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Sample records for aligned currents facs

  1. Field-aligned currents onboard the Intercosmos Bulgaria-1300 satellite in comparison with modeled FAC

    NASA Astrophysics Data System (ADS)

    Danov, Dimitar

    2008-02-01

    The statistical field-aligned current (FAC) distribution has been demonstrated by [Iijima, T., Potemra, T.A., 1976. The amplitude distribution of field-aligned currents at northern high latitudes observed by Triad. Journal of Geophysical Research 81(13), 2165-2174] and many other authors. The large-scale (LS) FACs have been described by different empirical/statistical models [Feldstein, Ya. I., Levitin, A.E., 1986. Solar wind control of electric fields and currents in the ionosphere. Journal of Geomagnetism and Geoelectricity 38, 1143; Papitashvili, V.O., Rich, F.J., Heinemann, M.A., Hairston, M.R., 1999. Parameterization of the Defense Meteorological Satellite Program ionospheric electrostatic potentials by the interplanetary magnetic field strength and direction. Journal of Geophysical Research 104, 177-184; Papitashvili, V.O., Christiansen, F., Neubert, T., 2002. A new model of field-aligned currents derived from high-precision satellite magnetic field data. Geophysical Research Letters, 29(14), 1683, doi:10.1029/2001GL014207; Tsyganenko, N.A., 2001. A model of the near magnetosphere with a dawn-dusk asymetry (I. Mathematical structure). Journal of Geophysical Research 107(A8), doi:10.1029/2001JA000219; Weimer, D.R., 1996a. A new model for prediction of ionospheric electric potentials as a function of the IMF. In: Snowmass'96 Online Poster Session; Weimer, D.R., 1996b. Substorm influence on the ionospheric convection patterns. In: Snowmass'96 Online Poster Session; Weimer, D.R., 2001. Maps of ionospheric field-aligned currents as a function of the interplanetary magnetic field derived from Dynamic Explorer 2 data. Journal of Geophysical Research 106, 12,889-12,902; Weimer, D.R., 2005. Improved ionospheric electrodynamic models and application to calculating Joule heating rates. Journal of Geophysical Research 110, A05306, doi:10.1029/2004JA010884]. In the present work, we compare two cases of LS FAC obtained from magnetic field measurements onboard the

  2. Generation of field-aligned current (FAC) and convection through the formation of pressure regimes: Correction for the concept of Dungey's convection

    NASA Astrophysics Data System (ADS)

    Tanaka, T.; Watanabe, M.; Den, M.; Fujita, S.; Ebihara, Y.; Kikuchi, T.; Hashimoto, K. K.; Kataoka, R.

    2016-09-01

    In this paper, we try to elucidate the generation mechanism of the field-aligned current (FAC) and coexisting convection. From the comparison between the theoretical prediction and the state of numerical solution from the high-resolution global simulation, we obtain the following conclusions about the distribution of dynamo, the magnetic field structure along the flow path that diverges Poynting flux, and energy conversion promoting the generation of electromagnetic energy. The dynamo for the region 1 FAC, which is in the high-latitude-side cusp-mantle region, has a structure in which magnetic field is compressed along the convection path by the slow mode motion. The dynamo for the region 2 FAC is in the ring current region at the inner edge of the plasma sheet, and has a structure in which magnetic field is curved outward along the convection path. Under these structures, electromagnetic energy is generated from the work done by pressure gradient force, in both dynamos for the region 1 and region 2 FACs. In these generation processes of the FACs, the excitation of convection and the formation of pressure regimes occur as interdependent processes. This structure leads to a modification in the way of understanding the Dungey's convection. Generation of the FAC through the formation of pressure regimes is essential even for the case of substorm onset.

  3. Relationships between Geomagnetic Induced Currents and Field Aligned Currents

    NASA Astrophysics Data System (ADS)

    Waters, C. L.; Barnett, R.; Anderson, B. J.; Gjerloev, J. W.; Korth, H.; Barnes, R. J.

    2015-12-01

    Geomagnetic Induced Currents (GICs) appear in the ground due to time varying magnetic fields that occur during periods of enhanced geomagnetic activity. The resultant time varying electric fields at Earth's surface drive very low frequency, currents through electricity supply transformers which reduces transforming capacity. In extreme cases, electricity supply grids can collapse as multiple transformers are affected. GICs have larger magnitudes at auroral latitudes and should be related to the field aligned current (FAC) and auroral ionosphere currents systems. At ground locations under the regions between upward and downward FACs, the GIC related fields show a direct relationship with the time derivative of the FACs. This allows a conversion factor between FAC and GIC magnitudes. Examples of the relationship between FAC and GIC related fields are presented using data derived from the Active Magnetosphere and Planetary Electrodynamics Response Experiment (AMPERE) and SuperMAG.

  4. Coordinated Coverage of the Ring Current, Cusp and Adjacent FACs with Cluster and Swarm

    NASA Astrophysics Data System (ADS)

    Xiong, C.; Dunlop, M. W.; Bogdanova, Y.; Yang, J.; Yang, Y.; Shen, C.; Luhr, H.; Olsen, N.; Zhang, Q. H.; Ritter, P.; Kauristie, K.; Masson, A.; Haagmans, R.

    2014-12-01

    We explore the capability of Swarm-Cluster coordination for probing the behavior of the ring current (RC), field aligned currents (FAC) and cusp currents at medium and low orbits. The RC and connecting R2 FACs influence the geomagnetic field at low Earth orbit (LEO) and are sampled in situ by the four Cluster spacecraft every perigee pass. Coordination of the configuration of the three Swarm spacecraft with the constellation of the four Cluster spacecraft has been planned through joint operations; providing a set of distributed, multi-point measurements covering this region. A particularly close coordination of all spacecraft has been achieved during the start of the Swarm operations. We show preliminary study of the morphology and influence of the ring current from the in-situ RC and associated FACs determined directly from the 4-spacecraft Cluster perigee observations. We report here preliminary results of joint science targets, including coordinated cusp encounters; the comparative significance of the connecting R2 FACs, and the use and application of new analysis techniques derived from the calculation of curl B and magnetic gradients to compare estimates of the current distributions. For context, we will report on the coordination of Champ and Cluster data to interpret and resolve the R1 and R2 FACs using Champ derived models of the associated auroral boundaries.

  5. The detailed spatial structure of field-aligned currents comprising the substorm current wedge

    NASA Astrophysics Data System (ADS)

    Murphy, Kyle R.; Mann, Ian R.; Rae, I. Jonathan; Waters, Colin L.; Frey, Harald U.; Kale, Andy; Singer, Howard J.; Anderson, Brian J.; Korth, Haje

    2013-12-01

    We present a comprehensive two-dimensional view of the field-aligned currents (FACs) during the late growth and expansion phases for three isolated substorms utilizing in situ observations from the Active Magnetosphere and Planetary Electrodynamics Response Experiment and from ground-based magnetometer and optical instrumentation from the Canadian Array for Realtime Investigations of Magnetic Activity and Time History of Events and Macroscale Interactions during Substorms ground-based arrays. We demonstrate that the structure of FACs formed during the expansion phase and associated with the substorm current wedge is significantly more complex than a simple equivalent line current model comprising a downward FAC in the east and upward FAC in the west. This two-dimensional view demonstrates that azimuthal bands of upward and downward FACs with periodic structuring in latitude form across midnight and can span up to 8 h of magnetic local time. However, when averaged over latitude, the overall longitudinal structure of the net FACs resembles the simpler equivalent line current description of the substorm current wedge (SCW). In addition, we demonstrate that the upward FAC elements of the structured SCW are spatially very well correlated with discrete aurora during the substorm expansion phase and that discrete changes in the FAC topology are observed in the late growth phase prior to auroral substorm expansion phase onset. These observations have important implications for determining how the magnetosphere and ionosphere couple during the late growth phase and expansion phase, as well as providing important constraints on the magnetospheric generator of the FACs comprising the SCW.

  6. Swarm Observations of Field-Aligned Currents: Case Studies

    NASA Astrophysics Data System (ADS)

    Le, G.; Chi, P. J.; Gjerloev, J. W.; Stolle, C.; Luhr, H.; Park, J.; Rauberg, J.

    2014-12-01

    In this paper, we report the results of a few case studies of multi-point magnetic field measurements of field-aligned currents (FACs) from Swarm constellation mission to understand their temporal and spatial characteristics. During the commissioning phase, the three Swarm spacecraft were in an identical polar orbit with a string-of-pearl configuration with small separations. During the science operational phase (since April, 2014), the three spacecraft were placed in slightly different polar orbits: one spacecraft in a higher altitude orbit (507km x 512km) and two side-by-side in lower altitude orbits (459km x 462km). We analyze a few FAC events in both orbital phases and during periods of active geomagnetic conditions. The multi-point observations enable us to examine the FACs' temporal evolution and separate their temporal and spatial variations.

  7. A High-resolution Model of Field-aligned Currents Through Empirical Orthogonal Functions Analysis (MFACE)

    NASA Technical Reports Server (NTRS)

    He, Maosheng; Vogt, Joachim; Luehr, Hermann; Sorbalo, Eugen; Blagau, Adrian; Le, Guan; Lu, Gang

    2012-01-01

    Ten years of CHAMP magnetic field measurements are integrated into MFACE, a model of field-aligned currents (FACs) using empirical orthogonal functions (EOFs). EOF1 gives the basic Region-1/Region-2 pattern varying mainly with the interplanetary magnetic field Bz component. EOF2 captures separately the cusp current signature and By-related variability. Compared to existing models, MFACE yields significantly better spatial resolution, reproduces typically observed FAC thickness and intensity, improves on the magnetic local time (MLT) distribution, and gives the seasonal dependence of FAC latitudes and the NBZ current signature. MFACE further reveals systematic dependences on By, including 1) Region-1/Region-2 topology modifications around noon; 2) imbalance between upward and downward maximum current density; 3) MLT location of the Harang discontinuity. Furthermore, our procedure allows quantifying response times of FACs to solar wind driving at the bow shock nose: we obtain 20 minutes and 35-40 minutes lags for the FAC density and latitude, respectively.

  8. Field-aligned currents and large-scale magnetospheric electric fields

    NASA Technical Reports Server (NTRS)

    Dangelo, N.

    1979-01-01

    The existence of field-aligned currents (FAC) at northern and southern high latitudes was confirmed by a number of observations, most clearly by experiments on the TRIAD and ISIS 2 satellites. The high-latitude FAC system is used to relate what is presently known about the large-scale pattern of high-latitude ionospheric electric fields and their relation to solar wind parameters. Recently a simplified model was presented for polar cap electric fields. The model is of considerable help in visualizing the large-scale features of FAC systems. A summary of the FAC observations is given. The simplified model is used to visualize how the FAC systems are driven by their generators.

  9. Lobe cell convection and field-aligned currents poleward of the region 1 current system

    NASA Astrophysics Data System (ADS)

    Eriksson, S.; Bonnell, J. W.; Blomberg, L. G.; Ergun, R. E.; Marklund, G. T.; Carlson, C. W.

    2002-08-01

    We present a case and statistical study of plasma convection in the Northern Hemisphere during summer conditions using electric field, magnetic field, and particle data taken during dawn-dusk directed orbits of the FAST satellite. To our knowledge, this set provides the most comprehensive combination of data as yet presented in support of lobe cell convection from an ionospheric perspective this far from the noon sector. In particular, we study the current systems and convection patterns for all passes in July 1997 that show evidence for six large-scale field-aligned currents (FACs) rather than the usual system of four FACs associated with the region 1/region 2 current systems. A total of 71 passes out of 232 in the study had the extra pair of FACs. The extra pair of FACs in 30 of the 71 cases lies either on the dawnside or on the duskside of the noon-midnight meridian, and their position is strongly correlated with the polarity of the IMF By (negative and positive, respectively). This is consistent with the IMF dependence of a three-cell convection pattern of coexisting merging, viscous, and lobe-type convection cells. The occurrence of the asymmetric FAC pair was also strongly linked to conditions of IMF |By/Bz| > 1. The extra pair of FACs in these cases was clearly associated with the lobe cell of the three-cell convection system. The remaining 41 cases had the pair of FACs straddling the noon-midnight meridian. The extra pair of FACs was often (20 cases out of 30) observed at magnetic local times more than three hours away from noon, rather than being confined to regions near noon and the typical location of the cusp. Such a current system consisting of a pair of FACs poleward of the nearest region 1 current is consistent with the IMF By-dependent global MHD model developed by Ogino et al. [1986] for southward IMF conditions, as well as with other magnetospheric and ionospheric convection models that include the effects of merging occuring simultaneously at

  10. Field-Aligned Current at Plasma Sheet Boundary Layers During Storm Time: Cluster Observation

    NASA Astrophysics Data System (ADS)

    Shi, J.; Cheng, Z.; Zhang, T.; Dunlop, M.; Liu, Z.

    2007-05-01

    The magnetic field data from the FGM instruments on board the four Cluster spacecrafts were used to study Field Aligned Current (FAC) at the Plasma Sheet Boundary Layers (PSBLs) with the so called "curlometer technique". We analyzed the date obtained in 2001 in the magnetotail and only two cases were found in the storm time. One (August 17, 2001) occurred from sudden commencement to main phase, and the other (October 1, 2001) lay in the main phase and recovery phase. The relationship between the FAC density and the AE index was studied and the results are shown as follows. (1) In the sudden commencement and the main phase the density of the FAC increases obviously, in the recovery phase the density of the FAC increases slightly. (2) From the sudden commencement to the initial stage of the main phase the FAC increases with decreasing AE index and decreases with increasing AE index. From the late stage of the main phase to initial stage of the recovery phase, the FAC increases with increasing AE index and decreases with decreasing AE index. In the late stage of the recovery phase the disturbance of the FAC is not so violent, so that the FAC varying with the AE index is not very obvious.

  11. Localized field-aligned currents in the polar cap associated with airglow patches

    NASA Astrophysics Data System (ADS)

    Zou, Ying; Nishimura, Yukitoshi; Burchill, Johnathan K.; Knudsen, David J.; Lyons, Larry R.; Shiokawa, Kazuo; Buchert, Stephan; Chen, Steve; Nicolls, Michael J.; Ruohoniemi, J. Michael; McWilliams, Kathryn A.; Nishitani, Nozomu

    2016-10-01

    Airglow patches have been recently associated with channels of enhanced antisunward ionospheric flows propagating across the polar cap from the dayside to nightside auroral ovals. However, how these flows maintain their localized nature without diffusing away remains unsolved. We examine whether patches and collocated flows are associated with localized field-aligned currents (FACs) in the polar cap by using coordinated observations of the Swarm spacecraft, a polar cap all-sky imager, and Super Dual Auroral Radar Network (SuperDARN) radars. We commonly (66% of cases) identify substantial FAC enhancements around patches, particularly near the patches' leading edge and center, in contrast to what is seen in the otherwise quiet polar cap. These FACs have densities of 0.1-0.2 μA/m-2 and have a distribution of width peaking at 75 km. They can be approximated as infinite current sheets that are orientated roughly parallel to patches. They usually exhibit a Region 1 sense, i.e., a downward FAC lying eastward of an upward FAC. With the addition of Resolute Bay Incoherent Scatter radar data, we find that the FACs can close through Pedersen currents in the ionosphere, consistent with the locally enhanced dawn-dusk electric field across the patch. Our results suggest that ionospheric polar cap flow channels are imposed by structures in the magnetospheric lobe via FACs, and thus manifest mesoscale magnetosphere-ionosphere coupling embedded in large-scale convection.

  12. Field-aligned current signatures during the March 13-14, 1989, great magnetic storm

    SciTech Connect

    Fujii, R. ); Fukunishi, H. ); Kokubun, S. ); Sugiura, M. ); Tohyama, F. ); Hayakawa, H.; Tsuruda, K. ); Okada, T. )

    1992-07-01

    Characteristics of field-aligned currents (FACs) in the evening and morning regions during the March 13-14, 1989, great magnetic storm have been determined using magnetic and electric field data obtained from the EXOS D spacecraft. This storm began with an SSC at 0128 UT on March 13, and the second SSC occurred at 0747 UT on the same day. The storm continued until March 14. The equatorward boundary of the FAC region began to move equatorward right after the first SSC in both the evening and morning sectors, but the poleward boundary did not immediately respond to the SSC. The equatorward boundary of the FAC system reached as low as below 48{degree} invariant latitude, which corresponds to L = 2.2, and the latitudinal width of the FAC region increased greatly, particularly in the morning sector ({approximately}33{degree} in invariant latitude). In the evening sector the conventional current system characterized by a pair of upward region 1 and downward region 2 FACs changed into complicated patterns consisting of many pairs of upward and downward FACs with the development of the storm, particularly around 22 UT on March 13 when an intense eastward electrojet was observed as low as 50{degree} invariant latitude on the ground. In the morning sector an additional large-scale upward FAC was observed poleward of the conventional downward region 1 and upward region 2 FAC system throughout the storm. In addition, a pair of FACs with a narrow latitudinal width ({approximately}1.5{degree}) was observed at the poleward boundary of the extra upward FAC.

  13. Comparison of field-aligned currents at ionospheric and magnetospheric altitudes

    NASA Technical Reports Server (NTRS)

    Spence, H. E.; Kivelson, M. G.; Walker, R. J.

    1988-01-01

    Using the empirical terrestrial magnetospheric magnetic field models of Tsyganenko and Usmanov (1982) and Tsyganenko (1987) the average field-aligned currents (FACs) in the magnetosphere were determined as a function of the Kp index. Three major model FAC systems were identified, namely, the dayside region 1, the nightside region 1, and the nightside polar cap. The models provide information about the sources of the current systems. Mapped ionospheric model FACs are compared with low-altitude measurements obtained by the spacecraft. It is found that low-altitude data can reveal either classic region 1/2 or more highly structured FAC patterns. Therefore, statistical results either obtained from observations or inferred from models are expected to be averages over temporally and spatially shifting patterns.

  14. Space Technology 5 observations of auroral field-aligned currents

    NASA Astrophysics Data System (ADS)

    Slavin, James

    During its three month long technology validation mission, Space Technology 5 (ST-5) returned high quality multi-point measurements of the near-Earth magnetic field. Its three micro-satellites were launched into a 300 x 4500 km, dawn - dusk, sun synchronous orbit (inclination = 105.6o) orbit with a period of 138 min by a Pegasus launch vehicle on March 22, 2006. The spacecraft were maintained in a "pearls on a sting" constellation with controlled spacings ranging from just over 5000 km down to under 50 km. The individual micro-satellites were 48 cm tall octagons with diameters of 50 cm. They were spin-stabilized at approximately 20 rpm at deployment and slowly spun-down to about 15 rpm by the end of the mission. Each spacecraft carried a miniature tri-axial fluxgate magnetometer (MAG) provided by the University of California at Los Angeles mounted at the end of a ultra-low mass 72 cm boom. These data allow, for the first time, the separation of temporal and spatial variations in field-aligned current (FAC) perturbations measured in low-Earth orbit on time scales of 10 sec to 10 min. The constellation measurements are used to directly determine field-aligned current sheet motion, thickness, and current density. Two multi-point methods for the inference of FAC current density that have not previously been possible in low-Earth orbit are demonstrated: 1) the "standard method," based upon s/c velocity, but corrected for FAC current sheet motion, and 2) the "gradiometer method" which uses simultaneous magnetic field measurements at two points with known separation. Future studies will apply these methods to the entire ST-5 data set and expand to include horizontal ionospheric currents, ULF waves and geomagnetic field gradient analyses.

  15. Space Technology 5 Observations of Auroral Field-Aligned Currents

    NASA Technical Reports Server (NTRS)

    Slavin, James

    2008-01-01

    During its three month long technology validation mission, Space Technology 5 (ST-5) returned high quality multi-point measurements of the near-Earth magnetic field. Its three micro-satellites were launched into a 300 x 4500 km, dawn - dusk, sun synchronous orbit (inclination = 105.60) orbit with a period of 138 min by a Pegasus launch vehicle on March 22, 2006. The spacecraft were maintained in a "pearls on a sting" constellation with controlled spacings ranging from just over 5000 km down to under 50 km. The individual micro-satellites were 48 cm tall octagons with diameters of 50 cm. They were spin-stabilized at approximately 20 rpm at deployment and slowly spun-down to about 15 rpm by the end of the mission. Each spacecraft carried a miniature tri-axial fluxgate magnetometer (MAG) provided by the University of California at Los Angeles mounted at the end of a ultra-low mass 72 cm boom. These data allow, for the first time, the separation of temporal and spatial variations in field-aligned current (FAC) perturbations measured in low-Earth orbit on time scales of 10 sec to 10 min. The constellation measurements are used to directly determine field-aligned current sheet motion, thickness. and current density. Two multi-point methods for the inference of FAC current density that have not previously been possible in low-Earth orbit are demonstrated: 1) the -standard method." based upon s/c velocity, but corrected for FAC current sheet motion. and 2) the "gradiometer method" which uses simultaneous magnetic field measurements at two points with known separation. Future studies will apply these methods to the entire ST-5 data sct and expand to include horizontal ionospheric currents. ULF waves and geomagnetic field gradient analyses.

  16. Field-aligned currents distribution as derived from the Swarm satellite constellation

    NASA Astrophysics Data System (ADS)

    Luhr, H.; Kervalishvili, G.; Rauberg, J.; Michaelis, I.

    2015-12-01

    The seminal studies of Iijima and Potemra have outlined the major distribution features of field-aligned currents (FACs) in a local time versus magnetic latitude frame. The related plot showing the Region 1 and 2 FAC belts has been the reference in many studies as the baseline configuration during the past decades. What did we learn more since then? ESA's constellation mission Swarm provides the opportunity to derive more reliable FAC estimates from multi-satellite magnetic field measurements. We make use of the Swarm A/C satellite pair, which flies side-by-side at a separation of 1.4° in longitude. By considering along-track differences over 5 s the four readings at the corners of an almost symmetrical quad are used for calculating the mean vertical current density flowing through the encircled area. FACs are estimated by mapping the vertical current component onto the field direction. Within the auroral oval current estimates from single and dual-satellite solutions agree generally well. Significant differences are frequently observed in the polar cap. Here underlying assumptions for single-satellite solutions are obviously not well satisfied. Another characteristic derived from the multi-satellite observations: FACs can be divided into two classes. For scale sizes up to some ten kilometers rapid temporal variations are observed. These FACs are related to kinetic Alfvén waves. The other class with scale lengths of more than 150 km can be regarded as stationary current systems lasting for more than a minute.

  17. Filamentary field-aligned currents at the polar cap region during northward interplanetary magnetic field derived with the Swarm constellation

    NASA Astrophysics Data System (ADS)

    Lühr, Hermann; Huang, Tao; Wing, Simon; Kervalishvili, Guram; Rauberg, Jan; Korth, Haje

    2016-10-01

    ESA's Swarm constellation mission makes it possible for the first time to determine field-aligned currents (FACs) in the ionosphere uniquely. In particular at high latitudes, the dual-satellite approach can reliably detect some FAC structures which are missed by the traditional single-satellite technique. These FAC events occur preferentially poleward of the auroral oval and during times of northward interplanetary magnetic field (IMF) orientation. Most events appear on the nightside. They are not related to the typical FAC structures poleward of the cusp, commonly termed NBZ. Simultaneously observed precipitating particle spectrograms and auroral images from Defense Meteorological Satellite Program (DMSP) satellites are consistent with the detected FACs and indicate that they occur on closed field lines mostly adjacent to the auroral oval. We suggest that the FACs are associated with Sun-aligned filamentary auroral arcs. Here we introduce in an initial study features of the high-latitude FAC structures which have been observed during the early phase of the Swarm mission. A more systematic survey over longer times is required to fully characterize the so far undetected field aligned currents.

  18. Effect of Interhemispheric Field-Aligned Currents on Region-1 Currents

    NASA Technical Reports Server (NTRS)

    Lyatsky, Sonya; Lyatsky, Wladislaw; Khazanov, George V.

    2015-01-01

    An asymmetry in ionospheric conductivity between two hemispheres results in the formation of additional, interhemispheric field-aligned currents flowing between conjugate ionospheres within two auroral zones. These interhemispheric currents are especially significant during summer-winter conditions when there is a significant asymmetry in ionospheric conductivity in two hemispheres. In such conditions, these currents may be comparable in magnitude with the Region 1 field-aligned currents. In this case, the R1 current is the sum of two FACs: one is going from to the solar wind, and another is flowing between conjugate ionospheres. These interhemispheric currents can also cause the formation of auroras extended along the nightside polar cap boundary, which may be related to the so-called double auroral oval. In this study, we present the results of analytical and numerical solutions for the interhemispheric currents and their effect on the Region 1 currents.

  19. Space Technology 5 Multi-Point Field-Aligned Current Measurements (Invited)

    NASA Astrophysics Data System (ADS)

    Slavin, J. A.; Le, G.; Gjerloev, J. W.

    2013-12-01

    NASA's Space Technology 5 (ST 5) microsatellite constellation technology mission was launched by a Pegasus launch vehicle on March 22, 2006. The three small (48 cm tall, 50 cm diameter, 25 kg mass, spin stabilized at 20 rpm) satellites were placid in a 300 x 4500 km, dawn to dusk, sun synchronous orbit (inclination = 105.6 deg) orbit with a period of 138 min. They were maintained in this 'pearls on a sting' formation with inter-satellite spacings ranging from over 5000 km to under 50 km. Each satellite carried a miniature tri-axial fluxgate magnetometer (MAG) provided by the University of California at Los Angeles. Field aligned currents (FACs) form in response to the stress exerted on the magnetosphere by the solar wind and act as the primary mechanism for dissipating solar wind energy into the ionosphere and upper atmosphere during the solar wind magnetosphere ionosphere coupling process. ST 5 returned the first direct, simultaneous, multipoint measurements of FAC motion, thickness, and temporal variability. Current density was measured using both 1) the 'standard method' based upon s/c velocity, but corrected for FAC current sheet motion, with the assumption of a time-stationary current density profile, and 2) for the first time at low altitudes, the 'gradiometer method' which uses simultaneous magnetic field measurements at two points with known separation. Here we review the ST 5 scientific results concerning FACs and discuss their implications for future investigations of field aligned currents systems using distributed systems of spaceborne magnetometers.

  20. Influences of the interplanetary magnetic field clock angle and cone angle on the field-aligned currents in the magnetotail

    NASA Astrophysics Data System (ADS)

    Cheng, Z. W.; Shi, J. K.; Dunlop, M.; Liu, Z. X.

    2013-10-01

    The influences of the interplanetary magnetic field (IMF) cone angle θ and clock angle ϕ on the field-aligned currents (FACs) at the plasma sheet boundary layers (PSBLs) have been investigated using Cluster Data. The FAC occurrence increases monotonically with IMF cone angle and has two peaks at -90° and +110° clock angle, respectively. The peak at +110° is distinctly larger than that at -90°. Overall, there are more FACs between 0° < ϕ < 180°, indicating that FACs occurrence is closely associated with duskward IMF. More FACs occur when 90° < |ϕ| < 180°, implying that FAC is closely associated with southward IMF. The large FAC densities occur when 60° < |ϕ| < 120°. The density also has two peaks and the peak at +90° clock angle (duskward IMF) is larger than that at -90° (dawnward IMF). These results indicate that the IMF influence on the FACs is from all IMF components and not only from a single component.

  1. Alfven Wave Reflection Model of Field-Aligned Currents at Mercury

    NASA Technical Reports Server (NTRS)

    Lyatsky, Wladislaw; Khazanov, George V.; Slavin, James

    2010-01-01

    An Alfven Wave Reflection (AWR) model is proposed that provides closure for strong field-aligned currents (FACs) driven by the magnetopause reconnection in the magnetospheres of planets having no significant ionospheric and surface electrical conductance. The model is based on properties of the Alfven waves, generated at high altitudes and reflected from the low-conductivity surface of the planet. When magnetospheric convection is very slow, the incident and reflected Alfven waves propagate along approximately the same path. In this case, the net field-aligned currents will be small. However, as the convection speed increases. the reflected wave is displaced relatively to the incident wave so that the incident and reflected waves no longer compensate each other. In this case, the net field-aligned current may be large despite the lack of significant ionospheric and surface conductivity. Our estimate shows that for typical solar wind conditions at Mercury, the magnitude of Region 1-type FACs in Mercury's magnetosphere may reach hundreds of kilo-Amperes. This AWR model of field-aligned currents may provide a solution to the long-standing problem of the closure of FACs in the Mercury's magnetosphere. c2009 Elsevier Inc. All rights reserved.

  2. Plasma Sheet Response to the Ionosphere's Demand for Field-Aligned Current

    NASA Astrophysics Data System (ADS)

    Coroniti, F. V.; Pritchett, P. L.

    2007-12-01

    Magnetospheric convection electric fields and plasma stresses are transmitted to the ionosphere by Alfvén wave electric fields and field-aligned currents (FACs). The closure of the FACs by ionospheric Hall and Pedersen currents drives the ionospheric convection system. However, the ionospheric system does not necessarily mesh smoothly with the magnetospheric drivers, and the magnetosphere must respond by altering its convection and plasma stress configuration, thereby creating self-consistent closure paths for the complete coupled system of currents and electric potentials. Three-dimensional particle-in-cell plasma kinetic simulations are used to determine the plasma sheet response to various current systems imposed as boundary conditions at the near-Earth boundary. These systems consist of separate downward and upward tubes of FAC and a substorm current wedge configuration. The results demonstrate that the creation of closure paths for ionospheric FACs can result in large configuration changes within the near-Earth plasma sheet. The plasma sheet is forced to establish polarization electric fields that locally increase the cross-tail current by producing a duskward Hall electron current; this results in the formation of thin (in z), spatially localized (in y) electron-dominated Hall current sheets. The observed complex magnetic field configuration with opposite polarity Bz fields in close proximity separated by electron scale thin current sheets is reminiscent of the turbulent magnetic fields that are observed within the near-Earth current disruption region at substorm breakup [ Lui et al., 1988, 1992].

  3. The particle carriers of field-aligned currents in the Earth's magnetotail during a substorm

    NASA Astrophysics Data System (ADS)

    Cheng, Z. W.; Zhang, J. C.; Shi, J. K.; Kistler, L. M.; Dunlop, M.; Dandouras, I.; Fazakerley, A.

    2016-04-01

    Although the particle carriers of field-aligned currents (FACs) in the Earth's magnetotail play an important role in the transfer of momentum and energy between the solar wind, magnetosphere, and ionosphere, the characteristics of the FAC carriers have been poorly understood. Taking advantage of multiinstrument magnetic field and plasma data collected by the four spacecraft of the Cluster constellation as they traversed the northern plasma sheet boundary layer in the magnetotail on 14 September 2004, we identified the species type and energy range of the FAC carriers for the first time. The results indicate that part of tailward FACs is carried by energetic keV ions, which are probably originated from the ionosphere through outflow, and they are not too small (~2 nA/m2) to be ignored. The earthward (tailward) FACs are mainly carried by the dominant tailward (earthward) motion of electrons, and higher-energy electrons (from ~0.5 to 26 keV) are the main carriers.

  4. Complexities of determining the Field-Aligned current density from LEO satellites.

    NASA Astrophysics Data System (ADS)

    Gjerloev, J. W.; Friel, M. M.; Ohtani, S.; Muhleisen, M.; Gjerloev, A. W.; Martin, P.; Barnes, R. J.

    2015-12-01

    We show results from a study of the field-aligned currents (FAC) as derived from SWARM magnetic field perturbations. We calculate the FAC density using four different techniques and explain why they provide different results. Theoretical work, simulations and data are used to show that widely used techniques can provide current density estimates with errors of 1000%. These errors can be explained by spatial gradients in the currents and temporal variability of the currents as well as a breakdown of other fundamental assumptions. We apply the techniques to auroral crossings with THEMIS ASI coverage and use the SWARM magnetic field observations to calculate the current density. Finally, we show how to estimate the errors in the current density calculations.

  5. Four large-scale field-aligned current systmes in the dayside high-latitude region

    NASA Technical Reports Server (NTRS)

    Ohtani, S.; Potemra, T. A.; Newell, P.T.; Zanetti, L. J.; Iijima, T.; Watanabe, M.; Blomberg, L. G.; Elphinstone, R. D.; Murphree, J. S.; Yamauchi, M.

    1995-01-01

    A system of four current sheets of large-scale field-aligned currents (FACs) was discovered in the data set of simultaneous Viking and Defense Meteorological Satellire Program-F7 (DMSP-F7) crossing of the dayside high-latitude region. This paper reports four examples of this system that were observed in the prenoon sector. The flow polarities of FACs are upward, downward, upward, and downward, from equatorward to poleward. The lowest-latitude upward current is flowing mostly in the central plasma sheet (CPS) precipitation region, often overlapping with the boundary plasma sheet (BPS) at its poleward edge, andis interpreted as a region 2 current. The pair of downward and upward FACs in the middle of te structure are collocated with structured electron precipitation. The precipitation of high-energy (greater than 1 keV) electrons is more intense in the lower-latitude downward current sheet. The highest-latitude downward flowing current sheet is located in a weak, low-energy particle precipitation region, suggesting that this current is flowing on open field lines. Simulaneous observations in the postnoon local time sector reveal the standard three-sheet structure of FACs, sometimes described as region 2, region 1, and mantle (referred to the midday region O) currents. A high correlation was found between the occurrence of the four FAC sheet structure and negative interplanetary magnetic field (IMF) B(sub Y). We discuss the FAC structurein terms of three types of convection cells: the merging, viscous, andlobe cells. During strongly negative IMF B(sub Y), two convection reversals exist in the prenoon sector; one is inside the viscous cell, and the other is between the viscous cell and the lobe cell. This structure of convection flow is supported by the Viking electric field and auroral UV image data. Based on the convection pattern, the four FAC sheet structure is interpreted as the latitude overlap of midday and morning FAC systems. We suggest that the for-current

  6. Quantitative patterns of large-scale field-aligned currents in the auroral ionosphere

    SciTech Connect

    Foster, J.C.; Fuller-Rowell, T.; Evans, D.S.

    1989-03-01

    Quantitative patterns of the distribution of field-aligned current (FAC) density have been derived from gradients of the average patterns of the Hall and Pedersen currents at high latitudes under the assumption that the total current is divergence-free. The horizontal currents were calculated from empirical convection electric field models, derived from Millstone Hill radar observations, and the ionospheric Hall and Pedersen conductances, based on satellite observations of the precipitating particle energy flux and spectrum and including an average (equinox) solar contribution. These independent empirical models, and the resultant patterns of the field-aligned currents, are keyed to an auroral precipitation index which quantifies the intensity and spatial extent of high-latitude particle precipitation and which is determined from a single satellite crossing of the auroral precipitation pattern. The patterns detail the spatial distribution of the currents as a function of increasing disturbance level. The magnitudes of the total single-hemisphere currents into or out of the ionosphere are closely balanced at each activity level and increase exponentially between 0.1 and 6 MA with increasing values of the precipitation index. The interplanetary magnetic field (IMF) sector dependence of the FAC patterns is investigated for disturbed conditions. A large portion of the FAC pattern is closed by local Pedersen currents (current into the ionosphere is balanced by an equal current out of the ionosphere at that local time). This locally balanced portion of the FAC system is enhanced in the prenoon (postnoon) sector for IMF B/sub v/>+1 nT (B/sub y/<-1 nT). In addition, there are net currents into the ionosphere postnoon and out of the ionosphere in the premidnight sector.

  7. Laboratory simulation of field-aligned currents

    NASA Technical Reports Server (NTRS)

    Wessel, Frank J.; Rostoker, Norman

    1993-01-01

    A summary of progress during the period Apr. 1992 to Mar. 1993 is provided. Objectives of the research are (1) to simulate, via laboratory experiments, the three terms of the field-aligned current equation; (2) to simulate auroral-arc formation processes by configuring the boundary conditions of the experimental chamber and plasma parameters to produce highly localized return currents at the end of a field-aligned current system; and (3) to extrapolate these results, using theoretical and computational techniques, to the problem of magnetospheric-ionospheric coupling and to compare them with published literature signatures of auroral-arc phenomena.

  8. Observations of Field-Aligned Current Spatial and Temporal Variations by Space Technology 5

    NASA Astrophysics Data System (ADS)

    Le, G.; Slavin, J. A.; Strangeway, R. J.; Wang, Y.

    2013-12-01

    In this paper, we report the results of magnetic field measurements of field-aligned currents (FACs) using multi-point magnetic field data from Space Technology 5 (ST-5) mission. ST-5 is a three micro-satellite constellation deployed into a 300 x 4500 km, dawn-dusk, sun synchronous polar orbit. The spacecraft were maintained in a 'pearls on a sting' constellation with controlled spacings ranging from just over 5000 km down to under 50 km. During the three-month mission duration, the constellation mission returned high quality multi-point measurements of the magnetic field through Earth's dynamic ionospheric current systems over a range of inter-satellite spacing. In this study, we use the ST-5 magnetic field measurements to separate spatial and temporal variations of FACs and to quantify the imbalance between the region 1 (R1) and the region 2 (R2) currents.

  9. Global ionospheric current patterns associated with the development of the R1 and R2 FACs deduced by the GEMSIS-POT

    NASA Astrophysics Data System (ADS)

    Nakamizo, A.; Hiraki, Y.; Hori, T.; Seki, K.; Ieda, A.; Tsuji, Y.; Miyoshi, Y.; Ebihara, Y.; Kikuchi, T.

    2011-12-01

    As part of the GEMSIS project (Geospace Environment Modeling System for Integrated Studies), we have developed a two-dimensional ionospheric global potential solver. There has been considerable research on the mid-and low-latitude ionospheric system driven by neutral wind [e.g., Richmond, 1973]. However, there are few researches on the relationship between the high-latitude system and middle and low latitude system, which is important for the integrated studies of the magnetosphere-inner magnetosphere system coupled through the ionosphere. Our model basically follows a methodology provided by Tsunomura [1999]; it solves the Ohm's law under the thin-shell approximated 2-D ionosphere, with FACs in the polar region and height-integrated ionospheric conductivities. The most important extension from previous studies is that our model covers both hemispheres without a boundary at the equator. The values of Pedersen and Hall conductivities are calculated as exactly as possible with the MSIS-2000, IRI-2007, and IGRF-2005 reference models. In addition, we consider the effect of auroral particle precipitation on conductivities with reference to the empirical models [e.g., Hardy et al., 1987]. Although the FACs and ionospheric conductivity are intrinsically related to each other, we set them a priori at present because there is still no theory describing the development of the FACs-conductivity coupled system self-consistently. By using the solver, we investigate (1) the relationship between the conductivity and electric field in the middle and low latitude ionosphere and (2) how the current density ratio and latitudinal/longitudinal distribution of R1-FAC and R2-FAC affect the electric field distribution and current pattern in the middle and low latitude ionosphere. Here, FACs are distributed with reference to the empirical model by Hori et al. [in preparation] and the location of the conductivity enhancement associated with auroral activities given by empirical models is

  10. Field-aligned currents, convection electric fields, and ULF-ELF waves in the cusp

    NASA Technical Reports Server (NTRS)

    Saflekos, N. A.; Potemra, T. A.; Kintner, P. M., Jr.; Green, J. L.

    1979-01-01

    Nearly simultaneous observations from the Triad and Hawkeye satellites over the Southern Hemisphere, at low altitudes near the noon meridian and close to the usual polar cusp latitudes, show that in and near the polar cusp there exist several relationships between field-aligned currents (FACs), convection electric fields, ULF-ELF magnetic noise, broadband electrostatic noise and interplanetary magnetic fields. The most important findings are (1) the FACs directed into the ionosphere in the noon-to-dusk local time sector and directed away from the ionosphere in the noon-to-dawn local time sector and identified as region-1 permanent FACs (Iijima and Potemra, 1976a) and are located equatorward of the regions of antisunward (westward) convection; (2) the observations are consistent with a two-cell convection pattern symmetric in one case (throat positioned at noon) and asymmetric in another (throat located in a sector on the forenoon side in juxtaposition to the region of strong convection on the afternoon side); and (3) fine-structure FACs are responsible for the generation of ULF-ELF noise in the polar cusp.

  11. Multi-point Magnetic Field Observations of Field-Aligned Currents from Swarm Constellation Mission

    NASA Astrophysics Data System (ADS)

    Le, Guan; Chi, Peter; Lühr, Hermann; Gjerloev, Jesper; Stolle, Claudia; Park, Jaeheung; Rauberg, Jan

    2015-04-01

    In this paper, we report the results of case studies of multi-point magnetic field measurements of field-aligned currents (FACs) from Swarm constellation mission to understand their temporal characteristics and hemispheric asymmetry. For science operations (since April, 2014), the three spacecraft were placed in slightly different polar orbits: Swarm B spacecraft in a higher altitude orbit (507km x 512km) and Swarm A and C side-by-side in lower altitude orbits (459km x 462km). In the beginning of the science operational phase, the longitudinal separations of the orbital planes were small, and Swarm A/C pair and Swarm B were nearly out of phase in the orbit. This unique orbit configuration provides opportunities to study some new features of FACs. Specifically, the Swarm satellites make multiple crossings of a FAC region within a few hours. Such data enable us to study temporal variations in several time scales, from 1 minute up to about 3 hours. Furthermore, the three satellites make nearly simultaneous observations of FACs in northern and southern hemispheres, which provide us an opportunity to study the hemispheric asymmetry.

  12. The Four-Part Field-Aligned Current System in the Ionosphere at Substorm Onset

    NASA Astrophysics Data System (ADS)

    McWilliams, K. A.; Sofko, G. J.; Bristow, W. A.; Hussey, G. C.

    2015-12-01

    Whereas the plasma circulation in the ionosphere is driven by convective drift which is the same for ions and electrons, the magnetospheric plasma circulation includes curvature and gradient drifts, which are charge-dependent. There is even a region of the Neutral Sheet in which the ions, but not the electrons, are "unmagnetized" and where charge separation can occur even for convective drift, which the electrons execute but the ions do not. Due to the charge separations in the magnetosphere, field-aligned currents are generated. The FACs and the associated electric fields play an important role in producing the convection pattern in the ionosphere. Here we argue that there are two pairs of FACs near substorm onset. One pair involves the auroral zone portion of the convection. There, a downward D FAC occurs in the poleward part of the auroral zone and an upward U FAC occurs in the equatorward part. We show that the D-U auroral FAC pair results from the odd situation in the INSh, where the electrons can convect earthward while the unmagnetized ions do not and so remain further tailward of the electrons. The equatorward edge of the auroral zone is marked by a convection reversal, because the auroral zone flows have an eastward velocity component, whereas subauroral flows have a westward component. At the convection reversal, the flow is strictly southward and the electric field strictly westward. The subauroral zone maps out to the outer radiation belt, where the high-energy electrons precipitate tailward of the energetic electron trapping boundary,and high-energy ions precipitate tailward of the energetic ion trapping boundary, the latter being earthward of the former. As a result, another FAC pair forms on field lines in the ORB/subauroral regions. The U FAC of the latter region is adjacent but earthward of the U FAC of the auroral zone pair. The D-U auroral zone pair is poleward of the U-D subauroral (Radiation Belt) pair. Finally, we note that the electric field

  13. ST5 Observations of the Imbalance of Region 1 and 2 Field-Aligned Currents and its Implication to Ionospheric Closure Currents

    NASA Technical Reports Server (NTRS)

    Le, G.

    2008-01-01

    A major unsolved question in the physics of ionosphere-magnetosphere coupling is how field-aligned currents (FACs) close. In order to maintain the divergence free condition, overall downward FACs (carried mainly by upward electrons) must eventually balance the overall upward FACs associated with the precipitating electrons through ionospheric Pedersen currents. Although much of the current closure may take place via local Pedersen currents flowing between Region 1 (R1) and Region 2 (R2) FACs, there is a generally an imbalance, i.e., more currents in R1 than in R2, in total currents between them. The net currents may be closed within R1 via cross-polar cap Pedersen currents. In this study, we use the magnetic field observations from Space Technology 5 mission to quantify the imbalance of R1 and R2 currents. We will determine the net R1-R2 currents under various solar wind conditions and discuss the implication of such imbalance to the ionospheric closure currents.

  14. Field-Aligned Current Reconfiguration and Magnetospheric Response to an Impulse in the Interplanetary Magnetic Field BY Component

    NASA Astrophysics Data System (ADS)

    Wilder, F. D.; Eriksson, S.; Korth, H.; Hairston, M. R.; Baker, J. B.; Heinselman, C. J.

    2013-12-01

    When the interplanetary magnetic field (IMF) is dawnward or duskward, magnetic merging between the IMF and the geomagnetic field occurs near the cusp on the dayside flanks of the magnetosphere. During these intervals, flow channels in the ionosphere with velocities in excess of 2 km/s have been observed, which can deposit large amounts of energy into the high-latitude thermosphere. In this study, we analyze an interval on 5 April 2010 where there was a strong dawnward impulse in the IMF, followed by a gradual decay in IMF magnitude at constant clock angle. Data from the Sondrestrom incoherent scatter radar and the DMSP spacecraft were used to investigate ionospheric convection during this interval, and data from the Active Magnetospheric and Planetary Electrodynamics Response Experiment (AMPERE) were used to investigate the associated Field-Aligned Current (FAC) system. Additionally, data from AMPERE were used to investigate the time response of the dawn-side FAC pair. We find there is a delay of approximately 1.25 hours between the arrival of the dawnward IMF impulse at the magnetopause and strength of the dawnward FAC pair, which is comparable to substorm growth and expansion time scales under southward IMF. Additionally, we find at the time of the peak FAC, there is evidence of a reconfiguring four-sheet FAC system in the morning local time sector of the ionosphere. Additionally, we find an inverse correlation between the dawn FAC strength and both the solar wind Alfvénic Mach number and the SYM-H index. No statistically significant correlation between the FAC strength and the solar wind dynamic pressure was found.

  15. Alfven Wave - DC Dualism in Description of Stationary Field-Aligned Currents

    NASA Technical Reports Server (NTRS)

    Khazanov, George V.

    2009-01-01

    In many cases, the field-aligned currents (FACs) in the Earth's magnetosphere and heliosphere may be described in terms of both DC currents and the currents of a propagating Alfven wave. The simplest example is when a propagating Alfven wave transports a potential hop along the magnetic fieid: between the source of the wave and its front, the problem is well stationary and includes the stationary field-aligned currents, transporting the electric charges along the magnetic field, which may be described as a DC problem, and only at the front of the wave there are the polarization (inertial) currents, closing across the magnetic field. In some cases, the Alfven wave approach brings better understanding to many problems. We will consider here the results of the applications of this approach to two long-staying problems: the effect of saturation of the transpolar voltage in the Earth's magnetosphere, and the experimentally-observed existence of the strong field-aligned currents in the subtle Mercury's magnetosphere which is not able tc close the measured field-aligned currents.

  16. A Science Mission for QSAT Project: Study of FACs in the Polar and Equatorial Regions

    NASA Astrophysics Data System (ADS)

    Fujimoto, Akiko; Ueno, Tamiki; Yumoto, Kiyohumi

    2009-04-01

    Kyushu University, Kyushu Institute of Technology and Fukuoka Institute of Technology are now designing, developing and building a micro-satellite called “QSAT”. The primary objective of QSAT is understanding the mechanism of spacecraft charging, which can be achieved with the onboard magnetometer, high-frequency probe (HP) and Langmuir probe (LP). The magnetometer measures the magnetic field variations caused by field-aligned currents (FACs) in the polar and equatorial regions. Polar FACs are well understood, while equatorial FACs are not. The science goals are as follows: (1) to better understand FACs in the polar region, (2) to compare the FACs observed in orbit with ground-based MAGDAS observations, (3) to investigate spatial distribution of FACs in the equatorial region. FACs play a crucial role in the coupling between solar wind, magnetosphere and ionosphere in terms of energy transfer. Also if we understand the relationship between the space and ground-based FACs data, then we can conduct long-term study on the solar wind-magnetosphere-ionosphere coupling in the future by mainly using data from ground-based magnetometer arrays.

  17. Sources of field-aligned currents in the auroral plasma

    SciTech Connect

    Marshall, J.A.; Burch, J.L. ); Kan, J.R. ); Reiff, P.H. ); Slavin, J.A. )

    1991-01-01

    Data from the Dynamics Explorer 1 High Altitude Plasma Instrument (HAPI) and magnetometer are used to investigate the sources of field-aligned currents in the nightside auroral zone. It is found that the formula developed by S. Knight predicts the field-aligned current density fairly accurately in regions where a significant potential drop can be inferred from the HAPI data; there are, however, regions in which the proportionality between potential drop and field-aligned current does not hold. In particular, the authors note occurrences of strong upward field-aligned current associated not with inverted-V events but instead with suprathermal bursts. In addition, upward field-aligned currents are often observed to peak near the edges of inverted-V events, rather than in the center as would be predicted by Knight.

  18. Sources of field-aligned currents in the auroral plasma

    NASA Astrophysics Data System (ADS)

    Marshall, J. A.; Burch, J. L.; Kan, J. R.; Reiff, P. H.; Slavin, J. A.

    1991-01-01

    Data from the Dynamics Explorer 1 High Altitude Plasma Instrument (HAPI) and magnetometer are used to investigate the sources of field-aligned currents in the nightside auroral zone. It is found that the formula developed by S. Knight predicts the field-aligned current density fairly accurately in regions where a significant potential drop can be inferred from the HAPI data; there are, however, regions in which the proportionality between potential drop and field-aligned current does not hold. In particular, occurrences of strong upward field-aligned current associated not with inverted-V events but instead with suprathermal bursts are noted. In addition, upward field-aligned currents are often observed to peak near the edges of inverted-V events, rather than in the center as would be predicted by Knight.

  19. Business-IT Alignment: A Current-State Evaluation of Strategic Alignment within the Hospital Organization

    ERIC Educational Resources Information Center

    Evers, Kevin W.

    2010-01-01

    More than thirty years of research has shown that the practical value of business-IT alignment is significant and that its importance derives from strategic impact on business outcomes. The purpose of this exploratory study is to identify the current-state of business-IT alignment maturity within the hospital organization. Data for this study was…

  20. Field-aligned currents and large scale magnetospheric electric fields

    NASA Technical Reports Server (NTRS)

    Dangelo, N.

    1980-01-01

    D'Angelo's model of polar cap electric fields (1977) was used to visualize how high-latitude field-aligned currents are driven by the solar wind generator. The region 1 and region 2 currents of Iijima and Potemra (1976) and the cusp field-aligned currents of Wilhjelm et al. (1978) and McDiarmid et al. (1978) are apparently driven by different generators, although in both cases the solar wind is their ultimate source.

  1. Field aligned current observations in the polar cusp ionosphere

    NASA Technical Reports Server (NTRS)

    Ledley, B. G.; Farthing, W. H.

    1973-01-01

    Vector magnetic field measurements made during a sounding rocket flight in the polar cusp ionosphere show field fluctuations in the lower F-region which are interpreted as being caused by the payload's passage through a structured field aligned current system. The field aligned currents have a characteristic horizontal scale size of one kilometer. Analysis of one large field fluctuation gives a current density of 0.0001 amp/m sq.

  2. Alfvénic field-aligned currents, ion upflow and electron precipitation during large geomagnetic storms

    NASA Astrophysics Data System (ADS)

    Hatch, Spencer; LaBelle, James; Chaston, Christopher

    2016-04-01

    We present four years of FAST observations of Alfvénic field-aligned currents (FACs) in the Northern Hemisphere coincident with 40 moderate (Dst < -50 nT) to very large geomagnetic storms. Superposed epoch analysis of Alfvénic activity of storm periods demonstrate a sharp increase in the probability of AlfvÉn wave occurrence just after storm commencement, and analysis based on storm phase shows that the probability of Alfvén wave occurrence increases by more than a factor of 5 on both dayside and nightside. Additionally, recently reported Van Allen Probes measurements in the magnetosphere imply a region (˜60-68 degrees invariant latitude) in the nightside ionosphere where Alfvén waves are statistically likely to be observed during storm main phase; we report statistical observations during main phase showing that this region instead corresponds to both intense electron precipitation (>10 mW m-2) and strong upflowing ion number flux (> 108 cm^{-2 s-1), while observed Alfvénic FAC occurrence rates are diminished relative to Van Allen Probes measurements. FAST observations also indicate that the most intense electron precipitation associated with Alfvénic FACs occurs pre-midnight during storm recovery phase.

  3. PC-FACS.

    PubMed

    Zhukovsky, Donna S

    2016-10-01

    PC-FACS(FastArticleCriticalSummaries for Clinicians inPalliativeCare) provides hospice and palliative care clinicians with concise summaries of the most important findings from more than 100 medical and scientific journals. If you have colleagues who would benefit from receiving PC-FACS, please encourage them to join the AAHPM at aahpm.org. Comments from readers are welcomed at pc-facs@aahpm.org.

  4. PC-FACS.

    PubMed

    Zhukovsky, Donna S

    2016-12-01

    PC-FACS(FastArticleCriticalSummaries for Clinicians inPalliativeCare) provides hospice and palliative care clinicians with concise summaries of the most important findings from more than 100 medical and scientific journals. If you have colleagues who would benefit from receiving PC-FACS, please encourage them to join the AAHPM at aahpm.org. Comments from readers are welcomed at pc-facs@aahpm.org.

  5. PC-FACS.

    PubMed

    Zhukovsky, Donna S

    2016-11-01

    PC-FACS(FastArticleCriticalSummaries for Clinicians inPalliativeCare) provides hospice and palliative care clinicians with concise summaries of the most important findings from more than 100 medical and scientific journals. If you have colleagues who would benefit from receiving PC-FACS, please encourage them to join the AAHPM at aahpm.org. Comments from readers are welcomed at pc-facs@aahpm.org.

  6. PC-FACS.

    PubMed

    Zhukovsky, Donna S

    2017-03-01

    PC-FACS(FastArticleCriticalSummaries for Clinicians inPalliativeCare) provides hospice and palliative care clinicians with concise summaries of the most important findings from more than 100 medical and scientific journals. If you have colleagues who would benefit from receiving PC-FACS, please encourage them to join the AAHPM at aahpm.org. Comments from readers are welcomed at pc-facs@aahpm.org.

  7. PC-FACS.

    PubMed

    Zhukovsky, Donna S

    2016-07-01

    PC-FACS(FastArticleCriticalSummaries for Clinicians inPalliativeCare) provides hospice and palliative care clinicians with concise summaries of the most important findings from more than 100 medical and scientific journals. If you have colleagues who would benefit from receiving PC-FACS, please encourage them to join the AAHPM at aahpm.org. Comments from readers are welcomed at pc-facs@aahpm.org.

  8. PC-FACS.

    PubMed

    Zhukovsky, Donna S

    2016-06-01

    PC-FACS(FastArticleCriticalSummaries for Clinicians inPalliativeCare) provides hospice and palliative care clinicians with concise summaries of the most important findings from more than 100 medical and scientific journals. If you have colleagues who would benefit from receiving PC-FACS, please encourage them to join the AAHPM at aahpm.org. Comments from readers are welcomed at pc-facs@aahpm.org.

  9. PC-FACS.

    PubMed

    Zhukovsky, Donna S

    2017-02-01

    PC-FACS(FastArticleCriticalSummaries for Clinicians inPalliativeCare) provides hospice and palliative care clinicians with concise summaries of the most important findings from more than 100 medical and scientific journals. If you have colleagues who would benefit from receiving PC-FACS, please encourage them to join the AAHPM at aahpm.org. Comments from readers are welcomed at pc-facs@aahpm.org.

  10. Simultaneous particle and field observations of field-aligned currents

    NASA Technical Reports Server (NTRS)

    Berko, F. W.; Hoffman, R. A.; Burton, R. K.; Holzer, R. E.

    1973-01-01

    Simultaneous measurements of low energy precipitating electrons and magnetic fluctuations from the low altitude polar orbiting satellite OGO-4 have been compared. Analysis of the two sets of experimental data for isolated events led to the classification of high latitude field-aligned currents as purely temporal or purely spatial variations. Magnetic field disturbances calculated using these simple current models and the measured particle fluxes were in good agreement with measured field values. While fluxes of greater than 1 keV electrons are detected primarily on the nightside, magnetometer disturbances indicative of field-aligned currents were seen at all local times, both in the visual auroral regions and dayside polar cusp. Thus electrons with energies less than approximately 1 keV are the prime charge carriers in high latitude dayside field-aligned currents. The satellite measurements are in good agreement with previously measured field-aligned current values and with values predicted from several models involving magnetospheric field-aligned currents.

  11. Changes in Magnetosphere-Ionosphere Coupling and FACs Associated with Substorm Onset (Invited)

    NASA Astrophysics Data System (ADS)

    Murphy, K. R.; Mann, I. R.; Rae, I. J.; Waters, C. L.; Anderson, B. J.; Korth, H.; Milling, D. K.; Singer, H. J.; Frey, H. U.

    2013-12-01

    Field aligned currents (FACs) are crucial for the communication of information between the ionosphere and magnetosphere. Utilising in-situ observations from the Iridium constellation and Active Magnetosphere and Planetary Electrodynamics Response Experiment (AMPERE) we provide detailed observations of the FAC topology through the substorm growth and expansion phases. In particular, for an isolated substorm on 16 February 2010 we demonstrate a clear and localized reduction in the FACs at least 6 minutes prior to auroral onset. A new auroral arc forms in the region of reduced FAC on closed field lines and initially expands azimuthally in wave like fashion. This newly formed arc continues to brighten and expands poleward signifying the start of the substorm expansion phase. We argue that the change in FACs observed prior to onset is the result of a change in the magnetosphere-ionosphere (M-I) coupling in a region local to the subsequent auroral onset. Such a change implies an important role for M-I coupling in destabilising the near-Earth tail during magnetospheric substorms and perhaps more importantly in selecting the location in the ionosphere where auroral onset begins. Further, we provide, a comprehensive in-situ two-dimensional view of the FAC topology associated with the substorm current wedge and westward traveling surge during the substorm expansion phase. We demonstrate that these current structures, when integrated with latitude to produce a net FAC as a function of MLT, have the same structure as the equivalent line current system comprising the SCW. Moreover, regions of upward FAC are associated with discrete auroral forms during the substorm expansion phase.

  12. Simultaneous prenoon and postnoon observations of three field-aligned current systems from Viking and DMSP-F7

    NASA Technical Reports Server (NTRS)

    Ohtani, S.; Potemra, T. A.; Newell, P. T.; Zanetti, L. J.; Iijima, T.; Watanabe, M.; Yamauchi, M.; Elphinstone, R. D.; De La Beauijardie, O.; Blomberg, L. G.

    1995-01-01

    The spatial structure of dayside large-scale field-aligned current (FAC) systems is examined by using Viking and Defense Meteorological Satellite Program-F7 (DMSP-F7) data. We focus on four events in which the satellites simultaneously observed postnoon and prenoon three FAC systems: the region 2, the region 1, and the mantle (referred to as midday region O) systems, from equatorward to poleward. These events provide the most solid evidence to date that the midday region O system is a separate and unique FAC system, and is not an extension of the region 1 system from other local times. The events are examined comprehensively by making use of a mulit-instrumental data set, which includes magnetic field, particle flux, electric field, auroral UV image data from the satellites, and the Sondrestrom convection data. The results are summarized as follows: (1) Region 2 currents flow mostly in the central plasma sheet (CPS) precipitation region, often overlapping with the boundary plasma sheet (BPD) at their poleward edge. (2) The region 1 system is located in the core part of the auroral oval and is confined in a relatively narrow range in latitude which includes the convection reversal. The low-latitude boundary layer, possibly including the outer part of the plasma sheet, and the external cusp are the major source regions of dayside region 1 currents. (2) Midday region O currents flow on open field lines and are collocated with the shear of antisunward convection flows with velocites decreasing poleward. On the basis of these results we support the view that both prenoon and postnoon current systems consist of the three-sheet structure when the disctortion ofthe convection pattern associated with interplanetary magnetic field (IMF) B(sub Y) is small and both morningside and eveningside convection cells are crescent-shaped. We also propose that the midday region O and a part of the region 1 systems are closely coupled to the same source.

  13. Field-aligned currents and ionospheric electric fields

    NASA Technical Reports Server (NTRS)

    Yasuhara, F.; Akasofu, S.-I.

    1977-01-01

    It is shown that the observed distribution of the ionospheric electric field can be deduced from an equation combining Ohm's law with the current continuity equation by using the 'observed' distribution of field-aligned currents as the boundary condition for two models of the ionosphere. The first model has one conductive annular ring representing the quiet-time auroral precipitation belt; the second has two conductive annular rings that simulate the discrete and diffuse auroral regions. An analysis is performed to determine how well the electric-field distribution can be reproduced. The results indicate that the first model reproduces the Sq(p)-type distribution, the second model reproduces reasonably well a substorm-type potential and ionospheric current patterns together with the Harang discontinuity, and that the distribution of field-aligned currents is the same for both models.

  14. Generation of field-aligned current in the auroral zone

    NASA Technical Reports Server (NTRS)

    Okuda, Hideo

    1991-01-01

    Generation of a magnetic field-aligned current in the auroral zone connecting the magnetospheric and ionospheric plasmas has been studied by means of a three dimensional particle simulation model. The model is of a magnetostatic variety appropriate for a low beta plasma in which the high frequency transverse displacement current has been eliminated. The simulation model is highly elongated along the magnetic field lines in order to model a highly elongated flux tube in the auroral zone. An enhanced field-aligned current was generated by injection of a magnetospheric plasma across the auroral zone magnetic field at the center of the model. Such a plasma injection may correspond to a plasmoid injection at the geomagnetic tail associated with magnetic reconnection during a substorm or a transverse plasma flow along the low latitude magnetopause boundary layer. The results of the simulations show that the field-aligned current can be enhanced over the thermal current by a factor of 5 - 10 via such injection. Associated with the enhanced current are the electrostatic ion cyclotron waves and shear Alfven waves excited in the auroral zone.

  15. Net field-aligned currents observed by Triad

    NASA Technical Reports Server (NTRS)

    Sugiura, M.; Potemra, T. A.

    1975-01-01

    From the Triad magnetometer observation of a step-like level shift in the east-west component of the magnetic field at 800 km altitude, the existence of a net current flowing into or away from the ionosphere in a current layer was inferred. The current direction is toward the ionosphere on the morning side and away from it on the afternoon side. The field aligned currents observed by Triad are considered as being an important element in the electro-dynamical coupling between the distant magnetosphere and the ionosphere. The current density integrated over the thickness of the layer increases with increasing magnetic activity, but the relation between the current density and Kp in individual cases is not a simple linear relation. An extrapolation of the statistical relation to Kp = 0 indicates existence of a sheet current of order 0.1 amp/m even at extremely quiet times. During periods of higher magnetic activity an integrated current of approximately 1 amp/m and average current density of order 0.000001 amp/sq m are observed. The location and the latitudinal width of the field aligned current layer carrying the net current very roughly agree with those of the region of high electron intensities in the trapping boundary.

  16. SuperDARN-derived plasma convection: Comparison with other data and application to field-aligned current measurements

    NASA Astrophysics Data System (ADS)

    Xu, Liang

    In this thesis, several aspects of the SuperDARN HF radar observations at high latitudes are investigated in cooperation with measurements performed by three other instruments, the Sondrestrom incoherent scatter radar, the ion drift meter onboard of the DMSP satellite and the CADI ionosonde. The first issue under investigation was consistency of plasma convection data provided by these instruments. First, routine measurements by the Goose Bay and Stokkseyri SuperDARN radar pair ("merge" velocity estimates) were compared with the Sondrestrom incoherent scatter radar data. Three different levels of assessment were used; by looking at the line-of-sight velocities, by comparing the SuperDARN vectors and corresponding Sondrestrom line-of-sight velocities and by comparing the end products of the instruments, the convection maps. All three comparisons showed overall reasonable agreement of the convection measurements though the data spread was significant and for some points a strong disagreement was obvious. Importantly, the convection map comparison showed a tendency for the SuperDARN velocities to be often less than the Sondrestrom drifts for strong flows (velocities > 1000 m/s) and larger for weak flows (velocities < 500 m/s). The second issue under investigation was the configuration of the ionospheric plasma convection and field-aligned currents (FACs) in the dayside ionosphere at small IMF B2 and By. By merging SuperDARN convection data for a number of events, it was found that convection tends to be compressed to the poleward edge of the polar cap with a noticeable decrease of the flow velociity inside the central polar cap for this condition. Also, for individual events, existence of three sheets of FACs was illustrated. FACs had similar appearance as region 1, region 2, and region 0 currents known from satellite magnetometer observations for the disturbed magnetosphere. Spatially, sheets of region 1 FACs were co-located with a line separating the plasma flow of

  17. PC-FACS.

    PubMed

    Abernethy, Amy P

    2012-03-01

    PC-FACS (Fast Article Critical Summaries for Clinicians in Palliative Care), an electronic publication of the American Academy of Hospice and Palliative Medicine, provides palliative care clinicians with concise summaries of the most important findings from more than 50 medical and scientific journals. Each month, structured summaries and insightful commentaries on 6-10 articles help palliative care clinicians stay on top of the research that is critical to contemporary practice. PC-FACS is free to AAHPM members and members can earn up to 3 CME credits quarterly. Following are excerpts from recent issues, and comments from readers are welcomed at resources@aahpm.org.

  18. PC-FACS.

    PubMed

    Zhukovsky, Donna S

    2012-04-01

    PC-FACS (Fast Article Critical Summaries for Clinicians in Palliative Care), an electronic publication of the American Academy of Hospice and Palliative Medicine, provides palliative care clinicians with concise summaries of the most important findings from more than 50 medical and scientific journals. Each month, structured summaries and insightful commentaries on 6-10 articles help palliative care clinicians stay on top of the research that is critical to contemporary practice. PC-FACS is free to AAHPM members. Following are excerpts from recent issues, and comments from readers are welcomed at resources@aahpm.org.

  19. Terrestrial ionospheric signatures of field-aligned currents

    NASA Technical Reports Server (NTRS)

    Friis-Christensen, E.

    1990-01-01

    The occurrence of traveling field-aligned current filaments and twin-vortex patterns is suggested to be related to sudden changes in solar wind dynamic pressure and/or the IMF. Greenland magnetometer observations of the cleft region magnetic perturbations associated with small-scale twin-vortex patterns show that these events occur on both sides of the magnetic local noon, contradicting Glassmeier at al.'s (1989) statistical analysis of 82 twin-vortex subauroral-latitude events obtained by the Scandinavian Magnetometer Array; the stations are closer to the ionospheric projection of the cleft earlier in magnetic local time, relative to the across-the-cleft-located Greenland stations.

  20. Three-dimensional structure of ionospheric currents produced by field-aligned currents

    NASA Astrophysics Data System (ADS)

    Takeda, M.

    1982-08-01

    Ionospheric currents caused by field-aligned currents are calculated three-dimensionally under quiet conditions at the equinox, using a magnetic field line coordinate system and with the assumption of infinite parallel conductivity. Input field-aligned currents are assumed to be distributed only in the daytime and the whole system is assumed to be symmetric about the equator. Calculated currents are comparable with those of the ionospheric dynamo in higher latitudes, but much weaker in lower latitudes including the equatorial electrojet region. Hence, if the model is valid these currents may have a considerable effect on the day-to-day variation of Sq currents in higher latitudes, but little effect on those in lower latitudes such as the counter-electrojet.

  1. Asymmetric field-aligned currents in the conjugate hemispheres

    NASA Astrophysics Data System (ADS)

    Reistad, J. P.; Ostgaard, N.; Oksavik, K.; Laundal, K. M.

    2012-12-01

    Earlier studies using simultaneous imaging from space of the Aurora Borealis (Northern Hemisphere) and Aurora Australis (Southern Hemisphere) have revealed that the aurora can experience a high degree of asymmetry between the two hemispheres. Using 19 hours of simultaneous global imaging from both hemispheres (IMAGE satellite in north and Polar satellite in south) in conjunction with the entire IMAGE WIC database, we investigate the importance of various mechanisms thought to generate the asymmetries seen in global imaging. In terms of asymmetric or interhemispheric field-aligned currents, three candidate mechanisms have been suggested: 1) Hemispheric differences in solar wind dynamo efficiency mainly controlled by IMF Bx leading to asymmetric region 1 currents; 2) conductivity differences in conjugate areas; and 3) penetration of IMF By into the closed magnetosphere possibly generating a pair of oppositely directed interhemispheric currents. From the 19 hour conjugate dataset we find that the solar wind dynamo is likely to be the most important controlling mechanism for asymmetric bright aurora in the polar part of the nightside oval. Here we present statistical analyses of candidates 1) and 3). Using the entire IMAGE WIC database, a statistical analysis of the auroral brightness distribution along and across the Northern Hemisphere oval is carried out. For each candidate, two extreme cases (+/- IMF Bx for 1) and +/- IMF By for 3)) are compared during times non-favorable for the other two mechanisms. Our results indicate that solar wind dynamo induced currents play an important role for the nightside auroral brightness in an average sense. Also, signatures of interhemispheric currents due to IMF By penetration are seen in our statistics, although this effect is somehow weaker.

  2. FACS binding assay for analysing GDNF interactions.

    PubMed

    Quintino, Luís; Baudet, Aurélie; Larsson, Jonas; Lundberg, Cecilia

    2013-08-15

    Glial cell-line derived neurotrophic factor (GDNF) is a secreted protein with great therapeutic potential. However, in order to analyse the interactions between GDNF and its receptors, researchers have been mostly dependent of radioactive binding assays. We developed a FACS-based binding assay for GDNF as an alternative to current methods. We demonstrated that the FACS-based assay using TGW cells allowed readily detection of GDNF binding and displacement to endogenous receptors. The dissociation constant and half maximal inhibitory concentration obtained were comparable to other studies using standard binding assays. Overall, this FACS-based, simple to perform and adaptable to high throughput setup, provides a safer and reliable alternative to radioactive methods.

  3. A subauroral polarization stream driven by field-aligned currents associated with precipitating energetic ions caused by EMIC waves: A case study

    NASA Astrophysics Data System (ADS)

    Yuan, Zhigang; Xiong, Ying; Qiao, Zheng; Li, Haimeng; Huang, Shiyong; Wang, Dedong; Deng, Xiaohua; Raita, Tero; Wang, Jingfang

    2016-02-01

    During the energetic ion injection event observed by the Los Alamos National Laboratory geosynchronous spacecraft, observations of the NOAA 15 satellite and Finnish network of search coil magnetometers have shown that a sharp enhancement of precipitating ring current (RC) ion flux is contributed to the pitch angle scattering caused by electromagnetic ion cyclotron (EMIC) waves. At subauroral latitudes, lower than the equatorward edge of precipitating electrons from the plasma sheet, the DMSP F13 satellite observed a subauroral polarization stream (SAPS) with a peak velocity of 688 m/s. When passing the region of EMIC waves derived by the Finnish network of search coil magnetometers and NOAA 15 satellite, the DMSP F13 satellite simultaneously observed field-aligned currents (FACs) flowing into the ionosphere and precipitating RC ions in the region of the SAPS. The peak of the SAPS accords to the minimum of the ion density in the region of the SAPS. Our result suggests that loss of RC ions caused by EMIC waves would possibly lead to FACs flowing into the ionosphere and drive the SAPS in the evening sector.

  4. 76 FR 19282 - Direct Investment Surveys: Alignment of Regulations With Current Practices

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-04-07

    ... Surveys: Alignment of Regulations With Current Practices AGENCY: Bureau of Economic Analysis, Commerce.... Current OMB 15 CFR section where identified and described Control No. 806.1 through 806.17 0608-0004...

  5. Small-scale field-aligned currents and ionospheric disturbances induced by vertical acoustic resonance during the 2015 eruption of Chile's Calbuco volcano

    NASA Astrophysics Data System (ADS)

    Aoyama, T.; Iyemori, T.; Nakanishi, K.; Nishioka, M.

    2015-12-01

    Wave packet structure of small-scale magnetic fluctuations were observed by SWARM satellites just above the volcano and it's magnetic conjugate point after the eruption of Chile's Calbuco volcano on April 22, 2015. These magnetic fluctuations in low and middle latitudes generated by small-scale field aligned currents (FACs), and have about 10-30 seconds period along the satellites' orbit [Nakanishi et al., 2014] and about 200 (340) seconds temporal scale for meridional (longitudinal) magnetic components [Iyemori et al., 2015]. We also observed ionospheric disturbances and ground geomagnetic fluctuations just after the eruption. The 4-min period oscillations of total electron content (TEC) were observed by GPS receivers near the volcano. The 260 and 215 seconds spectral peaks in D component of ground based geomagnetic observation were found. Such oscillations and spectral peaks didn't exist before the eruption. All of these observations may have the same origin, i.e., vertical acoustic resonance between the ionosphere and the ground. In this presentation, we estimate the propagation velocity of the TEC oscillations and the spatial scale of the disturbance region in the E-layer where the FACs are generated by the ionospheric dynamo.

  6. Dynamics of field-aligned currents reconstructed by the ground-based and satellite data

    NASA Astrophysics Data System (ADS)

    Nikolaeva, V. D.; Kotikov, A. L.; Sergienko, T. I.

    2014-09-01

    Parameters of field-aligned currents reconstructed by ground-based measurements of magnetic field in the Scandinavian countries (IMAGE) and ionospheric conductivity for specific events of the 6 and 8 December 2004 are represented here. Ionospheric conductivity was calculated from precipitating electron flux measured at DMSP-13 satellite and electron density EISCAT incoherent scattering radar direct measurements. There is a high correlation between field-aligned currents, calculated from DMSP-13 satellite data and field-aligned currents calculated from radar measurements for the December 6, 2004 in the presence of developed ionospheric current system. The comparison of field-aligned currents, reconstructed by the proposed method, with the currents calculated by the variation of magnetic field on the DMSP satellites, confirms correctness of the offered algorithm.

  7. Influence of the electron source distribution on field-aligned currents

    NASA Astrophysics Data System (ADS)

    Bruening, K.; Goertz, C. K.

    1985-01-01

    The field-aligned current density above a discrete auroral arc has been deduced from the downward electron flux and magnetic field measurements onboard the rocket Porcupine flight 4. Both measurements show that the field-aligned current density is, in spite of decreasing peak energies towards the edge of the arc, about 4 times higher there than in the center of the arc. This can be explained by using the single particle description for an anisotropic electron source distribution.

  8. Modeling magnetic perturbation fields associated with ionospheric and geomagnetic-field-aligned currents

    NASA Astrophysics Data System (ADS)

    Richmond, A. D.; Maute, A.

    2003-04-01

    The National Center for Atmospheric Research Thermosphere-Ionosphere-Electrodynamics General-Circulation Model calculates ionospheric and geomagnetic-field-aligned electric currents produced by ionospheric wind dynamo action, taking into account magnetospheric sources at high latitudes. The associated magnetic perturbations at the ground and at low-Earth-orbit (LEO) satellite altitudes are calculated by representing the height-integrated horizontal ionospheric current as a current sheet at 110 km, connected to geomagnetic-field-aligned currents flowing into and out of the top. The horizontal sheet current can be divided into two components: a divergence-free equivalent current which, together with the associated induced Earth currents, is responsible for all of the magnetic perturbations below the current sheet, and a divergent (but not irrotational) current that closes the field-aligned currents above. We call the combination of the field-aligned currents and their closing ionospheric currents the ``nonequivalent'' currents. By definition, these produce no magnetic effect at the ground, but they do produce important magnetic effects at LEO altitudes, generally dominating the component of LEO magnetic perturbations perpendicular to the main geomagnetic field. At high magnetic latitudes the nonequivalent LEO magnetic perturbations are largely toroidal, and are associated with the strong field-aligned currents that couple the ionosphere with the outer magnetosphere. At middle and low magnetic latitudes the nonequivalent LEO magnetic perturbations are largely associated with field-aligned currents that flow between the northern and southern hemispheres, and that can produce east-west perturbations of tens of nanoteslas.

  9. FACS Sorting Mammary Stem Cells.

    PubMed

    Iriondo, Oihana; Rábano, Miriam; Vivanco, María D M

    2015-01-01

    Fluorescent-activated cell sorting (FACS) represents one of the key techniques that have been used to isolate and characterize stem cells, including cells from the mammary gland. A combination of approaches, including recognition of cell surface antigens and different cellular activities, has facilitated the identification of stem cells from the healthy mammary gland and from breast tumors. In this chapter we describe the protocol to use FACS to separate breast cancer stem cells, but most of the general principles discussed could be applied to sort other types of cells.

  10. Origins of enhanced field-aligned current at the edge of an auroral arc

    NASA Astrophysics Data System (ADS)

    Greenspan, M. E.

    1989-09-01

    Consideration is given to observations showing that the upward field-aligned currents associated with auroral arcs are larger at their edges than within the arcs, focusing on the observations made with the Porcupine F4 rocket (Bruning and Geortz, 1985). It is found that an increase in the altitude of the top of the parallel electric field region does not sufficiently explain the increase in the upward field-aligned current at the edge of the arc crossed by the Porcupine F4. Other explanations are discussed, including the adiabatic acceleration of magnetospheric electrons through a field-aligned electrostatic potential. It is suggested that an increase in the density and/or a decrease in the perpendicular temperature of the magnetospheric electron population at the edge of the arc may explain the observed increase in upward field-aligned current.

  11. The evolution of arguments regarding the existence of field-aligned currents

    NASA Technical Reports Server (NTRS)

    Dessler, A. J.

    1984-01-01

    The present understanding of Birkeland (magnetically-field-aligned) currents was not obtained by a direct, logical course. The story is rather more complex. Starting at the end of the 19th century, the Norwegian scientist Kristian Birkeland laid out a compelling case, supported by both theory and experiment, for the existence of field-aligned currents that cause both the aurora and polar geomagnetic disturbances. Sydney Chapman, the British geophysicist, became the acknowledged leader and opinion maker in the field in the decades following Birkeland's death. Chapman proposed, in contradistinction to Birkeland's ideas, equivalent currents that were restricted to flow in the ionosphere with no vertical or field-aligned components. Birkeland's ideas may have faded completely if it had not been for Hannes Alfven, who became involved well after Chapman's ideas gained predominance. Alfven kept insisting that Birkeland's current system made more sense because field-aligned currents were required to drive most of the ionospheric currents. The author became personally involved when Zmuda et al. (1966) submitted to the Journal of Geophysical Research a paper reporting satellite data showing magnetic disturbances above the ionosphere that were consistent with field-aligned Birkeland currents, but which they did not interpret as being due to such currents.

  12. Field-aligned electric currents and their measurement by the incoherent backscatter technique

    NASA Technical Reports Server (NTRS)

    Bauer, P.; Cole, K. D.; Lejeume, G.

    1975-01-01

    Field aligned electric currents flow in the magnetosphere in many situations of fundamental geophysical interest. It is shown here that the incoherent backscatter technique can be used to measure these currents when the plasma line can be observed. The technique provides a ground based means of measuring these currents which complements the rocket and satellite ones.

  13. 76 FR 39260 - Direct Investment Surveys: Alignment of Regulations With Current Practices

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-07-06

    ... Regulations With Current Practices AGENCY: Bureau of Economic Analysis, Commerce. ACTION: Final rule. SUMMARY... align its regulations for direct investment surveys with current practices. No comments on the proposed... Reduction Act. * * * * * (b) Display. Current OMB 15 CFR section where identified and described control...

  14. A numerical model of ionospheric convection derived from field-alignment currents and the corresponding conductivity

    NASA Astrophysics Data System (ADS)

    Blomberg, L. G.; Marklund, G. T.

    1991-08-01

    A numerical model for the calculation of ionospheric convection patterns from given distributions of field aligned current and ionospheric conductivity is described. The model includes a coupling between the conductivity and the field aligned current. The input contributions, the field aligned current and the conductivity, are parametrized. From the primary model output a number of other quantities can be computed: the potential in the inertial frame, the potential in the magnetospheric equatorial plane, the distribution of ionosheric current, and the Joule heating in the ionosphere. This model was used together with a technique to caculate the high latitude potential distribution prevailing during a particular event by combining information from global auroral images and local measurements of fields and particles. The model potential variation along the satellite orbit was found to be in agreement with that calculated from the measured electric field. The model was also used to study some fundamental properties of the electrodynamics of the high latitude ionosphere.

  15. Does FACS perturb gene expression?

    PubMed

    Richardson, Graham M; Lannigan, Joanne; Macara, Ian G

    2015-02-01

    Fluorescence activated cell sorting is the technique most commonly used to separate primary mammary epithelial sub-populations. Many studies incorporate this technique before analyzing gene expression within specific cellular lineages. However, to our knowledge, no one has examined the effects of fluorescence activated cell sorting (FACS) separation on short-term transcriptional profiles. In this study, we isolated a heterogeneous mixture of cells from the mouse mammary gland. To determine the effects of the isolation and separation process on gene expression, we harvested RNA from the cells before enzymatic digestion, following enzymatic digestion, and following a mock FACS sort where the entire cohort of cells was retained. A strict protocol was followed to minimize disruption to the cells, and to ensure that no subpopulations were enriched or lost. Microarray analysis demonstrated that FACS causes minimal disruptions to gene expression patterns, but prior steps in the mammary cell isolation process are followed by upregulation of 18 miRNA's and rapid decreases in their predicted target transcripts. © 2015 International Society for Advancement of Cytometry.

  16. Characteristics of ionospheric convection and field-aligned current in the dayside cusp region

    NASA Technical Reports Server (NTRS)

    Lu, G.; Lyons, L. R.; Reiff, P. H.; Denig, W. F.; Beaujardiere, O. De LA; Kroehl, H. W.; Newell, P. T.; Rich, F. J.; Opgenoorth, H.; Persson, M. A. L.

    1995-01-01

    The assimilative mapping of ionospheric electrodynamics (AMIE) technique has been used to estimate global distributions of high-latitude ionospheric convection and field-aligned current by combining data obtained nearly simultaneously both from ground and from space. Therefore, unlike the statistical patterns, the 'snapshot' distributions derived by AMIE allow us to examine in more detail the distinctions between field-aligned current systems associated with separate magnetospheric processes, especially in the dayside cusp region. By comparing the field-aligned current and ionospheric convection patterns with the corresponding spectrograms of precipitating particles, the following signatures have been identified: (1) For the three cases studied, which all had an IMF with negative y and z components, the cusp precipitation was encountered by the DMSP satellites in the postnoon sector in the northern hemisphere and in the prenoon sector in the southern hemisphere. The equatorward part of the cusp in both hemispheres is in the sunward flow region and marks the beginning of the flow rotation from sunward to antisunward. (2) The pair of field-aligned currents near local noon, i.e., the cusp/mantle currents, are coincident with the cusp or mantle particle precipitation. In distinction, the field-aligned currents on the dawnside and duskside, i.e., the normal region 1 currents, are usually associated with the plasma sheet particle precipitation. Thus the cusp/mantle currents are generated on open field lines and the region 1 currents mainly on closed field lines. (3) Topologically, the cusp/mantle currents appear as an expansion of the region 1 currents from the dawnside and duskside and they overlap near local noon. When B(sub y) is negative, in the northern hemisphere the downward field-aligned current is located poleward of the upward current; whereas in the southern hemisphere the upward current is located poleward of the downward current. (4) Under the assumption of

  17. Space Technology 5 Multi-Point Observations of Temporal Variability of Field-Aligned Currents

    NASA Technical Reports Server (NTRS)

    Le, Guan; Wang, Yongli; Slavin, James A.; Strangeway, Robert J.

    2008-01-01

    Space Technology 5 (ST5) is a three micro-satellite constellation deployed into a 300 x 4500 km, dawn-dusk, sun-synchronous polar orbit from March 22 to June 21, 2006, for technology validations. In this paper, we present a study of the temporal variability of field-aligned currents using multi-point magnetic field measurements from ST5. The data demonstrate that meso-scale current structures are commonly embedded within large-scale field-aligned current sheets. The meso-scale current structures are very dynamic with highly variable current density and/or polarity in time scales of approximately 10 min. They exhibit large temporal variations during both quiet and disturbed times in such time scales. On the other hand, the data also shown that the time scales for the currents to be relatively stable are approximately 1 min for meso-scale currents and approximately 10 min for large scale current sheets. These temporal features are obviously associated with dynamic variations of their particle carriers (mainly electrons) as they respond to the variations of the parallel electric field in auroral acceleration region. The characteristic time scales for the temporal variability of meso-scale field-aligned currents are found to be consistent with those of auroral parallel electric field.

  18. Space Technology 5 (ST-5) Observations of Field-Aligned Currents: Temporal Variability

    NASA Technical Reports Server (NTRS)

    Le, Guan

    2010-01-01

    Space Technology 5 (ST-5) is a three micro-satellite constellation deployed into a 300 x 4500 km, dawn-dusk, sun-synchronous polar orbit from March 22 to June 21, 2006, for technology validations. In this paper, we present a study of the temporal variability of field-aligned currents using multi-point magnetic field measurements from STS. The data demonstrate that masoscale current structures are commonly embedded within large-scale field-aligned current sheets. The meso-scale current structures are very dynamic with highly variable current density and/or polarity in time scales of about 10 min. They exhibit large temporal variations during both quiet and disturbed times in such time scales. On the other hand, the data also shown that the time scales for the currents to be relatively stable are about I min for meso-scale currents and about 10 min for large scale current sheets. These temporal features are obviously associated with dynamic variations of their particle carriers (mainly electrons) as they respond to the variations of the parallel electric field in auroral acceleration region. The characteristic time scales for the temporal variability of meso-scale field-aligned currents are found to be consistent with those of auroral parallel electric field.

  19. Space Technology 5 Multipoint Observations of Temporal and Spatial Variability of Field-Aligned Currents

    NASA Technical Reports Server (NTRS)

    Le, G.; Wang, Y.; Slavin, J. A.; Strangeway, R. L.

    2009-01-01

    Space Technology 5 (ST5) is a constellation mission consisting of three microsatellites. It provides the first multipoint magnetic field measurements in low Earth orbit, which enables us to separate spatial and temporal variations. In this paper, we present a study of the temporal variability of field-aligned currents using the ST5 data. We examine the field-aligned current observations during and after a geomagnetic storm and compare the magnetic field profiles at the three spacecraft. The multipoint data demonstrate that mesoscale current structures, commonly embedded within large-scale current sheets, are very dynamic with highly variable current density and/or polarity in approx.10 min time scales. On the other hand, the data also show that the time scales for the currents to be relatively stable are approx.1 min for mesoscale currents and approx.10 min for large-scale currents. These temporal features are very likely associated with dynamic variations of their charge carriers (mainly electrons) as they respond to the variations of the parallel electric field in auroral acceleration region. The characteristic time scales for the temporal variability of mesoscale field-aligned currents are found to be consistent with those of auroral parallel electric field.

  20. Statistical relationship between large-scale upward field-aligned currents and electron precipitation

    NASA Astrophysics Data System (ADS)

    Korth, Haje; Zhang, Yongliang; Anderson, Brian J.; Sotirelis, Thomas; Waters, Colin L.

    2014-08-01

    Simultaneous observations of Birkeland currents by the constellation of Iridium satellites and N2 Lyman-Birge-Hopfield (LBH) auroral emissions measured by the Global Ultraviolet Imager (GUVI) onboard the Thermosphere, Ionosphere, and Mesosphere Energetics and Dynamics (TIMED) satellite are used to establish relationships between large-scale upward field-aligned currents and electron precipitation during stable current configurations. The electron precipitation was inferred from GUVI data using a statistical relationship between LBH intensity and electron energy flux. LBH emissions with >5% contribution from protons, identified by Lyman-alpha intensity, were excluded from the analysis. The Birkeland currents were derived with a spatial resolution of 3° in latitude and 2 h in local time. For southward interplanetary magnetic field (IMF), the electron precipitation occurred primarily within and near large-scale upward currents. The correspondence was less evident for northward IMF, presumably because the spatial variability is large compared to the areas of interest so that the number of events identified is smaller and the derived statistical distributions are less reliable. At dusk, the correlation between upward current and precipitation was especially high, where a larger fraction of the electron precipitation is accelerated downward by a field-aligned potential difference. Unaccelerated electron precipitation dominated in the morning sector, presumably induced by scattering of eastward-drifting energetic electrons into the loss cone through interaction with whistler-mode waves (diffuse precipitation) rather than by field-aligned acceleration. In the upward Region 1 on the dayside, where the electron precipitation is almost exclusively due to field-aligned acceleration, a quadratic relationship between current density and electron energy flux was observed, implying a linear current-voltage relationship in this region. Current density and electron energy flux in

  1. EquiFACS: The Equine Facial Action Coding System

    PubMed Central

    Wathan, Jen; Burrows, Anne M.; Waller, Bridget M.; McComb, Karen

    2015-01-01

    Although previous studies of horses have investigated their facial expressions in specific contexts, e.g. pain, until now there has been no methodology available that documents all the possible facial movements of the horse and provides a way to record all potential facial configurations. This is essential for an objective description of horse facial expressions across a range of contexts that reflect different emotional states. Facial Action Coding Systems (FACS) provide a systematic methodology of identifying and coding facial expressions on the basis of underlying facial musculature and muscle movement. FACS are anatomically based and document all possible facial movements rather than a configuration of movements associated with a particular situation. Consequently, FACS can be applied as a tool for a wide range of research questions. We developed FACS for the domestic horse (Equus caballus) through anatomical investigation of the underlying musculature and subsequent analysis of naturally occurring behaviour captured on high quality video. Discrete facial movements were identified and described in terms of the underlying muscle contractions, in correspondence with previous FACS systems. The reliability of others to be able to learn this system (EquiFACS) and consistently code behavioural sequences was high—and this included people with no previous experience of horses. A wide range of facial movements were identified, including many that are also seen in primates and other domestic animals (dogs and cats). EquiFACS provides a method that can now be used to document the facial movements associated with different social contexts and thus to address questions relevant to understanding social cognition and comparative psychology, as well as informing current veterinary and animal welfare practices. PMID:26244573

  2. Field-aligned currents in Saturn's northern nightside magnetosphere: Evidence for interhemispheric current flow associated with planetary period oscillations

    NASA Astrophysics Data System (ADS)

    Hunt, G. J.; Cowley, S. W. H.; Provan, G.; Bunce, E. J.; Alexeev, I. I.; Belenkaya, E. S.; Kalegaev, V. V.; Dougherty, M. K.; Coates, A. J.

    2015-09-01

    We investigate the magnetic perturbations associated with field-aligned currents observed on 34 Cassini passes over the premidnight northern auroral region during 2008. These are found to be significantly modulated not only by the northern planetary-period oscillation (PPO) system, similar to the southern currents by the southern PPO system found previously, but also by the southern PPO system as well, thus providing the first clear evidence of PPO-related interhemispheric current flow. The principal field-aligned currents of the two PPO systems are found to be co-located in northern ionospheric colatitude, together with the currents of the PPO-independent (subcorotation) system, located between the vicinity of the open-closed field boundary and field lines mapping to ~9 Saturn radius (Rs) in the equatorial plane. All three systems are of comparable magnitude, ~3 MA in each PPO half-cycle. Smaller PPO-related field-aligned currents of opposite polarity also flow in the interior region, mapping between ~6 and ~9 Rs in the equatorial plane, carrying a current of ~ ±2 MA per half-cycle, which significantly reduce the oscillation amplitudes in the interior region. Within this interior region the amplitudes of the northern and southern oscillations are found to fall continuously with distance along the field lines from the corresponding hemisphere, thus showing the presence of cross-field currents, with the southern oscillations being dominant in the south, and modestly lower in amplitude than the northern oscillations in the north. As in previous studies, no oscillations related to the opposite hemisphere are found on open field lines in either hemisphere.

  3. A numerical model of ionospheric convection derived from field-aligned currents and the corresponding conductivity

    NASA Astrophysics Data System (ADS)

    Blomberg, L. G.; Marklund, G. T.

    1988-03-01

    A numerical model for the calculation of ionospheric convection patterns from given distributions of field-aligned current and ionospheric conductivity is described. The model includes a coupling between the conductivity and the field-aligned current, so that the conductivity peaks in regions of upward current, as usually observed by measurements. The model is very flexible in that the input distributions, the field-aligned current, and the conductivity are parameterized in a convenient way. From the primary model output, namely the ionospheric electrostatic potential (or convection) in the corotating frame, a number of other quantities can be computed. These include: the potential in a Sun-fixed frame (the transformation takes into account the nonalignment of the Earth's magnetic and geographic axes); the potential in the magnetospheric equatorial plane (projected using either a dipole magnetic field model or the Tsyganenko-Usmanov model, and the assumption of vanishing parallel electric field); the distribution of ionospheric (horizontal) current; and Joule heating in the ionosphere. The model was used with input data inferred from satellite measurements to calculate the high-latitude potential distribution prevailing during a particular event. The model potential variation along the satellite orbit is found to be in excellent agreement with the measured electric field.

  4. High current density and low turn-on field from aligned Cd(OH)2 nanosheets

    NASA Astrophysics Data System (ADS)

    Bagal, Vivekanand S.; Patil, Girish P.; Deore, Amol B.; Baviskar, Prashant K.; Suryawanshi, Sachin R.; More, Mahendra A.; Chavan, Padmakar G.

    2016-04-01

    High current density of 9.8 mA/cm2 was drawn at an applied field of 4.1 V/μm from aligned Cd(OH)2 nanosheets and low turn-on field of 1.4 V/μm was found for the emission current density of 10 μA/cm2. The aligned Cd(OH)2 nanosheets were synthesized by CBD technique on Cadmium foil. To the best of our knowledge this is the first report on the field emission studies of Cd(OH)2 nanosheets. Simple synthesis route coupled with superior field emission properties indicate the possible use of Cd(OH)2 nanosheets for micro/nanoelectronic devices.

  5. On the relationship between morning sector irregular magnetic pulsations and field aligned currents

    NASA Technical Reports Server (NTRS)

    Engebretson, M. J.; Cahill, L. J., Jr.; Potemra, T. A.; Zanetti, L. J.; Arnoldy, R. L.; Mende, S. B.; Rosenberg, T. J.

    1984-01-01

    For three magnetically disturbed days in early 1980, data from south polar masses of the Magsat satellite are compared with data from search coil magnetometer, riometer, and photometer instrumentation at Siple, Antarctica. It is found that during each Magsat polar pass in the morning sector, the level of Pi 1 activity correlates well with the intensities of three-dimensional current systems. Fine structure is often observed in the field-aligned currents during periods of intense Pi activity. Among the Birkeland currents are 2-s to 10-s (16-80 km) structured perturbations; these are evident in the transverse components of the field and are thought to indicate filamentary currents. Pi 1 amplitudes are found to be considerably larger when region 2 Birkeland currents are overhead than when they are not. In one case, detailed features are identified in the high-resolution Magsat magnetic field data that may be current fluctuations related to asymmetric Pi 1.

  6. Relationships between field-aligned currents, electric fields, and particle precipitation as observed by Dynamics Explorer-2

    NASA Technical Reports Server (NTRS)

    Sugiura, M.; Iyemori, T.; Hoffman, R. A.; Maynard, N. C.; Burch, J. L.; Winningham, J. D.

    1984-01-01

    The relationships between field-aligned currents, electric fields, and particle fluxes are determined using observations from the polar orbiting low-altitude satellite Dynamics Explorer-2. It is shown that the north-south electric field and the east-west magnetic field components are usually highly correlated in the field-aligned current regions. This proportionality observationally proves that the field-aligned current equals the divergence of the height-integrated ionospheric Pedersen current in the meridional plane to a high degree of approximation. As a general rule, in the evening sector the upward field-aligned currents flow in the boundary plasma sheet region and the downward currents flow in the central plasma sheet region. The current densities determined independently from the plasma and magnetic field measurements are compared. Although the current densities deduced from the two methods are in general agreement, the degree and extent of the agreement vary in individual cases.

  7. Relationships between field-aligned currents, electric fields and particle precipitation as observed by dynamics Explorer-2

    NASA Technical Reports Server (NTRS)

    Sugiura, M.; Iyemori, T.; Hoffman, R. A.; Maynard, N. C.; Burch, J. L.; Winningham, J. D.

    1983-01-01

    The relationships between field-aligned currents, electric fields, and particle fluxes are determined using observations from the polar orbiting low-altitude satellite Dynamics Explorer-2. It is shown that the north-south electric field and the east-west magnetic field components are usually highly correlated in the field-aligned current regions. This proportionality observationally proves that the field-aligned current equals the divergence of the height-integrated ionospheric Pedersen current in the meridional plane to a high degree of approximation. As a general rule, in the evening sector the upward field-aligned currents flow in the boundary plasma sheet region and the downward currents flow in the central plasma sheet region. The current densities determined independently from the plasma and magnetic field measurements are compared. Although the current densities deduced from the two methods are in general agreement, the degree and extent of the agreement vary in individual cases.

  8. Dynamics of the field-aligned current distribution during a magnetic storm: AMPERE

    NASA Astrophysics Data System (ADS)

    Vassiliadis, D.; Tepke, B. P.

    2015-12-01

    Field-aligned current density in the ionosphere can be used to identify the location and intensity of solar wind-magnetosphere-ionosphere coupling, and help identify the large-scale processes that contribute to this coupling. The Active Magnetosphere and Planetary Electrodynamics Response Experiment (AMPERE) mission effectively provides high-resolution spatial and temporal measurements of the radial current during magnetic storms. These in situ measurements are complementary to magnetic remote sensing from the ground using magnetometer arrays. Here we examine two storms, on May 29, 2010 and August 5, 2011, using AMPERE and solar wind data. We identify the regions whose radial current density has the greatest correlation with solar wind coupling functions and individual magnetic and plasma variables. We develop a statistical model of the radial current density from the magnetospheric and solar wind data which is then used to represent regions of outflowing and inflowing current in the two hemispheres. While the model is limited in representing high spatial resolution, time series of regional and global field-aligned current are reproduced with relatively large correlation coefficients (0.70-0.90) in each event.

  9. Field-aligned currents observed in the vicinity of a moving auroral arc

    NASA Astrophysics Data System (ADS)

    Goertz, C. K.; Bruening, K.

    1984-09-01

    The sounding rocket Porcupine F4 was launched into an auroral arc and the field aligned currents were independently deduced from magnetic field measurements; the horizontal current deduced from the electric field measurements and height integrated conductivity calculations; and measurements of electron fluxes. Above the arc the different methods agree. The magnetosphere acts as generator and the ionosphere as load. North of the arc, the first two methods disagree, possibly due to an Alfven wave carrying the observed magnetic field perturbation. The energy flow is out of the ionosphere. Here the ionosphere acts as generator and the magnetosphere as load.

  10. Field-aligned currents observed in the vicinity of a moving auroral arc

    NASA Technical Reports Server (NTRS)

    Goertz, C. K.; Bruening, K.

    1984-01-01

    The sounding rocket Porcupine F4 was launched into an auroral arc and the field aligned currents were independently deduced from magnetic field measurements; the horizontal current deduced from the electric field measurements and height integrated conductivity calculations; and measurements of electron fluxes. Above the arc the different methods agree. The magnetosphere acts as generator and the ionosphere as load. North of the arc, the first two methods disagree, possibly due to an Alfven wave carrying the observed magnetic field perturbation. The energy flow is out of the ionosphere. Here the ionosphere acts as generator and the magnetosphere as load.

  11. Field-Aligned Currents in Saturn's Southern Nightside Magnetosphere: Sub-Corotation and Planetary Period Oscillation Currents

    NASA Astrophysics Data System (ADS)

    Hunt, G. J.; Cowley, S. W. H.; Provan, G.; Bunce, E. J.; Alexeev, I. I.; Belenkaya, E. S.; Kalegaev, V. V.; Dougherty, M. K.; Coates, A. J.

    2014-12-01

    We have investigated azimuthal magnetic field data showing the presence of field-aligned current sheets on 31 similar Cassini passes during the 2008 interval of near polar orbits across Saturn's southern post-midnight auroral region at radial distances ~3-5 RS. The currents are found to be strongly modulated in magnitude, form, and position by the phase of the southern planetary period oscillations (PPOs). We separate currents independent of PPO phase from PPO-related currents, by exploiting the expected anti-symmetry of the latter with respect to PPO phase. The PPO-independent current system is thought to be associated mainly with sub-corotation of magnetospheric plasma, and consists of a weak distributed downward current over the whole polar region, enhanced downward currents in a layer mapping to the outer magnetosphere where the ionospheric conductivity is elevated, and a main upward-directed current layer ~2° wide centered at ~18° co-latitude with respect to the southern pole carrying ~2.5 MA per radian of azimuth. The latter current maps to the main region of the hot plasma in Saturn's magnetosphere and is co-located with Saturn's main UV oval in this hemisphere and local time sector. No major currents are detected mapping to the inner equatorial magnetosphere ~4-8 RS dominated by cool Enceladus plasma. The PPO-related currents map to the inner part of the hot plasma region at ~18°-20° co-latitude, and carry rotating upward and downward currents peaking at ~1.7 MA rad-1. The co-latitude of the current layers is also modulated by 1° amplitude in the PPO cycle, with maximum equatorward and poleward excursions adjacent to maximum upward and downward PPO currents, respectively. It is shown that this phasing requires the current system to be driven upward from the planetary atmosphere rather than downward from the magnetosphere.

  12. Observations of field-aligned currents, waves, and electric fields at substorm onset

    NASA Technical Reports Server (NTRS)

    Smits, D. P.; Hughes, W. J.; Cattell, C. A.; Russell, C. T.

    1986-01-01

    Substorm onsets, identified Pi 2 pulsations observed on the Air Force Geophysics Laboratory Magnetometer Network, are studied using magnetometer and electric field data from ISEE 1 as well as magnetometer data from the geosynchronous satellites GOES 2 and 3. The mid-latitude magnetometer data provides the means of both timing and locating the substorm onset so that the spacecraft locations with respect to the substorm current systems are known. During two intervals, each containing several onsets or intensifications, ISEE 1 observed field-aligned current signatures beginning simultaneously with the mid-latitude Pi 2 pulsation. Close to the earth broadband bursts of wave noise were observed in the electric field data whenever field-aligned currents were detected. One onset occurred when ISEE 1 and GOES 2 were on the same field line but in opposite hemispheres. During this onset ISEE 1 and GOES 2 saw magnetic signatures which appear to be due to conjugate field-aligned currents flowing out of the western end of the westward auroral electrojets. The ISEE 1 signature is of a line current moving westward past the spacecraft. During the other interval, ISEE 1 was in the near-tail region near the midnight meridian. Plasma data confirms that the plasma sheet thinned and subsequently expanded at onset. Electric field data shows that the plasma moved in the opposite direction to the plasma sheet boundary as the boundary expanded which implies that there must have been an abundant source of hot plasma present. The plasma motion was towards the center of the plasma sheet and earthwards and consisted of a series of pulses rather than a steady flow.

  13. Cross-tail current, field-aligned current, and B(y)

    NASA Technical Reports Server (NTRS)

    Kaufmann, Richard L.; Lu, Chen; Larson, Douglas J.

    1994-01-01

    Orbits of individual charged particles were traced in a one-dimensional magnetic field model that included a uniform cross-tail component B(sub yo). The effects of B(sub yo) on the cross-tail current distribution j(sub y)(z), the average cross-tail drift velocity(nu(sub y)z), and the average pitch angle change(delta alpha) experienced during current sheet encounters were calculated. The addition of a B(sub yo) that exceeded several tenths of one nanotesla completely eliminated all resonance effects for odd-N orbits. An odd-N resonance involves ions that enter and exit the current sheet on the same side. Pitch angles of nearly all such ions changed substantially during a typical current sheet interaction, and there was no region of large cross-tail drift velocity in the presence of a modest B(sub yo). the addition of a very large B(sub yo) guide field in the direction that enhances the natural drift produces a large j(y) and small (Delta alpha) for ions with all energies. The addition of a modest B(sub yo) had less effect near even-N resonances. In this case, ions in a small energy range were found to undergo so little change in pitch angle that particles which originated in the ionosphere would pass through the current sheet and return to the conjugate ionosphere. Finally, the cross-tail drift of ions from regions dominated by stochastic orbits to regions dominated by either resonant or guiding center orbits was considered. The ion drift speed changed substantially during such transitions. The accompanying electrons obey the guiding center equations, so electron drift is more uniform. Any difference between gradients in the fluxes associated with electron and ion drifts requires the presence of a Birkeland current in order to maintain charge neutrality. This plasma sheet region therefore serves as a current generator. The analysis predicts that the resulting Birkeland current connects to the lowest altitude equatorial regions in which ions drift to or from a point

  14. Field-aligned current associated with a distorted two-cell convection pattern during northward interplanetary magnetic field

    NASA Technical Reports Server (NTRS)

    Zhu, L.; Schunk, R. W.; Sojka, J. J.

    1991-01-01

    The influence of the ionospheric conductance on the field-aligned current associated with a distorted two-cell convection pattern during northward IMF was investigated using the Heppner-Maynard (1987) convection model and the Utah State University conductivity model described by Rasmussen and Schunk (1987). Results show that the variation of the ionospheric conductivity distribution can significantly affect the features of the field-aligned current for northward IMF, where matching or mismatching between the conductance gradient and the convection electric field plays a key role. It was found that the increase of the field-aligned current in the polar cap observed during summer is mainly due to the increasing contribution from the Pedersen current, and that the increase of the field-aligned current in both the oval region and the evening-midnight sector during the active aurora period is mainly due to the increasing contribution from the Hall current.

  15. Field-aligned currents in Saturn's southern nightside magnetosphere: Subcorotation and planetary period oscillation components

    NASA Astrophysics Data System (ADS)

    Hunt, G. J.; Cowley, S. W. H.; Provan, G.; Bunce, E. J.; Alexeev, I. I.; Belenkaya, E. S.; Kalegaev, V. V.; Dougherty, M. K.; Coates, A. J.

    2014-12-01

    We investigate magnetic data showing the presence of field-aligned magnetosphere-ionosphere coupling currents on 31 Cassini passes across Saturn's southern postmidnight auroral region. The currents are strongly modulated in magnitude, form, and position by the phase of the southern planetary period oscillations (PPOs). PPO-independent currents are separated from PPO-related currents using the antisymmetry of the latter with respect to PPO phase. PPO-independent downward currents ~1.1 MA per radian of azimuth flow over the polar open field region indicative of significant plasma subcorotation are enhanced in an outer plasma sheet layer of elevated ionospheric conductivity carrying ~0.8 MA rad-1 and close principally in an upward directed current sheet at ~17°-19° ionospheric colatitude carrying ~2.3 MA rad-1 that maps to the outer hot plasma region in Saturn's magnetosphere (equatorial range ~11-16 Saturn radii (RS)) colocated with the UV oval. Subsidiary downward and upward currents ~0.5 MA rad-1 lie at ~19°-20.5° colatitude mapping to the inner hot plasma region, but no comparable currents are detected at larger colatitudes mapping to the cool plasma regime inside ~8 RS. PPO-related currents at ~17.5°-20° colatitude overlap the main upward and subsidiary downward currents and carry comparable rotating upward and downward currents peaking at ~1.7 MA rad-1. The overall current layer colatitude is also modulated with 1° amplitude in the PPO cycle, maximum equatorward adjacent to the peak upward PPO current and maximum poleward adjacent to peak downward PPO current. This phasing requires the current system to be driven from the planetary atmosphere rather than directly from the magnetosphere.

  16. Field-aligned currents and magnetospheric convection - A comparison between MHD simulations and observations

    NASA Technical Reports Server (NTRS)

    Walker, Raymond J.; Ogino, Tatsuki

    1988-01-01

    A time-dependent three-dimensional MHD model was used to investigate the magnetospheric configuration as a function of the interplanetary magnetic field direction when it was in the y-z plane in geocentric solar magnetospheric coordinates. The model results show large global convection cells, tail lobe cells, high-latitude polarcap cells, and low latitude cells. The field-aligned currents generated in the model magnetosphere and the model convection system are compared with observations from low-altitude polar orbiting satellites.

  17. Joule heating and field-aligned currents: Preliminary results from DE-2

    NASA Technical Reports Server (NTRS)

    Sugiura, M.

    1986-01-01

    There are three main processes by which energy is transferred from the magnetosphere to the thermosphere: (1) charge exchange of the ring current particles; (2) precipitation of charged particles; and (3) joule dissipation by the magnetosphere-ionosphere current systems. The importance of this last process has been recognized and the rate of joule heating has been estimated by many workers. Observations of the electric (E) and magnetic (B) fields from Dynamics Explorer Satellite 2 are providing a new set of data on field-aligned currents. One of the remarkable features found in these observations is the high correlation between an orthogonal pair of the E and B field components. In recent years, observational data have accrued concerning the relationship between the interplanetary magnetic field and the size of the polar cap and also about the evolution of a substorm or a magnetic storm. It is suggested that these findings be incorporated in future model calculations.

  18. Studies of Westward Electrojets and Field-Aligned Currents in the Magnetotail during Substorms: Implications for Magnetic Field Models

    NASA Technical Reports Server (NTRS)

    1996-01-01

    Our studies elucidated the relationship between the auroral arcs and magnetotail phenomena. One paper examined particle energization in the source region of the field-aligned currents that intensify at substorm onset when the arc brightens to form the westward electrojet. A second paper examined the relationship between the precipitating particles in the arcs, the location of the westward electrojet, and magnetospheric source regions. Two earlier papers also investigated the roles that field aligned currents and particle acceleration have during substorms.

  19. Validation of a new plasmapause model derived from CHAMP field-aligned current signatures

    NASA Astrophysics Data System (ADS)

    Heilig, Balázs; Darrouzet, Fabien; Vellante, Massimo; Lichtenberger, János; Lühr, Hermann

    2014-05-01

    Recently a new model for the plasmapause location in the equatorial plane was introduced based on magnetic field observations made by the CHAMP satellite in the topside ionosphere (Heilig and Lühr, 2013). Related signals are medium-scale field-aligned currents (MSFAC) (some 10km scale size). An empirical model for the MSFAC boundary was developed as a function of Kp and MLT. The MSFAC model then was compared to in situ plasmapause observations of IMAGE RPI. By considering this systematic displacement resulting from this comparison and by taking into account the diurnal variation and Kp-dependence of the residuals an empirical model of the plasmapause location that is based on MSFAC measurements from CHAMP was constructed. As a first step toward validation of the new plasmapause model we used in-situ (Van Allen Probes/EMFISIS, Cluster/WHISPER) and ground based (EMMA) plasma density observations. Preliminary results show a good agreement in general between the model and observations. Some observed differences stem from the different definitions of the plasmapause. A more detailed validation of the method can take place as soon as SWARM and VAP data become available. Heilig, B., and H. Lühr (2013) New plasmapause model derived from CHAMP field-aligned current signatures, Ann. Geophys., 31, 529-539, doi:10.5194/angeo-31-529-2013

  20. Time-dependent modeling of field-aligned current-generated ion transients in the polar wind

    NASA Technical Reports Server (NTRS)

    Gombosi, T. I.; Nagy, A. F.

    1989-01-01

    The time evolution of field-aligned current-generated transient features in the high-latitude ionosphere is investigated. Ionospheric return currents generate significant downward heavy ion flows in the topside ionosphere with peak values well exceeding 10 to the 8th sq cm/s. When the return current ceases, the polar ionosphere rapidly returns to its previous equilibrium state. During the recovery phase of the return current event, an upward propagating heavy ion transient is formed, which is mainly characterized by a relatively short O(+) upwelling event. On the other hand, the H(+) escape flux remains relatively constant (within 10-20 percent) during field-aligned current events. It is also found that upward currents generate a transient heavy ion outflow, which exceeds the ambient H(+) escape flux by a factor of 3 to 5, depending on the duration and strength of the field-aligned current event.

  1. Observations of field-aligned currents, particles, and plasma drift in the polar cusps near solstice

    NASA Technical Reports Server (NTRS)

    Bythrow, P. F.; Potemra, T. A.; Hoffman, R. A.

    1982-01-01

    Magnetic perturbations observed by the TRIAD magnetometer within two hours of an AE-C spacecraft pass provide field-aligned current data, from the same local time in the northern hemisphere, for a study of the polar cusp. The AE-C spinning mode has allowed the use of the Z-axis magnetometer for Birkeland current observations, in conjunction with particle and drift measurements. The average B(z) were found to be 1.9 nT and -1.1 nT during the first two hourly intervals on January 15, 1977. Measurements from the low energy electron experiment revealed intense fluxes of soft, cusp-like 100 eV Maxwellian electrons throughout the prenoon polar cap. The upward directed current can be identified as the dominant cusp current appropriate for B(y) values lower than zero, while the downward directed current, which has the appropriate sign of a dayside region 1 current, is observed to lie entirely within a westerly, antisunward-convecting plasma.

  2. Terminator field-aligned current system: A new finding from model-assimilated data set (MADS)

    NASA Astrophysics Data System (ADS)

    Zhu, L.; Schunk, R. W.; Scherliess, L.; Sojka, J. J.; Gardner, L. C.; Eccles, J. V.; Rice, D.

    2013-12-01

    Physics-based data assimilation models have been recognized by the space science community as the most accurate approach to specify and forecast the space weather of the solar-terrestrial environment. The model-assimilated data sets (MADS) produced by these models constitute an internally consistent time series of global three-dimensional fields whose accuracy can be estimated. Because of its internal consistency of physics and completeness of descriptions on the status of global systems, the MADS has also been a powerful tool to identify the systematic errors in measurements, reveal the missing physics in physical models, and discover the important dynamical physical processes that are inadequately observed or missed by measurements due to observational limitations. In the past years, we developed a data assimilation model for the high-latitude ionospheric plasma dynamics and electrodynamics. With a set of physical models, an ensemble Kalman filter, and the ingestion of data from multiple observations, the data assimilation model can produce a self-consistent time-series of the complete descriptions of the global high-latitude ionosphere, which includes the convection electric field, horizontal and field-aligned currents, conductivity, as well as 3-D plasma densities and temperatures, In this presentation, we will show a new field-aligned current system discovered from the analysis of the MADS produced by our data assimilation model. This new current system appears and develops near the ionospheric terminator. The dynamical features of this current system will be described and its connection to the active role of the ionosphere in the M-I coupling will be discussed.

  3. Transient, small-scale field-aligned currents in the plasma sheet boundary layer during storm time substorms.

    PubMed

    Nakamura, R; Sergeev, V A; Baumjohann, W; Plaschke, F; Magnes, W; Fischer, D; Varsani, A; Schmid, D; Nakamura, T K M; Russell, C T; Strangeway, R J; Leinweber, H K; Le, G; Bromund, K R; Pollock, C J; Giles, B L; Dorelli, J C; Gershman, D J; Paterson, W; Avanov, L A; Fuselier, S A; Genestreti, K; Burch, J L; Torbert, R B; Chutter, M; Argall, M R; Anderson, B J; Lindqvist, P-A; Marklund, G T; Khotyaintsev, Y V; Mauk, B H; Cohen, I J; Baker, D N; Jaynes, A N; Ergun, R E; Singer, H J; Slavin, J A; Kepko, E L; Moore, T E; Lavraud, B; Coffey, V; Saito, Y

    2016-05-28

    We report on field-aligned current observations by the four Magnetospheric Multiscale (MMS) spacecraft near the plasma sheet boundary layer (PSBL) during two major substorms on 23 June 2015. Small-scale field-aligned currents were found embedded in fluctuating PSBL flux tubes near the separatrix region. We resolve, for the first time, short-lived earthward (downward) intense field-aligned current sheets with thicknesses of a few tens of kilometers, which are well below the ion scale, on flux tubes moving equatorward/earthward during outward plasma sheet expansion. They coincide with upward field-aligned electron beams with energies of a few hundred eV. These electrons are most likely due to acceleration associated with a reconnection jet or high-energy ion beam-produced disturbances. The observations highlight coupling of multiscale processes in PSBL as a consequence of magnetotail reconnection.

  4. Current mechanism and band alignment of Al (Pt)/HfGdO/Ge capacitors

    NASA Astrophysics Data System (ADS)

    Junjun, Yuan; Zebo, Fang; Yanyan, Zhu; Bo, Yao; Shiyan, Liu; Gang, He; Yongsheng, Tan

    2016-03-01

    HfGdO high-k gate dielectric thin films were deposited on Ge substrates by radio-frequency magnetron sputtering. The current transport properties of Al(Pt)/HfGdO/Ge MOS structures were investigated at room temperature. The results show that the leakage currents are mainly induced by Frenkel-Poole emissions at a low electric field. At a high electric field, Fowler Nordheim tunneling dominates the current. The energy barriers were obtained by analyzing the Fowler Nordheim tunneling characteristics, which are 1.62 eV and 2.77 eV for Al/HfGdO and Pt/HfGdO, respectively. The energy band alignments for metal/HfGdO/Ge capacitors are summarized together with the results of current-voltage and the x-ray photoelectron spectroscopy. Project supported by the Natural Science Foundation of Shanghai (No. 15ZR1418700), the Natural Science Foundation of China (Nos. 51272159, 61405118), and the Natural Science Foundation of Zhejiang (Nos. LY15A040001, LQ13A040004).

  5. Field line twist and field-aligned currents in an axially symmetric equilibrium magnetosphere. [of Uranus

    NASA Technical Reports Server (NTRS)

    Voigt, Gerd-Hannes

    1986-01-01

    Field-aligned Birkeland currents and the angle of the magnetic line twist were calculated for an axially symmetric pole-on magnetosphere (assumed to be in MHD equilibrium). The angle of the field line twist was shown to have a strong radial dependence on the axisymmetric magnetotail as well as on the ionospheric conductivity and the amount of thermal plasma contained in closed magnetotail flux tubes. The field line twist results from the planetary rotation, which leads to the development of a toroidal magnetic B-sub-phi component and to differentially rotating magnetic field lines. It was shown that the time development of the toroidal magnetic B-sub-phi component and the rotation frequency are related through an induction equation.

  6. An MHD simulation of By-dependent magnetospheric convection and field-aligned currents during northward IMF

    NASA Technical Reports Server (NTRS)

    Ogino, T.; Walker, R. J.; Ashour-Abdalla, M.; Dawson, J. M.

    1985-01-01

    A three-dimensional MHD simulation code is used to model the magnetospheric configuration when the IMF has both a northward B(z) component and a B(y) component in the east-west direction. Projections of the plasma pressure, the field-aligned velocity, the field-aligned vorticity, and the field-aligned current along the magnetic field lines into the northern ionosphere are shown and discussed. Cross-sectional patterns of these parameters are shown. The results demonstrate that the B(y) component of the IMF strongly influences the plasma sheet configuration and the magnetospheric convection pattern.

  7. KINETIC ALFVEN WAVE INSTABILITY DRIVEN BY FIELD-ALIGNED CURRENTS IN SOLAR CORONAL LOOPS

    SciTech Connect

    Chen, L.; Wu, D. J. E-mail: djwu@pmo.ac.cn

    2012-08-01

    Magneto-plasma loops, which trace closed solar magnetic field lines, are the primary structural elements of the solar corona. Kinetic Alfven wave (KAW) can play an important role in inhomogeneous heating of these magneto-plasma structures in the corona. By the use of a low-frequency kinetic dispersion equation, which is presented in this paper and is valid in a finite-{beta} plasma with Q < {beta} < 1 plasma (where {beta} is the kinetic to magnetic pressure ratio and Q = m{sub e} /m{sub i} is the mass ratio of electrons to ions), KAW instability driven by a field-aligned current in the current-carrying loops in the solar corona is investigated. The results show that the KAW instability can occur in wave number regimes 0 < k{sub z} < k{sup c}{sub z} and 0 < k < k{sup c} , and that the critical wave numbers k{sup c}{sub z} and k{sup c} and the growth rate both considerably increase as the drift velocity V{sub D} of the current-carrying electrons increases in the loops. In particular, for typical parameters of the current-carrying loops in the solar corona this instability mechanism results in a high growth rate of KAWs, {omega}{sub i} {approx} 0.01-0.1{omega}{sub ci} {approx} 10{sup 3}-10{sup 4} s{sup -1}. The results are of importance in understanding the physics of the electric current dissipation and plasma heating of the current-carrying loops in the solar corona.

  8. Optical Alignment of the JWST ISIM to the OTE Simulator (OSIM): Current Concept and Design Studies

    NASA Technical Reports Server (NTRS)

    Frey, Bradley J.; Davila, Pamela S.; Marsh, James M.; Ohl, Raymond G.; Sullivan, Joseph

    2007-01-01

    The James Webb Space Telescope's (JWST) Integrated Science Instrument Module (ISIM) is the scientific payload of the observatory and contai ns four science instruments. During alignment and test of the integrated ISIM (i.e. ISIM + science instruments) at NASA's Goddard Space Fli ght Center (GSFC), the Optical telescope element SIMulator (OSIM) wil l be used to optically stimulate the science instruments to verify their operation and performance. In this paper we present the design of two cryogenic alignment fixtures that will be used to determine and verify the proper alignment of OSIM to ISIM during testing at GSFC. The se fixtures, the Master Alignment Target Fixture (MATF) and the ISIM Alignment Target Fixture (IATF), will provide continuous, 6 degree of freedom feedback to OSIM during initial ambient alignment as well as during cryogenic vacuum testing.

  9. Ion gyroradius effects on Alfvenic field aligned currents and electron energization in planetary magnetospheres.

    NASA Astrophysics Data System (ADS)

    Damiano, P. A.; Johnson, J.; Chaston, C. C.; Fox, W. R., II; Delamere, P. A.; Stauffer, B. H.

    2015-12-01

    Alfvenic current systems are a ubiquitous feature of planetary magnetospheres that can be generated by several mechanisms including the braking of flows (e.g. associated with reconnection at substorm onset) and via moon-planet interactions. The energetic electrons needed to carry the field-aligned currents are generally thought to be accelerated on either electron inertial or ion acoustic gyroradius scale lengths in the limit of inertial and kinetic Alfven waves respectively. Recent 2D dipolar hybrid gyrofluid-kinetic electron simulations of kinetic Alfven waves (Damiano et al., JGR, 2015), associated with the braking of fast flows in the terrestrial magnetotail, have illustrated that hot ion effects can act to limit the extent of the parallel current (all along the field line) from what would be expected in the cold ion limit. This correspondingly affects the characteristics of the electron energization, reducing both the parallel elongation in the electron distribution function associated with electron trapping in the kinetic Alfven wave regime and the extent of high energy tails evident in the inertial Alfven wave region above the ionosphere. In this presentation, we build on these initial simulation results analyzing the characteristics of the parallel current system and electron acceleration (associated with both inertial and kinetic Alfven waves) for a range of wave amplitudes and ratios of the electron to ion temperature. One finding is that for a given ion temperature, increasing wave amplitude recovers some of the features of the electron energization evident in the cold ion limit, but this is modulated by the effect of wave energy dispersion perpendicular to the ambient magnetic field. These results will be summarized and the relevance and extension of this work to consider Alfvenic aurora in the Jupiter magnetosphere (e.g. via either interchange motion or the Io-Jupiter interaction) will also be discussed.

  10. Space Technology 5 (ST-5) Multipoint Observations of Temporal and Spatial Variability of Field-Aligned Currents

    NASA Technical Reports Server (NTRS)

    Le, Guan

    2010-01-01

    Space Technology 5 (ST-5) is a three micro-satellite constellation deployed into a 300 x 4500 km, dawn-dusk, sun-synchronous polar orbit from March 22 to June 21, 2006, for technology validations. In this paper, we present a study of the temporal variability of field-aligned currents using multi-point magnetic field measurements from ST5. The data demonstrate that mesoscale current structures are commonly embedded within large-scale field-aligned current sheets. The meso-scale current structures are very dynamic with highly variable current density and/or polarity in time scales of about 10 min. They exhibit large temporal variations during both quiet and disturbed times in such time scales. On the other hand, the data also shown that the time scales for the currents to be relatively stable are about 1 min for meso-scale currents and about 10 min for large scale current sheets. These temporal features are obviously associated with dynamic variations of their particle carriers (mainly electrons) as they respond to the variations of the parallel electric field in auroral acceleration region. The characteristic time scales for the temporal variability of meso-scale field-aligned currents are found to be consistent with those of auroral parallel electric field.

  11. Space Technology 5 Multi-point Observations of Field-aligned Currents: Temporal Variability of Meso-Scale Structures

    NASA Technical Reports Server (NTRS)

    Le, Guan; Wang, Yongli; Slavin, James A.; Strangeway, Robert J.

    2007-01-01

    Space Technology 5 (ST5) is a three micro-satellite constellation deployed into a 300 x 4500 km, dawn-dusk, sun-synchronous polar orbit from March 22 to June 21, 2006, for technology validations. In this paper, we present a study of the temporal variability of field-aligned currents using multi-point magnetic field measurements from ST5. The data demonstrate that meso-scale current structures are commonly embedded within large-scale field-aligned current sheets. The meso-scale current structures are very dynamic with highly variable current density and/or polarity in time scales of - 10 min. They exhibit large temporal variations during both quiet and disturbed times in such time scales. On the other hand, the data also shown that the time scales for the currents to be relatively stable are approx. 1 min for meso-scale currents and approx. 10 min for large scale current sheets. These temporal features are obviously associated with dynamic variations of their particle carriers (mainly electrons) as they respond to the variations of the parallel electric field in auroral acceleration region. The characteristic time scales for the temporal variability of meso-scale field-aligned currents are found to be consistent with those of auroral parallel electric field.

  12. Alternating current impedance spectroscopic analysis of biofunctionalized vertically-aligned silica nanospring surface for biosensor applications

    NASA Astrophysics Data System (ADS)

    Timalsina, Yukta P.

    In this dissertation, a process of vertically-aligned (silica) nanosprings (VANS) based biosensor development is presented. Alternating current (AC) impedance spectroscopy has been used to analyze sensor response as a function of saline phosphate (SP) buffer and biological solutions. The sensor is a parallel plate capacitor consisting of two glass substrates coated with indium tin oxide (ITO), where the VANS [or randomly-aligned nanosprings (RANS)] grown on one substrate serve as the dielectric spacer layer. The response of a VANS device as a function of ionic concentration in SP buffer was examined and an equivalent circuit model was developed. The results demonstrated that VANS sensors exhibited greater sensitivity to the changes in SP concentration relative to the ITO sensors, which serve as controls. The biofunctionalized VANS surface via physisorption and the cross-linker method demonstrates the repeatability, specificity, and selectivity of the binding. The physisorption of biotinylated immunoglobulin G (B-IgG) onto the VANS surface simplifies the whole sensing procedure for the detection of glucose oxidase, since the avidin-conjugated glucose oxidase (Av-GOx) can directly be immobilized on the B-IgG. The cross linker method involves the covalent attachment of antibodies onto the functionalized VANS surface via imine bond. The experiments revealed that the VANS sensor response is solely the result of the interaction of target molecule i.e. mouse IgG with the probe layer, i.e. goat antimouse IgG (GalphaM IgG). It was determined that VANS-based sensors exhibit a greater magnitude of change between successive bio-layers relative to the controls above 100 Hz, which indicates that the addition of biomolecules inhibits the diffusion of ions and changes the effective dielectric response of the VANS via biomolecular polarization. The study of ionic transport in nanosprings suggested that conductance follows a scaling law. It was demonstrated that a VANS-based device

  13. Euler potentials for two layers with non-constant current densities in the ambient magnetic field aligned to the layers

    NASA Astrophysics Data System (ADS)

    Vandas, Marek; Romashets, Eugene P.

    2016-12-01

    The Euler potentials for two current layers aligned to an ambient homogeneous magnetic field are found. Previous treatment of such a system assumed constant current density in the layers. However, the magnetic field becomes infinite at the edges. The new approach eliminates this inconsistency by introducing an inhomogeneous current density. Euler potentials are constructed semi-analytically for such a system. Charged-particle motion and trapping in it are examined by this representation. Using Euler potentials, the influence of current sheets of zero and non-zero thicknesses on energetic-particle fluxes is investigated, and characteristic flux variations near the sheets are presented. The results can be applied to Birkeland currents.

  14. Kinetic Alfven Waves Carrying Intense Field Aligned Currents: Particle Trapping and Electron Acceleration

    NASA Astrophysics Data System (ADS)

    Rankin, R.; Artemyev, A.

    2015-12-01

    It is now common knowledge that dispersive scale Alfvén waves can drive parallel electron acceleration [Lotko et al., JGR, 1998; Samson et al., Ann. Geophys., 2003; Wygant et al., JGR, 2002] and transverse ion energization in the auroral zone and inner magnetosphere [Johnson and Cheng, JGR, 2001; Chaston et al., 2004]. In this paper we show that relatively low energy electrons (plasma sheet electrons with energies ranging up to ˜100 eV) can be accelerated very efficiently as they interact nonlinearly with kinetic Alfvén waves (KAWs) that carry intense field aligned currents from the equatorial plane toward the ionosphere in the inner magnetosphere. We propose a theoretical model describing electron trapping into an effective wave potential generated by parallel wave electric fields (with perpendicular wavelengths on the order of the ion gyro-radius) and the mirror force acting on electrons as they propagate along geomagnetic field lines. We demonstrate that waves with an electric potential amplitude between ~100 - 400 V can trap and accelerate electrons to energies approaching several keVs. Trapping acceleration corresponds to conservation of the electron magnetic moment and, thus, results in a significant decrease of the electron equatorial pitch-angle with time. Analytical and numerical estimates of the maximum energy and probability of trapping are presented. We discuss the application of the proposed model in light of recent observations of electromagnetic fluctuations in the inner magnetosphere that are present during periods of strong geomagnetic activity [Chaston et al., GRL, 2014; Califf et al., JGR, 2015].

  15. Alternating current impedance spectroscopic analysis of biofunctionalized vertically-aligned silica nanospring surface for biosensor applications

    NASA Astrophysics Data System (ADS)

    Timalsina, Yukta P.; Branen, Joshua; Aston, D. Eric; Noren, Kenneth; Corti, Giancarlo; Schumacher, Randi; McIlroy, David N.

    2011-07-01

    In this study, alternating current impedance spectroscopic analysis of the biofunctionalization process of a vertically-aligned (silica) nanosprings (VANS) surface is presented. The VANS surface is functionalized with a biotinylated immunoglobulin G (B-IgG) layer formed by physisorption of B-IgG from the solution phase. Bovine serum albumin passivation of the B-IgG layer reduces additional surface adsorption by blocking the potential sites of weak bond formation via electrostatic and hydrophobic interactions. As avidin acts as a receptor of biotinylated compounds, avidin conjugated glucose oxidase (Av-GOx) binds to the B-IgG layer via biotin. This avidin-biotin bond is a stable bond with high association affinity (Ka = 1015 M-1) that withstands wide variations in chemistry and pH. An IgG layer without biotin shows no binding to the Av-GOx, indicating that bonding is through the avidin-biotin interaction. Finally, fluoroscein iso-thiocyanate (FITC) labeled biotinylated bovine serum albumin (B-BSA) added to the Av-GOx surface is used to fluorescently label Av-GOx for fluorescent measurements that allow for the correlation of surface binding with impedance measurements. Modeling of impedance spectra measured after the addition of each biological solution indicates that the bimolecular layers behave as insulating layers. The impedance spectra for the VANS-based sensor are compared to simple parallel capacitor sensors, sans VANS, and serve as controls. VANS-based sensors exhibit a greater magnitude of change between successive bio-layers relative to the controls below 10 kHz. Changes in the magnitudes of the components of the VANS equivalent circuit indicate that the addition of biological layers changes the effective dielectric response of the VANS via the impediment of ionic motion and biomolecule polarization.

  16. A Comprehensive Benchmark Study of Multiple Sequence Alignment Methods: Current Challenges and Future Perspectives

    PubMed Central

    Thompson, Julie D.; Linard, Benjamin; Lecompte, Odile; Poch, Olivier

    2011-01-01

    Multiple comparison or alignmentof protein sequences has become a fundamental tool in many different domains in modern molecular biology, from evolutionary studies to prediction of 2D/3D structure, molecular function and inter-molecular interactions etc. By placing the sequence in the framework of the overall family, multiple alignments can be used to identify conserved features and to highlight differences or specificities. In this paper, we describe a comprehensive evaluation of many of the most popular methods for multiple sequence alignment (MSA), based on a new benchmark test set. The benchmark is designed to represent typical problems encountered when aligning the large protein sequence sets that result from today's high throughput biotechnologies. We show that alignmentmethods have significantly progressed and can now identify most of the shared sequence features that determine the broad molecular function(s) of a protein family, even for divergent sequences. However,we have identified a number of important challenges. First, the locally conserved regions, that reflect functional specificities or that modulate a protein's function in a given cellular context,are less well aligned. Second, motifs in natively disordered regions are often misaligned. Third, the badly predicted or fragmentary protein sequences, which make up a large proportion of today's databases, lead to a significant number of alignment errors. Based on this study, we demonstrate that the existing MSA methods can be exploited in combination to improve alignment accuracy, although novel approaches will still be needed to fully explore the most difficult regions. We then propose knowledge-enabled, dynamic solutions that will hopefully pave the way to enhanced alignment construction and exploitation in future evolutionary systems biology studies. PMID:21483869

  17. Microfluidics microFACS for Life Detection

    NASA Technical Reports Server (NTRS)

    Platt, Donald W.; Hoover, Richard B.

    2010-01-01

    A prototype micro-scale Fluorescent Activated Cell Sorter (microFACS) for life detection has been built and is undergoing testing. A functional miniature microfluidics instrument with the ability to remotely distinguish live or dead bacterial cells from abiotic particulates in ice or permafrost of icy bodies of the solar system would be of fundamental value to NASA. The use of molecular probes to obtain the bio-signature of living or dead cells could answer the most fundamental question of Astrobiology: Does life exist beyond Earth? The live-dead fluorescent stains to be used in the microFACS instrument function only with biological cell walls. The detection of the cell membranes of living or dead bacteria (unlike PAH's and many other Biomarkers) would provide convincing evidence of present or past life. This miniature device rapidly examine large numbers of particulates from a polar ice or permafrost sample and distinguish living from dead bacteria cells and biological cells from mineral grains and abiotic particulates and sort the cells and particulates based on a staining system. Any sample found to exhibit fluorescence consistent with living cells could then be used in conjunction with a chiral labeled release experiment or video microscopy system to seek addition evidence for cellular metabolism or motility. Results of preliminary testing and calibration of the microFACS prototype instrument system with pure cultures and enrichment assemblages of microbial extremophiles will be reported.

  18. Comparison of auroral ionospheric and field-aligned currents derived from Swarm and ground magnetic field measurements

    NASA Astrophysics Data System (ADS)

    Juusola, L.; Kauristie, K.; Vanhamäki, H.; Aikio, A.; Kamp, M.

    2016-09-01

    Derivation of the auroral ionospheric currents from magnetic field measurements can produce drastically different results depending on the data and method used. We have cross tested several methods for obtaining instantaneous field-aligned and horizontal currents from Swarm satellite and International Monitor for Auroral Geomagnetic Effects (IMAGE) ground magnetic field measurements. We found that Swarm can yield latitude profiles of the east-west component of the divergence-free current density at most at ˜200 km resolution, typically resolving the electrojets. The north-south divergence-free component, on the other hand, is not always well reproduced due to the small longitudinal distance between the side-by-side flying satellite pair. Swarm can yield the field-aligned and curl-free current density at a wider range of latitude resolutions (˜7.5-200 km) than the divergence-free current density. While 7.5 km is suitable for comparison with auroras, 200 km typically resolves the Regions 1 and 2 field-aligned currents. IMAGE can yield maps of the divergence-free current density at ˜50 km resolution. Induced telluric currents should be accounted for in the derivation. Not accounting for them in the Swarm analysis, however, does not appear to introduce significant errors. Ionospheric conductances can be estimated by combining the total horizontal current density, consisting of the curl-free and divergence-free components, with the electric field measurements. Our results indicate that Swarm can only yield these at ˜200 km scale size when there is no significant dependence on longitude. However, combining the divergence-free current from IMAGE with the curl-free current and electric field from Swarm could yield conductance maps at ˜50 km resolution.

  19. The Dependence of the Strength and Thickness of Field-Aligned Currents on Solar Wind and Ionospheric Parameters

    SciTech Connect

    Johnson, Jay R.; Wing, Simon

    2014-08-01

    Sheared plasma flows at the low-latitude boundary layer correlate well with early afternoon auroral arcs and eld-aligned currents [Sonnerup, 1980; Lundin and Evans, 1985]. We present a simple analytic model that relates solar wind and ionospheric parameters to the strength and thickness of field-aligned currents in a region of sheared velocity, such as the low latitude boundary layer. We compare the predictions of the model with DMSP observations and nd remarkably good scaling of the currents with solar wind and ionospheric parameters. The sheared boundary layer thickness is inferred to be around 3000km consistent with observational studies. The analytic model provides a simple way to organize data and to infer boundary layer structures from ionospheric data.

  20. Dynamics of debye-scale nonstationary plasma structures in the region of auroral field-aligned currents

    NASA Astrophysics Data System (ADS)

    Bespalov, P. A.; Mizonova, V. G.

    2017-01-01

    We consider the formation of small-scale nonstationary plasma structures in the region of relatively strong field-aligned electric currents. The formation of these structures has been shown to be associated with the density instability developed when the current velocity exceeds a critical value. The conditions for the development of this instability can be most favorable in the region of low-density plasma. Numerical calculations have been performed for the initial nonlinear stage of the structure development. The main parameters of the structure, i.e., the times of its formation and destruction, spatial scales, and electric field, have been estimated. The features of the structures are consistent with the existing data from space experiments in the region of auroral field-aligned currents of the Earth.

  1. Space Technology 5 (ST-5) Observations of the Imbalance of Region 1 and 2 Field-Aligned Currents

    NASA Technical Reports Server (NTRS)

    Le, Guan

    2010-01-01

    Space Technology 5 (ST-5) is a three micro-satellite constellation deployed into a 300 x 4500 km, dawn-dusk, sun-synchronous polar orbit from March 22 to June 21, 2006, for technology validations. In this study, we use the in-situ magnetic field observations from Space Technology 5 mission to quantify the imbalance of Region 1 (R1) and Region 2 (R2) currents. During the three-month duration of the ST5 mission, geomagnetic conditions range from quiet to moderately active. We find that the R1 current intensity is consistently stronger than the R2 current intensity both for the dawnside and the duskside large-scale field-aligned current system. The net currents flowing into (out of) the ionosphere in the dawnside (duskside) are in the order of 5% of the total RI currents. We also find that the net currents flowing into or out of the ionosphere are controlled by the solar wind-magnetosphere interaction in the same way as the field-aligned currents themselves are. Since the net currents due to the imbalance of the R1 and R2 currents require that their closure currents flow across the polar cap from dawn to dusk as Pedersen currents, our results indicate that the total amount of the cross-polar cap Pedersen currents is in the order of approx. 0.1 MA. This study, although with a very limited dataset, is one of the first attempts to quantify the cross-polar cap Pedersen currents. Given the importance of the Joule heating due to Pedersen currents to the high-latitude ionospheric electrodynamics, quantifying the cross-polar cap Pedersen currents and associated Joule heating is needed for developing models of the magnetosphere-ionosphere coupling.

  2. Strong IMF By-Related Plasma Convection in the Ionosphere and Cusp Field-Aligned Currents Under Northward IMF Conditions

    NASA Technical Reports Server (NTRS)

    Le, G.; Lu, G.; Strangeway, R. J.; Pfaff, R. F., Jr.; Vondrak, Richard R. (Technical Monitor)

    2001-01-01

    We present in this paper an investigation of IMF-By related plasma convection and cusp field-aligned currents using FAST data and AMIE model during a prolonged interval with large positive IMF By and northward Bz conditions (By/Bz much greater than 1). Using the FAST single trajectory observations to validate the global convection patterns at key times and key locations, we have demonstrated that the AMIE procedure provides a reasonably good description of plasma circulations in the ionosphere during this interval. Our results show that the plasma convection in the ionosphere is consistent with the anti-parallel merging model. When the IMF has a strongly positive By component under northward conditions, we find that the global plasma convection forms two cells oriented nearly along the Sun-earth line in the ionosphere. In the northern hemisphere, the dayside cell has clockwise convection mainly circulating within the polar cap on open field lines. A second cell with counterclockwise convection is located in the nightside circulating across the polar cap boundary, The observed two-cell convection pattern appears to be driven by the reconnection along the anti-parallel merging lines poleward of the cusp extending toward the dusk side when IMF By/Bz much greater than 1. The magnetic tension force on the newly reconnected field lines drives the plasma to move from dusk to dawn in the polar cusp region near the polar cap boundary. The field-aligned currents in the cusp region flow downward into the ionosphere. The return field-aligned currents extend into the polar cap in the center of the dayside convection cell. The field-aligned currents are closed through the Peterson currents in the ionosphere, which flow poleward from the polar cap boundary along the electric field direction.

  3. 3D model of small-scale density cavities in the auroral magnetosphere with field-aligned current

    NASA Astrophysics Data System (ADS)

    Bespalov, P. A.; Misonova, V. G.; Savina, O. N.

    2016-09-01

    We propose a 3D model of small-scale density cavities stimulated by an auroral field-aligned current and an oscillating field-aligned current of kinetic Alfvén waves. It is shown that when the field-aligned current increases so that the electron drift velocity exceeds a value of the order of the electron thermal velocity, the plasma becomes unstable to the formation of cavities with low density and strong electric field. The condition of instability is associated with the value of the background magnetic field. In the case of a relatively weak magnetic field (where the electron gyro-radius is greater than the ion acoustic wavelength), the current instability can lead to the formation of one-dimensional cavities along the magnetic field. In the case of a stronger magnetic field (where the ion acoustic wavelength is greater than the electron gyro-radius, but still is less than the ion gyro-radius), the instability can lead to the formation of 3D density cavities. In this case, the spatial scales of the cavity, both along and across the background magnetic field, can be comparable, and at the earlier stage of the cavity formation they are of the order of the ion acoustic wavelength. Rarefactions of the cavity density are accompanied by an increase in the electric field and are limited by the pressure of bipolar electric fields that occur within them. The estimates of typical density cavity characteristics and the results of numerical solutions agree with known experimental data: small-scale structures with a sufficiently strong electric field are observed in the auroral regions with strong field-aligned current.

  4. Small spatial scale field aligned currents in middle and low latitudes as observed by the CHAMP satellite and verification of their current circuit model

    NASA Astrophysics Data System (ADS)

    Nakanishi, K.; Iyemori, T.; Luhr, H.

    2013-12-01

    The magnetic field observation by the CHAMP satellite shows the global and frequent appearance of small scale (1-5 nT) magnetic fluctuations with period around a few tens seconds along the satellites. They have the following characteristics. 1. The signal is perpendicular to the geomagnetic main field, and the amplitude of the zonal component is larger than that of the meridional component. 2. Around the dip equator, as the latitude becomes lower, the period and amplitudes of the two components perpendicular to the main field respectively tend to become longer and smaller (to nearly zero on the dip equator). 3. The amplitude of the magnetic fluctuations on the dayside is larger than that on the night side by around one order in magnitude, which highly correlates to the electric conductivity of the ionospheric dynamo layer. 4. The amplitude shows symmetry about the magnetic dip equator which indicates a magnetic conjugacy to a certain extent. 5. The amplitude shows almost no dependence on the solar wind parameters such as the IMF cone angle nor the solar wind speed, which strongly suggests no association with the Pc3 micro pulsation. 6. The amplitude also shows almost no dependence on the geomagnetic activity. 7. The amplitude has a clear seasonal dependence with topographical characteristics. They can be interpreted as the spatial structure of small scale field-aligned currents generated by the ionospheric dynamo driven by atmospheric gravity waves propagating from the lower atmosphere. The mechanism is the following; first, the gravity waves generated by the lower atmospheric disturbance propagate to the ionosphere; the neutral winds oscillate, cause ionospheric dynamo and Pedersen and Hall currents flow; because the dynamo region is finite, the currents cause polarized electric fields; and the polarized electric fields propagate along the geomagnetic filed as Alfven waves accompanied by field-aligned currents, at the same time, the ionospheric currents divert to

  5. ST5 Observations of the Imbalance of Region 1 and 2 Field-Aligned Currents and Its Implication to the Cross-Polar Cap Pedersen Currents

    NASA Technical Reports Server (NTRS)

    Le, Guan; Slavin, J. A.; Strangeway, Robert

    2011-01-01

    In this study, we use the in-situ magnetic field observations from Space Technology 5 mission to quantify the imbalance of Region 1 (R1) and Region 2 (R2) currents. During the three-month duration of the ST5 mission, geomagnetic conditions range from quiet to moderately active. We find that the R1 current intensity is consistently stronger than the R2 current intensity both for the dawnside and the duskside large-scale field-aligned current system. The net currents flowing into (out of) the ionosphere in the dawnside (duskside) are in the order of 5% of the total R1 currents. We also find that the net currents flowing into or out of the ionosphere are controlled by the solar wind-magnetosphere interaction in the same way as the field-aligned currents themselves are. Since the net currents due to the imbalance of the R1 and R2 currents require that their closure currents flow across the polar cap from dawn to dusk as Pedersen currents, our results indicate that the total amount of the cross-polar cap Pedersen currents is in the order of 0.1 MA. This study, although with a very limited dataset, is one of the first attempts to quantify the cross-polar cap Pedersen currents. Given the importance of the Joule heating due to Pedersen currents to the high-latitude ionospheric electrodynamics, quantifying the cross-polar cap Pedersen currents and associated Joule heating is needed for developing models of the magnetosphere-ionosphere coupling.

  6. Future Aeronautical Communication System (FACS): Report

    NASA Astrophysics Data System (ADS)

    Hof, H. J.

    1985-06-01

    The feasibility of a FACS design, particularly with regard to application possibilities of satellites, was investigated. It was assumed that communication between airborne stations and air traffic control centers is exclusively possible via satellites using mainly voice communication (possibly completed by data communication). It is concluded that integration possibilities of satellites are mainly limited by the airborne antenna chosen. As a solution, phase steered microstrip antenna arrays are presented. However, the use of these antennas is limited to large (long-distance) aircraft. For operational feasibility, it is concluded that communication should take place in the high frequency band.

  7. Quasi-steady current sheet structures with field-aligned flow

    NASA Technical Reports Server (NTRS)

    Birn, J.

    1992-01-01

    The paper discusses the characteristics of quasi-steady plasma and field structures with field-aligned flow. Explicit solutions are developed for modeling the compressible flow around a plasmoid in the distant magnetotail. The expected and observed plasmoid signatures are found. Field signatures outside the plasmoid are typically those of encounters of traveling compression region: a north-south signature of Bz accompanied by an enhancement of Bx.

  8. Effects of field-aligned potential drops on region-2 currents, shielding, and the decoupling of magnetospheric and ionospheric flows

    NASA Astrophysics Data System (ADS)

    Wolf, R.; Sazykin, S. Y.

    2013-12-01

    It is technically difficult to include field-aligned potential drops in simulations of inner-magnetospheric electric fields, because the potential drops are most important in thin, intense sheets of Birkeland current, which are hard to resolve accurately on a large-scale grid. However, we have found a highly idealized situation that can be treated almost completely analytically, with the numerical work confined to solving a 1D differential equation. The calculation is set up as follows: (i) in the zero-order configuration, the inner edge of the plasma-sheet ions is circular, and the ions near the inner edge all gradient/curvature-drift west at the same angular rate; (ii) the convection potential is a small perturbation, in the sense that ExB drift near the inner edge is slow compared to gradient/curvature drift; (iii) the field-aligned potential drop is proportional to the density of field-aligned current; (iv) we look for steady-state solutions. The results indicate that the field-aligned potential drop has the following effects: (i) it decreases the total region-2 current but spreads it out in latitude; (ii) it reduces the efficiency with which the inner edge shields the inner magnetosphere from magnetospheric convection; (iii) it causes particles on the magnetospheric portions of field lines near the inner edge to ExB drift zonally at different rates than particles in the topside ionosphere. Results from these quasi-analytic calculations will be compared with compared with Rice Convection Model simulations of the same idealized physical situation.

  9. Proteomics of FACS-sorted heterogeneous Corynebacterium glutamicum populations.

    PubMed

    Harst, Andreas; Albaum, Stefan P; Bojarzyn, Tanja; Trötschel, Christian; Poetsch, Ansgar

    2017-03-18

    The metabolic status of individual cells in microbial cultures can differ, being relevant for biotechnology, environmental and medical microbiology. However, it is hardly understood in molecular detail due to limitations of current analytical tools. Here, we demonstrate that FACS in combination with proteomics can be used to sort and analyze cell populations based on their metabolic state. A previously established GFP reporter system was used to detect and sort single Corynebacterium glutamicum cells based on the concentration of branched chain amino acids (BCAA) using FACS. A proteomics workflow optimized for small cell numbers was used to quantitatively compare proteomes of a ΔaceE mutant, lacking functional pyruvate dehydrogenase (PD), and the wild type. About 800 proteins could be quantified from 1,000,000 cells. In the ΔaceE mutant BCAA production was coordinated with upregulation of the glyoxylate cycle and TCA cycle to counter the lack of acetyl CoA resulting from the deletion of aceE.

  10. Avoiding Tokamak Disruptions by Applying Static Magnetic Fields That Align Locked Modes with Stabilizing Wave-Driven Currents.

    PubMed

    Volpe, F A; Hyatt, A; La Haye, R J; Lanctot, M J; Lohr, J; Prater, R; Strait, E J; Welander, A

    2015-10-23

    Nonrotating ("locked") magnetic islands often lead to complete losses of confinement in tokamak plasmas, called major disruptions. Here locked islands were suppressed for the first time, by a combination of applied three-dimensional magnetic fields and injected millimeter waves. The applied fields were used to control the phase of locking and so align the island O point with the region where the injected waves generated noninductive currents. This resulted in stabilization of the locked island, disruption avoidance, recovery of high confinement, and high pressure, in accordance with the expected dependencies upon wave power and relative phase between the O point and driven current.

  11. Spatial relationships between region 2 field-aligned currents and electron and ion precipitation in the evening sector

    NASA Technical Reports Server (NTRS)

    Fujii, R.; Hoffman, R. A.; Sugiura, M.

    1990-01-01

    The equatorward cutoff of ion and electron precipitation in relation to the evening region 2 field-aligned current during isolated substorms has been investigated using the magnetic field and plasma data obtained from the Dynamics Explorer 2 satellite. The equatorward boundaries of the region 2 currents relative to those of central plasma sheet (CPS) electron precipitation are determined predominantly by magnetic local time and subsequently change with substorm phases. With approaching midnight, the equatorward boundary of CPS electron precipitation extends toward and eventually equatorward of that of the region 2 current. On the other hand, the equatorward boundary of the region 2 current coincides well with that of 10-20 keV ion precipitation during the whole course of substorms. It is proposed that these ions originate in the so-called Alfven layer and that the location of this inner boundary determines the lower latitude boundary of the region 2 current.

  12. Direct current injection and thermocapillary flow for purification of aligned arrays of single-walled carbon nanotubes

    SciTech Connect

    Xie, Xu; Islam, Ahmad E.; Seabron, Eric; Dunham, Simon N.; Du, Frank; Lin, Jonathan; Wilson, William L.; Rogers, John A.; Wahab, Muhammad A.; Alam, Muhammad A.; Li, Yuhang; Tomic, Bojan; Huang, Jiyuan; Burns, Branden; Song, Jizhou; Huang, Yonggang

    2015-04-07

    Aligned arrays of semiconducting single-walled carbon nanotubes (s-SWNTs) represent ideal configurations for use of this class of material in high performance electronics. Development of means for removing the metallic SWNTs (m-SWNTs) in as-grown arrays represents an essential challenge. Here, we introduce a simple scheme that achieves this type of purification using direct, selective current injection through interdigitated electrodes into the m-SWNTs, to allow their complete removal using processes of thermocapillarity and dry etching. Experiments and numerical simulations establish the fundamental aspects that lead to selectivity in this process, thereby setting design rules for optimization. Single-step purification of arrays that include thousands of SWNTs demonstrates the effectiveness and simplicity of the procedures. The result is a practical route to large-area aligned arrays of purely s-SWNTs with low-cost experimental setups.

  13. Current products and practices: curriculum development in orthodontic specialist registrar training: can orthodontics achieve constructive alignment?

    PubMed

    Chadwick, S M

    2004-09-01

    This paper aims to encourage a debate on the learning outcomes that have been developed for orthodontic specialist education. In outcome-based education the learning outcomes are clearly defined. They determine curriculum content and its organization, the teaching and learning approaches, the assessment techniques and hope to focus the minds of the students on ensuring all the learning outcomes are met. In Orthodontic Specialist Registrar training, whether constructive alignment can be achieved depends on the relationship between these aspects of the education process and the various bodies responsible for their delivery in the UK.

  14. Nanofabrication of arrays of silicon field emitters with vertical silicon nanowire current limiters and self-aligned gates

    NASA Astrophysics Data System (ADS)

    Guerrera, S. A.; Akinwande, A. I.

    2016-07-01

    We developed a fabrication process for embedding a dense array (108 cm-2) of high-aspect-ratio silicon nanowires (200 nm diameter and 10 μm tall) in a dielectric matrix and then structured/exposed the tips of the nanowires to form self-aligned gate field emitter arrays using chemical mechanical polishing (CMP). Using this structure, we demonstrated a high current density (100 A cm-2), uniform, and long lifetime (>100 h) silicon field emitter array architecture in which the current emitted by each tip is regulated by the silicon nanowire current limiter connected in series with the tip. Using the current voltage characteristics and with the aid of numerical device models, we estimated the tip radius of our field emission arrays to be ≈4.8 nm, as consistent with the tip radius measured using a scanning electron microscope (SEM).

  15. The evolution of high-latitude field-aligned currents and magnetospheric dynamics in response to solar wind drivers

    NASA Astrophysics Data System (ADS)

    Bogdanova, Yulia; Vennerstrøm, Susanne; Wild, James; Korth, Haje; Lühr, Hermann; Wing, Simon; Pitout, Frederic

    2016-04-01

    While the statistical behaviour of the solar wind-magnetosphere-ionosphere system is well defined by the Dungey cycle, questions remain on the behaviour of this coupled system during extreme conditions, for example during magnetic storms or periods with long lasting northward IMF, and on how, and how fast, the system reacts to abrupt changes in the solar wind driver. Field-aligned currents play a crucial role in the dynamics of this coupled system as they provide connectivity between different regions and act as channels for energy and momentum transfer. These currents have been investigated in the last decade thanks to observations from low-orbiting satellites, such as CHAMP, Ørsted, DMSP, and the Iridium constellation. However, many previous studies concentrated on the statistical behavior of the current systems or measurements from individual observatories. In this paper we will employ data from Swarm, AMPERE, DMSP, Cluster, SuperDARN and SuperMAG to perform a multi-point study of high-latitude field-aligned current systems evolution and properties and magnetospheric dynamics in response to the solar wind driver, concentrating on the intervals of changes in the IMF orientation and extreme IMF and solar wind conditions.

  16. PSBL filed-aligned plasma structures related to auroras

    NASA Astrophysics Data System (ADS)

    Koleva, Rositza; Zelenyi, Lev; Grigorenko, Elena; Sauvaud, Jean-André

    The plasma sheet boundary layer (PSBL) is characterised by field-aligned high-velocity ion beams and it is naturally to expect field-aligned currents (FAC) associated with them. Recent statistical analysis revealed two different types of ion beams. The first type (further - Type I) are collimated in energy, accompanied by isotropic electrons and no FACs or FACs of very small current density are registered with them. Type II are powerful field-aligned ion beams with large parallel temperatures streaming along with anisotropic electron fluxes, the distributions of the latter bear the signature of a separatrix. The electrons produce a pair of FACs: at the lobeward edge directed earthward, and inside PSBL - tailward. Two different acceleration mechanisms were suggested: Type I ion beams, observed under quiet or slightly disturbed conditions, are accelerated in spatially localized resonant sources located in the current sheet in the region of closed magnetic field lines and rather far from the distant X-line; Type II ion beams, observed under active conditions, are accelerated in the vicinity of a near-Earth X-line. To prove this hypothesis we studied the auroral and ground based events related to 364 CLUSTER observations of PSBL ion beams. The auroral and ground manifestations were investigated using POLAR and IMAGE UV images and magnetograms of appropriate ground stations. As a rule in cases of Type I ion beams CLUSTER footprints are in the region of soft diffuse precipitation, poleward of the region of discreet auroral forms, and the magnetograms exhibit no or small variations in the horizontal magnetic field component. In cases of Type II beams (with currents), CLUSTER footprints are located adjacent to the brightest auroral spot and the magnetograms exhibit large negative variations of the horizontal magnetic field component. However, in considerable number of cases PSBL currents are observed under quiet or slightly disturbed conditions. CLUSTER spectrograms for

  17. The impact of intrinsic alignment on current and future cosmic shear surveys

    NASA Astrophysics Data System (ADS)

    Krause, Elisabeth; Eifler, Tim; Blazek, Jonathan

    2016-02-01

    Intrinsic alignment (IA) of source galaxies is one of the major astrophysical systematics for weak lensing surveys. Several IA models have been proposed and their impact on cosmological constraints has been examined using the Fisher information matrix in conjunction with approximate, Gaussian covariances. This paper presents the first forecasts of the impact of IA on cosmic shear measurements for future surveys using simulated likelihood analyses and covariances that include higher order moments of the density field. We consider a range of possible IA scenarios and test mitigation schemes which parametrize IA by the fraction of red galaxies, normalization, luminosity and redshift dependence of the IA signal. Compared to previous studies, we find smaller biases in time-dependent dark energy models if IA is ignored in the analysis. The amplitude and significance of these biases vary as a function of survey properties (depth, statistical uncertainties), luminosity function and IA scenario. Due to its small statistical errors and relatively shallow depth, Euclid is significantly impacted by IA. Large Synoptic Survey Telescope (LSST) and Wide-Field Infrared Survey Telescope (WFIRST) benefit from increased survey depth, while larger statistical errors for Dark Energy Survey (DES) decrease IA's relative impact on cosmological parameters. The proposed IA mitigation scheme removes parameter biases for DES, LSST and WFIRST even if the shape of the IA power spectrum is only poorly known; successful IA mitigation for Euclid requires more prior information. We explore several alternative IA mitigation strategies for Euclid; in the absence of alignment of blue galaxies we recommend the exclusion of red (IA-contaminated) galaxies in cosmic shear analyses.

  18. Correlation between magnetic and electric field perturbations in the field-aligned current regions deduced from DE 2 observations

    NASA Technical Reports Server (NTRS)

    Ishii, M.; Sugiura, M.; Iyemori, T.; Slavin, J. A.

    1992-01-01

    The satellite-observed high correlations between magnetic and electric field perturbations in the high-latitude field-aligned current regions are investigated by examining the dependence of the relationship between Delta-B and E on spatial scale, using the electric and magnetic field data obtained by DE 2 in the polar regions. The results are compared with the Pedersen conductivity inferred from the international reference ionosphere model and the Alfven wave velocity calculated from the in situ ion density and magnetic field measurements.

  19. Fibro/Adipogenic Progenitors (FAPs): Isolation by FACS and Culture.

    PubMed

    Low, Marcela; Eisner, Christine; Rossi, Fabio

    2017-01-01

    Fibro/adipogenic progenitors (FAPs ) are tissue-resident mesenchymal stromal cells (MSCs). Current literature supports a role for these cells in the homeostasis and repair of multiple tissues suggesting that FAPs may have extensive therapeutic potential in the treatment of numerous diseases. In this context, it is crucial to establish efficient and reproducible procedures to purify FAP populations from various tissues. Here, we describe a protocol for the isolation and cell culture of FAPs from murine skeletal muscle using fluorescence -activated cell sorting (FACS), which is particularly useful for experiments where high cell purity is an essential requirement. Identification, isolation, and cell culture of FAPs represent powerful tools that will help us to understand the role of these cells in different conditions and facilitate the development of safe and effective new treatments for diseases.

  20. FACS selection of valuable mutant mouse round spermatids and strain rescue via round spermatid injection.

    PubMed

    Zhu, Lian; Zhou, Wei; Kong, Peng-Cheng; Wang, Mei-Shan; Zhu, Yan; Feng, Li-Xin; Chen, Xue-Jin; Jiang, Man-Xi

    2015-06-01

    Round spermatid injection (ROSI) into mammalian oocytes can result in the development of viable embryos and offspring. One current limitation to this technique is the identification of suitable round spermatids. In the current paper, round spermatids were selected from testicular cells with phase contrast microscopy (PCM) and fluorescence-activated cell sorting (FACS), and ROSI was performed in two strains of mice. The rates of fertilization, embryonic development and offspring achieved were the same in all strains. Significantly, round spermatids selected by PCM and FACS were effectively used to rescue the infertile Pten-null mouse. The current results indicate that FACS selection of round spermatids can not only provide high-purity and viable round spermatids for use in ROSI, but also has no harmful effects on the developmental capacity of subsequently fertilized embryos. It was concluded that round spermatids selected by FACS are useful for mouse strain rederivation and rescue of infertile males; ROSI should be considered as a powerful addition to the armamentarium of assisted reproduction techniques applicable in the mouse.

  1. Northward IMF and patterns of high-latitude precipitation and field-aligned currents: The February 1986 storm

    SciTech Connect

    Rich, F.J.; Hardy, D.A.; Redus, R.H.; Gussenhoven, M.S. )

    1990-06-01

    On February 7, 1986, during a major geomagnetic storm the B{sub z} component of the interplanetary magnetic field (IMF) turned strongly northward for several hours. Following the northward turning, the equatorward boundary of the auroral zone on the nightside contracted sharply poleward and polar cap arcs were observed. The strength of the region 1 / region 2 currents decreased markedly and became immeasurably small at the time of the maximum contraction of the auroral oval. An NBZ current system was observed to grow and expand in the southern (summer) high latitude region over a period of more than 2 hours. Simultaneously, an irregular pattern of field-aligned currents was observed in the northern (winter) hemisphere. During the contraction, the latitudinal width of the auroral region mapping to the central plasma sheet (CPS) decreased dramatically while the width of the area mapping to the boundary plasma regions (BPR) in the magnetosphere increased greatly. At the time of the maximum contraction the BPR extended up to a latitude of at least 87.1{degree}. The NBZ currents expanded with and were entirely located within the BPR precipitation. Polar cap arcs were observed in both regions of BPR precipitation and polar cap precipitation and were not correlated with the location of the large-scale field-aligned currents. There was no indication of the CPS intruding to high latitudes, and thus no evidence for bifurcation of the magnetotail. The boundary between the CPS and BPR showed little change. If this implies that the boundary between open and closed field lines contracted slowly or not at all, then a significant portion of the observed BPR precipitation was observed along open field lines.

  2. Magnetosphere-ionosphere-thermosphere coupling: Effect of neutral winds on energy transfer and field-aligned current

    SciTech Connect

    Lu, G.; Richmond, A.D.; Emery, B.A.

    1995-10-01

    The assimilative mapping of ionospheric electrodynamics (AMIE) algorithm has been applied to derive the realistic time-dependent large-scale global distributions of the ionospheric convection and particle precipitation during a recent Geospace Environment Modeling (GEM) campaign period: March 28-29, 1992. The AMIE outputs are then used as the inputs of the National Center for Atmospheric Research thermosphere-ionosphere general circulation model to estimate the electrodynamic quantities in the ionosphere and thermosphere. It is found that the magnetospheric electromagnetic energy dissipated in the high-latitude ionosphere is mainly converted into Joule heating, with only a small fraction (6%) going to acceleration of thermospheric neutral winds. This study also reveals that the thermospheric winds can have significant influence on the ionospheric electrodynamics. On the average for these 2 days, the neutral winds have approximately a 28% negative effect on Joule heating and approximately a 27% negative effect on field-aligned currents. The field-aligned currents driven by the neutral wind flow in the opposite direction to those driven by the plasma convection. On the average, the global electromagnetic energy input is about 4 times larger than the particle energy input. 65 refs., 10 figs.

  3. Enhanced critical-current in P-doped BaFe2As2 thin films on metal substrates arising from poorly aligned grain boundaries

    PubMed Central

    Sato, Hikaru; Hiramatsu, Hidenori; Kamiya, Toshio; Hosono, Hideo

    2016-01-01

    Thin films of the iron-based superconductor BaFe2(As1−xPx)2 (Ba122:P) were fabricated on polycrystalline metal-tape substrates with two kinds of in-plane grain boundary alignments (well aligned (4°) and poorly aligned (8°)) by pulsed laser deposition. The poorly aligned substrate is not applicable to cuprate-coated conductors because the in-plane alignment >4° results in exponential decay of the critical current density (Jc). The Ba122:P film exhibited higher Jc at 4 K when grown on the poorly aligned substrate than on the well-aligned substrate even though the crystallinity was poorer. It was revealed that the misorientation angles of the poorly aligned samples were less than 6°, which are less than the critical angle of an iron-based superconductor, cobalt-doped BaFe2As2 (~9°), and the observed strong pinning in the Ba122:P is attributed to the high-density grain boundaries with the misorientation angles smaller than the critical angle. This result reveals a distinct advantage over cuprate-coated conductors because well-aligned metal-tape substrates are not necessary for practical applications of the iron-based superconductors. PMID:27833118

  4. The dynamics of region 1 field-aligned currents during periods of dayside and nightside reconnection

    NASA Astrophysics Data System (ADS)

    Clausen, L. B. N.; Ruohoniemi, J. M.; Baker, J. B. H.; Milan, S. E.; Coxon, J.; Anderson, B. J.

    2015-12-01

    We use current density data from the Active Magnetosphere and Planetary Electrodynamics Response Experiment (AMPERE) to identify the location of maximum region 1 current at all magnetic local times. We term this location the R1 oval. Comparing the R1 oval location with particle precipitation boundaries identified in DMSP data, we find that the R1 oval is located on average within 1° of particle signatures associated with the open/closed field line boundary (OCB) across dayside and nightside MLTs. We hence conclude that the R1 oval can be used as a proxy for the location of the OCB. Studying the amount of magnetic flux enclosed by the R1 oval during the substorm cycle, we find that the R1 oval flux is well organized by it: during the growth phase the R1 oval location moves equatorward as the amount of magnetic flux increases whereas after substorm expansion phase onset significant flux closure occurs as the R1 current location retreats to higher latitudes. For about 15 minutes after expansion phase onset the amount of open magnetic flux continues to increase indicating that dayside reconnection dominates over nightside reconnection. In the current density data we find evidence of the substorm current wedge and also show that the dayside R1 currents are stronger than their nightside counterpart during the substorm growth phase whereas after expansion phase onset the nightside R1 currents dominate. Our observations of the current distribution and OCB movement during the substorm cycle are in excellent agreement with the expanding/contracting polar cap paradigm.

  5. A fast alignment method for breast MRI follow-up studies using automated breast segmentation and current-prior registration

    NASA Astrophysics Data System (ADS)

    Wang, Lei; Strehlow, Jan; Rühaak, Jan; Weiler, Florian; Diez, Yago; Gubern-Merida, Albert; Diekmann, Susanne; Laue, Hendrik; Hahn, Horst K.

    2015-03-01

    In breast cancer screening for high-risk women, follow-up magnetic resonance images (MRI) are acquired with a time interval ranging from several months up to a few years. Prior MRI studies may provide additional clinical value when examining the current one and thus have the potential to increase sensitivity and specificity of screening. To build a spatial correlation between suspicious findings in both current and prior studies, a reliable alignment method between follow-up studies is desirable. However, long time interval, different scanners and imaging protocols, and varying breast compression can result in a large deformation, which challenges the registration process. In this work, we present a fast and robust spatial alignment framework, which combines automated breast segmentation and current-prior registration techniques in a multi-level fashion. First, fully automatic breast segmentation is applied to extract the breast masks that are used to obtain an initial affine transform. Then, a non-rigid registration algorithm using normalized gradient fields as similarity measure together with curvature regularization is applied. A total of 29 subjects and 58 breast MR images were collected for performance assessment. To evaluate the global registration accuracy, the volume overlap and boundary surface distance metrics are calculated, resulting in an average Dice Similarity Coefficient (DSC) of 0.96 and root mean square distance (RMSD) of 1.64 mm. In addition, to measure local registration accuracy, for each subject a radiologist annotated 10 pairs of markers in the current and prior studies representing corresponding anatomical locations. The average distance error of marker pairs dropped from 67.37 mm to 10.86 mm after applying registration.

  6. Alignment validation

    SciTech Connect

    ALICE; ATLAS; CMS; LHCb; Golling, Tobias

    2008-09-06

    The four experiments, ALICE, ATLAS, CMS and LHCb are currently under constructionat CERN. They will study the products of proton-proton collisions at the Large Hadron Collider. All experiments are equipped with sophisticated tracking systems, unprecedented in size and complexity. Full exploitation of both the inner detector andthe muon system requires an accurate alignment of all detector elements. Alignmentinformation is deduced from dedicated hardware alignment systems and the reconstruction of charged particles. However, the system is degenerate which means the data is insufficient to constrain all alignment degrees of freedom, so the techniques are prone to converging on wrong geometries. This deficiency necessitates validation and monitoring of the alignment. An exhaustive discussion of means to validate is subject to this document, including examples and plans from all four LHC experiments, as well as other high energy experiments.

  7. A three-dimensional MHD simulation of the interaction of the solar wind with the earth's magnetosphere - The generation of field-aligned currents

    NASA Technical Reports Server (NTRS)

    Ogino, T.

    1986-01-01

    The time-dependent interaction of the solar wind with the earth's magnetosphere is simulated using a three-dimensional MHD model. The bow shock, magnetopause, magnetotail, and plasma sheet of the magnetosphere and Birkeland field-aligned currents that are dependent on the polarity of the z component of the IMF are produced. Twin convection cells and a dawn to dusk electric potential of 30-100 kV are detected at the equator in the magnetosphere. Four types of field-aligned currents are observed: region 1, region 2, dayside magnetopause currents in the dayside cusp region, and the dayside cusp currents for southward IMF. Region 1 and 2 field-aligned currents generated for all IMF conditions are 0.6-1.0 x 10 to the 6th A and 0.15-0.61 x 10 to the 6th A, respectively. The relationship between region 1 currents and field-aligned vorticity, and region 2 currents and pressure gradients are studied. The simulated data are compared with a theoretical analysis of the field-aligned currents and good correlation is observed.

  8. FACS Analysis of Memory T Lymphocytes.

    PubMed

    Lugli, Enrico; Zanon, Veronica; Mavilio, Domenico; Roberto, Alessandra

    2017-01-01

    Flow cytometry is a powerful and robust technology for detecting and monitoring multiple markers at the level of single cells. Since its early development, flow cytometry has been used to assess heterogeneity in a cell suspension. Over the years, the increasing number of parameters that could be included in a single assay combined with physical separation by fluorescence-activated cell sorting (FACS) revealed that the T cell compartment is extremely heterogenous in terms of phenotypic diversity, functional capacity, and transcriptional regulation. While naïve T cells are fairly homogenous, diversity becomes extreme in the antigen-experienced memory compartment. The precise identification of memory subsets by the simultaneous analysis of multiple markers by flow cytometry is key not only to basic science but also for the correct immunomonitoring of patients undergoing immunotherapy or for T cell-based therapeutic approaches. In this chapter, we provide guidelines to optimize complex flow cytometry panels, to achieve correct fluorescence compensation and determine positivity for a given antigen. Correct selection of reagents and their validation is essential to the success of the assay. Despite having been developed for the identification of human naïve and memory T cell subsets, the concepts illustrated here can be applied to any experiment aiming to investigate n parameters by flow cytometry.

  9. Murine Dermal Fibroblast Isolation by FACS.

    PubMed

    Walmsley, Graham G; Maan, Zeshaan N; Hu, Michael S; Atashroo, David A; Whittam, Alexander J; Duscher, Dominik; Tevlin, Ruth; Marecic, Owen; Lorenz, H Peter; Gurtner, Geoffrey C; Longaker, Michael T

    2016-01-07

    Fibroblasts are the principle cell type responsible for secreting extracellular matrix and are a critical component of many organs and tissues. Fibroblast physiology and pathology underlie a spectrum of clinical entities, including fibroses in multiple organs, hypertrophic scarring following burns, loss of cardiac function following ischemia, and the formation of cancer stroma. However, fibroblasts remain a poorly characterized type of cell, largely due to their inherent heterogeneity. Existing methods for the isolation of fibroblasts require time in cell culture that profoundly influences cell phenotype and behavior. Consequently, many studies investigating fibroblast biology rely upon in vitro manipulation and do not accurately capture fibroblast behavior in vivo. To overcome this problem, we developed a FACS-based protocol for the isolation of fibroblasts from the dorsal skin of adult mice that does not require cell culture, thereby preserving the physiologic transcriptional and proteomic profile of each cell. Our strategy allows for exclusion of non-mesenchymal lineages via a lineage negative gate (Lin(-)) rather than a positive selection strategy to avoid pre-selection or enrichment of a subpopulation of fibroblasts expressing specific surface markers and be as inclusive as possible across this heterogeneous cell type.

  10. Onset of Antarctic Circumpolar Current 30 million years ago as Tasmanian Gateway aligned with westerlies.

    PubMed

    Scher, Howie D; Whittaker, Joanne M; Williams, Simon E; Latimer, Jennifer C; Kordesch, Wendy E C; Delaney, Margaret L

    2015-07-30

    Earth's mightiest ocean current, the Antarctic Circumpolar Current (ACC), regulates the exchange of heat and carbon between the ocean and the atmosphere, and influences vertical ocean structure, deep-water production and the global distribution of nutrients and chemical tracers. The eastward-flowing ACC occupies a unique circumglobal pathway in the Southern Ocean that was enabled by the tectonic opening of key oceanic gateways during the break-up of Gondwana (for example, by the opening of the Tasmanian Gateway, which connects the Indian and Pacific oceans). Although the ACC is a key component of Earth's present and past climate system, the timing of the appearance of diagnostic features of the ACC (for example, low zonal gradients in water-mass tracer fields) is poorly known and represents a fundamental gap in our understanding of Earth history. Here we show, using geophysically determined positions of continent-ocean boundaries, that the deep Tasmanian Gateway opened 33.5 ± 1.5 million years ago (the errors indicate uncertainty in the boundary positions). Following this opening, sediments from Indian and Pacific cores recorded Pacific-type neodymium isotope ratios, revealing deep westward flow equivalent to the present-day Antarctic Slope Current. We observe onset of the ACC at around 30 million years ago, when Southern Ocean neodymium isotopes record a permanent shift to modern Indian-Atlantic ratios. Our reconstructions of ocean circulation show that massive reorganization and homogenization of Southern Ocean water masses coincided with migration of the northern margin of the Tasmanian Gateway into the mid-latitude westerly wind band, which we reconstruct at 64° S, near to the northern margin. Onset of the ACC about 30 million years ago coincided with major changes in global ocean circulation and probably contributed to the lower atmospheric carbon dioxide levels that appear after this time.

  11. Onset of Antarctic Circumpolar Current 30 million years ago as Tasmanian Gateway aligned with westerlies

    NASA Astrophysics Data System (ADS)

    Scher, Howie D.; Whittaker, Joanne M.; Williams, Simon E.; Latimer, Jennifer C.; Kordesch, Wendy E. C.; Delaney, Margaret L.

    2015-07-01

    Earth's mightiest ocean current, the Antarctic Circumpolar Current (ACC), regulates the exchange of heat and carbon between the ocean and the atmosphere, and influences vertical ocean structure, deep-water production and the global distribution of nutrients and chemical tracers. The eastward-flowing ACC occupies a unique circumglobal pathway in the Southern Ocean that was enabled by the tectonic opening of key oceanic gateways during the break-up of Gondwana (for example, by the opening of the Tasmanian Gateway, which connects the Indian and Pacific oceans). Although the ACC is a key component of Earth's present and past climate system, the timing of the appearance of diagnostic features of the ACC (for example, low zonal gradients in water-mass tracer fields) is poorly known and represents a fundamental gap in our understanding of Earth history. Here we show, using geophysically determined positions of continent-ocean boundaries, that the deep Tasmanian Gateway opened 33.5 +/- 1.5 million years ago (the errors indicate uncertainty in the boundary positions). Following this opening, sediments from Indian and Pacific cores recorded Pacific-type neodymium isotope ratios, revealing deep westward flow equivalent to the present-day Antarctic Slope Current. We observe onset of the ACC at around 30 million years ago, when Southern Ocean neodymium isotopes record a permanent shift to modern Indian-Atlantic ratios. Our reconstructions of ocean circulation show that massive reorganization and homogenization of Southern Ocean water masses coincided with migration of the northern margin of the Tasmanian Gateway into the mid-latitude westerly wind band, which we reconstruct at 64° S, near to the northern margin. Onset of the ACC about 30 million years ago coincided with major changes in global ocean circulation and probably contributed to the lower atmospheric carbon dioxide levels that appear after this time.

  12. Interplanetary magnetic field control of mantle precipitation and associated field-aligned currents

    NASA Technical Reports Server (NTRS)

    Xu, Dingan; Kivelson, Margaret G.; Walker, Ray J.; Newell, Patrick T.; Meng, C.-I.

    1995-01-01

    Dayside reconnection, which is particularly effective for a southward interplanetary magnetic field (IMF), allows magnetosheath particles to enter the magnetosphere where they form the plasma mantle. The motions of the reconnected flux tube produce convective flows in the ionosphere. It is known that the convection patterns in the polar cap are skewed to the dawnside for a positive IMF B(sub y) (or duskside for a negative IMF B(sub y)) in the northern polar cap. Correspondingly, one would expect to find asymmetric distributions of mantle particle precipitation, but previous results have been unclear. In this paper the correlation between B(sub y) and the distribution of mantle particle precipitation is studied for steady IMF conditions with southward IMF. Ion and electron data from the Defense Meteorological Satellite Program (DMSP) F6 and F7 satellites are used to identify the mantle region and IMP 8 is used as a solar wind monitor to characterize the IMF. We study the local time extension of mantle precipitation in the prenoon and postnoon regions. We find that, in accordance with theoretical expectations for a positive (negative) IMF B(sub y), mantle particle precipitation mainly appears in the prenoon region of the northern (southern) hemisphere. The mantle particle precipitation can extend to as early as 0600 magnetic local time (MLT) in the prenoon region but extends over a smaller local time region in the postnoon sector (we did not find mantle plasma beyond 1600 MLT in our data set although coverage is scant in this area). Magnetometer data from F7 are used to determine whether part of the region 1 current flows on open field lines. We find that at times part of the region 1 sense current extends into the region of mantle particle precipitation, and is therefore on open field lines. In other cases, region 1 currents are absent on open field lines. Most of the observed features can be readily interpreted in terms of the open magnetosphere model.

  13. Electric fields and field-aligned currents in polar regions of the solar corona: 3-D MHD consideration

    NASA Technical Reports Server (NTRS)

    Pisanko, Yu. V.

    1995-01-01

    The calculation of the solar rotation electro-dynamical effects in the near-the-Sun solar wind seems more convenient from the non-inertial corotating reference frame. This implies some modification of the 3-D MHD equations generally on the base of the General Theory of Relativity. The paper deals with the search of stationary (in corotating non-inertial reference frame) solutions of the modified 3-D MHD equations for the in near-the-Sun high latitude sub-alfvenic solar wind. The solution is obtained requiring electric fields and field-aligned electric currents in the high latitude near-the-Sun solar wind. Various scenario are explored self-consistently via a number of numerical experiments. The analogy with the high latitude Earth's magnetosphere is used for the interpretation of the results. Possible observational manifestations are discussed.

  14. Artificial riboswitch selection: A FACS-based approach.

    PubMed

    Ghazi, Zohaib; Fowler, Casey C; Li, Yingfu

    2014-01-01

    Riboswitches have a number of characteristics that make them ideal regulatory elements for a wide range of synthetic biology applications. To maximize their utility, methods are required to create custom riboswitches de novo or to modify existing riboswitches to suit specific experimental needs. This chapter describes such a method, which exploits fluorescence-activated cell sorting (FACS) to quickly and efficiently sort through large libraries of riboswitch-like sequences to identify those with the desired activity. Suggestions for the experimental setup are provided, along with detailed protocols for testing and optimizing FACS conditions FACS selection steps, and follow-up assays to identify and characterize individual riboswitches.

  15. Field-aligned currents in Saturn's magnetosphere: Local time dependence of southern summer currents in the dawn sector between midnight and noon

    NASA Astrophysics Data System (ADS)

    Hunt, G. J.; Cowley, S. W. H.; Provan, G.; Bunce, E. J.; Alexeev, I. I.; Belenkaya, E. S.; Kalegaev, V. V.; Dougherty, M. K.; Coates, A. J.

    2016-08-01

    We examine and compare the magnetic field perturbations associated with field-aligned ionosphere-magnetosphere coupling currents at Saturn, observed by the Cassini spacecraft during two sequences of highly inclined orbits in 2006/2007 and 2008 under late southern summer conditions. These sequences explore the southern currents in the dawn-noon and midnight sectors, respectively, thus allowing investigation of possible origins of the local time (LT) asymmetry in auroral Saturn kilometric radiation (SKR) emissions, which peak in power at ~8 h LT in the dawn-noon sector. We first show that the dawn-noon field data generally have the same four-sheet current structure as found previously in the midnight data and that both are similarly modulated by "planetary period oscillation" (PPO) currents. We then separate the averaged PPO-independent (e.g., subcorotation) and PPO-related currents for both LT sectors by using the current system symmetry properties. Surprisingly, we find that the PPO-independent currents are essentially identical within uncertainties in the dawn-dusk and midnight sectors, thus providing no explanation for the LT dependence of the SKR emissions. The main PPO-related currents are, however, found to be slightly stronger and narrower in latitudinal width at dawn-noon than at midnight, leading to estimated precipitating electron powers, and hence emissions, that are on average a factor of ~1.3 larger at dawn-noon than at midnight, inadequate to account for the observed LT asymmetry in SKR power by a factor of ~2.7. Some other factors must also be involved, such as a LT asymmetry in the hot magnetospheric auroral source electron population.

  16. Northward IMF and patterns of high-latitude precipitation and field-aligned currents: The February 1986 storm

    SciTech Connect

    Rich, F.J.; Hardy, D.A.; Redus, R.H.; Gussenhoven, M.S.

    1990-06-01

    On February 7, 1986, during a major geomagnetic storm the Bz component of the interplanetary magnetic field (IMF) turned strongly northward for several hours. Data from the Defense Meteorological Satellite Program F6 and F7 satellites and the HILAT satellite were used to study the evolution of the pattern of high-latitude precipitation and field-aligned currents in response to this change. Prior to the northward IMF period, the auroral zone was observed down to mid-latitudes and was very wide in latitude, and strong, large-scale region 1 / region 2 currents were clearly present. Following the northward turning, the equatorward boundary of the auroral zone on the nightside contracted sharply poleward and polar cap arcs were observed. The strength of the region 1 / region 2 currents decreased markedly and became immeasurably small at the time of the maximum contraction of the auroral oval. An NBZ current system was observed to grow and expand in the southern (summer) high latitude region over a period of more than 2 hours. When the IMF turned southward again, the pattern quickly reversed. The BPR contracted; the CPS precipitation regions expanded; the equatorward boundary of the auroral oval moved to lower latitudes; the NBZ currents disappeared in less than 30 min; and the region 1 / region 2 currents reappeared. Again, the BPR/CPS boundary did not move as rapidly and thus may indicate that the changes are due more to a reconfiguration within the magnetosphere than a change in the portion of the magnetosphere that is open or closed.

  17. Structure of High Latitude Currents in Magnetosphere-Ionosphere Models

    NASA Astrophysics Data System (ADS)

    Wiltberger, M.; Rigler, E. J.; Merkin, V.; Lyon, J. G.

    2017-03-01

    Using three resolutions of the Lyon-Fedder-Mobarry global magnetosphere-ionosphere model (LFM) and the Weimer 2005 empirical model we examine the structure of the high latitude field-aligned current patterns. Each resolution was run for the entire Whole Heliosphere Interval which contained two high speed solar wind streams and modest interplanetary magnetic field strengths. Average states of the field-aligned current (FAC) patterns for 8 interplanetary magnetic field clock angle directions are computed using data from these runs. Generally speaking the patterns obtained agree well with results obtained from the Weimer 2005 computing using the solar wind and IMF conditions that correspond to each bin. As the simulation resolution increases the currents become more intense and narrow. A machine learning analysis of the FAC patterns shows that the ratio of Region 1 (R1) to Region 2 (R2) currents decreases as the simulation resolution increases. This brings the simulation results into better agreement with observational predictions and the Weimer 2005 model results. The increase in R2 current strengths also results in the cross polar cap potential (CPCP) pattern being concentrated in higher latitudes. Current-voltage relationships between the R1 and CPCP are quite similar at the higher resolution indicating the simulation is converging on a common solution. We conclude that LFM simulations are capable of reproducing the statistical features of FAC patterns.

  18. Three-dimensional MHD simulation of the interaction of the solar wind with the earth's magnetosphere: The generation of field-aligned currents

    SciTech Connect

    Ogino, T.

    1986-06-01

    A global computer simulation of the interaction of the solar wind with the earth's magnetosphere was executed by using a three-dimensional magnetohydrodynamic model. As a result, we were able to reproduce quasi-steady-state magnetospheric configurations and a Birkeland field-aligned current system which depend on the polarity of the z-italic component of the interplanetary magnetic field (IMF). Twin convection cells and a dawn to dusk electric potential of 30--100 kV appeared at the equator in the magnetosphere. Four types of field-aligned currents were observed. Region 1 and 2 field-aligned currents generated for all IMF conditions were 0.6--1.0 x 10/sup 6/ A and 0.15--0.61 x 10/sup 6/ A, respectively, in the total current. Region 1 currents at high latitudes are generated from the field-aligned vorticity at the flanks through a viscous interaction and are strengthened by a twisting of open magnetic field lines in the tail region for southward IMF. On the other hand, the low-latitude region 2 currents probably are generated mainly from the inner pressure gradient of the plasma sheet. The region 1 current obtained from the simulation was in good agreement with an estimate from our theoretical analysis of the localized Alfve-acute-accentn mode. The other two types of field-aligned currents are the dayside magnetopause currents in the dayside cusp region, which increase for northward IMF, and the dayside cusp currents for southward IMF. The cusp currents are associated with a twisting of open magnetic field lines in the magnetopause region.

  19. By-controlled convection and field-aligned currents near midnight auroral oval for northward interplanetary magnetic field

    NASA Technical Reports Server (NTRS)

    Taguchi, S.; Sugiura, M.; Iyemori, T.; Winningham, J. D.; Slavin, J. A.

    1994-01-01

    Using the Dynamics Explorer (DE) 2 magnetic and electric field and plasma data, B(sub y)- controlled convection and field-aligned currents in the midnight sector for northward interplanetary magnetic field (IMF) are examined. The results of an analysis of the electric field data show that when IMF is stable and when its magnitude is large, a coherent B(sub y)-controlled convection exists near the midnight auroral oval in the ionosphere having adequate conductivities. When B(sub y) is negative, the convection consists of a westward (eastward) plasma flow at the lower latitudes and an eastward (westward) plasma flow at the higher latitudes in the midnight sector in the northern (southern) ionosphere. When B(sub y) is positive, the flow directions are reversed. The distribution of the field-aligned currents associated with the B(sub y)-controlled convection, in most cases, shows a three-sheet structure. In accordance with the convection the directions of the three sheets are dependent on the sign of B(sub y). The location of disappearance of the precipitating intense electrons having energies of a few keV is close to the convection reversal surface. However, the more detailed relationship between the electron precipitation boundary and the convection reversal surface depends on the case. In some cases the precipitating electrons extend beyond the convection reversal surface, and in others the poleward boundary terminates at a latitude lower than the reversal surface. Previous studies suggest that the poleward boundary of the electrons having energies of a few keV is not necessarily coincident with an open/closed bounary. Thus the open/closed boundary may be at a latitude higher than the poleward boundary of the electron precipitation, or it may be at a latitude lower than the poleward boundary of the electron precipitation. We discuss relationships between the open/closed boundary and the convection reversal surface. When as a possible choice we adopt a view that the

  20. Principal component analysis of Birkeland currents determined by the Active Magnetosphere and Planetary Electrodynamics Response Experiment

    NASA Astrophysics Data System (ADS)

    Milan, S. E.; Carter, J. A.; Korth, H.; Anderson, B. J.

    2015-12-01

    Principal component analysis is performed on Birkeland or field-aligned current (FAC) measurements from the Active Magnetosphere and Planetary Electrodynamics Response Experiment. Principal component analysis (PCA) identifies the patterns in the FACs that respond coherently to different aspects of geomagnetic activity. The regions 1 and 2 current system is shown to be the most reproducible feature of the currents, followed by cusp currents associated with magnetic tension forces on newly reconnected field lines. The cusp currents are strongly modulated by season, indicating that their strength is regulated by the ionospheric conductance at the foot of the field lines. PCA does not identify a pattern that is clearly characteristic of a substorm current wedge. Rather, a superposed epoch analysis of the currents associated with substorms demonstrates that there is not a single mode of response, but a complicated and subtle mixture of different patterns.

  1. Principle Component Analysis of Birkeland Currents Determined by the Active Magnetosphere and Planetary Electrodynamics Response Experiment

    NASA Astrophysics Data System (ADS)

    Milan, S. E.; Carter, J. A.; Korth, H.; Anderson, B. J.

    2015-12-01

    Principle Component Analysis is performed on northern and southern hemisphere Birkeland or field-aligned current (FAC) measurements from the Active Magnetosphere and Planetary Electrodynamics Response Experiment (AMPERE). PCA identifies the patterns in the FACs that respond coherently to different aspects of geomagnetic activity. The region 1 and 2 current system is shown to be the most reproducible feature of the currents, followed by cusp currents associated with magnetic tension forces on newly-reconnected field lines. The cusp currents are strongly modulated by season, indicating that their strength is regulated by the ionospheric conductance at the foot of the field lines. PCA does not identify a pattern that is clearly characteristic of a substorm current wedge. Rather, a superposed epoch analysis of the currents associated with substorms demonstrates that there is not a single mode of response, but a complicated and subtle mixture of different patterns. Other interhemispheric differences are discussed.

  2. 48 CFR 301.603-72 - FAC-C and HHS SAC certification requirements.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 48 Federal Acquisition Regulations System 4 2010-10-01 2010-10-01 false FAC-C and HHS SAC... Responsibilities 301.603-72 FAC-C and HHS SAC certification requirements. (a) The FAC-C certification program is... thereunder are not required to re-take training courses, but shall follow FAC-C training requirements...

  3. Investigation of the Influence of Magnetospheric Sources of Field-Aligned Currents on the Equatorial Electric Fields

    NASA Astrophysics Data System (ADS)

    Beloushko, Konstantin; Knyazeva, Mariya

    The urgency of studying electrodynamic processes related to the influence of spatial and temporal heterogeneities of the electromagnetic field in the Earth's upper atmosphere to the functioning of modern technological systems , satellite navigation systems , radio propagation Fundamentally new is the use of various third-party electrodynamic models in the total open loop model of the atmosphere based on the Upper Atmosphere Model (UAM) [1,2]. Performing calculations on model UAM using different spatial and temporal distributions of field-aligned currents and brands Lukianova and Papitashvili. A comparison of model results with data Jicamarca Incoherent Scatter Radar (Peru). References begin{enumerate} Namgaladze A.A., Korenkov Yu.N., Klimenko V.V., Karpov I.V., Bessarab F.S., Surotkin V.A., Gluschenko T.A., Naumova N.M. Global model of the thermosphere-ionosphere-protonosphere system. Pure and Applied Geophysics. № 2/3, 127, 219-254, 1988. Namgaladze A.A., Martynenko O.V., Namgaladze A.N. Global model of the upper atmosphere with variable latitudinal steps of numerical integration, IUGG XXI General Assembly, Boulder, 1995, Abstracts, GAB41F-6, B150, 1995, and (in Russian) Geamagn. Aeron., 36, 89-95, 1996a.

  4. FACS-style detection for real-time cell viscoelastic cytometry.

    PubMed

    Kasukurti, A; Eggleton, C D; Desai, S A; Marr, D W M

    Cell mechanical properties have been established as a label-free biophysical marker of cell viability and health; however, real-time methods with significant throughput for accurately and non-destructively measuring these properties remain widely unavailable. Without appropriate labels for use with fluorescence activated cell sorters (FACS), easily implemented real-time technology for tracking cell-level mechanical properties remains a current need. Employing modulated optical forces and enabled by a low-dimensional FACS-style detection method introduced here, we present a viscoelasticity cytometer (VC) capable of real-time and continuous measurements. We demonstrate the utility of this approach by tracking the high-frequency cell physical properties of populations of chemically-modified cells at rates of ~ 1 s(-1) and explain observations within the context of a simple theoretical model.

  5. Obtaining genomes from uncultivated environmental microorganisms using FACS-based single-cell genomics.

    PubMed

    Rinke, Christian; Lee, Janey; Nath, Nandita; Goudeau, Danielle; Thompson, Brian; Poulton, Nicole; Dmitrieff, Elizabeth; Malmstrom, Rex; Stepanauskas, Ramunas; Woyke, Tanja

    2014-05-01

    Single-cell genomics is a powerful tool for exploring the genetic makeup of environmental microorganisms, the vast majority of which are difficult, if not impossible, to cultivate with current approaches. Here we present a comprehensive protocol for obtaining genomes from uncultivated environmental microbes via high-throughput single-cell isolation by FACS. The protocol encompasses the preservation and pretreatment of differing environmental samples, followed by the physical separation, lysis, whole-genome amplification and 16S rRNA-based identification of individual bacterial and archaeal cells. The described procedure can be performed with standard molecular biology equipment and a FACS machine. It takes <12 h of bench time over a 4-d time period, and it generates up to 1 μg of genomic DNA from an individual microbial cell, which is suitable for downstream applications such as PCR amplification and shotgun sequencing. The completeness of the recovered genomes varies, with an average of ∼50%.

  6. FACS purification of immunolabeled cell types from adult rat brain.

    PubMed

    Guez-Barber, Danielle; Fanous, Sanya; Harvey, Brandon K; Zhang, Yongqing; Lehrmann, Elin; Becker, Kevin G; Picciotto, Marina R; Hope, Bruce T

    2012-01-15

    Molecular analysis of brain tissue is greatly complicated by having many different classes of neurons and glia interspersed throughout the brain. Fluorescence-activated cell sorting (FACS) has been used to purify selected cell types from brain tissue. However, its use has been limited to brain tissue from embryos or transgenic mice with promoter-driven reporter genes. To overcome these limitations, we developed a FACS procedure for dissociating intact cell bodies from adult wild-type rat brains and sorting them using commercially available antibodies against intracellular and extracellular proteins. As an example, we isolated neurons using a NeuN antibody and confirmed their identity using microarray and real time PCR of mRNA from the sorted cells. Our FACS procedure allows rapid, high-throughput, quantitative assays of molecular alterations in identified cell types with widespread applications in neuroscience.

  7. Average pattern of auroral particle precipitation, its associated conductivity and field aligned currents. (Reannouncement with new availability information)

    SciTech Connect

    Hardy, D.A.; Gussenhoven, M.S.; Rich, F.J.; Brautigam, D.H.

    1991-12-31

    A series of statistical studies has been completed to determine the global pattern of auroral electron and ion precipitation and their resultant Hall and Pedersen conductivities as a function of geomagnetic activity, solar wind velocity, the orientation of the Interplanetary Magnetic Field (IMF) and season. In addition, studies were performed relating these global patterns in particle precipitation to similar global determinations of the average delta beta vector produced by the auroral field aligned currents. The data for these studies were from instruments flown on the satellites of the Defense Meteorological Satellite Program (DMSP). In all cases the studies were performed by dividing the high latitude region into a series spatial bins in Magnetic Local Time (MLT) and corrected geomagnetic latitude (CGL). One such matrix of spatial bins was created for each different value or range of values of chosen sort parameter. For geomagnetic activity the sort parameter was one of seven levels of Kp. For the IMF and solar wind velocity the sort parameters consisted of 30 paired ranges of the solar wind velocity and the beta z component of the IMF. A rough separation by the IMF beta was performed by using the IMF sector structure and Kp together as the sort parameter. Seasonal separations were made with Kp and for time periods centered on the summer and winter solstices and the equinoxes. In all cases the large DMSP data sets were used to determine the average spectrum of precipitating electrons and ions and the average delta beta vector for each spatial bin and for each sort parameter used. In this paper the authors review the results of these studies.

  8. Chemometric Analysis of Gas Chromatography – Mass Spectrometry Data using Fast Retention Time Alignment via a Total Ion Current Shift Function

    SciTech Connect

    Nadeau, Jeremy S.; Wright, Bob W.; Synovec, Robert E.

    2010-04-15

    A critical comparison of methods for correcting severely retention time shifted gas chromatography-mass spectrometry (GC-MS) data is presented. The method reported herein is an adaptation to the Piecewise Alignment Algorithm to quickly align severely shifted one-dimensional (1D) total ion current (TIC) data, then applying these shifts to broadly align all mass channels throughout the separation, referred to as a TIC shift function (SF). The maximum shift varied from (-) 5 s in the beginning of the chromatographic separation to (+) 20 s toward the end of the separation, equivalent to a maximum shift of over 5 peak widths. Implementing the TIC shift function (TIC SF) prior to Fisher Ratio (F-Ratio) feature selection and then principal component analysis (PCA) was found to be a viable approach to classify complex chromatograms, that in this study were obtained from GC-MS separations of three gasoline samples serving as complex test mixtures, referred to as types C, M and S. The reported alignment algorithm via the TIC SF approach corrects for large dynamic shifting in the data as well as subtle peak-to-peak shifts. The benefits of the overall TIC SF alignment and feature selection approach were quantified using the degree-of-class separation (DCS) metric of the PCA scores plots using the type C and M samples, since they were the most similar, and thus the most challenging samples to properly classify. The DCS values showed an increase from an initial value of essentially zero for the unaligned GC-TIC data to a value of 7.9 following alignment; however, the DCS was unchanged by feature selection using F-Ratios for the GC-TIC data. The full mass spectral data provided an increase to a final DCS of 13.7 after alignment and two-dimensional (2D) F-Ratio feature selection.

  9. Ion-beam-spurted dimethyl-sulfate-doped PEDOT:PSS composite-layer-aligning liquid crystal with low residual direct-current voltage

    NASA Astrophysics Data System (ADS)

    Liu, Yang; Lee, Ju Hwan; Seo, Dae-Shik; Li, Xiang-Dan

    2016-09-01

    Thin ion-beam (IB)-spurted dimethyl sulfate/poly(3,4-ethylenedioxythiophene) polystyrene sulfonate (DMS/PEDOT:PSS) layers with improved electro-optic performance are presented for aligning liquid crystals. IB spurting is effective for enhancing the conductivity of such layers, as well as the anchoring energy of the liquid crystals sandwiched between them. Compared with a commercial twisted-nematic cell assembled with polyimide alignment layers, the same cell assembled with 3.0-keV IB-spurted DMS/PEDOT:PSS alignment layers shows a 38% faster switching and a 93% lower residual direct current. The improved electro-optic performance here is likely due to the enhanced electric field effect and the charge-releasing ability of thin IB-spurted DMS/PEDOT:PSS layers.

  10. Source Driver Channel Reduction Schemes Employing Corresponding Pixel Alignments for Current Programming Active-Matrix Organic Light-Emitting Diode Displays

    NASA Astrophysics Data System (ADS)

    Hong, Soon-Kwang; Oh, Du-Hwan; Jeong, Seok-Hee; Park, Young-Ju; Kim, Byeong-Koo; Ha, Yong-Min; Jang, Jin

    2008-03-01

    We propose two types of novel scheme for reducing the number of output channels of driver-integrated circuit (D-IC) for the current programming compensation pixel structures of active-matrix organic light-emitting diodes (AMOLEDs). One is a 2:1 data demultiplexing technique that can reduce the number of output channels of D-IC by half. The proposed second scheme is a vertically aligned red (R), green (G), and blue (B) subpixel scheme instead of a horizontally aligned R-G-B subpixel one, which is regarded as the conventional pixel alignment scheme. We have also successfully implemented these schemes in a 2.4-in.-sized QCIF + (176 × RGB × 220) AMOLED using p-type excimer laser annealing (ELA) low-temperature polycrystalline silicon (LTPS) technology and evaluated key performance characteristics.

  11. Structure of high latitude currents in global magnetospheric-ionospheric models

    USGS Publications Warehouse

    Wiltberger, M; Rigler, E. J.; Merkin, V; Lyon, J. G

    2016-01-01

    Using three resolutions of the Lyon-Fedder-Mobarry global magnetosphere-ionosphere model (LFM) and the Weimer 2005 empirical model we examine the structure of the high latitude field-aligned current patterns. Each resolution was run for the entire Whole Heliosphere Interval which contained two high speed solar wind streams and modest interplanetary magnetic field strengths. Average states of the field-aligned current (FAC) patterns for 8 interplanetary magnetic field clock angle directions are computed using data from these runs. Generally speaking the patterns obtained agree well with results obtained from the Weimer 2005 computing using the solar wind and IMF conditions that correspond to each bin. As the simulation resolution increases the currents become more intense and narrow. A machine learning analysis of the FAC patterns shows that the ratio of Region 1 (R1) to Region 2 (R2) currents decreases as the simulation resolution increases. This brings the simulation results into better agreement with observational predictions and the Weimer 2005 model results. The increase in R2 current strengths also results in the cross polar cap potential (CPCP) pattern being concentrated in higher latitudes. Current-voltage relationships between the R1 and CPCP are quite similar at the higher resolution indicating the simulation is converging on a common solution. We conclude that LFM simulations are capable of reproducing the statistical features of FAC patterns.

  12. MAC/FAC: A Model of Similarity-Based Retrieval.

    ERIC Educational Resources Information Center

    Forbus, Kenneth D.; And Others

    1995-01-01

    Presents MAC/FAC, a model of similarity-based retrieval that attempts to capture psychological phenomena; discusses its limitations and extensions, its relationship with other retrieval models, and its placement in the context of other work on the nature of similarity. Examines the utility of the model through psychological experiments and…

  13. Cationic fac-tris(pyrazole) complexes as anion receptors.

    PubMed

    Nieto, Sonia; Pérez, Julio; Riera, Víctor; Miguel, Daniel; Alvarez, Celedonio

    2005-01-28

    New receptors fac-[Re(CO)3(pz)3]BAr'4 (pz = 3,5-dimethylpyrazole or 3(5)-tert-butylpyrazole, Ar' = 3,5-(CF3)2C6H3), synthesized from [Re(OTf)(CO)5] and the pyrazoles, have been found to show a high affinity for chloride.

  14. Statistical Association: Alignment of Current U.S. High School Textbooks with the Common Core State Standards for Mathematics

    ERIC Educational Resources Information Center

    Tran, Dung

    2016-01-01

    This study examined the alignment of three selected U.S. high school textbooks series with the Common Core State Standards for Mathematics (CCSSM) regarding the treatment of statistical association. A framework grounded in the literature for inclusion and exclusion of reasoning about association topics was developed, and textbook entries were…

  15. Developing a New Teaching Approach for the Chemical Bonding Concept Aligned with Current Scientific and Pedagogical Knowledge

    ERIC Educational Resources Information Center

    Nahum, Tami Levy; Mamlok-Naaman, Rachel; Hofstein, Avi; Krajcik, Joseph

    2007-01-01

    The traditional pedagogical approach for teaching chemical bonding is often overly simplistic and not aligned with the most up-to-date scientific models. As a result, high-school students around the world lack fundamental understanding of chemical bonding. In order to improve students' understanding of this concept, it was essential to propose a…

  16. Sensitivity analysis and evaluation of MicroFacPM: a microscale motor vehicle emission factor model for particulate matter emissions.

    PubMed

    Singh, Rakesh B; Huber, Alan H; Braddock, James N

    2007-04-01

    A microscale emission factor model (MicroFacPM) for predicting real-time site-specific motor vehicle particulate matter emissions was presented in the companion paper titled "Development of a Microscale Emission Factor Model for Particulate Matter (MicroFacPM) for Predicting Real-Time Motor Vehicle Emissions". The emission rates discussed are in mass per unit distance with the model providing estimates of fine particulate matter (PM2.5) and coarse particulate matter. This paper complements the companion paper by presenting a sensitivity analysis of the model to input variables and evaluation model outputs using data from limited field studies. The sensitivity analysis has shown that MicroFacPM emission estimates are very sensitive to vehicle fleet composition, speed, and the percentage of high-emitting vehicles. The vehicle fleet composition can affect fleet emission rates from 8 mg/mi to 1215 mg/mi; an increase of 5% in the smoking (high-emitting) current average U.S. light-duty vehicle fleet (compared with 0%) increased PM2.5 emission rates by -272% for 2000; and for the current U.S. fleet, PM2.5 emission rates are reduced by a factor of -0.64 for speeds >50 miles per hour (mph) relative to a speed of 10 mph. MicroFacPM can also be applied to examine the contribution of emission rates per vehicle class, model year, and sources of PM. The model evaluation is presented for the Tuscarora Mountain Tunnel, Pennsylvania Turnpike, PA, and some limited evaluations at two locations: Sepulveda Tunnel, Los Angeles, CA, and Van Nuys Tunnel, Van Nuys, CA. In general, the performance of MicroFacPM has shown very encouraging results.

  17. FACS separation of non-compromised forensically relevant biological mixtures.

    PubMed

    Verdon, Timothy J; Mitchell, R John; Chen, Weisan; Xiao, Kun; van Oorschot, Roland A H

    2015-01-01

    Although focusing attention on the statistical analysis of complex mixture profiles is important, the forensic science community will also benefit from directing research to improving the reduction of the incidence of mixtures before DNA extraction. This preliminary study analysed the use of fluorescence assisted cell sorting (FACS) for separation of cellular mixtures before DNA extraction, specifically mixtures of relatively fresh blood and saliva from two donors, prepared in 14 different mixture ratios. Improvements in the number of detectable alleles from the targeted cell type and overall profile quality were seen when compared to the results from unseparated samples. STRmix calculations revealed increases in likelihood ratios after separation, demonstrating the potential for higher probative values to be obtained from forensically relevant mixtures after subjecting them to FACS than from unsorted samples.

  18. 48 CFR 301.607-76 - FAC-P/PM application process.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 48 Federal Acquisition Regulations System 4 2014-10-01 2014-10-01 false FAC-P/PM application... 301.607-76 FAC-P/PM application process. The P/PM Handbook contains application procedures and forms...; recertification; and certification waiver. Applicants for HHS FAC-P/PM certification actions shall comply with...

  19. 48 CFR 301.607-76 - FAC-P/PM application process.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 48 Federal Acquisition Regulations System 4 2011-10-01 2011-10-01 false FAC-P/PM application... 301.607-76 FAC-P/PM application process. The P/PM Handbook contains application procedures and forms...; recertification; and certification waiver. Applicants for HHS FAC-P/PM certification actions shall comply with...

  20. 48 CFR 301.607-76 - FAC-P/PM application process.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 48 Federal Acquisition Regulations System 4 2012-10-01 2012-10-01 false FAC-P/PM application... 301.607-76 FAC-P/PM application process. The P/PM Handbook contains application procedures and forms...; recertification; and certification waiver. Applicants for HHS FAC-P/PM certification actions shall comply with...

  1. 48 CFR 301.607-76 - FAC-P/PM application process.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 48 Federal Acquisition Regulations System 4 2013-10-01 2013-10-01 false FAC-P/PM application... 301.607-76 FAC-P/PM application process. The P/PM Handbook contains application procedures and forms...; recertification; and certification waiver. Applicants for HHS FAC-P/PM certification actions shall comply with...

  2. 48 CFR 301.607-76 - FAC-P/PM application process.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 48 Federal Acquisition Regulations System 4 2010-10-01 2010-10-01 false FAC-P/PM application... 301.607-76 FAC-P/PM application process. The P/PM Handbook contains application procedures and forms...; recertification; and certification waiver. Applicants for HHS FAC-P/PM certification actions shall comply with...

  3. Isolating specific embryonic cells of the sea urchin by FACS.

    PubMed

    Juliano, Celina; Swartz, S Zachary; Wessel, Gary

    2014-01-01

    Isolating cells based on specific gene expression enables a focused biochemical and molecular analysis. While cultured cells and hematopoietic cells, for example, are routinely isolated by fluorescence activated cell sorting (FACS), early embryonic cells are a relatively untapped source for FACS applications often because the embryos of many animals are quite limiting. Furthermore, many applications require genetic model organisms in which cells can be labeled by fluorescent transgenes, or antibodies against cell surface antigens. Here we define conditions in the sea urchin embryo for isolation of embryonic cells based on expression of specific proteins. We use the sea urchin embryo for which a nearly unlimited supply of embryonic cells is available and demonstrate the conditions for separation of the embryo into single cells, fixation of the cells for antibody penetration into the cells, and conditions for FACS of a rare cell type in the embryo. This protocol may be adapted for analysis of mRNA, chromatin, protein, or carbohydrates and depends only on the probe availability for the cell of interest. We anticipate that this protocol will be broadly applicable to embryos of other species.

  4. On Alfvenic Waves and Stochastic Ion Heating with 1Re Observations of Strong Field-aligned Currents, Electric Fields, and O+ ions

    NASA Technical Reports Server (NTRS)

    Coffey, Victoria; Chandler, Michael; Singh, Nagendra

    2008-01-01

    The role that the cleft/cusp has in ionosphere/magnetosphere coupling makes it a very dynamic region having similar fundamental processes to those within the auroral regions. With Polar passing through the cusp at 1 Re in the Spring of 1996, we observe a strong correlation between ion heating and broadband ELF (BBELF) emissions. This commonly observed relationship led to the study of the coupling of large field-aligned currents, burst electric fields, and the thermal O+ ions. We demonstrate the role of these measurements to Alfvenic waves and stochastic ion heating. Finally we will show the properties of the resulting density cavities.

  5. The magnitudes of the regions 1 and 2 Birkeland currents observed by AMPERE and their role in solar wind-magnetosphere-ionosphere coupling

    NASA Astrophysics Data System (ADS)

    Coxon, J. C.; Milan, S. E.; Clausen, L. B. N.; Anderson, B. J.; Korth, H.

    2014-12-01

    In this paper we present the first large-scale statistical study of the influence of magnetic reconnection on the magnitude of the regions 1 and 2 Birkeland field-aligned currents (FACs). While previous studies have employed single spacecraft measurements to construct a statistical picture of the location and density of the Birkeland currents, it has hitherto been difficult to compare in situ measurements of the solar wind with instantaneous global field-aligned current measurements. To that end, we utilize the Active Magnetosphere Planetary Electrodynamics Response Experiment (AMPERE), which yields field-aligned current density in both hemispheres at a cadence of 10 min. We quantify the amount of current flowing in the regions 1 (R1) and 2 (R2) FACs, and we compare these with the dayside reconnection rate ΦD deduced from interplanetary parameters from the OMNI data set and with the AL index to examine whether magnetic reconnection is responsible for driving currents in the coupled magnetosphere-ionosphere system. We find that current magnitudes are strongly correlated with both ΦD and AL index. We also find that R1 currents tend to be higher than R2 currents during periods of magnetic reconnection, suggesting leakage of current across the polar cap or an association with the substorm current wedge.

  6. The Fear-avoidance Components Scale (FACS): Development and Psychometric Evaluation of a New Measure of Pain-related Fear Avoidance.

    PubMed

    Neblett, Randy; Mayer, Tom G; Hartzell, Meredith M; Williams, Mark J; Gatchel, Robert J

    2016-04-01

    Pain-related fear avoidance (FA), a common problem for patients with painful medical conditions, involves pain-related catastrophizing cognitions, hypervigilance, and avoidance behaviors, which can ultimately lead to decreased functioning, depression, and disability. Several patient-reported instruments have been developed to measure FA, but they have been criticized for limited construct validity, inadequate item specificity, lack of cutoff scores, and missing important FA components. The Fear-Avoidance Components Scale (FACS) is a new patient-reported measure designed to comprehensively evaluate FA in patients with painful medical conditions. It combines important components of FA found in prior FA scales, while trying to correct some of their deficiencies, within a framework of the most current FA model. Psychometric evaluation of the FACS found high internal consistency (α = 0.92) and high test/retest reliability (r = 0.90-0.94, P < 0.01). FACS scores differentiated between 2 separate chronic pain patient samples and a nonpatient comparison group. When clinically relevant severity levels were created, FACS severity scores were highly associated with FA-related patient-reported psychosocial and objective lifting performance variables. These results suggest that the FACS is a psychometrically strong and reliable measure that can help healthcare providers assess FA-related barriers to function and recovery.

  7. mer and fac isomerism in tris chelate diimine metal complexes.

    PubMed

    Dabb, Serin L; Fletcher, Nicholas C

    2015-03-14

    In this perspective, we highlight the issue of meridional (mer) and facial (fac) orientation of asymmetrical diimines in tris-chelate transition metal complexes. Diimine ligands have long been the workhorse of coordination chemistry, and whilst there are now good strategies to isolate materials where the inherent metal centered chirality is under almost complete control, and systematic methodologies to isolate heteroleptic complexes, the conceptually simple geometrical isomerism has not been widely investigated. In systems where the two donor atoms are significantly different in terms of the σ-donor and π-accepting ability, the fac isomer is likely to be the thermodynamic product. For the diimine complexes with two trigonal planar nitrogen atoms there is much more subtlety to the system, and external factors such as the solvent, lattice packing and the various steric considerations play a delicate role in determining the observed and isolable product. In this article we discuss the possibilities to control the isomeric ratio in labile systems, consider the opportunities to separate inert complexes and discuss the observed differences in their spectroscopic properties. Finally we report on the ligand orientation in supramolecular systems where facial coordination leads to simple regular structures such as helicates and tetrahedra, but the ability of the ligand system to adopt a mer orientation enables self-assembled structures of considerable beauty and complexity.

  8. The modified FACS calcein AM retention assay: A high throughput flow cytometer based method to measure cytotoxicity.

    PubMed

    Gillissen, M A; Yasuda, E; de Jong, G; Levie, S E; Go, D; Spits, H; van Helden, P M; Hazenberg, M D

    2016-07-01

    Current methods to determine cellular cytotoxicity in vitro are hampered by background signals that are caused by auto-fluorescent target and effector cells and by non-specific cell death. We combined and adjusted existing cell viability assays to develop a method that allows for highly reproducible, accurate, single cell analysis by high throughput FACS, in which non-specific cell death is corrected for. In this assay the number of living, calcein AM labeled cells that are green fluorescent are quantified by adding a fixed number of unlabeled calibration beads to the analysis. Using this modified FACS calcein AM retention method, we found EC50 values to be highly reproducible and considerably lower compared to EC50 values obtained by conventional assays, displaying the high sensitivity of this assay.

  9. The facC Gene of Aspergillus nidulans Encodes an Acetate-Inducible Carnitine Acetyltransferase

    PubMed Central

    Stemple, Christopher J.; Davis, Meryl A.; Hynes, Michael J.

    1998-01-01

    Mutations in the facC gene of Aspergillus nidulans result in an inability to use acetate as a sole carbon source. This gene has been cloned by complementation. The proposed translation product of the facC gene has significant similarity to carnitine acetyltransferases (CAT) from other organisms. Total CAT activity was found to be inducible by acetate and fatty acids and repressed by glucose. Acetate-inducible activity was found to be absent in facC mutants, while fatty acid-inducible activity was absent in an acuJ mutant. Acetate induction of facC expression was dependent on the facB regulatory gene, and an expressed FacB fusion protein was demonstrated to bind to 5′ facC sequences. Carbon catabolite repression of facC expression was affected by mutations in the creA gene and a CreA fusion protein bound to 5′ facC sequences. Mutations in the acuJ gene led to increased acetate induction of facC expression and also of an amdS-lacZ reporter gene, and it is proposed that this results from accumulation of acetate, as well as increased expression of facB. A model is presented in which facC encodes a cytosolic CAT enzyme, while a different CAT enzyme, which is acuJ dependent, is present in peroxisomes and mitochondria, and these activities are required for the movement of acetyl groups between intracellular compartments. PMID:9829933

  10. Nanofabrication of Arrays of Silicon Field Emitters with Vertical Silicon Nanowire Current Limiters and Self-Aligned Gates

    DTIC Science & Technology

    2016-08-19

    polysilicon is deposited at 625 °C using low-pressure chemical vapor deposition (LPCVD). At this temperature, the polysilicon has columnar growth and large...results, as the transconductance for a cathode scales exponentially with the gate voltage, and the currents for which they report transconductance were...radius and perhaps a tighter distribution principally due to the exponential relationship between the field factor (and hence the tip radius) on the

  11. Blend Shape Interpolation and FACS for Realistic Avatar

    NASA Astrophysics Data System (ADS)

    Alkawaz, Mohammed Hazim; Mohamad, Dzulkifli; Basori, Ahmad Hoirul; Saba, Tanzila

    2015-03-01

    The quest of developing realistic facial animation is ever-growing. The emergence of sophisticated algorithms, new graphical user interfaces, laser scans and advanced 3D tools imparted further impetus towards the rapid advancement of complex virtual human facial model. Face-to-face communication being the most natural way of human interaction, the facial animation systems became more attractive in the information technology era for sundry applications. The production of computer-animated movies using synthetic actors are still challenging issues. Proposed facial expression carries the signature of happiness, sadness, angry or cheerful, etc. The mood of a particular person in the midst of a large group can immediately be identified via very subtle changes in facial expressions. Facial expressions being very complex as well as important nonverbal communication channel are tricky to synthesize realistically using computer graphics. Computer synthesis of practical facial expressions must deal with the geometric representation of the human face and the control of the facial animation. We developed a new approach by integrating blend shape interpolation (BSI) and facial action coding system (FACS) to create a realistic and expressive computer facial animation design. The BSI is used to generate the natural face while the FACS is employed to reflect the exact facial muscle movements for four basic natural emotional expressions such as angry, happy, sad and fear with high fidelity. The results in perceiving the realistic facial expression for virtual human emotions based on facial skin color and texture may contribute towards the development of virtual reality and game environment of computer aided graphics animation systems.

  12. Cluster Multipoint Observations of the Spatial Structure and Time Development of Auroral Acceleration Region Field-aligned Current Systems, Potentials, and Plasma

    NASA Astrophysics Data System (ADS)

    Hull, A. J.; Chaston, C. C.; Fillingim, M. O.; Frey, H. U.; Bonnell, J. W.; Mozer, F.; Goldstein, M. L.

    2014-12-01

    The auroral acceleration region is an integral part of the magnetosphere-ionosphere electrodynamic system, and plays a key role in the transport of plasma and energy between Earth and space. This region is embedded with field-aligned currents that couple the magnetosphere to the ionosphere and is where parallel electric fields form that accelerate plasma to and from these regions. Though considerable progress has been made, the complex interplay between field-aligned current system formation, the development of parallel electric fields, changes in the plasma constituents, and auroral emissions consequences are not fully understood. The Cluster mission is well suited for studying the structure and dynamics of the auroral acceleration region. Over its lifetime, Cluster has sampled much of this region with closely spaced probes enabling the distinction between temporal effects from spatial variations. Moreover, this data when combined with auroral images from IMAGE or THEMIS GBO-ASI enable an assessment of the auroral emission response to spatial morphology and temporal development of structures seeded in the auroral acceleration region. In this study we present a survey of Cluster multi-point traversals within and just above the auroral acceleration region (≤ 3 Re altitude). In particular we highlight the spatial morphology and developmental sequence of auroral acceleration current systems, potentials and plasma constituents, with the aim of identifying controlling factors, and assessing ionospheric consequences under different conditions. Our results suggest that the "Alfvénic" activity may be an important precursor and perhaps may be playing an essential role in the development of "quasi-static" current systems during quiet and substorm active times. Such events are generally the result of an injection mediated process at or near the plasma sheet boundary layer, resulting in the local expansion of the plasma sheet. Key features of the conversion from Alfv

  13. A 3.5 V lithium-iodine hybrid redox battery with vertically aligned carbon nanotube current collector.

    PubMed

    Zhao, Yu; Hong, Misun; Bonnet Mercier, Nadège; Yu, Guihua; Choi, Hee Cheul; Byon, Hye Ryung

    2014-02-12

    A lithium-iodine (Li-I2) cell using the triiodide/iodide (I3(-)/I(-)) redox couple in an aqueous cathode has superior gravimetric and volumetric energy densities (∼ 330 W h kg(-1) and ∼ 650 W h L(-1), respectively, from saturated I2 in an aqueous cathode) to the reported aqueous Li-ion batteries and aqueous cathode-type batteries, which provides an opportunity to construct cost-effective and high-performance energy storage. To apply this I3(-)/I(-) aqueous cathode for a portable and compact 3.5 V battery, unlike for grid-scale storage as general target of redox flow batteries, we use a three-dimensional and millimeter thick carbon nanotube current collector for the I3(-)/I(-) redox reaction, which can shorten the diffusion length of the redox couple and provide rapid electron transport. These endeavors allow the Li-I2 battery to enlarge its specific capacity, cycling retention, and maintain a stable potential, thereby demonstrating a promising candidate for an environmentally benign and reusable portable battery.

  14. Electric Field, Field-aligned Current and Electromagnetic Waves in the Dip Region in front of the Dipolarization Front

    NASA Astrophysics Data System (ADS)

    Fu, S.; Sun, W.; Zhou, X.; Zhao, D.; Zong, Q.; Yao, Z.; Pu, Z.; Parks, G. K.

    2015-12-01

    Dipolarization front (DF) is characterized by a strong increase of magnetic field Bz component often observed before the arrival of high-speed flows in the Earth's plasma sheet. The DF interfaces between the high-speed flowing transient plasma and the ambient plasma. Ahead of the DFs, magnetic field Bz decreases and it is, called the "dip region." However, unlike in the high-speed flow and the ambient plasma which can be described by MHD theory, kinetic effects are important in the dip region because the spatial scale is less than the ion gyroradius. Observation and simulation have demonstrated that the dip region is formed by the reflecting ions at the sharp front. Short lived electromagnetic waves are also observed here generated by the reflected ions. In addition, Hall electric field observed in this region is in the opposite direction of the electric field inside the DF. The dipolarization front and the dip region ahead of it formed a set of current systems and they are fundamentally important for understanding the cause of flow braking in the plasma sheet.

  15. Increased universality of Lepidopteran elicitor compounds across insects: Identification of fatty acid amino acid conjugates (FACs)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Fatty acid amino acid conjugates (FACs) are known elicitors of induced release of volatile compounds in plants that, in turn, attract foraging parasitoids. Since the discovery of volicitin [N-(17-hydroxylinolenoyl)-L-glutamine] in the regurgitant of larval Spodoptera exigua1, a series of related FAC...

  16. [FACS-mQ as a powerful clinical test in the cancer stem cell era].

    PubMed

    Takano, Toru; Hidaka, Yoh; Iwatani, Yoshinori

    2012-08-01

    Stem cells are pluripotent and self renewing, and possess an ability to differentiate into the various cell types of a particular tissue. In cancer tissues, existence of cells showing biological similarities with stem cells, named cancer stem cells (CSC), are known to regulate the growth of the tissue and determine its prognosis. Stem cells and CSCs usually exist as minor populations of cells in a tissue. Detection and analysis of these cells are usually laborious even using fluorescence activated cell sorting (FACS) with the conventional protocols. Considering these drawbacks, we developed a novel analytical method named mRNA quantification after FACS (FACS-mQ). In FACS-mQ, cells are labeled with a fluorescent dye in a manner that minimizes RNA degradation, then cells sorted by FACS are examined by analyzing their gene expression profile. We established protocols to obtain single cells from clinical samples for flow cytometry analysis. Further, we performed FACS-mQ analysis using fluorescence-labeled antibodies, cRNA probes and locked nucleic acid (LNA) probes. Evident decrease of intracellular RNAs did not observed in FACS-mQ using immunocytochemistry. Approximately 60% of intracellular RNA was preserved after in situ hybridization using cRNA probes. These RNAs from a small number of sorted cells were suitable for quantitative analysis to establish gene expression profiles. FACS-mQ does not require laborious and time-consuming procedures; thus, it is expected to facilitate research on stem cells or cancer stem cells.

  17. A new FACS approach isolates hESC derived endoderm using transcription factors.

    PubMed

    Pan, Yuqiong; Ouyang, Zhengqing; Wong, Wing Hung; Baker, Julie C

    2011-03-09

    We show that high quality microarray gene expression profiles can be obtained following FACS sorting of cells using combinations of transcription factors. We use this transcription factor FACS (tfFACS) methodology to perform a genomic analysis of hESC-derived endodermal lineages marked by combinations of SOX17, GATA4, and CXCR4, and find that triple positive cells have a much stronger definitive endoderm signature than other combinations of these markers. Additionally, SOX17(+) GATA4(+) cells can be obtained at a much earlier stage of differentiation, prior to expression of CXCR4(+) cells, providing an important new tool to isolate this earlier definitive endoderm subtype. Overall, tfFACS represents an advancement in FACS technology which broadly crosses multiple disciplines, most notably in regenerative medicine to redefine cellular populations.

  18. Relation of the auroral substorm to the substorm current wedge

    NASA Astrophysics Data System (ADS)

    McPherron, Robert L.; Chu, Xiangning

    2016-12-01

    The auroral substorm is an organized sequence of events seen in the aurora near midnight. It is a manifestation of the magnetospheric substorm which is a disturbance of the magnetosphere brought about by the solar wind transfer of magnetic flux from the dayside to the tail lobes and its return through the plasma sheet to the dayside. The most dramatic feature of the auroral substorm is the sudden brightening and poleward expansion of the aurora. Intimately associated with this expansion is a westward electrical current flowing across the bulge of expanding aurora. This current is fed by a downward field-aligned current (FAC) at its eastern edge and an upward current at its western edge. This current system is called the substorm current wedge (SCW). The SCW forms within a minute of auroral expansion. FAC are created by pressure gradients and field line bending from shears in plasma flow. Both of these are the result of pileup and diversion of plasma flows in the near-earth plasma sheet. The origins of these flows are reconnection sites further back in the tail. The auroral expansion can be explained by a combination of a change in field line mapping caused by the substorm current wedge and a tailward growth of the outer edge of the pileup region. We illustrate this scenario with a complex substorm and discuss some of the problems associated with this interpretation.

  19. High-Current and High-Transconductance Self-Aligned P+-GaAs Junction HFET of Complete Enhancement-Mode Operation

    NASA Astrophysics Data System (ADS)

    Nishii, Katsunori; Yokoyama, Mitsuru; Yamamoto, Shinji; Tamura, Akiyoshi; Inoue, Kaoru

    1999-04-01

    High-current and high-transconductance self-aligned p+-GaAs junction HFETs (PJ-HFETs) of a complete enhancement-mode operation have been developed for the first time. Due to the advantages of the p/n junction, the barrier height of 1.12 eV has been obtained. To obtain high activation for the Si implanted epitaxial layers, we optimized theannealing conditions. The 0.8 µm-gate complete enhancement mode PJ-HFET with a large forward gate voltage swing of more than 1.5 V exhibited a K-value of 400 mS/Vmm, a maximum transconductance (gmMAX) of 410 mS/mm and a maximum drain current (IMAX) of 380 mA/mm with a threshold voltage (Vth) of 0.2 V. The standard deviation of Vth was 18.4 mV across a 3 inch wafer. Operated with a drain bias of 3.3 V, the PJ-HFET demonstrated a power-added efficiency (PAE) of 39.5% with an adjacent channel leakage ratio (ACPR) of -57.4 dBc at an output power (Pout) of 21.5 dBm and a frequency of 1.9 GHz.

  20. Fair Access to Care Services (FACS): implementation in the mental health context of the UK.

    PubMed

    Cestari, L; Munroe, M; Evans, S; Smith, A; Huxley, P

    2006-11-01

    Since April 2003, all adults requiring social care services must have an assessment to determine their eligibility, which is set within the four-level framework of Fair Access to Care Services [FACS; LAC (2002)13]. This paper examines the implementation of FACS by community mental health teams in eight sites in mental health partnership trusts, and one in a mental health and social care trust in the UK. Twenty-eight respondents (managers within trusts and social services departments) participated in in-depth qualitative interviews, which were undertaken between August 2004 and February 2005. The interviews covered: consultation with users and partner organisations; training and briefings for staff; FACS thresholds; integration of FACS and the Care Programme Approach; and the impact of implementing FACS on budgetary arrangements between health and social care. Using the framework analysis approach to analyse data, it was found that FACS implementation in mental health services has been somewhat haphazard, and has identified real differences between health and social care approaches to eligibility determination, assessment and priorities. In particular, the type and amount of consultation, training and induction into FACS was variable, and in some cases, unacceptably poor. While FACS may have reduced variability between authorities, the exercise of professional judgement in the operation of FACS and the lack of high-quality preventative services remain as potential sources of inequity within the system. The authors conclude that FACS has revealed and reinforced a growing separation rather than an integration of mental health and social care ideas and practices, at least in the participating sites.

  1. Alignment of CEBAF cryomodules

    SciTech Connect

    Schneider, W.J.; Bisognano, J.J.; Fischer, J.

    1993-06-01

    CEBAF, the Continuous Electron Beam Accelerator Facility, when completed, will house a 4 GeV recirculating accelerator. Each of the accelerator`s two linacs contains 160 superconducting radio frequency (SRF) 1497 MHz niobium cavities in 20 cryomodules. Alignments of the cavities within the cryomodule with respect to beam axis is critical to achieving the optimum accelerator performance. This paper discusses the rationale for the current specification on cavity mechanical alignment: 2 mrad (rms) applied to the 0.5 m active length cavities. We describe the tooling that was developed to achieve the tolerance at the time of cavity pair assembly, to preserve and integrate alignment during cryomodule assembly, and to translate alignment to appropriate installation in the beam line.

  2. Time development of high-altitude auroral acceleration region plasma, potentials, and field-aligned current systems observed by Cluster during a substorm

    NASA Astrophysics Data System (ADS)

    Hull, A. J.; Chaston, C. C.; Fillingim, M. O.; Mozer, F.; Frey, H. U.

    2013-12-01

    The auroral acceleration region is an integral link in the chain of events that transpire during substorms, and the currents, plasma and electric fields undergo significant changes driven by complex dynamical processes deep in the magnetotail. These auroral acceleration processes in turn accelerate and heat the plasma that ultimately leads to some of the most intense global substorm auroral displays. The complex interplay between field-aligned current system formation, the development of parallel electric fields, and resultant changes in the plasma constituents that occur during substorms within or just above the auroral acceleration zone remain unclear. We present Cluster multi-point observations within the high-altitude acceleration region (> 3 Re altitude) at key instances during the development of a substorm. Of particular emphasis is on the time-development of the plasma, potentials and currents that occur therein with the aim of ascertaining high-altitude drivers of substorm active auroral acceleration processes and auroral emission consequences. Preliminary results show that the initial onset is dominated by Alfvenic activity as evidenced by the sudden occurrence of relatively intense, short-spatial scale Alfvenic currents and attendant energy dispersed, counterstreaming electrons poleward of the growth-phase arc. The Alfvenic currents are locally planar structures with characteristic thicknesses on the order of a few tens of kilometers. In subsequent passages by the other spacecraft, the plasma sheet region became hotter and thicker via the injection of new hot, dense plasma of magnetospheric origins poleward of the pre-existing growth phase arc. In association with the heating and/or thickening of the plasma sheet, the currents appeared to broaden to larger scales as Alfven dominated activity gave way to either inverted-V dominated or mixed inverted-V and Alfvenic behavior depending on location. The transition from Alfven dominated to inverted-V dominated

  3. Configuration and Generation of Substorm Current Wedge

    NASA Astrophysics Data System (ADS)

    Chu, Xiangning

    The substorm current wedge (SCW), a core element of substorm dynamics coupling the magnetotail to the ionosphere, is crucial in understanding substorms. It has been suggested that the field-aligned currents (FACs) in the SCW are caused by either pressure gradients or flow vortices, or both. Our understanding of FAC generations is based predominately on numerical simulations, because it has not been possible to organize spacecraft observations in a coordinate system determined by the SCW. This dissertation develops an empirical inversion model of the current wedge and inverts midlatitude magnetometer data to obtain the parameters of the current wedge for three solar cycles. This database enables statistical data analysis of spacecraft plasma and magnetic field observations relative to the SCW coordinate. In chapter 2, a new midlatitude positive bay (MPB) index is developed and calculated for three solar cycles of data. The MPB index is processed to determine the substorm onset time, which is shown to correspond to the auroral breakup onset with at most 1-2 minutes difference. Substorm occurrence rate is found to depend on solar wind speed while substorm duration is rather constant, suggesting that substorm process has an intrinsic pattern independent of external driving. In chapter 3, an SCW inversion technique is developed to determine the strength and locations of the FACs in an SCW. The inversion parameters for FAC strength and location, and ring current strength are validated by comparison with other measurements. In chapter 4, the connection between earthward flows and auroral poleward expansion is examined using improved mapping, obtained from a newly-developed dynamic magnetospheric model by superimposing a standard magnetospheric field model with substorm current wedge obtained from the inversion technique. It is shown that the ionospheric projection of flows observed at a fixed point in the equatorial plane map to the bright aurora as it expands poleward

  4. The Norwegian Façade Insulation Study: the efficacy of façade insulation in reducing noise annoyance due to road traffic.

    PubMed

    Amundsen, Astrid H; Klæboe, Ronny; Aasvang, Gunn Marit

    2011-03-01

    The efficacy of façade insulation in providing an improved indoor noise environment and in reducing indoor noise annoyance was examined in a socio-acoustic before-and-after study with a control group. An average equivalent noise reduction inside the dwellings of 7 dB was obtained from the façade insulation. Whereas 42% of the respondents were highly annoyed in the before-situation, this dropped to 16% in the after study. The conclusion is therefore that the façade insulation provided a substantial improvement in the indoor noise environment. The advantage with respect to indoor noise annoyance, of having the bedroom facing the least noise-exposed side of the dwelling corresponded to a 6 dB noise reduction. The changes in annoyance from noise reduction due to the façade insulation were in accordance with what would be expected from the exposure-response curves obtained in the before-situation. A total of 637 respondents participated in the before-study. Of these, 415 also participated in the after study. Indoor and outdoor noise exposure calculations for each of the dwellings were undertaken before and after the façade insulation was implemented.

  5. Two-stage bile preparation with acetone for recovery of fluorescent aromatic compounds (FACs).

    PubMed

    Karami, Ali; Syed, Mohd A; Christianus, Annie; Willett, Kristine L; Mazzeo, Jeffrey R; Courtenay, Simon C

    2012-07-15

    In this study we sought to optimize recovery of fluorescent aromatic compounds (FACs) from the bile of African catfish (Clarias gariepinus) injected with 10mg/kg benzo[a]pyrene (BaP). Fractions of pooled bile were hydrolyzed, combined with ten volumes of methanol, ethanol, acetonitrile, or acetone, centrifuged and supernatants were analyzed by high-performance liquid chromatography with fluorescent detection (HPLC/FL). As well, to test whether FACs were being lost in solids from the centrifugation, pellets were resuspended, hydrolyzed and mixed with six volumes of the organic solvent that produced best FAC recovery from the supernatant, and subjected to HPLC/FL. Highest FAC concentrations were obtained with 2000μl and 1250μl acetone for supernatants and resuspended pellets respectively. FACs concentrations were negatively correlated with biliary protein content but were unaffected by addition of bovine serum albumin (BSA) followed by no incubation indicating that the presence of proteins in the biliary mixture does not simply interfere with detection of FACs. In another experiment, efficiency of acetone addition was compared to two different liquid-liquid extractions (L-LEs). Acetone additions provided significantly higher biliary FACs than the L-LE methods. The new two-stage bile preparation with acetone is an efficient, inexpensive and easily performed method.

  6. 48 CFR 301.603-74 - Requirement for retention of FAC-C and HHS SAC certification.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... of FAC-C and HHS SAC certification. 301.603-74 Section 301.603-74 Federal Acquisition Regulations..., Contracting Authority, and Responsibilities 301.603-74 Requirement for retention of FAC-C and HHS SAC certification. To maintain FAC-C certification, all warranted Contracting Officers, regardless of series,...

  7. The alignment strategy of HADES

    NASA Astrophysics Data System (ADS)

    Pechenova, O.; Pechenov, V.; Galatyuk, T.; Hennino, T.; Holzmann, R.; Kornakov, G.; Markert, J.; Müntz, C.; Salabura, P.; Schmah, A.; Schwab, E.; Stroth, J.

    2015-06-01

    The global as well as intrinsic alignment of any spectrometer impacts directly on its performance and the quality of the achievable physics results. An overview of the current alignment procedure of the DiElectron Spectrometer HADES is presented with an emphasis on its main features and its accuracy. The sequence of all steps and procedures is given, including details on photogrammetric and track-based alignment.

  8. Automated alignment of optical components for high-power diode lasers

    NASA Astrophysics Data System (ADS)

    Brecher, C.; Pyschny, N.; Haag, S.; Guerrero Lule, V.

    2012-03-01

    Despite major progress in developing brilliant laser sources a huge potential for cost reductions can be found in simpler setups and automated assembly processes, especially for large volume applications. In this presentation, a concept for flexible automation in optics assembly is presented which is based on standard micro assembly systems with relatively large workspace and modular micromanipulators to enhance the system with additional degrees of freedom and a very high motion resolution. The core component is a compact flexure-based micromanipulator especially designed for the alignment of micro optical components which will be described in detail. The manipulator has been applied in different scenarios to develop and investigate automated alignment processes. This paper focuses on the automated alignment of fast axis collimation (FAC) lenses which is a crucial step during the production of diode lasers. The handling and positioning system, the measuring arrangement for process feedback during active alignment as well as the alignment strategy will be described. The fine alignment of the FAC lens is performed with the micromanipulator under concurrent analysis of the far and the near field intensity distribution. An optimization of the image processing chains for the alignment of a FAC in front of a diode bar led to cycle times of less than 30 seconds. An outlook on other applications and future work regarding the development of automated assembly processes as well as new ideas for flexible assembly systems with desktop robots will close the talk.

  9. Complement dependent cytotoxicity (CDC) activity of a humanized anti Lewis-Y antibody: FACS-based assay versus the 'classical' radioactive method -- qualification, comparison and application of the FACS-based approach.

    PubMed

    Nechansky, A; Szolar, O H J; Siegl, P; Zinoecker, I; Halanek, N; Wiederkum, S; Kircheis, R

    2009-05-01

    The fully humanized Lewis-Y carbohydrate specific monoclonal antibody (mAb) IGN311 is currently tested in a passive immunotherapy approach in a clinical phase I trail and therefore regulatory requirements demand qualified assays for product analysis. To demonstrate the functionality of its Fc-region, the capacity of IGN311 to mediate complement dependent cytotoxicity (CDC) against human breast cancer cells was evaluated. The "classical" radioactive method using chromium-51 and a FACS-based assay were established and qualified according to ICH guidelines. Parameters evaluated were specificity, response function, bias, repeatability (intra-day precision), intermediate precision (operator-time different), and linearity (assay range). In the course of a fully nested design, a four-parameter logistic equation was identified as appropriate calibration model for both methods. For the radioactive assay, the bias ranged from -6.1% to -3.6%. The intermediate precision for future means of duplicate measurements revealed values from 12.5% to 15.9% and the total error (beta-expectation tolerance interval) of the method was found to be <40%. For the FACS-based assay, the bias ranged from -8.3% to 0.6% and the intermediate precision for future means of duplicate measurements revealed values from 4.2% to 8.0%. The total error of the method was found to be <25%. The presented data demonstrate that the FACS-based CDC is more accurate than the radioactive assay. Also, the elimination of radioactivity and the 'real-time' counting of apoptotic cells further justifies the implementation of this method which was subsequently applied for testing the influence of storage at 4 degrees C and 25 degrees C ('stability testing') on the potency of IGN311 drug product. The obtained results demonstrate that the qualified functional assay represents a stability indicating test method.

  10. ALIGNING JIG

    DOEpatents

    Culver, J.S.; Tunnell, W.C.

    1958-08-01

    A jig or device is described for setting or aligning an opening in one member relative to another member or structure, with a predetermined offset, or it may be used for measuring the amount of offset with which the parts have previously been sct. This jig comprises two blocks rabbeted to each other, with means for securing thc upper block to the lower block. The upper block has fingers for contacting one of the members to be a1igmed, the lower block is designed to ride in grooves within the reference member, and calibration marks are provided to determine the amount of offset. This jig is specially designed to align the collimating slits of a mass spectrometer.

  11. Purification of specific cell population by fluorescence activated cell sorting (FACS).

    PubMed

    Basu, Sreemanti; Campbell, Hope M; Dittel, Bonnie N; Ray, Avijit

    2010-07-10

    Experimental and clinical studies often require highly purified cell populations. FACS is a technique of choice to purify cell populations of known phenotype. Other bulk methods of purification include panning, complement depletion and magnetic bead separation. However, FACS has several advantages over other available methods. FACS is the preferred method when very high purity of the desired population is required, when the target cell population expresses a very low level of the identifying marker or when cell populations require separation based on differential marker density. In addition, FACS is the only available purification technique to isolate cells based on internal staining or intracellular protein expression, such as a genetically modified fluorescent protein marker. FACS allows the purification of individual cells based on size, granularity and fluorescence. In order to purify cells of interest, they are first stained with fluorescently-tagged monoclonal antibodies (mAb), which recognize specific surface markers on the desired cell population (1). Negative selection of unstained cells is also possible. FACS purification requires a flow cytometer with sorting capacity and the appropriate software. For FACS, cells in suspension are passed as a stream in droplets with each containing a single cell in front of a laser. The fluorescence detection system detects cells of interest based on predetermined fluorescent parameters of the cells. The instrument applies a charge to the droplet containing a cell of interest and an electrostatic deflection system facilitates collection of the charged droplets into appropriate collection tubes (2). The success of staining and thereby sorting depends largely on the selection of the identifying markers and the choice of mAb. Sorting parameters can be adjusted depending on the requirement of purity and yield. Although FACS requires specialized equipment and personnel training, it is the method of choice for isolation of

  12. Image alignment

    DOEpatents

    Dowell, Larry Jonathan

    2014-04-22

    Disclosed is a method and device for aligning at least two digital images. An embodiment may use frequency-domain transforms of small tiles created from each image to identify substantially similar, "distinguishing" features within each of the images, and then align the images together based on the location of the distinguishing features. To accomplish this, an embodiment may create equal sized tile sub-images for each image. A "key" for each tile may be created by performing a frequency-domain transform calculation on each tile. A information-distance difference between each possible pair of tiles on each image may be calculated to identify distinguishing features. From analysis of the information-distance differences of the pairs of tiles, a subset of tiles with high discrimination metrics in relation to other tiles may be located for each image. The subset of distinguishing tiles for each image may then be compared to locate tiles with substantially similar keys and/or information-distance metrics to other tiles of other images. Once similar tiles are located for each image, the images may be aligned in relation to the identified similar tiles.

  13. Onorbit IMU alignment error budget

    NASA Technical Reports Server (NTRS)

    Corson, R. W.

    1980-01-01

    The Star Tracker, Crew Optical Alignment Sight (COAS), and Inertial Measurement Unit (IMU) from a complex navigation system with a multitude of error sources were combined. A complete list of the system errors is presented. The errors were combined in a rational way to yield an estimate of the IMU alignment accuracy for STS-1. The expected standard deviation in the IMU alignment error for STS-1 type alignments was determined to be 72 arc seconds per axis for star tracker alignments and 188 arc seconds per axis for COAS alignments. These estimates are based on current knowledge of the star tracker, COAS, IMU, and navigation base error specifications, and were partially verified by preliminary Monte Carlo analysis.

  14. Use of spherical elementary currents to map the polar current systems associated with the geomagnetic sudden commencements on 2013 and 2015 St. Patrick's Day storms

    NASA Astrophysics Data System (ADS)

    Marsal, S.; Torta, J. M.; Segarra, A.; Araki, T.

    2017-01-01

    Araki's model of geomagnetic sudden commencements (SCs) establishes that the ground magnetic signatures globally observed after the onset produced by an increased solar wind dynamic pressure impacting on the Earth's magnetosphere are caused by the setting up of a system of electric currents in the coupled magnetosphere-ionosphere. This current system consists of a particular evolving set of magnetopause currents closing in the ionosphere through geomagnetic field-aligned currents (FACs) and their induced counterpart. The present paper confirms the starting assumptions of the referred model by use of spherical elementary current systems (SECS), namely, the existence of FACs reversing polarity during the first couple of minutes of the SC. It is the first time that SECS have been applied to the study of SCs. The method has been fed with data from more than 100 stations of the global network of geomagnetic observatories and variometer sites in the northern hemisphere so as to provide a reliable pattern of the equivalent current system flowing at ionospheric heights on the occasion of the SCs associated with the 2013 and 2015 St. Patrick's Day storms. The combined analysis of solar wind data and the synoptic view of the SC current patterns provided by SECS allows it to explain some of the differences observed between both events.

  15. The two-way relationship between ionospheric outflow and the ring current

    DOE PAGES

    Welling, Daniel T.; Jordanova, Vania Koleva; Glocer, Alex; ...

    2015-06-01

    It is now well established that the ionosphere, because it acts as a significant source of plasma, plays a critical role in ring current dynamics. However, because the ring current deposits energy into the ionosphere, the inverse may also be true: the ring current can play a critical role in the dynamics of ionospheric outflow. This study uses a set of coupled, first-principles-based numerical models to test the dependence of ionospheric outflow on ring current-driven region 2 field-aligned currents (FACs). A moderate magnetospheric storm event is modeled with the Space Weather Modeling Framework using a global MHD code (Block Adaptivemore » Tree Solar wind Roe-type Upwind Scheme, BATS-R-US), a polar wind model (Polar Wind Outflow Model), and a bounce-averaged kinetic ring current model (ring current atmosphere interaction model with self-consistent magnetic field, RAM-SCB). Initially, each code is two-way coupled to all others except for RAM-SCB, which receives inputs from the other models but is not allowed to feed back pressure into the MHD model. The simulation is repeated with pressure coupling activated, which drives strong pressure gradients and region 2 FACs in BATS-R-US. It is found that the region 2 FACs increase heavy ion outflow by up to 6 times over the non-coupled results. The additional outflow further energizes the ring current, establishing an ionosphere-magnetosphere mass feedback loop. This study further demonstrates that ionospheric outflow is not merely a plasma source for the magnetosphere but an integral part in the nonlinear ionosphere-magnetosphere-ring current system.« less

  16. The two-way relationship between ionospheric outflow and the ring current

    SciTech Connect

    Welling, Daniel T.; Jordanova, Vania Koleva; Glocer, Alex; Toth, Gabor; Liemohn, Michael W.; Weimer, Dan R.

    2015-06-01

    It is now well established that the ionosphere, because it acts as a significant source of plasma, plays a critical role in ring current dynamics. However, because the ring current deposits energy into the ionosphere, the inverse may also be true: the ring current can play a critical role in the dynamics of ionospheric outflow. This study uses a set of coupled, first-principles-based numerical models to test the dependence of ionospheric outflow on ring current-driven region 2 field-aligned currents (FACs). A moderate magnetospheric storm event is modeled with the Space Weather Modeling Framework using a global MHD code (Block Adaptive Tree Solar wind Roe-type Upwind Scheme, BATS-R-US), a polar wind model (Polar Wind Outflow Model), and a bounce-averaged kinetic ring current model (ring current atmosphere interaction model with self-consistent magnetic field, RAM-SCB). Initially, each code is two-way coupled to all others except for RAM-SCB, which receives inputs from the other models but is not allowed to feed back pressure into the MHD model. The simulation is repeated with pressure coupling activated, which drives strong pressure gradients and region 2 FACs in BATS-R-US. It is found that the region 2 FACs increase heavy ion outflow by up to 6 times over the non-coupled results. The additional outflow further energizes the ring current, establishing an ionosphere-magnetosphere mass feedback loop. This study further demonstrates that ionospheric outflow is not merely a plasma source for the magnetosphere but an integral part in the nonlinear ionosphere-magnetosphere-ring current system.

  17. The two-way relationship between ionospheric outflow and the ring current

    NASA Astrophysics Data System (ADS)

    Welling, D. T.; Jordanova, V. K.; Glocer, A.; Toth, G.; Liemohn, M. W.; Weimer, D. R.

    2015-06-01

    It is now well established that the ionosphere, because it acts as a significant source of plasma, plays a critical role in ring current dynamics. However, because the ring current deposits energy into the ionosphere, the inverse may also be true: the ring current can play a critical role in the dynamics of ionospheric outflow. This study uses a set of coupled, first-principles-based numerical models to test the dependence of ionospheric outflow on ring current-driven region 2 field-aligned currents (FACs). A moderate magnetospheric storm event is modeled with the Space Weather Modeling Framework using a global MHD code (Block Adaptive Tree Solar wind Roe-type Upwind Scheme, BATS-R-US), a polar wind model (Polar Wind Outflow Model), and a bounce-averaged kinetic ring current model (ring current atmosphere interaction model with self-consistent magnetic field, RAM-SCB). Initially, each code is two-way coupled to all others except for RAM-SCB, which receives inputs from the other models but is not allowed to feed back pressure into the MHD model. The simulation is repeated with pressure coupling activated, which drives strong pressure gradients and region 2 FACs in BATS-R-US. It is found that the region 2 FACs increase heavy ion outflow by up to 6 times over the noncoupled results. The additional outflow further energizes the ring current, establishing an ionosphere-magnetosphere mass feedback loop. This study further demonstrates that ionospheric outflow is not merely a plasma source for the magnetosphere but an integral part in the nonlinear ionosphere-magnetosphere-ring current system.

  18. Temporal and spatial developments of global ionospheric current associated with storm-time overshielding

    NASA Astrophysics Data System (ADS)

    Tsuji, Y.; Shinbori, A.; Nishimura, Y.; Kikuchi, T.; Nagatsuma, T.; Watari, S.

    2010-12-01

    During the strong southward interplanetary magnetic field (IMF), the convection electric field originating from the region-1 field-aligned currents (R1 FACs) causes a two-cell ionospheric Hall current at high latitudes. The convection electric field penetrates to the magnetic equator, and drives the eastward equatorial electrojet (EEJ). Subsequently, when the southward IMF weakens, the reversed ionospheric current in the equatorial ionosphere, called equatorial counter electrojet (CEJ), is driven by the developed shielding electric field originating from the region-2 field-aligned currents (R2 FACs). Its state is called ‘overshielding’ because the shielding electric field overcomes the reduced convection field in lower latitudes of the R2 FACs [e.g., Kelley et al., 1979]. However, the temporal and spatial relationship of the global ionospheric current system has not been established during the storm-time overshielding yet. In this paper, we investigated magnetic field variations in high-low latitudes in the 21 CEJ events (overshielding events) during storms occurred during a period from 2001 to 2002. In high-middle latitudes during the period, the developed auroral electrojet (AEJ) moved poleward with ~3-8 degrees in magnetic latitude, maintaining the strength. This indicates a contraction of the auroral oval. Subsequently, the strength rapidly decreased without such a poleward shift. This result supports that the overshielding electric field is strengthened by the poleward shift of the R1 FACs [Kikuchi et al., 2008]. Moreover, in the 8 of 21 CEJ events, the magnetic field variation in lower latitudes than the AEJ region changed the direction with magnitudes one order smaller than the AEJ. This variation was generated by the ionospheric Hall currents associated with the overshielding electric field. We also found that the observed life time of CEJ, about 15-470 min, was either equal to or up to 3.8 times longer than that of the overshielding current at the

  19. Fuel Accident Condition Simulator (FACS) Furnace for Post-Irradiation Heating Tests of VHTR Fuel Compacts

    SciTech Connect

    Paul A Demkowicz; Paul Demkowicz; David V Laug

    2010-10-01

    Abstract –Fuel irradiation testing and post-irradiation examination are currently in progress as part of the Next Generation Nuclear Plant Fuels Development and Qualification Program. The PIE campaign will include extensive accident testing of irradiated very high temperature reactor fuel compacts to verify fission product retention characteristics at high temperatures. This work will be carried out at both the Idaho National Laboratory (INL) and the Oak Ridge National Laboratory, beginning with accident tests on irradiated fuel from the AGR-1 experiment in 2010. A new furnace system has been designed, built, and tested at INL to perform high temperature accident tests. The Fuel Accident Condition Simulator furnace system is designed to heat fuel specimens at temperatures up to 2000°C in helium while monitoring the release of volatile fission metals (e.g. Cs, Ag, Sr, Eu, and I) and fission gases (Kr, Xe). Fission gases released from the fuel to the sweep gas are monitored in real time using dual cryogenic traps fitted with high purity germanium detectors. Condensable fission products are collected on a plate attached to a water-cooled cold finger that can be exchanged periodically without interrupting the test. Analysis of fission products on the condensation plates involves dry gamma counting followed by chemical analysis of selected isotopes. This paper will describe design and operational details of the Fuel Accident Condition Simulator (FACS) furnace system, as well as preliminary system calibration results.

  20. MUSE optical alignment procedure

    NASA Astrophysics Data System (ADS)

    Laurent, Florence; Renault, Edgard; Loupias, Magali; Kosmalski, Johan; Anwand, Heiko; Bacon, Roland; Boudon, Didier; Caillier, Patrick; Daguisé, Eric; Dubois, Jean-Pierre; Dupuy, Christophe; Kelz, Andreas; Lizon, Jean-Louis; Nicklas, Harald; Parès, Laurent; Remillieux, Alban; Seifert, Walter; Valentin, Hervé; Xu, Wenli

    2012-09-01

    MUSE (Multi Unit Spectroscopic Explorer) is a second generation VLT integral field spectrograph (1x1arcmin² Field of View) developed for the European Southern Observatory (ESO), operating in the visible wavelength range (0.465-0.93 μm). A consortium of seven institutes is currently assembling and testing MUSE in the Integration Hall of the Observatoire de Lyon for the Preliminary Acceptance in Europe, scheduled for 2013. MUSE is composed of several subsystems which are under the responsibility of each institute. The Fore Optics derotates and anamorphoses the image at the focal plane. A Splitting and Relay Optics feed the 24 identical Integral Field Units (IFU), that are mounted within a large monolithic instrument mechanical structure. Each IFU incorporates an image slicer, a fully refractive spectrograph with VPH-grating and a detector system connected to a global vacuum and cryogenic system. During 2011, all MUSE subsystems were integrated, aligned and tested independently in each institute. After validations, the systems were shipped to the P.I. institute at Lyon and were assembled in the Integration Hall This paper describes the end-to-end optical alignment procedure of the MUSE instrument. The design strategy, mixing an optical alignment by manufacturing (plug and play approach) and few adjustments on key components, is presented. We depict the alignment method for identifying the optical axis using several references located in pupil and image planes. All tools required to perform the global alignment between each subsystem are described. The success of this alignment approach is demonstrated by the good results for the MUSE image quality. MUSE commissioning at the VLT (Very Large Telescope) is planned for 2013.

  1. Validation of ASHA FACS-functional assessment of communication skills for Alzheimer disease population.

    PubMed

    de Carvalho, Isabel Albuquerque M; Mansur, Letícia Lessa

    2008-01-01

    This study was aimed to validate the American Speech-Language-Hearing Association Functional Assessment of Communication Skills (ASHA FACS) for a Brazilian population. The scale was translated and adapted into Portuguese. Thirty-two patients with mild Alzheimer disease (AD), 25 patients with moderate AD, and 51 elderly without dementia were examined with Mini Mental State Examination, Geriatric Depression Scale, and Alzheimer Disease Assessment Scale-cognitive subscale (ADAS-cog). The ASHA FACS was answered by their relative/caregiver. The scale's internal consistency, its inter-examiner and intra-examiner's reproducibility, and scale's criterion validity were researched by correlation with ADAS-cog. The sensitivity and specificity were also researched. Statistical analyses indicated that the ASHA FACS has excellent internal consistency (Cronbach [alpha]=0.955), test-retest reliability (interclass correlation coefficient=0.995; P<0.001), and inter-examiners (interclass correlation coefficient=0.998; P<0.001). It showed excellent criterion validity when correlated with ADAS-cog. The ASHA FACS scale showed good sensitivity (75.0%) and specificity (82.4%) values once it is an ecologic and broad evaluation. The ASHA FACS Portuguese version is a valid and reliable instrument to verify communication alterations in AD patients and fills an important gap of efficiency indicators for speech language therapy in our country.

  2. GS-align for glycan structure alignment and similarity measurement

    PubMed Central

    Lee, Hui Sun; Jo, Sunhwan; Mukherjee, Srayanta; Park, Sang-Jun; Skolnick, Jeffrey; Lee, Jooyoung; Im, Wonpil

    2015-01-01

    Motivation: Glycans play critical roles in many biological processes, and their structural diversity is key for specific protein-glycan recognition. Comparative structural studies of biological molecules provide useful insight into their biological relationships. However, most computational tools are designed for protein structure, and despite their importance, there is no currently available tool for comparing glycan structures in a sequence order- and size-independent manner. Results: A novel method, GS-align, is developed for glycan structure alignment and similarity measurement. GS-align generates possible alignments between two glycan structures through iterative maximum clique search and fragment superposition. The optimal alignment is then determined by the maximum structural similarity score, GS-score, which is size-independent. Benchmark tests against the Protein Data Bank (PDB) N-linked glycan library and PDB homologous/non-homologous N-glycoprotein sets indicate that GS-align is a robust computational tool to align glycan structures and quantify their structural similarity. GS-align is also applied to template-based glycan structure prediction and monosaccharide substitution matrix generation to illustrate its utility. Availability and implementation: http://www.glycanstructure.org/gsalign. Contact: wonpil@ku.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25857669

  3. Nearly monotonic problems: A key to effective FA/C distributed sensor interpretation?

    SciTech Connect

    Carver, N.; Lesser, V.; Whitehair, R.

    1996-12-31

    The functionally-accurate, cooperative (FA/C) distributed problem-solving paradigm is one approach for organizing distributed problem solving among homogeneous, cooperating agents. A key assumption of the FA/C model has been that the agents` local solutions can substitute for the raw data in determining the global solutions. This is not the case in general, however. Does this mean that researchers` intuitions have been wrong and/or that FA/C problem solving is not likely to be effective? We suggest that some domains have a characteristic that can account for the success of exchanging mainly local solutions. We call such problems nearly monotonic. This concept is discussed in the context of FA/C-based distributed sensor interpretation.

  4. ENDEAVOUR: Phase 3 Multicenter Study of Revusiran (ALN-TTRSC) in Patients With Transthyretin (TTR) Mediated Familial Amyloidotic Cardiomyopathy (FAC)

    ClinicalTrials.gov

    2016-10-11

    Transthyretin (TTR) Mediated Familial Amyloidotic Cardiomyopathy (FAC); Amyloidosis, Hereditary; Amyloid Neuropathies, Familial; Amyloid Neuropathies; Amyloidosis, Hereditary, Transthyretin-Related; Familial Transthyretin Cardiac Amyloidosis

  5. RF Jitter Modulation Alignment Sensing

    NASA Astrophysics Data System (ADS)

    Ortega, L. F.; Fulda, P.; Diaz-Ortiz, M.; Perez Sanchez, G.; Ciani, G.; Voss, D.; Mueller, G.; Tanner, D. B.

    2017-01-01

    We will present the numerical and experimental results of a new alignment sensing scheme which can reduce the complexity of alignment sensing systems currently used, while maintaining the same shot noise limited sensitivity. This scheme relies on the ability of electro-optic beam deflectors to create angular modulation sidebands in radio frequency, and needs only a single-element photodiode and IQ demodulation to generate error signals for tilt and translation degrees of freedom in one dimension. It distances itself from current techniques by eliminating the need for beam centering servo systems, quadrant photodetectors and Gouy phase telescopes. RF Jitter alignment sensing can be used to reduce the complexity in the alignment systems of many laser optical experiments, including LIGO and the ALPS experiment.

  6. The Consequences of Saturn’s Rotating Asymmetric Ring Current

    NASA Astrophysics Data System (ADS)

    Southwood, D. J.; Kivelson, M. G.

    2009-12-01

    The plasma and field behavior in the dipolar region of the Saturnian magnetosphere is described, based primarily on interpretation of the magnetic field behavior measured by the Cassini spacecraft. Previous authors, such as Provan and Khurana, have pointed out that the regular pulses in field strength at around 10.8 hrs period detected in this region imply the existence not only of a symmetric ring current but also of a partial ring current. Once spacecraft motion in local time has been allowed for, one finds a close to sinusoidal variation with azimuth and time of the magnetic signal. Hence the partial ring current appears to quasi-rigidly rotate about the planetary axis at the same 10.8 hr period as the pulsing of the Saturn kilometric radiation. We point out that, independent of whether the excess current is due to asymmetry in flux tube population or in plasma beta (pressure normalized to field pressure), such a current gives rise to a rotating circulation system. The compressional field pattern is consistent with an m = 1 pattern of circulation. The fairly uniform inner magnetosphere cam magnetic signature predicted on the basis of inner magnetosphere transverse field components in our past work is modified in a systematic way by the partial ring current effects. The circulation due to the partial ring current has its own set of distributed field aligned currents (FACs). The rotating transverse perturbation field components are twisted by the FACs so that the radial field is reduced at low L-shells and increased at larger L. Overall the cam field is depressed at low L and enhanced as one approaches the boundary of the cam region at L = 10-12. In practice the system must also respond to some local time effects. Loss of plasma is easier on the night-side and flanks than on the day-side and so a day-night asymmetry is imposed tending to increase the perturbation field amplitudes by night. The FACs driven by the asymmetric ring current should be broadly

  7. FacPad: Bayesian sparse factor modeling for the inference of pathways responsive to drug treatment

    PubMed Central

    Ma, Haisu; Zhao, Hongyu

    2012-01-01

    Motivation: It is well recognized that the effects of drugs are far beyond targeting individual proteins, but rather influencing the complex interactions among many relevant biological pathways. Genome-wide expression profiling before and after drug treatment has become a powerful approach for capturing a global snapshot of cellular response to drugs, as well as to understand drugs’ mechanism of action. Therefore, it is of great interest to analyze this type of transcriptomic profiling data for the identification of pathways responsive to different drugs. However, few computational tools exist for this task. Results: We have developed FacPad, a Bayesian sparse factor model, for the inference of pathways responsive to drug treatments. This model represents biological pathways as latent factors and aims to describe the variation among drug-induced gene expression alternations in terms of a much smaller number of latent factors. We applied this model to the Connectivity Map data set (build 02) and demonstrated that FacPad is able to identify many drug–pathway associations, some of which have been validated in the literature. Although this method was originally designed for the analysis of drug-induced transcriptional alternation data, it can be naturally applied to many other settings beyond polypharmacology. Availability and implementation: The R package ‘FacPad’ is publically available at: http://cran.open-source-solution.org/web/packages/FacPad/ Contact: hongyu.zhao@yale.edu Supplementary Information: Supplementary data are available at Bioinformatics online. PMID:22923307

  8. 7 CFR 1945.18 - United States Department of Agriculture (USDA) Food and Agriculture Council (FAC).

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 13 2011-01-01 2009-01-01 true United States Department of Agriculture (USDA) Food and Agriculture Council (FAC). 1945.18 Section 1945.18 Agriculture Regulations of the Department of Agriculture (Continued) RURAL HOUSING SERVICE, RURAL BUSINESS-COOPERATIVE SERVICE, RURAL UTILITIES...

  9. 7 CFR 1945.18 - United States Department of Agriculture (USDA) Food and Agriculture Council (FAC).

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 13 2012-01-01 2012-01-01 false United States Department of Agriculture (USDA) Food and Agriculture Council (FAC). 1945.18 Section 1945.18 Agriculture Regulations of the Department of Agriculture (Continued) RURAL HOUSING SERVICE, RURAL BUSINESS-COOPERATIVE SERVICE, RURAL UTILITIES...

  10. 7 CFR 1945.18 - United States Department of Agriculture (USDA) Food and Agriculture Council (FAC).

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 13 2010-01-01 2009-01-01 true United States Department of Agriculture (USDA) Food and Agriculture Council (FAC). 1945.18 Section 1945.18 Agriculture Regulations of the Department of Agriculture (Continued) RURAL HOUSING SERVICE, RURAL BUSINESS-COOPERATIVE SERVICE, RURAL UTILITIES...

  11. Fac-Back-OPAC: An Open Source Interface to Your Library System

    ERIC Educational Resources Information Center

    Beccaria, Mike; Scott, Dan

    2007-01-01

    The new Fac-Back-OPAC (a faceted backup OPAC) is built on code that was originally developed by Casey Durfee in February 2007. It represents the convergence of two prominent trends in library tools: the decoupling of discovery tools from the traditional integrated library system (ILS) and the use of readily available open source components to…

  12. Substrate Engineering Enabling Fluorescence Droplet Entrapment for IVC-FACS-Based Ultrahigh-Throughput Screening.

    PubMed

    Ma, Fuqiang; Fischer, Michael; Han, Yunbin; Withers, Stephen G; Feng, Yan; Yang, Guang-Yu

    2016-09-06

    In vitro compartmentalization-based fluorescence-activated cell sorting (IVC-FACS) is a powerful screening tool for directed evolution of enzymes. However, the efficiency of IVC-FACS is limited by the tendency of the fluorescent reporter to diffuse out of the droplets, which decouples the genotype and phenotype of the target gene. Herein we present a new strategy called fluorescence droplet entrapment (FDE) to solve this problem. The substrate is designed with a polarity that enables it to pass through the oil phase, react with the enzyme and generate an oil-impermeable and fluorescent product that remains entrapped inside the droplet. Several FDE substrates were designed, using two distinct substrate engineering strategies, for the detection of phosphotriesterases, carboxylesterases, and glycosidases activities. Model screening assays in which rare phosphotriesterase-active cells were enriched from large excesses of inactive cells showed that the enrichment efficiency achievable using an FDE substrate was as high as 900-fold: the highest yet reported in such an IVC-FACS system. Thus, FDE provides a means to tightly control the onset of the enzymatic reaction, minimize droplet cross-talk, and lower the background fluorescence. It therefore may serve as a useful strategy for the IVC-FACS screening of enzymes, antibodies, and other proteins.

  13. Critical assessment of fluorescence polarization measurements with a FACS IV cell sorter

    NASA Astrophysics Data System (ADS)

    Muller, Claude P.; Krabichler, Gert

    1988-09-01

    The usefulness and limitations of the Becton-Dickinson fluorescence-activated cell sorter FACS IV for fluorescence polarization measurements were examined. A set of tests to determine the characteristics of the detection geometry, the optical properties of the beam splitter, and the capability to process fluorescence polarization data is presented. Recommendations are provided for correcting instrumental deficiencies.

  14. Function and evolutionary diversity of fatty acid amino acid conjugates (FACs)in Lepidopteran caterpillars

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Fatty acid amino acid conjugates (FACs) in regurgitant of larval Spodoptera exigua1 were initially identified as plant volatile elicitors and research has been focused on this apparent ecological disadvantage rather than on possible benefit for the caterpillar itself. Recently, we demonstrated that...

  15. The Framework for an Information Technology Strategic Roadmap for the United States Marine Corps: How Current Acquisitions Align to the Current Strategic Direction of the Department of Defense, Department of the Navy, and United States Marine Corps

    DTIC Science & Technology

    2008-06-01

    environmental) and internal organizational components affect and determine overall performance (Senge, 2006). Broadbent and Weill (1993) refer to alignment...base_level. Boot, M. (2007). War made new: Weapons, warfare, and the making of the modern world. New York, NY: Gotham Books. Broadbent , M

  16. Aligning for Innovation - Alignment Strategy to Drive Innovation

    NASA Technical Reports Server (NTRS)

    Johnson, Hurel; Teltschik, David; Bussey, Horace, Jr.; Moy, James

    2010-01-01

    With the sudden need for innovation that will help the country achieve its long-term space exploration objectives, the question of whether NASA is aligned effectively to drive the innovation that it so desperately needs to take space exploration to the next level should be entertained. Authors such as Robert Kaplan and David North have noted that companies that use a formal system for implementing strategy consistently outperform their peers. They have outlined a six-stage management systems model for implementing strategy, which includes the aligning of the organization towards its objectives. This involves the alignment of the organization from the top down. This presentation will explore the impacts of existing U.S. industrial policy on technological innovation; assess the current NASA organizational alignment and its impacts on driving technological innovation; and finally suggest an alternative approach that may drive the innovation needed to take the world to the next level of space exploration, with NASA truly leading the way.

  17. MUSE alignment onto VLT

    NASA Astrophysics Data System (ADS)

    Laurent, Florence; Renault, Edgard; Boudon, Didier; Caillier, Patrick; Daguisé, Eric; Dupuy, Christophe; Jarno, Aurélien; Lizon, Jean-Louis; Migniau, Jean-Emmanuel; Nicklas, Harald; Piqueras, Laure

    2014-07-01

    MUSE (Multi Unit Spectroscopic Explorer) is a second generation Very Large Telescope (VLT) integral field spectrograph developed for the European Southern Observatory (ESO). It combines a 1' x 1' field of view sampled at 0.2 arcsec for its Wide Field Mode (WFM) and a 7.5"x7.5" field of view for its Narrow Field Mode (NFM). Both modes will operate with the improved spatial resolution provided by GALACSI (Ground Atmospheric Layer Adaptive Optics for Spectroscopic Imaging), that will use the VLT deformable secondary mirror and 4 Laser Guide Stars (LGS) foreseen in 2015. MUSE operates in the visible wavelength range (0.465-0.93 μm). A consortium of seven institutes is currently commissioning MUSE in the Very Large Telescope for the Preliminary Acceptance in Chile, scheduled for September, 2014. MUSE is composed of several subsystems which are under the responsibility of each institute. The Fore Optics derotates and anamorphoses the image at the focal plane. A Splitting and Relay Optics feed the 24 identical Integral Field Units (IFU), that are mounted within a large monolithic structure. Each IFU incorporates an image slicer, a fully refractive spectrograph with VPH-grating and a detector system connected to a global vacuum and cryogenic system. During 2012 and 2013, all MUSE subsystems were integrated, aligned and tested to the P.I. institute at Lyon. After successful PAE in September 2013, MUSE instrument was shipped to the Very Large Telescope in Chile where that was aligned and tested in ESO integration hall at Paranal. After, MUSE was directly transported, fully aligned and without any optomechanical dismounting, onto VLT telescope where the first light was overcame the 7th of February, 2014. This paper describes the alignment procedure of the whole MUSE instrument with respect to the Very Large Telescope (VLT). It describes how 6 tons could be move with accuracy better than 0.025mm and less than 0.25 arcmin in order to reach alignment requirements. The success

  18. Multiple protein structure alignment.

    PubMed Central

    Taylor, W. R.; Flores, T. P.; Orengo, C. A.

    1994-01-01

    A method was developed to compare protein structures and to combine them into a multiple structure consensus. Previous methods of multiple structure comparison have only concatenated pairwise alignments or produced a consensus structure by averaging coordinate sets. The current method is a fusion of the fast structure comparison program SSAP and the multiple sequence alignment program MULTAL. As in MULTAL, structures are progressively combined, producing intermediate consensus structures that are compared directly to each other and all remaining single structures. This leads to a hierarchic "condensation," continually evaluated in the light of the emerging conserved core regions. Following the SSAP approach, all interatomic vectors were retained with well-conserved regions distinguished by coherent vector bundles (the structural equivalent of a conserved sequence position). Each bundle of vectors is summarized by a resultant, whereas vector coherence is captured in an error term, which is the only distinction between conserved and variable positions. Resultant vectors are used directly in the comparison, which is weighted by their error values, giving greater importance to the matching of conserved positions. The resultant vectors and their errors can also be used directly in molecular modeling. Applications of the method were assessed by the quality of the resulting sequence alignments, phylogenetic tree construction, and databank scanning with the consensus. Visual assessment of the structural superpositions and consensus structure for various well-characterized families confirmed that the consensus had identified a reasonable core. PMID:7849601

  19. Ferroplasma acidarmanus RPA2 facilitates efficient unwinding of forked DNA substrates by monomers of FacXPD helicase.

    PubMed

    Pugh, Robert A; Lin, Yuyen; Eller, Chelcie; Leesley, Haley; Cann, Isaac K O; Spies, Maria

    2008-11-28

    The strand-separation activity that is important for many cellular DNA processing machineries is provided by DNA helicases. In order to understand the physiological properties of a helicase acting in the context of its macromolecular machinery, it is imperative to identify the proteins that interact with the enzyme and to analyze how these proteins affect its helicase activities. The archaeal Rad3 helicase XPD (xeroderma pigmentosum group D protein) from Ferroplasma acidarmanus (FacXPD) is a superfamily II 5'-->3' DNA helicase. Similar to its mammalian homolog working as an integral part of the transcription factor IIH complex, FacXPD may play an important role in nucleotide excision repair (NER) and transcription initiation. Interaction between FacXPD and other archaeal NER proteins likely modulates their respective activities. Replication protein A (RPA), a single-stranded DNA (ssDNA)-binding protein, is one of the NER proteins that functionally interact with the human transcription factor IIH complex. There are two RPA proteins in F. acidarmanus: FacRPA1, a homodimer of two monomers consisting of two oligonucleotide/oligosaccharide binding folds, and FacRPA2, a monomer containing a single oligonucleotide/oligosaccharide binding fold. In this study, we analyzed the effect of these ssDNA-binding proteins on FacXPD helicase activity. We found that FacRPA2 stimulates DNA unwinding by FacXPD helicase through a novel mechanism by providing a helix-destabilizing function. In contrast, FacRPA1 fails to stimulate helicase activity to the same extent as FacRPA2 and competes with FacXPD for binding to the ssDNA-double-stranded DNA junction. We conclude that the FacRPA2-coated fork is a preferred and likely physiological substrate that a monomer of FacXPD can unwind with a processivity sufficient for expansion of the NER or transcription bubble. We also suggest that duplex melting by a cognate ssDNA-binding protein coordinated with translocation by a helicase may represent

  20. Oblique electron-cyclotron-emission radial and phase detector of rotating magnetic islands applied to alignment and modulation of electron-cyclotron-current-drive for neoclassical tearing mode stabilization.

    PubMed

    Volpe, F; Austin, M E; Campbell, G; Deterly, T

    2012-10-01

    A two channel oblique electron cyclotron emission (ECE) radiometer was installed on the DIII-D tokamak and interfaced to four gyrotrons. Oblique ECE was used to toroidally and radially localize rotating magnetic islands and so assist their electron cyclotron current drive (ECCD) stabilization. In particular, after manipulations operated by the interfacing analogue circuit, the oblique ECE signals directly modulated the current drive in synch with the island rotation and in phase with the island O-point, for a more efficient stabilization. Apart from the different toroidal location, the diagnostic view is identical to the ECCD launch direction, which greatly simplified the real-time use of the signals. In fact, a simple toroidal extrapolation was sufficient to lock the modulation to the O-point phase. This was accomplished by a specially designed phase shifter of nearly flat response over the 1-7 kHz range. Moreover, correlation analysis of two channels slightly above and below the ECCD frequency allowed checking the radial alignment to the island, based on the fact that for satisfactory alignment the two signals are out of phase.

  1. Oblique electron-cyclotron-emission radial and phase detector of rotating magnetic islands applied to alignment and modulation of electron-cyclotron-current-drive for neoclassical tearing mode stabilization

    SciTech Connect

    Volpe, F.; Austin, M. E.; Campbell, G.; Deterly, T.

    2012-10-15

    A two channel oblique electron cyclotron emission (ECE) radiometer was installed on the DIII-D tokamak and interfaced to four gyrotrons. Oblique ECE was used to toroidally and radially localize rotating magnetic islands and so assist their electron cyclotron current drive (ECCD) stabilization. In particular, after manipulations operated by the interfacing analogue circuit, the oblique ECE signals directly modulated the current drive in synch with the island rotation and in phase with the island O-point, for a more efficient stabilization. Apart from the different toroidal location, the diagnostic view is identical to the ECCD launch direction, which greatly simplified the real-time use of the signals. In fact, a simple toroidal extrapolation was sufficient to lock the modulation to the O-point phase. This was accomplished by a specially designed phase shifter of nearly flat response over the 1-7 kHz range. Moreover, correlation analysis of two channels slightly above and below the ECCD frequency allowed checking the radial alignment to the island, based on the fact that for satisfactory alignment the two signals are out of phase.

  2. FACS-based Satellite Cell Isolation From Mouse Hind Limb Muscles.

    PubMed

    Gromova, Anastasia; Tierney, Matthew T; Sacco, Alessandra

    2015-08-20

    Fluorescence Activated Cell Sorting (FACS) is a sensitive and accurate method for purifying satellite cells, or muscle stem cells, from adult mouse skeletal muscle (Liu et al., 2013; Sacco et al., 2008; Tierney et al., 2014). Mechanical and enzymatic digestion of hind limb muscles releases mononuclear muscle cells into suspension. This protocol employs fractionation strategies to deplete cells expressing the cell surface markers CD45, CD31, CD11b and Ly-6A/E-Sca1, both by magnetic separation and FACS-based exclusion, and positively select for cells expressing a7-integrin and CD34. This enables the researcher to successfully enrich satellite cells that uniformly express the paired-box transcription factor Pax7 and are capable of long-term self-renewal, skeletal muscle repair and muscle stem cell pool repopulation.

  3. Re-Casting the FAC Net: People, Platforms, and Policy in Forward Air Control

    DTIC Science & Technology

    2015-06-01

    radar-guided surface-to air-missiles (SAMs), anti-aircraft artillery ( AAA ), and small arms deny the use of airspace.8 Threats force FACs to circle...keep supporting fighters at greater distances from targets, while AAA keeps aircraft at higher altitudes. Furthermore, the enemy can employ both...pointing at the target, they could remain above certain AAA threats from the ground. In the early years of laser-guided deliveries, the Vietnamese shot

  4. Engraftment of FACS Isolated Muscle Stem Cells into Injured Skeletal Muscle.

    PubMed

    Tierney, Matthew; Sacco, Alessandra

    2017-01-01

    Skeletal muscle stem cell (MuSC) isolation and transplantation are invaluable tools to assess their capacity for self-renewal and tissue repair. Significant technical advances in recent years have led to the optimization of these approaches, improving our ability to assess MuSC regenerative potential. Here, we describe the procedures for Fluorescent Activated Cell Sorting (FACS)-based isolation of MuSC, their intramuscular transplantation, and analysis of their engraftment into host tissues.

  5. Re-casting the FAC Net: People, Platforms, and Policy in Forward Air Control

    DTIC Science & Technology

    2015-06-01

    An officer ( aviator /pilot) member of the tactical air control party who, from a forward ground or airborne position, controls aircraft in close air...Officers (ALOs) perform the functions of the FAC but may be enlisted and not aviators . Therefore, unless specifically denoted, this analysis uses the term...17 i While military aviation developed initially from the needs of ground commanders, advocates of airpower theory quickly sought independence

  6. Use FACS sorting in metabolic engineering of Escherichia coli for increased peptide production.

    PubMed

    Cheng, Qiong; Ruebling-Jass, Kristin; Zhang, Jianzhong; Chen, Qi; Croker, Kevin M

    2012-01-01

    Many proteins and peptides have been used in therapeutic or industrial applications. They are often produced as recombinant forms by microbial fermentation. Targeted metabolic engineering of the production strains has usually been the approach taken to increase protein production, and this approach requires sufficient knowledge about cell metabolism and regulation. Random screening is an alternative approach that could circumvent the knowledge requirement, but is hampered by lack of suitable high-throughput screening methods. We developed a novel fluorescence-activated cell sorting (FACS) method to screen for cells with increased peptide production. Using a model peptide rich in certain amino acids, we showed that increased fluorescence clones sorted from a plasmid expression library contained genes encoding rate-limiting enzymes for amino acid synthesis. These expression clones showed increased peptide production. This demonstrated that FACS could be used as a very powerful tool for metabolic engineering. It can be generally applied to other products or processes if the desired phenotype could be correlated with a fluorescence or light scattering parameter on the FACS.

  7. Evaluation of EBV transformation of human memory B-cells isolated by FACS and MACS techniques.

    PubMed

    Sadreddini, Sanam; Jadidi-Niaragh, Farhad; Younesi, Vahid; Pourlak, Tala; Afkham, Amir; Shokri, Fazel; Yousefi, Mehdi

    2016-07-01

    Several studies have been performed to develop effective neutralizing monoclonal antibodies. The Epstein-Barr virus (EBV) can efficiently immortalize B-cells to establish lymphoblastoid cell lines (LCL) and so it has been used extensively for transformation of B-cells to produce and secrete immunoglobulin. The present study addressed the effect of TLR7/8 agonist (R848), feeder cells layer and fluorescence-activated cell sorting (FACS) and magnetic-activated cell sorting (MACS) cell separation methods on the transformation efficiency of antibody-producing memory B-cells. For these studies, the antigen used for analyses of antibody formation was the tetanus neurotoxin (TeNT) derived from Clostridium tetani. The results here showed that employing an HFFF.PI6 feeder cell layer, R848 agonist and FACS-mediated purification of memory B-cells led to increased transformation efficiency. Altogether, the effects of the R848 and the feeder cells provided an efficient method for EBV transformation of human B-cells. Moreover, there was an advantage in using FACS sorting of B-cells over the MACS method in the context of EBV transformation and immortalization of precursors of antigen-specific B-cells.

  8. Understanding M-ligand bonding and mer-/fac-isomerism in tris(8-hydroxyquinolinate) metallic complexes.

    PubMed

    Lima, Carlos F R A C; Taveira, Ricardo J S; Costa, José C S; Fernandes, Ana M; Melo, André; Silva, Artur M S; Santos, Luís M N B F

    2016-06-28

    Tris(8-hydroxyquinolinate) metallic complexes, Mq3, are one of the most important classes of organic semiconductor materials. Herein, the nature of the chemical bond in Mq3 complexes and its implications on their molecular properties were investigated by a combined experimental and computational approach. Various Mq3 complexes, resulting from the alteration of the metal and substitution of the 8-hydroxyquinoline ligand in different positions, were prepared. The mer-/fac-isomerism in Mq3 was explored by FTIR and NMR spectroscopy, evidencing that, irrespective of the substituent, mer- and fac-are the most stable molecular configurations of Al(iii) and In(iii) complexes, respectively. The relative M-ligand bond dissociation energies were evaluated experimentally by electrospray ionization tandem mass spectrometry (ESI-MS-MS), showing a non-monotonous variation along the group (Al > In > Ga). The results reveal a strong covalent character in M-ligand bonding, which allows for through-ligand electron delocalization, and explain the preferred molecular structures of Mq3 complexes as resulting from the interplay between bonding and steric factors. The mer-isomer reduces intraligand repulsions, being preferred for smaller metals, while the fac-isomer is favoured for larger metals where stronger covalent M-ligand bonds can be formed due to more extensive through-ligand conjugation mediated by metal "d" orbitals.

  9. Aligning Assessments for COSMA Accreditation

    ERIC Educational Resources Information Center

    Laird, Curt; Johnson, Dennis A.; Alderman, Heather

    2015-01-01

    Many higher education sport management programs are currently in the process of seeking accreditation from the Commission on Sport Management Accreditation (COSMA). This article provides a best-practice method for aligning student learning outcomes with a sport management program's mission and goals. Formative and summative assessment procedures…

  10. Air Power Versus a Fielded Force: The Misty Facs Of Vietnam and the A-10 Facs of Kosovo a Comparative Analysis

    DTIC Science & Technology

    2002-06-01

    42 16 A-1H/J Sandy sitting alert………………………………………………………….44 17 HH-3 Jolly Green Helicopter ………………………………………………………46 18 Serbia, Kosovo and Montenegro...80 Momyer, 319. 27 helicopters .82 The versatility of the Misty FACs was further demonstrated in May and July when they began spotting for naval...Jolly Green helicopter during a rescue mission. 47 Figure 13: Camouflaged AAA Site in Route Package I on 19 Nov 67. The final quality of a

  11. Free-air ionization chamber, FAC-IR-300, designed for medium energy X-ray dosimetry

    NASA Astrophysics Data System (ADS)

    Mohammadi, S. M.; Tavakoli-Anbaran, H.; Zeinali, H. Z.

    2017-01-01

    The primary standard for X-ray photons is based on parallel-plate free-air ionization chamber (FAC). Therefore, the Atomic Energy Organization of Iran (AEOI) is tried to design and build the free-air ionization chamber, FAC-IR-300, for low and medium energy X-ray dosimetry. The main aim of the present work is to investigate specification of the FAC-IR-300 ionization chamber and design it. FAC-IR-300 dosimeter is composed of two parallel plates, a high voltage (HV) plate and a collector plate, along with a guard electrode that surrounds the collector plate. The guard plate and the collector were separated by an air gap. For obtaining uniformity in the electric field distribution, a group of guard strips was used around the ionization chamber. These characterizations involve determining the exact dimensions of the ionization chamber by using Monte Carlo simulation and introducing correction factors.

  12. Effect of HNT on the Microstructure, Thermal and Mechanical Properties of Al/FACS-HNT Composites Produced by GPI

    NASA Astrophysics Data System (ADS)

    Siewiorek, A.; Malczyk, P.; Sobczak, N.; Sobczak, J. J.; Czulak, A.; Kozera, R.; Gude, M.; Boczkowska, A.; Homa, M.

    2016-08-01

    To develop an optimised manufacturing method of fly ash-reinforced metal matrix composites, the preliminary tests were performed on the cenospheres selected from fly ash (FACS) with halloysite nanotubes (HNTs) addition. The preform made out of FACS with and without the addition of HNT (with 5 and 10 wt.%) has been infiltrated by the pure aluminium (Al) via adapted gas pressure infiltration process. This paper reveals the influence of HNT addition on the microstructure (analysis was done by computed tomography and scanning electron microscopy combined with energy-dispersive x-ray spectroscopy), thermal properties (thermal expansion coefficient, thermal conductivity and specific heat) and the mechanical properties (hardness and compression test) of manufactured composites. The analysis of structure-property relationships for Al/FACS-HNT composites produced shows that the addition of 5 wt.% of HNT to FACS preform contributes to receiving of the best mechanical and structural properties of investigated composites.

  13. Alignment Tool For Inertia Welding

    NASA Technical Reports Server (NTRS)

    Snyder, Gary L.

    1991-01-01

    Compact, easy-to-use tool aligns drive bar of inertia welder over hole in stub. Ensures drive bar concentric to hole within 0.002 in. (0.051 mm.). Holds two batteries and light bulb. Electrical circuit completed, providing current to bulb when pin in contact with post. When pin centered in post hole, it does not touch post, and lamp turns off. Built for use in making repair welds on liquid-oxygen-injector posts in Space Shuttle main engine. Version having suitably modified dimensions used to facilitate alignment in other forests of post.

  14. Alignment of Developments in Higher Education

    ERIC Educational Resources Information Center

    Cowan, John; George, Judith W.; Pinheiro-Torres, Andreia

    2004-01-01

    This study builds upon the concept of alignment within the curriculum (due to Biggs) and suggests, in the context of two current examples, an integrated methodology for effectively aligned development activities within universities. Higher Education institutions face important challenges. Firstly, quality enhancement of the curriculum is now an…

  15. Cavity alignment using fringe scanning

    NASA Astrophysics Data System (ADS)

    Sinkunaite, Laura Paulina; Kawabe, Keita; Landry, Michael

    2017-01-01

    LIGO employs two 4-km long Fabry-Pérot arm cavities, which need to be aligned in order for an interferometer to be locked on a TEM00 mode. Once the cavity is locked, alignment signals can be derived from wave-front sensors which measure the TEM01 mode content. However, the alignment state is not always good enough for locking on TEM00. Even when this is the case, the alignment can be evaluated using a free swinging cavity, that shows flashes when higher-order modes become resonant. By moving test masses, small changes are made to the mirror orientation, and hence the TEM00 mode can be optimized iteratively. Currently, this is a manual procedure, and thus it is very time-consuming. Therefore, this project is aimed to study another possible way to lock the cavity on the TEM00 mode. Misalignment information can also be extracted from the power of the higher-order modes transmitted through the cavity. This talk will present an algorithm for this alternative and faster way to derive the alignment state of the arm cavities. Supported by APS FIP, NSF, and Caltech SFP.

  16. MP-Align: alignment of metabolic pathways

    PubMed Central

    2014-01-01

    Background Comparing the metabolic pathways of different species is useful for understanding metabolic functions and can help in studying diseases and engineering drugs. Several comparison techniques for metabolic pathways have been introduced in the literature as a first attempt in this direction. The approaches are based on some simplified representation of metabolic pathways and on a related definition of a similarity score (or distance measure) between two pathways. More recent comparative research focuses on alignment techniques that can identify similar parts between pathways. Results We propose a methodology for the pairwise comparison and alignment of metabolic pathways that aims at providing the largest conserved substructure of the pathways under consideration. The proposed methodology has been implemented in a tool called MP-Align, which has been used to perform several validation tests. The results showed that our similarity score makes it possible to discriminate between different domains and to reconstruct a meaningful phylogeny from metabolic data. The results further demonstrate that our alignment algorithm correctly identifies subpathways sharing a common biological function. Conclusion The results of the validation tests performed with MP-Align are encouraging. A comparison with another proposal in the literature showed that our alignment algorithm is particularly well-suited to finding the largest conserved subpathway of the pathways under examination. PMID:24886436

  17. Girder Alignment Plan

    SciTech Connect

    Wolf, Zackary; Ruland, Robert; LeCocq, Catherine; Lundahl, Eric; Levashov, Yurii; Reese, Ed; Rago, Carl; Poling, Ben; Schafer, Donald; Nuhn, Heinz-Dieter; Wienands, Uli; /SLAC

    2010-11-18

    The girders for the LCLS undulator system contain components which must be aligned with high accuracy relative to each other. The alignment is one of the last steps before the girders go into the tunnel, so the alignment must be done efficiently, on a tight schedule. This note documents the alignment plan which includes efficiency and high accuracy. The motivation for girder alignment involves the following considerations. Using beam based alignment, the girder position will be adjusted until the beam goes through the center of the quadrupole and beam finder wire. For the machine to work properly, the undulator axis must be on this line and the center of the undulator beam pipe must be on this line. The physics reasons for the undulator axis and undulator beam pipe axis to be centered on the beam are different, but the alignment tolerance for both are similar. In addition, the beam position monitor must be centered on the beam to preserve its calibration. Thus, the undulator, undulator beam pipe, quadrupole, beam finder wire, and beam position monitor axes must all be aligned to a common line. All relative alignments are equally important, not just, for example, between quadrupole and undulator. We begin by making the common axis the nominal beam axis in the girder coordinate system. All components will be initially aligned to this axis. A more accurate alignment will then position the components relative to each other, without incorporating the girder itself.

  18. Localized field-aligned currents and 4-min TEC and ground magnetic oscillations during the 2015 eruption of Chile's Calbuco volcano

    NASA Astrophysics Data System (ADS)

    Aoyama, Tadashi; Iyemori, Toshihiko; Nakanishi, Kunihito; Nishioka, Michi; Rosales, Domingo; Veliz, Oscar; Safor, Erick Vidal

    2016-08-01

    The Calbuco volcano in southern Chile erupted on April 22, 2015. About 2 h after the first eruption, a Swarm satellite passed above the volcano and observed enhancement of small-amplitude (~0.5 nT) magnetic fluctuations with wave-packet structure which extends 15° in latitude. Similar wave packet is seen at the geomagnetic conjugate point of the volcano. Just after the eruption, geomagnetic fluctuations with the spectral peaks around the vertical acoustic resonance periods, 215 and 260 s, were also observed at Huancayo Geomagnetic Observatory located on the magnetic equator. Besides these observations, around 4-min, i.e., 175, 205 and 260 s, oscillations of total electron content (TEC) were observed at global positioning system stations near the volcano. The horizontal propagation velocity and the spatial scale of the TEC oscillation are estimated to be 720 m/s and 1600 km, respectively. These observations strongly suggest that the atmospheric waves induced by explosive volcanic eruption generate TEC variation and electric currents. The Swarm observation may be explained as a manifestation of their magnetic effects observed in the topside ionosphere.

  19. Water-stable fac-{TcO₃}⁺ complexes - a new field of technetium chemistry.

    PubMed

    Braband, Henrik

    2011-01-01

    The development of technetium chemistry has been lagging behind that of its heavier congener rhenium, primarily because the inherent radioactivity of all Tc isotopes has limited the number of laboratories that can study the chemistry of this fascinating element. Although technetium is an artificial element, it is not rare. Significant amounts of the isotope (99)Tc are produced every day as a fission byproduct in nuclear power plants. Therefore, a fundamental understanding of the chemistry of (99)Tc is essential to avoid its release into the environment. In this article the chemistry of technetium at its highest oxidation state (+VII) is reviewed with a special focus on recent developments which make water-stable complexes of the general type [TcO(3)(tacn-R)](+) (tacn-R = 1,4,7-triazacyclononane or derivatives) accessible. Complexes containing the fac-{TcO(3)}(+) core display a unique reactivity. In analogy to [OsO(4)] and [RuO(4)], complexes containing the fac-{TcO(3)}(+) core undergo with alkenes metal-mediated, vicinal cis-dihydroxylation reactions (alkene-glycol interconversion) in water via a (3+2)-cycloaddition reaction. Therefore, water-stable fac-{(99m)TcO(3)}(+) complexes pave the way for a new labeling strategy for radiopharmaceutical applications, based on (3+2)-cycloaddition reactions. This new concept for the labeling of biomolecules with small [(99m)TcO(3)(tacn-R)](+)-type complexes by way of a (3+2)-cycloaddition with alkenes is discussed in detail. The herein reported developments in high-valent technetium chemistry create a new field of research with this artificial element. This demonstrates the potential of fundamental research to provide new impetus of innovation for the development of new methods for radiopharmaceutical applications.

  20. RNA expression profiling from FACS-isolated cells of the Drosophila intestine.

    PubMed

    Dutta, Devanjali; Xiang, Jinyi; Edgar, Bruce A

    2013-11-13

    This unit describes a protocol for the isolation of Drosophila intestinal cell populations for the purpose of cell type-specific transcriptome profiling. A method to select a cell type of interest labeled with green or yellow fluorescent protein (GFP, YFP) by making use of the GAL4-UAS bipartite system and fluorescent-activated cell sorting (FACS) is presented. Total RNA is isolated from the sorted cells and linear RNA amplification is used to obtain sufficient amounts of high-quality RNA for analysis by microarray, RT-PCR, or RNA sequencing. This method will be useful for quantitative transcriptome comparison across intestinal cell types under normal and various experimental conditions.

  1. Expanding the Utility of FUCCI Reporters Using FACS-Based Omics Analysis.

    PubMed

    Chappell, James; Boward, Ben; Dalton, Stephen

    2016-01-01

    The FUCCI indicator system is a powerful tool for spatio-temporal analysis of the cell cycle, but its utility has been restricted so far to a limited range of applications. Here, we describe how to establish and validate the FUCCI system in murine pluripotent stem cells (PSCs) and describe the utility of transgenic FUCCI mice. We then describe how the FUCCI system can be used to generate material for a wide-range of omics-based applications in conjunction with FACS isolation of cells. This significantly broadens the potential applications of FUCCI reporters for studying the molecular basis of development and disease.

  2. A comparison of locally adaptive multigrid methods: LDC, FAC and FIC

    NASA Technical Reports Server (NTRS)

    Khadra, Khodor; Angot, Philippe; Caltagirone, Jean-Paul

    1993-01-01

    This study is devoted to a comparative analysis of three 'Adaptive ZOOM' (ZOom Overlapping Multi-level) methods based on similar concepts of hierarchical multigrid local refinement: LDC (Local Defect Correction), FAC (Fast Adaptive Composite), and FIC (Flux Interface Correction)--which we proposed recently. These methods are tested on two examples of a bidimensional elliptic problem. We compare, for V-cycle procedures, the asymptotic evolution of the global error evaluated by discrete norms, the corresponding local errors, and the convergence rates of these algorithms.

  3. Flow Pattern relative to the Substorm Current Wedge

    NASA Astrophysics Data System (ADS)

    Chu, X.; McPherron, R. L.; Hsu, T.

    2013-12-01

    Magnetospheric substorms play a key role in the coupling of the solar wind and the magnetosphere. The Substorm Current Wedge (SCW) is a key element in the present physical model of substorms. It is widely accepted that the SCW is created by earthward busty flows, but the generation mechanism is still unknown. Previous studies suggest pressure gradients and magnetic vortices are possible candidates. Due to the sparse coverage of satellites in space, these studies were strongly dependent on the assumption that the satellites were in the generation region of the field-aligned currents (FAC) forming the SCW. In this work, we take advantage of an inversion technique that determines the parameters describing the SCW and perform a statistical study on the plasma and magnetic field parameters of the flow pattern relative to the SCW. The inversion technique finds the location and the intensity of the SCW from midlatitude magnetic data. The technique has been validated using auroral observations, Equivalent Ionospheric Currents (EIC), SYM-H index from SuperMAG, and magnetic perturbations at geosynchronous orbit by the GOES satellite. A database of substorm events has been created using midlatitude positive bays, which are the ground signature of the SCW at lower latitudes. The inversion technique is applied to each event in the database to determine the location of the origin of the SCW. The inversion results are also used to find conjunction events with space observations from VAP (RBSP), THEMIS and GOES. The plasma and magnetic field parameters such as the pressure gradient and magnetic vorticity are then categorized as a function of their location relative to the origin of the SCW. How the distribution/pattern of the pressure gradient and vorticity are related to the properties of the SCW (locations and intensity of the FAC), and flows (entropy, velocity and density) will be determined.

  4. Multifunctionalization of cetuximab with bioorthogonal chemistries and parallel EGFR profiling of cell-lines using imaging, FACS and immunoprecipitation approaches.

    PubMed

    Reschke, Melanie L; Uprety, Rajendra; Bodhinayake, Imithri; Banu, Matei; Boockvar, John A; Sauve, Anthony A

    2014-12-01

    The ability to derivatize antibodies is currently limited by the chemical structure of antibodies as polypeptides. Modern methods of bioorthogonal and biocompatible chemical modifications could make antibody functionalization more predictable and easier, without compromising the functions of the antibody. To explore this concept, we modified the well-known anti-epidermal growth factor receptor (EGFR) drug, cetuximab (Erbitux®), with 5-azido-2-nitro-benzoyl (ANB) modifications by optimization of an acylation protocol. We then show that the resulting ANB-cetuximab can be reliably modified with dyes (TAMRA and carboxyrhodamine) or a novel synthesized cyclooctyne modified biotin. The resulting dye- and biotin-modified cetuximabs were then tested across several assay platforms with several cell lines including U87, LN229, F98EGFR, F98WT and HEK293 cells. The assay platforms included fluorescence microscopy, FACS and biotin-avidin based immunoprecipitation methods. The modified antibody performs consistently in all of these assay platforms, reliably determining relative abundances of EGFR expression on EGFR expressing cells (LN229 and F98EGFR) and failing to cross react with weak to negative EGFR expressing cells (U87, F98WT and HEK293). The ease of achieving diverse and assay relevant functionalizations as well as the consequent rapid construction of highly correlated antigen expression data sets highlights the power of bioorthogonal and biocompatible methods to conjugate macromolecules. These data provide a proof of concept for a multifunctionalization strategy that leverages the biochemical versatility and antigen specificity of antibodies.

  5. Plant volatile eliciting FACs in lepidopteran caterpillars, fruit flies, and crickets: a convergent evolution or phylogenetic inheritance?

    PubMed

    Yoshinaga, Naoko; Abe, Hiroaki; Morita, Sayo; Yoshida, Tetsuya; Aboshi, Takako; Fukui, Masao; Tumlinson, James H; Mori, Naoki

    2014-01-01

    Fatty acid amino acid conjugates (FACs), first identified in lepidopteran caterpillar spit as elicitors of plant volatile emission, also have been reported as major components in gut tracts of Drosophila melanogaster and cricket Teleogryllus taiwanemma. The profile of FAC analogs in these two insects was similar to that of tobacco hornworm Manduca sexta, showing glutamic acid conjugates predominantly over glutamine conjugates. The physiological function of FACs is presumably to enhance nitrogen assimilation in Spodoptera litura larvae, but in other insects it is totally unknown. Whether these insects share a common synthetic mechanism of FACs is also unclear. In this study, the biosynthesis of FACs was examined in vitro in five lepidopteran species (M. sexta, Cephonodes hylas, silkworm, S. litura, and Mythimna separata), fruit fly larvae and T. taiwanemma. The fresh midgut tissues of all of the tested insects showed the ability to synthesize glutamine conjugates in vitro when incubated with glutamine and sodium linolenate. Such direct conjugation was also observed for glutamic acid conjugates in all the insects but the product amount was very small and did not reflect the in vivo FAC patterns in each species. In fruit fly larvae, the predominance of glutamic acid conjugates could be explained by a shortage of substrate glutamine in midgut tissues, and in M. sexta, a rapid hydrolysis of glutamine conjugates has been reported. In crickets, we found an additional unique biosynthetic pathway for glutamic acid conjugates. T. taiwanemma converted glutamine conjugates to glutamic acid conjugates by deaminating the side chain of the glutamine moiety. Considering these findings together with previous results, a possibility that FACs in these insects are results of convergent evolution cannot be ruled out, but it is more likely that the ancestral insects had the glutamine conjugates and crickets and other insects developed glutamic acid conjugates in a different way.

  6. Plant volatile eliciting FACs in lepidopteran caterpillars, fruit flies, and crickets: a convergent evolution or phylogenetic inheritance?

    PubMed Central

    Yoshinaga, Naoko; Abe, Hiroaki; Morita, Sayo; Yoshida, Tetsuya; Aboshi, Takako; Fukui, Masao; Tumlinson, James H.; Mori, Naoki

    2013-01-01

    Fatty acid amino acid conjugates (FACs), first identified in lepidopteran caterpillar spit as elicitors of plant volatile emission, also have been reported as major components in gut tracts of Drosophila melanogaster and cricket Teleogryllus taiwanemma. The profile of FAC analogs in these two insects was similar to that of tobacco hornworm Manduca sexta, showing glutamic acid conjugates predominantly over glutamine conjugates. The physiological function of FACs is presumably to enhance nitrogen assimilation in Spodoptera litura larvae, but in other insects it is totally unknown. Whether these insects share a common synthetic mechanism of FACs is also unclear. In this study, the biosynthesis of FACs was examined in vitro in five lepidopteran species (M. sexta, Cephonodes hylas, silkworm, S. litura, and Mythimna separata), fruit fly larvae and T. taiwanemma. The fresh midgut tissues of all of the tested insects showed the ability to synthesize glutamine conjugates in vitro when incubated with glutamine and sodium linolenate. Such direct conjugation was also observed for glutamic acid conjugates in all the insects but the product amount was very small and did not reflect the in vivo FAC patterns in each species. In fruit fly larvae, the predominance of glutamic acid conjugates could be explained by a shortage of substrate glutamine in midgut tissues, and in M. sexta, a rapid hydrolysis of glutamine conjugates has been reported. In crickets, we found an additional unique biosynthetic pathway for glutamic acid conjugates. T. taiwanemma converted glutamine conjugates to glutamic acid conjugates by deaminating the side chain of the glutamine moiety. Considering these findings together with previous results, a possibility that FACs in these insects are results of convergent evolution cannot be ruled out, but it is more likely that the ancestral insects had the glutamine conjugates and crickets and other insects developed glutamic acid conjugates in a different way. PMID

  7. Synthesis and characterization of fac-Re(CO)3-aspartic-N-monoacetic acid, a structural analogue of a potential new renal tracer, fac-(99m)Tc(CO)3(ASMA).

    PubMed

    Klenc, Jeffrey; Lipowska, Malgorzata; Taylor, Andrew T; Marzilli, Luigi G

    2012-09-01

    The reaction of an aminopolycarboxylate ligand, aspartic-N-monoacetic acid (ASMA), with [Re(CO)3(H2O)3](+) was examined. The tridentate coordination of ASMA to this Re(I) tricarbonyl precursor yielded fac-Re(CO)3(ASMA) as a mixture of diastereomers. The chemistry is analogous to that of the Tc(I) tricarbonyl complex, which yields fac-(99m)Tc(CO)3(ASMA) under similar conditions. The formation, structure, and isomerization of fac-Re(CO)3(ASMA) products were characterized by HPLC, (1)H NMR spectroscopy, and X-ray crystallography. The two major fac-Re(CO)3(ASMA) diastereomeric products each have a linear ONO coordination mode with two adjacent five-membered chelate rings, but they differ in the endo or exo orientation of the uncoordinated acetate group, in agreement with expectations based on previous studies. Conditions have been identified for the expedient isomerization of fac-Re(CO)3(ASMA) to a mixture consisting primarily of one major product. Because different isomeric species typically have different pharmacokinetic characteristics, these conditions may provide for the practical isolation of a single (99m)Tc(CO)3(ASMA) species, thus allowing the isolation of the isomer that has optimal imaging and pharmacokinetic characteristics. This information will aid in the design of future (99m)Tc radiopharmaceuticals.

  8. Technology Alignment and Portfolio Prioritization (TAPP)

    NASA Technical Reports Server (NTRS)

    Funaro, Gregory V.; Alexander, Reginald A.

    2015-01-01

    Technology Alignment and Portfolio Prioritization (TAPP) is a method being developed by the Advanced Concepts Office, at NASA Marshall Space Flight Center. The TAPP method expands on current technology assessment methods by incorporating the technological structure underlying technology development, e.g., organizational structures and resources, institutional policy and strategy, and the factors that motivate technological change. This paper discusses the methods ACO is currently developing to better perform technology assessments while taking into consideration Strategic Alignment, Technology Forecasting, and Long Term Planning.

  9. Quantitative analysis of mammalian translation initiation sites by FACS-seq.

    PubMed

    Noderer, William L; Flockhart, Ross J; Bhaduri, Aparna; Diaz de Arce, Alexander J; Zhang, Jiajing; Khavari, Paul A; Wang, Clifford L

    2014-08-28

    An approach combining fluorescence-activated cell sorting and high-throughput DNA sequencing (FACS-seq) was employed to determine the efficiency of start codon recognition for all possible translation initiation sites (TIS) utilizing AUG start codons. Using FACS-seq, we measured translation from a genetic reporter library representing all 65,536 possible TIS sequences spanning the -6 to +5 positions. We found that the motif RYMRMVAUGGC enhanced start codon recognition and translation efficiency. However, dinucleotide interactions, which cannot be conveyed by a single motif, were also important for modeling TIS efficiency. Our dataset combined with modeling allowed us to predict genome-wide translation initiation efficiency for all mRNA transcripts. Additionally, we screened somatic TIS mutations associated with tumorigenesis to identify candidate driver mutations consistent with known tumor expression patterns. Finally, we implemented a quantitative leaky scanning model to predict alternative initiation sites that produce truncated protein isoforms and compared predictions with ribosome footprint profiling data. The comprehensive analysis of the TIS sequence space enables quantitative predictions of translation initiation based on genome sequence.

  10. Analysis of the advantages of cis reporters in optimized FACS-Gal.

    PubMed

    Sánchez-Luengo, Miguel Ángel; Rovira, Miguel; Serrano, Manuel; Fernandez-Marcos, Pablo Jose; Martinez, Lola

    2017-04-04

    Flow cytometry is a powerful multiparametric technology, widely used for the identification, quantification, and isolation of defined populations of cells based on the expression of target proteins. It also allows for the use of surrogate reporters, either enzymatic or fluorescent, to indirectly monitor the expression of these target proteins. In this work, we optimised the dissociation protocol for the detection of the enzymatic reporter LacZ using the FACS-Gal detection system with the fluorogenic substrate FDG to compare cis- versus trans-positioned reporters efficiency. Particularly, for the FACS-Gal optimization, we studied lung and haematopoietic tissues, focusing on cell recovery, viability, FDG loading conditions and distribution of cellular populations. Reporter genes such as LacZ can be placed together with the gene of interest in the same polycistronic mRNA (in cis), or in independent alleles (in trans), which can strongly affect the correlation with the reporter readout. To address this issue, we generated a mouse model containing both types of reporters for the same gene, and compared them. Our results clearly indicate that trans-positioned reporters can be misleading, and that using a reporter gene in cis rather than trans is a much more specific method to sort for cells undergoing Cre-mediated recombination. © 2017 International Society for Advancement of Cytometry.

  11. Multipoint Observations of Oval-aligned Transpolar Arc Formation

    NASA Astrophysics Data System (ADS)

    Cumnock, J. A.; Le, G.; Zhang, Y.; Slavin, J. A.

    2013-12-01

    We analyze changes in field-aligned currents associated with auroral oval-aligned transpolar arc formation during quiet times on time scales of a few minutes. This is accomplished using observations from the highly accurate multipoint magnetic field measurements provided by the Space Technology 5 mission which consists of three micro-satellites in low Earth orbit. Simultaneous measurements of precipitating particles are provided by three DMSP satellites. We analyze field-aligned currents associated with the dusk oval. For the first time we observe the field-aligned currents associated with the formation of an oval-aligned transpolar arc poleward of the auroral oval which in one case are large compared with the field-aligned currents associated with the auroral oval measured 10 minutes earlier. These events clearly illustrate the dynamic nature of oval-aligned arc formation.

  12. FACSGen 2.0 animation software: generating three-dimensional FACS-valid facial expressions for emotion research.

    PubMed

    Krumhuber, Eva G; Tamarit, Lucas; Roesch, Etienne B; Scherer, Klaus R

    2012-04-01

    In this article, we present FACSGen 2.0, new animation software for creating static and dynamic three-dimensional facial expressions on the basis of the Facial Action Coding System (FACS). FACSGen permits total control over the action units (AUs), which can be animated at all levels of intensity and applied alone or in combination to an infinite number of faces. In two studies, we tested the validity of the software for the AU appearance defined in the FACS manual and the conveyed emotionality of FACSGen expressions. In Experiment 1, four FACS-certified coders evaluated the complete set of 35 single AUs and 54 AU combinations for AU presence or absence, appearance quality, intensity, and asymmetry. In Experiment 2, lay participants performed a recognition task on emotional expressions created with FACSGen software and rated the similarity of expressions displayed by human and FACSGen faces. Results showed good to excellent classification levels for all AUs by the four FACS coders, suggesting that the AUs are valid exemplars of FACS specifications. Lay participants' recognition rates for nine emotions were high, and comparisons of human and FACSGen expressions were very similar. The findings demonstrate the effectiveness of the software in producing reliable and emotionally valid expressions, and suggest its application in numerous scientific areas, including perception, emotion, and clinical and neuroscience research.

  13. Tidal alignment of galaxies

    SciTech Connect

    Blazek, Jonathan; Vlah, Zvonimir; Seljak, Uroš

    2015-08-01

    We develop an analytic model for galaxy intrinsic alignments (IA) based on the theory of tidal alignment. We calculate all relevant nonlinear corrections at one-loop order, including effects from nonlinear density evolution, galaxy biasing, and source density weighting. Contributions from density weighting are found to be particularly important and lead to bias dependence of the IA amplitude, even on large scales. This effect may be responsible for much of the luminosity dependence in IA observations. The increase in IA amplitude for more highly biased galaxies reflects their locations in regions with large tidal fields. We also consider the impact of smoothing the tidal field on halo scales. We compare the performance of this consistent nonlinear model in describing the observed alignment of luminous red galaxies with the linear model as well as the frequently used "nonlinear alignment model," finding a significant improvement on small and intermediate scales. We also show that the cross-correlation between density and IA (the "GI" term) can be effectively separated into source alignment and source clustering, and we accurately model the observed alignment down to the one-halo regime using the tidal field from the fully nonlinear halo-matter cross correlation. Inside the one-halo regime, the average alignment of galaxies with density tracers no longer follows the tidal alignment prediction, likely reflecting nonlinear processes that must be considered when modeling IA on these scales. Finally, we discuss tidal alignment in the context of cosmic shear measurements.

  14. Tidal alignment of galaxies

    SciTech Connect

    Blazek, Jonathan; Vlah, Zvonimir; Seljak, Uroš E-mail: zvlah@stanford.edu

    2015-08-01

    We develop an analytic model for galaxy intrinsic alignments (IA) based on the theory of tidal alignment. We calculate all relevant nonlinear corrections at one-loop order, including effects from nonlinear density evolution, galaxy biasing, and source density weighting. Contributions from density weighting are found to be particularly important and lead to bias dependence of the IA amplitude, even on large scales. This effect may be responsible for much of the luminosity dependence in IA observations. The increase in IA amplitude for more highly biased galaxies reflects their locations in regions with large tidal fields. We also consider the impact of smoothing the tidal field on halo scales. We compare the performance of this consistent nonlinear model in describing the observed alignment of luminous red galaxies with the linear model as well as the frequently used 'nonlinear alignment model,' finding a significant improvement on small and intermediate scales. We also show that the cross-correlation between density and IA (the 'GI' term) can be effectively separated into source alignment and source clustering, and we accurately model the observed alignment down to the one-halo regime using the tidal field from the fully nonlinear halo-matter cross correlation. Inside the one-halo regime, the average alignment of galaxies with density tracers no longer follows the tidal alignment prediction, likely reflecting nonlinear processes that must be considered when modeling IA on these scales. Finally, we discuss tidal alignment in the context of cosmic shear measurements.

  15. Daily Bone Alignment With Limited Repeat CT Correction Rivals Daily Ultrasound Alignment for Prostate Radiotherapy

    SciTech Connect

    O'Daniel, Jennifer C.; Dong Lei Zhang Lifei; Wang He; Tucker, Susan L.; Kudchadker, Rajat J.; Lee, Andrew K.; Cheung, Rex; Cox, James D.; Kuban, Deborah A.; Mohan, Radhe

    2008-05-01

    Purpose: To compare the effectiveness of daily ultrasound (US)- and computed tomography (CT)-guided alignments with an off-line correction protocol using daily bone alignment plus a correction factor for systematic internal prostate displacement (CF{sub ID}). Methods and Materials: Ten prostate cancer patients underwent CT scans three times weekly using an integrated CT-linear accelerator system, followed by alignment using US for daily radiotherapy. Intensity-modulated radiotherapy plans were designed with our current clinical margins. The treatment plan was copied onto the repeat CT images and aligned using several methods: (1) bone alignment plus CF{sub ID} after three off-line CT scans (bone+3CT), (2) bone alignment plus CF{sub ID} after six off-line CT scans (bone+6CT), (3) US alignment, and (4) CT alignment. The accuracy of the repeated US and CT measurements to determine the CF{sub ID} was compared. The target dosimetric effect was quantified. Results: The CF{sub ID} for internal systematic prostate displacements was more accurately measured with limited repeat CT scans than with US (residual error, 0.0 {+-} 0.7 mm vs. 2.0 {+-} 3.2 mm). Bone+3CT, bone+6CT, and US provided equivalent prostate and seminal vesicle dose coverage, but bone+3CT and bone+6CT produced more precise daily alignments. Daily CT alignment provided the greatest target dose coverage. Conclusion: Daily bone alignment plus CF{sub ID} for internal systematic prostate displacement provided better daily alignment precision and equivalent dose coverage compared with daily US alignment. The CF{sub ID} should be based on at least three repeat CT scans, which could be collected before the start of treatment or during the first 3 treatment days. Daily bone alignment plus CF{sub ID} provides another option for accurate prostate cancer patient positioning.

  16. The application of silicalite-1/fly ash cenosphere (S/FAC) zeolite composite for the adsorption of methyl tert-butyl ether (MTBE).

    PubMed

    Lu, Jia; Xu, Fang; Wang, Deju; Huang, Jue; Cai, Weimin

    2009-06-15

    Silicalite-1/fly ash cenosphere (S/FAC) zeolite composite has been applied for batch adsorption of methyl tert-butyl ether (MTBE) from water systems. Here the key experimental conditions, including the ratio of initial MTBE concentration to the amount weight of S/FAC, adsorption time and temperature, have been discussed in detail. The results show that approximately 93-95% MTBE could be adsorbed with initial concentration of MTBE solution 1000 microg l(-1). The column flow-through experiments also prove the high capacity of S/FAC composite for MTBE removal. The distinct advantages of S/FAC zeolite composite as adsorbent lie in (1) enhanced adsorption rate and capacity based on hierarchical micro and meso/macroporosity of S/FAC; (2) more easily operation and recycling process by assembly of nano-sized silicalite-1 zeolite on FAC support.

  17. Flow Accelerated Erosion-Corrosion (FAC) considerations for secondary side piping in the AP1000{sup R} nuclear power plant design

    SciTech Connect

    Vanderhoff, J. F.; Rao, G. V.; Stein, A.

    2012-07-01

    The issue of Flow Accelerated Erosion-Corrosion (FAC) in power plant piping is a known phenomenon that has resulted in material replacements and plant accidents in operating power plants. Therefore, it is important for FAC resistance to be considered in the design of new nuclear power plants. This paper describes the design considerations related to FAC that were used to develop a safe and robust AP1000{sup R} plant secondary side piping design. The primary FAC influencing factors include: - Fluid Temperature - Pipe Geometry/layout - Fluid Chemistry - Fluid Velocity - Pipe Material Composition - Moisture Content (in steam lines) Due to the unknowns related to the relative impact of the influencing factors and the complexities of the interactions between these factors, it is difficult to accurately predict the expected wear rate in a given piping segment in a new plant. This paper provides: - a description of FAC and the factors that influence the FAC degradation rate, - an assessment of the level of FAC resistance of AP1000{sup R} secondary side system piping, - an explanation of options to increase FAC resistance and associated benefits/cost, - discussion of development of a tool for predicting FAC degradation rate in new nuclear power plants. (authors)

  18. On the generation/decay of the storm-enhanced density plumes: Role of the convection flow and field-aligned ion flow

    NASA Astrophysics Data System (ADS)

    Zou, Shasha; Moldwin, Mark B.; Ridley, Aaron J.; Nicolls, Michael J.; Coster, Anthea J.; Thomas, Evan G.; Ruohoniemi, J. Michael

    2014-10-01

    Storm-enhanced density (SED) plumes are prominent ionospheric electron density increases at the dayside middle and high latitudes. The generation and decay mechanisms of the plumes are still not clear. We present observations of SED plumes during six storms between 2010 and 2013 and comprehensively analyze the associated ionospheric parameters within the plumes, including vertical ion flow, field-aligned ion flow and flux, plasma temperature, and field-aligned currents, obtained from multiple instruments, including GPS total electron content (TEC), Poker Flat Incoherent Scatter Radar (PFISR), Super Dual Auroral Radar Network, and Active Magnetosphere and Planetary Electrodynamics Response Experiment. The TEC increase within the SED plumes at the PFISR site can be 1.4-5.5 times their quiet time value. The plumes are usually associated with northwestward E × B flows ranging from a couple of hundred m s-1 to > 1 km s-1. Upward vertical flows due to the projection of these E × B drifts are mainly responsible for lifting the plasma in sunlit regions to higher altitude and thus leading to plume density enhancement. The upward vertical flows near the poleward part of the plumes are more persistent, while those near the equatorward part are more patchy. In addition, the plumes can be collocated with either upward or downward field-aligned currents (FACs) but are usually observed equatorward of the peak of the Region 1 upward FAC, suggesting that the northwestward flows collocated with plumes can be either subauroral or auroral flows. Furthermore, during the decay phase of the plume, large downward ion flows, as large as ~200 m s-1, and downward fluxes, as large as 1014 m-2 s-1, are often observed within the plumes. In our study of six storms, enhanced ambipolar diffusion due to an elevated pressure gradient is able to explain two of the four large downward flow/flux cases, but this mechanism is not sufficient for the other two cases where the flows are of larger

  19. Long-term outcomes of phakic patients with diabetic macular oedema treated with intravitreal fluocinolone acetonide (FAc) implants

    PubMed Central

    Yang, Y; Bailey, C; Holz, F G; Eter, N; Weber, M; Baker, C; Kiss, S; Menchini, U; Ruiz Moreno, J M; Dugel, P; Lotery, A

    2015-01-01

    Purpose Diabetic macular oedema (DMO) is a leading cause of blindness in working-age adults. Slow-release, nonbioerodible fluocinolone acetonide (FAc) implants have shown efficacy in the treatment of DMO; however, the National Institute for Health and Care Excellence recommends that FAc should be used in patients with chronic DMO considered insufficiently responsive to other available therapies only if the eye to be treated is pseudophakic. The goal of this analysis was to examine treatment outcomes in phakic patients who received 0.2 μg/day FAc implant. Methods This analysis of the phase 3 FAME (Fluocinolone Acetonide in Diabetic Macular Edema) data examines the safety and efficacy of FAc implants in patients who underwent cataract extraction before (cataract before implant (CBI) group) or after (cataract after implant (CAI) group) receiving the implant. The data were further examined by DMO duration. Results Best corrected visual acuity (BCVA) after 36 months was comparable in the CAI and CBI groups. Both the percentage of patients gaining ≥3 lines of vision and mean change in BCVA letter score were numerically greater in the CAI group. In addition, most patients who underwent cataract surgery experienced a net gain in BCVA from presurgery baseline as well as from original study baseline. Conclusions These data support the use of 0.2 μg/day FAc implants in phakic as well as in pseudophakic patients. These findings will serve as a pilot for design of future studies to evaluate the potential protective effect of FAc implants before cataract surgery in patients with DMO and cataract. PMID:26113503

  20. Rotational Alignment Altered by Source Position Correlations

    NASA Technical Reports Server (NTRS)

    Jacobs, Chris S.; Heflin, M. B.; Lanyi, G. E.; Sovers, O. J.; Steppe, J. A.

    2010-01-01

    In the construction of modern Celestial Reference Frames (CRFs) the overall rotational alignment is only weakly constrained by the data. Therefore, common practice has been to apply a 3-dimensional No-Net-Rotation (NNR) constraint in order to align an under-construction frame to the ICRF. We present evidence that correlations amongst source position parameters must be accounted for in order to properly align a CRF at the 5-10 (mu)as level of uncertainty found in current work. Failure to do so creates errors at the 10-40 (mu)as level.

  1. Shuttle onboard IMU alignment methods

    NASA Technical Reports Server (NTRS)

    Henderson, D. M.

    1976-01-01

    The current approach to the shuttle IMU alignment is based solely on the Apollo Deterministic Method. This method is simple, fast, reliable and provides an accurate estimate for the present cluster to mean of 1,950 transformation matrix. If four or more star sightings are available, the application of least squares analysis can be utilized. The least squares method offers the next level of sophistication to the IMU alignment solution. The least squares method studied shows that a more accurate estimate for the misalignment angles is computed, and the IMU drift rates are a free by-product of the analysis. Core storage requirements are considerably more; estimated 20 to 30 times the core required for the Apollo Deterministic Method. The least squares method offers an intermediate solution utilizing as much data that is available without a complete statistical analysis as in Kalman filtering.

  2. Unequivocal Identification of Subpopulations in Putative Multiclonal Trypanosoma cruzi Strains by FACs Single Cell Sorting and Genotyping

    PubMed Central

    Valadares, Helder Magno Silva; Pimenta, Juliana Ramos; Segatto, Marcela; Veloso, Vanja Maria; Gomes, Mônica Lúcia; Chiari, Egler; Gollob, Kenneth John; Bahia, Maria Terezinha; de Lana, Marta; Franco, Glória Regina; Machado, Carlos Renato; Pena, Sérgio Danilo Junho; Macedo, Andréa Mara

    2012-01-01

    Trypanosoma cruzi, the etiological agent of Chagas disease, is a polymorphic species. Evidence suggests that the majority of the T. cruzi populations isolated from afflicted humans, reservoir animals, or vectors are multiclonal. However, the extent and the complexity of multiclonality remain to be established, since aneuploidy cannot be excluded and current conventional cloning methods cannot identify all the representative clones in an infection. To answer this question, we adapted a methodology originally described for analyzing single spermatozoids, to isolate and study single T. cruzi parasites. Accordingly, the cloning apparatus of a Fluorescence-Activated Cell Sorter (FACS) was used to sort single T. cruzi cells directly into 96-wells microplates. Cells were then genotyped using two polymorphic genomic markers and four microsatellite loci. We validated this methodology by testing four T. cruzi populations: one control artificial mixture composed of two monoclonal populations – Silvio X10 cl1 (TcI) and Esmeraldo cl3 (TcII) – and three naturally occurring strains, one isolated from a vector (A316A R7) and two others derived from the first reported human case of Chagas disease. Using this innovative approach, we were able to successfully describe the whole complexity of these natural strains, revealing their multiclonal status. In addition, our results demonstrate that these T. cruzi populations are formed of more clones than originally expected. The method also permitted estimating of the proportion of each subpopulation of the tested strains. The single-cell genotyping approach allowed analysis of intrapopulation diversity at a level of detail not achieved previously, and may thus improve our comprehension of population structure and dynamics of T. cruzi. Finally, this methodology is capable to settle once and for all controversies on the issue of multiclonality. PMID:22802979

  3. Unequivocal identification of subpopulations in putative multiclonal Trypanosoma cruzi strains by FACs single cell sorting and genotyping.

    PubMed

    Valadares, Helder Magno Silva; Pimenta, Juliana Ramos; Segatto, Marcela; Veloso, Vanja Maria; Gomes, Mônica Lúcia; Chiari, Egler; Gollob, Kenneth John; Bahia, Maria Terezinha; de Lana, Marta; Franco, Glória Regina; Machado, Carlos Renato; Pena, Sérgio Danilo Junho; Macedo, Andréa Mara

    2012-01-01

    Trypanosoma cruzi, the etiological agent of Chagas disease, is a polymorphic species. Evidence suggests that the majority of the T. cruzi populations isolated from afflicted humans, reservoir animals, or vectors are multiclonal. However, the extent and the complexity of multiclonality remain to be established, since aneuploidy cannot be excluded and current conventional cloning methods cannot identify all the representative clones in an infection. To answer this question, we adapted a methodology originally described for analyzing single spermatozoids, to isolate and study single T. cruzi parasites. Accordingly, the cloning apparatus of a Fluorescence-Activated Cell Sorter (FACS) was used to sort single T. cruzi cells directly into 96-wells microplates. Cells were then genotyped using two polymorphic genomic markers and four microsatellite loci. We validated this methodology by testing four T. cruzi populations: one control artificial mixture composed of two monoclonal populations--Silvio X10 cl1 (TcI) and Esmeraldo cl3 (TcII)--and three naturally occurring strains, one isolated from a vector (A316A R7) and two others derived from the first reported human case of Chagas disease. Using this innovative approach, we were able to successfully describe the whole complexity of these natural strains, revealing their multiclonal status. In addition, our results demonstrate that these T. cruzi populations are formed of more clones than originally expected. The method also permitted estimating of the proportion of each subpopulation of the tested strains. The single-cell genotyping approach allowed analysis of intrapopulation diversity at a level of detail not achieved previously, and may thus improve our comprehension of population structure and dynamics of T. cruzi. Finally, this methodology is capable to settle once and for all controversies on the issue of multiclonality.

  4. Precision alignment device

    DOEpatents

    Jones, N.E.

    1988-03-10

    Apparatus for providing automatic alignment of beam devices having an associated structure for directing, collimating, focusing, reflecting, or otherwise modifying the main beam. A reference laser is attached to the structure enclosing the main beam producing apparatus and produces a reference beam substantially parallel to the main beam. Detector modules containing optical switching devices and optical detectors are positioned in the path of the reference beam and are effective to produce an electrical output indicative of the alignment of the main beam. This electrical output drives servomotor operated adjustment screws to adjust the position of elements of the structure associated with the main beam to maintain alignment of the main beam. 5 figs.

  5. Precision alignment device

    DOEpatents

    Jones, Nelson E.

    1990-01-01

    Apparatus for providing automatic alignment of beam devices having an associated structure for directing, collimating, focusing, reflecting, or otherwise modifying the main beam. A reference laser is attached to the structure enclosing the main beam producing apparatus and produces a reference beam substantially parallel to the main beam. Detector modules containing optical switching devices and optical detectors are positioned in the path of the reference beam and are effective to produce an electrical output indicative of the alignment of the main beam. This electrical output drives servomotor operated adjustment screws to adjust the position of elements of the structure associated with the main beam to maintain alignment of the main beam.

  6. Hybrid vehicle motor alignment

    DOEpatents

    Levin, Michael Benjamin

    2001-07-03

    A rotor of an electric motor for a motor vehicle is aligned to an axis of rotation for a crankshaft of an internal combustion engine having an internal combustion engine and an electric motor. A locator is provided on the crankshaft, a piloting tool is located radially by the first locator to the crankshaft. A stator of the electric motor is aligned to a second locator provided on the piloting tool. The stator is secured to the engine block. The rotor is aligned to the crankshaft and secured thereto.

  7. Implementation of a parallel protein structure alignment service on cloud.

    PubMed

    Hung, Che-Lun; Lin, Yaw-Ling

    2013-01-01

    Protein structure alignment has become an important strategy by which to identify evolutionary relationships between protein sequences. Several alignment tools are currently available for online comparison of protein structures. In this paper, we propose a parallel protein structure alignment service based on the Hadoop distribution framework. This service includes a protein structure alignment algorithm, a refinement algorithm, and a MapReduce programming model. The refinement algorithm refines the result of alignment. To process vast numbers of protein structures in parallel, the alignment and refinement algorithms are implemented using MapReduce. We analyzed and compared the structure alignments produced by different methods using a dataset randomly selected from the PDB database. The experimental results verify that the proposed algorithm refines the resulting alignments more accurately than existing algorithms. Meanwhile, the computational performance of the proposed service is proportional to the number of processors used in our cloud platform.

  8. Shod wear and foot alignment in clinical gait analysis.

    PubMed

    Louey, Melissa Gar Yee; Sangeux, Morgan

    2016-09-01

    Sagittal plane alignment of the foot presents challenges when the subject wears shoes during gait analysis. Typically, visual alignment is performed by positioning two markers, the heel and toe markers, aligned with the foot within the shoe. Alternatively, software alignment is possible when the sole of the shoe lies parallel to the ground, and the change in the shoe's sole thickness is measured and entered as a parameter. The aim of this technical note was to evaluate the accuracy of visual and software foot alignment during shod gait analysis. We calculated the static standing ankle angles of 8 participants (mean age: 8.7 years, SD: 2.9 years) wearing bilateral solid ankle foot orthoses (BSAFOs) with and without shoes using the visual and software alignment methods. All participants were able to stand with flat feet in both static trials and the ankle angles obtained in BSAFOs without shoes was considered the reference. We showed that the current implementation of software alignment introduces a bias towards more ankle dorsiflexion, mean=3°, SD=3.4°, p=0.006, and proposed an adjusted software alignment method. We found no statistical differences using visual alignment and adjusted software alignment between the shoe and shoeless conditions, p=0.19 for both. Visual alignment or adjusted software alignment are advised to represent foot alignment accurately.

  9. Human mammalian cell sorting using a highly integrated micro-fabricated fluorescence-activated cell sorter (microFACS).

    PubMed

    Cho, Sung Hwan; Chen, Chun H; Tsai, Frank S; Godin, Jessica M; Lo, Yu-Hwa

    2010-06-21

    We demonstrate a high performance microfabricated FACS system with highly integrated microfluidics, optics, acoustics, and electronics. Single cell manipulation at a high speed is made possible by the fast response time (approximately 0.1 ms) of the integrated PZT actuator and the nozzle structure at the sorting junction. A Teflon AF-coated optofluidic waveguide along the microfluidic channel guides the illumination light, enabling multi-spot detection, while a novel space-time coding technology enhances the detection sensitivity of the microFACS system. The real-time control loop system is implemented using a field-programmable-gate-array (FPGA) for automated and accurate sorting. The microFACS achieves a high purification enrichment factor: up to approximately 230 fold for both polystyrene microbeads and suspended human mammalian cells (K562) at a high throughput (>1000 cells s(-1)). The sorting mechanism is independent of cell properties such as size, density, and shape, thus the presented system can be applied to sort out any pure sub-populations. This new lab-on-a-chip FACS system, therefore, holds promise to revolutionize microfluidic cytometers to meet cost, size, and performance goals.

  10. Community shifts of actively growing lake bacteria after N-acetyl-glucosamine addition: improving the BrdU-FACS method.

    PubMed

    Tada, Yuya; Grossart, Hans-Peter

    2014-02-01

    In aquatic environments, community dynamics of bacteria, especially actively growing bacteria (AGB), are tightly linked with dissolved organic matter (DOM) quantity and quality. We analyzed the community dynamics of DNA-synthesizing and accordingly AGB by linking an improved bromodeoxyuridine immunocytochemistry approach with fluorescence-activated cell sorting (BrdU-FACS). FACS-sorted cells of even oligotrophic ecosystems in winter were characterized by 16S rRNA gene analysis. In incubation experiments, we examined community shifts of AGB in response to the addition of N-acetyl-glucosamine (NAG), one of the most abundant aminosugars in aquatic systems. Our improved BrdU-FACS analysis revealed that AGB winter communities of oligotrophic Lake Stechlin (northeastern Germany) substantially differ from those of total bacteria and consist of Alpha-, Beta-, Gamma-, Deltaproteobacteria, Actinobacteria, Candidatus OP10 and Chloroflexi. AGB populations with different BrdU-fluorescence intensities and cell sizes represented different phylotypes suggesting that single-cell growth potential varies at the taxon level. NAG incubation experiments demonstrated that a variety of widespread taxa related to Alpha-, Beta-, Gammaproteobacteria, Bacteroidetes, Actinobacteria, Firmicutes, Planctomycetes, Spirochaetes, Verrucomicrobia and Chloroflexi actively grow in the presence of NAG. The BrdU-FACS approach enables detailed phylogenetic studies of AGB and, thus, to identify those phylotypes which are potential key players in aquatic DOM cycling.

  11. Photochemical reactions of fac-[Mn(CO)3(phen)imidazole]+: evidence for long-lived radical species intermediates.

    PubMed

    de Aguiar, Inara; Inglez, Simone D; Lima, Francisco C A; Daniel, Juliana F S; McGarvey, Bruce R; Tedesco, Antônio C; Carlos, Rose M

    2008-12-15

    The electronic absorption spectrum of fac-[Mn(CO)(3)(phen)imH](+), fac-1 in CH(2)Cl(2) is characterized by a strong absorption band at 378 nm (epsilon(max) = 3200 mol(-1) L cm(-1)). On the basis of quantum mechanical calculations, the visible absorption band has been assigned to ligand-to-ligand charge-transfer (LLCT, im-->phen) and metal-to-ligand charge-transfer (MLCT, Mn-->phen) charge transfer transition. When fac-1 in CH(2)Cl(2) is irradiated with 350 nm continuous light, the absorption features are gradually shifted to represent those of the meridional complex mer-[Mn(CO)(3)(phen)imH](+), mer-1 (lambda(max) = 556 nm). The net photoreaction under these conditions is a photoisomerization, although, the presence of the long-lived radical species was also detected by (1)H NMR and FTIR spectroscopy. 355 nm continuous photolysis of fac-1 in CH(3)CN solution also gives the long-lived intermediate which is readily trapped by metylviologen (MV(2+)) giving rise to the formation of the one-electron reduced methyl viologen (MV(*+)). The UV-vis spectra monitored during the slow (45 min) thermal back reaction exhibited isosbestic conversion at 426 nm. On the basis of spectroscopic techniques and quantum mechanical calculations, the role of the radicals produced is analyzed.

  12. Synthesis of novel CeO2-BiVO4/FAC composites with enhanced visible-light photocatalytic properties.

    PubMed

    Zhang, Jin; Wang, Bing; Li, Chuang; Cui, Hao; Zhai, Jianping; Li, Qin

    2014-09-01

    To utilize visible light more effectively in photocatalytic reactions, a fly ash cenosphere (FAC)-supported CeO2-BiVO4 (CeO2-BiVO4/FAC) composite photocatalyst was prepared by modified metalorganic decomposition and impregnation methods. The physical and photophysical properties of the composite have been characterized by X-ray diffraction (XRD), scanning electron microscope (SEM) and energy dispersive X-ray spectroscopy (EDX), X-ray photoelectron spectroscopy (XPS), and UV-Visible diffuse reflectance spectra. The XRD patterns exhibited characteristic diffraction peaks of both BiVO4 and CeO2 crystalline phases. The XPS results showed that Ce was present as both Ce(4+) and Ce(3+) oxidation states in CeO2 and dispersed on the surface of BiVO4 to constitute a p-n heterojunction composite. The absorption threshold of the CeO2-BiVO4/FAC composite shifted to a longer wavelength in the UV-Vis absorption spectrum compared to the pure CeO2 and pure BiVO4. The composites exhibited enhanced photocatalytic activity for Methylene Blue (MB) degradation under visible light irradiation. It was found that the 7.5wt.% CeO2-BiVO4/FAC composite showed the highest photocatalytic activity for MB dye wastewater treatment.

  13. MaqFACS (Macaque Facial Action Coding System) can be used to document facial movements in Barbary macaques (Macaca sylvanus)

    PubMed Central

    Julle-Danière, Églantine; Whitehouse, Jamie; Joly, Marine; Gass, Carolin; Burrows, Anne M.; Waller, Bridget M.

    2015-01-01

    Human and non-human primates exhibit facial movements or displays to communicate with one another. The evolution of form and function of those displays could be better understood through multispecies comparisons. Anatomically based coding systems (Facial Action Coding Systems: FACS) are developed to enable such comparisons because they are standardized and systematic and aid identification of homologous expressions underpinned by similar muscle contractions. To date, FACS has been developed for humans, and subsequently modified for chimpanzees, rhesus macaques, orangutans, hylobatids, dogs, and cats. Here, we wanted to test whether the MaqFACS system developed in rhesus macaques (Macaca mulatta) could be used to code facial movements in Barbary macaques (M. sylvanus), a species phylogenetically close to the rhesus macaques. The findings show that the facial movement capacity of Barbary macaques can be reliably coded using the MaqFACS. We found differences in use and form of some movements, most likely due to specializations in the communicative repertoire of each species, rather than morphological differences. PMID:26401458

  14. Pairwise Sequence Alignment Library

    SciTech Connect

    Jeff Daily, PNNL

    2015-05-20

    Vector extensions, such as SSE, have been part of the x86 CPU since the 1990s, with applications in graphics, signal processing, and scientific applications. Although many algorithms and applications can naturally benefit from automatic vectorization techniques, there are still many that are difficult to vectorize due to their dependence on irregular data structures, dense branch operations, or data dependencies. Sequence alignment, one of the most widely used operations in bioinformatics workflows, has a computational footprint that features complex data dependencies. The trend of widening vector registers adversely affects the state-of-the-art sequence alignment algorithm based on striped data layouts. Therefore, a novel SIMD implementation of a parallel scan-based sequence alignment algorithm that can better exploit wider SIMD units was implemented as part of the Parallel Sequence Alignment Library (parasail). Parasail features: Reference implementations of all known vectorized sequence alignment approaches. Implementations of Smith Waterman (SW), semi-global (SG), and Needleman Wunsch (NW) sequence alignment algorithms. Implementations across all modern CPU instruction sets including AVX2 and KNC. Language interfaces for C/C++ and Python.

  15. FACS-based isolation, propagation and characterization of mouse embryonic cardiomyocytes based on VCAM-1 surface marker expression.

    PubMed

    Pontén, Annica; Walsh, Stuart; Malan, Daniela; Xian, Xiaojie; Schéele, Susanne; Tarnawski, Laura; Fleischmann, Bernd K; Jovinge, Stefan

    2013-01-01

    Purification of cardiomyocytes from the embryonic mouse heart, embryonic stem (ES) or induced pluripotent stem cells (iPS) is a challenging task and will require specific isolation procedures. Lately the significance of surface markers for the isolation of cardiac cell populations with fluorescence activated cell sorting (FACS) has been acknowledged, and the hunt for cardiac specific markers has intensified. As cardiomyocytes have traditionally been characterized by their expression of specific transcription factors and structural proteins, and not by specific surface markers, this constitutes a significant bottleneck. Lately, Flk-1, c-kit and the cellular prion protein have been reported to specify cardiac progenitors, however, no surface markers have so far been reported to specify a committed cardiomyocyte. Herein show for the first time, that embryonic cardiomyocytes can be isolated with 98% purity, based on their expression of vascular cell adhesion molecule-1 (VCAM-1). The FACS-isolated cells express phenotypic markers for embryonic committed cardiomyocytes but not cardiac progenitors. An important aspect of FACS is to provide viable cells with retention of functionality. We show that VCAM-1 positive cardiomyocytes can be isolated with 95% viability suitable for in vitro culture, functional assays or expression analysis. In patch-clamp experiments we provide evidence of functionally intact cardiomyocytes of both atrial and ventricular subtypes. This work establishes that cardiomyocytes can be isolated with a high degree of purity and viability through FACS, based on specific surface marker expression as has been done in the hematopoietic field for decades. Our FACS protocol represents a significant advance in which purified populations of cardiomyocytes may be isolated and utilized for downstream applications, such as purification of ES-cell derived cardiomyocytes.

  16. Theoretical study on mechanism of the photochemical ligand substitution of fac-[Re(I)(bpy)(CO)3(PR3)](+) complex.

    PubMed

    Saita, Kenichiro; Harabuchi, Yu; Taketsugu, Tetsuya; Ishitani, Osamu; Maeda, Satoshi

    2016-07-14

    The mechanism of the CO ligand dissociation of fac-[Re(I)(bpy)(CO)3P(OMe)3](+) has theoretically been investigated, as the dominant process of the photochemical ligand substitution (PLS) reactions of fac-[Re(I)(bpy)(CO)3PR3](+), by using the (TD-)DFT method. The PLS reactivity can be determined by the topology of the T1 potential energy surface because the photoexcited complex is able to decay into the T1 state by internal conversions (through conical intersections) and intersystem crossings (via crossing seams) with sufficiently low energy barriers. The T1 state has a character of the metal-to-ligand charge-transfer ((3)MLCT) around the Franck-Condon region, and it changes to the metal-centered ((3)MC) state as the Re-CO bond is elongated and bent. The equatorial CO ligand has a much higher energy barrier to leave than that of the axial CO, so that the axial CO ligand selectively dissociates in the PLS reaction. The single-component artificial force induced reaction (SC-AFIR) search reveals the CO dissociation pathway in photostable fac-[Re(I)(bpy)(CO)3Cl]; however, the dissociation barrier on the T1 state is substantially higher than that in fac-[Re(I)(bpy)(CO)3PR3](+) and the minimum-energy seams of crossings (MESXs) are located before and below the barrier. The MESXs have also been searched in fac-[Re(I)(bpy)(CO)3PR3](+) and no MESXs were found before and below the barrier.

  17. Curriculum Alignment Research Suggests that Alignment Can Improve Student Achievement

    ERIC Educational Resources Information Center

    Squires, David

    2012-01-01

    Curriculum alignment research has developed showing the relationship among three alignment categories: the taught curriculum, the tested curriculum and the written curriculum. Each pair (for example, the taught and the written curriculum) shows a positive impact for aligning those results. Following this, alignment results from the Third…

  18. Genome editing using FACS enrichment of nuclease-expressing cells and indel detection by amplicon analysis.

    PubMed

    Lonowski, Lindsey A; Narimatsu, Yoshiki; Riaz, Anjum; Delay, Catherine E; Yang, Zhang; Niola, Francesco; Duda, Katarzyna; Ober, Elke A; Clausen, Henrik; Wandall, Hans H; Hansen, Steen H; Bennett, Eric P; Frödin, Morten

    2017-03-01

    This protocol describes methods for increasing and evaluating the efficiency of genome editing based on the CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats-CRISPR-associated 9) system, transcription activator-like effector nucleases (TALENs) or zinc-finger nucleases (ZFNs). First, Indel Detection by Amplicon Analysis (IDAA) determines the size and frequency of insertions and deletions elicited by nucleases in cells, tissues or embryos through analysis of fluorophore-labeled PCR amplicons covering the nuclease target site by capillary electrophoresis in a sequenator. Second, FACS enrichment of cells expressing nucleases linked to fluorescent proteins can be used to maximize knockout or knock-in editing efficiencies or to balance editing efficiency and toxic/off-target effects. The two methods can be combined to form a pipeline for cell-line editing that facilitates the testing of new nuclease reagents and the generation of edited cell pools or clonal cell lines, reducing the number of clones that need to be generated and increasing the ease with which they are screened. The pipeline shortens the time line, but it most prominently reduces the workload of cell-line editing, which may be completed within 4 weeks.

  19. Single-cell Gene Expression Profiling Using FACS and qPCR with Internal Standards.

    PubMed

    Porter, Joshua R; Telford, William G; Batchelor, Eric

    2017-02-25

    Gene expression measurements from bulk populations of cells can obscure the considerable transcriptomic variation of individual cells within those populations. Single-cell gene expression measurements can help assess the role of noise in gene expression, identify correlations in the expression of pairs of genes, and reveal subpopulations of cells that respond differently to a stimulus. Here, we describe a procedure to measure the expression of up to 96 genes in single mammalian cells isolated from a population growing in tissue culture. Cells are sorted into lysis buffer by fluorescence-activated cell sorting (FACS), and the mRNA species of interest are reverse-transcribed and amplified. Gene expression is then measured using a microfluidic real-time PCR machine, which performs up to 96 qPCR assays on up to 96 samples at a time. We also describe the generation and use of PCR amplicon standards to enable the estimation of the absolute number of each transcript. Compared with other methods of measuring gene expression in single cells, this approach allows for the quantification of more distinct transcripts than RNA FISH at a lower cost than RNA-Seq.

  20. Regional Cell Specific RNA Expression Profiling of FACS Isolated Drosophila Intestinal Cell Populations.

    PubMed

    Dutta, Devanjali; Buchon, Nicolas; Xiang, Jinyi; Edgar, Bruce A

    2015-08-03

    The adult Drosophila midgut is built of five distinct cell types, including stem cells, enteroblasts, enterocytes, enteroendocrine cells, and visceral muscles, and is divided into five major regions (R1 to R5), which are morphologically and functionally distinct from each other. This unit describes a protocol for the isolation of Drosophila intestinal cell populations for the purpose of cell type-specific transcriptome profiling from the five different regions. A method to select a cell type of interest labeled with green or yellow fluorescent protein (GFP, YFP) by making use of the GAL4-UAS bipartite system and fluorescent-activated cell sorting (FACS) is presented. Total RNA is isolated from the sorted cells of each region, and linear RNA amplification is used to obtain sufficient amounts of high-quality RNA for analysis by microarray, RT-PCR, or RNA sequencing. This method will be useful for quantitative transcriptome comparison across intestinal cell types in the different regions under normal and various experimental conditions.

  1. Fluorescent protein pair emit intracellular FRET signal suitable for FACS screening

    SciTech Connect

    Johansson, Daniel X.; Brismar, Hjalmar . E-mail: mats.persson@ki.se

    2007-01-12

    The fluorescent proteins ECFP and HcRed were shown to give an easily resolved FRET-signal when expressed as a fusion inside mammalian cells. HeLa-tat cells expressing ECFP, pHcRed, or the fusion protein pHcRed-ECFP were analyzed by flow cytometry after excitation of ECFP. Cells expressing HcRed-ECFP, or ECFP and HcRed, were mixed and FACS-sorted for FRET positive cells: HcRed-ECFP cells were greatly enriched (72 times). Next, cloned human antibodies were fused with ECFP and expressed anchored to the ER membrane. Their cognate antigens (HIV-1 gp120 or gp41) were fused to HcRed and co-expressed in the ER. An increase of 13.5 {+-} 1.5% (mean {+-} SEM) and 8.0 {+-} 0.7% in ECFP fluorescence for the specific antibodies reacting with gp120 or gp41, respectively, was noted after photobleaching. A positive control (HcRed-ECFP) gave a 14.8 {+-} 2.6% increase. Surprisingly, the unspecific antibody (anti-TT) showed 12.1 {+-} 1.1% increase, possibly because overexpression in the limited ER compartment gave false FRET signals.

  2. Magnetically Aligned Supramolecular Hydrogels

    PubMed Central

    Wallace, Matthew; Cardoso, Andre Zamith; Frith, William J; Iggo, Jonathan A; Adams, Dave J

    2014-01-01

    The magnetic-field-induced alignment of the fibrillar structures present in an aqueous solution of a dipeptide gelator, and the subsequent retention of this alignment upon transformation to a hydrogel upon the addition of CaCl2 or upon a reduction in solution pH is reported. Utilising the switchable nature of the magnetic field coupled with the slow diffusion of CaCl2, it is possible to precisely control the extent of anisotropy across a hydrogel, something that is generally very difficult to do using alternative methods. The approach is readily extended to other compounds that form viscous solutions at high pH. It is expected that this work will greatly expand the utility of such low-molecular-weight gelators (LMWG) in areas where alignment is key. PMID:25345918

  3. Improved docking alignment system

    NASA Technical Reports Server (NTRS)

    Monford, Leo G. (Inventor)

    1988-01-01

    Improved techniques are provided for the alignment of two objects. The present invention is particularly suited for 3-D translation and 3-D rotational alignment of objects in outer space. A camera is affixed to one object, such as a remote manipulator arm of the spacecraft, while the planar reflective surface is affixed to the other object, such as a grapple fixture. A monitor displays in real-time images from the camera such that the monitor displays both the reflected image of the camera and visible marking on the planar reflective surface when the objects are in proper alignment. The monitor may thus be viewed by the operator and the arm manipulated so that the reflective surface is perpendicular to the optical axis of the camera, the roll of the reflective surface is at a selected angle with respect to the camera, and the camera is spaced a pre-selected distance from the reflective surface.

  4. PILOT optical alignment

    NASA Astrophysics Data System (ADS)

    Longval, Y.; Mot, B.; Ade, P.; André, Y.; Aumont, J.; Baustista, L.; Bernard, J.-Ph.; Bray, N.; de Bernardis, P.; Boulade, O.; Bousquet, F.; Bouzit, M.; Buttice, V.; Caillat, A.; Charra, M.; Chaigneau, M.; Crane, B.; Crussaire, J.-P.; Douchin, F.; Doumayrou, E.; Dubois, J.-P.; Engel, C.; Etcheto, P.; Gélot, P.; Griffin, M.; Foenard, G.; Grabarnik, S.; Hargrave, P..; Hughes, A.; Laureijs, R.; Lepennec, Y.; Leriche, B.; Maestre, S.; Maffei, B.; Martignac, J.; Marty, C.; Marty, W.; Masi, S.; Mirc, F.; Misawa, R.; Montel, J.; Montier, L.; Narbonne, J.; Nicot, J.-M.; Pajot, F.; Parot, G.; Pérot, E.; Pimentao, J.; Pisano, G.; Ponthieu, N.; Ristorcelli, I.; Rodriguez, L.; Roudil, G.; Salatino, M.; Savini, G.; Simonella, O.; Saccoccio, M.; Tapie, P.; Tauber, J.; Torre, J.-P.; Tucker, C.

    2016-07-01

    PILOT is a balloon-borne astronomy experiment designed to study the polarization of dust emission in the diffuse interstellar medium in our Galaxy at wavelengths 240 μm with an angular resolution about two arcminutes. Pilot optics is composed an off-axis Gregorian type telescope and a refractive re-imager system. All optical elements, except the primary mirror, are in a cryostat cooled to 3K. We combined the optical, 3D dimensional measurement methods and thermo-elastic modeling to perform the optical alignment. The talk describes the system analysis, the alignment procedure, and finally the performances obtained during the first flight in September 2015.

  5. Erasing Errors due to Alignment Ambiguity When Estimating Positive Selection

    PubMed Central

    Redelings, Benjamin

    2014-01-01

    Current estimates of diversifying positive selection rely on first having an accurate multiple sequence alignment. Simulation studies have shown that under biologically plausible conditions, relying on a single estimate of the alignment from commonly used alignment software can lead to unacceptably high false-positive rates in detecting diversifying positive selection. We present a novel statistical method that eliminates excess false positives resulting from alignment error by jointly estimating the degree of positive selection and the alignment under an evolutionary model. Our model treats both substitutions and insertions/deletions as sequence changes on a tree and allows site heterogeneity in the substitution process. We conduct inference starting from unaligned sequence data by integrating over all alignments. This approach naturally accounts for ambiguous alignments without requiring ambiguously aligned sites to be identified and removed prior to analysis. We take a Bayesian approach and conduct inference using Markov chain Monte Carlo to integrate over all alignments on a fixed evolutionary tree topology. We introduce a Bayesian version of the branch-site test and assess the evidence for positive selection using Bayes factors. We compare two models of differing dimensionality using a simple alternative to reversible-jump methods. We also describe a more accurate method of estimating the Bayes factor using Rao-Blackwellization. We then show using simulated data that jointly estimating the alignment and the presence of positive selection solves the problem with excessive false positives from erroneous alignments and has nearly the same power to detect positive selection as when the true alignment is known. We also show that samples taken from the posterior alignment distribution using the software BAli-Phy have substantially lower alignment error compared with MUSCLE, MAFFT, PRANK, and FSA alignments. PMID:24866534

  6. Isolation of circulating tumor cells by immunomagnetic enrichment and fluorescence-activated cell sorting (IE/FACS) for molecular profiling.

    PubMed

    Magbanua, Mark Jesus M; Park, John W

    2013-12-01

    Circulating tumor cells (CTCs) are cells shed by the primary tumor into the blood stream capable of initiating distant metastasis. In the past decade, numerous assays have been developed to reliably detect these extremely rare cells. However, methods for purification of CTCs with little or no contamination of normal blood cells for molecular profiling are limited. We have developed a novel protocol to isolate CTCs by combining immunomagnetic enrichment and fluorescence-activated cell sorting (IE/FACS). The two-part assay includes (1) immunomagnetic capture using magnetic beads conjugated to monoclonal antibody against an epithelial cell adhesion marker (EpCAM) to enrich for tumor cells; and (2) FACS analysis using EpCAM to purify tumor cells away from mononuclear cells of hematopoietic lineage. Downstream molecular analyses of single and pooled cells confirmed the isolation of highly pure CTCs with characteristics typical that of malignant cells.

  7. Investigation of electron-loss and photon scattering correction factors for FAC-IR-300 ionization chamber

    NASA Astrophysics Data System (ADS)

    Mohammadi, S. M.; Tavakoli-Anbaran, H.; Zeinali, H. Z.

    2017-02-01

    The parallel-plate free-air ionization chamber termed FAC-IR-300 was designed at the Atomic Energy Organization of Iran, AEOI. This chamber is used for low and medium X-ray dosimetry on the primary standard level. In order to evaluate the air-kerma, some correction factors such as electron-loss correction factor (ke) and photon scattering correction factor (ksc) are needed. ke factor corrects the charge loss from the collecting volume and ksc factor corrects the scattering of photons into collecting volume. In this work ke and ksc were estimated by Monte Carlo simulation. These correction factors are calculated for mono-energy photon. As a result of the simulation data, the ke and ksc values for FAC-IR-300 ionization chamber are 1.0704 and 0.9982, respectively.

  8. The diagnostic accuracy of a single CEA blood test in detecting colorectal cancer recurrence: Results from the FACS trial

    PubMed Central

    Nicholson, Brian D.; Primrose, John; Perera, Rafael; James, Timothy; Pugh, Sian; Mant, David

    2017-01-01

    Objective To evaluate the diagnostic accuracy of a single CEA (carcinoembryonic antigen) blood test in detecting colorectal cancer recurrence. Background Patients who have undergone curative resection for primary colorectal cancer are typically followed up with scheduled CEA testing for 5 years. Decisions to investigate further (usually by CT imaging) are based on single test results, reflecting international guidelines. Methods A secondary analysis was undertaken of data from the FACS trial (two arms included CEA testing). The composite reference standard applied included CT-CAP imaging, clinical assessment and colonoscopy. Accuracy in detecting recurrence was evaluated in terms of sensitivity, specificity, likelihood ratios, predictive values, time-dependent area under the ROC curves, and operational performance when used prospectively in clinical practice are reported. Results Of 582 patients, 104 (17.9%) developed recurrence during the 5 year follow-up period. Applying the recommended threshold of 5μg/L achieves at best 50.0% sensitivity (95% CI: 40.1–59.9%); in prospective use in clinical practice it would lead to 56 missed recurrences (53.8%; 95% CI: 44.2–64.4%) and 89 false alarms (56.7% of 157 patients referred for investigation). Applying a lower threshold of 2.5μg/L would reduce the number of missed recurrences to 36.5% (95% CI: 26.5–46.5%) but would increase the false alarms to 84.2% (924/1097 referred). Some patients are more prone to false alarms than others—at the 5μg/L threshold, the 89 episodes of unnecessary investigation were clustered in 29 individuals. Conclusion Our results demonstrated very low sensitivity for CEA, bringing to question whether it could ever be used as an independent triage test. It is not feasible to improve the diagnostic performance of a single test result by reducing the recommended action threshold because of the workload and false alarms generated. Current national and international guidelines merit re

  9. Aligned-or Not?

    ERIC Educational Resources Information Center

    Roseman, Jo Ellen; Koppal, Mary

    2015-01-01

    When state leaders and national partners in the development of the Next Generation Science Standards met to consider implementation strategies, states and school districts wanted to know which materials were aligned to the new standards. The answer from the developers was short but not sweet: You won't find much now, and it's going to…

  10. Optically Aligned Drill Press

    NASA Technical Reports Server (NTRS)

    Adderholdt, Bruce M.

    1994-01-01

    Precise drill press equipped with rotary-indexing microscope. Microscope and drill exchange places when turret rotated. Microscope axis first aligned over future hole, then rotated out of way so drill axis assumes its precise position. New procedure takes less time to locate drilling positions and produces more accurate results. Apparatus adapted to such other machine tools as milling and measuring machines.

  11. Curriculum Alignment: Establishing Coherence

    ERIC Educational Resources Information Center

    Gagné, Philippe; Dumont, Laurence; Brunet, Sabine; Boucher, Geneviève

    2013-01-01

    In this paper, we present a step-by-step guide to implement a curricular alignment project, directed at professional development and student support, and developed in a higher education French as a second language department. We outline best practices and preliminary results from our experience and provide ways to adapt our experience to other…

  12. INTRINSIC ALIGNMENT OF CLUSTER GALAXIES: THE REDSHIFT EVOLUTION

    SciTech Connect

    Hao Jiangang; Kubo, Jeffrey M.; Feldmann, Robert; Annis, James; Johnston, David E.; Lin Huan; McKay, Timothy A.

    2011-10-10

    We present measurements of two types of cluster galaxy alignments based on a volume limited and highly pure ({>=}90%) sample of clusters from the GMBCG catalog derived from Data Release 7 of the Sloan Digital Sky Survey (SDSS DR7). We detect a clear brightest cluster galaxy (BCG) alignment (the alignment of major axis of the BCG toward the distribution of cluster satellite galaxies). We find that the BCG alignment signal becomes stronger as the redshift and BCG absolute magnitude decrease and becomes weaker as BCG stellar mass decreases. No dependence of the BCG alignment on cluster richness is found. We can detect a statistically significant ({>=}3{sigma}) satellite alignment (the alignment of the major axes of the cluster satellite galaxies toward the BCG) only when we use the isophotal fit position angles (P.A.s), and the satellite alignment depends on the apparent magnitudes rather than the absolute magnitudes of the BCGs. This suggests that the detected satellite alignment based on isophotal P.A.s from the SDSS pipeline is possibly due to the contamination from the diffuse light of nearby BCGs. We caution that this should not be simply interpreted as non-existence of the satellite alignment, but rather that we cannot detect them with our current photometric SDSS data. We perform our measurements on both SDSS r-band and i-band data, but do not observe a passband dependence of the alignments.

  13. Time scale of FAC variations estimated by SWARM and a comparison with ground based geomagnetic and micro-barometric observations

    NASA Astrophysics Data System (ADS)

    Iyemori, T.; Nakanishi, K.; Aoyama, T.; Luhr, H.; Odagi, Y.; Yokoyama, Y.; Iguchi, M.; Sugitani, S.; Hashiguchi, H.; Utsugi, M.; Ono, T.; Sanoo, Y.

    2015-12-01

    The low altitude magnetic satellites such as Oersted, CHAMP or SWARM observed small scale magnetic fluctuations having period about 10 to 30 sec along their orbits in middle or low latitudes. The amplitude is usually less than a few nT and they were observed almost always on the dayside. Most of them are interpreted as the spatial structure of small scale FACs probably generated by atmospheric gravity waves (Nakanishi et al., 2014). From a statistical analysis of correlation coefficients between a pair of the SWARM satellites, Iyemori et al. (2015) estimated the temporal scale of FAC variation to be roughly about 200 secs for meridional magnetic components and about 340 secs for longitudinal, i.e., east-west component. Based on a spectral analysis of ground geomagnetic and micro-barometric observations, we found that the spectral peaks with similar periods, i.e., 200sec or 320-350sec tend to appear statistically. This tendency supports the idea that the source of the FACs is mainly the acoustic mode of gravity waves. We discuss the characteristics of the power spectra, in particular, those of micro-barometric observations.

  14. Lysis matters: red cell lysis with FACS Lyse affects the flow cytometric enumeration of circulating leukemic blasts.

    PubMed

    Einwallner, Elisa; Subasic, Almira; Strasser, Andrea; Augustin, Dorothea; Thalhammer, Renate; Steiner, Irene; Schwarzinger, Ilse

    2013-04-30

    The whole blood lysis method has become a standard procedure to remove red cells prior to immunophenotypic analysis of leukocytes. In the present study we investigated the influence of four different lysis protocols on the flow cytometric recovery of leukemic blasts. 32 blast cells containing blood samples were stained with anti-CD45 and anti-CD34 monoclonal antibody combinations. Red cell lysis was performed with FACS Lysing Solution and BD PharmLyse™ (Becton Dickinson and Company BD Biosciences, San Jose, CA; n=32) as well as Optilyse C and IOTest 3 (Immunotech SAS, Marseille; n=15 out of 32). Flow cytometric enumeration of blasts was performed on a FACS-Canto flow cytometer. The percentage of blasts after treatment with FACS Lyse was significantly smaller than after PharmLyse™ (p<0.0001), Optilyse C (p<0.0001), or IOTest 3 (p<0.0001), respectively. The difference between PharmLyse™ and Optilyse C (p=0.93), PharmLyse™ and IOTest 3 (p=0.31), and Optilyse C and IOTest 3 (p=0.34) was not significant. These results emphasize the importance of harmonization of red cell lysis protocols for the application of flow cytometry in hematological neoplasms.

  15. Combination of FACS and homologous recombination for the generation of stable and high-expression engineered cell lines.

    PubMed

    Shi, Lei; Chen, Xuesi; Tang, Wenying; Li, Zhenyi; Liu, Jin; Gao, Feng; Sang, Jianli

    2014-01-01

    Traditionally, cell line generation requires several months and involves screening of over several hundred cell clones for high productivity before dozens are selected as candidate cell lines. Here, we have designed a new strategy for the generation of stable and high-expression cell lines by combining homologous recombination (HR) and fluorescence-activated cell sorting (FACS). High expression was indicated by the expression of secreted green fluorescent protein (SEGFP). Parental cell lines with the highest expression of SEGFP were then selected by FACS and identified by stability analysis. Consequently, HR vectors were constructed using the cassette for SEGFP as the HR region. After transfecting the HR vector, the cells with negative SEGFP expression were enriched by FACS. The complete exchange between SEGFP and target gene (TNFR-Fc) cassettes was demonstrated by DNA analysis. Compared with the traditional method, by integrating the cassette containing the gene of interest into the pre-selected site, the highest producing cells secreted a more than 8-fold higher titer of target protein. Hence, this new strategy can be applied to isolated stable cell lines with desirable expression of any gene of interest. The stable cell lines can rapidly produce proteins for researching protein structure and function and are even applicable in drug discovery.

  16. FACS-purified myoblasts producing controlled VEGF levels induce safe and stable angiogenesis in chronic hind limb ischemia.

    PubMed

    Wolff, Thomas; Mujagic, Edin; Gianni-Barrera, Roberto; Fueglistaler, Philipp; Helmrich, Uta; Misteli, Heidi; Gurke, Lorenz; Heberer, Michael; Banfi, Andrea

    2012-01-01

    We recently developed a method to control the in vivo distribution of vascular endothelial growth factor (VEGF) by high throughput Fluorescence-Activated Cell Sorting (FACS) purification of transduced progenitors such that they homogeneously express specific VEGF levels. Here we investigated the long-term safety of this method in chronic hind limb ischemia in nude rats. Primary myoblasts were transduced to co-express rat VEGF-A(164) (rVEGF) and truncated ratCD8a, the latter serving as a FACS-quantifiable surface marker. Based on the CD8 fluorescence of a reference clonal population, which expressed the desired VEGF level, cells producing similar VEGF levels were sorted from the primary population, which contained cells with very heterogeneous VEGF levels. One week after ischemia induction, 12 × 10(6) cells were implanted in the thigh muscles. Unsorted myoblasts caused angioma-like structures, whereas purified cells only induced normal capillaries that were stable after 3 months. Vessel density was doubled in engrafted areas, but only approximately 0.1% of muscle volume showed cell engraftment, explaining why no increase in total blood flow was observed. In conclusion, the use of FACS-purified myoblasts granted the cell-by-cell control of VEGF expression levels, which ensured long-term safety in a model of chronic ischemia. Based on these results, the total number of implanted cells required to achieve efficacy will need to be determined before a clinical application.

  17. Towards and FVE-FAC Method for Determining Thermocapillary Effects on Weld Pool Shape

    NASA Technical Reports Server (NTRS)

    Canright, David; Henson, Van Emden

    1996-01-01

    Several practical materials processes, e.g., welding, float-zone purification, and Czochralski crystal growth, involve a pool of molten metal with a free surface, with strong temperature gradients along the surface. In some cases, the resulting thermocapillary flow is vigorous enough to convect heat toward the edges of the pool, increasing the driving force in a sort of positive feedback. In this work we examine this mechanism and its effect on the solid-liquid interface through a model problem: a half space of pure substance with concentrated axisymmetric surface heating, where surface tension is strong enough to keep the liquid free surface flat. The numerical method proposed for this problem utilizes a finite volume element (FVE) discretization in cylindrical coordinates. Because of the axisymmetric nature of the model problem, the control volumes used are torroidal prisms, formed by taking a polygonal cross-section in the (r, z) plane and sweeping it completely around the z-axis. Conservation of energy (in the solid), and conservation of energy, momentum, and mass (in the liquid) are enforced globally by integrating these quantities and enforcing conservation over each control volume. Judicious application of the Divergence Theorem and Stokes' Theorem, combined with a Crank-Nicolson time-stepping scheme leads to an implicit algebraic system to be solved at each time step. It is known that near the boundary of the pool, that is, near the solid-liquid interface, the full conduction-convection solution will require extremely fine length scales to resolve the physical behavior of the system. Furthermore, this boundary moves as a function of time. Accordingly, we develop the foundation of an adaptive refinement scheme based on the principles of Fast Adaptive Composite Grid methods (FAC). Implementation of the method and numerical results will appear in a later report.

  18. FACS Fractionation and Differentiation of Skeletal-Muscle Resident Multipotent Tie2+ Progenitors.

    PubMed

    Biswas, Arpita A; Goldhamer, David J

    2016-01-01

    The skeletal muscle niche is complex and heterogeneous. Over the past few decades, various groups have reported the existence of multiple adult stem cell populations within this environment. Techniques commonly used to identify and assess the differentiation capacities of these cellular fractions, oftentimes rare populations, include the use of lineage tracers, immunofluorescence and histochemistry, flow cytometry, gene expression assays, and phenotypic analysis in culture or in vivo. In 2012, our lab identified and characterized a skeletal-muscle resident Tie2+ progenitor that exhibits adipogenic, chondrogenic, and osteogenic differentiation potentials (Wosczyna et al., J Bone Miner Res 27:1004-1017, 2012). This Tie2+ progenitor also expresses the markers PDGFRα and Sca-1 which in turn label a population of muscle-resident fibro/adipogenic progenitors (FAPs) (Joe et al., Nat Cell Biol 12:153-163, 2010; Uezumi et al., Nat Cell Biol 12:143-152, 2010), suggesting similar identities or overlap in the two mesenchymal progenitor populations. Our study demonstrated that these Tie2-expressing mesenchymal progenitors contribute robustly to BMP-induced heterotopic ossification (HO) in mice, and therefore could represent a key cellular target for therapeutic intervention in HO treatment (Wosczyna et al., J Bone Miner Res 27:1004-1017, 2012). In this chapter, we provide a detailed description of our updated fluorescence-activated cell sorting (FACS) strategy and describe cell culture methods for differentiation of Tie2+ progenitors to adipogenic and osteogenic fates. This strategy is easily adaptable for the prospective isolation of other rare subpopulations resident in skeletal muscle.

  19. EST Reading Curriculum & Instruction: An Alignment Analysis

    ERIC Educational Resources Information Center

    Mohammed, Lubna Ali; Sidek, H. M.

    2015-01-01

    In order for a curriculum to achieve its goals, it is imperative that the curriculum is coherent at all levels. In order to determine the coherency of a curriculum, the alignment of its theoretical underpinning and the label of a curriculum is one of the aspects that can be examined. The purpose of the current study was to examine if the…

  20. Constructing Aligned Assessments Using Automated Test Construction

    ERIC Educational Resources Information Center

    Porter, Andrew; Polikoff, Morgan S.; Barghaus, Katherine M.; Yang, Rui

    2013-01-01

    We describe an innovative automated test construction algorithm for building aligned achievement tests. By incorporating the algorithm into the test construction process, along with other test construction procedures for building reliable and unbiased assessments, the result is much more valid tests than result from current test construction…

  1. Inflation by alignment

    SciTech Connect

    Burgess, C.P.; Roest, Diederik

    2015-06-08

    Pseudo-Goldstone bosons (pGBs) can provide technically natural inflatons, as has been comparatively well-explored in the simplest axion examples. Although inflationary success requires trans-Planckian decay constants, f≳M{sub p}, several mechanisms have been proposed to obtain this, relying on (mis-)alignments between potential and kinetic energies in multiple-field models. We extend these mechanisms to a broader class of inflationary models, including in particular the exponential potentials that arise for pGB potentials based on noncompact groups (and so which might apply to moduli in an extra-dimensional setting). The resulting potentials provide natural large-field inflationary models and can predict a larger primordial tensor signal than is true for simpler single-field versions of these models. In so doing we provide a unified treatment of several alignment mechanisms, showing how each emerges as a limit of the more general setup.

  2. Automatic Word Alignment

    DTIC Science & Technology

    2014-02-18

    strategy was evalu­ ated in the context of English -to-Pashto (E2P) and Pashto-to- English (P2E), a low-resource language pair. For E2P, the training and...improves the quality of automatic word alignment, for example for resource poor language pairs, thus improving Statistical Machine Translation (SMT...example for resource poor language pairs, thus improving Statistical Machine Translation (SMT) performance. 15. SUBJECT TERMS 16. SECURITY

  3. Orbit IMU alignment: Error analysis

    NASA Technical Reports Server (NTRS)

    Corson, R. W.

    1980-01-01

    A comprehensive accuracy analysis of orbit inertial measurement unit (IMU) alignments using the shuttle star trackers was completed and the results are presented. Monte Carlo techniques were used in a computer simulation of the IMU alignment hardware and software systems to: (1) determine the expected Space Transportation System 1 Flight (STS-1) manual mode IMU alignment accuracy; (2) investigate the accuracy of alignments in later shuttle flights when the automatic mode of star acquisition may be used; and (3) verify that an analytical model previously used for estimating the alignment error is a valid model. The analysis results do not differ significantly from expectations. The standard deviation in the IMU alignment error for STS-1 alignments was determined to the 68 arc seconds per axis. This corresponds to a 99.7% probability that the magnitude of the total alignment error is less than 258 arc seconds.

  4. Nuclear reactor alignment plate configuration

    SciTech Connect

    Altman, David A; Forsyth, David R; Smith, Richard E; Singleton, Norman R

    2014-01-28

    An alignment plate that is attached to a core barrel of a pressurized water reactor and fits within slots within a top plate of a lower core shroud and upper core plate to maintain lateral alignment of the reactor internals. The alignment plate is connected to the core barrel through two vertically-spaced dowel pins that extend from the outside surface of the core barrel through a reinforcement pad and into corresponding holes in the alignment plate. Additionally, threaded fasteners are inserted around the perimeter of the reinforcement pad and into the alignment plate to further secure the alignment plate to the core barrel. A fillet weld also is deposited around the perimeter of the reinforcement pad. To accomodate thermal growth between the alignment plate and the core barrel, a gap is left above, below and at both sides of one of the dowel pins in the alignment plate holes through with the dowel pins pass.

  5. Dynamic Alignment at SLS

    SciTech Connect

    Ruland, Robert E.

    2003-04-23

    The relative alignment of components in the storage ring of the Swiss Light Source (SLS) is guaranteed by mechanical means. The magnets are rigidly fixed to 48 girders by means of alignment rails with tolerances of less than {+-}15 {micro}m. The bending magnets, supported by 3 point ball bearings, overlap adjacent girders and thus establish virtual train links between the girders, located near the bending magnet centres. Keeping the distortion of the storage ring geometry within a tolerance of {+-}100 {micro}m in order to guarantee sufficient dynamic apertures, requires continuous monitoring and correction of the girder locations. Two monitoring systems for the horizontal and the vertical direction will be installed to measure displacements of the train link between girders, which are due to ground settings and temperature effects: The hydrostatic levelling system (HLS) gives an absolute vertical reference, while the horizontal positioning system (HPS), which employs low cost linear encoders with sub-micron resolution, measures relative horizontal movements. The girder mover system based on five DC motors per girder allows a dynamic realignment of the storage ring within a working window of more than {+-}1 mm for girder translations and {+-}1 mrad for rotations. We will describe both monitoring systems (HLS and HPS) as well as the applied correction scheme based on the girder movers. We also show simulations indicating that beam based girder alignment takes care of most of the static closed orbit correction.

  6. Alignment of Content and Effectiveness of Mathematics Assessment Items

    ERIC Educational Resources Information Center

    Kulm, Gerald; Dager Wilson, Linda; Kitchen, Richard

    2005-01-01

    Alignment has taken on increased importance given the current high-stakes nature of assessment. To make well-informed decisions about student learning on the basis of test results, assessment items need to be well aligned with standards. Project 2061 of the American Association for the Advancement of Science (AAAS) has developed a procedure for…

  7. Method for alignment of microwires

    DOEpatents

    Beardslee, Joseph A.; Lewis, Nathan S.; Sadtler, Bryce

    2017-01-24

    A method of aligning microwires includes modifying the microwires so they are more responsive to a magnetic field. The method also includes using a magnetic field so as to magnetically align the microwires. The method can further include capturing the microwires in a solid support structure that retains the longitudinal alignment of the microwires when the magnetic field is not applied to the microwires.

  8. Alignment as a Teacher Variable

    ERIC Educational Resources Information Center

    Porter, Andrew C.; Smithson, John; Blank, Rolf; Zeidner, Timothy

    2007-01-01

    With the exception of the procedures developed by Porter and colleagues (Porter, 2002), other methods of defining and measuring alignment are essentially limited to alignment between tests and standards. Porter's procedures have been generalized to investigating the alignment between content standards, tests, textbooks, and even classroom…

  9. Derivation of three clones from human embryonic stem cell lines by FACS sorting and their characterization.

    PubMed

    Sidhu, Kuldip S; Tuch, Bernard E

    2006-02-01

    of genes, with only one, hES 3.2, expressing the endodermal markers, i.e., alpha-fetoprotein and GATA6. The ability to produce clones from a parent hESC line rapidly by FACS sorting will help provide a homogeneous population of cells for achieving uniformed lineage specifications for future transplantation therapies and biomedical research.

  10. FRESCO: flexible alignment with rectangle scoring schemes.

    PubMed

    Dalca, A V; Brudno, M

    2008-01-01

    While the popular DNA sequence alignment tools incorporate powerful heuristics to allow for fast and accurate alignment of DNA, most of them still optimize the classical Needleman Wunsch scoring scheme. The development of novel scoring schemes is often hampered by the difficulty of finding an optimizing algorithm for each non-trivial scheme. In this paper we define the broad class of rectangle scoring schemes, and describe an algorithm and tool that can align two sequences with an arbitrary rectangle scoring scheme in polynomial time. Rectangle scoring schemes encompass some of the popular alignment scoring metrics currently in use, as well as many other functions. We investigate a novel scoring function based on minimizing the expected number of random diagonals observed with the given scores and show that it rivals the LAGAN and Clustal-W aligners, without using any biological or evolutionary parameters. The FRESCO program, freely available at http://compbio.cs.toronto.edu/fresco, gives bioinformatics researchers the ability to quickly compare the performance of other complex scoring formulas without having to implement new algorithms to optimize them.

  11. Precision alignment and mounting apparatus

    NASA Technical Reports Server (NTRS)

    Preston, Dennis R. (Inventor)

    1993-01-01

    An alignment and mounting apparatus for mounting two modules (10,12) includes a first portion having a cylindrical alignment pin (16) projecting normal to a module surface, a second portion having a three-stage alignment guide (18) including a shoehorn flange (34), a Y-slot (42) and a V-block (22) which sequentially guide the alignment pin (16) with successively finer precision and a third portion in the form of a spring-loaded captive fastener (20) for connecting the two modules after alignment is achieved.

  12. Magnetotail flux accumulation leading to auroral expansion and a substorm current wedge: case study

    NASA Astrophysics Data System (ADS)

    Chu, X.; McPherron, R. L.; Hsu, T. S.; Angelopoulos, V.; Weygand, J. M.; Strangeway, R. J.; Liu, J.

    2015-12-01

    Magnetotail burst busty flows, magnetic field dipolarization, and auroral poleward expansion are linked to the development of substorm current wedges (SCW). Although auroral brightening is often attributed to field-aligned currents (FACs) in the SCW produced by flow vorticity and pressure redistribution, in-situ observations addressing the mechanism that generates these currents have been scarce. Conjugate observations and modelling results utilizing magnetotail satellites, inversion technique for SCW, and auroral imagers were used to study the release, transport, and accumulation of magnetic flux by flows; dipolarization associated with substorm current wedge formation; and auroral poleward expansion during an isolated substorm on 13 February 2008. During early expansion phase, magnetic flux released by magnetic reconnection was transported by earthward flows. Some magnetic flux was accumulated in the near-Earth region, and the remainder was transported azimuthally by flow diversion. The accumulated flux created a high pressure region with vertically dipolarized and azimuthally bent magnetic field lines. The rotation of the magnetic field lines was consistent with the polarity of the SCW. In the near-Earth region, good agreement was found among the magnetic flux transported by the flows, the accumulated flux causing dipolarization inside the SCW, and the flux enclosed within the poleward-expanded auroral oval. This agreement demonstrates that magnetic flux from the flows accumulated and generated the SCW, the magnetic dipolarization, and the auroral poleward expansion. The quantity of accumulated flux appears to determine the amplitudes of these phenomena.

  13. Engineering cell alignment in vitro.

    PubMed

    Li, Yuhui; Huang, Guoyou; Zhang, Xiaohui; Wang, Lin; Du, Yanan; Lu, Tian Jian; Xu, Feng

    2014-01-01

    Cell alignment plays a critical role in various cell behaviors including cytoskeleton reorganization, membrane protein relocation, nucleus gene expression, and ECM remodeling. Cell alignment is also known to exert significant effects on tissue regeneration (e.g., neuron) and modulate mechanical properties of tissues including skeleton, cardiac muscle and tendon. Therefore, it is essential to engineer cell alignment in vitro for biomechanics, cell biology, tissue engineering and regenerative medicine applications. With advances in nano- and micro-scale technologies, a variety of approaches have been developed to engineer cell alignment in vitro, including mechanical loading, topographical patterning, and surface chemical treatment. In this review, we first present alignments of various cell types and their functionality in different tissues in vivo including muscle and nerve tissues. Then, we provide an overview of recent approaches for engineering cell alignment in vitro. Finally, concluding remarks and perspectives are addressed for future improvement of engineering cell alignment.

  14. TSGC and JSC Alignment

    NASA Technical Reports Server (NTRS)

    Sanchez, Humberto

    2013-01-01

    NASA and the SGCs are, by design, intended to work closely together and have synergistic Vision, Mission, and Goals. The TSGC affiliates and JSC have been working together, but not always in a concise, coordinated, nor strategic manner. Today we have a couple of simple ideas to present about how TSGC and JSC have started to work together in a more concise, coordinated, and strategic manner, and how JSC and non-TSG Jurisdiction members have started to collaborate: Idea I: TSGC and JSC Technical Alignment Idea II: Concept of Clusters.

  15. Frequency alterations in key innate immune cell components in the peripheral blood of dengue patients detected by FACS analysis.

    PubMed

    Tsai, Jih-Jin; Jen, Yen-Hua; Chang, Jung-San; Hsiao, Hui-Mien; Noisakran, Sansanee; Perng, Guey Chuen

    2011-01-01

    Dengue is a timing disease, and frequently dengue patients do not seek help until 2-3 days after prodrome. Thus, the innate immune parameters in dengue patients remain largely unexplored. A comprehensive FACS profiling of key innate immune cells in the peripheral blood of dengue patients was performed. Twenty-seven dengue patients varying in days of fever onset were enrolled and the majority of them had primary infection based on serological results. FACS panels were used to evaluate NK cells, platelet-leukocyte aggregates (PLA), inflammatory monocytes, and plasmacytoid (pDC) and myeloid dendritic cells (mDC). FACS results showed the following findings: (i) NK cells significantly dropped on day 5 after the onset of fever and gradually returned to normal within 2 weeks of illness; (ii) biphasic PLA were observed, maximum levels were reached on days 6-8 and 11-16, and platelet-monocyte aggregates (PMA) were the most frequent event; (iii) inflammatory monocytes were consistently lower on days 5-8 and gradually returned to the normal level in the second week of illness, and (iv) pDC reached the maximum level on day 5 and gradually declined to the baseline level after 1 week of illness. In contrast, mDC fluctuated somewhat during the first week of illness and returned to the baseline level in the second week of illness. The most interesting finding was the biphasic PLA, in particular the PMA. These innate immunological parameters could be a crucial factor dictating the complicated pathogenesis of dengue disease.

  16. Fac-Re(bpy)(CO){sub 3}(COOMe): A model metallocarboxylate complex of rhenium with a bipyridyl ligand

    SciTech Connect

    Gibson, D.H.; Sleadd, B.A.; Vij, A.

    1999-05-01

    The title compound fac-(2,2{prime}-bipyridyl)(carbomethoxy)rhenium tricarbonyl, crystallizes in the monoclinic system, space group P2{sub 1}/c with the following crystal data: a = 8.37551(1), b = 6.6934(1), c = 26.2098(1) {angstrom}, V({angstrom}{sup 3}) = 1,535.93(3), Z = 4, and {beta} = 90.0971(2). The metal environment is slightly distorted octahedral with a chelating bipyridyl ligand and a facial arrangement of the carbon monoxide ligands.

  17. Proceedings of the first international workshop on accelerator alignment

    SciTech Connect

    Not Available

    1990-10-01

    This report contains papers on the following accelerator topics: current alignment topics; toolboxes: instrumentation, software, and methods; fiducialization of conventional magnets; fiducialization of superconducting magnets; and next generation linear colliders.

  18. Ontology Alignment Repair through Modularization and Confidence-Based Heuristics.

    PubMed

    Santos, Emanuel; Faria, Daniel; Pesquita, Catia; Couto, Francisco M

    2015-01-01

    Ontology Matching aims at identifying a set of semantic correspondences, called an alignment, between related ontologies. In recent years, there has been a growing interest in efficient and effective matching methods for large ontologies. However, alignments produced for large ontologies are often logically incoherent. It was only recently that the use of repair techniques to improve the coherence of ontology alignments began to be explored. This paper presents a novel modularization technique for ontology alignment repair which extracts fragments of the input ontologies that only contain the necessary classes and relations to resolve all detectable incoherences. The paper presents also an alignment repair algorithm that uses a global repair strategy to minimize both the degree of incoherence and the number of mappings removed from the alignment, while overcoming the scalability problem by employing the proposed modularization technique. Our evaluation shows that our modularization technique produces significantly small fragments of the ontologies and that our repair algorithm produces more complete alignments than other current alignment repair systems, while obtaining an equivalent degree of incoherence. Additionally, we also present a variant of our repair algorithm that makes use of the confidence values of the mappings to improve alignment repair. Our repair algorithm was implemented as part of AgreementMakerLight, a free and open-source ontology matching system.

  19. Ontology Alignment Repair through Modularization and Confidence-Based Heuristics

    PubMed Central

    Santos, Emanuel; Faria, Daniel; Pesquita, Catia; Couto, Francisco M.

    2015-01-01

    Ontology Matching aims at identifying a set of semantic correspondences, called an alignment, between related ontologies. In recent years, there has been a growing interest in efficient and effective matching methods for large ontologies. However, alignments produced for large ontologies are often logically incoherent. It was only recently that the use of repair techniques to improve the coherence of ontology alignments began to be explored. This paper presents a novel modularization technique for ontology alignment repair which extracts fragments of the input ontologies that only contain the necessary classes and relations to resolve all detectable incoherences. The paper presents also an alignment repair algorithm that uses a global repair strategy to minimize both the degree of incoherence and the number of mappings removed from the alignment, while overcoming the scalability problem by employing the proposed modularization technique. Our evaluation shows that our modularization technique produces significantly small fragments of the ontologies and that our repair algorithm produces more complete alignments than other current alignment repair systems, while obtaining an equivalent degree of incoherence. Additionally, we also present a variant of our repair algorithm that makes use of the confidence values of the mappings to improve alignment repair. Our repair algorithm was implemented as part of AgreementMakerLight, a free and open-source ontology matching system. PMID:26710335

  20. Saturn's Periodic Magnetosphere: The Relation Between Periodic Hot Plasma Injections, a Rotating Partial Ring Current, Global Magnetic Field Distortions, Plasmapause Motion, and Radio Emissions

    NASA Astrophysics Data System (ADS)

    Brandt, P. C.; Mitchell, D. G.; Gurnett, D. A.; Persoon, A. M.; Tsyganenko, N. A.

    2012-04-01

    It has been know for some time that the large-scale energetic particle injections (~3-200 keV) on the nigh side of Saturn observed by Cassini/INCA are closely tracked by the periodic Saturn Kilometric Radiation (SKR). The resulting energetic particle pressure is comparable to that of the colder plasma and it therefore distorts the global magnetic field significantly as the energetic particle population drifts around Saturn. In this presentation we discuss the important consequences this has for the large-scale dynamics and configuration of the entire inner magnetosphere of Saturn. We begin by reviewing the observational correlations between remote, global INCA observations of energetic particles, magnetic field distortions, and radio emissions. We present examples of how the magnetic field measurements and the INCA observations show direct implications of a rotating 3D electrical current system associated with, not only, the energetic particle pressure, but also with an interhemispheric field-aligned current (FAC) system. Recently, we found an intriguing high correlation also between the periodic motion of the high-latitude plasmapause-like boundary reported by Gurnett et al. [2011] and the energetic particles observed remotely by INCA that are periodically injected on the night side and then drift around Saturn according to their energy. In our preliminary analysis we see a direct correlation in at least 75% of the case with the center of drifting energetic particle distribution [Brandt et al., 2010] and the encounter with the rotating plasmapause-like density boundary [Gurnett et al., 2011]. However, the remaining, low-correlation cases suggest that we do not fully understand the global, 3D current system that produces the periodic perturbations in Saturn's magnetosphere. We will use these observations to constrain the underlying 3D current system and in particular, assess the role of interhemispheric FACs in reproducing the observations.

  1. Fluorescent activated cell sorting (FACS) combined with gene expression microarrays for transcription enrichment profiling of zebrafish lateral line cells.

    PubMed

    Gallardo, Viviana E; Behra, Martine

    2013-08-15

    Transgenic lines carrying fluorescent reporter genes like GFP have been of great value in the elucidation of developmental features and physiological processes in various animal models, including zebrafish. The lateral line (LL), which is a fish specific superficial sensory organ, is an emerging organ model for studying complex cellular processes in the context of the whole living animal. Cell migration, mechanosensory cell development/differentiation and regeneration are some examples. This sensory system is made of superficial and sparse small sensory patches called neuromasts, with less than 50 cells in any given patch. The paucity of cells is a real problem in any effort to characterize those cells at the transcriptional level. We describe here a method which we applied to efficiently separate subpopulation of cells of the LL, using two distinct stable transgenic zebrafish lines, Tg(cldnb:gfp) and Tg(tnks1bp1:EGFP). In both cases, the GFP positive (GFP+) cells were separated from the remainder of the animal by using a Fluorescent Activated Cell Sorter (FACS). The transcripts of the GFP+ cells were subsequently analyzed on gene expression microarrays. The combination of FACS and microarrays is an efficient method to establish a transcriptional signature for discrete cell populations which would otherwise be masked in whole animal preparation.

  2. Rapid isolation of antibody from a synthetic human antibody library by repeated fluorescence-activated cell sorting (FACS).

    PubMed

    Yim, Sung Sun; Bang, Hyun Bae; Kim, Young Hwan; Lee, Yong Jae; Jeong, Gu Min; Jeong, Ki Jun

    2014-01-01

    Antibodies and their derivatives are the most important agents in therapeutics and diagnostics. Even after the significant progress in the technology for antibody screening from huge libraries, it takes a long time to isolate an antibody, which prevents a prompt action against the spread of a disease. Here, we report a new strategy for isolating desired antibodies from a combinatorial library in one day by repeated fluorescence-activated cell sorting (FACS). First, we constructed a library of synthetic human antibody in which single-chain variable fragment (scFv) was expressed in the periplasm of Escherichia coli. After labeling the cells with fluorescent antigen probes, the highly fluorescent cells were sorted by using a high-speed cell sorter, and these cells were reused without regeneration in the next round of sorting. After repeating this sorting, the positive clones were completely enriched in several hours. Thus, we screened the library against three viral antigens, including the H1N1 influenza virus, Hepatitis B virus, and Foot-and-mouth disease virus. Finally, the potential antibody candidates, which show K(D) values between 10 and 100 nM against the target antigens, could be successfully isolated even though the library was relatively small (∼ 10(6)). These results show that repeated FACS screening without regeneration of the sorted cells can be a powerful method when a rapid response to a spreading disease is required.

  3. FACS-sorted particles reduce the data variance in optical tweezers-assisted dynamic force spectroscopy measurements.

    PubMed

    Stangner, T; Singer, D; Wagner, C; Gutsche, C; Ueberschär, O; Hoffmann, R; Kremer, F

    2013-08-01

    By combining optical tweezers-assisted dynamic force spectroscopy experiments with fluorescence activated cell sorting (FACS), we demonstrate a new approach to reducing the data variance in measuring receptor-ligand interactions on a single molecule level by ensuring similar coating densities. Therefore, the carboxyfluorescein-labelled monophosphorylated peptide tau226-240[pThr231] is anchored on melamine resin beads and these beads are sorted by FACS to achieve a homogeneous surface coverage. To quantify the impact of the fluorescence dye on the bond parameters between the phosphorylated peptide and the corresponding phosphorylation specific anti-human tau monoclonal antibody HPT-104, we perform dynamic force spectroscopy and compare the results to data using unsorted beads covered with the non-fluorescence peptide analogue. Finally, we demonstrate that the data variance of the relative binding frequency is significantly decreased by a factor of 3.4 using pre-sorted colloids with a homogeneous ligand coating compared to using unsorted colloids.

  4. Paired image- and FACS-based toxicity assays for high content screening of spheroid-type tumor cell cultures.

    PubMed

    Trumpi, Kari; Egan, David A; Vellinga, Thomas T; Borel Rinkes, Inne H M; Kranenburg, Onno

    2015-01-01

    Novel spheroid-type tumor cell cultures directly isolated from patients' tumors preserve tumor characteristics better than traditionally grown cell lines. However, such cultures are not generally used for high-throughput toxicity drug screens. In addition, the assays that are commonly used to assess drug-induced toxicity in such screens usually measure a proxy for cell viability such as mitochondrial activity or ATP-content per culture well, rather than actual cell death. This generates considerable assay-dependent differences in the measured toxicity values. To address this problem we developed a robust method that documents drug-induced toxicity on a per-cell, rather than on a per-well basis. The method involves automated drug dispensing followed by paired image- and FACS-based analysis of cell death and cell cycle changes. We show that the two methods generate toxicity data in 96-well format which are highly concordant. By contrast, the concordance of these methods with frequently used well-based assays was generally poor. The reported method can be implemented on standard automated microscopes and provides a low-cost approach for accurate and reproducible high-throughput toxicity screens in spheroid type cell cultures. Furthermore, the high versatility of both the imaging and FACS platforms allows straightforward adaptation of the high-throughput experimental setup to include fluorescence-based measurement of additional cell biological parameters.

  5. FACS-sorted particles reduce the data variance in optical tweezers-assisted dynamic force spectroscopy measurements

    NASA Astrophysics Data System (ADS)

    Stangner, T.; Singer, D.; Wagner, C.; Gutsche, C.; Ueberschär, O.; Hoffmann, R.; Kremer, F.

    2013-08-01

    By combining optical tweezers-assisted dynamic force spectroscopy experiments with fluorescence activated cell sorting (FACS), we demonstrate a new approach to reducing the data variance in measuring receptor-ligand interactions on a single molecule level by ensuring similar coating densities. Therefore, the carboxyfluorescein-labelled monophosphorylated peptide tau226-240[pThr231] is anchored on melamine resin beads and these beads are sorted by FACS to achieve a homogeneous surface coverage. To quantify the impact of the fluorescence dye on the bond parameters between the phosphorylated peptide and the corresponding phosphorylation specific anti-human tau monoclonal antibody HPT-104, we perform dynamic force spectroscopy and compare the results to data using unsorted beads covered with the non-fluorescence peptide analogue. Finally, we demonstrate that the data variance of the relative binding frequency is significantly decreased by a factor of 3.4 using pre-sorted colloids with a homogeneous ligand coating compared to using unsorted colloids.

  6. Nova laser alignment control system

    SciTech Connect

    Van Arsdall, P.J.; Holloway, F.W.; McGuigan, D.L.; Shelton, R.T.

    1984-03-29

    Alignment of the Nova laser requires control of hundreds of optical components in the ten beam paths. Extensive application of computer technology makes daily alignment practical. The control system is designed in a manner which provides both centralized and local manual operator controls integrated with automatic closed loop alignment. Menudriven operator consoles using high resolution color graphics displays overlaid with transport touch panels allow laser personnel to interact efficiently with the computer system. Automatic alignment is accomplished by using image analysis techniques to determine beam references points from video images acquired along the laser chain. A major goal of the design is to contribute substantially to rapid experimental turnaround and consistent alignment results. This paper describes the computer-based control structure and the software methods developed for aligning this large laser system.

  7. Nuclear reactor internals alignment configuration

    DOEpatents

    Gilmore, Charles B.; Singleton, Norman R.

    2009-11-10

    An alignment system that employs jacking block assemblies and alignment posts around the periphery of the top plate of a nuclear reactor lower internals core shroud to align an upper core plate with the lower internals and the core shroud with the core barrel. The distal ends of the alignment posts are chamfered and are closely received within notches machined in the upper core plate at spaced locations around the outer circumference of the upper core plate. The jacking block assemblies are used to center the core shroud in the core barrel and the alignment posts assure the proper orientation of the upper core plate. The alignment posts may alternately be formed in the upper core plate and the notches may be formed in top plate.

  8. Aligned Defrosting Dunes

    NASA Technical Reports Server (NTRS)

    2004-01-01

    17 August 2004 This July 2004 Mars Global Surveyor (MGS) Mars Orbiter Camera (MOC) image shows a group of aligned barchan sand dunes in the martian north polar region. At the time, the dunes were covered with seasonal frost, but the frost had begun to sublime away, leaving dark spots and dark outlines around the dunes. The surrounding plains exhibit small, diffuse spots that are also the result of subliming seasonal frost. This northern spring image, acquired on a descending ground track (as MGS was moving north to south on the 'night' side of Mars) is located near 78.8oN, 34.8oW. The image covers an area about 3 km (1.9 mi) across and sunlight illuminates the scene from the upper left.

  9. Lunar Alignments - Identification and Analysis

    NASA Astrophysics Data System (ADS)

    González-García, A. César

    Lunar alignments are difficult to establish given the apparent lack of written accounts clearly pointing toward lunar alignments for individual temples. While some individual cases are reviewed and highlighted, the weight of the proof must fall on statistical sampling. Some definitions for the lunar alignments are provided in order to clarify the targets, and thus, some new tools are provided to try to test the lunar hypothesis in several cases, especially in megalithic astronomy.

  10. Alignment of Helical Membrane Protein Sequences Using AlignMe

    PubMed Central

    Khafizov, Kamil; Forrest, Lucy R.

    2013-01-01

    Few sequence alignment methods have been designed specifically for integral membrane proteins, even though these important proteins have distinct evolutionary and structural properties that might affect their alignments. Existing approaches typically consider membrane-related information either by using membrane-specific substitution matrices or by assigning distinct penalties for gap creation in transmembrane and non-transmembrane regions. Here, we ask whether favoring matching of predicted transmembrane segments within a standard dynamic programming algorithm can improve the accuracy of pairwise membrane protein sequence alignments. We tested various strategies using a specifically designed program called AlignMe. An updated set of homologous membrane protein structures, called HOMEP2, was used as a reference for optimizing the gap penalties. The best of the membrane-protein optimized approaches were then tested on an independent reference set of membrane protein sequence alignments from the BAliBASE collection. When secondary structure (S) matching was combined with evolutionary information (using a position-specific substitution matrix (P)), in an approach we called AlignMePS, the resultant pairwise alignments were typically among the most accurate over a broad range of sequence similarities when compared to available methods. Matching transmembrane predictions (T), in addition to evolutionary information, and secondary-structure predictions, in an approach called AlignMePST, generally reduces the accuracy of the alignments of closely-related proteins in the BAliBASE set relative to AlignMePS, but may be useful in cases of extremely distantly related proteins for which sequence information is less informative. The open source AlignMe code is available at https://sourceforge.net/projects/alignme/, and at http://www.forrestlab.org, along with an online server and the HOMEP2 data set. PMID:23469223

  11. Survey and alignment at the ALS

    SciTech Connect

    Krebs, G.F.; Lauritzen, T.; Thur, W.

    1995-11-01

    This paper describes survey and alignment at the Lawrence Berkeley National Laboratory`s Advanced Light Source (ALS) accelerators from 1993 to 1995. The ALS is a 1.0 - 1.9 GeV electron accelerator producing extremely bright synchrotron light in the UV and soft-X-ray wavelengths. At the ALS, electrons are accelerated in a LINAC to 50 MeV, injected into a booster ring for further acceleration and finally injected into the storage ring. This is shown schematically in Figure 1. The storage ring, some 200 m in circumference, has been run with electron currents above 400 mA with lifetimes as high as 24 hours. The ALS is a third generation light source and requires for efficient storage ring operation, magnets aligned to within 150 mm of their ideal position. To accomplish this a network of monuments was established and their positions measured with respect to one another. The data was reduced using GEONET`` and STAR*NET`` software. Using the monuments as reference points, magnet positions were measured and alignment confirmed using the Kem Electronic Coordinate Determination System (ECDS``). A number of other papers dealing with survey and alignment (S&A) at the ALS have been written that may further elucidate some details of the methods and systems described in this paper.

  12. Scalable cell alignment on optical media substrates.

    PubMed

    Anene-Nzelu, Chukwuemeka G; Choudhury, Deepak; Li, Huipeng; Fraiszudeen, Azmall; Peh, Kah-Yim; Toh, Yi-Chin; Ng, Sum Huan; Leo, Hwa Liang; Yu, Hanry

    2013-07-01

    Cell alignment by underlying topographical cues has been shown to affect important biological processes such as differentiation and functional maturation in vitro. However, the routine use of cell culture substrates with micro- or nano-topographies, such as grooves, is currently hampered by the high cost and specialized facilities required to produce these substrates. Here we present cost-effective commercially available optical media as substrates for aligning cells in culture. These optical media, including CD-R, DVD-R and optical grating, allow different cell types to attach and grow well on them. The physical dimension of the grooves in these optical media allowed cells to be aligned in confluent cell culture with maximal cell-cell interaction and these cell alignment affect the morphology and differentiation of cardiac (H9C2), skeletal muscle (C2C12) and neuronal (PC12) cell lines. The optical media is amenable to various chemical modifications with fibronectin, laminin and gelatin for culturing different cell types. These low-cost commercially available optical media can serve as scalable substrates for research or drug safety screening applications in industry scales.

  13. Mask alignment system for semiconductor processing

    DOEpatents

    Webb, Aaron P.; Carlson, Charles T.; Weaver, William T.; Grant, Christopher N.

    2017-02-14

    A mask alignment system for providing precise and repeatable alignment between ion implantation masks and workpieces. The system includes a mask frame having a plurality of ion implantation masks loosely connected thereto. The mask frame is provided with a plurality of frame alignment cavities, and each mask is provided with a plurality of mask alignment cavities. The system further includes a platen for holding workpieces. The platen may be provided with a plurality of mask alignment pins and frame alignment pins configured to engage the mask alignment cavities and frame alignment cavities, respectively. The mask frame can be lowered onto the platen, with the frame alignment cavities moving into registration with the frame alignment pins to provide rough alignment between the masks and workpieces. The mask alignment cavities are then moved into registration with the mask alignment pins, thereby shifting each individual mask into precise alignment with a respective workpiece.

  14. Alignment of Iron Nanoparticles in a Magnetic Field Due to Shape Anisotropy

    SciTech Connect

    Radhakrishnan, Balasubramaniam; Nicholson, Don M; Eisenbach, Markus; Ludtka, Gerard Michael; Rios, Orlando; Parish, Chad M

    2015-07-09

    During high magnetic field processing there is evidence for alignment of non-spherical metallic particles above the Curie temperature in alloys with negligible magneto-crystalline anisotropy. The main driving force for alignment is the magnetic shape anisotropy. Current understanding of the phenomenon is not adequate to quantify the effect of particle size, aspect ratio, temperature and the magnetic field on particle alignment. We demonstrate a Monte Carlo approach coupled with size scaling to show the conditions under which alignment is possible.

  15. Lexical alignment in triadic communication

    PubMed Central

    Foltz, Anouschka; Gaspers, Judith; Thiele, Kristina; Stenneken, Prisca; Cimiano, Philipp

    2015-01-01

    Lexical alignment refers to the adoption of one’s interlocutor’s lexical items. Accounts of the mechanisms underlying such lexical alignment differ (among other aspects) in the role assigned to addressee-centered behavior. In this study, we used a triadic communicative situation to test which factors may modulate the extent to which participants’ lexical alignment reflects addressee-centered behavior. Pairs of naïve participants played a picture matching game and received information about the order in which pictures were to be matched from a voice over headphones. On critical trials, participants did or did not hear a name for the picture to be matched next over headphones. Importantly, when the voice over headphones provided a name, it did not match the name that the interlocutor had previously used to describe the object. Participants overwhelmingly used the word that the voice over headphones provided. This result points to non-addressee-centered behavior and is discussed in terms of disrupting alignment with the interlocutor as well as in terms of establishing alignment with the voice over headphones. In addition, the type of picture (line drawing vs. tangram shape) independently modulated lexical alignment, such that participants showed more lexical alignment to their interlocutor for (more ambiguous) tangram shapes compared to line drawings. Overall, the results point to a rather large role for non-addressee-centered behavior during lexical alignment. PMID:25762955

  16. Well-pump alignment system

    DOEpatents

    Drumheller, Douglas S.

    1998-01-01

    An improved well-pump for geothermal wells, an alignment system for a well-pump, and to a method for aligning a rotor and stator within a well-pump, wherein the well-pump has a whistle assembly formed at a bottom portion thereof, such that variations in the frequency of the whistle, indicating misalignment, may be monitored during pumping.

  17. CATO: The Clone Alignment Tool.

    PubMed

    Henstock, Peter V; LaPan, Peter

    2016-01-01

    High-throughput cloning efforts produce large numbers of sequences that need to be aligned, edited, compared with reference sequences, and organized as files and selected clones. Different pieces of software are typically required to perform each of these tasks. We have designed a single piece of software, CATO, the Clone Alignment Tool, that allows a user to align, evaluate, edit, and select clone sequences based on comparisons to reference sequences. The input and output are designed to be compatible with standard data formats, and thus suitable for integration into a clone processing pipeline. CATO provides both sequence alignment and visualizations to facilitate the analysis of cloning experiments. The alignment algorithm matches each of the relevant candidate sequences against each reference sequence. The visualization portion displays three levels of matching: 1) a top-level summary of the top candidate sequences aligned to each reference sequence, 2) a focused alignment view with the nucleotides of matched sequences displayed against one reference sequence, and 3) a pair-wise alignment of a single reference and candidate sequence pair. Users can select the minimum matching criteria for valid clones, edit or swap reference sequences, and export the results to a summary file as part of the high-throughput cloning workflow.

  18. Drive alignment pays maintenance dividends

    SciTech Connect

    Fedder, R.

    2008-12-15

    Proper alignment of the motor and gear drive on conveying and processing equipment will result in longer bearing and coupling life, along with lower maintenance costs. Selecting an alignment free drive package instead of a traditional foot mounted drive and motor is a major advancement toward these goals. 4 photos.

  19. Alignment of the MINOS FD

    SciTech Connect

    Becker, B.; Boehnlein, D.; /Fermilab

    2004-11-01

    The results and procedure of the alignment of the MINOS Far Detector are presented. The far detector has independent alignments of SM1 and SM2. The misalignments have an estimated uncertainty of {approx}850 {micro}m for SM1 and {approx}750 {micro}m for SM2. The alignment has as inputs the average rotations of U and V as determined by optical survey and strip positions within modules measured from the module mapper. The output of this is a module-module correction for transverse mis-alignments. These results were verified by examining an independent set of data. These alignment constants on average contribute much less then 1% to the total uncertainty in the transverse strip position.

  20. Splign: algorithms for computing spliced alignments with identification of paralogs

    PubMed Central

    Kapustin, Yuri; Souvorov, Alexander; Tatusova, Tatiana; Lipman, David

    2008-01-01

    Background The computation of accurate alignments of cDNA sequences against a genome is at the foundation of modern genome annotation pipelines. Several factors such as presence of paralogs, small exons, non-consensus splice signals, sequencing errors and polymorphic sites pose recognized difficulties to existing spliced alignment algorithms. Results We describe a set of algorithms behind a tool called Splign for computing cDNA-to-Genome alignments. The algorithms include a high-performance preliminary alignment, a compartment identification based on a formally defined model of adjacent duplicated regions, and a refined sequence alignment. In a series of tests, Splign has produced more accurate results than other tools commonly used to compute spliced alignments, in a reasonable amount of time. Conclusion Splign's ability to deal with various issues complicating the spliced alignment problem makes it a helpful tool in eukaryotic genome annotation processes and alternative splicing studies. Its performance is enough to align the largest currently available pools of cDNA data such as the human EST set on a moderate-sized computing cluster in a matter of hours. The duplications identification (compartmentization) algorithm can be used independently in other areas such as the study of pseudogenes. Reviewers This article was reviewed by: Steven Salzberg, Arcady Mushegian and Andrey Mironov (nominated by Mikhail Gelfand). PMID:18495041

  1. Magnetic alignment and the Poisson alignment reference system

    NASA Astrophysics Data System (ADS)

    Griffith, L. V.; Schenz, R. F.; Sommargren, G. E.

    1990-08-01

    Three distinct metrological operations are necessary to align a free-electron laser (FEL): the magnetic axis must be located, a straight line reference (SLR) must be generated, and the magnetic axis must be related to the SLR. This article begins with a review of the motivation for developing an alignment system that will assure better than 100-μm accuracy in the alignment of the magnetic axis throughout an FEL. The 100-μm accuracy is an error circle about an ideal axis for 300 m or more. The article describes techniques for identifying the magnetic axes of solenoids, quadrupoles, and wiggler poles. Propagation of a laser beam is described to the extent of revealing sources of nonlinearity in the beam. Development of a straight-line reference based on the Poisson line, a diffraction effect, is described in detail. Spheres in a large-diameter laser beam create Poisson lines and thus provide a necessary mechanism for gauging between the magnetic axis and the SLR. Procedures for installing FEL components and calibrating alignment fiducials to the magnetic axes of the components are also described. The Poisson alignment reference system should be accurate to 25 μm over 300 m, which is believed to be a factor-of-4 improvement over earlier techniques. An error budget shows that only 25% of the total budgeted tolerance is used for the alignment reference system, so the remaining tolerances should fall within the allowable range for FEL alignment.

  2. Testing the tidal alignment model of galaxy intrinsic alignment

    SciTech Connect

    Blazek, Jonathan; Seljak, Uroš; McQuinn, Matthew E-mail: mmcquinn@berkeley.edu

    2011-05-01

    Weak gravitational lensing has become a powerful probe of large-scale structure and cosmological parameters. Precision weak lensing measurements require an understanding of the intrinsic alignment of galaxy ellipticities, which can in turn inform models of galaxy formation. It is hypothesized that elliptical galaxies align with the background tidal field and that this alignment mechanism dominates the correlation between ellipticities on cosmological scales (in the absence of lensing). We use recent large-scale structure measurements from the Sloan Digital Sky Survey to test this picture with several statistics: (1) the correlation between ellipticity and galaxy overdensity, w{sub g+}; (2) the intrinsic alignment auto-correlation functions; (3) the correlation functions of curl-free, E, and divergence-free, B, modes, the latter of which is zero in the linear tidal alignment theory; (4) the alignment correlation function, w{sub g}(r{sub p},θ), a recently developed statistic that generalizes the galaxy correlation function to account for the angle between the galaxy separation vector and the principle axis of ellipticity. We show that recent measurements are largely consistent with the tidal alignment model and discuss dependence on galaxy luminosity. In addition, we show that at linear order the tidal alignment model predicts that the angular dependence of w{sub g}(r{sub p},θ) is simply w{sub g+}(r{sub p})cos (2θ) and that this dependence is consistent with recent measurements. We also study how stochastic nonlinear contributions to galaxy ellipticity impact these statistics. We find that a significant fraction of the observed LRG ellipticity can be explained by alignment with the tidal field on scales ∼> 10 \\hMpc. These considerations are relevant to galaxy formation and evolution.

  3. Explaining compact groups as change alignments

    NASA Technical Reports Server (NTRS)

    Mamon, Gary A.

    1990-01-01

    The physical nature of the apparently densest groups of galaxies, known as compact groups is a topic of some recent controversy, despite the detailed observations of a well-defined catalog of 100 isolated compact groups compiled by Hickson (1982). Whereas many authors have espoused the view that compact groups are bound systems, typically as dense as they appear in projection on the sky (e.g., Williams & Rood 1987; Sulentic 1987; Hickson & Rood 1988), others see them as the result of chance configurations within larger systems, either in 1D (chance alignments: Mamon 1986; Walke & Mamon 1989), or in 3D (transient cores: Rose 1979). As outlined in the companion review to this contribution (Mamon, in these proceedings), the implication of Hickson's compact groups (HCGs) being dense bound systems is that they would then constitute the densest isolated systems of galaxies in the Universe and the privileged site for galaxy interactions. In a previous paper (Mamon 1986), the author reviewed the arguments given for the different theories of compact groups. Since then, a dozen papers have been published on the subject, including a thorough and perceptive review by White (1990), thus more than doubling the amount written on the subject. Here, the author first enumerates the arguments that he brought up in 1986 substantiating the chance alignment hypothesis, then he reviews the current status of the numerous recent arguments arguing against chance alignments and/or for the bound dense group hypothesis (both for the majority of HCGs but not all of them), and finally he reconsiders each one of these anti-chance alignment arguments and shows that, rather than being discredited, the chance alignment hypothesis remains a fully consistent explanation for the nature of compact groups.

  4. Robust temporal alignment of multimodal cardiac sequences

    NASA Astrophysics Data System (ADS)

    Perissinotto, Andrea; Queirós, Sandro; Morais, Pedro; Baptista, Maria J.; Monaghan, Mark; Rodrigues, Nuno F.; D'hooge, Jan; Vilaça, João. L.; Barbosa, Daniel

    2015-03-01

    Given the dynamic nature of cardiac function, correct temporal alignment of pre-operative models and intraoperative images is crucial for augmented reality in cardiac image-guided interventions. As such, the current study focuses on the development of an image-based strategy for temporal alignment of multimodal cardiac imaging sequences, such as cine Magnetic Resonance Imaging (MRI) or 3D Ultrasound (US). First, we derive a robust, modality-independent signal from the image sequences, estimated by computing the normalized cross-correlation between each frame in the temporal sequence and the end-diastolic frame. This signal is a resembler for the left-ventricle (LV) volume curve over time, whose variation indicates different temporal landmarks of the cardiac cycle. We then perform the temporal alignment of these surrogate signals derived from MRI and US sequences of the same patient through Dynamic Time Warping (DTW), allowing to synchronize both sequences. The proposed framework was evaluated in 98 patients, which have undergone both 3D+t MRI and US scans. The end-systolic frame could be accurately estimated as the minimum of the image-derived surrogate signal, presenting a relative error of 1.6 +/- 1.9% and 4.0 +/- 4.2% for the MRI and US sequences, respectively, thus supporting its association with key temporal instants of the cardiac cycle. The use of DTW reduces the desynchronization of the cardiac events in MRI and US sequences, allowing to temporally align multimodal cardiac imaging sequences. Overall, a generic, fast and accurate method for temporal synchronization of MRI and US sequences of the same patient was introduced. This approach could be straightforwardly used for the correct temporal alignment of pre-operative MRI information and intra-operative US images.

  5. Image Correlation Method for DNA Sequence Alignment

    PubMed Central

    Curilem Saldías, Millaray; Villarroel Sassarini, Felipe; Muñoz Poblete, Carlos; Vargas Vásquez, Asticio; Maureira Butler, Iván

    2012-01-01

    The complexity of searches and the volume of genomic data make sequence alignment one of bioinformatics most active research areas. New alignment approaches have incorporated digital signal processing techniques. Among these, correlation methods are highly sensitive. This paper proposes a novel sequence alignment method based on 2-dimensional images, where each nucleic acid base is represented as a fixed gray intensity pixel. Query and known database sequences are coded to their pixel representation and sequence alignment is handled as object recognition in a scene problem. Query and database become object and scene, respectively. An image correlation process is carried out in order to search for the best match between them. Given that this procedure can be implemented in an optical correlator, the correlation could eventually be accomplished at light speed. This paper shows an initial research stage where results were “digitally” obtained by simulating an optical correlation of DNA sequences represented as images. A total of 303 queries (variable lengths from 50 to 4500 base pairs) and 100 scenes represented by 100 x 100 images each (in total, one million base pair database) were considered for the image correlation analysis. The results showed that correlations reached very high sensitivity (99.01%), specificity (98.99%) and outperformed BLAST when mutation numbers increased. However, digital correlation processes were hundred times slower than BLAST. We are currently starting an initiative to evaluate the correlation speed process of a real experimental optical correlator. By doing this, we expect to fully exploit optical correlation light properties. As the optical correlator works jointly with the computer, digital algorithms should also be optimized. The results presented in this paper are encouraging and support the study of image correlation methods on sequence alignment. PMID:22761742

  6. Image correlation method for DNA sequence alignment.

    PubMed

    Curilem Saldías, Millaray; Villarroel Sassarini, Felipe; Muñoz Poblete, Carlos; Vargas Vásquez, Asticio; Maureira Butler, Iván

    2012-01-01

    The complexity of searches and the volume of genomic data make sequence alignment one of bioinformatics most active research areas. New alignment approaches have incorporated digital signal processing techniques. Among these, correlation methods are highly sensitive. This paper proposes a novel sequence alignment method based on 2-dimensional images, where each nucleic acid base is represented as a fixed gray intensity pixel. Query and known database sequences are coded to their pixel representation and sequence alignment is handled as object recognition in a scene problem. Query and database become object and scene, respectively. An image correlation process is carried out in order to search for the best match between them. Given that this procedure can be implemented in an optical correlator, the correlation could eventually be accomplished at light speed. This paper shows an initial research stage where results were "digitally" obtained by simulating an optical correlation of DNA sequences represented as images. A total of 303 queries (variable lengths from 50 to 4500 base pairs) and 100 scenes represented by 100 x 100 images each (in total, one million base pair database) were considered for the image correlation analysis. The results showed that correlations reached very high sensitivity (99.01%), specificity (98.99%) and outperformed BLAST when mutation numbers increased. However, digital correlation processes were hundred times slower than BLAST. We are currently starting an initiative to evaluate the correlation speed process of a real experimental optical correlator. By doing this, we expect to fully exploit optical correlation light properties. As the optical correlator works jointly with the computer, digital algorithms should also be optimized. The results presented in this paper are encouraging and support the study of image correlation methods on sequence alignment.

  7. Isolated digit recognition without time alignment

    NASA Astrophysics Data System (ADS)

    Gay, Jeffrey Mark

    1994-12-01

    This thesis examines methods for isolated digit recognition without using time alignment. Resource requirements for isolated word recognizers that use time alignment can become prohibitively large as the vocabulary to be classified grows. Thus, methods capable of achieving recognition rates comparable to those obtained with current methods using these techniques are needed. The goals of this research are to find feature sets for speech recognition that perform well without using time alignment, and to identify classifiers that provide good performance with these features. Using the digits from the TI46 database, baseline speaker-independent recognition rates of 95.2% for the complete speaker set and 98.1% for the male speaker set are established using dynamic time warping (DTW). This work begins with features derived from spectrograms of each digit. Based on a critical band frequency scale covering the telephone bandwidth (300-3000 Hz), these critical band energy features are classified alone and in combination with several other feature sets, with several different classifiers. With this method, there is one 'short' feature vector per word. For speaker-independent recognition using the complete speaker set and a multi-layer perceptron (MLP) classifier, a recognition rate of 92.4% is achieved. For the same classifier with the male speaker set, a recognition rate of 97.1% is achieved. For the male speaker set, there is no statistical difference between results using DTW, and those using the MLP and no time alignment. This shows that there are feature sets that may provide high recognition rates for isolated word recognition without the need for time alignment.

  8. Cosmological information in the intrinsic alignments of luminous red galaxies

    SciTech Connect

    Chisari, Nora Elisa; Dvorkin, Cora E-mail: cdvorkin@ias.edu

    2013-12-01

    The intrinsic alignments of galaxies are usually regarded as a contaminant to weak gravitational lensing observables. The alignment of Luminous Red Galaxies, detected unambiguously in observations from the Sloan Digital Sky Survey, can be reproduced by the linear tidal alignment model of Catelan, Kamionkowski and Blandford (2001) on large scales. In this work, we explore the cosmological information encoded in the intrinsic alignments of red galaxies. We make forecasts for the ability of current and future spectroscopic surveys to constrain local primordial non-Gaussianity and Baryon Acoustic Oscillations (BAO) in the cross-correlation function of intrinsic alignments and the galaxy density field. For the Baryon Oscillation Spectroscopic Survey, we find that the BAO signal in the intrinsic alignments is marginally significant with a signal-to-noise ratio of 1.8 and 2.2 with the current LOWZ and CMASS samples of galaxies, respectively, and increasing to 2.3 and 2.7 once the survey is completed. For the Dark Energy Spectroscopic Instrument and for a spectroscopic survey following the EUCLID redshift selection function, we find signal-to-noise ratios of 12 and 15, respectively. Local type primordial non-Gaussianity, parametrized by f{sub NL} = 10, is only marginally significant in the intrinsic alignments signal with signal-to-noise ratios < 2 for the three surveys considered.

  9. MRD detection of leukemia relapse using HLA typing by FACS in combination with FISH after mismatched allogeneic stem cell transplantation.

    PubMed

    Miyachi, Mitsuru; Watanabe, Eri; Watanabe, Nobukazu; Tsuma, Yusuke; Kawashima-Goto, Sachiko; Tamura, Shinichi; Imamura, Toshihiko; Ishida, Hiroyuki; Hosoi, Hajime

    2014-08-01

    Loss of mismatched HLA is a cause of relapse following HLA-mismatched allo-SCT. We directly detected the loss of mismatched HLA alleles in relapsed leukemic cells at a MRD level using HLA typing by multicolor FACS (HLA-Flow) in combination with FISH in the BM of two patients with MLL-AF9-positive AML, at 6 and 10 months after mismatched allo-SCT. HLA-Flow with FISH analysis detected relapsed leukemic cells not expressing a mismatched HLA allele and harboring the MLL rearrangement. Simultaneously, real-time quantitative RT-PCR detected a low copy number of MLL-AF9 transcripts, consistent with MRD detection. HLA-Flow with FISH is a powerful method for detecting molecular relapse after mismatched allo-SCT and provides important information on the HLA expression status of the relapsed leukemic cells to help determine the next intervention.

  10. Combining Yeast Display and Competitive FACS to Select Rare Hapten-Specific Clones from Recombinant Antibody Libraries.

    PubMed

    Sun, Yue; Ban, Bhupal; Bradbury, Andrew; Ansari, G A Shakeel; Blake, Diane A

    2016-09-20

    The development of antibodies to low molecular weight haptens remains challenging due to both the low immunogenicity of many haptens and the cross-reactivity of the protein carriers used to generate the immune response. Recombinant antibodies and novel display technologies have greatly advanced antibody development; however, new techniques are still required to select rare hapten-specific antibodies from large recombinant libraries. In the present study, we used a combination of phage and yeast display to screen an immune antibody library (size, 4.4 × 10(6)) against hapten markers for petroleum contamination (phenanthrene and methylphenanthrenes). Selection via phage display was used first to enrich the library between 20- and 100-fold for clones that bound to phenanthrene-protein conjugates. The enriched libraries were subsequently transferred to a yeast display system and a newly developed competitive FACS procedure was employed to select rare hapten-specific clones. Competitive FACS increased the frequency of hapten-specific scFvs in our yeast-displayed scFvs from 0.025 to 0.005% in the original library to between 13 and 35% in selected pools. The presence of hapten-specific scFvs was confirmed by competitive ELISA using periplasmic protein. Three distinct antibody clones that recognize phenanthrene and methylphenanthrenes were selected, and their distinctive binding properties were characterized. To our knowledge, these are first antibodies that can distinguish between methylated (petrogenic) versus unmethylated (pyrogenic) phenanthrenes; such antibodies will be useful in detecting the sources of environmental contamination. This selection method could be generally adopted in the selection of other hapten-specific recombinant antibodies.

  11. Combining Yeast Display and Competitive FACS to Select Rare Hapten-Specific Clones from Recombinant Antibody Libraries

    PubMed Central

    2016-01-01

    The development of antibodies to low molecular weight haptens remains challenging due to both the low immunogenicity of many haptens and the cross-reactivity of the protein carriers used to generate the immune response. Recombinant antibodies and novel display technologies have greatly advanced antibody development; however, new techniques are still required to select rare hapten-specific antibodies from large recombinant libraries. In the present study, we used a combination of phage and yeast display to screen an immune antibody library (size, 4.4 × 106) against hapten markers for petroleum contamination (phenanthrene and methylphenanthrenes). Selection via phage display was used first to enrich the library between 20- and 100-fold for clones that bound to phenanthrene–protein conjugates. The enriched libraries were subsequently transferred to a yeast display system and a newly developed competitive FACS procedure was employed to select rare hapten-specific clones. Competitive FACS increased the frequency of hapten-specific scFvs in our yeast-displayed scFvs from 0.025 to 0.005% in the original library to between 13 and 35% in selected pools. The presence of hapten-specific scFvs was confirmed by competitive ELISA using periplasmic protein. Three distinct antibody clones that recognize phenanthrene and methylphenanthrenes were selected, and their distinctive binding properties were characterized. To our knowledge, these are first antibodies that can distinguish between methylated (petrogenic) versus unmethylated (pyrogenic) phenanthrenes; such antibodies will be useful in detecting the sources of environmental contamination. This selection method could be generally adopted in the selection of other hapten-specific recombinant antibodies. PMID:27571429

  12. Association studies to transporting proteins of fac-Re(I)(CO)3(pterin)(H2O) complex.

    PubMed

    Ragone, Fabricio; Saavedra, Héctor H Martínez; García, Pablo F; Wolcan, Ezequiel; Argüello, Gerardo A; Ruiz, Gustavo T

    2017-01-01

    A new synthetic route to acquire the water soluble complex fac-Re(I)(CO)3(pterin)(H2O) was carried out in aqueous solution. The complex has been obtained with success via the fac-[Re(I)(CO)3(H2O)3]Cl precursor complex. Re(I)(CO)3(pterin)(H2O) has been found to bind strongly with bovine and human serum albumins (BSA and HSA) with intrinsic-binding constants, Kb, of 6.5 × 10(5) M(-1) and 5.6 × 10(5) M(-1) at 310 K, respectively. The interactions of serum albumins with Re(I)(CO)3(pterin)(H2O) were evaluated employing UV-vis fluorescence and absorption spectroscopy and circular dichroism. The results suggest that the serum albumins-Re(I)(CO)3(pterin)(H2O) interactions occurred in the domain IIA-binding pocket without loss of helical stability of the proteins. The comparison of the fluorescence quenching of BSA and HSA due to the binding to the Re(I) complex suggested that local interaction around the Trp 214 residue had taken place. The analysis of the thermodynamic parameters ΔG(0), ΔH(0), and ΔS(0) indicated that the hydrophobic interactions played a major role in both HSA-Re(I) and BSA-Re(I) association processes. All these experimental results suggest that these proteins can be considered as good carriers for transportation of Re(I)(CO)3(pterin)(H2O) complex. This is of significant importance in relation to the use of this Re(I) complex in several biomedical fields, such as photodynamic therapy and radiopharmacy.

  13. BAYESIAN PROTEIN STRUCTURE ALIGNMENT1

    PubMed Central

    RODRIGUEZ, ABEL; SCHMIDLER, SCOTT C.

    2015-01-01

    The analysis of the three-dimensional structure of proteins is an important topic in molecular biochemistry. Structure plays a critical role in defining the function of proteins and is more strongly conserved than amino acid sequence over evolutionary timescales. A key challenge is the identification and evaluation of structural similarity between proteins; such analysis can aid in understanding the role of newly discovered proteins and help elucidate evolutionary relationships between organisms. Computational biologists have developed many clever algorithmic techniques for comparing protein structures, however, all are based on heuristic optimization criteria, making statistical interpretation somewhat difficult. Here we present a fully probabilistic framework for pairwise structural alignment of proteins. Our approach has several advantages, including the ability to capture alignment uncertainty and to estimate key “gap” parameters which critically affect the quality of the alignment. We show that several existing alignment methods arise as maximum a posteriori estimates under specific choices of prior distributions and error models. Our probabilistic framework is also easily extended to incorporate additional information, which we demonstrate by including primary sequence information to generate simultaneous sequence–structure alignments that can resolve ambiguities obtained using structure alone. This combined model also provides a natural approach for the difficult task of estimating evolutionary distance based on structural alignments. The model is illustrated by comparison with well-established methods on several challenging protein alignment examples. PMID:26925188

  14. Alignment of the Fermilab D0 Detector

    SciTech Connect

    Babatunde O'Sheg Oshinowo

    2001-07-20

    The Fermilab D0 detector was used for the discovery of the top quark during Run I in 1996. It is currently being upgraded to exploit the physics potential to be presented by the Main Injector and the Tevatron Collider during Run II in the Fall of 2000. Some of the essential elements of this upgrade is the upgrade of the Solenoid Magnet, the Central Fiber Tracker, the Preshower Detectors, the Calorimeter System, and the Muon System. This paper discusses the survey and alignment of the these detectors with emphasis on the Muon detector system. The alignment accuracy is specified as better than 0.5mm. A combination of the Laser Tracker, BETS, and V-STARS systems are used for the survey.

  15. Evryscope Robotilter automated camera / ccd alignment system

    NASA Astrophysics Data System (ADS)

    Ratzloff, Jeff K.; Law, Nicholas M.; Fors, Octavi; Ser, Daniel d.; Corbett, Henry T.

    2016-08-01

    We have deployed a new class of telescope, the Evryscope, which opens a new parameter space in optical astronomy - the ability to detect short time scale events across the entire sky simultaneously. The system is a gigapixel-scale array camera with an 8000 sq. deg. field of view, 13 arcsec per pixel sampling, and the ability to detect objects brighter than g = 16 in each 2-minute exposure. The Evryscope is designed to find transiting exoplanets around exotic stars, as well as detect nearby supernovae and provide continuous records of distant relativistic explosions like gamma-ray-bursts. The Evryscope uses commercially available CCDs and optics; the machine and assembly tolerances inherent in the mass production of these parts introduce problematic variations in the lens / CCD alignment which degrades image quality. We have built an automated alignment system (Robotilters) to solve this challenge. In this paper we describe the Robotilter system, mechanical and software design, image quality improvement, and current status.

  16. Development of a new transformant selection system for Penicillium chrysogenum: isolation and characterization of the P. chrysogenum acetyl-coenzyme A synthetase gene (facA) and its use as a homologous selection marker.

    PubMed

    Gouka, R J; van Hartingsveldt, W; Bovenberg, R A; van Zeijl, C M; van den Hondel, C A; van Gorcom, R F

    1993-01-01

    A new transformation system for the filamentous fungus Penicillium chrysogenum is described, based on the use of the homologous acetyl-coenzyme A synthetase (facA) gene as a selection marker. Acetate-non-utilizing (Fac-) strains of P. chrysogenum were obtained by positive selection for spontaneous resistance to fluoroacetate. Among these fac mutants putative facA strains were selected for a loss of acetyl-coenzyme A (CoA) synthetase activity. The facA gene, coding for the enzyme acetyl-CoA synthetase, was isolated from a P. chrysogenum genomic library using synthetic oligonucleotides derived from conserved regions from the corresponding genes of Aspergillus nidulans and Neurospora crassa. Vector pPC2-3, comprising a genomic 6.5 kb PstI fragment, was able to complement P. chrysogenum facA strains with frequencies up to 27 transformants.micrograms-1 DNA. Direct selection of transformants was accomplished using acetate and low amounts (0.001%) of glucose as carbon sources. About 50% of the transformants arose by integration of pPC2-3 DNA at the homologous facA locus and 50% by integration elsewhere in the genome. Determination of the nucleotide sequence of part of the cloned fragment showed the presence of an open reading frame of 2007 nucleotides, interrupted by five putative introns. Comparison of the nucleotide and the amino acid sequence of the facA gene of P. chrysogenum with the facA gene of A. nidulans reveals similarities of 80% and 89%, respectively. The putative introns present in the P. chrysogenum facA gene appear at identical positions as those in the A. nidulans facA gene, but show no significant sequence similarity.

  17. Fusion bonding and alignment fixture

    DOEpatents

    Ackler, Harold D.; Swierkowski, Stefan P.; Tarte, Lisa A.; Hicks, Randall K.

    2000-01-01

    An improved vacuum fusion bonding structure and process for aligned bonding of large area glass plates, patterned with microchannels and access holes and slots, for elevated glass fusion temperatures. Vacuum pumpout of all the components is through the bottom platform which yields an untouched, defect free top surface which greatly improves optical access through this smooth surface. Also, a completely non-adherent interlayer, such as graphite, with alignment and location features is located between the main steel platform and the glass plate pair, which makes large improvements in quality, yield, and ease of use, and enables aligned bonding of very large glass structures.

  18. On the Efficiency of Grain Alignment in Dark Clouds

    NASA Astrophysics Data System (ADS)

    Lazarian, A.; Goodman, Alyssa A.; Myers, Philip C.

    1997-11-01

    A quantitative analysis of grain alignment in the filamentary dark cloud L1755 in Ophiuchus is presented. We show that the observed decrease of the polarization-to-extinction ratio for the inner parts of this quiescent dark cloud can be explained as a result of the decrease of the efficiency of grain alignment. We make quantitative estimates of grain alignment efficiency for six mechanisms involving grains with either thermal or suprathermal rotation, interacting with either magnetic field or gaseous flow. We also make semiquantitative estimates of grain alignment by radiative torques. We show that in conditions typical of dark cloud interiors, all known major mechanisms of grain alignment fail. All the studied mechanisms predict polarization at least an order of magnitude below the currently detectable levels of ~1%. On the contrary, in the dark cloud environments where Av < 1, the grain alignment can be much more efficient. There the alignment of suprathermally rotating grains with superparamagnetic inclusions, and possibly also radiative torques, account for observed polarization. These results apply to L1755, which we model in detail, and probably also to B216 and other similar dark clouds. Our study suggests an explanation for the difference in results obtained through polarimetry of background starlight and polarized thermal emission from the dust itself. We conjecture that the emission polarimetry selectively reveals aligned grains in the environment far from thermodynamic equilibrium, as opposed to starlight polarization studies that probe the alignment of grains all the way along the line of sight, including the interiors of dark quiescent clouds, where no alignment is possible. We dedicate this paper to the memory of Edward M. Purcell and Lyman Spitzer, Jr., two pioneers in the quantitative study of the interstellar medium.

  19. Magnetic axis alignment and the Poisson alignment reference system

    NASA Astrophysics Data System (ADS)

    Griffith, Lee V.; Schenz, Richard F.; Sommargren, Gary E.

    1989-01-01

    Three distinct metrological operations are necessary to align a free-electron laser (FEL): the magnetic axis must be located, a straight line reference (SLR) must be generated, and the magnetic axis must be related to the SLR. This paper begins with a review of the motivation for developing an alignment system that will assure better than 100 micrometer accuracy in the alignment of the magnetic axis throughout an FEL. The paper describes techniques for identifying the magnetic axis of solenoids, quadrupoles, and wiggler poles. Propagation of a laser beam is described to the extent of revealing sources of nonlinearity in the beam. Development and use of the Poisson line, a diffraction effect, is described in detail. Spheres in a large-diameter laser beam create Poisson lines and thus provide a necessary mechanism for gauging between the magnetic axis and the SLR. Procedures for installing FEL components and calibrating alignment fiducials to the magnetic axes of the components are also described. An error budget shows that the Poisson alignment reference system will make it possible to meet the alignment tolerances for an FEL.

  20. Transmission of the electric fields to the low latitude ionosphere in the magnetosphere-ionosphere current circuit

    NASA Astrophysics Data System (ADS)

    Kikuchi, Takashi; Hashimoto, Kumiko K.

    2016-12-01

    The solar wind energy is transmitted to low latitude ionosphere in a current circuit from a dynamo in the magnetosphere to the equatorial ionosphere via the polar ionosphere. During the substorm growth phase and storm main phase, the dawn-to-dusk convection electric field is intensified by the southward interplanetary magnetic field (IMF), driving the ionospheric DP2 currents composed of two-cell Hall current vortices in high latitudes and Pedersen currents amplified at the dayside equator (EEJ). The EEJ-Region-1 field-aligned current (R1 FAC) circuit is completed via the Pedersen currents in midlatitude. On the other hand, the shielding electric field and the Region-2 FACs develop in the inner magnetosphere, tending to cancel the convection electric field at the mid-equatorial latitudes. The shielding often causes overshielding when the convection electric field reduces substantially and the EEJ is overcome by the counter electrojet (CEJ), leading to that even the quasi-periodic DP2 fluctuations are contributed by the overshielding as being composed of the EEJ and CEJ. The overshielding develop significantly during substorms and storms, leading to that the mid and low latitude ionosphere is under strong influence of the overshielding as well as the convection electric fields. The electric fields on the day- and night sides are in opposite direction to each other, but the electric fields in the evening are anomalously enhanced in the same direction as in the day. The evening anomaly is a unique feature of the electric potential distribution in the global ionosphere. DP2-type electric field and currents develop during the transient/short-term geomagnetic disturbances like the geomagnetic sudden commencements (SC), which appear simultaneously at high latitude and equator within the temporal resolution of 10 s. Using the SC, we can confirm that the electric potential and currents are transmitted near-instantaneously to low latitude ionosphere on both day- and night

  1. Laser beam alignment apparatus and method

    DOEpatents

    Gruhn, C.R.; Hammond, R.B.

    The disclosure related to an apparatus and method for laser beam alignment. Thermoelectric properties of a disc in a laser beam path are used to provide an indication of beam alignment and/or automatic laser alignment.

  2. Laser beam alignment apparatus and method

    DOEpatents

    Gruhn, Charles R.; Hammond, Robert B.

    1981-01-01

    The disclosure relates to an apparatus and method for laser beam alignment. Thermoelectric properties of a disc in a laser beam path are used to provide an indication of beam alignment and/or automatic laser alignment.

  3. Theory of grain alignment in molecular clouds

    NASA Technical Reports Server (NTRS)

    Roberge, Wayne G.

    1993-01-01

    Research accomplishments are presented and include the following: (1) mathematical theory of grain alignment; (2) super-paramagnetic alignment of molecular cloud grains; and (3) theory of grain alignment by ambipolar diffusion.

  4. Isothiocyanate-functionalized bifunctional chelates and fac-[MI(CO)3]+ (M = Re, 99mTc) complexes for targeting uPAR in prostate cancer

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Developing strategies to rapidly incorporate the fac-[MI(CO)3]+ (M = Re, 99mTc) core into biological targeting vectors is a growing realm in radiopharmaceutical development. This work presents the preparation of a novel isothiocyanate-functionalized bifunctional chelate based on 2,2´-dipicolylamine ...

  5. Synthesis and characterization of 5-bis(benzyl thio)-1, 3, 4-thiadiazole complexes with fac-ReBr3(CO) 32-

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Reactions of 2,5-bis(benzylthio)-1,3,4-thiadiazole (Compound 1) with a common organometallic rhenium starting material [NEt4]2[fac-[Re(I)Br3(CO)3] yielded two distinct types of complexes. Both complexes coordinate only through the nitrogen of the thiadiazole ring. Reaction of Compound 1 with the rhe...

  6. False positive tumor markers: elevation in patients with breast cancer on FAC-type chemotherapy and correlation with the development of hand-foot syndrome.

    PubMed

    Tyshler, L B; Longton, G M; Ellis, G K; Livingston, R B

    1996-01-01

    Breast cancer patients on dose-intensive chemotherapy often have elevated tumor markers during the course of treatment. Our objective was to estimate the incidence of a "false positive" tumor marker screen and to determine whether hand-foot epithelial damage was correlated. Data from 53 patients with high risk primary breast cancer who had undergone adjuvant or neoadjuvant 5FU-containing chemotherapy (FAC or FAC plus G-CSF) for 3 to 12 months were reviewed. The relationship between tumor marker elevation and disease recurrence, regimen intensity, and the occurrence of hand-foot syndrome was examined. Thirty-three of the 53 patients had elevated tumor markers in the absence of recurrent disease. The false positive rate was higher in patients who underwent FAC plus G-CSF chemotherapy than in patients who underwent FAC chemotherapy (92% vs 55%, p = .01). A false positive marker screen was associated with the occurrence of hand-foot syndrome even when the effect of regimen was accounted for by stratification (p = .01). Tumor marker screening of breast cancer patients on this type of adjuvant chemotherapy has poor specificity for recurrent malignancy. These data suggest tumor marker elevation may be an indicator of epithelial toxicity during chemotherapy, manifested clinically as hand-foot syndrome.

  7. Fixture for aligning motor assembly

    SciTech Connect

    Shervington, Roger M.; Vaghani, Vallabh V.; Vanek, Laurence D.; Christensen, Scott A.

    2009-12-08

    An alignment fixture includes a rotor fixture, a stator fixture and a sensor system which measures a rotational displacement therebetween. The fixture precisely measures rotation of a generator stator assembly away from a NULL position referenced by a unique reference spline on the rotor shaft. By providing an adjustable location of the stator assembly within the housing, the magnetic axes within each generator shall be aligned to a predetermined and controlled tolerance between the generator interface mounting pin and the reference spline on the rotor shaft. Once magnetically aligned, each generator is essentially a line replaceable unit which may be readily mounted to any input of a multi-generator gearbox assembly with the assurance that the magnetic alignment will be within a predetermined tolerance.

  8. Stellar Alignments - Identification and Analysis

    NASA Astrophysics Data System (ADS)

    Ruggles, Clive L. N.

    Fortuitous stellar alignments can be fitted to structural orientations with relative ease by the unwary. Nonetheless, cautious approaches taking into account a broader range of cultural evidence, as well as paying due attention to potential methodological pitfalls, have been successful in identifying credible stellar alignments—and constructing plausible assessments of their cultural significance—in a variety of circumstances. These range from single instances of alignments upon particular asterisms where the corroborating historical or ethnographic evidence is strong to repeated instances of oriented structures with only limited independent cultural information but where systematic, data-driven approaches can be productive. In the majority of cases, the identification and interpretation of putative stellar alignments relates to groups of similar monuments or complex single sites and involves a balance between systematic studies of the alignments themselves, backed up by statistical analysis where appropriate, and the consideration of a range of contextual evidence, either derived from the archaeological record alone or from other relevant sources.

  9. Well-pump alignment system

    DOEpatents

    Drumheller, D.S.

    1998-10-20

    An improved well-pump for geothermal wells, an alignment system for a well-pump, and to a method for aligning a rotor and stator within a well-pump are disclosed, wherein the well-pump has a whistle assembly formed at a bottom portion thereof, such that variations in the frequency of the whistle, indicating misalignment, may be monitored during pumping. 6 figs.

  10. The Rigors of Aligning Performance

    DTIC Science & Technology

    2015-06-01

    bearing in mind customer perceptions. Recommendations include employee training centered on goal alignment, which is vital to highlight the...appeared to be lacking in some areas when bearing in mind customer perceptions. Recommendations include employee training centered on goal alignment...through the strategic plan and CONOPS. However, the extent of goal accomplishment appears to be lacking in some areas when bearing in mind the

  11. National Ignition Facility system alignment.

    PubMed

    Burkhart, S C; Bliss, E; Di Nicola, P; Kalantar, D; Lowe-Webb, R; McCarville, T; Nelson, D; Salmon, T; Schindler, T; Villanueva, J; Wilhelmsen, K

    2011-03-10

    The National Ignition Facility (NIF) is the world's largest optical instrument, comprising 192 37 cm square beams, each generating up to 9.6 kJ of 351 nm laser light in a 20 ns beam precisely tailored in time and spectrum. The Facility houses a massive (10 m diameter) target chamber within which the beams converge onto an ∼1 cm size target for the purpose of creating the conditions needed for deuterium/tritium nuclear fusion in a laboratory setting. A formidable challenge was building NIF to the precise requirements for beam propagation, commissioning the beam lines, and engineering systems to reliably and safely align 192 beams within the confines of a multihour shot cycle. Designing the facility to minimize drift and vibration, placing the optical components in their design locations, commissioning beam alignment, and performing precise system alignment are the key alignment accomplishments over the decade of work described herein. The design and positioning phases placed more than 3000 large (2.5 m×2 m×1 m) line-replaceable optics assemblies to within ±1 mm of design requirement. The commissioning and alignment phases validated clear apertures (no clipping) for all beam lines, and demonstrated automated laser alignment within 10 min and alignment to target chamber center within 44 min. Pointing validation system shots to flat gold-plated x-ray emitting targets showed NIF met its design requirement of ±50 μm rms beam pointing to target chamber. Finally, this paper describes the major alignment challenges faced by the NIF Project from inception to present, and how these challenges were met and solved by the NIF design and commissioning teams.

  12. Binocular collimation vs conditional alignment

    NASA Astrophysics Data System (ADS)

    Cook, William J.

    2012-10-01

    As binocular enthusiasts share their passion, topics related to collimation abound. Typically, we find how observers, armed only with a jeweler's screwdriver, can "perfectly collimate" his or her binocular, make it "spot on," or other verbiage of similar connotation. Unfortunately, what most are addressing is a form of pseudo-collimation I have referred to since the mid-1970s as "Conditional Alignment." Ignoring the importance of the mechanical axis (hinge) in the alignment process, this "condition," while having the potential to make alignment serviceable, or even outstanding—within a small range of IPD (Interpupillary Distance) settings relative to the user's spatial accommodation (the ability to accept small errors in parallelism of the optical axes)—may take the instrument farther from the 3-axis collimation conscientious manufacturers seek to implement. Becoming more optically savvy—and especially with so many mechanically inferior binoculars entering the marketplace— the consumer contemplating self-repair and alignment has a need to understand the difference between clinical, 3-axis "collimation" (meaning both optical axes are parallel with the axis of the hinge) and "conditional alignment," as differentiated in this paper. Furthermore, I believe there has been a long-standing need for the term "Conditional Alignment," or some equivalent, to be accepted as part of the vernacular of those who use binoculars extensively, whether for professional or recreational activities. Achieving that acceptance is the aim of this paper.

  13. Projection-Based Volume Alignment

    PubMed Central

    Yu, Lingbo; Snapp, Robert R.; Ruiz, Teresa; Radermacher, Michael

    2013-01-01

    When heterogeneous samples of macromolecular assemblies are being examined by 3D electron microscopy (3DEM), often multiple reconstructions are obtained. For example, subtomograms of individual particles can be acquired from tomography, or volumes of multiple 2D classes can be obtained by random conical tilt reconstruction. Of these, similar volumes can be averaged to achieve higher resolution. Volume alignment is an essential step before 3D classification and averaging. Here we present a projection-based volume alignment (PBVA) algorithm. We select a set of projections to represent the reference volume and align them to a second volume. Projection alignment is achieved by maximizing the cross-correlation function with respect to rotation and translation parameters. If data are missing, the cross-correlation functions are normalized accordingly. Accurate alignments are obtained by averaging and quadratic interpolation of the cross-correlation maximum. Comparisons of the computation time between PBVA and traditional 3D cross-correlation methods demonstrate that PBVA outperforms the traditional methods. Performance tests were carried out with different signal-to-noise ratios using modeled noise and with different percentages of missing data using a cryo-EM dataset. All tests show that the algorithm is robust and highly accurate. PBVA was applied to align the reconstructions of a subcomplex of the NADH: ubiquinone oxidoreductase (Complex I) from the yeast Yarrowia lipolytica, followed by classification and averaging. PMID:23410725

  14. Accurate multiple network alignment through context-sensitive random walk

    PubMed Central

    2015-01-01

    Background Comparative network analysis can provide an effective means of analyzing large-scale biological networks and gaining novel insights into their structure and organization. Global network alignment aims to predict the best overall mapping between a given set of biological networks, thereby identifying important similarities as well as differences among the networks. It has been shown that network alignment methods can be used to detect pathways or network modules that are conserved across different networks. Until now, a number of network alignment algorithms have been proposed based on different formulations and approaches, many of them focusing on pairwise alignment. Results In this work, we propose a novel multiple network alignment algorithm based on a context-sensitive random walk model. The random walker employed in the proposed algorithm switches between two different modes, namely, an individual walk on a single network and a simultaneous walk on two networks. The switching decision is made in a context-sensitive manner by examining the current neighborhood, which is effective for quantitatively estimating the degree of correspondence between nodes that belong to different networks, in a manner that sensibly integrates node similarity and topological similarity. The resulting node correspondence scores are then used to predict the maximum expected accuracy (MEA) alignment of the given networks. Conclusions Performance evaluation based on synthetic networks as well as real protein-protein interaction networks shows that the proposed algorithm can construct more accurate multiple network alignments compared to other leading methods. PMID:25707987

  15. Camber Angle Inspection for Vehicle Wheel Alignments

    PubMed Central

    Young, Jieh-Shian; Hsu, Hong-Yi; Chuang, Chih-Yuan

    2017-01-01

    This paper introduces an alternative approach to the camber angle measurement for vehicle wheel alignment. Instead of current commercial approaches that apply computation vision techniques, this study aims at realizing a micro-control-unit (MCU)-based camber inspection system with a 3-axis accelerometer. We analyze the precision of the inspection system for the axis misalignments of the accelerometer. The results show that the axes of the accelerometer can be aligned to the axes of the camber inspection system imperfectly. The calibrations that can amend these axis misalignments between the camber inspection system and the accelerometer are also originally proposed since misalignments will usually happen in fabrications of the inspection systems. During camber angle measurements, the x-axis or z-axis of the camber inspection system and the wheel need not be perfectly aligned in the proposed approach. We accomplished two typical authentic camber angle measurements. The results show that the proposed approach is applicable with a precision of ±0.015∘ and therefore facilitates the camber measurement process without downgrading the precision by employing an appropriate 3-axis accelerometer. In addition, the measured results of camber angles can be transmitted via the medium such as RS232, Bluetooth, and Wi-Fi. PMID:28165365

  16. Camber Angle Inspection for Vehicle Wheel Alignments.

    PubMed

    Young, Jieh-Shian; Hsu, Hong-Yi; Chuang, Chih-Yuan

    2017-02-03

    This paper introduces an alternative approach to the camber angle measurement for vehicle wheel alignment. Instead of current commercial approaches that apply computation vision techniques, this study aims at realizing a micro-control-unit (MCU)-based camber inspection system with a 3-axis accelerometer. We analyze the precision of the inspection system for the axis misalignments of the accelerometer. The results show that the axes of the accelerometer can be aligned to the axes of the camber inspection system imperfectly. The calibrations that can amend these axis misalignments between the camber inspection system and the accelerometer are also originally proposed since misalignments will usually happen in fabrications of the inspection systems. During camber angle measurements, the x-axis or z-axis of the camber inspection system and the wheel need not be perfectly aligned in the proposed approach. We accomplished two typical authentic camber angle measurements. The results show that the proposed approach is applicable with a precision of ± 0.015 ∘ and therefore facilitates the camber measurement process without downgrading the precision by employing an appropriate 3-axis accelerometer. In addition, the measured results of camber angles can be transmitted via the medium such as RS232, Bluetooth, and Wi-Fi.

  17. An Improved Method for Completely Uncertain Biological Network Alignment

    PubMed Central

    Shen, Bin; Zhao, Muwei; Zhong, Wei; He, Jieyue

    2015-01-01

    With the continuous development of biological experiment technology, more and more data related to uncertain biological networks needs to be analyzed. However, most of current alignment methods are designed for the deterministic biological network. Only a few can solve the probabilistic network alignment problem. However, these approaches only use the part of probabilistic data in the original networks allowing only one of the two networks to be probabilistic. To overcome the weakness of current approaches, an improved method called completely probabilistic biological network comparison alignment (C_PBNA) is proposed in this paper. This new method is designed for complete probabilistic biological network alignment based on probabilistic biological network alignment (PBNA) in order to take full advantage of the uncertain information of biological network. The degree of consistency (agreement) indicates that C_PBNA can find the results neglected by PBNA algorithm. Furthermore, the GO consistency (GOC) and global network alignment score (GNAS) have been selected as evaluation criteria, and all of them proved that C_PBNA can obtain more biologically significant results than those of PBNA algorithm. PMID:26000284

  18. mer, fac, and Bidentate Coordination of an Alkyl-POP Ligand in the Chemistry of Nonclassical Osmium Hydrides.

    PubMed

    Esteruelas, Miguel A; García-Yebra, Cristina; Martín, Jaime; Oñate, Enrique

    2017-01-03

    Nonclassical and classical osmium polyhydrides containing the diphosphine 9,9-dimethyl-4,5-bis(diisopropylphosphino)xanthene (xant(P(i)Pr2)2), coordinated in κ(3)-mer, κ(3)-fac, and κ(2)-P,P fashions, have been isolated during the cyclic formation of H2 by means of the sequential addition of H(+) and H(-) or H(-) and H(+) to the classical trihydride OsH3Cl{xant(P(i)Pr2)2} (1). This complex adds H(+) to form the compressed dihydride dihydrogen complex [OsCl(H···H)(η(2)-H2){xant(P(i)Pr2)2}](+) (2). Under argon, cation 2 loses H2 and the resulting unsaturated fragment dimerizes to give [(Os(H···H){xant(P(i)Pr2)2})2(μ-Cl)2](2+) (3). During the transformation the phosphine changes its coordination mode from mer to fac. The benzofuran counterpart of 1, OsH3Cl{dbf(P(i)Pr2)2} (4; dbf(P(i)Pr2)2 = 4,6-bis(diisopropylphosphino)dibenzofuran), also adds H(+) to afford the benzofuran counterpart of 2, [OsCl(H···H)(η(2)-H2){xant(P(i)Pr2)2}](+) (5), which in contrast to the latter is stable and does not dimerize. Acetonitrile breaks the chloride bridge of 3 to form the dihydrogen [OsCl(η(2)-H2)(CH3CN){xant(P(i)Pr2)2}](+) (6), regenerating the mer coordination of the diphosphine. The hydride ion also breaks the chloride bridge of 3. The addition of KH to 3 leads to 1, closing a cycle for the formation of H2. Complex 1 reacts with a second hydride ion to give OsH4{xant(P(i)Pr2)2} (7) as consequence of the displacement of the chloride. Similarly to the latter, the oxygen atom of the mer-coordinated diphosphine of 7 has a tendency to be displaced by the hydride ion. Thus, the addition of KH to 7 yields [OsH5{xant(P(i)Pr2)2}](-) (8), containing a κ(2)-P,P-diphosphine. Complex 8 is easily protonated to afford OsH6{xant(P(i)Pr2)2} (9), which releases H2 to regenerate 7, closing a second cycle for the formation of molecular hydrogen.

  19. Experiments in Aligning Threaded Parts Using a Robot Hand

    NASA Technical Reports Server (NTRS)

    Diftler, M. A.; Walker, I. D.

    1999-01-01

    Techniques for determining and correcting threaded part alignment using force and angular position data are developed to augment currently limited techniques for align- ing threaded parts. These new techniques are based on backspinning a nut with respect to a bolt and measuring the force change that occurs when the bolt "falls" into the nut. Kinematic models that describe the relationship between threaded parts during backspinning are introduced and are used to show how angular alignment may be determined. The models indicate how to distinguish between the aligned and misaligned cases of a bolt and a nut connection by using axial force data only. In addition, by tracking the in-plane relative attitude of the bolt during spinning, data can be obtained on the direction of the angular misalignment which, in turn, is used to correct the misalignment. Results from experiments using a bolt held in a specialized fixture and a three fingers Stanford/JPL hand are presented.

  20. Magnetic Alignment of Pulsed Solenoids Using the Pulsed Wire Method

    SciTech Connect

    Arbelaez, D.; Madur, A.; Lipton, T.M.; Waldron, W.L.; Kwan, J.W.

    2011-04-01

    A unique application of the pulsed-wire measurement method has been implemented for alignment of 2.5 T pulsed solenoid magnets. The magnetic axis measurement has been shown to have a resolution of better than 25 {micro}m. The accuracy of the technique allows for the identification of inherent field errors due to, for example, the winding layer transitions and the current leads. The alignment system is developed for the induction accelerator NDCX-II under construction at LBNL, an upgraded Neutralized Drift Compression experiment for research on warm dense matter and heavy ion fusion. Precise alignment is essential for NDCX-II, since the ion beam has a large energy spread associated with the rapid pulse compression such that misalignments lead to corkscrew deformation of the beam and reduced intensity at focus. The ability to align the magnetic axis of the pulsed solenoids to within 100 pm of the induction cell axis has been demonstrated.

  1. Spontaneous magnetic alignment behaviour in free-living lizards

    NASA Astrophysics Data System (ADS)

    Diego-Rasilla, Francisco J.; Pérez-Mellado, Valentín; Pérez-Cembranos, Ana

    2017-04-01

    Several species of vertebrates exhibit spontaneous longitudinal body axis alignment relative to the Earth's magnetic field (i.e., magnetic alignment) while they are performing different behavioural tasks. Since magnetoreception is still not fully understood, studying magnetic alignment provides evidence for magnetoreception and broadens current knowledge of magnetic sense in animals. Furthermore, magnetic alignment widens the roles of magnetic sensitivity in animals and may contribute to shed new light on magnetoreception. In this context, spontaneous alignment in two species of lacertid lizards ( Podarcis muralis and Podarcis lilfordi) during basking periods was monitored. Alignments in 255 P. muralis and 456 P. lilfordi were measured over a 5-year period. The possible influence of the sun's position (i.e., altitude and azimuth) and geomagnetic field values corresponding to the moment in which a particular lizard was observed on lizards' body axis orientation was evaluated. Both species exhibited a highly significant bimodal orientation along the north-northeast and south-southwest magnetic axis. The evidence from this study suggests that free-living lacertid lizards exhibit magnetic alignment behaviour, since their body alignments cannot be explained by an effect of the sun's position. On the contrary, lizard orientations were significantly correlated with geomagnetic field values at the time of each observation. We suggest that this behaviour might provide lizards with a constant directional reference while they are sun basking. This directional reference might improve their mental map of space to accomplish efficient escape behaviour. This study is the first to provide spontaneous magnetic alignment behaviour in free-living reptiles.

  2. The Effect of Alignment Changes on Unilateral Transtibial Amputee’s Gait: A Systematic Review

    PubMed Central

    Jonkergouw, Niels; Prins, Maarten R.; Buis, Arjan W. P.; van der Wurff, Peter

    2016-01-01

    Introduction Prosthetic alignment, positioning of a prosthetic foot relative to a socket, is an iterative process in which an amputee’s gait is optimized through repetitive optical gait observation and induction of alignment adjustments when deviations are detected in spatiotemporal and kinematic gait parameters. An important limitation of the current prosthetic alignment approach is the subjectivity and the lack of standardized quantifiable baseline values. The purpose of this systematic review is to investigate if an optimal alignment criterion can be derived from published articles. Moreover, we investigated the effect of alignment changes on spatiotemporal, kinematic and kinetic gait parameters. Results A total of 11 studies were included, two controlled before-and-after studies and nine-interrupted time series studies. Discussion The results demonstrate that alignment changes have a predictable influence on the included kinetic parameters. However, the effect of alignment changes on spatio-temporal and kinematic gait parameters are generally unpredictable. These findings suggest that it is imperative to include kinetics in the process of dynamic prosthetic alignment. Partially this can be established by communication with the prosthetic user in terms of perceived socket comfort, but the use of measurement tools should also be considered. While current literature is not conclusive about an optimal alignment, future alignment research should focus on alignment optimisation based on kinetic outcomes. PMID:27923050

  3. Automated whole-genome multiple alignment of rat, mouse, and human

    SciTech Connect

    Brudno, Michael; Poliakov, Alexander; Salamov, Asaf; Cooper, Gregory M.; Sidow, Arend; Rubin, Edward M.; Solovyev, Victor; Batzoglou, Serafim; Dubchak, Inna

    2004-07-04

    We have built a whole genome multiple alignment of the three currently available mammalian genomes using a fully automated pipeline which combines the local/global approach of the Berkeley Genome Pipeline and the LAGAN program. The strategy is based on progressive alignment, and consists of two main steps: (1) alignment of the mouse and rat genomes; and (2) alignment of human to either the mouse-rat alignments from step 1, or the remaining unaligned mouse and rat sequences. The resulting alignments demonstrate high sensitivity, with 87% of all human gene-coding areas aligned in both mouse and rat. The specificity is also high: <7% of the rat contigs are aligned to multiple places in human and 97% of all alignments with human sequence > 100kb agree with a three-way synteny map built independently using predicted exons in the three genomes. At the nucleotide level <1% of the rat nucleotides are mapped to multiple places in the human sequence in the alignment; and 96.5% of human nucleotides within all alignments agree with the synteny map. The alignments are publicly available online, with visualization through the novel Multi-VISTA browser that we also present.

  4. Clickable, hydrophilic ligand for fac-[M(I)(CO)3](+) (M = Re/(99m)Tc) applied in an S-functionalized α-MSH peptide.

    PubMed

    Kasten, Benjamin B; Ma, Xiaowei; Liu, Hongguang; Hayes, Thomas R; Barnes, Charles L; Qi, Shibo; Cheng, Kai; Bottorff, Shalina C; Slocumb, Winston S; Wang, Jing; Cheng, Zhen; Benny, Paul D

    2014-03-19

    The copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC) click reaction was used to incorporate alkyne-functionalized dipicolylamine (DPA) ligands (1 and 3) for fac-[M(I)(CO)3](+) (M = Re/(99m)Tc) complexation into an α-melanocyte stimulating hormone (α-MSH) peptide analogue. A novel DPA ligand with carboxylate substitutions on the pyridyl rings (3) was designed to increase the hydrophilicity and to decrease in vivo hepatobiliary retention of fac-[(99m)Tc(I)(CO)3](+) complexes used in single photon emission computed tomography (SPECT) imaging studies with targeting biomolecules. The fac-[Re(I)(CO)3(3)] complex (4) was used for chemical characterization and X-ray crystal analysis prior to radiolabeling studies between 3 and fac-[(99m)Tc(I)(OH2)3(CO)3](+). The corresponding (99m)Tc complex (4a) was obtained in high radiochemical yields, was stable in vitro for 24 h during amino acid challenge and serum stability assays, and showed increased hydrophilicity by log P analysis compared to an analogous complex with nonfunctionalized pyridine rings (2a). An α-MSH peptide functionalized with an azide was labeled with fac-[M(I)(CO)3](+) using both click, then chelate (CuAAC reaction with 1 or 3 followed by metal complexation) and chelate, then click (metal complexation of 1 and 3 followed by CuAAC with the peptide) strategies to assess the effects of CuAAC conditions on fac-[M(I)(CO)3](+) complexation within a peptide framework. The peptides from the click, then chelate strategy had different HPLC tR's and in vitro stabilities compared to those from the chelate, then click strategy, suggesting nonspecific coordination of fac-[M(I)(CO)3](+) using this synthetic route. The fac-[M(I)(CO)3](+)-complexed peptides from the chelate, then click strategy showed >90% stability during in vitro challenge conditions for 6 h, demonstrated high affinity and specificity for the melanocortin 1 receptor (MC1R) in IC50 analyses, and led to moderately high uptake in B16F10 melanoma cells

  5. A Nonlinear Observer for Gyro Alignment Estimation

    NASA Technical Reports Server (NTRS)

    Thienel, J.; Sanner, R. M.

    2003-01-01

    A nonlinear observer for gyro alignment estimation is presented. The observer is composed of two error terms, an attitude error and an alignment error. The observer is globally stable with exponential convergence of the attitude errors. The gyro alignment estimate converges to the true alignment when the system is completely observable.

  6. A mammalian cell based FACS-panning platform for the selection of HIV-1 envelopes for vaccine development.

    PubMed

    Bruun, Tim-Henrik; Mühlbauer, Katharina; Benen, Thomas; Kliche, Alexander; Wagner, Ralf

    2014-01-01

    An increasing number of broadly neutralizing monoclonal antibodies (bnMAb) against the HIV-1 envelope (Env) protein has been discovered recently. Despite this progress, vaccination efforts with the aim to re-elicit bnMAbs that provide protective immunity have failed so far. Herein, we describe the development of a mammalian cell based FACS-panning method in which bnMAbs are used as tools to select surface-exposed envelope variants according to their binding affinity. For that purpose, an HIV-1 derived lentiviral vector was developed to infect HEK293T cells at low multiplicity of infection (MOI) in order to link Env phenotype and genotype. For proof of principle, a gp145 Env model-library was established in which the complete V3 domain was substituted by five strain specific V3 loop sequences with known binding affinities to nMAb 447-52D, respectively. Env genes were recovered from selected cells by PCR, subcloned into a lentiviral vector (i) to determine and quantify the enrichment nMAb binders and (ii) to generate a new batch of transduction competent particles. After 2 selection cycles the Env variant with highest affinity was enriched 20-fold and represented 80% of the remaining Env population. Exploiting the recently described bnMAbs, this procedure might prove useful in selecting Env proteins from large Env libraries with the potential to elicit bnMAbs when used as vaccine candidates.

  7. Alignment method for parabolic trough solar concentrators

    DOEpatents

    Diver, Richard B.

    2010-02-23

    A Theoretical Overlay Photographic (TOP) alignment method uses the overlay of a theoretical projected image of a perfectly aligned concentrator on a photographic image of the concentrator to align the mirror facets of a parabolic trough solar concentrator. The alignment method is practical and straightforward, and inherently aligns the mirror facets to the receiver. When integrated with clinometer measurements for which gravity and mechanical drag effects have been accounted for and which are made in a manner and location consistent with the alignment method, all of the mirrors on a common drive can be aligned and optimized for any concentrator orientation.

  8. An introduction to the Lagan alignment toolkit.

    PubMed

    Brudno, Michael

    2007-01-01

    The Lagan Toolkit is a software package for comparison of genomic sequences. It includes the CHAOS local alignment program, LAGAN global alignment program for two, or more sequences and Shuffle-LAGAN, a "glocal" alignment method that handles genomic rearrangements in a global alignment framework. The alignment programs included in the Lagan Toolkit have been widely used to compare genomes of many organisms, from bacteria to large mammalian genomes. This chapter provides an overview of the algorithms used by the LAGAN programs to construct genomic alignments, explains how to build alignments using either the standalone program or the web server, and discusses some of the common pitfalls users encounter when using the toolkit.

  9. Combining Multiple Pairwise Structure-based Alignments

    SciTech Connect

    2014-11-12

    CombAlign is a new Python code that generates a gapped, one-to-many, multiple structure-based sequence alignment(MSSA) given a set of pairwise structure-based alignments. In order to better define regions of similarity among related protein structures, it is useful to detect the residue-residue correspondences among a set of pairwise structure alignments. Few codes exist for constructing a one-to-many, multiple sequence alignment derived from a set of structure alignments, and we perceived a need for creating a new tool for combing pairwise structure alignments that would allow for insertion of gaps in the reference structure.

  10. Reactions of fac-[Re(CO)3(H2O)3]+ with nucleoside diphosphates and thiamine diphosphate in aqueous solution investigated by multinuclear NMR spectroscopy.

    PubMed

    Adams, Kristie M; Marzilli, Patricia A; Marzilli, Luigi G

    2007-10-29

    Products formed between monoester diphosphates (MDPs) and fac-[Re(CO)3(H2O)3]OTf at pH 3.6 were examined. Such adducts of the fac-[Re(CO)3]+ moiety have an uncommon combination of properties for an "inert" metal center in that sharp NMR signals can be observed, yet the products are equilibrating at rates allowing NMR EXSY cross-peaks to be observed. Thiamine diphosphate (TDP) and uridine 5'-diphosphate (5'-UDP) form 1:1 bidentate {Palpha,Pbeta} chelates, in which the MDP binds Re(I) via Palpha and Pbeta phosphate groups. Asymmetric centers are created at Re(I) (RRe/SRe) and Palpha (Delta/Lambda), leading to four diastereomers. The two mirror pairs of diastereomers (RReDelta/SReLambda) and (RReLambda/SReDelta) for TDP (no ribose) and for all four diastereomers (RReDelta, RReLambda, SReDelta, SReLambda) for 5'-UDP (asymmetric ribose) gave two and four sets of NMR signals for the bound MDP, respectively. 31Palpha-31Palpha EXSY cross-peaks indicate that the fac-[Re(CO)3(H2O)({Palpha,Pbeta}MDP)]- isomers interchange slowly on the NMR time scale, with an average k approximately equal to 0.8 s(-1) at 32 degrees C; the EXSY cross-peaks could arise from chirality changes at only Re(I) or at only Palpha. Guanosine 5'-diphosphate (5'-GDP), with a ribose moiety and a Re(I)-binding base, formed both possible diastereomers (RRe and SRe) of the fac-[Re(CO)3(H2O)({N7,Pbeta}GDP)]- macrochelate, with one slightly more abundant diastereomer suggested to be RRe by Mn2+ ion 1H NMR signal line-broadening combined with distances from molecular models. Interchange of the diastereomers requires that the coordination site of either N7 or Pbeta move to the H2O site. 31Palpha-31Palpha EXSY cross-peaks indicate a k approximately equal to 0.5 s(-1) at 32 degrees C for RRe-to-SRe interchange. The similarity of the rate constants for interchange of fac-[Re(CO)3(H2O)({Palpha,Pbeta}MDP)]- and fac-[Re(CO)3(H2O)({N7,Pbeta}GDP)]- adducts suggest strongly that interchange of Pbeta and H2O coordination

  11. Multiple sequence alignment with hierarchical clustering.

    PubMed Central

    Corpet, F

    1988-01-01

    An algorithm is presented for the multiple alignment of sequences, either proteins or nucleic acids, that is both accurate and easy to use on microcomputers. The approach is based on the conventional dynamic-programming method of pairwise alignment. Initially, a hierarchical clustering of the sequences is performed using the matrix of the pairwise alignment scores. The closest sequences are aligned creating groups of aligned sequences. Then close groups are aligned until all sequences are aligned in one group. The pairwise alignments included in the multiple alignment form a new matrix that is used to produce a hierarchical clustering. If it is different from the first one, iteration of the process can be performed. The method is illustrated by an example: a global alignment of 39 sequences of cytochrome c. PMID:2849754

  12. Constructing sequence alignments from a Markov decision model with estimated parameter values.

    PubMed

    Hunt, Fern Y; Kearsley, Anthony J; O'Gallagher, Agnes

    2004-01-01

    Current methods for aligning biological sequences are based on dynamic programming algorithms. If large numbers of sequences or a number of long sequences are to be aligned, the required computations are expensive in memory and central processing unit (CPU) time. In an attempt to bring the tools of large-scale linear programming (LP) methods to bear on this problem, we formulate the alignment process as a controlled Markov chain and construct a suggested alignment based on policies that minimise the expected total cost of the alignment. We discuss the LP associated with the total expected discounted cost and show the results of a solution of the problem based on a primal-dual interior point method. Model parameters, estimated from aligned sequences, along with cost function parameters are used to construct the objective and constraint conditions of the LP problem. This article concludes with a discussion of some alignments obtained from the LP solutions of problems with various cost function parameter values.

  13. Intrinsic galaxy shapes and alignments - II. Modelling the intrinsic alignment contamination of weak lensing surveys

    NASA Astrophysics Data System (ADS)

    Joachimi, B.; Semboloni, E.; Hilbert, S.; Bett, P. E.; Hartlap, J.; Hoekstra, H.; Schneider, P.

    2013-11-01

    Intrinsic galaxy alignments constitute the major astrophysical systematic of forthcoming weak gravitational lensing surveys but also yield unique insights into galaxy formation and evolution. We build analytic models for the distribution of galaxy shapes based on halo properties extracted from the Millennium Simulation, differentiating between early- and late-type galaxies as well as central galaxies and satellites. The resulting ellipticity correlations are investigated for their physical properties and compared to a suite of current observations. The best-faring model is then used to predict the intrinsic alignment contamination of planned weak lensing surveys. We find that late-type galaxy models generally have weak intrinsic ellipticity correlations, marginally increasing towards smaller galaxy separation and higher redshift. The signal for early-type models at fixed halo mass strongly increases by three orders of magnitude over two decades in galaxy separation, and by one order of magnitude from z = 0 to z = 2. The intrinsic alignment strength also depends strongly on halo mass, but not on galaxy luminosity at fixed mass, or galaxy number density in the environment. We identify models that are in good agreement with all observational data, except that all models overpredict alignments of faint early-type galaxies. The best model yields an intrinsic alignment contamination of a Euclid-like survey between 0.5 and 10 per cent at z > 0.6 and on angular scales larger than a few arcminutes. Cutting 20 per cent of red foreground galaxies using observer-frame colours can suppress this contamination by up to a factor of 2.

  14. Status report on the survey and alignment activities at Fermilab

    SciTech Connect

    Oshinowo, Babatunde O'Sheg; /Fermilab

    2004-10-01

    The surveying and alignment activities at Fermilab are the responsibility of the Alignment and Metrology Group. The Group supports and interacts with physicists and engineers working on any particular project, from the facility construction phase to the installation and final alignment of components in the beam line. One of the goals of the Alignment and Metrology Group is to upgrade the old survey networks in the tunnel using modern surveying technology, such as the Laser Tracker for tunnel networks and GPS for the surface networks. According to the job needs, all surveys are done with Laser Trackers and/or Videogrammetry (V-STARS) systems for spatial coordinates; optical and electronic levels are used for elevations, Gyro-Theodolite for azimuths, Mekometer for distances and GPS for baseline vectors. The group has recently purchased two new API Laser Trackers, one INCA3 camera for the V-Stars, and one DNA03 digital level. This report presents the projects and major activities of the Alignment and Metrology Group at Fermilab during the period of 2000 to 2004. It focuses on the most important current projects, especially those that have to be completed during the currently scheduled three-month shutdown period. Future projects, in addition to the status of the current projects, are also presented.

  15. The alignment-distribution graph

    NASA Technical Reports Server (NTRS)

    Chatterjee, Siddhartha; Gilbert, John R.; Schreiber, Robert

    1993-01-01

    Implementing a data-parallel language such as Fortran 90 on a distributed-memory parallel computer requires distributing aggregate data objects (such as arrays) among the memory modules attached to the processors. The mapping of objects to the machine determines the amount of residual communication needed to bring operands of parallel operations into alignment with each other. We present a program representation called the alignment-distribution graph that makes these communication requirements explicit. We describe the details of the representation, show how to model communication cost in this framework, and outline several algorithms for determining object mappings that approximately minimize residual communication.

  16. The alignment-distribution graph

    NASA Technical Reports Server (NTRS)

    Chatterjee, Siddhartha; Gilbert, John R.; Schreiber, Robert

    1993-01-01

    Implementing a data-parallel language such as Fortran 90 on a distributed-memory parallel computer requires distributing aggregate data objects (such as arrays) among the memory modules attached to the processors. The mapping of objects to the machine determines the amount of residual communication needed to bring operands of parallel operations into alignment with each other. We present a program representation called the alignment distribution graph that makes these communication requirements explicit. We describe the details of the representation, show how to model communication cost in this framework, and outline several algorithms for determining object mappings that approximately minimize residual communication.

  17. XUV ionization of aligned molecules

    SciTech Connect

    Kelkensberg, F.; Siu, W.; Gademann, G.; Rouzee, A.; Vrakking, M. J. J.; Johnsson, P.; Lucchini, M.; Lucchese, R. R.

    2011-11-15

    New extreme-ultraviolet (XUV) light sources such as high-order-harmonic generation (HHG) and free-electron lasers (FELs), combined with laser-induced alignment techniques, enable novel methods for making molecular movies based on measuring molecular frame photoelectron angular distributions. Experiments are presented where CO{sub 2} molecules were impulsively aligned using a near-infrared laser and ionized using femtosecond XUV pulses obtained by HHG. Measured electron angular distributions reveal contributions from four orbitals and the onset of the influence of the molecular structure.

  18. Measurements of magnetic field alignment

    SciTech Connect

    Kuchnir, M.; Schmidt, E.E.

    1987-11-06

    The procedure for installing Superconducting Super Collider (SSC) dipoles in their respective cryostats involves aligning the average direction of their field with the vertical to an accuracy of 0.5 mrad. The equipment developed for carrying on these measurements is described and the measurements performed on the first few prototypes SSC magnets are presented. The field angle as a function of position in these 16.6 m long magnets is a characteristic of the individual magnet with possible feedback information to its manufacturing procedure. A comparison of this vertical alignment characteristic with a magnetic field intensity (by NMR) characteristic for one of the prototypes is also presented. 5 refs., 7 figs.

  19. Vectorcardiographic loop alignment for fetal movement detection using the expectation-maximization algorithm and support vector machines.

    PubMed

    Vullings, R; Mischi, M

    2013-01-01

    Reduced fetal movement is an important parameter to assess fetal distress. Currently, no suitable methods are available that can objectively assess fetal movement during pregnancy. Fetal vectorcardiographic (VCG) loop alignment could be such a method. In general, the goal of VCG loop alignment is to correct for motion-induced changes in the VCGs of (multiple) consecutive heartbeats. However, the parameters used for loop alignment also provide information to assess fetal movement. Unfortunately, current methods for VCG loop alignment are not robust against low-quality VCG signals. In this paper, a more robust method for VCG loop alignment is developed that includes a priori information on the loop alignment, yielding a maximum a posteriori loop alignment. Classification, based on movement parameters extracted from the alignment, is subsequently performed using support vector machines, resulting in correct classification of (absence of) fetal movement in about 75% of cases. After additional validation and optimization, this method can possibly be employed for continuous fetal movement monitoring.

  20. ALIGN_MTX--an optimal pairwise textual sequence alignment program, adapted for using in sequence-structure alignment.

    PubMed

    Vishnepolsky, Boris; Pirtskhalava, Malak

    2009-06-01

    The presented program ALIGN_MTX makes alignment of two textual sequences with an opportunity to use any several characters for the designation of sequence elements and arbitrary user substitution matrices. It can be used not only for the alignment of amino acid and nucleotide sequences but also for sequence-structure alignment used in threading, amino acid sequence alignment, using preliminary known PSSM matrix, and in other cases when alignment of biological or non-biological textual sequences is required. This distinguishes it from the majority of similar alignment programs that make, as a rule, alignment only of amino acid or nucleotide sequences represented as a sequence of single alphabetic characters. ALIGN_MTX is presented as downloadable zip archive at http://www.imbbp.org/software/ALIGN_MTX/ and available for free use. As application of using the program, the results of comparison of different types of substitution matrix for alignment quality in distantly related protein pair sets were presented. Threading matrix SORDIS, based on side-chain orientation in relation to hydrophobic core centers with evolutionary change-based substitution matrix BLOSUM and using multiple sequence alignment information position-specific score matrices (PSSM) were taken for test alignment accuracy. The best performance shows PSSM matrix, but in the reduced set with lower sequence similarity threading matrix SORDIS shows the same performance and it was shown that combined potential with SORDIS and PSSM can improve alignment quality in evolutionary distantly related protein pairs.

  1. Improving pairwise sequence alignment accuracy using near-optimal protein sequence alignments

    PubMed Central

    2010-01-01

    Background While the pairwise alignments produced by sequence similarity searches are a powerful tool for identifying homologous proteins - proteins that share a common ancestor and a similar structure; pairwise sequence alignments often fail to represent accurately the structural alignments inferred from three-dimensional coordinates. Since sequence alignment algorithms produce optimal alignments, the best structural alignments must reflect suboptimal sequence alignment scores. Thus, we have examined a range of suboptimal sequence alignments and a range of scoring parameters to understand better which sequence alignments are likely to be more structurally accurate. Results We compared near-optimal protein sequence alignments produced by the Zuker algorithm and a set of probabilistic alignments produced by the probA program with structural alignments produced by four different structure alignment algorithms. There is significant overlap between the solution spaces of structural alignments and both the near-optimal sequence alignments produced by commonly used scoring parameters for sequences that share significant sequence similarity (E-values < 10-5) and the ensemble of probA alignments. We constructed a logistic regression model incorporating three input variables derived from sets of near-optimal alignments: robustness, edge frequency, and maximum bits-per-position. A ROC analysis shows that this model more accurately classifies amino acid pairs (edges in the alignment path graph) according to the likelihood of appearance in structural alignments than the robustness score alone. We investigated various trimming protocols for removing incorrect edges from the optimal sequence alignment; the most effective protocol is to remove matches from the semi-global optimal alignment that are outside the boundaries of the local alignment, although trimming according to the model-generated probabilities achieves a similar level of improvement. The model can also be used to

  2. Isolation of full-size mRNA from ethanol-fixed cells after cellular immunofluorescence staining and fluorescence-activated cell sorting (FACS)

    SciTech Connect

    Esser, C.; Kremer, J.; Hundeiker, C.; Goettlinger, C.; Radbruch, A.

    1995-12-01

    Preparation of intact, full-size RNA from tissues or cells requires stringent precautions against ubiquitous and rather stable RNases. Fluorescence-activated cell sorting (FACS) usually aims at the isolation of cells according to cell surface markers on living cells, from which RNA can be obtained by standard protocols. The separation of cells according to intracellular immunofluorescence markers, such as intranuclear, intracytoplasmic, or secreted molecules, requires permeation of the cell membrane for the staining antibodies, which is usually achieved by fixation. However, commonly used fixatives such as ethanol, methanol, or formaldehyde do not inactivate RNases completely, thereby hampering the analysis of complete RNA molecules from fixed cells. We report isolation of intact, full size RNA suitable for Northern blotting from cells that were fixed by 95% ethanol/5% acetic acid containing RNase inhibitors, stained intracellularly, and sorted by FACS. 21 refs., 2 figs., 1 tab.

  3. Tonal Alignment in Irish Dialects

    ERIC Educational Resources Information Center

    Dalton, Martha; Ni Chasaide, Ailbhe

    2005-01-01

    A comparison of the contour alignment of nuclear and initial prenuclear accents was carried out for the Irish dialects of Gaoth Dobhair in Ulster (GD-U) and Cois Fharraige in Connaught (CF-C). This was done across conditions where the number of unstressed syllables following the nuclear and preceding the initial prenuclear accents was varied from…

  4. Alignment in Second Language Dialogue

    ERIC Educational Resources Information Center

    Costa, Albert; Pickering, Martin; Sorace, Antonella

    2008-01-01

    This paper considers the nature of second language dialogues, involving at least one non-native (L2) speaker. We assume that dialogue is characterised by a process in which interlocutors develop similar mental states to each other (Pickering & Garrod, 2004). We first consider various means in which interlocutors align their mental states, and…

  5. First evidence of anisotropy of GPS phase slips caused by the mid-latitude field-aligned ionospheric irregularities

    NASA Astrophysics Data System (ADS)

    Afraimovich, E. L.; Ishin, A. B.; Tinin, M. V.; Yasyukevich, Yu. V.; Jin, S. G.

    2011-05-01

    The mid-latitude field-aligned irregularity (FAI) along the magnetic field line is a common phenomenon in the ionosphere. However, few data reveal the field-aligned ionospheric irregularities. They are insufficient to identify FAIs effects so far, particularly effect on global positioning system (GPS) signals. In this paper, the mid-latitude FAIs by line-of-sight angular scanning relative to the local magnetic field vector are investigated using the denser GPS network observations in Japan. It has been the first found that total GPS L2 phase slips over Japan, during the recovery phase of the 12 Feb 2000 geomagnetic storm were caused by GPS signal scattering on FAIs both for the lines-of-sight aligned to the magnetic field line (the field of aligned scattering, FALS) and across the magnetic field line (the field of across scattering, FACS). The FALS results are also in a good agreement with the data of the magnetic field orientation control of GPS occultation observations of equatorial scintillation during thorough low earth orbit (LEO) satellites measurements, e.g. Challenging Minisatellite Payload (CHAMP) and Satellite de Aplicaciones Cientificas-C (SAC-C). The role of large-angle scattering almost along the normal to the magnetic field line in GPS scintillation is determined by attenuation of the irregularity anisotropy factor as compared with the other factors.

  6. Laser-optic instruments improve machinery alignment

    SciTech Connect

    Bloch, H.P.

    1987-10-12

    Laser-optic alignment systems are fast becoming cost-effective devices that improve the accuracy and speed of machinery shaft alignment. Because of the difficulty, if not impossibility, of aligning operating machinery, cold alignment specifications must be determined to compensate for thermal growth so that the shaft alignment remains within tolerances when the machine reaches normal operating temperature. Some methods for accomplishing this are reviewed here. Three years' field experience with laser-optic alignment systems shows that many of these limitations can be eliminated, resulting in a more accurate alignment in less time. Some actual field alignments are given as examples of the improvement achieved by the use of laser equipment, and a procedure is given that shows how the laser-optic system may be used to determine running alignment changes caused by thermal growth.

  7. Progressive multiple sequence alignments from triplets

    PubMed Central

    Kruspe, Matthias; Stadler, Peter F

    2007-01-01

    Background The quality of progressive sequence alignments strongly depends on the accuracy of the individual pairwise alignment steps since gaps that are introduced at one step cannot be removed at later aggregation steps. Adjacent insertions and deletions necessarily appear in arbitrary order in pairwise alignments and hence form an unavoidable source of errors. Research Here we present a modified variant of progressive sequence alignments that addresses both issues. Instead of pairwise alignments we use exact dynamic programming to align sequence or profile triples. This avoids a large fractions of the ambiguities arising in pairwise alignments. In the subsequent aggregation steps we follow the logic of the Neighbor-Net algorithm, which constructs a phylogenetic network by step-wisely replacing triples by pairs instead of combining pairs to singletons. To this end the three-way alignments are subdivided into two partial alignments, at which stage all-gap columns are naturally removed. This alleviates the "once a gap, always a gap" problem of progressive alignment procedures. Conclusion The three-way Neighbor-Net based alignment program aln3nn is shown to compare favorably on both protein sequences and nucleic acids sequences to other progressive alignment tools. In the latter case one easily can include scoring terms that consider secondary structure features. Overall, the quality of resulting alignments in general exceeds that of clustalw or other multiple alignments tools even though our software does not included heuristics for context dependent (mis)match scores. PMID:17631683

  8. Fluorescence Activated Cell Sorting (FACS) and Gene Expression Analysis of Fos-expressing Neurons from Fresh and Frozen Rat Brain Tissue.

    PubMed

    Rubio, F Javier; Li, Xuan; Liu, Qing-Rong; Cimbro, Raffaello; Hope, Bruce T

    2016-08-27

    The study of neuroplasticity and molecular alterations in learned behaviors is switching from the study of whole brain regions to the study of specific sets of sparsely distributed activated neurons called neuronal ensembles that mediate learned associations. Fluorescence Activated Cell Sorting (FACS) has recently been optimized for adult rat brain tissue and allowed isolation of activated neurons using antibodies against the neuronal marker NeuN and Fos protein, a marker of strongly activated neurons. Until now, Fos-expressing neurons and other cell types were isolated from fresh tissue, which entailed long processing days and allowed very limited numbers of brain samples to be assessed after lengthy and complex behavioral procedures. Here we found that yields of Fos-expressing neurons and Fos mRNA from dorsal striatum were similar between freshly dissected tissue and tissue frozen at -80 ºC for 3 - 21 days. In addition, we confirmed the phenotype of the NeuN-positive and NeuN-negative sorted cells by assessing gene expression of neuronal (NeuN), astrocytic (GFAP), oligodendrocytic (Oligo2) and microgial (Iba1) markers, which indicates that frozen tissue can also be used for FACS isolation of glial cell types. Overall, it is possible to collect, dissect and freeze brain tissue for multiple FACS sessions. This maximizes the amount of data obtained from valuable animal subjects that have often undergone long and complex behavioral procedures.

  9. Randomized trial comparing protracted infusion of 5-fluorouracil with weekly doxorubicin and cyclophosphamide with a monthly bolus FAC regimen in metastatic breast carcinoma (SPM90).

    PubMed Central

    Pierga, J. Y.; Jouve, M.; Asselain, B.; Livartowski, A.; Beuzeboc, P.; Diéras, V.; Scholl, S.; Dorval, T.; Palangié, T.; Garcia-Giralt, E.; Pouillart, P.

    1998-01-01

    Infusional 5-fluorouracil in advanced breast cancer has been associated with improved clinical response rates when compared with conventional bolus therapy. As a first line of chemotherapy in proven metastatic breast carcinoma, 258 women were randomly assigned to receive FAC consisting of 5-fluorouracil (F) 600 mg m(-2) intravenously (i.v.) over 1 h on days 1, 2 and 3, doxorubicin (A) 50 mg m(-2) i.v. bolus on day 1 and cyclophosphamide (C), 400 mg m(-2) i.v. bolus on days 1, 2 and 3 or 'FULON' consisting of 5-fluorouracil 250 mg m(-2) day(-1) continuously infused from day 1 to day 22, doxorubicin 15 mg m(-2) i.v. bolus on days 1, 8, 15 and 22 and cyclophosphamide 300 mg m(-2) i.v. bolus on days 1, 8, 15 and 22. Chemotherapy courses were administered 4-weekly for the bolus regimen and 6-weekly for FULON. Pretreatment characteristics were identical between the two groups. Response rates were 54% in the FAC arm and 53% in the FULON arm. Time to progression was 14 months in the FAC arm and 12 months in the FULON arm. Differences were not statistically significant. Median overall survival duration for all patients was 22 months. Haematological toxicity was more severe in the bolus-treated group (P = 0.05), as were nausea and vomiting (P < or = 0.01). We conclude that the two regimens appeared equally effective but have different toxicities. PMID:9652764

  10. Isolating intestinal stem cells from adult Drosophila midguts by FACS to study stem cell behavior during aging.

    PubMed

    Tauc, Helen M; Tasdogan, Alpaslan; Pandur, Petra

    2014-12-16

    Aging tissue is characterized by a continuous decline in functional ability. Adult stem cells are crucial in maintaining tissue homeostasis particularly in tissues that have a high turnover rate such as the intestinal epithelium. However, adult stem cells are also subject to aging processes and the concomitant decline in function. The Drosophila midgut has emerged as an ideal model system to study molecular mechanisms that interfere with the intestinal stem cells' (ISCs) ability to function in tissue homeostasis. Although adult ISCs can be easily identified and isolated from midguts of young flies, it has been a major challenge to study endogenous molecular changes of ISCs during aging. This is due to the lack of a combination of molecular markers suitable to isolate ISCs from aged intestines. Here we propose a method that allows for successful dissociation of midgut tissue into living cells that can subsequently be separated into distinct populations by FACS. By using dissociated cells from the esg-Gal4, UAS-GFP fly line, in which both ISCs and the enteroblast (EB) progenitor cells express GFP, two populations of cells are distinguished based on different GFP intensities. These differences in GFP expression correlate with differences in cell size and granularity and represent enriched populations of ISCs and EBs. Intriguingly, the two GFP-positive cell populations remain distinctly separated during aging, presenting a novel technique for identifying and isolating cell populations enriched for either ISCs or EBs at any time point during aging. The further analysis, for example transcriptome analysis, of these particular cell populations at various time points during aging is now possible and this will facilitate the examination of endogenous molecular changes that occur in these cells during aging.

  11. An efficient method for multiple sequence alignment

    SciTech Connect

    Kim, J.; Pramanik, S.

    1994-12-31

    Multiple sequence alignment has been a useful method in the study of molecular evolution and sequence-structure relationships. This paper presents a new method for multiple sequence alignment based on simulated annealing technique. Dynamic programming has been widely used to find an optimal alignment. However, dynamic programming has several limitations to obtain optimal alignment. It requires long computation time and cannot apply certain types of cost functions. We describe detail mechanisms of simulated annealing for multiple sequence alignment problem. It is shown that simulated annealing can be an effective approach to overcome the limitations of dynamic programming in multiple sequence alignment problem.

  12. Bokeh mirror alignment for Cherenkov telescopes

    NASA Astrophysics Data System (ADS)

    Mueller, S. A.; Adam, J.; Ahnen, M. L.; Baack, D.; Balbo, M.; Bergmann, M.; Biland, A.; Blank, M.; Bretz, T.; Bruegge, K. A.; Buss, J.; Dmytriiev, A.; Dorner, D.; Einecke, S.; Hempfling, C.; Hildebrand, D.; Hughes, G.; Linhoff, L.; Mannheim, K.; Neise, D.; Neronov, A.; Noethe, M.; Paravac, A.; Pauss, F.; Rhode, W.; Shukla, A.; Temme, F.; Thaele, J.; Walter, R.

    2016-08-01

    Segmented imaging reflectors are a great choice for Imaging Atmospheric Cherenkov Telescopes (IACTs). However, the alignment of the individual mirror facets is challenging. We align a segmented reflector by observing and optimizing its Bokeh function. Bokeh alignment can already be done with very little resources and little preparation time. Further, Bokeh alignment can be done anytime, even during the day. We present a first usage of Bokeh alignment on FACT, a 4m IACT on Canary Island La Palma, Spain and further a first Bokeh alignment test on the CTA MST IACT prototype in Brelin Adlershof.

  13. DAPS: Database of Aligned Protein Structures

    DOE Data Explorer

    Mallick, Parag; Rice, Danny; Eisenberg, David

    DAPS is based on the FSSP, DSSP, PDB and CATH databases. There also exists a subset of DAPS known as DDAPS (also pronounced DAPS) - Database of Distant Aligned Protein Structures. It is a database of structures that have low sequence similarity but share a similar fold. There are a number of filters used to make the DDAPS list more useful. The algorithm requires that an FSSP file exists for one of the members of a pair and that the other member is listed in that FSSP file. It requires that each member of the pair be within the CATH database and share a common CAT classification. It also requires that the secondary structure can be determined by DSSP. How is DAPS constructed? We begin with the set of all chains from the current release of the PDB. An all on all search is done on the list to find pairs that have the same fold acoording to both the FSSP and CATH databases and clustered into groups by a representative structure (representative structures have less than 25% sequence identity to each other). For each protein pair, regions aligned by the DALI program are extracted from the corresponding FSSP file, or recomputed using DALI-lite. In domain DAPS, only regions that are called "domains" by CATH are included in the alignment. The amino acid type, secondary structure type, and solvent accessibility are extracted from the DSSP file and written pairwise into the database. DAPS is updated with updates of CATH.[Taken from http://nihserver.mbi.ucla.edu/DAPS/daps_help.html

  14. Alignment of Elementary Geometry Curriculum with Current Standards.

    ERIC Educational Resources Information Center

    Pickreign, Jamar; Capps, Lelon R.

    2000-01-01

    Examines geometry language used in K-6 textbooks and compares the findings to language used in modern mathematics standards documents. Finds a substantial misalignment between the geometry presented in textbooks, the geometry teaching expectations of mathematics education professionals, and the geometry being assessed in student performance…

  15. Mid-latitude field-aligned ionospheric irregularities and its impact on GPS

    NASA Astrophysics Data System (ADS)

    Yasyukevich, Yury; Afraimovich, Edward; Ishin, Artem; Tinin, Mikhail

    2010-05-01

    Strong scintillations of amplitude and phase of transionospheric radio signals occur due to signal scattering on intensive small scale irregularities. Scintillation can have an adverse effect on GPS signals and cause a GPS receiver to lose lock on the signal in some extreme cases. Although the plasma bubble is a common phenomenon and it has been studied for years, precise observed data of ionospheric scintillations and loss of lock to GPS receivers due to plasma bubble at mid-latitude are still limited. In most papers there are no data regarding the space geometry of field-aligned irregularities. For the first time, we propose a GPS method to detect mid-latitude field-aligned irregularities (FAIs) by line-of-sight angular scanning regarding the local magnetic field vector. We show that total GPS L2 phase slips over Japan during the recovery phase of the 12 February, 2000 geomagnetic storm (Ma and Maruyama, 2006, doi:10.1029/2006GL027512) were caused by GPS signal scattering on FAIs for the line-of-sight of both aligned to magnetic field line (the field of aligned scattering, FALS), and across it or at large angles to magnetic field line (the field of across scattering, FACS). Our FALS results confirm well with data of investigation of magnetic field orientation control of GPS occultation observations of equatorial scintillation during detailed LEO CHAMP, SAC-C and PICOSat measurements, realized by Anderson and Strauss (2005, doi:10.1029/2005GL023781). The role of large-angle scattering almost along the normal to the magnetic field line in GPS scintillation is determined by attenuation of the irregularity anisotropy factor as compared with the other factors. The work was supported by the Fundamental Research Program of RAS Physical Science Department (Project IV.12 "Modern problems of radiophysics").

  16. Comparative Analysis of Circulating Endothelial Progenitor Cells in Age-Related Macular Degeneration Patients Using Automated Rare Cell Analysis (ARCA) and Fluorescence Activated Cell Sorting (FACS)

    PubMed Central

    Say, Emil Anthony T.; Melamud, Alex; Esserman, Denise Ann; Povsic, Thomas J.; Chavala, Sai H.

    2013-01-01

    Background Patients with age-related macular degeneration (ARMD) begin with non-neovascular (NNV) phenotypes usually associated with good vision. Approximately 20% of NNV-ARMD patients will convert to vision debilitating neovascular (NV) ARMD, but precise timing of this event is unknown. Developing a clinical test predicting impending conversion to NV-ARMD is necessary to prevent vision loss. Endothelial progenitor cells (EPCs), defined as CD34+VEGR2+ using traditional fluorescence activated cell sorting (FACS), are rare cell populations known to be elevated in patients with NV-ARMD compared to NNV-ARMD. FACS has high inter-observer variability and subjectivity when measuring rare cell populations precluding development into a diagnostic test. We hypothesized that automated rare cell analysis (ARCA), a validated and FDA-approved technology for reproducible rare cell identification, can enumerate EPCs in ARMD patients more reliably. This pilot study serves as the first step in developing methods for reproducibly predicting ARMD phenotype conversion. Methods We obtained peripheral venous blood samples in 23 subjects with NNV-ARMD or treatment naïve NV-ARMD. Strict criteria were used to exclude subjects with known angiogenic diseases to minimize confounding results. Blood samples were analyzed in masked fashion in two separate laboratories. EPCs were independently enumerated using ARCA and FACS within 24 hours of blood sample collection, and p<0.2 was considered indicative of a trend for this proof of concept study, while statistical significance was established at 0.05. Results We measured levels of CD34+VEGFR2+ EPCs suggestive of a trend with higher values in patients with NV compared to NNV-ARMD (p = 0.17) using ARCA. Interestingly, CD34+VEGR2+ EPC analysis using FACS did not produce similar results (p = 0.94). Conclusions CD34+VEGR2+ may have predictive value for EPC enumeration in future ARCA studies. EPC measurements in a small sample size were

  17. Prism Window for Optical Alignment

    NASA Technical Reports Server (NTRS)

    Tang, Hong

    2008-01-01

    A prism window has been devised for use, with an autocollimator, in aligning optical components that are (1) required to be oriented parallel to each other and/or at a specified angle of incidence with respect to a common optical path and (2) mounted at different positions along the common optical path. The prism window can also be used to align a single optical component at a specified angle of incidence. Prism windows could be generally useful for orienting optical components in manufacture of optical instruments. "Prism window" denotes an application-specific unit comprising two beam-splitter windows that are bonded together at an angle chosen to obtain the specified angle of incidence.

  18. Aligned mesoporous architectures and devices.

    SciTech Connect

    Brinker, C. Jeffrey; Lu, Yunfeng

    2011-03-01

    This is the final report for the Presidential Early Career Award for Science and Engineering - PECASE (LDRD projects 93369 and 118841) awarded to Professor Yunfeng Lu (Tulane University and University of California-Los Angeles). During the last decade, mesoporous materials with tunable periodic pores have been synthesized using surfactant liquid crystalline as templates, opening a new avenue for a wide spectrum of applications. However, the applications are somewhat limited by the unfavorabe pore orientation of these materials. Although substantial effort has been devoted to align the pore channels, fabrication of mesoporous materials with perpendicular pore channels remains challenging. This project focused on fabrication of mesoporous materials with perpendicularly aligned pore channels. We demonstrated structures for use in water purification, separation, sensors, templated synthesis, microelectronics, optics, controlled release, and highly selective catalysts.

  19. Normalized entropy measure for multimodality image alignment

    NASA Astrophysics Data System (ADS)

    Studholme, Colin; Hawkes, David J.; Hill, Derek L.

    1998-06-01

    Automated multi-modality 3D medical image alignment has been an active area of research for many years. There have been a number of recent papers proposing and investigating the use of entropy derived measures of brain image alignment. Any registration measure must allow us to choose between transformation estimates based on the similarity of images within their volume of overlap. Since 3D medical images often have a limited extent and overlap, the similarity measure for the two transformation estimates may be derived from two very different regions within the images. Direct measures of information such as the joint entropy and mutual information will therefore be a function of, not only image similarity in the region of overlap, but also of the local image content within the overlap. In this paper we present a new measure, normalized mutual information, which is simply the ratio of the sum of the marginal entropies and the joint entropy. The effect of changing overlap on current entropy measures and this normalized measure are compared using a simple image model and experiments on clinical MR-PET and MR-CT image data. Results indicate that the normalized entropy measure provides significantly improved behavior over a range of imaged fields of view.

  20. Aligning incentives in supply chains.

    PubMed

    Narayanan, V G; Raman, Ananth

    2004-11-01

    Most companies don't worry about the behavior of their supply chain partners. Instead, they expect the supply chain to work efficiently without interference, as if guided by Adam Smith's famed invisible hand. In their study of more than 50 supply networks, V.G. Narayanan and Ananth Raman found that companies often looked out for their own interests and ignored those of their network partners. Consequently, supply chains performed poorly. Those results aren't shocking when you consider that supply chains extend across several functions and many companies, each with its own priorities and goals. Yet all those functions and firms must pull in the same direction for a chain to deliver goods and services to consumers quickly and cost-effectively. According to the authors, a supply chain works well only if the risks, costs, and rewards of doing business are distributed fairly across the network. In fact, misaligned incentives are often the cause of excess inventory, stock-outs, incorrect forecasts, inadequate sales efforts, and even poor customer service. The fates of all supply chain partners are interlinked: If the firms work together to serve consumers, they will all win. However, they can do that only if incentives are aligned. Companies must acknowledge that the problem of incentive misalignment exists and then determine its root cause and align or redesign incentives. They can improve alignment by, for instance, adopting revenue-sharing contracts, using technology to track previously hidden information, or working with intermediaries to build trust among network partners. It's also important to periodically reassess incentives, because even top-performing networks find that changes in technology or business conditions alter the alignment of incentives.

  1. Fiber alignment apparatus and method

    DOEpatents

    Kravitz, S.H.; Warren, M.E.; Snipes, M.B. Jr.; Armendariz, M.G.; Word, J.C. V

    1997-08-19

    A fiber alignment apparatus includes a micro-machined nickel spring that captures and locks arrays of single mode fibers into position. The design consists of a movable nickel leaf shaped spring and a fixed pocket where fibers are held. The fiber is slid between the spring and a fixed block, which tensions the spring. When the fiber reaches the pocket, it automatically falls into the pocket and is held by the pressure of the leaf spring. 8 figs.

  2. Fiber alignment apparatus and method

    DOEpatents

    Kravitz, Stanley H.; Warren, Mial Evans; Snipes, Jr., Morris Burton; Armendariz, Marcelino Guadalupe; Word, V., James Cole

    1997-01-01

    A fiber alignment apparatus includes a micro-machined nickel spring that captures and locks arrays of single mode fibers into position. The design consists of a movable nickel leaf shaped spring and a fixed pocket where fibers are held. The fiber is slid between the spring and a fixed block, which tensions the spring. When the fiber reaches the pocket, it automatically falls into the pocket and is held by the pressure of the leaf spring.

  3. Threaded pilot insures cutting tool alignment

    NASA Technical Reports Server (NTRS)

    Goldman, R.; Schneider, W. E.

    1966-01-01

    Threaded pilot allows machining of a port component, or boss, after the reciprocating hole has been threaded. It is used to align cutting surfaces with the boss threads, thus insuring precision alignment.

  4. Interactive Alignment of Multisyllabic Stress Patterns in a Second Language Classroom

    ERIC Educational Resources Information Center

    Trofimovich, Pavel; McDonough, Kim; Foote, Jennifer A.

    2014-01-01

    The current study explored the occurrence of stress pattern alignment during peer interaction in a second language (L2) classroom. Interactive alignment is a sociocognitive phenomenon in which interlocutors reuse each other's expressions, structures, and pronunciation patterns during conversation. Students (N = 41) enrolled in a…

  5. State Standards and State Assessment Systems: A Guide to Alignment. Series on Standards and Assessments.

    ERIC Educational Resources Information Center

    La Marca, Paul M.; Redfield, Doris; Winter, Phoebe C.

    Alignment of content standards, performance standards, and assessments is crucial. This guide contains information to assist states and districts in aligning their assessment systems to their content and performance standards. It includes a review of current literature, both published and fugitive. The research is woven together with a few basic…

  6. Aligning Plasma-Arc Welding Oscillations

    NASA Technical Reports Server (NTRS)

    Norris, Jeff; Fairley, Mike

    1989-01-01

    Tool aids in alignment of oscillator probe on variable-polarity plasma-arc welding torch. Probe magnetically pulls arc from side to side as it moves along joint. Tensile strength of joint depends on alignment of weld bead and on alignment of probe. Operator installs new tool on front of torch body, levels it with built-in bubble glass, inserts probe in slot on tool, and locks probe in place. Procedure faster and easier and resulting alignment more accurate and repeatable.

  7. Use laser-optics for machinery alignment

    SciTech Connect

    Bloch, H.P.

    1987-10-01

    Many sources attribute most bearing overload and destructive vibration in industrial machinery to shaft misalignment. There is considerable disagreement as to the alignment quality required. There is also little agreement on suitable calculation methods and achievable accuracy for anticipated thermal growth of machinery (necessary if running alignment is to remain acceptable). This article examines existing alignment quality guidelines for relevance and consistency, and reviews the application of laser-optic alignment systems based on three years of field experience.

  8. Strategy for alignment of electron beam trajectory in LEReC cooling section

    SciTech Connect

    Seletskiy, S.; Blaskiewicz, M.; Fedotov, A.; Kayran, D.; Kewisch, J.; Michnoff, R.; Pinayev, I.

    2016-09-23

    We considered the steps required to align the electron beam trajectory through the LEReC cooling section. We devised a detailed procedure for the beam-based alignment of the cooling section solenoids. We showed that it is critical to have an individual control of each CS solenoid current. Finally, we modeled the alignment procedure and showed that with two BPM fitting the solenoid shift can be measured with 40 um accuracy and the solenoid inclination can be measured with 30 urad accuracy. These accuracies are well within the tolerances of the cooling section solenoid alignment.

  9. A fast cross-validation method for alignment of electron tomography images based on Beer-Lambert law.

    PubMed

    Yan, Rui; Edwards, Thomas J; Pankratz, Logan M; Kuhn, Richard J; Lanman, Jason K; Liu, Jun; Jiang, Wen

    2015-11-01

    In electron tomography, accurate alignment of tilt series is an essential step in attaining high-resolution 3D reconstructions. Nevertheless, quantitative assessment of alignment quality has remained a challenging issue, even though many alignment methods have been reported. Here, we report a fast and accurate method, tomoAlignEval, based on the Beer-Lambert law, for the evaluation of alignment quality. Our method is able to globally estimate the alignment accuracy by measuring the goodness of log-linear relationship of the beam intensity attenuations at different tilt angles. Extensive tests with experimental data demonstrated its robust performance with stained and cryo samples. Our method is not only significantly faster but also more sensitive than measurements of tomogram resolution using Fourier shell correlation method (FSCe/o). From these tests, we also conclude that while current alignment methods are sufficiently accurate for stained samples, inaccurate alignments remain a major limitation for high resolution cryo-electron tomography.

  10. A fast cross-validation method for alignment of electron tomography images based on Beer-Lambert law

    PubMed Central

    Yan, Rui; Edwards, Thomas J.; Pankratz, Logan M.; Kuhn, Richard J.; Lanman, Jason K.; Liu, Jun; Jiang, Wen

    2015-01-01

    In electron tomography, accurate alignment of tilt series is an essential step in attaining high-resolution 3D reconstructions. Nevertheless, quantitative assessment of alignment quality has remained a challenging issue, even though many alignment methods have been reported. Here, we report a fast and accurate method, tomoAlignEval, based on the Beer-Lambert law, for the evaluation of alignment quality. Our method is able to globally estimate the alignment accuracy by measuring the goodness of log-linear relationship of the beam intensity attenuations at different tilt angles. Extensive tests with experimental data demonstrated its robust performance with stained and cryo samples. Our method is not only significantly faster but also more sensitive than measurements of tomogram resolution using Fourier shell correlation method (FSCe/o). From these tests, we also conclude that while current alignment methods are sufficiently accurate for stained samples, inaccurate alignments remain a major limitation for high resolution cryo-electron tomography. PMID:26455556

  11. Vertically aligned nanostructure scanning probe microscope tips

    DOEpatents

    Guillorn, Michael A.; Ilic, Bojan; Melechko, Anatoli V.; Merkulov, Vladimir I.; Lowndes, Douglas H.; Simpson, Michael L.

    2006-12-19

    Methods and apparatus are described for cantilever structures that include a vertically aligned nanostructure, especially vertically aligned carbon nanofiber scanning probe microscope tips. An apparatus includes a cantilever structure including a substrate including a cantilever body, that optionally includes a doped layer, and a vertically aligned nanostructure coupled to the cantilever body.

  12. Ultrafast electron diffraction from aligned molecules

    SciTech Connect

    Centurion, Martin

    2015-08-17

    The aim of this project was to record time-resolved electron diffraction patterns of aligned molecules and to reconstruct the 3D molecular structure. The molecules are aligned non-adiabatically using a femtosecond laser pulse. A femtosecond electron pulse then records a diffraction pattern while the molecules are aligned. The diffraction patterns are then be processed to obtain the molecular structure.

  13. Solid-state thermolysis of a fac-rhenium(I) carbonyl complex with a redox non-innocent pincer ligand.

    PubMed

    Jurca, Titel; Chen, Wen-Ching; Michel, Sheila; Korobkov, Ilia; Ong, Tiow-Gan; Richeson, Darrin S

    2013-03-25

    The development of rhenium(I) chemistry has been restricted by the limited structural and electronic variability of the common pseudo-octahedral products fac-[ReX(CO)3L2] (L2 = α-diimine). We address this constraint by first preparing the bidentate bis(imino)pyridine complexes [(2,6-{2,6-Me2C6H3N=CPh}2C5H3N)Re(CO)3X] (X = Cl 2, Br 3), which were characterized by spectroscopic and X-ray crystallographic means, and then converting these species into tridentate pincer ligand compounds, [(2,6-{2,6-Me2C6H3N=CPh}2C5H3N)Re(CO)2X] (X = Cl 4, Br 5). This transformation was performed in the solid-state by controlled heating of 2 or 3 above 200 °C in a tube furnace under a flow of nitrogen gas, giving excellent yields (≥95 %). Compounds 4 and 5 define a new coordination environment for rhenium(I) carbonyl chemistry where the metal center is supported by a planar, tridentate pincer-coordinated bis(imino)pyridine ligand. The basic photophysical features of these compounds show significant elaboration in both number and intensity of the d-π* transitions observed in the UV/Vis spec tra relative to the bidentate starting materials, and these spectra were analyzed using time-dependent DFT computations. The redox nature of the bis(imino)pyridine ligand in compounds 2 and 4 was examined by electrochemical analysis, which showed two ligand reduction events and demonstrated that the ligand reduction shifts to a more positive potential when going from bidentate 2 to tridentate 4 (+160 mV for the first reduction step and +90 mV for the second). These observations indicate an increase in electrostatic stabilization of the reduced ligand in the tridentate conformation. Elaboration on this synthetic methodology documented its generality through the preparation of the pseudo-octahedral rhenium(I) triflate complex [(2,6-{2,6-Me2C6H3N=CPh}2C5H3N)Re(CO)2OTf] (7, 93 % yield).

  14. RegiStax: Alignment, stacking and processing of images

    NASA Astrophysics Data System (ADS)

    Berrevoets, Cor; DeClerq, Bart; George, Tony; Makolkin, Dmitry; Maxson, Paul; Pilz, Bob; Presnyakov, Pavel; Roel, Eric; Weiller, Sylvain

    2012-06-01

    RegiStax is software for alignment/stacking/processing of images; it was released over 10 years ago and continues to be developed and improved. The current version is RegiStax 6, which supports the following formats: AVI, SER, RFL (RegiStax Framelist), BMP, JPG, TIF, and FIT. This version has a shorter and simpler processing sequence than its predecessor, and optimizing isn't necessary anymore as a new image alignment method optimizes directly. The interface of RegiStax 6 has been simplified to look more uniform in appearance and functionality, and RegiStax 6 now uses Multi-core processing, allowing the user to have up to have multiple cores(recommended to use maximally 4) working simultaneous during alignment/stacking.

  15. GATA: A graphic alignment tool for comparative sequenceanalysis

    SciTech Connect

    Nix, David A.; Eisen, Michael B.

    2005-01-01

    Several problems exist with current methods used to align DNA sequences for comparative sequence analysis. Most dynamic programming algorithms assume that conserved sequence elements are collinear. This assumption appears valid when comparing orthologous protein coding sequences. Functional constraints on proteins provide strong selective pressure against sequence inversions, and minimize sequence duplications and feature shuffling. For non-coding sequences this collinearity assumption is often invalid. For example, enhancers contain clusters of transcription factor binding sites that change in number, orientation, and spacing during evolution yet the enhancer retains its activity. Dotplot analysis is often used to estimate non-coding sequence relatedness. Yet dot plots do not actually align sequences and thus cannot account well for base insertions or deletions. Moreover, they lack an adequate statistical framework for comparing sequence relatedness and are limited to pairwise comparisons. Lastly, dot plots and dynamic programming text outputs fail to provide an intuitive means for visualizing DNA alignments.

  16. The alignment and assembly of the DESI prime focus corrector

    NASA Astrophysics Data System (ADS)

    Brooks, David; Doel, Peter; Besuner, Robert; Flaugher, Brenna; Gallo, Giuseppe; Gutierrez, Gaston; Kent, Stephen; Lampton, Michael; Levi, Michael; Liang, Ming; Miller, Timothy N.; Sprayberry, David; Stefanik, Andrew

    2016-08-01

    The Dark Energy Spectroscopic Instrument (DESI), which is currently under construction, is designed to measure the expansion history of the Universe using the Baryon Acoustic Oscillation technique. The spectra of 40 million galaxies over 14000 sq deg will be measured during the life of the experiment. A new prime focus corrector for the KPNO Mayall telescope will deliver light to 5000 fibre optic positioners. The fibres in turn feed ten broad-band spectrographs. The prime focus corrector for DESI consists of six lenses that range in diameter from 0.80 - 1.14 meters and from 83 - 237 kg in weight. The alignment of the large lenses of the optical corrector poses a significant challenge as in order to meet the fibre throughput requirements they have to be aligned to within a tolerance of 50 micrometres. This paper details the design for the cells that will hold the lenses and the alignment and assembly procedure for the mounting of the lenses into the cells and into the complete barrel assembly. This is based on the experience obtained from the alignment of the Dark Energy Camera (DECam) instrument which was successfully assembled and aligned by the same team and we include in the paper the lessons learnt and design modifications that will be implemented on the DESI system.

  17. Sim4cc: a cross-species spliced alignment program.

    PubMed

    Zhou, Leming; Pertea, Mihaela; Delcher, Arthur L; Florea, Liliana

    2009-06-01

    Advances in sequencing technologies have accelerated the sequencing of new genomes, far outpacing the generation of gene and protein resources needed to annotate them. Direct comparison and alignment of existing cDNA sequences from a related species is an effective and readily available means to determine genes in the new genomes. Current spliced alignment programs are inadequate for comparing sequences between different species, owing to their low sensitivity and splice junction accuracy. A new spliced alignment tool, sim4cc, overcomes problems in the earlier tools by incorporating three new features: universal spaced seeds, to increase sensitivity and allow comparisons between species at various evolutionary distances, and powerful splice signal models and evolutionarily-aware alignment techniques, to improve the accuracy of gene models. When tested on vertebrate comparisons at diverse evolutionary distances, sim4cc had significantly higher sensitivity compared to existing alignment programs, more than 10% higher than the closest competitor for some comparisons, while being comparable in speed to its predecessor, sim4. Sim4cc can be used in one-to-one or one-to-many comparisons of genomic and cDNA sequences, and can also be effectively incorporated into a high-throughput annotation engine, as demonstrated by the mapping of 64,000 Fagus grandifolia 454 ESTs and unigenes to the poplar genome.

  18. Constraints on the alignment of galaxies in galaxy clusters from ~14 000 spectroscopic members

    NASA Astrophysics Data System (ADS)

    Sifón, Cristóbal; Hoekstra, Henk; Cacciato, Marcello; Viola, Massimo; Köhlinger, Fabian; van der Burg, Remco F. J.; Sand, David J.; Graham, Melissa L.

    2015-03-01

    Torques acting on galaxies lead to physical alignments, but the resulting ellipticity correlations are difficult to predict. As they constitute a major contaminant for cosmic shear studies, it is important to constrain the intrinsic alignment signal observationally. We measured the alignments of satellite galaxies within 90 massive galaxy clusters in the redshift range 0.05 alignment: the radial alignment of satellite galaxies toward the brightest cluster galaxies (BCGs), the common orientations of satellite galaxies and BCGs, and the radial alignments of satellites with each other. Residual systematic effects are much smaller than the statistical uncertainties. We detect no galaxy alignment of any kind out to at least 3r200. The signal is consistent with zero for both blue and red galaxies, bright and faint ones, and also for subsamples of clusters based on redshift, dynamical mass, and dynamical state. These conclusions are unchanged if we expand the sample with bright cluster members from the red sequence. We augment our constraints with those from the literature to estimate the importance of the intrinsic alignments of satellites compared to those of central galaxies, for which the alignments are described by the linear alignment model. Comparison of the alignment signals to the expected uncertainties of current surveys such as the Kilo-Degree Survey suggests that the linear alignment model is an adequate treatment of intrinsic alignments, but it is not clear whether this will be the case for larger surveys. Table is available in electronic form at

  19. Aligning Two Genomic Sequences That Contain Duplications

    NASA Astrophysics Data System (ADS)

    Hou, Minmei; Riemer, Cathy; Berman, Piotr; Hardison, Ross C.; Miller, Webb

    It is difficult to properly align genomic sequences that contain intra-species duplications. With this goal in mind, we have developed a tool, called TOAST (two-way orthologous alignment selection tool), for predicting whether two aligned regions from different species are orthologous, i.e., separated by a speciation event, as opposed to a duplication event. The advantage of restricting alignment to orthologous pairs is that they constitute the aligning regions that are most likely to share the same biological function, and most easily analyzed for evidence of selection. We evaluate TOAST on 12 human/mouse gene clusters.

  20. Accelerator and transport line survey and alignment

    SciTech Connect

    Ruland, R.E.

    1991-10-01

    This paper summarizes the survey and alignment processes of accelerators and transport lines and discusses the propagation of errors associated with these processes. The major geodetic principles governing the survey and alignment measurement space are introduced and their relationship to a lattice coordinate system shown. The paper continues with a broad overview about the activities involved in the step sequence from initial absolute alignment to final smoothing. Emphasis is given to the relative alignment of components, in particular to the importance of incorporating methods to remove residual systematic effects in surveying and alignment operations. Various approaches to smoothing used at major laboratories are discussed. 47 refs., 19 figs., 1 tab.

  1. Antares beam-alignment-system performance

    SciTech Connect

    Appert, Q.D.; Bender, S.C.

    1983-01-01

    The beam alignment system for the 24-beam-sector Antares CO/sub 2/ fusion laser automatically aligns more than 200 optical elements. A visible-wavelength alignment technique is employed which uses a telescope/TV system to view point-light sources appropriately located down the beamline. The centroids of the light spots are determined by a video tracker, which generates error signals used by the computer control system to move appropriate mirrors in a closed-loop system. Final touch-up alignment is accomplished by projecting a CO/sub 2/ alignment laser beam through the system and sensing its position at the target location. The techniques and control algorithms employed have resulted in alignment accuracies exceeding design requirements. By employing video processing to determine the centroids of diffraction images and by averaging over multiple TV frames, we achieve alignment accuracies better than 0.1 times system diffraction limits in the presence of air turbulence.

  2. FOGSAA: Fast Optimal Global Sequence Alignment Algorithm

    NASA Astrophysics Data System (ADS)

    Chakraborty, Angana; Bandyopadhyay, Sanghamitra

    2013-04-01

    In this article we propose a Fast Optimal Global Sequence Alignment Algorithm, FOGSAA, which aligns a pair of nucleotide/protein sequences faster than any optimal global alignment method including the widely used Needleman-Wunsch (NW) algorithm. FOGSAA is applicable for all types of sequences, with any scoring scheme, and with or without affine gap penalty. Compared to NW, FOGSAA achieves a time gain of (70-90)% for highly similar nucleotide sequences (> 80% similarity), and (54-70)% for sequences having (30-80)% similarity. For other sequences, it terminates with an approximate score. For protein sequences, the average time gain is between (25-40)%. Compared to three heuristic global alignment methods, the quality of alignment is improved by about 23%-53%. FOGSAA is, in general, suitable for aligning any two sequences defined over a finite alphabet set, where the quality of the global alignment is of supreme importance.

  3. Pupil Alignment Measuring Technique and Alignment Reference for Instruments or Optical Systems

    NASA Technical Reports Server (NTRS)

    Hagopian, John G.

    2010-01-01

    A technique was created to measure the pupil alignment of instruments in situ by measuring calibrated pupil alignment references (PARs) in instruments. The PAR can also be measured using an alignment telescope or an imaging system. PAR allows the verification of the science instrument (SI) pupil alignment at the integrated science instrument module (ISIM) level of assembly at ambient and cryogenic operating temperature. This will allow verification of the ISIM+SI alignment, and provide feedback to realign the SI if necessary.

  4. Aligned interactions in cosmic rays

    NASA Astrophysics Data System (ADS)

    Kempa, J.

    2015-12-01

    The first clean Centauro was found in cosmic rays years many ago at Mt Chacaltaya experiment. Since that time, many people have tried to find this type of interaction, both in cosmic rays and at accelerators. But no one has found a clean cases of this type of interaction.It happened finally in the last exposure of emulsion at Mt Chacaltaya where the second clean Centauro has been found. The experimental data for both the Centauros and STRANA will be presented and discussed in this paper. We also present our comments to the intriguing question of the existence of a type of nuclear interactions at high energy with alignment.

  5. MEANS FOR DETERMINING CENTRIFUGE ALIGNMENT

    DOEpatents

    Smith, W.Q.

    1958-08-26

    An apparatus is presented for remotely determining the alignment of a centrifuge. The centrifage shaft is provided with a shoulder, upon which two followers ride, one for detecting radial movements, and one upon the shoulder face for determining the axial motion. The followers are attached to separate liquid filled bellows, and a tube connects each bellows to its respective indicating gage at a remote location. Vibrations produced by misalignment of the centrifuge shaft are transmitted to the bellows, and tbence through the tubing to the indicator gage. This apparatus is particularly useful for operation in a hot cell where the materials handled are dangerous to the operating personnel.

  6. Aligned interactions in cosmic rays

    SciTech Connect

    Kempa, J.

    2015-12-15

    The first clean Centauro was found in cosmic rays years many ago at Mt Chacaltaya experiment. Since that time, many people have tried to find this type of interaction, both in cosmic rays and at accelerators. But no one has found a clean cases of this type of interaction.It happened finally in the last exposure of emulsion at Mt Chacaltaya where the second clean Centauro has been found. The experimental data for both the Centauros and STRANA will be presented and discussed in this paper. We also present our comments to the intriguing question of the existence of a type of nuclear interactions at high energy with alignment.

  7. Method for protein structure alignment

    DOEpatents

    Blankenbecler, Richard; Ohlsson, Mattias; Peterson, Carsten; Ringner, Markus

    2005-02-22

    This invention provides a method for protein structure alignment. More particularly, the present invention provides a method for identification, classification and prediction of protein structures. The present invention involves two key ingredients. First, an energy or cost function formulation of the problem simultaneously in terms of binary (Potts) assignment variables and real-valued atomic coordinates. Second, a minimization of the energy or cost function by an iterative method, where in each iteration (1) a mean field method is employed for the assignment variables and (2) exact rotation and/or translation of atomic coordinates is performed, weighted with the corresponding assignment variables.

  8. Separation of uncompromised whole blood mixtures for single source STR profiling using fluorescently-labeled human leukocyte antigen (HLA) probes and fluorescence activated cell sorting (FACS).

    PubMed

    Dean, Lee; Kwon, Ye Jin; Philpott, M Katherine; Stanciu, Cristina E; Seashols-Williams, Sarah J; Dawson Cruz, Tracey; Sturgill, Jamie; Ehrhardt, Christopher J

    2015-07-01

    Analysis of biological mixtures is a significant problem for forensic laboratories, particularly when the mixture contains only one cell type. Contributions from multiple individuals to biologic evidence can complicate DNA profile interpretation and often lead to a reduction in the probative value of DNA evidence or worse, its total loss. To address this, we have utilized an analytical technique that exploits the intrinsic immunological variation among individuals to physically separate cells from different sources in a mixture prior to DNA profiling. Specifically, we applied a fluorescently labeled antibody probe to selectively bind to one contributor in a mixture through allele-specific interactions with human leukocyte antigen (HLA) proteins that are expressed on the surfaces of most nucleated cells. Once the contributor's cells were bound to the probe, they were isolated from the mixture using fluorescence activated cell sorting (FACS)-a high throughput technique for separating cell populations based on their optical properties-and then subjected to STR analysis. We tested this approach on two-person and four-person whole blood mixtures where one contributor possessed an HLA allele (A*02) that was not shared by other contributors to the mixture. Results showed that hybridization of the mixture with a fluorescently-labeled antibody probe complimentary to the A*02 allele's protein product created a cell population with a distinct optical profile that could be easily differentiated from other cells in the mixture. After sorting the cells with FACS, genetic analysis showed that the STR profile of this cell population was consistent with that of the contributor who possessed the A*02 allele. Minor peaks from the A*02 negative contributor(s) were observed but could be easily distinguished from the profile generated from A*02 positive cells. Overall, this indicates that HLA antibody probes coupled to FACS may be an effective approach for generating STR profiles of

  9. Strategies for active alignment of lenses

    NASA Astrophysics Data System (ADS)

    Langehanenberg, Patrik; Heinisch, Josef; Wilde, Chrisitan; Hahne, Felix; Lüerß, Bernd

    2015-10-01

    Today's optical systems require up-to-date assembly and joining technology. The trend of keeping dimensions as small as possible while maintaining or increasing optical imaging performance leaves little to no room for mechanical lens adjustment equipment that may remain in the final product. In this context active alignment of optical elements opens up possibilities for the fast and cost-economic manufacturing of lenses and lens assemblies with highest optical performance. Active alignment for lens manufacturing is the precise alignment of the optical axis of a lens with respect to an optical or mechanical reference axis (e.g. housing) including subsequent fixation by glue. In this contribution we will describe different approaches for active alignment and outline strengths and limitations of the different methods. Using the SmartAlign principle, highest quality cemented lenses can be manufactured without the need for high precision prealignment, while the reduction to a single alignment step greatly reduces the cycle time. The same strategies can also be applied to bonding processes. Lenses and lens groups can be aligned to both mechanical and optical axes to maximize the optical performance of a given assembly. In hybrid assemblies using both mechanical tolerances and active alignment, SmartAlign can be used to align critical lens elements anywhere inside the system for optimized total performance. Since all geometrical parameters are re-measured before each alignment, this process is especially suited for complex and time-consuming production processes where the stability of the reference axis would otherwise be critical. For highest performance, lenses can be actively aligned using up to five degrees of freedom. In this way, SmartAlign enables the production of ultra-precise mounted lenses with an alignment precision below 1 μm.

  10. Detection of molecular alterations in methamphetamine-activated Fos-expressing neurons from a single rat dorsal striatum using fluorescence-activated cell sorting (FACS).

    PubMed

    Liu, Qing-Rong; Rubio, Francisco J; Bossert, Jennifer M; Marchant, Nathan J; Fanous, Sanya; Hou, Xingyu; Shaham, Yavin; Hope, Bruce T

    2014-01-01

    Methamphetamine and other drugs activate a small proportion of all neurons in the brain. We previously developed a fluorescence-activated cell sorting (FACS)-based method to characterize molecular alterations induced selectively in activated neurons that express the neural activity marker Fos. However, this method requires pooling samples from many rats. We now describe a modified FACS-based method to characterize molecular alterations in Fos-expressing dorsal striatal neurons from a single rat using a multiplex pre-amplification strategy. Fos and NeuN (a neuronal marker) immunohistochemistry indicate that 5-6% of dorsal striatum neurons were activated 90 min after acute methamphetamine injections (5 mg/kg, i.p.) while less than 0.5% of neurons were activated by saline injections. We used FACS to separate NeuN-labeled neurons into Fos-positive and Fos-negative neurons and assessed mRNA expression using RT-qPCR from as little as five Fos-positive neurons. Methamphetamine induced 3-20-fold increases of immediate early genes arc, homer-2, c-fos, fosB, and its isoforms (ΔfosB and a novel isoform ΔfosB-2) in Fos-positive but not Fos-negative neurons. Immediate early gene mRNA induction was 10-fold lower or absent when assessed in unsorted samples from single dorsal striatum homogenates. Our modified method makes it feasible to study unique molecular alterations in neurons activated by drugs or drug-associated cues in complex addiction models. Methamphetamine and other drugs activate a small proportion of all neurons in the brain. We here report an improved method to characterize molecular alterations induced selectively in activated neurons that express the neural activity marker Fos. We used FACS along with targeted PCR pre-amplification to assess acute methamphetamine-induced gene expression from as few as 5 Fos-expressing neurons from a single rat dorsal striatum. Methamphetamine induced 3-20-fold increases of immediate early genes (IEGs) in Fos-positive but not

  11. Correction of both spontaneous and DEB-induced chromosome instability in Fanconi anemia FA-C cells by FACC cDNA

    SciTech Connect

    Stavropoulos, D.J.; Tomkins, D.J.; Allingham-Hawkins, D.J.; Buchwald, M.

    1994-09-01

    Cells from all four Fanconi anemia complementation groups show hypersensitivity to cell-killing by mitomycin C (MMC), diepoxybutane (DEB) and other DNA cross-linking agents, and increased spontaneous and DEB-induced chromosome aberrations (CA). The extent of these phenotypes varies between lymphoblastoid cell lines from different complementation groups. Our data showed that the difference in MMC hypersensitivity and DEB-CA was not always coupled. While 230N (FA-B) had higher DEB-induced CA/cell than 536N (FA-C) (7.42 vs. 4.46 respectively), that latter was much more sensitive to cell-killing by MMC (dose at 10% survival, D{sub 10}: 5.2 vs. 1.2 ng/ml respectively). Strathdes et al. (1992) cloned a cDNA Fanconi anemia complementation group C (FACC) which complemented the hypersensitivity to MMC and DEB cell-killing of FA-C cells (536N) but not cells from the other three complementation groups. The present study was initiated to determine whether chromosome instability in 536N is also complemented by the FACC (FAC3) cDNA. The pREP4-FAC3 vector was transfected into 536N and transfectants selected with hygromycin B. The DEB D{sub 10} of 536N (1.0 {mu}M) was corrected to the control level (16.2 {mu}M for 3TO) by FACC (15.1 {mu}M for 536N-FACC), as previously demonstrated. Chromosome instability (cab, cse, ctb, cte) was determined without and with 0.1 {mu}g/ml DEB treatment. Spontaneous CA of 536N (0.30 aberrations/cell) was corrected to the control level (0.04 for 3TO) by FACC (0.06 for 536N-FACC). Similarly, the DEB-induced CA was corrected (2.74 for 536N vs. 0.06 and 0.02 for 3TO and 536N-FACC respectively). Thus, at least for FA complementation group C, hypersensitivity to cell-killing and chromosome instability are not dissociated and are most likely caused by the same gene defect.

  12. Measuring alignment of loading fixture

    DOEpatents

    Scavone, Donald W.

    1989-01-01

    An apparatus and method for measuring the alignment of a clevis and pin type loading fixture for compact tension specimens include a pair of substantially identical flat loading ligaments. Each loading ligament has two apertures for the reception of a respective pin of the loading fixture and a thickness less than one-half of a width of the clevis opening. The pair of loading ligaments are mounted in the clevis openings at respective sides thereof. The loading ligaments are then loaded by the pins of the loading fixture and the strain in each loading ligament is measured. By comparing the relative strain of each loading ligament, the alignment of the loading fixture is determined. Preferably, a suitable strain gage device is located at each longitudinal edge of a respective loading ligament equidistant from the two apertures in order to determine the strain thereat and hence the strain of each ligament. The loading ligaments are made substantially identical by jig grinding the loading ligaments as a matched set. Each loading ligament can also be individually calibrated prior to the measurement.

  13. Apse-Alignment of the Uranian Rings

    NASA Technical Reports Server (NTRS)

    Mosqueira, I.; Estrada, P. R.

    2000-01-01

    An explanation of the dynamical mechanism for apse-alignment of the eccentric Uranian rings is necessary before observations can be used to determine properties such as ring masses, particle sizes, and elasticities. The leading model relies on the ring self-gravity to accomplish this task, yet it yields equilibrium masses which are not in accord with Voyager radio measurements. We explore possible solutions such that the self-gravity and the collisional terms are both involved in the process of apse-alignment. We consider limits that correspond to a hot and a cold ring, and show that pressure terms may play a significant role in the equilibrium conditions for the narrow Uranian rings. In the cold ring case, where the scale height of the ring near periapse is comparable to the ring particle size, we introduce a new pressure correction pertaining to a region of the ring where the particles are locked in their relative positions and jammed against their neighbors, and the velocity dispersion is so low that the collisions are nearly elastic. In this case, we find a solution such that the ring self-gravity maintains apse-alignment against both differential precession (m = 1 mode) and the fluid pressure. We apply this model to the Uranian alpha ring, and show that, compared to the previous self-gravity model, the mass estimate for this ring increases by an order of magnitude. In the case of a hot ring, where the scale height can reach a value as much as fifty times larger than a particle size, we find velocity dispersion profiles that result in pressure forces which act in such a way as to alter the ring equilibrium conditions, again leading to a ring mass increase of an order of magnitude; however, such a velocity dispersion profile would require a different mechanism than is currently envisioned for establishing heating/cooling balance in a finite-sized, inelastic particle ring. Finally, we introduce an important correction to the model of Chiang and Goldreich.

  14. Coval: Improving Alignment Quality and Variant Calling Accuracy for Next-Generation Sequencing Data

    PubMed Central

    Kosugi, Shunichi; Natsume, Satoshi; Yoshida, Kentaro; MacLean, Daniel; Cano, Liliana; Kamoun, Sophien; Terauchi, Ryohei

    2013-01-01

    Accurate identification of DNA polymorphisms using next-generation sequencing technology is challenging because of a high rate of sequencing error and incorrect mapping of reads to reference genomes. Currently available short read aligners and DNA variant callers suffer from these problems. We developed the Coval software to improve the quality of short read alignments. Coval is designed to minimize the incidence of spurious alignment of short reads, by filtering mismatched reads that remained in alignments after local realignment and error correction of mismatched reads. The error correction is executed based on the base quality and allele frequency at the non-reference positions for an individual or pooled sample. We demonstrated the utility of Coval by applying it to simulated genomes and experimentally obtained short-read data of rice, nematode, and mouse. Moreover, we found an unexpectedly large number of incorrectly mapped reads in ‘targeted’ alignments, where the whole genome sequencing reads had been aligned to a local genomic segment, and showed that Coval effectively eliminated such spurious alignments. We conclude that Coval significantly improves the quality of short-read sequence alignments, thereby increasing the calling accuracy of currently available tools for SNP and indel identification. Coval is available at http://sourceforge.net/projects/coval105/. PMID:24116042

  15. Modeling amyotrophic lateral sclerosis in pure human iPSc-derived motor neurons isolated by a novel FACS double selection technique.

    PubMed

    Toli, Diana; Buttigieg, Dorothée; Blanchard, Stéphane; Lemonnier, Thomas; Lamotte d'Incamps, Boris; Bellouze, Sarah; Baillat, Gilbert; Bohl, Delphine; Haase, Georg

    2015-10-01

    Amyotrophic lateral sclerosis (ALS) is a severe and incurable neurodegenerative disease. Human motor neurons generated from induced pluripotent stem cells (iPSc) offer new perspectives for disease modeling and drug testing in ALS. In standard iPSc-derived cultures, however, the two major phenotypic alterations of ALS--degeneration of motor neuron cell bodies and axons--are often obscured by cell body clustering, extensive axon criss-crossing and presence of unwanted cell types. Here, we succeeded in isolating 100% pure and standardized human motor neurons by a novel FACS double selection based on a p75(NTR) surface epitope and an HB9::RFP lentivirus reporter. The p75(NTR)/HB9::RFP motor neurons survive and grow well without forming clusters or entangled axons, are electrically excitable, contain ALS-relevant motor neuron subtypes and form functional connections with co-cultured myotubes. Importantly, they undergo rapid and massive cell death and axon degeneration in response to mutant SOD1 astrocytes. These data demonstrate the potential of FACS-isolated human iPSc-derived motor neurons for improved disease modeling and drug testing in ALS and related motor neuron diseases.

  16. High-throughput FACS-based mutant screen identifies a gain-of-function allele of the Fusarium graminearum adenylyl cyclase causing deoxynivalenol over-production.

    PubMed

    Blum, Ailisa; Benfield, Aurélie H; Stiller, Jiri; Kazan, Kemal; Batley, Jacqueline; Gardiner, Donald M

    2016-05-01

    Fusarium head blight and crown rot, caused by the fungal plant pathogen Fusarium graminearum, impose a major threat to global wheat production. During the infection, plants are contaminated with mycotoxins such as deoxynivalenol (DON), which can be toxic for humans and animals. In addition, DON is a major virulence factor during wheat infection. However, it is not fully understood how DON production is regulated in F. graminearum. In order to identify regulators of DON production, a high-throughput mutant screen using Fluorescence Activated Cell Sorting (FACS) of a mutagenised TRI5-GFP reporter strain was established and a mutant over-producing DON under repressive conditions identified. A gain-of-function mutation in the F. graminearum adenylyl cyclase (FAC1), which is a known positive regulator of DON production, was identified as the cause of this phenotype through genome sequencing and segregation analysis. Our results show that the high-throughput mutant screening procedure developed here can be applied for identification of fungal proteins involved in diverse processes.

  17. Exposure to hydrocarbons 10 years after the Exxon Valdez oil spill: evidence from cytochrome P4501A expression and biliary FACs in nearshore demersal fishes.

    PubMed

    Jewett, Stephen C; Dean, Thomas A; Woodin, Bruce R; Hoberg, Max K; Stegeman, John J

    2002-01-01

    Three biomarkers of hydrocarbon exposure, CYP1A in liver vascular endothelium, liver ethoxyresorufin O-deethylase (EROD), and biliary fluorescent aromatic compounds (FACs), were examined in the nearshore fishes, masked greenling (Hexagrammos octogrammus) and crescent gunnel (Pholis laeta), collected in Prince William Sound, Alaska, 7-10 years after the Exxon Valdez oil spill (EVOS). All biomarkers were elevated in fish collected from sites originally oiled, in comparison to fish from unoiled sites. In 1998, endothelial CYP1A in masked greenling from sites that were heavily oiled in 1989 was significantly higher than in fish collected outside the spill trajectory. In 1999, fishes collected from sites adjacent to intertidal mussel beds containing lingering Exxon Valdez oil had elevated endothelial CYP1A and EROD, and high concentrations of biliary FACs. Fishes from sites near unoiled mussel beds, but within the original spill trajectory, also showed evidence of hydrocarbon exposure, although there were no correlations between sediment petroleum hydrocarbon and any of the biomarkers. Our data show that 10 years after the spill, nearshore fishes within the original spill zone were still exposed to residual EVOS hydrocarbons.

  18. Automated interferometric alignment system for paraboloidal mirrors

    DOEpatents

    Maxey, L.C.

    1993-09-28

    A method is described for a systematic method of interpreting interference fringes obtained by using a corner cube retroreflector as an alignment aid when aligning a paraboloid to a spherical wavefront. This is applicable to any general case where such alignment is required, but is specifically applicable in the case of aligning an autocollimating test using a diverging beam wavefront. In addition, the method provides information which can be systematically interpreted such that independent information about pitch, yaw and focus errors can be obtained. Thus, the system lends itself readily to automation. Finally, although the method is developed specifically for paraboloids, it can be seen to be applicable to a variety of other aspheric optics when applied in combination with a wavefront corrector that produces a wavefront which, when reflected from the correctly aligned aspheric surface will produce a collimated wavefront like that obtained from the paraboloid when it is correctly aligned to a spherical wavefront. 14 figures.

  19. Inertial currents in isotropic plasma

    NASA Technical Reports Server (NTRS)

    Heinemann, M.; Erickson, G. M.; Pontius, D. H., Jr.

    1994-01-01

    The magnetospheric convection electric field contributes to Birkeland currents. The effects of the field are to polarize the plasma by displacing the bounce paths of the ions from those of electrons, to redistribute the pressure so that it is not constant along magnetic field lines, and to enhance the pressure gradient by the gradient of the bulk speed. Changes in the polarization charge during the convection of the plasma are neutralized by electrons in the form of field-aligned currents that close through the ionosphere. The pressure drives field-aligned currents through its gradient in the same manner as in quasi-static plasmas, but with modifications that are important if the bulk speed is of the order of the ion thermal speed; the variations in the pressure along field lines are maintained by a weak parallel potential drop. These effects are described in terms of the field-aligned currents in steady state, isotropic, MHD plasma. Solutions are developed by taking the MHD limit ot two-fluid solutions and illustrated in the special case of Maxwellian plasma for which the temperature is constant along magnetic field lines. The expression for the Birkeland current density is a generalization of Vasyliunas' expression for the field-aligned current density in quasi-static plasma and provides a unifying expression when both pressure gradients and ion inertia operate simultaneously as sources of field-aligned currents. It contains a full account of different aspects of the ion flow (parallel and perpendicular velocity and vorticity) that contribute to the currents. Contributions of ion inertia to field-aligned currents will occur in regions of strong velocity shear, electric field reversal, or large gradients in the parallel velocity or number density, and may be important in the low-latitude boundary layer, plasma sheet boundary layer, and the inner edge region of the plasma sheet.

  20. The Alignment of Galaxy Structures

    NASA Astrophysics Data System (ADS)

    Biernacka, M.; Panko, E.; Bajan, K.; Godłowski, W.; Flin, P.

    2015-11-01

    We analyzed the orientation of the sample of ACO galaxy clusters. We examined the alignment in a subsample of 1056 galaxy structures taken from the Panko-Flin (2006) Catalog with known BM morphological types. We were looking for a correlation between the orientation of the cluster and the positions of neighboring clusters. The Binggeli effect (the excess of small values of the Δθ angles between the direction toward neighboring clusters and the cluster position angle) is observed, having a range up to about 45 h-1 Mpc. The strongest effect was found for elongated BM type I clusters. This is probably connected with the origins of the supergiant galaxy and with cluster formation along a long filament or plane in a supercluster.

  1. AIMFAST: Alignment Implementation for Manufacturing

    SciTech Connect

    2012-09-13

    AIMFAST is a software code used to align facets on a dish concentrator to a specific aimpoint strategy to minimize peak fluxes and maximize system optical performance. AIMFAST uses a large monitor or projections screen to display fringe patterns, and a machine vision camera to image the reflection of these patterns in the subject dish mirrors. From these images, a detailed map of surface normals can be generated and compared to design or fitted mirror shapes. This fitted comparison is then used to develop a single vector representing the orientation of the facets relative to the design orientation, and provide near-real-time adjustment information to a communicating computer. The communicating computer can display adjustments or directly interface with adjustment tools. The software for the communicating computer is specific to the implementation and is not a part of AIMFAST.

  2. IAIMFAST: Alignment Implementation for Manufacturing

    SciTech Connect

    Andraka, Charles E.

    2013-08-29

    AIMFAST is a software code used to align facets on a dish concentrator to a specific aimpoint strategy to minimize peak fluxes and maximize system optical performance. AIM FAST uses a large monitor to display fringe patterns, and a machine vision camera to image the reflection of these patterns in the subject dish mirrors. From these images, a detailed map of surface normals can be generated and compared to design or fitted mirror shapes. This fitted comparison is then used to develop a single vector representing the orientation of the facets relative to the design orientation, and provide near-real-time adjustment information to a communicating computer. The communicating computer can display adjustments or directly interface with adjustment tools.

  3. Tonal alignment in Irish dialects.

    PubMed

    Dalton, Martha; Chasaide, Ailbhe Ní

    2005-01-01

    A comparison of the contour alignment of nuclear and initial prenuclear accents was carried out for the Irish dialects of Gaoth Dobhair in Ulster (GD-U) and Cois Fharraige in Connaught (CF-C). This was done across conditions where the number of unstressed syllables following the nuclear and preceding the initial prenuclear accents was varied from 2-0. This tests a variable peak hypothesis prompted by findings for other languages, that peak timing drifts as a function of the number of syllables preceding (the prenuclear) and following (the nuclear) accent. These data also test a second hypothesis that the L*+H dominant accent of GD-U might be viewed as being underlyingly the same as the dominant H* or H*+L accent of the CF-C dialect. According to this realignment hypothesis, the difference between these Ulster and Connaught dialects lies in the way that the melodic tier is aligned to the segmental tier: GD-U would be viewed as having a delayed realization of the peak relative to the Connaught dialect. Results do not support the variable peak hypothesis for Irish, as in either dialect, the peak appeared to be rather fixed across the three conditions examined (though not necessarily identical for prenuclear and nuclear positions). The results also militate against the realignment hypothesis, which rather than providing a more simple unifying account, would greatly complicate it. One reason is that there is a peak timing difference between the nuclear and prenuclear accents of CF-C, not mirrored in GD-U. Furthermore, even if one were to limit consideration to a single (e.g., prenuclear) context, a simple realignment of the accents in one dialect does not generate the appropriate contour in the other.

  4. DNAAlignEditor: DNA alignment editor tool

    PubMed Central

    Sanchez-Villeda, Hector; Schroeder, Steven; Flint-Garcia, Sherry; Guill, Katherine E; Yamasaki, Masanori; McMullen, Michael D

    2008-01-01

    Background With advances in DNA re-sequencing methods and Next-Generation parallel sequencing approaches, there has been a large increase in genomic efforts to define and analyze the sequence variability present among individuals within a species. For very polymorphic species such as maize, this has lead to a need for intuitive, user-friendly software that aids the biologist, often with naïve programming capability, in tracking, editing, displaying, and exporting multiple individual sequence alignments. To fill this need we have developed a novel DNA alignment editor. Results We have generated a nucleotide sequence alignment editor (DNAAlignEditor) that provides an intuitive, user-friendly interface for manual editing of multiple sequence alignments with functions for input, editing, and output of sequence alignments. The color-coding of nucleotide identity and the display of associated quality score aids in the manual alignment editing process. DNAAlignEditor works as a client/server tool having two main components: a relational database that collects the processed alignments and a user interface connected to database through universal data access connectivity drivers. DNAAlignEditor can be used either as a stand-alone application or as a network application with multiple users concurrently connected. Conclusion We anticipate that this software will be of general interest to biologists and population genetics in editing DNA sequence alignments and analyzing natural sequence variation regardless of species, and will be particularly useful for manual alignment editing of sequences in species with high levels of polymorphism. PMID:18366684

  5. Free-space optical communication alignment system

    NASA Astrophysics Data System (ADS)

    Mariola, M.; Petruccione, F.

    2016-10-01

    Optical communication systems in free space require a coarse and fine alignment system to align the receiver and transmitter. In general a coarse alignment is not entirely accurate to transmit the laser beacon in the exact direction of the visible field of the camera. During this process, some algorithms such as the raster, spiral and raster spiral scan algorithm can be used to find the spot of the laser beacon. Applications that require to transmit data in form of polarization signals, such as quantum cryptography, requires a polarisation bases alignment system to transmit and receive the photons. In this paper we present a fine alignment system using a polarised laser beacon. The system proposed was subdivided into a coarse and fine alignment system. The coarse alignment was implemented by using the GPS to acquire the geographical position of the transmitter, receiver and a reference point. The fine alignment was achieved by using a polarised laser beacon from the receiver to the transmitter and a camera located on the transmitter side. The algorithm presented was capable of excluding the background noise. Furthermore the polarisation of the laser beacon was used to align the polarisation bases of the transmitter and the receiver.

  6. Some aspects of SR beamline alignment

    NASA Astrophysics Data System (ADS)

    Gaponov, Yu. A.; Cerenius, Y.; Nygaard, J.; Ursby, T.; Larsson, K.

    2011-09-01

    Based on the Synchrotron Radiation (SR) beamline optical element-by-element alignment with analysis of the alignment results an optimized beamline alignment algorithm has been designed and developed. The alignment procedures have been designed and developed for the MAX-lab I911-4 fixed energy beamline. It has been shown that the intermediate information received during the monochromator alignment stage can be used for the correction of both monochromator and mirror without the next stages of alignment of mirror, slits, sample holder, etc. Such an optimization of the beamline alignment procedures decreases the time necessary for the alignment and becomes useful and helpful in the case of any instability of the beamline optical elements, storage ring electron orbit or the wiggler insertion device, which could result in the instability of angular and positional parameters of the SR beam. A general purpose software package for manual, semi-automatic and automatic SR beamline alignment has been designed and developed using the developed algorithm. The TANGO control system is used as the middle-ware between the stand-alone beamline control applications BLTools, BPMonitor and the beamline equipment.

  7. VIRUS spectrograph assembly and alignment procedures

    NASA Astrophysics Data System (ADS)

    Prochaska, Travis; Allen, Richard D.; Boster, Emily; DePoy, D. L.; Herbig, Benjamin; Hill, Gary J.; Lee, Hanshin; Marshall, Jennifer L.; Martin, Emily C.; Meador, William; Rheault, Jean-Philippe; Tuttle, Sarah E.; Vattiat, Brian L.

    2012-09-01

    We describe the mechanical assembly and optical alignment processes used to construct the Visual Integral-Field Replicable Unit Spectrograph (VIRUS) instrument. VIRUS is a set of 150+ optical spectrographs designed to support observations for the Hobby-Eberly Telescope Dark Energy Experiment (HETDEX). To meet the instrument's manufacturing constraints, a production line will be set up to build subassemblies in parallel. To aid in the instrument's assembly and alignment, specialized fixtures and adjustment apparatuses have been developed. We describe the design and operations of the various optics alignment apparatuses, as well as the mirrors' alignment and bonding fixtures.

  8. Optimizing femorotibial alignment in high tibial osteotomy

    PubMed Central

    Rudan, John; Harrison, Mark; Simurda, Michael A

    Objective To study factors that affect femorotibial (F-T) alignment after valgus closing wedge tibial osteotomy. Study design A review of standardized standing radiographs. Femorotibial alignment was measured 1 year postoperatively for over- and under-correction. Changes in F–T alignment and in tibial plateau angle were measured. Setting An urban hospital and orthopedic clinic. Patients Eighty-two patients with osteoarthritis and varus femorotibial alignment underwent valgus closing wedge tibial osteotomy. Patients having a diagnosis of inflammatory arthritis or a prior osteotomy about the knee were excluded. Results A 1° wedge removed from the tibia resulted in an average correction of F–T alignment of 1.2°. A knee that had increased valgus orientation of the distal femur had a greater degree of correction, averaging 1.46° in F–T alignment per degree of tibial wedge. This resulted in excessive postoperative valgus alignment for some patients who had increased valgus tilt of the distal femur. Optimal F–T alignment of 6° to 14° of valgus occurred when the postoperative tibial inclination was 4° to 8° of valgus. Conclusions There was a trend for knees with increased valgus orientation of the distal femur to have greater correction in F–T alignment after tibial osteotomy, likely because of a greater opening up of the medial joint space during stance. Surgeons need to account for this in their preoperative planning. PMID:10526522

  9. Triangular Alignment (TAME). A Tensor-based Approach for Higher-order Network Alignment

    SciTech Connect

    Mohammadi, Shahin; Gleich, David F.; Kolda, Tamara G.; Grama, Ananth

    2015-11-01

    Network alignment is an important tool with extensive applications in comparative interactomics. Traditional approaches aim to simultaneously maximize the number of conserved edges and the underlying similarity of aligned entities. We propose a novel formulation of the network alignment problem that extends topological similarity to higher-order structures and provide a new objective function that maximizes the number of aligned substructures. This objective function corresponds to an integer programming problem, which is NP-hard. Consequently, we approximate this objective function as a surrogate function whose maximization results in a tensor eigenvalue problem. Based on this formulation, we present an algorithm called Triangular AlignMEnt (TAME), which attempts to maximize the number of aligned triangles across networks. We focus on alignment of triangles because of their enrichment in complex networks; however, our formulation and resulting algorithms can be applied to general motifs. Using a case study on the NAPABench dataset, we show that TAME is capable of producing alignments with up to 99% accuracy in terms of aligned nodes. We further evaluate our method by aligning yeast and human interactomes. Our results indicate that TAME outperforms the state-of-art alignment methods both in terms of biological and topological quality of the alignments.

  10. The effects of alignment error and alignment filtering on the sitewise detection of positive selection.

    PubMed

    Jordan, Gregory; Goldman, Nick

    2012-04-01

    When detecting positive selection in proteins, the prevalence of errors resulting from misalignment and the ability of alignment filters to mitigate such errors are not well understood, but filters are commonly applied to try to avoid false positive results. Focusing on the sitewise detection of positive selection across a wide range of divergence levels and indel rates, we performed simulation experiments to quantify the false positives and false negatives introduced by alignment error and the ability of alignment filters to improve performance. We found that some aligners led to many false positives, whereas others resulted in very few. False negatives were a problem for all aligners, increasing with sequence divergence. Of the aligners tested, PRANK's codon-based alignments consistently performed the best and ClustalW performed the worst. Of the filters tested, GUIDANCE performed the best and Gblocks performed the worst. Although some filters showed good ability to reduce the error rates from ClustalW and MAFFT alignments, none were found to substantially improve the performance of PRANK alignments under most conditions. Our results revealed distinct trends in error rates and power levels for aligners and filters within a biologically plausible parameter space. With the best aligner, a low false positive rate was maintained even with extremely divergent indel-prone sequences. Controls using the true alignment and an optimal filtering method suggested that performance improvements could be gained by improving aligners or filters to reduce the prevalence of false negatives, especially at higher divergence levels and indel rates.

  11. High performance triboelectric nanogenerators with aligned carbon nanotubes.

    PubMed

    Wang, Huan; Shi, Mayue; Zhu, Kai; Su, Zongming; Cheng, Xiaoliang; Song, Yu; Chen, Xuexian; Liao, Zhiqiang; Zhang, Min; Zhang, Haixia

    2016-11-03

    As the essential element of a triboelectric nanogenerator (TENG), friction layers play key roles that determine the device performance, which can be enhanced by material selection and surface modification. In this work, we have embedded aligned carbon nanotubes (CNTs) on the polydimethylsiloxane (PDMS) surface as the effective dielectric layer to donate electrons. This layer not only increases the electron generation for the output, but also shows notable stretchability. The length and the properties of the aligned CNTs can be controlled precisely. Using the 40 μm CNT as an example, the fabricated CNT-PDMS TENG shows an output voltage of 150 V and a current density of 60 mA m(-2), which are 250% and 300% enhancement compared to the TENG using directly doped PDMS/multiwall carbon nanotubes, respectively. The maximum power density of this TENG reaches 4.62 W m(-2) at an external load of 30 MΩ. The TENG has demonstrated superior stability during cyclic measurement of over 12 000 cycles. Besides, the aligned CNT-PDMS film shows superhydrophobicity (154°) and good sheet resistance of 280 Ω sq(-1). This stretchable aligned CNT-PDMS film can be universally utilized as a positive triboelectric layer pairing with polymeric materials such as polyethylene terephthalate, polyimide, PDMS and polytetrafluoroethylene for TENGs. This work provides an effective method of structure design for flexible and stretchable nanogenerators.

  12. Effects On Beam Alignment Due To Neutron-Irradiated CCD Images At The National Ignition Facility

    SciTech Connect

    Awwal, A; Manuel, A; Datte, P; Burkhart, S

    2011-02-28

    The 192 laser beams in the National Ignition Facility (NIF) are automatically aligned to the target-chamber center using images obtained through charged coupled device (CCD) cameras. Several of these cameras are in and around the target chamber during an experiment. Current experiments for the National Ignition Campaign are attempting to achieve nuclear fusion. Neutron yields from these high energy fusion shots expose the alignment cameras to neutron radiation. The present work explores modeling and predicting laser alignment performance degradation due to neutron radiation effects, and demonstrates techniques to mitigate performance degradation. Camera performance models have been created based on the measured camera noise from the cumulative single-shot fluence at the camera location. We have found that the effect of the neutron-generated noise for all shots to date have been well within the alignment tolerance of half a pixel, and image processing techniques can be utilized to reduce the effect even further on the beam alignment.

  13. Shear alignment of a disordered lamellar mesophase.

    PubMed

    Kumaran, V; Raman, D S S

    2011-03-01

    The shear alignment of an initially disordered lamellar phase is examined using lattice Boltzmann simulations of a mesoscopic model based on a free-energy functional for the concentration modulation. For a small shear cell of width 8λ, the qualitative features of the alignment process are strongly dependent on the Schmidt number Sc=ν/D (ratio of kinematic viscosity and mass diffusion coefficient). Here, λ is the wavelength of the concentration modulation. At low Schmidt number, it is found that there is a significant initial increase in the viscosity, coinciding with the alignment of layers along the extensional axis, followed by a decrease at long times due to the alignment along the flow direction. At high Schmidt number, alignment takes place due to the breakage and reformation of layers because diffusion is slow compared to shear deformation; this results in faster alignment. The system size has a strong effect on the alignment process; perfect alignment takes place for a small systems of width 8λ and 16λ, while a larger system of width 32λ does not align completely even at long times. In the larger system, there appears to be a dynamical steady state in which the layers are not perfectly aligned--where there is a balance between the annealing of defects due to shear and the creation due to an instability of the aligned lamellar phase under shear. We observe two types of defect creation mechanisms: the buckling instability under dilation, which was reported earlier, as well as a second mechanism due to layer compression.

  14. Alignment of Short Reads: A Crucial Step for Application of Next-Generation Sequencing Data in Precision Medicine

    PubMed Central

    Ye, Hao; Meehan, Joe; Tong, Weida; Hong, Huixiao

    2015-01-01

    Precision medicine or personalized medicine has been proposed as a modernized and promising medical strategy. Genetic variants of patients are the key information for implementation of precision medicine. Next-generation sequencing (NGS) is an emerging technology for deciphering genetic variants. Alignment of raw reads to a reference genome is one of the key steps in NGS data analysis. Many algorithms have been developed for alignment of short read sequences since 2008. Users have to make a decision on which alignment algorithm to use in their studies. Selection of the right alignment algorithm determines not only the alignment algorithm but also the set of suitable parameters to be used by the algorithm. Understanding these algorithms helps in selecting the appropriate alignment algorithm for different applications in precision medicine. Here, we review current available algorithms and their major strategies such as seed-and-extend and q-gram filter. We also discuss the challenges in current alignment algorithms, including alignment in multiple repeated regions, long reads alignment and alignment facilitated with known genetic variants. PMID:26610555

  15. Implementation of two-state alignment system into CXrL aligner (Poster Paper)

    NASA Astrophysics Data System (ADS)

    Chen, Guan-Jye; Bodoh, D.; Wallace, John P.; Anderson, Paul D.; Reilly, Michael T.; Nachman, Ramez; Cerrina, Franco

    1992-07-01

    We describe the implementation of the two-state alignment system into the CXrL aligner, which is developed at our Center for X-ray Lithography. The CXrL aligner is designed to expose sub 0.25 μm feature size integrated circuits. The aligner consists of a three-axes two-state alignment system for alignment error detection and a piezo based precision mechanical stage for alignment error correction. The wafer is held by a precision vacuum chuck, while the mask is held by three vacuum suction cups located around the glass ring. In the prototype, the mask to wafer relative positioning is achieved by 3 motorized stages (for gap setting) and 3 piezo-actuators (for lateral alignment). Since the optical system is designed to be located outside of the synchrotron radiation path, alignment can be performed during exposure. We present the results of the alignment system performance, such as noise equivalent displacement and alignment signal response time. An alignment signal repeatibility of much better than 3σ = 0.07μm is achieved. We also briefly describe the future evaluation of the system, such as overlay measurement of the system using verniers and SEM inspection of some specially designed patterns.

  16. Phylogenetic Inference From Conserved sites Alignments

    SciTech Connect

    grundy, W.N.; Naylor, G.J.P.

    1999-08-15

    Molecular sequences provide a rich source of data for inferring the phylogenetic relationships among species. However, recent work indicates that even an accurate multiple alignment of a large sequence set may yield an incorrect phylogeny and that the quality of the phylogenetic tree improves when the input consists only of the highly conserved, motif regions of the alignment. This work introduces two methods of producing multiple alignments that include only the conserved regions of the initial alignment. The first method retains conserved motifs, whereas the second retains individual conserved sites in the initial alignment. Using parsimony analysis on a mitochondrial data set containing 19 species among which the phylogenetic relationships are widely accepted, both conserved alignment methods produce better phylogenetic trees than the complete alignment. Unlike any of the 19 inference methods used before to analyze this data, both methods produce trees that are completely consistent with the known phylogeny. The motif-based method employs far fewer alignment sites for comparable error rates. For a larger data set containing mitochondrial sequences from 39 species, the site-based method produces a phylogenetic tree that is largely consistent with known phylogenetic relationships and suggests several novel placements.

  17. Nonvisual Cues for Aligning to Cross Streets

    ERIC Educational Resources Information Center

    Scott, Alan C.; Barlow, Janet M.; Guth, David A.; Bentzen, Billie Louise; Cunningham, Christopher M.; Long, Richard

    2011-01-01

    Accurately aligning to a crosswalk is an important component of safe street crossing for pedestrians who are blind. Six alignment cues were evaluated in a simulated crosswalk environment in which the angle of the crosswalk was not always in line with the slope of the ramp. The effectiveness of each cue is reported and implications are discussed.…

  18. Instructional Alignment under No Child Left Behind

    ERIC Educational Resources Information Center

    Polikoff, Morgan S.

    2012-01-01

    The alignment of instruction with the content of standards and assessments is the key mediating variable separating the policy of standards-based reform (SBR) from the outcome of improved student achievement. Few studies have investigated SBR's effects on instructional alignment, and most have serious methodological limitations. This research uses…

  19. Probabilistic sequence alignment of stratigraphic records

    NASA Astrophysics Data System (ADS)

    Lin, Luan; Khider, Deborah; Lisiecki, Lorraine E.; Lawrence, Charles E.

    2014-10-01

    The assessment of age uncertainty in stratigraphically aligned records is a pressing need in paleoceanographic research. The alignment of ocean sediment cores is used to develop mutually consistent age models for climate proxies and is often based on the δ18O of calcite from benthic foraminifera, which records a global ice volume and deep water temperature signal. To date, δ18O alignment has been performed by manual, qualitative comparison or by deterministic algorithms. Here we present a hidden Markov model (HMM) probabilistic algorithm to find 95% confidence bands for δ18O alignment. This model considers the probability of every possible alignment based on its fit to the δ18O data and transition probabilities for sedimentation rate changes obtained from radiocarbon-based estimates for 37 cores. Uncertainty is assessed using a stochastic back trace recursion to sample alignments in exact proportion to their probability. We applied the algorithm to align 35 late Pleistocene records to a global benthic δ18O stack and found that the mean width of 95% confidence intervals varies between 3 and 23 kyr depending on the resolution and noisiness of the record's δ18O signal. Confidence bands within individual cores also vary greatly, ranging from ~0 to >40 kyr. These alignment uncertainty estimates will allow researchers to examine the robustness of their conclusions, including the statistical evaluation of lead-lag relationships between events observed in different cores.

  20. Galaxy Alignments: Observations and Impact on Cosmology

    NASA Astrophysics Data System (ADS)

    Kirk, Donnacha; Brown, Michael L.; Hoekstra, Henk; Joachimi, Benjamin; Kitching, Thomas D.; Mandelbaum, Rachel; Sifón, Cristóbal; Cacciato, Marcello; Choi, Ami; Kiessling, Alina; Leonard, Adrienne; Rassat, Anais; Schäfer, Björn Malte

    2015-11-01

    Galaxy shapes are not randomly oriented, rather they are statistically aligned in a way that can depend on formation environment, history and galaxy type. Studying the alignment of galaxies can therefore deliver important information about the physics of galaxy formation and evolution as well as the growth of structure in the Universe. In this review paper we summarise key measurements of galaxy alignments, divided by galaxy type, scale and environment. We also cover the statistics and formalism necessary to understand the observations in the literature. With the emergence of weak gravitational lensing as a precision probe of cosmology, galaxy alignments have taken on an added importance because they can mimic cosmic shear, the effect of gravitational lensing by large-scale structure on observed galaxy shapes. This makes galaxy alignments, commonly referred to as intrinsic alignments, an important systematic effect in weak lensing studies. We quantify the impact of intrinsic alignments on cosmic shear surveys and finish by reviewing practical mitigation techniques which attempt to remove contamination by intrinsic alignments.