood, Eric F.; Beven, Keith J.

    1993-01-01

    One of the shortcomings of the original theory of the geomorphologic unit hydrograph (GUH) is that it assumes that runoff is generated uniformly from the entire catchment area. It is now recognized that in many catchments much of the runoff during storm events is produced on partial areas which usually form on narrow bands along the stream network. A storm response model that includes runoff generation on partial areas by both Hortonian and Dunne mechanisms was recently developed by the authors. In this paper a methodology for integrating this partial area runoff generation model with the GUH-based runoff routing model is presented; this leads to a generalized GUH. The generalized GUH and the storm response model are then used to estimate physically based flood frequency distributions. In most previous work the initial moisture state of the catchment had been assumed to be constant for all the storms. In this paper we relax this assumption and allow the initial moisture conditions to vary between storms. The resulting flood frequency distributions are cast in a scaled dimensionless framework where issues such as catchment scale and similarity can be conveniently addressed. A number of experiments are performed to study the sensitivity of the flood frequency response to some of the 'similarity' parameters identified in this formulation. The results indicate that one of the most important components of the derived flood frequency model relates to the specification of processes within the runoff generation model; specifically the inclusion of both saturation excess and Horton infiltration excess runoff production mechanisms. The dominance of these mechanisms over different return periods of the flood frequency distribution can significantly affect the distributional shape and confidence limits about the distribution. Comparisons with observed flood distributions seem to indicate that such mixed runoff production mechanisms influence flood distribution shape. The

  5. Effects of copy number variable regions on local gene expression in white blood cells of Mexican Americans

    PubMed Central

    Blackburn, August; Almeida, Marcio; Dean, Angela; Curran, Joanne E; Johnson, Matthew P; Moses, Eric K; Abraham, Lawrence J; Carless, Melanie A; Dyer, Thomas D; Kumar, Satish; Almasy, Laura; Mahaney, Michael C; Comuzzie, Anthony; Williams-Blangero, Sarah; Blangero, John; Lehman, Donna M; Göring, Harald H H

    2015-01-01

    Only few systematic studies on the contribution of copy number variation to gene expression variation have been published to date. Here we identify effects of copy number variable regions (CNVRs) on nearby gene expression by investigating 909 CNVRs and expression levels of 12059 nearby genes in white blood cells from Mexican-American participants of the San Antonio Family Heart Study. We empirically evaluate our ability to detect the contribution of CNVs to proximal gene expression (presumably in cis) at various window sizes (up to a 10 Mb distance) between the gene and CNV. We found a ~1-Mb window size to be optimal for capturing cis effects of CNVs. Up to 10% of the CNVs in this study were found to be significantly associated with the expression of at least one gene within their vicinity. As expected, we find that CNVs that directly overlap gene sequences have the largest effects on gene expression (compared with non-overlapping CNVRs located nearby), with positive correlation (except for a few exceptions) between estimated genomic dosage and expression level. We find that genes whose expression level is significantly influenced by nearby CNVRs are enriched for immunity and autoimmunity related genes. These findings add to the currently limited catalog of CNVRs that are recognized as expression quantitative trait loci, and have implications for future study designs as well as for prioritizing candidate causal variants in genomic regions associated with disease. PMID:25585699

  6. A dimensionless analysis of a 2DOF piezoelectric vibration energy harvester

    NASA Astrophysics Data System (ADS)

    Xiao, Han; Wang, Xu; John, Sabu

    2015-06-01

    In this study, a dimensionless analysis method is proposed to predict the output voltage and harvested power for a 2DOF vibration energy harvesting system. This method allows us to compare the harvesting power and efficiency of the 2DOF vibration energy harvesting system and to evaluate the harvesting system performance regardless the sizes or scales. The analysis method is a hybrid of time domain simulation and frequency response analysis approaches, which would be a useful tool for parametric study, design and optimisation of a 2DOF piezoelectric vibration energy harvester. In a case study, a quarter car suspension model with a piezoelectric material insert is chosen to be studied. The 2DOF vibration energy harvesting system could potentially be applied in a vehicle to convert waste or harmful ambient vibration energy into electrical energy for charging the battery. Especially for its application in a hybrid vehicle or an electrical vehicle, the 2DOF vibration energy harvesting system could improve charge mileage, comfort and reliability.

  7. Dimensionless scaling of the critical beta for onset of a neoclassical tearing mode

    SciTech Connect

    La Haye, R. J.; Buttery, R. J.; Huysmans, G. T. A.; Maraschek, M.; Wilson, H. R.

    2000-08-01

    The islands from tearing modes driven unstable and sustained by the helically perturbed neoclassical bootstrap current often provide the practical limit to long-pulse, high confinement tokamak operation. The destabilization of such ''metastable'' plasmas depends on a ''seed'' island exceeding a threshold. A database from similar regimes [high confinement H-mode with periodic edge localized modes (ELMs) and periodic central sawteeth] was compiled from the tokamaks ASDEX Upgrade (AUG) [Plasma Phys. Controlled Fusion 41, 767 (1999)], DIII-D [Nucl. Fusion 38, 987 (1998)], and JET (Joint European Torus) [Plasma Phys. Controlled Fusion 41, B1 (1999)]. A comparison is made of the measured critical beta for onset of the m/n=3/2 mode (m and n being the poloidal and toroidal Fourier harmonics, respectively) to a model in terms of dimensionless parameters for the seed and threshold islands. This modeling is then used for extrapolation to a reactor-grade tokamak design such as ITER/FDR (International Thermonuclear Experimental Reactor/Final Design Report) [Nucl. Fusion 39, 2137 (1999)]; this indicates that the seed island from sawteeth could be too small to sufficiently disturb the metastable plasma and excite the m/n=3/2 neoclassical tearing mode. (c) 2000 American Institute of Physics.

  8. Optimization of Dimensionless Figure of Merit in Oxide Thin Film Thermoelectrics

    NASA Astrophysics Data System (ADS)

    Osborne, Daniel; Huxtable, Scott; Tiwari, Ashutosh; Abiade, Jeremiah

    2010-03-01

    The ability of uniquely functional thermoelectric materials to convert waste heat directly into electricity is critical considering the global energy economy. Profitable, energy-efficient thermoelectrics possess thermoelectric figures of merit ZT >= 1. We examined the effect of metal nanoparticle -- oxide film interfaces on the thermal conductivity κ and Seebeck coefficient S in bilayer and multilayer thin film oxide thermoelectrics in an effort to improve the dimensionless figure of merit ZT. Since a thermoelectric's figure of merit ZT is directly proportional to S/κ, reducing κ and increasing S are key strategies to optimize ZT. We reduced κ by phonon scattering due to the inclusion of metal nanoparticles in the bulk of the thermoelectric thin film, and increased S due to energy-dependent electron scattering at the metal - oxide interfaces. Doped strontium titanate (STO) thin film/Au nanoparticle composites were synthesized by alternate ablation of Au and Nb-doped STO targets during pulsed laser deposition. Characterization of the thermoelectric films involve XRD, XPS, and TEM analyses, Seebeck coefficient measurements, and also measurements of the thermal conductivity via time-domain thermoreflectance. The measured thermal conductivities and Seebeck coefficients of the thin films shows a strong dependence on the nanoscale interfaces of the films.

  9. Influence of starch steeping period on dimensionless disintegration values of a paracetamol tablet formulation.

    PubMed

    Alebiowu, Gbenga; Adeyemi, Ayoade O

    2009-01-01

    In this study, tapioca starches obtained after different steeping periods, i.e. TS 24, TS 48 and TS 72, were used as disintegrants with corn starch BP as the standard disintegrant in a paracetamol tablet formulation. Two dimensionless disintegration quantities, T(N) and T(C) were used in the determination of the influence that steeping period of starch disintegrant would have on the crushing strength friability-disintegration time ratio (CSFR/DT). These quantities were used to assess the influence of steeping period, relative density and disintegrant concentration on CSFR/DT as well as to compare disintegrant efficiency. The results suggest that the CSFR/DT is more dependent on the disintegrant concentration than on steeping period and relative density. The study further showed that TS 72 is a more reliable disintegrant because its activity would not be influenced by changes in relative density of tablets. This work concludes that the T(N) would be more useful for quantitative assessment while T(C) is more relevant for qualitative assessment.

  10. Integrative genome-wide analysis reveals a robust genomic glioblastoma signature associated with copy number driving changes in gene expression.

    PubMed

    de Tayrac, Marie; Etcheverry, Amandine; Aubry, Marc; Saïkali, Stephan; Hamlat, Abderrahmane; Quillien, Veronique; Le Treut, André; Galibert, Marie-Dominique; Mosser, Jean

    2009-01-01

    Glioblastoma multiforme shows multiple chromosomal aberrations, the impact of which on gene expression remains unclear. To investigate this relationship and to identify putative initiating genomic events, we integrated a paired copy number and gene expression survey in glioblastoma using whole human genome arrays. Loci of recurrent copy number alterations were combined with gene expression profiles obtained on the same tumor samples. We identified a set of 406 "cis-acting DNA targeted genes" corresponding to genomic aberrations with direct copy-number-driving changes in gene expression, defined as genes with either significantly concordant or correlated changes in DNA copy number and expression. Functional annotation revealed that these genes participate in key processes of cancer cell biology, providing insights into the genetic mechanisms driving glioblastoma. The robustness of the gene selection was validated on an external microarray data set including 81 glioblastomas and 23 non-neoplastic brain samples. The integration of array CGH and gene expression data highlights a robust cis-acting DNA targeted genes signature that may be critical for glioblastoma progression, with two tumor suppressor genes PCDH9 and STARD13 that could be involved in tumor invasiveness and resistance to etoposide.

  11. Dimensionless Model of a Thermoelectric Cooling Device Operating at Real Heat Transfer Conditions: Maximum Cooling Capacity Mode

    NASA Astrophysics Data System (ADS)

    Melnikov, A. A.; Kostishin, V. G.; Alenkov, V. V.

    2016-09-01

    Real operating conditions of a thermoelectric cooling device are in the presence of thermal resistances between thermoelectric material and a heat medium or cooling object. They limit performance of a device and should be considered when modeling. Here we propose a dimensionless mathematical steady state model, which takes them into account. Analytical equations for dimensionless cooling capacity, voltage, and coefficient of performance (COP) depending on dimensionless current are given. For improved accuracy a device can be modeled with use of numerical or combined analytical-numerical methods. The results of modeling are in acceptable accordance with experimental results. The case of zero temperature difference between hot and cold heat mediums at which the maximum cooling capacity mode appears is considered in detail. Optimal device parameters for maximal cooling capacity, such as fraction of thermal conductance on the cold side y, fraction of current relative to maximal j' are estimated in range of 0.38-0.44 and 0.48-0.95, respectively, for dimensionless conductance K' = 5-100. Also, a method for determination of thermal resistances of a thermoelectric cooling system is proposed.

  12. Dimensionless Model of a Thermoelectric Cooling Device Operating at Real Heat Transfer Conditions: Maximum Cooling Capacity Mode

    NASA Astrophysics Data System (ADS)

    Melnikov, A. A.; Kostishin, V. G.; Alenkov, V. V.

    2017-05-01

    Real operating conditions of a thermoelectric cooling device are in the presence of thermal resistances between thermoelectric material and a heat medium or cooling object. They limit performance of a device and should be considered when modeling. Here we propose a dimensionless mathematical steady state model, which takes them into account. Analytical equations for dimensionless cooling capacity, voltage, and coefficient of performance (COP) depending on dimensionless current are given. For improved accuracy a device can be modeled with use of numerical or combined analytical-numerical methods. The results of modeling are in acceptable accordance with experimental results. The case of zero temperature difference between hot and cold heat mediums at which the maximum cooling capacity mode appears is considered in detail. Optimal device parameters for maximal cooling capacity, such as fraction of thermal conductance on the cold side y, fraction of current relative to maximal j' are estimated in range of 0.38-0.44 and 0.48-0.95, respectively, for dimensionless conductance K' = 5-100. Also, a method for determination of thermal resistances of a thermoelectric cooling system is proposed.

  13. The correlation of reproduction-related gene expression with germ cell number in DM and PLL gilts.

    PubMed

    Hu, Yan-Biao; Pan, Zeng-Xiang; Xu, Dan; Xu, Yin-Xue; Liu, Hong-Lin; Huang, Rui-Hua; Hu, Zhi-Gang

    2006-09-01

    In this study, the ovarian germ cell number was counted in 3-week-old Duroc x Meishan (DM, n=30) and PIC x (Landrace x Large White) (PLL, n=53) gilts, and the mRNA expression levels of four reproduction-related genes were investigated by quantitative RT-PCR. Correlation of germ cell number with the expression level of these genes was analyzed. Results showed that the germ cell number of DM was significantly higher than that of PLL gilts (P<0.01), although there was no significant difference between the ovarian weight of DM and PLL gilts (P=0.269). No significant correlation existed between germ cell number and ovarian weight in the two gilt groups (R=0.335, P=0.07; R=0.119, P=0.398, respectively). A significant correlation was found between the germ cell number and expression level of ESR and IGF1R mRNA in DM gilts (R=0.648, P<0.05; R=0.757, P<0.01, respectively), but the correlation between the germ cell number and expression level of FSHR and INHBA mRNA did not reach statistical significance. Significant correlation was found between the germ cell number and the expression level of ESR, FSHR, and IGF1R mRNA in PLL gilts (R=0.435, P<0.01; R=0.438, P<0.01; R=0.292, P<0.05, respectively), but not with INHBA mRNA in PLL gilts.

  14. PHOTOSPHERE EMISSION FROM A HYBRID RELATIVISTIC OUTFLOW WITH ARBITRARY DIMENSIONLESS ENTROPY AND MAGNETIZATION IN GRBs

    SciTech Connect

    Gao, He; Zhang, Bing E-mail: zhang@physics.unlv.edu

    2015-03-10

    In view of the recent Fermi observations of gamma-ray burst (GRB) prompt emission spectra, we develop a theory of photosphere emission of a hybrid relativistic outflow with a hot fireball component (defined by dimensionless entropy η) and a cold Poynting-flux component (defined by magnetization σ{sub 0} at the central engine). We consider the scenarios both without and with sub-photospheric magnetic dissipations. Based on a simplified toy model of jet dynamics, we develop two approaches: a 'bottom-up' approach to predict the temperature (for a non-dissipative photosphere) and luminosity of the photosphere emission and its relative brightness for a given pair of (η, σ{sub 0}); and a 'top-down' approach to diagnose central engine parameters (η and σ{sub 0}) based on the observed quasi-thermal photosphere emission properties. We show that a variety of observed GRB prompt emission spectra with different degrees of photosphere thermal emission can be reproduced by varying η and σ{sub 0} within the non-dissipative photosphere scenario. In order to reproduce the observed spectra, the outflows of most GRBs need to have a significant σ, both at the central engine and at the photosphere. The σ value at 10{sup 15} cm from the central engine (a possible non-thermal emission site) is usually also greater than unity, so that internal-collision-induced magnetic reconnection and turbulence (ICMART) may be the mechanism to power the non-thermal emission. We apply our top-down approach to GRB 110721A and find that the temporal evolution behavior of its blackbody component can be well interpreted with a time-varying (η, σ{sub 0}) at the central engine, instead of invoking a varying engine base size r {sub 0} as proposed by previous authors.

  15. A parametric study of wind chill equivalent temperatures by a dimensionless steady-state analysis

    NASA Astrophysics Data System (ADS)

    Shitzer, Avraham

    2006-03-01

    A first order analytical approximation of steady-state heat conduction in a hollow cylinder exchanging heat at its external surface by convection with a cold and windy environment is presented. The model depicts the thermal behavior of certain body elements, e.g., head/face, when exposed to such environments. The results are presented by dimensionless parameters and facilitate the estimation of wind chill equivalent temperatures (WCETs). The effects of several variables on determining WCETs were studied using specific examples, leading to the following generalizations: (1) the conditions assumed for "calm" wind speed appear to be a dominant factor in determining WCET; (2) the effects, on both (skin) surface temperature and on WCET, of a 1°C change in environmental temperature appear to be more pronounced than those of a 1 m/s change in wind speed; (3) similarly, predicted WCETs are more sensitive to the geometrical dimensions assumed for the modeled entity than they are to wind speeds; and (4) tissue thermal conductivity, the angle at which the convective heat transfer coefficient is measured relative to wind direction, and the factor used to establish "effective" wind speeds in the domain occupied by humans relative to reported values, all seem to have relatively small effects on the determination of WCET. These conclusions strongly suggest, among other things, that for any given combination of environmental conditions, wind chill indices may best be presented as ranges rather than as single values. This seems to apply even when worst-case scenarios are considered. Also emphasized is the need for careful and realistic selection of all the parameter values used in the determination of WCETs.

  16. A parametric study of wind chill equivalent temperatures by a dimensionless steady-state analysis.

    PubMed

    Shitzer, Avraham

    2006-03-01

    A first order analytical approximation of steady-state heat conduction in a hollow cylinder exchanging heat at its external surface by convection with a cold and windy environment is presented. The model depicts the thermal behavior of certain body elements, e.g., head/face, when exposed to such environments. The results are presented by dimensionless parameters and facilitate the estimation of wind chill equivalent temperatures (WCETs). The effects of several variables on determining WCETs were studied using specific examples, leading to the following generalizations: (1) the conditions assumed for "calm" wind speed appear to be a dominant factor in determining WCET; (2) the effects, on both (skin) surface temperature and on WCET, of a 1 degrees C change in environmental temperature appear to be more pronounced than those of a 1 m/s change in wind speed; (3) similarly, predicted WCETs are more sensitive to the geometrical dimensions assumed for the modeled entity than they are to wind speeds; and (4) tissue thermal conductivity, the angle at which the convective heat transfer coefficient is measured relative to wind direction, and the factor used to establish "effective" wind speeds in the domain occupied by humans relative to reported values, all seem to have relatively small effects on the determination of WCET. These conclusions strongly suggest, among other things, that for any given combination of environmental conditions, wind chill indices may best be presented as ranges rather than as single values. This seems to apply even when worst-case scenarios are considered. Also emphasized is the need for careful and realistic selection of all the parameter values used in the determination of WCETs.

  17. Photosphere Emission from a Hybrid Relativistic Outflow with Arbitrary Dimensionless Entropy and Magnetization in GRBs

    NASA Astrophysics Data System (ADS)

    Gao, He; Zhang, Bing

    2015-03-01

    In view of the recent Fermi observations of gamma-ray burst (GRB) prompt emission spectra, we develop a theory of photosphere emission of a hybrid relativistic outflow with a hot fireball component (defined by dimensionless entropy η) and a cold Poynting-flux component (defined by magnetization σ0 at the central engine). We consider the scenarios both without and with sub-photospheric magnetic dissipations. Based on a simplified toy model of jet dynamics, we develop two approaches: a "bottom-up" approach to predict the temperature (for a non-dissipative photosphere) and luminosity of the photosphere emission and its relative brightness for a given pair of (η, σ0) and a "top-down" approach to diagnose central engine parameters (η and σ0) based on the observed quasi-thermal photosphere emission properties. We show that a variety of observed GRB prompt emission spectra with different degrees of photosphere thermal emission can be reproduced by varying η and σ0 within the non-dissipative photosphere scenario. In order to reproduce the observed spectra, the outflows of most GRBs need to have a significant σ, both at the central engine and at the photosphere. The σ value at 1015 cm from the central engine (a possible non-thermal emission site) is usually also greater than unity, so that internal-collision-induced magnetic reconnection and turbulence (ICMART) may be the mechanism to power the non-thermal emission. We apply our top-down approach to GRB 110721A and find that the temporal evolution behavior of its blackbody component can be well interpreted with a time-varying (η, σ0) at the central engine, instead of invoking a varying engine base size r 0 as proposed by previous authors.

  18. Individual and combined effects of DNA methylation and copy number alterations on miRNA expression in breast tumors

    PubMed Central

    2013-01-01

    Background The global effect of copy number and epigenetic alterations on miRNA expression in cancer is poorly understood. In the present study, we integrate genome-wide DNA methylation, copy number and miRNA expression and identify genetic mechanisms underlying miRNA dysregulation in breast cancer. Results We identify 70 miRNAs whose expression was associated with alterations in copy number or methylation, or both. Among these, five miRNA families are represented. Interestingly, the members of these families are encoded on different chromosomes and are complementarily altered by gain or hypomethylation across the patients. In an independent breast cancer cohort of 123 patients, 41 of the 70 miRNAs were confirmed with respect to aberration pattern and association to expression. In vitro functional experiments were performed in breast cancer cell lines with miRNA mimics to evaluate the phenotype of the replicated miRNAs. let-7e-3p, which in tumors is found associated with hypermethylation, is shown to induce apoptosis and reduce cell viability, and low let-7e-3p expression is associated with poorer prognosis. The overexpression of three other miRNAs associated with copy number gain, miR-21-3p, miR-148b-3p and miR-151a-5p, increases proliferation of breast cancer cell lines. In addition, miR-151a-5p enhances the levels of phosphorylated AKT protein. Conclusions Our data provide novel evidence of the mechanisms behind miRNA dysregulation in breast cancer. The study contributes to the understanding of how methylation and copy number alterations influence miRNA expression, emphasizing miRNA functionality through redundant encoding, and suggests novel miRNAs important in breast cancer. PMID:24257477

  19. Integration of mRNA expression profile, copy number alterations, and microRNA expression levels in breast cancer to improve grade definition.

    PubMed

    Cava, Claudia; Bertoli, Gloria; Ripamonti, Marilena; Mauri, Giancarlo; Zoppis, Italo; Della Rosa, Pasquale Anthony; Gilardi, Maria Carla; Castiglioni, Isabella

    2014-01-01

    Defining the aggressiveness and growth rate of a malignant cell population is a key step in the clinical approach to treating tumor disease. The correct grading of breast cancer (BC) is a fundamental part in determining the appropriate treatment. Biological variables can make it difficult to elucidate the mechanisms underlying BC development. To identify potential markers that can be used for BC classification, we analyzed mRNAs expression profiles, gene copy numbers, microRNAs expression and their association with tumor grade in BC microarray-derived datasets. From mRNA expression results, we found that grade 2 BC is most likely a mixture of grade 1 and grade 3 that have been misclassified, being described by the gene signature of either grade 1 or grade 3. We assessed the potential of the new approach of integrating mRNA expression profile, copy number alterations, and microRNA expression levels to select a limited number of genomic BC biomarkers. The combination of mRNA profile analysis and copy number data with microRNA expression levels led to the identification of two gene signatures of 42 and 4 altered genes (FOXM1, KPNA4, H2AFV and DDX19A) respectively, the latter obtained through a meta-analytical procedure. The 42-based gene signature identifies 4 classes of up- or down-regulated microRNAs (17 microRNAs) and of their 17 target mRNA, and the 4-based genes signature identified 4 microRNAs (Hsa-miR-320d, Hsa-miR-139-5p, Hsa-miR-567 and Hsa-let-7c). These results are discussed from a biological point of view with respect to pathological features of BC. Our identified mRNAs and microRNAs were validated as prognostic factors of BC disease progression, and could potentially facilitate the implementation of assays for laboratory validation, due to their reduced number.

  20. Changes in mast cell number and stem cell factor expression in human skin after radiotherapy for breast cancer.

    PubMed

    Westbury, Charlotte B; Freeman, Alex; Rashid, Mohammed; Pearson, Ann; Yarnold, John R; Short, Susan C

    2014-05-01

    Mast cells are involved in the pathogenesis of radiation fibrosis and may be a therapeutic target. The mechanism of increased mast cell number in relation to acute and late tissue responses in human skin was investigated. Punch biopsies of skin 1 and 15-18 months after breast radiotherapy and a contralateral control biopsy were collected. Mast cells were quantified by immunohistochemistry using the markers c-Kit and tryptase. Stem cell factor (SCF) and collagen-1 expression was analysed by qRT-PCR. Clinical photographic scores were performed at post-surgical baseline and 18 months and 5 years post-radiotherapy. Primary human dermal microvascular endothelial cell (HDMEC) cultures were exposed to 2Gy ionising radiation and p53 and SCF expression was analysed by Western blotting and ELISA. Dermal mast cell numbers were increased at 1 (p=0.047) and 18 months (p=0.040) using c-Kit, and at 18 months (p=0.024) using tryptase immunostaining. Collagen-1 mRNA in skin was increased at 1 month (p=0.047) and 18 months (p=0.032) and SCF mRNA increased at 1 month (p=0.003). None of 16 cases scored had a change in photographic appearance at 5 years, compared to baseline. SCF expression was not increased in HDMECs irradiated in vitro. Increased mast cell number was associated with up-regulated collagen-1 expression in human skin at early and late time points. This increase could be secondary to elevated SCF expression at 1 month after radiotherapy. Although mast cells accumulate around blood vessels, no endothelial cell secretion of SCF was seen after in vitro irradiation. Modification of mast cell number and collagen-1 expression may be observed in skin at 1 and 18 months after radiotherapy in breast cancer patients with no change in photographic breast appearance at 5 years. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  1. Integrative analysis of copy number and transcriptional expression profiles in esophageal cancer to identify a novel driver gene for therapy

    PubMed Central

    Dong, Gaochao; Mao, Qixing; Yu, Decai; Zhang, Yi; Qiu, Mantang; Dong, Gaoyue; Chen, Qiang; Xia, Wenjie; Wang, Jie; Xu, Lin; Jiang, Feng

    2017-01-01

    An increasing amount of evidence has highlighted the critical roles that copy number variants play in cancer progression. Here, we systematically analyzed the copy number alterations and differentially transcribed genes. Integrative analysis of the association between copy number variants and differential gene expression suggested that copy number variants will lead to aberrant expression of the corresponding genes. We performed a KEGG pathway and GO analysis, which revealed that cell cycle may have an effective role in the progression of esophageal cancer. FAM60A was then screened out as a potential prognostic factor through survival analysis and correlation analysis with clinical-pathological parameters. We subsequently showed that silencing of FAM60A could inhibit esophageal carcinoma tumor cell growth, migration and invasion in vitro. Through the bioinformatic analysis, we predict that FAM60A may act as a transcriptional factor to regulate genes that are correlated with each cell cycle. In summary, we comprehensively analyzed copy number segments and transcriptional expression profiles, which provided a novel approach to identify clinical biomarkers and therapeutic targets of esophageal carcinoma. PMID:28169357

  2. Assigning numbers to the arrows: Parameterizing a gene regulation network by using accurate expression kinetics

    NASA Astrophysics Data System (ADS)

    Ronen, Michal; Rosenberg, Revital; Shraiman, Boris I.; Alon, Uri

    2002-08-01

    A basic challenge in systems biology is to understand the dynamical behavior of gene regulation networks. Current approaches aim at determining the network structure based on genomic-scale data. However, the network connectivity alone is not sufficient to define its dynamics; one needs to also specify the kinetic parameters for the regulation reactions. Here, we ask whether effective kinetic parameters can be assigned to a transcriptional network based on expression data. We present a combined experimental and theoretical approach based on accurate high temporal-resolution measurement of promoter activities from living cells by using green fluorescent protein (GFP) reporter plasmids. We present algorithms that use these data to assign effective kinetic parameters within a mathematical model of the network. To demonstrate this, we employ a well defined network, the SOS DNA repair system of Escherichia coli. We find a strikingly detailed temporal program of expression that correlates with the functional role of the SOS genes and is driven by a hierarchy of effective kinetic parameter strengths for the various promoters. The calculated parameters can be used to determine the kinetics of all SOS genes given the expression profile of just one representative, allowing a significant reduction in complexity. The concentration profile of the master SOS transcriptional repressor can be calculated, demonstrating that relative protein levels may be determined from purely transcriptional data. This finding opens the possibility of assigning kinetic parameters to transcriptional networks on a genomic scale.

  3. Genes and Small RNA Transcripts Exhibit Dosage-Dependent Expression Pattern in Maize Copy-Number Alterations.

    PubMed

    Zuo, Tao; Zhang, Jianbo; Lithio, Andrew; Dash, Sudhansu; Weber, David F; Wise, Roger; Nettleton, Dan; Peterson, Thomas

    2016-07-01

    Copy-number alterations are widespread in animal and plant genomes, but their immediate impact on gene expression is still unclear. In animals, copy-number alterations usually exhibit dosage effects, except for sex chromosomes which tend to be dosage compensated. In plants, genes within small duplications (<100 kb) often exhibit dosage-dependent expression, whereas large duplications (>50 Mb) are more often dosage compensated. However, little or nothing is known about expression in moderately-sized (1-50 Mb) segmental duplications, and about the response of small RNAs to dosage change. Here, we compared maize (Zea mays) plants with two, three, and four doses of a 14.6-Mb segment of chromosome 1 that contains ∼300 genes. Plants containing the duplicated segment exhibit dosage-dependent effects on ear length and flowering time. Transcriptome analyses using GeneChip and RNA-sequencing methods indicate that most expressed genes and unique small RNAs within the duplicated segments exhibit dosage-dependent transcript levels. We conclude that dosage effect is the predominant regulatory response for both genes and unique small RNA transcripts in the segmental dosage series we tested. To our knowledge this is the first analysis of small RNA expression in plant gene dosage variants. Because segmental duplications comprise a significant proportion of eukaryotic genomes, these findings provide important new insight into the regulation of genes and small RNAs in response to dosage changes. Copyright © 2016 by the Genetics Society of America.

  4. The Beta-Binomial Distribution for Estimating the Number of False Rejections in Microarray Gene Expression Studies.

    PubMed

    Hunt, Daniel L; Cheng, Cheng; Pounds, Stanley

    2009-03-15

    In differential expression analysis of microarray data, it is common to assume independence among null hypotheses (and thus gene expression levels). The independence assumption implies that the number of false rejections V follows a binomial distribution and leads to an estimator of the empirical false discovery rate (eFDR). The number of false rejections V is modeled with the beta-binomial distribution. An estimator of the beta-binomial false discovery rate (bbFDR) is then derived. This approach accounts for how the correlation among non-differentially expressed genes influences the distribution of V. Permutations are used to generate the observed values for V under the null hypotheses and a beta-binomial distribution is fit to the values of V. The bbFDR estimator is compared to the eFDR estimator in simulation studies of correlated non-differentially expressed genes and is found to outperform the eFDR for certain scenarios. As an example, this method is also used to perform an analysis that compares the gene expression of soft tissue sarcoma samples to normal tissue samples.

  5. Connected Representations of Knowledge: Do Undergraduate Students Relate Algebraic Rational Expressions to Rational Numbers?

    ERIC Educational Resources Information Center

    Yantz. Jennifer

    2013-01-01

    The attainment and retention of later algebra skills in high school has been identified as a factor significantly impacting students' postsecondary success as STEM majors. Researchers maintain that learners develop meaning for algebraic procedures by forming connections to the basic number system properties. In the present study, the connections…

  6. Connected Representations of Knowledge: Do Undergraduate Students Relate Algebraic Rational Expressions to Rational Numbers?

    ERIC Educational Resources Information Center

    Yantz. Jennifer

    2013-01-01

    The attainment and retention of later algebra skills in high school has been identified as a factor significantly impacting students' postsecondary success as STEM majors. Researchers maintain that learners develop meaning for algebraic procedures by forming connections to the basic number system properties. In the present study, the connections…

  7. Interaction-Based Feature Selection for Uncovering Cancer Driver Genes Through Copy Number-Driven Expression Level.

    PubMed

    Park, Heewon; Niida, Atsushi; Imoto, Seiya; Miyano, Satoru

    2017-02-01

    Driver gene selection is crucial to understand the heterogeneous system of cancer. To identity cancer driver genes, various statistical strategies have been proposed, especially the L1-type regularization methods have drawn a large amount of attention. However, the statistical approaches have been developed purely from algorithmic and statistical point, and the existing studies have applied the statistical approaches to genomic data analysis without consideration of biological knowledge. We consider a statistical strategy incorporating biological knowledge to identify cancer driver gene. The alterations of copy number have been considered to driver cancer pathogenesis processes, and the region of strong interaction of copy number alterations and expression levels was known as a tumor-related symptom. We incorporate the influence of copy number alterations on expression levels to cancer driver gene-selection processes. To quantify the dependence of copy number alterations on expression levels, we consider [Formula: see text] and [Formula: see text] effects of copy number alterations on expression levels of genes, and incorporate the symptom of tumor pathogenesis to gene-selection procedures. We then proposed an interaction-based feature-selection strategy based on the adaptive L1-type regularization and random lasso procedures. The proposed method imposes a large amount of penalty on genes corresponding to a low dependency of the two features, thus the coefficients of the genes are estimated to be small or exactly 0. It implies that the proposed method can provide biologically relevant results in cancer driver gene selection. Monte Carlo simulations and analysis of the Cancer Genome Atlas (TCGA) data show that the proposed strategy is effective for high-dimensional genomic data analysis. Furthermore, the proposed method provides reliable and biologically relevant results for cancer driver gene selection in TCGA data analysis.

  8. Effect of passage number on cellular response to DNA-damaging agents: Cell survival and gene expression

    SciTech Connect

    Chang-Liu, C.M.; Woloschak, G.E.

    1997-08-01

    The effect of different passage numbers on plating efficiency, doubling time, cell growth, and radiation sensitivity was assessed in Syrian hamster embryo (SHE) cells. Changes in gene expression after UV or {gamma}-ray irradiation at different passage numbers were also examined. The SHE cells were maintained in culture medium for up to 64 passages. Cells were exposed to {sup 60}Co {gamma} rays or 254-nm UV radiation. Differential display of cDNAs and northern blots were used for the study of gene expression. With increasing passage number, SHE cells demonstrated decreased doubling time, increased plating efficiency, and a decreased yield in the number of cells per plate. Between passages 41 and 48 a crisis period was evident during which time cell growth in high serum was no longer optimal, and serum concentrations were reduced to maintain cell growth. Sensitivity to ionizing radiation was no different between early- and intermediate-passage cells. However, after UV exposure at low passages (passage 3), confluent cells were more sensitive to the killing effects of UV than were log-phase cells. At intermediate passages (passages 43, 48), confluent cells were slightly more radioresistant than were log-phase cells. By passage 64, however, both confluent and log-phase cells showed similar patterns of UV sensitivity. Expression of {gamma}-actin, PCNA, and p53 transcripts did not change following UV exposure. p53 mRNA was induced following {gamma}-ray exposure of the intermediate (passage 45) epithelial cells. The observed differences in radiation sensitivity associated with increasing passage number may be influenced by radiation-induced gene expression. The authors are conducted experiments to identify these genes.

  9. The number of preproghrelin mRNA expressing cells is increased in mice with activity-based anorexia.

    PubMed

    François, Marie; Barde, Swapnali; Achamrah, Najate; Breton, Jonathan; do Rego, Jean-Claude; Coëffier, Moïse; Hökfelt, Tomas; Déchelotte, Pierre; Fetissov, Sergueï O

    2015-06-01

    Plasma levels of ghrelin, an orexigenic peptide, are increased during conditions of chronic starvation, such as in patients with anorexia nervosa. However, it is not known whether such increase can be related to the number of preproghrelin mRNA-expressing cells in the stomach, and if chronic starvation may activate a tentative central ghrelin production. In this work, in situ hybridization technique was used to analyze the presence and number of preproghrelin mRNA-expressing cells in the stomach and the hypothalamus of mice with activity-based anorexia (ABA) induced by the combination of running wheel activity with progressive, during 10 days, feeding-time restriction (FTR) and compared with sedentary FTR, ABA pair-fed (PF) and ad libitum-fed control mice. All food-restricted mice lost more than 20% of body weight. Body weight loss was similar in ABA and PF mice, but it was more pronounced than in FTR mice. Food intake was also lower in ABA than in FTR mice. Preproghrelin mRNA-expressing cells in the stomach were increased proportionally to the body weight loss in all food-restricted groups with the highest number in ABA mice. No preproghrelin mRNA-producing cells were detectable in the hypothalamus of either control or food-restricted mice. Thus, the increased number of gastric preproghrelin mRNA-producing cells during chronic starvation proportionally to the body weight loss and reduced food intake may underlie increased plasma ghrelin. Hyperactivity-induced anorexia appears to further increase the number of preproghrelin mRNA-producing cells in the stomach. No evidence was found for ghrelin expression in the hypothalamus, not even in any of the present experimental models. Copyright © 2015 Elsevier Ltd. All rights reserved.

  10. Integrative analysis of DNA copy number, DNA methylation and gene expression in multiple myeloma reveals alterations related to relapse

    PubMed Central

    Krzeminski, Patryk; Corchete, Luis A.; García, Juan L.; López-Corral, Lucía; Fermiñán, Encarna; García, Eva M.; Martín, Ana A.; Hernández-Rivas, Jesús M.; García-Sanz, Ramón; Miguel, Jesús F. San; Gutiérrez, Norma C.

    2016-01-01

    Multiple myeloma (MM) remains incurable despite the introduction of novel agents, and a relapsing course is observed in most patients. Although the development of genomic technologies has greatly improved our understanding of MM pathogenesis, the mechanisms underlying relapse have been less thoroughly investigated. In this study, an integrative analysis of DNA copy number, DNA methylation and gene expression was conducted in matched diagnosis and relapse samples from MM patients. Overall, the acquisition of abnormalities at relapse was much more frequent than the loss of lesions present at diagnosis, and DNA losses were significantly more frequent in relapse than in diagnosis samples. Interestingly, copy number abnormalities involving more than 100 Mb of DNA at relapse significantly affect the gene expression of these samples, provoking a particular deregulation of the IL-8 pathway. On the other hand, no significant modifications of gene expression were observed in those samples with less than 100 Mb affected by chromosomal changes. Although several statistical approaches were used to identify genes whose abnormal expression at relapse was regulated by methylation, only two genes that were significantly deregulated in relapse samples (SORL1 and GLT1D1) showed a negative correlation between methylation and expression. Further analysis revealed that DNA methylation was involved in regulating SORL1 expression in MM. Finally, relevant changes in gene expression observed in relapse samples, such us downregulation of CD27 and P2RY8, were most likely not preceded by alterations in the corresponding DNA. Taken together, these results suggest that the genomic heterogeneity described at diagnosis remains at relapse. PMID:27811368

  11. Integrative analysis of DNA copy number, DNA methylation and gene expression in multiple myeloma reveals alterations related to relapse.

    PubMed

    Krzeminski, Patryk; Corchete, Luis A; García, Juan L; López-Corral, Lucía; Fermiñán, Encarna; García, Eva M; Martín, Ana A; Hernández-Rivas, Jesús M; García-Sanz, Ramón; San Miguel, Jesús F; Gutiérrez, Norma C

    2016-12-06

    Multiple myeloma (MM) remains incurable despite the introduction of novel agents, and a relapsing course is observed in most patients. Although the development of genomic technologies has greatly improved our understanding of MM pathogenesis, the mechanisms underlying relapse have been less thoroughly investigated. In this study, an integrative analysis of DNA copy number, DNA methylation and gene expression was conducted in matched diagnosis and relapse samples from MM patients. Overall, the acquisition of abnormalities at relapse was much more frequent than the loss of lesions present at diagnosis, and DNA losses were significantly more frequent in relapse than in diagnosis samples. Interestingly, copy number abnormalities involving more than 100 Mb of DNA at relapse significantly affect the gene expression of these samples, provoking a particular deregulation of the IL-8 pathway. On the other hand, no significant modifications of gene expression were observed in those samples with less than 100 Mb affected by chromosomal changes. Although several statistical approaches were used to identify genes whose abnormal expression at relapse was regulated by methylation, only two genes that were significantly deregulated in relapse samples (SORL1 and GLT1D1) showed a negative correlation between methylation and expression. Further analysis revealed that DNA methylation was involved in regulating SORL1 expression in MM. Finally, relevant changes in gene expression observed in relapse samples, such us downregulation of CD27 and P2RY8, were most likely not preceded by alterations in the corresponding DNA. Taken together, these results suggest that the genomic heterogeneity described at diagnosis remains at relapse.

  12. Effects of Biofilm Growth on Plasmid Copy Number and Expression of Antibiotic Resistance Genes in Enterococcus faecalis

    PubMed Central

    Cook, L. C.

    2013-01-01

    Biofilm growth causes increased average plasmid copy number as well as increased copy number heterogeneity in Enterococcus faecalis cells carrying plasmid pCF10. In this study, we examined whether biofilm growth affected the copy number and expression of antibiotic resistance determinants for several plasmids with diverse replication systems. Four different E. faecalis plasmids, unrelated to pCF10, demonstrated increased copy number in biofilm cells. In biofilm cells, we also observed increased transcription of antibiotic resistance genes present on these plasmids. The increase in plasmid copy number correlated with increased plating efficiency on high concentrations of antibiotics. Single-cell analysis of strains carrying two different plasmids suggested that the increase in plasmid copy number associated with biofilm growth was restricted to a subpopulation of biofilm cells. Regrowth of harvested biofilm cells in liquid culture resulted in a rapid reduction of plasmid copy number to that observed in the planktonic state. These results suggest a possible mechanism by which biofilm growth could reduce susceptibility to antibiotics in clinical settings. PMID:23380728

  13. Assessment of the number and expression of P-type H(+)-ATPase genes in tomato.

    PubMed

    Ewing, N N; Bennett, A B

    1994-10-01

    Seven genomic fragments encoding isoforms of tomato (Lycopersicon esculentum) plasma membrane H(+)-ATPase were cloned and characterized. Genomic DNA gel-blot analysis indicated that probes corresponding to LHA1 through LHA7 hybridized to a common set of seven to nine restriction fragments at moderate stringency and to single, distinct fragments at high stringency. RNA gel-blot and polymerase chain reaction (PCR)-based RNA analyses indicated that LHA1, LHA2, and LHA4 transcripts were present in all organs examined (roots, hypocotyls, stems, immature leaves, mature leaves, green fruit, and red ripe fruit). LHA1 mRNA was present at similar abundance in all organs, LHA2 mRNA was most abundant in hypocotyls and leaves, and LHA4 mRNA was most abundant in roots and hypocotyls. RNA gel-blot and RNA-based PCR assays indicated that LHA3, LHA5, LHA6, and LHA7 mRNA was present at very low or nondetectable levels in all organs, suggesting that these genes are either expressed at very low levels or in organs not examined or that they are regulated by hormonal or environmental cues that were not tested. Indoleacetic acid (IAA) treatment of tomato hypocotyl segments resulted in modest changes in abundance of LHA1, LHA2, and LHA4 transcripts, but these changes were not correlated with the time course of IAA-induced growth. In addition, constitutively silent LHA genes were not activated by IAA. These results indicate that at least seven genomic sequences are present in tomato that may encode plasma membrane H(+)-ATPases, at least three of which are expressed relatively abundantly at the mRNA level.

  14. MET expression and copy number status in clear-cell renal cell carcinoma: prognostic value and potential predictive marker

    PubMed Central

    Macher-Goeppinger, Stephan; Keith, Martina; Endris, Volker; Penzel, Roland; Tagscherer, Katrin E.; Pahernik, Sascha; Hohenfellner, Markus; Gardner, Humphrey; Grüllich, Carsten; Schirmacher, Peter; Roth, Wilfried

    2017-01-01

    Multiple targeted therapy for advanced clear-cell renal cell carcinoma (RCC) has substantially improved patient outcome, but complete remission is uncommon and many tumors eventually develop resistance. Mechanistic, preclinical, and early clinical data highlight c-Met / hepatocyte growth factor receptor as a promising target for RCC therapeutic agents. We have examined MET expression, frequency of MET gene copy gains and MET gene mutation in a large, hospital-based series of renal cell carcinomas with long-term follow-up information. Out of a total of 572 clear-cell RCC, only 17% were negative for MET expression whereas 32% showed high protein levels. High MET expression and MET copy number gains were associated with an aggressive phenotype and an unfavorable patient outcome. Elevated protein levels in absence of gene amplification were not attributed to mutations, based on results of targeted next-generation sequencing. Our data reveal that clear-cell RCC with MET upregulation show an aggressive behavior and MET copy number increase is evident in a substantial percentage of patients with high-grade carcinomas and metastatic disease. Diagnostic assessment of MET expression and amplification may be of predictive value to guide targeted therapy against MET signaling in patients with clear-cell RCC. PMID:27894094

  15. Association study and expression analysis of CYP4A11 gene copy number variation in Chinese cattle

    PubMed Central

    Yang, Mingjuan; Lv, Jingqiao; Zhang, Liangzhi; Li, Mingxun; Zhou, Yang; Lan, Xianyong; Lei, Chuzhao; Chen, Hong

    2017-01-01

    The identification of copy number variations (CNVs) allow us to explore genomic polymorphisms. In recent years, significant progress in understanding CNVs has been made in studies of human and animals, however, association and expression studies of CNVs are still in the early stage. It was previously reported that the Cytochrome P-450 4A11 (CYP4A11) gene is located within a copy number variable region (CNVR) that encompasses quantitative trait loci (QTLs) for economic traits like meat quality and milk production. So, this study was performed to determine the presence of CYP4A11 CNV in six distinct cattle breeds, identify its relationship with growth, and explore the biological effects of gene expression. For three CYP4A11 CNV types, Normal was more frequent than Gain or Loss. Association analysis revealed a positive effect of CYP4A11 copy number on growth traits (P < 0.05). One-way analysis of variance (ANOVA) analysis revealed that more CYP4A11 copies increased the gene expression level. Moreover, overexpression of CYP4A11 in vitro revealed its effect on lipid deposit. The data provide evidence for the functional role of CYP4A11 CNV and provide the basis for future applications in cattle breeding. PMID:28492277

  16. Expression of epithelial-mesenchymal transition-related genes increases with copy number in multiple cancer types

    PubMed Central

    Qu, Hong

    2016-01-01

    Epithelial-mesenchymal transition (EMT) is a cellular process through which epithelial cells transform into mesenchymal cells. EMT-implicated genes initiate and promote cancer metastasis because mesenchymal cells have greater invasive and migration capacities than epithelial cells. In this pan-cancer analysis, we explored the relationship between gene expression changes and copy number variations (CNVs) for EMT-implicated genes. Based on curated 377 EMT-implicated genes from the literature, we identified 212 EMT-implicated genes associated with more frequent copy number gains (CNGs) than copy number losses (CNLs) using data from The Cancer Genome Atlas (TCGA). Then by correlating these CNV data with TCGA gene expression data, we identified 71 EMT-implicated genes with concordant CNGs and gene up-regulation in 20 or more tumor samples. Of those, 14 exhibited such concordance in over 110 tumor samples. These 14 genes were predominantly apoptosis regulators, which may implies that apoptosis is critical during EMT. Moreover, the 71 genes with concordant CNG and up-regulation were largely involved in cellular functions such as phosphorylation cascade signaling. This is the first observation of concordance between CNG and up-regulation of specific genes in hundreds of samples, which may indicate that somatic CNGs activate gene expression by increasing the gene dosage. PMID:27029057

  17. Critical Eotvos numbers for buoyancy-induced oil drop detachment based on shape analysis.

    PubMed

    Chatterjee, Jaideep

    2002-08-05

    Critical values of the Eotvos number, which is half the Bond number, above which buoyancy induced drop detachment occurs, are estimated based on force balance equations available in the literature [Colloids Surf. A: Physicochem. Eng. Aspects 178 (2001) 249]. Since there are two significantly different expressions of the capillary retention force responsible for holding oil drops on a solid substrate in an aqueous phase, the critical dimensionless number is estimated with these two distinct equations. The differential equation defining the drop shape, with the constraints of the drop volume and the 'pinned' or 'receding' contact line, is numerically solved. The equilibrium drop shapes predicted are shown to match the experimentally observed variations in drop shape. From the numerical solution, it is observed that for interfacial tension (IFT) values lower than a certain limit for a given drop size, no numerically estimated drop shape can fulfil the drop volume constraint. Similarly, for the dimensionless number above a critical value, no shape can meet all the constraints. These critical Eotvos numbers are estimated, based on the above numerical approach, for initial contact angles measured in oil varying from 20 degrees to 90 degrees. It is found that the critical Eotvos numbers estimated from the numerical shape analysis are between the critical values estimated from the two force-balance equations. Near 90 degrees, the critical values estimated from the drop shape analysis matches the values from one of the force balance estimates, but merges with the critical values of the dimensionless number, estimated from the other force balance model near 10 degrees. From this analysis, it appears that a combination of the two equations for the capillary retention force is required, with one dominating when the contact angles are high, while the other applies for low values of the contact angle.

  18. Summary of dimensionless Texas hyetographs and distribution of storm depth developed for Texas Department of Transportation research project 0–4194

    USGS Publications Warehouse

    Asquith, William H.; Roussel, Meghan C.; Thompson, David B.; Cleveland, Theodore G.; Fang, Xing

    2005-01-01

    Hyetographs and storm depth distributions are important elements of hydraulic design by Texas Department of Transportation engineers. Design hyetographs are used in conjunction with unit hydrographs to obtain peak discharge and hydrograph shape for hydraulic design. Storm-depth distributions can be used to assess the probability of a total rainfall depth for a storm. A research project from 2000–2004 has been conducted to (1) determine if existing Natural Resources Conservation Service (NRCS) dimensionless hyetographs are representative of storms in Texas, (2) provide new procedures for dimensionless hyetograph estimation if the NRCS hyetographs are not representative, and (3) provide a procedure to estimate the distribution of storm depth for Texas. This report summarizes the research activities and results of the research project. The report documents several functional models of dimensionless hyetographs and provides curves and tabulated ordinates of empirical (nonfunctional) dimensionless hyetographs for a database of runoff-producing storms in Texas. The dimensionless hyetographs are compared to the NRCS dimensionless hyetographs. The distribution of storm depth is documented for seven values of minimum interevent time through dimensionless frequency curves and tables of mean storm depth for each county in Texas. Conclusions regarding application of the research results are included in the report.

  19. Column Number Density Expressions Through M = 0 and M = 1 Point Source Plumes Along Any Straight Path

    NASA Technical Reports Server (NTRS)

    Woronowicz, Michael

    2016-01-01

    Analytical expressions for column number density (CND) are developed for optical line of sight paths through a variety of steady free molecule point source models including directionally-constrained effusion (Mach number M = 0) and flow from a sonic orifice (M = 1). Sonic orifice solutions are approximate, developed using a fair simulacrum fitted to the free molecule solution. Expressions are also developed for a spherically-symmetric thermal expansion (M = 0). CND solutions are found for the most general paths relative to these sources and briefly explored. It is determined that the maximum CND from a distant location through directed effusion and sonic orifice cases occurs along the path parallel to the source plane that intersects the plume axis. For the effusive case this value is exactly twice the CND found along the ray originating from that point of intersection and extending to infinity along the plume's axis. For sonic plumes this ratio is reduced to about 4/3. For high Mach number cases the maximum CND will be found along the axial centerline path. Keywords: column number density, plume flows, outgassing, free molecule flow.

  20. Copy Number Variation and Differential Expression of a Protective Endogenous Retrovirus in Sheep

    PubMed Central

    Viginier, Barbara; Dolmazon, Christine; Lantier, Isabelle; Lantier, Frédéric; Archer, Fabienne; Leroux, Caroline; Terzian, Christophe

    2012-01-01

    The Jaagsiekte sheep retrovirus exJSRV and its endogenous counterpart enJSRV co-exist in sheep. exJSRV, a betaretrovirus, is the etiological agent of ovine pulmonary adenocarcinoma, and it has been demonstrated in vitro that an enJSRV Gag variant bearing the R-to-W amino acid change at position 21 was able to block exJSRV budding from the cells, providing a potential protective role for the host. In this work, we developed a fast mutation detection assay based on the oligo ligation assay (OLA) that permits the quantification of the relative proportions of the R21 and W21 Gag variants present in individual genomes and in cDNA obtained from normal and exJSRV-induced lung tumors. We have shown that the W21/R21 ratio is variable within and between breeds. We also describe for the first time that putative protecting enJSRV variants were expressed in alveolar type II cells (AECII), the major target of exJSRV. PMID:22911867

  1. Chromosome 15q11-13 duplication syndrome brain reveals epigenetic alterations in gene expression not predicted from copy number

    PubMed Central

    Hogart, Amber; Leung, Karen N.; Wang, Nicholas J.; Wu, David J.; Driscoll, Jennette; Vallero, Roxanne O.; Schanen, N. Carolyn

    2008-01-01

    Background Chromosome 15q11-13 contains a cluster of imprinted genes essential for normal mammalian neurodevelopment. Deficiencies in paternal or maternal 15q11-13 alleles result in Prader-Willi or Angelman syndromes, respectively, and maternal duplications lead to a distinct condition that often includes autism. Overexpression of maternally expressed imprinted genes is predicted to cause 15q11-13-associated autism, but a link between gene dosage and expression has not been experimentally determined in brain. Methods Post-mortem brain tissue was obtained from a male with 15q11-13 hexasomy and a female with 15q11-13 tetrasomy. Quantitative RT-PCR was used to measure ten 15q11-13 transcripts in maternal 15q11-13 duplication, Prader-Willi syndrome, and control brain samples. Southern blot, bisulfite sequencing and fluorescence in situ hybridization were used to investigate epigenetic mechanisms of gene regulation. Results Gene expression and DNA methylation correlated with parental gene dosage in the male 15q11-13 duplication sample with severe cognitive impairment and seizures. Strikingly, the female with autism and milder Prader-Willi-like characteristics demonstrated unexpected deficiencies in the paternally expressed transcripts SNRPN, NDN, HBII85, and HBII52 and unchanged levels of maternally expressed UBE3A compared to controls. Paternal expression abnormalities in the female duplication sample were consistent with elevated DNA methylation of the 15q11-13 imprinting control region (ICR). Expression of nonimprinted 15q11-13 GABA receptor subunit genes was significantly reduced specifically in the female 15q11-13 duplication brain without detectable GABRB3 methylation differences. Conclusion Our findings suggest that genetic copy number changes combined with additional genetic or environmental influences on epigenetic mechanisms impact outcome and clinical heterogeneity of 15q11-13 duplication syndromes. PMID:18835857

  2. Flower-enhanced expression of a nuclear-encoded mitochondrial respiratory protein is associated with changes in mitochondrion number.

    PubMed Central

    Huang, J; Struck, F; Matzinger, D F; Levings, C S

    1994-01-01

    The mitochondrial Rieske iron-sulfur protein is an obligatory component of the respiratory electron transport chain that is encoded by a single-copy gene in mammals and fungi. In contrast, this protein is encoded by a small gene family in dicotyledonous tobacco and monocotyledonous maize. We cloned four cDNAs from tobacco that encode the mitochondrial Rieske iron-sulfur protein. These clones, along with a previously isolated cDNA, represent five independent members of the gene family that can be divided into three subfamilies. All of these genes were derived from the two progenitor species and were expressed in amphidiploid tobacco. The proteins encoded by these five genes are probably functional because they all contain the universally conserved hexyl peptides necessary for the 2Fe-2S cluster formation. The expression of the Rieske protein gene family is differentially regulated; a 6- to 11-fold higher level of steady state transcripts was found in flowers than in leaves, stems, and roots. Members of at least two subfamilies were preferentially expressed in flowers, indicating that they share a common cis-regulatory element(s), which can respond to a flower-specific signal(s). Although approximately 10 times more transcripts occurred in flowers than in leaves, flower and leaf mitochondria contained a similar amount of the Rieske protein. Flowers, however, contained seven times more Rieske proteins than leaves. These results indicated an increase in mitochondrion number in flowers. High-energy demands during anther development might bring about an increase in mitochondrion numbers in flowers and the flower-enhanced expression of the Rieske protein gene family. Our results suggested that nuclear genes encoding mitochondrial respiratory proteins could sense and respond to changes in energy metabolism and/or changes in mitochondrion numbers. PMID:8180500

  3. Copy number and gene expression alterations in radiation-induced papillary thyroid carcinoma from chernobyl pediatric patients.

    PubMed

    Stein, Leighton; Rothschild, Jenniffer; Luce, Jesse; Cowell, John K; Thomas, Geraldine; Bogdanova, Tatania I; Tronko, Mycola D; Hawthorn, Lesleyann

    2010-05-01

    Following exposure to radiation during the Chernobyl fallout tragedy, papillary thyroid carcinoma (PTC) increased significantly in individuals who were children at the time of the accident. We have used two high-throughput, whole genome platforms to analyze radiation-induced PTCs from pediatric patients from the Chernobyl region. We performed comparative genomic hybridization using Affymetrix 50K Mapping arrays and gene expression profiling on 10 pediatric post-Chernobyl PTCs obtained from patients living in the region. We performed an overlay analysis of these two data sets. Many regions of copy number alterations (CNAs) were detected including novel regions that had never been associated with PTCs. Increases in copy numbers were consistently found on chromosomes 1p, 5p, 9q, 12q, 13q, 16p, 21q, and 22q. Deletions were observed less frequently and were mapped to 1q, 6q, 9q, 10q, 13q, 14q, 21q, and 22q. Gene expression analysis revealed that most of the altered genes were also perturbed in sporadic adult PTC; however, 141 gene expression changes were found to be unique to the post-Chernobyl tumors. The genes with the highest increases in expression that were novel to the pediatric post-Chernobyl tumors were TESC, PDZRN4, TRAa/TRDa, GABBR2, and CA12. The genes showing the largest expression decreases included PAPSS2, PDLIM3, BEXI, ANK2, SORBS2, and PPARGCIA. An overlay analysis of the gene expression and CNA profiles was then performed. This analysis identified genes showing both CNAs and concurrent gene expression alterations. Many of these are commonly seen in sporadic PTC such as SERPINA, COL8A, and PDX, while others were unique to the radiation-induced profiles including CAMK2N1, AK1, DHRS3, and PDE9A. This type of analysis allows an assessment of gene expression changes that are associated with a physical mechanism. These genes and chromosomal regions are potential markers for radiation-induced PTC.

  4. HAWAIIAN SKIRT controls size and floral organ number by modulating CUC1 and CUC2 expression.

    PubMed

    González-Carranza, Zinnia H; Zhang, Xuebin; Peters, Janny L; Boltz, Veronique; Szecsi, Judit; Bendahmane, Mohammed; Roberts, Jeremy A

    2017-01-01

    The Arabidopsis thaliana F-box gene HAWAIIAN SKIRT (HWS) affects organ growth and the timing of floral organ abscission. The loss-of-function hws-1 mutant exhibits fused sepals and increased organ size. To understand the molecular mechanisms of HWS during plant development, we mutagenized hws-1 seeds with ethylmethylsulphonate (EMS) and screened for mutations suppressing hws-1 associated phenotypes. We isolated the shs1/hws-1 (suppressor of hws-1) mutant in which hws-1 sepal fusion phenotype was suppressed. The shs1/hws-1 mutant carries a G→A nucleotide substitution in the MIR164 binding site of CUP-SHAPED COTYLEDON 1 (CUC1) mRNA. CUC1 and CUP-SHAPED COTYLEDON 2 (CUC2) transcript levels were altered in shs1, renamed cuc1-1D, and in hws-1 mutant. Genetic interaction analyses using single, double and triple mutants of cuc1-1D, cuc2-1D (a CUC2 mutant similar to cuc1-1D), and hws-1, demonstrate that HWS, CUC1 and CUC2 act together to control floral organ number. Loss of function of HWS is associated with larger petal size due to alterations in cell proliferation and mitotic growth, a role shared with the CUC1 gene.

  5. Integrated Analysis of Genome-Wide Copy Number Alterations and Gene Expression Profiling of Lung Cancer in Xuanwei, China

    PubMed Central

    Zhang, Yanliang; Xue, Qiuyue; Pan, Guoqing; Meng, Qing H.; Tuo, Xiaoyu; Cai, Xuemei; Chen, Zhenghui; Li, Ya; Huang, Tao; Duan, Xincen; Duan, Yong

    2017-01-01

    Objectives Lung cancer in Xuanwei (LCXW), China, is known throughout the world for its distinctive characteristics, but little is known about its pathogenesis. The purpose of this study was to screen potential novel “driver genes” in LCXW. Methods Genome-wide DNA copy number alterations (CNAs) were detected by array-based comparative genomic hybridization and differentially expressed genes (DEGs) by gene expression microarrays in 8 paired LCXW and non-cancerous lung tissues. Candidate driver genes were screened by integrated analysis of CNAs and DEGs. The candidate genes were further validated by real-time quantitative polymerase chain reaction. Results Large numbers of CNAs and DEGs were detected, respectively. Some of the most frequently occurring CNAs included gains at 5p15.33-p15.32, 5p15.1-p14.3, and 5p14.3-p14.2 and losses at 11q24.3, 21q21.1, 21q22.12-q22.13, and 21q22.2. Integrated analysis of CNAs and DEGs identified 24 candidate genes with frequent copy number gains and concordant upregulation, which were considered potential oncogenes, including CREB3L4, TRIP13, and CCNE2. In addition, the analysis identified 19 candidate genes with a negative association between copy number change and expression change, considered potential tumor suppressor genes, including AHRR, NKD2, and KLF10. One of the most studied oncogenes, MYC, may not play a carcinogenic role in LCXW. Conclusions This integrated analysis of CNAs and DEGs identified several potential novel LCXW-related genes, laying an important foundation for further research on the pathogenesis of LCXW and identification of novel biomarkers or therapeutic targets. PMID:28056099

  6. Hypoxia induces arginase II expression and increases viable human pulmonary artery smooth muscle cell numbers via AMPKα1 signaling.

    PubMed

    Xue, Jianjing; Nelin, Leif D; Chen, Bernadette

    2017-04-01

    Pulmonary artery smooth muscle cell (PASMC) proliferation is one of the hallmark features of hypoxia-induced pulmonary hypertension. With only supportive treatment options available for this life-threatening disease, treating and preventing the proliferation of PASMCs is a viable therapeutic option. A key promoter of hypoxia-induced increases in the number of viable human PASMCs is arginase II, with attenuation of viable cell numbers following pharmacologic inhibition or siRNA knockdown of the enzyme. Additionally, increased levels of arginase have been demonstrated in the pulmonary vasculature of patients with pulmonary hypertension. The signaling pathways responsible for the hypoxic induction of arginase II in PASMCs, however, remain unknown. Hypoxia is a recognized activator of AMPK, which is known to be expressed in human PASMCs (hPASMCs). Activation of AMPK by hypoxia has been shown to promote cell survival in PASMCs. In addition, pharmacologic agents targeting AMPK have been shown to attenuate chronic hypoxia-induced pulmonary hypertension in animal models. The present studies tested the hypothesis that hypoxia-induced arginase II expression in hPASMCs is mediated through AMPK signaling. We found that pharmacologic inhibitors of AMPK, as well as siRNA knockdown of AMPKα1, prevented hypoxia-induced arginase II. The hypoxia-induced increase in viable hPASMC numbers was also prevented following both pharmacologic inhibition and siRNA knockdown of AMPK. Furthermore, we demonstrate that overexpression of AMPK induced arginase II protein expression and viable cells numbers in hPASMCs. Copyright © 2017 the American Physiological Society.

  7. Dimensionless scalings of confinement, heat transport and pedestal stability in JET-ILW and comparison with JET-C

    NASA Astrophysics Data System (ADS)

    Frassinetti, L.; Saarelma, S.; Lomas, P.; Nunes, I.; Rimini, F.; Beurskens, M. N. A.; Bilkova, P.; Boom, J. E.; de la Luna, E.; Delabie, E.; Drewelow, P.; Flanagan, J.; Garzotti, L.; Giroud, C.; Hawks, N.; Joffrin, E.; Kempenaars, M.; Kim, Hyun-Tae; Kruezi, U.; Loarte, A.; Lomanowski, B.; Lupelli, I.; Meneses, L.; Maggi, C. F.; Menmuir, S.; Peterka, M.; Rachlew, E.; Romanelli, M.; Stefanikova, E.; Contributors, JET

    2017-01-01

    Three dimensionless scans in the normalized Larmor radius ρ *, normalized collisionality ν * and normalized plasma pressure β have been performed in JET with the ITER-like wall (JET-ILW). The normalized energy confinement and the thermal diffusivity exhibit a scaling with ρ * consistent with the earlier results obtained in the carbon wall JET (JET-C) and with a gyro-Bohm scaling. In the pedestal, experimental results show that the stability is not dependent on ρ *, qualitatively in agreement with the peeling-ballooning (P-B) model. The ν * dimensionless scaling shows that JET-ILW normalized confinement has a stronger dependence on collisionality than JET-C. This leads to a reduction of the difference in the confinement between JET-ILW and JET-C to  ≈10% at low ν *. The pedestal stability shows an improvement with decreasing ν *. This is ascribed to the increase of the bootstrap current, to the reduction of the pedestal width and to the reduction of the relative shift between pedestal density and temperature position. The β dimensionless scan shows that, at low collisionality, JET-ILW normalized confinement has no clear dependence with β, in agreement with part of the earlier scalings. At high collisionality, a reduction of the normalized confinement with increasing β is observed. This behaviour is driven mainly by the pedestal where the stability is reduced with increasing β. The P-B analysis shows that the stability reduction with increasing β at high ν * is due to the destabilizing effect of the increased relative shift.

  8. Alterations in gene expression of proprotein convertases in human lung cancer have a limited number of scenarios.

    PubMed

    Demidyuk, Ilya V; Shubin, Andrey V; Gasanov, Eugene V; Kurinov, Alexander M; Demkin, Vladimir V; Vinogradova, Tatyana V; Zinovyeva, Marina V; Sass, Alexander V; Zborovskaya, Irina B; Kostrov, Sergey V

    2013-01-01

    Proprotein convertases (PCs) is a protein family which includes nine highly specific subtilisin-like serine endopeptidases in mammals. The system of PCs is involved in carcinogenesis and levels of PC mRNAs alter in cancer, which suggests expression status of PCs as a possible marker for cancer typing and prognosis. The goal of this work was to assess the information value of expression profiling of PC genes. Quantitative polymerase chain reaction was used for the first time to analyze mRNA levels of all PC genes as well as matrix metalloproteinase genes MMP2 and MMP14, which are substrates of PCs, in 30 matched pairs of samples of human lung cancer tumor and adjacent tissues without pathology. Significant changes in the expression of PCs have been revealed in tumor tissues: increased FURIN mRNA level (p<0.00005) and decreased mRNA levels of PCSK2 (p<0.007), PCSK5 (p<0.0002), PCSK7 (p<0.002), PCSK9 (p<0.00008), and MBTPS1 (p<0.00004) as well as a tendency to increase in the level of PCSK1 mRNA. Four distinct groups of samples have been identified by cluster analysis of the expression patterns of PC genes in tumor vs. normal tissue. Three of these groups covering 80% of samples feature a strong elevation in the expression of a single gene in cancer: FURIN, PCSK1, or PCSK6. Thus, the changes in the expression of PC genes have a limited number of scenarios, which may reflect different pathways of tumor development and cryptic features of tumors. This finding allows to consider the mRNAs of PC genes as potentially important tumor markers.

  9. Plant-specific Histone Deacetylases HDT½ Regulate GIBBERELLIN 2-OXIDASE 2 Expression to Control Arabidopsis Root Meristem Cell Number.

    PubMed

    Li, Huchen; Torres-Garcia, Jesus; Latrasse, David; Benhamed, Moussa; Schilderink, Stefan; Zhou, Wenkun; Kulikova, Olga; Hirt, Heribert; Bisseling, Ton

    2017-08-30

    Root growth is modulated by environmental factors and depends on cell production in the root meristem (RM). New cells in the meristem are generated by stem cells and transit-amplifying cells, which together determine RM cell number. Transcription factors and chromatin-remodelling factors have been implicated in regulating the switch from stem cells to transit-amplifying cells. Here we show that two Arabidopsis thaliana paralogs encoding plant-specific histone deacetylases, HDT1 and HDT2, regulate a second switch from transit-amplifying cells to expanding cells. Knockdown of HDT½ (hdt1,2i) results in an earlier switch and causes a reduced RM cell number. Our data show that HDT½ negatively regulate the acetylation level of the C19-GIBBERELLIN 2-OXIDASE 2 (GA2ox2) locus and repress the expression of GA2ox2 in the RM and elongation zone. Overexpression of GA2ox2 in the RM phenocopies the hdt1,2i phenotype. Conversely, knockout of GA2ox2 partially rescues the root growth defect of hdt1,2i. These results suggest that by repressing the expression of GA2ox2, HDT½ likely fine-tune gibberellin metabolism and they are crucial for regulating the switch from cell division to expansion to determine RM cell number. We propose that HDT½ function as part of a mechanism that modulates root growth in response to environmental factors. © 2017 American Society of Plant Biologists. All rights reserved.

  10. Column number density expressions through M = 0 and M = 1 point source plumes along any straight path

    NASA Astrophysics Data System (ADS)

    Woronowicz, Michael

    2016-11-01

    Analytical expressions for column number density (CND) are developed for optical line of sight paths through a variety of steady free molecule point source models including directionally-constrained effusion (Mach number M = 0) and flow from a sonic orifice (M = 1). Sonic orifice solutions are approximate, developed using a fair simulacrum fitted to the free molecule solution. Expressions are also developed for a spherically-symmetric thermal expansion (M = 0). CND solutions are found for the most general paths relative to these sources and briefly explored. It is determined that the maximum CND from a distant location through directed effusion and sonic orifice cases occurs along the path parallel to the source plane that intersects the plume axis. For the effusive case this value is exactly twice the CND found along the ray originating from that point of intersection and extending to infinity along the plume's axis. For sonic plumes this ratio is reduced to about 4/3. For high Mach number cases the maximum CND will be found along the axial centerline path.

  11. Column Number Density Expressions Through M = 0 and M = 1 Point Source Plumes Along Any Straight Path

    NASA Technical Reports Server (NTRS)

    Woronowicz, Michael S.

    2016-01-01

    Analytical expressions for column number density (CND) are developed for optical line of sight paths through a variety of steady free molecule point source models including directionally-constrained effusion (Mach number M = 0) and flow from a sonic orifice (M 1). Sonic orifice solutions are approximate, developed using a fair simulacrum fitted to the free molecule solution. Expressions are also developed for a spherically-symmetric thermal expansion (M = 0). CND solutions are found for the most general paths relative to these sources and briefly explored. It is determined that the maximum CND from a distant location through directed effusion and sonic orifice cases occurs along the path parallel to the source plane that intersects the plume axis. For the effusive case this value is exactly twice the CND found along the ray originating from that point of intersection and extending to infinity along the plumes axis. For sonic plumes this ratio is reduced to about 43. For high Mach number cases the maximum CND will be found along the axial centerline path.

  12. Multiplex titration RT-PCR: rapid determination of gene expression patterns for a large number of genes

    NASA Technical Reports Server (NTRS)

    Nebenfuhr, A.; Lomax, T. L.

    1998-01-01

    We have developed an improved method for determination of gene expression levels with RT-PCR. The procedure is rapid and does not require extensive optimization or densitometric analysis. Since the detection of individual transcripts is PCR-based, small amounts of tissue samples are sufficient for the analysis of expression patterns in large gene families. Using this method, we were able to rapidly screen nine members of the Aux/IAA family of auxin-responsive genes and identify those genes which vary in message abundance in a tissue- and light-specific manner. While not offering the accuracy of conventional semi-quantitative or competitive RT-PCR, our method allows quick screening of large numbers of genes in a wide range of RNA samples with just a thermal cycler and standard gel analysis equipment.

  13. Multiplex titration RT-PCR: rapid determination of gene expression patterns for a large number of genes

    NASA Technical Reports Server (NTRS)

    Nebenfuhr, A.; Lomax, T. L.

    1998-01-01

    We have developed an improved method for determination of gene expression levels with RT-PCR. The procedure is rapid and does not require extensive optimization or densitometric analysis. Since the detection of individual transcripts is PCR-based, small amounts of tissue samples are sufficient for the analysis of expression patterns in large gene families. Using this method, we were able to rapidly screen nine members of the Aux/IAA family of auxin-responsive genes and identify those genes which vary in message abundance in a tissue- and light-specific manner. While not offering the accuracy of conventional semi-quantitative or competitive RT-PCR, our method allows quick screening of large numbers of genes in a wide range of RNA samples with just a thermal cycler and standard gel analysis equipment.

  14. Parvalbumin and neuropeptide Y expressing hippocampal GABA-ergic inhibitory interneuron numbers decline in a model of Gulf War illness

    PubMed Central

    Megahed, Tarick; Hattiangady, Bharathi; Shuai, Bing; Shetty, Ashok K.

    2015-01-01

    Cognitive dysfunction is amongst the most conspicuous symptoms in Gulf War illness (GWI). Combined exposure to the nerve gas antidote pyridostigmine bromide (PB), pesticides and stress during the Persian Gulf War-1 (PGW-1) are presumed to be among the major causes of GWI. Indeed, our recent studies in rat models have shown that exposure to GWI-related (GWIR) chemicals and mild stress for 4 weeks engenders cognitive impairments accompanied with several detrimental changes in the hippocampus. In this study, we tested whether reduced numbers of hippocampal gamma-amino butyric acid (GABA)-ergic interneurons are among the pathological changes induced by GWIR-chemicals and stress. Animals were exposed to low doses of GWIR-chemicals and mild stress for 4 weeks. Three months after this exposure, subpopulations of GABA-ergic interneurons expressing the calcium binding protein parvalbumin (PV), the neuropeptide Y (NPY) and somatostatin (SS) in the hippocampus were stereologically quantified. Animals exposed to GWIR-chemicals and stress for 4 weeks displayed reduced numbers of PV-expressing GABA-ergic interneurons in the dentate gyrus and NPY-expressing interneurons in the CA1 and CA3 subfields. However, no changes in SS+ interneuron population were observed in the hippocampus. Furthermore, GABA-ergic interneuron deficiency in these animals was associated with greatly diminished hippocampus neurogenesis. Because PV+ and NPY+ interneurons play roles in maintaining normal cognitive function and neurogenesis, and controlling the activity of excitatory neurons in the hippocampus, reduced numbers of these interneurons may be one of the major causes of cognitive dysfunction and reduced neurogenesis observed in GWI. Hence, strategies that improve inhibitory neurotransmission in the hippocampus may prove beneficial for reversing cognitive dysfunction in GWI. PMID:25620912

  15. Parvalbumin and neuropeptide Y expressing hippocampal GABA-ergic inhibitory interneuron numbers decline in a model of Gulf War illness.

    PubMed

    Megahed, Tarick; Hattiangady, Bharathi; Shuai, Bing; Shetty, Ashok K

    2014-01-01

    Cognitive dysfunction is amongst the most conspicuous symptoms in Gulf War illness (GWI). Combined exposure to the nerve gas antidote pyridostigmine bromide (PB), pesticides and stress during the Persian Gulf War-1 (PGW-1) are presumed to be among the major causes of GWI. Indeed, our recent studies in rat models have shown that exposure to GWI-related (GWIR) chemicals and mild stress for 4 weeks engenders cognitive impairments accompanied with several detrimental changes in the hippocampus. In this study, we tested whether reduced numbers of hippocampal gamma-amino butyric acid (GABA)-ergic interneurons are among the pathological changes induced by GWIR-chemicals and stress. Animals were exposed to low doses of GWIR-chemicals and mild stress for 4 weeks. Three months after this exposure, subpopulations of GABA-ergic interneurons expressing the calcium binding protein parvalbumin (PV), the neuropeptide Y (NPY) and somatostatin (SS) in the hippocampus were stereologically quantified. Animals exposed to GWIR-chemicals and stress for 4 weeks displayed reduced numbers of PV-expressing GABA-ergic interneurons in the dentate gyrus and NPY-expressing interneurons in the CA1 and CA3 subfields. However, no changes in SS+ interneuron population were observed in the hippocampus. Furthermore, GABA-ergic interneuron deficiency in these animals was associated with greatly diminished hippocampus neurogenesis. Because PV+ and NPY+ interneurons play roles in maintaining normal cognitive function and neurogenesis, and controlling the activity of excitatory neurons in the hippocampus, reduced numbers of these interneurons may be one of the major causes of cognitive dysfunction and reduced neurogenesis observed in GWI. Hence, strategies that improve inhibitory neurotransmission in the hippocampus may prove beneficial for reversing cognitive dysfunction in GWI.

  16. The effect of visitor number and spice provisioning in pacing expression by jaguars evaluated through a case study.

    PubMed

    Vidal, L S; Guilherme, F R; Silva, V F; Faccio, M C S R; Martins, M M; Briani, D C

    2016-06-01

    Captive animals exhibit stereotypic pacing in response to multiple causes, including the inability to escape from human contact. Environmental enrichment techniques can minimize pacing expression. By using an individual-based approach, we addressed whether the amount of time two males and a female jaguar (Panthera onca) devote to pacing varied with the number of visitors and tested the effectiveness of cinnamon and black pepper in reducing pacing. The amount of time that all jaguars engaged in pacing increased significantly with the number of visitors. Despite the difference between the males regarding age and housing conditions, both devoted significantly less time to pacing following the addition of both spices, which indicates their suitability as enrichment techniques. Mean time devoted to pacing among the treatments did not differ for the female. Our findings pointed out to the validity of individual-based approaches, as they can reveal how suitable olfactory stimuli are to minimizing stereotypies irrespective of particular traits.

  17. Number and regional distribution of GAD65 mRNA-expressing interneurons in the rat hippocampal formation.

    PubMed

    Czéh, B; Abrahám, Hajnalka; Tahtakran, Siroun; Houser, Carolyn R; Seress, L

    2013-12-01

    In rodent models for neuropsychiatric disorders reduced number of hippocampal interneurons have been reported, but the total number of GABAergic neurons in the normal rat hippocampus is yet unknown. We used in situ hybridization method to label the 65 isoform of glutamic acid decarboxylase (GAD65) and counted the number of GAD65 mRNA-expressing neurons along the entire septo-temporal axis of the hippocampus. We found that 2/3 of the interneurons were in Ammon's horn (61,590) and 1/3 in the dentate gyrus (28,000). We observed the following numbers in Ammon's horn: CA3 area 33,400, CA2 area 4,190, CA1 area 24,000 and in the dentate gyrus: 6,000 in the molecular and 9,000 in the granule cell layers and 13,000 in the hilus. GAD65 mRNA-expressing neurons were significantly more numerous in dorsal than in ventral hippocampus. The ratio between interneurons and principal cells was lowest in the granule cell layer (0.9%) and highest in hilus (21%). In Ammon's horn this ratio was constant being 13% in CA3 and 8% in CA1-2 areas. In the entire hippocampal formation, the interneuron/principal cell ratio was 6%, with a significant difference between Ammon's horn (9.5%) and the dentate gyrus (2.8%) including the hilus. Such low ratios could suggest that even a limited loss of GABAergic neurons in the hippocampus may have a considerable functional impact.

  18. Diversification of spatiotemporal expression and copy number variation of the echinoid hbox12/pmar1/micro1 multigene family

    PubMed Central

    Geraci, Fabiana; Spinelli, Giovanni

    2017-01-01

    Changes occurring during evolution in the cis-regulatory landscapes of individual members of multigene families might impart diversification in their spatiotemporal expression and function. The archetypal member of the echinoid hbox12/pmar1/micro1 family is hbox12-a, a homeobox-containing gene expressed exclusively by dorsal blastomeres, where it governs the dorsal/ventral gene regulatory network during embryogenesis of the sea urchin Paracentrotus lividus. Here we describe the inventory of the hbox12/pmar1/micro1 genes in P. lividus, highlighting that gene copy number variation occurs across individual sea urchins of the same species. We show that the various hbox12/pmar1/micro1 genes group into three subfamilies according to their spatiotemporal expression, which ranges from broad transcription throughout development to transient expression in either the animal hemisphere or micromeres of the early embryo. Interestingly, the promoter regions of those genes showing comparable expression patterns are highly similar, while differing from those of the other subfamilies. Strikingly, phylogenetic analysis suggests that the hbox12/pmar1/micro1 genes are species-specific, exhibiting extensive divergence in their noncoding, but not in their coding, sequences across three distinct sea urchin species. In spite of this, two micromere-specific genes of P. lividus possess a TCF/LEF-binding motif in a similar position, and their transcription relies on Wnt/β-catenin signaling, similar to the pmar1 and micro1 genes, which in other sea urchin species are involved in micromere specification. Altogether, our findings suggest that the hbox12/pmar1/micro1 gene family evolved rather rapidly, generating paralogs whose cis-regulatory sequences diverged following multiple rounds of duplication from a common ancestor. PMID:28350855

  19. Development of a dimensionless parameter for characterization of dielectric barrier discharge devices with respect to geometrical features

    NASA Astrophysics Data System (ADS)

    Lim, Mook Tzeng; Zuklifli, Ahmad Zulazlan Shah; Jayapalan, Kanesh Kumar; Chin, Oihoong

    2017-09-01

    Non-thermal plasma (NTP) devices produce excited and radical species that have higher energy levels than their ground state and are utilized for various applications. There are various types of NTP devices, with dielectric barrier discharge (DBD) reactors being widely used. These DBD devices vary in geometrical configuration and operating parameters, making a comparison of their performance in terms of discharge power characteristics difficult. Therefore, this study proposes a dimensionless parameter that is related to the geometrical features, and is a function of the discharge power with respect to the frequency, voltage, and capacitance of a DBD. The dimensionless parameter, in the form of a ratio of the discharge energy per cycle to the gap capacitive energy, will be useful for engineers and designers to compare the energy characteristics of devices systematically, and could also be used for scaling up DBD devices. From the results in this experiment and from the literature, different DBD devices are categorized into three separate groups according to different levels of the energy ratio. The larger DBD devices have lower energy ratios due to their lower estimated surface discharge areas and capacitive reactance. Therefore, the devices can be categorized according to the energy ratio due to the effects of the geometrical features of the DBD devices, since it affects the surface discharge area and capacitance of the DBD. The DBD devices are also categorized into three separate groups using the Kriegseis factor, but the categorization is different from that of the energy ratio.

  20. Deciphering the associations between gene expression and copy number alteration using a sparse double Laplacian shrinkage approach

    PubMed Central

    Shi, Xingjie; Zhao, Qing; Huang, Jian; Xie, Yang; Ma, Shuangge

    2015-01-01

    Motivation: Both gene expression levels (GEs) and copy number alterations (CNAs) have important biological implications. GEs are partly regulated by CNAs, and much effort has been devoted to understanding their relations. The regulation analysis is challenging with one gene expression possibly regulated by multiple CNAs and one CNA potentially regulating the expressions of multiple genes. The correlations among GEs and among CNAs make the analysis even more complicated. The existing methods have limitations and cannot comprehensively describe the regulation. Results: A sparse double Laplacian shrinkage method is developed. It jointly models the effects of multiple CNAs on multiple GEs. Penalization is adopted to achieve sparsity and identify the regulation relationships. Network adjacency is computed to describe the interconnections among GEs and among CNAs. Two Laplacian shrinkage penalties are imposed to accommodate the network adjacency measures. Simulation shows that the proposed method outperforms the competing alternatives with more accurate marker identification. The Cancer Genome Atlas data are analysed to further demonstrate advantages of the proposed method. Availability and implementation: R code is available at http://works.bepress.com/shuangge/49/ Contact: shuangge.ma@yale.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26342102

  1. The top-scoring 'N' algorithm: a generalized relative expression classification method from small numbers of biomolecules.

    PubMed

    Magis, Andrew T; Price, Nathan D

    2012-09-11

    Relative expression algorithms such as the top-scoring pair (TSP) and the top-scoring triplet (TST) have several strengths that distinguish them from other classification methods, including resistance to overfitting, invariance to most data normalization methods, and biological interpretability. The top-scoring 'N' (TSN) algorithm is a generalized form of other relative expression algorithms which uses generic permutations and a dynamic classifier size to control both the permutation and combination space available for classification. TSN was tested on nine cancer datasets, showing statistically significant differences in classification accuracy between different classifier sizes (choices of N). TSN also performed competitively against a wide variety of different classification methods, including artificial neural networks, classification trees, discriminant analysis, k-Nearest neighbor, naïve Bayes, and support vector machines, when tested on the Microarray Quality Control II datasets. Furthermore, TSN exhibits low levels of overfitting on training data compared to other methods, giving confidence that results obtained during cross validation will be more generally applicable to external validation sets. TSN preserves the strengths of other relative expression algorithms while allowing a much larger permutation and combination space to be explored, potentially improving classification accuracies when fewer numbers of measured features are available.

  2. The top-scoring ‘N’ algorithm: a generalized relative expression classification method from small numbers of biomolecules

    PubMed Central

    2012-01-01

    Background Relative expression algorithms such as the top-scoring pair (TSP) and the top-scoring triplet (TST) have several strengths that distinguish them from other classification methods, including resistance to overfitting, invariance to most data normalization methods, and biological interpretability. The top-scoring ‘N’ (TSN) algorithm is a generalized form of other relative expression algorithms which uses generic permutations and a dynamic classifier size to control both the permutation and combination space available for classification. Results TSN was tested on nine cancer datasets, showing statistically significant differences in classification accuracy between different classifier sizes (choices of N). TSN also performed competitively against a wide variety of different classification methods, including artificial neural networks, classification trees, discriminant analysis, k-Nearest neighbor, naïve Bayes, and support vector machines, when tested on the Microarray Quality Control II datasets. Furthermore, TSN exhibits low levels of overfitting on training data compared to other methods, giving confidence that results obtained during cross validation will be more generally applicable to external validation sets. Conclusions TSN preserves the strengths of other relative expression algorithms while allowing a much larger permutation and combination space to be explored, potentially improving classification accuracies when fewer numbers of measured features are available. PMID:22966958

  3. Loss of p16 expression and copy number changes of CDKN2A in a spectrum of spitzoid melanocytic lesions.

    PubMed

    Harms, Paul W; Hocker, Thomas L; Zhao, Lili; Chan, May P; Andea, Aleodor A; Wang, Min; Harms, Kelly L; Wang, Michael L; Carskadon, Shannon; Palanisamy, Nallasivam; Fullen, Douglas R

    2016-12-01

    Spitzoid melanocytic lesions, including Spitz nevi (benign), spitzoid melanoma (malignant), and borderline atypical Spitz tumors (ASTs), frequently present challenges for accurate diagnosis and prognosis. Evaluation for loss of the tumor suppressor p16, encoded by CDKN2A gene on chromosome 9p21.3, has been proposed to be useful for evaluation of spitzoid melanocytic lesions. However, reports on the utility of p16 immunohistochemistry for spitzoid lesions have been conflicting, and few studies have directly compared p16 immunohistochemistry with fluorescence in situ hybridization (FISH) for CDKN2A genomic status. We analyzed a spectrum of benign (n=24), borderline (n=27), and malignant (n=19) spitzoid lesions for p16 protein expression by immunohistochemistry and CDKN2A copy number by FISH. Immunohistochemistry was evaluated by 2 scoring methods: H score and 2-tiered score (positive or negative for p16 loss). By immunohistochemistry, loss of p16 expression was not observed in Spitz nevi (0/24) but was seen in ASTs (7/27; 26%) and spitzoid melanomas (3/19; 16%). By H score, p16 expression was significantly higher in Spitz nevi relative to ASTs or spitzoid melanomas. Similarly, copy number aberrations of CDKN2A by FISH were absent in Spitz nevi but were found in 2 (9.5%) of 21 ASTs and 4 (33%) of 12 spitzoid melanomas. Our findings from this large cohort suggest that p16 aberrations are highly specific for borderline and malignant spitzoid neoplasms relative to Spitz nevi. Similar to ASTs, p16 loss in spitzoid melanomas may occur in the presence or absence of genomic CDKN2A loss.

  4. Development of Dimensionless Surge Response Functions for Hazard Assessment at Panama City, Florida

    NASA Astrophysics Data System (ADS)

    Taylor, N. R.; Irish, J. L.; Hagen, S. C.; Kaihatu, J. M.; McLaughlin, P. W.

    2013-12-01

    Reliable and robust methods of extreme value analysis in hurricane surge forecasting are of high importance in the coastal engineering profession. The Joint Probability Method (JPM) has become the preferred statistical method over the Historical Surge Population (HSP) method, due to its ability to give more accurate surge predictions, as demonstrated by Irish et. al in 2011 (J. Geophys. Res.). One disadvantage to this method is its high computational cost; a single location can require hundreds of simulated storms, each needing one thousand computational hours or more to complete. One way of overcoming this issue is to use an interpolating function, called a surge response function, to reduce the required number of simulations to a manageable number. These sampling methods, which use physical scaling laws, have been shown to significantly reduce the number of simulated storms needed for application of the JPM method. In 2008, Irish et. al. (J. Phys. Oceanogr.) demonstrated that hurricane surge scales primarily as a function of storm size and intensity. Additionally, Song et. al. in 2012 (Nat. Hazards) has shown that surge response functions incorporating bathymetric variations yield highly accurate surge estimates along the Texas coastline. This study applies the Song. et. al. model to 73 stations along the open coast, and 273 stations within the bays, in Panama City, Florida. The model performs well for the open coast and bay areas; surge levels at most stations along the open coast were predicted with RMS errors below 0.40 meters, and R2 values at or above 0.80. The R2 values for surge response functions within bays were consistently at or above 0.75. Surge levels at most stations within the North Bay and East Bay were predicted with RMS errors below 0.40 meters; within the West Bay, surge was predicted with RMS errors below 0.52 meters. Accurately interpolating surge values along the Panama City coast and bays enables efficient use of the JPM model in order to

  5. Effect of induction of SOS response on expression of pBR322 genes and on plasmid copy number

    SciTech Connect

    Bertrand-Burggraf, E.; Oertel, P.; Schnarr, M.; Daune, M.; Granger-Schnarr, M. )

    1989-09-01

    Several lines of evidence are presented that indicate that the level of tetracycline resistance of Esherichia coli strains harboring plasmid pBR322 varies according to whether the SOS system of the host bacteria has been induced. These include use of strains in which the SOS system is expressed constitutively (lexA def.), is thermoinducible (recA441) or noninducible (lexA ind-), or is highly repressed (multiple copies of lexA+). Similar induction was observed with the product of another plasmid gene, beta-lactamase. The amounts of extractable plasmid DNA were also increased by SOS induction, and we propose that the SOS-induced increases in levels of tetracycline resistance and beta-lactamase activity are due to an increased plasmid copy number.

  6. A dimensionless relative trajectory estimation algorithm for autonomous imaging of a small astronomical body in a close distance flyby

    NASA Astrophysics Data System (ADS)

    Ariu, Kaito; Inamori, Takaya; Funase, Ryu; Nakasuka, Shinichi

    2016-08-01

    The world's first micro-spacecraft, ;Proximate Object Close flYby with Optical Navigation; (PROCYON) has the advanced mission to approach an asteroid in dozen km (a one-order closer imaging distance compared with previous probes). In such a close distance encounter, the estimation of the relative trajectory of the target is necessary to perform autonomous imaging. However, the estimation is difficult owing to rapid changes of the line-of-sight direction of the target body. To overcome this problem, a novel dimensionless or direction only relative trajectory estimation algorithm, which uses a least square method, is proposed. The evaluation function for the least square method coincides with the error property of picture information to enable all of its calculations to be recursive and linear. It is suited for the implementation on the limited on-board computer. Numerical simulation results indicate that the proposed algorithm should enable the one-order closer flyby observation.

  7. Comparative analyses of gene copy number and mRNA expression in GBM tumors and GBM xenografts

    SciTech Connect

    Hodgson, J. Graeme; Yeh, Ru-Fang; Ray, Amrita; Wang, Nicholas J.; Smirnov, Ivan; Yu, Mamie; Hariono, Sujatmi; Silber, Joachim; Feiler, Heidi S.; Gray, Joe W.; Spellman, Paul T.; Vandenberg, Scott R.; Berger, Mitchel S.; James, C. David

    2009-04-03

    Development of model systems that recapitulate the molecular heterogeneity observed among glioblastoma multiforme (GBM) tumors will expedite the testing of targeted molecular therapeutic strategies for GBM treatment. In this study, we profiled DNA copy number and mRNA expression in 21 independent GBM tumor lines maintained as subcutaneous xenografts (GBMX), and compared GBMX molecular signatures to those observed in GBM clinical specimens derived from the Cancer Genome Atlas (TCGA). The predominant copy number signature in both tumor groups was defined by chromosome-7 gain/chromosome-10 loss, a poor-prognosis genetic signature. We also observed, at frequencies similar to that detected in TCGA GBM tumors, genomic amplification and overexpression of known GBM oncogenes, such as EGFR, MDM2, CDK6, and MYCN, and novel genes, including NUP107, SLC35E3, MMP1, MMP13, and DDX1. The transcriptional signature of GBMX tumors, which was stable over multiple subcutaneous passages, was defined by overexpression of genes involved in M phase, DNA replication, and chromosome organization (MRC) and was highly similar to the poor-prognosis mitosis and cell-cycle module (MCM) in GBM. Assessment of gene expression in TCGA-derived GBMs revealed overexpression of MRC cancer genes AURKB, BIRC5, CCNB1, CCNB2, CDC2, CDK2, and FOXM1, which form a transcriptional network important for G2/M progression and/or checkpoint activation. Our study supports propagation of GBM tumors as subcutaneous xenografts as a useful approach for sustaining key molecular characteristics of patient tumors, and highlights therapeutic opportunities conferred by this GBMX tumor panel for testing targeted therapeutic strategies for GBM treatment.

  8. Column Number Density Expressions Through M = 0 and M = 1 Point Source Plumes Along Any Straight Path

    NASA Technical Reports Server (NTRS)

    Woronowicz, Michael

    2017-01-01

    Providers of payloads carried aboard the International Space Station must conduct analyses to demonstrate that any planned gaseous venting events generate no more than a certain level of material that may interfere with optical measurements from other experiments or payloads located nearby. This requirement is expressed in terms of a maximum column number density (CND). Depending on the level of rarefaction, such venting may be characterized by effusion for low flow rates, or by a sonic distribution at higher levels. Since the relative locations of other sensitive payloads are often unknown because they may refer to future projects, this requirement becomes a search for the maximum CND along any path.In another application, certain astronomical observations make use of CND to estimate light attenuation from a distant star through gaseous plumes, such as the Fermi Bubbles emanating from the vicinity of the black hole at the center of our Milky Way galaxy, in order to infer the amount of material being expelled via those plumes.This paper presents analytical CND expressions developed for general straight paths based upon a free molecule point source model for steady effusive flow and for a distribution fitted to model flows from a sonic orifice. Among other things, in this Mach number range it is demonstrated that the maximum CND from a distant location occurs along the path parallel to the source plane that intersects the plume axis. For effusive flows this value is exactly twice the CND found along the ray originating from that point of intersection and extending to infinity along the plumes axis. For sonic plumes this ratio is reduced to about 43.

  9. Differential viral levels and immune gene expression in three stocks of Apis mellifera induced by different numbers of Varroa destructor.

    PubMed

    Khongphinitbunjong, Kitiphong; de Guzman, Lilia I; Tarver, Matthew R; Rinderer, Thomas E; Chen, Yanping; Chantawannakul, Panuwan

    2015-01-01

    The viral levels and immune responses of Italian honey bees (IHB), Russian honey bees (RHB) and an outcross of Varroa Sensitive Hygienic bees (POL) deliberately infested with one or two foundress Varroa were compared. We found that the Deformed wing virus (DWV) level in IHB inoculated with one or two foundress Varroa increased to about 10(3) or 10(5) fold the levels of their uninfested brood. In contrast, POL (10(2) or 10(4) fold) and RHB (10(2) or l0(4) fold) supported a lower increase in DWV levels. The feeding of different stages of Varroa nymphs did not increase DWV levels of their pupal hosts. Analyses of their corresponding Varroa mites showed the same trends: two foundress Varroa yielded higher DWV levels than one foundress, and the addition of nymphs did not increase viral levels. Using the same pupae examined for the presence of viruses, 16 out of 24 genes evaluated showed significant differential mRNA expression levels among the three honey bee stocks. However, only four genes (Defensin, Dscam, PPOact and spaetzle), which were expressed at similar levels in uninfested pupae, were altered by the number of feeding foundress Varroa and levels of DWV regardless of stocks. This research provides the first evidence that immune response profiles of different honey bee stocks are induced by Varroa parasitism.

  10. Breast cancer cell cyclooxygenase-2 expression alters extracellular matrix structure and function and numbers of cancer associated fibroblasts.

    PubMed

    Krishnamachary, Balaji; Stasinopoulos, Ioannis; Kakkad, Samata; Penet, Marie-France; Jacob, Desmond; Wildes, Flonne; Mironchik, Yelena; Pathak, Arvind P; Solaiyappan, Meiyappan; Bhujwalla, Zaver M

    2017-01-31

    Cyclooxygenase-2 (COX-2) is a critically important mediator of inflammation that significantly influences tumor angiogenesis, invasion, and metastasis. We investigated the role of COX-2 expressed by triple negative breast cancer cells in altering the structure and function of the extracellular matrix (ECM). COX-2 downregulation effects on ECM structure and function were investigated using magnetic resonance imaging (MRI) and second harmonic generation (SHG) microscopy of tumors derived from triple negative MDA-MB-231 breast cancer cells, and a derived clone stably expressing a short hairpin (shRNA) molecule downregulating COX-2. MRI of albumin-GdDTPA was used to characterize macromolecular fluid transport in vivo and SHG microscopy was used to quantify collagen 1 (Col1) fiber morphology. COX-2 downregulation decreased Col1 fiber density and altered macromolecular fluid transport. Immunohistochemistry identified significantly fewer activated cancer associated fibroblasts (CAFs) in low COX-2 expressing tumors. Metastatic lung nodules established by COX-2 downregulated cells were infrequent, smaller, and contained fewer Col1 fibers.COX-2 overexpression studies were performed with tumors derived from triple negative SUM-149 breast cancer cells lentivirally transduced to overexpress COX-2. SHG microscopy identified significantly higher Col1 fiber density in COX-2 overexpressing tumors with an increase of CAFs. These data expand upon the roles of COX-2 in shaping the structure and function of the ECM in primary and metastatic tumors, and identify the potential role of COX-2 in modifying the number of CAFs in tumors that may have contributed to the altered ECM.

  11. The dose dependence of glucocorticoid-inducible gene expression results from changes in the number of transcriptionally active templates.

    PubMed Central

    Ko, M S; Nakauchi, H; Takahashi, N

    1990-01-01

    Glucocorticoid hormones induce the transcription of genes having glucocorticoid response elements in a dose dependent manner. To determine whether this dose dependence represents a response of individual templates or of the mass of templates, we introduced a bacterial beta-galactosidase gene linked to the glucocorticoid-inducible enhancer/promoter of the mouse mammary tumor virus (MTV) into Ltk- cells and obtained stable transformants containing a single or a few templates per cell. Visual inspection and flow cytometry analysis by enzyme histochemistry assay for beta-galactosidase revealed that individual cells showed very heterogeneous beta-galactosidase activity after 48 h induction with dexamethasone. When the glucocorticoid concentration was increased, an increasing cell population producing beta-galactosidase was observed. These phenomena were probably not due to heterogeneity of template copy number or to a predetermined cellular state among individual cells, since cells forming a single small colony gave similar results. This was also supported by data showing that recloned cells retained both their responsiveness to the glucocorticoid hormone and their digestion pattern in Southern blotting analyses. These results indicate that the dose dependent increase of glucocorticoid-inducible gene expression is caused by an increase in the number of transcriptionally active templates. Images Fig. 1. Fig. 3. Fig. 4. Fig. 5. Fig. 8. PMID:2167833

  12. Nusselt numbers of laminar, oscillating flows in stacks and regenerators with pores of arbitrary cross-sectional geometry.

    PubMed

    Brady, John F

    2013-04-01

    Though widely used in steady-flow heat transfer applications, the Nusselt number-a dimensionless heat transfer coefficient-has not been studied as thoroughly in oscillating flows and is therefore not generally used in thermoacoustic applications. This paper presents expressions for the Nusselt numbers of laminar oscillating flows within the pores of stacks and regenerators, derived from thermoacoustic theory developed by Rott and Swift. These expressions are based on bulk (velocity-weighted, cross-sectionally averaged) temperature, rather than the cross-sectionally averaged temperature. Results are shown for parallel plates, circular pores, rectangular pores, and within the boundary layer limit. It is shown that bulk temperature does not become infinite during an acoustic cycle and that the Nusselt number is a complex constant at all times. In addition, steady-flow Nusselt numbers are recovered when velocity and temperature profiles are like those in steady flows.

  13. A Coursewriter II Function (FCALC) For the Manipulation of Numerical and Algebraic Expressions. Systems Memo Number One.

    ERIC Educational Resources Information Center

    Smith, Authella; And Others

    Documentation of the Coursewriter II Function FCALC is provided. The function is designed for use on the IBM 1500 instructional system and has three major applications: 1) comparison of a numeric expression in buffer 5 with a numeric expression in buffer 0; 2) comparison of an algebraic expression in buffer 5 with an algebraic expression in buffer…

  14. Empirical, dimensionless, cumulative-rainfall hyetographs developed from 1959-86 storm data for selected small watersheds in Texas

    USGS Publications Warehouse

    Williams-Sether, Tara; Asquith, William H.; Thompson, David B.; Cleveland, Theodore G.; Fang, Xing

    2004-01-01

    A database of incremental cumulative-rainfall values for storms that occurred in small urban and rural watersheds in north and south central Texas during the period from 1959 to 1986 was used to develop empirical, dimensionless, cumulative-rainfall hyetographs. Storm-quartile classifications were determined from the cumulative-rainfall values, which were divided into data groups on the basis of storm-quartile classification (first, second, third, fourth, and first through fourth combined), storm duration (0 to 6, 6 to 12, 12 to 24, 24 to 72, and 0 to 72 hours), and rainfall amount (1 inch or more). Removal of long leading tails, in effect, shortened the storm duration and, in some cases, affected the storm-quartile classification. Therefore, two storm groups, untrimmed and trimmed, were used for analysis. The trimmed storms generally are preferred for interpretation. For a 12-hour or less trimmed storm duration, approximately 49 percent of the storms are first quartile. For trimmed storm durations of 12 to 24 and 24 to 72 hours, 47 and 38 percent, respectively, of the storms are first quartile. For a trimmed storm duration of 0 to 72 hours, the first-, second-, third-, and fourth-quartile storms accounted for 46, 21, 20, and 13 percent of all storms, respectively. The 90th-percentile curve for first-quartile storms indicated about 90 percent of the cumulative rainfall occurs during the first 20 percent of the storm duration. The 10th-percentile curve for first-quartile storms indicated about 30 percent of the cumulative rainfall occurs during the first 20 percent of the storm duration. The 90th-percentile curve for fourth-quartile storms indicated about 33 percent of the cumulative rainfall occurs during the first 20 percent of the storm duration. The 10th-percentile curve for fourth-quartile storms indicated less than 5 percent of the cumulative rainfall occurs during the first 20 percent of the storm duration. Statistics for the empirical, dimensionless

  15. Empirical, dimensionless, cumulative-rainfall hyetographs developed from 1959-86 storm data for selected small watersheds in Texas

    USGS Publications Warehouse

    Williams-Sether, Tara; Asquith, William H.; Thompson, David B.; Cleveland, Theodore G.; Fang, Xing

    2004-01-01

    A database of incremental cumulative-rainfall values for storms that occurred in small urban and rural watersheds in north and south central Texas during the period from 1959 to 1986 was used to develop empirical, dimensionless, cumulative-rainfall hyetographs. Storm-quartile classifications were determined from the cumulative-rainfall values, which were divided into data groups on the basis of storm-quartile classification (first, second, third, fourth, and first through fourth combined), storm duration (0 to 6, 6 to 12, 12 to 24, 24 to 72, and 0 to 72 hours), and rainfall amount (1 inch or more). Removal of long leading tails, in effect, shortened the storm duration and, in some cases, affected the storm-quartile classification. Therefore, two storm groups, untrimmed and trimmed, were used for analysis. The trimmed storms generally are preferred for interpretation. For a 12-hour or less trimmed storm duration, approximately 49 percent of the storms are first quartile. For trimmed storm durations of 12 to 24 and 24 to 72 hours, 47 and 38 percent, respectively, of the storms are first quartile. For a trimmed storm duration of 0 to 72 hours, the first-, second-, third-, and fourth-quartile storms accounted for 46, 21, 20, and 13 percent of all storms, respectively. The 90th-percentile curve for first-quartile storms indicated about 90 percent of the cumulative rainfall occurs during the first 20 percent of the storm duration. The 10th-percentile curve for first-quartile storms indicated about 30 percent of the cumulative rainfall occurs during the first 20 percent of the storm duration. The 90th-percentile curve for fourth-quartile storms indicated about 33 percent of the cumulative rainfall occurs during the first 20 percent of the storm duration. The 10th-percentile curve for fourth-quartile storms indicated less than 5 percent of the cumulative rainfall occurs during the first 20 percent of the storm duration. Statistics for the empirical, dimensionless

  16. bla(KPC) RNA expression correlates with two transcriptional start sites but not always with gene copy number in four genera of Gram-negative pathogens.

    PubMed

    Roth, Amanda L; Kurpiel, Philip M; Lister, Philip D; Hanson, Nancy D

    2011-08-01

    Klebsiella pneumoniae carbapenemase (KPC)-producing organisms are therapeutically and diagnostically challenging. It is possible that bla(KPC) gene expression plays a role in the variability observed in clinical susceptibility testing. bla(KPC) transformants together with 10 clinical isolates representing four genera were evaluated for bla(KPC) copy number and gene expression and correlated with β-lactam MIC data. The data suggest that mechanisms other than gene copy number and expression of bla(KPC) contribute to variability in susceptibility when testing KPC-producing isolates.

  17. Characterization of gear faults in variable rotating speed using Hilbert-Huang Transform and instantaneous dimensionless frequency normalization

    NASA Astrophysics Data System (ADS)

    Wu, T. Y.; Chen, J. C.; Wang, C. C.

    2012-07-01

    The objective of this research is to investigate the feasibility of utilizing the instantaneous dimensionless frequency (DLF) normalization and Hilbert-Huang Transform (HHT) to characterize the different gear faults in case of variable rotating speed. The normalized DLF of the vibration signals are calculated based on the rotating speed of shaft and the instantaneous frequencies of Intrinsic Mode Functions (IMFs) which are decomposed by Empirical Mode Decomposition (EMD) process. The faulty gear features on DLF-energy distribution of vibration signal can be extracted without the presence of shaft rotating speed, so that the proposed approach can be applied for characterizing the malfunctions of gearbox system under variable shaft rotating speed. A test rig of gear transmission system is performed to illustrate the gear faults, including worn tooth, broken tooth and gear unbalance. Different methods to determine the instantaneous frequency are employed to verify the consistence of characterization results. The DLF-energy distributions of vibration signals are investigated in different faulty gear conditions. The analysis results demonstrate the capability and effectiveness of the proposed approach for characterizing the gear malfunctions at the DLFs corresponding to the meshing frequency as well as the shaft rotating frequency. The support vector machine (SVM) is then employed to classify the vibration patterns of gear transmission system at different malfunctions. Using the energy distribution at the characteristic DLFs as the features, the different fault types of gear can be identified by SVM with high accuracy.

  18. Maternal and cord blood miR-223 expression associates with prenatal tobacco smoke exposure and low regulatory T-cell numbers.

    PubMed

    Herberth, Gunda; Bauer, Mario; Gasch, Michaela; Hinz, Denise; Röder, Stefan; Olek, Sven; Kohajda, Tibor; Rolle-Kampczyk, Ulrike; von Bergen, Martin; Sack, Ulrich; Borte, Michael; Lehmann, Irina

    2014-02-01

    There is evidence that microRNAs (miRNAs) are sensitive to environmental stressors, including tobacco smoke. On the other hand, miRNAs are involved in immune regulation, such as regulatory T (Treg) cell differentiation. The aim of the present study was to investigate the association between prenatal tobacco smoke exposure, miRNAs, and Treg cell numbers. Within a prospective mother-child study (Lifestyle and Environmental Factors and Their Influence on Newborns Allergy Risk), we analyzed the expression of miR-155 and miR-223 together with Treg cell numbers in maternal blood during pregnancy, as well as in cord blood (n = 441). Tobacco smoke exposure was assessed based on questionnaire answers and maternal urine cotinine levels. Additionally, the concentration of smoking-related volatile organic compounds was measured in dwellings of study participants. Both maternal and cord blood miR-223 expressions were positively correlated with maternal urine cotinine levels. An association was also found between maternal miR-223 expression and indoor concentrations of benzene and toluene. High miR-223 expression was associated with lower Treg cell numbers in maternal and cord blood. Furthermore, children with lower Treg cell numbers at birth had a higher risk of atopic dermatitis during the first 3 years of life. The concentration of the toluene metabolite S-benzylmercapturic acid in maternal urine was associated with decreased cord blood, but not maternal blood, miR-155 expression. A relationship between miR-155 expression and Treg cell numbers was not found. For the first time, we show that maternal tobacco smoke exposure during pregnancy correlates with the level of miRNA-223 expression in blood, with an effect on children's cord blood Treg cell numbers and subsequent allergy risk. Copyright © 2013 American Academy of Allergy, Asthma & Immunology. Published by Mosby, Inc. All rights reserved.

  19. Partition resampling and extrapolation averaging: approximation methods for quantifying gene expression in large numbers of short oligonucleotide arrays.

    PubMed

    Goldstein, Darlene R

    2006-10-01

    Studies of gene expression using high-density short oligonucleotide arrays have become a standard in a variety of biological contexts. Of the expression measures that have been proposed to quantify expression in these arrays, multi-chip-based measures have been shown to perform well. As gene expression studies increase in size, however, utilizing multi-chip expression measures is more challenging in terms of computing memory requirements and time. A strategic alternative to exact multi-chip quantification on a full large chip set is to approximate expression values based on subsets of chips. This paper introduces an extrapolation method, Extrapolation Averaging (EA), and a resampling method, Partition Resampling (PR), to approximate expression in large studies. An examination of properties indicates that subset-based methods can perform well compared with exact expression quantification. The focus is on short oligonucleotide chips, but the same ideas apply equally well to any array type for which expression is quantified using an entire set of arrays, rather than for only a single array at a time. Software implementing Partition Resampling and Extrapolation Averaging is under development as an R package for the BioConductor project.

  20. Bioinformatic identification of prognostic signature defined by copy number alteration and expression of CCNE1 in non-muscle invasive bladder cancer

    PubMed Central

    Song, Bic-Na; Kim, Seon-Kyu; Chu, In-Sun

    2017-01-01

    Non-muscle invasive bladder cancer (NMIBC) patients frequently fail to respond to treatment and experience disease progression because of their clinical and biological diversity. In this study, we identify a prognostic molecular signature for predicting the heterogeneity of NMIBC by using an integrative analysis of copy number and gene expression data. We analyzed the copy number and gene expression profiles of 404 patients with bladder cancer obtained from The Cancer Genome Atlas (TCGA) consortium. Of the 14 molecules with significant copy number alterations that were previously reported, 13 were significantly correlated with copy number and expression changes. Prognostic gene sets based on the 13 genes were developed, and their prognostic values were verified in three independent patient cohorts (n=501). Among them, a signature of CCNE1 and its coexpressed genes was significantly associated with disease progression and validated in the independent cohorts. The CCNE1 signature was an independent risk factor based on the result of a multivariate analysis (hazard ratio=6.849, 95% confidence interval=1.613–29.092, P=0.009). Finally, gene network and upstream regulator analyses revealed that NMIBC progression is potentially mediated by CCND1-CCNE1-SP1 pathways. The prognostic molecular signature defined by copy number and expression changes of CCNE1 suggests a novel diagnostic tool for predicting the likelihood of NMIBC progression. PMID:28082741

  1. Integrative analysis of copy number and gene expression in breast cancer using formalin-fixed paraffin-embedded core biopsy tissue: a feasibility study.

    PubMed

    Iddawela, Mahesh; Rueda, Oscar; Eremin, Jenny; Eremin, Oleg; Cowley, Jed; Earl, Helena M; Caldas, Carlos

    2017-07-11

    An absence of reliable molecular markers has hampered individualised breast cancer treatments, and a major limitation for translational research is the lack of fresh tissue. There are, however, abundant banks of formalin-fixed paraffin-embedded (FFPE) tissue. This study evaluated two platforms available for the analysis of DNA copy number and gene expression using FFPE samples. The cDNA-mediated annealing, selection, extension, and ligation assay (DASL™) has been developed for gene expression analysis and the Molecular Inversion Probes assay (Oncoscan™), were used for copy number analysis using FFPE tissues. Gene expression and copy number were evaluated in core-biopsy samples from patients with breast cancer undergoing neoadjuvant chemotherapy (NAC). Forty-three core-biopsies were evaluated and characteristic copy number changes in breast cancers, gains in 1q, 8q, 11q, 17q and 20q and losses in 6q, 8p, 13q and 16q, were confirmed. Regions that frequently exhibited gains in tumours showing a pathological complete response (pCR) to NAC were 1q (55%), 8q (40%) and 17q (40%), whereas 11q11 (37%) gain was the most frequent change in non-pCR tumours. Gains associated with poor survival were 11q13 (62%), 8q24 (54%) and 20q (47%). Gene expression assessed by DASL correlated with immunohistochemistry (IHC) analysis for oestrogen receptor (ER) [area under the curve (AUC) = 0.95], progesterone receptor (PR)(AUC = 0.90) and human epidermal growth factor type-2 receptor (HER-2) (AUC = 0.96). Differential expression analysis between ER+ and ER- cancers identified over-expression of TTF1, LAF-4 and C-MYB (p ≤ 0.05), and between pCR vs non-pCRs, over-expression of CXCL9, AREG, B-MYB and under-expression of ABCG2. This study was an integrative analysis of copy number and gene expression using FFPE core biopsies and showed that molecular marker data from FFPE tissues were consistent with those in previous studies using fresh-frozen samples. FFPE tissue can provide

  2. Number Guessing

    ERIC Educational Resources Information Center

    Sezin, Fatin

    2009-01-01

    It is instructive and interesting to find hidden numbers by using different positional numeration systems. Most of the present guessing techniques use the binary system expressed as less-than, greater-than or present-absent type information. This article describes how, by employing four cards having integers 1-64 written in different colours, one…

  3. Tissue expression map of a large number of expressed sequence tags and its application to in silico screening of stress response genes in common wheat.

    PubMed

    Mochida, Keiichi; Kawaura, Kanako; Shimosaka, Etsuo; Kawakami, Naoto; Shin-I, Tadasu; Kohara, Yuji; Yamazaki, Yukiko; Ogihara, Yasunari

    2006-09-01

    In order to assess global changes in gene expression patterns in stress-induced tissues, we conducted large-scale analysis of expressed sequence tags (ESTs) in common wheat. Twenty-one cDNA libraries derived from stress-induced tissues, such as callus, as well as liquid cultures and abiotic stress conditions (temperature treatment, desiccation, photoperiod, moisture and ABA) were constructed. Several thousand colonies were randomly selected from each of these 21 cDNA libraries and sequenced from both the 5' and 3' ends. By computing abundantly expressed ESTs, correlated expression patterns of genes across the tissues were monitored. Furthermore, the relationships between gene expression profiles among the stress-induced tissues were inferred from the gene expression patterns. Multi-dimensional analysis of EST data is analogous to microarray experiments. As an example, genes specifically induced and/or suppressed by cold acclimation and heat-shock treatments were selected in silico. Four hundred and ninety genes showing fivefold induction or 218 genes for suppression in comparison to the control expression level were selected. These selected genes were annotated with the BLAST search. Furthermore, gene ontology was conducted for these genes with the InterPro search. Because genes regulated in response to temperature treatment were successfully selected, this method can be applied to other stress-treated tissues. Then, the method was applied to screen genes in response to abiotic stresses such as drought and ABA treatments. In silico selection of screened genes from virtual display should provide a powerful tool for functional plant genomics.

  4. Long-term effects of a neonatal low-protein diet in rats on the number of macrophages in culture and the expression/production of fusion proteins.

    PubMed

    de Melo, Juliana Félix; da Costa, Thacianna Barreto; da Costa Lima, Tamara D; Chaves, Maria E C; Vayssade, Muriel; Nagel, Marie-Danielle; de Castro, Célia M M B

    2013-08-01

    To investigate the effects of a neonatal low-protein diet on the number of macrophages in culture and the expression/production of proteins that regulate macrophage fusion in young and adult rats. Male Wistar rats (n = 18) were suckled by mothers fed diets containing 17 % protein (controls, C) or 8 % protein (undernourished, UN). All rats were fed a normal protein diet after weaning. Bronchoalveolar lavage was collected from 42-, 60- and 90-day-old rats. Alveolar macrophages were cultured for 4 days to assess the number of cells and the expression of cadherins, key proteins involved in macrophage fusion, by western blotting. IL-4 and IFN-γ levels in culture supernatants were measured by ELISA. Offspring from mothers fed a low-protein diet showed a lower body weight gain. The number of cells in cultured macrophages from UN was reduced at 42 and 60 days and increased at 90 days. IL-4 production was increased in the supernatants from UN group at 60 days but did not affect the expression of cadherins. IFN-γ production was increased in the supernatants from UN group at 42 and 60 days and reduced at 90 days. This study thus demonstrated that dietary restriction during lactation altered the number of alveolar macrophages in culture and the production of fusion proteins of offspring aged 42, 60 or 90 days but did not modify the expression of adhesion molecules important for the fusion of these cells.

  5. Approximate expressions that describe the profiles of sessile and pendent drops for the cases of small Bond numbers and strong wetting

    NASA Astrophysics Data System (ADS)

    Galaktionov, E. V.; Galaktionova, N. E.; Tropp, E. A.

    2016-12-01

    Variational formulations of the problems of sessile and pendent drops are given taking into account the force of gravity in the axially symmetric case. Approximate expressions that describe the surface profiles of these drops by the asymptotic method for small Bond numbers have been obtained by the linearization method in the case of strong wetting.

  6. Identification of Novel Breast Cancer Subtype-Specific Biomarkers by Integrating Genomics Analysis of DNA Copy Number Aberrations and miRNA-mRNA Dual Expression Profiling.

    PubMed

    Li, Dongguo; Xia, Hong; Li, Zhen-ya; Hua, Lin; Li, Lin

    2015-01-01

    Breast cancer is a heterogeneous disease with well-defined molecular subtypes. Currently, comparative genomic hybridization arrays (aCGH) techniques have been developed rapidly, and recent evidences in studies of breast cancer suggest that tumors within gene expression subtypes share similar DNA copy number aberrations (CNA) which can be used to further subdivide subtypes. Moreover, subtype-specific miRNA expression profiles are also proposed as novel signatures for breast cancer classification. The identification of mRNA or miRNA expression-based breast cancer subtypes is considered an instructive means of prognosis. Here, we conducted an integrated analysis based on copy number aberrations data and miRNA-mRNA dual expression profiling data to identify breast cancer subtype-specific biomarkers. Interestingly, we found a group of genes residing in subtype-specific CNA regions that also display the corresponding changes in mRNAs levels and their target miRNAs' expression. Among them, the predicted direct correlation of BRCA1-miR-143-miR-145 pairs was selected for experimental validation. The study results indicated that BRCA1 positively regulates miR-143-miR-145 expression and miR-143-miR-145 can serve as promising novel biomarkers for breast cancer subtyping. In our integrated genomics analysis and experimental validation, a new frame to predict candidate biomarkers of breast cancer subtype is provided and offers assistance in order to understand the potential disease etiology of the breast cancer subtypes.

  7. Integrative analysis of DNA copy number and gene expression in metastatic oral squamous cell carcinoma identifies genes associated with poor survival

    PubMed Central

    2010-01-01

    Background Lymphotropism in oral squamous cell carcinoma (OSCC) is one of the most important prognostic factors of 5-year survival. In an effort to identify genes that may be responsible for the initiation of OSCC lymphotropism, we examined DNA copy number gains and losses and corresponding gene expression changes from tumor cells in metastatic lymph nodes of patients with OSCC. Results We performed integrative analysis of DNA copy number alterations (CNA) and corresponding mRNA expression from OSCC cells isolated from metastatic lymph nodes of 20 patients using Affymetrix 250 K Nsp I SNP and U133 Plus 2.0 arrays, respectively. Overall, genome CNA accounted for expression changes in 31% of the transcripts studied. Genome region 11q13.2-11q13.3 shows the highest correlation between DNA CNA and expression. With a false discovery rate < 1%, 530 transcripts (461 genes) demonstrated a correlation between CNA and expression. Among these, we found two subsets that were significantly associated with OSCC (n = 122) when compared to controls, and with survival (n = 27), as tested using an independent dataset with genome-wide expression profiles for 148 primary OSCC and 45 normal oral mucosa. We fit Cox models to calculate a principal component analysis-derived risk-score for these two gene sets ('122-' or '27-transcript PC'). The models combining the 122- or 27-transcript PC with stage outperformed the model using stage alone in terms of the Area Under the Curve (AUC = 0.82 or 0.86 vs. 0.72, with p = 0.044 or 0.011, respectively). Conclusions Genes exhibiting CNA-correlated expression may have biological impact on carcinogenesis and cancer progression in OSCC. Determination of copy number-associated transcripts associated with clinical outcomes in tumor cells with an aggressive phenotype (i.e., cells metastasized to the lymph nodes) can help prioritize candidate transcripts from high-throughput data for further studies. PMID:20537188

  8. Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome

    PubMed Central

    Ravasi, Timothy; Suzuki, Harukazu; Pang, Ken C.; Katayama, Shintaro; Furuno, Masaaki; Okunishi, Rie; Fukuda, Shiro; Ru, Kelin; Frith, Martin C.; Gongora, M. Milena; Grimmond, Sean M.; Hume, David A.; Hayashizaki, Yoshihide; Mattick, John S.

    2006-01-01

    Recent large-scale analyses of mainly full-length cDNA libraries generated from a variety of mouse tissues indicated that almost half of all representative cloned sequences did not contain an apparent protein-coding sequence, and were putatively derived from non-protein-coding RNA (ncRNA) genes. However, many of these clones were singletons and the majority were unspliced, raising the possibility that they may be derived from genomic DNA or unprocessed pre-mRNA contamination during library construction, or alternatively represent nonspecific “transcriptional noise.” Here we show, using reverse transcriptase-dependent PCR, microarray, and Northern blot analyses, that many of these clones were derived from genuine transcripts of unknown function whose expression appears to be regulated. The ncRNA transcripts have larger exons and fewer introns than protein-coding transcripts. Analysis of the genomic landscape around these sequences indicates that some cDNA clones were produced not from terminal poly(A) tracts but internal priming sites within longer transcripts, only a minority of which is encompassed by known genes. A significant proportion of these transcripts exhibit tissue-specific expression patterns, as well as dynamic changes in their expression in macrophages following lipopolysaccharide stimulation. Taken together, the data provide strong support for the conclusion that ncRNAs are an important, regulated component of the mammalian transcriptome. PMID:16344565

  9. Assessment of Tumor Heterogeneity, as Evidenced by Gene Expression Profiles, Pathway Activation, and Gene Copy Number, in Patients with Multifocal Invasive Lobular Breast Tumors.

    PubMed

    Norton, Nadine; Advani, Pooja P; Serie, Daniel J; Geiger, Xochiquetzal J; Necela, Brian M; Axenfeld, Bianca C; Kachergus, Jennifer M; Feathers, Ryan W; Carr, Jennifer M; Crook, Julia E; Moreno-Aspitia, Alvaro; Anastasiadis, Panos Z; Perez, Edith A; Thompson, E Aubrey

    2016-01-01

    Invasive lobular carcinoma (ILC) comprises approximately ~10-20% of breast cancers. In general, multifocal/multicentric (MF/MC) breast cancer has been associated with an increased rate of regional lymph node metastases. Tumor heterogeneity between foci represents a largely unstudied source of genomic variation in those rare patients with MF/MC ILC. We characterized gene expression and copy number in 2 or more foci from 11 patients with MF/MC ILC (all ER+, HER2-) and adjacent normal tissue. RNA and DNA were extracted from 3x1.5 mm cores from all foci. Gene expression (730 genes) and copy number (80 genes) were measured using Nanostring PanCancer and Cancer CNV panels. Linear mixed models were employed to compare expression in tumor versus normal samples from the same patient, and to assess heterogeneity (variability) in expression among multiple ILC within an individual. 35 and 34 genes were upregulated (FC>2) and down-regulated (FC<0.5) respectively in ILC tumor relative to adjacent normal tissue, q<0.05. 9/34 down-regulated genes (FIGF, RELN, PROM1, SFRP1, MMP7, NTRK2, LAMB3, SPRY2, KIT) had changes larger than CDH1, a hallmark of ILC. Copy number changes in these patients were relatively few but consistent across foci within each patient. Amplification of three genes (CCND1, FADD, ORAOV1) at 11q13.3 was present in 2/11 patients in both foci. We observed significant evidence of within-patient between-foci variability (heterogeneity) in gene expression for 466 genes (p<0.05 with FDR 8%), including CDH1, FIGF, RELN, SFRP1, MMP7, NTRK2, LAMB3, SPRY2 and KIT. There was substantial variation in gene expression between ILC foci within patients, including known markers of ILC, suggesting an additional level of complexity that should be addressed.

  10. Novel copy number variation of the TGFβ3 gene is associated with TGFβ3 gene expression and duration of fertility traits in hens

    PubMed Central

    Gu, Lantao; Sun, Chenghao; Gong, Yangzhang; Yu, Mei; Li, Shijun

    2017-01-01

    Improvements in the duration of fertility (DF) could increase the interval between successive artificial inseminations, thereby decreasing the cost associated with production of hatching eggs. The molecular mechanisms involved in DF in hens remains under-explored. In this study, expression levels of the transforming growth factor-β genes (TGFβs: TGFβ1, TGFβ2, TGFβ3) were investigated in utero-vaginal junctions (UVJs) of hens with long DF (Group L, n = 10) and short DF (Group S, n = 10). TGFβ1 and 2 tended to exhibit higher expression levels in UVJs from Group L hens. The expression levels of TGFβ3 mRNA and protein were significantly increased in UVJs of hens from Group L compared to hens in Group S. Consistently, six TGFβs downstream genes (DAXX, MEKK1, T-BET, GATA-3, TAK1, and FOXP3) associated with the immune response were found to be significantly differentially expressed in UVJs of Group L than Group S hens. In addition, four SNPs were identified in intron 1 of TGFβ3, and these SNPs were significantly associated with DF traits (P < 0.05). Furthermore, we identified multi-copy and copy number variants (CNVs) in chicken TGFβ3 and later determined significant associations between TGFβ3 CNVs and DF traits in hens. Specifically, TGFβ3 copy number exhibited a significant positive correlation with its expression (P < 0.05). Collectively, our results suggest that chicken DF traits may be regulated by the expression of TGFβ3 in UVJ. Meanwhile, the copy number variation in the TGFβ3 gene identified in this study seems to be one marker for DF traits. PMID:28301526

  11. Adenovirus-mediated ectopic expression of Msx2 in even-numbered rhombomeres induces apoptotic elimination of cranial neural crest cells in ovo.

    PubMed

    Takahashi, K; Nuckolls, G H; Tanaka, O; Semba, I; Takahashi, I; Dashner, R; Shum, L; Slavkin, H C

    1998-05-01

    Distinct cranial neural crest-derived cell types (a number of neuronal as well as non-neuronal cell lineages) are generated at characteristic times and positions in the rhombomeres of the hindbrain in developing vertebrate embryos. To examine this developmental process, we developed a novel strategy designed to test the efficacy of gain-of-function Msx2 expression within rhombomeres in ovo prior to the emigration of cranial neural crest cells (CNCC). Previous studies indicate that CNCC from odd-numbered rhombomeres (r3 and r5) undergo apoptosis in response to exogenous BMP4. We provide evidence that targeted infection in ovo using adenovirus containing Msx2 and a reporter molecule indicative of translation can induce apoptosis in either even- or odd-numbered rhombomeres. Furthermore, infected lacZ-control explants indicated that CNCC emigrated, and that 20% of these cells were double positive for crest cell markers HNK-1 and beta-gal. In contrast, there were no HNK-1 and Msx2 double positive cells emigrating from Msx2 infected explants. These results support the hypothesis that apoptotic elimination of CNCC can be induced by 'gain-of-function' Msx2 expression in even-numbered rhombomeres. These inductive interactions involve qualitative, quantitative, positional and temporal differences in TGF-beta-related signals, Msx2 expression and other transcriptional control.

  12. Integrated Genome-wide DNA Copy Number and Expression Analysis Identifies Distinct Mechanisms of Primary Chemo-resistance in Ovarian Carcinomas

    PubMed Central

    Etemadmoghadam, Dariush; deFazio, Anna; Beroukhim, Rameen; Mermel, Craig; George, Joshy; Getz, Gaddy; Tothill, Richard; Okamoto, Aikou; Raeder, Maria B; Harnett, Paul; Lade, Stephen; Akslen, Lars A; Tinker, Anna; Locandro, Bianca; Alsop, Kathryn; Chiew, Yoke-Eng; Traficante, Nadia; Fereday, Sian; Johnson, Daryl; Fox, Stephen; Sellers, William; Urashima, Mitsuyoshi; Salvesen, Helga B; Meyerson, Matthew; Bowtell, David

    2009-01-01

    Purpose A significant number of women with serous ovarian cancer are intrinsically refractory to platinum-taxol based treatment. We analyzed somatic DNA copy number variation (CNV) and gene expression data to identify key mechanisms associated with primary resistance in advanced-stage serous cancers. Experimental Design Genome-wide CNV was measured in 118 ovarian tumors using high-resolution oligonucleotide microarrays. A well-defined subset of 85 advanced-stage serous tumors was then used to relate CNV to primary resistance to treatment. The discovery-based approach was complemented by quantitative-PCR copy number analysis of twelve candidate genes as independent validation of previously reported associations with clinical outcome. Likely CNV targets and tumor molecular subtypes were further characterized by gene expression profiling. Results Amplification of 19q12, containing Cyclin E (CCNE1) and 20q11.22-q13.12, mapping immediately adjacent to the steroid receptor co-activator NCOA3, were significantly associated with poor response to primary treatment. Other genes previously associated with CNV and clinical outcome in ovarian cancer were not associated with primary treatment resistance. Chemoresistant tumors with high CCNE1 copy number and protein expression were associated with increased cellular proliferation but so too were a subset of treatment responsive patients, suggesting a cell-cycle independent role for CCNE1 in modulating chemoresponse. Patients with a poor clinical outcome without CCNE1 amplification over expressed genes involved in extracellular matrix deposition. Conclusions We have identified two distinct mechanisms of primary treatment failure in serous ovarian cancer, involving CCNE1 amplification and enhanced extracellular matrix deposition. CCNE1 copy number is validated as a dominant marker of patient outcome in ovarian cancer. PMID:19193619

  13. The number of cells expressing the myelin-supporting oligodendrocyte marker PLP-exon 3b remains unchanged in Wallerian degeneration.

    PubMed

    Li, G; Blakemore, W F

    2004-08-01

    Following spinal cord trauma there is controversy as to whether myelin-supporting oligodendrocytes at a distance from areas of spinal cord damage undergo apoptosis. To examine the response of oligodendrocytes to axon degeneration, we counted the number of oligodendrocytes and oligodendrocyte precursors in the dorsal funiculi during the course of Wallerian degeneration. Axons were disrupted at T13 and the number of labelled cells in the dorsal funiculi counted at T12, 4 days and 2, 4, and 8 weeks after injury using riboprobes to exon-3b of the PLP gene whose expression is considered to restricted to myelin-supporting oligodendrocytes, PDGFRalpha which is regarded as a marker of oligodendrocyte precursors, and MOG a marker previously used to identify myelin-supporting oligodendrocytes. We found that the number of PLP-exon-3b labelled cells remained constant during the course of Wallerian degeneration while the number of cells labelled with the riboprobes to PDGFRalpha and MOG increased. Significantly the number of MOG-positive cells was increased at times when the number of PDGFRalpha labelled cells was highest. The number of PDGFRalpha labelled cells decreased with time while the number PLP-exon-3b labelled cells remained constant. It is therefore possible that the apoptotic oligodendrocytes identified in previous studies could represent degenerating oligodendrocyte precursors or their progeny rather than degenerating myelin-supporting oligodendrocytes.

  14. Increased levels of prolactin receptor expression correlate with the early onset of lupus symptoms and increased numbers of transitional-1 B cells after prolactin treatment

    PubMed Central

    2012-01-01

    Background Prolactin is secreted from the pituitary gland and other organs, as well as by cells such as lymphocytes. Prolactin has an immunostimulatory effect and is associated with autoimmune diseases that are characterised by abnormal B cell activation, such as systemic lupus erythematosus (SLE). Our aim was to determine if different splenic B cell subsets express the prolactin receptor and if the presence of prolactin influences these B cell subsets and correlates with development of lupus. Results Using real-time PCR and flow cytometry, we found that different subsets of immature (transitional) and mature (follicular, marginal zone) B cells express different levels of the prolactin receptor and are differentially affected by hyperprolactinaemia. We found that transitional B cells express the prolactin receptor at higher levels compared to mature B cells in C57BL/6 mice and the lupus-prone MRL/lpr and MRL mouse strains. Transitional-1 (T1) B cells showed a higher level of prolactin receptor expression in both MRL/lpr and MRL mice compared to C57BL/6 mice. Hyperprolactinaemia was induced using metoclopramide, which resulted in the development of early symptoms of SLE. We found that T1 B cells are the main targets of prolactin and that prolactin augments the absolute number of T1 B cells, which reflects the finding that this B cell subpopulation expresses the highest level of the prolactin receptor. Conclusions We found that all B cell subsets express the prolactin receptor but that transitional B cells showed the highest prolactin receptor expression levels. Hyperprolactinaemia in mice susceptible to lupus accelerated the disease and increased the absolute numbers of T1 and T3 B cells but not of mature B cells, suggesting a primary effect of prolactin on the early stages of B cell maturation in the spleen and a role of prolactin in B cell differentiation, contributing to SLE onset. PMID:22404893

  15. Influence of the number of vehicles in the emergence of sound events on the annoyance expressed - experimental study

    NASA Technical Reports Server (NTRS)

    Vallet, M.

    1982-01-01

    The acoustical index leg was studied to determine its accuracy in predicting annoyance from traffic noise. Annoyance was tested in experimental situations where the frequency of the number of heavy vehicles varied from 3 to 30 HV/30 min for different classes of the Leg level at 50, 55, 60 dB(A) of traffic noise. The results showed that: (1) for a constant Leg level the annoyance increases as a function of the number of HV up to a certain threshold at which the annoyance is stabilized; (2) for a constant frequency of passage of HV, the annoyance increases with the Leg level; (3) composite indexes of the type Leg + Log NHV, L1 + EMER or L1 + L10 give a predictive value greater than that of the Leg pr Log nHV taken alone.

  16. Expression of platelet-bound stromal-cell derived factor-1 (SDF-1) and number of CD34(+) progenitor cells in patients with congestive heart failure.

    PubMed

    Jorbenadze, Rezo; Schleicher, Erwin; Bigalke, Boris; Stellos, Konstantinos; Gawaz, Meinrad

    2014-01-01

    Platelet-bound stromal cell-derived factor-1 (SDF-1) plays a crucial role in attachment of circulating CD34(+) progenitor cells to the vascular wall, facilitating tissue healing after injury. However there is no evidence about expression of platelet-bound SDF-1 in patients with congestive heart failure (CHF). The aim of our study was to evaluate expression of platelet-bound SDF-1 and number of CD34(+) progenitor cells in patients with CHF. Forty-eight patients with idiopathic dilated cardiomyopathy (DCM) and 61 patients with ischaemic cardiomyopathy (ICM) were consecutively enrolled into the study. Blood taken from 109 consecutive patients was studied for surface expression of platelet-bound SDF-1 and number of CD34(+) progenitor cells by flow cytometry. The highest expression of platelet-bound SDF-1 was observed in patients with severe impairment of left ventricular systolic function compared with patients with mild or moderate impairment of left ventricular systolic function (mild vs. moderate vs. severe impairment of left ventricular systolic function: MFI ± SD: 35.6 ± 34 vs. 101.45 ± 73 vs. 124.86 ± 86.7, Kruskal-Wallis p < 0.001). Similar to platelet-bound SDF-1 number of CD34(+) progenitor cells was the highest in severe impairment of left ventricular systolic function (mild vs. moderate vs. severe impairment of left ventricular systolic function: mean ± SD: 260.4 ± 177.5 vs. 580.7 ± 340.5 vs. 640.82 ± 370.6, Kruskal-Wallis p < 0.001). Platelet-bound SDF-1 expression was associated with number of circulating CD34(+) progenitor cells (r = 0.454, p < 0.001) in patients with CHF. Expression of platelet-bound SDF-1 and number of CD34(+) cells were higher in patients with DCM compared with patients with ICM (p < 0.001 for both) and inversely correlated with age and aspirin therapy. Platelet-bound SDF-1 and CD34(+) progenitor cells are especially increased in patients with severe impairment of left

  17. Correlation of p16(INK4A) expression and HPV copy number with cellular FTIR spectroscopic signatures of cervical cancer cells.

    PubMed

    Ostrowska, Kamila M; Garcia, Amaya; Meade, Aidan D; Malkin, Alison; Okewumi, Ifeoluwapo; O'Leary, John J; Martin, Cara; Byrne, Hugh J; Lyng, Fiona M

    2011-04-07

    Cervical cancer, a potentially preventable disease, has its main aetiology in infection by high risk human papillomavirus (HR-HPV). Approaches to improving cervical cancer screening and diagnostic methodologies include molecular biological analysis, targeting of biomarker proteins, but also exploration and implementation of new techniques such as vibrational spectroscopy. This study correlates the biomarker protein p16(INK4A) expression levels dependent on HPV copy number with the infrared absorption spectral signatures of the cervical cancer cell lines, HPV negative C33A, HPV-16 positive SiHa and CaSki and HPV-18 positive HeLa. Confocal fluorescence microscopy demonstrated that p16(INK4A) is expressed in all investigated cell lines in both nuclear and cytoplasmic regions, although predominantly in the cytoplasm. Flow cytometry was used to quantify the p16(INK4A) expression levels and demonstrated a correlation, albeit nonlinear, between the reported number of integrated HPV copies and p16(INK4A) expression levels. CaSki cells were found to have the highest level of expression, HeLa intermediate levels, and SiHa and C33A the lowest levels. FTIR spectra revealed differences in nucleic acid, lipid and protein signatures between the cell lines with varying HPV copy number. Peak intensities exhibited increasing tendency in nucleic acid levels and decreasing tendency in lipid levels with increasing HPV copy number, and although they were found to be nonlinearly correlated with the HPV copy number, their dependence on p16(INK4A) levels was found to be close to linear. Principal Component Analysis (PCA) of the infrared absorption spectra revealed differences between nuclear and cytoplasmic spectroscopic signatures for all cell lines, and furthermore clearly differentiated the groups of spectra representing each cell line. Finally, Partial Least Squares (PLS) analysis was employed to construct a model which can predict the p16(INK4A) expression level based on a spectral

  18. Low temperature-induced DNA hypermethylation attenuates expression of RhAG, an AGAMOUS homolog, and increases petal number in rose (Rosa hybrida).

    PubMed

    Ma, Nan; Chen, Wen; Fan, Tiangang; Tian, Yaran; Zhang, Shuai; Zeng, Daxing; Li, Yonghong

    2015-10-05

    Flower development is central to angiosperm reproduction and is regulated by a broad range of endogenous and exogenous stimuli. It has been well documented that ambient temperature plays a key role in controlling flowering time; however, the mechanisms by which temperature regulates floral organ differentiation remain largely unknown. In this study, we show that low temperature treatment significantly increases petal number in rose (Rosa hybrida) through the promotion of stamen petaloidy. Quantitative RT-PCR analysis revealed that the expression pattern of RhAG, a rose homolog of the Arabidopsis thaliana AGAMOUS C-function gene, is associated with low temperature regulated flower development. Silencing of RhAG mimicked the impact of low temperature treatments on petal development by significantly increasing petal number through an increased production of petaloid stamens. In situ hybridization studies further revealed that low temperature restricts its spatial expression area. Analysis of DNA methylation level showed that low temperature treatment enhances the methylation level of the RhAG promoter, and a specific promoter region that was hypermethylated at CHH loci under low temperature conditions, was identified by bisulfite sequencing. This suggests that epigenetic DNA methylation contributes to the ambient temperature modulation of RhAG expression. Our results provide highlights in the role of RhAG gene in petal number determination and add a new layer of complexity in the regulation of floral organ development. We propose that RhAG plays an essential role in rose flower patterning by regulating petal development, and that low temperatures increase petal number, at least in part, by suppressing RhAG expression via enhancing DNA CHH hypermethylation of the RhAG promoter.

  19. Photoperiod affects the expression of sex and species differences in leukocyte number and leukocyte trafficking in congeneric hamsters.

    PubMed

    Bilbo, S D; Dhabhar, F S; Viswanathan, K; Saul, A; Nelson, R J

    2003-11-01

    Sex differences in immune function are well documented. These sex differences may be modulated by social and environmental factors. Individuals of polygynous species generally exhibit more pronounced sex differences in immune parameters than individuals of monogamous species, often displaying an energetic trade-off between enhanced immunity and high mating success. During winter, animals contend with environmental conditions (e.g. low temperatures and decreased food availability) that evoke energetic-stress responses; many mammals restrict reproduction in response to photoperiod as part of an annual winter coping strategy. To test the hypothesis that extant sex and species differences in immune surveillance may be modulated by photoperiod, we examined leukocyte numbers in males and females of two closely related hamster species (Phodopus). As predicted, uniparental P. sungorus exhibited a robust sex difference, with total white blood cells, total lymphocytes, T cells, and B cells higher in females than males, during long days when reproduction occurs, but not during short days when reproduction usually stops. In contrast, biparental male and female P. campbelli exhibited comparable leukocyte numbers during both long and short days. To study sex differences in stress responses, we also examined immune cell trafficking in response to an acute (2 h) restraint stressor. During stressful challenges, it appears beneficial for immune cells to exit the blood and move to primary immune defense areas such as the skin, in preparation for potential injury or infection. Acute stress moved lymphocytes and monocytes out of the blood in all animals. Blood cortisol concentrations were increased in P. sungorus females compared to males at baseline (52%) and in response to restraint stress (38%), but only in long days. P. campbelli males and females exhibited comparable blood cortisol and stress responses during both long and short days. Our results suggest that interactions among

  20. Increased Uterine NK cell numbers and perforin expression during the implantation phase in IVF Cycles with GnRH Antagonist Protocol

    PubMed Central

    Xu, Bufang; Wang, Jingwen; Xia, Lan; Zhang, Dan; Wu, Xian; Zhang, Aijun

    2017-01-01

    GnRH antagonist negatively affects endometrial receptivity in in vitro fertilization (IVF) cycles, however, its underlying mechanism remains unclear. To explore its target molecules, we studied endometria in the window phase of fixed GnRH antagonist, low-dose flexible GnRH antagonist, GnRH agonist long protocol, and untreated control groups. There were 384 differentially expressed genes (DEGs) in the fixed antagonist group with greater than twofold expression change compared with the control group and 197 DEGs between the fixed antagonist and agonist groups, the majority of which were associated with the natural killer (NK) cell-mediated cytotoxicity pathway. We then analysed the PRF1 and FASLG protein levels. The perforin level were significantly higher in both the antagonist groups than in other two groups, and was higher in the fixed antagonist group. Similarly, the uNK cell numbers were higher in the antagonist groups, and the highest uNK cell number occurred in the fixed group (p < 0.05). No significant differences existed in the Fas ligand levels and apoptosis rates among the three treatment groups, but were higher in the treatment groups than the control group. Together, these data indicate that GnRH antagonist may increase the uNK cell numbers and perforin expression, and this effect may be dose-dependent. PMID:28045093

  1. ON THE ELECTRON-TO-NEUTRAL NUMBER DENSITY RATIO IN THE COMA OF COMET 67P/CHURYUMOV–GERASIMENKO: GUIDING EXPRESSION AND SOURCES FOR DEVIATIONS

    SciTech Connect

    Vigren, E.; Eriksson, A. I.; Edberg, N. J. T.; Odelstad, E.; Galand, M.; Schwartz, S. J.

    2015-10-10

    We compute partial photoionization frequencies of H{sub 2}O, CO{sub 2}, and CO, the major molecules in the coma of comet 67P/Churyumov–Gerasimenko, the target comet of the ongoing ESA Rosetta mission. Values are computed from Thermosphere Ionosphere Mesosphere Energy and Dynamics/Solar EUV Experiment solar EUV spectra for 2014 August 1, 2015 March 1, and for perihelion (2015 August, as based on prediction). From the varying total photoionization frequency of H{sub 2}O, as computed from 2014 August 1 to 2015 May 20, we derive a simple analytical expression for the electron-to-neutral number density ratio as a function of cometocentric and heliocentric distance. The underlying model assumes radial movement of the coma constituents and does not account for chemical loss or the presence of electric fields. We discuss various effects/processes that can cause deviations between values from the analytical expression and actual electron-to-neutral number density ratios. The analytical expression is thus not strictly meant as predicting the actual electron-to-neutral number density ratio, but is useful in comparisons with observations as an indicator of processes at play in the cometary coma.

  2. CBF2A-CBF4B genomic region copy numbers alongside the circadian clock play key regulatory mechanisms driving expression of FR-H2 CBFs.

    PubMed

    Dhillon, Taniya; Morohashi, Kengo; Stockinger, Eric J

    2017-06-01

    The C-Repeat Binding Factors (CBFs) are DNA-binding transcriptional activators that were identified using Arabidopsis thaliana. In barley, Hordeum vulgare, a cluster of CBF genes reside at FROST RESISTANCE-H2, one of two loci having major effects on winter-hardiness. FR-H2 was revealed in a population derived from the winter barley 'Nure' and the spring barley 'Trèmois'. 'Nure' harbors two to three copies of CBF2A and CBF4B as a consequence of tandem iteration of the genomic region encompassing these genes whereas 'Trèmois' harbors single copies, and these copy number differences are associated with their transcript level differences. Here we explore further the relationship between FR-H2 CBF gene copy number and transcript levels using 'Admire', a winter barley accumulating FR-H2 CBF gene transcripts to very high levels, and a group of lines related to 'Admire' through descent. DNA blot hybridization indicated the CBF2A-CBF4B genomic region is present in 7-8 copies in 'Admire' and is highly variable in copy number across the lines related to 'Admire'. At normal growth temperatures transcript levels of CBF12, CBF14, and CBF16 were higher in lines having greater CBF2A-CBF4B genomic region copy numbers than in lines having fewer copy numbers at peak expression level time points controlled by the circadian clock. Chromatin immunoprecipitation indicated CBF2 was at the CBF12 and CBF16 promoters at normal growth temperatures. These data support a scenario in which CBF2A-CBF4B genomic region copy numbers affect expression of other FR-H2 CBFs through a mechansim in which these other FR-H2 CBFs are activated by those in the copy number variable unit.

  3. Increased expression and copy number amplification of LINE-1 and SINE B1 retrotransposable elements in murine mammary carcinoma progression

    PubMed Central

    Gualtieri, Alberto; Andreola, Federica; Sciamanna, Ilaria; Sinibaldi-Vallebona, Paola; Serafino, Annalucia; Spadafora, Corrado

    2013-01-01

    In higher eukaryotic genomes, Long Interspersed Nuclear Element 1 (LINE-1) retrotransposons and endogenous retroviruses represent large families of repeated elements encoding reverse transcriptase (RT) proteins. Short Interspersed Nuclear Element B1 (SINE B1) retrotrasposons do not encode RT, but use LINE-1-derived RT for their retrotransposition. We previously showed that many cancer types have an abundant endogenous RT activity. Inhibition of that activity, by either RNA interference-dependent silencing of active LINE-1 elements or by RT inhibitory drugs, reduced proliferation and promoted differentiation in cancer cells, indicating that LINE-1-encoded RT is required for tumor progression. Using MMTV-PyVT transgenic mice as a well-defined model of breast cancer progression, we now report that both LINE-1 and SINE B1 retrotransposons are up-regulated at a very early stage of tumorigenesis; LINE-1-encoded RT product and enzymatic activity were detected in tumor tissues as early as stage 1, preceding the widespread appearance of histological alterations and specific cancer markers, and further increased in later progression stages, while neither was present in non-pathological breast tissues. Importantly, both LINE-1 and SINE B1 retrotransposon families undergo copy number amplification during tumor progression. These findings therefore indicate that RT activity is distinctive of breast cancer cells and that, furthermore, LINE-1 and SINE B1 undergo copy number amplification during cancer progression. PMID:24231191

  4. Increased expression and copy number amplification of LINE-1 and SINE B1 retrotransposable elements in murine mammary carcinoma progression.

    PubMed

    Gualtieri, Alberto; Andreola, Federica; Sciamanna, Ilaria; Sinibaldi-Vallebona, Paola; Serafino, Annalucia; Spadafora, Corrado

    2013-11-01

    In higher eukaryotic genomes, Long Interspersed Nuclear Element 1 (LINE-1) retrotransposons and endogenous retroviruses represent large families of repeated elements encoding reverse transcriptase (RT) proteins. Short Interspersed Nuclear Element B1 (SINE B1) retrotrasposons do not encode RT, but use LINE-1-derived RT for their retrotransposition. We previously showed that many cancer types have an abundant endogenous RT activity. Inhibition of that activity, by either RNA interference-dependent silencing of active LINE-1 elements or by RT inhibitory drugs, reduced proliferation and promoted differentiation in cancer cells, indicating that LINE-1-encoded RT is required for tumor progression. Using MMTV-PyVT transgenic mice as a well-defined model of breast cancer progression, we now report that both LINE-1 and SINE B1 retrotransposons are up-regulated at a very early stage of tumorigenesis; LINE-1-encoded RT product and enzymatic activity were detected in tumor tissues as early as stage 1, preceding the widespread appearance of histological alterations and specific cancer markers, and further increased in later progression stages, while neither was present in non-pathological breast tissues. Importantly, both LINE-1 and SINE B1 retrotransposon families undergo copy number amplification during tumor progression. These findings therefore indicate that RT activity is distinctive of breast cancer cells and that, furthermore, LINE-1 and SINE B1 undergo copy number amplification during cancer progression.

  5. Correlations of the cycle-averaged Nusselt number in a periodically reversing pipe flow

    SciTech Connect

    Xiaoguo Tang; Cheng, P. )

    1993-03-01

    An experiment has been initiated to study oscillatory heat transfer in a periodically reversing pipe flow. A multivariate statistical analysis was employed to obtain a correlation equation for the cycle-averaged Nusselt number in terms of the three similarity parameters: the Reynolds number, the dynamic Reynolds number, and the dimensionless fluid displacement.

  6. Low lamin A expression in lung adenocarcinoma cells from pleural effusions is a pejorative factor associated with high number of metastatic sites and poor Performance status.

    PubMed

    Kaspi, Elise; Frankel, Diane; Guinde, Julien; Perrin, Sophie; Laroumagne, Sophie; Robaglia-Schlupp, Andrée; Ostacolo, Kevin; Harhouri, Karim; Tazi-Mezalek, Rachid; Micallef, Joelle; Dutau, Hervé; Tomasini, Pascale; De Sandre-Giovannoli, Annachiara; Lévy, Nicolas; Cau, Pierre; Astoul, Philippe; Roll, Patrice

    2017-01-01

    The type V intermediate filament lamins are the principal components of the nuclear matrix, including the nuclear lamina. Lamins are divided into A-type and B-type, which are encoded by three genes, LMNA, LMNB1, and LMNB2. The alternative splicing of LMNA produces two major A-type lamins, lamin A and lamin C. Previous studies have suggested that lamins are involved in cancer development and progression. A-type lamins have been proposed as biomarkers for cancer diagnosis, prognosis, and/or follow-up. The aim of the present study was to investigate lamins in cancer cells from metastatic pleural effusions using immunofluorescence, western blotting, and flow cytometry. In a sub-group of lung adenocarcinomas, we found reduced expression of lamin A but not of lamin C. The reduction in lamin A expression was correlated with the loss of epithelial membrane antigen (EMA)/MUC-1, an epithelial marker that is involved in the epithelial to mesenchymal transition (EMT). Finally, the lamin A expression was inversely correlated with the number of metastatic sites and the WHO Performance status, and association of pleural, bone and lung metastatic localizations was more frequent when lamin A expression was reduced. In conclusion, low lamin A but not lamin C expression in pleural metastatic cells could represent a major actor in the development of metastasis, associated with EMT and could account for a pejorative factor correlated with a poor Performance status.

  7. Patients with acute-on-chronic liver failure have increased numbers of regulatory immune cells expressing the receptor tyrosine kinase MERTK.

    PubMed

    Bernsmeier, Christine; Pop, Oltin T; Singanayagam, Arjuna; Triantafyllou, Evangelos; Patel, Vishal C; Weston, Christopher J; Curbishley, Stuart; Sadiq, Fouzia; Vergis, Nikhil; Khamri, Wafa; Bernal, William; Auzinger, Georg; Heneghan, Michael; Ma, Yun; Jassem, Wayel; Heaton, Nigel D; Adams, David H; Quaglia, Alberto; Thursz, Mark R; Wendon, Julia; Antoniades, Charalambos G

    2015-03-01

    Characteristics of decompensated cirrhosis and acute-on-chronic liver failure (ACLF) include susceptibility to infection, immuneparesis, and monocyte dysfunction. MER receptor tyrosine kinase (MERTK) is expressed by monocytes and macrophages and contributes to down-regulation of innate immune responses. We investigated whether MERTK expression is altered on monocytes from patients with liver failure. We analyzed blood and liver samples collected from patients admitted to the liver intensive therapy unit at King's College Hospital in London from December 2012 through July 2014. Patients had either ACLF (n = 41), acute decompensation of cirrhosis without ACLF (n = 9), cirrhosis without decompensation (n = 17), or acute liver failure (n = 23). We also analyzed samples from healthy individuals (controls, n = 29). We used flow cytometry to determine the level of innate immune function, and associated the findings with disease severity. We developed an assay to measure recruitment and migration of immune cells from the tissue parenchyma. Immunohistochemistry and confocal microscopy were used to determine levels of MERTK in bone marrow, liver, and lymph node tissues. We performed immunophenotype analyses and measured the production of tumor necrosis factor and interleukin 6 and intracellular killing of Escherichia coli by monocytes and peritoneal macrophages incubated with lipopolysaccharide, with or without an inhibitor of MERTK (UNC569). The number of monocytes and macrophages that expressed MERTK was greatly increased in the circulation, livers, and lymph nodes of patients with ACLF, compared with patients with stable cirrhosis and controls. MERTK expression (mean fluorescence intensity) correlated with the severity of hepatic and extrahepatic disease and systemic inflammatory responses. Based on immunophenotype, migration, and functional analyses, MERTK-expressing monocytes migrate across the endothelia to localize into tissue sites and regional lymph nodes

  8. Roux-en-Y gastric bypass surgery increases number but not density of CCK-, GLP-1-, 5-HT-, and neurotensin-expressing enteroendocrine cells in rats

    PubMed Central

    Mumphrey, M. B.; Patterson, L. M.; Zheng, H.; Berthoud, H.-R.

    2013-01-01

    Background Roux-en-Y gastric bypass (RYGB) surgery is very effective in reducing excess body weight and improving glucose homeostasis in obese subjects. Changes in the pattern of gut hormone secretion are thought to play a major role, but the mechanisms leading to both changed hormone secretion and beneficial effects remain unclear. Specifically, it is not clear whether changes in the number of hormone-secreting enteroendocrine cells, or changes in the releasing stimuli, or both, are important. Methods We estimated numbers of enteroendocrine cells after immunohistochemical staining in fixed tissue samples from rats at 10–11 months after RYGB. Key Results Numbers of glucagon-like peptide-1 (GLP-1) (L-cells, co-expressing peptide YY (PYY)), cholecystokinin (CCK), neurotensin, and 5-HT-immunoreactive cells were significantly increased in the Roux and common limbs, but not the biliopancreatic limb in RYGB rats compared with sham-operated, obese rats fed high-fat diet, and chow-fed controls. This increase was mostly accounted for by general hyperplasia of all intestinal wall layers of the nutrient-perfused Roux and common limbs, and less to increased density of expression. The number of ghrelin cells in the bypassed stomach was not different among the three groups. Conclusions & Inferences The findings suggest that the number of enteroendocrine cells increases passively as the gut adapts, and that the increased total number of L- and I-cells is likely to contribute to the higher circulating levels of GLP-1, PYY, and CCK, potentially leading to suppression of food intake and stimulation of insulin secretion. Whether changes in releasing stimuli also contribute to altered circulating levels will have to be determined in future studies. PMID:23095091

  9. Age-Dependent Brain Gene Expression and Copy Number Anomalies in Autism Suggest Distinct Pathological Processes at Young Versus Mature Ages

    PubMed Central

    Winn, Mary E.; Barnes, Cynthia Carter; Li, Hai-Ri; Weiss, Lauren; Fan, Jian-Bing; Murray, Sarah; April, Craig; Belinson, Haim; Fu, Xiang-Dong; Wynshaw-Boris, Anthony; Schork, Nicholas J.; Courchesne, Eric

    2012-01-01

    Autism is a highly heritable neurodevelopmental disorder, yet the genetic underpinnings of the disorder are largely unknown. Aberrant brain overgrowth is a well-replicated observation in the autism literature; but association, linkage, and expression studies have not identified genetic factors that explain this trajectory. Few studies have had sufficient statistical power to investigate whole-genome gene expression and genotypic variation in the autistic brain, especially in regions that display the greatest growth abnormality. Previous functional genomic studies have identified possible alterations in transcript levels of genes related to neurodevelopment and immune function. Thus, there is a need for genetic studies involving key brain regions to replicate these findings and solidify the role of particular functional pathways in autism pathogenesis. We therefore sought to identify abnormal brain gene expression patterns via whole-genome analysis of mRNA levels and copy number variations (CNVs) in autistic and control postmortem brain samples. We focused on prefrontal cortex tissue where excess neuron numbers and cortical overgrowth are pronounced in the majority of autism cases. We found evidence for dysregulation in pathways governing cell number, cortical patterning, and differentiation in young autistic prefrontal cortex. In contrast, adult autistic prefrontal cortex showed dysregulation of signaling and repair pathways. Genes regulating cell cycle also exhibited autism-specific CNVs in DNA derived from prefrontal cortex, and these genes were significantly associated with autism in genome-wide association study datasets. Our results suggest that CNVs and age-dependent gene expression changes in autism may reflect distinct pathological processes in the developing versus the mature autistic prefrontal cortex. Our results raise the hypothesis that genetic dysregulation in the developing brain leads to abnormal regional patterning, excess prefrontal neurons

  10. BAP1 Is Altered by Copy Number Loss, Mutation, and/or Loss of Protein Expression in More Than 70% of Malignant Peritoneal Mesotheliomas.

    PubMed

    Leblay, Noémie; Leprêtre, Frédéric; Le Stang, Nolwenn; Gautier-Stein, Amandine; Villeneuve, Laurent; Isaac, Sylvie; Maillet, Denis; Galateau-Sallé, Françoise; Villenet, Céline; Sebda, Shéhérazade; Goracci, Alexandra; Byrnes, Graham; McKay, James D; Figeac, Martin; Glehen, Olivier; Gilly, François-Noël; Foll, Matthieu; Fernandez-Cuesta, Lynnette; Brevet, Marie

    2017-04-01

    Malignant mesothelioma is a deadly disease that is strongly associated with asbestos exposure. Peritoneal mesotheliomas account for 10% of all the cases. BRCA1 associated protein 1 (BAP1) is a deubiquitinating hydrolase that plays a key role in various cellular processes. Germline and somatic inactivation of BRCA1 associated protein 1 gene (BAP1) is frequent in pleural mesothelioma; however, little is known about its status in peritoneal mesothelioma. Taking advantage of the extensive French National Network for the Diagnosis of Malignant Pleural Mesothelioma and Rare Peritoneal Tumors and the French National Network for the Treatment of Rare Peritoneal Surface Malignancies, we collected biological material and clinical and epidemiological data for 46 patients with peritoneal mesothelioma. The status of BAP1 was evaluated at the mutational and protein expression levels and combined with our previous data on copy number alterations assessed in the same samples. We detected mutations in 32% of the malignant peritoneal mesotheliomas analyzed. In addition, we have previously reported that copy number losses occurred in 42% of the samples included in this series. Overall, 73% of the malignant peritoneal mesotheliomas analyzed carried at least one inactivated BAP1 allele, but only 57% had a complete loss of its protein nuclear expression. Better overall survival was observed for patients with BAP1 mutations (p = 0.04), protein expression loss (p = 0.016), or at least one of these alterations (p = 0.007) independently of tumor histological subtype, age, and sex. As in pleural mesothelioma, inactivation of BAP1 is frequent in peritoneal mesotheliomas. We found that BAP1 protein nuclear expression is a good prognostic factor and a more reliable marker for the complete loss of BAP1 activity than mutation or copy number loss. Copyright © 2017 International Association for the Study of Lung Cancer. Published by Elsevier Inc. All rights reserved.

  11. Age-dependent brain gene expression and copy number anomalies in autism suggest distinct pathological processes at young versus mature ages.

    PubMed

    Chow, Maggie L; Pramparo, Tiziano; Winn, Mary E; Barnes, Cynthia Carter; Li, Hai-Ri; Weiss, Lauren; Fan, Jian-Bing; Murray, Sarah; April, Craig; Belinson, Haim; Fu, Xiang-Dong; Wynshaw-Boris, Anthony; Schork, Nicholas J; Courchesne, Eric

    2012-01-01

    Autism is a highly heritable neurodevelopmental disorder, yet the genetic underpinnings of the disorder are largely unknown. Aberrant brain overgrowth is a well-replicated observation in the autism literature; but association, linkage, and expression studies have not identified genetic factors that explain this trajectory. Few studies have had sufficient statistical power to investigate whole-genome gene expression and genotypic variation in the autistic brain, especially in regions that display the greatest growth abnormality. Previous functional genomic studies have identified possible alterations in transcript levels of genes related to neurodevelopment and immune function. Thus, there is a need for genetic studies involving key brain regions to replicate these findings and solidify the role of particular functional pathways in autism pathogenesis. We therefore sought to identify abnormal brain gene expression patterns via whole-genome analysis of mRNA levels and copy number variations (CNVs) in autistic and control postmortem brain samples. We focused on prefrontal cortex tissue where excess neuron numbers and cortical overgrowth are pronounced in the majority of autism cases. We found evidence for dysregulation in pathways governing cell number, cortical patterning, and differentiation in young autistic prefrontal cortex. In contrast, adult autistic prefrontal cortex showed dysregulation of signaling and repair pathways. Genes regulating cell cycle also exhibited autism-specific CNVs in DNA derived from prefrontal cortex, and these genes were significantly associated with autism in genome-wide association study datasets. Our results suggest that CNVs and age-dependent gene expression changes in autism may reflect distinct pathological processes in the developing versus the mature autistic prefrontal cortex. Our results raise the hypothesis that genetic dysregulation in the developing brain leads to abnormal regional patterning, excess prefrontal neurons

  12. Short-chain fatty acid level and field cancerization show opposing associations with enteroendocrine cell number and neuropilin expression in patients with colorectal adenoma

    PubMed Central

    2011-01-01

    Background Previous reports have suggested that the VEGF receptor neuropilin-1 (NRP-1) is expressed in a singly dispersed subpopulation of cells in the normal colonic epithelium, but that expression becomes dysregulated during colorectal carcinogenesis, with higher levels in tumour suggestive of a poor prognosis. We noted that the spatial distribution and morphology if NRP-1 expressing cells resembles that of enteroendocrine cells (EEC) which are altered in response to disease state including cancer and irritable bowel syndrome (IBS). We have shown that NRP-1 is down-regulated by butyrate in colon cancer cell lines in vitro and we hypothesized that butyrate produced in the lumen would have an analogous effect on the colon mucosa in vivo. Therefore we sought to investigate whether NRP-1 is expressed in EEC and how NRP-1 and EEC respond to butyrate and other short-chain fatty acids (SCFA - principally acetate and propionate). Additionally we sought to assess whether there is a field effect around adenomas. Methodology Biopsies were collected at the mid-sigmoid, at the adenoma and at the contralateral wall (field) of 28 subjects during endoscopy. Samples were fixed for IHC and stained for either NRP-1 or for chromogranin A (CgA), a marker of EEC. Stool sampling was undertaken to assess individuals' butyrate, acetate and propionate levels. Result NRP-1 expression was inversely related to SCFA concentration at the colon landmark (mid-sigmoid), but expression was lower and not related to SCFA concentration at the field. Likewise CgA+ cell number was also inversely related to SCFA at the landmark, but was lower and unresponsive at the field. Crypt cellularity was unaltered by field effect. A colocalisation analysis showed only a small subset of NRP-1 localised with CgA. Adenomas showed extensive, weaker staining for NRP-1 which contrastingly correlated positively with butyrate level. Field effects cause this relationship to be lost. Adenoma tissue shows dissociation of

  13. Maternal undernutrition does not alter Sertoli cell numbers or the expression of key developmental markers in the mid-gestation ovine fetal testis

    PubMed Central

    2013-01-01

    Background The aim of this study was to determine the effects of maternal undernutrition on ovine fetal testis morphology and expression of relevant histological indicators. Maternal undernutrition, in sheep, has been reported, previously, to alter fetal ovary development, as indicated by delayed folliculogenesis and the altered expression of ovarian apoptosis-regulating gene products, at day 110 of gestation. It is not known whether or not maternal undernutrition alters the same gene products in the day 110 fetal testis. Design and methods Mature Scottish Blackface ewes were fed either 100% (Control; C) or 50% (low; L) of estimated metabolisable energy requirements of a pregnant ewe, from mating to day 110 of gestation. All pregnant ewes were euthanized at day 110 and a sub-set of male fetuses was randomly selected (6 C and 9 L) for histology studies designed to address the effect of nutritional state on several indices of testis development. Sertoli cell numbers were measured using a stereological method and Ki67 (cell proliferation index), Bax (pro-apoptosis), Mcl-1 (anti-apoptosis), SCF and c-kit ligand (development and apoptosis) gene expression was measured in Bouins-fixed fetal testis using immunohistochemistry. Results No significant differences were observed in numbers of Sertoli cells or testicular Ki67 positive cells. The latter were localised to the testicular cords and interstitium. Bax and Mcl-1 were localised specifically to the germ cells whereas c-kit was localised to both the cords and interstitium. SCF staining was very sparse. No treatment effects were observed for any of the markers examined. Conclusions These data suggest that, unlike in the fetal ovary, maternal undernutrition for the first 110 days of gestation affects neither the morphology of the fetal testis nor the expression of gene products which regulate apoptosis. It is postulated that the effects of fetal undernutrition on testis function may be expressed through hypothalamic

  14. Decreased Numbers of Somatostatin-Expressing Neurons in the Amygdala of Subjects With Bipolar Disorder or Schizophrenia: Relationship to Circadian Rhythms.

    PubMed

    Pantazopoulos, Harry; Wiseman, Jason T; Markota, Matej; Ehrenfeld, Lucy; Berretta, Sabina

    2017-03-15

    Growing evidence points to a key role for somatostatin (SST) in schizophrenia (SZ) and bipolar disorder (BD). In the amygdala, neurons expressing SST play an important role in the regulation of anxiety, which is often comorbid in these disorders. We tested the hypothesis that SST-immunoreactive (IR) neurons are decreased in the amygdala of subjects with SZ and BD. Evidence for circadian SST expression in the amygdala and disrupted circadian rhythms and rhythmic peaks of anxiety in BD suggest a disruption of rhythmic expression of SST in this disorder. Amygdala sections from 12 SZ, 15 BD, and 15 control subjects were processed for immunocytochemistry for SST and neuropeptide Y, a neuropeptide partially coexpressed in SST-IR neurons. Total numbers (Nt) of IR neurons were measured. Time of death was used to test associations with circadian rhythms. SST-IR neurons were decreased in the lateral amygdala nucleus in BD (Nt, p = .003) and SZ (Nt, p = .02). In normal control subjects, Nt of SST-IR neurons varied according to time of death. This pattern was altered in BD subjects, characterized by decreases of SST-IR neurons selectively in subjects with time of death corresponding to the day (6:00 am to 5:59 pm). Numbers of neuropeptide Y-IR neurons were not affected. Decreased SST-IR neurons in the amygdala of patients with SZ and BD, interpreted here as decreased SST expression, may disrupt responses to fear and anxiety regulation in these individuals. In BD, our findings raise the possibility that morning peaks of anxiety depend on a disruption of circadian regulation of SST expression in the amygdala. Copyright © 2016 Society of Biological Psychiatry. Published by Elsevier Inc. All rights reserved.

  15. Potentialities of laser systems for remote sensing of the atmosphere at a wide variability of optical and physical characteristics: dimensionless-parametric modelling

    NASA Astrophysics Data System (ADS)

    Agishev, R. R.

    2017-02-01

    Within the framework of generalisation of different approaches to the modelling of atmospheric lidars, the methodology capabilities for dimensionless-parametric analysis are expanded. The developed approach simplifies the analysis of the signal-to-noise ratio and potential capabilities of existing and newly developed monitoring systems with a wide variability of atmospheric and optical conditions and a great variety of modern lidars. Its applicability to the problems of remote atmospheric sensing, environmental monitoring and lidar navigation in providing the eye safety, noise immunity and reliability is discussed.

  16. Inhibitory transmission in locus coeruleus neurons expressing GABAA receptor epsilon subunit has a number of unique properties.

    PubMed

    Belujon, P; Baufreton, J; Grandoso, L; Boué-Grabot, E; Batten, T F C; Ugedo, L; Garret, M; Taupignon, A I

    2009-10-01

    Fast inhibitory synaptic transmission in the brain relies on ionotropic GABA(A) receptors (GABA(A)R). Eighteen genes code for GABA(A)R subunits, but little is known about the epsilon subunit. Our aim was to identify the synaptic transmission properties displayed by native receptors incorporating epsilon. Immunogold localization detected epsilon at synaptic sites on locus coeruleus (LC) neurons. In situ hybridization revealed prominent signals from epsilon, and mRNAs, some low beta1 and beta3 signals, and no gamma signal. Using in vivo extracellular and in vitro patch-clamp recordings in LC, we established that neuron firing rates, GABA-activated currents, and mIPSC charge were insensitive to the benzodiazepine flunitrazepam (FLU), in agreement with the characteristics of recombinant receptors including an epsilon subunit. Surprisingly, LC provided binding sites for benzodiazepines, and GABA-induced currents were potentiated by diazepam (DZP) in the micromolar range. A number of GABA(A)R ligands significantly potentiated GABA-induced currents, and zinc ions were only active at concentrations above 1 muM, further indicating that receptors were not composed of only alpha and beta subunits, but included an epsilon subunit. In contrast to recombinant receptors including an epsilon subunit, GABA(A)R in LC showed no agonist-independent opening. Finally, we determined that mIPSCs, as well as ensemble currents induced by ultra-fast GABA application, exhibited surprisingly slow rise times. Our work thus defines the signature of native GABA(A)R with a subunit composition including epsilon: differential sensitivity to FLU and DZP and slow rise time of currents. We further propose that alpha(3,) beta(1/3,) and epsilon subunits compose GABA(A)R in LC.

  17. Mesodermal Gene Expression in the Acoel Isodiametra pulchra Indicates a Low Number of Mesodermal Cell Types and the Endomesodermal Origin of the Gonads

    PubMed Central

    Chiodin, Marta; Børve, Aina; Berezikov, Eugene; Ladurner, Peter; Martinez, Pedro; Hejnol, Andreas

    2013-01-01

    Acoelomorphs are bilaterally symmetric small marine worms that lack a coelom and possess a digestive system with a single opening. Two alternative phylogenetic positions of this group within the animal tree are currently debated. In one view, Acoelomorpha is the sister group to all remaining Bilateria and as such, is a morphologically simple stepping stone in bilaterian evolution. In the other, the group is a lineage within the Deuterostomia, and therefore, has derived a simple morphology from a more complex ancestor. Acoels and the closely related Nemertodermatida and Xenoturbellida, which together form the Acoelomorpha, possess a very limited number of cell types. To further investigate the diversity and origin of mesodermal cell types we describe the expression pattern of 12 orthologs of bilaterian mesodermal markers including Six1/2, Twist, FoxC, GATA4/5/6, in the acoel Isodiametra pulchra. All the genes are expressed in stem cells (neoblasts), gonads, and at least subsets of the acoel musculature. Most are expressed in endomesodermal compartments of I. pulchra developing embryos similar to what has been described in cnidarians. Our molecular evidence indicates a very limited number of mesodermal cell types and suggests an endomesodermal origin of the gonads and the stem cell system. We discuss our results in light of the two prevailing phylogenetic positions of Acoelomorpha. PMID:23405161

  18. An assessment of the malignant potential of actinic keratoses and Bowen's disease: p53 and PCNA expression pattern correlate with the number of desmosomes.

    PubMed

    Ramzi, Saeef Taher; Maruno, Motoyoshi; Khaskhely, Noor Mohammad; Khan, Mohammed Abul Kasem; Takamiyagi, Atsushi; Uezato, Hiroshi; Nonaka, Shigeo

    2002-09-01

    Actinic keratoses (AK) and Bowen's disease (BD), both intraepidermal skin tumors, have a potential progression to squamous cell carcinoma (SCC). To evaluate the malignant potential of AK and BD, the expression pattern of p53 protein and proliferating cell nuclear antigen (PCNA) were examined in five types of AK and BD by immunohistochemistry. The ultrastructural difference of epidermal cells between AK and BD lesions was investigated. In the study of p53 and PCNA expression, the atrophic and acantholytic types of AK showed lower positive rates compared to others. These two types did not demonstrate all layers expression pattern. The number of desmosomes of the epidermal cells was significantly reduced in BD, and in the bowenoid and hypertrophic types of AK compared with other types of AK The number of hemi-desmosomes showed greatest reduction in BD and the bowenoid type of AK On the basis of our findings, it is hypothesized that atrophic and acantholytic types of AK may have the lowest, and the bowenoid type of AK and BD may have the highest, malignant potential.

  19. Association of high HLA-E expression during acute cellular rejection and numbers of HLA class I leader peptide mismatches with reduced renal allograft survival.

    PubMed

    Guberina, Hana; Rebmann, Vera; Wagner, Bettina; da Silva Nardi, Fabiola; Dziallas, Phillip; Dolff, Sebastian; Bienholz, Anja; Wohlschlaeger, Jeremias; Bankfalvi, Agnes; Heinemann, Falko M; Witzke, Oliver; Zoet, Yvonne M; Claas, Frans H J; Horn, Peter A; Kribben, Andreas; Doxiadis, Ilias I N

    2017-03-01

    Non-classical Human Leukocyte Antigen (HLA)-E preferentially presents leader peptides derived from classical HLA-class I molecules. HLA-E can trigger opposed immune responses by interacting with inhibitory NKG2A or by activating NKG2C receptors on NK and T-cells. We studied the impact of HLA-E on renal allograft survival during acute cellular rejection. HLA-E expression was up-regulated in acute cellular rejection (ACR) biopsies (n=12) compared to biopsies from 13 renal allografts with no rejection-signs. HLA-E up-regulation was correlated with numbers of HLA-class I leader peptide mismatches (p=0.04). CD8+ and CD56+ infiltrating cells correlated with HLA-E expression (p<0.0001 and p=0.0009, respectively). Activating NKG2C receptor dominated on effector cells in biopsies and peripheral blood during ACR potentially allowing HLA-E-mediated immune activation. Moreover, HLA-E expression correlated with deterioration in renal allograft function (p<0.008) and reduced allograft survival (p=0.002). Our findings provide evidence that during renal allograft rejection HLA-E along with high numbers of mismatched HLA-class I leader peptides might represent additional targets for immune-activating responses.

  20. Kif3a controls murine nephron number via GLI3 repressor, cell survival, and gene expression in a lineage-specific manner.

    PubMed

    Chi, Lijun; Galtseva, Alevtina; Chen, Lin; Mo, Rong; Hui, Chi-Chung; Rosenblum, Norman D

    2013-01-01

    The primary cilium is required during early embryo patterning, epithelial tubulogenesis, and growth factor-dependent signal transduction. The requirement for primary cilia during renal epithelial-mesenchymal tissue interactions that give rise to nephrons is undefined. Here, we used Cre-mediated recombination to generate mice with Kif3a deficiency targeted to the ureteric and/or metanephric mesenchyme cell lineages in the embryonic kidney. Gradual loss of primary cilia in either lineage leads to a phenotype of reduced nephron number. Remarkably, in addition to cyst formation, loss of primary cilia in the ureteric epithelial cell leads to decreased expression of Wnt11 and Ret and reduced ureteric branching. Constitutive expression of GLI3 repressor (Gli3(Δ699/+) ) rescues these abnormalities. In embryonic metanephric mesenchyme cells, Kif3a deficiency limits survival of nephrogenic progenitor cells and expression of genes required for nephron formation. Together, our data demonstrate that Kif3a controls nephron number via distinct cell lineage-specific mechanisms.

  1. Kif3a Controls Murine Nephron Number Via GLI3 Repressor, Cell Survival, and Gene Expression in a Lineage-Specific Manner

    PubMed Central

    Chi, Lijun; Galtseva, Alevtina; Chen, Lin; Mo, Rong; Hui, Chi-chung; Rosenblum, Norman D.

    2013-01-01

    The primary cilium is required during early embryo patterning, epithelial tubulogenesis, and growth factor-dependent signal transduction. The requirement for primary cilia during renal epithelial-mesenchymal tissue interactions that give rise to nephrons is undefined. Here, we used Cre-mediated recombination to generate mice with Kif3a deficiency targeted to the ureteric and/or metanephric mesenchyme cell lineages in the embryonic kidney. Gradual loss of primary cilia in either lineage leads to a phenotype of reduced nephron number. Remarkably, in addition to cyst formation, loss of primary cilia in the ureteric epithelial cell leads to decreased expression of Wnt11 and Ret and reduced ureteric branching. Constitutive expression of GLI3 repressor (Gli3Δ699/+) rescues these abnormalities. In embryonic metanephric mesenchyme cells, Kif3a deficiency limits survival of nephrogenic progenitor cells and expression of genes required for nephron formation. Together, our data demonstrate that Kif3a controls nephron number via distinct cell lineage-specific mechanisms. PMID:23762375

  2. Maternal age and ovarian stimulation independently affect oocyte mtDNA copy number and cumulus cell gene expression in bovine clones.

    PubMed

    Cree, Lynsey M; Hammond, Elizabeth R; Shelling, Andrew N; Berg, Martin C; Peek, John C; Green, Mark P

    2015-06-01

    Does maternal ageing and ovarian stimulation alter mitochondrial DNA (mtDNA) copy number and gene expression of oocytes and cumulus cells from a novel bovine model for human IVF? Oocytes collected from females with identical nuclear genetics show decreased mtDNA copy number and increased expression of an endoplasmic reticulum (ER) stress gene with repect to ovarian stimulation, whilst differences in the expression of genes involved in mitochondrial function, antioxidant protection and apoptosis were evident in relation to maternal ageing and the degree of ovarian stimulation in cumulus cells. Oocyte quality declines with advancing maternal age; however, the underlying mechanism, as well as the effects of ovarian stimulation are poorly understood. Human studies investigating these effects are often limited by differences in age and ovarian stimulation regimens within a patient cohort, as well as genetic and environmental variability. A novel bovine cross-sectional maternal age model for human IVF was undertaken. Follicles were aspirated from young (3 years of age; n = 7 females) and old (10 years of age; n = 5 females) Holstein Freisian clones following multiple unstimulated, mild and standard ovarian stimulation cycles. These bovine cloned females were generated by the process of somatic cell nuclear transfer (SCNT) from the same founder and represent a homogeneous population with reduced genetic and environmental variability. Maternal age and ovarian stimulation effects were investigated in relation to mtDNA copy number, and the expression of 19 genes involved in mitochondrial function, antioxidant protection, oocyte-cumulus cell signalling and follicle development in both oocytes and cumulus cells. Young (3 years of age; n = 7 females) and old (10 years of age; n = 5 females) Holstein Freisian bovine clones were maintained as one herd. Stimulation cycles were based on the long GnRH agonist down-regulation regimen used in human fertility clinics. Follicle growth

  3. A significant effect of the TSPY1 copy number on spermatogenesis efficiency and the phenotypic expression of the gr/gr deletion.

    PubMed

    Shen, Ying; Yan, Yuanlong; Liu, Yunqiang; Zhang, Sizhong; Yang, Dong; Zhang, Peng; Li, Lei; Wang, Yan; Ma, Yongxin; Tao, Dachang; Yang, Yuan

    2013-04-15

    AZFc deletions cause a significant phenotypic heterogeneity with respect to spermatogenesis; however, the reason for this is poorly understood. Recently, testis-specific protein Y-encoded 1 (TSPY1) copy number variation (CNV) was determined to be a potential genetic modifier of spermatogenesis. We performed a large-scale cohort study to investigate the effect of TSPY1 CNV on spermatogenesis and to elucidate the possible contribution of TSPY1 genetic variation to the phenotypic expression of AZFc deletions. Haplogrouping of the Y-chromosome and quantification of the TSPY1 copy number were performed in 2272 Han Chinese males with different spermatogenic statuses (704 males with the b2/b4 or gr/gr deletion and 1568 non-AZFc-deleted males). Our data revealed that the TSPY1 copy number distributions were significantly different among non-AZFc-deleted males with different spermatogenic phenotypes. Lower sperm production and an elevated risk of spermatogenic failure were observed in males with fewer than 21 TSPY1 copies and in those with more than 55 copies relative to men with 21-35 copies. Similar results were observed in males with the gr/gr deletion. These findings indicate that TSPY1 CNV affects an individual's susceptibility to spermatogenic failure by modulating the efficiency of spermatogenesis and strongly suggest that there is a significant quantity effect of the TSPY1 copy number on the phenotypic expression of the gr/gr deletion. To our knowledge, this CNV is the first independent genetic factor that has been clearly observed to influence the spermatogenic status of gr/gr deletion carriers. A combined genetic analysis of the TSPY1 copy number and the gr/gr deletion could inform the clinical counselling of infertile couples.

  4. Maternal high-protein diet during pregnancy, but not during suckling, induced altered expression of an increasing number of hepatic genes in adult mouse offspring.

    PubMed

    Vanselow, Jens; Kucia, Marzena; Langhammer, Martina; Koczan, Dirk; Metges, Cornelia C

    2016-04-01

    Indirect effects of a high-protein maternal diet are not well understood. In this study, we analyzed short-term and sustainable effects of a prenatal versus early postnatal maternal high-protein diet on growth and hepatic gene expression in mouse offspring. Dams were exposed to an isoenergetic high-protein (HP, 40 % w/w) diet during pregnancy or lactation. Growth and hepatic expression profiles of male offspring were evaluated directly after weaning and 150 days after birth. Offspring from two dietary groups, high-protein diet during pregnancy and control diet during lactation (HPC), and control diet during pregnancy and high-protein diet during lactation (CHP), were compared with offspring (CC) from control-fed dams. Maternal CHP treatment was associated with sustained offspring growth retardation, but decreased numbers of affected hepatic genes in adults compared to weanlings. In contrast, offspring of the HPC group did not show persistent effects on growth parameters, but the number of affected hepatic genes was even increased at adult age. In both dietary groups, however, only a small subset of genes was affected in weanlings as well as in adults. We conclude that (1) prenatal and early postnatal maternal HP diet caused persistent, but (2) different effects and partially complementary trends on growth characteristics and on the hepatic transcriptome and associated pathways and that (3) only a small number of genes and associated upstream regulators might be involved in passing early diet-induced imprints to adulthood.

  5. Estimating the number of plasmids taken up by a eukaryotic cell during transfection and evidence that antisense RNA abolishes gene expression in Physarum polycephalum.

    PubMed

    Materna, Stefan C; Marwan, Wolfgang

    2005-02-01

    We have estimated the statistical distribution of the number of plasmids taken up by individual Jurkat lymphoma cells during electroporation in the presence of two plasmids, one encoding for yellow (EYFP) the other for cyan (ECFP) fluorescent protein. The plasmid concentration at which most of the cells take up only one plasmid or several molecules was determined by statistical analysis. We found that cells behaved slightly heterogeneous in plasmid uptake and describe how the homogeneity of a cell population can be quantified by Poisson statistics in order to identify experimental conditions that yield homogeneously transfection-competent cell populations. The experimental procedure worked out with Jurkat cells was applied to assay the effectiveness of antisense RNA in knocking down gene expression in Physarum polycephalum. Double transfection of flagellates with vectors encoding EYFP and antisense-EYFP revealed for the first time that gene expression can be suppressed by co-expression of antisense RNA in Physarum. Quantitative analysis revealed that one copy of antisense expressing gene per EYFP gene was sufficient to completely suppress formation of the EYFP protein in Physarum.

  6. DNA copy number alterations, gene expression changes and disease-free survival in patients with colorectal cancer: a 10 year follow-up.

    PubMed

    Bigagli, Elisabetta; De Filippo, Carlotta; Castagnini, Cinzia; Toti, Simona; Acquadro, Francesco; Giudici, Francesco; Fazi, Marilena; Dolara, Piero; Messerini, Luca; Tonelli, Francesco; Luceri, Cristina

    2016-12-01

    DNA copy number alterations (CNAs) and gene expression changes have amply been encountered in colorectal cancers (CRCs), but the extent at which CNAs affect gene expression, as well as their relevance for tumor development, are still poorly defined. Here we aimed at assessing the clinical relevance of these parameters in a 10 year follow-up study. Tumors and normal adjacent colon mucosa, obtained at primary surgery from 21 CRC patients, were subjected to (i) high-resolution array CGH (a-CGH) for the detection of CNAs and (ii) microarray-based transcriptome profiling for the detection of gene expression (GE) changes. Correlations between these genomic and transcriptomic changes and their associations with clinical and histopathological parameters were assessed with the aim to identify molecular signatures associated with disease-free survival of the CRC patients during a 10 year follow-up. DNA copy number gains were frequently detected in chromosomes 7, 8q, 13, 19, 20q and X, whereas DNA copy number losses were frequently detected in chromosomes 1p, 4, 8p, 15, 17p, 18, 19 and 22q. None of these alterations were observed in all samples. In addition, we found that 2,498 genes were up- and that 1,094 genes were down-regulated in the tumor samples compared to their corresponding normal mucosa (p < 0.01). The expression of 65 genes was found to be significantly associated with prognosis (p < 0.01). Specifically, we found that up-regulation of the IL17RA, IGF2BP2 and ABCC2 genes, and of genes acting in the mTOR and cytokine receptor pathways, were strongly associated with a poor survival. Subsequent integrated analyses revealed that increased expression levels of the MMP9, BMP7, UBE2C, I-CAM, NOTCH3, NOTCH1, PTGES2, HMGB1 and ERBB3 genes were associated with copy number gains, whereas decreased expression levels of the MUC1, E2F2, HRAS and SIRT3 genes were associated with copy number losses. Pathways related to cell cycle progression, eicosanoid metabolism, and

  7. Decreased number of CD4{sup +} and CD8{sup +} T cells that express the interleukin-7 receptor in blood and tissues of SIV-infected macaques

    SciTech Connect

    Moniuszko, Marcin; Edghill-Smith, Yvette; Stevceva, Liljana; Tsai, Wen-Po . E-mail: franchig@mail.nih.gov

    2006-12-20

    Acute HIV/SIV (human/simian immunodeficiency virus) infection results in severe CD4{sup +} T cell depletion in lymphoid compartments. During the chronic phase of infection, CD4{sup +} T cell numbers rebound in blood but remain low in the gut-associated lymphoid tissue (GALT), even when viral replication is suppressed by antiretroviral therapy (ART). Thus, strategies to repopulate lymphoid compartments may ameliorate the clinical outcome of HIV/SIV infection. Interleukin (IL)-7 is a key cytokine for the maintenance of homeostatic proliferation of T cells. In HIV/SIV infection, IL-7 expression is increased, likely to compensate for T cell loss, suggesting that supraphysiological administration of IL-7 could provide additional benefit. However, the ability of T cells to respond to IL-7 is dependent on the level of expression of the IL-7 receptor (IL-7R) in T cells in various body compartments. In here, we investigated the proportion of IL-7R{sup +} T cells in blood, spleen, gut, and genitourinary tract of healthy and SIV-infected macaques with various degrees of CD4{sup +} T cell depletion. We found that the percentage of T cells expressing IL-7R was significantly lower in both CD4{sup +} and CD8{sup +} T cell subsets in SIV-infected macaques than in healthy animals and this decrease directly correlated with the CD4{sup +} T cell number. Importantly, the proportion of CD4{sup +} and CD8{sup +} T cells expressing IL-7R in blood paralleled that found in tissues. IL-7R{sup +} T cells within the SIV-specific CD8{sup +} T cells varied and were lowest in most tissues of viremic macaques, likely reflecting continuous antigen stimulation of effector cells.

  8. Probiotic Treatment Decreases the Number of CD14-Expressing Cells in Porcine Milk Which Correlates with Several Intestinal Immune Parameters in the Piglets

    PubMed Central

    Scharek-Tedin, Lydia; Kreuzer-Redmer, Susanne; Twardziok, Sven Olaf; Siepert, Bianca; Klopfleisch, Robert; Tedin, Karsten; Zentek, Jürgen; Pieper, Robert

    2015-01-01

    Modulating the mucosal immune system of neonates by probiotic treatment of their mothers is a promising approach which can only be investigated through the use of animal models. Here, we used sows and their piglets to investigate the impact of a bacterial treatment on the sow’s milk and on the neonate piglet intestinal immune system. In previous experiments, feed supplementation of sows with the probiotic Enterococcus faecium NCIMB 10415 during pregnancy and lactation had been shown to affect intestinal microbiota and cytokine expression of the offspring during the suckling and weaning periods. We therefore investigated the composition of the milk from treated sows in comparison to samples from a control group. In treated sows, the amount of lactose increased, and the somatic cell numbers were reduced. In all milk samples, the percentage of cells expressing membranous CD14 (mCD14) was greater than the fractions of immune cells, indicating expression of mCD14 on mammary epithelial cells. However, in the milk of E. faecium-treated sows, mCD14+ cells were reduced. Furthermore, the number of CD14+ milk cells was positively correlated with the percentages of B cells and activated T cells in the ileal MLN of the piglets. This study provides evidence for the expression of mCD14 by the porcine mammary epithelium, and suggests an immunological effect of mCD14+ milk cells on the piglets’ intestinal immune system. Our study further suggests that mCD14+ mammary epithelial cell populations can be modulated by probiotic feed supplementation of the sow. PMID:25806034

  9. Dimensionless parameterization of lidar for laser remote sensing of the atmosphere and its application to systems with SiPM and PMT detectors.

    PubMed

    Agishev, Ravil; Comerón, Adolfo; Rodriguez, Alejandro; Sicard, Michaël

    2014-05-20

    In this paper, we show a renewed approach to the generalized methodology for atmospheric lidar assessment, which uses the dimensionless parameterization as a core component. It is based on a series of our previous works where the problem of universal parameterization over many lidar technologies were described and analyzed from different points of view. The modernized dimensionless parameterization concept applied to relatively new silicon photomultiplier detectors (SiPMs) and traditional photomultiplier (PMT) detectors for remote-sensing instruments allowed predicting the lidar receiver performance with sky background available. The renewed approach can be widely used to evaluate a broad range of lidar system capabilities for a variety of lidar remote-sensing applications as well as to serve as a basis for selection of appropriate lidar system parameters for a specific application. Such a modernized methodology provides a generalized, uniform, and objective approach for evaluation of a broad range of lidar types and systems (aerosol, Raman, DIAL) operating on different targets (backscatter or topographic) and under intense sky background conditions. It can be used within the lidar community to compare different lidar instruments.

  10. FGFR1 mRNA and protein expression, not gene copy number, predict FGFR TKI sensitivity across all lung cancer histologies.

    PubMed

    Wynes, Murry W; Hinz, Trista K; Gao, Dexiang; Martini, Michael; Marek, Lindsay A; Ware, Kathryn E; Edwards, Michael G; Böhm, Diana; Perner, Sven; Helfrich, Barbara A; Dziadziuszko, Rafal; Jassem, Jacek; Wojtylak, Szymon; Sejda, Aleksandra; Gozgit, Joseph M; Bunn, Paul A; Camidge, D Ross; Tan, Aik-Choon; Hirsch, Fred R; Heasley, Lynn E

    2014-06-15

    FGFR1 gene copy number (GCN) is being evaluated as a biomarker for FGFR tyrosine kinase inhibitor (TKI) response in squamous cell lung cancers (SCC). The exclusive use of FGFR1 GCN for predicting FGFR TKI sensitivity assumes increased GCN is the only mechanism for biologically relevant increases in FGFR1 signaling. Herein, we tested whether FGFR1 mRNA and protein expression may serve as better biomarkers of FGFR TKI sensitivity in lung cancer. Histologically diverse lung cancer cell lines were submitted to assays for ponatinib sensitivity, a potent FGFR TKI. A tissue microarray composed of resected lung tumors was submitted to FGFR1 GCN, and mRNA analyses and the results were validated with The Cancer Genome Atlas (TCGA) lung cancer data. Among 58 cell lines, 14 exhibited ponatinib sensitivity (IC50 values ≤ 50 nmol/L) that correlated with FGFR1 mRNA and protein expression, but not with FGFR1 GCN or histology. Moreover, ponatinib sensitivity associated with mRNA expression of the ligands, FGF2 and FGF9. In resected tumors, 22% of adenocarcinomas and 28% of SCCs expressed high FGFR1 mRNA. Importantly, only 46% of SCCs with increased FGFR1 GCN expressed high mRNA. Lung cancer TCGA data validated these findings and unveiled overlap of FGFR1 mRNA positivity with KRAS and PIK3CA mutations. FGFR1 dependency is frequent across various lung cancer histologies, and FGFR1 mRNA may serve as a better biomarker of FGFR TKI response in lung cancer than FGFR1 GCN. The study provides important and timely insight into clinical testing of FGFR TKIs in lung cancer and other solid tumor types. ©2014 American Association for Cancer Research.

  11. Porcine MAP3K5 analysis: molecular cloning, characterization, tissue expression pattern, and copy number variations associated with residual feed intake.

    PubMed

    Pu, L; Zhang, L C; Zhang, J S; Song, X; Wang, L G; Liang, J; Zhang, Y B; Liu, X; Yan, H; Zhang, T; Yue, J W; Li, N; Wu, Q Q; Wang, L X

    2016-08-12

    Mitogen-activated protein kinase kinase kinase 5 (MAP3K5) is essential for apoptosis, proliferation, differentiation, and immune responses, and is a candidate marker for residual feed intake (RFI) in pig. We cloned the full-length cDNA sequence of porcine MAP3K5 by rapid-amplification of cDNA ends. The 5451-bp gene contains a 5'-untranslated region (UTR) (718 bp), a coding region (3738 bp), and a 3'-UTR (995 bp), and encodes a peptide of 1245 amino acids, which shares 97, 99, 97, 93, 91, and 84% sequence identity with cattle, sheep, human, mouse, chicken, and zebrafish MAP3K5, respectively. The deduced MAP3K5 protein sequence contains two conserved domains: a DUF4071 domain and a protein kinase domain. Phylogenetic analysis showed that porcine MAP3K5 forms a separate branch to vicugna and camel MAP3K5. Tissue expression analysis using real-time quantitative polymerase chain reaction (qRT-PCR) revealed that MAP3K5 was expressed in the heart, liver, spleen, lung, kidney, muscle, fat, pancrea, ileum, and stomach tissues. Copy number variation was detected for porcine MAP3K5 and validated by qRT-PCR. Furthermore, a significant increase in average copy number was detected in the low RFI group when compared to the high RFI group in a Duroc pig population. These results provide useful information regarding the influence of MAP3K5 on RFI in pigs.

  12. Nonallelic homologous recombination of the FCGR2/3 locus results in copy number variation and novel chimeric FCGR2 genes with aberrant functional expression.

    PubMed

    Nagelkerke, S Q; Tacke, C E; Breunis, W B; Geissler, J; Sins, J W R; Appelhof, B; van den Berg, T K; de Boer, M; Kuijpers, T W

    2015-09-01

    The human FCGR2/3 locus, containing five highly homologous genes encoding the major IgG receptors, shows extensive copy number variation (CNV) associated with susceptibility to autoimmune diseases. Having genotyped >4000 individuals, we show that all CNV at this locus can be explained by nonallelic homologous recombination (NAHR) of the two paralogous repeats that constitute the majority of the locus, and describe four distinct CNV regions (CNRs) with a highly variable prevalence in the population. Apart from CNV, NAHR events also created several hitherto unidentified chimeric FCGR2 genes. These include an FCGR2A/2C chimeric gene that causes a decreased expression of FcγRIIa on phagocytes, resulting in a decreased production of reactive oxygen species in response to immune complexes, compared with wild-type FCGR2A. Conversely, FCGR2C/2A chimeric genes were identified to lead to an increased expression of FCGR2C. Finally, a rare FCGR2B null-variant allele was found, in which a polymorphic stop codon of FCGR2C is introduced into one FCGR2B gene, resulting in a 50% reduction in protein expression. Our study on CNRs and the chimeric genes is essential for the correct interpretation of association studies on FCGR genes as a determinant for disease susceptibility, and may explain some as yet unidentified extreme phenotypes of immune-mediated disease.

  13. Analyses of chromosome copy number and expression level of four genes in the ciliate Chilodonella uncinata reveal a complex pattern that suggests epigenetic regulation.

    PubMed

    Bellec, Laure; Katz, Laura A

    2012-08-10

    Chilodonella uncinata, like all ciliates, contains two distinct nuclei in every cell: a germline micronucleus and a somatic macronucleus. The macronucleus develops from the zygotic nucleus through a series of chromosomal rearrangements. Macronuclear development in C. uncinata yields a nucleus with highly amplified gene-sized chromosomes. The macronucleus is transcriptionally active during vegetative growth while there is no expression in the micronucleus except during a brief period following conjugation. Gene family evolution in ciliates occurs through complex processes including gene duplication and an alternative processing of scrambled genes. Here we use quantitative PCR to compare relative expression levels of eight genes (SSU-rDNA, actin, α-tubulin and five β-tubulin sequences) to their abundance as macronuclear chromosomes. We show that three strains of the morphospecies C. uncinata share similar patterns across all loci. For example, we find an inverse correlation among five β-tubulin genes whereby the more abundant macronuclear chromosomes have lower levels of expression compared to less abundant chromosomes. We discuss the implication of our findings, which suggest that epigenetic mechanisms maintain chromosome copy number in C. uncinata.

  14. A retrospective analysis of RET translocation, gene copy number gain and expression in NSCLC patients treated with vandetanib in four randomized Phase III studies.

    PubMed

    Platt, Adam; Morten, John; Ji, Qunsheng; Elvin, Paul; Womack, Chris; Su, Xinying; Donald, Emma; Gray, Neil; Read, Jessica; Bigley, Graham; Blockley, Laura; Cresswell, Carl; Dale, Angela; Davies, Amanda; Zhang, Tianwei; Fan, Shuqiong; Fu, Haihua; Gladwin, Amanda; Harrod, Grace; Stevens, James; Williams, Victoria; Ye, Qingqing; Zheng, Li; de Boer, Richard; Herbst, Roy S; Lee, Jin-Soo; Vasselli, James

    2015-03-23

    To determine the prevalence of RET rearrangement genes, RET copy number gains and expression in tumor samples from four Phase III non-small-cell lung cancer (NSCLC) trials of vandetanib, a selective inhibitor of VEGFR, RET and EGFR signaling, and to determine any association with outcome to vandetanib treatment. Archival tumor samples from the ZODIAC ( NCT00312377 , vandetanib ± docetaxel), ZEAL ( NCT00418886 , vandetanib ± pemetrexed), ZEPHYR ( NCT00404924 , vandetanib vs placebo) and ZEST ( NCT00364351 , vandetanib vs erlotinib) studies were evaluated by fluorescence in situ hybridization (FISH) and immunohistochemistry (IHC) in 944 and 1102 patients. The prevalence of RET rearrangements by FISH was 0.7% (95% CI 0.3-1.5%) among patients with a known result. Seven tumor samples were positive for RET rearrangements (vandetanib, n = 3; comparator, n = 4). 2.8% (n = 26) of samples had RET amplification (innumerable RET clusters, or ≥7 copies in > 10% of tumor cells), 8.1% (n = 76) had low RET gene copy number gain (4-6 copies in ≥40% of tumor cells) and 8.3% (n = 92) were RET expression positive (signal intensity ++ or +++ in >10% of tumor cells). Of RET-rearrangement-positive patients, none had an objective response in the vandetanib arm and one patient responded in the comparator arm. Radiologic evidence of tumor shrinkage was observed in two patients treated with vandetanib and one treated with comparator drug. The objective response rate was similar in the vandetanib and comparator arms for patients positive for RET copy number gains or RET protein expression. We have identified prevalence for three RET biomarkers in a population predominated by non-Asians and smokers. RET rearrangement prevalence was lower than previously reported. We found no evidence of a differential benefit for efficacy by IHC and RET gene copy number gains. The low prevalence of RET rearrangements (0.7%) prevents firm conclusions regarding association of vandetanib treatment with

  15. A human sleep homeostasis phenotype in mice expressing a primate-specific PER3 variable-number tandem-repeat coding-region polymorphism

    PubMed Central

    Hasan, Sibah; van der Veen, Daan R.; Winsky-Sommerer, Raphaelle; Hogben, Alexandra; Laing, Emma E.; Koentgen, Frank; Dijk, Derk-Jan; Archer, Simon N.

    2014-01-01

    In humans, a primate-specific variable-number tandem-repeat (VNTR) polymorphism (4 or 5 repeats 54 nt in length) in the circadian gene PER3 is associated with differences in sleep timing and homeostatic responses to sleep loss. We investigated the effects of this polymorphism on circadian rhythmicity and sleep homeostasis by introducing the polymorphism into mice and assessing circadian and sleep parameters at baseline and during and after 12 h of sleep deprivation (SD). Microarray analysis was used to measure hypothalamic and cortical gene expression. Circadian behavior and sleep were normal at baseline. The response to SD of 2 electrophysiological markers of sleep homeostasis, electroencephalography (EEG) θ power during wakefulness and δ power during sleep, were greater in the Per35/5 mice. During recovery, the Per35/5 mice fully compensated for the SD-induced deficit in δ power, but the Per34/4 and wild-type mice did not. Sleep homeostasis-related transcripts (e.g., Homer1, Ptgs2, and Kcna2) were differentially expressed between the humanized mice, but circadian clock genes were not. These data are in accordance with the hypothesis derived from human data that the PER3 VNTR polymorphism modifies the sleep homeostatic response without significantly influencing circadian parameters.—Hasan, S., van der Veen, D. R., Winsky-Sommerer, R., Hogben, A., Laing, E. E., Koentgen, F., Dijk, D.-J., Archer, S. N. A human sleep homeostasis phenotype in mice expressing a primate-specific PER3 variable-number tandem-repeat coding-region polymorphism. PMID:24577121

  16. Quality improvement of transgenic cloned bovine embryos using an aggregation method: Effects on cell number, cell ratio, embryo perimeter, mitochondrial distribution, and gene expression profile.

    PubMed

    Bang, J I; Jin, J I; Ghanem, N; Choi, B H; Fakruzzaman, M; Ha, A N; Lee, K L; Uhm, S J; Ko, D H; Koo, B C; Lee, J G; Kong, I K

    2015-09-01

    The production of cloned embryos using conventional methods has extremely low success rates owing to low embryo quality. To improve the quality of cloned bovine embryos expressing enhanced green fluorescent protein (EGFP), we applied an aggregation culture method. The EGFP gene was transfected into bovine fetal fibroblasts using a retroviral vector system. Somatic cell nuclear transfer was performed using these cells, and the resulting embryos were cultured in aggregates or individually. Gene expression was analyzed by a microarray, and differentially expressed genes were validated by quantitative real-time polymerase chain reaction. The total number of cells per blastocyst and the ratio of inner cell mass cells to trophectoderm cells were higher in aggregated transgenic cloned blastocysts (agBL; 368.7 ± 109.6 and 1:4.8, respectively) than in in vitro-fertilized blastocysts (ivfBL; 189.8 ± 65.8 and 1:2.6, respectively) and nonaggregated transgenic cloned blastocysts (sBL; 113.1 ± 36.3 and 1:1.5, respectively; P < 0.05 and P < 0.01, respectively). Moreover, the blastocyst perimeter was larger in the agBL group than in the ivfBL and sBL groups (1168.8 ± 200.23 vs. 887.33 ± 187.62 and 678 ± 226.1 μm; P < 0.05). In addition, mitochondrial fluorescence intensity was higher in the agBL group than in the ivfBL and sBL groups (P < 0.05). The number of apoptotic cells per blastocyst was lower in the ivfBL and agBL groups than in the sBL group (3.7 ± 2.2 and 3.4 ± 2.1 vs. 6.7 ± 6.8; P < 0.05). The genes identified in the microarray belonged to 18 categories. Expression of the Krüppel-like factor 4 gene, which is associated with cell proliferation, development, and transcription, was 7.2-fold higher in the agBL group than in the ivfBL group (P < 0.05) but did not differ between the sBL and ivfBL groups (P > 0.05). Expression of the heat shock 70-kDa protein 1A gene, which is associated with apoptosis, was 12-fold higher in the s

  17. Integrated Copy Number and Expression Analysis Identifies Profiles of Whole-Arm Chromosomal Alterations and Subgroups with Favorable Outcome in Ovarian Clear Cell Carcinomas

    PubMed Central

    Uehara, Yuriko; Oda, Katsutoshi; Ikeda, Yuji; Koso, Takahiro; Tsuji, Shingo; Yamamoto, Shogo; Asada, Kayo; Sone, Kenbun; Kurikawa, Reiko; Makii, Chinami; Hagiwara, Otoe; Tanikawa, Michihiro; Maeda, Daichi; Hasegawa, Kosei; Nakagawa, Shunsuke; Wada-Hiraike, Osamu; Kawana, Kei; Fukayama, Masashi; Fujiwara, Keiichi; Yano, Tetsu; Osuga, Yutaka; Fujii, Tomoyuki; Aburatani, Hiroyuki

    2015-01-01

    Ovarian clear cell carcinoma (CCC) is generally associated with chemoresistance and poor clinical outcome, even with early diagnosis; whereas high-grade serous carcinomas (SCs) and endometrioid carcinomas (ECs) are commonly chemosensitive at advanced stages. Although an integrated genomic analysis of SC has been performed, conclusive views on copy number and expression profiles for CCC are still limited. In this study, we performed single nucleotide polymorphism analysis with 57 epithelial ovarian cancers (31 CCCs, 14 SCs, and 12 ECs) and microarray expression analysis with 55 cancers (25 CCCs, 16 SCs, and 14 ECs). We then evaluated PIK3CA mutations and ARID1A expression in CCCs. SNP array analysis classified 13% of CCCs into a cluster with high frequency and focal range of copy number alterations (CNAs), significantly lower than for SCs (93%, P < 0.01) and ECs (50%, P = 0.017). The ratio of whole-arm to all CNAs was higher in CCCs (46.9%) than SCs (21.7%; P < 0.0001). SCs with loss of heterozygosity (LOH) of BRCA1 (85%) also had LOH of NF1 and TP53, and LOH of BRCA2 (62%) coexisted with LOH of RB1 and TP53. Microarray analysis classified CCCs into three clusters. One cluster (CCC-2, n = 10) showed more favorable prognosis than the CCC-1 and CCC-3 clusters (P = 0.041). Coexistent alterations of PIK3CA and ARID1A were more common in CCC-1 and CCC-3 (7/11, 64%) than in CCC-2 (0/10, 0%; P < 0.01). Being in cluster CCC-2 was an independent favorable prognostic factor in CCC. In conclusion, CCC was characterized by a high ratio of whole-arm CNAs; whereas CNAs in SC were mainly focal, but preferentially caused LOH of well-known tumor suppressor genes. As such, expression profiles might be useful for sub-classification of CCC, and might provide useful information on prognosis. PMID:26043110

  18. Relativistic theory of tidal Love numbers

    SciTech Connect

    Binnington, Taylor; Poisson, Eric

    2009-10-15

    In Newtonian gravitational theory, a tidal Love number relates the mass multipole moment created by tidal forces on a spherical body to the applied tidal field. The Love number is dimensionless, and it encodes information about the body's internal structure. We present a relativistic theory of Love numbers, which applies to compact bodies with strong internal gravities; the theory extends and completes a recent work by Flanagan and Hinderer, which revealed that the tidal Love number of a neutron star can be measured by Earth-based gravitational-wave detectors. We consider a spherical body deformed by an external tidal field, and provide precise and meaningful definitions for electric-type and magnetic-type Love numbers; and these are computed for polytropic equations of state. The theory applies to black holes as well, and we find that the relativistic Love numbers of a nonrotating black hole are all zero.

  19. Coordinate regulation of glucose transporter function, number, and gene expression by insulin and sulfonylureas in L6 rat skeletal muscle cells.

    PubMed Central

    Wang, P H; Moller, D; Flier, J S; Nayak, R C; Smith, R J

    1989-01-01

    The extrapancreatic actions of sulfonylureas on the glucose transport system were studied in the L6 line of cultured rat skeletal muscle cells. Insulin (10(-7) M) increased 2-deoxyglucose uptake in differentiated L6 myotubes by 30-40% after 8 h of incubation. The sulfonylurea tolazamide (0.6 mg/ml, 22 h) had no effect on glucose uptake in the absence of insulin, but increased insulin-stimulated 2-deoxyglucose uptake twofold. The total cellular content of glucose transporters was assessed with a monoclonal anti-transporter antibody by a solid-phase ELISA method. Insulin (8 h) increased the quantity of glucose transporters, with a maximal twofold increase at 10(-7) M and a dose-response curve similar to that for insulin stimulation of glucose uptake. In spite of its lack of effect on glucose uptake, tolazamide alone (0.6 mg/ml) increased the cellular content of transporters by 70%. The effects of insulin and tolazamide on transporter gene expression were studied with probes derived from Hep G2 glucose transporter cDNA. Insulin increased the transporter mRNA level 1.7-fold, tolazamide increased it 1.5-fold, and the combination of insulin and tolazamide increased transporter mRNA 3-fold. It is concluded that sulfonylureas, together with insulin, enhance glucose uptake in L6 skeletal muscle cells by increasing the number of functioning glucose transport molecules. The long-term regulation of the glucose transport system in skeletal muscle by insulin and sulfonylureas in vivo may involve similar changes in transporter function, number, and gene expression. Images PMID:2661591

  20. Variation in HMA4 gene copy number and expression among Noccaea caerulescens populations presenting different levels of Cd tolerance and accumulation.

    PubMed

    Craciun, Adrian R; Meyer, Claire-Lise; Chen, Jiugeng; Roosens, Nancy; De Groodt, Ruth; Hilson, Pierre; Verbruggen, Nathalie

    2012-06-01

    There is huge variability among populations of the hyperaccumulator Noccaea caerulescens (formerly Thlaspi caerulescens) in their capacity to tolerate and accumulate cadmium. To gain new insights into the mechanisms underlying this variability, we estimated cadmium fluxes and further characterized the N. caerulescens heavy metal ATPase 4 (NcHMA4) gene in three populations (two calamine, Saint-Félix-de-Pallières, France and Prayon, Belgium; one serpentine, Puente Basadre, Spain) presenting contrasting levels of tolerance and accumulation. Cadmium uptake and translocation varied among populations in the same way as accumulation; the population with the highest cadmium concentration in shoots (Saint Félix-de-Pallières) presented the highest capacity for uptake and translocation. We demonstrated that the four NcHMA4 copies identified in a previous study are not fixed at the species level, and that the copy truncated in the C-terminal part encodes a functional protein. NcHMA4 expression and gene copy number was lower in the serpentine population, which was the least efficient in cadmium translocation compared to the calamine populations. NcHMA4 expression was associated with the vascular tissue in all organs, with a maximum at the crown. Overall, our results indicate that differences in cadmium translocation ability of the studied populations appear to be controlled, at least partially, by NcHMA4, while the overexpression of NcHMA4 in the two calamine populations may result from convergent evolution.

  1. Development of a fed-batch fermentation process to overproduce phosphoenolpyruvate carboxykinase using an expression vector with promoter and plasmid copy number controllable by heat.

    PubMed

    Chao, Yun-Peng; Chern, Jong-Tzer; Lin, Wei Shing; Wang, Zei Wen

    2003-11-20

    To effectively achieve tight regulation and high-level expression of cloned genes, a novel expression plasmid has been developed to contain the promoter and allow the plasmid copy number to be controlled by heat. The feasibility of the plasmid was tested by overproducing the pck gene product (Pck), a protein responsible for cell growth on gluconeogenic carbons and with potential toxicity. By fusing the pck gene with the promoter on the plasmid, the Escherichia coli strain harboring the composite vector was shown to produce various amounts of Pck in response to different degrees of heat shock. With the use of a 30 degrees -->41 degrees C stepwise upshift, the shake-flask culture of recombinant cells enabled production of maximal Pck in soluble form accounting for 20% of total cell protein. In sharp contrast, Pck production was undetectable in the uninduced cell, and this was further confirmed by the failed growth of strain JCL1305, defective in the essential genes for gluconeogenesis, carrying the composite vector on succinate at 30 degrees C. By exploiting the fed-batch fermentation approach, the recombinant cell batch initially kept at 30 degrees C in a lab-scale fermentor was exposed to 41 degrees C for 2 h at the batch fermentation stage, followed by a reduction in temperature to 37 degrees C throughout the remainder of the culturing process. Consequently, this resulted in Pck production equivalent to 15% of total cell protein. The total Pck yield thus calculated was amplified 1880-fold over that obtained at the shake-flask scale. Overall, there is great promise for this expression system due to its tight control, high production, simple thermomodulation, and feasible scale-up of recombinant proteins.

  2. Distinct patterns of DNA copy number alteration are associated with different clinicopathological features and gene-expression subtypes of breast cancer.

    PubMed

    Bergamaschi, Anna; Kim, Young H; Wang, Pei; Sørlie, Therese; Hernandez-Boussard, Tina; Lonning, Per E; Tibshirani, Robert; Børresen-Dale, Anne-Lise; Pollack, Jonathan R

    2006-11-01

    Breast cancer is a leading cause of cancer-death among women, where the clinicopathological features of tumors are used to prognosticate and guide therapy. DNA copy number alterations (CNAs), which occur frequently in breast cancer and define key pathogenetic events, are also potentially useful prognostic or predictive factors. Here, we report a genome-wide array-based comparative genomic hybridization (array CGH) survey of CNAs in 89 breast tumors from a patient cohort with locally advanced disease. Statistical analysis links distinct cytoband loci harboring CNAs to specific clinicopathological parameters, including tumor grade, estrogen receptor status, presence of TP53 mutation, and overall survival. Notably, distinct spectra of CNAs also underlie the different subtypes of breast cancer recently defined by expression-profiling, implying these subtypes develop along distinct genetic pathways. In addition, higher numbers of gains/losses are associated with the "basal-like" tumor subtype, while high-level DNA amplification is more frequent in "luminal-B" subtype tumors, suggesting also that distinct mechanisms of genomic instability might underlie their pathogenesis. The identified CNAs may provide a basis for improved patient prognostication, as well as a starting point to define important genes to further our understanding of the pathobiology of breast cancer. This article contains Supplementary Material available at http://www.interscience.wiley.com/jpages/1045-2257/suppmat

  3. Express

    Integrated Risk Information System (IRIS)

    Express ; CASRN 101200 - 48 - 0 Human health assessment information on a chemical substance is included in the IRIS database only after a comprehensive review of toxicity data , as outlined in the IRIS assessment development process . Sections I ( Health Hazard Assessments for Noncarcinogenic Effect

  4. Alterations of LKB1 and KRAS and Risk of Brain Metastasis: Comprehensive Characterization by Mutation Analysis, Copy Number, and Gene Expression in Non-Small-Cell Lung Carcinoma

    PubMed Central

    Zhao, Ni; Wilkerson, Matthew D.; Shah, Usman; Yin, Xiaoying; Wang, Anyou; Hayward, Michele C.; Roberts, Patrick; Lee, Carrie B.; Parsons, Alden M.; Thorne, Leigh B.; Haithcock, Benjamin E.; Grilley-Olson, Juneko E.; Stinchcombe, Thomas E.; Funkhouser, William K.; Wong, Kwok K.; Sharpless, Norman E.; Hayes, D. Neil

    2015-01-01

    Background Brain metastases are one of the most malignant complications of lung cancer and constitute a significant cause of cancer related morbidity and mortality worldwide. Recent years of investigation suggested a role of LKB1 in NSCLC development and progression, in synergy with KRAS alteration. In this study, we systematically analyzed how LKB1 and KRAS alteration, measured by mutation, gene expression (GE) and copy number (CN), are associated with brain metastasis in NSCLC. Materials and Methods Patients treated at University of North Carolina Hospital from 1990 to 2009 with NSCLC provided frozen, surgically extracted tumors for analysis. GE was measured using Agilent 44,000 custom-designed arrays, CN was assessed by Affymetrix GeneChip Human Mapping 250K Sty Array or the Genome-Wide Human SNP Array 6.0 and gene mutation was detected using ABI sequencing. Integrated analysis was conducted to assess the relationship between these genetic markers and brain metastasis. A model was proposed for brain metastasis prediction using these genetic measurements. Results 17 of the 174 patients developed brain metastasis. LKB1 wild type tumors had significantly higher LKB1 CN (p < 0.001) and GE (p = 0.002) than the LKB1 mutant group. KRAS wild type tumors had significantly lower KRAS GE (p < 0.001) and lower CN, although the latter failed to be significant (p = 0.295). Lower LKB1 CN (p = 0.039) and KRAS mutation (p = 0.007) were significantly associated with more brain metastasis. The predictive model based on nodal (N) stage, patient age, LKB1 CN and KRAS mutation had a good prediction accuracy, with area under the ROC curve of 0.832 (p < 0.001). Conclusion LKB1 CN in combination with KRAS mutation predicted brain metastasis in NSCLC. PMID:25224251

  5. Optimal Strouhal number for swimming animals

    NASA Astrophysics Data System (ADS)

    Eloy, Christophe

    2012-04-01

    To evaluate the swimming performances of aquatic animals, an important dimensionless quantity is the Strouhal number, St=fA/U, with f the tail-beat frequency, A the peak-to-peak tail amplitude, and U the swimming velocity. Experiments with flapping foils have exhibited maximum propulsive efficiency in the interval 0.25number increases from 0.15 to 0.8 for animals spanning from the largest cetaceans to the smallest tadpoles. To assess the validity of this model, the swimming kinematics of 53 different species of aquatic animals have been compiled from the literature and it shows that their Strouhal numbers are consistently near the predicted optimum.

  6. Series of Reciprocal Triangular Numbers

    ERIC Educational Resources Information Center

    Bruckman, Paul; Dence, Joseph B.; Dence, Thomas P.; Young, Justin

    2013-01-01

    Reciprocal triangular numbers have appeared in series since the very first infinite series were summed. Here we attack a number of subseries of the reciprocal triangular numbers by methodically expressing them as integrals.

  7. Series of Reciprocal Triangular Numbers

    ERIC Educational Resources Information Center

    Bruckman, Paul; Dence, Joseph B.; Dence, Thomas P.; Young, Justin

    2013-01-01

    Reciprocal triangular numbers have appeared in series since the very first infinite series were summed. Here we attack a number of subseries of the reciprocal triangular numbers by methodically expressing them as integrals.

  8. Convoluted Convolved Fibonacci Numbers

    NASA Astrophysics Data System (ADS)

    Moree, Pieter

    2004-04-01

    The convolved Fibonacci numbers F_j^(r) are defined by (1-x-x^2)^{-r}=sum_{j>= 0}F_{j+1}^(r)x^j. In this note we consider some related numbers that can be expressed in terms of convolved Fibonacci numbers. These numbers appear in the numerical evaluation of a constant arising in the study of the average density of elements in a finite field having order congruent to a (mod d). We derive a formula expressing these numbers in terms of ordinary Fibonacci and Lucas numbers. The non-negativity of these numbers can be inferred from Witt's dimension formula for free Lie algebras. This note is a case study of the transform 1/n sum_{d|}n mu(d)f(z^d)^{n/d} (with f any formal series), which was introduced and studied in a companion paper by Moree.

  9. Global and pedestal confinement and pedestal structure in dimensionless collisionality scans of low-triangularity H-mode plasmas in JET-ILW

    NASA Astrophysics Data System (ADS)

    Frassinetti, L.; Beurskens, M. N. A.; Saarelma, S.; Boom, J. E.; Delabie, E.; Flanagan, J.; Kempenaars, M.; Giroud, C.; Lomas, P.; Meneses, L.; Maggi, C. S.; Menmuir, S.; Nunes, I.; Rimini, F.; Stefanikova, E.; Urano, H.; Verdoolaege, G.; Contributors, JET

    2017-01-01

    A dimensionless collisionality scan in low-triangularity plasmas in the Joint European Torus with the ITER-like wall (JET-ILW) has been performed. The increase of the normalized energy confinement (defined as the ratio between thermal energy confinement and Bohm confinement time) with decreasing collisionality is observed. Moreover, at low collisionality, a confinement factor H98, comparable to JET-C, is achieved. At high collisionality, the low normalized confinement is related to a degraded pedestal stability and a reduction in the density-profile peaking. The increase of normalized energy confinement is due to both an increase in the pedestal and in the core regions. The improvement in the pedestal is related to the increase of the stability. The improvement in the core is driven by (i) the core temperature increase via the temperature-profile stiffness and by (ii) the density-peaking increase driven by the low collisionality. Pedestal stability analysis performed with the ELITE (edge-localized instabilities in tokamak equilibria) code has a reasonable qualitative agreement with the experimental results. An improvement of the pedestal stability with decreasing collisionality is observed. The improvement is ascribed to the reduction of the pedestal width, the increase of the bootstrap current and the reduction of the relative shift between the positions of the pedestal density and pedestal temperature. The EPED1 model predictions for the pedestal pressure height are qualitatively well correlated with the experimental results. Quantitatively, EPED1 overestimates the experimental pressure by 15-35%. In terms of the pedestal width, a correct agreement (within 10-15%) between the EPED1 and the experimental width is found at low collisionality. The experimental pedestal width increases with collisionality. Nonetheless, an extrapolation to low-collisionality values suggests that the width predictions from the KBM constraint are reasonable for ITER.

  10. Evaluation of gene expression and DNA copy number profiles of adipose tissue-derived stromal cells and consecutive neurosphere-like cells generated from dogs with naturally occurring spinal cord injury.

    PubMed

    Lim, Ji-Hey; Koh, Sehwon; Thomas, Rachael; Breen, Matthew; Olby, Natasha J

    2017-03-01

    OBJECTIVE To evaluate gene expression and DNA copy number in adipose tissue-derived stromal cells (ADSCs) and in ADSC-derived neurosphere-like cell clusters (ADSC-NSCs) generated from tissues of chronically paraplegic dogs. ANIMALS 14 client-owned paraplegic dogs. PROCEDURES Dorsal subcutaneous adipose tissue (< 1 cm(3)) was collected under general anesthesia; ADSCs were isolated and cultured. Third-passage ADSCs were cultured in neural cell induction medium to generate ADSC-NSCs. Relative gene expression of mesenchymal cell surface marker CD90 and neural progenitor marker nestin was assessed in ADSCs and ADSC-NSCs from 3 dogs by quantitative real-time PCR assay; expression of these and various neural lineage genes was evaluated for the same dogs by reverse transcription PCR assay. Percentages of cells expressing CD90, nestin, glial fibrillary acidic protein (GFAP), and tubulin β 3 class III (TUJ1) proteins were determined by flow cytometry for all dogs. The DNA copy number stability (in samples from 6 dogs) and neural cell differentiation (14 dogs) were assessed with array-comparative genomic hybridization analysis and immunocytochemical evaluation, respectively. RESULTS ADSCs and ADSC-NSCs expressed neural cell progenitor and differentiation markers; GFAP and microtubule-associated protein 2 were expressed by ADSC-NSCs but not ADSCs. Relative gene expression of CD90 and nestin was subjectively higher in ADSC-NSCs than in ADSCs. Percentages of ADSC-NSCs expressing nestin, GFAP, and TUJ1 proteins were substantially higher than those of ADSCs. Cells expressing neuronal and glial markers were generated from ADSC-NSCs and had no DNA copy number instability detectable by the methods used. CONCLUSIONS AND CLINICAL RELEVANCE Results suggested ADSCs can potentially be a safe and clinically relevant autologous source for canine neural progenitor cells. Further research is needed to verify these findings.

  11. Number Time

    ERIC Educational Resources Information Center

    Herrera, Terese A.

    2004-01-01

    This article features Number Time, a site developed by the British Broadcasting Corporation (BBC) for young mathematics learners, located at www.bbc.co.uk/schools/numbertime. The site uses interactive animation to help children in pre-K through grade 2 understand and practice number basics. Users will find online games, videos that tell number…

  12. Number Time

    ERIC Educational Resources Information Center

    Herrera, Terese A.

    2004-01-01

    This article features Number Time, a site developed by the British Broadcasting Corporation (BBC) for young mathematics learners, located at www.bbc.co.uk/schools/numbertime. The site uses interactive animation to help children in pre-K through grade 2 understand and practice number basics. Users will find online games, videos that tell number…

  13. Application of dimensionless sediment rating curves to predict suspended-sediment concentrations, bedload, and annual sediment loads for rivers in Minnesota

    USGS Publications Warehouse

    Ellison, Christopher A.; Groten, Joel T.; Lorenz, David L.; Koller, Karl S.

    2016-10-27

    Consistent and reliable sediment data are needed by Federal, State, and local government agencies responsible for monitoring water quality, planning river restoration, quantifying sediment budgets, and evaluating the effectiveness of sediment reduction strategies. Heightened concerns about excessive sediment in rivers and the challenge to reduce costs and eliminate data gaps has guided Federal and State interests in pursuing alternative methods for measuring suspended and bedload sediment. Simple and dependable data collection and estimation techniques are needed to generate hydraulic and water-quality information for areas where data are unavailable or difficult to collect.The U.S. Geological Survey, in cooperation with the Minnesota Pollution Control Agency and the Minnesota Department of Natural Resources, completed a study to evaluate the use of dimensionless sediment rating curves (DSRCs) to accurately predict suspended-sediment concentrations (SSCs), bedload, and annual sediment loads for selected rivers and streams in Minnesota based on data collected during 2007 through 2013. This study included the application of DSRC models developed for a small group of streams located in the San Juan River Basin near Pagosa Springs in southwestern Colorado to rivers in Minnesota. Regionally based DSRC models for Minnesota also were developed and compared to DSRC models from Pagosa Springs, Colorado, to evaluate which model provided more accurate predictions of SSCs and bedload in Minnesota.Multiple measures of goodness-of-fit were developed to assess the effectiveness of DSRC models in predicting SSC and bedload for rivers in Minnesota. More than 600 dimensionless ratio values of SSC, bedload, and streamflow were evaluated and delineated according to Pfankuch stream stability categories of “good/fair” and “poor” to develop four Minnesota-based DSRC models. The basis for Pagosa Springs and Minnesota DSRC model effectiveness was founded on measures of goodness

  14. Experimental studies on the effect of Reynolds and Weber numbers on the impact forces of low-speed droplets colliding with a solid surface

    NASA Astrophysics Data System (ADS)

    Zhang, Bin; Li, Jingyin; Guo, Penghua; Lv, Qian

    2017-09-01

    The impact force of low-speed droplets colliding with a solid surface was recorded with an experimental setup involving a highly sensitive piezoelectric force transducer and a high-speed camera recording the droplet shape. Water, ethanol, pure glycerin and aqueous glycerin solutions were used. Experimental results showed that dimensionless force is independent of the Weber number in the experimental range of 68-858 but varies with the Reynolds number. The impact is categorized into three types of processes according to the data on dimensionless peak force against the Reynolds number. The first type is a viscosity-dominated one, in which the Reynolds number ranges between 2.9 and 20. In the second type, transition process, the Reynolds number is in the range of 20-230. In the inertia-dominated type, the Reynolds number is larger than 230. In the viscosity-dominated impact, dimensionless peak force decreases rapidly with increasing Reynolds number, and the effect of viscosity could not be ignored. In the inertia-dominated impact, dimensionless peak force remains constant with varying the Reynolds number, that is, impact force is directly proportional to the product of liquid density, velocity squared and diameter squared but is unaffected by the changes in viscosity and surface tension. Furthermore, the deformation of droplet shape due to oscillation affects the impact force; a small horizontal-to-vertical ratio results in small impact force and vice versa.

  15. Genome-wide Copy Number Variation and Temporal Genes Expression Analysis in Marek's Disease-Resistant or -Susceptible Inbred Lines of Chickens

    USDA-ARS?s Scientific Manuscript database

    Viruses that cause cancers are a great threat to human and animal health. Marek’s disease (MD) in chickens is a lymphoproliferative disease caused by Marek’s disease virus (MDV). The over-expression of Hodgkin’s disease antigen in MD makes it an ideal model to study the progression mechanism of Hodg...

  16. RhoE deficiency alters postnatal subventricular zone development and the number of calbindin-expressing neurons in the olfactory bulb of mouse.

    PubMed

    Ballester-Lurbe, Begoña; González-Granero, Susana; Mocholí, Enric; Poch, Enric; García-Manzanares, María; Dierssen, Mara; Pérez-Roger, Ignacio; García-Verdugo, José M; Guasch, Rosa M; Terrado, José

    2015-11-01

    The subventricular zone represents an important reservoir of progenitor cells in the adult brain. Cells from the subventricular zone migrate along the rostral migratory stream and reach the olfactory bulb, where they originate different types of interneurons. In this work, we have analyzed the role of the small GTPase RhoE/Rnd3 in subventricular zone cell development using mice-lacking RhoE expression. Our results show that RhoE null mice display a remarkable postnatal broadening of the subventricular zone and caudal rostral migratory stream. This broadening was caused by an increase in progenitor proliferation, observed in the second postnatal week but not before, and by an altered migration of the cells, which appeared in disorganized cell arrangements that impaired the appropriate contact between cells in the rostral migratory stream. In addition, the thickness of the granule cell layer in the olfactory bulb was reduced, although the density of granule cells did not differ between wild-type and RhoE null mice. Finally, the lack of RhoE expression affected the olfactory glomeruli inducing a severe reduction of calbindin-expressing interneurons in the periglomerular layer. This was already evident in the newborns and even more pronounced 15 days later when RhoE null mice displayed 89% less cells than control mice. Our results indicate that RhoE has pleiotropic functions on subventricular cells because of its role in proliferation and tangential migration, affecting mainly the development of calbindin-expressing cells in the olfactory bulb.

  17. Number 85.

    PubMed

    Cornel, Veronica M

    2007-07-06

    Reviews are listed in order of appearance in the sources indicated. In multidisciplinary review journals, only those reviews which fall within the scope of this Journal are included. Sources are listed alphabetically in three categories: regularly issued review journals and series volumes, contributed volumes, and other monographs. Titles are numbered serially, and these numbers are used for reference in the index. Major English-language sources of critical reviews are covered. Encyclopedic treatises, annual surveys such as Specialist Periodical Reports, and compilations of symposia proceedings are omitted. This installment of Recent Reviews covers principally the early part of the 2007 literature. Previous installment: J. Org. Chem. 2007, 72 (7), 2699-706.

  18. Number 84.

    PubMed

    Cornel, Veronica M

    2007-03-30

    Reviews are listed in order of appearance in the sources indicated. In multidisciplinary review journals, only those reviews which fall within the scope of this Journal are included. Sources are listed alphabetically in three categories: regularly issued review journals and series volumes, contributed volumes, and other monographs. Titles are numbered serially, and these numbers are used for reference in the index. Major English-language sources of critical reviews are covered. Encyclopedic treatises, annual surveys such as Specialist Periodical Reports, and compilations of symposia proceedings are omitted. This installment of Recent Reviews covers principally the latter part of the 2006 literature. Previous installment: J. Org. Chem. 2007, 72(1), 303-12.

  19. Number 83.

    PubMed

    Cornel, Veronica M

    2007-01-05

    Reviews are listed in order of appearance in the sources indicated. In multidisciplinary review journals, only those reviews which fall within the scope of this Journal are included. Sources are listed alphabetically in three categories: regularly issued review journals and series volumes, contributed volumes, and other monographs. Titles are numbered serially, and these numbers are used for reference in the index. Major English-language sources of critical reviews are covered. Encyclopedic treatises, annual surveys such as Specialist Periodical Reports, and compilations of symposia proceedings are omitted. This installment of Recent Reviews covers principally the middle part of the 2006 literature. Previous installment: J. Org. Chem. 2006, 71(20), 7923-30.

  20. Number 75.

    PubMed

    Cornel, Veronica M

    2005-01-07

    Reviews are listed in order of appearance in the sources indicated. In multidisciplinary review journals, only those reviews which fall within the scope of this Journal are included. Sources are listed alphabetically in three categories: regularly issued review journals and series volumes, contributed volumes, and other monographs. Titles are numbered serially, and these numbers are used for reference in the index. Major English-language sources of critical reviews are covered. Encyclopedic treatises, annual surveys such as Specialist Periodical Reports, and compilations of symposia proceedings are omitted. This installment of Recent Reviews covers principally the middle part of the 2004 literature. Previous installment: J. Org. Chem. 2004, 69(20), 6957-66.

  1. Numbers Sense

    ERIC Educational Resources Information Center

    Kathotia, Vinay

    2009-01-01

    This article reports on work undertaken by schools as part of Qualifications and Curriculum Authority's (QCA's) "Engaging mathematics for all learners" project. The goal was to use in the classroom, materials and approaches from a Royal Institution (Ri) Year 10 master-class, "Number Sense", which was inspired by examples from…

  2. Numbers, Please!

    ERIC Educational Resources Information Center

    Thelin, John R.

    2013-01-01

    What topic would you choose if you had the luxury of writing forever? In this article, John Thelin provides his response: He would opt to write about the history of higher education in a way that relies on quantitative data. "Numbers, please!" is his research request in taking on a longitudinal study of colleges and universities over…

  3. Numbers, Please!

    ERIC Educational Resources Information Center

    Thelin, John R.

    2013-01-01

    What topic would you choose if you had the luxury of writing forever? In this article, John Thelin provides his response: He would opt to write about the history of higher education in a way that relies on quantitative data. "Numbers, please!" is his research request in taking on a longitudinal study of colleges and universities over…

  4. Numbers? Borrinnnggg!!!

    ERIC Educational Resources Information Center

    Buscemi, William I.

    1997-01-01

    Suggests that political apathy among young people is the result of not having the conceptual tools necessary to comprehend present issues. Argues that to grasp many issues, students need to be mathematically literate, which many are not. Suggests that instructors should expose students to comparative numbers more often. (DSK)

  5. Numbers Sense

    ERIC Educational Resources Information Center

    Kathotia, Vinay

    2009-01-01

    This article reports on work undertaken by schools as part of Qualifications and Curriculum Authority's (QCA's) "Engaging mathematics for all learners" project. The goal was to use in the classroom, materials and approaches from a Royal Institution (Ri) Year 10 master-class, "Number Sense", which was inspired by examples from…

  6. Negative Numbers

    ERIC Educational Resources Information Center

    Galbraith, Mary J.

    1974-01-01

    Examination of models for representing integers demonstrates that formal operational thought is required for establishing the operations on integers. Advocated is the use of many models for introducing negative numbers but, apart from addition, it is recommended that operations on integers be delayed until the formal operations stage. (JP)

  7. Transcriptome and Expression Profiling Analysis of the Hemocytes Reveals a Large Number of Immune-Related Genes in Mud Crab Scylla paramamosain during Vibrio parahaemolyticus Infection

    PubMed Central

    Xie, Chuping; Chen, Yaping; Sun, Wanwei; Ding, Jun; Zhou, Lizhen; Wang, Shasha; Wang, Shuqi; Zhang, Yueling; Zhu, Dashi; Wen, Xiaobo; Hu, Songnian; Li, Shengkang

    2014-01-01

    Background Mud crab Scylla paramamosain is an economically important marine species in China. However, frequent outbreaks of infectious diseases caused by marine bacteria, such as Vibrio parahaemolyticus, result in great economic losses. Methodology/Principal Findings Comparative de novo transcriptome analysis of S. paramamosain infected with V. parahaemolyticus was carried out to investigate the molecular mechanisms underlying the immune response to pathogenic bacteria by using the Illumina paired-end sequencing platform. A total of 52,934,042 clean reads from the hemocytes of V. parahaemolyticus-infected mud crabs and controls were obtained and assembled into 186,193 contigs. 59,120 unigenes were identified from 81,709 consensus sequences of mud crabs and 48,934 unigenes were matched proteins in the Nr or Swissprot databases. Among these, 10,566 unigenes belong to 3 categories of Gene Ontology, 25,349 to 30 categories of KEGG, and 15,191 to 25 categories of COG database, covering almost all functional categories. By using the Solexa/Illumina's DGE platform, 1213 differentially expressed genes (P<0.05), including 538 significantly up-regulated and 675 down-regulated, were detected in V. parahaemolyticus-infected crabs as compared to that in the controls. Transcript levels of randomly-chosen genes were further measured by quantitative real-time PCR to confirm the expression profiles. Many differentially expressed genes are involved in various immune processes, including stimulation of the Toll pathway, Immune Deficiency (IMD) pathway, Ras-regulated endocytosis, and proPO-activating system. Conclusions/Significance Analysis of the expression profile of crabs under infection provides invaluable new data for biological research in S. paramamosain, such as the identification of novel genes in the hemocytes during V. parahaemolyticus infection. These results will facilitate our comprehensive understanding of the mechanisms involved in the immune response to bacterial

  8. Tandem Repeats, High Copy Number and Remarkable Diel Expression Rhythm of Form II RuBisCO in Prorocentrum donghaiense (Dinophyceae)

    PubMed Central

    Shi, Xinguo; Zhang, Huan; Lin, Senjie

    2013-01-01

    Gene structure and expression regulation of form II RuBisCO (rbcII) in dinoflagellates are still poorly understood. Here we isolated this gene (Pdrbc) and investigated its diel expression pattern in a harmful algal bloom forming dinoflagellate Prorocentrum donghaiense. We obtained cDNA sequences with triple tandem repeats of the coding unit (CU); the 5′ region has the sequence of a typical dinoflagellate plastid gene, encoding an N-terminus with two transmembrane regions separated by a plastid transit peptide. The CUs (1,455 bp except 1464 bp in last CU) are connected through a 63 bp spacer. Phylogenetic analysis showed that rbcII CUs within species formed monophyletic clusters, indicative of intraspecific gene duplication or purifying evolution. Using quantitative PCR (qPCR) we estimated 117±40 CUs of Pdrbc in the P. donghaiense genome. Although it is commonly believed that most dinoflagellate genes lack transcriptional regulation, our RT-qPCR analysis on synchronized cultures revealed remarkable diel rhythm of Pdrbc expression, showing significant correlations of transcript abundance with the timing of the dark-to-light transition and cell cycle G2M-phase. When the cultures were shifted to continuous light, Pdrbc expression remained significantly correlated with the G2M-phase. Under continuous darkness the cell cycle was arrested at the G1 phase, and the rhythm of Pdrbc transcription disappeared. Our results suggest that dinoflagellate rbcII 1) undergoes duplication or sequence purification within species, 2) is organized in tandem arrays in most species probably to facilitate efficient translation and import of the encoded enzyme, and 3) is regulated transcriptionally in a cell cycle-dependent fashion at least in some dinoflagellates. PMID:23976999

  9. Enhanced expression of trim14 gene suppressed Sindbis virus reproduction and modulated the transcription of a large number of genes of innate immunity.

    PubMed

    Nenasheva, V V; Kovaleva, G V; Uryvaev, L V; Ionova, K S; Dedova, A V; Vorkunova, G K; Chernyshenko, S V; Khaidarova, N V; Tarantul, V Z

    2015-07-01

    In the present research, we have studied an influence of enhanced expression TRIM14 on alphavirus Sindbis (SINV, Togaviridae family) infection. In the HEK293 cells transfected with human trim14 gene (HEK-trim14), SINV yield after infection was decreased 1000-10,000 times (3-4 lg of TCD50/ml) at 24 h p.i. and considerably less (1-2 lg of TCD50/ml) at 48 h p.i. Analysis of the expression of 43 genes directly or indirectly involved in innate immune machine in HEK-trim14 non-infected cells comparing with the control (non-transfected) HEK293 cells revealed that stable trim14 transfection in HEK293 cells caused increased transcription of 18 genes (ifna, il6 (ifnβ2), isg15, raf-1, NF-kB (nf-kb1, rela, nf-kb2, relb), grb2, grb3-3, traf3ip2, junB, c-myb, pu.1, akt1, tyk2, erk2, mek2) and lowered transcription of 3 genes (ifnγ, gata1, il-17a). The similar patterns of genes expression observe in SINV-infected non-transfected HEK293 cells. However, SINV infection of HEK-trim14 cells caused inhibition of the most interferon cascade genes as well as subunits of transcription factor NF-κB. Thus, stable enhanced expression of trim14 gene in cells activates the transcription of many immunity genes and suppresses the SINV reproduction, but SINV infection of HEK-trim14 cells promotes inhibition of some genes involved in innate immune system.

  10. Systematic Review of Micro-RNA Expression in Pre-Eclampsia Identifies a Number of Common Pathways Associated with the Disease

    PubMed Central

    Sheikh, Adam M.; Currie, Gemma; Delles, Christian

    2016-01-01

    Background Pre-eclampsia (PE) is a complex, multi-systemic condition of pregnancy which greatly impacts maternal and perinatal morbidity and mortality. MicroRNAs (miRs) are differentially expressed in PE and may be important in helping to understand the condition and its pathogenesis. Methods Case-control studies investigating expression of miRs in PE were collected through a systematic literature search. Data was extracted and compared from 58 studies to identify the most promising miRs associated with PE pathogenesis and identify areas of methodology which could account for often conflicting results. Results Some of the most frequently differentially expressed miRs in PE include miR-210, miR-223 and miR-126/126* which associate strongly with the etiological domains of hypoxia, immunology and angiogenesis. Members of the miR-515 family belonging to the imprinted chromosome 19 miR cluster with putative roles in trophoblast invasion were also found to be differentially expressed. Certain miRs appear to associate with more severe forms of PE such as miR-210 and the immune-related miR-181a and miR-15 families. Patterns of miR expression may help pinpoint key pathways (e.g. IL-6/miR-223/STAT3) and aid in untangling the heterogeneous nature of PE. The detectable presence of many PE-associated miRs in antenatal circulatory samples suggests their usefulness as predictive biomarkers. Further progress in ascertaining the clinical value of miRs and in understanding how they might contribute to pathogenesis is predicated upon resolving current methodological challenges in studies. These include differences in diagnostic criteria, cohort characteristics, sampling technique, RNA isolation and platform-dependent variation in miR profiling. Conclusion Reviewing studies of PE-associated miRs has revealed their potential as informants of underlying target genes and pathways relating to PE pathogenesis. However, the incongruity in results across current studies hampers their

  11. Developing Meaning for Algebraic Procedures: An Exploration of the Connections Undergraduate Students Make between Algebraic Rational Expressions and Basic Number Properties

    ERIC Educational Resources Information Center

    Yantz, Jennifer

    2013-01-01

    The attainment and retention of later algebra skills in high school has been identified as a factor significantly impacting the postsecondary success of students majoring in STEM fields. Researchers maintain that learners develop meaning for algebraic procedures by forming connections to the basic number system properties. The present study…

  12. Generalized Knudsen Number for Unsteady Fluid Flow

    NASA Astrophysics Data System (ADS)

    Kara, V.; Yakhot, V.; Ekinci, K. L.

    2017-02-01

    We explore the scaling behavior of an unsteady flow that is generated by an oscillating body of finite size in a gas. If the gas is gradually rarefied, the Navier-Stokes equations begin to fail and a kinetic description of the flow becomes more appropriate. The failure of the Navier-Stokes equations can be thought to take place via two different physical mechanisms: either the continuum hypothesis breaks down as a result of a finite size effect or local equilibrium is violated due to the high rate of strain. By independently tuning the relevant linear dimension and the frequency of the oscillating body, we can experimentally observe these two different physical mechanisms. All the experimental data, however, can be collapsed using a single dimensionless scaling parameter that combines the relevant linear dimension and the frequency of the body. This proposed Knudsen number for an unsteady flow is rooted in a fundamental symmetry principle, namely, Galilean invariance.

  13. Magellan: a web based system for the integrated analysis of heterogeneous biological data and annotations; application to DNA copy number and expression data in ovarian cancer.

    PubMed

    Kingsley, Chris B; Kuo, Wen-Lin; Polikoff, Daniel; Berchuck, Andy; Gray, Joe W; Jain, Ajay N

    2007-02-05

    Recent advances in high throughput biological methods allow researchers to generate enormous amounts of data from a single experiment. In order to extract meaningful conclusions from this tidal wave of data, it will be necessary to develop analytical methods of sufficient power and utility. It is particularly important that biologists themselves be able to perform many of these analyses, such that their background knowledge of the experimental system under study can be used to interpret results and direct further inquiries. We have developed a web-based system, Magellan, which allows the upload, storage, and analysis of multivariate data and textual or numerical annotations. Data and annotations are treated as abstract entities, to maximize the different types of information the system can store and analyze. Annotations can be used in analyses/visualizations, as a means of subsetting data to reduce dimensionality, or as a means of projecting variables from one data type or data set to another. Analytical methods are deployed within Magellan such that new functionalities can be added in a straightforward fashion. Using Magellan, we performed an integrated analysis of genome-wide comparative genomic hybridization (CGH), mRNA expression, and clinical data from ovarian tumors. Analyses included the use of permutation-based methods to identify genes whose mRNA expression levels correlated with patient survival, a nearest neighbor classifier to predict patient survival from CGH data, and curated annotations such as genomic position and derived annotations such as statistical computations to explore the quantitative relationship between CGH and mRNA expression data.

  14. Selective populations of hippocampal interneurons express ErbB4 and their number and distribution is altered in ErbB4 knockout mice

    PubMed Central

    Neddens, Jörg; Buonanno, Andrés

    2010-01-01

    Neuregulins (NRGs) are ligands of ErbB receptor tyrosine kinases. The NRG1-ErbB4 pathway has been shown to modulate hippocampal synaptic plasticity and network oscillations in the adult rodent brain. In order to identify cells that mediate these effects here we determine the expression pattern of ErbB4 in four functionally distinct classes of interneurons that represent the majority of all inhibitory neurons in the hippocampus. Based on data from 15 mice and 25,000 cells, we show that ErbB4 is expressed in cells that are positive for cholecystokinin (CCK, 54%), parvalbumin (PV, 42%), or neuronal nitric oxide synthase (nNOS, 39%) in a layer-specific and region-specific manner, whereas cells expressing somatostatin (SOM) are rarely immunoreactive for ErbB4 (1%). We next compared the numerical density (cells/mm3) and the distribution of interneurons between ErbB4−/− mice and wildtype controls. Based on data from 25 mice and 56,000 cells, we detected reductions of PV-positive and nNOS-positive cells in knockouts (−24% and −27%, respectively) but only a minor reduction of CCK-positive cells; no changes in SOM-positive cells were observed. The overall reduction of interneurons was verified by quantification of GAD67-immunoreactive cells (−24% in ErbB4−/− mice). The reduction of interneurons along the dorsoventral axis was more severe in intermediate and ventral portions than in the dorsal hippocampus, and regional reductions occurred in the CA1-3 regions and subiculum, whereas we found no significant changes in the dentate gyrus. The expression by different populations of interneurons suggests that ErbB4 can modulate several microcircuits within the hippocampus and mediate the previously reported effects of NRG1 on network oscillations and synaptic plasticity. The selective reduction of GABAergic cells in ErbB4−/− mice is consistent with the role of NRG-ErbB4 signaling in the generation and migration of interneurons during development, and with neuronal

  15. Testosterone and trenbolone enanthate increase mature myostatin protein expression despite increasing skeletal muscle hypertrophy and satellite cell number in rodent muscle.

    PubMed

    Dalbo, V J; Roberts, M D; Mobley, C B; Ballmann, C; Kephart, W C; Fox, C D; Santucci, V A; Conover, C F; Beggs, L A; Balaez, A; Hoerr, F J; Yarrow, J F; Borst, S E; Beck, D T

    2017-04-01

    The androgen-induced alterations in adult rodent skeletal muscle fibre cross-sectional area (fCSA), satellite cell content and myostatin (Mstn) were examined in 10-month-old Fisher 344 rats (n = 41) assigned to Sham surgery, orchiectomy (ORX), ORX + testosterone (TEST; 7.0 mg week(-1) ) or ORX + trenbolone (TREN; 1.0 mg week(-1) ). After 29 days, animals were euthanised and the levator ani/bulbocavernosus (LABC) muscle complex was harvested for analyses. LABC muscle fCSA was 102% and 94% higher in ORX + TEST and ORX + TREN compared to ORX (p < .001). ORX + TEST and ORX + TREN increased satellite cell numbers by 181% and 178% compared to ORX, respectively (p < .01), with no differences between conditions for myonuclear number per muscle fibre (p = .948). Mstn protein was increased 159% and 169% in the ORX + TEST and ORX + TREN compared to ORX (p < .01). pan-SMAD2/3 protein was ~30-50% greater in ORX compared to SHAM (p = .006), ORX + TEST (p = .037) and ORX + TREN (p = .043), although there were no between-treatment effects regarding phosphorylated SMAD2/3. Mstn, ActrIIb and Mighty mRNAs were lower in ORX, ORX + TEST and ORX + TREN compared to SHAM (p < .05). Testosterone and trenbolone administration increased muscle fCSA and satellite cell number without increasing myonuclei number, and increased Mstn protein levels. Several genes and signalling proteins related to myostatin signalling were differentially regulated by ORX or androgen therapy.

  16. Study of Nonlinear MHD Tribological Squeeze Film at Generalized Magnetic Reynolds Numbers Using DTM.

    PubMed

    Rashidi, Mohammad Mehdi; Freidoonimehr, Navid; Momoniat, Ebrahim; Rostami, Behnam

    2015-01-01

    In the current article, a combination of the differential transform method (DTM) and Padé approximation method are implemented to solve a system of nonlinear differential equations modelling the flow of a Newtonian magnetic lubricant squeeze film with magnetic induction effects incorporated. Solutions for the transformed radial and tangential momentum as well as solutions for the radial and tangential induced magnetic field conservation equations are determined. The DTM-Padé combined method is observed to demonstrate excellent convergence, stability and versatility in simulating the magnetic squeeze film problem. The effects of involved parameters, i.e. squeeze Reynolds number (N1), dimensionless axial magnetic force strength parameter (N2), dimensionless tangential magnetic force strength parameter (N3), and magnetic Reynolds number (Rem) are illustrated graphically and discussed in detail. Applications of the study include automotive magneto-rheological shock absorbers, novel aircraft landing gear systems and biological prosthetics.

  17. Study of Nonlinear MHD Tribological Squeeze Film at Generalized Magnetic Reynolds Numbers Using DTM

    PubMed Central

    Rashidi, Mohammad Mehdi; Freidoonimehr, Navid; Momoniat, Ebrahim; Rostami, Behnam

    2015-01-01

    In the current article, a combination of the differential transform method (DTM) and Padé approximation method are implemented to solve a system of nonlinear differential equations modelling the flow of a Newtonian magnetic lubricant squeeze film with magnetic induction effects incorporated. Solutions for the transformed radial and tangential momentum as well as solutions for the radial and tangential induced magnetic field conservation equations are determined. The DTM-Padé combined method is observed to demonstrate excellent convergence, stability and versatility in simulating the magnetic squeeze film problem. The effects of involved parameters, i.e. squeeze Reynolds number (N1), dimensionless axial magnetic force strength parameter (N2), dimensionless tangential magnetic force strength parameter (N3), and magnetic Reynolds number (Rem) are illustrated graphically and discussed in detail. Applications of the study include automotive magneto-rheological shock absorbers, novel aircraft landing gear systems and biological prosthetics. PMID:26267247

  18. Number 8

    NASA Technical Reports Server (NTRS)

    2006-01-01

    29 January 2006 This Mars Global Surveyor (MGS) Mars Orbiter Camera (MOC) image shows a spotted, high latitude plain, south of the Argyre basin. When the image was received from Mars by the MOC operations team, they noticed -- with a sense of humor -- the number '8' on this martian surface. The '8' is located at the center-right and is formed by the rims of two old impact craters that have been eroded and partly-filled and partly-buried beneath the surface.

    Location near: 68.6oS, 38.4oW Image width: 3 km (1.9 mi) Illumination from: upper left Season: Southern Summer

  19. Deductions about the Number, Organization, and Evolution of Genes in the Tomato Genome Based on Analysis of a Large Expressed Sequence Tag Collection and Selective Genomic Sequencing

    PubMed Central

    Van der Hoeven, Rutger; Ronning, Catherine; Giovannoni, James; Martin, Gregory; Tanksley, Steven

    2002-01-01

    Analysis of a collection of 120,892 single-pass ESTs, derived from 26 different tomato cDNA libraries and reduced to a set of 27,274 unique consensus sequences (unigenes), revealed that 70% of the unigenes have identifiable homologs in the Arabidopsis genome. Genes corresponding to metabolism have remained most conserved between these two genomes, whereas genes encoding transcription factors are among the fastest evolving. The majority of the 10 largest conserved multigene families share similar copy numbers in tomato and Arabidopsis, suggesting that the multiplicity of these families may have occurred before the divergence of these two species. An exception to this multigene conservation was observed for the E8-like protein family, which is associated with fruit ripening and has higher copy number in tomato than in Arabidopsis. Finally, six BAC clones from different parts of the tomato genome were isolated, genetically mapped, sequenced, and annotated. The combined analysis of the EST database and these six sequenced BACs leads to the prediction that the tomato genome encodes ∼35,000 genes, which are sequestered largely in euchromatic regions corresponding to less than one-quarter of the total DNA in the tomato nucleus. PMID:12119366

  20. Grasping numbers.

    PubMed

    Moretto, Giovanna; di Pellegrino, Giuseppe

    2008-07-01

    Both theoretical and empirical studies suggest that numerical processing is intimately linked to representations of goal-directed hand actions. Further evidence for this possibility is provided here by the results of two experiments, both of which revealed a powerful influence of numerical magnitude on the selection of hand grasping movements. Human participants performed either power or precision grip responses based on the semantic properties (e.g., parity) of visual Arabic numerals, in Experiment 1, or depending on their surface characteristics (e.g., colour), in Experiment 2. In both the experiments, it was found that small numerical values facilitated precision grip (commonly used to grasp small objects), while large numerical value potentiated power grip (commonly used to grasp large objects). These findings reveal that perceiving numbers can automatically prime grasping gestures, in a similar manner to viewing physical objects. This result is coherent with the view that processing of symbolic (numerical) and physical quantitative information converges onto a shared magnitude system representing the coordinates of action.

  1. Evolutionary Changes in Gene Expression, Coding Sequence and Copy-Number at the Cyp6g1 Locus Contribute to Resistance to Multiple Insecticides in Drosophila

    PubMed Central

    Harrop, Thomas W. R.; Sztal, Tamar; Lumb, Christopher; Good, Robert T.; Daborn, Phillip J.; Batterham, Philip; Chung, Henry

    2014-01-01

    Widespread use of insecticides has led to insecticide resistance in many populations of insects. In some populations, resistance has evolved to multiple pesticides. In Drosophila melanogaster, resistance to multiple classes of insecticide is due to the overexpression of a single cytochrome P450 gene, Cyp6g1. Overexpression of Cyp6g1 appears to have evolved in parallel in Drosophila simulans, a sibling species of D. melanogaster, where it is also associated with insecticide resistance. However, it is not known whether the ability of the CYP6G1 enzyme to provide resistance to multiple insecticides evolved recently in D. melanogaster or if this function is present in all Drosophila species. Here we show that duplication of the Cyp6g1 gene occurred at least four times during the evolution of different Drosophila species, and the ability of CYP6G1 to confer resistance to multiple insecticides exists in D. melanogaster and D. simulans but not in Drosophila willistoni or Drosophila virilis. In D. virilis, which has multiple copies of Cyp6g1, one copy confers resistance to DDT and another to nitenpyram, suggesting that the divergence of protein sequence between copies subsequent to the duplication affected the activity of the enzyme. All orthologs tested conferred resistance to one or more insecticides, suggesting that CYP6G1 had the capacity to provide resistance to anthropogenic chemicals before they existed. Finally, we show that expression of Cyp6g1 in the Malpighian tubules, which contributes to DDT resistance in D. melanogaster, is specific to the D. melanogaster–D. simulans lineage. Our results suggest that a combination of gene duplication, regulatory changes and protein coding changes has taken place at the Cyp6g1 locus during evolution and this locus may play a role in providing resistance to different environmental toxins in different Drosophila species. PMID:24416303

  2. Effects of Zidovudine Treatment on Heart mRNA Expression and Mitochondrial DNA Copy Number Associated with Alterations in Deoxynucleoside Triphosphate Composition in a Neonatal Rat Model.

    PubMed

    Snowdin, Jacob W; Hsiung, Chia-Heng; Kesterson, Daniel G; Kamath, Vasudeva G; McKee, Edward E

    2015-10-01

    The prevention of mother-to-child transmission (MTCT) of HIV is a crucial component in HIV therapy. Nucleoside reverse transcriptase inhibitors (NRTIs), primarily 3'-azido-3'-thymidine (AZT [zidovudine]), have been used to treat both mothers and neonates. While AZT is being replaced with less toxic drugs in treating mothers in MTCT prevention, it is still commonly used to treat neonates. Problems related to mitochondrial toxicity and potential mutagenesis associated with AZT treatment have been reported in treated cohorts. Yet little is known concerning the metabolism and potential toxicity of AZT on embryonic and neonatal tissues, especially considering that the enzymes of nucleoside metabolism change dramatically as many tissues convert from hyperplastic to hypertrophic growth during this period. AZT is known to inhibit thymidine phosphorylation and potentially alter deoxynucleoside triphosphate (dNTP) pools in adults. This study examines the effects of AZT on dNTP pools, mRNA expression of deoxynucleoside/deoxynucleotide metabolic enzymes, and mitochondrial DNA levels in a neonatal rat model. Results show that AZT treatment dramatically altered dNTP pools in the first 7 days of life after birth, which normalized to age-matched controls in the second and third weeks. Additionally, AZT treatment dramatically increased the mRNA levels of many enzymes involved in deoxynucleotide synthesis and mitochondrial biogenesis during the first week of life, which normalized to age-matched controls by the third week. These results were correlated with depletion of mitochondrial DNA noted in the second week. Taken together, results demonstrated that AZT treatment has a powerful effect on the deoxynucleotide synthesis pathways that may be associated with toxicity and mutagenesis.

  3. Decreased expression of brain-derived neurotrophic factor in BDNF(+/-) mice is associated with enhanced recovery of motor performance and increased neuroblast number following experimental stroke.

    PubMed

    Nygren, Josefine; Kokaia, Merab; Wieloch, Tadeusz

    2006-08-15

    Brain-derived neurotrophic factor (BDNF) is involved in brain plasticity and neuronal survival. Generally, BDNF enhances synaptic activity and neurite growth, although the effect of BDNF on neuronal survival and brain plasticity following injury is equivocal. Housing rats in an enriched environment after experimental stroke enhances recovery of sensory-motor function, which is associated with a decrease in the BDNF mRNA and protein levels. We used BDNF(+/-) mice and wild-type littermate mice to investigate whether the decrease in the brain levels of BDNF affected motor function or infarct volume following transient occlusion of the middle cerebral artery (tMCAO) for 40 min. We found that the BDNF(+/-) mice had a significantly improved motor function on the rotating pole test 2 weeks after tMCAO compared with wild-type mice. When intermittently exposed to an enriched environment following tMCAO, the wild-type mice improved motor function to the same degree as BDNF(+/-) mice. There was no effect of BDNF reduction on infarct volume. Neurogenesis is induced following experimental stroke, and in the striatum of BDNF(+/-) mice significantly increased numbers of neuroblasts compared with wild-type mice were seen, both in standard and in enriched conditions. We conclude that decreasing brain levels of BDNF enhances the recovery of function following experimental stroke.

  4. Rayleigh- and Prandtl-number dependence of the large-scale flow-structure in weakly-rotating turbulent thermal convection

    NASA Astrophysics Data System (ADS)

    Weiss, Stephan; Wei, Ping; Ahlers, Guenter

    2015-11-01

    Turbulent thermal convection under rotation shows a remarkable variety of different flow states. The Nusselt number (Nu) at slow rotation rates (expressed as the dimensionless inverse Rossby number 1/Ro), for example, is not a monotonic function of 1/Ro. Different 1/Ro-ranges can be observed with different slopes ∂Nu / ∂ (1 / Ro) . Some of these ranges are connected by sharp transitions where ∂Nu / ∂ (1 / Ro) changes discontinuously. We investigate different regimes in cylindrical samples of aspect ratio Γ = 1 by measuring temperatures at the sidewall of the sample for various Prandtl numbers in the range 3 < Pr < 35 and Rayleigh numbers in the range of 108 < Ra < 4 ×1011 . From these measurements we deduce changes of the flow structure. We learn about the stability and dynamics of the large-scale circulation (LSC), as well as about its breakdown and the onset of vortex formation close to the top and bottom plate. We shall examine correlations between these measurements and changes in the heat transport. This work was supported by NSF grant DRM11-58514. SW acknowledges support by the Deutsche Forschungsgemeinschaft.

  5. The importance of the number of transplanted cells with dipeptidyl peptidase-4 expression on the haematopoietic recovery and lymphocyte reconstitution in patients with multiple myeloma after autologous haematopoietic stem-cell transplantation.

    PubMed

    Kopinska, Anna; Krawczyk-Kulis, Małgorzata; Dziaczkowska-Suszek, Joanna; Bieszczad, Katarzyna; Jagoda, Krystyna; Kyrcz-Krzemien, Slawomira

    2017-06-01

    Autologous haematopoietic stem cell transplantation (AHSCT) remains recommended treatment in the first remission in multiple myeloma (MM). In earlier research it has been suggested that there is an influence of the expression of dipeptidyl peptidase-4 (CD26) on both the homing and lymphocyte reconstitution after AHSCT. The aim of the study is to investigate the influence of transplanted cells CD26+ on the haematopoietic recovery and lymphocyte reconstitution after AHSCT in MM. Forty eight patients with MM underwent AHSCT in our centre. Number of all CD26+ cells, CD26+ lymphocytes, CD26+ monocytes and CD26+ and CD34+ cells were measured in the harvested material. Number of lymphocyte's subpopulations (all lymphocytes CD3+, helpers, suppressors, natural killer (NK), cytotoxic NK and lymphocytes B) were measured in peripheral blood during regeneration after AHSCT. In both flow cytometry was used. On the basis of the analysis there was, as regards regeneration of haematopoietic cells after AHSCT, it was shown that a higher number of monocytes CD26+ improves the reconstitution of helper, suppressor and NK lymphocytes. A higher number of transplanted CD26+ lymphocytes accelerates the reconstitution of NK lymphocytes, whereas a higher number of all the cells CD26+ has a positive impact on the regeneration of cytotoxic NK lymphocytes. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

  6. Effect of Temperature, pH, and Initial Cell Number on luxCDABE and nah Gene Expression during Naphthalene and Salicylate Catabolism in the Bioreporter Organism Pseudomonas putida RB1353

    PubMed Central

    Dorn, Jonathan G.; Frye, Robert J.; Maier, Raina M.

    2003-01-01

    One limitation of employing lux bioreporters to monitor in situ microbial gene expression in dynamic, laboratory-scale systems is the confounding variability in the luminescent responses. For example, despite careful control of oxygen tension, growth stage, and cell number, luminescence from Pseudomonas putida RB1353, a naphthalene-degrading lux bioreporter, varied by more than sevenfold during saturated flow column experiments in our laboratory. Therefore, this study was conducted to determine what additional factors influence the luminescent response. Specifically, this study investigated the impact of temperature, pH, and initial cell number (variations within an order of magnitude) on the peak luminescence of P. putida RB1353 and the maximum degradation rate (Vmax) during salicylate and naphthalene catabolism. Statistical analyses based on general linear models indicated that under constant oxygen tension, temperature and pH accounted for 98.1% of the variability in luminescence during salicylate catabolism and 94.2 and 49.5% of the variability in Vmax during salicylate and naphthalene catabolism, respectively. Temperature, pH, and initial substrate concentration accounted for 99.9% of the variability in luminescence during naphthalene catabolism. Initial cell number, within an order of magnitude, did not have a significant influence on either peak luminescence or Vmax during salicylate and naphthalene catabolism. Over the ranges of temperature and pH evaluated, peak luminescence varied by more than 4 orders of magnitude. The minimum parameter deviation required to alter lux gene expression during salicylate and naphthalene catabolism was a change in temperature of 1°C, a change in pH of 0.2, or a change in initial cell number of 1 order of magnitude. Results from this study indicate that there is a need for careful characterization of the impact of environmental conditions on both the expression of the reporter and catabolic genes and the activities of the

  7. Genome-wide scan identifies a copy number variable region at 3p21.1 that influences the TLR9 expression levels in IgA nephropathy patients

    PubMed Central

    Sallustio, Fabio; Cox, Sharon N; Serino, Grazia; Curci, Claudia; Pesce, Francesco; De Palma, Giuseppe; Papagianni, Aikaterini; Kirmizis, Dimitrios; Falchi, Mario; Schena, Francesco P

    2015-01-01

    Immunoglobulin A nephropathy (IgAN) is a complex multifactorial disease characterized by genetic factors that influence the pathogenesis of the disease. In this context, an intriguing role could be ascribed to copy number variants (CNVs). We performed the whole-genome screening of CNVs in familial IgAN patients, their healthy relatives and healthy subjects (HSs). In the initial screening, we included 217 individuals consisting of 51 biopsy-proven familial IgAN cases and 166 healthy relatives. We identified 148 IgAN-specific aberrations, specifically 105 loss and 43 gain, using a new statistical approach that allowed us to identify aberrations that were concordant across multiple samples. Several CNVs overlapped with regions evidenced by previous genome-wide genetic studies. We focused our attention on a CNV located in chromosome 3, which contains the TLR9 gene and found that IgAN patients characterized by deteriorated renal function carried low copy number of this CNV. Moreover, the TLR9 gene expression was low and significantly correlated with the loss aberration. Conversely, IgAN patients with normal renal function had no aberration and the TLR9 mRNA was expressed at the same level as in HSs. We confirmed our data in another cohort of Greek subjects. In conclusion, here we performed the first genome-wide CNV study in IgAN identifying structural variants that could help the genetic dissection of this complex disease, and pointed out a loss aberration in the chromosome 3, which is responsible for the downregulation of TLR9 expression that, in turn, could contribute to the deterioration of the renal function in IgAN patients. PMID:25293716

  8. Down-Regulation of KCC2 Expression and Phosphorylation in Motoneurons, and Increases the Number of in Primary Afferent Projections to Motoneurons in Mice with Post-Stroke Spasticity

    PubMed Central

    Toda, Takuya; Ishida, Kazuto; Kiyama, Hiroshi; Yamashita, Toshihide; Lee, Sachiko

    2014-01-01

    Spasticity obstructs motor function recovery post-stroke, and has been reported to occur in spinal cord injury and electrophysiological studies. The purpose of the present study was to assess spinal cord circuit spasticity in post-stroke mice. At 3, 7, 21, and 42 d after photothrombotic ischemic cortical injury in C57BL/6J mice, we observed decreased rate-dependent depression (RDD) of the Hoffmann reflex (H reflex) in the affected forelimb of mice compared with the limbs of sham mice and the non-affected forelimb. This finding suggests a hyper-excitable stretch reflex in the affected forelimb. We then performed immunohistochemical and western blot analyses to examine the expression of the potassium-chloride cotransporter 2 (KCC2) and phosphorylation of the KCC2 serine residue, 940 (S940), since this is the main chloride extruder that affects neuronal excitability. We also performed immunohistochemical analyses on the number of vesicular glutamate transporter 1 (vGluT1)-positive boutons to count the number of Ia afferent fibers that connect to motoneurons. Western bolts revealed that, compared with sham mice, experimental mice had significantly reduced KCC2 expression at 7 d post-stroke, and dephosphorylated S940 at 3 and 7 d post-stroke in motoneuron plasma membranes. We also observed a lower density of KCC2-positive areas in the plasma membrane of motoneurons at 3 and 7 d post-stroke. However, western blot and immunohistochemical analyses revealed that there were no differences between groups 21 and 42 d post-stroke, respectively. In addition, at 7 and 42 d post-stroke, experimental mice exhibited a significant increase in vGluT1 boutons compared with sham mice. Our findings suggest that both the down-regulation of KCC2 and increases in Ia afferent fibers are involved in post-stroke spasticity. PMID:25546454

  9. The RNA-Binding Chaperone Hfq Is an Important Global Regulator of Gene Expression in Pasteurella multocida and Plays a Crucial Role in Production of a Number of Virulence Factors, Including Hyaluronic Acid Capsule

    PubMed Central

    Mégroz, Marianne; Kleifeld, Oded; Wright, Amy; Powell, David; Harrison, Paul; Adler, Ben; Harper, Marina

    2016-01-01

    The Gram-negative bacterium Pasteurella multocida is the causative agent of a number of economically important animal diseases, including avian fowl cholera. Numerous P. multocida virulence factors have been identified, including capsule, lipopolysaccharide (LPS), and filamentous hemagglutinin, but little is known about how the expression of these virulence factors is regulated. Hfq is an RNA-binding protein that facilitates riboregulation via interaction with small noncoding RNA (sRNA) molecules and their mRNA targets. Here, we show that a P. multocida hfq mutant produces significantly less hyaluronic acid capsule during all growth phases and displays reduced in vivo fitness. Transcriptional and proteomic analyses of the hfq mutant during mid-exponential-phase growth revealed altered transcript levels for 128 genes and altered protein levels for 78 proteins. Further proteomic analyses of the hfq mutant during the early exponential growth phase identified 106 proteins that were produced at altered levels. Both the transcript and protein levels for genes/proteins involved in capsule biosynthesis were reduced in the hfq mutant, as were the levels of the filamentous hemagglutinin protein PfhB2 and its secretion partner LspB2. In contrast, there were increased expression levels of three LPS biosynthesis genes, encoding proteins involved in phosphocholine and phosphoethanolamine addition to LPS, suggesting that these genes are negatively regulated by Hfq-dependent mechanisms. Taken together, these data provide the first evidence that Hfq plays a crucial role in regulating the global expression of P. multocida genes, including the regulation of key P. multocida virulence factors, capsule, LPS, and filamentous hemagglutinin. PMID:26883595

  10. Simple expressions for the maximum omnidirectional bandgap of bilayer photonic crystals.

    PubMed

    Hsueh, W J; Wun, S J

    2011-05-01

    We propose three dimensionless approximate expressions to predict the thickness filling factor, gap center, and gap width of the maximum omnidirectional gap (MODG) for various refractive indices in one-dimensional photonic crystals. These expressions are simple and do not include trigonometric or inverse trigonometric functions. It is easy to obtain the MODG from given refractive indices but also to estimate the refractive indices from the MODG based on the results.

  11. Filament actuation by an active colloid at low Reynolds number

    NASA Astrophysics Data System (ADS)

    Laskar, Abhrajit; Adhikari, R.

    2017-03-01

    Active colloids and externally actuated semi-flexible filaments provide basic building blocks for designing autonomously motile micro-machines. Here, we show that a passive semi-flexible filament can be actuated and transported by attaching an active colloid to its terminus. We study the dynamics of this assembly when it is free, tethered, or clamped using overdamped equations of motion that explicitly account for active fluid flow and the forces it mediates. Linear states are destabilised by buckling instabilities to produce stable states of non-zero curvature and writhe. We demarcate boundaries of these states in the two-dimensional parameter space representing dimensionless measures of polar and apolar activity. Our proposed assembly can be used as a novel component in the design of micro-machines at low Reynolds number and to study elastic instabilities driven by ‘follower’ forces.

  12. Number Concepts with "Number Worlds": Thickening Understandings

    ERIC Educational Resources Information Center

    Liljedahl, Peter; Sinclair, Nathalie; Zazkis, Rina

    2006-01-01

    This study focuses on the nature of preservice elementary school teachers' understandings of several concepts in elementary number theory that are evoked by a computer-based microworld called "Number Worlds". In particular, the focus is on the concepts of factor, multiple and prime number. The notion of "thickness" is examined with respect to…

  13. Novel methods for evaluation of the Reynolds number of synthetic jets

    NASA Astrophysics Data System (ADS)

    Kordík, J.; Broučková, Z.; Vít, T.; Pavelka, M.; Trávníček, Z.

    2014-06-01

    The paper proposes four novel methods of evaluation of synthetic jet velocity amplitude (Reynolds number in dimensionless form). The methods are based on the measurement of synthetic jet actuator electrical input (alternating current and voltage) and are applicable for loudspeaker-based actuators with air as the working fluid. Experimental validations are performed by means of hot-wire anemometry and laser Doppler vibrometry. Uncertainty and limitation of the methods are discussed, including a proposal of an adequate incompressibility criterion. Ranges of applicability are specified. Additionally, the results are compared with available literature, namely with another method based on cavity pressure measurements, a good consistency is found.

  14. A new approach to the formulation and validation of scaling expressions for plasma confinement in tokamaks

    NASA Astrophysics Data System (ADS)

    Murari, A.; Peluso, E.; Gelfusa, M.; Lupelli, I.; Gaudio, P.

    2015-07-01

    The extrapolation of the energy confinement time to the next generation of devices has been investigated both theoretically and experimentally for several decades in the tokamak community. Various scaling expressions have been proposed using dimensional and dimensionless quantities. They are all based on the assumption that the scalings are in power law form. In this paper, an innovative methodology is proposed to extract the scaling expressions for the energy confinement time in tokamaks directly from experimental databases, without any previous assumption about the mathematical form of the scalings. The approach to obtain the scaling expressions is based on genetic programming and symbolic regression. These techniques have been applied to the ITPA database of H-mode discharges and the results have been validated with a series of established statistical tools. The soundest results, using dimensional variables, are not in the form of power laws but contain a multiplicative saturation term. Also the scalings, expressed in terms of the traditional dimensionless quantities, are not in power law form and contain additive saturation terms. The extrapolation to ITER of both dimensional and dimensionless quantities indicate that the saturation effects are quite significant and could imply a non-negligible reduction in the confinement time to be expected in the next generation of devices. The results obtained with the proposed techniques therefore motivate a systematic revisiting of the scaling expressions for plasma confinement in tokamaks.

  15. On Multiplying Negative Numbers.

    ERIC Educational Resources Information Center

    Crowley, Mary L.; Dunn, Kenneth A.

    1985-01-01

    Comments on the history of negative numbers, some methods that can be used to introduce the multiplication of negative numbers to students, and an explanation of why the product of two negative numbers is a positive number are included. (MNS)

  16. A universal number for wave reflection optimization of the mammalian cardiovascular system.

    NASA Astrophysics Data System (ADS)

    Pahlevan, Niema; Gharib, Morteza

    2015-11-01

    Quantifying the optimum arterial wave reflection and systemic arterial function is essential to the evaluation of optimal cardiovascular system (CVS) operation. The CVS function depends on both the dynamics of the heart and wave dynamics of the arterial network. Here, we are introducing a universal dimensionless number, called wave condition number (α) that quantifies the arterial wave reflection. An in-vitro experimental approach, utilizing a unique hydraulic model was used to quantify α in human aortas with a wide range of aortic rigidities. Our results indicate that the optimum value of the wave condition number is 0.1 at each level of aortic rigidity. Looking into mammals of various size (from mice to elephant), our results show that the optimum wave condition number remains 0.1 and is universal among all mammals. Clinical applications and the relevancy of the wave condition number will also be discussed.

  17. All Square Chiliagonal Numbers

    ERIC Educational Resources Information Center

    A?iru, Muniru A.

    2016-01-01

    A square chiliagonal number is a number which is simultaneously a chiliagonal number and a perfect square (just as the well-known square triangular number is both triangular and square). In this work, we determine which of the chiliagonal numbers are perfect squares and provide the indices of the corresponding chiliagonal numbers and square…

  18. All Square Chiliagonal Numbers

    ERIC Educational Resources Information Center

    A?iru, Muniru A.

    2016-01-01

    A square chiliagonal number is a number which is simultaneously a chiliagonal number and a perfect square (just as the well-known square triangular number is both triangular and square). In this work, we determine which of the chiliagonal numbers are perfect squares and provide the indices of the corresponding chiliagonal numbers and square…

  19. Promote Number Sense

    ERIC Educational Resources Information Center

    Gurganus, Susan

    2004-01-01

    "Number sense" is "an intuition about numbers that is drawn from all varied meanings of number" (NCTM, 1989, p. 39). Students with number sense understand that numbers are representative of objects, magnitudes, relationships, and other attributes; that numbers can be operated on, compared, and used for communication. It is fundamental knowledge…

  20. Stationary shapes of deformable particles moving at low Reynolds numbers

    NASA Astrophysics Data System (ADS)

    Boltz, Horst-Holger; Kierfeld, Jan

    2016-11-01

    We introduce an iterative solution scheme in order to calculate stationary shapes of deformable elastic capsules which are steadily moving through a viscous fluid at low Reynolds numbers. The iterative solution scheme couples hydrodynamic boundary integral methods and elastic shape equations to find the stationary axisymmetric shape and the velocity of an elastic capsule moving in a viscous fluid governed by the Stokes equation. We use this approach to systematically study dynamical shape transitions of capsules with Hookean stretching and bending energies and spherical resting shape sedimenting under the influence of gravity or centrifugal forces. We find three types of possible axisymmetric stationary shapes for sedimenting capsules with fixed volume: a pseudospherical state, a pear-shaped state, and buckled shapes. Capsule shapes are controlled by two dimensionless parameters, the Föppl-von-Kármán number characterizing the elastic properties and a Bond number characterizing the driving force. For increasing gravitational force the spherical shape transforms into a pear shape. For very large bending rigidity (very small Föppl-von-Kármán number) this transition is discontinuous with shape hysteresis. The corresponding transition line terminates, however, in a critical point, such that the discontinuous transition is not present at typical Föppl-von-Kármán numbers of synthetic capsules. In an additional bifurcation, buckled shapes occur upon increasing the gravitational force.

  1. IMPACT OF CAPILLARY AND BOND NUMBERS ON RELATIVE PERMEABILITY

    SciTech Connect

    Kishore K. Mohanty

    2002-09-30

    Recovery and recovery rate of oil, gas and condensates depend crucially on their relative permeability. Relative permeability in turn depends on the pore structure, wettability and flooding conditions, which can be represented by a set of dimensionless groups including capillary and bond numbers. The effect of flooding conditions on drainage relative permeabilities is not well understood and is the overall goal of this project. This project has three specific objectives: to improve the centrifuge relative permeability method, to measure capillary and bond number effects experimentally, and to develop a pore network model for multiphase flows. A centrifuge has been built that can accommodate high pressure core holders and x-ray saturation monitoring. The centrifuge core holders can operate at a pore pressure of 6.9 MPa (1000 psi) and an overburden pressure of 17 MPa (2500 psi). The effect of capillary number on residual saturation and relative permeability in drainage flow has been measured. A pore network model has been developed to study the effect of capillary numbers and viscosity ratio on drainage relative permeability. Capillary and Reynolds number dependence of gas-condensate flow has been studied during well testing. A method has been developed to estimate relative permeability parameters from gas-condensate well test data.

  2. Numbers Defy the Law of Large Numbers

    ERIC Educational Resources Information Center

    Falk, Ruma; Lann, Avital Lavie

    2015-01-01

    As the number of independent tosses of a fair coin grows, the rates of heads and tails tend to equality. This is misinterpreted by many students as being true also for the absolute numbers of the two outcomes, which, conversely, depart unboundedly from each other in the process. Eradicating that misconception, as by coin-tossing experiments,…

  3. Numbers Defy the Law of Large Numbers

    ERIC Educational Resources Information Center

    Falk, Ruma; Lann, Avital Lavie

    2015-01-01

    As the number of independent tosses of a fair coin grows, the rates of heads and tails tend to equality. This is misinterpreted by many students as being true also for the absolute numbers of the two outcomes, which, conversely, depart unboundedly from each other in the process. Eradicating that misconception, as by coin-tossing experiments,…

  4. Hall Effect Thruster Interactions Data From the Russian Express-A2 and Express-A3 Satellites. Part 2; Acquire TM Date for Type B Sensors for "Express-A" Number 2 Satellite for the Period of March 12, 2000 to and Including June 15, 2000, Task 25

    NASA Technical Reports Server (NTRS)

    Dunning, John (Technical Monitor); Sitnikova, N.; Volkov, D.; Maximov, I.; Petrusevich, V.; Allen, D.

    2003-01-01

    This 12-part report documents the data obtained from various sensor measurements taken aboard the Russian Express-A2 and Express-A3 spacecraft in Geosynchronous Earth Orbit (GEO). These GEO communications satellites, which were designed and built by NPO Prikladnoy Mekhaniki (NPO PM) of Zheleznogorsk, Russia, utilize Hall thruster propulsion systems for north-south and east-west stationkeeping and as of June 2002, were still operating at 80 E. and 11 W., respectively. Express-A2 was launched on March 12, 2000, while Express-A3 was launched on June 24, 2000. The diagnostic equipment from which these data were taken includes electric field strength sensors, ion current and energy sensors, and pressure sensors. The diagnostics and the Hall thruster propulsion systems are described in detail along with lists of tabular data from those diagnostics and propulsion system and other satellite systems. Space Power, Inc., now part of Pratt & Whitney's Chemical Systems Division, under contract NAS3 99151 to the NASA Glenn Research Center, obtained these data over several periods from March 12, 2000, through September 30, 2001. Each of the 12 individual reports describe, in detail, the propulsion systems as well as the diagnostic sensors utilized. Finally, parts 11 and 12 include the requirements to which NPO PM prepared and delivered these data.

  5. Hall Effect Thruster Interactions Data from the Russian Express-A2 and Express-A3 Satellites. Part 4; Acquire TM-Data for Type A and Type B Sensors for "Express-A" Number 3 Satellite, Task 27A

    NASA Technical Reports Server (NTRS)

    Sitnikova, N.; Volkov, D.; Maximov, I.; Petrusevich, V.; Allen, D.

    2003-01-01

    This 12-part report documents the data obtained from various sensor measurements taken aboard the Russian Express-A2 and Express-A3 spacecraft in Geosynchronous Earth Orbit (GEO). These GEO communications satellites, which were designed and built by NPO Prikladnoy Mekhaniki (NPO PM) of Zheleznogorsk, Russia, utilize Hall thruster propulsion systems for north-south and east-west stationkeeping and as of June 2002, were still operating at 80deg E., and 11deg W., respectively. Express-A2 was launched on March 12, 2000, while Express-A3 was launched on June 24, 2000. The diagnostic equipment from which these data were taken includes electric field strength sensors, ion current and energy sensors, and pressure sensors. The diagnostics and the Hall thruster propulsion systems are described in detail along with lists of tabular data from those diagnostics and propulsion system and other satellite systems. Space Power, Inc., now part of Pratt & Whitney's Chemical Systems Division, under contract NAS3-99151 to the NASA Glenn Research Center, obtained these data over several periods from March 12, 2000, through September 30, 2001. Each of the 12 individual reports describe, in detail, the propulsion systems as well as the diagnostic sensors utilized. Finally, parts 11 and 12 include the requirements to which NPO PM prepared and delivered these data.

  6. Hall Effect Thruster Interactions Data from the Russian Express-A2 and Express-A3 Satellites. Part 8; Acquire TM-Data for Type A and Type B Sensors for "Express A" Number 3 Satellite for the Period of January 1, 2001 to and Including March 31, 2001, Task 27C

    NASA Technical Reports Server (NTRS)

    Dunning, John (Technical Monitor); Sitnikova, N.; Volkov, D.; Maximov, I.; Petrusevich, V.; Allen, D.

    2003-01-01

    This 12-part report documents the data obtained from various sensor measurements taken aboard the Russian Express-A2 and Express-A3 spacecraft in Geosynchronous Earth Orbit (GEO). These GEO communications satellites, which were designed and built by NPO Prikladnoy Mekhaniki (NPO PM) of Zheleznogorsk, Russia, utilize Hall thruster propulsion systems for north-south and east-west stationkeeping and as of June 2002, were still operating at 80deg E. and 11deg W., respectively. Express-A2 was launched on March 12, 2000, while Express-A3 was launched on June 24, 2000. The diagnostic equipment from which these data were taken includes electric field strength sensors, ion current and energy sensors, and pressure sensors. The diagnostics and the Hall thruster propulsion systems are described in detail along with lists of tabular data from those diagnostics and propulsion system and other satellite systems. Space Power, Inc., now part of Pratt & Whitney's Chemical Systems Division, under contract NAS3 99151 to the NASA Glenn Research Center, obtained these data over several periods from March 12, 2000, through September 30, 2001. Each of the 12 individual reports describe, in detail, the propulsion systems as well as the diagnostic sensors utilized. Finally, parts 11 and 12 include the requirements to which NPO PM prepared and delivered these data.

  7. Hall Effect Thruster Interactions Data From the Russian Express-A2 and Express-A3 Satellites. Part 10; Acquire TM-Data for Type A and Type B Sensors for "Express-A" Number 3 Satellite for the Period of July 1, 2001 to and Including September 30, 2001, Task 27D

    NASA Technical Reports Server (NTRS)

    Dunning, John (Technical Monitor); Sitnikova, N.; Volkov, D.; Maximov, I.; Petrusevich, V.; Allen, D.

    2003-01-01

    This 12-part report documents the data obtained from various sensor measurements taken aboard the Russian Express-A2 and Express-A3 spacecraft in Geosynchronous Earth Orbit (GEO). These GEO communications satellites, which were designed and built by NPO Prikladnoy Mekhaniki (NPO PM) of Zheleznogorsk, Russia, utilize Hall thruster propulsion systems for north-south and east-west stationkeeping and as of June 2002, were still operating at 80 E. and 11 W., respectively. Express-A2 was launched on March 12, 2000, while Express-A3 was launched on June 24, 2000. The diagnostic equipment from which these data were taken includes electric field strength sensors, ion current and energy sensors, and pressure sensors. The diagnostics and the Hall thruster propulsion systems are described in detail along with lists of tabular data from those diagnostics and propulsion system and other satellite systems. Space Power, Inc., now part of Pratt & Whitney's Chemical Systems Division, under contract NAS3 99151 to the NASA Glenn Research Center, obtained these data over several periods from March 12, 2000, through September 30, 2001. Each of the 12 individual reports describe, in detail, the propulsion systems as well as the diagnostic sensors utilized. Finally, parts 11 and 12 include the requirements to which NPO PM prepared and delivered these data.

  8. Lipid-Free Apolipoprotein A-I Reduces Progression of Atherosclerosis by Mobilizing Microdomain Cholesterol and Attenuating the Number of CD131 Expressing Cells: Monitoring Cholesterol Homeostasis Using the Cellular Ester to Total Cholesterol Ratio.

    PubMed

    Kaul, Sushma; Xu, Hao; Zabalawi, Manal; Maruko, Elisa; Fulp, Brian E; Bluemn, Theresa; Brzoza-Lewis, Kristina L; Gerelus, Mark; Weerasekera, Ranjuna; Kallinger, Rachel; James, Roland; Zhang, Yi Sherry; Thomas, Michael J; Sorci-Thomas, Mary G

    2016-11-07

    Atherosclerosis is a chronic inflammatory disorder whose development is inversely correlated with high-density lipoprotein concentration. Current therapies involve pharmaceuticals that significantly elevate plasma high-density lipoprotein cholesterol concentrations. Our studies were conducted to investigate the effects of low-dose lipid-free apolipoprotein A-I (apoA-I) on chronic inflammation. The aims of these studies were to determine how subcutaneously injected lipid-free apoA-I reduces accumulation of lipid and immune cells within the aortic root of hypercholesterolemic mice without sustained elevations in plasma high-density lipoprotein cholesterol concentrations. Ldlr(-/-) and Ldlr(-/-) apoA-I(-/-) mice were fed a Western diet for a total of 12 weeks. After 6 weeks, a subset of mice from each group received subcutaneous injections of 200 μg of lipid-free human apoA-I 3 times a week, while the other subset received 200 μg of albumin, as a control. Mice treated with lipid-free apoA-I showed a decrease in cholesterol deposition and immune cell retention in the aortic root compared with albumin-treated mice, regardless of genotype. This reduction in atherosclerosis appeared to be directly related to a decrease in the number of CD131 expressing cells and the esterified cholesterol to total cholesterol content in several immune cell compartments. In addition, apoA-I treatment altered microdomain cholesterol composition that shifted CD131, the common β subunit of the interleukin 3 receptor, from lipid raft to nonraft fractions of the plasma membrane. ApoA-I treatment reduced lipid and immune cell accumulation within the aortic root by systemically reducing microdomain cholesterol content in immune cells. These data suggest that lipid-free apoA-I mediates beneficial effects through attenuation of immune cell lipid raft cholesterol content, which affects numerous types of signal transduction pathways that rely on microdomain integrity for assembly and

  9. Experimental investigation of terminal velocity and Sherwood number of rising droplet in an extraction column

    NASA Astrophysics Data System (ADS)

    Azizi, Zoha

    2017-10-01

    Mass transfer and terminal velocity of toluene drops rising in an extraction column was studied experimentally. The impact of packing was investigated by inserting a structured packing in three different heights of 10, 25 and 40 cm inside the column. The effect of packing height, flow rate and drop size on terminal velocity and Sherwood number were investigated and the results were also compared with the case of non-packed column. It was discussed that a 30% increase in Sherwood number could be achieved using the packing with 40 cm in height. It was also found that for Eötvös number, Eö, higher than 0.4, the deformation of drops and velocity oscillation appeared, which affected the terminal velocity. Finally, two correlations were proposed, which permitted the prediction of deformation and extraction ratio versus the dimensionless numbers of Reynolds, Eötvös and the packing height ratio.

  10. Similarity states of homogeneous stably-stratified turbulence at infinite Froude number

    NASA Technical Reports Server (NTRS)

    Chasnov, Jeffrey R.

    1993-01-01

    We present evidence of similarity states which may develop inhomogeneous stably-stratified flows if a dimensionless group in addition to the Reynolds number, the so-called Froude number, is sufficiently large. Here, we define the Froude number as the ratio of the internal wave time-scale to the turbulence time-scale. We examine three different similarity states which may develop depending on the initial conditions of the velocity and density fields. Theoretical arguments and results of large-eddy simulations will be presented. We will conclude this report with some speculative thoughts on similarity states which may develop in stably-stratified turbulence at arbitrary Froude number as well as our future research plans in this area.

  11. 32 CFR 1602.19 - Numbers.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 32 National Defense 6 2012-07-01 2012-07-01 false Numbers. 1602.19 Section 1602.19 National Defense Other Regulations Relating to National Defense SELECTIVE SERVICE SYSTEM DEFINITIONS § 1602.19 Numbers. Cardinal numbers may be expressed by Arabic or Roman symbols....

  12. 32 CFR 1602.19 - Numbers.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 32 National Defense 6 2014-07-01 2014-07-01 false Numbers. 1602.19 Section 1602.19 National Defense Other Regulations Relating to National Defense SELECTIVE SERVICE SYSTEM DEFINITIONS § 1602.19 Numbers. Cardinal numbers may be expressed by Arabic or Roman symbols....

  13. 32 CFR 1602.19 - Numbers.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 32 National Defense 6 2010-07-01 2010-07-01 false Numbers. 1602.19 Section 1602.19 National Defense Other Regulations Relating to National Defense SELECTIVE SERVICE SYSTEM DEFINITIONS § 1602.19 Numbers. Cardinal numbers may be expressed by Arabic or Roman symbols....

  14. 32 CFR 1602.19 - Numbers.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 32 National Defense 6 2011-07-01 2011-07-01 false Numbers. 1602.19 Section 1602.19 National Defense Other Regulations Relating to National Defense SELECTIVE SERVICE SYSTEM DEFINITIONS § 1602.19 Numbers. Cardinal numbers may be expressed by Arabic or Roman symbols....

  15. 32 CFR 1602.19 - Numbers.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 32 National Defense 6 2013-07-01 2013-07-01 false Numbers. 1602.19 Section 1602.19 National Defense Other Regulations Relating to National Defense SELECTIVE SERVICE SYSTEM DEFINITIONS § 1602.19 Numbers. Cardinal numbers may be expressed by Arabic or Roman symbols....

  16. Flying and swimming animals cruise at a Strouhal number tuned for high power efficiency.

    PubMed

    Taylor, Graham K; Nudds, Robert L; Thomas, Adrian L R

    2003-10-16

    Dimensionless numbers are important in biomechanics because their constancy can imply dynamic similarity between systems, despite possible differences in medium or scale. A dimensionless parameter that describes the tail or wing kinematics of swimming and flying animals is the Strouhal number, St = fA/U, which divides stroke frequency (f) and amplitude (A) by forward speed (U). St is known to govern a well-defined series of vortex growth and shedding regimes for airfoils undergoing pitching and heaving motions. Propulsive efficiency is high over a narrow range of St and usually peaks within the interval 0.2 < St < 0.4 (refs 3-8). Because natural selection is likely to tune animals for high propulsive efficiency, we expect it to constrain the range of St that animals use. This seems to be true for dolphins, sharks and bony fish, which swim at 0.2 < St < 0.4. Here we show that birds, bats and insects also converge on the same narrow range of St, but only when cruising. Tuning cruise kinematics to optimize St therefore seems to be a general principle of oscillatory lift-based propulsion.

  17. Flying and swimming animals cruise at a Strouhal number tuned for high power efficiency

    NASA Astrophysics Data System (ADS)

    Taylor, Graham K.; Nudds, Robert L.; Thomas, Adrian L. R.

    2003-10-01

    Dimensionless numbers are important in biomechanics because their constancy can imply dynamic similarity between systems, despite possible differences in medium or scale. A dimensionless parameter that describes the tail or wing kinematics of swimming and flying animals is the Strouhal number, St = fA/U, which divides stroke frequency (f) and amplitude (A) by forward speed (U). St is known to govern a well-defined series of vortex growth and shedding regimes for airfoils undergoing pitching and heaving motions. Propulsive efficiency is high over a narrow range of St and usually peaks within the interval 0.2 < St < 0.4 (refs 3-8). Because natural selection is likely to tune animals for high propulsive efficiency, we expect it to constrain the range of St that animals use. This seems to be true for dolphins, sharks and bony fish, which swim at 0.2 < St < 0.4. Here we show that birds, bats and insects also converge on the same narrow range of St, but only when cruising. Tuning cruise kinematics to optimize St therefore seems to be a general principle of oscillatory lift-based propulsion.

  18. Building Numbers from Primes

    ERIC Educational Resources Information Center

    Burkhart, Jerry

    2009-01-01

    Prime numbers are often described as the "building blocks" of natural numbers. This article shows how the author and his students took this idea literally by using prime factorizations to build numbers with blocks. In this activity, students explore many concepts of number theory, including the relationship between greatest common factors and…

  19. Are Numbers Gendered?

    ERIC Educational Resources Information Center

    Wilkie, James E. B.; Bodenhausen, Galen V.

    2012-01-01

    We examined the possibility that nonsocial, highly generic concepts are gendered. Specifically, we investigated the gender connotations of Arabic numerals. Across several experiments, we show that the number 1 and other odd numbers are associated with masculinity, whereas the number 2 and other even numbers are associated with femininity, in ways…

  20. Are Numbers Gendered?

    ERIC Educational Resources Information Center

    Wilkie, James E. B.; Bodenhausen, Galen V.

    2012-01-01

    We examined the possibility that nonsocial, highly generic concepts are gendered. Specifically, we investigated the gender connotations of Arabic numerals. Across several experiments, we show that the number 1 and other odd numbers are associated with masculinity, whereas the number 2 and other even numbers are associated with femininity, in ways…

  1. Building Numbers from Primes

    ERIC Educational Resources Information Center

    Burkhart, Jerry

    2009-01-01

    Prime numbers are often described as the "building blocks" of natural numbers. This article shows how the author and his students took this idea literally by using prime factorizations to build numbers with blocks. In this activity, students explore many concepts of number theory, including the relationship between greatest common factors and…

  2. Sierpinski and Carmichael Numbers

    DTIC Science & Technology

    2013-01-16

    prove that almost all odd natural numbers k have the property that 2nk + 1 is not a Carmichael number for any n 2 N; this implies the existence of a...Sierpiński and Riesel numbers. First, we prove that almost all odd natural numbers k have the property that 2nk + 1 is not a Carmichael number for any n...Sierpiński [25] showed that there are infinitely many odd natural numbers k with the property that 2nk + 1 is composite for every natural number n; such an

  3. PET: [number sign]1 is number one

    SciTech Connect

    Miller, C.

    1994-09-01

    Subsidized in the beginning by bottle deposits, now spurred by the ability of curbside recycling to collect more than soda bottles, polyethylene terephthalate (PET) recycling has made great strides in the last 10 years. Its growth rate and increased market demand are the envy of many other materials. Appropriate, if not deliberately, this number-one resin is listed under the Society for the Plastics Industry's resin identification code as [number sign]1. Unlike most recyclables, the market demand for recycled PET is greater than the supply. As a result, demand not supply, is fueling the increase in PET recycling.

  4. Possible number systems.

    PubMed

    Rips, Lance J; Thompson, Samantha

    2014-03-01

    Number systems-such as the natural numbers, integers, rationals, reals, or complex numbers-play a foundational role in mathematics, but these systems can present difficulties for students. In the studies reported here, we probed the boundaries of people's concept of a number system by asking them whether "number lines" of varying shapes qualify as possible number systems. In Experiment 1, participants rated each of a set of number lines as a possible number system, where the number lines differed in their structures (a single straight line, a step-shaped line, a double line, or two branching structures) and in their boundedness (unbounded, bounded below, bounded above, bounded above and below, or circular). Participants also rated each of a group of mathematical properties (e.g., associativity) for its importance to number systems. Relational properties, such as associativity, predicted whether participants believed that particular forms were number systems, as did the forms' ability to support arithmetic operations, such as addition. In Experiment 2, we asked participants to produce properties that were important for number systems. Relational, operation, and use-based properties from this set again predicted ratings of whether the number lines were possible number systems. In Experiment 3, we found similar results when the number lines indicated the positions of the individual numbers. The results suggest that people believe that number systems should be well-behaved with respect to basic arithmetic operations, and that they reject systems for which these operations produce ambiguous answers. People care much less about whether the systems have particular numbers (e.g., 0) or sets of numbers (e.g., the positives).

  5. Number Sense Made Simple Using Number Patterns

    ERIC Educational Resources Information Center

    Su, Hui Fang Huang; Marinas, Carol; Furner, Joseph

    2011-01-01

    This article highlights investigating intriguing number patterns utilising an emerging technology called the Square Tool. Mathematics teachers of grades K-12 will find the Square Tool useful in making connections and bridging the gap from the concrete to the abstract. Pattern recognition helps students discover various mathematical concepts. With…

  6. Gas absorption in pulmonary airways at low Peclet number

    SciTech Connect

    Grotberg, J.B. )

    1990-05-01

    A mathematical model is presented that investigates the mass transport of a diffusible and soluble gas contaminant through a liquid-lined tube when the Peclet number is small. The transport is determined by four dimensionless parameters: lambda, the tube aspect ratio; d, the relative difference in end concentrations; gamma, the radial transport coefficient; and Pe, the Peclet number. The problem is formulated for arbitrary gamma, but in the case of ozone and nitrous oxides the value of gamma is small. An asymptotic analysis for Pe much less than 1 and gamma much less than 1 is presented which yields the concentration field and transport characteristics we seek. It also provides a low Peclet number analysis for the conjugate problem of mass and heat transfer that is not currently available in the literature. The application to transport in the small airways of the lung is discussed, particularly the radial absorption differences in inspiratory and expiratory flow. Depending on the relative sizes of gamma and Pe, fractional uptake decreases with increasing Pe during inspiration but can increase during expiration.

  7. Effect of the capillary number and its constituents on two-phase relative permeabilities

    SciTech Connect

    Fulcher, R.A. Jr.

    1983-03-01

    One of the primary goals of any enhanced recovery project is to maximize the ability of the fluids to flow through a porous medium, i.e., the reservoir. The topic of this study is the effect of the capillary number, a dimensionless group describing the ratio of viscous to capillary forces, on 2-phase (oil-water) relative permeability curves. Specifically, a series of steady-state measurements were performed to determine if the capillary number causes changes in the 2-phase permeabilities or if any one of its constituents, such as flow velocity, fluid viscosity, or interfacial tension, are the controlling variables. For the core tests, run in fired Berea Sandstone, a Soltrol 170 oil-calcium chloride brine- isopropyl alcohol-glycerin system was utilized. Alcohol was the tension reducer and glycerin was used as the wetting phase viscosifier. It was found that the nonwetting phase (oil) relative permeability shows no correlation with the capillary number.

  8. Generalized Fibonacci Numbers and Dimer Statistics

    NASA Astrophysics Data System (ADS)

    Lu, W. T.; Wu, F. Y.

    2003-04-01

    We establish new product identities involving the q-analogue of the Fibonacci numbers. We show that the identities lead to alternate expressions of generating functions for close-packed dimers on non-orientable surfaces.

  9. Generalized Fibonacci Numbers and Dimer Statistics

    NASA Astrophysics Data System (ADS)

    Lu, W. T.; Wu, F. Y.

    We establish new product identities involving the q-analogue of the Fibonacci numbers. We show that the identities lead to alternate expressions of generating functions for close-packed dimers on non-orientable surfaces.

  10. Making decisions from numbers

    SciTech Connect

    Somers, E.

    1987-03-01

    Regulatory agencies require numbers to provide health protection. The manner in which these numbers are derived from animal experiments and human epidemiology is considered together with the limitations and inadequacies of these numbers. Some recent examples of risk assessment in Canada are given including asbestos, drinking water, and indoor air quality. The value of these numbers in providing a measure of the hazard in a wider perspective is stressed, although they can never be the sole determinant of public policy.

  11. Expressed Philosophical, Value, and/or Attitudinal Orientations Toward Educational Practice of Student Teachers Preparing to Teach Minority and Mainstream Ethnic Groups. Teacher Education Forum; Volume 4, Number 15.

    ERIC Educational Resources Information Center

    Harty, Harold

    This study examined the expressed orientations toward education of (1) preservice teachers who opted to participate in student teaching programs in minority settings; (2) preservice teachers who selected conventional student teaching placements; and (3) inservice supervising teachers from both settings. Four student teaching programs provided the…

  12. Estimating Large Numbers

    ERIC Educational Resources Information Center

    Landy, David; Silbert, Noah; Goldin, Aleah

    2013-01-01

    Despite their importance in public discourse, numbers in the range of 1 million to 1 trillion are notoriously difficult to understand. We examine magnitude estimation by adult Americans when placing large numbers on a number line and when qualitatively evaluating descriptions of imaginary geopolitical scenarios. Prior theoretical conceptions…

  13. Sum-Difference Numbers

    ERIC Educational Resources Information Center

    Shi, Yixun

    2010-01-01

    Starting with an interesting number game sometimes used by school teachers to demonstrate the factorization of integers, "sum-difference numbers" are defined. A positive integer n is a "sum-difference number" if there exist positive integers "x, y, w, z" such that n = xy = wz and x ? y = w + z. This paper characterizes all sum-difference numbers…

  14. The Remarkable Number "1"

    ERIC Educational Resources Information Center

    Allen, G. Donald

    2014-01-01

    In human history, the origin of the numbers came from definite practical needs. Indeed, there is strong evidence that numbers were created before writing. The number "1", dating back at least 20,000 years, was found as a counting symbol on a bone. The famous statement by the German mathematician Leopold Kronecker (1823-1891), "God…

  15. Sum-Difference Numbers

    ERIC Educational Resources Information Center

    Shi, Yixun

    2010-01-01

    Starting with an interesting number game sometimes used by school teachers to demonstrate the factorization of integers, "sum-difference numbers" are defined. A positive integer n is a "sum-difference number" if there exist positive integers "x, y, w, z" such that n = xy = wz and x ? y = w + z. This paper characterizes all sum-difference numbers…

  16. Discovery: Prime Numbers

    ERIC Educational Resources Information Center

    de Mestre, Neville

    2008-01-01

    Prime numbers are important as the building blocks for the set of all natural numbers, because prime factorisation is an important and useful property of all natural numbers. Students can discover them by using the method known as the Sieve of Eratosthenes, named after the Greek geographer and astronomer who lived from c. 276-194 BC. Eratosthenes…

  17. The Numbered Forest.

    ERIC Educational Resources Information Center

    Kissner, Emily

    2000-01-01

    Describes the activity of numbering trees in which students number trees or find the numbered trees and observe other features according to class time. This activity aims to increase student tracking, mapping, and writing skills and integrate them with math skills. Suggests follow up activities that focus on reading, writing, and language skills.…

  18. Estimating Large Numbers

    ERIC Educational Resources Information Center

    Landy, David; Silbert, Noah; Goldin, Aleah

    2013-01-01

    Despite their importance in public discourse, numbers in the range of 1 million to 1 trillion are notoriously difficult to understand. We examine magnitude estimation by adult Americans when placing large numbers on a number line and when qualitatively evaluating descriptions of imaginary geopolitical scenarios. Prior theoretical conceptions…

  19. The Remarkable Number "1"

    ERIC Educational Resources Information Center

    Allen, G. Donald

    2014-01-01

    In human history, the origin of the numbers came from definite practical needs. Indeed, there is strong evidence that numbers were created before writing. The number "1", dating back at least 20,000 years, was found as a counting symbol on a bone. The famous statement by the German mathematician Leopold Kronecker (1823-1891), "God…

  20. Estimating large numbers.

    PubMed

    Landy, David; Silbert, Noah; Goldin, Aleah

    2013-07-01

    Despite their importance in public discourse, numbers in the range of 1 million to 1 trillion are notoriously difficult to understand. We examine magnitude estimation by adult Americans when placing large numbers on a number line and when qualitatively evaluating descriptions of imaginary geopolitical scenarios. Prior theoretical conceptions predict a log-to-linear shift: People will either place numbers linearly or will place numbers according to a compressive logarithmic or power-shaped function (Barth & Paladino, ; Siegler & Opfer, ). While about half of people did estimate numbers linearly over this range, nearly all the remaining participants placed 1 million approximately halfway between 1 thousand and 1 billion, but placed numbers linearly across each half, as though they believed that the number words "thousand, million, billion, trillion" constitute a uniformly spaced count list. Participants in this group also tended to be optimistic in evaluations of largely ineffective political strategies, relative to linear number-line placers. The results indicate that the surface structure of number words can heavily influence processes for dealing with numbers in this range, and it can amplify the possibility that analogous surface regularities are partially responsible for parallel phenomena in children. In addition, these results have direct implications for lawmakers and scientists hoping to communicate effectively with the public. Copyright © 2013 Cognitive Science Society, Inc.

  1. The Soybean Rhg1 Locus for Resistance to the Soybean Cyst Nematode Heterodera glycines Regulates the Expression of a Large Number of Stress- and Defense-Related Genes in Degenerating Feeding Cells1[C][W][OA

    PubMed Central

    Kandoth, Pramod Kaitheri; Ithal, Nagabhushana; Recknor, Justin; Maier, Tom; Nettleton, Dan; Baum, Thomas J.; Mitchum, Melissa G.

    2011-01-01

    To gain new insights into the mechanism of soybean (Glycine max) resistance to the soybean cyst nematode (Heterodera glycines), we compared gene expression profiles of developing syncytia in soybean near-isogenic lines differing at Rhg1 (for resistance to Heterodera glycines), a major quantitative trait locus for resistance, by coupling laser capture microdissection with microarray analysis. Gene expression profiling revealed that 1,447 genes were differentially expressed between the two lines. Of these, 241 (16.8%) were stress- and defense-related genes. Several stress-related genes were up-regulated in the resistant line, including those encoding homologs of enzymes that lead to increased levels of reactive oxygen species and proteins associated with the unfolded protein response. These results indicate that syncytia induced in the resistant line are undergoing severe oxidative stress and imbalanced endoplasmic reticulum homeostasis, both of which likely contribute to the resistance reaction. Defense-related genes up-regulated within syncytia of the resistant line included those predominantly involved in apoptotic cell death, the plant hypersensitive response, and salicylic acid-mediated defense signaling; many of these genes were either partially suppressed or not induced to the same level by a virulent soybean cyst nematode population for successful nematode reproduction and development on the resistant line. Our study demonstrates that a network of molecular events take place during Rhg1-mediated resistance, leading to a highly complex defense response against a root pathogen. PMID:21335526

  2. The Soybean Rhg1 locus for resistance to the soybean cyst nematode Heterodera glycines regulates the expression of a large number of stress- and defense-related genes in degenerating feeding cells.

    PubMed

    Kandoth, Pramod Kaitheri; Ithal, Nagabhushana; Recknor, Justin; Maier, Tom; Nettleton, Dan; Baum, Thomas J; Mitchum, Melissa G

    2011-04-01

    To gain new insights into the mechanism of soybean (Glycine max) resistance to the soybean cyst nematode (Heterodera glycines), we compared gene expression profiles of developing syncytia in soybean near-isogenic lines differing at Rhg1 (for resistance to Heterodera glycines), a major quantitative trait locus for resistance, by coupling laser capture microdissection with microarray analysis. Gene expression profiling revealed that 1,447 genes were differentially expressed between the two lines. Of these, 241 (16.8%) were stress- and defense-related genes. Several stress-related genes were up-regulated in the resistant line, including those encoding homologs of enzymes that lead to increased levels of reactive oxygen species and proteins associated with the unfolded protein response. These results indicate that syncytia induced in the resistant line are undergoing severe oxidative stress and imbalanced endoplasmic reticulum homeostasis, both of which likely contribute to the resistance reaction. Defense-related genes up-regulated within syncytia of the resistant line included those predominantly involved in apoptotic cell death, the plant hypersensitive response, and salicylic acid-mediated defense signaling; many of these genes were either partially suppressed or not induced to the same level by a virulent soybean cyst nematode population for successful nematode reproduction and development on the resistant line. Our study demonstrates that a network of molecular events take place during Rhg1-mediated resistance, leading to a highly complex defense response against a root pathogen.

  3. Genome Wide Copy Number Analysis of Paediatric Burkitt Lymphoma Using Formalin-Fixed Tissues Reveals a Subset with Gain of Chromosome 13q and Corresponding miRNA Over Expression

    PubMed Central

    Schiffman, Joshua D.; Lorimer, Patrick D.; Rodic, Vladimir; Jahromi, Mona S.; Downie, Jonathan M.; Bayerl, Michael G.; Sanmann, Jennifer N.; Althof, Pamela A.; Sanger, Warren G.; Barnette, Phillip; Perkins, Sherrie L.; Miles, Rodney R.

    2011-01-01

    SUMMARY The majority of paediatric Burkitt lymphoma (pBL) patients that relapse will die of disease, but markers for this high-risk subset are unknown. MYC translocations characterize pBL, but additional genetic changes may relate to prognosis and serve as potential biomarkers. We utilized a molecular inversion probe single nucleotide polymorphism assay to perform high resolution, genome-wide copy number analysis on archival formalin-fixed, paraffin-embedded pBL and germline tissues. We identified copy number abnormalities (CNAs) in 18/28 patients (64%) with a total of 62 CNAs that included 32 gains and 30 copy number losses. We identified 7 recurrent CNAs including 1q gain (7/28, 25%), 13q gain (3/28, 11%), and 17p loss (4/28, 14%). The minimum common amplified region on 13q was at 13q31 and included the MIR17HG (MIR17-92) locus. Samples with this gain had higher levels of MIR17 RNA and showed a tendency for early relapse. Tumour-specific uniparental disomy was identified in 32% of cases and usually was recurrent. These results demonstrate that high-resolution copy number analysis can be performed on archival lymphoma tissue specimens, which has significance for the study of rare diseases. PMID:21981616

  4. Versatile page numbering analysis

    NASA Astrophysics Data System (ADS)

    Déjean, Hervé; Meunier, Jean-Luc

    2008-01-01

    In this paper, we revisit the problem of detecting the page numbers of a document. This work is motivated by a need for a generic method which applies on a large variety of documents, as well as the need for analyzing the document page numbering scheme rather than spotting one number per page. We propose here a novel method, based on the notion of sequence, which goes beyond any previous described work, and we report on an extensive evaluation of its performance.

  5. Curvature and Tachibana numbers

    SciTech Connect

    Stepanov, Sergey E

    2011-07-31

    The aim of this paper is to define the rth Tachibana number t{sub r} of an n-dimensional compact oriented Riemannian manifold as the dimension of the space of conformally Killing r-forms, for r=1,2,...,n-1. We also describe properties of these numbers, by analogy with properties of the Betti numbers b{sub r} of a compact oriented Riemannian manifold. Bibliography: 25 titles.

  6. High-Reynolds Number Taylor-Couette Turbulence

    NASA Astrophysics Data System (ADS)

    Grossmann, Siegfried; Lohse, Detlef; Sun, Chao

    2016-01-01

    Taylor-Couette flow, the flow between two coaxial co- or counter-rotating cylinders, is one of the paradigmatic systems in the physics of fluids. The (dimensionless) control parameters are the Reynolds numbers of the inner and outer cylinders, the ratio of the cylinder radii, and the aspect ratio. One key response of the system is the torque required to retain constant angular velocities, which can be connected to the angular velocity transport through the gap. Whereas the low-Reynolds number regime was well explored in the 1980s and 1990s of the past century, in the fully turbulent regime major research activity developed only in the past decade. In this article, we review this recent progress in our understanding of fully developed Taylor-Couette turbulence from the experimental, numerical, and theoretical points of view. We focus on the parameter dependence of the global torque and on the local flow organization, including velocity profiles and boundary layers. Next, we discuss transitions between different (turbulent) flow states. We also elaborate on the relevance of this system for astrophysical disks (quasi-Keplerian flows). The review ends with a list of challenges for future research on turbulent Taylor-Couette flow.

  7. Hacking DNA copy number for circuit engineering.

    PubMed

    Wu, Feilun; You, Lingchong

    2017-07-27

    DNA copy number represents an essential parameter in the dynamics of synthetic gene circuits but typically is not explicitly considered. A new study demonstrates how dynamic control of DNA copy number can serve as an effective strategy to program robust oscillations in gene expression circuits.

  8. High Reynolds Number Research

    NASA Technical Reports Server (NTRS)

    Baals, D. D. (Editor)

    1977-01-01

    Fundamental aerodynamic questions for which high Reynolds number experimental capability is required are discussed. The operational characteristics and design features of the National Transonic Facility are reviewed.

  9. Universal Number Library

    SciTech Connect

    Lloyd, G. Scott

    2016-09-17

    This floating-point arithmetic library contains a software implementation of Universal Numbers (unums) as described by John Gustafson [1]. The unum format is a superset of IEEE 754 floating point with several advantages. Computing with unums provides more accurate answers without rounding errors, underflow or overflow. In contrast to fixed-sized IEEE numbers, a variable number of bits can be used to encode unums. This all allows number with only a few significant digits or with a small dynamic range to be represented more compactly.

  10. Rarefaction waves in van der Waals fluids with an arbitrary number of degrees of freedom.

    PubMed

    Yuen, Albert; Barnard, John J

    2015-09-01

    The isentropic expansion of an instantaneously and homogeneously heated foil is calculated using a 1D fluid model. The initial temperature and density are assumed to be in the vicinity of the critical temperature and solid density, respectively. The fluid is assumed to satisfy the van der Waals equation of state with an arbitrary number of degrees of freedom. Self-similar Riemann solutions are found. With a larger number of degrees of freedom f, depending on the initial dimensionless entropy s[over ̃]_{0}, a richer family of foil expansion behaviors have been found. We calculate the domain in parameter space where these behaviors occur. In total, eight types of rarefaction waves are found and described.

  11. Details of Exact Low Prandtl Number Boundary-Layer Solutions for Forced and For Free Convection

    NASA Technical Reports Server (NTRS)

    Sparrow, E. M.; Gregg, J. L.

    1959-01-01

    A detailed report is given of exact (numerical) solutions of the laminar-boundary-layer equations for the Prandtl number range appropriate to liquid metals (0.003 to 0.03). Consideration is given to the following situations: (1) forced convection over a flat plate for the conditions of uniform wall temperature and uniform wall heat flux, and (2) free convection over an isothermal vertical plate. Tabulations of the new solutions are given in detail. Results are presented for the heat-transfer and shear-stress characteristics; temperature and velocity distributions are also shown. The heat-transfer results are correlated in terms of dimensionless parameters that vary only slightly over the entire liquid-metal range. Previous analytical and experimental work on low Prandtl number boundary layers is surveyed and compared with the new exact solutions.

  12. Geoid and topography for infinite Prandtl number convection in a spherical shell

    NASA Technical Reports Server (NTRS)

    Bercovici, D.; Schubert, G.; Zebib, A.

    1988-01-01

    Geoid anomalies and surface and lower-boundary topographies are calculated for numerically generated thermal convection for an infinite Prandtl number, Boussinesq, axisymmetric spherical fluid shell with constant gravity and viscosity, for heating both entirely from below and entirely from within. Convection solutions are obtained for Rayleigh numbers Ra up to 20 times the critical Ra in heating from below and 27 times critical for heating from within. Geoid parallels surface undulations, and boundary deformation generally increases with increasing cell wavelength. Dimensionless geoid and topography in heating from below are about 5 times greater than in heating from within. Values for heating from within correlate more closely with geophysical data than values from heating from below, suggesting a predominance of internal heating in the mantle. The study emphasizes that dynamically induced topography and geoid are sensitive to the mode of heating in the earth's mantle.

  13. Education by the Numbers

    ERIC Educational Resources Information Center

    Leadership, 2007

    2007-01-01

    Education, it seems, is increasingly driven by the numbers. Whether it is measuring student performance or a school district's ability to balance the books, one will find data out there about it. So much data, in fact, that it is difficult to sort through all the numbers to get the needed information. This article describes California's Ed-Data…

  14. The Fibonacci Numbers.

    ERIC Educational Resources Information Center

    Onstad, Torgeir

    1991-01-01

    After a brief historical account of Leonardo Pisano Fibonacci, some basic results concerning the Fibonacci numbers are developed and proved, and entertaining examples are described. Connections are made between the Fibonacci numbers and the Golden Ratio, biological nature, and other combinatorics examples. (MDH)

  15. The Fibonacci Numbers.

    ERIC Educational Resources Information Center

    Onstad, Torgeir

    1991-01-01

    After a brief historical account of Leonardo Pisano Fibonacci, some basic results concerning the Fibonacci numbers are developed and proved, and entertaining examples are described. Connections are made between the Fibonacci numbers and the Golden Ratio, biological nature, and other combinatorics examples. (MDH)

  16. Avogadro's Number Ferromagnetically

    ERIC Educational Resources Information Center

    Houari, Ahmed

    2010-01-01

    Avogadro's number, usually denoted by N[subscript A], plays a fundamental role in both physics and chemistry. It defines the extremely useful concept of the mole, which is the base unit of the amount of matter in the international system of units. The fundamental character of this number can also be illustrated by its appearance in the definitions…

  17. Avogadro's Number Ferromagnetically

    ERIC Educational Resources Information Center

    Houari, Ahmed

    2010-01-01

    Avogadro's number, usually denoted by N[subscript A], plays a fundamental role in both physics and chemistry. It defines the extremely useful concept of the mole, which is the base unit of the amount of matter in the international system of units. The fundamental character of this number can also be illustrated by its appearance in the definitions…

  18. Templates, Numbers & Watercolors.

    ERIC Educational Resources Information Center

    Clemesha, David J.

    1990-01-01

    Describes how a second-grade class used large templates to draw and paint five-digit numbers. The lesson integrated artistic knowledge and vocabulary with their mathematics lesson in place value. Students learned how draftspeople use templates, and they studied number paintings by Charles Demuth and Jasper Johns. (KM)

  19. Numbers Are Not Everything

    ERIC Educational Resources Information Center

    Cole, Milton W.

    2009-01-01

    Numbers--of publications, grant money, PhD students, and invited talks, for example--play too large a role in assessments of faculty. The author's thirty-five years of experience in higher education have convinced him that overreliance on such numbers is a big problem, especially, but not exclusively, in the sciences. Every scientist recognizes…

  20. Templates, Numbers & Watercolors.

    ERIC Educational Resources Information Center

    Clemesha, David J.

    1990-01-01

    Describes how a second-grade class used large templates to draw and paint five-digit numbers. The lesson integrated artistic knowledge and vocabulary with their mathematics lesson in place value. Students learned how draftspeople use templates, and they studied number paintings by Charles Demuth and Jasper Johns. (KM)

  1. Squirming At Finite Reynolds Number

    NASA Astrophysics Data System (ADS)

    Chisholm, Nicholas; Zhu, Ziyi; Khair, Aditya

    2013-11-01

    The dynamics of swimming microorganisms at zero Reynolds number (Re = 0) has been the subject of extensive theoretical and experimental investigation over the past decade, and the study of locomotion at high Reynolds number (Re >> 1), where inertial forces are dominant, has a venerable history. In this talk, we consider swimming between these limits, i.e. at finite Reynolds numbers, using the popular ``squirmer'' model of self-propulsion, wherein locomotion is achieved through surface distortions. We first utilize matched asymptotic expansions to derive an analytical expression for the swimming velocity of a squirmer through O (Re2) , which highlights that inertia affects so-called ``pusher'' and ``puller'' swimmers in fundamentally different manners. (The equivalent of Whitehead's paradox for a self-propelled object is elucidated in the process.) Next, we employ numerical methods to compute the swimming velocity of pushers and pullers for higher Reynolds numbers. Finally, we demonstrate that inertia causes squirmers (which are non-chiral) to drift across the streamlines of an imposed shear flow.

  2. DNA vaccines expressing the duck hepatitis B virus surface proteins lead to reduced numbers of infected hepatocytes and protect ducks against the development of chronic infection in a virus dose-dependent manner.

    PubMed

    Miller, Darren S; Kotlarski, Ieva; Jilbert, Allison R

    2006-07-20

    We tested the efficacy of DNA vaccines expressing the duck hepatitis B virus (DHBV) pre-surface (pre-S/S) and surface (S) proteins in modifying the outcome of infection in 14-day-old ducks. In two experiments, Pekin Aylesbury ducks were vaccinated on days 4 and 14 of age with plasmid DNA vaccines expressing either the DHBV pre-S/S or S proteins, or the control plasmid vector, pcDNA1.1Amp. All ducks were then challenged intravenously on day 14 of age with 5 x 10(7) or 5 x 10(8) DHBV genomes. Levels of initial DHBV infection were assessed using liver biopsy tissue collected at day 4 post-challenge (p.c.) followed and immunostained for DHBV surface antigen to determine the percentage of infected hepatocytes. All vector vaccinated ducks challenged with 5 x 10(7) and 5 x 10(8) DHBV genomes had an average of 3.21% and 20.1% of DHBV-positive hepatocytes respectively at day 4 p.c. and 16 out of 16 ducks developed chronic DHBV infection. In contrast, pre-S/S and S vaccinated ducks challenged with 5 x 10(7) DHBV genomes had reduced levels of initial infection with an average of 1.38% and 1.93% of DHBV-positive hepatocytes at day 4 p.c. respectively and 10 of 18 ducks were protected against chronic infection. The pre-S/S and the S DNA vaccinated ducks challenged with 5 x 10(8) DHBV genomes had an average of 31.5% and 9.2% of DHBV-positive hepatocytes on day 4 p.c. respectively and only 4 of the 18 vaccinated ducks were protected against chronic infection. There was no statistically significant difference in the efficacy of the DHBV pre-S/S or S DNA vaccines. In conclusion, vaccination of young ducks with DNA vaccines expressing the DHBV pre-S/S and S proteins induced rapid immune responses that reduced the extent of initial DHBV infection in the liver and prevented the development of chronic infection in a virus dose-dependent manner.

  3. Numbers in Action.

    PubMed

    Rugani, Rosa; Sartori, Luisa

    2016-01-01

    Humans show a remarkable tendency to describe and think of numbers as being placed on a mental number line (MNL), with smaller numbers located on the left and larger ones on the right. Faster responses to small numbers are indeed performed on the left side of space, while responses to large numbers are facilitated on the right side of space (spatial-numerical association of response codes, SNARC effect). This phenomenon is considered the experimental demonstration of the MNL and has been extensively replicated throughout a variety of paradigms. Nevertheless, the majority of previous literature has mainly investigated this effect by means of response times and accuracy, whereas studies considering more subtle and automatic measures such as kinematic parameters are rare (e.g., in a reaching-to-grasp movement, the grip aperture is enlarged in responding to larger numbers than in responding to small numbers). In this brief review we suggest that numerical magnitude can also affect the what and how of action execution (i.e., temporal and spatial components of movement). This evidence could have large implications in the strongly debated issue concerning the effect of experience and culture on the orientation of MNL.

  4. Numbers in Action

    PubMed Central

    Rugani, Rosa; Sartori, Luisa

    2016-01-01

    Humans show a remarkable tendency to describe and think of numbers as being placed on a mental number line (MNL), with smaller numbers located on the left and larger ones on the right. Faster responses to small numbers are indeed performed on the left side of space, while responses to large numbers are facilitated on the right side of space (spatial-numerical association of response codes, SNARC effect). This phenomenon is considered the experimental demonstration of the MNL and has been extensively replicated throughout a variety of paradigms. Nevertheless, the majority of previous literature has mainly investigated this effect by means of response times and accuracy, whereas studies considering more subtle and automatic measures such as kinematic parameters are rare (e.g., in a reaching-to-grasp movement, the grip aperture is enlarged in responding to larger numbers than in responding to small numbers). In this brief review we suggest that numerical magnitude can also affect the what and how of action execution (i.e., temporal and spatial components of movement). This evidence could have large implications in the strongly debated issue concerning the effect of experience and culture on the orientation of MNL. PMID:27524965

  5. Discovering Avogadro's Number.

    ERIC Educational Resources Information Center

    Rieck, William A.

    1997-01-01

    Illustrates the use of an inductive approach that leads students to the discovery of Avogadro's number while integrating thinking, mathematical, and calculator skills in the process. An understanding of scientific notation and a calculator are required. (DDR)

  6. Quantum random number generator

    SciTech Connect

    Pooser, Raphael C.

    2016-05-10

    A quantum random number generator (QRNG) and a photon generator for a QRNG are provided. The photon generator may be operated in a spontaneous mode below a lasing threshold to emit photons. Photons emitted from the photon generator may have at least one random characteristic, which may be monitored by the QRNG to generate a random number. In one embodiment, the photon generator may include a photon emitter and an amplifier coupled to the photon emitter. The amplifier may enable the photon generator to be used in the QRNG without introducing significant bias in the random number and may enable multiplexing of multiple random numbers. The amplifier may also desensitize the photon generator to fluctuations in power supplied thereto while operating in the spontaneous mode. In one embodiment, the photon emitter and amplifier may be a tapered diode amplifier.

  7. Quantum random number generators

    NASA Astrophysics Data System (ADS)

    Herrero-Collantes, Miguel; Garcia-Escartin, Juan Carlos

    2017-01-01

    Random numbers are a fundamental resource in science and engineering with important applications in simulation and cryptography. The inherent randomness at the core of quantum mechanics makes quantum systems a perfect source of entropy. Quantum random number generation is one of the most mature quantum technologies with many alternative generation methods. This review discusses the different technologies in quantum random number generation from the early devices based on radioactive decay to the multiple ways to use the quantum states of light to gather entropy from a quantum origin. Randomness extraction and amplification and the notable possibility of generating trusted random numbers even with untrusted hardware using device-independent generation protocols are also discussed.

  8. Computer Corner: Growing Numbers.

    ERIC Educational Resources Information Center

    Shumway, Richard J.

    1983-01-01

    Exponential growth provides an interesting setting for exploration. A sequence of activities and questions which will help students become better acquainted with large numbers and scientific notation, as well as computer notions, is given. (MNS)

  9. Discovering Avogadro's Number.

    ERIC Educational Resources Information Center

    Rieck, William A.

    1997-01-01

    Illustrates the use of an inductive approach that leads students to the discovery of Avogadro's number while integrating thinking, mathematical, and calculator skills in the process. An understanding of scientific notation and a calculator are required. (DDR)

  10. Genetics by the Numbers

    MedlinePlus

    ... genome is larger than any other known species. Credit: Open Cage That's how many base pairs—or ... of chromosomes, which are made up of DNA. Credit: NHGRI That's the approximate number of genes in ...

  11. Shear rotation numbers

    NASA Astrophysics Data System (ADS)

    Doeff, E.; Misiurewicz, M.

    1997-11-01

    This paper presents results on rotation numbers for orientation-preserving torus homeomorphisms homotopic to a Dehn twist. Rotation numbers and the rotation set for such homeomorphisms have been defined and initially investigated by the first author in a previous paper. Here we prove that each rotation number 0951-7715/10/6/017/img5 in the interior of the rotation set is realized by some compact invariant set, and that there is an ergodic measure on that set with mean rotation number 0951-7715/10/6/017/img5. It is also proved that the function which assigns its rotation set to such a homeomorphism is continuous. Finally, a counterexample is presented that shows that rational extremal points of the shear rotation set do not necessarily correspond to any periodic orbits.

  12. The Numbers Game.

    ERIC Educational Resources Information Center

    Lustick, David

    1997-01-01

    Describes a simple activity that explores and reveals the principles of significant figures and scientific notation using a 500 gram bag of unpopped popcorn. Students must devise a method for determining the number of kernels in the bag. (DDR)

  13. Logo and Negative Numbers.

    ERIC Educational Resources Information Center

    Strawn, Candace A.

    1998-01-01

    Describes LOGO's turtle graphics capabilities based on a sixth-grade classroom's activities with negative numbers and Logo programming. A sidebar explains LOGO and offers suggestions to teachers for using LOGO effectively. (LRW)

  14. High Reynolds number and turbulence effects on aerodynamics and heat transfer in a turbine cascade

    NASA Technical Reports Server (NTRS)

    Yeh, Frederick C.; Hippensteele, Steven A.; Vanfossen, G. James; Poinsatte, Philip E.; Ameri, Ali

    1993-01-01

    Experimental data on pressure distribution and heat transfer on a turbine airfoil were obtained over a range of Reynolds numbers from 0.75 to 7.5 x 10 exp 6 and a range of turbulence intensities from 1.8 to about 15 percent. The purpose of this study was to obtain fundamental heat transfer and pressure distribution data over a wide range of high Reynolds numbers and to extend the heat transfer data base to include the range of Reynolds numbers encountered in the Space Shuttle main engine (SSME) turbopump turbines. Specifically, the study aimed to determine (1) the effect of Reynolds number on heat transfer, (2) the effect of upstream turbulence on heat transfer and pressure distribution, and (3) the relationship between heat transfer at high Reynolds numbers and the current data base. The results of this study indicated that Reynolds number and turbulence intensity have a large effect on both the transition from laminar to turbulent flow and the resulting heat transfer. For a given turbulence intensity, heat transfer for all Reynolds numbers at the leading edge can be correlated with the Frossling number developed for lower Reynolds numbers. For a given turbulence intensity, heat transfer for the airfoil surfaces downstream of the leading edge can be approximately correlated with a dimensionless parameter. Comparison of the experimental results were also made with a numerical solution from a two-dimensional Navier-Stokes code.

  15. Fibonacci's Forgotten Number

    ERIC Educational Resources Information Center

    Brown, Ezra; Brunson, Cornelius

    2008-01-01

    Fibonacci's forgotten number is the sexagesimal number 1;22,7,42,33,4,40, which he described in 1225 as an approximation to the real root of x[superscript 3] + 2x[superscript 2] + 10x - 20. In decimal notation, this is 1.36880810785...and it is correct to nine decimal digits. Fibonacci did not reveal his method. How did he do it? There is also a…

  16. Low Reynolds Number Vehicles

    DTIC Science & Technology

    1985-02-01

    numbers. At high altitudes aircraft gas turbine engine fan, compressor, and turbine blades with their small chords encounter Reynolds numhers...light man-carrying/man-powered aircraft , minl-RPVs at low altitude, and wind turbines . Since the airfoil section forms the basic element in the...Wind turbine blades also require high aerodynamic efficiency and all-weather capabilities. The need for efficient low Reynolds number airfoils which

  17. Fibonacci's Forgotten Number

    ERIC Educational Resources Information Center

    Brown, Ezra; Brunson, Cornelius

    2008-01-01

    Fibonacci's forgotten number is the sexagesimal number 1;22,7,42,33,4,40, which he described in 1225 as an approximation to the real root of x[superscript 3] + 2x[superscript 2] + 10x - 20. In decimal notation, this is 1.36880810785...and it is correct to nine decimal digits. Fibonacci did not reveal his method. How did he do it? There is also a…

  18. [Projection of prisoner numbers].

    PubMed

    Metz, Rainer; Sohn, Werner

    2015-01-01

    The past and future development of occupancy rates in prisons is of crucial importance for the judicial administration of every country. Basic factors for planning the required penal facilities are seasonal fluctuations, minimum, maximum and average occupancy as well as the present situation and potential development of certain imprisonment categories. As the prisoner number of a country is determined by a complex set of interdependent conditions, it has turned out to be difficult to provide any theoretical explanations. The idea accepted in criminology for a long time that prisoner numbers are interdependent with criminal policy must be regarded as having failed. Statistical and time series analyses may help, however, to identify the factors having influenced the development of prisoner numbers in the past. The analyses presented here, first describe such influencing factors from a criminological perspective and then deal with their statistical identification and modelling. Using the development of prisoner numbers in Hesse as an example, it has been found that modelling methods in which the independent variables predict the dependent variable with a time lag are particularly helpful. A potential complication is, however, that for predicting the number of prisoners the different dynamics in German and foreign prisoners require the development of further models.

  19. Report number codes

    SciTech Connect

    Nelson, R.N.

    1985-05-01

    This publication lists all report number codes processed by the Office of Scientific and Technical Information. The report codes are substantially based on the American National Standards Institute, Standard Technical Report Number (STRN)-Format and Creation Z39.23-1983. The Standard Technical Report Number (STRN) provides one of the primary methods of identifying a specific technical report. The STRN consists of two parts: The report code and the sequential number. The report code identifies the issuing organization, a specific program, or a type of document. The sequential number, which is assigned in sequence by each report issuing entity, is not included in this publication. Part I of this compilation is alphabetized by report codes followed by issuing installations. Part II lists the issuing organization followed by the assigned report code(s). In both Parts I and II, the names of issuing organizations appear for the most part in the form used at the time the reports were issued. However, for some of the more prolific installations which have had name changes, all entries have been merged under the current name.

  20. Viscous range of turbulent scalar of large Prandtl number

    NASA Astrophysics Data System (ADS)

    Qian, J.

    1995-02-01

    The analytical theory of a turbulent scalar, developed in previous papers is extended to the case of large Prandtl number. The fluctuation character of the least principal rate of strain gamma has an important effect upon the scalar spectrum. The scalar variance spectrum in the viscous range is F(k) = 4.472 (nu/epsilon)(exp 1/2) chi k(exp -1) H(x), X is identical to (k/k(sub b))(exp 2), H(x) is a dimensionless universal function and is determined by solving numerically the closed spectral dynamical equations. A simple fitting formula of the numerical result is H(x) = 0.7687 exp(- 3.79x) + 0.2313 exp(-11.13 x), which corresponds a two-values fluctuation model of gamma. Here upsilon is the kinematic viscosity, k(sub b) is identical to (epsilon/upsilon mu(exp 2))(exp 1/4) is the Batchelor wavenumber, mu is the scalar diffusivity, and epsilon and eni are respectively the energy and variance dissipation rates.

  1. Quantum random number generation

    SciTech Connect

    Ma, Xiongfeng; Yuan, Xiao; Cao, Zhu; Zhang, Zhen; Qi, Bing

    2016-06-28

    Quantum physics can be exploited to generate true random numbers, which play important roles in many applications, especially in cryptography. Genuine randomness from the measurement of a quantum system reveals the inherent nature of quantumness -- coherence, an important feature that differentiates quantum mechanics from classical physics. The generation of genuine randomness is generally considered impossible with only classical means. Based on the degree of trustworthiness on devices, quantum random number generators (QRNGs) can be grouped into three categories. The first category, practical QRNG, is built on fully trusted and calibrated devices and typically can generate randomness at a high speed by properly modeling the devices. The second category is self-testing QRNG, where verifiable randomness can be generated without trusting the actual implementation. The third category, semi-self-testing QRNG, is an intermediate category which provides a tradeoff between the trustworthiness on the device and the random number generation speed.

  2. Quantum random number generation

    DOE PAGES

    Ma, Xiongfeng; Yuan, Xiao; Cao, Zhu; ...

    2016-06-28

    Quantum physics can be exploited to generate true random numbers, which play important roles in many applications, especially in cryptography. Genuine randomness from the measurement of a quantum system reveals the inherent nature of quantumness -- coherence, an important feature that differentiates quantum mechanics from classical physics. The generation of genuine randomness is generally considered impossible with only classical means. Based on the degree of trustworthiness on devices, quantum random number generators (QRNGs) can be grouped into three categories. The first category, practical QRNG, is built on fully trusted and calibrated devices and typically can generate randomness at a highmore » speed by properly modeling the devices. The second category is self-testing QRNG, where verifiable randomness can be generated without trusting the actual implementation. The third category, semi-self-testing QRNG, is an intermediate category which provides a tradeoff between the trustworthiness on the device and the random number generation speed.« less

  3. Beyond the Number Domain

    PubMed Central

    Cantlon, Jessica F.; Platt, Michael L.; Brannon, Elizabeth M.

    2009-01-01

    In a world without numbers, we would be unable to build a skyscraper, hold a national election, plan a wedding, or pay for a chicken at the market. The numerical symbols used in all these behaviors build on the approximate number system (ANS) which represents the number of discrete objects or events as a continuous mental magnitude. In this review, we first discuss evidence that the ANS bears a set of behavioral and brain signatures that are universally displayed across animal species, human cultures, and development. We then turn to the question of whether the ANS constitutes a specialized cognitive and neural domain--a question central to understanding how this system works, the nature of its evolutionary and developmental trajectory, and its physical instantiation in the brain. PMID:19131268

  4. Safety in glomerular numbers.

    PubMed

    Schreuder, Michiel F

    2012-10-01

    A low nephron number is, according to Brenner's hyperfiltration hypothesis, associated with hypertension, glomerular damage and proteinuria, and starts a vicious cycle that ends in renal failure over the long term. Nephron endowment is set during foetal life, and there is no formation of nephrons after 34-36 weeks of gestation, indicating that many factors before that time-point may have an impact on kidney development and reduce nephron numbers. Such factors include maternal malnutrition, stress, diseases, such as diabetes, uteroplacental insufficiency, maternal and neonatal drugs and premature birth. However, other congenital anomalies, such as renal hypoplasia, unilateral renal agenesis or multicystic dysplastic kidney, may also lead to a reduced nephron endowment, with an increased risk for hypertension, renal dysfunction and the need for renal replacement therapy. This review focuses on the causes and consequences of a low nephron endowment and will illustrate why there is safety in glomerular numbers.

  5. Quantum random number generation

    NASA Astrophysics Data System (ADS)

    Ma, Xiongfeng; Yuan, Xiao; Cao, Zhu; Qi, Bing; Zhang, Zhen

    2016-06-01

    Quantum physics can be exploited to generate true random numbers, which have important roles in many applications, especially in cryptography. Genuine randomness from the measurement of a quantum system reveals the inherent nature of quantumness—coherence, an important feature that differentiates quantum mechanics from classical physics. The generation of genuine randomness is generally considered impossible with only classical means. On the basis of the degree of trustworthiness on devices, quantum random number generators (QRNGs) can be grouped into three categories. The first category, practical QRNG, is built on fully trusted and calibrated devices and typically can generate randomness at a high speed by properly modelling the devices. The second category is self-testing QRNG, in which verifiable randomness can be generated without trusting the actual implementation. The third category, semi-self-testing QRNG, is an intermediate category that provides a tradeoff between the trustworthiness on the device and the random number generation speed.

  6. Minimal Niven Numbers

    DTIC Science & Technology

    2007-12-26

    265–275. [7] H. G. Grundman, ‘ Sequences of consecutive Niven numbers’, Fibonacci Quart. 32 (1994), 174–175. [8] D. R. Heath-Brown and S. Konyagin...paper, we define a natural sequence in relation to q-Niven numbers. For a fixed but arbitrary k ∈ N and a base q ≥ 2, one may ask whether or not there...other words, ak is the smallest Niven number whose sum of the digits is a given positive integer k. We denote by ck the companion sequence ck = ak/k

  7. Earthquake number forecasts testing

    NASA Astrophysics Data System (ADS)

    Kagan, Yan Y.

    2017-10-01

    We study the distributions of earthquake numbers in two global earthquake catalogues: Global Centroid-Moment Tensor and Preliminary Determinations of Epicenters. The properties of these distributions are especially required to develop the number test for our forecasts of future seismic activity rate, tested by the Collaboratory for Study of Earthquake Predictability (CSEP). A common assumption, as used in the CSEP tests, is that the numbers are described by the Poisson distribution. It is clear, however, that the Poisson assumption for the earthquake number distribution is incorrect, especially for the catalogues with a lower magnitude threshold. In contrast to the one-parameter Poisson distribution so widely used to describe earthquake occurrences, the negative-binomial distribution (NBD) has two parameters. The second parameter can be used to characterize the clustering or overdispersion of a process. We also introduce and study a more complex three-parameter beta negative-binomial distribution. We investigate the dependence of parameters for both Poisson and NBD distributions on the catalogue magnitude threshold and on temporal subdivision of catalogue duration. First, we study whether the Poisson law can be statistically rejected for various catalogue subdivisions. We find that for most cases of interest, the Poisson distribution can be shown to be rejected statistically at a high significance level in favour of the NBD. Thereafter, we investigate whether these distributions fit the observed distributions of seismicity. For this purpose, we study upper statistical moments of earthquake numbers (skewness and kurtosis) and compare them to the theoretical values for both distributions. Empirical values for the skewness and the kurtosis increase for the smaller magnitude threshold and increase with even greater intensity for small temporal subdivision of catalogues. The Poisson distribution for large rate values approaches the Gaussian law, therefore its skewness

  8. Analogies for Avogadro's Number.

    ERIC Educational Resources Information Center

    Poskozim, Paul S.; And Others

    1986-01-01

    Reviews analogies used to try to capture the concept of the magnitude of Avogadro's number, including analogies related to small/tiny objects, counting, people, water, and money. Also presents several new ones which are based on modern computers and printers. (JN)

  9. Playing the Numbers

    ERIC Educational Resources Information Center

    Doyle, William R.

    2010-01-01

    Some say that the educators now have a gender-stratified system of higher education, with nearly 60 percent of all undergraduates being women and fewer men attending each year. The battle for gender equity for women in higher education has been a long and contentious one. In the decades since, increasing numbers of women have gone to college, to…

  10. Paint by Numbers Revived!

    ERIC Educational Resources Information Center

    Hahn, Nic

    2012-01-01

    Remember paint by numbers? This revived trend was a perfect solution to teaching geometric shapes to the author's first-grade students. Geometric shapes are identified and used in early elementary art classrooms, but this lesson gives students a deeper understanding of shape, encourages problem-solving, and makes a strong correlation between math…

  11. Introducing Complex Numbers

    ERIC Educational Resources Information Center

    Trudgian, Timothy

    2009-01-01

    One of the difficulties in any teaching of mathematics is to bridge the divide between the abstract and the intuitive. Throughout school one encounters increasingly abstract notions, which are more and more difficult to relate to everyday experiences. This article examines a familiar approach to thinking about negative numbers, that is an…

  12. ALARA notes, Number 8

    SciTech Connect

    Khan, T.A.; Baum, J.W.; Beckman, M.C.

    1993-10-01

    This document contains information dealing with the lessons learned from the experience of nuclear plants. In this issue the authors tried to avoid the `tyranny` of numbers and concentrated on the main lessons learned. Topics include: filtration devices for air pollution abatement, crack repair and inspection, and remote handling equipment.

  13. Preschoolers' Number Sense

    ERIC Educational Resources Information Center

    Moomaw, Sally; Carr, Victoria; Boat, Mary; Barnett, David

    2010-01-01

    A child's demonstration of his conceptual understanding of number bodes well for his future success in school mathematics. As youngsters' thinking becomes more logical, they apply one-to-one correspondence relationships to quantification. Yet, reliable assessment of young children's mathematical ability is difficult because of social and emotional…

  14. "Better than Their Numbers"

    ERIC Educational Resources Information Center

    Cech, Scott J.

    2008-01-01

    This article discusses College Summit, a nonprofit effort centered around the premise that there is a sizable number of students who are more capable of college academics than their test scores and grade point averages suggest. Its four-day summer sessions are focused not on ramping up students' academic performance but in mining students'…

  15. "Better than Their Numbers"

    ERIC Educational Resources Information Center

    Cech, Scott J.

    2008-01-01

    This article discusses College Summit, a nonprofit effort centered around the premise that there is a sizable number of students who are more capable of college academics than their test scores and grade point averages suggest. Its four-day summer sessions are focused not on ramping up students' academic performance but in mining students'…

  16. The Net by Numbers.

    ERIC Educational Resources Information Center

    McMurdo, George

    1996-01-01

    The expansion of the commercial Internet has encouraged the interpretation of the Internet and its uses as a potential marketing medium. Examines statistical and demographic information about the Internet including number of Internet hosts and World Wide Web servers, and estimates of Internet users; and raises questions about definitions and…

  17. Paint by Numbers Revived!

    ERIC Educational Resources Information Center

    Hahn, Nic

    2012-01-01

    Remember paint by numbers? This revived trend was a perfect solution to teaching geometric shapes to the author's first-grade students. Geometric shapes are identified and used in early elementary art classrooms, but this lesson gives students a deeper understanding of shape, encourages problem-solving, and makes a strong correlation between math…

  18. Number in Classifier Languages

    ERIC Educational Resources Information Center

    Nomoto, Hiroki

    2013-01-01

    Classifier languages are often described as lacking genuine number morphology and treating all common nouns, including those conceptually count, as an unindividuated mass. This study argues that neither of these popular assumptions is true, and presents new generalizations and analyses gained by abandoning them. I claim that no difference exists…

  19. Chippy's Computer Numbers.

    ERIC Educational Resources Information Center

    Girard, Suzanne; Willing, Kathlene R.

    Intended for young children just becoming familiar with computers, this counting book introduces and reinforces new computer vocabulary and concepts. The numbers, from one to twelve, are presented along with words and illustrations from the world of computers, allowing for different activities in which children can count or match and name the…

  20. The Net by Numbers.

    ERIC Educational Resources Information Center

    McMurdo, George

    1996-01-01

    The expansion of the commercial Internet has encouraged the interpretation of the Internet and its uses as a potential marketing medium. Examines statistical and demographic information about the Internet including number of Internet hosts and World Wide Web servers, and estimates of Internet users; and raises questions about definitions and…

  1. High Reynolds Number Effects on Multi-Hole Probes and Hot Wire Anemometers

    NASA Technical Reports Server (NTRS)

    Ramachandran, N.; Smith, A.; Gerry, G.; Kauffman, W.

    1995-01-01

    The paper reports on the results from an experimental investigation of the response of multi-hole and hot wire probes at high flow Reynolds numbers (Re approx. 10(exp 6)). The limited results available in literature for 5-hole probes are restricted to Re approx. 10(exp 4). The experiment aims to investigate the probe response (in terms of dimensionless pressure ratios, characterizing pitch, and yaw angles and the total and static pressures) at high Re values and to gauge their effect on the calculated velocity vector. Hot wire calibrations were also undertaken with a parametric variation of the flow pressure, velocity and temperature. Different correction and calibration schemes are sought to be tested against the acquired data set. The data is in the analysis stage at the present time. The test provided good benchmark quality data that can be used to test future calibration and testing methods.

  2. Vortex shedding from a hydrofoil at high Reynolds number

    NASA Astrophysics Data System (ADS)

    Bourgoyne, Dwayne A.; Ceccio, Steven L.; Dowling, David R.

    2005-05-01

    High Reynolds number (Re) wall-bounded turbulent flows occur in many hydro- and aerodynamic applications. However, the limited amount of high-Re experimental data has hampered the development and validation of scaling laws and modelling techniques applicable to such flows. This paper presents measurements of the turbulent flow near the trailing edge of a two-dimensional lifting surface at chord-based Reynolds numbers, Re_{C}, typical of heavy-lift aircraft wings and full-scale ship propellers. The experiments were conducted in the William B. Morgan Large Cavitation Channel at flow speeds from 0.50 to 18.3ms(-1) with a cambered hydrofoil having a 3.05m span and a 2.13m chord that generated 60 metric tons of lift at the highest flow speed, Re_{C}{≈}50{×}10(6) . Flow-field measurements concentrated on the foil's near wake and include results from trailing edges having terminating bevel angles of 44(°) and 56(°) . Although generic turbulent boundary layer and wake characteristics were found at any fixed Re_{C} in the trailing-edge region, the variable strength of near-wake vortex shedding caused the flow-field fluctuations to be Reynolds-number and trailing-edge-geometry dependent. In the current experiments, vortex-shedding strength peaked at Re_{C}{=}4{×}10(6) with the 56(°) bevel-angle trailing edge. A dimensionless scaling for this phenomenon constructed from the free-stream speed, the wake thickness, and an average suction-side shear-layer vorticity at the trailing edge collapses the vortex-shedding strength measurements for 1.4{×}10(6}{≤) Re_{C}{≤}50{×}10(6) from both trailing edges and from prior measurements on two-dimensional struts at Re_{C}{˜}2{×}10(6) with asymmetrical trailing edges.

  3. Transcriptional regulation by the numbers: models.

    PubMed

    Bintu, Lacramioara; Buchler, Nicolas E; Garcia, Hernan G; Gerland, Ulrich; Hwa, Terence; Kondev, Jané; Phillips, Rob

    2005-04-01

    The expression of genes is regularly characterized with respect to how much, how fast, when and where. Such quantitative data demands quantitative models. Thermodynamic models are based on the assumption that the level of gene expression is proportional to the equilibrium probability that RNA polymerase (RNAP) is bound to the promoter of interest. Statistical mechanics provides a framework for computing these probabilities. Within this framework, interactions of activators, repressors, helper molecules and RNAP are described by a single function, the "regulation factor". This analysis culminates in an expression for the probability of RNA polymerase binding at the promoter of interest as a function of the number of regulatory proteins in the cell.

  4. CT number definition

    NASA Astrophysics Data System (ADS)

    Bryant, J. A.; Drage, N. A.; Richmond, S.

    2012-04-01

    The accuracy of CT number plots has been found lacking in several medical applications. This is of concern since the ability to compare and evaluate results on a reproducible and standard basis is essential to long term development. Apart from the technical limitations arising from the CT scanner and the data treatment, there are fundamental issues with the definition of the Hounsfield number, namely the absence of a standard photon energy and the need to specify the attenuation mechanism for standard measurements. This paper presents calculations to demonstrate the shortcomings of the present definition with a brief discussion. The remedy is straightforward, but probably of long duration as it would require an international agreement.

  5. The Remarkable Number "1"

    NASA Astrophysics Data System (ADS)

    Allen, G. Donald

    2014-09-01

    In human history, the origin of the numbers came from definite practical needs. Indeed, there is strong evidence that numbers were created before writing. The number "1", dating back at least 20,000 years, was found as a counting symbol on a bone. The famous statement by the German mathematician Leopold Kronecker (1823-1891), "God made the integers; all else is the work of man," has spawned a lively modern philosophical discussion, and this discussion begins by trying to get a philosophical handle on "1." This approach remains under heavy discussion, and is more-or-less unresolved (Frege in Die Grundlagen der Arithmetik (English: The foundations of arithmetic). Polhman, 1884). In this note, we consider the many facets of "one" in it many guises and applications. Nonetheless, "one" has multiple meanings, from the very practical to the abstract, from mathematics to science to basically everything. We examine here a mere slice of mathematical history with a focus on the most basic and applicable concept therein. It troubles many, particularly students, even today.

  6. Neither Name, Nor Number

    NASA Astrophysics Data System (ADS)

    Holik, Federico

    2014-03-01

    Since its origins, quantum mechanics has presented problems with the concept of individuality. It is argued that quantum particles do not have individuality, and so, one can speak about "entities without identity". On the contrary, we claim that the problem of quantum non individuality goes deeper, and that one of its most important features is the fact that there are quantum systems for which particle number is not well defined. In this work, we continue this discussion in relation to the problem about the one and the many.

  7. High Reynolds Number Turbulence

    DTIC Science & Technology

    2007-03-27

    wall relation of McKeon et al. (2005), and the results for the smallest sandgrain roughness used by Nikuradse (1933). 3 57xI03 "eI : uhp - 2 8 1 6 8 x l 0...Reynolds Number Turbulent Pipe Flow," ASME International Mechanical Engineering Conference and Exposition, Washington, D.C., November 16-21, 2003... Engineering Sciences, Vol. 365 (1852) pp. 699-714, 2007. 14 ’Pipe flow roughness Allen, J.J., Shockling, M.A. and Smits, A.J. "Effects of a machined rough

  8. Experimental investigation of free-convection heat transfer in vertical tube at large Grashof numbers / E. R. G. Eckert, A. J. Diaguila

    NASA Technical Reports Server (NTRS)

    Eckert, E R G; Diaguila, A J

    1952-01-01

    Local free-convection heat-transfer coefficients and temperature fields in the turbulent flow range were obtained within a vertical, stationary tube closed at the boom, heated along its walls, and having a length-to-diameter ratio of 5. Convective heat-transfer coefficients were correlated by the general relations for free-convection heat transfer. These coefficients, converted to dimensionless Nusselt numbers were 35 percent below known relations for vertical flat plates. Air temperature measurements within the tube indicated a thin boundary layer along the heated wall surface and unstable conditions in the air flow.

  9. Importance of wave-number dependence of Biot numbers in one-sided models of evaporative Marangoni instability: Horizontal layer and spherical droplet

    NASA Astrophysics Data System (ADS)

    Machrafi, H.; Rednikov, A.; Colinet, P.; Dauby, P. C.

    2015-05-01

    A one-sided model of the thermal Marangoni instability owing to evaporation into an inert gas is developed. Two configurations are studied in parallel: a horizontal liquid layer and a spherical droplet. With the dynamic gas properties being admittedly negligible, one-sided approaches typically hinge upon quantifying heat and mass transfer through the gas phase by means of transfer coefficients (like in the Newton's cooling law), which in dimensionless terms eventually corresponds to using Biot numbers. Quite a typical arrangement encountered in the literature is a constant Biot number, the same for perturbations of different wavelengths and maybe even the same as for the reference state. In the present work, we underscore the relevance of accounting for its wave-number dependence, which is especially the case in the evaporative context with relatively large values of the resulting effective Biot number. We illustrate the effect in the framework of the Marangoni instability thresholds. As a concrete example, we consider HFE-7100 (a standard refrigerant) for the liquid and air for the inert gas.

  10. Importance of wave-number dependence of Biot numbers in one-sided models of evaporative Marangoni instability: Horizontal layer and spherical droplet.

    PubMed

    Machrafi, H; Rednikov, A; Colinet, P; Dauby, P C

    2015-05-01

    A one-sided model of the thermal Marangoni instability owing to evaporation into an inert gas is developed. Two configurations are studied in parallel: a horizontal liquid layer and a spherical droplet. With the dynamic gas properties being admittedly negligible, one-sided approaches typically hinge upon quantifying heat and mass transfer through the gas phase by means of transfer coefficients (like in the Newton's cooling law), which in dimensionless terms eventually corresponds to using Biot numbers. Quite a typical arrangement encountered in the literature is a constant Biot number, the same for perturbations of different wavelengths and maybe even the same as for the reference state. In the present work, we underscore the relevance of accounting for its wave-number dependence, which is especially the case in the evaporative context with relatively large values of the resulting effective Biot number. We illustrate the effect in the framework of the Marangoni instability thresholds. As a concrete example, we consider HFE-7100 (a standard refrigerant) for the liquid and air for the inert gas.

  11. Low Reynolds number multiple-time-scale turbulence model and calculations of steady and pulsating shear layers

    NASA Technical Reports Server (NTRS)

    Kim, Sang-Wook

    1992-01-01

    A low Reynolds number multiple-time-scale turbulence model (LMS) and its application to fully developed turbulent channel flows and pulsating pipe flows are presented. The LMS can describe the inequilibrium turbulence phenomena down to the viscous sublayer. The calculated fluid flow and turbulence fields for the channel flows are in better agreement with the direct numerical simulation (DNS) results than those obtained using a Reynolds stress turbulence model, and the calculated near-wall dissipation rates are in qualitatively correct agreement with the DNS results. The LMS also successfully predicts the rapidly varying phase-lead of the wall shearing stress that occurs in a narrow range of the dimensionless frequency omega (+) = (omega x nu)/(upsilon x tau(exp2)) for the pulsating pipe flows while various other turbulence models fail to predict this phenomenon, and the LMS yields significantly improved numerical results for a wide range of the dimensionless frequency compared with those obtained using a rapid distortion theory (RDT).

  12. An introduction to hyperharmonic numbers

    NASA Astrophysics Data System (ADS)

    Cereceda, José Luis

    2015-04-01

    In this note, we deal with a generalization of the harmonic numbers proposed by Conway and Guy in their Book of Numbers, namely, the so-called hyperharmonic numbers. Our main aim is to prove, by mathematical induction, the formula defining the hyperharmonic numbers in terms of ordinary harmonic numbers. Moreover, we calculate the hyperharmonic numbers as the derivative of a certain binomial coefficient.

  13. Energy Dependence of the Hounsfield Number

    PubMed Central

    Brooks, Rodney A.

    1977-01-01

    A standard definition is proposed for the Hounsfield number. Any CT number can be converted to the Hounsfield scale after performing a simple calibration using air and water. The energy dependence of the Hounsfield number H is given by the expression H = (Hc + Hp Q)/(1 + Q), where Hc and Hp are the Compton and photoelectric coefficients of the material being measured, expressed in Hounsfield units, and Q is the “quality factor” of the scanner. Q can be measured by performing a scan of a single calibrating material, such as a KI solution. By applying this analysis to dual-energy scans, the Compton and photoelectric coefficients of an unknown substance may easily be obtained. This can lead to a limited degree of chemical identification.

  14. 7 CFR 29.9205 - Identification number (farm serial number).

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 2 2014-01-01 2014-01-01 false Identification number (farm serial number). 29.9205 Section 29.9205 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE... number (farm serial number). The serial number assigned to an individual farm by the appropriate office...

  15. 7 CFR 29.9205 - Identification number (farm serial number).

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 2 2012-01-01 2012-01-01 false Identification number (farm serial number). 29.9205 Section 29.9205 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE... number (farm serial number). The serial number assigned to an individual farm by the appropriate office...

  16. 7 CFR 29.9205 - Identification number (farm serial number).

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 2 2013-01-01 2013-01-01 false Identification number (farm serial number). 29.9205 Section 29.9205 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE... number (farm serial number). The serial number assigned to an individual farm by the appropriate office...

  17. 7 CFR 29.9205 - Identification number (farm serial number).

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 2 2011-01-01 2011-01-01 false Identification number (farm serial number). 29.9205 Section 29.9205 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE... number (farm serial number). The serial number assigned to an individual farm by the appropriate office...

  18. 7 CFR 29.9205 - Identification number (farm serial number).

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Identification number (farm serial number). 29.9205 Section 29.9205 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE... number (farm serial number). The serial number assigned to an individual farm by the appropriate office...

  19. The effect of Bond number on pool boiling for mini-fin surfaces and different working fluids

    NASA Astrophysics Data System (ADS)

    Strąk, Ewelina; Pastuszko, Robert

    2016-03-01

    Experimental nucleate pool boiling data were collected for structures in the form of extended surfaces sintered with perforated foil. The article describes experimental investigations for two kinds of surfaces: smooth and mini-fins with sintered perforated foil (MFP). The MFP surfaces were manufactured out of perforated copper foil (pore diameters: 0.05 - 0.3 mm) sintered with the mini-fins, uniformly spaced on the base surface. The experiments were carried out at atmospheric pressure for four kinds of the fluids: water, ethanol, FC-72 and Novec 649. The results for these working fluids were compared in terms of the Bond number and other dimensionless parameters. For all working fluids, the heat transfer coefficients obtained for the MFP surfaces were from 2 to 5 times higher than those for the smooth surface. Using a regression analysis with reference to selected physical properties and several characteristic dimensions, it was possible to develop a correlation for the Nusselt number.

  20. CRC octane-number-requirement survey, 1990

    SciTech Connect

    Not Available

    1991-07-01

    An annual statistical survey of octane number requirements of current model vehicles is conducted by the Coordinating Research Council, Inc. Test data have been obtained by seventeen companies on 356 1990 vehicles including passenger cars and light-duty trucks and vans, of which 169 were equipped with knock sensors. Octane number requirements were determined by testing at maximum-throttle conditions, as well as at part-throttle, with three unleaded fuel series of varying sensitivities. Requirements are expressed as the (R+M)/2 octane number, Research octane number, and Motor octane number of the reference fuel producing knock which was recurrent and repeatable at the lowest audible level. Estimated octane number requirements for the total vehicles are weighted in proportion to the 1990 vehicle model production and/or sales figures. The octane number requirements of 1990 models with average sensitivity unleaded fuels were 85.4 (R+M)/2 octane numbers at the 50 percent satisfaction level, and 89.2 (R+M)/2 octane numbers at the 90 percent satisfaction level.

  1. CRC octane number requirement survey for 1989

    SciTech Connect

    Not Available

    1990-08-01

    An annual statistical survey of octane number requirements of current model vehicles is conducted by the Coordinating Research Council, Inc. Test data have been obtained by eighteen companies on 391 1989 vehicles including passenger cars and light-duty trucks and vans, of which 179 were equipped with knock sensors. Maximum octane number requirements were determined by testing at maximum-throttle conditions, as well as at part-throttle, with three unleaded fuel series of varying sensitivities. Requirements are expressed as the (R+M)/2 octane number, Research octane number, and Motor octane number of the reference fuel producing knock which was recurrent and repeatable at the lowest audible level. Estimated octane number requirements for the total vehicles are weighted in proportion to the 1989 vehicle model production and/or sales figures. The maximum octane number requirements of 1989 models with average sensitivity unleaded fuels were 85.1 (R+M)/2 octane numbers at the 50 percent satisfaction level, and 89.2 (R+M)/2 octane numbers at the 90 percent satisfaction level. Comparison with previous Surveys are made in this report.

  2. CRC octane number requirement survey 1992

    SciTech Connect

    Not Available

    1993-08-01

    An annual statistical survey of octane number requirements of current model vehicles is conducted by the Coordinating Research Council, Inc. Test data have been obtained by ten companies on 184 1992 vehicles including passenger cars and light-duty trucks and vans, of which 88 were equipped with knock sensors. Octane number requirements were determined by testing at maximum-throttle conditions, as well as at part-throttle, with four unleaded fuel series of varying sensitivities, one containing 15 percent methyl tertiary butyl ether. Requirements are expressed as the (R+M)/2 octane number, Research octane number, and Motor octane number of the reference fuel producing knock which was recurrent and repeatable at the lowest audible level. Estimated octane number requirements for the total vehicles are weighted in proportion to the 1992 vehicle model production and/or sales figures. The octane number requirements of 1992 models with average sensitivity unleaded fuels were 85.1 (R+M)/2 octane numbers at the 50 percent satisfaction level, and 92.0 (R+M)/2 octane numbers at the 90 percent satisfaction level. In order to make a more powerful test of statistical significance of the FBRUM fuel series, the 1991 ONRS was pooled with the 1992 ONRS and compared with the pooled data for the FBRU fuel series. There was no significant difference between the two fuel series up to about 90 percent satisfaction. Beyond 90 percent satisfaction, the variability in the data is high.

  3. Beyond Natural Numbers: Negative Number Representation in Parietal Cortex

    PubMed Central

    Blair, Kristen P.; Rosenberg-Lee, Miriam; Tsang, Jessica M.; Schwartz, Daniel L.; Menon, Vinod

    2012-01-01

    Unlike natural numbers, negative numbers do not have natural physical referents. How does the brain represent such abstract mathematical concepts? Two competing hypotheses regarding representational systems for negative numbers are a rule-based model, in which symbolic rules are applied to negative numbers to translate them into positive numbers when assessing magnitudes, and an expanded magnitude model, in which negative numbers have a distinct magnitude representation. Using an event-related functional magnetic resonance imaging design, we examined brain responses in 22 adults while they performed magnitude comparisons of negative and positive numbers that were quantitatively near (difference <4) or far apart (difference >6). Reaction times (RTs) for negative numbers were slower than positive numbers, and both showed a distance effect whereby near pairs took longer to compare. A network of parietal, frontal, and occipital regions were differentially engaged by negative numbers. Specifically, compared to positive numbers, negative number processing resulted in greater activation bilaterally in intraparietal sulcus (IPS), middle frontal gyrus, and inferior lateral occipital cortex. Representational similarity analysis revealed that neural responses in the IPS were more differentiated among positive numbers than among negative numbers, and greater differentiation among negative numbers was associated with faster RTs. Our findings indicate that despite negative numbers engaging the IPS more strongly, the underlying neural representation are less distinct than that of positive numbers. We discuss our findings in the context of the two theoretical models of negative number processing and demonstrate how multivariate approaches can provide novel insights into abstract number representation. PMID:22363276

  4. Beyond natural numbers: negative number representation in parietal cortex.

    PubMed

    Blair, Kristen P; Rosenberg-Lee, Miriam; Tsang, Jessica M; Schwartz, Daniel L; Menon, Vinod

    2012-01-01

    Unlike natural numbers, negative numbers do not have natural physical referents. How does the brain represent such abstract mathematical concepts? Two competing hypotheses regarding representational systems for negative numbers are a rule-based model, in which symbolic rules are applied to negative numbers to translate them into positive numbers when assessing magnitudes, and an expanded magnitude model, in which negative numbers have a distinct magnitude representation. Using an event-related functional magnetic resonance imaging design, we examined brain responses in 22 adults while they performed magnitude comparisons of negative and positive numbers that were quantitatively near (difference <4) or far apart (difference >6). Reaction times (RTs) for negative numbers were slower than positive numbers, and both showed a distance effect whereby near pairs took longer to compare. A network of parietal, frontal, and occipital regions were differentially engaged by negative numbers. Specifically, compared to positive numbers, negative number processing resulted in greater activation bilaterally in intraparietal sulcus (IPS), middle frontal gyrus, and inferior lateral occipital cortex. Representational similarity analysis revealed that neural responses in the IPS were more differentiated among positive numbers than among negative numbers, and greater differentiation among negative numbers was associated with faster RTs. Our findings indicate that despite negative numbers engaging the IPS more strongly, the underlying neural representation are less distinct than that of positive numbers. We discuss our findings in the context of the two theoretical models of negative number processing and demonstrate how multivariate approaches can provide novel insights into abstract number representation.

  5. PCR-Based Detection of DNA Copy Number Variation.

    PubMed

    Mehrotra, Meenakshi

    2016-01-01

    Copy number variations are important polymorphisms that can influence gene expression within and close to the rearranged region, and results in phenotypic variation. Techniques that detect abnormalities in DNA copy number are therefore useful for studying the associations between DNA aberrations and disease phenotype and for locating critical genes. PCR-based detection of copy number of target gene using TaqMan copy number assay offers a reliable method to measure copy number variation in human genome.

  6. On Fibonacci Numbers Which Are Elliptic Korselt Numbers

    DTIC Science & Technology

    2014-11-17

    On Fibonacci numbers which are elliptic Korselt numbers Florian Luca School of Mathematics University of the Witwatersrand P. O. Box Wits 2050, South...is a CM elliptic curve with CM field Q( √ −d), then the set of n for which the nth Fibonacci number Fn satisfies an elliptic Korselt criterion for Q...SUBTITLE On Fibonacci Numbers Which Are Elliptic Korselt Numbers 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d

  7. Stochastic variation in Cardamine hirsuta petal number.

    PubMed

    Monniaux, Marie; Pieper, Bjorn; Hay, Angela

    2016-04-01

    Floral development is remarkably robust in terms of the identity and number of floral organs in each whorl, whereas vegetative development can be quite plastic. This canalization of flower development prevents the phenotypic expression of cryptic genetic variation, even in fluctuating environments. A cruciform perianth with four petals is a hallmark of the Brassicaceae family, typified in the model species Arabidopsis thaliana However, variable petal loss is found in Cardamine hirsuta, a genetically tractable relative of A. thaliana Cardamine hirsuta petal number varies in response to stochastic, genetic and environmental perturbations, which makes it an interesting model to study mechanisms of decanalization and the expression of cryptic variation. Multitrait quantitative trait locus (QTL) analysis in recombinant inbred lines (RILs) was used to identify whether the stochastic variation found in C. hirsuta petal number had a genetic basis. Stochastic variation (standard error of the average petal number) was found to be a heritable phenotype, and four QTL that influenced this trait were identified. The sensitivity to detect these QTL effects was increased by accounting for the effect of ageing on petal number variation. All QTL had significant effects on both average petal number and its standard error, indicating that these two traits share a common genetic basis. However, for some QTL, a degree of independence was found between the age of the flowers where allelic effects were significant for each trait. Stochastic variation in C. hirsuta petal number has a genetic basis, and common QTL influence both average petal number and its standard error. Allelic variation at these QTL can, therefore, modify petal number in an age-specific manner via effects on the phenotypic mean and stochastic variation. These results are discussed in the context of trait evolution via a loss of robustness. © The Author 2015. Published by Oxford University Press on behalf of the Annals

  8. Stochastic variation in Cardamine hirsuta petal number

    PubMed Central

    Monniaux, Marie; Pieper, Bjorn; Hay, Angela

    2016-01-01

    Background and Aims Floral development is remarkably robust in terms of the identity and number of floral organs in each whorl, whereas vegetative development can be quite plastic. This canalization of flower development prevents the phenotypic expression of cryptic genetic variation, even in fluctuating environments. A cruciform perianth with four petals is a hallmark of the Brassicaceae family, typified in the model species Arabidopsis thaliana. However, variable petal loss is found in Cardamine hirsuta, a genetically tractable relative of A. thaliana. Cardamine hirsuta petal number varies in response to stochastic, genetic and environmental perturbations, which makes it an interesting model to study mechanisms of decanalization and the expression of cryptic variation. Methods Multitrait quantitative trait locus (QTL) analysis in recombinant inbred lines (RILs) was used to identify whether the stochastic variation found in C. hirsuta petal number had a genetic basis. Key Results Stochastic variation (standard error of the average petal number) was found to be a heritable phenotype, and four QTL that influenced this trait were identified. The sensitivity to detect these QTL effects was increased by accounting for the effect of ageing on petal number variation. All QTL had significant effects on both average petal number and its standard error, indicating that these two traits share a common genetic basis. However, for some QTL, a degree of independence was found between the age of the flowers where allelic effects were significant for each trait. Conclusions Stochastic variation in C. hirsuta petal number has a genetic basis, and common QTL influence both average petal number and its standard error. Allelic variation at these QTL can, therefore, modify petal number in an age-specific manner via effects on the phenotypic mean and stochastic variation. These results are discussed in the context of trait evolution via a loss of robustness. PMID:26346720

  9. Percents Are Not Natural Numbers

    ERIC Educational Resources Information Center

    Jacobs, Jennifer A.

    2013-01-01

    Adults are prone to treating percents, one representational format of rational numbers, as novel cases of natural number. This suggests that percent values are not differentiated from natural numbers; a conceptual shift from the natural numbers to the rational numbers has not yet occurred. This is most surprising, considering people are inundated…

  10. Percents Are Not Natural Numbers

    ERIC Educational Resources Information Center

    Jacobs, Jennifer A.

    2013-01-01

    Adults are prone to treating percents, one representational format of rational numbers, as novel cases of natural number. This suggests that percent values are not differentiated from natural numbers; a conceptual shift from the natural numbers to the rational numbers has not yet occurred. This is most surprising, considering people are inundated…

  11. Number sense in the transition from natural to rational numbers.

    PubMed

    Van Hoof, Jo; Verschaffel, Lieven; Van Dooren, Wim

    2017-03-01

    Rational numbers are of critical importance both in mathematics and in other fields of science. However, they form a stumbling block for learners. One widely known source of the difficulty learners have with rational numbers is the natural number bias, that is the tendency to (inappropriately) apply natural number properties in rational number tasks. Still, it has been shown that a good understanding of natural numbers is highly predictive for mathematics achievement in general, and for performance on rational number tasks in particular. In this study, we further investigated the relation between learners' natural and rational number knowledge, specifically in cases where a natural number bias may lead to errors. Participants were 140 sixth graders from six different primary schools. Participants completed a symbolic and a non-symbolic natural number comparison task, a number line estimation task, and a rational number sense test. Learners' natural number knowledge was found to be a good predictor of their rational number knowledge. However, after first controlling for learners' general mathematics achievement, their natural number knowledge only predicted the subaspect of operations with rational numbers. The results of this study suggest that the relation between learners' natural and rational number knowledge can largely be explained by their relation with learners' general mathematics achievement. © 2016 The British Psychological Society.

  12. Number Sense in the Transition from Natural to Rational Numbers

    ERIC Educational Resources Information Center

    Van Hoof, Jo; Verschaffel, Lieven; Van Dooren, Wim

    2017-01-01

    Background: Rational numbers are of critical importance both in mathematics and in other fields of science. However, they form a stumbling block for learners. One widely known source of the difficulty learners have with rational numbers is the natural number bias, that is the tendency to (inappropriately) apply natural number properties in…

  13. Number Sense in the Transition from Natural to Rational Numbers

    ERIC Educational Resources Information Center

    Van Hoof, Jo; Verschaffel, Lieven; Van Dooren, Wim

    2017-01-01

    Background: Rational numbers are of critical importance both in mathematics and in other fields of science. However, they form a stumbling block for learners. One widely known source of the difficulty learners have with rational numbers is the natural number bias, that is the tendency to (inappropriately) apply natural number properties in…

  14. Number Games, Magnitude Representation, and Basic Number Skills in Preschoolers

    ERIC Educational Resources Information Center

    Whyte, Jemma Catherine; Bull, Rebecca

    2008-01-01

    The effect of 3 intervention board games (linear number, linear color, and nonlinear number) on young children's (mean age = 3.8 years) counting abilities, number naming, magnitude comprehension, accuracy in number-to-position estimation tasks, and best-fit numerical magnitude representations was examined. Pre- and posttest performance was…

  15. [Intel random number generator-based true random number generator].

    PubMed

    Huang, Feng; Shen, Hong

    2004-09-01

    To establish a true random number generator on the basis of certain Intel chips. The random numbers were acquired by programming using Microsoft Visual C++ 6.0 via register reading from the random number generator (RNG) unit of an Intel 815 chipset-based computer with Intel Security Driver (ISD). We tested the generator with 500 random numbers in NIST FIPS 140-1 and X(2) R-Squared test, and the result showed that the random number it generated satisfied the demand of independence and uniform distribution. We also compared the random numbers generated by Intel RNG-based true random number generator and those from the random number table statistically, by using the same amount of 7500 random numbers in the same value domain, which showed that the SD, SE and CV of Intel RNG-based random number generator were less than those of the random number table. The result of u test of two CVs revealed no significant difference between the two methods. Intel RNG-based random number generator can produce high-quality random numbers with good independence and uniform distribution, and solves some problems with random number table in acquisition of the random numbers.

  16. Number theory meets high energy physics

    NASA Astrophysics Data System (ADS)

    Todorov, Ivan

    2017-03-01

    Feynman amplitudes in perturbative quantum field theory are being expressed in terms of an algebra of functions, extending the familiar logarithms, and associated numbers— periods. The study of these functions (including hyperlogarithms) and numbers (like the multiple zeta values), that dates back to Leibniz and Euler, has attracted anew the interest of algebraic geometers and number theorists during the last decades. The two originally independent developments are recently coming together in an unlikely collaboration between particle physics and what were regarded as the most abstruse branches of mathematics.

  17. Gene copy number and malaria biology

    PubMed Central

    Anderson, Tim J.C.; Patel, Jigar; Ferdig, Michael T.

    2010-01-01

    Alteration in gene copy number provides a simple way to change expression levels and alter phenotype. This was fully appreciated by bacteriologists more than 25 years ago, but the extent and implications of copy number polymorphism (CNP) have only recently become apparent in other organisms. New methods demonstrate the ubiquity of CNPs in eukaryotes and their medical importance in humans. CNP is also widespread in the Plasmodium falciparum genome and has an important and underappreciated role in determining phenotype. In this review, we summarize the distribution of CNP, its evolutionary dynamics within populations, its functional importance and its mode of evolution. PMID:19559648

  18. Parametric number covariance in quantum chaotic spectra.

    PubMed

    Vinayak; Kumar, Sandeep; Pandey, Akhilesh

    2016-03-01

    We study spectral parametric correlations in quantum chaotic systems and introduce the number covariance as a measure of such correlations. We derive analytic results for the classical random matrix ensembles using the binary correlation method and obtain compact expressions for the covariance. We illustrate the universality of this measure by presenting the spectral analysis of the quantum kicked rotors for the time-reversal invariant and time-reversal noninvariant cases. A local version of the parametric number variance introduced earlier is also investigated.

  19. Representing Numbers: Prime and Irrational

    ERIC Educational Resources Information Center

    Zazkis, Rina

    2005-01-01

    This article draws an analogy between prime and irrational numbers with respect to how these numbers are defined and how they are perceived by learners. Excerpts are presented from two research studies: a study on understanding prime numbers by pre-service elementary school teachers and a study on understanding irrational numbers by pre-service…

  20. New expressions to describe solution nonideal osmotic pressure, freezing point depression, and vapor pressure.

    PubMed

    Fullerton, G D; Zimmerman, R J; Cantu, C; Cameron, I L

    1992-12-01

    New empirical expressions for osmotic pressure, freezing point depression, and vapor pressure are proposed based on the concepts of volume occupancy and (or) hydration force. These expressions are in general inverse relationships in comparison to the standard ideal expressions for the same properties. The slopes of the new equations are determined by the molecular weight of the solute and known constants. The accuracy and precision of the molecular weights calculated from the slope are identical and approximately 1% for the experiments reported here. The nonideality of all three colligative expressions is described by a dimensionless constant called the solute-solvent interaction parameter I. The results on sucrose have the same I = 0.26 for all three solution properties. The nonideality parameter I increased from 0.26 on sucrose to 1.7 on hemoglobin to successfully describe the well-known nonideal response of macromolecules.

  1. Turbulent Skin Friction at High Mach Numbers and Reynolds Numbers

    NASA Technical Reports Server (NTRS)

    Matting, Fred W.; Chapman, Dean R.

    1958-01-01

    For a number of years now, experimenters have been making measurements of skin friction. Formerly, the main interest was at low Mach numbers; later, measurements were made at supersonic Mach numbers. However, almost all of these measurements were over a limited range of Reynolds numbers. On the other hand, these measurements fairly well determined the effects of Mach number and heat transfer on skin friction. The purpose of this paper is to give the results of skin-friction measurements in turbulent boundary layers at high Mach numbers and high Reynolds numbers where data have not previously existed. The equipment used was expressly designed to provide these conditions. As is well known, it is difficult to obtain high Mach numbers and high Reynolds numbers simultaneously with air in a wind tunnel. In order to avoid condensation, it is necessary to heat the air, with a resulting loss in density and Reynolds number. It is desirable, then, to use a gas that does not condense at high Mach numbers. This suggested helium, which was used as a working fluid in some of the tests. At high Mach numbers in a given wind tunnel, higher Reynolds numbers can be obtained with helium than with air, principally because no heating of the helium is required. The different ratios of specific heats also contribute to the increase. In using helium as a working fluid, it is, of course, necessary to determine the equivalence of air and helium in the turbulent boundary layer.

  2. 15. Stress Sheet, Truss number 2, span number 6, Superior ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    15. Stress Sheet, Truss number 2, span number 6, Superior Avenue viaduct. Drawing courtesy Engineering Dept., City of Cleveland. - Superior Avenue Viaduct, Cleveland East & West side, Cuyahoga Valley Vicinity, Cleveland, Cuyahoga County, OH

  3. Lattice animals on a staircase and Fibonacci numbers

    NASA Astrophysics Data System (ADS)

    Turban, L.

    2000-04-01

    We study the statistics of column-convex lattice animals resulting from the stacking of squares on a single or double staircase. We obtain exact expressions for the number of animals with a given length and area, their mean length and their mean height. These objects are closely related to Fibonacci numbers. On a single staircase, the total number of animals with area k is given by the Fibonacci number Fk .

  4. Ordering of Z-numbers

    NASA Astrophysics Data System (ADS)

    Mohamad, Daud; Shaharani, Saidatull Akma; Kamis, Nor Hanimah

    2017-08-01

    The concept of Z-number which was introduced by Zadeh in 2010 has captured attention by many due to its enormous applications in the area of Computing with Words (CWW). A Z-number is an ordered pair of fuzzy numbers, (A, R), where A essentially plays the role of fuzzy restriction which is a real-valued uncertain variable and R is a measure of reliability of the first component. Besides its theoretical development, Z-numbers have been successfully applied to decision making problems under uncertain environment. In any decision making evaluation using Z-number, ideally the final outcome of the calculation should also be in Z-number. A question will arise: how do we order the Z-numbers so that the preference of the alternatives can be ranked appropriately? In this paper, we propose a method of ordering the Z-number via the transformation of the Z-numbers to fuzzy numbers. The Z-number will then be ranked using a ranking fuzzy number method. The proposed method will be tested in several combinations of Z-numbers to investigate its effectiveness. The effect of different values of A and R towards the ordering of Z-numbers is analyzed and discussed.

  5. Reynolds and froude number effect on the flow past an interface-piercing circular cylinder

    NASA Astrophysics Data System (ADS)

    Koo, Bonguk; Yang, Jianming; Yeon, Seong Mo; Stern, Frederick

    2014-09-01

    The two-phase turbulent flow past an interface-piercing circular cylinder is studied using a high-fidelity orthogonal curvilinear grid solver with a Lagrangian dynamic subgrid-scale model for large-eddy simulation and a coupled level set and volume of fluid method for air-water interface tracking. The simulations cover the sub-critical and critical and post critical regimes of the Reynolds and sub and super-critical Froude numbers in order to investigate the effect of both dimensionless parameters on the flow. Significant changes in flow features near the air-water interface were observed as the Reynolds number was increased from the sub-critical to the critical regime. The interface makes the separation point near the interface much delayed for all Reynolds numbers. The separation region at intermediate depths is remarkably reduced for the critical Reynolds number regime. The deep flow resembles the single-phase turbulent flow past a circular cylinder, but includes the effect of the free-surface and the limited span length for sub-critical Reynolds numbers. At different Froude numbers, the air-water interface exhibits significantly changed structures, including breaking bow waves with splashes and bubbles at high Froude numbers. Instantaneous and mean flow features such as interface structures, vortex shedding, Reynolds stresses, and vorticity transport are also analyzed. The results are compared with reference experimental data available in the literature. The deep flow is also compared with the single-phase turbulent flow past a circular cylinder in the similar ranges of Reynolds numbers. Discussion is provided concerning the limitations of the current simulations and available experimental data along with future research

  6. Natural Number Bias in Operations with Missing Numbers

    ERIC Educational Resources Information Center

    Christou, Konstantinos P.

    2015-01-01

    This study investigates the hypothesis that there is a natural number bias that influences how students understand the effects of arithmetical operations involving both Arabic numerals and numbers that are represented by symbols for missing numbers. It also investigates whether this bias correlates with other aspects of students' understanding of…

  7. Natural Number Bias in Operations with Missing Numbers

    ERIC Educational Resources Information Center

    Christou, Konstantinos P.

    2015-01-01

    This study investigates the hypothesis that there is a natural number bias that influences how students understand the effects of arithmetical operations involving both Arabic numerals and numbers that are represented by symbols for missing numbers. It also investigates whether this bias correlates with other aspects of students' understanding of…

  8. Toddlers' Spontaneous Attention to Number and Verbal Number Quantification

    ERIC Educational Resources Information Center

    Li, Xia

    2009-01-01

    "S"pontaneous "a"ttention to "n"umber (SAN) is the tendency to notice the relatively abstract attribute of number despite the presence of other attributes. According to nativists, an innate concept of one to three directs young children's attention to these "intuitive numbers" in everyday situations--even before they acquire language. According to…

  9. Irrational Numbers on the Number Line--Where Are They?

    ERIC Educational Resources Information Center

    Sirotic, N.; Zazkis, R.

    2007-01-01

    This paper reports part of an ongoing investigation into the understanding of irrational numbers by prospective secondary school teachers. It focuses on the representation of irrational numbers as points on a number line. In a written questionnaire, followed by a clinical interview, participants were asked to indicate the exact location of the…

  10. Introducing Number and Arithmetic Concepts with Number Sticks.

    ERIC Educational Resources Information Center

    Baroody, Arthur J.

    1993-01-01

    This article compares the relative merits of using Cuisenaire rods (unsegmented, unnumbered, and representing continuous quantities) and number sticks (segmented, numbered, and representing discrete quantities) to introduce number and arithmetic concepts to beginning students or students with learning difficulties or mental disabilities. (DB)

  11. Stability of the shape of a translating viscoelastic drop at low Reynolds number

    NASA Astrophysics Data System (ADS)

    Wu, H.; Haj-Hariri, H.; Borhan, A.

    2012-11-01

    We examine the stability of the shape of a viscoelastic drop translating in an immiscible, otherwise quiescent Newtonian fluid at low Reynolds number. Non-Newtonian stresses in the drop phase are characterized by the finitely extensible nonlinear elastic-Chilcott-Rallison model. A boundary integral method is used to numerically examine the time-evolution of initially perturbed drop shapes over a range of dimensionless parameters. For sufficiently small capillary numbers, the drop achieves an oblate spheroidal steady shape. For large initial deformations or capillary numbers, however, the drop deforms continuously and eventually breaks up through either the formation of an elongated tail or the development of a re-entrant cavity at its trailing end. These mechanisms of drop breakup are qualitatively similar to those reported earlier for Newtonian drops [C. J. Koh and L. G. Leal, Phys. Fluids A 1, 1309 (1989), 10.1063/1.857359; C. Pozrikidis, J. Fluid Mech. 210, 1 (1990), 10.1017/S0022112090001203; H. A. Stone, Annu. Rev. Fluid Mech. 26, 65 (1994), 10.1146/annurev.fl.26.010194.000433]. Compared to the case of a Newtonian drop, drop phase elasticity is found to have a stabilizing (destabilizing) effect for initially oblate (prolate) shape perturbations, due to the development of polymeric stresses caused by deformation of polymer chains in alignment with streamlines of the flow. Polymer viscosity has a strong influence on the stability of the shape of drops, whereas polymer relaxation time and extensibility have relatively weak influences.

  12. Number Tracks, Number Lines, Number Strips Are They All the Same?

    ERIC Educational Resources Information Center

    Iannone, Paola

    2006-01-01

    In this article, the author argues that there is a big conceptual difference between number lines and number strips and that number lines should be consistently used as early as Y1. Her interest in the use of the number line as a powerful image of the real numbers, and how this is introduced in the early years, comes from her own experience as a…

  13. A Laboratory Experiment on How to Create Dimensionless Correlations

    ERIC Educational Resources Information Center

    Edwards, Robert V.

    2010-01-01

    An experiment is described that illustrates how chemical engineering correlations are created. Balls of different diameters and different specific gravities (all less than one) are dropped from several heights into a pool of water, and the maximum depth reached by the ball is measured. This data is used to estimate the coefficients for a…

  14. On the Role of Dimensionless Elastic Fracture Mechanics.

    DTIC Science & Technology

    1985-07-03

    34.’ . . . .- . . - . . . - ... - . .. . . . . . -8-.V 6. B.M. Wundt , "A Unified Interpretation of Room Temperature Strength of Notched...Fracture mechanics technology applied to heavy section steel structures. Proc. Second Int. Conf. Fracture, Brighton, U.K., 825-850 (1969). J.G. Williams ...207s (1948). D.H. Winne and B.M. Wundt , Application of the Griffith-Irwin theory of crack propagation to the bursting behavior of disks, including

  15. Dimensionless form for Goodwin's equation of business cycle

    NASA Astrophysics Data System (ADS)

    Antonova, A. O.; Reznik, S. N.; Todorov, M. D.

    2012-10-01

    We have conducted numerically a comparative analysis of two models of the business cycle proposed by R. Goodwin, Econometrica, 19, 1-17 (1951): in form of the neutral differential equation with fixed delay and in form of the second order nonlinear ordinary differential equation. Both models demonstrate the possibility of oscillations of income (so-called Goodwin's oscillations). We have shown that for these models the excitation conditions for Goodwin's oscillations and the some its properties may be very different.

  16. A Laboratory Experiment on How to Create Dimensionless Correlations

    ERIC Educational Resources Information Center

    Edwards, Robert V.

    2010-01-01

    An experiment is described that illustrates how chemical engineering correlations are created. Balls of different diameters and different specific gravities (all less than one) are dropped from several heights into a pool of water, and the maximum depth reached by the ball is measured. This data is used to estimate the coefficients for a…

  17. Relating Mason number to Bingham number in magnetorheological fluids

    NASA Astrophysics Data System (ADS)

    Sherman, Stephen G.; Becnel, Andrew C.; Wereley, Norman M.

    2015-04-01

    Magnetorheological (MR) fluids are described using two nondimensional numbers, the Bingham and Mason numbers. The Mason number is the ratio of particle magnetic forces to viscous forces and describes the behavior of MR fluids at the microscopic, particle level scale. At the macroscopic, continuum scale, Bingham number is the ratio of yield stress to viscous stress, and describes the bulk motion of the fluid. If these two nondimensional numbers can be related, then microscopic models can be directly compared to macroscopic results. We show that if microscopic and macroscopic forces are linearly related, then Bingham and Mason number are inversely related, or, alternatively, that the product of the Bingham number and the Mason number is a constant. This relationship is experimentally validated based on measurements of apparent viscosity on a high shear rate, γ ˙ ≈ 10 000s-1, Searle cell rheometer. This relationship between Mason number and Bingham number is then used to analyze a Mason number based result, and is also used to inform the MR fluid device design process.

  18. Number games, magnitude representation, and basic number skills in preschoolers.

    PubMed

    Whyte, Jemma Catherine; Bull, Rebecca

    2008-03-01

    The effect of 3 intervention board games (linear number, linear color, and nonlinear number) on young children's (mean age = 3.8 years) counting abilities, number naming, magnitude comprehension, accuracy in number-to-position estimation tasks, and best-fit numerical magnitude representations was examined. Pre- and posttest performance was compared following four 25-min intervention sessions. The linear number board game significantly improved children's performance in all posttest measures and facilitated a shift from a logarithmic to a linear representation of numerical magnitude, emphasizing the importance of spatial cues in estimation. Exposure to the number card games involving nonsymbolic magnitude judgments and association of symbolic and nonsymbolic quantities, but without any linear spatial cues, improved some aspects of children's basic number skills but not numerical estimation precision.

  19. Identifying Fractions on Number Lines.

    ERIC Educational Resources Information Center

    Bright, George W.; And Others

    1988-01-01

    This study investigated the ways students represented fractions on number lines and the effects of instruction on those representations. The instruction primarily concerned representing fractions and ordering fractions on number lines. (Author/PK)

  20. The Mental Number Line in Dyscalculia: Impaired Number Sense or Access From Symbolic Numbers?

    PubMed

    Lafay, Anne; St-Pierre, Marie-Catherine; Macoir, Joël

    2016-03-25

    Numbers may be manipulated and represented mentally over a compressible number line oriented from left to right. According to numerous studies, one of the primary reasons for dyscalculia is related to improper understanding of the mental number line. Children with dyscalculia usually show difficulty when they have to place Arabic numbers on a physical number line. However, it remains unclear whether they have a deficit with the mental number line per se or a deficit with accessing it from nonsymbolic and/or symbolic numbers. Quebec French-speaking 8- to 9-year-old children with (24) and without (37) dyscalculia were assessed with transcoding tasks (number-to-positionandposition-to-number) designed to assess the acuity of the mental number line with Arabic and spoken numbers as well as with analogic numerosities. Results showed that children with dyscalculia produced a larger percentage absolute error than children without mathematics difficulties in every task except the number-to-position transcoding task with analogic numerosities. Hence, these results suggested that children with dyscalculia do not have a general deficit of the mental number line but rather a deficit with accessing it from symbolic numbers. © Hammill Institute on Disabilities 2016.

  1. Random Numbers and Quantum Computers

    ERIC Educational Resources Information Center

    McCartney, Mark; Glass, David

    2002-01-01

    The topic of random numbers is investigated in such a way as to illustrate links between mathematics, physics and computer science. First, the generation of random numbers by a classical computer using the linear congruential generator and logistic map is considered. It is noted that these procedures yield only pseudo-random numbers since…

  2. A Lesson in Number Pattern

    ERIC Educational Resources Information Center

    Fletcher, Rodney

    2008-01-01

    This article presents a guided investigation into the spacial relationships between the centres of the squares in a Fibonacci tiling. It is essentially a lesson in number pattern, but includes work with surds, coordinate geometry, and some elementary use of complex numbers. The investigation could be presented to students in a number of ways…

  3. Numbers and Math. Beginnings Workshop.

    ERIC Educational Resources Information Center

    Gross, Fred E.; Elkind, CavidEpstein, Ann S.; Copley, Juanita V.; Haugen, Ginny; Haugen, Kirsten

    2003-01-01

    Presents five articles addressing numbers and math instruction for young children: "Math Talk with Young Children: One Parent's Experience" (Fred E. Gross); "How Children Build Their Understanding of Numbers" (David Elkind); "Early Math: It's More than Numbers" (Ann S. Epstein); "Assessing Mathematical Learning: Observing and Listening to…

  4. Linear or Exponential Number Lines

    ERIC Educational Resources Information Center

    Stafford, Pat

    2011-01-01

    Having decided to spend some time looking at one's understanding of numbers, the author was inspired by "Alex's Adventures in Numberland," by Alex Bellos to look at one's innate appreciation of number. Bellos quotes research studies suggesting that an individual's natural appreciation of numbers is more likely to be exponential rather…

  5. Simple Remarks on Carmichael Numbers

    NASA Astrophysics Data System (ADS)

    Uchiyama, Shigenori

    An odd composite number n for which an-1 ≡ 1 (mod n) for all integers a coprime to n is called a Carmichael number. This paper shows that some class of Carmichael numbers which have relatively large prime factors can be recognized in deterministic polynomial time under the assumption of the Extended Riemann Hypothesis (ERH). Also some related problems are discussed.

  6. Numbers and Math. Beginnings Workshop.

    ERIC Educational Resources Information Center

    Gross, Fred E.; Elkind, CavidEpstein, Ann S.; Copley, Juanita V.; Haugen, Ginny; Haugen, Kirsten

    2003-01-01

    Presents five articles addressing numbers and math instruction for young children: "Math Talk with Young Children: One Parent's Experience" (Fred E. Gross); "How Children Build Their Understanding of Numbers" (David Elkind); "Early Math: It's More than Numbers" (Ann S. Epstein); "Assessing Mathematical Learning: Observing and Listening to…

  7. Three Cubes in One Number

    ERIC Educational Resources Information Center

    Jue, Brian

    2010-01-01

    Separate a three-digit number into its component digits. After raising each digit to the third power and computing the sum of the cubes, determine how often the original number reappears. Modular arithmetic is used to reduce the number of potential solutions to a more manageable quantity. (Contains 4 tables.)

  8. Random Numbers and Quantum Computers

    ERIC Educational Resources Information Center

    McCartney, Mark; Glass, David

    2002-01-01

    The topic of random numbers is investigated in such a way as to illustrate links between mathematics, physics and computer science. First, the generation of random numbers by a classical computer using the linear congruential generator and logistic map is considered. It is noted that these procedures yield only pseudo-random numbers since…

  9. What Exactly Do Numbers Mean?

    ERIC Educational Resources Information Center

    Huang, Yi Ting; Spelke, Elizabeth; Snedeker, Jesse

    2013-01-01

    Number words are generally used to refer to the exact cardinal value of a set, but cognitive scientists disagree about their meanings. Although most psychological analyses presuppose that numbers have exact semantics ("two" means exactly two), many linguistic accounts propose that numbers have lower-bounded semantics (at least two), and…

  10. Linear or Exponential Number Lines

    ERIC Educational Resources Information Center

    Stafford, Pat

    2011-01-01

    Having decided to spend some time looking at one's understanding of numbers, the author was inspired by "Alex's Adventures in Numberland," by Alex Bellos to look at one's innate appreciation of number. Bellos quotes research studies suggesting that an individual's natural appreciation of numbers is more likely to be exponential rather…

  11. Cognitive representation of negative numbers.

    PubMed

    Fischer, Martin H

    2003-05-01

    To understand negative numbers, must we refer to positive number representations (the phylogenetic hypothesis), or do we acquire a negative mental number line (the ontogenetic hypothesis)? In the experiment reported here, participants made lateralized button responses to indicate the larger of two digits from the range -9 to 9. Digit pairs were displayed spatially congruent or incongruent with either a phylogenetic or an ontogenetic mental number line. The pattern of decision latencies suggests that negative numbers become associated with left space, thus supporting the ontogenetic view.

  12. Generalized Bernoulli-Hurwitz numbers and the universal Bernoulli numbers

    NASA Astrophysics Data System (ADS)

    Ônishi, Yoshihiro

    2011-10-01

    The three fundamental properties of the Bernoulli numbers, namely, the von Staudt-Clausen theorem, von Staudt's second theorem, and Kummer's original congruence, are generalized to new numbers that we call generalized Bernoulli-Hurwitz numbers. These are coefficients in the power series expansion of a higher-genus algebraic function with respect to a suitable variable. Our generalization differs strongly from previous works. Indeed, the order of the power of the modulus prime in our Kummer-type congruences is exactly the same as in the trigonometric function case (namely, Kummer's own congruence for the original Bernoulli numbers), and as in the elliptic function case (namely, H. Lang's extension for the Hurwitz numbers). However, in other past results on higher-genus algebraic functions, the modulus was at most half of its value in these classical cases. This contrast is clarified by investigating the analogue of the three properties above for the universal Bernoulli numbers. Bibliography: 34 titles.

  13. Quantum random number generator using photon-number path entanglement

    NASA Astrophysics Data System (ADS)

    Kwon, Osung; Cho, Young-Wook; Kim, Yoon-Ho

    2010-08-01

    We report an experimental implementation of quantum random number generator based on the photon-number-path entangled state. The photon-number-path entangled state is prepared by means of two-photon Hong-Ou-Mandel quantum interference at a beam splitter. The randomness in our scheme is of truly quantum mechanical origin as it comes from the projection measurement of the entangled two-photon state. The generated bit sequences satisfy the standard randomness test.

  14. Approximate Number Sense, Symbolic Number Processing, or Number-Space Mappings: What Underlies Mathematics Achievement?

    ERIC Educational Resources Information Center

    Sasanguie, Delphine; Gobel, Silke M.; Moll, Kristina; Smets, Karolien; Reynvoet, Bert

    2013-01-01

    In this study, the performance of typically developing 6- to 8-year-old children on an approximate number discrimination task, a symbolic comparison task, and a symbolic and nonsymbolic number line estimation task was examined. For the first time, children's performances on these basic cognitive number processing tasks were explicitly contrasted…

  15. Betti Numbers of Gaussian Fields

    NASA Astrophysics Data System (ADS)

    Park, Changbom; Pranav, Pratyush; Chingangbam, Pravabati; van de Weygaert, Rien; Jones, Bernard; Vegter, Gert; Kim, Inkang; Hidding, Johan; Hellwing, Wojciech A.

    2013-06-01

    We present the relation between the genus in cosmology and the Betti numbers for excursion sets of three- and two-dimensional smooth Gaussian random fields, and numerically investigate the Betti numbers as a function of threshold level. Betti numbers are topological invariants of figures that can be used to distinguish topological spaces. In the case of the excursion sets of a three-dimensional field there are three possibly non-zero Betti numbers; β_0 is the number of connected regions, β_1 is the number of circular holes (i.e., complement of solid tori), and β_2 is the number of three-dimensional voids (i.e., complement of three-dimensional excursion regions). Their sum with alternating signs is the genus of the surface of excursion regions. It is found that each Betti number has a dominant contribution to the genus in a specific threshold range. β_0 dominates the high-threshold part of the genus curve measuring the abundance of high density regions (clusters). β_1 dominates the genus near the median thresholds which measures the topology of negatively curved iso-density surfaces, and β_2 corresponds to the low-threshold part measuring the void abundance. We average the Betti number curves (the Betti numbers as a function of the threshold level) over many realizations of Gaussian fields and find that both the amplitude and shape of the Betti number curves depend on the slope of the power spectrum n in such a way that their shape becomes broader and their amplitude drops less steeply than the genus as n decreases. This behaviour contrasts with the fact that the shape of the genus curve is fixed for all Gaussian fields regardless of the power spectrum. Even though the Gaussian Betti number curves should be calculated for each given power spectrum, we propose to use the Betti numbers for better specification of the topology of large scale structures in the universe.

  16. Catalan Numbers, the Hankel Transform, and Fibonacci Numbers

    NASA Astrophysics Data System (ADS)

    Cvetkovic, Aleksandar; Rajkovic, Predrag; Ivkovic, Milos

    2002-05-01

    We prove that the Hankel transformation of a sequence whose elements are the sums of two adjacent Catalan numbers is a subsequence of the Fibonacci numbers. This is done by finding the explicit form for the coefficients in the three-term recurrence relation that the corresponding orthogonal polynomials satisfy.

  17. Schizophrenia copy number variants and associative learning.

    PubMed

    Clifton, N E; Pocklington, A J; Scholz, B; Rees, E; Walters, J T R; Kirov, G; O'Donovan, M C; Owen, M J; Wilkinson, L S; Thomas, K L; Hall, J

    2017-02-01

    Large-scale genomic studies have made major progress in identifying genetic risk variants for schizophrenia. A key finding from these studies is that there is an increased burden of genomic copy number variants (CNVs) in schizophrenia cases compared with controls. The mechanism through which these CNVs confer risk for the symptoms of schizophrenia, however, remains unclear. One possibility is that schizophrenia risk CNVs impact basic associative learning processes, abnormalities of which have long been associated with the disorder. To investigate whether genes in schizophrenia CNVs impact on specific phases of associative learning we combined human genetics with experimental gene expression studies in animals. In a sample of 11 917 schizophrenia cases and 16 416 controls, we investigated whether CNVs from patients with schizophrenia are enriched for genes expressed during the consolidation, retrieval or extinction of associative memories. We show that CNVs from cases are enriched for genes expressed during fear extinction in the hippocampus, but not genes expressed following consolidation or retrieval. These results suggest that CNVs act to impair inhibitory learning in schizophrenia, potentially contributing to the development of core symptoms of the disorder.

  18. Schizophrenia copy number variants and associative learning

    PubMed Central

    Clifton, N E; Pocklington, A J; Scholz, B; Rees, E; Walters, J T R; Kirov, G; O'Donovan, M C; Owen, M J; Wilkinson, L S; Thomas, K L; Hall, J

    2017-01-01

    Large-scale genomic studies have made major progress in identifying genetic risk variants for schizophrenia. A key finding from these studies is that there is an increased burden of genomic copy number variants (CNVs) in schizophrenia cases compared with controls. The mechanism through which these CNVs confer risk for the symptoms of schizophrenia, however, remains unclear. One possibility is that schizophrenia risk CNVs impact basic associative learning processes, abnormalities of which have long been associated with the disorder. To investigate whether genes in schizophrenia CNVs impact on specific phases of associative learning we combined human genetics with experimental gene expression studies in animals. In a sample of 11 917 schizophrenia cases and 16 416 controls, we investigated whether CNVs from patients with schizophrenia are enriched for genes expressed during the consolidation, retrieval or extinction of associative memories. We show that CNVs from cases are enriched for genes expressed during fear extinction in the hippocampus, but not genes expressed following consolidation or retrieval. These results suggest that CNVs act to impair inhibitory learning in schizophrenia, potentially contributing to the development of core symptoms of the disorder. PMID:27956746

  19. What exactly do numbers mean?

    PubMed Central

    Huang, Yi Ting; Spelke, Elizabeth; Snedeker, Jesse

    2014-01-01

    Number words are generally used to refer to the exact cardinal value of a set, but cognitive scientists disagree about their meanings. Although most psychological analyses presuppose that numbers have exact semantics (two means EXACTLY TWO), many linguistic accounts propose that numbers have lower-bounded semantics (AT LEAST TWO), and that speakers restrict their reference through a pragmatic inference (scalar implicature). We address this debate through studies of children who are in the process of acquiring the meanings of numbers. Adults and 2- and 3-year-olds were tested in a novel paradigm that teases apart semantic and pragmatic aspects of interpretation (the covered box task). Our findings establish that when scalar implicatures are cancelled in the critical trials of this task, both adults and children consistently give exact interpretations for number words. These results, in concert with recent work on real-time processing, provide the first unambiguous evidence that number words have exact semantics. PMID:25285053

  20. Dynamic Virtual Credit Card Numbers

    NASA Astrophysics Data System (ADS)

    Molloy, Ian; Li, Jiangtao; Li, Ninghui

    Theft of stored credit card information is an increasing threat to e-commerce. We propose a dynamic virtual credit card number scheme that reduces the damage caused by stolen credit card numbers. A user can use an existing credit card account to generate multiple virtual credit card numbers that are either usable for a single transaction or are tied with a particular merchant. We call the scheme dynamic because the virtual credit card numbers can be generated without online contact with the credit card issuers. These numbers can be processed without changing any of the infrastructure currently in place; the only changes will be at the end points, namely, the card users and the card issuers. We analyze the security requirements for dynamic virtual credit card numbers, discuss the design space, propose a scheme using HMAC, and prove its security under the assumption the underlying function is a PRF.