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Sample records for field slab gel

  1. Optimization of separation and detection schemes for DNA with pulsed field slab gel and capillary electrophoresis

    SciTech Connect

    McGregor, D.A.

    1993-07-01

    The purpose of the Human Genome Project is outlined followed by a discussion of electrophoresis in slab gels and capillaries and its application to deoxyribonucleic acid (DNA). Techniques used to modify electroosmotic flow in capillaries are addressed. Several separation and detection schemes for DNA via gel and capillary electrophoresis are described. Emphasis is placed on the elucidation of DNA fragment size in real time and shortening separation times to approximate real time monitoring. The migration of DNA fragment bands through a slab gel can be monitored by UV absorption at 254 nm and imaged by a charge coupled device (CCD) camera. Background correction and immediate viewing of band positions to interactively change the field program in pulsed-field gel electrophoresis are possible throughout the separation. The use of absorption removes the need for staining or radioisotope labeling thereby simplifying sample preparation and reducing hazardous waste generation. This leaves the DNA in its native state and further analysis can be performed without de-staining. The optimization of several parameters considerably reduces total analysis time. DNA from 2 kb to 850 kb can be separated in 3 hours on a 7 cm gel with interactive control of the pulse time, which is 10 times faster than the use of a constant field program. The separation of {Phi}X174RF DNA-HaeIII fragments is studied in a 0.5% methyl cellulose polymer solution as a function of temperature and applied voltage. The migration times decreased with both increasing temperature and increasing field strength, as expected. The relative migration rates of the fragments do not change with temperature but are affected by the applied field. Conditions were established for the separation of the 271/281 bp fragments, even without the addition of intercalating agents. At 700 V/cm and 20{degrees}C, all fragments are separated in less than 4 minutes with an average plate number of 2.5 million per meter.

  2. Hybrid slab-microchannel gel electrophoresis system

    DOEpatents

    Balch, Joseph W.; Carrano, Anthony V.; Davidson, James C.; Koo, Jackson C.

    1998-01-01

    A hybrid slab-microchannel gel electrophoresis system. The hybrid system permits the fabrication of isolated microchannels for biomolecule separations without imposing the constraint of a totally sealed system. The hybrid system is reusable and ultimately much simpler and less costly to manufacture than a closed channel plate system. The hybrid system incorporates a microslab portion of the separation medium above the microchannels, thus at least substantially reducing the possibility of non-uniform field distribution and breakdown due to uncontrollable leakage. A microslab of the sieving matrix is built into the system by using plastic spacer materials and is used to uniformly couple the top plate with the bottom microchannel plate.

  3. A Simple Vertical Slab Gel Electrophoresis Apparatus.

    ERIC Educational Resources Information Center

    Carter, J. B.; And Others

    1983-01-01

    Describes an inexpensive, easily constructed, and safe vertical slab gel kit used routinely for sodium dodecyl sulphate-polyacrylamide gel electrophoresis research and student experiments. Five kits are run from a single transformer. Because toxic solutions are used, students are given plastic gloves and closely supervised during laboratory…

  4. Hybrid slab-microchannel gel electrophoresis system

    DOEpatents

    Balch, J.W.; Carrano, A.V.; Davidson, J.C.; Koo, J.C.

    1998-05-05

    A hybrid slab-microchannel gel electrophoresis system is described. The hybrid system permits the fabrication of isolated microchannels for biomolecule separations without imposing the constraint of a totally sealed system. The hybrid system is reusable and ultimately much simpler and less costly to manufacture than a closed channel plate system. The hybrid system incorporates a microslab portion of the separation medium above the microchannels, thus at least substantially reducing the possibility of non-uniform field distribution and breakdown due to uncontrollable leakage. A microslab of the sieving matrix is built into the system by using plastic spacer materials and is used to uniformly couple the top plate with the bottom microchannel plate. 4 figs.

  5. Polyacrylamide Slab Gel Electrophoresis of Soluble Proteins for Studies of Bacterial Floras

    PubMed Central

    Moore, W. E. C.; Hash, D. E.; Holdeman, Lillian V.; Cato, Elizabeth P.

    1980-01-01

    A polyacrylamide slab gel electrophoresis procedure was used to compare cellular proteins from bacterial isolates of gingival crevice floras. Isolates with identical protein patterns consistently were shown to be members of the same species. When used to screen isolates, the procedure reduced total analytical time and expense without sacrificing accuracy, and it provided additional verification of the identity of strains characterized by conventional phenotypic tests. Images PMID:16345555

  6. Differentiation of Campylobacter species by protein banding patterns in polyacrylamide slab gels.

    PubMed Central

    Ferguson, D A; Lambe, D W

    1984-01-01

    Soluble protein extracts of 37 catalase-positive strains of Campylobacter species were examined by polyacrylamide slab gel electrophoresis (PAGE). Electrophoretic banding patterns showed good correlation with biochemical tests and with available DNA homology data in distinguishing species of Campylobacter but did not differentiate subspecies or biotypes. PAGE patterns indicated that Campylobacter coli is a distinct species. Furthermore, the PAGE patterns indicated that C. jejuni and nalidixic acid-resistant thermophilic Campylobacter species (C. laridis) are each distinct species. The protein banding patterns of C. fetus subsp. venerealis and C. fetus subsp. fetus strains were distinctly different from those of the three thermophilic species. Images PMID:6490829

  7. Field Study and Numerical Simulation of Sub Slab Ventilation Systems

    SciTech Connect

    Bonnefous, Y.C.; Gadgil, A.J.; Fisk, W.J.; Prill, R.J.; Nematollahi, A.R.

    1992-05-01

    The effectiveness of the technique of subslab ventilation (SSV) for limiting radon entry into basements was investigated through complementary experimentation and numerical modeling. Subslab pressure fields resulting from SSV were measured in six well-characterized basements, each with a different combination of soil and aggregate permeability. The relationship between air velocity and pressure gradient was measured in the laboratory for the three types of aggregate installed beneath the basement slabs. A new numerical model of SSV was developed and verified with the field data. This model simulates non-Darcy flow in the aggregate. We demonstrate that non-Darcy effects significantly impact SSV performance. Field data and numerical simulations indicate that increasing the aggregate permeability within the investigated range of 2 x 10{sup -8} m{sup 2} to 3 x 10{sup -7} m{sup 2} substantially improves the extension of the subslab pressure field due to SSV operation. Sealing of cracks in the slab and excavation of a small pit where the SSV pipe penetrates the slab also dramatically improve this pressure field extension. Our findings are consistent with the results of prior field studies; however, the studies reported here have improved our understanding of factors affecting SSV performance. The dependence of SSV performance on the relevant parameters are currently under investigation with the model.

  8. The gravitational field of an infinite flat slab

    NASA Astrophysics Data System (ADS)

    Fulling, S. A.; Bouas, J. D.; Carter, H. B.

    2015-08-01

    We study Einstein's equations with a localized plane-symmetric source, with close attention to gauge freedom/fixing and to listing all physically distinct solutions. In the vacuum regions there are only two qualitatively different solutions, one curved and one flat; in addition, on each of the two sides there is a free parameter describing how the slab is embedded into the vacuum region. Surprisingly, for a generic slab source the solution must be curved on one side and flat on the other. We treat infinitely thin slabs in full detail and indicate how thick slabs can increase the variety of external geometry pairs. Positive energy density seems to force external geometries with curvature singularities at some distance from the slab; we speculate that such singularities occur in regions where the solution cannot be physically relevant anyway.

  9. Effects of triggering mechanism on snow avalanche slope angles and slab depths from field data

    NASA Astrophysics Data System (ADS)

    McClung, David M.

    2013-04-01

    Field data from snow avalanche fracture lines for slope angle and slab depth (measured perpendicular to the weak layer) were analyzed for different triggering mechanisms. For slope angle, the results showed that the same probability density function (pdf) (of log-logistic type) and range (25 - 55 degrees) apply independent of triggering mechanism. For slab depth, the same pdf (generalized extreme value) applies independent of triggering mechanism. For both slope angle and slab depth, the data skewness differentiated between triggering mechanism and increased with applied triggering load. For slope angle, skewness is lowest for natural triggering by snow loads and highest for triggering from human intervention. For slab depth, the skewness is lowest for natural triggering and highest for a mix of triggers including explosive control with skier triggering being intermediate. The results reveal the effects of triggering mechanism which are important for risk analyses and to guide avalanche forecasting.

  10. Pulsed field gel electrophoresis for dairy propionibacteria.

    PubMed

    Chuat, Victoria; de Freitas, Rosangela; Dalmasso, Marion

    2015-01-01

    Pulsed field gel electrophoresis (PFGE) is a technique using alternating electric fields to migrate high molecular weight DNA fragments with a high resolution. This method consists of the digestion of bacterial chromosomal DNA with rare-cutting restriction enzymes and in applying an alternating electrical current between spatially distinct pairs of electrodes. DNA molecules migrate at different speeds according to the size of the fragments. Among other things, this technique is considered as the "gold standard" for genotyping, genetic fingerprinting, epidemiological studies, genome size estimation, and studying radiation-induced DNA damage and repair. This chapter describes a PFGE method that can be used to differentiate dairy propionibacteria. PMID:25862063

  11. Optimization of electric field strength for DNA sequencing in capillary gel electrophoresis

    NASA Astrophysics Data System (ADS)

    Luckey, John A.; Smith, Lloyd M.

    1993-06-01

    Since its development, capillary gel electrophoresis has demonstrated the ability to separate DNA sequencing reactions at speeds roughly 25 times as great as conventional slab gel electrophoresis. These increased speeds are the result of using the more efficient dissipation of Joule heating by capillaries. However, to date there have been no studies which quantitate the advantages of disadvantages in operating these gels at high electric field strength. This work addresses this question by investigating the band-broadening of DNA sequencing reactions as they are separated through a fixed distance of gel at field strengths ranging from 50 V/cm to 400 V/cm. It is found that the bandwidths of DNA fragments do decrease with the higher field strengths due to a reduction in diffusional broadening. However, at sufficiently high electric field strengths, the bands begin to broaden again under the influence of an increasing thermal gradient across the diameter of the capillary. The result is an optimum electric field strength in the intermediate range of 100 - 250 V/cm depending on the length of fragments being separated. The relative importance of diffusion and thermal gradients are discussed and used to generate an equation that models the observed band broadening of DNA in capillary gel electrophoresis (CGE).

  12. High electric field measurement using slab-coupled optical sensors.

    PubMed

    Stan, Nikola; Seng, Frederick; Shumway, LeGrand; King, Rex; Selfridge, Richard; Schultz, Stephen

    2016-01-20

    A fiber-optic electric field sensor was developed to measure electric field up to 18 MV/m. The sensor uses resonant coupling between an optical fiber and a nonlinear electro-optical crystal. The sensing system uses high dielectric strength materials to eliminate dielectric breakdown. A postprocessing nonlinear calibration method is developed that maps voltage change to wavelength shift and then converts the wavelength shift to electric field using the transmission spectrum. The nonlinear calibration method is compared against the linear method with electric field pulses having magnitudes from 1.5 to 18 MV/m. PMID:26835936

  13. Electric field-induced deformation of polyelectrolyte gels

    SciTech Connect

    Adolf, D.; Hance, B.G.

    1995-08-01

    Water-swollen polyelectrolyte gels deform in an electric field. We observed that the sign and magnitude of the deformation is dependent on the nature of the salt bath in which the gel is immersed and electrocuted. These results are compatible with a deformation mechanism based upon creation of ion density gradients by the field which, in turn, creates osmotic pressure gradients within the gel. A consistent interpretation results only if gel mobility is allowed as well as free ion diffusion and migration.

  14. Stacking gels: A method for maximising output for pulsed-field gel electrophoresis.

    PubMed

    Heng, See Kah; Heng, Chua Kek; Puthucheary, S D

    2009-01-01

    Pulsed field gel electrophoresis (PFGE), the gold standard of molecular typing methods, has a major disadvantage of an unusually long electrophoretic time. From the original protocol of 6 days, it was modified to 3 days and subsequently to a single day. We describe the procedure of stacking five to six gels one on top of another in order to increase and maximize the output in a shorter time without compromising the resolution and reproducibility. All the variables that affect pulsed field gels during electrophoresis were taken into consideration. We firstly optimized the parameters to be used and secondly determined whether stacking of five to six gels had any effect on the molecular separation during electrophoresis in comparison with a single gel run. DNA preparation, restriction, electrophoresis, staining and gel documentation was carried out based on previously published methods. Gels were analysed using BioNumerics and dice coefficient and unweighted pair group methods were used to generate dendrograms based on 1.5% tolerance values. Identical band profiles and band resolution-separation were seen in the PFGE patterns with single gel and multiple stacking gels. Cluster analysis further strengthened the fact that results from stacking gels were reproducible and comparable with a single gel run. This method of stacking gels saves time and maximizes the output at the same time. The run time for a single gel was about 28 hours, but with six stacked gels the run time was 54 hours compared with 28 x 6 = 168 hours if they were run separately as single gels thus saving time of 67.86%. Beside the big factor of saving time, stacking gels save resources (electricity, reagents, water, chemicals and working time) by increasing the sample throughput in a shorter time without compromising on quality of data. But optimization of working parameters is vital depending on the PFGE system used. PMID:19384038

  15. Sub-slab pressure field extension in schools and other large buildings

    NASA Astrophysics Data System (ADS)

    Harris, D. B.; Craig, A. B.; Leovic, K. W.

    1991-09-01

    The experiences of EPA are discussed in using pressure field extension (PFE) to design active subslab depressurization (ASD) systems to reduce radon levels in old and new schools, including instances where the data collected resulted in the installation of smaller systems than expected and selection of high vacuum fans instead of normal mitigation fans. A central collection system for use under very large slabs is discussed and PFE data are given for a hospital under construction. The most direct method of projecting or measuring the performance of an ASD system is to measure the strength and extent of the pressure field established under the slab. The PFE can be determined (during diagnostics) to help design an ASD system and (following installation) to ascertain system performance. In schools and other large buildings, these data are invaluable to provide a system that will mitigate the building without undue cost escalation.

  16. Effects of magnetic field on the interaction between terahertz wave and non-uniform plasma slab

    NASA Astrophysics Data System (ADS)

    Tian, Yuan; Ai, Xia; Han, YiPing; Guo, LiXin

    2015-10-01

    In this paper, the interaction between terahertz electromagnetic wave and a non-uniform magnetized plasma slab is investigated. Different from most of the published literatures, the plasma employed in this work is inhomogeneous in both collision frequency and electron density. Profiles are introduced to describe the non-uniformity of the plasma slab. At the same time, magnetic field is applied to the background of the plasma slab. It came out with an interesting phenomenon that there would be a valley in the absorption band as the plasma's electromagnetic characteristic is affected by the magnetic field. In addition, the valley located just near the middle of the absorption peak. The cause of the valley's appearance is inferred in this paper. And the influences of the variables, such as magnetic field strength, electron density, and collision frequency, are discussed in detail. The objective of this work is also pointed out, such as the applications in flight communication, stealth, emissivity, plasma diagnose, and other areas of plasma.

  17. Effects of magnetic field on the interaction between terahertz wave and non-uniform plasma slab

    SciTech Connect

    Tian, Yuan; Han, YiPing; Guo, LiXin; Ai, Xia

    2015-10-15

    In this paper, the interaction between terahertz electromagnetic wave and a non-uniform magnetized plasma slab is investigated. Different from most of the published literatures, the plasma employed in this work is inhomogeneous in both collision frequency and electron density. Profiles are introduced to describe the non-uniformity of the plasma slab. At the same time, magnetic field is applied to the background of the plasma slab. It came out with an interesting phenomenon that there would be a valley in the absorption band as the plasma's electromagnetic characteristic is affected by the magnetic field. In addition, the valley located just near the middle of the absorption peak. The cause of the valley's appearance is inferred in this paper. And the influences of the variables, such as magnetic field strength, electron density, and collision frequency, are discussed in detail. The objective of this work is also pointed out, such as the applications in flight communication, stealth, emissivity, plasma diagnose, and other areas of plasma.

  18. Self-consistent solution for a collisionless plasma slab in motion across a magnetic field

    SciTech Connect

    Echim, Marius M.; Lemaire, Joseph F.; Roth, Michel

    2005-07-15

    The problem of the dynamics of a plasma slab moving across a magnetic field is treated in the framework of the kinetic theory. A velocity distribution function (VDF) is found for each plasma species, electrons and protons, in terms of the constants of motion defined by the geometry of the problem. The zero- and first-order moments of the VDF are introduced into the right-hand side term of Maxwell's equations to compute the electric and magnetic vector potentials and corresponding fields. The solutions are found numerically. We obtain a region of plasma convection--the slab proper--where the plasma moves with a uniform velocity, V{sub x}=V{sub 0}=(ExB/B{sup 2}){sub x}. At the core margins two plasma 'wings' are formed, each being the result of a pair of interpenetrated boundary layers with different transition lengths. Inside these wings, the plasma velocity is not uniform, V{sub x}{ne}(ExB/B{sup 2}){sub x}. It decreases from the maximum value obtained in the core to a minimum value in the central region of the wings where a flow reversal is found with the plasma convecting in the opposite direction to the core motion. There is also an asymmetry of the velocity gradient at the borders of the core, which results in a corresponding asymmetry in the thickness of the wings. Furthermore, it is found that the reversed plasma flow in the thinner wing is larger than that in the broader wing. For a fixed direction of the magnetic field the two plasma wings interchange position with respect to the center of the slab when the plasma bulk velocity reverses sign.

  19. Tailoring of spectral response and spatial field distribution with corrugated photonic crystal slab.

    PubMed

    Gad, Raanan; Lau, Wah Tung; Nicholaou, Costa; Ahmadi, Soroosh; Sigal, Iliya; Levi, Ofer

    2015-08-15

    We report a new physical mechanism for simultaneous tuning of quality factors, spectral responses, and field distributions in photonic crystal slabs through removal of polarization mode degeneracy using a lattice of elliptical nano-holes. The quality factors in these structures can become higher than those obtained with much smaller circular nano-holes. Furthermore, the modes can be superimposed by either rotating or morphing the elliptical nano-holes into a corrugated grating. These findings will enable improved radiation-matter interaction in optical, microwave, and THZ frequencies along with enhanced opto-acoustic coupling. PMID:26274642

  20. Capacity degradation of field-tested silica gel samples

    NASA Astrophysics Data System (ADS)

    Penney, T. R.; Pesaran, A. A.; Thomas, T. M.

    1985-06-01

    Researchers at the Solar Energy Research Institute (SERI) have begun preliminary studies to quantify the effect of contamination of silica gel used in dehumidification processes of desiccant cooling systems. Sorption capacity degradation of field tested samples was measured, and the source of degradation was quantified using surface analysis experimental methods.

  1. Pulsed-field gel electrophoresis typing of Staphylococcus aureus isolates

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Pulsed-field gel electrophoresis (PFGE) is the most applied and effective genetic typing method for epidemiological studies and investigation of foodborne outbreaks caused by different pathogens, including Staphylococcus aureus. The technique relies on analysis of large DNA fragments generated by th...

  2. Tunable Lamb wave band gaps in two-dimensional magnetoelastic phononic crystal slabs by an applied external magnetostatic field.

    PubMed

    Zhou, Changjiang; Sai, Yi; Chen, Jiujiu

    2016-09-01

    This paper theoretically investigates the band gaps of Lamb mode waves in two-dimensional magnetoelastic phononic crystal slabs by an applied external magnetostatic field. With the assumption of uniformly oriented magnetization, an equivalent piezomagnetic material model is used. The effects of magnetostatic field on phononic crystals are considered carefully in this model. The numerical results indicate that the width of the first band gap is significantly changed by applying the external magnetic field with different amplitude, and the ratio between the maximum and minimum gap widths reaches 228%. Further calculations demonstrate that the orientation of the magnetic field obviously affects the width and location of the first band gap. The contactless tunability of the proposed phononic crystal slabs shows many potential applications of vibration isolation in engineering. PMID:27281285

  3. Field-Theoretic Studies of Nanostructured Triblock Polyelectrolyte Gels

    NASA Astrophysics Data System (ADS)

    Audus, Debra; Fredrickson, Glenn

    2012-02-01

    Recently, experimentalists have developed nanostructured, reversible gels formed from triblock polyelectrolytes (Hunt et al. 2011, Lemmers et al. 2010, 2011). These gels have fascinating and tunable properties that reflect a heterogeneous morphology with domains on the order of tens of nanometers. The complex coacervate domains, aggregated oppositely charged end-blocks, are embedded in a continuous aqueous matrix and are bridged by uncharged, hydrophilic polymer mid-blocks. We report on simulation studies that employ statistical field theory models of triblock polyelectrolytes, and we explore the equilibrium self-assembly of these remarkable systems. As the charge complexation responsible for the formation of coacervate domains is driven by electrostatic correlations, we have found it necessary to pursue full ``field-theoretic simulations'' of the models, as opposed to the familiar self-consistent field theory approach. Our investigations have focused on morphological trends with mid- and end-block lengths, polymer concentration, salt concentration and charge density.

  4. Sub-slab pressure-field extension in schools and other large buildings. Rept. for 1988-91

    SciTech Connect

    Harris, D.B.; Craig, A.B.; Leovic, K.W.

    1991-01-01

    The paper discusses EPA's experiences using pressure field extension (PFE) to design active subslab depressurization (ASD) systems to reduce radon levels in old and new schools, including instances where the data collected resulted in the installation of smaller systems than expected and selection of high vacuum fans instead of 'normal' mitigation fans. A central collection system for use under very large slabs is discussed and PFE data are given for a hospital under construction. The most direct method of projecting or measuring the performance of an ASD system is to measure the strength and extent of the pressure field established under the slab. The PFE can be determined (during diagnostics) to help design an ASD system and (following installation) to ascertain system performance. In schools and other large buildings, these data are invaluable to provide a system that will mitigate the building without undue cost escalation.

  5. The electromagnetic field in conductive slabs and cylinders submitted to a harmonic longitudinal magnetic field

    NASA Astrophysics Data System (ADS)

    Íñiguez, J.; Raposo, V.; Zazo, M.; García-Flores, A.; Hernández-Gómez, P.

    2009-11-01

    The analysis of the induced current distribution in conducting wires subjected to a harmonic axial voltage is important in designing many electrical devices such as transformers and transmission lines. The azimuthal magnetic field induces axial electric currents and therefore the impedance of the wire depends on the excitation frequency. The current density is increasingly confined to a thin layer at the boundary of the wire as the frequency increases. To minimize this effect at higher frequencies it is necessary to enhance the surface-to-volume ratio by using thin high-conductivity wires. The study of induction phenomena in conducting samples subjected to a harmonic longitudinal magnetic field has attracted less attention. The time-varying magnetic flux induces eddy currents, which flow perpendicularly to the axis of the sample. We study the electromagnetic field in samples of simple geometry, making the usual approximations in good conductors. The validity of our calculations extends to several GHz and allows us to propose a method for determining the electrical conductivity by measuring the phase angle of the complex mutual inductance between a primary coil, responsible for the external magnetic field, and a secondary winding around the sample.

  6. The Application of Pulsed Field Gel Electrophoresis in Clinical Studies

    PubMed Central

    Parizad, Eskandar Gholami; Valizadeh, Azar

    2016-01-01

    Pulsed-field gel electrophoresis is a method applied in separating large segments of deoxyribonucleotide using an alternating and cross field. In a uniform magnetic field, components larger than 50kb pass a route through the gel and since the movement of DNA (Deoxyribonucleic acid) molecules are in a Zigzag form, separation of DNAs as bands carried out better via gel. PFGE in microbiology is a standard method which is used for typing of bacteria. It is also a very useful tool in epidemiological studies and gene mapping in microbes and mammalian cell, also motivated development of large-insert cloning system such as bacterial and yeast artifical chromosomes. In this method, close and similar species in terms of genetic patterns show alike profiles regarding DNA separation, and those ones which don’t have similarity or are less similar, reveal different separation profiles. So this feature can be used to determine the common species as the prevalence agent of a disease. PFGE can be utilized for monitoring and evaluating different micro-organisms in clinical samples and existing ones in soil and water. This method can also be a reliable and standard method in vaccine preparation. In recent decades, PFGE is highly regarded as a powerful tool in control, prevention and monitoring diseases in different populations. PMID:26894068

  7. High field magnetic resonance imaging-based gel dosimetry for small radiation fields

    NASA Astrophysics Data System (ADS)

    Ding, Xuanfeng

    Small megavoltage photon radiation fields (< 3cm diameter) are used in advanced radiation therapy techniques, such as intensity modulated radiotherapy, and stereotactic radiosurgery, as well as for cellular and preclinical radiobiology studies (very small fields, <1 mm diameter). Radiation dose characteristics for these small fields are difficult to determine in multiple dimensions because of steep dose gradients (30--40% per mm) and conditions of electronic disequilibrium. Conventional radiation dosimetry techniques have limitations for small fields because detector size may be large compared to radiation field size and/or dose acquisition may be restricted to one or two dimensions. Polymer gel dosimetry, is a three-dimensional (3D) dosimeter based on radiation-induced polymerization of tissue equivalent gelatin. Polymer gel dosimeters can be read using magnetic resonance imaging (MRI), which detects changes in relaxivity due to gel polymerization. Spatial resolution for dose readout is limited to 0.25--0.5mm pixel size because of available the magnetic field strengths (1.5T and 3T) and the stability of polymer gelatin at room temperature. A reliable glucose-based MAGIC (methacrylic and ascorbic acid in gelatine initiated by copper) gel dosimeter was formulated and evaluated for small field 3D dosimetry using 3T and 7T high field MRI for dose readout. The melting point of the original recipe MAGIC gel was increased by 4°C by adding 10% glucose to improve gel stability. Excellent spatial resolution of 79um (1.5 hr scan) and 39um (12 hr scan) was achieved using 7T MRI, proving gel stability for long scan times and high resolution 3D dosimetry.

  8. Slow light, open-cavity formation, and large longitudinal electric field on a slab waveguide made of indefinite permittivity metamaterials

    NASA Astrophysics Data System (ADS)

    Lu, W. T.; Sridhar, S.

    2010-07-01

    The optical properties of slab waveguides made of indefinite permittivity (ɛ) materials (IEMs) are considered. In this medium, the real part of the transverse permittivity is negative while that of the longitudinal permittivity is positive. At any given frequency, the IEM waveguide supports an infinite number of transverse magnetic (TM) eigenmodes. For a slab waveguide with a fixed thickness, at most only one TM mode is forward wave. The remainder are backward waves which can have a very large phase index. At a critical thickness, the waveguide supports degenerate forward- and backward-wave modes with zero group velocity if loss is absent. Above the critical thickness, the waveguide supports complex-conjugate decay modes instead of propagating modes. The presence of loss in IEMs will lift the TM mode degeneracy, resulting in modes with finite group velocity. A feasible realization is proposed. The performance of the IEM waveguide is analyzed and possible applications are discussed, which are supported by numerical calculations. These slab waveguides can be used to make optical delay lines in optical buffers to slow down and trap light, to form open cavities, to generate strong longitudinal electric fields, and as phase shifters in optical integrated circuits. Although the presence of loss will hinder these applications, gain can be introduced to compensate the loss and enhance the performance.

  9. Interaction of electromagnetic fields with chondrocytes in gel culture

    NASA Astrophysics Data System (ADS)

    Grodzinsky, Alan J.; Buschmann, Michael D.; Gluzband, Yehezkiel A.

    1992-01-01

    The specific objectives of this research period were: (1) to quantify the effect of applied electric fields on chondrocyte metabolism, using a range of stimulation frequencies and amplitudes; (2) to compare the chondrocyte biosynthetic response to applied fields at early times in agarose gel culture before an extracellular matrix has accumulated and at later times after significant deposition of matrix around and between the cells; and (3) to begin to interpret the biosynthetic response to applied fields in terms of models of physical mechanisms. The results of these studies suggest that electric fields applied to chondrocytes in agarose can modulate the synthesis of proteoglycans and protein constituents. Biosynthesis may be inhibited or stimulated depending on the amplitude of the applied current density. In addition, the presence of extracellular matrix may enhance the ability of normal chondrocytes and cells in intact cartilage to respond to electric fields, although the presence of matrix was not required for the stimulatory response to be observed with Swarm rat chondrosarcoma cells.

  10. ELECTROMAGNETISM, OPTICS, ACOUSTICS, HEAT TRANSFER, CLASSICAL MECHANICS, AND FLUID DYNAMICS: Analysis on Far-Field of Slab Waveguide and Its Gaussian Approximation

    NASA Astrophysics Data System (ADS)

    Li, Lian-Huang; Guo, Fu-Yuan; Peng, Yu-Jia; Tang, Xiao-Shan; Gao, Rui

    2010-02-01

    This paper researches end diffraction of slab waveguide and then matching efficiency between the far-field and its Gaussian approximate field is analyzed leads to a new definition of divergence half-angle. Finally, why the far-field can be approximated by a Gaussian function is presented according to characteristic of beam propagation factor.

  11. Field lines and magnetic surfaces in a two-component slab/2D model of interplanetary magnetic fluctuations

    NASA Technical Reports Server (NTRS)

    Matthaeus, W. H.; Pontius, D. H., Jr.; Gray, P. C.; Bieber, J. W.

    1995-01-01

    A two-component model for the spectrum of interplanetary magnetic fluctuations was proposed on the basis of ISEE observations, and has found an intriguing level of application in other solar wind studies. The model fluctuations consist of a fraction of 'slab' fluctuations, varying only in the direction parallel to the locally uniform mean magnetic field B(0) and a complement of 2D (two-dimensional) fluctuations that vary in the directions transverse to B(0). We have developed an spectral method computational algorithm for computing the magnetic flux surfaces (flux tubes) associated with the composite model, based upon a precise analogy with equations for ideal transport of a passive scalar in planar two dimensional geometry. Visualization of various composite models will be presented, including the 80 percent 2D/ 20 percent slab model with delta B/B(0) approximately equals 1 and a minus 5/3 spectral law, that is thought to approximately represent a snapshot of solar wind turbulence. Characteristically, the visualizations show that flux tubes, even when defined as regular on some plane, shred and disperse rapidly as they are viewed along the parallel direction. This diffusive process, which generalizes the standard picture of field line random walk, will be discussed in detail. Evidently, the traditional picture that flux tubes randomize like strands of spaghetti with a uniform tangle along the axial direction is in need of modification.

  12. Oriented fibrin gels formed by polymerization in strong magnetic fields

    NASA Astrophysics Data System (ADS)

    Torbet, J.

    1981-01-01

    Fibrinogen is a soluble plasma protein which, after cleavage by the specific proteolytic enzyme thrombin, polymerizes to form the filamentous fibrin network during blood clotting (see refs 1 and 2 for reviews). Fibrinogen has a molecular weight of 340,000 and is composed of two identical halves, each containing three peptide chains designated Aα, Bβ and γ. Fibrin monomers are produced by thrombin which releases the small negatively charged fibrinopeptides A and B. The overall shape of the fibrinogen molecule has not been unequivocally established1,2. The trinodular, elongated (~450 Å long) structure proposed by Hall and Slayter3 is the most widely accepted model and it has obtained additional support from recent work4-6. Fibrin monomers are also about 450 Å long7 and in fibres they probably have a half-staggered arrangement along the axis7,8. The fibres are an assembly of protofibrils whose structure and packing are not reliably known. We report here that highly oriented fibrin gels are formed when polymerization takes place slowly in a strong magnetic field. It is shown that the protofibrils pack into a three-dimensional crystalline lattice. We introduce magnetically induced birefringence as a potential tool for studying polymerization and briefly speculate on the applications of strong magnetic fields.

  13. The textural properties and microstructure of konjac glucomannan - tungsten gels induced by DC electric fields.

    PubMed

    Wang, Lixia; Zhuang, Yuanhong; Li, Jingliang; Pang, Jie; Liu, Xiangyang

    2016-12-01

    Konjac glucomannan - tungsten (KGM-T) gels were successfully prepared under DC electric fields, in the presence of sodium tungstate. The textural properties and microstructure of the gels were investigated by Texture Analyzer, Rheometer and SEM. Based on the response surface methodology (RSM) results, the optimum conditions for KGM-T gel springiness is 0.32% sodium tungstate concentration, 0.54% KGM concentration, 24.66V voltage and 12.37min treatment time. Under these conditions, the maximum springiness value of KGM-T gel is 1.21mm. Steady flow measurement indicated that KGM-T gel showed characteristic non-Newtonian pseudoplastic behaviour, with low flow behaviour indexes in the shear thinning region. SEM demonstrated the porosity of the freeze-dried samples. These findings may pave the way to use DC electric fields for the design and development of KGM gels and to apply KGM gels for practical applications. PMID:27374531

  14. Temperature field inside an absorbing-emitting semi-transparent slab at radiative equilibrium with variable spatial refractive index.

    NASA Astrophysics Data System (ADS)

    Abdallah, P. B.; Le Dez, V.

    2000-05-01

    The temperature field inside an absorbing-emitting slab of semi-transparent grey medium at radiative equilibrium has been determined with the help of a curved ray-tracing technique when the spatial variation of the refractive index in the medium is assumed to be linear. The integration of the radiative transfer equation has been carried out on the trajectories on which radiation propagates inside the medium, leading to the absorbed radiative energy at an internal point. For a linear refractive index, existence of totally reflected internal trajectories producing mirage effects have to be taken into account in the resolution of the radiative problem. Results obtained for different optical depths with low and strong gradients of refractive index display significant differences from the case of a constant refractive index.

  15. Effect of gel structure of matrix orientation in pulsed alternating electric fields

    SciTech Connect

    Stellwagen, N.C.; Stellwagen, J.

    1993-12-31

    Four polymeric gels with different structures, LE agarose, HEEO agarose, beta-carrageenan, and polyacrylamide, were studied by transient electric birefringence to determine the importance of various structural features on the orientation of the gels in pulsed alternating electric fields. The birefrigence relaxation times observed for agarose gels in low voltage electric fields suggest that long fibers and/or domains, ranging up to tens of microns in size, are oriented by the electric field. The sign of the birefringence reverses when the direction of the electric field is reversed, suggesting that the oriented domains change their direction of orientation from parallel to perpendicular (or vice versa) when the polarity of the electric field is reversed. These anamalous orientation effects are observed with both types of agarose gels, but not with beta-carrageenan or polyacrylamide gels, suggesting that the alternating D,L galactose residues in the agarose backbone are responsible for the anomalies.

  16. Numerical modeling of deep oceanic slab dehydration: Implications for the possible origin of far field intra-continental volcanoes in northeastern China

    NASA Astrophysics Data System (ADS)

    Sheng, Jian; Liao, Jie; Gerya, Taras

    2016-03-01

    Intra-continental volcanoes have different origins compared to arc volcanoes, and several conflicting geodynamic mechanisms of intra-continental magmatism have been proposed, which require quantitative testing. In this paper, we investigate numerically possible influences of deep subducted slab dehydration processes for the development of intra-continental volcanoes distributed in northeastern China. We employ 2D thermo-mechanical numerical models to investigate the complex dynamics of long-term subduction process, including slab interaction with mantle transition zone, deep oceanic plate dehydration, trench rollback, and back-arc extension. Our experiments show systematically that water can be transported to the transition zone by stagnant slabs hydrating the overlaying deep asthenospheric mantle. Positively buoyant partially molten hydrous plumes arising from the hydrated area formed atop the slabs can propagate upwards and form partially molten mantle regions under the far field continental plate. Our numerical models thus suggest that the development of widely distributed intra-continental volcanism in northeastern China could be related to the rising of multiple relatively small hydrous plumes triggered by stagnant paleo-Pacific slab dehydration in the transition zone.

  17. Mechanical Properties of Electroactive Polymer Gels and Their Behavior in DC Electric Fields

    NASA Astrophysics Data System (ADS)

    Yao, Li; Krause, Sonja

    2000-03-01

    We have reported the bending deformation of swollen crosslinked partially sulfonated triblock copolymer poly(styrene-b-ethylene-co-butylene-b-styrene) (S-SEBS) hydrogels in DC electric fields in previous APS meetings(Bull. Am. Phys. Soc., 43 (1), 598, 1998 and 44 (1), 757, 1999). However, very little force was generated from the bending of the S-SEBS gel due to the low modulus of this highly elastic material. For the present study, partially sulfonated crosslinked polystyrene gels (XL-S-PS) were prepared. The gel bending behavior of XL-S-PS gels was studied in four different sulfonated solutions with varied cations including Na^+, Cs^+, (CH_3)_4NH^+ and (Bu)_4NH^+. Comparison of gel bending of S-SEBS and XL-S-PS gels indicated qualitative similarities and quantitative differences. The bending motion of the XL-S-PS gels in electric fields was slower than that of the S-SEBS gels but more force was generated in the XL-S-PS gel system. Nanoparticles were used as fillers in some of the XL-S-PS gels to modify their mechanical properties which will be discussed in the presentation.

  18. Electromagnetic eigenstates and the field of an oscillating point electric dipole in a flat-slab composite structure

    NASA Astrophysics Data System (ADS)

    Farhi, Asaf; Bergman, David J.

    2016-06-01

    An exact calculation of the local electric field E (r ) is described for the case of a time-dependent point electric dipole p e-i ω t in the top layer of an ɛ2, ɛ1, ɛ2 three parallel slabs composite structure, where the ɛ1 layer has a finite thickness 2 d but the ɛ2 layers are infinitely thick. For this purpose we first calculate all the eigenstates of the full Maxwell equations for the case where μ =1 everywhere in the system. The eigenvalues appear as special, nonphysical values of ɛ1 when ɛ2 is given. These eigenstates are then used to develop an exact expansion for the physical values of E (r ) in the system characterized by physical values of ɛ1(ω ) and ɛ2(ω ) . Results are compared with those of a previous calculation of the local field of a time-dependent point charge in the quasistatic regime. Numerical results are shown for the local electric field in practically important configurations where attaining an optical image with subwavelength resolution has practical significance.

  19. Push-pull slab coupled optical sensor for measuring electric fields in a vibrational environment.

    PubMed

    Seng, Frederick; Stan, Nikola; Josephson, Chad; King, Rex; Shumway, LeGrand; Selfridge, Richard; Schultz, Stephen

    2015-06-01

    Vibration-insensitive fiber optic electric field sensor is created by fabricating two sensing elements in close proximity onto the same optical fiber and subtracting the two signals. The device is used to measure an electric field of 10  kV/m, while the sensor is being bent and impacted. PMID:26192684

  20. Full-field dye concentration measurement within saturated/unsaturated thin slabs of porous media

    SciTech Connect

    Norton, D.L.; Glass, R.J.

    1992-12-31

    This paper presents a full-field dye concentration measurement technique that extends our experimental capabilities to the measurement of transient dye concentration fields within steady state flow fields under unsaturated or saturated conditions. Simple light absorption theory provides a basis for translating images into high resolution dye concentration fields. A series of dye pulse experiments that demonstrate the combined use of the full-field saturation and dye concentration techniques was conducted at four different degrees of saturation. Each of these experimental sequences was evaluated with respect to mass balance, the results being within 5% of the known dye mass input. An image windowing technique allowed us to see increased dispersion due to decreasing moisture content, tailing of concentration at the rear of the dye pulse and slight velocity changes of the dispersive front due to changes in moisture content. The exceptional resolution of dye concentration in space and time provided by this laboratory technique allows systematic experimentation for examining basic processes affecting solute transport within saturated/unsaturated porous media. Future challenges for this work will be to use these techniques to analyze more complex systems involving heterogeneities, scaling laws, and detailed investigations of the relationship between transverse and longitudinal dispersion in unsaturated media.

  1. SUB-SLAB PRESSURE FIELD EXTENSION IN SCHOOLS AND OTHER LARGE BUILDINGS

    EPA Science Inventory

    The paper discusses EPA's experiences using pressure field extension (PFE) to design active subslab depressurization (ASD) systems to reduce radon levels in old and new schools, including instances where the data collected resulted in the installation of smaller systems than expe...

  2. Slab reformer

    DOEpatents

    Spurrier, Francis R.; DeZubay, Egon A.; Murray, Alexander P.; Vidt, Edward J.

    1984-02-07

    Slab-shaped high efficiency catalytic reformer configurations particularly useful for generation of fuels to be used in fuel cell based generation systems. A plurality of structures forming a generally rectangular peripheral envelope are spaced about one another to form annular regions, an interior annular region containing a catalytic bed and being regeneratively heated on one side by a hot comubstion gas and on the other side by the gaseous products of the reformation. An integrally mounted combustor is cooled by impingement of incoming oxidant.

  3. Slab reformer

    DOEpatents

    Spurrier, Francis R.; DeZubay, Egon A.; Murray, Alexander P.; Vidt, Edward J.

    1985-03-12

    Slab-shaped high efficiency catalytic reformer configurations particularly useful for generation of fuels to be used in fuel cell based generation systems. A plurality of structures forming a generally rectangular peripheral envelope are spaced about one another to form annular regions, an interior annular region containing a catalytic bed and being regeneratively heated on one side by a hot combustion gas and on the other side by the gaseous products of the reformation. An integrally mounted combustor is cooled by impingement of incoming oxidant.

  4. Slab reformer

    NASA Technical Reports Server (NTRS)

    Spurrier, Francis R. (Inventor); DeZubay, Egon A. (Inventor); Murray, Alexander P. (Inventor); Vidt, Edward J. (Inventor)

    1984-01-01

    Slab-shaped high efficiency catalytic reformer configurations particularly useful for generation of fuels to be used in fuel cell based generation systems. A plurality of structures forming a generally rectangular peripheral envelope are spaced about one another to form annular regions, an interior annular region containing a catalytic bed and being regeneratively heated on one side by a hot comubstion gas and on the other side by the gaseous products of the reformation. An integrally mounted combustor is cooled by impingement of incoming oxidant.

  5. Rheological properties and formation mechanism of DC electric fields induced konjac glucomannan-tungsten gels.

    PubMed

    Wang, Lixia; Jiang, Yaoping; Lin, Youhui; Pang, Jie; Liu, Xiang Yang

    2016-05-20

    Konjac glucomannan-tungsten (KGM-T) hydrogel of electrochemical reversibility was successfully produced under DC electric fields in the presence of sodium tungstate. The structure and the effects of sodium tungstate concentration, KGM concentration, voltage and electric processing time on the rheological properties of the gels were investigated. pH experiments showed that KGM sol containing Na2WO4·2H2O in the vicinity of the positive electrode became acidic and the negative electrode basic after the application of DC electric fields. Under acid conditions, WO4(2-) ions transformed into isopoly-tungstic acid ions. FTIR and Raman studies indicated that isopoly-tungstic acid ions absorbed on KGM molecular chain and cross-linked with -OH groups at C-6 position on sugar units of KGM. Frequency sweep data showed with increasing sodium tungstate concentration, voltage, and electric processing time, the viscoelastic moduli, i.e., the storage and the loss moduli of the gel increased, whereas an increase in KGM concentration led to a decrease in gel viscoelastic moduli. The temperature sweep measurements indicated the obtained gel exhibited high thermal stability. Finally, the mechanism of gel formation was proposed. Our work may pave the way to use DC electric fields for the design and development of KGM gels as well as polysaccharide gels. PMID:26917402

  6. Diode end-pumped high-power Q-switched double Nd:YAG slab laser and its efficient near-field second-harmonic generation.

    PubMed

    Zhu, Peng; Li, Daijun; Qi, Bingsong; Schell, Alexander; Shi, Peng; Haas, Claus; Fu, Shaojun; Wu, Nianle; Du, Keming

    2008-10-01

    We reported on an all-solid-state double Nd:YAG slab laser. The laser was based on two diode end-pumped Nd:YAG slabs and a stable-unstable hybrid resonator. A cw output of 189 W and an average Q-switched output of 169 W at 10 kHz with an M(2) factor of 1.5 in the slow direction and 1.7 in the fast direction were obtained. We demonstrated efficient near-field frequency doubling by imaging the one-dimensional top-hat near-field to a lithium triborate frequency doubler. We obtained 93 W green light at 10 kHz with a pulse width of 10.7 ns. The efficiency of second-harmonic generation was up to 57%. PMID:18830367

  7. Molecular stretching of long DNA in agarose gel using alternating current electric fields.

    PubMed Central

    Kaji, Noritada; Ueda, Masanori; Baba, Yoshinobu

    2002-01-01

    We demonstrate a novel method for stretching a long DNA molecule in agarose gel with alternating current (AC) electric fields. The molecular motion of a long DNA (T4 DNA; 165.6 kb) in agarose gel was studied using fluorescence microscopy. The effects of a wide range of field frequencies, field strengths, and gel concentrations were investigated. Stretching was only observed in the AC field when a frequency of approximately 10 Hz was used. The maximal length of the stretched DNA had the longest value when a field strength of 200 to 400 V/cm was used. Stretching was not sensitive to a range of agarose gel concentrations from 0.5 to 3%. Together, these experiments indicate that the optimal conditions for stretching long DNA in an AC electric field are a frequency of 10 Hz with a field strength of 200 V/cm and a gel concentration of 1% agarose. Using these conditions, we were able to successfully stretch Saccharomyces cerevisiae chromosomal DNA molecules (225-2,200 kb). These results may aid in the development of a novel method to stretch much longer DNA, such as human chromosomal DNA, and may contribute to the analysis of a single chromosomal DNA from a single cell. PMID:11751320

  8. IMPROVED APPROACHES TO DESIGN OF POLYMER GEL TREATMENTS IN MATURE OIL FIELDS: FIELD DEMONSTRATION IN DICKMAN FIELD, NESS COUNTY, KANSAS

    SciTech Connect

    Ronald Fowler

    2004-11-30

    This report describes the results of the one-year project entitled ''Improved Approaches to Design of Polymer Gel Treatments in Mature Oil Fields: Field Demonstration in Dickman Field, Ness County, Kansas''. The project was a 12-month collaboration of Grand Mesa Operating Company (a small independent), TIORCO Inc. (a company focused on improved recovery technology) and the University of Kansas. The study undertook tasks to determine an optimum polymer gel treatment design in Mississippian reservoirs, demonstrate application, and evaluate the success of the program. The project investigated geologic and engineering parameters and cost-effective technologies required for design and implementation of effective polymer gel treatment programs in the Mississippian reservoir in the Midcontinent. The majority of Mississippian production in Kansas occurs at or near the top of the Mississippian section just below the regional sub-Pennsylvanian unconformity and karst surface. Dickman Field with the extremely high water cuts and low recovery factors is typical of Mississippian reservoirs. Producibility problems in these reservoirs include inadequate reservoir characterization, drilling and completion design problems, and most significantly extremely high water cuts and low recovery factors that place continued operations at or near their economic limits. Geologic, geophysical and engineering data were integrated to provide a technical foundation for candidate selection and treatment design. Data includes core, engineering data, and 3D seismic data. Based on technical and economic considerations a well was selected for gel-polymer treatment (Grand Mesa Operating Company Tilley No.2). The treatment was not successful due to the small amount of polymer that could be injected. Data from the initial well and other candidates in the demonstration area was analyzed using geologic, geophysical and engineering data. Based on the results of the treatment and the integrated reservoir

  9. Polymer gel dosimetry of an electron beam in the presence of a magnetic field

    NASA Astrophysics Data System (ADS)

    Vandecasteele, J.; De Deene, Y.

    2013-06-01

    The effect of a strong external magnetic field on 4 MeV electron beam was measured with polymer gel dosimetry. The measured entrance dose distribution was compared with a calculated fluence map. The magnetic field was created by use of two permanent Neodymium (NdFeB) magnets that were positioned perpendicular to the electron beam. The magnetic field between the magnets was measured with Hall sensors. Based on the magnetic field measurement and the law of Biot-Savart, the magnetic field distribution was extrapolated. Electron trajectories were calculated using a relativistic Lorentz force operator. Although the simplified computational model that was applied, the shape and position of the calculated entrance fluence map are found to be in good agreement with the measured dose distribution in the first layer of the phantom. In combination with the development of low density polymer gel dosimeters, these preliminary results show the potential of 3D gel dosimetry in MRI-linac applications.

  10. Adaptation of radiation field analyser (RFA) as optical CT scanner for gel dosimetry

    PubMed Central

    Brindha, S.; Kumar, Vinoth; Vasanth, S.; Ravindran Paul, B.

    2006-01-01

    Optical scanning is one of the emerging evaluation tools used for obtaining dose distributions in gel dosimetry. A radiation field analyzer adapted into an optical CT scanner to evaluate an irradiated Fricke gel has been already reported by others. This prototype optical CT scanner functions like a first generation x-ray CT scanner in the translate-rotate fashion. A similar scanner was constructed in our department for optical scanning of irradiated FX gel. At first, an aquarium was constructed and fitted into the water phantom of the RFA with provision to place the gel phantom to be scanned along with a light source and detector. The movements of the RFA were utilized to scan the gel phantom. A scan of a cuvette filled with colored solution was carried out and the resulting images were reconstructed and profiles obtained to evaluate the working of the optical scanner. A scan of the gel phantom was then obtained to evaluate the performance of the scanner. Thus a radiation field analyzer (DYNASCAN) was successfully adapted to an optical scanner to evaluate Fricke gels in our department. PMID:21206636

  11. Gel Electrophoresis of DNA --- New Measurements and the Repton Model at High Fields

    NASA Astrophysics Data System (ADS)

    Krawczyk, M. J.; Pasciak, P.; Dydejczyk, A.; Kulakowski, K.; Dulak, J.

    2005-05-01

    New experimental data are presented on the gel electrophoresis of DNA. Experiment was made for molecules of length 173 kbp, in 1 percent agarose gel, in TAE 1 × buffer and the field intensity between 5 and 9 V/cm. The results are compared with our computer simulations, performed within the repton model of Duke and Rubinstein. The ranges of field and molecule length are determined, where the geometration effect appears. We investigate also the field dependence of the velocity and the diffusion coefficient at the border of the geometration regime.

  12. Small-Field Measurements of 3D Polymer Gel Dosimeters through Optical Computed Tomography

    PubMed Central

    Shih, Cheng-Ting; Lee, Yao-Ting; Wu, Shin-Hua; Yao, Chun-Hsu; Hsieh, Bor-Tsung

    2016-01-01

    With advances in therapeutic instruments and techniques, three-dimensional dose delivery has been widely used in radiotherapy. The verification of dose distribution in a small field becomes critical because of the obvious dose gradient within the field. The study investigates the dose distributions of various field sizes by using NIPAM polymer gel dosimeter. The dosimeter consists of 5% gelatin, 5% monomers, 3% cross linkers, and 5 mM THPC. After irradiation, a 24 to 96 hour delay was applied, and the gel dosimeters were read by a cone beam optical computed tomography (optical CT) scanner. The dose distributions measured by the NIPAM gel dosimeter were compared to the outputs of the treatment planning system using gamma evaluation. For the criteria of 3%/3 mm, the pass rates for 5 × 5, 3 × 3, 2 × 2, 1 × 1, and 0.5 × 0.5 cm2 were as high as 91.7%, 90.7%, 88.2%, 74.8%, and 37.3%, respectively. For the criteria of 5%/5 mm, the gamma pass rates of the 5 × 5, 3 × 3, and 2 × 2 cm2 fields were over 99%. The NIPAM gel dosimeter provides high chemical stability. With cone-beam optical CT readouts, the NIPAM polymer gel dosimeter has potential for clinical dose verification of small-field irradiation. PMID:26974434

  13. Pulsed-field gel electrophoresis for epidemiologic studies of Campylobacter hyointestinalis isolates.

    PubMed Central

    Salama, S M; Tabor, H; Richter, M; Taylor, D E

    1992-01-01

    Campylobacter hyointestinalis was isolated from five members of the same family who had previously consumed raw milk. Pulsed-field gel electrophoresis of genomic DNAs from the five strains, after digestion with restriction endonuclease SalI, revealed that three strains had identical genome patterns and therefore appeared to be related, whereas the other two had completely different genome patterns and appeared to be unrelated. We report here for the first time the isolation of C. hyointestinalis from family members who had consumed raw milk. Our study also demonstrates the usefulness of pulsed-field gel electrophoresis for epidemiologic studies of this unusual campylobacter. Images PMID:1500503

  14. Progress on slab lasers

    NASA Astrophysics Data System (ADS)

    Albrecht, G. F.; Eggleston, J. M.; Petr, R. A.

    1986-01-01

    After a brief overview of slab geometry work published to date, zig-zag optical path slab laser development toward a 100-Hz slab YAG system ('Centurion') and a 10-Hz dual slab glass system ('Gemini') is described. Some of the major diagnostic work performed and in the process is also described to illustrate the major mechanisms responsible for beam distortion observed in these types of slab lasers.

  15. Three-dimensional dosimetry of small megavoltage radiation fields using radiochromic gels and optical CT scanning

    NASA Astrophysics Data System (ADS)

    Babic, Steven; McNiven, Andrea; Battista, Jerry; Jordan, Kevin

    2009-04-01

    The dosimetry of small fields as used in stereotactic radiotherapy, radiosurgery and intensity-modulated radiation therapy can be challenging and inaccurate due to partial volume averaging effects and possible disruption of charged particle equilibrium. Consequently, there exists a need for an integrating, tissue equivalent dosimeter with high spatial resolution to avoid perturbing the radiation beam and artificially broadening the measured beam penumbra. In this work, radiochromic ferrous xylenol-orange (FX) and leuco crystal violet (LCV) micelle gels were used to measure relative dose factors (RDFs), percent depth dose profiles and relative lateral beam profiles of 6 MV x-ray pencil beams of diameter 28.1, 9.8 and 4.9 mm. The pencil beams were produced via stereotactic collimators mounted on a Varian 2100 EX linear accelerator. The gels were read using optical computed tomography (CT). Data sets were compared quantitatively with dosimetric measurements made with radiographic (Kodak EDR2) and radiochromic (GAFChromic® EBT) film, respectively. Using a fast cone-beam optical CT scanner (Vista™), corrections for diffusion in the FX gel data yielded RDFs that were comparable to those obtained by minimally diffusing LCV gels. Considering EBT film-measured RDF data as reference, cone-beam CT-scanned LCV gel data, corrected for scattered stray light, were found to be in agreement within 0.5% and -0.6% for the 9.8 and 4.9 mm diameter fields, respectively. The validity of the scattered stray light correction was confirmed by general agreement with RDF data obtained from the same LCV gel read out with a laser CT scanner that is less prone to the acceptance of scattered stray light. Percent depth dose profiles and lateral beam profiles were found to agree within experimental error for the FX gel (corrected for diffusion), LCV gel (corrected for scattered stray light), and EBT and EDR2 films. The results from this study reveal that a three-dimensional dosimetry method

  16. Comparison of restriction enzymes for pulsed-field gel electrophoresis typing of Moraxella catarrhalis.

    PubMed

    Marti, Sara; Puig, Carmen; Domenech, Arnau; Liñares, Josefina; Ardanuy, Carmen

    2013-07-01

    NotI, the most prevalent restriction enzyme used for typing Moraxella catarrhalis, failed to digest genomic DNA from respiratory samples. An improved pulsed-field gel electrophoresis (PFGE) methodology determined SpeI as the best choice for typing this bacterial species, with a good restriction of clinical samples and a good clustering correlation with NotI. PMID:23678064

  17. Pulsed-field gel electrophoresis as a discriminatory typing technique for the biothreat agent burkholderia mallei.

    PubMed

    Chantratita, Narisara; Vesaratchavest, Mongkol; Wuthiekanun, Vanaporn; Tiyawisutsri, Rachaneeporn; Ulziitogtokh, Tsedev; Akcay, Erhan; Day, Nicholas P J; Peacock, Sharon J

    2006-03-01

    Pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) was used to type 21 laboratory strains of Burkholderia mallei. We demonstrated good resolution by PFGE together with clustering of some geographically related isolates, and confirmed previous observations that B. mallei is clonal as defined by MLST. PMID:16525089

  18. Preface: Deep Slab and Mantle Dynamics

    NASA Astrophysics Data System (ADS)

    Suetsugu, Daisuke; Bina, Craig R.; Inoue, Toru; Wiens, Douglas A.

    2010-11-01

    We are pleased to publish this special issue of the journal Physics of the Earth and Planetary Interiors entitled "Deep Slab and Mantle Dynamics". This issue is an outgrowth of the international symposium "Deep Slab and Mantle Dynamics", which was held on February 25-27, 2009, in Kyoto, Japan. This symposium was organized by the "Stagnant Slab Project" (SSP) research group to present the results of the 5-year project and to facilitate intensive discussion with well-known international researchers in related fields. The SSP and the symposium were supported by a Grant-in-Aid for Scientific Research (16075101) from the Ministry of Education, Culture, Sports, Science and Technology of the Japanese Government. In the symposium, key issues discussed by participants included: transportation of water into the deep mantle and its role in slab-related dynamics; observational and experimental constraints on deep slab properties and the slab environment; modeling of slab stagnation to constrain its mechanisms in comparison with observational and experimental data; observational, experimental and modeling constraints on the fate of stagnant slabs; eventual accumulation of stagnant slabs on the core-mantle boundary and its geodynamic implications. This special issue is a collection of papers presented in the symposium and other papers related to the subject of the symposium. The collected papers provide an overview of the wide range of multidisciplinary studies of mantle dynamics, particularly in the context of subduction, stagnation, and the fate of deep slabs.

  19. A dosimetric study of small photon fields using polymer gel and Gafchromic EBT films

    SciTech Connect

    Hassani, Hossein; Nedaie, Hassan Ali; Zahmatkesh, Mohammad Hassan; Shirani, Kaveh

    2014-04-01

    The use of small field sizes is increasingly becoming important in radiotherapy particularly since the introduction of stereotactic radiosurgery and intensity-modulated radiation therapy techniques. The reliable measurement of delivered dose from such fields with conventional dosimeters, such as ionization chambers, is a challenging task. In this work, methacrylic and ascorbic acid in gelatin initiated by copper polymer gel dosimeters are employed to measure dose in 3 dimensions. Field sizes of 5 × 5 mm{sup 2}, 10 × 10 mm{sup 2}, 20 × 20 mm{sup 2}, and 30 × 30 mm{sup 2} are investigated for a 6-MV x-rays. The results show an agreement with Gafchromic film, with some variation in measured doses near the edge of the fields, where the film data decrease more rapidly than the other methods. Dose penumbra widths obtained with gel dosimeters and Gafchormic film were generally in agreement with each other. The results of this work indicate that polymer gel dosimetry could be invaluable for the quantification of the 3-dimensional dose distribution in small field size.

  20. Trapping and breaking of in vivo nicked DNA during pulsed field gel electrophoresis.

    PubMed

    Khan, Sharik R; Kuzminov, Andrei

    2013-12-15

    Pulsed field gel electrophoresis (PFGE) offers a high-resolution approach to quantify chromosomal fragmentation in bacteria, measured as percentage of chromosomal DNA entering the gel. The degree of separation in pulsed field gel (PFG) depends on the size of DNA as well as various conditions of electrophoresis such as electric field strength, time of electrophoresis, switch time, and buffer composition. Here we describe a new parameter, the structural integrity of the sample DNA itself, that influences its migration through PFGs. We show that subchromosomal fragments containing both spontaneous and DNA damage-induced nicks are prone to breakage during PFGE. Such breakage at single-strand interruptions results in artifactual decrease in molecular weight of linear DNA making accurate determination of the number of double-strand breaks difficult. Although breakage of nicked subchromosomal fragments is field strength independent, some high-molecular-weight subchromosomal fragments are also trapped within wells under the standard PFGE conditions. This trapping can be minimized by lowering the field strength and increasing the time of electrophoresis. We discuss how breakage of nicked DNA may be mechanistically linked to trapping. Our results suggest how to optimize conditions for PFGE when quantifying chromosomal fragmentation induced by DNA damage. PMID:23770235

  1. Simplified protocol for pulsed-field gel electrophoresis analysis of Streptococcus pneumoniae.

    PubMed

    McEllistrem, M C; Stout, J E; Harrison, L H

    2000-01-01

    A variety of pulsed-field gel electrophoresis (PFGE) protocols for the molecular subtyping of Streptococcus pneumoniae have been reported; most are time-consuming and complex. We sought to modify reference PFGE protocols to reduce the time required while creating high-quality gels. Only protocol modifications that resulted in high-quality banding patterns were considered. The following protocol components were modified. Lysis enzymes (lysozyme, mutanolysin, and RNase A) were deleted in a stepwise fashion, and then the lysis buffer was deleted. Lysis and digestion were accomplished in a single step with EDTA and N-lauroyl sarcosine (ES; pH 8.5 to 9.3) incubation at 50 degrees C in the absence of proteinase K. All enzymes except the restriction enzyme were omitted. A minimum incubation time of 6 h was required to achieve high-quality gels. All of the reactions were performed within 9 h, and the total protocol time from lysis to gel completion was reduced from 3 days to only 36 h. Combining lysis and digestion into a single step resulted in a substantial reduction in the time required to perform PFGE for S. pneumoniae. The ES solution may have caused cell lysis by activating N-acetylmuramyl-L-alanine amidase, the pneumococcal autolysin. PMID:10618114

  2. Band gap control using electric field of photonic gel cells fabricated with block copolymer and hydrogel.

    PubMed

    Lee, Sung Nam; Baek, Young Bin; Shin, Dong Myung

    2014-08-01

    Optical and electrical characteristics of the devices using photonic gel film and hydrogel electrolyte were studied. Poly(styrene-b-2-vinylpyridine) (PS-b-P2VP) lamellar film with alternating hydrophobic block and hydrophilic polyelectrolyte block polymers (52 kg/mol-b-57 kg/mol) were prepared for the photonic gel. Poly(isobutylene-co-maleic acid) sodium salts were prepared for the hydrogel. This hydrogel fiber is common water swelling material and it owned ions for a device has conductivity. Photonic gel and hydrogel was spin coating onto Indium-tin-oxide (ITO) glass for make electric fields. The reflectance maximum wavelength of photonic crystal device shifted from 538 nm and reached to 557 nm, 585 nm and 604 nm during 30 min voltage applying time. The bandwidth variation was very limited. Loss of electrolyte was much less with hydrogel compared to the pure water. We can control color of hydrogel used photonic device by electric field with reasonable time range under moderate electric field by applying 2 V between two facing electrodes. PMID:25936055

  3. Field-theoretic model of inhomogeneous supramolecular polymer networks and gels

    NASA Astrophysics Data System (ADS)

    Mohan, Aruna; Elliot, Richard; Fredrickson, Glenn H.

    2010-11-01

    We present a field-theoretic model of the gelation transition in inhomogeneous reversibly bonding systems and demonstrate that our model reproduces the classical Flory-Stockmayer theory of gelation in the homogeneous limit. As an illustration of our model in the context of inhomogeneous gelation, we analyze the mean-field behavior of an equilibrium system of reacting trifunctional units in a good solvent confined within a slit bounded by parallel, repulsive walls. Our results indicate higher conversions and, consequently, higher concentrations of gel following the gelation transition near the center of the slit relative to the edges.

  4. Field-theoretic model of inhomogeneous supramolecular polymer networks and gels.

    PubMed

    Mohan, Aruna; Elliot, Richard; Fredrickson, Glenn H

    2010-11-01

    We present a field-theoretic model of the gelation transition in inhomogeneous reversibly bonding systems and demonstrate that our model reproduces the classical Flory-Stockmayer theory of gelation in the homogeneous limit. As an illustration of our model in the context of inhomogeneous gelation, we analyze the mean-field behavior of an equilibrium system of reacting trifunctional units in a good solvent confined within a slit bounded by parallel, repulsive walls. Our results indicate higher conversions and, consequently, higher concentrations of gel following the gelation transition near the center of the slit relative to the edges. PMID:21054065

  5. Short protocol for pulsed field gel electrophoresis of a variety of Clostridia species.

    PubMed

    Sperner, B; Schalch, B; Eisgruber, H; Stolle, A

    1999-07-01

    While pulsed field gel electrophoresis has become an important tool for genotyping of bacteria, one of its drawbacks is that standard methods are rather time-consuming. In order to overcome this problem, shortened procedures for DNA preparation have been developed for some bacterial species. The aim of this study was to examine if a short procedure used for pulsed field gel electrophoresis of Clostridium botulinum could be applied to other Clostridia species. For this, the protocol was modified and used to prepare the DNA of 34 strains of 25 different Clostridia species. In contrast to a standard procedure, which takes at least 5 days from DNA extraction to completion of the electrophoresis, this protocol yielded results within 2 days. In order to directly compare the results of the short protocol with those of the standard, long procedure, parallel DNA preparations were performed using both methods and the two DNA samples thus obtained per strain were then run on the same gel. Briefly, the procedure was as follows. After embedding the bacterial cells in agarose, the agarose blocks were incubated for 1 h in lysis solution containing lysozyme, mutanolysin, lysostaphin and RNase. This was followed by a 1-h proteinase K treatment. Then, slices were cut from the agarose blocks and washed for 15 min in TE buffer, these washes were repeated four times with fresh TE. After a 2-h restriction with SmaI, electrophoresis was carried out overnight. PMID:10397313

  6. Compliant random fields in gels formed from side-chain liquid crystalline polymers

    NASA Astrophysics Data System (ADS)

    Goldbart, Paul; Ye, Fangfu; Lu, Bing; Xing, Xiangjun

    2013-03-01

    Localized polymer-chain backbones in gels formed from side-chain liquid crystalline polymers serve to create random fields that induce local orientational order of the nematogenic pendants of the side chains. These random fields differ, however, from conventional ones, in that they are compliant, and thus themselves undergo thermal fluctuations. We develop a free energy that describes local nematic ordering in presence of such compliant random fields. In particular, we show that, as a result of this compliance, the free energy has a qualitatively new structure, unattainable via truly static random fields. We discuss the physical implications this free energy, focusing on the consequences of the compliant nature of the random fields.

  7. Interlaboratory Agreement of Pulsed-Field Gel Electrophoresis Identification of Leptospira Serovars

    PubMed Central

    Mende, Katrin; Galloway, Renee L.; Becker, Sara J.; Beckius, Miriam L.; Murray, Clinton K.; Hospenthal, Duane R.

    2013-01-01

    Leptospirosis may be caused by > 250 Leptospira serovars. Serovar classification is a complex task that most laboratories cannot perform. We assessed the interlaboratory reproducibility of a pulsed-field gel electrophoresis (PFGE) identification technique developed by the Centers for Disease Control and Prevention (CDC). Blinded exchange of 93 Leptospiraceae strains occurred between San Antonio Military Medical Center (SAMMC) and the CDC. PFGE was performed and gel images were analyzed and compared with patterns present in each laboratory's database (CDC database: > 800 strain patterns; SAMMC database: > 300 strain patterns). Overall, 93.7% (74 of 79) of strains present in each receiving laboratory's database were correctly identified. Five isolates were misidentified, and two isolates did not match serovar PFGE patterns in the receiving laboratory's database. Patterns for these seven isolates were identical between laboratories; four serovars represented misidentified reference strains. The PFGE methodology studied showed excellent interlaboratory reproducibility, enabling standardization and data sharing between laboratories. PMID:23817329

  8. Use of conductive gels for electric field homogenization increases the antitumor efficacy of electroporation therapies

    NASA Astrophysics Data System (ADS)

    Ivorra, Antoni; Al-Sakere, Bassim; Rubinsky, Boris; Mir, Lluis M.

    2008-11-01

    Electroporation is used in tissue for gene therapy, drug therapy and minimally invasive tissue ablation. The electrical field that develops during the application of the high voltage pulses needs to be precisely controlled. In the region to be treated, it is desirable to generate a homogeneous electric field magnitude between two specific thresholds whereas in other regions the field magnitude should be as low as possible. In the case of irregularly shaped tissue structures, such as bulky tumors, electric field homogeneity is almost impossible to be achieved with current electrode arrangements. We propose the use of conductive gels, matched to the conductivity of the tissues, to fill dead spaces between plate electrodes gripping the tissue so that the electric field distribution becomes less heterogeneous. Here it is shown that this technique indeed improves the antitumor efficacy of electrochemotherapy in sarcomas implanted in mice. Furthermore, we analyze, through finite element method simulations, how relevant the conductivity mismatches are. We found that conductivity mismatching errors are surprisingly well tolerated by the technique. Gels with conductivities ranging from 5 mS cm-1 to 10 mS cm-1 will be a proper solution for most cases.

  9. Strong Static Magnetic Fields Increase the Gel Signal in Partially Hydrated DPPC/DMPC Membranes.

    PubMed

    Tang, Jennifer; Alsop, Richard J; Schmalzl, Karin; Epand, Richard M; Rheinstädter, Maikel C

    2015-01-01

    NIt was recently reported that static magnetic fields increase lipid order in the hydrophobic membrane core of dehydrated native plant plasma membranes [Poinapen, Soft Matter 9:6804-6813, 2013]. As plasma membranes are multicomponent, highly complex structures, in order to elucidate the origin of this effect, we prepared model membranes consisting of a lipid species with low and high melting temperature. By controlling the temperature, bilayers coexisting of small gel and fluid domains were prepared as a basic model for the plasma membrane core. We studied molecular order in mixed lipid membranes made of dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) using neutron diffraction in the presence of strong static magnetic fields up to 3.5 T. The contribution of the hydrophobic membrane core was highlighted through deuterium labeling the lipid acyl chains. There was no observable effect on lipid organization in fluid or gel domains at high hydration of the membranes. However, lipid order was found to be enhanced at a reduced relative humidity of 43%: a magnetic field of 3.5 T led to an increase of the gel signal in the diffraction patterns of 5%. While all biological materials have weak diamagnetic properties, the corresponding energy is too small to compete against thermal disorder or viscous effects in the case of lipid molecules. We tentatively propose that the interaction between the fatty acid chains' electric moment and the external magnetic field is driving the lipid tails in the hydrophobic membrane core into a better ordered state. PMID:26426063

  10. Strong Static Magnetic Fields Increase the Gel Signal in Partially Hydrated DPPC/DMPC Membranes

    PubMed Central

    Tang, Jennifer; Alsop, Richard J.; Schmalzl, Karin; Epand, Richard M.; Rheinstädter, Maikel C.

    2015-01-01

    It was recently reported that static magnetic fields increase lipid order in the hydrophobic membrane core of dehydrated native plant plasma membranes [Poinapen, Soft Matter 9:6804-6813, 2013]. As plasma membranes are multicomponent, highly complex structures, in order to elucidate the origin of this effect, we prepared model membranes consisting of a lipid species with low and high melting temperature. By controlling the temperature, bilayers coexisting of small gel and fluid domains were prepared as a basic model for the plasma membrane core. We studied molecular order in mixed lipid membranes made of dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) using neutron diffraction in the presence of strong static magnetic fields up to 3.5 T. The contribution of the hydrophobic membrane core was highlighted through deuterium labeling the lipid acyl chains. There was no observable effect on lipid organization in fluid or gel domains at high hydration of the membranes. However, lipid order was found to be enhanced at a reduced relative humidity of 43%: a magnetic field of 3.5 T led to an increase of the gel signal in the diffraction patterns of 5%. While all biological materials have weak diamagnetic properties, the corresponding energy is too small to compete against thermal disorder or viscous effects in the case of lipid molecules. We tentatively propose that the interaction between the fatty acid chains’ electric moment and the external magnetic field is driving the lipid tails in the hydrophobic membrane core into a better ordered state. PMID:26426063

  11. Direct observation by laser scanning confocal microscopy of microstructure and phase migration of PVC gels in an applied electric field.

    PubMed

    Xia, Hong; Ueki, Takamitsu; Hirai, Toshihiro

    2011-02-01

    The fluorescent probe lucigenin was incorporated in poly(vinyl chloride) (PVC) gels, and laser scanning confocal microscopy (LSCM) was used to clarify the internal structures of the gels. From the two-dimensional and three-dimensional information by LSCM, we first observed the internal structure of the PVC gel at a wet status, where the PVC gels comprised a polymer-rich phase and a polymer-poor phase uniformly with a three-dimensional network structure. After an electric field was applied, an effect of the electric field resulted in the change of internal structure in the gels. The polymer-poor phase moved from the cathode to the anode and the polymer-rich phase formed linelike arrangement between electrodes due to the attraction force. On the other hand, the freeze-dried PVC gels with/without in-situ dc voltage casting were particularly fabricated to confirm above results by the field emission scanning electron microscopy (FE-SEM). It was found that many craters remained on the surface of the gel near the anode due to sublimation in freeze-drying. This phenomenon did not appear on the surface near the cathode. The results of in-situ dc voltage casting also suggested that a substantial amount of polymer-poor phase was moved and fixed at the anode. Thus, results of both LSCM and in-situ dc voltage casting corresponded to the effect of electric field on PVC gels and provided a convincing evidence for the interpretation of the deformation mechanism of PVC gel actuators by an applied electric field. PMID:21174424

  12. Linear Dichroism of Chlorosomes from Chloroflexus Aurantiacus in Compressed Gels and Electric Fields

    PubMed Central

    van Amerongen, H.; Vasmel, H.; van Grondelle, R.

    1988-01-01

    The linear dichroism of chlorosomes from Chloroflexus aurantiacus was measured between 250 and 800 nm. To orient the chlorosomes we used a new way of compressing polyacrylamide gels, where the dimension of the gel along the measuring light-beam is kept constant. The press required for such a way of compressing is relatively easy to construct. A theoretical description is given to interpret the measured linear dichroism in terms of the orientation of the transition moments. The results obtained with the polyacrylamide gels are compared with the linear dichroism measurements for chlorosomes oriented in electric fields. Both the spectral features as well as the absolute size of the linear dichroism signals are in reasonable agreement. We find that the transition moment corresponding to the 741 nm bacteriochlorophyll c (Bchl c) absorption band makes an angle of 20° with the long axis of the chlorosome. For the 461 nm Bchl c band an angle of 30° is found. Both angles are significantly lower than the values reported so far in literature and they imply that Bchl c is highly organized in the chlorosomes. PMID:19431726

  13. Small field dose delivery evaluations using cone beam optical computed tomography-based polymer gel dosimetry

    PubMed Central

    Olding, Timothy; Holmes, Oliver; DeJean, Paul; McAuley, Kim B.; Nkongchu, Ken; Santyr, Giles; Schreiner, L. John

    2011-01-01

    This paper explores the combination of cone beam optical computed tomography with an N-isopropylacrylamide (NIPAM)-based polymer gel dosimeter for three-dimensional dose imaging of small field deliveries. Initial investigations indicate that cone beam optical imaging of polymer gels is complicated by scattered stray light perturbation. This can lead to significant dosimetry failures in comparison to dose readout by magnetic resonance imaging (MRI). For example, only 60% of the voxels from an optical CT dose readout of a 1 l dosimeter passed a two-dimensional Low's gamma test (at a 3%, 3 mm criteria, relative to a treatment plan for a well-characterized pencil beam delivery). When the same dosimeter was probed by MRI, a 93% pass rate was observed. The optical dose measurement was improved after modifications to the dosimeter preparation, matching its performance with the imaging capabilities of the scanner. With the new dosimeter preparation, 99.7% of the optical CT voxels passed a Low's gamma test at the 3%, 3 mm criteria and 92.7% at a 2%, 2 mm criteria. The fitted interjar dose responses of a small sample set of modified dosimeters prepared (a) from the same gel batch and (b) from different gel batches prepared on the same day were found to be in agreement to within 3.6% and 3.8%, respectively, over the full dose range. Without drawing any statistical conclusions, this experiment gives a preliminary indication that intrabatch or interbatch NIPAM dosimeters prepared on the same day should be suitable for dose sensitivity calibration. PMID:21430853

  14. Equilibrium intermediate-state patterns in a type-I superconducting slab in an arbitrarily oriented applied magnetic field

    SciTech Connect

    Clem, John; Prozorov, Ruslan; Wijngaarden, Rinke J.

    2013-09-04

    The equilibrium topology of superconducting and normal domains in flat type-I superconductors is investigated. Important improvements with respect to previous work are that (1) the energy of the external magnetic field, as deformed by the presence of superconducting domains, is calculated in the same way for three different topologies and (2) calculations are made for arbitrary orientation of the applied field. A phase diagram is presented for the minimum-energy topology as a function of applied field magnitude and angle. For small (large) applied fields, normal (superconducting) tubes are found, while for intermediate fields, parallel domains have a lower energy. The range of field magnitudes for which the superconducting-tubes structure is favored shrinks when the field is more in-plane oriented.

  15. Equilibrium intermediate-state patterns in a type-I superconducting slab in an arbitrarily oriented applied magnetic field

    DOE PAGESBeta

    Clem, John; Prozorov, Ruslan; Wijngaarden, Rinke J.

    2013-09-04

    The equilibrium topology of superconducting and normal domains in flat type-I superconductors is investigated. Important improvements with respect to previous work are that (1) the energy of the external magnetic field, as deformed by the presence of superconducting domains, is calculated in the same way for three different topologies and (2) calculations are made for arbitrary orientation of the applied field. A phase diagram is presented for the minimum-energy topology as a function of applied field magnitude and angle. For small (large) applied fields, normal (superconducting) tubes are found, while for intermediate fields, parallel domains have a lower energy. Themore » range of field magnitudes for which the superconducting-tubes structure is favored shrinks when the field is more in-plane oriented.« less

  16. Genetic profiling of Klebsiella pneumoniae: comparison of pulsed field gel electrophoresis and random amplified polymorphic DNA

    PubMed Central

    Ashayeri-Panah, Mitra; Eftekhar, Fereshteh; Ghamsari, Maryam Mobarak; Parvin, Mahmood; Feizabadi, Mohammad Mehdi

    2013-01-01

    In this study, the discriminatory power of pulsed field gel electrophoresis (PFGE) and random amplified polymorphic DNA (RAPD) methods for subtyping of 54 clinical isolates of Klebsiella pneumoniae were compared. All isolates were typeable by RAPD, while 3.6% of them were not typeable by PFGE. The repeatability of both typing methods were 100% with satisfying reproducibility (≥ 95%). Although the discriminatory power of PFGE was greater than RAPD, both methods showed sufficient discriminatory power (DI > 0.95) which reflects the heterogeneity among the K. pneumoniae isolates. An optimized RAPD protocol is less technically demanding and time consuming that makes it a reliable typing method and competitive with PFGE. PMID:24516423

  17. Simple, time saving pulsed-field gel electrophoresis protocol for the typing of Stenotrophomonas maltophilia.

    PubMed

    Shueh, Chong Seng; Neela, Vasanthakumari; Hussin, Salasawati; Hamat, Rukman Awang

    2013-08-01

    We developed a time-saving and cost-efficient Pulsed Field Gel Electrophoresis (PFGE) method for the typing of Stenotrophomonas maltophilia by modifying the conventional procedures. Our modifications related to the cell suspension preparation, lysis of bacterial cells in plugs, washing steps, and consumption of restriction enzyme. Although few rapid PFGE protocols on Gram-negative bacteria are available, the use of comparatively large amounts of costly reagents prompted us to look for other alternative. Hence, by considering the speed, simplicity, and relatively low cost, the modified protocol may be of more practical value than other established protocols in investigating S. maltophilia nosocomial outbreaks. PMID:23756145

  18. Genome size of human oral Treponema species by pulsed-field gel electrophoresis.

    PubMed

    Correia, F F; Plummer, A R; Paster, B J; Dewhirst, F E

    2004-04-01

    The genome sizes of seven strains of oral treponemes were determined using pulsed-field gel electrophoresis (PFGE). These strains represent members from six of the currently known cultivable oral treponeme groups. The PFGE fragments were digitally recorded and then quantitated using GIMP v 1.2, an image manipulation program. The results show that the six oral treponeme genomes are comparable in size, ranging from approximately 2.2 to 2.5 Mbp. The genome sizes of these strains are 20-25% smaller than Treponema denticola strains, which have genome sizes of approximately 2.8-3.0 Mbp. PMID:14871355

  19. Molecular karyotype analysis of Perkinsus atlanticus (Phylum Perkinsozoa) by pulsed field gel electrophoresis.

    PubMed

    Leonor Teles-Grilo, M; Duarte, Sérgio M; Tato-Costa, Joana; Gaspar-Maia, Alexandre; Oliveira, Carla; Rocha, António A; Marques, Américo; Cordeiro-da-Silva, Anabela; Azevedo, Carlos

    2007-11-01

    Perkinsus atlanticus is a pathogenic protist that infects the clam Ruditapes decussatus. Although it was recently proposed that the genus Perkinsus belongs to a new phylum, Perkinsozoa, in the infra-kingdom Alveolata, there remain different opinions about whether this genus should form a phylum on its own and consequently divergent views about its taxonomic characterization. In this work, we have identified nine chromosomes by pulsed field gel electrophoresis (PFGE) combined with densitometry analysis. The obtained karyotype of Perkinsus atlanticus, like that of other early branches of the dinoflagellate lineage, displays a more conventional chromosome organization, different from that of most dinoflagellates. PMID:17822886

  20. Optimization of pulsed-field gel electrophoresis protocols for Salmonella Paratyphi A subtyping.

    PubMed

    Chen, Chunxia; Zhao, Yingwei; Han, Hui; Pang, Bo; Zhang, Jingyun; Yan, Meiying; Diao, Baowei; Cui, Zhigang; Zhou, Haijian; Liang, Weili; Feng, Yanfang; Kan, Biao

    2012-04-01

    Salmonella enterica serovar Paratyphi A infection has caused public health problems in some countries in recent years. Pulsed-field gel electrophoresis (PFGE) has been used for the subtyping and epidemiological investigations of some serotypes of Salmonella, mainly in outbreaks caused by non-typhoidal Salmonella. In this study, different restriction endonucleases and electrophoresis parameters were compared for the PFGE subtyping by using Salmonella Paratyphi A strain panels. Two protocols for the enzymes SpeI and XbaI showed higher discriminatory power, which may facilitate epidemiological analysis for more accurate case definition, and clonality study of Salmonella Paratyphi A. PMID:22443482

  1. Model and field studies of the degradation of cross-linked polyacrylamide gels used during the revegetation of slate waste.

    PubMed

    Holliman, Peter J; Clark, Jennifer A; Williamson, Julie C; Jones, Davey L

    2005-01-01

    Cross-linked polyacrylamide gels are increasingly being used in environmental restoration schemes and horticulture as a means of enhancing water supply to plants. However, the environmental impact of cross-linked polyacrylamide gel deployment in soil remains poorly understood. This study assessed the chemical, physical and biological properties of new and field-conditioned cross-linked polyacrylamide gels. Both monomeric acrylamide (11 microg l(-1)) and acrylic acid (285 microg l(-1)) were observed in new gel; however, the levels of monomers in field-conditioned gels (1-6 years old) were very low (acrylamide <1 microg l(-1); acrylic acid <7 microg l(-1)). Generally, freeze-thaw processes and exposure to UV radiation had little effect on gel acrylic acid and acrylamide concentrations. However, elevated temperatures (35 degrees C) caused a significant release of up to 144 mug l(-1) of acrylamide and 453 microg l(-1) of acrylic acid in new gel and up to 25 microg l(-1) of acrylamide and 157 microg l(-1) of acrylic acid in field-conditioned gels. In contrast, gel water holding capacity was highly dependent upon environmental conditions (UV exposure and freeze/thaw cycles produced the greatest loss of water holding in new gels) and gel age. Optical microscopy revealed that after placement in the field the gels became increasingly colonised over time by fungi and bacteria. In enrichment cultures, we were unable, however, to demonstrate microbial growth when cross-linked polyacrylamide was used as the sole nitrogen source. In summary, under a range of conditions cross-linked polyacrylamide did not release acrylamide above legally permitted limits, with the exception of gel subjected to elevated temperatures. However, their capacity for holding water decreased sharply within 18 months. We therefore conclude that cross-linked polyacrylamide placed in soil is relatively stable with respect to the production of potentially toxic acrylamide, a species with a short half

  2. XPCS study of dynamic correlation in polyurethane gel-carbonyl iron composite under magnetic field

    NASA Astrophysics Data System (ADS)

    Grigoriew, Helena; Wiegart, Lutz; Boczkowska, Anna; Mirkowska, Monika

    2010-10-01

    An X-ray photon correlation spectroscopy (XPCS) study of composite-type material consisting of polyurethane gel and carbonyl iron micrometric spheres was performed under magnetic fields of 0, 300 and 600 mT. The onion-like spheres structure was destroyed during the composite processing. The following conclusions were obtained from the study: -The polyurethane matrix is preferred as a source for the observed dynamic effects. -Below 300mT the material dynamics in direction of the outer magnetic field are very clear. -For 600 mT the dependence of the dynamics on magnetic field direction disappears, but the correlation rate is much higher. These findings may be caused by a disturbance of the polymer mesostructure by larger strain leading to its cross-linking.

  3. Conformational Entropy Mechanism for Periodic Motion of DNA under Constant-Field Gel Electrophoresis

    NASA Astrophysics Data System (ADS)

    Azuma, Ryuzo; Takayama, Hajime

    2006-06-01

    Entropic elasticity of a single charged polymer undergoing gel electrophoresis is a fundamental theme of polymer statistical physics since the discovery of “periodic” behavior in constant field gel electrophoresis (CFGE). In the present work we address the problem numerically by two steps. In the first step, we carry out Brownian dynamics (BD) simulations on CFGE by solving semi-microscopic Langevin equations of a polymer consisting of beads separated by a mean distance much smaller than the Kuhn length. Results are analyzed based on coarse-graining over the Kuhn length scale. We show the averaged elongation-contraction motion involves asymmetric V-shaped configurations whose shorter arm length depends on the field and the temperature consistently with what is expected when the BD chain is described by the freely-jointed chain (FJC) model with a suitable Kuhn length. To our knowledge, this is the first numerical confirmation of the FJC model itself from a submicroscopic description of polymer motion. The saturation of chain mobility in high fields agrees well with the nonlinear dependence of this shorter arm length on the field. In the second step, we discuss the periodic elongation-contraction motion of the coarse-grained chain by such a simplified model as a one-dimensional chain consisting of beads, elastic strings, and obstacles. The results from these two chain models indicate that the periodic elongation-contraction motion of DNA under CFGE is self-organized by a balance between the field force and the conformational entropic force.

  4. Theory of gel electrophoresis in high fields: Evolution of a population of hernias

    NASA Astrophysics Data System (ADS)

    Long, Didier; Viovy, Jean-Louis

    1997-02-01

    We consider long polyelectrolytes that are initially at rest in a gel and suddenly submitted to a strong electric field. The evolution of the conformation regime is described up to the final disengagement from the initial tube. Just after the field has been applied, the chain adopts a comb-like conformation with several “hernias”, which evolve in competition with each other. As long as the conformation has many hernias, the distribution of their size follows a self-similar law, first described by Deutsch. The number of hernias decreases, and ultimately the chain disengages from its initial tube. Various predictions for the conformation of the chain in this last stage and for time constants are proposed. In particular, the disengagement times are found to follow a self-similar law in the size of the chains.

  5. Molecular Epidemiology of Mycobacterium tuberculosis Isolates in 100 Patients With Tuberculosis Using Pulsed Field Gel Electrophoresis

    PubMed Central

    Pooideh, Mohammad; Jabbarzadeh, Ismail; Ranjbar, Reza; Saifi, Mahnaz

    2015-01-01

    Background: Tuberculosis (TB) is a widespread infectious disease. Today, TB has created a public health crisis in the world. Genotyping of Mycobacterium tuberculosis isolates is useful for surveying the dynamics of TB infection, identifying new outbreaks, and preventing the disease. Different molecular methods for clustering of M. tuberculosis isolates have been used. Objectives: During a one year study of genotyping, 100 M. tuberculosis isolates from patients referred to Pasteur Institute of Iran were collected and their genotyping was accomplished using pulsed field gel electrophoresis (PFGE) method. Materials and Methods: Identification of all M. tuberculosis isolates was accomplished using standard biochemical and species-specific polymerase chain reaction (PCR) methods. Antibiotic susceptibility tests were performed using proportional method. After preparing PFGE plaques for each isolate of M. tuberculosis, XbaI restriction enzyme was applied for genome digestion. Finally, the digested DNA fragments were separated on 1% agarose gel and analyzed with GelCompar II software. Results: Genotyping of the studied isolates in comparison with the molecular weight marker revealed two common types; pulsotype A with 71 isolates and one multidrug resistant mycobacterium (MDR) case, and pulsotype B including 29 isolates and three MDR cases. No correlation between the antibiotypes and pulsotypes was observed. Conclusions: Molecular epidemiology studies of infectious diseases have been useful when bacterial isolates have been clustered in a period of time and in different geographical regions with variable antibiotic resistance patterns. In spite of high geographical differences and different antibiotic resistant patterns, low genetic diversity among the studied TB isolates may refer to the low rate of mutations in XbaI restriction sites in the mycobacterial genome. We also identified three MDR isolates in low-incidence pulsotype B, which could be disseminated and is highly

  6. Dc to ac field conversion due to leaky-wave excitation in a plasma slab behind an ionization front

    NASA Astrophysics Data System (ADS)

    Kostin, V. A.; Vvedenskii, N. V.

    2015-03-01

    We present a way for generating coherent tunable electromagnetic radiation through dc to ac field conversion by an ionization front. The conversion is caused by the excitation of leaky waves behind the transversely limited ionization front propagating in a uniform electrostatic field. This differs significantly from the well-known dc-to-ac-radiation-converter models which consider Doppler-like frequency conversion by a transversely unlimited ionization front propagating in a spatially periodic electric field. We explore the dispersion properties and excitation of these leaky waves radiated through the transverse plasma boundary at the Cherenkov angle to the direction of propagation of a superluminal ionization front as dependent on the parameters of the plasma produced and on the speed of the ionization front. It is shown that not only the center frequency but also the duration and waveform of the generated pulse may significantly depend on the speed of the ionization front. The results indicate the possibility of using such converters based on planar photoconductive antennas to create sources of microwave and terahertz radiation with controllable waveforms that are transformed from video to radio pulse when the angle of incident ionizing radiation is tuned.

  7. Sausage oscillations of coronal plasma slabs

    NASA Astrophysics Data System (ADS)

    Hornsey, C.; Nakariakov, V. M.; Fludra, A.

    2014-07-01

    Context. Sausage oscillations are observed in plasma non-uniformities of the solar corona as axisymmetric perturbations of the non-uniformity. Often, these non-uniformities can be modelled as field-aligned slabs of the density enhancement. Aims: We perform parametric studies of sausage oscillations of plasma slabs, aiming to determine the dependence of the oscillation period on its parameters, and the onset of leaky and trapped regimes of the oscillations. Methods: Slabs with smooth transverse profiles of the density of a zero-beta plasma are perturbed by an impulsive localised perturbation of the sausage symmetry. In particular, the slab can contain an infinitely thin current sheet in its centre. The initial value problem is then solved numerically. The numerical results are subject to spectral analysis. The results are compared with analytical solutions for a slab with a step-function profile and also with sausage oscillations of a plasma cylinder. Results: We established that sausage oscillations in slabs generally have the same properties as in plasma cylinders. In the trapped regime, the sausage oscillation period increases with the increase in the longitudinal wavelength. In the leaky regime, the dependence of the period on the wavelength experiences saturation, and the period becomes independent of the wavelength in the long-wavelength limit. In the leaky regime the period is always longer than in the trapped regime. The sausage oscillation period in a slab is always longer than in a cylinder with the same transverse profile. In slabs with steeper transverse profiles, sausage oscillations have longer periods. The leaky regime occurs at shorter wavelengths in slabs with smoother profiles.

  8. 5 × 5 cm2 silicon photonic crystal slabs on glass and plastic foil exhibiting broadband absorption and high-intensity near-fields

    PubMed Central

    Becker, C.; Wyss, P.; Eisenhauer, D.; Probst, J.; Preidel, V.; Hammerschmidt, M.; Burger, S.

    2014-01-01

    Crystalline silicon photonic crystal slabs are widely used in various photonics applications. So far, the commercial success of such structures is still limited owing to the lack of cost-effective fabrication processes enabling large nanopatterned areas (≫ 1 cm2). We present a simple method for producing crystalline silicon nanohole arrays of up to 5 × 5 cm2 size with lattice pitches between 600 and 1000 nm on glass and flexible plastic substrates. Exclusively up-scalable, fast fabrication processes are applied such as nanoimprint-lithography and silicon evaporation. The broadband light trapping efficiency of the arrays is among the best values reported for large-area experimental crystalline silicon nanostructures. Further, measured photonic crystal resonance modes are in good accordance with light scattering simulations predicting strong near-field intensity enhancements greater than 500. Hence, the large-area silicon nanohole arrays might become a promising platform for ultrathin solar cells on lightweight substrates, high-sensitive optical biosensors, and nonlinear optics. PMID:25073935

  9. Separation of chromosomal DNA molecules from yeast by orthogonal-field-alternation gel electrophoresis.

    PubMed Central

    Carle, G F; Olson, M V

    1984-01-01

    A simple agarose-gel apparatus has been developed that allows the separation of DNA molecules in the size range from 50 kb to well over 750 kb, the largest size for which size standards were available. The apparatus is based on the recent discovery that large DNA molecules are readily fractionated on agarose gels if they are alternately subjected to two approximately orthogonal electric fields. The switching time, which was on the order of 20-50 sec in our experiments, can be adjusted to optimize fractionation in a given size range. The resolution of the technique is sufficient to allow the fractionation of a sample of self-ligated lambda DNA into a ladder of approximately 15 bands, spaced at 50 kb intervals. We have applied the technique to the fractionation of yeast DNA into 11 distinct bands, several of which have been shown by DNA-DNA hybridization to hybridize uniquely to different chromosome-specific hybridization probes. In this paper, we describe the design of the apparatus, the electrophoretic protocol, and the sample-handling procedures that we have employed. Images PMID:6379602

  10. Segmentation of 2D gel electrophoresis spots using a Markov random field

    NASA Astrophysics Data System (ADS)

    Hoeflich, Christopher S.; Corso, Jason J.

    2009-02-01

    We propose a statistical model-based approach for the segmentation of fragments of DNA as a first step in the automation of the primarily manual process of comparing two or more images resulting from the Restriction Landmark Genomic Scanning (RLGS) method. These 2D gel electrophoresis images are the product of the separation of DNA into fragments that appear as spots on X-ray films. The goal is to find instances where a spot appears in one image and not in another since a missing spot can be correlated with a region of DNA that has been affected by a disease such as cancer. The entire comparison process is typically done manually, which is tedious and very error prone. We pose the problem as the labeling of each image pixel as either a spot or non-spot and use a Markov Random Field (MRF) model and simulated annealing for inference. Neighboring spot labels are then connected to form spot regions. The MRF based model was tested on actual 2D gel electrophoresis images.

  11. Deepest hypocentral distributions associated with stagnant slabs and penetrated slabs

    NASA Astrophysics Data System (ADS)

    Fukao, Y.; Obayashi, M.

    2013-12-01

    We constructed a new P-wave tomographic model of the mantle, GAP_P4, using more than ten millions of travel time data, including waveform-based differential travel times from ocean bottoms, to all of which the finite frequency kernels were applied in the inversion. Based on this model, we made a systematic survey for subducted slab images around the Circum Pacific. This survey revealed a progressive lateral variation of slab configuration along arc(s), where a subducted slab is in general in one or two of the following four stages: I. slab stagnant above the 660, II. slab penetrating the 660, III. slab trapped in the uppermost lower mantle (660 to ˜1000 km in depth), and IV. slab descending well into the deep lower mantle. The majority of the slab images are either at stage I or III. We interpret I to IV as the successive stages of slab subduction through the transition region with the 660 at the middle. There is a remarkable correlation of the slab configuration with the deepest shock hypocentral distribution. Subhorizontal distributions of deepest shocks are associated with stagnant slabs in the transition zone (slabs at stage I). Their focal depths are limited to shallower than ˜620 km. Steeply dipping deepest shock distributions are associated with penetrating slabs across the 660-km discontinuity or trapped slabs below it (slabs at stages II and III). Their focal depths extend well beyond ˜620 km. There are no cases of association of either a stagnant slab (at stage I) with subvertical distribution of deepest shocks or a trapped slab (at stage II or III) with their subhorizontal distribution. Only steeply dipping slabs appear to penetrate the 660 to be trapped in the uppermost lower mantle. The along-arc variations of stagnant-slab configuration and deepest shock distribution beneath the Bonin arc indicate a process of how the slab begins to penetrate the 660-km discontinuity after the slab stagnation. Those beneath the Java arc and Kermadec arc commonly

  12. Laboratory and field evaluation of an indoxacarb gel bait against two cockroach species (Dictyoptera: Blattellidae, Blattidae) in Lagos, Nigeria.

    PubMed

    Anikwe, Joseph Chuks; Adetoro, Fouad Abidemi; Anogwih, Joy Anuri; Makanjuola, Winifred Ayinke; Kemabonta, Kehinde Abike; Akinwande, Kayode Lawrence

    2014-08-01

    Indoxacarb gel bait was evaluated for its efficacy in the laboratory and field against American cockroaches, Periplaneta americana (L.), and German cockroaches, Blattella germanica (L.). Advion 0.6% indoxacarb gel bait was toxic to both P. americana and B. germanica. There were no significant differences in the LT50 (h) values for treatment levels of 0.25 g, 0.5 g, and 1.0 g gel applied against P. americana, whereas gel applied at 0.5 g to B. germanica had a significantly greater LT50 (h) in the laboratory than the gel treatments on P. americana. The LT50 for both cockroach species ranged from 40.65 to 145.60 h. There was no control mortality in the laboratory bioassays. In the field, 55 houses were treated with 0.5 g of 6-8 spots of indoxacarb gel bait per kitchen of two or three bedroom bungalows from three Local Government Areas of Lagos State, comprising Surulere (22), Alimosho (12), and Shomolu (21). Mean reduction in cockroach populations varied from location to location based on the level of infestations. Percentage reductions in the indoxacarb gel-treated units ranged from 3.5% at 1 d after treatment to 99.8% at 14 d at Surulere, while reductions ranged from 8.9% at 1 d after treatment to 99.7% at 14 d at Shomolu; a similar trend was observed for Alimosho. Indoxacarb gel bait was highly effective in the control of cockroaches. PMID:25195457

  13. Campylobacter coli pulsed field gel electrophoresis genotypic diversity among sows and piglets in a farrowing barn.

    PubMed

    Hume, Michael E; Droleskey, Robert E; Sheffield, Cynthia L; Harvey, Roger B

    2002-08-01

    Genotypes of Campylobacter coli isolates from feces of three sows and rectal swabs of 17 piglets were examined by pulsed field gel electrophoresis (PFGE). All of the animals originated from a single farrowing barn of a farrow-to-finish swine operation. Five Campylobacter colonies were picked from a single agar plate for each sample after broth enrichment and growth on Campy-Cefex agar. Genotypes were examined by PFGE after genomic DNA digestion with SmaI and SacII restriction endonucleases. Twenty SmaI genotypes and 12 SacII genotypes were detected among 99 Campylobacter coli isolates. There was no pattern of shared genotypes between sows and their respective piglets, nor between littermates. Results indicate that a high number of Campylobacter genotypes may coexist in related pigs from a single housing facility. PMID:12070692

  14. Molecular analysis of chromosomal rearrangements using pulsed field gel electrophoresis and somatic cell hybrids

    SciTech Connect

    Davis, L.M. )

    1991-01-01

    Many human genetic diseases, including some cancers, are characterized by consistent chromosome abnormalities, such as deletions and translocations. Analyses of these mutations often prove crucial to the eventual cloning and characterization of the gene(s) responsible for the disease. Two methods for analyzing these chromosome abnormalities have been developed in recent years: somatic cell hybridization and pulsed field gel electrophoresis (PFGE). Somatic cell hybridization is a technique for segregating an aberrant chromosome from its normal homologue in a cell derived from an unrelated species, which is usually a rodent. Demonstrations of these analytic techniques are presented, using as an example chromosomal abnormalities involving human chromosome band 11p13, the locus for the Wilms' tumor, aniridia, genitourinary abnormality, and mental retardation (WAGR) syndrome.

  15. Epidemiological investigation of Salmonella tilene by pulsed-field gel electrophoresis and polymerase chain reaction

    PubMed Central

    Anand, Chandar M; Fonseca, Kevin; Longmore, Ken; Rennie, Robert; Chui, Linda; Lingley, Mike; Woodward, David

    1997-01-01

    Pulsed-field gel electrophoresis (PFGE) and DNA fingerprinting by the polymerase chain reaction (PCR) were performed on 11 isolates of Salmonella tilene. Five strains were from a cluster of human patients, six from sugar gliders and pygmy hedgehogs kept as family pets or from local pet retailers, and one isolate from the first North American case of S tilene described in Washington State in 1994. The PFGE restriction patterns showed all isolates to be similar. However, PCR using primers to the 16S and 23S rRNA genes of Escherichia coli demonstrated that the Washington State isolate differed from the rest of the other isolates, which were all similar based upon their DNA fingerprint. This study indicates that reliance on one technique alone may be insufficient to show nuances between strains that are, in many respects, closely related. PMID:22346526

  16. Epidemiological typing of Flavimonas oryzihabitans by PCR and pulsed-field gel electrophoresis.

    PubMed

    Liu, P Y; Shi, Z Y; Lau, Y J; Hu, B S; Shyr, J M; Tsai, W S; Lin, Y H; Tseng, C Y

    1996-01-01

    Flavimonas oryzihabitans has emerged as a potential nosocomial pathogen in recent years. The typing method for characterization of this species has never been reported before. Pulsed-field gel electrophoresis (PFGE) and enterobacterial repetitive intergenic consensus (ERIC)-based PCR were used to generate DNA fingerprints for 14F. oryzihabitans isolates obtained from eight episodes of nosocomial infections during a 2-year period. Both techniques successfully classified these clinical isolates into eight distinct genotypes, thus indicating that all of these episodes of infections were independent. In contrast, repeated isolates from the same patient were assigned to identical genotypes. The reproducibility of both techniques was good. Therefore, we conclude that both PFGE and ERIC-PCR have comparable reproducible and discriminatory powers for the typing of F. oryzihabitans and may be useful for clarifying the epidemiology of this species; however, ERIC-PCR has the advantages of both speed and simplicity. PMID:8748275

  17. Characterization of Listeria monocytogenes isolates from cattle and ground beef by pulsed-field gel electrophoresis.

    PubMed

    Foerster, Claudia; Vidal, Lorena; Troncoso, Miriam; Figueroa, Guillermo

    2012-01-01

    The aims of this study were to determine the occurrence of Listeria monocytogenes in cattle feces and ground beef, to characterize these strains by pulsed-field gel electrophoresis and to compare them to three listeria strains found in humans. Cattle from different origins (n = 250) and ground beef obtained from supermarkets (n = 40) were sampled. The results show low occurrence in cattle feces (0.4 %) but a higher presence in ground beef (37 %). An important part of the ground beef strains (80 %) had > 95 % similarity with a strain isolated from a human sporadic case and the ATCC 19115 used as control. The strain isolated from cattle feces had 93 % similarity to clone 009, previously associated with a listeriosis outbreak related to cheese. Cattle and ground beef can harbor virulent L. monocytogenes strains. Further studies in animals and animal products are needed to improve listeriosis control. PMID:23102469

  18. Derivation of clones close to met by preparative field inversion gel electrophoresis

    SciTech Connect

    Michiels, F.; Burmeister, M.; Lehrach, H.

    1987-06-05

    The molecular analysis of genes identified by mutations is a major problems in mammalian genetics. As a step toward this goal, preparative field inversion gel electrophoresis (FIGE) was used to selectively isolate clones from the environment of genetically linked markers, and to select a subset of these clones containing sequences next to specific restriction sites rare in mammalian DNA. This approach has been used to generate a library highly enriched in sequences closely linked to the cystic fibrosis marker met. One clone derived from the end of a Not I restriction fragment containing the met sequence was analyzed in detail and localized within a long range map to a position of 300 kilobase pairs 5' of the metD sequence.

  19. Austin Chalk: cross-link gel water, slick water fracs common in Giddings field

    SciTech Connect

    Mickey, V.

    1981-05-01

    Of the approx. 600 wells drilled in the Giddings field, Austin Chalk trend in the last year, most were probably completed by cross-link gel fracs or slick water fracs. Although open hole completions are not uncommon in the chalk, they are not really practical in most situations, given the 600 to 800 ft of gross pay usually encountered in the Austin Chalk trend. Most of the open hole completions occur when an operator takes a kick while drilling and decides to drop a mud pill over the zone, run casing above it, cement it in and produce the interval open hole. Chalk wells are subject to kick at any time during drilling because of natural fracturing systems throughout the trend. Mud weights are generally fairly light for faster drilling, approx. 9.4 to 9.8 lb, depending on the particular area.

  20. Epidemiologic study of Taylorella equigenitalis strains by field inversion gel electrophoresis of genomic restriction endonuclease fragments.

    PubMed

    Bleumink-Pluym, N; ter Laak, E A; van der Zeijst, B A

    1990-09-01

    Contagious equine metritis (CEM), a sexually transmitted bacterial disease, was first described in thoroughbred horses. It also occurs in nonthoroughbred horses, in which it produces isolated, apparently unrelated outbreaks. Thirty-two strains of Taylorella equigenitalis, the causative agent of CEM, from all over the world were characterized by field inversion gel electrophoresis of fragments of genomic DNA obtained by digestion with low-cleavage-frequency restriction enzymes. This resulted in a division into five clearly distinct groups. Strains from thoroughbred horses from all continents belonged to one group. Strains from nonthoroughbred horses from various countries were different from strains from thoroughbred horses; four groups could be determined. Two groups contained both streptomycin-resistant and streptomycin-susceptible strains. The data indicate that CEM in nonthoroughbreds did not originate from the thoroughbred population; also, the reverse was not demonstrated. Thus, extensive international transportation directives regarding the testing of nonthoroughbred horses for CEM may need reconsideration. PMID:2172296

  1. Micro gel column technique is fit for detecting mixed fields post ABO incompatible hematopoietic stem cell transplantation.

    PubMed

    Li, Min-Fang; Liu, Feng; Zhang, Min

    2015-04-01

    How to choose suitable serologic method for assessment of the actual stages of ABO chimera is more important to establish transfusion strategy for patients post-ABO incompatible hematopoietic stem cell transplantation. We reported ABO phenotypes of a patient post-ABO minor incompatible hematopoietic stem cell transplantation from 1+ weak agglutination by tube method was obviously reaffirmed to mixed fields with 4+ positive reaction by micro gel column card. Hence, blood bank technologists must continually work together with hematologist to establish appropriate transfusion strategy, and micro gel column technique can be more appropriate for detecting mixed fields during the whole period of transplantation. PMID:25578650

  2. DNA electrophoresis in agarose gels: Effects of electric field and gel concentration on the exponential dependence of reciprocal mobility on DNA length

    NASA Astrophysics Data System (ADS)

    Beheshti, Afshin; van Winkle, David; Randolph, Rill

    2002-03-01

    Electrophoresis was performed on double stranded DNA fragments ranging in length from 200 bp to 48502 bp at agarose gel concentrations T = 0.5% - 1.5% and electric fields E = 0.71 V/cm to 5 V/cm. A wide range of electric fields and gel concentrations were used to find what range of conditions work with the new interpolation equation, 1/μ(L) = 1/μl - (1/μl - 1/μ_s)e^-L/γ. The equation fit extremely well (\\chi^2 >= 0.999) to data with E = 2.5 V/cm to 5 V/cm and for lower fields (E < 2.5 V/cm) at low gel concentrations (T = 0.5% and 0.7%). This exponential relation seemed to hold when there is a smooth transition from the Ogston sieving regime to the reptation regime when looking at the “reptation plots” (plotting 3μL/μo vs. L) (Rousseau, J., Drouin, G., and Slater, G. W., Phys Rev Lett. 1997, 79, 1945-1948). For separations of single-stranded DNA in polyacrylamide, similar reptation plots have a region with a negative slope between the Ogston sieving regime and the reptation regime which has been interpreted as the signature of entropic trapping. When separating double-stranded DNA in agarose it was observed that fits deviate from the data when three different slopes are observed in the reptation plots. Failure of the simple exponential relationship between reciprocal mobility and DNA length appears to be the consequence of entropic trapping.

  3. Polyelectrolyte gels

    SciTech Connect

    Segalman, D.J.; Witkowski, W.R.

    1995-06-01

    Polyelectrolyte (PE) gels are swollen polymer/solvent networks that undergo a reversible volume collapse/expansion through various types of stimulation. Applications that could exploit this large deformation and solvent expulsion/absorption characteristics include robotic {open_quotes}fingers{close_quotes} and drug delivery systems. The goals of the research were to first explore the feasibility of using the PE gels as {open_quotes}smart materials{close_quotes} - materials whose response can be controlled by an external stimulus through a feedback mechanism. Then develop a predictive capability to simulate the dynamic behavior of these gels. This involved experimentally characterizing the response of well-characterized gels to an applied electric field and other stimuli to develop an understanding of the underlying mechanisms which cause the volume collapse. Lastly, the numerical analysis tool was used to simulate various potential engineering devices based on PE gels. This report discusses the pursuit of those goals through experimental and computational means.

  4. Safety Evaluation of Self-assembling Peptide Gel after Intracranial Administration to Rats Using the Open Field Test.

    PubMed

    Tsunoda, Masashi; Sugaya, Chiemi; Sugiura, Yumiko; Nagai, Yusuke; Sakanishi, Kotaro

    2016-01-01

    Self-assembling peptides have been developed as clinical materials, which could scaffold to regenerate nerve cells and hemostatic materials in vivo. However, there has not been enough information for their in vivo application. The safety of self-assembling peptides for the application on the brain was examined using behavioral tests for each rat in this study. Self-assembling peptide gel was administered to the surface of the brain at a volume of 20 µL at 1.5%. After 2 months, the open field test and the prepulse inhibition (PPI) test were performed. There were no significant differences between the peptide gel and the control groups in locomotor distances and in %PPIs in the PPI test. The mean values of the percentage of time the rats stayed in the central area of the open field during the first 5 min and instances of center rearing or face washing in the peptide gel group were significantly higher than those in the control. There were amorphous substance in the subarachnoid region, and infiltrations of mononuclear cells were also observed in the self-assembling peptide gel group. Although the meaning of the effects observed in this study was not fully elucidated, the self-assembling gel produced marginal but significant behavioral and histological effects. PMID:27582322

  5. Pulsed-field gel electrophoresis of the genomic restriction fragments of coagulase-negative staphylococci.

    PubMed

    Snopková, S; Götz, F; Doskar, J; Rosypal, S

    1994-12-01

    The genomes of 47 coagulase-negative staphylococcal strains assigned to different species were analysed by pulsed-field electrophoresis. The strains were clustered on the basis of their similarity in the SmaI restriction patterns into various groups, each group consisting of the type strain and the strains whose SmaI restriction patterns were similar to that of the type of strain. The SmaI restriction groups seem to correspond to the following species: Staphylococcus warneri, S. hominis, S. xylosus, S. lugdunensis, S. kloosii, S. haemolyticus, S. lentus, S. cohnii, S. equorum, S. chromogenes, S. saprophyticus, S. simulans, S. carnosus, S. capitis and S. auricularis. The species S. sciuri, S. caseolyticus, S. gallinarum, S. epidermidis and S. schleiferi were represented only by their type strains and showed no similarity in their SmaI restriction patterns neither to each other nor to all the other species investigated here. Thus, the classification of coagulase-negative staphylococcal strains into the above species seems to be confirmed also by genome restriction analysis carried out by pulsed-field gel electrophoresis. PMID:7813882

  6. Pulsed Field Gel Electrophoresis along with Antimicrobial Resistance pattern of Salmonella serotypes isolated from broiler whole carcass rinses

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Pulsed field gel electrophoresis (PFGE) and antibiogram patterns have been used to evaluate the diversity within and between individual Salmonella serotypes. The objectives of the study were to evaluate the PFGE along with antimicrobial resistance patterns of Salmonella isolates originating from br...

  7. Application of multiplex PCR, pulsed-field gel electrophoresis (PFGE), and BOX-PCR for molecular analysis of enterococci

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objective of the study was to use band-based molecular methods including BOX-PCR (Polymerase Chain Reaction) and Pulsed-Field Gel Electrophoresis (PFGE) to determine if genetically related enterococci were found among different stores, food types, or years. Enterococci were also characterized f...

  8. Implementation of Salmonella serotype determination using pulsed-field gel electrophoresis in a state public health laboratory.

    PubMed

    Bopp, Dianna J; Baker, Deborah J; Thompson, Lisa; Saylors, Amy; Root, Timothy P; Armstrong, Leeanna; Mitchell, Kara; Dumas, Nellie B; Musser, Kimberlee Arruda

    2016-08-01

    We examined the use of pulsed-field gel electrophoresis (PFGE) to predict serotype for Salmonella isolates. Between 2012 and 2014 we assessed 4481 isolates, resulting in >90% assigned serotypes. PFGE is efficient for determining serotype in the majority of cases and results in expedited serotype determination, as well as cost savings. PMID:27220605

  9. Characterization of Salmonella isolates from retail foods based on serotyping, pulse field gel electrophoresis, antibiotic resistance and other phenotypic properties

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Sixteen Salmonella strains isolated from a variety of foods during 2000 and 2003, by the Florida State Department of Agriculture, were characterized by various genotypic and phenotypic tests. Among 16 isolates, 15 different serotypes were identified. Pulse-Field Gel Electrophoresis (PFGE) fingerpr...

  10. Improved Pulsed-Field Gel Electrophoresis Procedure for the Analysis of F. columnare Isolates Previously Affected by DNA Degradation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Flavobacterium columnare is a fresh water bacterium that causes columnaris diseases in over 36 fish species. Intra-species typing of F. columnare can be performed by pulsed-field gel electrophoresis (PFGE). However, this method is hampered by the degradation of chromosomal DNA in about 10% of strain...

  11. Genetic diversity demonstrated by pulsed field gel electrophoresis of Salmonella enterica isolates obtained from diverse sources in Mexico

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This study was conducted to determine the genetic diversity of Salmonella isolates recovered from a variety of sources using pulsed-field gel electrophoresis (PFGE) to assess their possible relatedness. Salmonella was isolated from ca. 52% of samples from a pepper var. Bell production system. A to...

  12. Sample collection system for gel electrophoresis

    SciTech Connect

    Olivares, Jose A.; Stark, Peter C.; Dunbar, John M.; Hill, Karen K.; Kuske, Cheryl R.; Roybal, Gustavo

    2004-09-21

    An automatic sample collection system for use with an electrophoretic slab gel system is presented. The collection system can be used with a slab gel have one or more lanes. A detector is used to detect particle bands on the slab gel within a detection zone. Such detectors may use a laser to excite fluorescently labeled particles. The fluorescent light emitted from the excited particles is transmitted to low-level light detection electronics. Upon the detection of a particle of interest within the detection zone, a syringe pump is activated, sending a stream of buffer solution across the lane of the slab gel. The buffer solution collects the sample of interest and carries it through a collection port into a sample collection vial.

  13. Cordilleran slab windows

    SciTech Connect

    Thorkelson, D.J.; Taylor, R.P. )

    1989-09-01

    The geometry and geologic implications of subducted spreading ridges are topics that have bedeviled earth scientists ever since the recognition of plate tectonics. As a consequence of subduction of the Kula-Farallon and East Pacific rises, slab windows formed and migrated beneath the North American Cordillera. The probable shape and extent of these windows, which represent the asthenosphere-filled gaps between two separating, subducting oceanic plates, are depicted from the Late Cretaceous to the present. Possible effects of the existence and migration of slab windows on the Cordillera at various times include cessation of arc volcanism and replacement by rift or plate-edge volcanism; lithospheric uplift, attenuation, and extension; and increased intensity of compressional tectonism. Eocene extensional tectonism and alkaline magmatism in southern British Columbia and the northwestern United States were facilitated by slab-window development.

  14. Separation of long linear polymers in gel electrophoresis with alternating electric fields: A theoretical study using the necklace model

    NASA Astrophysics Data System (ADS)

    Terranova, G. R.; Mártin, H. O.; Aldao, C. M.

    2012-06-01

    The necklace model, which mimics the reptation of a chain of N beads in a square lattice, is used to study the drift velocity of charged linear polymers in gels under an applied electric field that periodically changes its direction. The characteristics of the model allow us to determine the effects of the alternating electric field on the chains’ dynamics. We explain why chains of different N can be made to move in opposite directions with a nonuniform electric field with certain values of intensity and frequency. The key point is that, when alternating electric fields are applied, longer chains spend more time out of the steady-state regime than lower chains. Numerical results are obtained by means of Monte Carlo simulations and they are qualitatively in agreement with experiments of DNA migration in gel electrophoresis.

  15. Molecular Analysis of Mycobacterium avium Isolates by Using Pulsed-Field Gel Electrophoresis and PCR

    PubMed Central

    Pestel-Caron, Martine; Graff, Gabriel; Berthelot, Gilles; Pons, Jean-Louis; Lemeland, Jean-François

    1999-01-01

    Genetic relationships among 46 isolates of Mycobacterium avium recovered from 37 patients in a 2,500-bed hospital from 1993 to 1998 were assessed by pulsed-field gel electrophoresis (PFGE) and PCR amplification of genomic sequences located between the repetitive elements IS1245 and IS1311. Each technique enabled the identification of 27 to 32 different patterns among the 46 isolates, confirming that the genetic heterogeneity of M. avium strains is high in a given community. Furthermore, this retrospective analysis of sporadic isolates allowed us (i) to suggest the existence of two remanent strains in our region, (ii) to raise the question of the possibility of nosocomial acquisition of M. avium strains, and (iii) to document laboratory contamination. The methods applied in the present study were found to be useful for the typing of M. avium isolates. In general, both methods yielded similar results for both related and unrelated isolates. However, the isolates in five of the six PCR clusters were distributed among two to three PFGE patterns, suggesting that this PCR-based method may have limitations for the analysis of strains with low insertion sequence copy numbers or for resolution of extended epidemiologic relationships. PMID:10405383

  16. Rapid identification of Pseudomonas aeruginosa by pulsed-field gel electrophoresis

    PubMed Central

    Selim, Samy; El Kholy, Iman; Hagagy, Nashwa; El Alfay, Sahar; Aziz, Mohamed Abdel

    2015-01-01

    Twenty clinical Pseudomonas aeruginosa isolates recovered from patients admitted to The General Hospital in Ismailia Governorate (Egypt) were examined in this study. We analysed P. aeruginosa ATCC 9027 (as a control strain) and 19 of the isolates after digestion with SpeI restriction endonuclease. After this we conducted a pulsed-field gel electrophoresis (PFGE) and typed the obtained 10 unique patterns, designated as A, A1, B, B1, C, C1, D, D1, E and F. We evaluated the genetic relatedness between all strains, based on ≥87% band identity. As a result, the isolates were grouped in the 10 clusters as follows: patterns A, A1, B, B1, C contained two strains each and patterns C1, D, D1, E contained a single strain each; the five remaining strains were closely related (genomic pattern F). One isolate belonged to antibiotype ‘b’. The genotype patterns of the P. aeruginosa ATCC 9027 control strain and isolate no. 11 were closely related and had two different antibiotypes ‘d’ and ‘c’, respectively. PMID:26019629

  17. Molecular epidemiologic analysis of Vibrio cholerae O1 isolates by pulsed-field gel electrophoresis.

    PubMed Central

    Mahalingam, S; Cheong, Y M; Kan, S; Yassin, R M; Vadivelu, J; Pang, T

    1994-01-01

    Isolates of Vibrio cholerae O1 El Tor from two well-defined cholera outbreaks in Malaysia were analyzed by using pulsed-field gel electrophoresis (PFGE). Isolates from sporadic cases occurring during the same time period were also studied. Digestion of chromosomal DNA from these isolates of V. cholerae O1 with restriction endonucleases NotI (5'-GCGGCCGC-3') and SfiI (5'-GGCCNNNN-3'), followed by PFGE, produced restriction endonuclease analysis (REA) patterns consisting of 13 to 24 bands (ranging in size from 46 to 398 kbp). Analysis of the REA patterns generated by PFGE after digestion with NotI and SfiI suggested the clonal nature and close genetic identity of the isolates obtained during each of the two outbreaks (Dice coefficient, 0.93 to 1.0). Although they had very similar REA patterns, the two outbreak clones were not identical. Isolates of V. cholerae O1 from sporadic cases, on the other hand, appeared to be much more heterogeneous (five different REA patterns detected in the five isolates tested; Dice coefficient, 0.31 to 0.81) than those obtained during the two outbreaks. We conclude that PFGE of V. cholerae O1 chromosomal DNA digested with infrequently cutting restriction endonucleases is a useful method for molecular typing of V. cholerae isolates for epidemiological purposes. Images PMID:7883885

  18. Characterization of Erwinia amylovora strains from Bulgaria by pulsed-field gel electrophoresis.

    PubMed

    Atanasova, Iliana; Urshev, Zoltan; Hristova, Petya; Bogatzevska, Nevena; Moncheva, Penka

    2012-01-01

    The aim of this study was to characterize genetically Bulgarian Erwinia amylovora strains using pulsed-field gel electrophoresis (PFGE) analysis. Fifty E. amylovora strains isolated from different hosts, locations, as well as in different years were analysed by PFGE after XbaI, SpeI, and XhoI digestion of the genomic DNA. The strains were distributed into four groups according to their XbaI-generated profile. About 82% of the strains displayed a PFGE profile identical to that of type Pt2. Three strains belonged to the Central Europe Pt1 type. Two new PFGE profiles, not reported so far, were established--one for a strain isolated from Malus domestica and another for all Fragaria spp. strains. The same grouping of the strains was obtained after analysis of the SpeI digestion patterns. On the basis of PFGE profiles, after XbaI and SpeI digestion, a genetic differentiation between the strains associated with subfamily Maloideae and subfamily Rosoideae was revealed. The presence of more than one PFGE profile in the population of E. amylovora in Bulgaria suggests a multiple source of inoculum. PMID:22624335

  19. Genome fingerprinting of Salmonella typhi by pulsed-field gel electrophoresis for subtyping common phage types.

    PubMed Central

    Nair, S.; Poh, C. L.; Lim, Y. S.; Tay, L.; Goh, K. T.

    1994-01-01

    The genomic DNA of 39 strains of Salmonella typhi isolated from local residents and patients who had visited countries in the Asian region was analysed for restriction fragment length polymorphisms (RFLP). Pulsed-field gel electrophoretic (PFGE) analysis of Xba I- and Spe I-generated genomic restriction fragments established 22 PFGE types whereas phage typing differentiated the 39 isolates into 9 distinct phage types. This study showed that PFGE is more discriminatory than phage typing as it is capable of subtyping S. typhi strains of the same phage types. Genetic relatedness among the isolates was determined. Seven major clusters were identified at SABs of > 0.80 and the remaining 13 isolates were distributed into minor clusters which were related at SABs of less than 0.80. In conclusion, PFGE analysis in conjunction with distance matrix analysis served as a useful tool for delineating common S. typhi phage types of diverse origins from different geographical locales and separated in time. Images Fig. 1 Fig. 2 Fig. 3 PMID:7995349

  20. Slab Leaf Bowls

    ERIC Educational Resources Information Center

    Suitor, Cheryl

    2012-01-01

    In science class, fourth graders investigate the structure of plants and leaves from trees and how the process of photosynthesis turns sunlight into sugar proteins. In this article, the author fuses art and science for a creative and successful clay slab project in her elementary art classroom. (Contains 1 online resource.)

  1. Characterization of Mannheimia haemolytica in beef calves via nasopharyngeal culture and pulsed-field gel electrophoresis.

    PubMed

    Capik, Sarah F; White, Brad J; Lubbers, Brian V; Apley, Michael D; Mosier, Derek A; Larson, Robert L; Murray, Robert W

    2015-09-01

    Mannheimia haemolytica is a major bacterial component of bovine respiratory disease (BRD); unfortunately, very little is known about M. haemolytica transmission dynamics among cattle. Identifying potential variation in M. haemolytica populations over time and induction of nasopharyngeal colonization and subsequent shedding are 2 areas where knowledge is lacking. In our study, 2 separate loads of 20 mixed-origin, male calves were purchased through an order buyer on different dates. Deep nasopharyngeal cultures (NPC) were performed on all calves on arrival and, if M. haemolytica-negative, a second screening culture was obtained. Calves that were negative on 2 initial NPCs (NEG; n = 4) were subsequently challenged with a previously isolated field strain of M. haemolytica in both the upper and lower respiratory tract, individually housed, and then monitored for M. haemolytica shedding via NPCs at 0.5, 1, 3, 5, 7, and 9 days postchallenge. Naturally M. haemolytica-positive calves (2 per load) were kept for additional daily cultures (POS; n = 4). Individual calf M. haemolytica status for both the POS and NEG groups was inconsistent between study days. Additionally, pulsed-field gel electrophoresis performed on isolates from the positive cultures showed that the NEG calves did not shed the M. haemolytica challenge strain, but rather 2 distinct clusters of M. haemolytica were shared among POS and NEG calves regardless of their initial status. Although sample sizes were small, these findings illustrate how variable the results of a single nasopharyngeal swab can be and the challenges of using an individual culture to truly represent animal M. haemolytica status. PMID:26330399

  2. Pulsed-field gel electrophoresis (PFGE): application in population structure studies of bovine mastitis-causing streptococci.

    PubMed

    Santos-Sanches, Ilda; Chambel, Lélia; Tenreiro, Rogério

    2015-01-01

    Pulsed-field gel electrophoresis (PFGE) separates large DNA molecules by the use of an alternating electrical field, such that greater size resolution can be obtained when compared to normal agarose gel electrophoresis. PFGE is often employed to track pathogens and is a valuable typing scheme to detect and differentiate strains. Particularly, the contour-clamped homogeneous electric field (CHEF) PFGE system is considered to be the gold standard for use in epidemiological studies of many bacterial pathogens. Here we describe a PFGE protocol that was applicable to the study of bovine streptococci, namely, Streptococcus agalactiae (group B Streptococcus, GBS), Streptococcus dysgalactiae subsp. dysgalactiae (group C Streptococcus, GCS), and Streptococcus uberis-which are relevant pathogens causing mastitis, a highly prevalent and costly disease in dairy industry due to antibiotherapy and loss in milk production. PMID:25399106

  3. Reduction of a high-field dielectric artifact with homemade gel.

    PubMed

    Takayama, Yukihisa; Nonaka, Hiroi; Nakajima, Manabu; Obata, Takayuki; Ikehira, Hiroo

    2008-01-01

    We developed an original dielectric-equivalent gel (Japanese Patent Application ID: P2004-236876A, February 6, 2003) pad that could improve inhomogeneous images caused primarily by B(1) homogeneity on a high-tesla magnetic resonance (MR) system. Made easily from various ingredients, our gel could reduce interference from radiofrequency waves at an object's surface and show changes in B(1) inhomogeneity. We herein assess the gel's effect using a plastic-bottle phantom on a 3T MR system. PMID:18460847

  4. High-Frequency Alternating-Crossed-Field Gel Electrophoresis WithNeutral or Slightly Charged Interpenetrating Networks to Improve DNASeparation

    SciTech Connect

    Boyd, B.; Prausnitz, J.; Blanch, H.

    1998-07-01

    Toward improving DNA separations, this work reports theeffects of high-frequency square-wave AC fields superimposedperpendicular to the direct current (DC) separation field on DNAmigration in both polyacrylamide-based interpenetrating networks (IPNs)and in agarose networks. Compared to standard polyacrylamide gels, IPNsallow the separation of larger DNA (9000 bp vs. 5000 bp at 5 V/cm). Innovel polyacrylamide-based IPNs, an alternating current (AC) field of 5Hz increased the maximum DNA size separable. This effect was extended tolarger DNA sizes with increasing electric-field strength up to andapparently beyond the power supply-limited maximum electric-fieldstrength of 48 V/cm. The orthogonal AC field also increased mobility.These two results combine to yield a reduction in separation time of upto a factor of 20 in novel polyacrylamide-based IPNs. When negativelycharged acrylic-acid groups were incorporated into the IPNs, the use ofthe AC field changed the DNA-network interaction, which altered the sizedependence of DNA mobility. In agarose gels, an AC field of 50 Hzincreased the size range separable; however, there was no increase in DNAmobility. There was no change in size dependence of mobility in an ACfield when the number of charged groups in the agarose network wasincreased. Based on results in the literature, possible mechanisms wereexamined for the effects of the AC field on DNA separation.

  5. Application of pulsed field gel electrophoresis to the 1993 epidemic of whooping cough in the UK.

    PubMed Central

    Syedabubakar, S. N.; Matthews, R. C.; Preston, N. W.; Owen, D.; Hillier, V.

    1995-01-01

    The purpose of this study was to DNA fingerprint the majority (64%) of isolates received at the Pertussis Reference Laboratory during the 1993 whooping cough epidemic by pulsed field gel electrophoresis of Xba I-generated restriction digests. Two DNA restriction patterns, types 1 and 3, predominated (40% and 23%, respectively, of 180 isolates) but type 2, identified in a previous study was notably absent. Twenty-one new DNA types occurred (24% of isolates), some being atypical as bands 155-230 kb were no longer conserved, but there was no statistically significant difference in their incidence in the upswing (June-September) compared to the downswing (October-December) phase of the epidemic. There was a relatively high proportion of new types, compared to type 1, at the peak (September). About 50% of isolates received were from the North Western Region, where 44% of isolates were DNA type 1. Whereas only 1 out of 10 isolates from Scotland were of this type, suggesting some geographic variation. Statistically significant findings included a higher proportion of isolates from female patients (P < 0.01), most marked in the 12-24 months age group (P < 0.05); a higher proportion of infants under 12 months requiring hospital admission compared to older children (P < 0.05); and a greater number of isolates from unvaccinated children (P < 0.01). Analysis of serotype according to four age groups (under 3 months, 3-12 months, 12-24 months and above 2 years) showed statistically significant differences (P < 0.05) with a noticeably lower proportion (38%) of serotype 1,3 in 3-12 months age group and higher prevalence (74%) of serotype 1,3 in the 12-24 months age group. There was no correlation between DNA type and serotype. Images Fig. 2 PMID:7641824

  6. Multilocus sequence typing scheme versus pulsed-field gel electrophoresis for typing Mycobacterium abscessus isolates.

    PubMed

    Machado, Gabriel Esquitini; Matsumoto, Cristianne Kayoko; Chimara, Erica; Duarte, Rafael da Silva; de Freitas, Denise; Palaci, Moises; Hadad, David Jamil; Lima, Karla Valéria Batista; Lopes, Maria Luiza; Ramos, Jesus Pais; Campos, Carlos Eduardo; Caldas, Paulo César; Heym, Beate; Leão, Sylvia Cardoso

    2014-08-01

    Outbreaks of infections by rapidly growing mycobacteria following invasive procedures, such as ophthalmological, laparoscopic, arthroscopic, plastic, and cardiac surgeries, mesotherapy, and vaccination, have been detected in Brazil since 1998. Members of the Mycobacterium chelonae-Mycobacterium abscessus group have caused most of these outbreaks. As part of an epidemiological investigation, the isolates were typed by pulsed-field gel electrophoresis (PFGE). In this project, we performed a large-scale comparison of PFGE profiles with the results of a recently developed multilocus sequence typing (MLST) scheme for M. abscessus. Ninety-three isolates were analyzed, with 40 M. abscessus subsp. abscessus isolates, 47 M. abscessus subsp. bolletii isolates, and six isolates with no assigned subspecies. Forty-five isolates were obtained during five outbreaks, and 48 were sporadic isolates that were not associated with outbreaks. For MLST, seven housekeeping genes (argH, cya, glpK, gnd, murC, pta, and purH) were sequenced, and each isolate was assigned a sequence type (ST) from the combination of obtained alleles. The PFGE patterns of DraI-digested DNA were compared with the MLST results. All isolates were analyzable by both methods. Isolates from monoclonal outbreaks showed unique STs and indistinguishable or very similar PFGE patterns. Thirty-three STs and 49 unique PFGE patterns were identified among the 93 isolates. The Simpson's index of diversity values for MLST and PFGE were 0.69 and 0.93, respectively, for M. abscessus subsp. abscessus and 0.96 and 0.97, respectively, for M. abscessus subsp. bolletii. In conclusion, the MLST scheme showed 100% typeability and grouped monoclonal outbreak isolates in agreement with PFGE, but it was less discriminative than PFGE for M. abscessus. PMID:24899019

  7. Multilocus Sequence Typing Scheme versus Pulsed-Field Gel Electrophoresis for Typing Mycobacterium abscessus Isolates

    PubMed Central

    Machado, Gabriel Esquitini; Matsumoto, Cristianne Kayoko; Chimara, Erica; Duarte, Rafael da Silva; de Freitas, Denise; Palaci, Moises; Hadad, David Jamil; Lima, Karla Valéria Batista; Lopes, Maria Luiza; Ramos, Jesus Pais; Campos, Carlos Eduardo; Caldas, Paulo César; Heym, Beate

    2014-01-01

    Outbreaks of infections by rapidly growing mycobacteria following invasive procedures, such as ophthalmological, laparoscopic, arthroscopic, plastic, and cardiac surgeries, mesotherapy, and vaccination, have been detected in Brazil since 1998. Members of the Mycobacterium chelonae-Mycobacterium abscessus group have caused most of these outbreaks. As part of an epidemiological investigation, the isolates were typed by pulsed-field gel electrophoresis (PFGE). In this project, we performed a large-scale comparison of PFGE profiles with the results of a recently developed multilocus sequence typing (MLST) scheme for M. abscessus. Ninety-three isolates were analyzed, with 40 M. abscessus subsp. abscessus isolates, 47 M. abscessus subsp. bolletii isolates, and six isolates with no assigned subspecies. Forty-five isolates were obtained during five outbreaks, and 48 were sporadic isolates that were not associated with outbreaks. For MLST, seven housekeeping genes (argH, cya, glpK, gnd, murC, pta, and purH) were sequenced, and each isolate was assigned a sequence type (ST) from the combination of obtained alleles. The PFGE patterns of DraI-digested DNA were compared with the MLST results. All isolates were analyzable by both methods. Isolates from monoclonal outbreaks showed unique STs and indistinguishable or very similar PFGE patterns. Thirty-three STs and 49 unique PFGE patterns were identified among the 93 isolates. The Simpson's index of diversity values for MLST and PFGE were 0.69 and 0.93, respectively, for M. abscessus subsp. abscessus and 0.96 and 0.97, respectively, for M. abscessus subsp. bolletii. In conclusion, the MLST scheme showed 100% typeability and grouped monoclonal outbreak isolates in agreement with PFGE, but it was less discriminative than PFGE for M. abscessus. PMID:24899019

  8. Carbon dioxide slab laser

    SciTech Connect

    Tulip, J.

    1988-01-12

    A gas slab laser is described comprising: first and second elongated electrodes each including a planar light reflecting surface disposed so as to form a light guide only in a plane perpendicular to the planar surface and to define a gas discharge gap therebetween; a laser gas disposed in the gap; and means for applying a radio frequency current between the first and second electrodes to establish a laser-exciting discharge in the laser gas.

  9. Water shutoff through fullbore placement of polymer gel in faulted and in hydraulically fractured producers of the Prudhoe Bay field

    SciTech Connect

    Lane, R.H.; Sanders, G.S.

    1995-12-31

    Selective shutoff of undesired water influx by nonselective (fullbore) placement of treating chemicals has been successfully demonstrated in production wells of the Prudhoe Bay field. This was accomplished through: (1) careful choice of candidates with known high conductivity water influx pathways (fault, hydraulic fracture, thief), (2) placement that exploited conductivity differences without zonal isolation, and (3) use of established polymer gel chemistry with previously demonstrated ability to shut off water preferentially to oil.

  10. Successful gas shutoff with polymer gel using temperature modeling and selective placement in the Prudhoe Bay field

    SciTech Connect

    Sanders, G.S.; Chambers, M.J.; Lane, R.H.

    1995-12-31

    A combination of known crosslinked gel chemistry with careful problem diagnosis, wellbore and formation temperature modeling, and zone isolation techniques yields a high success rate for shutting off unwanted gas influx into production wells in the Prudhoe Bay Field of Alaska. The paper includes candidate selection criteria, methodology of temperature simulation, job design, field operations case histories, and pre- and post-job production data for evaluation of success. This approach has led to a 60% technical success rate, primarily on wells that had cement squeeze failures. Job costs are about 75% those of comparable cement squeezes.

  11. [Investigation of Salmonella serotype Enteritidis isolates by plasmid profile analysis and pulsed field gel electrophoresis].

    PubMed

    Us, Ebru; Erdem, Birsel; Tekeli, Alper; Gerçeker, Devran; Saran, Begüm; Bayramova, Mehseti; Sahin, Fikret

    2011-04-01

    In this study a total of 122 Salmonella serotype Enteritidis stock strains selected from the culture collection of Enterobacteriaceae Laboratory of Ankara University Faculty of Medicine, Department of Medical Microbiology, were investigated by plasmid profile analysis with the method defined by Kado and Liu and pulsed field gel electrophoresis (PFGE) according to World Health Organization protocols using SpeI and XbaI macrorestriction enzymes, for better understanding of the molecular epidemiology of S. Enteritidis. The study strains were selected from a collection of previously isolated epidemic (n= 13) and sporadic (n= 109) strains (103 stool, 16 blood and one each bile, urine and cerebrospinal fluid) obtained from 10 different cities after the year 2000. PFGE patterns were analyzed with Gene Directory software (Syngene, UK) and a similarity index was determined by using Dice coefficient and the unweighted pair group method with mathematical averaging (UPGMA). Plasmid-carrying 110 (90%) strains that harbored 1-4 plasmids with sizes ranging from 2.0 to 100 kb were separated into patterns more than 14 (p1-p14). A total of 85 (69.7%) isolates harbored the 57 kb plasmid solely or in combination with other plasmids. By PFGE, 11 distinct patterns were shown with each enzyme SpeI and XbaI. S. Enteritidis strains after digestion with macrorestriction enzyme SpeI generated 11 different PFGE patterns (A to K), whereas XbaI generated also 11 different PFGE patterns (a to k). PFGE pattern A consisted of 93 strains (76.2%) after digestion with macrorestriction enzyme SpeI, while PFGE pattern a consisted 53 (43.4%) and PFGE pattern b 42 strains (34.4%) after digestion with macrorestriction enzyme XbaI. Using two macrorestriction enzymes two PFGE cluster profiles Aa (50 strains, 40.9%) and Ab (42 strains, 34.4%) were found to be predominating among 17 different PFGE clusters. Our results confirmed the clonal nature of S. Enteritidis strains in Turkey. The use of two enzymes in

  12. Mantle Response to a Slab Gap and Three-dimensional Slab Interaction in Central America

    NASA Astrophysics Data System (ADS)

    Jadamec, M. A.; Fischer, K. M.

    2013-12-01

    southern Cocos slab edge and a separate region of toroidal flow around the northern Nazca slab edge, together leading to east directed mantle flow through the slab gap. The geodynamic models suggest the counterclockwise toroidal flow around the southern Cocos plate may provide a solid state mantle flow framework leading to the observed northward decrease in anomalous isotopic signatures in the Costa Rican-Nicaraguan volcanic front. Adding a third slab into the models, the west-dipping Antilles slab, further modulates the mantle flow field, leading to increased eastward directed slab entrained flow beneath the Caribbean plate and enhancing the east-directed flow of the mantle through the Cocos-Nazca slab gap. The incorporation of the Antilles slab also leads to an increase in the east-directed surface velocity of the overriding Caribbean plate, suggesting coupling between the interior of the Caribbean plate and the mantle, and that the observed eastward motion of the Caribbean plate in geodetic studies (Lopez et al., 2006) is due in part to mantle flow related to subduction of the Antilles slab.

  13. Fatigue of concrete beams and slabs

    NASA Astrophysics Data System (ADS)

    Roesler, Jeffrey Raphael

    Traditionally, simply supported concrete beam (SSB) fatigue results have been used to characterize the fatigue resistance of fully supported concrete slabs (FSS). SSB concrete fatigue tests have been assumed to be equivalent to the fatigue resistance of concrete slabs in the field. The effect specimen size, boundary conditions, and loading configurations have on the fatigue of concrete beams and slabs have not been considered in the design of concrete pavements against fatigue. A laboratory study was undertaken to determine if the fatigue behavior of FSS and SSB were similar. A fully supported beam (FSB) was also tested under repeated loading, since it represented an intermediate specimen size and testing configuration between SSB and FSS. The best way to present fatigue results for all specimens was a stress ratio (S) to number of cycles to failure (N) curve (S-N curve). SSB fatigue behavior was similar to results obtained from the literature. FSB had similar fatigue behavior to SSB. The fatigue curve derived from repeated loading of FSS was 30 percent higher than the SSB fatigue curve. This suggested for a given number of cycles to failure, FSS could take a 30 percent higher bending stress as compared to SSB and FSB. The concrete modulus of rupture from a FSS test configuration was 30 percent greater than the concrete modulus of rupture from a SSB test setup. If the concrete modulus of rupture from a FSS test configuration was used in the slab's stress ratio, the slab's fatigue curve was the same as the SSB and FSB. This meant concrete behaved the same under fatigue loading, irrespective of specimen size and test configuration, as long as the correct concrete modulus of rupture was used in the stress ratio. Strain gages, attached to all specimens tested, indicated cracking in concrete occurred in a narrow band. Regions of high plastic strain were found in the plane of cracking, while adjacent areas experienced decreases in strain levels with cracking. Strain

  14. Diode-pumped efficient slab laser with two Nd:YLF crystals and second-harmonic generation by slab LBO.

    PubMed

    Li, Daijun; Ma, Zhe; Haas, Rüdiger; Schell, Alexander; Simon, Janosch; Diart, Robert; Shi, Peng; Hu, Peixin; Loosen, Peter; Du, Keming

    2007-05-15

    We demonstrate a diode-pumped electro-optical Q-switched slab laser with a high optical efficiency, high pulse energy, and short pulse width with two Nd:YLF crystals inside one resonator. The single compact slab resonator can generate a 1D top-hat beam at both the far field and the near field. With a slab-geometry-design lithium triborate (LBO) crystal, efficient critical phase-matching second-harmonic generation for a 1D top-hat beam with multiple transverse modes is achieved. PMID:17440558

  15. Use of Pulsed-Field Gel Electrophoresis of Conserved XbaI Fragments for Identification of Swine Salmonella Serotypes▿

    PubMed Central

    Gaul, Stephen B.; Wedel, Stephanie; Erdman, Matthew M.; Harris, D. L.; Harris, Isabel Turney; Ferris, Kathleen E.; Hoffman, Lorraine

    2007-01-01

    Swine Salmonella isolates (n = 674) from various locations throughout the United States and Canada were analyzed via pulsed-field gel electrophoresis (PFGE) with XbaI. PFGE subtypes were analyzed by cluster analysis and compared to conventional serotyping results. The analysis showed a correlation of serotype to PFGE subtype. In addition, conserved fragments were identified within the restriction patterns that were unique to each serotype. PFGE using XbaI restriction provided a possible alternative method for screening and identifying swine Salmonella serotypes. PMID:17166969

  16. The association of serotype and pulsed-field gel electrophoresis genotype in isolates of Streptococcus pneumoniae isolated in Israel.

    PubMed

    Bar-Meir, M; Naaman, G; Assous, M; Korenman, Z; Valinsky, L; Picard, E

    2015-05-01

    The relationship between Streptococcus pneumoniae isolates causing invasive infections in children admitted to a single center in central Israel was examined by pulsed-field gel electrophoresis (PFGE) and serotyping. Although there was a close correlation between serotype and PFGE clone, the genetic diversity varied by serotype, with some genotypes comprising multiple serotypes. Additionally, clones C and D were associated with higher penicillin minimum inhibitory concentrations. Serotyping alone may be insufficient for epidemiological mapping of pneumococcal isolates in the era of pneumococcal conjugate polysaccharide vaccines. PMID:25749648

  17. Preparation of α-mannoside hydrogel and electrical detection of saccharide-protein interactions using the smart gel-modified gate field effect transistor

    NASA Astrophysics Data System (ADS)

    Maeda, Yasuhiro; Matsumoto, Akira; Miura, Yoshiko; Miyahara, Yuji

    2012-02-01

    The purpose of this study was to detect saccharide-protein interaction capitalizing on the gel-modified field effect transistor [FET]. A lectin-sensitive polymer gel that undergoes volume changes in response to the formation of molecular complex between 'pendant' carbohydrate and a 'target' lectin concanavalin A [Con A] was synthesized. It was revealed that direction and magnitude of the gel response (swelling or deswelling) could be readily designed depending on composition and network density of the gel. The Con A-sensitive polymer gel has shown the ability to transduce the detection of saccharide-protein interactions into electrical signals for FET. PACS: 87.85.jf, bio-based materials

  18. SUB-SLAB PROBE INSTALLATION

    EPA Science Inventory

    Sub-slab sampling has become an integral part of vapor intrusion investigations. It is now recommended in guidance documents developed by EPA and most states. A method for sub-slab probe installation was devised in 2002, presented at conferences through 2005, and finally docume...

  19. [Thermoluminescence Slab Dosimeter].

    PubMed

    Shinsho, Kiyomitsu; Koba, Yusuke; Tamatsu, Satoshi; Sakurai, Noboru; Wakabayashi, Genichiro; Fukuda, Kazusige

    2013-01-01

    In 1953 F. Daniels et al. used the property of thermoluminescence in dosimetry for the first time. Since then, numerous TLD have been developed. 2D TLD was investigated for the first time in 1972 by P Broadhead. However, due to excessive fading, difficulties with handling and the time required for measurements, development stalled. At the current time, the majority of TLD are used in small scale, localized dosimetry with a wide dynamic range and personal dosimeters for exposure management. Urushiyama et. al. have taken advantage of the commoditization of CCD cameras in recent years--making large area, high resolution imaging easier--to introduce and develop a 2D TLD. It is expected that these developments will give rise to a new generation of applications for 2D TL dosimetry. This paper introduces the "TL Slab Dosimeter" developed jointly by Urushiyama et. al. and our team, its measurement system and several typical usage scenarios. PMID:24893451

  20. Quantitative hybridization to genomic DNA fractionated by pulsed-field gel electrophoresis.

    PubMed

    Leach, T J; Glaser, R L

    1998-10-15

    Hybridization to genomic DNA fractionated by CHEF electrophoresis can vary >100-fold if the DNA is acid depurinated prior to Southern blotting. The level of hybridization is high or low depending on whether the molecule being analyzed migrates at a size coincident with or different from the size of the majority of genomic DNA in the sample, respectively. Techniques that avoid acid depurination including in-gel hybridizations and UV irradiation of DNA prior to blotting provide more accurate quantitative results. CHEF analysis of DNA molecules containing repetitive satellite sequences is particularly prone to this effect. PMID:9753752

  1. Size-fractionation of the small chromosomes of Trypanozoon and Nannomonas trypanosomes by pulsed field gradient gel electrophoresis.

    PubMed

    Gibson, W C; Borst, P

    1986-02-01

    We have compared the molecular karyotypes of trypanosomes from different subgroups within subgenus Trypanozoon by pulsed field gradient (PFG) gel electrophoresis. Although the overall karyotype was similar, there was much variation in the size of chromosomes between different stocks. Two of three stocks of Trypanosoma (Trypanozoon) brucei gambiense had remarkably small mini-chromosomes: 25-50 kilobase pairs compared to 50-150 kilobase pairs for the mini-chromosomes of other Trypanozoon stocks. The relative amount of DNA in the mini-chromosomal fraction of different stocks correlated well with the amount of 177 base pair satellite DNA monomer per microgram nuclear DNA. Hybridisation of Southern blots of pulsed field gradient gels with a number of gene probes showed that the loci for tubulin and phosphoglycerate kinase in Trypanozoon probably lie on the same chromosome, together with some variant surface glycoprotein genes; the genes for triose phosphate isomerase and glyceraldehyde phosphate dehydrogenase are separately located both with respect to each other and the above housekeeping genes. Therefore, there are at minimum three pairs of chromosomes carrying housekeeping genes in Trypanozoon. In some stocks the chromosomes carrying the tubulin and phosphoglycerate kinase genes are split into two bands, suggesting that homologous chromosomes may differ substantially in size in trypanosomes. One Trypanosoma (Nannomonas) congolense stock examined had a similar pattern of chromosome distribution to that of Trypanozoon, but with very small mini-chromosomes (25-50 kilobase pairs.) PMID:3960051

  2. Optimization of Pulsed-field Gel Electrophoresis Procedure for Bacillus cereus.

    PubMed

    Zhang, Hui Juan; Pan, Zhuo; Wei, Jian Chun; Zhang, En Min; Cai, Hong; Liang, Xu Dong; Li, Wei

    2016-03-01

    In order to develop a rapid and reliable method for B. cereus genotyping, factors influencing PFGE results, including preparation of bacterial cells embedded in agarose, lysis of embedded cells, enzymatic digestion of intact genomic DNA, and electrophoresis parameters allowing for reproducible and meaningful DNA fragment separation, were controlled. Optimal cellular growth (Luria-Bertani agar plates for 12-18 h) and lysis conditions (4 h incubation with 500 µg/mL lysozyme) produced sharp bands on the gel. Restriction enzyme NotI was chosen as the most suitable. Twenty-two isolates were analyzed by NotI digestion, using three electrophoretic parameters (EPs). The EP-a was optimal for distinguishing between isolates. The optimized protocol could be completed within 40 h which is a significant improvement over the previous methods. PMID:27109136

  3. Leaky unstable modes and electromagnetic radiation amplification by an anisotropic plasma slab

    SciTech Connect

    Vagin, K. Yu. Uryupin, S. A.

    2015-09-15

    The interaction between electromagnetic radiation and a photoionized plasma slab with an anisotropic electron velocity distribution is studied. It is shown that the fields of leaky modes are amplified due to the development of aperiodic instability in the slab, which leads to an increase in both the reflected and transmitted fields. The transmitted field can significantly increase only if the slab thickness does not exceed the ratio of the speed of light to the electron plasma frequency, whereas there is no upper bound on the slab thickness for the reflected signal to be amplified.

  4. New Packaging for Amplifier Slabs

    SciTech Connect

    Riley, M.; Thorsness, C.; Suratwala, T.; Steele, R.; Rogowski, G.

    2015-03-18

    The following memo provides a discussion and detailed procedure for a new finished amplifier slab shipping and storage container. The new package is designed to maintain an environment of <5% RH to minimize weathering.

  5. Efficient second-harmonic generation in micrometer-thick slabs with indefinite permittivity

    NASA Astrophysics Data System (ADS)

    Ciattoni, A.; Spinozzi, E.

    2012-04-01

    We theoretically predict efficient optical second-harmonic generation (SHG) from a micrometer-thick slab consisting of a quadratic nonlinear anisotropic medium whose linear principal permittivities have, at the fundamental wavelength, real parts of different signs (indefinite permittivity) and magnitude smaller than 1. We show that, by illuminating the slab with a p-polarized fundamental wave (with intensity of a few MW/cm2), highly efficient scattering of the second-harmonic field occurs in conditions at which the slab is linearly fully transparent for the fundamental wave. The high efficiency of the SHG process stems from the enhancement of the longitudinal field, perpendicular to the slab surface, produced by the very small value of the slab dielectric permittivities. We investigate the role played by medium losses, showing that, even in the strong-absorption regime, the described process yields a second-harmonic field which is much stronger than that produced by a standard (not indefinite) nonlinear slab.

  6. Photo-Induced Anomalous Deformation of Poly(N-Isopropylacrylamide) Gel Hybridized with an Inorganic Nanosheet Liquid Crystal Aligned by Electric Field.

    PubMed

    Inadomi, Takumi; Ikeda, Shogo; Okumura, Yasushi; Kikuchi, Hirotsugu; Miyamoto, Nobuyoshi

    2014-09-16

    Poly-(N-isopropylacrylamide) (PNIPA) hydrogel films doped with uniaxially aligned liquid crystalline (LC) nanosheets adsorbed with a dye are synthesized and its anomalous photothermal deformation is demonstrated. The alignment of the nanosheet LC at the cm-scale is easily achieved by the application of an in-plane or out-of-plane AC electric field during photo-polymerization. A photoresponsive pattern is printable onto the gel with μm-scale resolution by adsorption of the dye through a pattern-holed silicone rubber. When the gel is irradiated with light, only the colored part is photothermally deformed. Interestingly, the photo-irradiated gel shows temporal expansion along one direction followed by anisotropic shrinkage, which is an anomalous behavior for a conventional PNIPA gel. PMID:25228493

  7. Diagnosis of an outbreak of Salmonella typhimurium in chinchillas (Chinchilla lanigera) by pulsed-field gel electrophoresis.

    PubMed

    Gornatti Churria, Carlos D; Vigo, Germán B; Origlia, Javier; Campos, Josefina; Caffer, María; Píscopo, Miguel; Herrero Loyola, Miguel; Petruccelli, Miguel; Pichel, Mariana

    2014-01-01

    Adult chinchillas (Chinchilla lanigera) that had suddenly died in a commercial farm located in La Plata City, Buenos Aires Province, Argentina, in July 2012 were macroscopically, histopathologically, and microbiologically examined. Salmonella enterica serovar Typhimurium (S. Typhimurium) was isolated from the liver, spleen, heart, lungs, kidneys and intestines from each of the five animals evaluated. The five strains were susceptible to ampicillin, cephalotin, cefotaxime, nalidixic acid, gentamicin, streptomycin, chloramphenicol, fosfomycin, nitrofurantoin and trimethoprim-sulfamethoxazole, and resistant to tetracycline. Each of the five S. Typhimurium isolates was analyzed by XbaI- pulsed-field gel electrophoresis (PFGE), showing an identical electrophoretic profile with 15 defined bands, which was found to be identical to pattern ARJPXX01.0220 of the PulseNet Argentine National database of Salmonella PFGE patterns. This is the first work describing the postmortem diagnosis of an outbreak of salmonellosis in chinchillas by using molecular methods such as PFGE. PMID:25444129

  8. Cost-Effective Application of Pulsed-Field Gel Electrophoresis to Typing of Salmonella enterica Serovar Typhimurium

    PubMed Central

    Doran, Geraldine; Morris, Dearbhaile; O'Hare, Colette; DeLappe, Niall; Bradshaw, Bernard; Corbett-Feeney, Geraldine; Cormican, Martin

    2005-01-01

    Salmonella enterica serovar Typhimurium is frequently isolated from humans and animals. Phage typing is historically the first-line reference typing technique in Europe. It is rapid and convenient for laboratories with appropriate training and experience, and costs of consumables are low. Phage typing and pulsed-field gel electrophoresis (PFGE) were performed on 503 isolates of serovar Typhimurium. Twenty-nine phage types and 53 PFGE patterns were observed. Most isolates of phage types DT104, DT104b, and U310 are not distinguishable from other members of their phage type by PFGE. By contrast, PFGE of isolates of phage types DT193 and U302 shows great heterogeneity. Analysis of experience with PFGE and phage typing can facilitate the selective application of PFGE to maximize the yield of epidemiologically relevant additional information while controlling costs. PMID:16332808

  9. Analysis of haemorrhagic septicaemia-causing isolates of Pasteurella multocida by ribotyping and field alternation gel electrophoresis (FAGE).

    PubMed

    Townsend, K M; Dawkins, H J; Papadimitriou, J M

    1997-10-16

    Ribotyping and field alternation gel electrophoresis (FAGE) were used to examine 19 Pasteurella multocida isolates, and to assess the ability of these techniques to differentiate P. multocida strains that cause haemorrhagic septicaemia (HS). Reproducible patterns were obtained from both methods, with FAGE demonstrating greater discriminatory power than ribotyping. FAGE analysis was particularly useful in distinguishing North American cultures originating from the 1922 Yellowstone National Park Buffalo 'B' strain, demonstrating the ability to detect genetic alterations induced by repeated subculture. A remarkable homogeneity was observed among Asian HS strains following ribotyping and FAGE analysis, with a clear distinction observed between virulent and avirulent HS isolates. This study has illustrated the value of genomic fingerprinting methods in distinguishing strains of similar serotype, and the capability of these methods to produce detailed characterisation of P. multocida isolates. PMID:9444075

  10. Changes in Predominance of Pulsed-Field Gel Electrophoresis Profiles of Bordetella pertussis Isolates, United States, 2000-2012.

    PubMed

    Cassiday, Pamela K; Skoff, Tami H; Jawahir, Selina; Tondella, M Lucia

    2016-03-01

    To clarify the characteristics of circulating Bordetella pertussis isolates, we used pulsed-field gel electrophoresis (PFGE) to analyze 5,262 isolates collected in the United States during 2000-2012. We found 199 PFGE profiles; 5 profiles accounted for 72% of isolates. The most common profile, CDC013, accounted for 35%-46% of isolates tested from 2000-2009; however, the proportion of isolates of this profile rapidly decreased in 2010. Profile CDC237, first seen in 2009, increased rapidly and accounted for 29% of 2012 isolates. No location bias was observed among profiles during 2000-2010, but differences were observed among isolates from different states during 2012. Predominant profiles match those observed in recent European PFGE studies. PFGE profile changes are concurrent with other recent molecular changes in B. pertussis and may be contributing to the reemergence of pertussis in the United States. Continued PFGE monitoring is critical for understanding the changing epidemiology of pertussis. PMID:26886905

  11. Changes in Predominance of Pulsed-Field Gel Electrophoresis Profiles of Bordetella pertussis Isolates, United States, 2000–2012

    PubMed Central

    Skoff, Tami H.; Jawahir, Selina; Tondella, M. Lucia

    2016-01-01

    To clarify the characteristics of circulating Bordetella pertussis isolates, we used pulsed-field gel electrophoresis (PFGE) to analyze 5,262 isolates collected in the United States during 2000–2012. We found 199 PFGE profiles; 5 profiles accounted for 72% of isolates. The most common profile, CDC013, accounted for 35%–46% of isolates tested from 2000–2009; however, the proportion of isolates of this profile rapidly decreased in 2010. Profile CDC237, first seen in 2009, increased rapidly and accounted for 29% of 2012 isolates. No location bias was observed among profiles during 2000–2010, but differences were observed among isolates from different states during 2012. Predominant profiles match those observed in recent European PFGE studies. PFGE profile changes are concurrent with other recent molecular changes in B. pertussis and may be contributing to the reemergence of pertussis in the United States. Continued PFGE monitoring is critical for understanding the changing epidemiology of pertussis. PMID:26886905

  12. Phenotypic and genotypic (pulsed-field gel electrophoresis) characteristics of enterotoxin-A-producing Staphylococcus aureus strains.

    PubMed

    Gouloumès, C; Bes, M; Renaud, F; Lina, B; Reverdy, M E; Brun, Y; Fleurette, J

    1996-05-01

    The phenotypic (antibiotype, serotype, phagetype) and genotypic (SmaI restriction patterns using pulsed-field gel electrophoresis) characters of 162 Staphylococcus aureus epidemiologically unrelated strains were studied. Eighty-two of the isolates produced enterotoxin-A (SEA+), while 80 produced none (SEA-). None of the phenotypic characters observed were characteristic of SEA+ strains. On the other hand, the electrophoretic profiles revealed a non-random distribution of the SEA+ strains (p < 0.01 in groups PI and PIII, and p < 0.03 in group PII). It can therefore reasonably be assumed that the enterotoxin-A-producing strains did not constitute a single clone, but rather, seemed to belong to strains derived from at least three clones with distinct genetic organization. PMID:8763613

  13. Slab coupled optical fiber sensor calibration

    NASA Astrophysics Data System (ADS)

    Whitaker, B.; Noren, J.; Chadderdon, S.; Wang, W.; Forber, R.; Selfridge, R.; Schultz, S.

    2013-02-01

    This paper presents a method for calibrating slab coupled optical fiber sensors (SCOS). An automated system is presented for selecting the optimal laser wavelength for use in SCOS interrogation. The wavelength calibration technique uses a computer sound card for both the creation of the applied electric field and the signal detection. The method used to determine the ratio between the measured SCOS signal and the applied electric field is also described along with a demonstration of the calibrated SCOS involving measuring the dielectric breakdown of air.

  14. Analysis of Genomic Diversity among Helicobacter pylori Strains Isolated from Iranian Children by Pulsed Field Gel Electrophoresis

    PubMed Central

    Falsafi, Tahereh; Sotoudeh, Nazli; Feizabadi, Mohammad-Mehdi; Mahjoub, Fatemeh

    2014-01-01

    Objective: Presence of genomic diversity among Helicobacter pylori (H. pylori) strains have been suggested by numerous investigators. Little is known about diversity of H. pylori strains isolated from Iranian children and their association with virulence of the strains. Our purpose was to assess the degree of genomic diversity among H. pylori strains isolated from Iranian-children, on the basis of vacA genotype, cagA status of the strains, sex, age as well as the pathological status of the patients. Methods: Genomic DNA from 44 unrelated H. pylori strains isolated during 1997–2009, was examined by pulse-field gel electrophoresis (PFGE). Pathological status of the patients was performed according to the modified Sydney-system and genotype/status of vacA/cagA genes was determined by PCR. PFGE was performed using XbaI restriction-endonuclease and the field inversion-gel electrophoresis system. Findings: No significant relationship was observed between the patterns of PFGE and the cagA/vacA status/genotype. Also no relationship was observed between age, sex, and pathological status of the children and the PFGE patterns of their isolates. Similar conclusion was obtained by Total Lab software. However, more relationship was observed between the strains isolated in the close period (1997–2009, 2001–2003, 2005–2007, and 2007–2009) and more difference was observed among those obtained in the distant periods (1997 and 2009). Conclusion: H. pylori strains isolated from children in Iran are extremely diverse and this diversity is not related to their virulence characteristics. Occurrence of this extreme diversity may be related to adaptation of H. pylori strains to variable living conditions during transmission between various host individuals. PMID:26019775

  15. The impact of slab dip variations, gaps and rollback on mantle wedge flow: insights from fluids experiments

    NASA Astrophysics Data System (ADS)

    MacDougall, Julia G.; Kincaid, Chris; Szwaja, Sara; Fischer, Karen M.

    2014-05-01

    Observed seismic anisotropy and geochemical anomalies indicate the presence of 3-D flow around and above subducting slabs. To investigate how slab geometry and velocity affect mantle flow, we conducted a set of experiments using a subduction apparatus in a fluid-filled tank. Our models comprise two independently adjustable, continuous belts to represent discrete sections of subducting slabs that kinematically drive flow in the surrounding glucose syrup that represents the upper mantle. We analyse how slab dip (ranging from 30° to 80°), slab dip difference between slab segments (ranging from 20° to 50°), rates of subduction (4-8 cm yr-1) and slab/trench rollback (0-3 cm yr-1) affect mantle flow. Whiskers were used to approximate mineral alignment induced by the flow, as well as to predict directions of seismic anisotropy. We find that dip variations between slab segments generate 3-D flow in the mantle wedge, where the path lines of trenchward moving mantle material above the slab are deflected towards the slab segment with the shallower dip. The degree of path line deflection increases as the difference in slab dip between the segments increases, and, for a fixed dip difference, as slab dip decreases. In cases of slab rollback and large slab dip differences, we observe intrusion of subslab material through the gap and into the wedge. Flow through the gap remains largely horizontal before eventual downward entrainment. Whisker alignment in the wedge flow is largely trench-normal, except near the lateral edges of the slab where toroidal flow dominates. In addition, whisker azimuths located above the slab gap deviate most strongly from trench-normal orientations when slab rollback does not occur. Such flow field complexities are likely sufficient to affect deep melt production and shallow melt delivery. However, none of the experiments produced flow fields that explain the trench-parallel shear wave splitting fast directions observed over broad arc and backarc

  16. Estimation of circular DNA size using gamma-irradiation and pulsed-field gel electrophoresis

    SciTech Connect

    Beverley, S.M. )

    1989-02-15

    A method is described for estimating the size of large circular DNAs found within complex chromosomal DNA preparations. DNAs are treated with low levels of gamma-irradiation, sufficient to introduce a single double-stranded break per circle, and the resulting linear DNA is sized by pulsed-field electrophoresis and blot hybridization. The method is fast, reproducible, and very conveniently applied to the agarose-enclosed chromosomal DNA preparations commonly used in pulsed field electrophoresis.

  17. Random amplified polymorphic DNA assay is less discriminant than pulsed-field gel electrophoresis for typing strains of methicillin-resistant Staphylococcus aureus.

    PubMed

    Saulnier, P; Bourneix, C; Prévost, G; Andremont, A

    1993-04-01

    Twenty-six strains of methicillin-resistant Staphylococcus aureus with different pulsed-field gel electrophoresis fingerprints were tested by random amplified polymorphic DNA assay with three primers, resulting in 15 to 20 different random amplified polymorphic DNA fingerprints. By summing the results for the three primers, the number of different fingerprints increased to 25, but two strains could not be differentiated. We conclude that pulsed-field gel electrophoresis remains the best method of typing methicillin-resistant S. aureus strains. PMID:8463406

  18. Random amplified polymorphic DNA assay is less discriminant than pulsed-field gel electrophoresis for typing strains of methicillin-resistant Staphylococcus aureus.

    PubMed Central

    Saulnier, P; Bourneix, C; Prévost, G; Andremont, A

    1993-01-01

    Twenty-six strains of methicillin-resistant Staphylococcus aureus with different pulsed-field gel electrophoresis fingerprints were tested by random amplified polymorphic DNA assay with three primers, resulting in 15 to 20 different random amplified polymorphic DNA fingerprints. By summing the results for the three primers, the number of different fingerprints increased to 25, but two strains could not be differentiated. We conclude that pulsed-field gel electrophoresis remains the best method of typing methicillin-resistant S. aureus strains. Images PMID:8463406

  19. Genotyping Campylobacter jejuni by comparative genome indexing: an evaluation with pulsed-field gel electrophoresis and flaA SVR sequencing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Aims: Comparative genome indexing (CGI) using whole-genome DNA microarrays was evaluated as a means of genotying Campylobacter jejuni relative to two standard methods, pulsed-field gel electrophoresis (PFGE) and flaA short variable region sequencing (flaA SVR typing). Methods and Results: Thirty-six...

  20. A comparison of BOX-PCR and pulsed-field gel electrophoresis to determine genetic relatedness of enterococci from different environments

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Aims: The genetic relatedness of enterococci from poultry litter to enterococci from nearby surface water and groundwater in the Lower Fraser Valley regions of British Columbia, Canada was determined. Methods and Results: BOX-PCR and Pulsed-Field Gel Electrophoresis (PFGE) were used to subtype en...

  1. A comparison of non-typhoidal Salmonella from humans and food animals using pulsed-field gel electrophoresis and antimicrobial susceptibility patterns

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Salmonellosis is one of the most important foodborne diseases affecting humans. To characterize the relationship between Salmonella causing human infections and their food animal reservoirs, we compared pulsed-field gel electrophoresis (PFGE) and antimicrobial susceptibility patterns of non-typhoida...

  2. Photonic crystal slab quantum cascade detector

    SciTech Connect

    Reininger, Peter Schwarz, Benedikt; Harrer, Andreas; Zederbauer, Tobias; Detz, Hermann; Maxwell Andrews, Aaron; Gansch, Roman; Schrenk, Werner; Strasser, Gottfried

    2013-12-09

    In this Letter, we demonstrate the design, fabrication, and characterization of a photonic crystal slab quantum cascade detector (PCS-QCD). By employing a specifically designed resonant cavity, the performance of the photodetector is improved in three distinct ways. The PCS makes the QCD sensitive to surface normal incident light. It resonantly enhances the photon lifetime inside the active zone, thus increasing the photocurrent significantly. And, the construction form of the device inherently decreases the noise. Finally, we compare the characteristics of the PCS-QCD to a PCS - quantum well infrared photodetector and outline the advantages for certain fields of applications.

  3. Phase conjugated slab laser designator

    SciTech Connect

    Chandra, S.; Paul, J.L.

    1989-06-06

    A laser designator is described comprising a laser pump means; a high power phase conjugated slab laser amplifier formed of GSGG:Cr:Nd as a lasing material on one side of the pump means; a low power rod shaped laser oscillator on the opposite side of the pump means; and a first plurality of optical reflecting and refracting means for directing and shaping a laser beam which surrounds the pump means and passes through the rod and slab; and a telescope means coupled to the beam to direct it to a distant target.

  4. A wrinkly phononic crystal slab

    NASA Astrophysics Data System (ADS)

    Bayat, Alireza; Gordaninejad, Faramarz

    2015-03-01

    The buckling induced surface instability is employed to propose a tunable phononic crystal slab composed of a stiff thin film bonded on a soft elastomer. Wrinkles formation is used to generate one-dimensional periodic scatterers at the surface of a finitely thick slab. Wrinkles' pattern change and corresponding stress is employed to control wave propagation triggered by a compressive strain. Simulation results show that the periodic wrinkly structure can be used as a transformative phononic crystal which can switch band diagram of the structure in a reversible behavior. Results of this study provide opportunities for the smart design of tunable switch and elastic wave filters at ultrasonic and hypersonic frequency ranges.

  5. A charge-coupled-device camera image analysis system for quantifying DNA distributions in agarose gels after pulsed-field gel electrophoresis

    SciTech Connect

    Dewey, W.C.; Thompson, L.L.; Trinh, M.L.; Latz, D.L. |; Ward, J.F.

    1994-10-01

    A charge-coupled-device camera system was coupled to a personal computer and, with uniformity in illumination and detection (within 4-8%) along each lane, was used for quantifying the distribution of DNA molecules that migrate from the PFGE well (plug) into the lane at distances varying from 1 to 50 mm (with 0.5 mm/pixel). By using a specially designed transmission filter for transmitting 470-725 nm fluorescence from ethidium bromide-stained DNA while eliminating most of the fluorescence (<400 nm) from the agarose gel, and by using neutral density filters to prevent saturation of the camera, the fluorescence intensity is linearly related to the amount of DNA varying from {approximately} 0.03 {mu}g in a 3-mm-diameter cylindrical plug 5 mm long (equal to background) to {approximately} 4 {mu}g (where ethidium bromide staining saturates). The percentage DNA released from the plug and distribution in the lane (with 1-2 mm resolution) obtained by quantifying DNA fluorescence were not significantly different from the same data obtained by analysis of radioactivity of the same DNA labeled with [{sup 3}H]dThd. However, scattering of fluorescence from one lane into an adjacent lane 3 mm away and as far as 10 mm from the plug into the lane presented a problem. This problem was overcome by using a form with slots to cover every other lane when the images were obtained and either (1) cutting the lane from the plug and moving it 15 mm away or (2) imaging the intact gel and applying a correction for {approximately} 7% of the fluorescence from the plug tailing out {approximately} 10 mm beyond the first 1 mm in the lane. In addition, the following were required: (1) carefully controlled staining and destaining procedures, and (2) a low background that is obtained as an average uniform background in each lane 5 mm beyond where DNA migration stops. 31 refs., 7 figs.

  6. Design and experimental testing of air slab caps which convert commercial electron diodes into dual purpose, correction-free diodes for small field dosimetry

    SciTech Connect

    Charles, P. H.; Cranmer-Sargison, G.; Thwaites, D. I.; Kairn, T.; Crowe, S. B.; Langton, C. M.; Trapp, J. V.; Pedrazzini, G.; Aland, T.; Kenny, J.

    2014-10-15

    Purpose: Two diodes which do not require correction factors for small field relative output measurements are designed and validated using experimental methodology. This was achieved by adding an air layer above the active volume of the diode detectors, which canceled out the increase in response of the diodes in small fields relative to standard field sizes. Methods: Due to the increased density of silicon and other components within a diode, additional electrons are created. In very small fields, a very small air gap acts as an effective filter of electrons with a high angle of incidence. The aim was to design a diode that balanced these perturbations to give a response similar to a water-only geometry. Three thicknesses of air were placed at the proximal end of a PTW 60017 electron diode (PTWe) using an adjustable “air cap”. A set of output ratios (OR{sub Det}{sup f{sub c}{sub l}{sub i}{sub n}}) for square field sizes of side length down to 5 mm was measured using each air thickness and compared to OR{sub Det}{sup f{sub c}{sub l}{sub i}{sub n}} measured using an IBA stereotactic field diode (SFD). k{sub Q{sub c{sub l{sub i{sub n,Q{sub m{sub s{sub r}{sup f{sub c}{sub l}{sub i}{sub n},f{sub m}{sub s}{sub r}}}}}}}}} was transferred from the SFD to the PTWe diode and plotted as a function of air gap thickness for each field size. This enabled the optimal air gap thickness to be obtained by observing which thickness of air was required such that k{sub Q{sub c{sub l{sub i{sub n,Q{sub m{sub s{sub r}{sup f{sub c}{sub l}{sub i}{sub n},f{sub m}{sub s}{sub r}}}}}}}}} was equal to 1.00 at all field sizes. A similar procedure was used to find the optimal air thickness required to make a modified Sun Nuclear EDGE detector (EDGEe) which is “correction-free” in small field relative dosimetry. In addition, the feasibility of experimentally transferring k{sub Q{sub c{sub l{sub i{sub n,Q{sub m{sub s{sub r}{sup f{sub c}{sub l}{sub i}{sub n},f{sub m}{sub s}{sub r

  7. Controlling of optical bistability and multistability in a defect slab

    NASA Astrophysics Data System (ADS)

    Jabbari, Masoud

    2016-02-01

    Optical bistability (OB) and optical multistability (OM) due to wide applications in all-optical switching and transistors is studied in this paper. Here, we study the OB and OM properties of incident light in a defect slab doped by a GaAs quantum well (QW) nanostructure. It is shown that OB and OM features can be manipulated by spin coherence created by circular polarized laser fields in GaAs QWs. The impacts of laser field features, such as intensity, frequency detuning, and relative phase, on OB and OM are simulated. Moreover, the dependence of OB and OM features of a probe light on the thickness of the slab, then, are analyzed. It is found that the thickness of the slab can provide a new way to optimize the intensity threshold of OB and OM. We hope that our proposed model may be useful for developing all-optical devices on nanoscales.

  8. How mantle slabs drive plate tectonics.

    PubMed

    Conrad, Clinton P; Lithgow-Bertelloni, Carolina

    2002-10-01

    The gravitational pull of subducted slabs is thought to drive the motions of Earth's tectonic plates, but the coupling between slabs and plates is not well established. If a slab is mechanically attached to a subducting plate, it can exert a direct pull on the plate. Alternatively, a detached slab may drive a plate by exciting flow in the mantle that exerts a shear traction on the base of the plate. From the geologic history of subduction, we estimated the relative importance of "pull" versus "suction" for the present-day plates. Observed plate motions are best predicted if slabs in the upper mantle are attached to plates and generate slab pull forces that account for about half of the total driving force on plates. Slabs in the lower mantle are supported by viscous mantle forces and drive plates through slab suction. PMID:12364804

  9. Frequencies of virulence genes and pulse field gel electrophoresis fingerprints in Escherichia coli isolates from canine pyometra.

    PubMed

    Maluta, Renato P; Borges, Clarissa A; Beraldo, Lívia G; Cardozo, Marita V; Voorwald, Fabiana A; Santana, André M; Rigobelo, Everlon C; Toniollo, Gilson H; Avila, Fernando A

    2014-11-01

    Escherichia coli is the most common bacterial agent isolated from canine pyometra. The frequencies of 24 virulence genes and pulsed field gel electrophoresis (PFGE) profiles were determined for 23 E. coli isolates from cases of canine pyometra in Brazil. The frequencies of virulence genes were 91.3% fimH, 91.3% irp-2, 82.6% fyuA, 56.5% iroN, 47.8% traT, 39.1% usp, 34.8% sfaD/E, 34.8% tsh, 30.4% papC, 30.4% hlyA, 26.1% papGIII, 26.1% cnf-1, 21.7% papE/F, 21.7% iss, 17.4% iutA, 17.4% ompT, 17.4% cvaC, 17.4% hlyF, 17.4% iucD, 13.0% iucC, 13.0% astA, 4.3% papGII, 0% afaB/C and 0% papGI. The high frequency of yersiniabactin (fyuA and irp2) and salmochelin (iroN) genes suggests that iron uptake systems might be important in the pathogenesis of canine pyometra. PFGE profiles of 19 isolates were heterogeneous, confirming that E. coli isolates from canine pyometra are unlikely to be epidemic clones. PMID:25201253

  10. Use of pulsed-field gel electrophoresis for epidemiological study of Bordetella pertussis in a whooping cough outbreak.

    PubMed Central

    de Moissac, Y R; Ronald, S L; Peppler, M S

    1994-01-01

    We used pulsed-field gel electrophoresis (PFGE) of chromosomal DNA digested with XbaI to determine the distribution of different Bordetella pertussis strains from clinical isolates obtained during a large whooping cough outbreak that occurred in Alberta, Canada, from December 1989 to May 1991. Our initial study analyzed 28 clinical isolates, 14 from the city of Edmonton and 1 from each of 14 northern Alberta towns. These clinical isolates were randomly chosen over the course of the 18-month outbreak. The DNA profiles were more heterogeneous than anticipated and caused concern that PFGE was too sensitive a technique to characterize strains. Further analysis showed that this was not the case, as clusters of similar PFGE patterns were observed in strains isolated from the same outlying town. Identical PFGE patterns were also seen in clinical strains obtained from different members of the same family. Two PFGE pattern types, a and b, predominated in the outbreak, accounting overall for 44 of 70 B. pertussis strains tested. Results from isolates from outlying towns, however, indicated involvement of local strains rather than a single, highly infectious strain in the whooping cough outbreak in Alberta. Images PMID:8150949

  11. Multilocus Sequence Typing Lacks the Discriminatory Ability of Pulsed-Field Gel Electrophoresis for Typing Salmonella enterica Serovar Typhimurium

    PubMed Central

    Fakhr, Mohamed K.; Nolan, Lisa K.; Logue, Catherine M.

    2005-01-01

    Nontyphoidal salmonellae are among the leading causes of food-borne disease in the United States. Because of the importance of Salmonella enterica in food-borne disease, numerous typing methodologies have been developed. Among the several molecular typing methods, pulsed-field gel electrophoresis (PFGE) is currently considered the “gold standard” technique in typing Salmonella. The aim of this study was to compare the discriminatory power of PFGE to multilocus sequence typing (MLST) in typing Salmonella enterica serovar Typhimurium clinical isolates. A total of 85 Salmonella Typhimurium clinical isolates from cattle were used in this study. PFGE using XbaI was performed on the 85 isolates by the Centers for Disease Control and Prevention method, and data were analyzed using the BioNumerics software package. Fifty PFGE profiles were observed among the isolates, and these grouped into three major clusters. For the MLST analysis, the manB, pduF, glnA, and spaM genes were amplified by PCR from the same 85 isolates. DNA sequencing of these four genes, manB, pduF, glnA, and spaM, showed no genetic diversity among the isolates tested, with a 100% identity in nucleotide sequence. Moreover, the DNA sequences of the aforementioned genes showed 100% identity to the sequence reported in GenBank for the S. enterica serovar Typhimurium LT2 strain. Therefore, MLST, using these genes, lacks the discriminatory power of PFGE for typing Salmonella enterica serovar Typhimurium. PMID:15872244

  12. Rapid estimation of chromosomal damage in yeast due to the effects of environmental chemicals using pulsed field gel electrophoresis.

    PubMed

    Ehlers, J; Tosch, M; AlBaz, I; Lochmann, E R

    1991-10-01

    We present a procedure to rapidly estimate the damage to yeast chromosomes by toxic chemicals. This procedure employs the following steps: incubation of yeast cells with the chemicals, DNA preparation in an agarose matrix, separation of chromosome-sized DNA molecules into reproducible band patterns by pulsed field gel electrophoresis, and quantification of the intensity of chromosomal bands by densitometry. Saccharomyces cerevisiae cells have been treated with N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) and cis-Platinum(II) diamminedichloride (cisPT), both of which are known to interact with DNA, and trichlorethylen (TCE), for which such an effect has not been shown in yeast. Treatment of cells with MNNG and cisPt led to an impairment of the intensity of the band pattern to an extent dependent on the concentration of the chemicals applied. For TCE a similar effect could not be discerned. This procedure will be useful as a screening test for the estimation of the biological hazards of toxic chemicals. PMID:1769347

  13. Random amplified polymorphic DNA typing versus pulsed-field gel electrophoresis for epidemiological typing of vancomycin-resistant enterococci.

    PubMed Central

    Barbier, N; Saulnier, P; Chachaty, E; Dumontier, S; Andremont, A

    1996-01-01

    Sixty vancomycin-resistant vanA mutant Enterococcus faecium (VRE) isolates, collected during a 40-month period from 48 patients hospitalized in a French Cancer Referral Center, were typed by using random amplified polymorphic DNA (RAPD), and the results were compared with those previously obtained by typing with SmaI pulsed-field gel electrophoresis (PFGE), which is currently recognized as the "gold standard." The discriminating power of RAPD typing, with seven primers and 11 combinations of primers, was tested on 18 strains, and only the most discriminating combination was further tested on the whole collection. We compared the epidemiological usefulness of RAPD typing of 60 clinical VRE isolates with that of SmaI PFGE typing. With primers AP4 and ERIC1R, RAPD generated 30 patterns versus the 36 patterns generated by SmaI PFGE. However, this did not hamper the epidemiologically correct clustering of 15 related strains and the detection of multiple colonization in nine patients. We conclude that this simple RAPD technique is well suited to the epidemiological typing of VRE and the monitoring of its nosocomial spread. PMID:8727883

  14. Multilocus sequence typing lacks the discriminatory ability of pulsed-field gel electrophoresis for typing Salmonella enterica serovar Typhimurium.

    PubMed

    Fakhr, Mohamed K; Nolan, Lisa K; Logue, Catherine M

    2005-05-01

    Nontyphoidal salmonellae are among the leading causes of food-borne disease in the United States. Because of the importance of Salmonella enterica in food-borne disease, numerous typing methodologies have been developed. Among the several molecular typing methods, pulsed-field gel electrophoresis (PFGE) is currently considered the "gold standard" technique in typing Salmonella. The aim of this study was to compare the discriminatory power of PFGE to multilocus sequence typing (MLST) in typing Salmonella enterica serovar Typhimurium clinical isolates. A total of 85 Salmonella Typhimurium clinical isolates from cattle were used in this study. PFGE using XbaI was performed on the 85 isolates by the Centers for Disease Control and Prevention method, and data were analyzed using the BioNumerics software package. Fifty PFGE profiles were observed among the isolates, and these grouped into three major clusters. For the MLST analysis, the manB, pduF, glnA, and spaM genes were amplified by PCR from the same 85 isolates. DNA sequencing of these four genes, manB, pduF, glnA, and spaM, showed no genetic diversity among the isolates tested, with a 100% identity in nucleotide sequence. Moreover, the DNA sequences of the aforementioned genes showed 100% identity to the sequence reported in GenBank for the S. enterica serovar Typhimurium LT2 strain. Therefore, MLST, using these genes, lacks the discriminatory power of PFGE for typing Salmonella enterica serovar Typhimurium. PMID:15872244

  15. Pulsed-Field Gel Electrophoresis Genotyping of Taylorella equigenitalis Isolates Collected in the United States from 1978 to 2010▿

    PubMed Central

    Aalsburg, Alan M.; Erdman, Matthew M.

    2011-01-01

    Taylorella equigenitalis is the etiologic agent of contagious equine metritis (CEM), a venereal disease of horses. A total of 82 strains of T. equigenitalis isolated in the United States were analyzed by pulsed-field gel electrophoresis (PFGE) after digestion of genomic DNA with restriction enzyme ApaI. Twenty-eight of those strains isolated from horses in the 2009 U.S. outbreak (CEM09) were further analyzed with NotI and NaeI enzymes. When ApaI alone was used for analysis, the 82 isolates clustered into 15 different genotypes that clearly defined groups of horses with known epidemiological connections. The PFGE profiles of the CEM09 isolates were indistinguishable after digestion with ApaI, NotI, and NaeI and did not match those of isolates from previous U.S. outbreaks in 1978 and 2006 or of any other isolate from the National Veterinary Services Laboratories (NVSL) culture library. Coupled with the fact that the CEM09 isolates are epidemiologically related, these results suggest a common source for the outbreak not linked to previous occurrences of CEM in the United States. PMID:21191049

  16. Subduction and slab detachment in the Mediterranean-Carpathian region.

    PubMed

    Wortel, M J; Spakman, W

    2000-12-01

    Seismic tomography models of the three-dimensional upper mantle velocity structure of the Mediterranean-Carpathian region provide a better understanding of the lithospheric processes governing its geodynamical evolution. Slab detachment, in particular lateral migration of this process along the plate boundary, is a key element in the lithospheric dynamics of the region during the last 20 to 30 million years. It strongly affects arc and trench migration, and causes along-strike variations in vertical motions, stress fields, and magmatism. In a terminal-stage subduction zone, involving collision and suturing, slab detachment is the natural last stage in the gravitational settling of subducted lithosphere. PMID:11110653

  17. Vibration characteristics of floating slab track

    NASA Astrophysics Data System (ADS)

    Kuo, Chen-Ming; Huang, Cheng-Hao; Chen, Yi-Yi

    2008-11-01

    Coupled equilibrium equations of suspended wheels and floating slab track system were solved with the fourth-order Runge-Kutta method to obtain the deflections, vibration velocities, and wheel-rail contact forces. The program was validated through several aspects. Cases with various vehicle speed, slab mass, and stiffness of slab bearing were analyzed to reveal the effects of slab bearing on track responses. The correlation between wheel-rail resonance and train speed was also discussed. It was found that rail deflections increase significantly as train speed increases. Although large slab mass may lower tuning frequency, it could also result in higher wheel-rail contact force and rail deflections. The floating slab track is effective in isolating loading above 10 Hz, which might present in some railway sections with irregularities. Adopting floating slab track for vibration control for environment along the railway may cause concerns about ride quality and track damages.

  18. Pulsed-Field Gel Electrophoresis characterization of Listeria monocytogenes isolates from cheese manufacturing plants in São Paulo, Brazil.

    PubMed

    Barancelli, Giovana V; Camargo, Tarsila M; Gagliardi, Natália G; Porto, Ernani; Souza, Roberto A; Campioni, Fabio; Falcão, Juliana P; Hofer, Ernesto; Cruz, Adriano G; Oliveira, Carlos A F

    2014-03-01

    This study aimed to evaluate the occurrence of Listeria monocytogenes in cheese and in the environment of three small-scale dairy plants (A, B, C) located in the Northern region state of São Paulo, Brazil, and to characterize the isolates using conventional serotyping and PFGE. A total of 393 samples were collected and analyzed from October 2008 to September 2009. From these, 136 came from dairy plant A, where only L. seeligeri was isolated. In dairy plant B, 136 samples were analyzed, and L. innocua, L. seeligeri and L. welshimeri were isolated together with L. monocytogenes. In dairy plant C, 121 samples were analyzed, and L. monocytogenes and L. innocua were isolated. Cheese from dairy plants B and C were contaminated with Listeria spp, with L. innocua being found in Minas frescal cheese from both dairy plants, and L. innocua and L. monocytogenes in Prato cheese from dairy plant C. A total of 85 L. monocytogenes isolates were classified in 3 serotypes: 1/2b, 1/2c, and 4b, with predominance of serotype 4b in both dairy plants. The 85 isolates found in the dairy plants were characterized by genomic macrorestriction using ApaI and AscI with Pulsed Field Gel Electrophoresis (PFGE). Macrorestriction yielded 30 different pulsotypes. The presence of indistinguishable profiles repeatedly isolated during a 12-month period indicated the persistence of L. monocytogenes in dairy plants B and C, which were more than 100 km away from each other. Brine used in dairy plant C contained more than one L. monocytogenes lineage. The routes of contamination were identified in plants B and C, and highlighted the importance of using molecular techniques and serotyping to track L. monocytogenes sources of contamination, distribution, and routes of contamination in dairy plants, and to develop improved control strategies for L. monocytogenes in dairy plants and dairy products. PMID:24412413

  19. Comparison of multilocus sequence typing and pulsed-field gel electrophoresis for Salmonella spp. identification in surface water

    NASA Astrophysics Data System (ADS)

    Kuo, Chun Wei; Hao Huang, Kuan; Hsu, Bing Mu; Tsai, Hsien Lung; Tseng, Shao Feng; Kao, Po Min; Shen, Shu Min; Chou Chiu, Yi; Chen, Jung Sheng

    2013-04-01

    Salmonella is one of the most important pathogens of waterborne diseases with outbreaks from contaminated water reported worldwide. In addition, Salmonella spp. can survive for long periods in aquatic environments. To realize genotypes and serovars of Salmonella in aquatic environments, we isolated the Salmonella strains by selective culture plates to identify the serovars of Salmonella by serological assay, and identify the genotypes by Multilocus sequence typing (MLST) based on the sequence data from University College Cork (UCC), respectively. The results show that 36 stream water samples (30.1%) and 18 drinking water samples (23.3%) were confirmed the existence of Salmonella using culture method combined PCR specific invA gene amplification. In this study, 24 cultured isolates of Salmonella from water samples were classified to fifteen Salmonella enterica serovars. In addition, we construct phylogenetic analysis using phylogenetic tree and Minimum spanning tree (MST) method to analyze the relationship of clinical, environmental, and geographical data. Phylogenetic tree showed that four main clusters and our strains can be distributed in all. The genotypes of isolates from stream water are more biodiversity while comparing the Salmonella strains genotypes from drinking water sources. According to MST data, we can found the positive correlation between serovars and genotypes of Salmonella. Previous studies revealed that the result of Pulsed field gel electrophoresis (PFGE) method can predict the serovars of Salmonella strain. Hence, we used the MLST data combined phylogenetic analysis to identify the serovars of Salmonella strain and achieved effectiveness. While using the geographical data combined phylogenetic analysis, the result showed that the dominant strains were existed in whole stream area in rainy season. Keywords: Salmonella spp., MLST, phylogenetic analysis, PFGE

  20. Kodamaea ohmeri isolates from patients in a university hospital: identification, antifungal susceptibility, and pulsed-field gel electrophoresis analysis.

    PubMed

    Lee, Jin Sol; Shin, Jong Hee; Kim, Mi-Na; Jung, Sook-In; Park, Kyung Hwa; Cho, Duck; Kee, Seung Jung; Shin, Myung Geun; Suh, Soon Pal; Ryang, Dong Wook

    2007-03-01

    Data on clinical isolates of Kodamaea (Pichia) ohmeri, an emerging fungal pathogen, are scarce. Over the past 5 years, we identified yeast isolates from nine patients with fungemia as K. ohmeri by using the API 20C system. Here, we reanalyzed these isolates first by sequencing the internal transcribed spacer 2 (ITS2) regions and then by growing the isolates on CHROMagar Candida medium and subjecting them to pulsed-field gel electrophoresis (PFGE). Based on their ITS2 sequences, six of the nine isolates were confirmed as K. ohmeri, while the others were identified as Candida haemulonii (n = 2) and Candida parapsilosis (n = 1). PFGE karyotyping of the K. ohmeri isolates revealed similar major bands, and their colonies showed a characteristic color change from pink to blue when grown on CHROMagar Candida medium for more than 48 h. For K. ohmeri, the ranges of MICs of fluconazole, voriconazole, caspofungin, and micafungin were 2 to 32 mug/ml, 0.03 to 0.5 mug/ml, 0.125 to 0.25 mug/ml, and 0.03 to 0.06 mug/ml, respectively. Restriction endonuclease analysis of genomic NotI-digested DNA (REAG-N) from isolates from different patients produced unique patterns, suggesting that the fungemia had occurred sporadically. This study determined that ITS2 sequence data, PFGE karyotypes, and CHROMagar Candida chromogenic culture medium are reliable diagnostic tools for identifying K. ohmeri while REAG-N is useful for genotyping the clinical isolates of K. ohmeri. PMID:17251396

  1. Analysis of Molecular Epidemiology of Chilean Salmonella enterica Serotype Enteritidis Isolates by Pulsed-Field Gel Electrophoresis and Bacteriophage Typing

    PubMed Central

    Fernandez, Jorge; Fica, Alberto; Ebensperger, German; Calfullan, Hector; Prat, Soledad; Fernandez, Alda; Alexandre, Marcela; Heitmann, Ingrid

    2003-01-01

    Human Salmonella enterica serotype Enteritidis infections emerged in Chile in 1994. S. enterica serotype Enteritidis phage type 1 isolates predominated in the north, and phage type 4 isolates predominated in the central and southern regions. A study was planned to characterize this epidemic using the best discriminatory typing technique. Research involved 441 S. enterica serotype Enteritidis isolates, including clinical preepidemic samples (n = 74; 1975 to 1993) and epidemic (n = 199), food (n = 72), poultry (n = 57), and some Latin American (n = 39) isolates. The best method was selected based on a sample of preepidemic isolates, analyzing the discriminatory power (DP) obtained by phage typing and randomly amplified polymorphic DNA and pulsed-field gel electophoresis (PFGE) analysis. The highest DP was associated with BlnI PFGE-bacteriophage typing analysis (0.993). A total of 38 BlnI patterns (B patterns) were identified before the epidemic period, 19 since 1994, and only 4 in both periods. Two major clusters were identified by phylogenetic analysis, and the predominant B patterns clustered in the same branch. Combined analysis revealed that specific B pattern-phage type combinations (subtypes) disappeared before 1994, that different genotypes associated with S. enterica serotype Enteritidis phage type 4 had been observed since 1988, and that strain diversity increased before the expansion of S. enterica serotype Enteritidis in 1994. Predominant subtype B3-phage type 4 was associated with the central and southern regions, and subtype B38-phage type 1 was associated with the north (P < 0.0001). Food and poultry isolates matched the predominant S. enterica serotype Enteritidis subtypes, but isolates identified in neighboring countries (Peru and Bolivia) did not match S. enterica serotype Enteritidis subtypes identified in the north of Chile. The results of this work demonstrate that genetic diversity, replacement, and expansion of specific S. enterica serotype

  2. Epidemiologic analysis of sporadic Salmonella typhi isolates and those from outbreaks by pulsed-field gel electrophoresis.

    PubMed Central

    Thong, K L; Cheong, Y M; Puthucheary, S; Koh, C L; Pang, T

    1994-01-01

    Pulsed-field gel electrophoresis (PFGE) was used to compare and analyze 158 isolates of Salmonella typhi from five well-defined outbreaks of typhoid fever in Malaysia and also isolates involved in sporadic cases of typhoid fever occurring during the same period. Digestion of chromosomal DNAs from these S. typhi isolates with the restriction endonucleases XbaI (5'-TCTAGA-3'), SpeI (5'-ACTAGT-3'), and AvrII (5'-CCTAGG-3') and then PFGE produced restriction endonuclease analysis (REA) patterns consisting of 11 to 24 DNA fragments ranging in size from 20 to 630 kbp. Analysis of the REA patterns generated by PFGE after digestion with XbaI and SpeI indicated that the S. typhi isolates obtained from sporadic cases of infection were much more heterogeneous (at least 13 different REA patterns were detected; Dice coefficient, between 0.73 and 1.0) than those obtained during outbreaks of typhoid fever. The clonal nature and the close genetic identities of isolates from outbreaks in Alor Setar, Penang, Kota Kinabalu, Johor Bahru, and Kota Bahru were suggested by the fact that only a limited number of REA patterns, which mostly differed by only a single band, were detected (one to four patterns; Dice coefficient, between 0.82 and 1.0), although a different pattern was associated with each of these outbreaks. Comparison of REA patterns with ribotyping for 18 S. typhi isolates involved in sporadic cases of infection showed a good correlation, in that 72% of the isolates were in the same group. There was no clear correlation of phage types with a specific REA pattern. We conclude that PFGE of s. typhi chromosomal DNA digested with infrequently cutting restriction endonucleases is a useful method for comparing and differentiating S. typhi isolates for epidemiological purposes. Images PMID:7914202

  3. Comparison of restriction endonuclease analysis, ribotyping, and pulsed-field gel electrophoresis for molecular differentiation of Clostridium difficile strains.

    PubMed Central

    Kristjánsson, M; Samore, M H; Gerding, D N; DeGirolami, P C; Bettin, K M; Karchmer, A W; Arbeit, R D

    1994-01-01

    A combined clinical and molecular epidemiologic analysis of 46 strains of Clostridium difficile, including 16 nosocomial isolates from one ward (outbreak ward) plus 17 other nosocomial isolates and 13 community-acquired isolates, was performed. HindIII digests of total cellular DNA were analyzed by restriction enzyme analysis (REA) and ribotyping; SmaI digests were analyzed by pulsed-field gel electrophoresis (PFGE). Isolates were assigned to typing groups on the basis of the profiles detected; isolates with closely related profiles were assigned to subgroups. The 16 isolates from the outbreak ward were resolved by both REA and PFGE into five distinct groups; 13 isolates represented two REA groups and three PFGE groups and two isolates were resolved as distinct groups by both techniques. DNA obtained from one isolate was persistently partially degraded, precluding analysis by PFGE. Seventeen sporadic nosocomial isolates were resolved by REA and PFGE into comparable numbers of groups (i.e., nine groups) and subgroups (i.e., 15 and 14 subgroups, respectively), with two isolates not evaluable by PFGE. The 13 epidemiologically unrelated community-acquired isolates were assigned to 11 groups by REA and to 12 groups by PFGE. Overall, ribotyping identified only nine groups among the 46 isolates. We conclude that REA and PFGE have comparable discriminatory powers for epidemiologic typing of C. difficile isolates and that ribotyping is appreciably less discriminatory. For a few isolates, partial DNA degradation prevented analysis by PFGE but not by REA or ribotyping; the cause of the degradation is unknown. Images PMID:7989550

  4. Analysis of molecular epidemiology of Chilean Salmonella enterica serotype enteritidis isolates by pulsed-field gel electrophoresis and bacteriophage typing.

    PubMed

    Fernandez, Jorge; Fica, Alberto; Ebensperger, German; Calfullan, Hector; Prat, Soledad; Fernandez, Alda; Alexandre, Marcela; Heitmann, Ingrid

    2003-04-01

    Human Salmonella enterica serotype Enteritidis infections emerged in Chile in 1994. S. enterica serotype Enteritidis phage type 1 isolates predominated in the north, and phage type 4 isolates predominated in the central and southern regions. A study was planned to characterize this epidemic using the best discriminatory typing technique. Research involved 441 S. enterica serotype Enteritidis isolates, including clinical preepidemic samples (n = 74; 1975 to 1993) and epidemic (n = 199), food (n = 72), poultry (n = 57), and some Latin American (n = 39) isolates. The best method was selected based on a sample of preepidemic isolates, analyzing the discriminatory power (DP) obtained by phage typing and randomly amplified polymorphic DNA and pulsed-field gel electophoresis (PFGE) analysis. The highest DP was associated with BlnI PFGE-bacteriophage typing analysis (0.993). A total of 38 BlnI patterns (B patterns) were identified before the epidemic period, 19 since 1994, and only 4 in both periods. Two major clusters were identified by phylogenetic analysis, and the predominant B patterns clustered in the same branch. Combined analysis revealed that specific B pattern-phage type combinations (subtypes) disappeared before 1994, that different genotypes associated with S. enterica serotype Enteritidis phage type 4 had been observed since 1988, and that strain diversity increased before the expansion of S. enterica serotype Enteritidis in 1994. Predominant subtype B3-phage type 4 was associated with the central and southern regions, and subtype B38-phage type 1 was associated with the north (P < 0.0001). Food and poultry isolates matched the predominant S. enterica serotype Enteritidis subtypes, but isolates identified in neighboring countries (Peru and Bolivia) did not match S. enterica serotype Enteritidis subtypes identified in the north of Chile. The results of this work demonstrate that genetic diversity, replacement, and expansion of specific S. enterica serotype

  5. The influence of particle size and static magnetic fields on the uptake of magnetic nanoparticles into three dimensional cell-seeded collagen gel cultures.

    PubMed

    Lewis, Emily E L; Child, Hannah W; Hursthouse, Andrew; Stirling, David; McCully, Mark; Paterson, David; Mullin, Margaret; Berry, Catherine C

    2015-08-01

    Over recent decades there has been and continues to be major advances in the imaging, diagnosis and potential treatment of medical conditions, by the use of magnetic nanoparticles. However, to date the majority of cell delivery studies employ a traditional 2D monolayer culture. This article aims to determine the ability of various sized magnetic nanoparticles to penetrate and travel through a cell seeded collagen gel model, in the presence or absence of a magnetic field. Three different sized (100, 200, and 500 nm) nanoparticles were employed in the study. The results showed cell viability was unaffected by the presence of nanoparticles over a 24-h test period. The initial uptake of the 100 nm nanoparticle into the collagen gel structure was superior compared to the larger sized nanoparticles under the influence of a magnetic field and incubated for 24 h. Interestingly, it was the 200 nm nanoparticles, which proved to penetrate the gel furthest, under the influence of a magnetic field, during the initial culture stage after 1-h incubation. PMID:25358626

  6. The transition from stress softening to stress hardening under cyclic loading induced by magnetic field for magneto-sensitive polymer gels

    NASA Astrophysics Data System (ADS)

    Xu, Yangguang; Liao, Guojiang; Zhang, Canyang; Wan, Qiang; Liu, Taixiang

    2016-04-01

    Magneto-sensitive polymer gel (MSPG) is a kind of ferromagnetic particle filled smart polymer composite, whose magneto-mechanical coupling mechanism has attracted increasing attention in recent years. In this work, the magneto-induced rheological response of MSPG under cyclic shear loading was investigated. It was found that magnetic field is the critical reason for the transition from stress softening to stress hardening under cyclic loading. Besides, the particle concentration and temperature are the controlling factors in the structure optimization of MSPG in the presence of magnetic field. The magneto-induced hardening mechanism was further proposed based on the related experimental results.

  7. Population Genetic Structure of Listeria monocytogenes Strains as Determined by Pulsed-Field Gel Electrophoresis and Multilocus Sequence Typing

    PubMed Central

    Henri, Clémentine; Félix, Benjamin; Guillier, Laurent; Leekitcharoenphon, Pimlapas; Michelon, Damien; Mariet, Jean-François; Aarestrup, Frank M.; Mistou, Michel-Yves; Hendriksen, René S.

    2016-01-01

    ABSTRACT Listeria monocytogenes is a ubiquitous bacterium that may cause the foodborne illness listeriosis. Only a small amount of data about the population genetic structure of strains isolated from food is available. This study aimed to provide an accurate view of the L. monocytogenes food strain population in France. From 1999 to 2014, 1,894 L. monocytogenes strains were isolated from food at the French National Reference Laboratory for L. monocytogenes and classified according to the five risk food matrices defined by the European Food Safety Authority (EFSA). A total of 396 strains were selected on the basis of different pulsed-field gel electrophoresis (PFGE) clusters, serotypes, and strain origins and typed by multilocus sequence typing (MLST), and the MLST results were supplemented with MLST data available from Institut Pasteur, representing human and additional food strains from France. The distribution of sequence types (STs) was compared between food and clinical strains on a panel of 675 strains. High congruence between PFGE and MLST was found. Out of 73 PFGE clusters, the two most prevalent corresponded to ST9 and ST121. Using original statistical analysis, we demonstrated that (i) there was not a clear association between ST9 and ST121 and the food matrices, (ii) serotype IIc, ST8, and ST4 were associated with meat products, and (iii) ST13 was associated with dairy products. Of the two major STs, ST121 was the ST that included the fewest clinical strains, which might indicate lower virulence. This observation may be directly relevant for refining risk analysis models for the better management of food safety. IMPORTANCE This study showed a very useful backward compatibility between PFGE and MLST for surveillance. The results enabled better understanding of the population structure of L. monocytogenes strains isolated from food and management of the health risks associated with L. monocytogenes food strains. Moreover, this work provided an accurate view

  8. Numerical Models of Subduction and Slab Detachment: Placing a Lower Bound on the Strength of Slabs

    NASA Astrophysics Data System (ADS)

    Billen, M. I.; Andrews, E.

    2007-12-01

    Subduction provides the main driving force for the motion of tectonic plates at the Earth's surface through slab- pull and sinking-induced flow in the surrounding mantle. The ability of the slab to directly transmit slab-pull forces to the tectonic plate at the surface depends on the minimum strength and rheology (e.g., viscous, plastic) of the slab. Previous models have shown that observations including the state of stress in slabs, dynamic topography and the geoid above slabs, the evolution of slab and the kinematic history of subduction can be well-matched by a variety of models with either low viscosity (i.e., 100-1,000 times more viscous than the surrounding mantle) or high viscosity slabs (i.e., more than 10,000 times more viscous than the surrounding mantle). However, in many of the models in which a good match to observations is found for low viscosity slabs, the maximum slab viscosity is imposed as a cut-off value, which forces the entire slab to have a more or less uniform viscosity independent of strain-rate or stress magnitude, rather than a plastic yielding-type rheology. We present numerical models demonstrating that when the non-Newtonian viscosity of the upper mantle and plastic yielding behavior of slabs are taken into account, the minimum yield strength that allows for continuous subduction is approximately 300- 500 MPa, which leads to high viscosity slabs with some localized lower viscosity regions. A yield stress of 10-100 MPa is required to form uniformly low viscosity slabs, but these slabs detach from the subducting plate, due to localized weakening, when the slab reaches a length of 200-300 km, even when subduction is facilitated by a low viscosity shear zone and kinematically-imposed surface velocities. In contrast, detachment of higher strength slabs in fully-dynamic models only occurs when the shear zone is removed and prevents further subduction.

  9. Role of Hydrogen in stagnant slabs and big mantle wedge

    NASA Astrophysics Data System (ADS)

    Ohtani, E.; Zhao, D.

    2008-12-01

    Eastern China, Europe, and United State (e.g., [7]). According to the BMW model by Zhao [2], the intra-plate volcanisms in Northeast China including Mt. Changbai are different from the hot plumes and they might be generated due to some processes related to the deep-seated dehydration from the stagnant slab. Recent geochemical studies on volcanic rocks and associated mantle xenoliths in Northeast China (e.g., [8]) indicated that there is no geochemical evidence for involvement of subducting slab in most basalts, i.e., no depletion of high field strength elements and no enrichment of large ion lithophile elements. There is no clear evidence for a high-3He/4He mantle plume component in these rocks, i.e., 3He/4He ratios are significantly below the high 3He/4He ratios of mantle plumes such as those beneath Hawaii and Iceland. The geochemical signatures of the deep dehydration should be different from those in the conventional mantle wedge, since the fluids generated at such depths are completely different from those at the shallow depths. Further studies including the element partitioning between fluids and mantle under the deep upper mantle and the transition zone conditions are necessary to clarify the possible role of the Big Mantle Wedge on the intra-plate volcanism. [1] Fukao, et al., J. G. R. 108, doi:10.1029/2001JB000989, 2003. [2] Zhao et al., Chin. Sci. Bulletin 49, 1401, 2004, [3] Ohtani, Elements, 1, 25, 2005. [4] Richard et al., EPSL, 251, 156, 2006. [5] Hae et al., EPSL, 243, 141, 2006. [6] Litasov and Ohtani, PEPI, 134, 105, 2002. [7] Song et al., Nature, 427, 530, 2004. [8] Chen et al., Lithos, 96, 108, 2007

  10. Slab melting versus slab dehydration in subduction-zone magmatism

    PubMed Central

    Mibe, Kenji; Kawamoto, Tatsuhiko; Matsukage, Kyoko N.; Fei, Yingwei; Ono, Shigeaki

    2011-01-01

    The second critical endpoint in the basalt-H2O system was directly determined by a high-pressure and high-temperature X-ray radiography technique. We found that the second critical endpoint occurs at around 3.4 GPa and 770 °C (corresponding to a depth of approximately 100 km in a subducting slab), which is much shallower than the previously estimated conditions. Our results indicate that the melting temperature of the subducting oceanic crust can no longer be defined beyond this critical condition and that the fluid released from subducting oceanic crust at depths greater than 100 km under volcanic arcs is supercritical fluid rather than aqueous fluid and/or hydrous melts. The position of the second critical endpoint explains why there is a limitation to the slab depth at which adakitic magmas are produced, as well as the origin of across-arc geochemical variations of trace elements in volcanic rocks in subduction zones. PMID:21536910

  11. Slab melting versus slab dehydration in subduction-zone magmatism.

    PubMed

    Mibe, Kenji; Kawamoto, Tatsuhiko; Matsukage, Kyoko N; Fei, Yingwei; Ono, Shigeaki

    2011-05-17

    The second critical endpoint in the basalt-H(2)O system was directly determined by a high-pressure and high-temperature X-ray radiography technique. We found that the second critical endpoint occurs at around 3.4 GPa and 770 °C (corresponding to a depth of approximately 100 km in a subducting slab), which is much shallower than the previously estimated conditions. Our results indicate that the melting temperature of the subducting oceanic crust can no longer be defined beyond this critical condition and that the fluid released from subducting oceanic crust at depths greater than 100 km under volcanic arcs is supercritical fluid rather than aqueous fluid and/or hydrous melts. The position of the second critical endpoint explains why there is a limitation to the slab depth at which adakitic magmas are produced, as well as the origin of across-arc geochemical variations of trace elements in volcanic rocks in subduction zones. PMID:21536910

  12. Nonlinear Shear Instabilities in an Infinite Slab

    NASA Astrophysics Data System (ADS)

    Nepveu, M.

    1982-08-01

    The dynamical evolution of an infinite slab moving in denser and noisy (turbulent) surroundings is investigated with a 2D hydrodynamic code. The applicability of the results to astrophysical jets is discussed. Inviscid beams show internal shocks at regular intervals of a few beamwidths. Kinks are not obvious. In viscous beams shocks are less outspoken, but turbulence is triggered with maximum scales of a few beamwidths. These viscous beams broaden. Linear stability analysis may hold up to a few e-folding times, although the seed disturbance field is not infinitesimal. The computations suggest that viscous astrophysical beams may become blurred quite suddenly and may give rise to sudden change in radiation patterns (NGC 1265).

  13. Laser applications in machining slab materials

    NASA Astrophysics Data System (ADS)

    Zhang, Xiaoping

    1990-10-01

    Since the invention of the laser back in 1960, laser technology has been extensively applied in many fields of science and technology. These has been a history of nearly two decades of using lasers as an energy source in machining materials, such as cutting, welding, ruling and boring, among other operations. With the development of flexible automation in production, the advantages of laser machining have has grown more and more obvious. The combination of laser technology and computer science further promotes the enhancement and upgrading of laser machining and related equipment. At present, many countries are building high quality laser equipment for machining slab materials, such as the Coherent and Spectra Physics corporations in the United States, the Trumpf Corporation in West Germany, the Amada Corporation in Japan, and the Bystronic Corporation in Switzerland, among other companies.

  14. Electrophoretic extraction of proteins from two-dimensional electrophoresis gel spots

    DOEpatents

    Zhang, Jian-Shi; Giometti, C.S.; Tollaksen, S.L.

    1987-09-04

    After two-dimensional electrophoresis of proteins or the like, resulting in a polyacrylamide gel slab having a pattern of protein gel spots thereon, an individual protein gel spot is cored out from the slab, to form a gel spot core which is placed in an extraction tube, with a dialysis membrane across the lower end of the tube. Replicate gel spots can be cored out from replicate gel slabs and placed in the extraction tube. Molten agarose gel is poured into the extraction tube where the agarose gel hardens to form an immobilizing gel, covering the gel spot cores. The upper end portion of the extraction tube is filled with a volume of buffer solution, and the upper end is closed by another dialysis membrane. Upper and lower bodies of a buffer solution are brought into contact with the upper and lower membranes and are provided with electrodes connected to the positive and negative terminals of a dc power supply, thereby producing an electrical current which flows through the upper membrane, the volume of buffer solution, the agarose, the gel spot cores and the lower membrane. The current causes the proteins to be extracted electrophoretically from the gel spot cores, so that the extracted proteins accumulate and are contained in the space between the agarose gel and the upper membrane. 8 figs.

  15. Slab Driven Mantle Deformation and Plate-Mantle Decoupling

    NASA Astrophysics Data System (ADS)

    Jadamec, M. A.; MacDougall, J.; Fischer, K. M.

    2015-12-01

    Observations of shear wave splitting derived from local sources in subduction zones suggest viscous flow in the mantle wedge is commonly non-parallel to both the subducting plate velocity vector and the motion of the overriding plate. However, far from the subduction zone trench, observations indicate the fast axis of shear wave splitting tends to align with the velocity vector of the surface plates. Similarly, previous 3D geodynamic models show the slab can drive local decoupling of the mantle and surface plates, in both direction and speed. This suggests that there is some distance from the trench over which there is significant decoupling of the mantle flow from surface plate motion, and that this decoupling zone then decays with continued distance from the trench, resulting in far-field plate-mantle coupling. Here we present results from geodynamic models of subduction coupled with calculations of olivine fabric deformation and synthetic splitting to 1) examine the influence of slab strength, slab dip, and non-Newtonian viscosity on the deformation fabric in the mantle wedge and subslab mantle and 2) quantify the spatial extent and intensity of this slab driven decoupling zone. We compare the deformation fabric in a 2D corner flow solution with varying dip to that of a 2D free subduction model with varying initial dip and slab strength. The results show that using an experimentally derived flow law to define viscosity (both diffusion creep and dislocation creep deformation mechanisms) has a first order effect on the viscosity structure and flow velocity in the upper mantle. The free subduction models using the composite viscosity formulation produce a zone of subduction induced mantle weakening that results in reduced viscous support of the slab and lateral variability in coupling of the mantle to the base of the surface plates. The maximum yield stress, which places an upper bound on the slab strength, can also have a significant impact on the viscosity

  16. A new model for yield stress of magneto-rheological greases/gels under combined effects of magnetic field and temperature

    NASA Astrophysics Data System (ADS)

    Sahin, Huseyin; Wang, Xiaojie; Gordaninejad, Faramarz

    2009-03-01

    The goal of this study is to develop a new model to describe the behavior of shear yield stress of magnetorheological greases/gels (MRGs) under the combined effects of applied magnetic field and temperature. MRGs are a class of field-responsive materials which consist of micron-size ferrous particles suspended in a grease/gel-like material. The main advantage of a MRG over a MR fluid is that in a MRG, ferrous particles do not settle. However, the rheological properties of grease carrier materials are very sensitive to temperature. Therefore, the temperature effect on the yield stress of MRGs may be one of the main concerns in developing these materials. In this study, the steady-shear magneto-rheological response of MRGs subject to various temperatures is investigated. All experimental data are obtained for magnetic fields ranging from 0.14T to 0.53T and temperatures ranging from 10°C to 70°C. It is observed that temperature has a pronounced effect on the field induced yield stress of MRGs. A new yield stress model for MRGs which is a function of magnetic field and temperature is proposed based on the Herschel-Bulkley constitutive equation and the Arrhenius relationship. Excellent agreement between the model predictions and experimental data is obtained.

  17. Dynamic uplift during slab flattening

    NASA Astrophysics Data System (ADS)

    Dávila, Federico M.; Lithgow-Bertelloni, Carolina

    2015-09-01

    Subduction exerts a strong control on surface topography and is the main cause of large vertical motions in continents, including past events of large-scale marine flooding and tilting. The mechanism is dynamic deflection: the sinking of dense subducted lithosphere gives rise to stresses that directly pull down the surface. Here we show that subduction does not always lead to downward deflections of the Earth's surface. Subduction of young lithosphere at shallow angles (flat subduction) leaves it neutrally or even positively buoyant with respect to underlying mantle because the lithosphere is relatively warm compared with older lithosphere, and because the thickened and hence drier oceanic crust does not undergo the transformation of basalt to denser eclogite. Accounting for neutrally buoyant flat segments along with large variations in slab morphology in the South American subduction zone explains along-strike and temporal changes in dynamic topography observed in the geologic record since the beginning of the Cenozoic. Our results show that the transition from normal subduction to slab flattening generates dynamic uplift, preventing back-arc marine flooding.

  18. A comparison of microseismicity induced by gel-proppant-and water-injected hydraulic fractures, Carthage Cotton Valley gas field, East Texas

    SciTech Connect

    Rutledge, J. T.; Phillips, W. S.

    2002-01-01

    In May and July, 1997, a consortia of operators and service companies conducted a series of hydraulic fracture imaging tests in the Carthage Cotton Valley gas field of East Texas (Walker, 1997). Microseismic data were collected and processed for six hydraulic fracture treatments in two wells (3 completion intervals per well) (Mayerhofer et al., 2000). One well was completed with gel-proppant treatments in which a viscous crosslink gel was injected to entrain high concentrations of sand proppant into formation. The second well was completed using treated water and very low proppant concentrations (waterfracs). Waterfracs have been shown to be just as effective as the conventional gel-proppant treatments in Cotton Valley reservoirs, but at greatly reduced cost. Mayerhofer and Meehan (1998) suggest two possible reasons why waterfracs are successful: (1) Induced shear displacement along natural and hydraulic fractures results in self-propping (shear dilation enhanced by fracture branching, proppant and spalled rock fragments), and (2) Fracture extension and cleanup is easier to achieve with low-viscosity fluids. With improved source location precision and focal mechanism determination (fracture plane orientation and sense of slip), we have reexamined the Cotton Valley data, comparing the seismicity induced by water and gel-proppant treatments at common depth intervals. We have improved the location precision and computed focal mechanism of microearthquakes induced during a series of hydraulic fracture completions within the Cotton Valley formation of East Texas. Conventional gel-proppant treatments and treatments using treated water and very low proppant concentrations (waterfracs) were monitored. Waterfracs have been shown to be just as effective as the conventional gel-proppant treatments in Cotton Valley reservoirs, but at greatly reduced cost (Mayerhofer and Meehan, 1998). Comparison of the seismicity induced by the two treatment types show similar distributions of

  19. Subducting Slabs: Jellyfishes in the Earth's Mantle

    NASA Astrophysics Data System (ADS)

    Loiselet, C.; Braun, J.; Husson, L.; Le Carlier de Veslud, C.; Thieulot, C.; Yamato, P.; Grujic, D.

    2010-12-01

    The constantly improving resolution of geophysical data, seismic tomography and seismicity in particular, shows that the lithosphere does not subduct as a slab of uniform thickness but is rather thinned in the upper mantle and thickened around the transition zone between the upper and lower mantle. This observation has traditionally been interpreted as evidence for the buckling and piling of slabs at the boundary between the upper and lower mantle, where a strong contrast in viscosity may exist and cause resistance to the penetration of slabs into the lower mantle. The distribution and character of seismicity reveal, however, that slabs undergo vertical extension in the upper mantle and compression near the transition zone. In this paper, we demonstrate that during the subduction process, the shape of low viscosity slabs (1 to 100 times more viscous than the surrounding mantle) evolves toward an inverted plume shape that we coin jellyfish. Results of a 3D numerical model show that the leading tip of slabs deform toward a rounded head skirted by lateral tentacles that emerge from the sides of the jellyfish head. The head is linked to the body of the subducting slab by a thin tail. A complete parametric study reveals that subducting slabs may achieve a variety of shapes, in good agreement with the diversity of natural slab shapes evidenced by seismic tomography. Our work also suggests that the slab to mantle viscosity ratio in the Earth is most likely to be lower than 100. However, the sensitivity of slab shapes to upper and lower mantle viscosities and densities, which remain poorly constrained by independent evidence, precludes any systematic deciphering of the observations.

  20. Subducting slabs: Jellyfishes in the Earth's mantle

    NASA Astrophysics Data System (ADS)

    Loiselet, Christelle; Braun, Jean; Husson, Laurent; Le Carlier de Veslud, Christian; Thieulot, Cedric; Yamato, Philippe; Grujic, Djordje

    2010-08-01

    The constantly improving resolution of geophysical data, seismic tomography and seismicity in particular, shows that the lithosphere does not subduct as a slab of uniform thickness but is rather thinned in the upper mantle and thickened around the transition zone between the upper and lower mantle. This observation has traditionally been interpreted as evidence for the buckling and piling of slabs at the boundary between the upper and lower mantle, where a strong contrast in viscosity may exist and cause resistance to the penetration of slabs into the lower mantle. The distribution and character of seismicity reveal, however, that slabs undergo vertical extension in the upper mantle and compression near the transition zone. In this paper, we demonstrate that during the subduction process, the shape of low viscosity slabs (1 to 100 times more viscous than the surrounding mantle) evolves toward an inverted plume shape that we coin jellyfish. Results of a 3D numerical model show that the leading tip of slabs deform toward a rounded head skirted by lateral tentacles that emerge from the sides of the jellyfish head. The head is linked to the body of the subducting slab by a thin tail. A complete parametric study reveals that subducting slabs may achieve a variety of shapes, in good agreement with the diversity of natural slab shapes evidenced by seismic tomography. Our work also suggests that the slab to mantle viscosity ratio in the Earth is most likely to be lower than 100. However, the sensitivity of slab shapes to upper and lower mantle viscosities and densities, which remain poorly constrained by independent evidence, precludes any systematic deciphering of the observations.

  1. Goos-Haenchen shifts of the reflected waves from a cold, inhomogeneous, and magnetized plasma slab

    SciTech Connect

    Xu Guoding; Zang Taocheng; Pan Tao

    2010-01-15

    We discuss theoretically the Goos-Haenchen (GH) shifts of the reflected waves from a cold, inhomogeneous, and magnetized plasma slab by using the invariant imbedding approach. Aiming at the linear and parabolic electron-density profiles, we demonstrate numerically the dependences of the co- and cross-polarized GH shifts on the angle of incidence, external static magnetic field, and the thickness of the plasma slab. The results show that the different electron-density profiles of plasma can result in the very different dependences of the GH shifts on the angle of incidence, external magnetic field, and the slab's thickness; the GH shifts can be switched between the considerably large positive and negative values under certain conditions. Particularly, without altering the structure of the plasma slab, the GH shifts can be manipulated by modifying the angle of incident or the external static magnetic field.

  2. Slab fluid release: localized in space and time

    NASA Astrophysics Data System (ADS)

    John, T.; Gussone, N. C.; Podladchikov, Y. Y.

    2012-12-01

    As subducting oceanic plates descend into the Earth's mantle, increasing pressures and temperatures lead to the progressive destabilization of hydrous mineral phases and the release of H2O-rich fluids. Some fraction of these fluids ascend into the overlying mantle wedge, inducing partial melting, and their "chemical freight" is thought to contribute to the distinctive chemical signature of the resulting arc magmas. Field evidences suggest that channelized fluid flow may be the dominant mechanism for intra-slab fluid flow. Along their pathways within slabs, these fluids can trigger mineral reactions and produce chemical changes in rocks with which they interact. However, the spatial and temporal scales of this fluid flow remain largely unknown. We employed the Ca and Li isotope systems on a fossil high-pressure fluid pathway and its associated reaction halo (Chinese Tianshan), formed at ~70 km depth during subduction of a coherent oceanic slab, allowing us to constrain the fluid flux, fluid source and the duration of the fluid-rock interaction. In the reaction halo, the degree of eclogitization along with Ca concentration increases towards the vein. A high fluid flux is required to obtain the observed Ca increase and changes in δ44/40Ca. The Ca isotope composition indicate mixing of two distinct Ca sources, the wall-rock blueschist and an external fluid source, the latter of which is enriched in heavy Ca isotopes. The relatively high δ44/40Ca (>1.3‰) of the infiltrating fluid is suggestive of partially hydrated slab mantle as the fluid source. Alternatively, Ca derived from MORB, (0.7 to 0.9‰) and AOC (0.6 to 1.0‰) might evolve towards heavier Ca isotope values while it is ascending through the slab and reacting with wall-rocks and forming carbonates, which are usually associated with the flow structures. This is because calcium carbonate precipitation preferentially removes light Ca from the fluid while the residual fluid will get heavier proportional to

  3. The slab geometry laser. I - Theory

    NASA Technical Reports Server (NTRS)

    Eggleston, J. M.; Kane, T. J.; Kuhn, K.; Byer, R. L.; Unternahrer, J.

    1984-01-01

    Slab geometry solid-state lasers offer significant performance improvements over conventional rod-geometry lasers. A detailed theoretical description of the thermal, stress, and beam-propagation characteristics of a slab laser is presented. The analysis includes consideration of the effects of the zig-zag optical path, which eliminates thermal and stress focusing and reduces residual birefringence.

  4. Rapid pulsed-field gel electrophoresis protocol for typing of Escherichia coli O157:H7 and other gram-negative organisms in 1 day.

    PubMed Central

    Gautom, R K

    1997-01-01

    Genomic DNA patterns generated by pulsed-field gel electrophoresis are highly specific for different strains of an organism and have significant value in epidemiologic investigations of infectious-disease outbreaks. Unfortunately, time-consuming and tedious specimen processing is an inherent problem which limits the use of this powerful technology as a real-time epidemic investigational tool. Here, I describe a rapid method to improve the response time and provide specific bacterial strain identification for the typing of Escherichia coli O157:H7 and other gram-negative organisms in a single day. PMID:9350772

  5. Electrophoretic extraction of proteins from two-dimensional electrophoresis gel spots

    DOEpatents

    Zhang, Jian-Shi; Giometti, Carol S.; Tollaksen, Sandra L.

    1989-01-01

    After two-dimensional electrophoresis of proteins or the like, resulting in a polyacrylamide gel slab having a pattern of protein gel spots thereon, an individual protein gel spot is cored out from the slab, to form a gel spot core which is placed in an extraction tube, with a dialysis membrane across the lower end of the tube. Replicate gel spots can be cored out from replicate gel slabs and placed in the extraction tube. Molten agarose gel is poured into the extraction tube where the agarose gel hardens to form an immobilizing gel, covering the gel spot cores. The upper end portion of the extraction tube is filled with a volume of buffer solution, and the upper end is closed by another dialysis membrane. Upper and lower bodies of a buffer solution are brought into contact with the upper and lower membranes and are provided with electrodes connected to the positive and negative terminals of a DC power supply, thereby producing an electrical current which flows through the upper membrane, the volume of buffer solution, the agarose, the gel spot cores and the lower membrane. The current causes the proteins to be extracted electrophoretically from the gel spot cores, so that the extracted proteins accumulate and are contained in the space between the agarose gel and the upper membrane. A high percentage extraction of proteins is achieved. The extracted proteins can be removed and subjected to partial digestion by trypsin or the like, followed by two-dimensional electrophoresis, resulting in a gel slab having a pattern of peptide gel spots which can be cored out and subjected to electrophoretic extraction to extract individual peptides.

  6. INDEPENDENT VERIFICATION OF THE BUILDING 3550 SLAB AT OAK RIDGE NATIONAL LABORATORY OAK RIDGE, TENNESSEE

    SciTech Connect

    Weaver, Phyllis C.

    2012-05-08

    The Oak Ridge Institute for Science and Education (ORISE) has completed the independent verification survey of the Building 3550 Slab. The results of this effort are provided. The objective of this verification survey is to provide independent review and field assessment of remediation actions conducted by Safety and Ecology Corporation (SEC) to document that the final radiological condition of the slab meets the release guidelines. Verification survey activities on the Building 3550 Slab that included scans, measurements, and the collection of smears. Scans for alpha, alpha plus beta, and gamma activity identified several areas that were investigated.

  7. Looking east inside of the 44" slab mill building at ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Looking east inside of the 44" slab mill building at the red hot slabs being conveyed to the hot beds. - U.S. Steel Edgar Thomson Works, 44" Slab Mill, Along Monongahela River, Braddock, Allegheny County, PA

  8. Magnetoelectric sensor excitations in hexaferrite slabs

    NASA Astrophysics Data System (ADS)

    Zare, Saba; Izadkhah, Hessam; Somu, Sivasubramanian; Vittoria, Carmine

    2015-06-01

    We developed techniques for H- and E-field sensors utilizing single phase magnetoelectric (ME) hexaferrite slabs in the frequency range of 100 Hz to 10 MHz. Novel circuit designs incorporating both spiral and solenoid coils and single and multi-capacitor banks were developed to probe the physics and properties of ME hexaferrites and explore ME effects for sensor detections. Fundamental measurements of the anisotropic tensor elements of the magneto-electric coupling parameter were performed using these novel techniques. In addition, for H-field sensing experiments we measured sensitivity of about 3000 Vm-1/G using solenoid coils and 8000 Vm-1/G using spiral coils. For E-field, sensing the sensitivity was 10-4 G/Vm-1 and using single capacitor detector. Sensitivity for multi-capacitor detectors was measured to be in the order of 10-3 G/Vm-1 and frequency dependent exhibiting a maximum value at ˜1 MHz. Tunability of 0.1%-90% was achieved for tunable inductor applications using both single and multi-capacitors excitation. We believe that significant (˜106) improvements in sensitivity and tunability are feasible with simple modifications of the fabrication process.

  9. A cryogenic slab CO laser

    SciTech Connect

    Ionin, Andrei A; Kozlov, A Yu; Seleznev, L V; Sinitsyn, D V

    2009-03-31

    A compact capacitive transverse RF-discharge-pumped slab CO laser with cryogenically cooled electrodes, which operates both in the cw and repetitively pulsed regimes, is fabricated. The laser operation is studied in the free running multifrequency regime at the vibrational - rotational transitions of the fundamental (V + 1 {yields} V) vibrational bands of the CO molecule in the spectral region from 5.1 to 5.4 {mu}m. Optimal operation conditions (gas mixture composition and pressure, RF pump parameters) are determined. It is shown that only gas mixtures with a high content of oxygen (up to 20% with respect to the concentration of CO molecules) can be used as an active medium of this laser. It is demonstrated that repetitively pulsed pumping is more efficient compared to cw pumping. In this case, quasi-cw lasing regime can be obtained. The maximum average output power of {approx}12 W was obtained for this laser operating on fundamental bands and its efficiency achieved {approx}14 %. The frequency-selective operation regime of the slab RF-discharge-pumped CO laser was realised at {approx} 100 laser lines in the spectral region from 5.0 to 6.5 {mu}m with the average output power of up to several tens of milliwatts in each line. Lasing at the transitions of the first vibrational overtone (V + 2 {yields} V) of the CO molecule is obtained in the spectral region from 2.5 to 3.9 {mu}m. The average output power of the overtone laser achieved 0.3 W. All the results were obtained without the forced gas mixture exchange in the discharge chamber. Under fixed experimental conditions, repetitively pulsed lasing (with fluctuations of the output characteristics no more than {+-}10 %) was stable for more than an hour. (lasers)

  10. Terminal Stage Subduction and Slab Detachment: From Structure to Dynamics

    NASA Astrophysics Data System (ADS)

    Wortel, M. J.; Spakman, W.; Govers, R.

    2007-12-01

    In this contribution we focus on terminal stage subduction, often triggered by continent-continent or arc-continent collision. Rupturing of subducted lithosphere, including slab detachment, is a key process in this stage. Seismic tomography information on the 3D structure of subduction zones has been key towards developing a better understanding of subduction processes. We show how structural information on lithosphere and mantle structure, obtained from seismic tomography, can be used to formulate hypotheses concerning the evolution and dynamics of subduction zones which (1) can be subjected to numerical modeling to investigate the physical soundness of the hypotheses, and (2) can subsequently be tested against geological, geophysical, and geodetical data to assess their general or regional validity. In combination, this approach increases our understanding of the relation between deep processes and the geological processes at the surface. The landlocked basin setting of the Mediterranean region provides unique opportunities to study terminal stage subduction and its consequences. Subducted lithosphere is subject to various types of rupturing: Slab detachment, vertical slab tearing and the formation of STEP (tear) faults have been identified and analysed. The different Mediterranean arc systems being in slightly different stages of evolution provides additional clues towards unraveling the dynamics of the process. Using examples from the western-central and eastern Mediterranean, we show how temporal and spatial variations in slab structure affect the dynamics and stress field of convergent plate boundaries, with arc migration and back-arc extension as a prominent expression. In addition, terminal stage subduction appears to be have played a crucial role in Italian magmatism. Terminal stage subduction involving slab detachment is a strongly transient stage with great impact on geological processes, on a wide variety of scales. The information obtained from

  11. Equilibrium Slab Models of Lyman-Alpha Clouds

    NASA Technical Reports Server (NTRS)

    Charlton, Jane C.; Salpeter, Edwin E.; Hogan, Craig J.

    1993-01-01

    We model the L(sub y(alpha)) clouds as slabs of hydrogen with an ionizing extragalactic radiation field incident from both sides. In general, the equilibrium configuration of a slab at redshift z approx. less than 5 is determined by a balance of the gas pressure, gravity (including the effects of a dark matter halo), and the pressure exerted by the inter-galactic medium, P(sub ext). These models have been used to make predictions of the number of slabs as a function of the neutral hydrogen column density, N(sub H). A break in the curve is predicted at the transition between regimes where gravity and pressure are the dominant confining forces, with a less rapid decrease at larger N(sub H). The transition from optically thin to optically thick slabs leads to a gap in the distribution, whose location is governed largely by the spectrum of ionizing radiation. There are certain parallels between lines of sight through the outer HI disk of spiral galaxy with increasing radius, and the progression from damped, to Lyman limit, to forest clouds. We discuss briefly the possibility that at least some of the observed low z forest clouds may be a separate population, associated with galaxies, as suggested by the observations of Bahcall et al. This population could dominate the forest at present if the dark matter attached to galaxies should lead to gravity confinement for this disk population, while the isolated clouds remain pressure confined. The formalism developed in this paper will allow a more detailed study. We also discuss a more general parameter study of the equilibrium configuration of slabs, including mock gravity and L(sub y(alpha)) photon trapping.

  12. On the Viability of Slab Melting

    NASA Astrophysics Data System (ADS)

    Van Hunen, J.; Bouilhol, P.; Magni, V.; Maunder, B. L.

    2014-12-01

    Melting subducted mafic crust is commonly assumed to be the main process leading to silicic melts with an adakitic signature, which may form Archaean granitoids and generate early continental crust. Alternatively, melting of the overriding lower mafic crust and near-Moho depth fractional crystallisation of mantle melts can form differentiated magmas with an adakitic signature. Previous work shows how only very young slabs melt through dehydration melting, or depict melting of dry eclogites via water addition from deeper slab dehydration. Alternatively, underplated subducted material via delamination and diapirism may be important in the generation of felsic continental crust. We quantify subduction dehydration and melting reactions in a warm subduction system using a thermo-mechanical subduction model with a thermodynamic database. We find that even young (hot) slabs dehydrate before reaching their solidus, which suppresses any slab dehydration melting and creates significant amounts of mantle wedge melting irrespective of slab age. Significant slab crust melting is only achieved in young slabs via water present melting if metamorphic fluids from the subducted mantle flux through the dry eclogites. These slab melts, however, interfere with massive mantle wedge melting and unlikely to participate in the overriding plate felsic magmatism, unlike the shallower, primitive mantle wedge melts. We also explore the conditions for delaminating the mafic subducted crust. For a wide range of ages, the uppermost part of the subducted slab might delaminate to form compositionally buoyant plumes that rise through the mantle wedge. Thick crust on young slabs (as perhaps representative for a hotter, early Earth) may delaminate entirely and reside in the mantle wedge. Under such conditions, this ponded crust might melts subsequently, forming "adakitic" felsic melts contributing to a significant amount of the overriding plate crustal volumes.

  13. Slab stagnation and detachment under northeast China

    NASA Astrophysics Data System (ADS)

    Honda, Satoru

    2016-03-01

    Results of tomography models around the Japanese Islands show the existence of a gap between the horizontally lying (stagnant) slab extending under northeastern China and the fast seismic velocity anomaly in the lower mantle. A simple conversion from the fast velocity anomaly to the low-temperature anomaly shows a similar feature. This feature appears to be inconsistent with the results of numerical simulations on the interaction between the slab and phase transitions with temperature-dependent viscosity. Such numerical models predict a continuous slab throughout the mantle. I extend previous analyses of the tomography model and model calculations to infer the origins of the gap beneath northeastern China. Results of numerical simulations that take the geologic history of the subduction zone into account suggest two possible origins for the gap: (1) the opening of the Japan Sea led to a breaking off of the otherwise continuous subducting slab, or (2) the western edge of the stagnant slab is the previous subducted ridge, which was the plate boundary between the extinct Izanagi and the Pacific plates. Origin (2) suggesting the present horizontally lying slab has accumulated since the ridge subduction, is preferable for explaining the present length of the horizontally lying slab in the upper mantle. Numerical models of origin (1) predict a stagnant slab in the upper mantle that is too short, and a narrow or non-existent gap. Preferred models require rather stronger flow resistance of the 660-km phase change than expected from current estimates of the phase transition property. Future detailed estimates of the amount of the subducted Izanagi plate and the present stagnant slab would be useful to constrain models. A systematic along-arc variation of the slab morphology from the northeast Japan to Kurile arcs is also recognized, and its understanding may constrain the 3D mantle flow there.

  14. The use of high field strength and parallel imaging techniques for MRI-based gel dosimetry in stereotactic radiosurgery

    NASA Astrophysics Data System (ADS)

    Seimenis, I.; Moutsatsos, A.; Petrokokkinos, L.; Kantemiris, I.; Benekos, O.; Efstathopoulos, E.; Papagiannis, P.; Spevacek, V.; Semnicka, J.; Dvorak, P.

    2009-07-01

    The poor clinical acceptance of polymer gel dosimetry for dose verification in stereotactic radio-surgery applications stems, inter alia, from the increased MRI acquisition times needed to meet the associated spatial resolution demands. To examine whether this could be partly alleviated by the employment of 3 Tesla imagers and parallel imaging techniques, a PolyAcrylamide Gel filled tube was irradiated in a Leksell Gamma Knife unit with two single irradiation shots (4 mm and 8 mm) and underwent four different scanning sessions using an optimised, volume selective, 32 echo CPMG pulse sequence: One performed on a 1.5 T imager with 0.5 × 0.5 mm2 in-plane spatial resolution and 0.75 mm slice thickness (scan A), while the rest three on a 3.0 T imager; one with the same spatial resolution as in scan A (scan B) and two with finer in-plane resolution (scans C and D). In scans B and C the sensitivity encoding (SENSE) parallel imaging technique was employed. Relative dose distributions derived by scan A were benchmarked against Monte Carlo and treatment planning system calculations, and then used as the reference for the comparison of 2D relative dose distributions derived by each scan in terms of dose difference and distance-to-agreement criteria (γ index tool). Findings suggest that careful MRI planning based on a figure of merit accounting for scanning time and precision for a given increase in spatial resolution, could facilitate the introduction of polymer gel dosimetry into the clinical setting as a practical quality assurance tool for complex radio-surgery techniques.

  15. Reflection and transmission of Gaussian beam by a chiral slab

    NASA Astrophysics Data System (ADS)

    Yan, Bing; Zhang, Huayong; Zhang, Jianyong

    2016-06-01

    Based on the generalized Lorenz-Mie theory framework, the reflection and transmission of an incident Gaussian beam by a chiral slab were investigated, by expanding the incident Gaussian beam, reflected beam, internal beam as well as transmitted beam in terms of cylindrical vector wave functions. The unknown expansion coefficients were determined by virtue of the boundary conditions. For a localized beam model, numerical results of the normalized field intensity distributions are presented, and the propagation characteristics are discussed concisely in this paper.

  16. Cretaceous Arctic magmatism: Slab vs. plume? Or slab and plume?

    NASA Astrophysics Data System (ADS)

    Gottlieb, E. S.; Miller, E. L.; Andronikov, A. V.; Brumley, K.; Mayer, L. A.; Mukasa, S. B.

    2010-12-01

    Tectonic models for the Cretaceous paleogeographic evolution of the Arctic Ocean and its adjacent landmasses propose that rifting in the Amerasia Basin (AB) began in Jura-Cretaceous time, accompanied by the development of the High Arctic Large Igneous Province (HALIP). During the same timespan, deformation and slab-related magmatism, followed by intra-arc rifting, took place along the Pacific side of what was to become the Arctic Ocean. A compilation and comparison of the ages, characteristics and space-time variation of circum-Arctic magmatism allows for a better understanding of the role of Pacific margin versus Arctic-Atlantic plate tectonics and the role of plume-related magmatism in the origin of the Arctic Ocean. In Jura-Cretaceous time, an arc built upon older terranes overthrust the Arctic continental margins of North America and Eurasia, shedding debris into foreland basins in the Brooks Range, Alaska, across Chukotka, Russia, to the Lena Delta and New Siberian Islands region of the Russian Arctic. These syn-tectonic sediments have some common sources (e.g., ~250-300 Ma magmatic rocks) as determined by U-Pb detrital zircon geochronology. They are as young as Valanginian-Berriasian (~136 Ma, Gradstein et al., 2004) and place a lower limit on the age of formation of the AB. Subsequent intrusions of granitoid plutons, inferred to be ultimately slab-retreat related, form a belt along the far eastern Russian Arctic continental margin onto Seward Peninsula and have yielded a continuous succession of zircon U-Pb ages from ~137-95 Ma (n=28) and a younger suite ~91-82 Ma (n=16). All plutons dated were intruded in an extensional tectonic setting based on their relations to wall-rock deformation. Regional distribution of ages shows a southward migration of the locus of magmatism during Cretaceous time. Basaltic lavas as old as 130 Ma and as young as 80 Ma (40Ar/39Ar)) erupted across the Canadian Arctic Islands, Svalbard and Franz Josef Land and are associated with

  17. The Casimir force between an ideal metal plate and a dissipative dielectric slab

    NASA Astrophysics Data System (ADS)

    Falinejad, H.; Bayat, F.

    2014-09-01

    In this research, a general formula for the Casimir force between ideal metal plate and a dissipative dielectric slab has been obtained. The dielectric function of the slab is assumed to be an arbitrary complex function of frequency satisfying Kramers-Kronig relations. A classical expression for the radiation pressure of the vacuum fields on the slab is presented by using the Maxwell stress tensor. With the transition to the quantum domain and using the fluctuation dissipation theorem and Kubo's formula, the resulting expression is written in terms of the imaginary part of the vector potential Green functions components of the system. Finally, by computing the Green function, the Casimir force on the slab is obtained. This formalism enables us to calculate the Casimir force without resorting to the explicit form of the field operators. The general expression is confirmed by limiting and comparing with one of the previous works.

  18. Crystallization from Gels

    NASA Astrophysics Data System (ADS)

    Narayana Kalkura, S.; Natarajan, Subramanian

    Among the various crystallization techniques, crystallization in gels has found wide applications in the fields of biomineralization and macromolecular crystallization in addition to crystallizing materials having nonlinear optical, ferroelectric, ferromagnetic, and other properties. Furthermore, by using this method it is possible to grow single crystals with very high perfection that are difficult to grow by other techniques. The gel method of crystallization provides an ideal technique to study crystal deposition diseases, which could lead to better understanding of their etiology. This chapter focuses on crystallization in gels of compounds that are responsible for crystal deposition diseases. The introduction is followed by a description of the various gels used, the mechanism of gelling, and the fascinating phenomenon of Liesegang ring formation, along with various gel growth techniques. The importance and scope of study on crystal deposition diseases and the need for crystal growth experiments using gel media are stressed. The various crystal deposition diseases, viz. (1) urolithiasis, (2) gout or arthritis, (3) cholelithiasis and atherosclerosis, and (4) pancreatitis and details regarding the constituents of the crystal deposits responsible for the pathological mineralization are discussed. Brief accounts of the theories of the formation of urinary stones and gallstones and the role of trace elements in urinary stone formation are also given. The crystallization in gels of (1) the urinary stone constituents, viz. calcium oxalate, calcium phosphates, uric acid, cystine, etc., (2) the constituents of the gallstones, viz. cholesterol, calcium carbonate, etc., (3) the major constituent of the pancreatic calculi, viz., calcium carbonate, and (4) cholic acid, a steroidal hormone are presented. The effect of various organic and inorganic ions, trace elements, and extracts from cereals, herbs, and fruits on the crystallization of major urinary stone and gallstone

  19. Hydrous manganese oxide doped gel probe sampler for measuring in situ reductive dissolution rates. 2. Field deployment.

    PubMed

    Farnsworth, Claire E; Griffis, Sarah D; Wildman, Richard A; Hering, Janet G

    2010-01-01

    In situ rates of reductive dissolution in submerged shoreline sediments at Lake Tegel (Berlin, Germany) were measured with a novel hydrous manganese (Mn) oxide-doped gel probe sampler in concert with equilibrium gel probe and sequential extraction measurements. Rates were low in the top 8 cm, then showed a peak from 8 to 14 cm, with a maximum at 12 cm depth. This rate corresponded with a peak in dissolved porewater iron (Fe) at 11 cm depth. Below 14 cm, the reductive dissolution rate reached an intermediate steady value. Lower rates at depth corresponded with increases in operationally defined fractions of carbonate-bound and organic- and sulfide-bound Mn and Fe as detected by sequential extraction. Observed rates of reductive dissolution, which reflect a capacity for Mn reduction rather than actual rates under ambient conditions, appear to correlate with porewater chemistry and sequential extraction fractions as expected in early sediment diagenesis, and are consistent with previous measurements of in situ reductive dissolution rates. Significant downward advection in this bank filtration setting depletes the Mn and Fe oxides in the sediments and enhances the transport of dissolved Fe and Mn into the infiltrating water. PMID:20039732

  20. Differential Single Nucleotide Polymorphism-Based Analysis of an Outbreak Caused by Salmonella enterica Serovar Manhattan Reveals Epidemiological Details Missed by Standard Pulsed-Field Gel Electrophoresis

    PubMed Central

    Scaltriti, Erika; Sassera, Davide; Comandatore, Francesco; Morganti, Marina; Mandalari, Carmen; Gaiarsa, Stefano; Bandi, Claudio; Zehender, Gianguglielmo; Bolzoni, Luca; Casadei, Gabriele

    2015-01-01

    We retrospectively analyzed a rare Salmonella enterica serovar Manhattan outbreak that occurred in Italy in 2009 to evaluate the potential of new genomic tools based on differential single nucleotide polymorphism (SNP) analysis in comparison with the gold standard genotyping method, pulsed-field gel electrophoresis. A total of 39 isolates were analyzed from patients (n = 15) and food, feed, animal, and environmental sources (n = 24), resulting in five different pulsed-field gel electrophoresis (PFGE) profiles. Isolates epidemiologically related to the outbreak clustered within the same pulsotype, SXB_BS.0003, without any further differentiation. Thirty-three isolates were considered for genomic analysis based on different sets of SNPs, core, synonymous, nonsynonymous, as well as SNPs in different codon positions, by Bayesian and maximum likelihood algorithms. Trees generated from core and nonsynonymous SNPs, as well as SNPs at the second and first plus second codon positions detailed four distinct groups of isolates within the outbreak pulsotype, discriminating outbreak-related isolates of human and food origins. Conversely, the trees derived from synonymous and third-codon-position SNPs clustered food and human isolates together, indicating that all outbreak-related isolates constituted a single clone, which was in line with the epidemiological evidence. Further experiments are in place to extend this approach within our regional enteropathogen surveillance system. PMID:25653407

  1. Three-dimensional Numerical Models of Slab Edges: Implications for Mantle Upwelling and Anomalous Volcanism

    NASA Astrophysics Data System (ADS)

    Jadamec, M.; Moresi, L. N.; Durance-Sie, P. M.; Mclean, K. A.

    2013-05-01

    addition, higher temperatures in the mantle wedge in regions of active back arc spreading and young oceanic lithosphere in the upper plate can enhance slab melting and lead to increased mantle flow velocities due to the reduction in the temperature-dependent viscosity. Models of this kind can provide a framework for interpreting how the 3D solid state flow field may influence melt migration patterns in subduction zones with slab edges.

  2. Down-dip and Along-strike Stress in Subducting Slabs

    NASA Astrophysics Data System (ADS)

    Petricca, P.; Carminati, E.; Basili, R.; Doglioni, C.

    2014-12-01

    The reconstructed stress fields for intermediate depths in slabs (between 100 and 300 km) remain enigmatic. Slab pull should enhance downdip tension, but downdip compression is often observed.Based on hotspot tracks (indicating a relative motion between the lithosphere and the mantle) several researchers proposed a westward drift of the lithosphere with debated velocities (2-13 cm/yr). Available data indicates that dominant down-dip tension occurs along E-directed subductions (e.g., Chile) sustained by the eastward relative mantle flow and down-dip compression along W-directed subductions (e.g., Tonga) encroached by the mantle motion. In this perspective, 3D viscoelastic models (FEM) were performed to investigate the origin of stress in slabs at intermediate depths. Geometries inspired to real subduction zones, were used to analyze the effect of the principal geodynamic forces (slab pull, mantle flow, plate convergence), the correlation between subduction polarity (i.e., how the mantle flow approaches the slab) and geometry, the nature of down-dip and along-strike stresses (poorly investigated in the literature).We conclude that, although the stress in slabs is controlled by several geodynamic processes, down-dip compression is favored by mantle flow opposing the slab, whereas down-dip tension is enhanced by mantle flow sustaining the slab. These predictions are in agreement with available geophysical observations.Substantial along-strike deformation affects intermediate and deeper regions of the slab when mantle flow is enhanced. Down-dip and along-strike axes form couples that tend to rotate approaching the slab sides. The larger the lateral extent of the plate the most this effect is evident. According to these findings, along-strike tension or compression comes out in response to the flexure (forward or backward) of the lithosphere depending on the slab longitudinal curvature. Along-strike tension occurs in case of slabs curved towards the mantle flow direction

  3. High-quality slab-based intermixing method for fusion rendering of multiple medical objects.

    PubMed

    Kim, Dong-Joon; Kim, Bohyoung; Lee, Jeongjin; Shin, Juneseuk; Kim, Kyoung Won; Shin, Yeong-Gil

    2016-01-01

    The visualization of multiple 3D objects has been increasingly required for recent applications in medical fields. Due to the heterogeneity in data representation or data configuration, it is difficult to efficiently render multiple medical objects in high quality. In this paper, we present a novel intermixing scheme for fusion rendering of multiple medical objects while preserving the real-time performance. First, we present an in-slab visibility interpolation method for the representation of subdivided slabs. Second, we introduce virtual zSlab, which extends an infinitely thin boundary (such as polygonal objects) into a slab with a finite thickness. Finally, based on virtual zSlab and in-slab visibility interpolation, we propose a slab-based visibility intermixing method with the newly proposed rendering pipeline. Experimental results demonstrate that the proposed method delivers more effective multiple-object renderings in terms of rendering quality, compared to conventional approaches. And proposed intermixing scheme provides high-quality intermixing results for the visualization of intersecting and overlapping surfaces by resolving aliasing and z-fighting problems. Moreover, two case studies are presented that apply the proposed method to the real clinical applications. These case studies manifest that the proposed method has the outstanding advantages of the rendering independency and reusability. PMID:26403436

  4. A numerical model for calculating vibration due to a harmonic moving load on a floating-slab track with discontinuous slabs in an underground railway tunnel

    NASA Astrophysics Data System (ADS)

    Hussein, M. F. M.; Hunt, H. E. M.

    2009-03-01

    This paper presents a new method for modelling floating-slab tracks with discontinuous slabs in underground railway tunnels. The track is subjected to a harmonic load moving with a constant velocity. The model consists of two sub-models. The first is an infinite track with periodic double-beam unit formulated as a periodic infinite structure. The second is modelled with a new version of the Pipe-in-Pipe (PiP) model that accounts for a tunnel wall embedded in a half-space. The two sub-models are coupled by writing the force transmitted from the track to the tunnel as a continuous function using Fourier series representation and satisfying the compatibility condition. The displacements at the free surface are calculated for a track with discontinuous slab and compared with those of a track with continuous slab. The results show that the far-field vibration can be significantly increased due to resonance frequencies of slabs for tracks with discontinuous slabs.

  5. SU-D-213-06: Dosimetry of Modulated Electron Radiation Therapy Using Fricke Gel Dosimeter

    SciTech Connect

    Gawad, M Abdel; Elgohary, M; Hassaan, M; Emam, M; Desouky, O; Eldib, A; Ma, C

    2015-06-15

    Purpose: Modulated electron radiation therapy (MERT) has been proposed as an effective modality for treatment of superficial targets. MERT utilizes multiple beams of different energies which are intensity modulated to deliver optimized dose distribution. Energy independent dosimeters are thus needed for quantitative evaluations of MERT dose distributions and measurements of absolute doses delivered to patients. Thus in the current work we study the feasibility of Fricke gel dosimeters in MERT dosimetry. Methods: Batches of radiation sensitive Fricke gel is fabricated and poured into polymethyl methacrylate cuvettes. The samples were irradiated in solid water phantom and a thick layer of bolus was used as a buildup. A spectrophotometer system was used for measuring the color changes (the absorbance) before and after irradiation and then we calculate net absorbance. We constructed calibration curves to relate the measured absorbance in terms of absorbed dose for all available electron energies. Dosimetric measurements were performed for mixed electron beam delivery and we also performed measurement for segmented field delivery with the dosimeter placed at the junction of two adjacent electron beams of different energies. Dose measured by our gel dosimetry is compared to that calculation from our precise treatment planning system. We also initiated a Monte Carlo study to evaluate the water equivalence of our dosimeters. MCBEAM and MCSIM codes were used for treatment head simulation and phantom dose calculation. PDDs and profiles were calculated for electron beams incident on a phantom designed with 1cm slab of Fricke gel. Results: The calibration curves showed no observed energy dependence with all studied electron beam energies. Good agreement was obtained between dose calculated and that obtained by gel dosimetry. Monte Carlo results illustrated the tissue equivalency of our Gel dosimeters. Conclusion: Fricke Gel dosimeters represent a good option for the dosimetric

  6. Detecting slab structure beneath the Mediterranean

    NASA Astrophysics Data System (ADS)

    Miller, Meghan S.; Sun, Daoyuan; Piana Agostinetti, Nicola

    2013-04-01

    The presence of subducted slabs in the Mediterranean has been well documented with seismic tomography, however, these images, which are produced by smoothed, damped inversions, underestimate the sharpness of the structures. The position and extent of the slabs and the presence possible tears or gaps in the subducted lithosphere are still debated, yet the shape and location these structures are important for kinematic reconstructions and evolution of the entire subduction zone system. Extensive distribution of broadband seismic instrumentation in the Mediterranean (Italian National Seismic Network in Italy and the NSF-PICASSO project in Spain and Morocco) has allowed us to use alternative methodologies to detect the position of the slabs and slab tears beneath the Central and Western Mediterranean. Using S receiver functions we are able to identify S-to-p conversions from the bottom of the subducted slab and a lack of these signals where there are gaps or tears in the slab. We also analyze broadband waveforms for changes in P wave coda from deep (> 300 km depth) local earthquakes. The waveform records for stations in southern Italy and around the Betic-Rif show large amplitude, high frequency (f > 5 Hz) late arrivals with long coda after relatively low-frequency onset. High frequency arrivals are the strongest from events whose raypaths travel within the slab to the stations where they are recorded allowing for mapping of where the subducted material is located within the upper mantle. These two methods, along with inferring the slab position from fast P-wave velocity perturbations in tomography and intermediate depth seismicity, provide additional geophysical evidence to aid in interpretation of the complex, segmented slab structure beneath the Mediterranean.

  7. Andean flat subduction maintained by slab tunneling

    NASA Astrophysics Data System (ADS)

    Schepers, Gerben; van Hinsbergen, Douwe; Kosters, Martha; Boschman, Lydian; McQuarrie, Nadine; Spakman, Wim

    2016-04-01

    In two segments below the Andean mountain belt, the Nazca Plate is currently subducting sub-horizontally below South America over a distance of 200-300 km before the plate bends into the mantle. Such flat slab segments have pronounced effects on orogenesis and magmatism and are widely believed to be caused by the downgoing plate resisting subduction due to its local positive buoyancy. In contrast, here we show that flat slabs primarily result from a local resistance against rollback rather than against subduction. From a kinematic reconstruction of the Andean fold-thrust belt we determine up to ~390 km of shortening since ~50 Ma. During this time the South American Plate moved ~1400 km westward relative to the mantle, thus forcing ~1000 km of trench retreat. Importantly, since the 11-12 Ma onset of flat slab formation, ~1000 km of Nazca Plate subduction occurred, much more than the flat slab lengths, which leads to our main finding that the flat slabs, while being initiated by arrival of buoyant material at the trench, are primarily maintained by locally impeded rollback. We suggest that dynamic support of flat subduction comes from the formation of slab tunnels below segments with the most buoyant material. These tunnels trap mantle material until tearing of the tunnel wall provides an escape route. Fast subduction of this tear is followed by a continuous slab and the process can recur during ongoing rollback of the 7000 km wide Nazca slab at segments with the most buoyant subducting material, explaining the regional and transient character of flat slabs. Our study highlights the importance of studying subduction dynamics in absolute plate motion context.

  8. From field to gel blot: teaching a holistic view of developmental phenomena to undergraduate biology students at the University of Tokyo.

    PubMed

    Ariizumi, Takashi; Asashima, Makoto

    2003-01-01

    We present here an outline of the lectures and laboratory exercises for undergraduate developmental biology students at the University of Tokyo. The main aim of our course is to help students fill the gap between natural history, classical embryology and molecular developmental biology. To achieve this aim, we take up various topics in the lectures, from fertilization and early development to developmental engineering. Our laboratory exercises begin with an introduction to the natural history of the organism. The entire class and the instructors collect newts in the field and discuss features of their mating behavior and so on. In the laboratory, students are absorbed by exercises such as a lampbrush chromosome preparation and an in vitro beating heart induction. After that, students choose their own research projects for which they will employ both classical embryological and modern molecular biological techniques. At the end of our course, the connectivity principle from field to gel blot will be part of the students' understanding. PMID:12705655

  9. Application of PCR-Denaturing-Gradient Gel Electrophoresis (DGGE) Method to Examine Microbial Community Structure in Asparagus Fields with Growth Inhibition due to Continuous Cropping

    PubMed Central

    Urashima, Yasufumi; Sonoda, Takahiro; Fujita, Yuko; Uragami, Atsuko

    2012-01-01

    Growth inhibition due to continuous cropping of asparagus is a major problem; the yield of asparagus in replanted fields is low compared to that in new fields, and missing plants occur among young seedlings. Although soil-borne disease and allelochemicals are considered to be involved in this effect, this is still controversial. We aimed to develop a technique for the biological field diagnosis of growth inhibition due to continuous cropping. Therefore, in this study, fungal community structure and Fusarium community structure in continuously cropped fields of asparagus were analyzed by polymerase chain reaction/denaturing-gradient gel electrophoresis (PCR-DGGE). Soil samples were collected from the Aizu region of Fukushima Prefecture, Japan. Soil samples were taken from both continuously cropped fields of asparagus with growth inhibition and healthy neighboring fields of asparagus. The soil samples were collected from the fields of 5 sets in 2008 and 4 sets in 2009. We were able to distinguish between pathogenic and non-pathogenic Fusarium by using Alfie1 and Alfie2GC as the second PCR primers and PCR-DGGE. Fungal community structure was not greatly involved in the growth inhibition of asparagus due to continuous cropping. By contrast, the band ratios of Fusarium oxysporum f. sp. asparagi in growth-inhibited fields were higher than those in neighboring healthy fields. In addition, there was a positive correlation between the band ratios of Fusarium oxysporum f. sp. asparagi and the ratios of missing asparagus plants. We showed the potential of biological field diagnosis of growth inhibition due to continuous cropping of asparagus using PCR-DGGE. PMID:22200640

  10. High transparent shape memory gel

    NASA Astrophysics Data System (ADS)

    Gong, Jin; Arai, Masanori; Kabir, M. H.; Makino, Masato; Furukawa, Hidemitsu

    2014-03-01

    Gels are a new material having three-dimensional network structures of macromolecules. They possess excellent properties as swellability, high permeability and biocompatibility, and have been applied in various fields of daily life, food, medicine, architecture, and chemistry. In this study, we tried to prepare new multi-functional and high-strength gels by using Meso-Decoration (Meso-Deco), one new method of structure design at intermediate mesoscale. High-performance rigid-rod aromatic polymorphic crystals, and the functional groups of thermoreversible Diels-Alder reaction were introduced into soft gels as crosslinkable pendent chains. The functionalization and strengthening of gels can be realized by meso-decorating the gels' structure using high-performance polymorphic crystals and thermoreversible pendent chains. New gels with good mechanical properties, novel optical properties and thermal properties are expected to be developed.

  11. Nonlocal microscopic theory of quantum friction between parallel metallic slabs

    SciTech Connect

    Despoja, Vito

    2011-05-15

    We present a new derivation of the friction force between two metallic slabs moving with constant relative parallel velocity, based on T=0 quantum-field theory formalism. By including a fully nonlocal description of dynamically screened electron fluctuations in the slab, and avoiding the usual matching-condition procedure, we generalize previous expressions for the friction force, to which our results reduce in the local limit. Analyzing the friction force calculated in the two local models and in the nonlocal theory, we show that for physically relevant velocities local theories using the plasmon and Drude models of dielectric response are inappropriate to describe friction, which is due to excitation of low-energy electron-hole pairs, which are properly included in nonlocal theory. We also show that inclusion of dissipation in the nonlocal electronic response has negligible influence on friction.

  12. Constraints of subducted slab geometries on trench migration and subduction velocities: flat slabs and slab curtains in the mantle under Asia

    NASA Astrophysics Data System (ADS)

    Wu, J. E.; Suppe, J.; Renqi, L.; Lin, C.; Kanda, R. V.

    2013-12-01

    The past locations, shapes and polarity of subduction trenches provide first-order constraints for plate tectonic reconstructions. Analogue and numerical models of subduction zones suggest that relative subducting (Vs) and overriding (Vor) plate velocities may strongly influence final subducted slab geometries. Here we have mapped the 3D geometries of subducted slabs in the upper and lower mantle of Asia from global seismic tomography. We have incorporated these slabs into plate tectonic models, which allows us to infer the subducting and overriding plate velocities. We describe two distinct slab geometry styles, ';flat slabs' and ';slab curtains', and show their implications for paleo-trench positions and subduction geometries in plate tectonic reconstructions. When compared to analogue and numerical models, the mapped slab styles show similarities to modeled slabs that occupy very different locations within Vs:Vor parameter space. ';Flat slabs' include large swaths of sub-horizontal slabs in the lower mantle that underlie the well-known northward paths of India and Australia from Eastern Gondwana, viewed in a moving hotspot reference. At India the flat slabs account for a significant proportion of the predicted lost Ceno-Tethys Ocean since ~100 Ma, whereas at Australia they record the existence of a major 8000km by 2500-3000km ocean that existed at ~43 Ma between East Asia, the Pacific and Australia. Plate reconstructions incorporating the slab constraints imply these flat slab geometries were generated when continent overran oceanic lithosphere to produce rapid trench retreat, or in other words, when subducting and overriding velocities were equal (i.e. Vs ~ Vor). ';Slab curtains' include subvertical Pacific slabs near the Izu-Bonin and Marianas trenches that extend from the surface down to 1500 km in the lower mantle and are 400 to 500 km thick. Reconstructed slab lengths were assessed from tomographic volumes calculated at serial cross-sections. The ';slab

  13. Ultra-low field T1 vs. T1rho at 3T and 7T: study of rotationally immobilized protein gels and animal brain tissues

    NASA Astrophysics Data System (ADS)

    Dong, Hui; Inglis, Ben; Barr, Ian; Clarke, John

    2015-03-01

    Clinical magnetic resonance imaging (MRI) machines operating in static fields of typically 1.5 T or 3 T can capture information on slow molecular dynamics utilizing the so-called T1rho technique. This technique, in which a radiofrequency (RF) spin-lock field is applied with microtesla amplitude, has been used, for example, to determine the onset time of stroke in studies on rats. The long RF pulse, however, may exceed the specific absorption rate (SAR) limit, putting subjects at risk. Ultra-low-field (ULF) MRI, based on Superconducting Quantum Interference Devices (SQUIDs), directly detects proton signals at a static magnetic field of typically 50-250 μT. Using our ULF MRI system with adjustable static field of typically 55 to 240 μT, we systematically measured the T1 and T2 dispersion profiles of rotationally immobilized protein gels (bovine serum albumin), ex vivo pig brains, and ex vivo rat brains with induced stroke. Comparing the ULF results with T1rho dispersion obtained at 3 T and 7 T, we find that the degree of protein immobilization determines the frequency-dependence of both T1 and T1rho. Furthermore, T1rho and ULF T1 show similar results for stroke, suggesting that ULF MRI may be used to image traumatic brain injury with negligible SAR. This research was supported by the Henry H. Wheeler, Jr. Brain Imaging Center and the Donaldson Trust.

  14. Use of a Ring Chromosome and Pulsed-Field Gels to Study Interhomolog Recombination, Double-Strand DNA Breaks and Sister-Chromatid Exchange in Yeast

    PubMed Central

    Game, J. C.; Sitney, K. C.; Cook, V. E.; Mortimer, R. K.

    1989-01-01

    We describe a system that uses pulsed-field gels for the physical detection of recombinant DNA molecules, double-strand DNA breaks (DSB) and sister-chromatid exchange in the yeast Saccharomyces cerevisiae. The system makes use of a circular variant of chromosome III (Chr. III). Meiotic recombination between this ring chromosome and a linear homolog produces new molecules of sizes distinguishable on gels from either parental molecule. We demonstrate that these recombinant molecules are not present either in strains with two linear Chr. III molecules or in rad50 mutants, which are defective in meiotic recombination. In conjunction with the molecular endpoints, we present data on the timing of commitment to meiotic recombination scored genetically. We have used x-rays to linearize circular Chr. III, both to develop a sensitive method for measuring frequency of DSB and as a means of detecting double-sized circles originating in part from sister-chromatid exchange, which we find to be frequent during meiosis. PMID:2693206

  15. Use of a ring chromosome and pulsed-field gels to study interhomolog recombination, double-strand DNA breaks and sister-chromatid exchange in yeast

    SciTech Connect

    Game, J.C. ); Sitney, K.C.; Cook, V.E.; Mortimer, R.K. )

    1989-12-01

    The authors describe a system that uses pulsed-field gels for the physical detection of recombinant DNA molecules, double-strand DNA breaks (DSB) and sister-chromatid exchange in the yeast Saccharomyces cerevisiae. The system makes use of a circular variant of chromosome II (Chr. III). Meiotic recombination between this ring chromosome and a linear homolog produces new molecules of sizes distinguishable on gels from either parental molecule. They demonstrate that these recombinant molecules are not present either in strains with two linear Chr. III molecules or in rad50 mutants, which are defective in meiotic recombination. In conjunction with the molecular endpoints. They present data on the timing of commitment to meiotic recombination scored genetically. They have used x-rays to linearize circular Chr. III, both to develop a sensitive method for measuring frequency of DSB and as a means of detecting double-size circles originating in part from sister-chromatid exchange, which they find to be frequent during meiosis.

  16. Separation performance of single-stranded DNA electrophoresis in photopolymerized cross-linked polyacrylamide gels.

    PubMed

    Lo, Roger C; Ugaz, Victor M

    2006-02-01

    Considerable effort has been directed toward optimizing performance and maximizing throughput in ssDNA electrophoresis because it is a critical analytical step in a variety of genomic assays. Ultimately, it would be desirable to quantitatively determine the achievable level of separation resolution directly from measurements of fundamental physical properties associated with the gel matrix rather than by the trial and error process often employed. Unfortunately, this predictive capability is currently lacking, due in large part to the need for a more detailed understanding of the fundamental parameters governing separation performance (mobility, diffusion, and dispersion). We seek to address this issue by systematically characterizing electrophoretic mobility, diffusion, and dispersion behavior of ssDNA fragments in the 70-1,000 base range in a photopolymerized cross-linked polyacrylamide matrix using a slab gel DNA sequencer. Data are collected for gel concentrations of 6, 9, and 12%T at electric fields ranging from 15 to 40 V/cm, and resolution predictions are compared with corresponding experimentally measured values. The data exhibit a transition from behavior consistent with the Ogston model for small fragments to behavior in agreement with the biased reptation model at larger fragment sizes. Mobility data are also used to estimate the mean gel pore size and compare the predictions of several models. PMID:16331587

  17. Photocatalytic, highly hydrophilic porcelain stoneware slabs

    NASA Astrophysics Data System (ADS)

    Raimondo, M.; Guarini, G.; Zanelli, C.; Marani, F.; Fossa, L.; Dondi, M.

    2011-10-01

    Photocatalytic, highly hydrophilic industrial porcelain stoneware large slabs were realized by deposition of nanostructured TiO2 coatings. Different surface finishing and experimental conditions were considered in order to assess the industrial feasibility. Photocatalytic and wetting behaviour of functionalized slabs mainly depends on surface phase composition in terms of anatase/rutile ratio, this involving - as a key issue - the deposition of TiO2 on industrially sintered products with an additional annealing step to strengthen coatings' performances and durability.

  18. Three-dimensional Numerical Models of Mantle Flow Through the Cocos-Nazca Slab Gap

    NASA Astrophysics Data System (ADS)

    Jadamec, M.; Fischer, K. M.

    2013-05-01

    , seafloor ages, and geologic history are used to construct the variable thickness of the overriding Caribbean and South American plates (Feng et al., 2007; Muller et al., 2008; Rychert et al., 2008; Abt et al., 2010b; Lekic and Romanowicz, 2011; Yuan et al., 2011). The predicted motion of the Cocos and Nazca plates are compared to observed plate motions (DeMets and Dixon, 1999) and the predicted mantle flow fields are compared to local S wave and teleseismic SK(K)S observations of seismic anisotropy (Abt et al., 2009, 2010a). The direction of Cocos and Nazca surface plate motion is reasonably well reproduced regardless of whether the Cocos and Nazca slabs are a continuous slab at depth or separated by a gap. However, the inclusion of a gap between the Cocos and Nazca slabs has a significant effect on the mantle flow field, reversing the direction of the slab entrained flow beneath the Caribbean plate and resulting in counterclockwise toroidal flow around the southern Cocos slab edge and clockwise toroidal flow around the northern Nazca slab edge. The results have implications for the initiation slab tears and indicate complexity in the coupling between the lithosphere and mantle in subduction zones.

  19. Dependency of slab geometry on absolute velocities and conditions for cyclicity: insights from numerical modelling

    NASA Astrophysics Data System (ADS)

    Gibert, G.; Gerbault, M.; Hassani, R.; Tric, E.

    2012-05-01

    The aim of this study is to quantify the relationship between the kinematics of subduction, deformation in the overriding plate and the evolution of slab geometry. A 2-D finite element numerical code is used, and a first objective consists in benchmarking previously published analogue models. Far-field plate velocities are applied, and once the subducting plate reaches the 660 km discontinuity, modelled as a rigid base, we obtain two different forms or styles of subduction that depend on the overriding plate velocity vop: if vop > 0, the slab lies forwards on the 660 km discontinuity (style 1), and if vop≤ 0, the slab lies backwards on the discontinuity (style 2). We also obtain a cyclic pattern with the slab folding on itself repeatedly when vsp > 0 and 2vop+vsp > 0 (where vsp is the subducting plate velocity). These conditions result from the analysis of several simulations in which the subduction velocities and plate viscosities are varied. When the slab periodically folds on the 660 km discontinuity, periods of shallow slab dip and compression in the overriding plate are followed by periods of slab steepening and relative extension in the overriding plate. Folding periodicity is controlled by the slab viscosity and subduction velocity. When a low-viscosity zone is included in the overriding plate, the trench motion is effectively decoupled from the overriding plate velocity, therefore allowing it to be directly controlled by the deep dynamics of the slab. For the cyclic style 2 corresponding to forward folding of the slab, the low-viscosity region in the overriding plate increases the stress amplitudes oscillations, the trench motion and the folding periodicity with time. Therefore the strength of the entire overriding plate is shown to directly control the dynamics of subduction. Using the Nazca and South American plate velocities we produce models of cyclic folding with a period of ca. 22 Ma and a minimal dip angle of ca. 10°. Episodic folding of the slab

  20. Tunable one-dimensional photonic crystal slabs

    NASA Astrophysics Data System (ADS)

    Beccherelli, R.; Bellini, B.; Zografopoulos, D.; Kriezis, E.

    2007-05-01

    A 1D photonic crystal slab based on preferential etching of commercially available silicon-on-insulator wafers is presented. Compared to dry etching, anisotropic wet etching is more tolerant to errors as it is self-stopping on crystallographic {111} planes and it produces a more precise geometry with symmetries and homothetic properties, with surface roughness close to 1 nm. The resulting grooves are infiltrated by low viscosity liquid crystal having large positive optical anisotropy. The use of slanted grooves provides advantages: first of all the complete filling of slanted grooves is simplified when compared to vertical walls structures. Furthermore alignment is significantly facilitated. Indeed the liquid crystal molecules tend to align with their long axis along the submicron grooves. Therefore by forcing reorientation out of a rest position, the liquid crystal presents a choice of refractive indices to the propagating optical field. The liquid crystal behavior is simulated by a finite element method, and coupled to a finite difference time domain method. We investigate different photonic crystal configurations. Large tunability of bandgap edge for TE polarization is demonstrated when switching the liquid crystal with an applied voltage. We have also studied the use of the same device geometry as a very compact microfluidic refractometric sensor.

  1. Nanoscale Electrical Imaging of Metal-Insulator Transition in Ion-Gel Gated ZnO Field Effect Transistors

    NASA Astrophysics Data System (ADS)

    Ren, Yuan; Yuan, Hongtao; Wu, Xiaoyu; Iwasa, Yoshihiro; Cui, Yi; Hwang, Harold; Lai, Keji

    2015-03-01

    Electric double-layer transistors (EDLTs) using ionic liquid as the gate dielectric have demonstrated a remarkably wide range of density modulation, a condition crucial for the study of novel electronic phases in complex quantum materials. Yet little is known microscopically when carriers are modulated in the EDLT structure because of the technical challenge to image the buried electrolyte-semiconductor interface with nanoscale resolution. Using a cryogenic microwave impedance microscope, we demonstrate the real-space conductivity mapping in ZnO EDLTs with a spatial resolution of 100nm. A thin layer of ion gel, which solidifies below the glass transition temperature of 200K, was spin-coated on the ZnO surface to induce the metal-insulator transition. The microwave images acquired at different channel conductance clearly showed the spatial evolution of local conductivity through the transition. In addition, by applying a large source-drain bias, electrical inhomogeneity was also observed across the source and drain electrodes.

  2. Three-dimensional necking during viscous slab detachment

    NASA Astrophysics Data System (ADS)

    Tscharner, M.; Schmalholz, S. M.; Duretz, T.

    2014-06-01

    We study the three-dimensional (3-D) deformation during detachment of a lithospheric slab with simple numerical models using the finite element method. An initially vertical layer of power law viscous fluid mimics the slab and is surrounded by a linear or power law viscous fluid representing asthenospheric mantle. We quantify the impact of slab size and shape (symmetric/asymmetric) on slab detachment and identify two processes that control the lateral (i.e., along-trench) slab deformation: (1) the horizontal deflection of the lateral, vertical slab sides (> 100 km with velocities up to 16 mm/yr) and (2) the propagation of localized thinning (necking) inside the slab (with velocities >9 cm/yr). The lateral propagation velocity is approximately constant during slab detachment. Larger slabs (here wider than approximately 300 km) detach with rates similar to those predicted by 2-D models, whereas smaller slabs detach slower. Implications for geodynamic processes and interpretations of seismic tomography are discussed.

  3. Molecular epidemiology of Salmonella spp. isolates from gulls, fish-meal factories, feed factories, animals and humans in Norway based on pulsed-field gel electrophoresis.

    PubMed Central

    Nesse, L. L.; Refsum, T.; Heir, E.; Nordby, K.; Vardund, T.; Holstad, G.

    2005-01-01

    The molecular epidemiology of 98 isolates of Salmonella serovar Agona (n = 27), S. Montevideo (n = 42) and S. Senftenberg (n = 29) from wild-living gulls, fish-meal factories, feed factories, humans and domestic animals was investigated using pulsed-field gel electrophoresis (PFGE) and computerized numerical analysis. Two of the S. Agona profiles were identified both in gulls and in two of the factories. In addition, one of these profiles was detected in two infected poultry farms. Two of the S. Montevideo profiles were also identified both in gulls and in two of the factories, and one of these profiles was observed in a human isolate. Four factories shared an identical S. Senftenberg profile. The S. Senftenberg profile found in gulls was not identified in any other source investigated. The presence of isolates with identical PFGE profiles indicates potential epidemiological links between different factories, as well as between gulls and factories. PMID:15724711

  4. Comparison of arbitrarily primed PCR and macrorestriction (pulsed-field gel electrophoresis) typing of Pseudomonas aeruginosa strains from cystic fibrosis patients.

    PubMed Central

    Kersulyte, D; Struelens, M J; Deplano, A; Berg, D E

    1995-01-01

    Arbitrarily primed PCR fingerprinting was carried out on 43 Pseudomonas aeruginosa isolates from cystic fibrosis (CF) patients. Seventeen major groups of strains that coincided with groups also distinguished by macrorestriction (pulsed-field gel electrophoresis) typing were identified. Our results illustrated that a CF patient can carry more than one strain and can carry a given strain for long periods of time and that strains can evolve by changes in drug resistance or other phenotypic traits during long-term colonization. The arbitrarily primed PCR method is recommended for first-pass screening of P. aeruginosa isolates from CF patients, especially when many strains are to be typed, because of its sensitivity and efficiency. PMID:7559985

  5. Comparative Analysis of Infrequent-Restriction-Site PCR and Pulsed-Field Gel Electrophoresis for Epidemiological Typing of Legionella pneumophila Serogroup 1 Strains

    PubMed Central

    Riffard, Serge; Presti, François Lo; Vandenesch, François; Forey, Françoise; Reyrolle, Monique; Etienne, Jerome

    1998-01-01

    Two methods were compared for the analysis of 48 unrelated and epidemiologically related Legionella pneumophila serogroup 1 isolates. These are the infrequent-restriction-site PCR (IRS-PCR) assay with adapters designed for XbaI and PstI restriction sites and the pulsed-field gel electrophoresis (PFGE) analysis determined after DNA restriction with SfiI. Both methods demonstrated a high level of discrimination with a similar capacity for differentiating 23 of the 24 unrelated isolates. PFGE analysis and IRS-PCR assay were both able to identify epidemiologically related isolates of L. pneumophila from three outbreaks. Hence, IRS-PCR assay appears to be a reproducible (intergel reproducibility, 100%) and discriminative (discriminatory index, ≥0.996) tool for typing of Legionella. Compared to PFGE, however, IRS-PCR presented an advantage through ease of performance and with attributes of rapidity and sensitivity of target DNA. PMID:9431941

  6. Monitoring fatigue life in concrete bridge deck slabs

    NASA Astrophysics Data System (ADS)

    Newhook, J.; Limaye, V.

    2007-04-01

    Concrete bridge deck slabs are the most common form of bridge deck construction in short and medium span bridge structures in North America. Understanding and monitoring the condition of these bridge decks is an important component of a bridge management strategy. Progressive deterioration due to fatigue occurs in concrete decks due to the large number of cycles of heavy wheels loads and normally manifests itself as the progressive growth of cracks in the top and underside of the deck slab. While some laboratory fatigue testing programs have been reported in the literature, there is very little information on proposed techniques to monitor this phenomenon. This paper discusses the issue of how fatigue monitoring may be included as part of a structural health monitoring system for bridges. The paper draws upon previously published experimental results to identify the main characteristics of fatigue damage and structural response for concrete bridge deck slabs. Several means of monitoring this response are then evaluated and monitoring methods are proposed. A specific field structure monitoring program is used to illustrate the application of the concept. The cases study examines several sensor systems and discusses the various limitations and needs in this area. The results are of interest to both the general area of structural health monitoring as well as fatigue monitoring specifically.

  7. Was there a Laramide "flat slab"?

    NASA Astrophysics Data System (ADS)

    Jones, C. H.

    2014-12-01

    Slab-continent interactions drive most non-collisional orogenies; this has led us to usually anticipate that temporal changes or spatial variations in orogenic style are related to changes in the slab, most especially in the slab's dip. This is most dramatically evident for orogenies in the foreland, well away from the trench, such as the Laramide orogeny. However, the physical means of connecting slab geometry to crustal deformation remain obscure. Dickinson and Snyder (1978) and Bird (1984) laid out a conceptually elegant means of creating foreland deformation from shear between a slab and overriding continental lithosphere, but such strong shear removed all of the continental lithosphere in the western U.S. when included in a numerical simulation of flat slab subduction (Bird, 1988), a removal in conflict with observations of volcanic rocks and xenoliths in many locations. Relying on an increase in edge normal stresses results, for the Laramide, in requiring the little-deformed Colorado Plateau to either be unusually strong or to have risen rapidly enough and high enough to balance edge stresses with body forces. Early deformation in the Plateau rules out unusual strength, and the accumulation and preservation of Late Cretaceous near-sea level sedimentary rocks makes profound uplift unlikely (though not impossible). Relying on comparisons with the Sierras Pampeanas is also fraught with problems: the Sierras are not separated from the Andean fold-and-thrust belt by several hundred kilometers of little-deformed crust, nor were they buried under kilometers of marine muds as were large parts of the Laramide foreland. We have instead suggested that some unusual interactions of an obliquely subducting plate with a thick Archean continental root might provide a better explanation than a truly flat slab (Jones et al., 2011). From this, and given that several flat-slab segments today are not associated with foreland orogenesis and noting that direct evidence for truly

  8. Polyclonal infections due to Mycobacterium avium complex in patients with AIDS detected by pulsed-field gel electrophoresis of sequential clinical isolates.

    PubMed Central

    Slutsky, A M; Arbeit, R D; Barber, T W; Rich, J; von Reyn, C F; Pieciak, W; Barlow, M A; Maslow, J N

    1994-01-01

    Invasive infection with organisms of the Mycobacterium avium complex (MAC) is common among patients with advanced human immunodeficiency virus infection. In previous studies, we analyzed multiple individual colonies of MAC isolated from specimens obtained at the same time and observed that 14 to 20% of patients are simultaneously infected with more than one strain. In this study, we examined sequential isolates from 12 patients with AIDS who had two or more MAC isolates available from clinical specimens collected more than 1 week apart; the intervals between the first and last specimens ranged from 8 to 192 (median, 46) days. For each isolate, restriction digests of genomic DNA were analyzed by pulsed-field gel electrophoresis; DNA was prepared by using a protocol, described here in detail, which had been optimized for conditions of bacterial growth and lysis. The pulsed-field gel electrophoresis analysis identified four patients (33%) infected with two different MAC strains. Both M. avium and M. intracellulare were cultured from blood specimens from two patients. In each of the four patients, the second strain was identified from a culture taken within 14 days of the initial study isolate, and in three of these patients, the first strain was detected again in a subsequent culture. These observations suggest that the presence of two different strains among isolates from sequential cultures may reflect ongoing polyclonal infection. We conclude that polyclonal infection with MAC is common among patients with AIDS. The identification of such infections may be critical in the development of effective treatments. Images PMID:7929773

  9. Water in the Slab: a Trilogy

    NASA Astrophysics Data System (ADS)

    Faccenda, M.; Burlini, L.; Gerya, T.; Mancktelow, N.

    2012-12-01

    In this presentation we summarize the results of a project started in 2007 from a brilliant intuition of Luigi Burlini that suggested an additional anisotropy source for the interpretation of seismic anisotropy patterns observed at subduction zones. Such an anisotropic body located in the upper part of the slab would result from the hydration of the oceanic plate at the trench outer-rise. The natural continuation of the project was to understand the mechanical processes behind slab hydration and the fluid flow patterns established during slab dehydration. In both cases, we found that tectonic pressure gradients due to the bending and unbending of the subducting oceanic plate are fundamental in driving fluid flow. This last part of the project led to the other two chapters of the final trilogy about the long route of water in the slab. This trilogy is here described in detail and a chronologically ordered series of events presented below. The first episode is related to slab hydration occurring during bending at the trench-outer rise. Here, fluids are driven downward along active normal faults by bending-related, sub-hydrostatic pressure gradients. Water can percolate down to 15-20 km below the seafloor, triggering hydrothermal reactions and the formation of hydrous minerals. This results in an elongated pattern of mostly trench-dipping hydrated faults with a strike parallel to the trench and whose orientation below the forearc becomes sub-vertical. The second episode is related to the geophysical implications of a hydrated slab below the forearc. Indeed, both the subvertical layering of closely spaced hydrated and dry levels (SPO) and the syn-deformational, fault-parallel alignment of highly anisotropic minerals (CPO) such as serpentine and talc may contribute to the SKS splitting patterns observed in the forearc. We suggest that the upper part of the slab may have a strong seismic anisotropy that can be approximated by a transverse isotropic body with a sub

  10. Aerosol gels

    NASA Technical Reports Server (NTRS)

    Sorensen, Christopher M. (Inventor); Chakrabarti, Amitabha (Inventor); Dhaubhadel, Rajan (Inventor); Gerving, Corey (Inventor)

    2010-01-01

    An improved process for the production of ultralow density, high specific surface area gel products is provided which comprises providing, in an enclosed chamber, a mixture made up of small particles of material suspended in gas; the particles are then caused to aggregate in the chamber to form ramified fractal aggregate gels. The particles should have a radius (a) of up to about 50 nm and the aerosol should have a volume fraction (f.sub.v) of at least 10.sup.-4. In preferred practice, the mixture is created by a spark-induced explosion of a precursor material (e.g., a hydrocarbon) and oxygen within the chamber. New compositions of matter are disclosed having densities below 3.0 mg/cc.