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Sample records for pre-main sequence phase

  1. THE HABITABLE ZONES OF PRE-MAIN-SEQUENCE STARS

    Energy Technology Data Exchange (ETDEWEB)

    Ramirez, Ramses M.; Kaltenegger, Lisa [Institute for Pale Blue Dots, Cornell University, Ithaca, NY (United States)

    2014-12-20

    We calculate the pre-main-sequence habitable zone (HZ) for stars of spectral classes F-M. The spatial distribution of liquid water and its change during the pre-main-sequence phase of protoplanetary systems is important for understanding how planets become habitable. Such worlds are interesting targets for future missions because the coolest stars could provide habitable conditions for up to 2.5 billion years post-accretion. Moreover, for a given star type, planetary systems are more easily resolved because of higher pre-main-sequence stellar luminosities, resulting in larger planet-star separation for cool stars than is the case for the traditional main-sequence (MS) HZ. We use one-dimensional radiative-convective climate and stellar evolutionary models to calculate pre-main-sequence HZ distances for F1-M8 stellar types. We also show that accreting planets that are later located in the traditional MS HZ orbiting stars cooler than a K5 (including the full range of M stars) receive stellar fluxes that exceed the runaway greenhouse threshold, and thus may lose substantial amounts of water initially delivered to them. We predict that M-star planets need to initially accrete more water than Earth did, or, alternatively, have additional water delivered later during the long pre-MS phase to remain habitable. Our findings are also consistent with recent claims that Venus lost its water during accretion.

  2. The Habitable Zones of Pre-Main-Sequence Stars

    CERN Document Server

    Ramirez, Ramses M

    2014-01-01

    We calculate the pre-main-sequence HZ for stars of spectral classes F to M. The spatial distribution of liquid water and its change during the pre-main-sequence phase of protoplanetary systems is important in understanding how planets become habitable. Such worlds are interesting targets for future missions because the coolest stars could provide habitable conditions for up to 2.5 billion years post-accretion. Moreover, for a given star type, planetary systems are more easily resolved because of higher pre-main-sequence stellar luminosities, resulting in larger planet to star separation for cool stars than is the case for the traditional main-sequence (MS) habitable zone (HZ). We use 1D radiative-convective climate and stellar evolutionary models to calculate pre-main-sequence HZ distances for F1 to M8 stellar types. We also show that accreting planets that are later located in the traditional MS HZ orbiting stars cooler than a K5 (including the full range of M-stars) receive stellar fluxes that exceed the ru...

  3. Lithium Depletion in Fully Convective Pre-Main Sequence Stars

    CERN Document Server

    Bildsten, L; Matzner, C D; Ushomirsky, G; Bildsten, Lars; Brown, Edward F.; Matzner, Christopher D.; Ushomirsky, Greg

    1996-01-01

    We present an analytic calculation of the thermonuclear depletion of lithium in contracting, fully convective, pre-main sequence stars of mass M 0.08 M_sun) and for constraining the masses of lithium depleted stars.

  4. Are pre-main-sequence stars older than we thought?

    CERN Document Server

    Naylor, Tim

    2009-01-01

    We fit the colour-magnitude diagrams of stars between the zero-age main-sequence and terminal-age main sequence in young clusters and associations. The ages we derive are a factor 1.5 to 2 longer than the commonly used ages for these regions, which are derived from the positions of pre-main-sequence stars in colour-magnitude diagrams. From an examination of the uncertainties in the main-sequence and pre-main-sequence models, we conclude that the longer age scale is probably the correct one, which implies we must revise upwards the commonly used ages for young clusters and associations. Such a revision would explain the discrepancy between the observational lifetimes of proto-planetary discs and theoretical calculations of the time to form planets. It would also explain the absence of clusters with ages between 5 and 30Myr. We use the $\\tau^2$ statistic to fit the main-sequence data, but find that we must make significant modifications if we are to fit sequences which have vertical segments in the colour-magni...

  5. The Effect of Pre-Main Sequence Stars on Star Cluster Dynamics

    CERN Document Server

    Wiersma, R; Zwart, S P

    2006-01-01

    We investigate the effects of the addition of pre-main sequence evolution to star cluster simulations. We allowed stars to follow pre-main sequence tracks that begin at the deuterium burning birthline and end at the zero age main sequence. We compared our simulations to ones in which the stars began their lives at the zero age main sequence, and also investigated the effects of particular choices for initial binary orbital parameters. We find that the inclusion of the pre-main sequence phase results in a slightly higher core concentration, lower binary fraction, and fewer hard binary systems. In general, the global properties of star clusters remain almost unchanged, but the properties of the binary star population in the cluster can be dramatically modified by the correct treatment of the pre-main sequence stage.

  6. Pre-main-sequence isochrones -- I. The Pleiades benchmark

    CERN Document Server

    Bell, Cameron P M; Mayne, N J; Jeffries, R D; Littlefair, S P

    2012-01-01

    We present a critical assessment of commonly used pre-main-sequence isochrones by comparing their predictions to a set of well-calibrated colour-magnitude diagrams of the Pleiades in the wavelength range 0.4 to 2.5 microns. Our analysis shows that for temperatures less than 4000 K the models systematically overestimate the flux by a factor two at 0.5 microns, though this decreases with wavelength, becoming negligible at 2.2 microns. In optical colours this will result in the ages for stars younger than 10 Myr being underestimated by factors between two and three. We show that using observations of standard stars to transform the data into a standard system can introduce significant errors in the positioning of pre-main-sequences in colour-magnitude diagrams. Therefore we have compared the models to the data in the natural photometric system in which the observations were taken. Thus we have constructed and tested a model of the system responses for the Wide-Field Camera on the Isaac Newton Telescope. As a ben...

  7. Structure and Evolution of Pre-Main Sequence Stars

    CERN Document Server

    Schulz, Norbert S; Bautz, Mark W; Canizares, Claude C; Davis, John; Dewey, Dan; Huenemoerder, David P; Heilmann, Ralf; Houck, John; Marshall, Herman L; Nowak, Mike; Schattenburg, Mark; Audard, Marc; Drake, Jeremy; Gagne, Marc; Kastner, Joel; Kallman, Tim; Lautenegger, Maurice; Lee, Julia; Miller, Jon; Montmerle, Thierry; Mukai, Koji; Osten, Rachel; Parerels, Frits; Pollock, Andy; Preibisch, Thomas; Raymond, John; Reale, Fabio; Smith, Randall; Testa, Paola; Weintraub, David

    2009-01-01

    Low-mass pre-main sequence (PMS) stars are strong and variable X-ray emitters, as has been well established by EINSTEIN and ROSAT observatories. It was originally believed that this emission was of thermal nature and primarily originated from coronal activity (magnetically confined loops, in analogy with Solar activity) on contracting young stars. Broadband spectral analysis showed that the emission was not isothermal and that elemental abundances were non-Solar. The resolving power of the Chandra and XMM X-ray gratings spectrometers have provided the first, tantalizing details concerning the physical conditions such as temperatures, densities, and abundances that characterize the X-ray emitting regions of young star. These existing high resolution spectrometers, however, simply do not have the effective area to measure diagnostic lines for a large number of PMS stars over required to answer global questions such as: how does magnetic activity in PMS stars differ from that of main sequence stars, how do they ...

  8. The coronal evolution of pre-main-sequence stars

    CERN Document Server

    Gregory, Scott G; Davies, Claire L

    2016-01-01

    The bulk of X-ray emission from pre-main-sequence (PMS) stars is coronal in origin. We demonstrate herein that stars on Henyey tracks in the Hertzsprung-Russell diagram have lower $\\log(L_X/L_\\ast)$, on average, than stars on Hayashi tracks. This effect is driven by the decay of $L_X$ once stars develop radiative cores. $L_X$ decays faster with age for intermediate mass PMS stars, the progenitors of main sequence A-type stars, compared to those of lower mass. As almost all main sequence A-type stars show no detectable X-ray emission, we may already be observing the loss of their coronae during their PMS evolution. Although there is no direct link between the size or mass of the radiative core and $L_X$, the longer stars have spent with partially convective interiors, the weaker their X-ray emission becomes. This conference paper is a synopsis of Gregory, Adams and Davies (2016).

  9. Massive pre-main-sequence stars in M17

    Science.gov (United States)

    Ramírez-Tannus, M. C.; Kaper, L.; de Koter, A.; Tramper, F.; Bik, A.; Ellerbroek, L. E.; Ochsendorf, B. B.; Ramírez-Agudelo, O. H.; Sana, H.

    2017-08-01

    The formation process of massive stars is still poorly understood. Massive young stellar objects (mYSOs) are deeply embedded in their parental clouds; these objects are rare, and thus typically distant, and their reddened spectra usually preclude the determination of their photospheric parameters. M17 is one of the best-studied H ii regions in the sky, is relatively nearby, and hosts a young stellar population. We have obtained optical to near-infrared spectra of previously identified candidate mYSOs and a few OB stars in this region with X-shooter on the ESO Very Large Telescope. The large wavelength coverage enables a detailed spectroscopic analysis of the photospheres and circumstellar disks of these candidate mYSOs. We confirm the pre-main-sequence (PMS) nature of six of the stars and characterise the O stars. The PMS stars have radii that are consistent with being contracting towards the main sequence and are surrounded by a remnant accretion disk. The observed infrared excess and the double-peaked emission lines provide an opportunity to measure structured velocity profiles in the disks. We compare the observed properties of this unique sample of young massive stars with evolutionary tracks of massive protostars and propose that these mYSOs near the western edge of the H ii region are on their way to become main-sequence stars ( 6-20 M⊙) after having undergone high mass accretion rates (Ṁacc 10-4-10-3M⊙yr-1). Their spin distribution upon arrival at the zero age main-sequence is consistent with that observed for young B stars, assuming conservation of angular momentum and homologous contraction. Based on observations collected at the European Southern Observatory at Paranal, Chile (ESO programmes 60.A-9404(A), 085.D-0741, 089.C-0874(A), and 091.C-0934(B)).The full normalised X-shooter spectra are available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/604/A78

  10. The potential of space observations for pulsating pre-main sequence stars

    CERN Document Server

    Zwintz, Konstanze

    2016-01-01

    The first asteroseismic studies of pre-main sequence (pre-MS) pulsators have been conducted based on data from the space telescopes MOST and CoRoT with typical time bases of less than 40 days. With these data, a relation between the pulsational properties of pre-MS delta Scuti stars and their relative evolutionary phase on their way from the birthline to the zero-age main sequence was revealed. But it is evident from comparison with the more evolved pulsators in their main sequence or post-main sequence stages observed by the main Kepler mission, that many more questions could be addressed with significantly longer time bases and ultra-high precision. Here, I will discuss the observational status of pre-MS asteroseismology and the potential of future space observations for this research field.

  11. ACCRETION RATES ON PRE-MAIN-SEQUENCE STARS IN THE YOUNG OPEN CLUSTER NGC 6530

    Energy Technology Data Exchange (ETDEWEB)

    Gallardo, Jose; Del Valle, Luciano; Ruiz, Maria Teresa, E-mail: gallardo@das.uchile.cl, E-mail: ldelvall@das.uchile.cl, E-mail: mtruiz@das.uchile.cl [Departamento de Astronomia, Universidad de Chile, Casilla 36-D, Santiago (Chile)

    2012-01-15

    It is well accepted that during the star formation process, material from a protoplanetary disk is accreted onto the central object during the first {approx}1-5 Myr. Different authors have published measurements of accretion rates for young low- and intermediate-mass stars in several nearby star-forming regions (SFRs). Due to its somewhat larger distance, the SFR M8 (the Lagoon Nebula) has not been studied to the same extent, despite its abundant population of young stellar objects. We have obtained optical band low-resolution spectra of a sample of pre-main-sequence stars in the open cluster NGC 6530 located in the aforementioned nebulae using the Gemini Multi Object Spectrograph at Gemini-South in multi-object mode. Spectra cover the H{sub {alpha}} emission line used to measure the accretion rate, following the method presented by Natta et al. The observed spectral characteristics are fully consistent with pre-main-sequence stars, showing lithium absorption lines, which are very common in young stellar objects, as well as prominent and broad H{sub {alpha}} emission lines, indicating a T Tauri evolutionary stage. This work presents the first determinations of mass accretion rates of young stellar objects in the open cluster NGC 6530, confirming that they are classical T Tauri stars going through the accretion phase. These observations contribute to a better understanding of the stellar content and evolutionary phase of the very active Lagoon Nebula SFR.

  12. Pulsation of Pre-Main Sequence Stars in Young Open Clusters

    Science.gov (United States)

    Zwintz, Konstanze; Weiss, Werner W.

    2001-08-01

    The aim of this proposal is to determine observationally the parameter space of the pre-main sequence instability strip. For that purpose we intend to obtain photometric timeseries with high time resolution and low noise level of the stars in young open clusters (IC 4996, NGC 6910 and NGC 6383) and to identify pre-main sequence pulsators. Several cluster members have the spectral types of interest (A-F) and lie between the birthline and the zero-age main sequence. Up to now the number of pre-main sequence pulsators is absolutely inadequate to determine reliably the hot and cool border of the according instability region. Its definition is indispensable for a better understanding of the internal structure and evolution of such stars.

  13. Theoretical seismic properties of pre-main sequence gamma Doradus pulsators

    CERN Document Server

    Bouabid, M -P; Miglio, A; Dupret, M -A; Grigahcene, A; Noels, A

    2011-01-01

    Context. gamma Doradus (gamma Dor) are late A and F-type stars pulsating with high order gravity modes (g-modes). The existence of different evolutionary phases crossing the gamma Dor instability strip raises the question of the existence of pre-main sequence (PMS) gamma Dor stars. Aims. We intend to study the differences between the asteroseismic behaviour of PMS and main sequence (MS) gamma Dor pulsators as it is predicted by the current theory of stellar evolution and stability. Methods. We explore the adiabatic and non-adiabatic properties of high order g-modes in a grid of PMS and MS models covering the mass range 1.2 Msun < Mstar < 2.5 Msun. Results. We derive the theoretical instability strip (IS) for the PMS gamma Dor pulsators. This IS covers the same effective temperature range as the MS gamma Dor one. Nevertheless, the frequency domain of unstable modes in PMS models with a fully radiative core is larger than in MS models, even if they present the same number of unstable modes. Moreover, the ...

  14. The Recurrent Eclipse of an Unusual Pre--Main-Sequence Star in IC 348

    CERN Document Server

    Nordhagen, S; Williams, E C; Semkov, E

    2006-01-01

    The recurrence of a previously documented eclipse of a solar-like pre--main-sequence star in the young cluster IC 348 has been observed. The recurrence interval is 4.7 $\\pm 0.1$ yr and portions of 4 cycles have now been seen. The duration of each eclipse is at least 3.5 years, or $\\sim 75$% of a cycle, verifying that this is not an eclipse by a stellar companion. The light curve is generally symmetric and approximately flat-bottomed. Brightness at maximum and minimum have been rather stable over the years but the light curve is not perfectly repetitive or smooth and small variations exist at all phases. We confirm that the star is redder when fainter. Models are discussed and it is proposed that this could be a system similar to KH 15D in NGC 2264. Specifically, it may be an eccentric binary in which a portion of the orbit of one member is currently occulted during some binary phases by a circumbinary disk. The star deserves sustained observational attention for what it may reveal about the circumstellar envi...

  15. EXPORT optical photometry and polarimetry of Vega-type and pre-main sequence stars

    CERN Document Server

    Oudmaijer, R D; Eiroa, C

    2001-01-01

    This paper presents optical UBVRI broadband photo-polarimetry of the EXPORT sample obtained at the 2.5m Nordic Optical Telescope. The database consists of multi-epoch photo-polarimetry of 68 pre-main-sequence and main-sequence stars. An investigation of the polarization variability indicates that 22 objects are variable at the 3sigma level in our data. All these objects are pre-main sequence stars, consisting of both T Tauri and Herbig Ae/Be objects while the main sequence, Vega type and post-T Tauri type objects are not variable. The polarization properties of the variable sources are mostly indicative of the UXOR-type behaviour; the objects show highest polarization when the brightness is at minimum. We add seven new objects to the class of UXOR variables (BH Cep, VX Cas, DK Tau, HK Ori, LkHa 234, KK Oph and RY Ori). The main reason for their discovery is the fact that our data-set is the largest in its kind, indicating that many more young UXOR-type pre-main sequence stars remain to be discovered. The set ...

  16. Low-mass pre--main-sequence stars in the Magellanic Clouds

    CERN Document Server

    Gouliermis, Dimitrios

    2012-01-01

    [Abridged] The stellar Initial Mass Function (IMF) suggests that sub-solar stars form in very large numbers. Most attractive places for catching low-mass star formation in the act are young stellar clusters and associations, still (half-)embedded in star-forming regions. The low-mass stars in such regions are still in their pre--main-sequence (PMS) evolutionary phase. The peculiar nature of these objects and the contamination of their samples by the evolved populations of the Galactic disk impose demanding observational techniques for the detection of complete numbers of PMS stars in the Milky Way. The Magellanic Clouds, the companion galaxies to our own, demonstrate an exceptional star formation activity. The low extinction and stellar field contamination in star-forming regions of these galaxies imply a more efficient detection of low-mass PMS stars than in the Milky Way, but their distance from us make the application of special detection techniques unfeasible. Nonetheless, imaging with the Hubble Space Te...

  17. A probable pre-main sequence chemically peculiar star in the open cluster Stock 16

    CERN Document Server

    Netopil, M; Paunzen, E; Zwintz, K; Pintado, O I; Bagnulo, S

    2014-01-01

    We used the Ultraviolet and Visual Echelle Spectrograph of the ESO-Very Large Telescope to obtain a high resolution and high signal-to-noise ratio spectrum of Stock 16-12, an early-type star which previous Delta-a photometric observations suggest being a chemically peculiar (CP) star. We used spectral synthesis to perform a detailed abundance analysis obtaining an effective temperature of 8400 +/- 400 K, a surface gravity of 4.1 +/- 0.4, a microturbulence velocity of 3.4 +0.7/-0.3 km/s, and a projected rotational velocity of 68 +/- 4 km/s. We provide photometric and spectroscopic evidence showing the star is most likely a member of the young Stock 16 open cluster (age 3-8 Myr). The probable cluster membership, the star's position in the Hertzsprung-Russell diagram, and the found infrared excess strongly suggest the star is still in the pre-main-sequence (PMS) phase. We used PMS evolutionary tracks to determine the stellar mass, which ranges between 1.95 and 2.3 Msun, depending upon the adopted spectroscopic o...

  18. Pre main sequence stars as UV sources for the World Space Observatory-UV mission

    Science.gov (United States)

    Gomez de Castro, Ana I.; Lamzin, Sergei A.

    2011-09-01

    Pre-main sequence stars are bright UV (UV) sources compared with their main sequence analogues. The source of this excess is the high energy processes associated with the physics of accretion/outflow during early stellar evolution. In this review, the main sources of UV excess are described as well as the most significant "unknowns" in the field. Special emphasis is made on the results from the last observations carried out with the Hubble Space Telescope and on the relevance of future dedicated monitoring programs with the World Space Observatory-UV.

  19. Differential rotation on both components of the pre main-sequence binary system HD 155555

    OpenAIRE

    Dunstone, N. J.; Hussain, G A J; Cameron, A. Collier; Marsden, S. C.; Jardine, M.; Barnes, J. R.; Vlex, J. C. Ramirez; Donati, J.-F.

    2008-01-01

    We present the first measurements of surface differential rotation on a pre-main sequence binary system. Using intensity (Stokes I) and circularly polarised (Stokes V) timeseries spectra, taken over eleven nights at the Anglo-Australian Telescope (AAT), we incorporate a solar-like differential rotation law into the surface imaging process. We find that both components of the young, 18 Myr, HD 155555 (V824 Ara, G5IV + K0IV) binary system show significant differential rotation. The equator-pole...

  20. Active phenomena in the pre-main sequence Herbig Ae star HD 163296

    Science.gov (United States)

    Catala, C.; Praderie, F.; Simon, T.; Talavera, A.; The, P. S.

    1989-01-01

    Observations by IUE of the short-term variability of the Mg II and Ca II resonance lines in the Herbig Ae star HD 163296 are presented. Evidence that these lines show a phenomenon of rotational modulation, similar to the one observed in AB Aur, another Herbig Ae star is found. The variations in the spectrum of HD 163296 are even more conspicuous than in the spectrum of AB Aur. Magnetically structured winds may thus be a widespread phenomenon among the pre-main sequence Herbig Ae/Be stars.

  1. Pre-main sequence variable stars in young open cluster NGC 1893

    OpenAIRE

    Lata, Sneh; Pandey, A.K.(Indian Institute of Technology Bombay (IIT), Mumbai, India); Chen, W. P.; Maheswar, G.; Chauhan, Neelam

    2012-01-01

    We present results of multi-epoch (fourteen nights during 2007-2010) $V$-band photometry of the cluster NGC 1893 region to identify photometric variable stars in the cluster. The study identified a total of 53 stars showing photometric variability. The members associated with the region are identified on the basis of spectral energy distribution, $J-H/H-K$ two colour diagram and $V/V-I$ colour-magnitude diagram. The ages and masses of the majority of pre-main-sequence sources are found to be ...

  2. Kinematic Distances of Pre-main Sequence Stars in the Lupus Star-Forming Region

    Science.gov (United States)

    Galli, P. A. B.; Teixeira, R.; Ducourant, C.; Bertout, C.

    2014-06-01

    The problem of the determination of distances has always played a central role in astronomy. However, little recent progress has been made in the distance determination of faint young stellar objects such as pre-main sequence (PMS) stars. Many of the PMS stars were neither observed by the Hipparcos satellite due to their magnitude nor have any trigonometric parallax measured from the ground due to their distance. Here we investigate the kinematic properties of the Lupus moving group with the primary objective of deriving individual parallaxes for each group member of this star-forming region.

  3. The first magnetic maps of a pre-main sequence binary star system - HD 155555

    OpenAIRE

    Dunstone, N. J.; Hussain, G. A. J.; Cameron, A. Collier; Marsden, S. C.; Jardine, M.; Stempels, H. C.; Vlex, J. C. Ramirez; Donati, J. -F.

    2008-01-01

    We present the first maps of the surface magnetic fields of a pre-main sequence binary system. Spectropolarimetric observations of the young, 18 Myr, HD 155555 (V824 Ara, G5IV + K0IV) system were obtained at the Anglo-Australian Telescope in 2004 and 2007. Both datasets are analysed using a new binary Zeeman Doppler imaging (ZDI) code. This allows us to simultaneously model the contribution of each component to the observed circularly polarised spectra. Stellar brightness maps are also produc...

  4. Differential rotation on both components of the pre main-sequence binary system HD 155555

    OpenAIRE

    Dunstone, N. J.; Hussain, G. A. J.; Cameron, A. Collier; Marsden, S. C.; Jardine, M.; Barnes, J.R.; Vlex, J. C. Ramirez; Donati, J. -F.

    2008-01-01

    We present the first measurements of surface differential rotation on a pre-main sequence binary system. Using intensity (Stokes I) and circularly polarised (Stokes V) timeseries spectra, taken over eleven nights at the Anglo-Australian Telescope (AAT), we incorporate a solar-like differential rotation law into the surface imaging process. We find that both components of the young, 18 Myr, HD 155555 (V824 Ara, G5IV + K0IV) binary system show significant differential rotation. The equator-pole...

  5. Evidence of accretion triggered oscillations in the pre-main-sequence interacting binary AK Sco

    CERN Document Server

    de Castro, Ana I Gomez; Talavera, Antonio

    2012-01-01

    Pre-main sequence (PMS) binaries are surrounded by circumbinary disks from which matter falls onto both components. The material dragged from the circumbinary disk flows onto each star through independent streams channelled by the variable gravitational field. The action of the bar-like potential is most prominent in high eccentricity systems made of two equal mass stars. AK Sco is a unique PMS system composed of two F5 stars in an orbit with e=0.47. Henceforth, it is an ideal laboratory to study matter infall in binaries and its role in orbit circularization. In this letter, we report the detection of a 1.3mHz ultra low frequency oscillation in the ultraviolet light curve at periastron passage. This oscillation last 7 ks being most likely fed by the gravitational energy released when the streams tails spiralling onto each star get in contact at periastron passage enhancing the accretion flow; this unveils a new mechanism for angular momentum loss during pre-main sequence evolution and a new type of interacti...

  6. An Unusual Eclipse of a Pre-Main Sequence Star in IC 348

    CERN Document Server

    Cohen, R E; Williams, E C

    2003-01-01

    A solar-like pre-main sequence star (TJ 108 = H 187 = LRLL 35 = HMW 15) in the extremely young cluster IC 348 has been found, which apparently experienced an eclipse lasting ~3.5 years, much longer than has ever been detected for any normal eclipsing binary. The light curve is flat-bottomed and rather symmetric, with a depth of 0.66 mag in Cousins I. During eclipse, the system reddened by \\~0.17 mag in R-I. We argue that the eclipsing body is not a star because of the small probability of detecting an eclipse in what would be a very widely separated binary. Instead, it appears that the eclipse was caused by a circumstellar or circumbinary cloud or disk feature which occulted the star, or one of its components, if it is a binary system. We emphasize the importance of more detailed study of this object, which appears to be a new member of a small class of pre-main sequence stars whose variability can be firmly linked to occultation by circumstellar (or circumbinary) matter.

  7. Pre-main sequence stars in the stellar association N11 in the Large Magellanic Cloud

    CERN Document Server

    Vallenari, Antonella; Sordo, Rosanna

    2009-01-01

    Magellanic Clouds are of extreme importance to the study of the star formation process in low metallicity environments. In this paper we report on the discovery of pre-main sequence candidates and young embedded stellar objects in N11 located in the Large Magellanic Cloud to cast light on the star formation scenario. We would like to remind that this comparison is complicated by the presence of a large age dispersion detected in the fields. Deep archive HST/ACS photometry is used to derive color-magnitude diagrams of the associations in N~11 and of the foreground field population. These data are complemented by archive IR Spitzer data which allow the detection of young embedded stellar objects. The spatial distribution of the pre-main sequence candidates and young embedded stellar objects is compared with literature data observed at different wavelengths, such as H$_{\\alpha}$ and CO maps, and with the distribution of OB and Herbig Ae/Be stars. The degree of clustering is derived using the Minimal Spanning Tre...

  8. Gaia-ESO Survey: The analysis of pre-main sequence stellar spectra

    CERN Document Server

    Lanzafame, A C; Damiani, F; Franciosini, E; Cottaar, M; Sousa, S G; Tabernero, H M; Klutsch, A; Spina, L; Biazzo, K; Prisinzano, L; Sacco, G G; Randich, S; Brugaletta, E; Mena, E Delgado; Adibekyan, V; Montes, D; Bonito, R; Gameiro, J F; Alcalá, J M; Hernández, J I González; Jeffries, R; Messina, S; Meyer, M; Gilmore, G; Asplund, M; Binney, J; Bonifacio, P; Drew, J E; Feltzing, S; Ferguson, A M N; Micela, G; Negueruela, I; Prusti, T; Rix, H-W; Vallenari, A; Alfaro, E J; Prieto, C Allende; Babusiaux, C; Bensby, T; Blomme, R; Bragaglia, A; Flaccomio, E; Francois, P; Hambly, N; Irwin, M; Koposov, S E; Korn, A J; Smiljanic, R; Van Eck, S; Walton, N; Bayo, A; Bergemann, M; Carraro, G; Costado, M T; Edvardsson, B; Heiter, U; Hill, V; Hourihane, A; Jackson, R J; Jofré, P; Lardo, C; Lewis, J; Lind, K; Magrini, L; Marconi, G; Martayan, C; Masseron, T; Monaco, L; Morbidelli, L; Sbordone, L; Worley, C C; Zaggia, S

    2015-01-01

    This paper describes the analysis of UVES and GIRAFFE spectra acquired by the Gaia-ESO Public Spectroscopic Survey in the fields of young clusters whose population includes pre-main sequence (PMS) stars. Both methods that have been extensively used in the past and new ones developed in the contest of the Gaia-ESO survey enterprise are available and used. The internal precision of these quantities is estimated by inter-comparing the results obtained by such different methods, while the accuracy is estimated by comparison with independent external data, like effective temperature and surface gravity derived from angular diameter measurements, on a sample of benchmarks stars. Specific strategies are implemented to deal with fast rotation, accretion signatures, chromospheric activity, and veiling. The analysis carried out on spectra acquired in young clusters' fields during the first 18 months of observations, up to June 2013, is presented in preparation of the first release of advanced data products. Stellar par...

  9. Theoretical study of $\\gamma$ Doradus pulsations in pre-main sequence stars

    CERN Document Server

    Bouabid, M -P; Miglio, A; Dupret, M -A; Grigahcène, A; Noels, A

    2010-01-01

    The question of the existence of pre-main sequence (PMS) $\\gamma$~Doradus ($\\gamma$~Dor) has been raised by the observations of young clusters such as NGC~884 hosting $\\gamma$~Dor members. We have explored the properties of $\\gamma$~Dor type pulsations in a grid of PMS models covering the mass range $1.2 M_\\odot < M_* < 2.5 M_\\odot$ and we derive the theoretical instability strip (IS) for the PMS $\\gamma$~Dor pulsators. We explore the possibility of distinguishing between PMS and MS $\\gamma$~Dor by the behaviour of the period spacing of their high order $gravity$-modes ($g$-modes).

  10. KH 15D: Gradual Occultation of a Pre-Main-Sequence Binary

    CERN Document Server

    Winn, J N; Johnson, J A; Stanek, K Z; Garnavich, P M; Winn, Joshua N.; Holman, Matthew J.; Johnson, John A.; Stanek, Krzysztof Z.; Garnavich, Peter M.

    2004-01-01

    We propose that the extraordinary "winking star" KH 15D is an eccentric pre-main-sequence binary that is gradually being occulted by an opaque screen. This model accounts for the periodicity, depth, duration, and rate of growth of the modern eclipses; the historical light curve from photographic plates; and the existing radial velocity measurements. It also explains the re-brightening events that were previously observed during mid-eclipse, and the subsequent disappearance of these events. We predict the future evolution of the system and its full radial velocity curve. Given the small velocity of the occulting screen relative to the center of mass of the binary, the screen is probably associated with the binary, and may be the edge of a precessing circumbinary disk.

  11. New radio detections of early-type pre-main-sequence stars

    Science.gov (United States)

    Skinner, Stephen L.; Brown, Alexander; Linsky, Jeffrey L.

    1990-01-01

    Results of VLA radio continuum observations of 13 early-type pre-main-sequence stars selected from the 1984 catalog of Finkenzeller and Mundt are presented. The stars HD 259431 and MWC 1080 were detected at 3.6 cm, while HD 200775 and TY CrA were detected at both 3.6 and 6 cm. The flux density of HD 200775 has a frequency dependence consistent with the behavior expected for free-free emission originating in a fully ionized wind. However, an observation in A configuration suggests that the source geometry may not be spherically symmetric. In contrast, the spectral index of TY CrA is negative with a flux behavior implying nonthermal emission. The physical mechanism responsible for the nonthermal emission has not yet been identified, although gyrosynchrotron and synchrotron processes cannot be ruled out.

  12. The magnetic field of the pre-main sequence Herbig Ae star HD 190073

    Science.gov (United States)

    Catala, C.; Alecian, E.; Donati, J.-F.; Wade, G. A.; Landstreet, J. D.; Böhm, T.; Bouret, J.-C.; Bagnulo, S.; Folsom, C.; Silvester, J.

    2007-01-01

    Context: The general context of this paper is the study of magnetic fields in the pre-main sequence intermediate mass Herbig Ae/Be stars. Magnetic fields are likely to play an important role in pre-main sequence evolution at these masses, in particular in controlling the gains and losses of stellar angular momentum. Aims: The particular aim of this paper is to announce the detection of a structured magnetic field in the Herbig Ae star HD 190073, and to discuss various scenarii for the geometry of the star, its environment and its magnetic field. Methods: We have used the ESPaDOnS spectropolarimeter at CFHT in 2005 and 2006 to obtain high-resolution, high signal-to-noise circular polarization spectra which demonstrate unambiguously the presence of a magnetic field in the photosphere of this star. Results: Nine circular polarization spectra were obtained, each one showing a clear Zeeman signature. This signature is suggestive of a magnetic field structured on large scales. The signature, which corresponds to a longitudinal magnetic field of 74± 10 G, does not vary detectably on a one-year timeframe, indicating either an azimuthally symmetric field, a zero inclination angle between the rotation axis and the line of sight, or a very long rotation period. The optical spectrum of HD 190073 exhibits a large number of emission lines. We discuss the formation of these emission lines in the framework of a model involving a turbulent heated region at the base of the stellar wind, possibly powered by magnetic accretion. Conclusions: .This magnetic detection contributes an important new observational discovery which will aid our understanding of stellar magnetism at intermediate masses. Based on observations obtained at the Canada-France-Hawaii Telescope (CFHT) which is operated by the National Research Council of Canada, the Institut National des Sciences de l'Univers of the Centre National de la Recherche Scientifique of France, and the University of Hawaii.

  13. Pre-main-sequence isochrones -- II. Revising star and planet formation timescales

    CERN Document Server

    Bell, Cameron P M; Mayne, N J; Jeffries, R D; Littlefair, S P

    2013-01-01

    We have derived ages for 13 young (<30 Myr) star-forming regions and find they are up to a factor two older than the ages typically adopted in the literature. This result has wide-ranging implications, including that circumstellar discs survive longer (~10-12 Myr) and that the average Class I lifetime is greater (~1 Myr) than currently believed. For each star-forming region we derived two ages from colour-magnitude diagrams. First we fitted models of the evolution between the zero-age main-sequence and terminal-age main-sequence to derive a homogeneous set of main-sequence ages, distances and reddenings with statistically meaningful uncertainties. Our second age for each star-forming region was derived by fitting pre-main-sequence stars to new semi-empirical model isochrones. For the first time (for a set of clusters younger than 50 Myr) we find broad agreement between these two ages, and since these are derived from two distinct mass regimes that rely on different aspects of stellar physics, it gives us c...

  14. Differential rotation on both components of the pre main-sequence binary system HD 155555

    CERN Document Server

    Dunstone, N J; Cameron, A Collier; Marsden, S C; Jardine, M; Barnes, J R; Vlex, J C Ramirez; Donati, J -F

    2008-01-01

    We present the first measurements of surface differential rotation on a pre-main sequence binary system. Using intensity (Stokes I) and circularly polarised (Stokes V) timeseries spectra, taken over eleven nights at the Anglo-Australian Telescope (AAT), we incorporate a solar-like differential rotation law into the surface imaging process. We find that both components of the young, 18 Myr, HD 155555 (V824 Ara, G5IV + K0IV) binary system show significant differential rotation. The equator-pole laptimes as determined from the intensity spectra are 80 days for the primary star and 163 days for the secondary. Similarly for the magnetic spectra we obtain equator-pole laptimes of 44 and 71 days respectively, showing that the shearing timescale of magnetic regions is approximately half that found for stellar spots. Both components are therefore found to have rates of differential rotation similar to those of the same spectral type main sequence single stars. The results for HD 155555 are therefore in contrast to tho...

  15. Pre-main-sequence isochrones -- III. The Cluster Collaboration isochrone server

    CERN Document Server

    Bell, Cameron P M; Naylor, Tim; Mayne, N J; Jeffries, R D; Mamajek, Eric E; Rowe, John

    2014-01-01

    We present an isochrone server for semi-empirical pre-main-sequence model isochrones in the following systems: Johnson-Cousins, Sloan Digital Sky Survey, Two-Micron All-Sky Survey, Isaac Newton Telescope (INT) Wide-Field Camera, and INT Photometric H$\\alpha$ Survey (IPHAS)/UV-Excess Survey (UVEX). The server can be accessed via the Cluster Collaboration webpage {http://www.astro.ex.ac.uk/people/timn/isochrones/}. To achieve this we have used the observed colours of member stars in young clusters with well-established age, distance and reddening to create fiducial loci in the colour-magnitude diagram. These empirical sequences have been used to quantify the discrepancy between the models and data arising from uncertainties in both the interior and atmospheric models, resulting in tables of semi-empirical bolometric corrections (BCs) in the various photometric systems. The model isochrones made available through the server are based on existing stellar interior models coupled with our newly derived semi-empiric...

  16. Pulsating pre-main sequence stars in IC 4996 and NGC 6530

    CERN Document Server

    Zwintz, K; Zwintz, Konstanze; Weiss, Werner W.

    2006-01-01

    Asteroseismology of pulsating pre-main sequence (PMS) stars has the potential of testing the validity of current models of PMS structure and evolution. As a first step, a sufficiently large sample of pulsating PMS stars has to be established, which allows to select candidates optimally suited for a detailed asteroseismological analysis based on photometry from space or ground based network data. A search for pulsating PMS members in the young open clusters IC 4996 and NGC 6530 has been performed to improve the sample of known PMS pulsators. As both clusters are younger than 10 million years, all members with spectral types later than A0 have not reached the zero-age main sequence yet. Hence, IC 4996 and NGC 6530 are most suitable to search for PMS pulsation among their A- and F-type cluster stars. CCD time series photometry in Johnson B and V filters has been obtained for IC 4996 and NGC 6530. The resulting light curves for 113 stars in IC 4996 and 194 stars in NGC 6530 have been subject to detailed frequency...

  17. Magnetic Activity of Pre-main Sequence Stars near the Stellar-Substellar Boundary

    CERN Document Server

    Principe, David A; Rodriguez, David

    2015-01-01

    X-ray observations of pre-main sequence (pre-MS) stars of M-type probe coronal emission and offer a means to investigate magnetic activity at the stellar-substellar boundary. Recent observations of main sequence (MS) stars at this boundary display a decrease in fractional X-ray luminosity ($L_{X}$/$L_{bol}$) by almost two orders of magnitude for spectral types M7 and later. We investigate magnetic activity and search for a decrease in X-ray emission in the pre-MS progenitors of these MS stars. We present XMM-Newton X-ray observations and preliminary results for ~10 nearby (30-70 pc), very low mass pre-MS stars in the relatively unexplored age range of 10-30 Myr. We compare the fractional X-ray luminosities of these 10-30 Myr old stars to younger (1-3 Myr) pre-MS brown dwarfs and find no dependence on spectral type or age suggesting that X-ray activity declines at an age later than ~30 Myr in these very low-mass stars.

  18. Magnetic Activity of Pre-main Sequence Stars near the Stellar-Substellar Boundary

    Science.gov (United States)

    Principe, David; Kastner, Joel. H.; Rodriguez, David

    2016-01-01

    X-ray observations of pre-main sequence (pre-MS) stars of M-type probe coronal emission and offer a means to investigate magnetic activity at the stellar-substellar boundary. Recent observations of main sequence (MS) stars at this boundary display a decrease in fractional X-ray luminosity (L X /L bol ) by almost two orders of magnitude for spectral types M7 and later. We investigate magnetic activity and search for a decrease in X-ray emission in the pre-MS progenitors of these MS stars. We present XMM-Newton X-ray observations and preliminary results for ~10 nearby (30-70 pc), very low mass pre-MS stars in the relatively unexplored age range of 10-30 Myr. We compare the fractional X-ray luminosities of these 10-30 Myr old stars to younger (1-3 Myr) pre-MS brown dwarfs and find no dependence on spectral type or age suggesting that X-ray activity declines at an age later than ~30 Myr in these very low-mass stars.

  19. The effect of starspots on the radii of low-mass pre-main sequence stars

    CERN Document Server

    Jackson, R J

    2014-01-01

    A polytropic model is used to investigate the effects of dark photospheric spots on the evolution and radii of magnetically active, low-mass (M<0.5Msun), pre-main sequence (PMS) stars. Spots slow the contraction along Hayashi tracks and inflate the radii of PMS stars by a factor of (1-beta)^{-N} compared to unspotted stars of the same luminosity, where beta is the equivalent covering fraction of dark starspots and N \\simeq 0.45+/-0.05. This is a much stronger inflation than predicted by the models of Spruit & Weiss (1986) for main sequence stars with the same beta, where N \\sim 0.2 to 0.3. These models have been compared to radii determined for very magnetically active K- and M-dwarfs in the young Pleiades and NGC 2516 clusters, and the radii of tidally-locked, low-mass eclipsing binary components. The binary components and ZAMS K-dwarfs have radii inflated by \\sim 10 per cent compared to an empirical radius-luminosity relation that is defined by magnetically inactive field dwarfs with interferometrica...

  20. Pre-main-sequence binaries with tidally disrupted discs: the Br gamma in HD 104237

    CERN Document Server

    Garcia, P J V; Dougados, C; Bacciotti, F; Clausse, J -M; Massi, F; Mérand, A; Petrov, R; Weigelt, G

    2013-01-01

    Active pre-main-sequence binaries with separations of around ten stellar radii present a wealth of phenomena unobserved in common systems. The study of these objects is extended from Classical T Tauri stars to the Herbig Ae star HD 104237. Spectro-interferometry with the VLTI/AMBER is presented. It is found that the K-band continuum squared visibilities are compatible with a circumbinary disc with a radius of ~0.5 AU. However, a significant fraction (~50 per cent) of the flux is unresolved and not fully accounted by the stellar photospheres. The stars probably don't hold circumstellar discs, in addition to the circumbinary disk, due to the combined effects of inner magnetospheric truncation and outer tidal truncation. This unresolved flux likely arises in compact structures inside the tidally disrupted circumbinary disc. Most ($\\gtrsim 90$ per cent) of the Br gamma line emission is unresolved. The line-to-continuum spectro-astrometry shifts in time, along the direction of the Ly alpha jet known to be driven b...

  1. The first magnetic maps of a pre-main sequence binary star system - HD 155555

    CERN Document Server

    Dunstone, N J; Cameron, A Collier; Marsden, S C; Jardine, M; Stempels, H C; Vlex, J C Ramirez; Donati, J -F

    2008-01-01

    We present the first maps of the surface magnetic fields of a pre-main sequence binary system. Spectropolarimetric observations of the young, 18 Myr, HD 155555 (V824 Ara, G5IV + K0IV) system were obtained at the Anglo-Australian Telescope in 2004 and 2007. Both datasets are analysed using a new binary Zeeman Doppler imaging (ZDI) code. This allows us to simultaneously model the contribution of each component to the observed circularly polarised spectra. Stellar brightness maps are also produced for HD 155555 and compared to previous Doppler images. Our radial magnetic maps reveal a complex surface magnetic topology with mixed polarities at all latitudes. We find rings of azimuthal field on both stars, most of which are found to be non-axisymmetric with the stellar rotational axis. We also examine the field strength and the relative fraction of magnetic energy stored in the radial and azimuthal field components at both epochs. A marked weakening of the field strength of the secondary star is observed between t...

  2. Exploring pre-main sequence variables of ONC: The new variables

    CERN Document Server

    Parihar, Padmakar; Distefano, Elisa; Shantikumar N S; Medhi, Biman J

    2009-01-01

    Since 2004, we have been engaged in a long-term observing program to monitor young stellar objects in the Orion Nebula Cluster. We have collected about two thousands frames in V, R, and I broad-band filters on more than two hundred nights distributed over five consecutive observing seasons. The high-quality and time-extended photometric data give us an opportunity to address various phenomena associated with young stars. The prime motivations of this project are i) to explore various manifestations of stellar magnetic activity in very young low-mass stars; ii) to search for new pre-main sequence eclipsing binaries; and iii) to look for any EXor and FUor like transient activities associated with YSOs. Since this is the first paper on this program, we give a detailed description of the science drivers, the observation and the data reduction strategies as well. In addition to these, we also present a large number of new periodic variables detected from our first five years of time-series photometric data. Our st...

  3. V4046 Sgr: Touchstone to Investigate Spectral Type Discrepancies for Pre-main Sequence Stars

    CERN Document Server

    Kastner, Joel H; Sargent, Benjamin; Smith, C T; Rayner, John

    2014-01-01

    Determinations of the fundamental properties (e.g., masses and ages) of late-type, pre-main sequence (pre-MS) stars are complicated by the potential for significant discrepancies between the spectral types of such stars as ascertained via optical vs. near-infrared observations. To address this problem, we have obtained near-IR spectroscopy of the nearby, close binary T Tauri system V4046 Sgr AB with the NASA Infrared Telescope Facility (IRTF) SPEX spectrometer. The V4046 Sgr close binary (and circumbinary disk) system provides an important test case for spectral type determination thanks to the stringent observational constraints on its component stellar masses (i.e., ~0.9 Msun each) as well as on its age (12-21 Myr) and distance (73 pc). Analysis of the IRTF data indicates that the composite near-IR spectral type for V4046 Sgr AB lies in the range M0-M1, i.e., significantly later than the K5+K7 composite type previously determined from optical spectroscopy. However, the K5+K7 composite type is in better agre...

  4. Hunting for millimeter flares from magnetic reconnection in pre-main sequence spectroscopic binaries

    CERN Document Server

    Kóspál, Á; Hogerheijde, M R; Moór, A; Blake, G A

    2010-01-01

    Recent observations of the low-mass pre-main sequence, eccentric spectroscopic binaries DQ Tau and V773 Tau A reveal that their millimeter spectrum is occasionally dominated by flares from non-thermal emission processes. The transient activity is believed to be synchrotron in nature, resulting from powerful magnetic reconnection events when the separate magnetic structures of the binary components are capable of interacting and forced to reorganize, typically near periastron. We conducted the first systematic study of the millimeter variability toward a sample of 12 PMS spectroscopic binaries with the aim to characterize the proliferation of flares amongst sources likely to experience similar interbinary reconnection events. The source sample consists of short-period, close-separation binaries that possess either a high orbital eccentricity or a circular orbit. Using the MAMBO2 array on the IRAM 30m telescope, we carried out continuous monitoring at 1.25 mm over a 4-night period during which all of the high-e...

  5. Tracing the potential planet-forming regions around seven pre-main-sequence stars

    CERN Document Server

    Schegerer, A A; Hummel, C A; Quanz, S P; Richichi, A

    2009-01-01

    We investigate the nature of the innermost regions of seven circumstellar disks around pre-main-sequence stars. Our object sample contains disks apparently at various stages of their evolution. Both single stars and spatially resolved binaries are considered. In particular, we search for inner disk gaps as proposed for several young stellar objects. When analyzing the underlying dust population in the atmosphere of circumstellar disks, the shape of the 10um feature is investigated. We performed interferometric observations in N band 8-13um with MIDI using baseline lengths of between 54m and 127m. The data analysis is based on radiative-transfer simulations using the Monte Carlo code MC3D by modeling simultaneously the SED, N band spectra, and interferometric visibilities. Correlated and uncorrelated N band spectra are compared to investigate the radial distribution of the dust composition of the disk atmosphere. Spatially resolved mid-infrared emission was detected in all objects. For four objects, the observ...

  6. RX J0942.7-7726AB: an isolated pre-main sequence wide binary

    CERN Document Server

    Murphy, Simon J; Bessell, Michael S

    2012-01-01

    We report the discovery of two young M-dwarfs, RX J0942.7-7726 (M1) and 2MASS J09424157-7727130 (M4.5), that were found only 42 arcsec apart in a survey for pre-main sequence stars surrounding the open cluster eta Chamaeleontis. Both stars have congruent proper motions and near-infrared photometry. Medium-resolution spectroscopy reveals that they are coeval (age 8-12 Myr), codistant (100-150 pc) and thus almost certainly form a true wide binary with a projected separation of 4000-6000 AU. The system appears too old and dynamically fragile to have originated in eta Cha and a traceback analysis argues for its birth in or near the Scorpius-Centaurus OB Association. RX J0942.7-7726AB joins a growing group of wide binaries kinematically linked to Sco-Cen, suggesting that such fragile systems can survive the turbulent environment of their natal molecular clouds while still being dispersed with large velocities. Conversely, the small radial velocity difference between the stars (2.7 \\pm 1.0 km/s) could mean the syst...

  7. The quadruple pre-main sequence system LkCa3: Implications for stellar evolution models

    CERN Document Server

    Torres, Guillermo; Badenas, Mariona; Prato, L; Schaefer, G H; Wasserman, Lawrence H; Mathieu, Robert D; Latham, David W

    2013-01-01

    We report the discovery that the pre-main sequence object LkCa3 in the Taurus-Auriga star-forming region is a hierarchical quadruple system of M stars. It was previously known to be a close (~0.5 arc sec) visual pair, with one component being a moderately eccentric 12.94-day single-lined spectroscopic binary. A re-analysis of archival optical spectra complemented with new near-infrared spectroscopy shows both visual components to be double-lined, the second one having a period of 4.06 days and a circular orbit. In addition to the orbital elements, we determine optical and near-infrared flux ratios, effective temperatures, and projected rotational velocities for all four stars. Using existing photometric monitoring observations of the system that had previously revealed the rotational period of the primary in the longer-period binary, we detect also the rotational signal of the primary in the 4.06-day binary, which is synchronized with the orbital motion. With only the assumption of coevality, a comparison of ...

  8. Older and Colder: The impact of starspots on pre-main sequence stellar evolution

    CERN Document Server

    Somers, Garrett

    2015-01-01

    We assess the impact of starspots on the evolution of late-type stars during the pre-main sequence (pre-MS) using a modified stellar evolution code. We find that heavily spotted models of mass 0.1-1.2\\msun\\ are inflated by up to $10$% during the pre-MS, and up to 4% and 9% for fully- and partially-convective stars at the zero-age MS, consistent with measurements from active eclipsing binary systems. Spots similarly decrease stellar luminosity and $T_{\\rm eff}$, causing isochrone-derived masses to be under-estimated by up to a factor of $2 \\times$, and ages to be under-estimated by a factor of 2-10$\\times$, at 3 Myr. Consequently, pre-MS clusters and their active stars are systematically older and more massive than often reported. Cluster ages derived with the lithium depletion boundary technique are erroneously young by $\\sim 15$% and $10$% at $30$ and $100$ Myr respectively, if 50% spotted stars are interpreted with un-spotted models. Finally, lithium depletion is suppressed in spotted stars with radiative c...

  9. Deep near-IR variability survey of pre-main-sequence stars in Rho Ophiuchi

    CERN Document Server

    de Oliveira, Catarina Alves

    2008-01-01

    Variability is a common characteristic of pre-main-sequence stars (PMS). Near-IR variability surveys of young stellar objects (YSOs) can probe stellar and circumstellar environments and provide information about the dynamics of the on going magnetic and accretion processes. Furthermore, variability can be used as a tool to uncover new cluster members in star formation regions. We hope to achieve the deepest near-IR variability study of YSOs targeting the Rho Ophiuchi cluster. Fourteen epochs of observations were obtained with the Wide Field Camera (WFCAM) at the UKIRT telescope scheduled in a manner that allowed the study of variability on timescales of days, months, and years. Statistical tools, such as the multi-band cross correlation index and the reduced chi-square, were used to disentangle signals of variability from noise. Variability characteristics are compared to existing models of YSOs in order to relate them to physical processes, and then used to select new candidate members of this star-forming r...

  10. Fundamental properties of pre-main sequence stars in young, southern star forming regions: metallicities

    CERN Document Server

    James, D J; Santos, N C; Bouvier, J; James, David J.; Melo, Claudio; Santos, Nuno C.; Bouvier, Jerome

    2005-01-01

    Aims: The primary motivation for this project is to search for metal-rich star forming regions, in which, stars of super-solar metallicity will be created, as hopefully, will be extra-solar planets orbiting them ! Results: We find (pre-main sequence) model-dependent isochronal ages of the Lupus, Chamaeleon and CrA targets to be $9.1 \\pm 2.1$ Myr, $4.5 \\pm 1.6$ Myr and $9.0 \\pm 3.9$ Myr respectively. The majority of the stars have Li I 6707.8A equivalent widths similar to, or above those of, their similar mass Pleiades counterparts, confirming their youthfulness. Most stars are kinematic members, either single or binary, of their regions. We find a mean radial velocity for objects in the Lupus cloud to be ${\\bar {RV}}=+2.6 \\pm 1.8$ km s$^{-1}$, for the Chamaeleon I & II clouds, ${\\bar {RV}}=+12.8 \\pm 3.6$ km s$^{-1}$ whereas for the CrA cloud, we find ${\\bar {RV}}=-1.1 \\pm 0.5$ km s$^{-1}$. All stars are coronally and chromospherically active, exhibiting X-ray and H$\\alpha$ emission levels marginally less,...

  11. Pre-main sequence stars older than 8 Myr in the Eagle Nebula

    CERN Document Server

    De Marchi, Guido; Guarcello, M G; Bonito, Rosaria

    2013-01-01

    Attention is given to a population of 110 stars in the NGC 6611 cluster of the Eagle Nebula that have prominent near-infrared (NIR) excess and optical colours typical of pre-main sequence (PMS) stars older than 8 Myr. At least half of those for which spectroscopy exists have a Halpha emission line profile revealing active accretion. In principle, the V-I colours of all these stars would be consistent with those of young PMS objects (< 1 Myr) whose radiation is heavily obscured by a circumstellar disc seen at high inclination and in small part scattered towards the observer by the back side of the disc. However, using theoretical models it is shown here that objects of this type can only account for a few percent of this population. In fact, the spatial distribution of these objects, their X-ray luminosities, their optical brightness, their positions in the colour-magnitude diagram and the weak Li absorption lines of the stars studied spectroscopically suggest that most of them are at least 8 times older th...

  12. An extensive VLT/X-shooter library of photospheric templates of pre-main sequence stars

    Science.gov (United States)

    Manara, C. F.; Frasca, A.; Alcalá, J. M.; Natta, A.; Stelzer, B.; Testi, L.

    2017-09-01

    Context. Studies of the formation and evolution of young stars and their disks rely on knowledge of the stellar parameters of the young stars. The derivation of these parameters is commonly based on comparison with photospheric template spectra. Furthermore, chromospheric emission in young active stars impacts the measurement of mass accretion rates, a key quantity for studying disk evolution. Aims: Here we derive stellar properties of low-mass (M⋆≲ 2 M⊙) pre-main sequence stars without disks, which represent ideal photospheric templates for studies of young stars. We also use these spectra to constrain the impact of chromospheric emission on the measurements of mass accretion rates. The spectra are reduced, flux-calibrated, and corrected for telluric absorption, and are made available to the community. Methods: We derive the spectral type for our targets by analyzing the photospheric molecular features present in their VLT/X-shooter spectra by means of spectral indices and comparison of the relative strength of photospheric absorption features. We also measure effective temperature, gravity, projected rotational velocity, and radial velocity from our spectra by fitting them with synthetic spectra with the ROTFIT tool. The targets have negligible extinction (AVhttp://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/605/A86

  13. Constraints on the height of the inner disk rim in pre-main-sequence stars

    CERN Document Server

    Vinković, Dejan

    2014-01-01

    The structure of inner region of protoplanetary disks around young pre-main-sequence stars is still poorly understood. This part of the disk is shaped by various forces influencing dust and gas dynamics and by dust sublimation, which creates abrupt drops in the dust density. This region also emits a strong near-infrared excess that cannot be explained by classical accretion disk models, which suggests the existence of some unusual dust distribution or disk shape. The most prevalent explanation to date is the puffed-up inner disk rim model, where the disk exhibits an optically thin cavity around the star up to the distance of dust sublimation. The critical parameter in this model is the inner disk rim height $z_{\\rm max}$ relative to the rim's distance from the star $R_{\\rm in}$. Observations often require $z_{\\rm max}/R_{\\rm in}\\gtrsim0.2$ to reproduce the near-infrared excess in the spectra. In this paper we put together a comprehensive list of processes that can shape the inner disk rim and combined them to...

  14. Exploring pre-main-sequence variables of the ONC: the new variables

    Science.gov (United States)

    Parihar, Padmakar; Messina, Sergio; Distefano, Elisa; Shantikumar, N. S.; Medhi, Biman J.

    2009-12-01

    Since 2004, we have been engaged in a long-term observing programme to monitor young stellar objects (YSOs) in the Orion Nebula Cluster (ONC). We have collected about 2000 frames in V, R and I broad-band filters on more than 200 nights distributed over five consecutive observing seasons. The high-quality and time-extended photometric data give us an opportunity to address various phenomena associated with young stars. The prime motivations of this project are (i) to explore various manifestations of stellar magnetic activity in very young low-mass stars, (ii) to search for new pre-main-sequence eclipsing binaries and (iii) to look for any EXor and FUor-like transient activities associated with YSOs. Since this is the first paper on this programme, we give a detailed description of the science drivers, the observation and the data reduction strategies as well. In addition to these, we also present a large number of new periodic variables detected from our first 5 yr of time-series photometric data. Our study reveals that about 72 per cent of classical T Tauri stars (CTTS) in our field of view are periodic, whereas only 32 per cent of weak-lined T Tauri stars (WTTS) are periodic. This indicates that inhomogeneity patterns on the surface of CTTS of the ONC stars are much more stable than on WTTS. From our multiyear monitoring campaign, we found that the photometric surveys based on single season are incapable of identifying all periodic variables. And any study on evolution of angular momentum based on single-season surveys must be carried out with caution.

  15. YSOVAR: SIX PRE-MAIN-SEQUENCE ECLIPSING BINARIES IN THE ORION NEBULA CLUSTER

    Energy Technology Data Exchange (ETDEWEB)

    Morales-Calderon, M.; Stauffer, J. R.; Rebull, L. M. [Spitzer Science Center, California Institute of Technology, 1200 E California Blvd., Pasadena, CA 91125 (United States); Stassun, K. G. [Physics and Astronomy Department, Vanderbilt University, 1807 Station B, Nashville, TN 37235 (United States); Vrba, F. J. [U. S. Naval Observatory, Flagstaff Station, 10391 W. Naval Observatory Road, Flagstaff, AZ 86001-8521 (United States); Prato, L. [Lowell Observatory, 1400 West Mars Hill Road, Flagstaff, AZ 86001 (United States); Hillenbrand, L. A.; Carpenter, J. M. [Astronomy Department, California Institute of Technology, 1200 E California Blvd., Pasadena, CA 91125 (United States); Terebey, S.; Angione, J. [Department of Physics and Astronomy, California State University at Los Angeles, Los Angeles, CA 90032 (United States); Covey, K. R. [Department of Astronomy, Cornell University, 226 Space Sciences Building, Ithaca, NY 14853 (United States); Terndrup, D. M. [Department of Astronomy, The Ohio State University, 140 West 18th Avenue, Columbus, OH 43210 (United States); Gutermuth, R. [Department of Astronomy, University of Massachusetts, Amherst, MA 01003 (United States); Song, I. [Physics and Astronomy Department, University of Georgia, Athens, GA 30602-2451 (United States); Plavchan, P. [NASA Exoplanet Science Institute, California Institute of Technology, Pasadena, CA 91125 (United States); Marchis, F. [SETI Institute, Carl Sagan Center, 189 N San Bernado Av, Mountain View, CA 94043 (United States); Garcia, E. V. [Department of Physics, Fisk University, 1000 17th Ave. N, Nashville, TN 37208 (United States); Margheim, S. [Gemini Observatory, Southern Operations Center, Casilla 603, La Serena (Chile); Luhman, K. L. [Department of Astronomy and Astrophysics, The Pennsylvania State University, University Park, PA 16802 (United States); Irwin, J. M., E-mail: mariamc@cab.inta-csic.es [Harvard-Smithsonian Center for Astrophysics, 60 Garden St., Cambridge, MA 02138 (United States)

    2012-07-10

    Eclipsing binaries (EBs) provide critical laboratories for empirically testing predictions of theoretical models of stellar structure and evolution. Pre-main-sequence (PMS) EBs are particularly valuable, both due to their rarity and the highly dynamic nature of PMS evolution, such that a dense grid of PMS EBs is required to properly calibrate theoretical PMS models. Analyzing multi-epoch, multi-color light curves for {approx}2400 candidate Orion Nebula Cluster (ONC) members from our Warm Spitzer Exploration Science Program YSOVAR, we have identified 12 stars whose light curves show eclipse features. Four of these 12 EBs are previously known. Supplementing our light curves with follow-up optical and near-infrared spectroscopy, we establish two of the candidates as likely field EBs lying behind the ONC. We confirm the remaining six candidate systems, however, as newly identified ONC PMS EBs. These systems increase the number of known PMS EBs by over 50% and include the highest mass ({theta}{sup 1} Ori E, for which we provide a complete set of well-determined parameters including component masses of 2.807 and 2.797 M{sub Sun }) and longest-period (ISOY J053505.71-052354.1, P {approx} 20 days) PMS EBs currently known. In two cases ({theta}{sup 1} Ori E and ISOY J053526.88-044730.7), enough photometric and spectroscopic data exist to attempt an orbit solution and derive the system parameters. For the remaining systems, we combine our data with literature information to provide a preliminary characterization sufficient to guide follow-up investigations of these rare, benchmark systems.

  16. THE QUADRUPLE PRE-MAIN-SEQUENCE SYSTEM LkCa 3: IMPLICATIONS FOR STELLAR EVOLUTION MODELS

    Energy Technology Data Exchange (ETDEWEB)

    Torres, Guillermo; Latham, David W. [Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138 (United States); Ruiz-Rodriguez, Dary; Prato, L.; Wasserman, Lawrence H. [Lowell Observatory, 1400 West Mars Hill Road, Flagstaff, AZ 86001 (United States); Badenas, Mariona [Department of Astronomy, Yale University, New Haven, CT 06520 (United States); Schaefer, G. H. [CHARA Array of Georgia State University, Mount Wilson Observatory, Mount Wilson, CA 91023 (United States); Mathieu, Robert D., E-mail: gtorres@cfa.harvard.edu [Department of Astronomy, University of Wisconsin-Madison, Madison, WI 53706 (United States)

    2013-08-10

    We report the discovery that the pre-main-sequence (PMS) object LkCa 3 in the Taurus-Auriga star-forming region is a hierarchical quadruple system of M stars. It was previously known to be a close ({approx}0.''5) visual pair, with one component being a moderately eccentric 12.94 day single-lined spectroscopic binary. A re-analysis of archival optical spectra complemented by new near-infrared (NIR) spectroscopy shows both visual components to be double lined; the second one has a period of 4.06 days and a circular orbit. In addition to the orbital elements, we determine optical and NIR flux ratios, effective temperatures, and projected rotational velocities for all four stars. Using existing photometric monitoring observations of the system that had previously revealed the rotational period of the primary in the longer-period binary, we also detect the rotational signal of the primary in the 4.06 day binary, which is synchronized with the orbital motion. With only the assumption of coevality, a comparison of all of these constraints with current stellar evolution models from the Dartmouth series points to an age of 1.4 Myr and a distance of 133 pc, consistent with previous estimates for the region and suggesting that the system is on the near side of the Taurus complex. Similar comparisons of the properties of LkCa 3 and the well-known quadruple PMS system GG Tau with the widely used models from the Lyon series for a mixing length parameter of {alpha}{sub ML} = 1.0 strongly favor the Dartmouth models.

  17. X-ray Emission Properties of Intermediate-Mass, Pre-Main-Sequence Stars

    Science.gov (United States)

    Povich, Matthew S.; Binder, Breanna; Townsley, Leisa K.; Broos, Patrick S.

    2017-08-01

    Intermediate-mass (2-8 M⊙) main-sequence stars with A to mid-B spectral types occupy an X-ray "desert" of weak intrinsic emission between low- and high-mass stars. Lacking the wind-shock driven emission of massive, O and early B stars or the convectively-driven magnetic reconnection flaring activity of later-type stars, X-ray detections of (non-peculiar) main-sequence AB stars are typically ascribed to the presence of unresolved, lower-mass binary companions. There is mounting evidence, however, that intermediate-mass, pre-main sequence stars (IMPS) with GK spectral types produce intrinsic X-ray emission that rapidly decays with time following the development of a radiative zone as IMPS approach the ZAMS as AB stars. This suggests that X-ray emission from IMPS may be a more luminous analog of the well-studied coronal X-ray emission from lower-mass, T Tauri stars. Statistical studies of young IMPS have been hampered by their scarcety in nearby, unobscured star-forming regions. We present the first results from a spectral-fitting study to measure absorption-corrected X-ray luminosities and plasma temperatures for hundreds of candidate X-ray emitting IMPS found in the MYStIX and MAGiX surveys of massive Galactic star forming regions. Candidate IMPS are placed on the HR diagram via a novel infrared spectral energy distribution modeling technique designed for highly-obscured, young massive star-forming regions. The rapid decay of X-ray emission from these objects has the potential to provide an independent chronometer to constrain star formation rates, and may produce an age-dependent bias in the relationship between the stellar X-ray luminosity function and mass function in distant (>2 kpc) regions observed with relatively shallow X-ray observations.This work is supported by the National Science Foundation under grant CAREER-1454334 and by NASA through Chandra Award 18200040.

  18. Hunting for millimeter flares from magnetic reconnection in pre-main sequence spectroscopic binaries

    Science.gov (United States)

    Kóspál, Á.; Salter, D. M.; Hogerheijde, M. R.; Moór, A.; Blake, G. A.

    2011-03-01

    Context. Recent observations of the low-mass pre-main sequence (PMS), eccentric spectroscopic binaries DQ Tau and V773 Tau A reveal that their millimeter spectrum is occasionally dominated by flares from non-thermal emission processes. The transient activity is believed to be synchrotron in nature, resulting from powerful magnetic reconnection events when the separate magnetic structures of the binary components are briefly capable of interacting and forced to reorganize, typically near periastron. Aims: We conducted the first systematic study of the millimeter variability toward a sample of 12 PMS spectroscopic binaries with the aim to characterize the proliferation of flares amongst sources likely to experience similar interbinary reconnection events. The source sample consists entirely of short-period, close-separation binaries that possess either a high orbital eccentricity (e > 0.1) or a circular orbit (e ≈ 0). Methods: Using the MAMBO2 array on the IRAM 30 m telescope, we carried out continuous monitoring at 1.25 mm (240 GHz) over a 4-night period during which all of the high-eccentricity binaries approached periastron. We also obtained simultaneous optical VRI measurements, since a strong link is often observed between stellar reconnection events (traced via X-rays) and optical brightenings. Results: UZ Tau E is the only source to be detected at millimeter wavelengths, and it exhibited significant variation (F1.25mm = 87-179 mJy); it is also the only source to undergo strong simultaneous optical variability (ΔR ≈ 0.9 mag). The binary possesses the largest orbital eccentricity in the current sample, a predicted factor in star-star magnetic interaction events. With orbital parameters and variable accretion activity similar to DQ Tau, the millimeter behavior of UZ Tau E draws many parallels to the DQ Tau model for colliding magnetospheres. However, on the basis of our observations alone, we cannot determine whether the variability is repetitive, or if it

  19. Pre-Main sequence Turn-On as a chronometer for young clusters: NGC346 as a benchmark

    CERN Document Server

    Cignoni, M; Sabbi, E; Nota, A; Degl'Innocenti, S; Moroni, P G Prada; Gallagher, J S

    2010-01-01

    We present a novel approach to derive the age of very young star clusters, by using the Turn-On (TOn). The TOn is the point in the color-magnitude diagram (CMD) where the pre-main sequence (PMS) joins the main sequence (MS). In the MS luminosity function (LF) of the cluster, the TOn is identified as a peak followed by a dip. We propose that by combining the CMD analysis with the monitoring of the spatial distribution of MS stars it is possible to reliably identify the TOn in extragalactic star forming regions. Compared to alternative methods, this technique is complementary to the turn-off dating and avoids the systematic biases affecting the PMS phase. We describe the method and its uncertainties, and apply it to the star forming region NGC346, which has been extensively imaged with the Hubble Space Telescope (HST). This study extends the LF approach in crowded extragalactic regions and opens the way for future studies with HST/WFC3, JWST and from the ground with adaptive optics.

  20. The Interior Structure Constants as an Age Diagnostic for Low-Mass, Pre-Main Sequence Detached Eclipsing Binary Stars

    CERN Document Server

    Feiden, Gregory A

    2013-01-01

    We propose a novel method for determining the ages of low-mass, pre-main sequence stellar systems using the apsidal motion of low-mass detached eclipsing binaries. The apsidal motion of a binary system with an eccentric orbit provides information regarding the interior structure constants of the individual stars. These constants are related to the normalized stellar interior density distribution and can be extracted from the predictions of stellar evolution models. We demonstrate that low-mass, pre-main sequence stars undergoing radiative core contraction display rapidly changing interior structure constants (greater than 5% per 10 Myr) that, when combined with observational determinations of the interior structure constants (with 5 -- 10% precision), allow for a robust age estimate. This age estimate, unlike those based on surface quantities, is largely insensitive to the surface layer where effects of magnetic activity are likely to be most pronounced. On the main sequence, where age sensitivity is minimal,...

  1. Age-Related Observations of Low Mass Pre-Main and Young Main Sequence Stars (Invited Review)

    CERN Document Server

    Hillenbrand, Lynne A

    2008-01-01

    This overview summarizes the age dating methods available for young sub-solar mass stars. Pre-main sequence age diagnostics include the Hertzsprung-Russell (HR) diagram, spectroscopic surface gravity indicators, and lithium depletion; asteroseismology is also showing recent promise. Near and beyond the zero-age main sequence, rotation period or vsini and activity (coronal and chromospheric) diagnostics along with lithium depletion serve as age proxies. Other authors in this volume present more detail in each of the aforementioned areas. Herein, I focus on pre-main sequence HR diagrams and address the questions: Do empirical young cluster isochrones match theoretical isochrones? Do isochrones predict stellar ages consistent with those derived via other independent techniques? Do the observed apparent luminosity spreads at constant effective temperature correspond to true age spreads? While definitive answers to these questions are not provided, some methods of progression are outlined.

  2. Analysis of flares in the chromosphere and corona of main- and pre-main-sequence M-type stars

    Science.gov (United States)

    Crespo-Chacón, I.

    2015-11-01

    This Ph.D. Thesis revolves around flares on main- and pre-main-sequence M-type stars. We use observations in different wavelength ranges with the aim of analysing the effects of flares at different layers of stellar atmospheres. In particular, optical and X-ray observations are used so that we can study how flares affect, respectively, the chromosphere and the corona of stars. In the optical range we carry out a high temporal resolution spectroscopic monitoring of UV Ceti-type stars aimed at detecting non-white-light flares (the most typical kind of solar flares) in stars other than the Sun. With these data we confirm that non-white-light flares are a frequent phenomenon in UV Ceti-type stars, as observed in the Sun. We study and interpret the behaviour of different chromospheric lines during the flares detected on AD Leo. By using a simplified slab model of flares (Jevremović et al. 1998), we are able to determine the physical parameters of the chromospheric flaring plasma (electron density and electron temperature), the temperature of the underlying source, and the surface area covered by the flaring plasma. We also search for possible relationships between the physical parameters of the flaring plasma and other properties such as the flare duration, area, maximum flux and released energy. This work considerably extends the existing sample of stellar flares analysed with good quality spectroscopy in the optical range. In X-rays we take advantage of the great sensitivity, wide energy range, high energy resolution, and continuous time coverage of the EPIC detectors - on-board the XMMNewton satellite - in order to perform time-resolved spectral analysis of coronal flares. In particular, in the UV Ceti-type star CC Eri we study two flares that are weaker than those typically reported in the literature (allowing us to speculate about the role of flares as heating agents of stellar atmospheres); while in the pre-main-sequence M-type star TWA 11B (with no signatures of

  3. The Effect of Screening Factors and Thermonuclear Reaction Rates in the Pre-main Sequence Evolution of Low Mass Stars

    Indian Academy of Sciences (India)

    İ. Küçük; Ş. Çalışkan

    2010-09-01

    In understanding the nucleosynthesis of the elements in stars, one of the most important quantities is the reaction rate and it must be evaluated in terms of the stellar temperature , and its determination involves the knowledge of the excitation function () of the specific nuclear reaction leading to the final nucleus. In this paper, the effect of thermonuclear reaction rates to the pre-main sequence evolution of low mass stars having masses 0.7, 0.8, 0.9 and 1 M⊙ are studied by using our modified Stellar Evolutionary Program.

  4. A Wide-Field Survey for Transiting Hot Jupiters and Eclipsing Pre-Main-Sequence Binaries in Young Stellar Associations

    CERN Document Server

    Oelkers, Ryan J; Marshall, Jennifer L; DePoy, Darren L; Lambas, Diego G; Colazo, Carlos; Stringer, Katelyn

    2016-01-01

    The past two decades have seen a significant advancement in the detection, classification and understanding of exoplanets and binaries. This is due, in large part, to the increase in use of small-aperture telescopes (< 20 cm) to survey large areas of the sky to milli-mag precision with rapid cadence. The vast majority of the planetary and binary systems studied to date consist of main-sequence or evolved objects, leading to a dearth of knowledge of properties at early times (< 50 Myr). Only a dozen binaries and one candidate transiting Hot Jupiter are known among pre-main sequence objects, yet these are the systems that can provide the best constraints on stellar formation and planetary migration models. The deficiency in the number of well-characterized systems is driven by the inherent and aperiodic variability found in pre-main-sequence objects, which can mask and mimic eclipse signals. Hence, a dramatic increase in the number of young systems with high-quality observations is highly desirable to gui...

  5. An unusual very low-mass high-amplitude pre-main sequence periodic variable

    CERN Document Server

    Rodriguez-Ledesma, Maria V; Ibrahimov, Mansur; Messina, Sergio; Parihar, Padmakar; Hessman, Frederic; de Oliveira, Catarina Alves; Herbst, William

    2012-01-01

    We have investigated the nature of the variability of CHS7797, an unusual periodic variable in the Orion Nebula Cluster. An extensive I-band photometric data set of CHS7797 was compiled between 2004-2010 using various telescopes. Further optical data have been collected in R and z' bands. In addition, simultaneous observations of the ONC region including CHS7797 were performed in the I, J, Ks and IRAC [3.6] and [4.5] bands over a time interval of about 40d. CHS7797 shows an unusual large-amplitude variation of about 1.7 mag in the R, I, and z' bands with a period 17.786. The amplitude of the brightness modulation decreases only slightly at longer wavelengths. The star is faint during 2/3 of the period and the shape of the phased light-curves for seven different observing seasons shows minor changes and small-amplitude variations. Interestingly, there are no significant colour-flux correlations for wavelengths smaller than 2microns, while the object becomes redder when fainter at longer wavelengths. CHS7797 ha...

  6. A statistical analysis of X-ray variability in pre-main sequence objects of the Taurus Molecular Cloud

    CERN Document Server

    Stelzer, B; Briggs, K; Micela, G; Scelsi, L; Audard, M; Pillitteri, I; Güdel, M

    2006-01-01

    This work is part of a systematic X-ray survey of the Taurus star forming complex with XMM-Newton. We study the time series of all X-ray sources associated with Taurus members, to statistically characterize their X-ray variability, and compare the results to those for pre-main sequence stars in the Orion Nebula Cluster and to expectations arising from a model where all the X-ray emission is the result of a large number of stochastically occurring flares. We find that roughly half of the detected X-ray sources show variability above our sensitivity limit, and in ~ 26 % of the cases this variability is recognized as flares. Variability is more frequently detected at hard than at soft energies. The variability statistics of cTTS and wTTS are undistinguishable, suggesting a common (coronal) origin for their X-ray emission. We have for the first time applied a rigorous maximum likelihood method in the analysis of the number distribution of flare energies on pre-main sequence stars. In its differential form this di...

  7. The Mdot - M* relation of pre-main sequence stars: a consequence of X-ray driven disc evolution

    CERN Document Server

    Ercolano, B; Owen, J E; Rosotti, G; Manara, C F

    2013-01-01

    We analyse current measurements of accretion rates onto pre-main sequence stars as a function of stellar mass, and conclude that the steep dependance of accretion rates on stellar mass is real and not driven by selection/detection threshold, as has been previously feared. These conclusions are reached by means of statistical tests including a survival analysis which can account for upper limits. The power-law slope of the Mdot-M* relation is found to be in the range of 1.6-1.9 for young stars with masses lower than 1 Msun. The measured slopes and distributions can be easily reproduced by means of a simple disc model which includes viscous accretion and X-ray photoevaporation. We conclude that the Mdot-M* relation in pre-main sequence stars bears the signature of disc dispersal by X-ray photoevaporation, suggesting that the relation is a straight- forward consequence of disc physics rather than an imprint of initial conditions.

  8. Pre-main sequence accretion in the low metallicity Galactic star-forming region Sh 2-284

    CERN Document Server

    Kalari, V M

    2014-01-01

    We present optical spectra of pre-main sequence (PMS) candidates around the H$\\alpha$ region taken with the Southern African Large Telescope, SALT, in the low metallicity ($Z$) Galactic region Sh 2-284, which includes the open cluster Dolidze 25 with an atypical low metallicity of $Z$ $\\sim$ 1/5 $Z_{\\odot}$. It has been suggested on the basis of both theory and observations that PMS mass-accretion rates, $\\dot M_{\\rm{acc}}$, are a function of $Z$. We present the first sample of spectroscopic estimates of mass-accretion rates for PMS stars in any low-$Z$ star-forming region. Our data-set was enlarged with literature data of H$\\alpha$ emission in intermediate-resolution R-band spectroscopy. Our total sample includes 24 objects spanning a mass range between 1 - 2 $M_{\\odot}$ and with a median age of approximately 3.5 Myr. The vast majority (21 out of 24) show evidence for a circumstellar disk on the basis of 2MASS and Spitzer infrared photometry. We find $\\dot M_{\\rm{acc}}$ in the 1 - 2 $M_{\\odot}$ interval to d...

  9. Measuring the mass of a pre-main sequence binary star through the orbit of TWA5A

    Energy Technology Data Exchange (ETDEWEB)

    Konopacky, Q; Ghez, A; Duchene, G; McCabe, C; Macintosh, B

    2007-01-18

    We present the results of a five year monitoring campaign of the close binary TWA 5Aab in the TW Hydrae association, using speckle and adaptive optics on the W.M. Keck 10 m telescopes. These measurements were taken as part of our ongoing monitoring of pre-main sequence (PMS) binaries in an effort to increase the number of dynamically determined PMS masses and thereby calibrate the theoretical PMS evolutionary tracks. Our observations have allowed us to obtain the first determination of this system's astrometric orbit. We find an orbital period of 5.94 {+-} 0.09 years and a semi-major axis of 0.''066 {+-} 0.''005. Combining these results with a kinematic distance, we calculate a total mass of 0.71 {+-} 0.14 M{sub {circle_dot}} (D/44 pc){sup 3}. for this system. This mass measurement, as well as the estimated age of this system, are consistent to within 2{sigma} of all theoretical models considered. In this analysis, we properly account for correlated uncertainties, and show that while these correlations are generally ignored, they increase the formal uncertainties by up to a factor of five and therefore are important to incorporate. With only a few more years of observation, this type of measurement will allow the theoretical models to be distinguished.

  10. Impact of internal gravity waves on the rotation profile inside pre-main sequence low-mass stars

    CERN Document Server

    Charbonnel, C; Amard, L; Palacios, A; Talon, S

    2013-01-01

    We study the impact of internal gravity waves (IGW), meridional circulation, shear turbulence, and stellar contraction on the internal rotation profile and surface velocity evolution of solar metallicity low-mass pre-main sequence stars. We compute a grid of rotating stellar evolution models with masses between 0.6 and 2.0Msun taking these processes into account for the transport of angular momentum, as soon as the radiative core appears and assuming no more disk-locking from that moment on.IGW generation along the PMS is computed taking Reynolds-stress and buoyancy into account in the bulk of the stellar convective envelope and convective core (when present). Redistribution of angular momentum within the radiative layers accounts for damping of prograde and retrograde IGW by thermal diffusivity and viscosity in corotation resonance. Over the whole mass range considered, IGW are found to be efficiently generated by the convective envelope and to slow down the stellar core early on the PMS. In stars more massi...

  11. Magnetic fields and differential rotation on the pre-main sequence III: The early-G star HD 106506

    CERN Document Server

    Waite, I A; Carter, B D; Hart, R; Donati, J -F; Vélez, J C Ramírez; Semel, M; Dunstone, N

    2011-01-01

    We present photometry and spectropolarimetry of the pre-main sequence star HD 106506. A photometric rotational period of ~1.416 +/- 0.133 days has been derived using observations at Mount Kent Observatory (MKO). Spectropolarimetric data taken at the 3.9-m Anglo-Australian Telescope (AAT) were used to derive spot occupancy and magnetic maps of the star through the technique of Zeeman Doppler imaging (ZDI). The resulting brightness maps indicate that HD 106506 displays photospheric spots at all latitudes including a predominant polar spot. Azimuthal and radial magnetic images of this star have been derived, and a significant azimuthal magnetic field is indicated, in line with other active young stars. A solar-like differential rotation law was incorporated into the imaging process. Using Stokes I information the equatorial rotation rate, $\\Omega_{eq}$, was found to be 4.54 +/- 0.01 rad/d, with a photospheric shear $\\delta\\Omega$ of $0.21_{-0.03}^{+0.02}$ rad/d. This equates to an equatorial rotation period of ~...

  12. On the origin of the correlations between the accretion luminosity and emission line luminosities in pre-main-sequence stars

    Science.gov (United States)

    Mendigutía, I.; Oudmaijer, R. D.; Rigliaco, E.; Fairlamb, J. R.; Calvet, N.; Muzerolle, J.; Cunningham, N.; Lumsden, S. L.

    2015-09-01

    Correlations between the accretion luminosity and emission line luminosities (Lacc and Lline) of pre-main-sequence (PMS) stars have been published for many different spectral lines, which are used to estimate accretion rates. Despite the origin of those correlations is unknown, this could be attributed to direct or indirect physical relations between the emission line formation and the accretion mechanism. This work shows that all (near-UV/optical/near-IR) Lacc-Lline correlations are the result of the fact that the accretion luminosity and the stellar luminosity (L*) are correlated, and are not necessarily related with the physical origin of the line. Synthetic and observational data are used to illustrate how the Lacc-Lline correlations depend on the Lacc-L* relationship. We conclude that because PMS stars show the Lacc-L* correlation immediately implies that Lacc also correlates with the luminosity of all emission lines, for which the Lacc-Lline correlations alone do not prove any physical connection with accretion but can only be used with practical purposes to roughly estimate accretion rates. When looking for correlations with possible physical meaning, we suggest that Lacc/L* and Lline/L* should be used instead of Lacc and Lline. Finally, the finding that Lacc has a steeper dependence on L* for T Tauri stars than for intermediate-mass Herbig Ae/Be stars is also discussed. That is explained from the magnetospheric accretion scenario and the different photospheric properties in the near-UV.

  13. On the origin of the correlations between the accretion luminosity and emission line luminosities in pre-main sequence stars

    CERN Document Server

    Mendigutía, I; Rigliaco, E; Fairlamb, J R; Calvet, N; Muzerolle, J; Cunningham, N; Lumsden, S L

    2015-01-01

    Correlations between the accretion luminosity and emission line luminosities (L_acc and L_line) of pre-main sequence (PMS) stars have been published for many different spectral lines, which are used to estimate accretion rates. Despite the origin of those correlations is unknown, this could be attributed to direct or indirect physical relations between the emission line formation and the accretion mechanism. This work shows that all (near-UV/optical/near-IR) L_acc-L_line correlations are the result of the fact that the accretion luminosity and the stellar luminosity (L_star) are correlated, and are not necessarily related with the physical origin of the line. Synthetic and observational data are used to illustrate how the L_acc-L_line correlations depend on the L_acc-L_star relationship. We conclude that because PMS stars show the L_acc-L_star correlation immediately implies that L_acc also correlates with the luminosity of all emission lines, for which the L_acc-L_line correlations alone do not prove any phy...

  14. Photometric determination of the mass accretion rate of pre-main sequence stars. IV. Recent star formation in NGC 602

    CERN Document Server

    De Marchi, Guido; Panagia, Nino

    2013-01-01

    We have studied the young stellar populations in NGC 602, in the Small Magellanic Cloud, using a novel method that we have developed to combine Hubble Space Telescope photometry in the V, I, and Halpha bands. We have identified about 300 pre-main sequence (PMS) stars, all of which are still undergoing active mass accretion, and have determined their physical parameters (effective temperature, luminosity, age, mass and mass accretion rate). Our analysis shows that star formation has been present in this field over the last 60 Myr. In addition, we can recognise at least two clear, distinct, and prominent episodes in the recent past: one about 2 Myr ago, but still ongoing in regions of higher nebulosity, and one (or more) older than 30 Myr, encompassing both stars dispersed in the field and two smaller clusters located about 100 arcsec north of the centre of NGC 602. The relative locations of younger and older PMS stars do not imply a causal effect or triggering of one generation on the other. The strength of th...

  15. An Internet server for update pre-main sequence tracks of low- and intermediate-mass stars

    CERN Document Server

    Siess, L; Forestini, M

    2000-01-01

    We present new grids of pre-main sequence (PMS) tracks for stars in the mass range 0.1 to 7.0 Msun. The computations were performed for four different metallicities (Z=0.01, 0.02, 0.03 and 0.04). A fifth table has been computed for the solar composition (Z=0.02), including a moderate overshooting. We describe the update in the physics of the Grenoble stellar evolution code which concerns mostly changes in the equation of state (EOS) adopting the formalism proposed by Pols et al. (1995) and in the treatment of the boundary condition. Comparisons of our models with other grids demonstrate the validity of this EOS in the domain of very low-mass stars. Finally, we present a new server dedicated to PMS stellar evolution which allows the determination of stellar parameters from observational data, the calculation of isochrones, the retrieval of evolutionary files and the possibility to generate graphic outputs. WWW site : http://www-laog.obs.ujf-grenoble.fr/activites/starevol/evol.html

  16. The influence of radiative core growth on coronal X-ray emission from pre-main sequence stars

    CERN Document Server

    Gregory, Scott G; Davies, Claire L

    2016-01-01

    Pre-main sequence (PMS) stars of mass $\\gtrsim0.35\\,{\\rm M}_\\odot$ transition from hosting fully convective interiors to configurations with a radiative core and outer convective envelope during their gravitational contraction. This stellar structure change influences the external magnetic field topology and, as we demonstrate herein, affects the coronal X-ray emission as a stellar analog of the solar tachocline develops. We have combined archival X-ray, spectroscopic, and photometric data for $\\sim$1000 PMS stars from five of the best studied star forming regions; the ONC, NGC 2264, IC 348, NGC 2362, and NGC 6530. Using a modern, PMS calibrated, spectral type-to-effective temperature and intrinsic colour scale, we deredden the photometry using colours appropriate for each spectral type, and determine the stellar mass, age, and internal structure consistently for the entire sample. We find that PMS stars on Henyey tracks have, on average, lower fractional X-ray luminosities ($L_{\\rm X}/L_\\ast$) than those on ...

  17. The Solar Neighborhood. XXVI. AP Col: The Closest (8.4 pc) Pre-Main-Sequence Star

    CERN Document Server

    Riedel, Adric R; Henry, Todd J; Melis, Carl; Jao, Wei-Chun; Subasavage, John P; 10.1088/0004-6256/142/4/104

    2011-01-01

    We present the results of a multi-technique investigation of the M4.5Ve flare star AP Col, which we discover to be the nearest pre-main-sequence star. These include astrometric data from the CTIO 0.9m, from which we derive a proper motion of 342.0+/-0.5 mas yr^-1, a trigonometric parallax of 119.21+/-0.98 mas (8.39+/-0.07 pc), and photometry and photometric variability at optical wavelengths. We also provide spectroscopic data, including radial velocity (22.4+/-0.3 km s^-1), lithium Equivalent Width (EW) (0.28+/-0.02 A), H-alpha EW (-6.0 to -35 A), {\\it vsini} (11+/-1 km s^-1), and gravity indicators from the Siding Spring 2.3-m WiFeS, Lick 3-m Hamilton echelle, and Keck-I HIRES echelle spectrographs. The combined observations demonstrate that AP Col is the closer of only two known systems within 10 pc of the Sun younger than 100 Myr. Given its space motion and apparent age of 12-50 Myr, AP Col is likely a member of the recently proposed ~40 Myr old Argus/IC 2391 association.

  18. The pre-main-sequence star V1184 Tauri (CB 34V) at the end of prolonged eclipse

    Science.gov (United States)

    Semkov, E. H.; Peneva, S. P.; Ibryamov, S. I.

    2015-10-01

    Aims: V1184 Tau (CB 34V) lies in the field of the Bok globule CB 34 and was discovered as a large amplitude variable in 1993. According to the first hypothesis of the variability of the star, it is a FU Orionis candidate erupted between 1951 and 1993. During subsequent observations, the star manifests large amplitude variability interpreted as obscuration from circumstellar clouds of dust. We included V1184 Tau (CB 34V) in our target list of highly variable pre-main-sequence stars to determine the reasons for the variations in the brightness of this object. Methods: Data from BVRI photometric observations of the young stellar object V1184 Tau, obtained in the period 2008-2015, are presented in the paper. These data are a continuation of our optical photometric monitoring of the star began in 2000 and continuing to date. The photometric observations of V1184 Tau were performed in two observatories with two medium-sized and two small telescopes. Results: Our results indicate that during periods of maximum light the star shows characteristics typical of T Tauri stars. During the observed deep minimum in brightness, however, V1184 Tau is rather similar to UX Orionis objects. The deep drop in brightness began in 2003 ended in 2015 as the star has returned to maximum light. The light curve during the drop is obviously asymmetric as the decrease in brightness lasts two times longer than the rise. The observed colour reverse on the colour-magnitude diagrams is also confirmation of obscuration from circumstellar clouds of dust as a reason for the large amplitude variability in the brightness. Appendix A is available in electronic form at http://www.aanda.org

  19. An IUE Atlas of Pre-Main-Sequence Stars. II. Far-Ultraviolet Accretion Diagnostics in T Tauri Stars

    Science.gov (United States)

    Johns-Krull, Christopher M.; Valenti, Jeff A.; Linsky, Jeffrey L.

    2000-08-01

    We use our ultraviolet (UV) atlas of pre-main-sequence stars constructed from all useful, short-wavelength, low-resolution spectra in the International Ultraviolet Explorer (IUE) satellite Final Archive to analyze the short-wavelength UV properties of 49 T Tauri stars (TTSs). We compare the line and continuum fluxes in these TTSs with each other and with previously published parameters of these systems, including rotation rate, infrared excess, and mass accretion rate. The short-wavelength continuum in the classical TTSs (CTTSs) appears to originate in a ~10,000 K optically thick plasma, while in the naked TTSs (NTTSs-stars without dusty disks) the continuum appears to originate in the stellar atmosphere. We show that all of the TTSs in our sample lie in the regime of ``saturated'' magnetic activity due to their small Rossby numbers. However, while some of the TTSs show emission line surface fluxes consistent with this saturation level, many CTTSs show significantly stronger emission than predicted by saturation. In these stars, the emission line luminosity in the high ionization lines present in the spectrum between 1200 and 2000 Å correlates well with the mass accretion rate. Therefore, we conclude that the bulk of the short-wavelength emission seen in CTTSs results from accretion related processes and not from dynamo-driven magnetic activity. Using CTTSs with known mass accretion rates, we calibrate the relationship between M and LC IV to derive the mass accretion rate for some CTTSs which for various reasons have never had their mass accretion rates measured. Finally, several of the CTTSs show strong emission from molecular hydrogen. While emission from H2 cannot form in gas at a temperature of ~105 K, the strength of the molecular hydrogen emission is nevertheless well correlated with all the other emissions displayed in the IUE short-wavelength bandpass. This suggests that the H2 emission is in fact fluorescent emission pumped by the emission (likely Ly

  20. Effect of accretion on the pre-main-sequence evolution of low-mass stars and brown dwarfs

    Science.gov (United States)

    Vorobyov, Eduard I.; Elbakyan, Vardan; Hosokawa, Takashi; Sakurai, Yuya; Guedel, Manuel; Yorke, Harold

    2017-09-01

    Aims: The pre-main-sequence evolution of low-mass stars and brown dwarfs is studied numerically starting from the formation of a protostellar or proto-brown dwarf seed and taking into account the mass accretion onto the central object during the initial several Myr of evolution. Methods: The stellar evolution was computed using the STELLAR evolution code with recent modifications. The mass accretion rates were taken from numerical hydrodynamics models by computing the circumstellar disk evolution starting from the gravitational collapse of prestellar cloud cores of various mass and angular momentum. The resulting stellar evolution tracks were compared with the isochrones and isomasses calculated using non-accreting models. Results: We find that mass accretion in the initial several Myr of protostellar evolution can have a strong effect on the subsequent evolution of young stars and brown dwarfs. The disagreement between accreting and non-accreting models in terms of the total stellar luminosity L∗, stellar radius R∗, and effective temperature Teff depends on the thermal efficiency of accretion, that is, on the fraction of accretion energy that is absorbed by the central object. The largest mismatch is found for the cold accretion case, in which essentially all accretion energy is radiated away. The relative deviations in L∗ and R∗ in this case can reach 50% for objects 1.0 Myr old, and they remain notable even for objects 10 Myr old. In the hot and hybrid accretion cases, in which a constant fraction of accretion energy is absorbed, the disagreement between accreting and non-accreting models becomes less pronounced, but still remains notable for objects 1.0 Myr old. These disagreements may lead to an incorrect age estimate for objects of (sub-)solar mass when using the isochrones that are based on non-accreting models, as has also been noted previously. We find that objects with strong luminosity bursts exhibit notable excursions in the L∗-Teff diagram

  1. Revisiting the pre-main-sequence evolution of stars. I. Importance of accretion efficiency and deuterium abundance

    Science.gov (United States)

    Kunitomo, Masanobu; Guillot, Tristan; Takeuchi, Taku; Ida, Shigeru

    2017-03-01

    Context. Protostars grow from the first formation of a small seed and subsequent accretion of material. Recent theoretical work has shown that the pre-main-sequence (PMS) evolution of stars is much more complex than previously envisioned. Instead of the traditional steady, one-dimensional solution, accretion may be episodic and not necessarily symmetrical, thereby affecting the energy deposited inside the star and its interior structure. Aims: Given this new framework, we want to understand what controls the evolution of accreting stars. Methods: We use the MESA stellar evolution code with various sets of conditions. In particular, we account for the (unknown) efficiency of accretion in burying gravitational energy into the protostar through a parameter, ξ, and we vary the amount of deuterium present. Results: We confirm the findings of previous works that, in terms of evolutionary tracks on an Hertzprung-Russell (H-R) diagram, the evolution changes significantly with the amount of energy that is lost during accretion. We find that deuterium burning also regulates the PMS evolution. In the low-entropy accretion scenario, the evolutionary tracks in the H-R diagram are significantly different from the classical tracks and are sensitive to the deuterium content. A comparison of theoretical evolutionary tracks and observations allows us to exclude some cold accretion models (ξ 0) with low deuterium abundances. Conclusions: We confirm that the luminosity spread seen in clusters can be explained by models with a somewhat inefficient injection of accretion heat. The resulting evolutionary tracks then become sensitive to the accretion heat efficiency, initial core entropy, and deuterium content. In this context, we predict that clusters with a higher D/H ratio should have less scatter in luminosity than clusters with a smaller D/H. Future work on this issue should include radiation-hydrodynamic simulations to determine the efficiency of accretion heating and further

  2. Extended Magnetospheres in Pre-main-sequence Evolution: From T Tauri Stars to the Brown Dwarf Limit

    Science.gov (United States)

    Gómez de Castro, Ana I.; Marcos-Arenal, Pablo

    2012-04-01

    Low-mass pre-main-sequence stars, i.e., T Tauri stars (TTSs), strongly radiate at high energies, from X-rays to the ultraviolet (UV). This excess radiation with respect to main-sequence cool stars (MSCSs) is associated with the accretion process, i.e., it is produced in the extended magnetospheres, in the accretion shocks on the stellar surface, and in the outflows. Although evidence of accretion shocks and outflow contribution to the high-energy excess have been recently addressed, there is not an updated revision of the magnetospheric contribution. This article addresses this issue. The UV observations of the TTSs in the well-known Taurus region have been analyzed together with the XMM-Newton observations compiled in the XEST survey. For the first time the high sensitivity of the Hubble Space Telescope UV instrumentation has allowed measurement of the UV line fluxes of TTSs to M8 type. UV- and X-ray-normalized fluxes have been determined to study the extent and properties of the TTS magnetospheres as a class. They have been compared with the atmospheres of the MSCSs. The main results from this analysis are (1) the normalized fluxes of all the tracers are correlated; this correlation is independent of the broad mass range and the hardness of the X-ray radiation field; (2) the TTS correlations are different than the MSCS correlations; (3) there is a very significant excess emission in O I in the TTSs compared with MSCSs that seems to be caused by recombination radiation from the disk atmosphere after photoionization by extreme UV radiation; the Fe II/Mg II recombination continuum has also been detected in several TTSs and most prominently in AA Tau; and (4) the normalized flux of the UV tracers anticorrelates with the strength of the X-ray flux, i.e., the stronger the X-ray surface flux is, the weaker the observed UV flux. This last behavior is counterintuitive within the framework of stellar dynamo theory and suggests that UV emission can be produced in the

  3. A Critical Assessment of Ages Derived Using Pre-Main-Sequence Isochrones in Colour-Magnitude Diagrams

    Science.gov (United States)

    Bell, Cameron P. M.

    2012-11-01

    In this thesis a critical assessment of the ages derived using theoretical pre-main-sequence (pre-MS) stellar evolutionary models is presented by comparing the predictions to the low-mass pre-MS population of 14 young star-forming regions (SFRs) in colour-magnitude diagrams (CMDs). Deriving pre-MS ages requires precise distances and estimates of the reddening. Therefore, the main-sequence (MS) members of the SFRs have been used to derive a self-consistent set of statistically robust ages, distances and reddenings with associated uncertainties using a maximum-likelihood fitting statistic and MS evolutionary models. A photometric method for de-reddening individual stars - known as the Q-method - in regions where the extinction is spatially variable has been updated and is presented. The effects of both the model dependency and the SFR composition on these derived parameters are also discussed. The problem of calibrating photometric observations of red pre-MS stars is examined and it is shown that using observations of MS stars to transform the data into a standard photometric system can introduce significant errors in the position of the pre-MS locus in CMD space. Hence, it is crucial that precise photometric studies - especially of pre-MS objects - be carried out in the natural photometric system of the observations. This therefore requires a robust model of the system responses for the instrument used, and thus the calculated responses for the Wide-Field Camera on the Isaac Newton Telescope are presented. These system responses have been tested using standard star observations and have been shown to be a good representation of the photometric system. A benchmark test for the pre-MS evolutionary models is performed by comparing them to a set of well-calibrated CMDs of the Pleiades in the wavelength regime 0.4-2.5 μm. The masses predicted by these models are also tested against dynamical masses using a sample of MS binaries by calculating the system magnitude in a

  4. MML 53: a new low-mass, pre-main sequence eclipsing binary in the Upper Centarus-Lupus Region discovered by SuperWASP

    CERN Document Server

    Hebb, L; Aigrain, S; Collier-Cameron, A; Hodgkin, S T; Irwin, J M; Maxted, P F L; Pollacco, D; Street, R A; Wilson, D M; Stassun, K G

    2010-01-01

    We announce the discovery of a new low-mass, pre-main sequence eclipsing binary, MML 53. Previous observations of MML 53 found it to be a pre-main sequence spectroscopic multiple associated with the 15-22 Myr Upper Centaurus Lupus cluster. We identify the object as an eclipsing binary for the first time through the analysis of multiple seasons of time series photometry from the SuperWASP transiting planet survey. Re-analysis of a single archive spectrum shows MML 53 to be a spatially unresolved triple system of young stars which all exhibit significant lithium absorption. Two of the components comprise an eclipsing binary with period, P = 2.097891(6) +- 0.000005 and mass ratio, q~0.8. Here, we present the analysis of the discovery data.

  5. Angular momentum transport by internal gravity waves. IV - Wave generation by surface convection zone, from the pre-main sequence to the early-AGB in intermediate mass stars

    CERN Document Server

    Talon, Suzanne

    2008-01-01

    This is the fourth in a series of papers that deal with angular momentum transport by internal gravity waves in stellar interiors. Here, we want to examine the potential role of waves in other evolutionary phases than the main sequence. We study the evolution of a 3Msun Population I model from the pre-main sequence to the early-AGB phase and examine whether waves can lead to angular momentum redistribution and/or element diffusion at the external convection zone boundary. We find that, although waves produced by the surface convection zone can be ignored safely for such a star during the main sequence, it is not the case for later evolutionary stages. In particular, angular momentum transport by internal waves could be quite important at the end of the sub-giant branch and during the early-AGB phase. Wave-induced mixing of chemicals is expected during the early-AGB phase.

  6. Investigation of the magnetic field characteristics of Herbig Ae/Be stars: Discovery of the pre-main sequence progenitors of the magnetic Ap/Bp stars

    CERN Document Server

    Wade, G A; Bagnulo, S; Landstreet, J D; Mason, E; Silvester, J; Alecian, E; Böhm, T; Bouret, J C; Catala, C; Donati, J F; Folsom, C; Bale, K

    2006-01-01

    We are investigating the magnetic characteristics of pre-main sequence Herbig Ae/Be stars, with the aim of (1) understanding the origin and evolution of magnetism in intermediate-mass stars, and (2) exploring the influence of magnetic fields on accretion, rotation and mass-loss at the early stages of evolution of A, B and O stars. We have begun by conducting 2 large surveys of Herbig Ae/Be stars, searching for direct evidence of photospheric magnetic fields via the longitudinal Zeeman effect. From observations obtained using FORS1 at the ESO-VLT and ESPaDOnS at the Canada-France-Hawaii Telescope, we report the confirmed detection of magnetic fields in 4 pre-main sequence A- and B-type stars, and the apparent (but as yet unconfirmed) detection of fields in 2 other such stars. We do not confirm the detection of magnetic fields in several stars reported by other authors to be magnetic: HD 139614, HD 144432 or HD 31649. One of the most evolved stars in the detected sample, HD 72106A, shows clear evidence of stron...

  7. Magnetic fields and differential rotation on the pre-main sequence I: The early-G star HD 141943 - brightness and magnetic topologies

    CERN Document Server

    Marsden, S C; Vélez, J C Ramírez; Alecian, E; Brown, C J; Carter, B D; Donati, J F; Dunstone, N; Hart, R; Semel, M; Waite, I A

    2011-01-01

    Spectroscopic and spectropolarimetric observations of the pre-main sequence early-G star HD 141943 were obtained at four observing epochs (in 2006, 2007, 2009 and 2010). The observations were undertaken at the 3.9-m Anglo-Australian Telescope using the UCLES echelle spectrograph and the SEMPOL spectropolarimeter visitor instrument. Brightness and surface magnetic field topologies were reconstructed for the star using the technique of least-squares deconvolution to increase the signal-to-noise of the data. The reconstructed brightness maps show that HD 141943 had a weak polar spot and a significant amount of low latitude features, with little change in the latitude distribution of the spots over the 4 years of observations. The surface magnetic field was reconstructed at three of the epochs from a high order (l <= 30) spherical harmonic expansion of the spectropolarimetric observations. The reconstructed magnetic topologies show that in 2007 and 2010 the surface magnetic field was reasonably balanced betwee...

  8. The clustered nature of star formation. Pre--main-sequence clusters in the star-forming region NGC 602/N90 in the Small Magellanic Cloud

    CERN Document Server

    Gouliermis, Dimitrios A; Dolphin, Andrew E; Gennaro, Mario; Tognelli, Emanuele; Moroni, Pier Giorgio Prada

    2012-01-01

    Located at the tip of the wing of the Small Magellanic Cloud (SMC), the star-forming region NGC602/N90 is characterized by the HII nebular ring N90 and the young cluster of pre--main-sequence (PMS) and early-type main sequence stars NGC602. We present a thorough cluster analysis of the stellar sample identified with HST/ACS camera in the region. We show that apart from the central cluster, low-mass PMS stars are congregated in thirteen additional small compact sub-clusters at the periphery of NGC602. We find that the spatial distribution of the PMS stars is bimodal, with an unusually large fraction (~60%) of the total population being clustered, while the remaining is diffusely distributed in the inter-cluster area. From the corresponding color-magnitude diagrams we disentangle an age-difference of ~2.5Myr between NGC602 and the compact sub-clusters which appear younger. The diffuse PMS population appears to host stars as old as those in NGC602. Almost all detected PMS sub-clusters appear to be centrally conc...

  9. Can we predict the global magnetic topology of a pre-main sequence star from its position in the Hertzsprung-Russell diagram?

    CERN Document Server

    Gregory, S G; Morin, J; Hussain, G A J; Mayne, N J; Hillenbrand, L A; Jardine, M

    2012-01-01

    ZDI studies have shown that the magnetic fields of T Tauri stars can be significantly more complex than a simple dipole and can vary markedly between sources. We collect and summarize the magnetic field topology information obtained to date and present Hertzsprung-Russell (HR) diagrams for the stars in the sample. Intriguingly, the large scale field topology of a given pre-main sequence (PMS) star is strongly dependent upon the stellar internal structure, with the strength of the dipole component of its multipolar magnetic field decaying rapidly with the development of a radiative core. Using the observational data as a basis, we argue that the general characteristics of the global magnetic field of a PMS star can be determined from its position in the HR diagram. Moving from hotter and more luminous to cooler and less luminous stars across the PMS of the HR diagram, we present evidence for four distinct magnetic topology regimes. Stars with large radiative cores, empirically estimated to be those with a core...

  10. Mid-IR spectra of Pre-Main Sequence Herbig stars: an explanation for the non-detections of water lines

    CERN Document Server

    Antonellini, S; Lahuis, F; Woitke, P; Thi, W -F; Meijerink, R; Aresu, G; Spaans, M; Güdel, M; Liebhart, A

    2016-01-01

    The mid-IR detection rate of water lines in disks around Herbig stars disks is about 5\\%, while it is around 50\\% for disks around TTauri stars. The reason for this is still unclear. In this study, we want to find an explanation for the different detection rates between low mass and high mass pre-main-sequence stars (PMSs) in the mid-IR regime. We run disk models with stellar parameters adjusted to spectral types B9 through M2, using the radiation thermo-chemical disk modeling code ProDiMo. We produce convolved spectra at the resolution of Spitzer IRS, JWST MIRI and VLT VISIR spectrographs. We apply random noise derived from typical Spitzer spectra for a direct comparison with observations. The strength of the mid-IR water lines correlates directly with the luminosity of the central star. We explored a small parameter space around a standard disk model, considering dust-to-gas mass ratio, disk gas mass, mixing coefficient for dust settling, flaring index, dust maximum size and size power law distribution inde...

  11. A constraint on the formation timescale of the young open cluster NGC 2264: Lithium abundance of pre-main sequence stars

    CERN Document Server

    Lim, Beomdu; Kim, Jinyoung S; Bessell, Michael S; Hwang, Narae; Park, Byeong-Gon

    2016-01-01

    The timescale of cluster formation is an essential parameter in order to understand the formation process of star clusters. Pre-main sequence (PMS) stars in nearby young open clusters reveal a large spread in brightness. If the spread were considered as a result of a real spread in age, the corresponding cluster formation timescale would be about 5 -- 20 Myr. Hence it could be interpreted that star formation in an open cluster is prolonged for up to a few tens of Myr. However, difficulties in reddening correction, observational errors, and systematic uncertainties introduced by imperfect evolutionary models for PMS stars, can result in an artificial age spread. Alternatively, we can utilize Li abundance as a relative age indicator of PMS star to determine the cluster formation timescale. The optical spectra of 134 PMS stars in NGC 2264 have been obtained with MMT/Hectochelle. The equivalent widths have been measured for 86 PMS stars with a detectable Li line (3500 < T_eff [K] <= 6500). Li abundance unde...

  12. Planetary Construction Zones in Occultation: Eclipses by Circumsecondary and Circumplanetary Disks and a Candidate Eclipse of a Pre-Main Sequence Star in Sco-Cen

    CERN Document Server

    Mamajek, Eric E; Pecaut, Mark; Moolekamp, Fred; Scott, Erin L; Kenworthy, Matthew; Cameron, Andrew Collier; Parley, Neil

    2011-01-01

    The large relative sizes of circumstellar and circumplanetary disks imply that they might be seen in eclipse in stellar light curves. We present photometric and spectroscopic data for a pre-main sequence K5 star (1SWASP J140747.93-394542.6 = ASAS J140748-3945.7), a newly discovered ~0.9 Msun member of the ~16 Myr-old Upper Centaurus-Lupus subgroup of Sco-Cen at a distance of 128+-13 pc. This star exhibited a remarkably long, deep, and complex eclipse event centered on 29 April 2007 (as discovered in SuperWASP photometry, and with portions of the dimming confirmed by ASAS data). At least 5 multi-day dimming events of >0.5 mag are identified, with a >3.3 mag deep eclipse bracketed by two pairs of ~1 mag eclipses symmetrically occurring +-12 days and +-26 days before and after. Hence, significant dimming of the star was taking place on and off over at least a ~54 day period in 2007, and a strong >1 mag dimming event occurring over a ~12 day span. We place a firm lower limit on the period of 850 days (i.e. the o...

  13. XMM-Newton monitoring of the close pre-main-sequence binary AK Sco. Evidence of tide driven filling of the inner gap in the circumbinary disk

    CERN Document Server

    de Castro, Ana I Gomez; Talavera, Antonio; Sytov, A Yu; Bisikalo, D

    2013-01-01

    AK~Sco stands out among pre-main sequence binaries because of its prominent ultraviolet excess, the high eccentricity of its orbit and the strong tides driven by it. AK Sco consists of two F5 type stars that get as close as 11R$_*$ at periastron passage. The presence of a dense ($n_e \\sim 10^{11}$~cm$^{-3}$) extended envelope has been unveiled recently. In this article, we report the results from a XMM-Newton based monitoring of the system. We show that at periastron, X-ray and UV fluxes are enhanced by a factor of $\\sim 3$ with respect to the apastron values. The X-ray radiation is produced in an optically thin plasma with T$\\sim 6.4\\times 10^{6}$ K and it is found that the N$_H$ column density rises from 0.35$\\times 10^{21}$~cm$^{-2}$ at periastron to 1.11$\\times 10^{21}$~cm$^{-2}$ at apastron, in good agreement with previous polarimetric observations. The UV emission detected in the Optical Monitor band seems to be caused by the reprocessing of the high energy magnetospheric radiation on the circumstellar ...

  14. The multipolar magnetic fields of accreting pre-main-sequence stars: B at the inner disk, B along the accretion flow, and B at the accretion shock

    CERN Document Server

    Gregory, Scott G; Hussain, Gaitee A J

    2016-01-01

    Zeeman-Doppler imaging studies have revealed the complexity of the large-scale magnetic fields of accreting pre-main-sequence stars. All have multipolar magnetic fields with the octupole component being the dominant field mode for many of the stars studied thusfar. Young accreting stars with fully convective interiors often feature simple axisymmetric magnetic fields with dipole components of order a kilo-Gauss (at least those of mass $\\gtrsim0.5\\,{\\rm M}_\\odot$), while those with substantially radiative interiors host more complex non-axisymmetric magnetic fields with dipole components of order a few 0.1 kilo-Gauss. Here, via several simple examples, we demonstrate that i). in most cases, the dipole component alone can be used to estimate the disk truncation radius (but little else); ii) due the presence of higher order magnetic field components, the field strength in the accretion spots is far in excess of that expected if a pure dipole magnetic field is assumed. (Fields of $\\sim$6$\\,{\\rm kG}$ have been mea...

  15. CoRoT 223992193: A new, low-mass, pre-main sequence eclipsing binary with evidence of a circumbinary disk

    CERN Document Server

    Gillen, Edward; McQuillan, Amy; Bouvier, Jerome; Hodgkin, Simon; Alencar, Silvia H P; Terquem, Caroline; Southworth, John; Gibson, Neale P; Cody, Ann Marie; Lendl, Monika; Morales-Calderón, Maria; Favata, Fabio; Stauffer, John; Micela, Giuseppina

    2013-01-01

    We present the discovery of CoRoT 223992193, a double-lined, detached eclipsing binary, comprising two pre-main sequence M dwarfs, discovered by the CoRoT space mission during a 23-day observation of the 3 Myr old NGC 2264 star-forming region. Using multi-epoch optical and near-IR follow-up spectroscopy with FLAMES on the Very Large Telescope and ISIS on the William Herschel Telescope we obtain a full orbital solution and derive the fundamental parameters of both stars by modelling the light curve and radial velocity data. The orbit is circular and has a period of $3.8745745 \\pm 0.0000014$ days. The masses and radii of the two stars are $0.67 \\pm 0.01$ and $0.495 \\pm 0.007$ $M_{\\odot}$ and $1.30 \\pm 0.04$ and $1.11 ~^{+0.04}_{-0.05}$ $R_{\\odot}$, respectively. This system is a useful test of evolutionary models of young low-mass stars, as it lies in a region of parameter space where observational constraints are scarce; comparison with these models indicates an apparent age of $\\sim$3.5-6 Myr. The systemic ve...

  16. The Multiple Young Stellar Objects of HBC 515: An X-ray and Millimeter-wave Imaging Study in (Pre-main Sequence) Diversity

    CERN Document Server

    Principe, D A; Kastner, J H; Wilner, D; Stelzer, B; Micela, G

    2016-01-01

    We present Chandra X-ray Observatory and Submillimeter Array (SMA) imaging of HBC 515, a system consisting of multiple young stellar objects (YSOs). The five members of HBC 515 represent a remarkably diverse array of YSOs, ranging from the low-mass Class I/II protostar HBC 515B, through Class II and transition disk objects (HBC 515D and C, respectively), to the "diskless", intermediate- mass, pre-main sequence binary HBC 515A. Our Chandra/ACIS imaging establishes that all five components are X-ray sources, with HBC 515A - a subarcsecond-separation binary that is partially resolved by Chandra - being the dominant X-ray source. We detect an X-ray flare associated with HBC 515B. In the SMA imaging, HBC 515B is detected as a strong 1.3 mm continuum emission source; a second, weaker mm continuum source is coincident with the position of the transition disk object HBC 515C. These results strongly support the protostellar nature of HBC 515B, and firmly establish HBC 515A as a member of the rare class of relatively m...

  17. The Gaia-ESO Survey: lithium depletion in the Gamma Velorum cluster and inflated radii in low-mass pre-main-sequence stars

    Science.gov (United States)

    Jeffries, R. D.; Jackson, R. J.; Franciosini, E.; Randich, S.; Barrado, D.; Frasca, A.; Klutsch, A.; Lanzafame, A. C.; Prisinzano, L.; Sacco, G. G.; Gilmore, G.; Vallenari, A.; Alfaro, E. J.; Koposov, S. E.; Pancino, E.; Bayo, A.; Casey, A. R.; Costado, M. T.; Damiani, F.; Hourihane, A.; Lewis, J.; Jofre, P.; Magrini, L.; Monaco, L.; Morbidelli, L.; Worley, C. C.; Zaggia, S.; Zwitter, T.

    2017-01-01

    We show that non-magnetic models for the evolution of pre-main-sequence (PMS) stars cannot simultaneously describe the colour-magnitude diagram (CMD) and the pattern of lithium depletion seen in the cluster of young, low-mass stars surrounding γ2 Velorum. The age of 7.5 ± 1 Myr inferred from the CMD is much younger than that implied by the strong Li depletion seen in the cluster M-dwarfs, and the Li depletion occurs at much redder colours than predicted. The epoch at which a star of a given mass depletes its Li and the surface temperature of that star are both dependent on its radius. We demonstrate that if the low-mass stars have radii ˜10 per cent larger at a given mass and age, then both the CMD and the Li-depletion pattern of the Gamma Velorum cluster are explained at a common age of ≃18-21 Myr. This radius inflation could be produced by some combination of magnetic suppression of convection and extensive cool starspots. Models that incorporate radius inflation suggest that PMS stars, similar to those in the Gamma Velorum cluster, in the range 0.2 30 per cent) than inferred from conventional, non-magnetic models in the Hertzsprung-Russell diagram. Systematic changes of this size may be of great importance in understanding the evolution of young stars, disc lifetimes and the formation of planetary systems.

  18. A High-Resolution Multiband Survey of Westerlund 2 With the Hubble Space Telescope. II. Mass accretion in the Pre-Main Sequence Population

    CERN Document Server

    Zeidler, Peter; Nota, Antonella; Sabbi, Elena; Pasquali, Anna; Tosi, Monica; Bonanos, Alceste Z; Christian, Carol

    2016-01-01

    We present a detailed analysis of the pre-main-sequence (PMS) population of the young star cluster Westerlund~2 (Wd2), the central ionizing cluster of the HII region RCW 49, using data from a high resolution multi-band survey with the Hubble Space Telescope. The data were acquired with the Advanced Camera for Surveys in the F555W, F814W, and F658N filters and with the Wide Field Camera 3 in the F125W, F160W, and F128N filters. We find a mean age of the region of 1.04+-0.72 Myr. The combination of dereddened F555W and F814W photometry in combination with F658N photometry allows us to study and identify stars with H_alpha excess emission. With a careful selection of 240 bona-fide PMS H_alpha excess emitters we were able to determine their H_alpha luminosity, which has a mean value L(H_alpha)=1.67 x 10^{-31} erg s^{-1}. Using the PARSEC 1.2S isochrones to obtain the stellar parameters of the PMS stars we determined a mean mass accretion rate \\dot M_acc=4.43 x 10^{-8} M_sun yr^{-1} per star. A careful analysis of...

  19. CoRoT 223992193: Investigating the variability in a low-mass, pre-main sequence eclipsing binary with evidence of a circumbinary disk

    CERN Document Server

    Gillen, Edward; Terquem, Caroline; Bouvier, Jerome; Alencar, Silvia H P; Gandolfi, Davide; Stauffer, John; Cody, Ann Marie; Venuti, Laura; Almeida, Pedro Viana; Micela, Giuseppina; Favata, Fabio; Deeg, Hans J

    2016-01-01

    CoRoT 223992193 is the only known low-mass, pre-main sequence eclipsing binary that shows evidence of a circumbinary disk. The system displays complex photometric and spectroscopic variability over a range of timescales and wavelengths. Using two optical CoRoT runs, and infrared Spitzer 3.6 and 4.5 $\\mu$m observations (simultaneous with the second CoRoT run), we model the out-of-eclipse light curves. The large scale structure in both CoRoT light curves is consistent with the constructive and destructive interference of starspot signals at two slightly different periods. Using the stellar $v\\sin i$ 's, we infer different rotation periods: the primary is consistent with synchronisation and the secondary is slightly supersynchronous. Comparison of the raw data to the residuals of our spot model in colour-magnitude space indicates additional contributions consistent with variable dust emission and obscuration. We also identify short-duration flux dips preceding secondary eclipse in all three CoRoT and Spitzer ban...

  20. Zodiacal Exoplanets in Time (ZEIT) III: A Neptune-sized planet orbiting a pre-main-sequence star in the Upper Scorpius OB Association

    CERN Document Server

    Mann, Andrew W; Rizzuto, Aaron C; Irwin, Jonathan; Feiden, Gregory A; Gaidos, Eric; Mace, Gregory N; Kraus, Adam L; James, David J; Ansdell, Megan; Charbonneau, David; Covey, Kevin R; Ireland, Michael J; Jaffe, Daniel T; Johnson, Marshall C; Kidder, Benjamin; Vanderburg, Andrew

    2016-01-01

    We confirm and characterize a close-in ($P_\\rm{orb}$ = 5.425 days), super-Neptune sized ($5.04^{+0.34}_{-0.37}$ Earth radii) planet transiting EPIC 205117205 (2MASS J16101473-1919095), a late-type (M3) pre-main sequence ($\\simeq$11 Myr-old) star in the Upper Scorpius subgroup of the Scorpius-Centaurus OB association. The host star has the kinematics of a member of the Upper Scorpius OB association, and its spectrum contains lithium absorption, an unambiguous sign of youth (<20 Myr) in late-type dwarfs. We combine photometry from K2 and the ground-based MEarth project to refine the planet's properties and constrain the average stellar density. We determine EPIC 205117205's bolometric flux and effective temperature from moderate resolution spectra. By utilizing isochrones that include the effects of magnetic fields, we derive a precise (6-7%) radius and mass for the host star, and a stellar age consistent with the established value for Upper Scorpius. Follow-up high-resolution imaging and Doppler spectroscop...

  1. Searching for young Jupiter analogs around AP Col: L-band high-contrast imaging of the closest pre-main sequence star

    CERN Document Server

    Quanz, Sascha P; Janson, Markus; Avenhaus, Henning; Meyer, Michael R; Hillenbrand, Lynne A

    2012-01-01

    The nearby M-dwarf AP Col was recently identified by Riedel et al. 2011 as a pre-main sequence star (age 12 - 50 Myr) situated only 8.4 pc from the Sun. The combination of its youth, distance, and intrinsically low luminosity make it an ideal target to search for extrasolar planets using direct imaging. We report deep adaptive optics observations of AP Col taken with VLT/NACO and Keck/NIRC2 in the L-band. Using aggressive speckle suppression and background subtraction techniques, we are able to rule out companions with mass m >= 0.5 - 1M_Jup for projected separations a>4.5 AU, and m >= 2 M_Jup for projected separations as small as 3 AU, assuming an age of 40 Myr using the COND theoretical evolutionary models. Using a different set of models the mass limits increase by a factor of ~2. The observations presented here are the deepest mass-sensitivity limits yet achieved within 20 AU on a star with direct imaging. While Doppler radial velocity surveys have shown that Jovian bodies with close-in orbits are rare ar...

  2. A New Method for the Assessment of Age and Age-Spread of Pre-Main Sequence Stars in Young Stellar Associations of the Magellanic Clouds

    CERN Document Server

    Da Rio, Nicola; Gennaro, Mario

    2010-01-01

    We present a new method for the evaluation of the age and age-spread among pre-main-sequence (PMS) stars in star-forming regions in the Magellanic Clouds, accounting simultaneously for photometric errors, unresolved binarity, differential extinction, stellar variability, accretion and crowding. The application of the method is performed with the statistical construction of synthetic color-magnitude diagrams using PMS evolutionary models. We convert each isochrone into 2D probability distributions of artificial PMS stars in the CMD by applying the aforementioned biases that dislocate these stars from their original CMD positions. A maximum-likelihood technique is then applied to derive the probability for each observed star to have a certain age, as well as the best age for the entire cluster. We apply our method to the photometric catalog of ~2000 PMS stars in the young association LH 95 in the LMC, based on the deepest HST/ACS imaging ever performed toward this galaxy, with a detection limit of V~28, corresp...

  3. Pre-Main Sequence variables in the VMR-D : identification of T Tauri-like accreting protostars through Spitzer-IRAC variability

    CERN Document Server

    Giannini, T; Elia, D; Strafella, F; De Luca, M; Fazio, G; Marengo, M; Nisini, B; Smith, H A

    2009-01-01

    We present a study of the infrared variability of young stellar objects by means of two Spitzer-IRAC images of the Vela Molecular Cloud D (VMR-D) obtained in observations separated in time by about six months. By using the same space-born IR instrumentation, this study eliminates all the unwanted effects usually unavoidable when comparing catalogs obtained from different instruments. The VMR-D map covers about 1.5 square deg. of a site where star formation is actively ongoing. We are interested in accreting pre-main sequence variables whose luminosity variations are due to intermittent events of disk accretion (i.e. active T Tauri stars and EXor type objects). The variable objects have been selected from a catalog of more than 170,000 sources detected at a S/N ratio > 5. We searched the sample of variables for ones whose photometric properties are close to those of known EXor's. These latter are monitored in a more systematic way than T Tauri stars and the mechanisms that regulate the observed phenomenology a...

  4. The Gaia-ESO Survey: Lithium depletion in the Gamma Velorum cluster and inflated radii in low-mass pre-main-sequence stars

    CERN Document Server

    Jeffries, R D; Franciosini, E; Randich, S; Barrado, D; Frasca, A; Klutsch, A; Lanzafame, A C; Prisinzano, L; Sacco, G G; Gilmore, G; Vallenari, A; Alfaro, E J; Koposov, S E; Pancino, E; Bayo, A; Casey, A R; Costado, M T; Damiani, F; Hourihane, A; Lewis, J; Jofre, P; Magrini, L; Monaco, L; Morbidelli, L; Worley, C C; Zaggia, S; Zwitter, T

    2016-01-01

    We show that non-magnetic models for the evolution of pre-main-sequence (PMS) stars *cannot* simultaneously describe the colour-magnitude diagram (CMD) and the pattern of lithium depletion seen in the cluster of young, low-mass stars surrounding $\\gamma^2$ Velorum. The age of 7.5+/-1 Myr inferred from the CMD is much younger than that implied by the strong Li depletion seen in the cluster M-dwarfs and the Li depletion occurs at much redder colours than predicted. The epoch at which a star of a given mass depletes its Li and the surface temperature of that star are both dependent on its radius. We demonstrate that if the low-mass stars have radii ~10 per cent larger at a given mass and age, then both the CMD and Li depletion pattern of the Gamma Vel cluster are explained at a common age of 18-21 Myr. This radius inflation could be produced by some combination of magnetic suppression of convection and extensive cool starspots. Models that incorporate radius inflation suggest that PMS stars similar to those in t...

  5. Zodiacal Exoplanets in Time (ZEIT). III. A Short-period Planet Orbiting a Pre-main-sequence Star in the Upper Scorpius OB Association

    Science.gov (United States)

    Mann, Andrew W.; Newton, Elisabeth R.; Rizzuto, Aaron C.; Irwin, Jonathan; Feiden, Gregory A.; Gaidos, Eric; Mace, Gregory N.; Kraus, Adam L.; James, David J.; Ansdell, Megan; Charbonneau, David; Covey, Kevin R.; Ireland, Michael J.; Jaffe, Daniel T.; Johnson, Marshall C.; Kidder, Benjamin; Vanderburg, Andrew

    2016-09-01

    We confirm and characterize a close-in ({P}{{orb}} = 5.425 days), super-Neptune sized ({5.04}-0.37+0.34 {R}\\oplus ) planet transiting K2-33 (2MASS J16101473-1919095), a late-type (M3) pre-main-sequence (11 Myr old) star in the Upper Scorpius subgroup of the Scorpius-Centaurus OB association. The host star has the kinematics of a member of the Upper Scorpius OB association, and its spectrum contains lithium absorption, an unambiguous sign of youth (\\lt 20 Myr) in late-type dwarfs. We combine photometry from K2 and the ground-based MEarth project to refine the planet’s properties and constrain the host star’s density. We determine K2-33’s bolometric flux and effective temperature from moderate-resolution spectra. By utilizing isochrones that include the effects of magnetic fields, we derive a precise radius (6%-7%) and mass (16%) for the host star, and a stellar age consistent with the established value for Upper Scorpius. Follow-up high-resolution imaging and Doppler spectroscopy confirm that the transiting object is not a stellar companion or a background eclipsing binary blended with the target. The shape of the transit, the constancy of the transit depth and periodicity over 1.5 yr, and the independence with wavelength rule out stellar variability or a dust cloud or debris disk partially occulting the star as the source of the signal; we conclude that it must instead be planetary in origin. The existence of K2-33b suggests that close-in planets can form in situ or migrate within ˜10 Myr, e.g., via interactions with a disk, and that long-timescale dynamical migration such as by Lidov-Kozai or planet-planet scattering is not responsible for all short-period planets.

  6. Photometric Determination of the Mass Accretion Rates of Pre-main-sequence Stars. V. Recent Star Formation in the 30 Dor Nebula

    Science.gov (United States)

    De Marchi, Guido; Panagia, Nino; Beccari, Giacomo

    2017-09-01

    We report on the properties of the low-mass stars that recently formed in the central ∼ 2\\buildrel{ \\prime}\\over{.} 7× 2\\buildrel{ \\prime}\\over{.} 7 of 30 Dor, including the R136 cluster. Using the photometric catalog of De Marchi et al., based on observations with the Hubble Space Telescope, and the most recent extinction law for this field, we identify 1035 bona fide pre-main-sequence (PMS) stars showing {{H}}α excess emission at the 4σ level with an {{H}}α equivalent width of 20 Å or more. We find a wide spread in age spanning the range ∼ 0.1{--}50 {Myr}. We also find that the older PMS objects are placed in front of the R136 cluster and are separated from it by a conspicuous amount of absorbing material, indicating that star formation has proceeded from the periphery into the interior of the region. We derive physical parameters for all PMS stars, including masses m, ages t, and mass accretion rates {\\dot{M}}{acc}. To identify reliable correlations between these parameters, which are intertwined, we use a multivariate linear regression fit of the type {log}{\\dot{M}}{acc}=a× {log}t+b× {log}m+c. The values of a and b for 30 Dor are compatible with those found in NGC 346 and NGC 602. We extend the fit to a uniform sample of 1307 PMS stars with 0.5contract NAS5-26555.

  7. THE CLUSTERED NATURE OF STAR FORMATION. PRE-MAIN-SEQUENCE CLUSTERS IN THE STAR-FORMING REGION NGC 602/N90 IN THE SMALL MAGELLANIC CLOUD

    Energy Technology Data Exchange (ETDEWEB)

    Gouliermis, Dimitrios A.; Gennaro, Mario [Max Planck Institute for Astronomy, Koenigstuhl 17, 69117 Heidelberg (Germany); Schmeja, Stefan [Zentrum fuer Astronomie der Universitaet Heidelberg, Institut fuer Theoretische Astrophysik, Albert-Ueberle-Str. 2, 69120 Heidelberg (Germany); Dolphin, Andrew E. [Raytheon Company, P.O. Box 11337, Tucson, AZ 85734 (United States); Tognelli, Emanuele; Prada Moroni, Pier Giorgio [Dipartimento di Fisica ' Enrico Fermi' , Universita di Pisa, largo Pontecorvo 3, Pisa I-56127 (Italy)

    2012-03-20

    Located at the tip of the wing of the Small Magellanic Cloud (SMC), the star-forming region NGC 602/N90 is characterized by the H II nebular ring N90 and the young cluster of pre-main-sequence (PMS) and early-type main-sequence stars NGC 602, located in the central area of the ring. We present a thorough cluster analysis of the stellar sample identified with Hubble Space Telescope/Advanced Camera for Surveys in the region. We show that apart from the central cluster low-mass PMS stars are congregated in 13 additional small, compact sub-clusters at the periphery of NGC 602, identified in terms of their higher stellar density with respect to the average background density derived from star counts. We find that the spatial distribution of the PMS stars is bimodal, with an unusually large fraction ({approx}60%) of the total population being clustered, while the remaining is diffusely distributed in the intercluster area, covering the whole central part of the region. From the corresponding color-magnitude diagrams we disentangle an age difference of {approx}2.5 Myr between NGC 602 and the compact sub-clusters, which appear younger, on the basis of comparison of the brighter PMS stars with evolutionary models, which we accurately calculated for the metal abundance of the SMC. The diffuse PMS population appears to host stars as old as those in NGC 602. Almost all detected PMS sub-clusters appear to be centrally concentrated. When the complete PMS stellar sample, including both clustered and diffused stars, is considered in our cluster analysis, it appears as a single centrally concentrated stellar agglomeration, covering the whole central area of the region. Considering also the hot massive stars of the system, we find evidence that this agglomeration is hierarchically structured. Based on our findings, we propose a scenario according to which the region NGC 602/N90 experiences an active clustered star formation for the last {approx}5 Myr. The central cluster NGC 602 was

  8. XMM-NEWTON MONITORING OF THE CLOSE PRE-MAIN-SEQUENCE BINARY AK SCO. EVIDENCE OF TIDE-DRIVEN FILLING OF THE INNER GAP IN THE CIRCUMBINARY DISK

    Energy Technology Data Exchange (ETDEWEB)

    Gomez de Castro, Ana Ines [S. D. Astronomia y Geodesia and Instituto de Matematica Interdisciplinar, Fac. de CC Matematicas, Universidad Complutense, E-28040 Madrid (Spain); Lopez-Santiago, Javier [Departamento de Astrofisica, Fac de CC Fisicas, Universidad Complutense, E-28040 Madrid (Spain); Talavera, Antonio [European Space Astronomy Center, Villanueva de la Canada, E-28691, Madrid (Spain); Sytov, A. Yu.; Bisikalo, D. [Institute of Astronomy of the Russian Academy of Sciences, Pyatnitskaya St. 48, 109017 Moscow (Russian Federation)

    2013-03-20

    AK Sco stands out among pre-main-sequence binaries because of its prominent ultraviolet excess, the high eccentricity of its orbit, and the strong tides driven by it. AK Sco consists of two F5-type stars that get as close as 11 R{sub *} at periastron passage. The presence of a dense (n{sub e} {approx} 10{sup 11} cm{sup -3}) extended envelope has been unveiled recently. In this article, we report the results from an XMM-Newton-based monitoring of the system. We show that at periastron, X-ray and UV fluxes are enhanced by a factor of {approx}3 with respect to the apastron values. The X-ray radiation is produced in an optically thin plasma with T {approx} 6.4 Multiplication-Sign 10{sup 6} K and it is found that the N{sub H} column density rises from 0.35 Multiplication-Sign 10{sup 21} cm{sup -2} at periastron to 1.11 Multiplication-Sign 10{sup 21} cm{sup -2} at apastron, in good agreement with previous polarimetric observations. The UV emission detected in the Optical Monitor band seems to be caused by the reprocessing of the high-energy magnetospheric radiation on the circumstellar material. Further evidence of the strong magnetospheric disturbances is provided by the detection of line broadening of 278.7 km s{sup -1} in the N V line with Hubble Space Telescope/Space Telescope Imaging Spectrograph. Numerical simulations of the mass flow from the circumbinary disk to the components have been carried out. They provide a consistent scenario with which to interpret AK Sco observations. We show that the eccentric orbit acts like a gravitational piston. At apastron, matter is dragged efficiently from the inner disk border, filling the inner gap and producing accretion streams that end as ring-like structures around each component of the system. At periastron, the ring-like structures come into contact, leading to angular momentum loss, and thus producing an accretion outburst.

  9. First determination of s-process element abundances in pre-main sequence clusters. Y, Zr, La, and Ce in IC 2391, the Argus association, and IC 2602

    Science.gov (United States)

    D'Orazi, V.; De Silva, G. M.; Melo, C. F. H.

    2017-02-01

    Context. Several high-resolution spectroscopic studies have provided compelling observational evidence that open clusters display a decreasing trend of their barium abundances as a function of the cluster's age. Young clusters (ages ≲ 200 Myr) exhibit significant enhancement in the [Ba/Fe] ratios, at variance with solar-age clusters where the Ba content has been found to be [Ba/Fe] 0 dex. Different viable solutions have been suggested in the literature; nevertheless, a conclusive interpretation of such a peculiar trend has not been found. Interestingly, it is debated whether the other species produced with Ba via s-process reactions follow the same trend with age. Aims: Pre-main sequence clusters (≈10-50 Myr) show the most extreme behaviour in this respect: their [Ba/Fe] ratios can reach 0.65 dex, which is higher than the solar value by a factor of four. Crucially, there are no investigations of the other s-process species for these young stellar populations. In this paper we present the first determination of Y, Zr, La, and Ce in clusters IC 2391, IC 2602, and the Argus association. The main objective of our work is to ascertain whether these elements reveal the same enhancement as Ba. Methods: We have exploited high-resolution, high signal-to-noise spectra in order to derive abundances for Y, Zr, La, and Ce via spectral synthesis calculations. Our sample includes only stars with very similar atmospheric parameters so that internal errors due to star-to-star inhomogeneity are negligible. The chemical analysis was carried out in a strictly differential way, as done in all our previous investigations, to minimise the impact of systematic uncertainties. Results: Our results indicate that, at variance with Ba, all the other s-process species exhibit a solar scaled pattern; these clusters confirm a similar trend discovered in the slightly older local associations (e.g. AB Doradus, Carina-Near), where only Ba exhibit enhanced value with all other s-process species

  10. MEASUREMENT OF SPIN-ORBIT MISALIGNMENT AND NODAL PRECESSION FOR THE PLANET AROUND PRE-MAIN-SEQUENCE STAR PTFO 8-8695 FROM GRAVITY DARKENING

    Energy Technology Data Exchange (ETDEWEB)

    Barnes, Jason W. [Department of Physics, University of Idaho, Moscow, ID 83844-0903 (United States); Van Eyken, Julian C. [Department of Physics, University of California Santa Barbara, Santa Barbara, CA 93106-9530 (United States); Jackson, Brian K. [Carnegie Institution of Washington, DTM, 5241 Broad Branch Road, NW Washington, DC 20015-1305 (United States); Ciardi, David R. [NASA Exoplanet Science Institute, Caltech M/S 100-22, Pasadena, CA 91125 (United States); Fortney, Jonathan J., E-mail: jwbarnes@uidaho.edu [Department of Astronomy, University of California Santa Cruz, Santa Cruz, CA 95064 (United States)

    2013-09-01

    PTFO 8-8695b represents the first transiting exoplanet candidate orbiting a pre-main-sequence star (van Eyken et al. 2012, ApJ, 755, 42). We find that the unusual lightcurve shapes of PTFO 8-8695 can be explained by transits of a planet across an oblate, gravity-darkened stellar disk. We develop a theoretical framework for understanding precession of a planetary orbit's ascending node for the case when the stellar rotational angular momentum and the planetary orbital angular momentum are comparable in magnitude. We then implement those ideas to simultaneously and self-consistently fit two separate lightcurves observed in 2009 December and 2010 December. Our two self-consistent fits yield M{sub p} = 3.0 M{sub Jup} and M{sub p} = 3.6 M{sub Jup} for assumed stellar masses of M{sub *} = 0.34 M{sub Sun} and M{sub *} = 0.44 M{sub Sun} respectively. The two fits have precession periods of 293 days and 581 days. These mass determinations (consistent with previous upper limits) along with the strength of the gravity-darkened precessing model together validate PTFO 8-8695b as just the second hot Jupiter known to orbit an M-dwarf. Our fits show a high degree of spin-orbit misalignment in the PTFO 8-8695 system: 69 Degree-Sign {+-} 2 Degree-Sign or 73. Degree-Sign 1 {+-} 0. Degree-Sign 5, in the two cases. The large misalignment is consistent with the hypothesis that planets become hot Jupiters with random orbital plane alignments early in a system's lifetime. We predict that as a result of the highly misaligned, precessing system, the transits should disappear for months at a time over the course of the system's precession period. The precessing, gravity-darkened model also predicts other observable effects: changing orbit inclination that could be detected by radial velocity observations, changing stellar inclination that would manifest as varying vsin i, changing projected spin-orbit alignment that could be seen by the Rossiter-McLaughlin effect, changing

  11. A Tale of Two Anomalies: Depletion, Dispersion, and the Connection Between the Stellar Lithium Spread and Inflated Radii on the Pre-Main Sequence

    CERN Document Server

    Somers, Garrett

    2014-01-01

    We investigate lithium depletion in standard stellar models (SSMs) and main sequence (MS) open clusters, and explore the origin of the Li dispersion in young, cool stars of equal mass, age and composition. We first demonstrate that SSMs accurately predict the Li abundances of solar analogs at the zero-age main sequence (ZAMS) within theoretical uncertainties. We then measure the rate of MS Li depletion by removing the [Fe/H]-dependent ZAMS Li pattern from three well-studied clusters, and comparing the detrended data. MS depletion is found to be mass dependent, in the sense of more depletion at low mass. A dispersion in Li abundance at fixed $T_{\\rm eff}$ is nearly universal, and sets in by $\\sim$200 Myr. We discuss mass and age dispersion trends, and the pattern is mixed. We argue that metallicity impacts the ZAMS Li pattern, in agreement with theoretical expectations but contrary to the findings of some previous studies, and suggest Li as a test of cluster metallicity. Finally, we argue that a radius dispers...

  12. A Tale of Two Anomalies: Depletion, Dispersion, and the Connection between the Stellar Lithium Spread and Inflated Radii on the Pre-main Sequence

    Science.gov (United States)

    Somers, Garrett; Pinsonneault, Marc H.

    2014-07-01

    We investigate lithium depletion in standard stellar models (SSMs) and main sequence (MS) open clusters, and explore the origin of the Li dispersion in young, cool stars of equal mass, age, and composition. We first demonstrate that SSMs accurately predict the Li abundances of solar analogs at the zero-age main sequence (ZAMS) within theoretical uncertainties. We then measure the rate of MS Li depletion by removing the [Fe/H]-dependent ZAMS Li pattern from three well-studied clusters, and comparing the detrended data. MS depletion is found to be mass-dependent, in the sense of more depletion at low mass. A dispersion in Li abundance at fixed T eff is nearly universal, and sets in by ~200 Myr. We discuss mass and age dispersion trends, and the pattern is mixed. We argue that metallicity impacts the ZAMS Li pattern, in agreement with theoretical expectations but contrary to the findings of some previous studies, and suggest Li as a test of cluster metallicity. Finally, we argue that a radius dispersion in stars of fixed mass and age, during the epoch of pre-MS Li destruction, is responsible for the spread in Li abundances and the correlation between rotation and Li in young cool stars, most well known in the Pleiades. We calculate stellar models, inflated to match observed radius anomalies in magnetically active systems, and the resulting range of Li abundances reproduces the observed patterns of young clusters. We discuss ramifications for pre-MS evolutionary tracks and age measurements of young clusters, and suggest an observational test.

  13. A tale of two anomalies: Depletion, dispersion, and the connection between the stellar lithium spread and inflated radii on the pre-main sequence

    Energy Technology Data Exchange (ETDEWEB)

    Somers, Garrett; Pinsonneault, Marc H., E-mail: somers@astronomy.ohio-state.edu, E-mail: pinsono@astronomy.ohio-state.edu [Department of Astronomy, The Ohio State University, 140 West 18th Avenue, Columbus, OH 43201 (United States)

    2014-07-20

    We investigate lithium depletion in standard stellar models (SSMs) and main sequence (MS) open clusters, and explore the origin of the Li dispersion in young, cool stars of equal mass, age, and composition. We first demonstrate that SSMs accurately predict the Li abundances of solar analogs at the zero-age main sequence (ZAMS) within theoretical uncertainties. We then measure the rate of MS Li depletion by removing the [Fe/H]-dependent ZAMS Li pattern from three well-studied clusters, and comparing the detrended data. MS depletion is found to be mass-dependent, in the sense of more depletion at low mass. A dispersion in Li abundance at fixed T{sub eff} is nearly universal, and sets in by ∼200 Myr. We discuss mass and age dispersion trends, and the pattern is mixed. We argue that metallicity impacts the ZAMS Li pattern, in agreement with theoretical expectations but contrary to the findings of some previous studies, and suggest Li as a test of cluster metallicity. Finally, we argue that a radius dispersion in stars of fixed mass and age, during the epoch of pre-MS Li destruction, is responsible for the spread in Li abundances and the correlation between rotation and Li in young cool stars, most well known in the Pleiades. We calculate stellar models, inflated to match observed radius anomalies in magnetically active systems, and the resulting range of Li abundances reproduces the observed patterns of young clusters. We discuss ramifications for pre-MS evolutionary tracks and age measurements of young clusters, and suggest an observational test.

  14. Evidence for variable, correlated X-ray and optical/IR extinction towards the nearby, pre-main-sequence binary TWA 30

    Science.gov (United States)

    Principe, David A.; Sacco, G.; Kastner, J. H.; Stelzer, B.; Alcalá, J. M.

    2016-06-01

    We present contemporaneous XMM-Newton X-ray and ground-based optical/near-IR spectroscopic observations of the nearby (D ≈ 42 pc), low-mass (mid-M) binary system TWA 30A and 30B. The components of this wide (separation ˜3400 au) binary are notable for their nearly edge-on disc viewing geometries, high levels of variability, and evidence for collimated stellar outflows. We obtained XMM-Newton X-ray observations of TWA 30A and 30B in 2011 June and July, accompanied (respectively) by Infrared Telescope Facility SpeX (near-IR) and VLT XSHOOTER (visible/near-IR) spectroscopy obtained within ˜20 h of the X-ray observations. TWA 30A was detected in both XMM-Newton observations at relatively faint intrinsic X-ray luminosities (LX ˜ 8 × 1027 erg s-1) compared to stars of similar mass and age. The intrinsic (0.15-2.0 keV) X-ray luminosities measured in 2011 had decreased by a factor 20-100 relative to a 1990 (ROSAT) X-ray detection. TWA 30B was not detected, and we infer an upper limit on its X-ray Luminosity of LX ≲ 3.0 × 1027 erg s-1. We measured a decrease in visual extinction towards TWA 30A (from AV ≈ 14.9 to AV ≈ 4.7) between the two 2011 observing epochs, and we find evidence for a corresponding significant decrease in X-ray absorbing column (NH). The apparent correlated change in AV and NH is suggestive of variable obscuration of the stellar photosphere by disc material composed of both gas and dust. However, in both observations, the inferred NH to AV ratio is lower than that typical of the interstellar medium, suggesting that the disc is either depleted of gas or is deficient in metals in the gas phase.

  15. Accretion and outflow activity on the late phases of pre-main-sequence evolution. The case of RZ Piscium

    Science.gov (United States)

    Potravnov, I. S.; Mkrtichian, D. E.; Grinin, V. P.; Ilyin, I. V.; Shakhovskoy, D. N.

    2017-03-01

    RZ Psc is an isolated high-latitude post-T Tauri star that demonstrates a UX Ori-type photometric activity. The star shows very weak spectroscopic signatures of accretion, but at the same time possesses the unusual footprints of the wind in Na i D lines. In the present work we investigate new spectroscopic observations of RZ Psc obtained in 2014 during two observation runs. We found variable blueshifted absorption components (BACs) in lines of the other alcali metals, K i 7699 Å and Ca ii IR triplet. We also confirmed the presence of a weak emission component in the Hα line, which allowed us to estimate the mass accretion rate on the star as Ṁ ≤ 7 × 10-12M⊙ yr-1. We could not reveal any clear periodicity in the appearance of BACs in sodium lines. Nevertheless, the exact coincidence of the structure and velocities of the Na i D absorptions observed with the interval of about one year suggests that such a periodicity should exist.

  16. Impact of initial models and variable accretion rates on the pre-main-sequence evolution of massive and intermediate-mass stars and the early evolution of HII regions

    CERN Document Server

    Haemmerlé, Lionel

    2016-01-01

    Massive star formation requires the accretion of gas at high rate while the star is already bright. Its actual luminosity depends sensitively on the stellar structure. We compute pre-main-sequence tracks for massive and intermediate-mass stars with variable accretion rates and study the evolution of stellar radius, effective temperature and ionizing luminosity, starting at $2\\,M_\\odot$ with convective or radiative structures. The radiative case shows a much stronger swelling of the protostar for high accretion rates than the convective case. For radiative structures, the star is very sensitive to the accretion rate and reacts quickly to accretion bursts, leading to considerable changes in photospheric properties on timescales as short as 100 - 1000 yr. The evolution for convective structures is much less influenced by the instantaneous accretion rate, and produces a monotonically increasing ionizing flux that can be many orders of magnitude smaller than in the radiative case. For massive stars, it results in ...

  17. Impact of initial models and variable accretion rates on the pre-main-sequence evolution of massive and intermediate-mass stars and the early evolution of H II regions

    Science.gov (United States)

    Haemmerlé, Lionel; Peters, Thomas

    2016-05-01

    Massive star formation requires the accretion of gas at high rate while the star is already bright. Its actual luminosity depends sensitively on the stellar structure. We compute pre-main-sequence tracks for massive and intermediate-mass stars with variable accretion rates and study the evolution of stellar radius, effective temperature and ionizing luminosity, starting at 2 M⊙ with convective or radiative structures. The radiative case shows a much stronger swelling of the protostar for high accretion rates than the convective case. For radiative structures, the star is very sensitive to the accretion rate and reacts quickly to accretion bursts, leading to considerable changes in photospheric properties on time-scales as short as 100-1000 yr. The evolution for convective structures is much less influenced by the instantaneous accretion rate, and produces a monotonically increasing ionizing flux that can be many orders of magnitude smaller than in the radiative case. For massive stars, it results in a delay of the H II region expansion by up to 10 000 yr. In the radiative case, the H II region can potentially be engulfed by the star during the swelling, which never happens in the convective case. We conclude that the early stellar structure has a large impact on the radiative feedback during the pre-main-sequence evolution of massive protostars and introduces an important uncertainty that should be taken into account. Because of their lower effective temperatures, our convective models may hint at a solution to an observed discrepancy between the luminosity distribution functions of massive young stellar objects and compact H II regions.

  18. High-precision Radio and Infrared Astrometry of LSPM J1314+1320AB. II. Testing Pre-main-sequence Models at the Lithium Depletion Boundary with Dynamical Masses

    Science.gov (United States)

    Dupuy, Trent J.; Forbrich, Jan; Rizzuto, Aaron; Mann, Andrew W.; Aller, Kimberly; Liu, Michael C.; Kraus, Adam L.; Berger, Edo

    2016-08-01

    We present novel tests of pre-main-sequence models based on individual dynamical masses for the M7 binary LSPM J1314+1320AB. Joint analysis of Keck adaptive optics astrometric monitoring along with Very Long Baseline Array radio data from a companion paper yield component masses of 92.8 ± 0.6 M Jup (0.0885 ± 0.0006 M ⊙) and 91.7 ± 1.0 M Jup (0.0875 ± 0.0010 M ⊙) and a parallactic distance of 17.249 ± 0.013 pc. We find component luminosities consistent with the system being coeval at 80.8 ± 2.5 Myr, according to BHAC15 evolutionary models. The presence of lithium is consistent with model predictions, marking the first test of the theoretical lithium depletion boundary using ultracool dwarfs of known mass. However, we find that the evolutionary model-derived average effective temperature (2950 ± 5 K) is 180 K hotter than that given by a spectral type-{T}{eff} relation based on BT-Settl models (2770 ± 100 K). We suggest that the dominant source of this discrepancy is model radii being too small by ≈13%. In a test mimicking the typical application of models by observers, we derive masses on the H-R diagram using luminosity and BT-Settl temperature. The estimated masses are lower by {46}-19+16 % (2.0σ) than we measure dynamically and would imply that this is a system of ≈50 M Jup brown dwarfs, highlighting the large systematic errors possible in H-R diagram properties. This is the first time masses have been measured for ultracool (≥M6) dwarfs displaying spectral signatures of low gravity. Based on features in the infrared, LSPM J1314+1320AB appears to have higher gravity than typical Pleiades and AB Dor members, opposite the expectation given its younger age. The components of LSPM J1314+1320AB are now the nearest, lowest mass pre-main-sequence stars with direct mass measurements. Data presented herein were obtained at the W. M. Keck Observatory, which is operated as a scientific partnership among the California Institute of Technology, the

  19. Magnetic fields and differential rotation on the pre-main sequence II: The early-G star HD 141943 - coronal magnetic field, H-alpha emission and differential rotation

    CERN Document Server

    Marsden, S C; Vélez, J C Ramírez; Alecian, E; Brown, C J; Carter, B D; Donati, J F; Dunstone, N; Hart, R; Semel, M; Waite, I A

    2011-01-01

    Spectropolarimetric observations of the pre-main sequence early-G star HD 141943 were obtained at three observing epochs (2007, 2009 and 2010). The observations were obtained using the 3.9-m Anglo-Australian telescope with the UCLES echelle spectrograph and the SEMPOL spectropolarimeter visitor instrument. The brightness and surface magnetic field topologies (given in Paper I) were used to determine the star's surface differential rotation and reconstruct the coronal magnetic field of the star. The coronal magnetic field at the 3 epochs shows on the largest scales that the field structure is dominated by the dipole component with possible evidence for the tilt of the dipole axis shifting between observations. We find very high levels of differential rotation on HD 141943 (~8 times the solar value for the magnetic features and ~5 times solar for the brightness features) similar to that evidenced by another young early-G star, HD 171488. These results indicate that a significant increase in the level of differe...

  20. High-Precision Radio and Infrared Astrometry of LSPM J1314+1320AB - II: Testing Pre--Main-Sequence Models at the Lithium Depletion Boundary with Dynamical Masses

    CERN Document Server

    Dupuy, Trent J; Rizzuto, Aaron; Mann, Andrew W; Aller, Kimberly; Liu, Michael C; Kraus, Adam L; Berger, Edo

    2016-01-01

    We present novel tests of pre$-$main-sequence models based on individual dynamical masses for the M7 binary LSPM J1314+1320AB. Joint analysis of our Keck adaptive optics astrometric monitoring along with Very Long Baseline Array radio data from a companion paper yield component masses of $0.0885\\pm0.0006$ $M_{\\odot}$ and $0.0875\\pm0.0010$ $M_{\\odot}$ and a parallactic distance of $17.249\\pm0.013$ pc. We also derive component luminosities that are consistent with the system being coeval at an age of $80.8\\pm2.5$ Myr, according to BHAC15 evolutionary models. The presence of lithium is consistent with model predictions, marking the first time the theoretical lithium depletion boundary has been tested with ultracool dwarfs of known mass. However, we find that the average evolutionary model-derived effective temperature ($2950\\pm5$ K) is 180 K hotter than we derive from a spectral type$-$$T_{\\rm eff}$ relation based on BT-Settl models ($2770\\pm100$ K). We suggest that the dominant source of this discrepancy is mod...

  1. Thermohaline instability and rotation-induced mixing. III - Grid of stellar models and asymptotic asteroseismic quantities from the pre-main sequence up to the AGB for low- and intermediate-mass stars at various metallicities

    CERN Document Server

    Lagarde, N; Charbonnel, C; Eggenberger, P; Ekström, S; Palacios, A

    2012-01-01

    The availability of asteroseismic constraints for a large sample of stars from the missions CoRoT and Kepler paves the way for various statistical studies of the seismic properties of stellar populations. In this paper, we evaluate the impact of rotation-induced mixing and thermohaline instability on the global asteroseismic parameters at different stages of the stellar evolution from the Zero Age Main Sequence to the Thermally Pulsating Asymptotic Giant Branch to distinguish stellar populations. We present a grid of stellar evolutionary models for four metallicities (Z = 0.0001, 0.002, 0.004, and 0.014) in the mass range between 0.85 to 6.0 Msun. The models are computed either with standard prescriptions or including both thermohaline convection and rotation-induced mixing. For the whole grid we provide the usual stellar parameters (luminosity, effective temperature, lifetimes, ...), together with the global seismic parameters, i.e. the large frequency separation and asymptotic relations, the frequency corre...

  2. Pre-main sequence spectroscopic binaries suitable for VLTI observations

    CERN Document Server

    Guenther, E W; Mundt, R; Covino, E; Alcalá, J M; Cusano, F; Stecklum, B

    2007-01-01

    A severe problem of the research in star-formation is that the masses of young stars are almost always estimated only from evolutionary tracks. Since the tracks published by different groups differ, it is often only possible to give a rough estimate of the masses of young stars. It is thus crucial to test and calibrate the tracks. Up to now, only a few tests of the tracks could be carried out. However, with the VLTI it is now possible to set constrains on the tracks by determining the masses of many young binary stars precisely. In order to use the VLTI efficiently, a first step is to find suitable targets, which is the purpose of this work. Given the distance of nearby star-forming regions, suitable VLTI targets are binaries with orbital periods between at least 50 days, and few years. Although a number of surveys for detecting spectroscopic binaries have been carried out, most of the binaries found so far have periods which are too short. We thus surveyed the Chamaeleon, Corona Australis, Lupus, Sco-Cen, rh...

  3. Orbital Parameters for a Pre-Main Sequence Binary System

    Science.gov (United States)

    Karnath, Nicole; Prato, L.; Wasserman, L.

    2011-01-01

    The young system VSB 111 was originally classified as a single-lined spectroscopic binary in the star forming region of NGC 2264. Using the Keck II telescope we measured radial velocities for both the primary and secondary components in the infrared. By combining these data with previous visible light observations of the primary star, we derived the period, eccentricity, and other orbital parameters, as well as the mass ratio of the system. With additional information gained from further observations, for example the inclination derived from the angularly resolved orbit, we will eventually obtain the individual stellar masses, necessary to help to calibrate models of young star evolution. Furthermore, by compiling dozens or even hundreds of mass ratios for young binaries we can use mass ratio distributions to improve our understanding of binary star formation. No infrared excess or any other indication of a circumstellar disk is in evidence for VSB 111, indicating that either the accretion rate has dropped to an undetectable value or that this system has aged enough that its disk has dissipated, if originally present. Given the approximately 900 day period of this system, and its relatively high eccentricity, 0.8, the action of the companion could have been responsible for early dissipation of any disk material.

  4. Chemical analysis of 24 dusty (pre-)main-sequence stars

    CERN Document Server

    Acke, B; Acke, Bram; Waelkens, Christoffel

    2004-01-01

    We have analysed the chemical photospheric composition of 24 Herbig Ae/Be and Vega-type stars in search for the lambda Bootis phenomenon. We present the results of the elemental abundances of the sample stars. Some of the stars were never before studied spectroscopically at optical wavelengths. We have determined the projected rotational velocities of our sample stars. Furthermore, we discuss stars that depict a (selective) depletion pattern in detail. HD 4881 and HD 139614 seem to display an overall deficiency. AB Aur and possibly HD 126367 have subsolar values for the iron abundance, but are almost solar in silicon. HD 100546 is the only clear lambda Bootis star in our sample.

  5. SNMR pulse sequence phase cycling

    Science.gov (United States)

    Walsh, David O; Grunewald, Elliot D

    2013-11-12

    Technologies applicable to SNMR pulse sequence phase cycling are disclosed, including SNMR acquisition apparatus and methods, SNMR processing apparatus and methods, and combinations thereof. SNMR acquisition may include transmitting two or more SNMR pulse sequences and applying a phase shift to a pulse in at least one of the pulse sequences, according to any of a variety cycling techniques. SNMR processing may include combining SNMR from a plurality of pulse sequences comprising pulses of different phases, so that desired signals are preserved and indesired signals are canceled.

  6. Solid phase sequencing of biopolymers

    Energy Technology Data Exchange (ETDEWEB)

    Cantor, Charles (Del Mar, CA); Koster, Hubert (La Jolla, CA)

    2010-09-28

    This invention relates to methods for detecting and sequencing target nucleic acid sequences, to mass modified nucleic acid probes and arrays of probes useful in these methods, and to kits and systems which contain these probes. Useful methods involve hybridizing the nucleic acids or nucleic acids which represent complementary or homologous sequences of the target to an array of nucleic acid probes. These probes comprise a single-stranded portion, an optional double-stranded portion and a variable sequence within the single-stranded portion. The molecular weights of the hybridized nucleic acids of the set can be determined by mass spectroscopy, and the sequence of the target determined from the molecular weights of the fragments. Nucleic acids whose sequences can be determined include DNA or RNA in biological samples such as patient biopsies and environmental samples. Probes may be fixed to a solid support such as a hybridization chip to facilitate automated molecular weight analysis and identification of the target sequence.

  7. Solid phase sequencing of biopolymers

    Science.gov (United States)

    Cantor, Charles R.; Hubert, Koster

    2014-06-24

    This invention relates to methods for detecting and sequencing target nucleic acid sequences, to mass modified nucleic acid probes and arrays of probes useful in these methods, and to kits and systems which contain these probes. Useful methods involve hybridizing the nucleic acids or nucleic acids which represent complementary or homologous sequences of the target to an array of nucleic acid probes. These probes comprise a single-stranded portion, an optional double-stranded portion and a variable sequence within the single-stranded portion. The molecular weights of the hybridized nucleic acids of the set can be determined by mass spectroscopy, and the sequence of the target determined from the molecular weights of the fragments. Probes may be affixed to a solid support such as a hybridization chip to facilitate automated molecular weight analysis and identification of the target sequence.

  8. Accretion in the Rho-Oph pre-main sequence stars

    CERN Document Server

    Natta, A; Testi, L

    2006-01-01

    The aim of this paper is to provide a measurement of the mass accretion rate in a large, complete sample of objects in the core of the star forming region Rho-Oph. The sample includes most of the objects (104 out of 111) with evidence of a circumstellar disk from mid-infrared photometry; it covers a stellar mass range from about 0.03 to 3 Msun and it is complete to a limiting mass of ~0.05 Msun. We used J and K-band spectra to derive the mass accretion rate of each object from the intensity of the hydrogen recombination lines, Pab or Brg. For comparison, we also obtained similar spectra of 35 diskless objects. The results show that emission in these lines is only seen in stars with disks, and can be used as an indicator of accretion. However, the converse does not hold, as about 50% of our disk objects do not have detectable line emission. The measured accretion rates show a strong correlation with the mass of the central object (Macc ~ Mstar^1.8+-0.2) and a large spread, of two orders of magnitude at least, ...

  9. Empirical Tests of Pre-Main-Sequence Stellar Evolution Models with Eclipsing Binaries

    CERN Document Server

    Stassun, Keivan G; Torres, Guillermo

    2014-01-01

    We examine the performance of standard PMS stellar evolution models against the accurately measured properties of a benchmark sample of 26 PMS stars in 13 EB systems. We provide a definitive compilation of all fundamental properties for the EBs. We also provide a definitive compilation of the various PMS model sets. In the H-R diagram, the masses inferred for the individual stars by the models are accurate to better than 10% above 1 Msun, but below 1 Msun they are discrepant by 50-100%. We find evidence that the failure of the models to match the data is linked to the triples in the EB sample; at least half of the EBs possess tertiary companions. Excluding the triples, the models reproduce the stellar masses to better than ~10% in the H-R diagram, down to 0.5 Msun, below which the current sample is fully contaminated by tertiaries. We consider several mechanisms by which a tertiary might cause changes in the EB properties and thus corrupt the agreement with stellar model predictions. We show that the energies...

  10. YSOVAR: Six Pre-main-sequence Eclipsing Binaries in the Orion Nebula Cluster

    Science.gov (United States)

    2012-06-25

    includes background subtraction, cosmic -hit removal, flat-fielding, and wavelength calibration. 23 http://www2.keck.hawaii.edu/inst/nirspec-old/redspec...Inclination and combined radius are highly degenerated; inclination and temperature ratio are less so, but also provide weaker constraints. (A color version of...example, the model isochrones of Siess et al. (2000) predict a radius sum of 11.1–14.5R for ages in the range of 0.3–2 Myr. 5.2. ISOY J0535−0447 ISOY

  11. Active Phenomena in the Pre-main Sequence Star AB AUR

    Science.gov (United States)

    Praderie, F.; Simon, T.; Boesgaard, A. M.; Felenbok, P.; Catala, C.; Czarny, J.; Talavera, A.

    1985-01-01

    The Herbig Ae star AB Aur presents short time scale variability in the Mg II and Ca II resonance lines. A qualitative model of the expanding envelope, involving fast and slow streams in a co-rotating structure, is proposed to explain the Mg II spectral variability.

  12. Old pre-main-sequence Stars: Disc reformation by Bondi-Hoyle accretion

    CERN Document Server

    Scicluna, P; Dale, J E; Testi, L

    2014-01-01

    Young stars show evidence of accretion discs which evolve quickly and disperse with an e-folding time of $\\sim$ 3Myr. This is in striking contrast with recent observations that suggest evidence for numerous $>30$ Myr old stars with an accretion disc in large star-forming complexes. We consider whether these observations of apparently old accretors could be explained by invoking Bondi-Hoyle accretion to rebuild a new disc around these stars during passage through a clumpy molecular cloud. We combine a simple Monte Carlo model to explore the capture of mass by such systems with a viscous evolution model to infer the levels of accretion that would be observed. We find that a significant fraction of stars may capture enough material via the Bondi-Hoyle mechanism to rebuild a disc of mass $\\gtrsim$ 1 minimum-mass solar nebula, and $\\lesssim 10\\%$ accrete at observable levels at any given time. A significant fraction of the observed old accretors may be explained with our proposed mechanism. Such accretion may prov...

  13. Pre-main sequence stars with disks in the Eagle Nebula observed in scattered light

    CERN Document Server

    Guarcello, M G; Micela, G; Peres, G; Prisinzano, L; Sciortino, S

    2010-01-01

    NGC6611 and its parental cloud, the Eagle Nebula (M16), are well-studied star-forming regions, thanks to their large content of both OB stars and stars with disks and the observed ongoing star formation. We identified 834 disk-bearing stars associated with the cloud, after detecting their excesses in NIR bands from J band to 8.0 micron. In this paper, we study in detail the nature of a subsample of disk-bearing stars that show peculiar characteristics. They appear older than the other members in the V vs. V-I diagram, and/or they have one or more IRAC colors at pure photospheric values, despite showing NIR excesses, when optical and infrared colors are compared. We confirm the membership of these stars to M16 by a spectroscopic analysis. The physical properties of these stars with disks are studied by comparing their spectral energy distributions (SEDs) with the SEDs predicted by models of T-Tauri stars with disks and envelopes. We show that the age of these stars estimated from the V vs. V-I diagram is unrel...

  14. The pre-main sequence population of NGC 6530 in M8

    Directory of Open Access Journals (Sweden)

    J. I. Arias

    2006-01-01

    Full Text Available Presentamos los resultados de una investigaci on de probables miembros d ebiles del c umulo abierto muy joven NGC 6530 en M8, basados en espectroscop a de resoluci on intermedia obtenida con el telescopio Magallanes I de 6.5 m del Observatorio Las Campanas. El an alisis de los espectros condujo al descubrimiento de 39 nuevas estrellas de pre-secuencia principal en la regi on. De acuerdo a los tipos espectrales, y a la presencia de l neas de emisi on y de l nea de absorci on de litio, identi camos 30 estrellas T-Tauri cl asicas, 7 estrellas T-Tauri d ebiles y dos objetos Herbig Ae/Be. Utilizando magnitudes infrarrojas de 2MASS y de nuestro trabajo previo, y las huellas evolutivas de Palla & Stahler (1999, estimamos las masas y edades de estas estrellas. Encontramos que casi todas las estrellas de nuestra muestra son m as j ovenes que 3 106 a~nos y abarcan un intervalo de masas de entre 0.8 y 2.0 M .

  15. Pre-main-sequence population in NGC 1893 region: X-ray properties

    CERN Document Server

    Pandey, A K; Yadav, Ram Kesh; Richichi, Andrea; Lata, Sneh; Pandey, J C; Ojha, D K; Chen, W P

    2013-01-01

    Continuing the attempt to understand the properties of the stellar content in the young cluster NGC 1893 we have carried out a comprehensive multi-wavelength study of the region. The present study focuses on the X-ray properties of T-Tauri Stars (TTSs) in the NGC 1893 region. We found a correlation between the X-ray luminosity, $L_X$, and the stellar mass (in the range 0.2$-$2.0 \\msun) of TTSs in the NGC 1893 region, similar to those reported in some other young clusters, however the value of the power-law slope obtained in the present study ($\\sim$ 0.9) for NGC 1893 is smaller than those ($\\sim$1.4 - 3.6) reported in the case of TMC, ONC, IC 348 and Chameleon star forming regions. However, the slope in the case of Class III sources (Weak line TTSs) is found to be comparable to that reported in the case of NGC 6611 ($\\sim$ 1.1). It is found that the presence of circumstellar disks has no influence on the X-ray emission. The X-ray luminosity for both CTTSs and WTTSs is found to decrease systematically with age...

  16. The Structure of the Accretion Flow on pre-main-sequence stars

    Science.gov (United States)

    Calvet, Nuria

    1999-07-01

    We propose to test an essential prediction of the magnetospheric accretion model for T Tauri stars. STIS echelle spectra will be used to search for the relatively narrow high-temperature emission lines that must result from the magnetospheric accretion shock, but are not expected in the previous, alternative boundary layer model. By combining the results from high temperature {10^5 K} lines, accessible only with HST, with optical lines and optical-UV continuum emission, we will develop physically self-consistent models of accretion shock structure. The geometrically distribution of the emitting gas as derived from our results will test theories of mass-loading of magnetic field lines at the magnetosphere-disk interface. Analysis of the UV emission lines will also provide improved calibrations between ultraviolet continuum emission and accretion luminosities, and thus improve estimates of mass accretion rates for T Tauri stars.

  17. Extreme value statistics for two-dimensional convective penetration in a pre-main sequence star

    Science.gov (United States)

    Pratt, J.; Baraffe, I.; Goffrey, T.; Constantino, T.; Viallet, M.; Popov, M. V.; Walder, R.; Folini, D.

    2017-08-01

    Context. In the interior of stars, a convectively unstable zone typically borders a zone that is stable to convection. Convective motions can penetrate the boundary between these zones, creating a layer characterized by intermittent convective mixing, and gradual erosion of the density and temperature stratification. Aims: We examine a penetration layer formed between a central radiative zone and a large convection zone in the deep interior of a young low-mass star. Using the Multidimensional Stellar Implicit Code (MUSIC) to simulate two-dimensional compressible stellar convection in a spherical geometry over long times, we produce statistics that characterize the extent and impact of convective penetration in this layer. Methods: We apply extreme value theory to the maximal extent of convective penetration at any time. We compare statistical results from simulations which treat non-local convection, throughout a large portion of the stellar radius, with simulations designed to treat local convection in a small region surrounding the penetration layer. For each of these situations, we compare simulations of different resolution, which have different velocity magnitudes. We also compare statistical results between simulations that radiate energy at a constant rate to those that allow energy to radiate from the stellar surface according to the local surface temperature. Results: Based on the frequency and depth of penetrating convective structures, we observe two distinct layers that form between the convection zone and the stable radiative zone. We show that the probability density function of the maximal depth of convective penetration at any time corresponds closely in space with the radial position where internal waves are excited. We find that the maximal penetration depth can be modeled by a Weibull distribution with a small shape parameter. Using these results, and building on established scalings for diffusion enhanced by large-scale convective motions, we propose a new form for the diffusion coefficient that may be used for one-dimensional stellar evolution calculations in the large Péclet number regime. These results should contribute to the 321D link.

  18. The discovery of a low mass, pre-main-sequence stellar association around $\\gamma$ Velorum

    CERN Document Server

    Pozzo, M; Naylor, T; Totten, E J; Harmer, S; Kenyon, M E

    2000-01-01

    We report the serendipitous discovery of a population of low mass, pre-mainsequence stars (PMS) in the direction of the Wolf-Rayet/O-star binary systemgamma^{2} Vel and the Vela OB2 association. We argue that gamma^{2} Vel and thelow mass stars are truly associated, are approximately coeval and that both areat distances between 360-490 pc, disagreeing at the 2 sigma level with therecent Hipparcos parallax of gamma^{2} Vel, but consistent with older distanceestimates. Our results clearly have implications for the physical parameters ofthe gamma^{2} Vel system, but also offer an exciting opportunity to investigatethe influence of high mass stars on the mass function and circumstellar disclifetimes of their lower mass PMS siblings.

  19. Thirty-two phase sequences design with good autocorrelation properties

    Indian Academy of Sciences (India)

    S P Singh; K Subba Rao

    2010-02-01

    Polyphase Barker Sequences are finite length, uniform complex sequences; the magnitude of their aperiodic autocorrelation sidelobes are bounded by 1. Such sequences have been used in numerous real-world applications such as channel estimation, radar and spread spectrum communication. In this paper, thirty-two phase Barker sequences up to length 24 with an alphabet size of only 32 are presented. The sequences from length 25 to 289 have autocorrelation properties better than well-known Frank codes. Because of the complex structure the sequences are very difficult to detect and analyse by an enemy’s electronic support measures (ESMs). The synthesized sequences are promising for practical application to radar and spread spectrum communication systems. These sequences are found using the Modified Simulated Annealing Algorithm (MSAA). The convergence rate of the algorithm is good.

  20. Temporal extension of phase screen sequences using proper orthogonal decomposition

    Science.gov (United States)

    Henriksson, Markus; Sjöqvist, Lars; Tidström, Jonas

    2016-10-01

    For performance modelling of optical countermeasure systems simulation of turbulence effects is necessary. Physical optics numerical beam propagation using phase screens is an established method in this respect. In some cases a short sequence of temporally resolved phase screens is available from Computational Fluid Dynamics (CFD) simulations or from wavefront sensor measurements. It is, however, seldom possible to provide enough sequences and sufficient sequence length for Monte Carlo simulations of system performance utilizing these methods. Therefore, we have investigated the possibility to generate an arbitrary number of longer temporal sequences of phase screens with the same statistical properties for simulation of turbulence, based on an available short phase screen sequence. The method apply Proper Orthogonal Decomposition (POD), a method used to generate orthogonal modes from a dataset. For discretely sampled sequences the Singular Value Decomposition (SVD) algorithm is suitable to extract the set of POD modes. This scheme provides a separate temporal sequence of coefficients for each spatial mode. The next step is to generate new, longer temporal sequences of coefficients with the same statistical properties as those extracted by the SVD algorithm. Finally a new sequence of phase screens is generated by adding all spatial modes. The method is illustrated using data from CFD calculations of a down-scaled jet engine plume. The method is especially suitable for very strong localized turbulence as in aero optics and engine exhaust plumes, but may be useful also for extended turbulence. The use to generate Power-In-Bucket (PIB) sequences for evaluation of turbulence distortion effects is demonstrated. PIB is an important quantity when evaluating e.g. the performance of directed infrared countermeasure (DIRCM) systems.

  1. Solid-Phase Purification of Synthetic DNA Sequences.

    Science.gov (United States)

    Grajkowski, Andrzej; Cieslak, Jacek; Beaucage, Serge L

    2016-08-05

    Although high-throughput methods for solid-phase synthesis of DNA sequences are currently available for synthetic biology applications and technologies for large-scale production of nucleic acid-based drugs have been exploited for various therapeutic indications, little has been done to develop high-throughput procedures for the purification of synthetic nucleic acid sequences. An efficient process for purification of phosphorothioate and native DNA sequences is described herein. This process consists of functionalizing commercial aminopropylated silica gel with aminooxyalkyl functions to enable capture of DNA sequences carrying a 5'-siloxyl ether linker with a "keto" function through an oximation reaction. Deoxyribonucleoside phosphoramidites functionalized with the 5'-siloxyl ether linker were prepared in yields of 75-83% and incorporated last into the solid-phase assembly of DNA sequences. Capture of nucleobase- and phosphate-deprotected DNA sequences released from the synthesis support is demonstrated to proceed near quantitatively. After shorter than full-length DNA sequences were washed from the capture support, the purified DNA sequences were released from this support upon treatment with tetra-n-butylammonium fluoride in dry DMSO. The purity of released DNA sequences exceeds 98%. The scalability and high-throughput features of the purification process are demonstrated without sacrificing purity of the DNA sequences.

  2. An investigation of Hebbian phase sequences as assembly graphs

    Directory of Open Access Journals (Sweden)

    Daniel Gomes Almeida Filho

    2014-04-01

    Full Text Available Hebb proposed that synapses between neurons that fire synchronously are strengthened, forming cell assemblies and phase sequences. The former, on a shorter scale, are ensembles of synchronized cells that function transiently as a closed processing system; the latter, on a larger scale, correspond to the sequential activation of cell assemblies able to represent percepts and behaviors. Nowadays, the recording of large neuronal populations allows for the detection of multiple cell assemblies. Within Hebb’s theory, the next logical step is the analysis of phase sequences. Here we detected phase sequences as consecutive assembly activation patterns, and then analyzed their graph attributes in relation to behavior. We investigated action potentials recorded from the adult rat hippocampus and neocortex before, during and after novel object exploration (experimental periods. Within assembly graphs, each assembly corresponded to a node, and each edge corresponded to the temporal sequence of consecutive node activations. The sum of all assembly activations was proportional to firing rates, but the activity of individual assemblies was not. Assembly repertoire was stable across experimental periods, suggesting that novel experience does not create new assemblies in the adult rat. Assembly graph attributes, on the other hand, varied significantly across behavioral states and experimental periods, and were separable enough to correctly classify experimental periods (Naïve Bayes classifier; maximum AUROCs ranging from 0.55 to 0.99 and behavioral states (waking, slow wave sleep, and rapid eye movement sleep; maximum AUROCs s ranging from 0.64 to 0.98. Our findings agree with Hebb’s view that assemblies correspond to primitive building blocks of representation, nearly unchanged in the adult, while phase sequences are labile across behavioral states and change after novel experience. The results are compatible with a role for phase sequences in behavior

  3. The Gaia-ESO Survey: the first abundance determination of the pre-main-sequence cluster Gamma Velorum

    CERN Document Server

    Spina, L; Palla, F; Sacco, G G; Magrini, L; Franciosini, E; Morbidelli, L; Prisinzano, L; Alfaro, E J; Biazzo, K; Frasca, A; Hernandez, J I Gonzalez; Sousa, S G; Adibekyan, V; Delgado-Mena, E; Montes, D; Tabernero, H; Klutsch, A; Gilmore, G; Feltzing, S; Jeffries, R D; Micela, G; Vallenari, A; Bensby, T; Bragaglia, A; Flaccomio, E; Koposov, S; Lanzafame, A C; Pancino, E; Recio-Blanco, A; Smiljanic, R; Costado, M T; Damiani, F; Hill, V; Hourihane, A; Jofre, P; de Laverny, P; Masseron, T; Worley, C

    2014-01-01

    Knowledge of the abundance distribution of star forming regions and young clusters is critical to investigate a variety of issues, from triggered star formation and chemical enrichment by nearby supernova explosions to the ability to form planetary systems.In spite of this, detailed abundance studies are currently available for relatively few regions. In this context, we present the analysis of the metallicity of the Gamma Velorum cluster, based on the products distributed in the first internal release of the Gaia-ESO Survey. The Gamma Velorum candidate members have been observed with FLAMES, using both UVES and Giraffe, depending on the target brightness and spectral type. In order to derive a solid metallicity determination for the cluster, membership of the observed stars must be first assessed. To this aim, we use several membership criteria including radial velocities, surface gravity estimates, and the detection of the photospheric lithium line. Out of the 80 targets observed with UVES, we identify 14 h...

  4. The Gaia-ESO Survey: pre-main-sequence stars in the young open cluster NGC 3293

    Science.gov (United States)

    Delgado, A. J.; Sampedro, L.; Alfaro, E. J.; Costado, M. T.; Yun, J. L.; Frasca, A.; Lanzafame, A. C.; Drew, J. E.; Eislöffel, J.; Blomme, R.; Morel, T.; Lobel, A.; Semaan, T.; Randich, S.; Jeffries, R. D.; Micela, G.; Vallenari, A.; Kalari, V.; Gilmore, G.; Flaccomio, E.; Carraro, G.; Lardo, C.; Monaco, L.; Prisinzano, L.; Sousa, S. G.; Morbidelli, L.; Lewis, J.; Koposov, S.; Hourihane, A.; Worley, C.; Casey, A.; Franciosini, E.; Sacco, G.; Magrini, L.

    2016-08-01

    The young open cluster NGC3293 is included in the observing program of the Gaia-ESO survey (GES). The radial velocity values provided have been used to assign cluster membership probabilities by means of a single-variable parametric analysis. These membership probabilities are compared to the results of the photometric membership assignment of NGC3293, based on UBVRI photometry. The agreement of the photometric and kinematic member samples amounts to 65 per cent, and could increase to 70 per cent as suggested by the analysis of the differences between both samples. A number of photometric PMS candidate members of spectral type F are found, which are confirmed by the results from VPHAS photometry and SED fitting for the stars in common with VPHAS and GES data sets. Excesses at mid- and near-infrared wavelengths, and signs of Hα emission, are investigated for them. Marginal presence of Hα emission or infilling is detected for the candidate members. Several of them exhibit moderate signs of U excess and weak excesses at mid-IR wavelengths. We suggest that these features originate from accretion discs in their last stages of evolution.

  5. Dust disks around old Pre Main-Sequence stars HST\\/NICMOS2 scattered light images and modeling

    CERN Document Server

    Augereau, J C; Mouillet, D; Ménard, F

    2000-01-01

    We present recent near-infrared detections of circumstellar disks around the two old PMS Herbig stars HD 141569 and HD 100546 obtained with the HST/NICMOS2 camera. They reveal extended structures larger than 350-400 AU in radius. While the HD 100546 disk appears as a continuous disk down to 40 AU, the HD 141569 environment seems more complex, splitted at least into two dust populations. As a convincing example, the full modeling of the disk surrounding HR 4796, another old PMS star, is detailed and confronted with more recent observations.

  6. EXPORT : Spectral classification and projected rotational velocities of Vega-type and pre-main sequence stars

    NARCIS (Netherlands)

    Mora, A; Merin, B; Solano, E; Montesinos, B; de Winter, D; Eiroa, C; Ferlet, R; Grady, CA; Miranda, LF; Oudmaijer, RD; Palacios, J; Quirrenbach, A; Harris, AW; Rauer, H; Cameron, A; Deeg, HJ; Garzon, F; Penny, A; Schneider, J; Tsapras, Y; Wesselius, PR

    2001-01-01

    In this paper we present the first comprehensive results extracted from the spectroscopic campaigns carried out by the EXPORT (EXoPlanetary Observational Research Team) consortium. During 1998-1999, EXPORT carried out an intensive observational effort in the framework of the origin and evolution of

  7. The fate of the pre-main sequence-rich clusters Collinder197 and vdB92: dissolution?

    CERN Document Server

    Bonatto, Charles

    2010-01-01

    We investigate the nature and possible evolution of the young Galactic star clusters Collinder 197 (Cr 197) and vdB 92. The colour-magnitude diagrams (CMDs) are basically characterised by a poorly-populated MS and a dominant fraction ($\\ga75%$) of PMS stars, and the combined MS and PMS CMD morphology in both clusters consistently constrains the age to within $5\\pm4$ Myr, with a $\\sim10$ Myr spread in the star formation process. The MS$ + $PMS stellar masses are $\\approx660^{+102}_{-59} \\ms$ (Cr 197) and $\\approx750^{+101}_{-51} \\ms$ (vdB 92). Cr 197 and vdB 92 appear to be abnormally large, when compared to clusters within the same age range. They have irregular stellar radial density distributions (RDPs) with a marked excess in the innermost region, a feature that, at less than 10 Myr, is more likely related to the star formation and/or molecular cloud fragmentation than to age-dependent dynamical effects. The velocity dispersion of both clusters, derived from proper motions, is in the range $\\sim15 - 22 \\km...

  8. Dynamo action and magnetic activity during the pre-main sequence: Influence of rotation and structural changes

    Science.gov (United States)

    Emeriau-Viard, Constance; Brun, Allan Sacha

    2017-10-01

    During the PMS, structure and rotation rate of stars evolve significantly. We wish to assess the consequences of these drastic changes on stellar dynamo, internal magnetic field topology and activity level by mean of HPC simulations with the ASH code. To answer this question, we develop 3D MHD simulations that represent specific stages of stellar evolution along the PMS. We choose five different models characterized by the radius of their radiative zone following an evolutionary track, from 1 Myr to 50 Myr, computed by a 1D stellar evolution code. We introduce a seed magnetic field in the youngest model and then we spread it through all simulations. First of all, we study the consequences that the increase of rotation rate and the change of geometry of the convective zone have on the dynamo field that exists in the convective envelop. The magnetic energy increases, the topology of the magnetic field becomes more complex and the axisymmetric magnetic field becomes less predominant as the star ages. The computation of the fully convective MHD model shows that a strong dynamo develops with a ratio of magnetic to kinetic energy reaching equipartition and even super-equipartition states in the faster rotating cases. Magnetic fields resulting from our MHD simulations possess a mixed poloidal-toroidal topology with no obvious dominant component. We also study the relaxation of the vestige dynamo magnetic field within the radiative core and found that it satisfies stability criteria. Hence it does not experience a global reconfiguration and instead slowly relaxes by retaining its mixed poloidal-toroidal topology.

  9. Stellar Activity on the Young Suns of Orion: COUP Observations of K5-7 Pre-Main Sequence Stars

    CERN Document Server

    Wolk, S J; Micela, G; Favata, F; Glassgold, A E; Shang, H; Feigelson, E D

    2005-01-01

    In January 2003, the Chandra Orion Ultradeep Project (COUP) detected about 1400 young stars during a 13.2 day observation of the Orion Nebula Cluster (ONC). This paper studies a well-defined sample of 28 solar-mass COUP sources to characterize the magnetic activity of analogs of the young Sun and thereby to improve understanding of the effects of solar X-rays on the solar nebula during the era of planet formation. We find that active young Suns spend 70% of their time in a characteristic state with relatively constant flux and magnetically confined plasma with temperatures kT_2 = 2.1 * kT_1. During characteristic periods, the 0.5-8 keV X-ray luminosity is about 0.03% of the bolometric luminosity. One or two powerful flares per week with peak luminosities logL_x ~ 30-32 erg/s are typically superposed on this characteristic emission accompanied by heating of the hot plasma component from ~2.4 keV to ~7 keV at the flare peak. The energy distribution of flares superposed on the characteristic emission level follo...

  10. Long-term BVRI light curves of 5 pre-main sequence stars in the field of "Gulf of Mexico"

    CERN Document Server

    Ibryamov, Sunay I; Peneva, Stoyanka P

    2014-01-01

    We present new data from BVRI photometric observations of five PMS stars during the period from April 2013 to July 2014. The stars are located in the field of NGC 7000/IC 5070 ("Gulf of Mexico") - a region with active star formation. The presented paper is a continuation of our long-term photometric investigations of the young stellar objects in this region. The long-term multicolor photometric observations of PMS stars are very important for their exact classification. Our results show that the studied stars exhibit different types of photometric variability in all bands. We tried to classify them using our data from the long-term photometry and data published by other authors.

  11. Long-term BVRI light curves of 5 pre-main sequence stars in the field of "Gulf of Mexico"

    OpenAIRE

    Ibryamov, Sunay I.; Semkov, Evgeni H.; Peneva, Stoyanka P.

    2014-01-01

    We present new data from BVRI photometric observations of five PMS stars during the period from April 2013 to July 2014. The stars are located in the field of NGC 7000/IC 5070 ("Gulf of Mexico") - a region with active star formation. The presented paper is a continuation of our long-term photometric investigations of the young stellar objects in this region. The long-term multicolor photometric observations of PMS stars are very important for their exact classification. Our results show that ...

  12. Automated detection of cardiac phase from intracoronary ultrasound image sequences.

    Science.gov (United States)

    Sun, Zheng; Dong, Yi; Li, Mengchan

    2015-01-01

    Intracoronary ultrasound (ICUS) is a widely used interventional imaging modality in clinical diagnosis and treatment of cardiac vessel diseases. Due to cyclic cardiac motion and pulsatile blood flow within the lumen, there exist changes of coronary arterial dimensions and relative motion between the imaging catheter and the lumen during continuous pullback of the catheter. The action subsequently causes cyclic changes to the image intensity of the acquired image sequence. Information on cardiac phases is implied in a non-gated ICUS image sequence. A 1-D phase signal reflecting cardiac cycles was extracted according to cyclical changes in local gray-levels in ICUS images. The local extrema of the signal were then detected to retrieve cardiac phases and to retrospectively gate the image sequence. Results of clinically acquired in vivo image data showed that the average inter-frame dissimilarity of lower than 0.1 was achievable with our technique. In terms of computational efficiency and complexity, the proposed method was shown to be competitive when compared with the current methods. The average frame processing time was lower than 30 ms. We effectively reduced the effect of image noises, useless textures, and non-vessel region on the phase signal detection by discarding signal components caused by non-cardiac factors.

  13. [Producing a sequence of movements in response to a sequence of visual stimuli. Inter-individual differences in early phase of sequence learning].

    Science.gov (United States)

    Kurganskiĭ, A V; Grigal, P P

    2009-01-01

    In this work, we studied the inter-individual variants at the early stage of serial learning in the sequence reproduction task where subjects were asked to produce a sequence of movements whose serial order was given by the sequence of visual stimuli. A total of 20 adults participated in the experiment where, besides the sequence reproduction task, each subject also performed the simple visuomotor reaction time task, the choice reaction time task and the serial reaction time task. It was found that individual latencies vs. trial number plots (learning curves) were characterized by one distinctive feature: the latency reduction, if any, took a form of either an abrupt decline down to a stationary level (fast phase) or a gradual approximately linear leveling off over the entire block of 60 trials (slow phase). The diversity of the individual learning curves were limited to the following four types: a flat curve, a curve with the fast phase only, a curve with the slow phase only, and a curve that combined both phases with the leading fast phase followed by the slow phase. All the subjects were subdivided into four groups according to the subject's type of learning curve. We analyzed the correlation pattern between temporal indices (latencies and inter-response intervals) and compared these indices to simple visuomotor reaction time, choice reaction time and the amount of learning in the serial reaction time task. The significant between-group differences found in this analysis suggest that there are some essential functional differences related to the group break up. It was suggested that inter-individual variants in the character of the early stage of sequence learning are determined mainly by the functional and structural complexity of the internal representation of the sequence and by the way the working memory operates in order to recognize the driving sequence of visual stimuli and to translate the internal representation of a sequence into motor commands.

  14. A hybrid approach for de novo human genome sequence assembly and phasing.

    Science.gov (United States)

    Mostovoy, Yulia; Levy-Sakin, Michal; Lam, Jessica; Lam, Ernest T; Hastie, Alex R; Marks, Patrick; Lee, Joyce; Chu, Catherine; Lin, Chin; Džakula, Željko; Cao, Han; Schlebusch, Stephen A; Giorda, Kristina; Schnall-Levin, Michael; Wall, Jeffrey D; Kwok, Pui-Yan

    2016-07-01

    Despite tremendous progress in genome sequencing, the basic goal of producing a phased (haplotype-resolved) genome sequence with end-to-end contiguity for each chromosome at reasonable cost and effort is still unrealized. In this study, we describe an approach to performing de novo genome assembly and experimental phasing by integrating the data from Illumina short-read sequencing, 10X Genomics linked-read sequencing, and BioNano Genomics genome mapping to yield a high-quality, phased, de novo assembled human genome.

  15. A High-Throughput Process for the Solid-Phase Purification of Synthetic DNA Sequences.

    Science.gov (United States)

    Grajkowski, Andrzej; Cieślak, Jacek; Beaucage, Serge L

    2017-06-19

    An efficient process for the purification of synthetic phosphorothioate and native DNA sequences is presented. The process is based on the use of an aminopropylated silica gel support functionalized with aminooxyalkyl functions to enable capture of DNA sequences through an oximation reaction with the keto function of a linker conjugated to the 5'-terminus of DNA sequences. Deoxyribonucleoside phosphoramidites carrying this linker, as a 5'-hydroxyl protecting group, have been synthesized for incorporation into DNA sequences during the last coupling step of a standard solid-phase synthesis protocol executed on a controlled pore glass (CPG) support. Solid-phase capture of the nucleobase- and phosphate-deprotected DNA sequences released from the CPG support is demonstrated to proceed near quantitatively. Shorter than full-length DNA sequences are first washed away from the capture support; the solid-phase purified DNA sequences are then released from this support upon reaction with tetra-n-butylammonium fluoride in dry dimethylsulfoxide (DMSO) and precipitated in tetrahydrofuran (THF). The purity of solid-phase-purified DNA sequences exceeds 98%. The simulated high-throughput and scalability features of the solid-phase purification process are demonstrated without sacrificing purity of the DNA sequences. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

  16. Spectrum analysis of complicated radiolocation signal with binary phase manipulation by Kasami sequence

    Directory of Open Access Journals (Sweden)

    O. D. Mrachkovskyi

    2015-06-01

    Full Text Available Introduction. This article contain short introduction to history of complicated signals and list of common sequences, used in spectrum spreading. Method of creating Kasami sequences. In this article is shown sequence creation method, based on method of creating maximum length sequence. Creating of the structural schema of Kasami sequences generator. Principles of construction of Kasami sequence generator are shown in this article. Example of generator for sequence with length 63 symbols, which are created using method, mentioned in previous article, is also shown. Spectrum of Kasami sequences. This article contain amplitude and phase spectrum of two Kasami sequences with lengths of 1023 and 255 symbols. Theoretical formulas are created using Discrete Fourier Transform operation, and graphics are plotted using Fast Fourier Transform operation. Phase spectrum data are also been changed by unwrap operation for better visibility. Conclusion. This article contain analysis of characteristics of previously shown spectrum. Several conclusions are made about correlation between sequence and spectrum characteristics. These conclusions include that made about amplitude spectrum form dependence of sequence length, type and basic impulse characteristics.

  17. Reference genome-independent assessment of mutation density using restriction enzyme-phased sequencing

    Science.gov (United States)

    Determining the mutation rates in single individuals is a significant challenge requiring a substantial amount of sequencing and analysis. We have developed a simple method based on restriction enzyme-phased sequencing to measure the mutation density by comparing a wild type to mutagenized individua...

  18. Phase-sensitive fat suppression steady-state free procession sequence with phase correction

    Institute of Scientific and Technical Information of China (English)

    Zu Zhong-Liang; Zhou Kun; Zhang Shi-Gang; Gao Song; Bao Shang-Lian

    2008-01-01

    Robust and fast fat suppression is a challenge in balanced steady-state free precession (SSFP) magnetic resonance imaging.Although single-acquisition phase-sensitive SSFP can provide fat-suppressed images in short scan time,phase errors,especially spatially-dependent phase shift,caused by a variety of factors may result in misplacement of fat and water voxels.In this paper,a novel phase correction algorithm was used to calibrate those phase errors during image reconstruction.This algorithm corrects phase by region growing,employing both the magnitude and the phase information of image pixels.Phantom and in vivo imagings were performed to validate the technique.As a result,excellent fat-suppressed images were acquired by using single-acquisition phase-seusitive SSFP with phase correction.

  19. Efficient Simulation of Quantum States Based on Classical Fields Modulated with Pseudorandom Phase Sequences

    CERN Document Server

    Fu, Jian

    2010-01-01

    We demonstrate that a tensor product structure could be obtained by introducing pseudorandom phase sequences into classical fields with two orthogonal modes. Using classical fields modulated with pseudorandom phase sequences, we discuss efficient simulation of several typical quantum states, including product state, Bell states, GHZ state, and W state. By performing quadrature demodulation scheme, we could obtain the mode status matrix of the simulating classical fields, based on which we propose a sequence permutation mechanism to reconstruct the simulated quantum states. The research on classical simulation of quantum states is important, for it not only enables potential practical applications in quantum computation, but also provides useful insights into fundamental concepts of quantum mechanics.

  20. A new RF tagging pulse based on the Frank poly-phase perfect sequence

    DEFF Research Database (Denmark)

    Laustsen, Christoffer; Greferath, Marcus; Ringgaard, Steffen

    2014-01-01

    Radio frequency (RF) spectrally selective multiband pulses or tagging pulses, are applicable in a broad range of magnetic resonance methods. We demonstrate through simulations and experiments a new phase-modulation-only RF pulse for RF tagging based on the Frank poly-phase perfect sequence...

  1. Multipacket Reception in Wireless Ad Hoc Networks Based on CDMA and Polynomial Phase-modulating Sequences

    Institute of Scientific and Technical Information of China (English)

    ZHANG Ji-dong; Wang Bao-yun; ZHENG Bao-yu

    2004-01-01

    Based on the polynomial phase-modulating sequences algorithm, this paper presents two schemes for the application of CDMA with polynomial phase signals to improve the signal separation performance. Simulation results illustrate the proposed approach have 1~3 dB improvement about signal-to-interference and noise ratio in most environment, compared with the PPS algorithm.

  2. Sequence heuristics to encode phase behaviour in intrinsically disordered protein polymers.

    Science.gov (United States)

    Quiroz, Felipe García; Chilkoti, Ashutosh

    2015-11-01

    Proteins and synthetic polymers that undergo aqueous phase transitions mediate self-assembly in nature and in man-made material systems. Yet little is known about how the phase behaviour of a protein is encoded in its amino acid sequence. Here, by synthesizing intrinsically disordered, repeat proteins to test motifs that we hypothesized would encode phase behaviour, we show that the proteins can be designed to exhibit tunable lower or upper critical solution temperature (LCST and UCST, respectively) transitions in physiological solutions. We also show that mutation of key residues at the repeat level abolishes phase behaviour or encodes an orthogonal transition. Furthermore, we provide heuristics to identify, at the proteome level, proteins that might exhibit phase behaviour and to design novel protein polymers consisting of biologically active peptide repeats that exhibit LCST or UCST transitions. These findings set the foundation for the prediction and encoding of phase behaviour at the sequence level.

  3. The rotation period distributions of 4--10 Myr T Tauri stars in Orion OB1: New constraints on pre-main-sequence angular momentum evolution

    CERN Document Server

    Karim, Md Tanveer; Briceno, Cesar; Vivas, A Katherina; Raetz, Stefanie; Mateu, Cecilia; Downes, Juan Jose; Calvet, Nuria; Hernandez, Jesus; Neuhauser, Ralph; Mugrauer, Markus; Takahashi, Hidenori; Tachihara, Kengo; Chini, Rolf; Cruz-Dias, Gustavo A; Aarnio, Alicia; James, David J; Hackstein, Moritz

    2016-01-01

    Most existing studies of the angular momentum evolution of young stellar populations have focused on the youngest (1-3 Myr) T Tauri stars. In contrast, the angular momentum distributions of older T Tauri stars (4-10 Myr) have been less studied, even though they hold key insight to understanding stellar angular momentum evolution at a time when protoplanetary disks have largely dissipated and when models therefore predict changes in the rotational evolution that can in principle be tested. We present a study of photometric variability among 1,974 confirmed T Tauri members of various sub-regions of the Orion OB1 association, and with ages spanning 4-10 Myr, using optical time-series from three different surveys. For 564 of the stars (~32% of the weak-lined T Tauri stars and ~13% of the classical T Tauri stars in our sample) we detect statistically significant periodic variations which we attribute to the stellar rotation periods, making this one of the largest samples of T Tauri star rotation periods yet publis...

  4. Evidence for Variable, Correlated X-ray and Optical/IR Extinction toward the Nearby, Pre-main Sequence Binary TWA 30

    CERN Document Server

    Principe, David A; Kastner, Joel H; Stelzer, Beate; Alcala, Juan

    2016-01-01

    We present contemporaneous XMM-Newton X-ray and ground-based optical/near-IR spectroscopic observations of the nearby ($D \\approx 42$ pc), low-mass (mid-M) binary system TWA 30A and 30B. The components of this wide (separation $\\sim$3400 AU) binary are notable for their nearly edge-on disk viewing geometries, high levels of variability, and evidence for collimated stellar outflows. We obtained XMM-Newton X-ray observations of TWA 30A and 30B in 2011 June and July, accompanied (respectively) by IRTF SpeX (near-IR) and VLT XSHOOTER (visible/near-IR) spectroscopy obtained within $\\sim$20 hours of the X-ray observations. TWA 30A was detected in both XMM-Newton observations at relatively faint intrinsic X-ray luminosities ($L_{X}$$\\sim$$8\\times10^{27}$ $erg$ $s^{-1}$) compared to stars of similar mass and age . The intrinsic (0.15-2.0 keV) X-ray luminosities measured in 2011 had decreased by a factor 20-100 relative to a 1990 (ROSAT) X-ray detection. TWA 30B was not detected, and we infer an upper limit of ($L_{X}...

  5. The Rotation Period Distributions of 4-10 Myr T Tauri Stars in Orion OB1: New Constraints on Pre-main-sequence Angular Momentum Evolution

    Science.gov (United States)

    Karim, Md Tanveer; Stassun, Keivan G.; Briceño, César; Vivas, A. Katherina; Raetz, Stefanie; Mateu, Cecilia; José Downes, Juan; Calvet, Nuria; Hernández, Jesús; Neuhäuser, Ralph; Mugrauer, Markus; Takahashi, Hidenori; Tachihara, Kengo; Chini, Rolf; Cruz-Dias, Gustavo A.; Aarnio, Alicia; James, David J.; Hackstein, Moritz

    2016-12-01

    Most existing studies of the angular momentum evolution of young stellar populations have focused on the youngest (≲1-3 Myr) T Tauri stars. In contrast, the angular momentum distributions of older T Tauri stars (˜4-10 Myr) have been less studied, even though they hold key insights to understanding stellar angular momentum evolution at a time when protoplanetary disks have largely dissipated and when models therefore predict changes in the rotational evolution that can in principle be tested. We present a study of photometric variability among 1974 confirmed T Tauri members of various subregions of the Orion OB1 association, and with ages spanning 4-10 Myr, using optical time series from three different surveys. For 564 of the stars (˜32% of the weak-lined T Tauri stars and ˜13% of the classical T Tauri stars in our sample) we detect statistically significant periodic variations, which we attribute to the stellar rotation periods, making this one of the largest samples of T Tauri star rotation periods yet published. We observe a clear change in the overall rotation period distributions over the age range 4-10 Myr, with the progressively older subpopulations exhibiting systematically faster rotation. This result is consistent with angular momentum evolution model predictions of an important qualitative change in the stellar rotation periods starting at ˜5 Myr, an age range for which very few observational constraints were previously available.

  6. TIME-SERIES PHOTOMETRY OF STARS IN AND AROUND THE LAGOON NEBULA. I. ROTATION PERIODS OF 290 LOW-MASS PRE-MAIN-SEQUENCE STARS IN NGC 6530

    Energy Technology Data Exchange (ETDEWEB)

    Henderson, Calen B. [Department of Astronomy, Ohio State University, 140 W. 18th Ave., Columbus, OH 43210 (United States); Stassun, Keivan G., E-mail: henderson@astronomy.ohio-state.edu [Department of Physics and Astronomy, Vanderbilt University, VU Station B 1807, Nashville, TN 37235 (United States)

    2012-03-01

    We have conducted a long-term, wide-field, high-cadence photometric monitoring survey of {approx}50,000 stars in the Lagoon Nebula H II region. This first paper presents rotation periods for 290 low-mass stars in NGC 6530, the young cluster illuminating the nebula, and for which we assemble a catalog of infrared and spectroscopic disk indicators, estimated masses and ages, and X-ray luminosities. The distribution of rotation periods we measure is broadly uniform for 0.5 days < P < 10 days; the short-period cutoff corresponds to breakup. We observe no obvious bimodality in the period distribution, but we do find that stars with disk signatures rotate more slowly on average. The stars' X-ray luminosities are roughly flat with rotation period, at the saturation level (log L{sub X} /L{sub bol} Almost-Equal-To -3.3). However, we find a significant positive correlation between L{sub X} /L{sub bol} and corotation radius, suggesting that the observed X-ray luminosities are regulated by centrifugal stripping of the stellar coronae. The period-mass relationship in NGC 6530 is broadly similar to that of the Orion Nebula Cluster (ONC), but the slope of the relationship among the slowest rotators differs from that in the ONC and other young clusters. We show that the slope of the period-mass relationship for the slowest rotators can be used as a proxy for the age of a young cluster, and we argue that NGC 6530 may be slightly younger than the ONC, making it a particularly important touchstone for models of angular momentum evolution in young, low-mass stars.

  7. Optical spectroscopy of X-ray sources in the Taurus molecular cloud: discovery of ten new pre-main sequence stars

    CERN Document Server

    Scelsi, L; Affer, L; Argiroffi, C; Pillitteri, I; Maggio, A; Micela, G

    2008-01-01

    We have analyzed optical spectra of 25 X-ray sources identified as potential new members of the Taurus molecular cloud (TMC), in order to confirm their membership in this SFR. Fifty-seven candidates were previously selected among the X-ray sources in the XEST survey, having a 2MASS counterpart compatible with a PMS star based on color-magnitude and color-color diagrams. We obtained high-resolution optical spectra for 7 of these candidates with the SARG spectrograph at the TNG telescope, which were used to search for Li absorption and to measure the Ha line and the radial and rotational velocities; 18 low-resolution optical spectra obtained with DOLORES for other candidate members were used for spectral classification, for Ha measurements, and to assess membership together with IR color-color and color-magnitude diagrams and additional information from the X-ray data. We found that 3 sources show Li absorption, with equivalent widths of ~500 mA, broad spectral line profiles, indicating v sin i ~20-40 km/s, rad...

  8. Time-Series Photometry of Stars in and around the Lagoon Nebula. I. Rotation Periods of 290 Low-Mass Pre-Main-Sequence Stars in NGC 6530

    CERN Document Server

    Henderson, Calen B

    2011-01-01

    We have conducted a long-term, wide-field, high-cadence photometric monitoring survey of ~50,000 stars in the Lagoon Nebula \\ion{H}{2} region. This first paper presents rotation periods for 290 low-mass stars in NGC 6530, the young cluster illuminating the nebula, and for which we assemble a catalog of infrared and spectroscopic disk indicators, estimated masses and ages, and X-ray luminosities. The distribution of rotation periods we measure is broadly uniform for 0.5 < P < 10 d; the short-period cutoff corresponds to breakup. We observe no obvious bimodality in the period distribution, but we do find that stars with disk signatures rotate more slowly on average. The stars' X-ray luminosities are roughly flat with rotation period, at the saturation level ($\\log L_X / L_{\\rm bol} \\approx -3.3$). However, we find a significant positive correlation between $L_X / L_{\\rm bol}$ and co-rotation radius, suggesting that the observed X-ray luminosities are regulated by centrifugal stripping of the stellar coron...

  9. LUMINOSITY DISCREPANCY IN THE EQUAL-MASS, PRE-MAIN-SEQUENCE ECLIPSING BINARY PAR 1802: NON-COEVALITY OR TIDAL HEATING?

    Energy Technology Data Exchange (ETDEWEB)

    Gomez Maqueo Chew, Yilen; Stassun, Keivan G.; Hebb, Leslie [Department of Physics and Astronomy, Vanderbilt University, Nashville, TN 37235 (United States); Prsa, Andrej [Department of Astronomy and Astrophysics, Villanova University, Villanova, PA 19085 (United States); Stempels, Eric [Department of Astronomy and Space Physics, Uppsala University, SE-752 67 Uppsala (Sweden); Barnes, Rory [Department of Astronomy, University of Washington, Seattle, WA 98195 (United States); Heller, Rene [Leibniz-Institut fuer Astrophysik Potsdam (AIP), An der Sternwarte 16, 14482 Potsdam (Germany); Mathieu, Robert D., E-mail: yilen.gomez@vanderbilt.edu [Department of Astronomy, University of Wisconsin-Madison, Madison, WI 53706 (United States)

    2012-01-20

    Parenago 1802, a member of the {approx}1 Myr Orion Nebula Cluster, is a double-lined, detached eclipsing binary in a 4.674 day orbit, with equal-mass components (M{sub 2}/M{sub 1} = 0.985 {+-} 0.029). Here we present extensive VI{sub C} JHK{sub S} light curves (LCs) spanning {approx}15 yr, as well as a Keck/High Resolution Echelle Spectrometer (HIRES) optical spectrum. The LCs evince a third light source that is variable with a period of 0.73 days, and is also manifested in the high-resolution spectrum, strongly indicating the presence of a third star in the system, probably a rapidly rotating Classical T Tauri star. We incorporate this third light into our radial velocity and LC modeling of the eclipsing pair, measuring accurate masses (M{sub 1} = 0.391 {+-} 0.032 and M{sub 2} = 0.385 {+-} 0.032 M{sub Sun }), radii (R{sub 1} = 1.73 {+-} 0.02 and R{sub 2} = 1.62 {+-} 0.02 R{sub Sun }), and temperature ratio (T{sub eff,1}/T{sub eff,2} = 1.0924 {+-} 0.0017). Thus, the radii of the eclipsing stars differ by 6.9% {+-} 0.8%, the temperatures differ by 9.2% {+-} 0.2%, and consequently the luminosities differ by 62% {+-} 3%, despite having masses equal to within 3%. This could be indicative of an age difference of {approx}3 Multiplication-Sign 10{sup 5} yr between the two eclipsing stars, perhaps a vestige of the binary formation history. We find that the eclipsing pair is in an orbit that has not yet fully circularized, e = 0.0166 {+-} 0.003. In addition, we measure the rotation rate of the eclipsing stars to be 4.629 {+-} 0.006 days; they rotate slightly faster than their 4.674 day orbit. The non-zero eccentricity and super-synchronous rotation suggest that the eclipsing pair should be tidally interacting, so we calculate the tidal history of the system according to different tidal evolution theories. We find that tidal heating effects can explain the observed luminosity difference of the eclipsing pair, providing an alternative to the previously suggested age difference.

  10. Variability of Disk Emission in Pre-Main Sequence and Related Stars. II. Variability in the Gas and Dust Emission of the Herbig Fe Star SAO 206462

    CERN Document Server

    Sitko, Michael L; Kimes, Robin L; Beerman, Lori C; Martus, Cameron; Lynch, David K; Russell, Ray W; Grady, Carol A; Schneider, Glenn; Lisse, Carey M; Nuth, Joseph A; Cure, Michel; Henden, Arne A; Kraus, Stefan; Motta, Veronica; Tamura, Motohide; Hornbeck, Jeremy; Williger, Gerard M; Fugazza, Dino

    2011-01-01

    We present thirteen epochs of near-infrared (0.8-5 micron) spectroscopic observations of the pre-transitional, "gapped" disk system in SAO 206462 (=HD 135344B). In all, six gas emission lines (including Br gamma, Pa beta, and the 0.8446 micron line of O I) along with continuum measurements made near the standard J, H, K, and L photometric bands were measured. A mass accretion rate of approximately 2 x 10^-8 solar masses per year was derived from the Br gamma and Pa beta lines. However, the fluxes of these lines varied by a factor of over two during the course of a few months. The continuum also varied, but by only ~30%, and even decreased at a time when the gas emission was increasing. The H I line at 1.083 microns was also found to vary in a manner inconsistent with that of either the hydrogen lines or the dust. Both the gas and dust variabilities indicate significant changes in the region of the inner gas and the inner dust belt that may be common to many young disk systems. If planets are responsible for d...

  11. Variability of Disk Emission in Pre-Main Sequence and Related Stars. III. Exploring Structural Changes in the Pre-transitional Disk in HD 169142

    CERN Document Server

    Wagner, Kevin R; Grady, Carol A; Whitney, Barbara A; Swearingen, Jeremy R; Champney, Elizabeth H; Johnson, Alexa N; Werren, Chelsea; Russell, Ray W; Schneider, Glenn H; Momose, Munetake; Muto, Takayuki; Inoue, Akio K; Lauroesch, James T; Brown, Alexander; Fukagawa, Misato; Currie, Thayne M; Hornbeck, Jeremy; Wisniewski, John P; Woodgate, Bruce E

    2014-01-01

    We present near-IR and far-UV observations of the pre-transitional (gapped) disk in HD 169142 using NASA's Infrared Telescope Facility and Hubble Space Telescope. The combination of our data along with existing data sets into the broadband spectral energy distribution reveals variability of up to 45% between ~1.5-10 {\\mu}m over a maximum timescale of 10 years. All observations known to us separate into two distinct states corresponding to a high near-IR state in the pre-2000 epoch and a low state in the post-2000 epoch, indicating activity within the <1 AU region of the disk. Through analysis of the Pa {\\beta} and Br {\\gamma} lines in our data we derive a mass accretion rate in May 2013 of (1.5 - 2.7) x 10^-9 Msun/yr. We present a theoretical modeling analysis of the disk in HD 169142 using Monte-Carlo radiative transfer simulation software to explore the conditions and perhaps signs of planetary formation in our collection of 24 years of observations. We find that shifting the outer edge (r = 0.3 AU) of t...

  12. Variability of Disk Emission in Pre-main Sequence and Related Stars. V. Changes in the Innermost Disk Structure of the Herbig AE Star HD 31648 = MWC 480

    Science.gov (United States)

    Fernandes, Rachel; Long, Zachary; Sitko, Michael L.; Grady, C. A.; Kusakabe, Nobuhiko

    2017-01-01

    We present five epochs of near IR observations of the protoplanetary disk around HD 31648 (MWC 480). A mass accretion rate of approximately 1.1×10-7 Msun/year was derived from Brγ and Paβ lines. The spectral energy distribution (SED) reveals a variability of about 30% between 1.5 and 10 microns. We present the theoretical modeling analysis of the disk in HD 31648 using Monte-Carlo Radiation Transfer Code (MRTC). We find that varying the height of the inner rim successfully produces a shift in the NIR flux.

  13. Phasing for medical sequencing using rare variants and large haplotype reference panels

    Science.gov (United States)

    Sharp, Kevin; Kretzschmar, Warren; Delaneau, Olivier; Marchini, Jonathan

    2016-01-01

    Motivation: There is growing recognition that estimating haplotypes from high coverage sequencing of single samples in clinical settings is an important problem. At the same time very large datasets consisting of tens and hundreds of thousands of high-coverage sequenced samples will soon be available. We describe a method that takes advantage of these huge human genetic variation resources and rare variant sharing patterns to estimate haplotypes on single sequenced samples. Sharing rare variants between two individuals is more likely to arise from a recent common ancestor and, hence, also more likely to indicate similar shared haplotypes over a substantial flanking region of sequence. Results: Our method exploits this idea to select a small set of highly informative copying states within a Hidden Markov Model (HMM) phasing algorithm. Using rare variants in this way allows us to avoid iterative MCMC methods to infer haplotypes. Compared to other approaches that do not explicitly use rare variants we obtain significant gains in phasing accuracy, less variation over phasing runs and improvements in speed. For example, using a reference panel of 7420 haplotypes from the UK10K project, we are able to reduce switch error rates by up to 50% when phasing samples sequenced at high-coverage. In addition, a single step rephasing of the UK10K panel, using rare variant information, has a downstream impact on phasing performance. These results represent a proof of concept that rare variant sharing patterns can be utilized to phase large high-coverage sequencing studies such as the 100 000 Genomes Project dataset. Availability and implementation: A webserver that includes an implementation of this new method and allows phasing of high-coverage clinical samples is available at https://phasingserver.stats.ox.ac.uk/. Contact: marchini@stats.ox.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27153703

  14. Separation of Quadruplex Polymorphism in DNA Sequences by Reversed-Phase Chromatography

    Science.gov (United States)

    Miller, M. Clarke; Ohrenberg, Carl J.; Kuttan, Ashani; Trent, John O.

    2015-01-01

    This unit describes a method for the separation of a mixture of quadruplex conformations formed from the same parent sequence via reversed-phase chromatography (RPC). Polymorphism is inherent to quadruplex formation and even relatively simple quadruplex-forming sequences can fold into a cornucopia of possible conformations and topologies. Isolation of a specific conformation for study can be problematic. This is especially true for conformations of the human telomere sequence d(GGG(TTAGGG)3), High Performance Liquid Chromatography (HPLC), especially reversed-phase chromatography, has been a mainstay of nucleic acids research and purification for many decades. We have successfully applied this method to the problem of separating individual quadruplex species in the ensemble from the same parent sequence. PMID:26344226

  15. Effective Simulation of Quantum Entanglement Based on Classical Fields Modulated with Pseudorandom Phase Sequences

    CERN Document Server

    Fu, Jian; Xu, Yingying; Dong, Hongtao

    2010-01-01

    We demonstrate that n classical fields modulated with n different pseudorandom phase sequences can constitute a 2^n-dimensional Hilbert space that contains tensor product structure. By using classical fields modulated with pseudorandom phase sequences, we discuss effective simulation of Bell states and GHZ state, and apply both correlation analysis and von Neumann entropy to characterize the simulation. We obtain similar results with the cases in quantum mechanics and find that the conclusions can be easily generalized to n quantum particles. The research on simulation of quantum entanglement may be important, for it not only provides useful insights into fundamental features of quantum entanglement, but also yields new insights into quantum computation.

  16. Three-Phase Multiple Harmonic Sequence Detection Based on Generalized Delayed Signal Superposition

    DEFF Research Database (Denmark)

    Lu, Yong; Xiao, Guochun; Wang, Xiongfei

    2016-01-01

    -phase multiple harmonic sequence detection method is proposed for estimating both the fundamental and harmonic sequence components under adverse grid conditions. This detection method is denoted as MG DSS-PLL since it contains Multiple Generalized Delayed Signal Superposition operators and a Phase-Locked Loop....... The proposed MGDSS-PLL can be flexibly tuned to extracting any harmonic components according to specific applications and it also exhibits great robustness to different grid disturbances. Simulations and experimental results are presented for verifying the performance of the MGDSS-PLL....

  17. Haplotype-Phased Synthetic Long Reads from Short-Read Sequencing.

    Directory of Open Access Journals (Sweden)

    James A Stapleton

    Full Text Available Next-generation DNA sequencing has revolutionized the study of biology. However, the short read lengths of the dominant instruments complicate assembly of complex genomes and haplotype phasing of mixtures of similar sequences. Here we demonstrate a method to reconstruct the sequences of individual nucleic acid molecules up to 11.6 kilobases in length from short (150-bp reads. We show that our method can construct 99.97%-accurate synthetic reads from bacterial, plant, and animal genomic samples, full-length mRNA sequences from human cancer cell lines, and individual HIV env gene variants from a mixture. The preparation of multiple samples can be multiplexed into a single tube, further reducing effort and cost relative to competing approaches. Our approach generates sequencing libraries in three days from less than one microgram of DNA in a single-tube format without custom equipment or specialized expertise.

  18. Efficacy of a single sequence of intermittent bright light pulses for delaying circadian phase in humans

    OpenAIRE

    2004-01-01

    It has been shown in animal studies that exposure to brief pulses of bright light can phase shift the circadian pacemaker, and that the resetting action of light is most efficient during the first minutes of light exposure. In humans, multiple consecutive days of exposure to brief bright light pulses have been shown to phase shift the circadian pacemaker. The aim of the present study was to determine if a single sequence of brief bright light pulses administered during the early biological ni...

  19. Episodic sequence memory is supported by a theta-gamma phase code.

    Science.gov (United States)

    Heusser, Andrew C; Poeppel, David; Ezzyat, Youssef; Davachi, Lila

    2016-10-01

    The meaning we derive from our experiences is not a simple static extraction of the elements but is largely based on the order in which those elements occur. Models propose that sequence encoding is supported by interactions between high- and low-frequency oscillations, such that elements within an experience are represented by neural cell assemblies firing at higher frequencies (gamma) and sequential order is encoded by the specific timing of firing with respect to a lower frequency oscillation (theta). During episodic sequence memory formation in humans, we provide evidence that items in different sequence positions exhibit greater gamma power along distinct phases of a theta oscillation. Furthermore, this segregation is related to successful temporal order memory. Our results provide compelling evidence that memory for order, a core component of an episodic memory, capitalizes on the ubiquitous physiological mechanism of theta-gamma phase-amplitude coupling.

  20. Phased whole-genome genetic risk in a family quartet using a major allele reference sequence.

    Directory of Open Access Journals (Sweden)

    Frederick E Dewey

    2011-09-01

    Full Text Available Whole-genome sequencing harbors unprecedented potential for characterization of individual and family genetic variation. Here, we develop a novel synthetic human reference sequence that is ethnically concordant and use it for the analysis of genomes from a nuclear family with history of familial thrombophilia. We demonstrate that the use of the major allele reference sequence results in improved genotype accuracy for disease-associated variant loci. We infer recombination sites to the lowest median resolution demonstrated to date (< 1,000 base pairs. We use family inheritance state analysis to control sequencing error and inform family-wide haplotype phasing, allowing quantification of genome-wide compound heterozygosity. We develop a sequence-based methodology for Human Leukocyte Antigen typing that contributes to disease risk prediction. Finally, we advance methods for analysis of disease and pharmacogenomic risk across the coding and non-coding genome that incorporate phased variant data. We show these methods are capable of identifying multigenic risk for inherited thrombophilia and informing the appropriate pharmacological therapy. These ethnicity-specific, family-based approaches to interpretation of genetic variation are emblematic of the next generation of genetic risk assessment using whole-genome sequencing.

  1. Effect of annealing on phase sequence and their composition in the Pt-coated Mo system

    Energy Technology Data Exchange (ETDEWEB)

    Khumalo, Z.M., E-mail: zakhele@tlabs.ac.za [Department of Physics, University of Cape Town, Private Bag X3, Rondebosch 7701 (South Africa); Materials Research Department, National Research Foundation, iThemba LABS, P.O. Box 722, Somerset West (South Africa); Topić, M. [Materials Research Department, National Research Foundation, iThemba LABS, P.O. Box 722, Somerset West (South Africa); Comrie, C.M. [Department of Physics, University of Cape Town, Private Bag X3, Rondebosch 7701 (South Africa); Materials Research Department, National Research Foundation, iThemba LABS, P.O. Box 722, Somerset West (South Africa); Blumenthal, M. [Department of Physics, University of Cape Town, Private Bag X3, Rondebosch 7701 (South Africa); Pineda-Vargas, C.A.; Bucher, R. [Materials Research Department, National Research Foundation, iThemba LABS, P.O. Box 722, Somerset West (South Africa); Kisslinger, K. [Center for Functional Nanomaterials, Brookhaven National Laboratory, P.O. Box 5000, Upton, NY USA (United States)

    2014-11-01

    Highlights: • Platinum coatings were prepared using electron beam evaporator. • The phase analysis revealed the presence of the MoPt{sub 2} and MoPt. • At low annealing time, the MoPt{sub 2} phase appeared to have more Pt content. • The MoPt{sub 2} phase disappeared as the annealing time increases. • It is believed that the MoPt phase was growing at the expense of the MoPt{sub 2}. - Abstract: The phase formation sequence and the composition of phases induced by thermal annealing in a platinum (Pt) coated molybdenum (Mo) system were investigated by X-ray diffraction (XRD), Rutherford backscattering spectrometry (RBS) and transmission electron microscopy (TEM). The X-ray diffraction study of a 0.2 μm thick platinum layer deposited on a Mo substrate and annealed at temperatures between 800 °C and 900 °C for different periods of time shows the formation of MoPt{sub 2} and MoPt phases. It was also found that these phases nucleate sequentially and the MoPt{sub 2} phase becomes unstable at 900 °C after a longer annealing time of 8 h. Rutherford backscattering spectroscopy and transmission electron microscopy showed that the coating thickness approximately doubled after thermal annealing, from 0.22 μm to 0.46 μm, due to the formation of the Pt–Mo phases.

  2. Default cycle phases determined after modifying discrete DNA sequences in plant cells

    Energy Technology Data Exchange (ETDEWEB)

    Sans, J.; Leyton, C. [Universidad de Chile, Santiago (Chile). Facultad de Medicina; Gimenez-Abian, M.I.; Gimenez-Abian, J.F.; Aller, P.; De La Torre, C. [Centro de Investigaciones Biologicas, CSIC, Madrid (Spain)

    1997-02-01

    After bromosubstituting DNA sequences replicated in the first, second, or third part of the S phase, in Allium cepa L. meristematic cells, radiation at 313 nm wavelength under anoxia allowed ascription of different sequences to both the positive and negative regulation of some cycle phase transitions. The present report shows that the radiation forced cells in late G{sub 1} phase to advance into S, while those in G{sub 2} remained in G{sub 2} and cells in prophase returned to G{sub 2} when both sets of sequences involved in the positive and negative controls were bromosubstituted and later irradiated. In this way, not only G{sub 2} but also the S phase behaved as cycle phases where cells accumulated by default when signals of different sign functionally cancelled out. The treatment did not halt the rates of replication or transcription of plant bromosubstituted DNA. The irradiation under hypoxia apparently prevents the binding of regulatory proteins to Br-DNA. (author).

  3. An Optimal Sorting of Pulse Amplitude Sequence Based on the Phased Array Radar Beam Tasks

    Institute of Scientific and Technical Information of China (English)

    Chuan Sheng∗,Yongshun Zhang; Wenlong Lu

    2016-01-01

    The study of phased array radar ( PAR) pulse amplitude sequence characteristics is the key to understand the radar’s working state and its beam’s scanning manner. According to the principle of antenna pattern formation and the searching and tracking modes of beams, this paper analyzes the characteristics and differences of pulse amplitude sequence when the radar beams work in searching and tracking modes respectively. Then an optimal sorting model of pulse amplitude sequence is established based on least⁃squares and curve⁃fitting methods. This method is helpful for acquiring the current working state of the radar and recognizing its instantaneous beam pointing by sorting the pulse amplitude sequence without the necessity to estimate the antenna pattern.

  4. Extracting flat-field images from scene-based image sequences using phase correlation

    Science.gov (United States)

    Caron, James N.; Montes, Marcos J.; Obermark, Jerome L.

    2016-06-01

    Flat-field image processing is an essential step in producing high-quality and radiometrically calibrated images. Flat-fielding corrects for variations in the gain of focal plane array electronics and unequal illumination from the system optics. Typically, a flat-field image is captured by imaging a radiometrically uniform surface. The flat-field image is normalized and removed from the images. There are circumstances, such as with remote sensing, where a flat-field image cannot be acquired in this manner. For these cases, we developed a phase-correlation method that allows the extraction of an effective flat-field image from a sequence of scene-based displaced images. The method uses sub-pixel phase correlation image registration to align the sequence to estimate the static scene. The scene is removed from sequence producing a sequence of misaligned flat-field images. An average flat-field image is derived from the realigned flat-field sequence.

  5. Selective Sequence for the Peptide-Triggered Phase Transition of Lyotropic Liquid-Crystalline Structures.

    Science.gov (United States)

    Liu, Qingtao; Dong, Yao-Da; Boyd, Ben J

    2016-05-24

    A novel concept of using mixed lipids to construct selective peptide-sequence-sensing lyotropic liquid-crystalline (LLC) dispersion systems was investigated. The LLC systems were constructed using a mixture of phytantriol, a lipid that forms lyotropic liquid-crystalline phases, and a novel synthesized peptide-lipid (peplipid) for sensing a target peptide with the RARAR sequence. The internal structure of the dispersed LLC particles was converted from the lamellar structure (liposomes) to the inverse bicontinuous cubic phase (cubosomes) in the presence of the target peptide. The addition of common human proteins did not induce any structural change, indicating a high selectivity of interaction with the target peptide. The concept has potential for the design of targeted controlled release drug delivery agents.

  6. Photometric amplitudes and phases of B-type main sequence pulsators: sources of inaccuracy

    CERN Document Server

    Szewczuk, Wojciech

    2010-01-01

    We discuss all possible sources of uncertainties in theoretical values of the photometric amplitudes and phases of B-type main sequence pulsators. These observables are of particular importance because they contain information about the mode geometry as well as about stellar physics. Here, we study effects of various parameters coming both from theory of linear nonadiabatic oscillations and from models of stellar atmospheres. In particular, we show effects of chemical composition, opacities and, for the first time, effects of the NLTE atmospheres.

  7. Predicting the Fluid Phase Behaviour of Aqueous Solutions of ELP (VPGVG) Sequences Using SAFT-VR.

    Science.gov (United States)

    Zhao, Binwu; Lindeboom, Tom; Benner, Steven W; Jackson, George; Galindo, Amparo; Hall, Carol K

    2017-08-08

    The statistical associating fluid theory for potentials of variable range (SAFT-VR) is used in this paper to predict the fluid phase behaviour of elastin-like polypeptides (ELPs) sequences in aqueous solution.with special focus on the loci of lower critical solution temperature (LCST) points. A SAFT-VR model for these solutions is obtained following a coarse-graining approach combining information from atomistic simulations and from previous SAFT models for relevant systems available in the literature. Constant-pressure temperature-composition phase diagrams for (VPGVG)n sequences + water are calculated for n =1 to 300. The SAFT-VR equation of state lends itself to the easy calculation of phase boundaries, so that complete fluid-phase diagrams can be calculated efficiently. A broad range of thermodynamic conditions of temperature and pressure are considered, and regions of vapour-liquid and liquid-liquid coexistence, including LCSTs are found. The calculated phase boundaries at low concentrations match those measured in experiments. The temperature-composition phase diagrams of the ELP + water systems at low pressure (0.1 MPa) are similar to those of types V and VI phase behaviour in the classification of Scott and van Konynenburg. Study of the high-pressure phase behaviour confirms however that a closed-loop liquid-liquid immiscibility region, separate from the gas-liquid envelope, is present for the (VPGVG)30-water system; such a phase diagram is typical of type VI phase behavior. ELPs with shorter lengths exhibit both liquid-liquid and gas-liquid regions, both of which shrink as the chain length of ELPs decrease. The strength of the hydrogen-bonding interaction is also found to affect the phase diagram of (VPGVG)30-water system in that the liquid-liquid and gas-liquid region expand as the H-bonding strength decreases and shrink as the H-bonding strength increases. The LCSTs of the mixtures are seen to decrease as the ELP chain length increases.

  8. [Phase I clinical trial design of anticancer agents--a Fibonacci and a modified Fibonacci sequence].

    Science.gov (United States)

    Kusaba, H; Tamura, T

    2000-05-01

    A Phase I clinical trial of an anticancer agent is the first evaluation in humans, and it is an important step in drug development. From the ethical point of view, the goal is to escalate to the maximum tolerated dose quickly, yet safely, to minimize the likelihood of treating patients at doses that are too low or high. It is expected that the contradictions between safety and efficacy in the Phase I clinical trials will be solved by developing methods. The modified Fibonacci sequence has been generally adopted for dose escalation, although it includes some problems. It is necessary to recognize that the method used for Phase I clinical trials for anticancer agents remains unsatisfactory, and that it is also necessary to develop more ethical and scientific methods.

  9. Two-Phase and Family-Based Designs for Next-Generation Sequencing Studies

    Directory of Open Access Journals (Sweden)

    Duncan C Thomas

    2013-12-01

    Full Text Available The cost of next-generation sequencing is now approaching that of early GWAS panels, but is still out of reach for large epidemiologic studies and the millions of rare variants expected poses challenges for distinguishing causal from non-causal variants. We review two types of designs for sequencing studies: two-phase designs for targeted follow-up of genomewide association studies using unrelated individuals; and family-based designs exploiting co-segregation for prioritizing variants and genes.Two-phase designs subsample subjects for sequencing from a larger case-control study jointly on the basis of their disease and carrier status; the discovered variants are then tested for association in the parent study. The analysis combines the full sequence data from the substudy with the more limited SNP data from the main study. We discuss various methods for selecting this subset of variants and describe the expected yield of true positive associations in the context of an on-going study of second breast cancers following radiotherapy.While the sharing of variants within families means that family-based designs are less efficient for discovery than sequencing unrelated individuals, the ability to exploit co-segregation of variants with disease within families helps distinguish causal from non-causal ones. Furthermore, by enriching for family history, the yield of causal variants can be improved and use of identity-by-descent information improves imputation of genotypes for other family members. We compare the relative efficiency of these designs with those using unrelated individuals for discovering and prioritizing variants or genes for testing association in larger studies. While associations can be tested with single variants, power is low for rare ones. Recent generalizations of burden or kernel tests for gene-level associations to family-based data are appealing. These approaches are illustrated in the context of a family-based study of

  10. THE EFFECT OF BLENDING SEQUENCE ON PHASE MORPHOLOGY OF NYLON 6/ABS/SMA BLENDS

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    The preparation process-dependent phase morphology of blends composed of nylon 6 and acryionitrile-butadienestyrene(ABS)over a composition range of 30-70 wt% using a styrene-maleic anhydride(SMA)copolymer as the compatibilizing agent with a constant content(5phr)was investigated.The results of the scanning electron microscope (SEM)observation revealed that compared with the binary blends of nylon 6 and ABS,the existence of SMA caused a composition shift of phase inversion to a higher weight fraction of nylon 6 when ABS was blended with the preblended nylon 6/SMA blend,while the co-continuous structures could be observed over a considerably narrower composition range when nylon 6 was blended with the pre-blended ABS/SMA blend.An examination through dynamic mechanical analysis (DMA)tests confirmed the results obtained with SEM.It is found that near the phase inversion region a remarkable change in the dynamic storage modulus(G')and the loss tangent(tanδ)appears.Moreover,the influence of blending sequence on the size of dispersed particles has been probed for uncompatibilized and compatibilized blends of nylon 6 and ABS over a wide range of compositions below or beyond the phase inversion points.For the blends of ABS dispersed in a nylon 6 matrix,little discernible effects of blending sequence on particle size could be observed.Furthermore,there exists a significant difference in morphologies of the blends prepared by nylon 6 particles dispersing in a ABS matrix in cases of different blending sequences used.Some possible factors responsible for the above asymmetric behaviors have been proposed.

  11. Solid-phase peptide synthesis: from standard procedures to the synthesis of difficult sequences.

    Science.gov (United States)

    Coin, Irene; Beyermann, Michael; Bienert, Michael

    2007-01-01

    This protocol for solid-phase peptide synthesis (SPPS) is based on the widely used Fmoc/tBu strategy, activation of the carboxyl groups by aminium-derived coupling reagents and use of PEG-modified polystyrene resins. A standard protocol is described, which was successfully applied in our lab for the synthesis of the corticotropin-releasing factor (CRF), >400 CRF analogs and a countless number of other peptides. The 41-mer peptide CRF is obtained within approximately 80 working hours. To achieve the so-called difficult sequences, special techniques have to be applied in order to reduce aggregation of the growing peptide chain, which is the main cause of failure for peptide chemosynthesis. Exemplary application of depsipeptide and pseudoproline units is shown for synthesizing an extremely difficult sequence, the Asn(15) analog of the WW domain FBP28, which is impossible to obtain using the standard protocol.

  12. Zero phase sequence impedance and tank heating model for three phase three leg core type power transformers coupling magnetic field and electric circuit equations in finite element software

    Energy Technology Data Exchange (ETDEWEB)

    Ngnegueu, T.; Mailhot, M.; Munar, A. [Jeumont Schneider Transformateurs, Lyon (France); Sacotte, M. [France-Transfo. Voie romaine, Mezieres-Les-Metz (France)

    1995-05-01

    In this paper, the authors present a finite element model for the calculation of zero phase sequence reactance for three phase three leg core type power transformers. An axisymmetrical approximation is assumed. A simplified model is used to assess the tank`s hottest spot temperature.

  13. Quantitative Analysis of Fundus-Image Sequences Reveals Phase of Spontaneous Venous Pulsations

    Science.gov (United States)

    Moret, Fabrice; Reiff, Charlotte M.; Lagrèze, Wolf A.; Bach, Michael

    2015-01-01

    Purpose Spontaneous venous pulsation correlates negatively with elevated intracranial pressure and papilledema, and it relates to glaucoma. Yet, its etiology remains unclear. A key element to elucidate its underlying mechanism is the time at which collapse occurs with respect to the heart cycle, but previous reports are contradictory. We assessed this question in healthy subjects using quantitative measurements of both vein diameters and artery lateral displacements; the latter being used as the marker of the ocular systole time. Methods We recorded 5-second fundus sequences with a near-infrared scanning laser ophthalmoscope in 12 young healthy subjects. The image sequences were coregistered, cleaned from microsaccades, and filtered via a principal component analysis to remove nonpulsatile dynamic features. Time courses of arterial lateral displacement and of diameter at sites of spontaneous venous pulsation or proximal to the disk were retrieved from those image sequences and compared. Results Four subjects displayed both arterial and venous pulsatile waveforms. On those, we observed venous diameter waveforms differing markedly among the subjects, ranging from a waveform matching the typical intraocular pressure waveform to a close replica of the arterial waveform. Conclusions The heterogeneity in waveforms and arteriovenous phases suggests that the mechanism governing the venous outflow resistance differs among healthy subjects. Translational relevance Further characterizations are necessary to understand the heterogeneous mechanisms governing the venous outflow resistance as this resistance is altered in glaucoma and is instrumental when monitoring intracranial hypertension based on fundus observations. PMID:26396929

  14. Theory of phase segregation in DNA assemblies containing two different base-pair sequence types

    Science.gov (United States)

    (O’ Lee, Dominic J.; Wynveen, Aaron; Kornyshev, Alexei A.

    2017-01-01

    Spontaneous pairing of homologous DNA sequences—a challenging subject in molecular biophysics, often referred to as ‘homology recognition’—has been observed in vitro for several DNA systems. One of these experiments involved liquid crystalline quasi-columnar phases formed by a mixture of two kinds of double stranded DNA oligomer. Both oligomer types were of the same length and identical stoichiometric base-pair composition, but the base-pairs followed a different order. Phase segregation of the two DNA types was observed in the experiments, with the formation of boundaries between domains rich in molecules of one type (order) of base pair sequence. We formulate here a modified ‘X–Y model’ for phase segregation in such assemblies, obtain approximate solutions of the model, compare analytical results to Monte Carlo simulations, and rationalise past experimental observations. This study, furthermore, reveals the factors that affect the degree of segregation. Such information could be used in planning new versions of similar segregation experiments, needed for deepening our understanding of forces that might be involved, e.g., in gene–gene recognition.

  15. Characterization of Shigella type 1 fimbriae: expression, FimA sequence, and phase variation.

    Science.gov (United States)

    Snellings, N J; Tall, B D; Venkatesan, M M

    1997-06-01

    This study documents the presence of type 1 fimbriae on Shigella and confirms these mannose-sensitive adherence structures to be bona fide components of the Shigella surface. While laboratory-passaged Shigella strains and lyophilized clinical isolates failed to express type 1 fimbriae, 6 of 20 recent clinical isolates, including 4 Shigella flexneri strains, 1 Shigella boydii strain, and 1 Shigella dysenteriae strain, produced type 1 fimbriae as detected by mannose-sensitive hemagglutination (MSHA) and electron microscopy. Optimal production of a predominantly Fim+ population required serial passage every 48 to 72 h in unshaken brain heart infusion broth at 37 degrees C. Fim+ Shigella cultures were capable of reversibly switching to a non-MSHA, afimbriated phase during serial aerobic cultivation on tryptic soy agar plates. The amino acid sequence of S. flexneri type 1 FimA contained 18 substitutions compared to that of Escherichia coli fimbrillin. Indirect immunoelectron microscopy suggested the presence of both shared and unique epitopes on E. coli and S. flexneri type 1 fimbriae. Random phase variation between fimbriated and afimbriated states in Shigella was accompanied by the genomic rearrangement associated with phase variation in E. coli.

  16. Information performances and illative sequences: Sequential organization of explanations of chemical phase equilibrium

    Science.gov (United States)

    Brown, Nathaniel James Swanton

    While there is consensus that conceptual change is surprisingly difficult, many competing theories of conceptual change co-exist in the literature. This dissertation argues that this discord is partly the result of an inadequate account of the unwritten rules of human social interaction that underlie the field's preferred methodology---semi-structured interviewing. To better understand the contributions of interaction during explanations, I analyze eight undergraduate general chemistry students as they attempt to explain to various people, for various reasons, why phenomena involving chemical phase equilibrium occur. Using the methods of interaction analysis, I characterize the unwritten, but systematic, rules that these participants follow as they explain. The result is a description of the contributions of interaction to explaining. Each step in each explanation is a jointly performed expression of a subject-predicate relation, an interactive accomplishment I call an information performance (in-form, for short). Unlike clauses, in-forms need not have a coherent grammatical structure. Unlike speaker turns, in-forms have the clear function of expressing information. Unlike both clauses and speaker turns, in-forms are a co-construction, jointly performed by both the primary speaker and the other interlocutor. The other interlocutor strongly affects the form and content of each explanation by giving or withholding feedback at the end of each in-form, moments I call feedback-relevant places. While in-forms are the bricks out of which the explanation is constructed, they are secured by a series of inferential links I call an illative sequence. Illative sequences are forward-searching, starting with a remembered fact or observation and following a chain of inferences in the hope it leads to the target phenomenon. The participants treat an explanation as a success if the illative sequence generates an in-form that describes the phenomenon. If the illative sequence does

  17. Efficacy of a single sequence of intermittent bright light pulses for delaying circadian phase in humans. : Phase delaying efficacy of intermittent bright light

    OpenAIRE

    2004-01-01

    International audience; It has been shown in animal studies that exposure to brief pulses of bright light can phase shift the circadian pacemaker and that the resetting action of light is most efficient during the first minutes of light exposure. In humans, multiple consecutive days of exposure to brief bright light pulses have been shown to phase shift the circadian pacemaker. The aim of the present study was to determine whether a single sequence of brief bright light pulses administered du...

  18. Dual-frequency tissue harmonic suppression using phase-coded pulse sequence: proof of concept using a phantom.

    Science.gov (United States)

    Shen, Che-Chou; Wang, Hui-Ting

    2013-03-01

    The presence of tissue harmonic generation during acoustic propagation is one major limitation in nonlinear detection of microbubble contrast agents. However, conventional solutions for tissue harmonic suppression are not applicable in dual-frequency (DF) harmonic imaging. In DF harmonic imaging, the second harmonic signal at second harmonic (2f(0)) frequency and the inter-modulation harmonic signal at fundamental (f(0)) frequency are simultaneously generated for imaging and both need to be suppressed to improve contrast-to-tissue ratio (CTR). In this study, a novel phase-coded pulse sequence is developed to accomplish DF tissue harmonic suppression. Phase-coded pulse sequence utilizes multiple firings with equidistant transmit phase for harmonic cancellation in the sum of respective echoes. For the f(0) transmit component, the transmit phase comes from the equidistant set of {-2π/3, 0, 2π/3} to suppress the second harmonic signal at 2f(0) frequency. Moreover, in order to provide the inter-modulation harmonic suppression at f(0) frequency, the 2f(0) transmit phase has to be particularly manipulated for the corresponding f(0) transmit phase. The proposed three-pulse sequence can remove not only the second-order harmonic signal but also other higher-order counterparts at both f(0) and 2f(0) frequencies. Measurements were performed at f(0) equal to 2.25 MHz and using hydrophone in water and contrast agents in tissue phantom. Experimental results indicate that the sequence reduces the tissue harmonic magnitude by about 20 dB along the entire axial depths and the corresponding CTR improves at both frequencies. In DF harmonic imaging, the proposed phase-coded sequence can effectively remove the tissue harmonic background at both f(0) and 2f(0) frequencies for improvement of contrast detection. Copyright © 2012 Elsevier B.V. All rights reserved.

  19. Signal intensity changes of the fetal liver on MRI in-phase and out-of-phase sequence.

    Science.gov (United States)

    Li, Xiaobing; Brugger, Peter C; Huang, Min; Kasprian, Gregor; Li, Hong; Bettelheim, Dieter; Prayer, Daniela

    2013-04-01

    To study signal intensity (SI) of the fetal liver by MRI in-phase and out-of-phase over gestational age (GA). A total of 91 pregnant women from 19 to 38 gestational weeks were imaged using MRI. Liver-to-spleen SI ratios of the right and left fetal liver lobes on in-phase and out-of-phase were measured, calculated, and compared with each other. Curves of liver-to-spleen SI ratio of the right and left liver lobe were plotted by GA. Liver-to-spleen SI ratio of the right lobe on in-phase was different from that of the left liver lobe (t = 3.95; p < 0.001). A statistically significant difference was also found for out-of-phase SI ratios (t = 3.69; p < 0.001). Curves of liver-to-spleen SI ratio of the fetal liver on in-phase and out-of-phase showed changes against GA. Liver-to-spleen SI ratio is different between the right and left liver lobe, which probably results from the different blood supply. Curves of liver-to-spleen SI ratios between 19 to 38 gestational weeks reflect the changes of decreasing function of blood production by fetal liver. In-phase and out-of-phase may have clinical use in the early detection of disordered fetal growth and metabolism. © 2013 John Wiley & Sons, Ltd.

  20. Analysis of autocorrelation and ambiguity function of complicated radiolocation signal with binary phase manipulation by Kasami sequence

    Directory of Open Access Journals (Sweden)

    O. D. Mrachkovskyi

    2015-09-01

    Full Text Available Introduction. Were reviewed publications dedicated to pseudorandom sequences in radiolocation, and was made conclusion about necessity of researching in this subject. Modeling of probing radiolocation signal with binary phase manipulation by Kasami sequence. Were considered the method of forming Kasami sequences and measuring their properties. Example of generator for sequence with length 63 symbols is also shown. Technique of research. Were shown graphical results for modeling of Kasami sequence with lengths of 255 binary values. Amplitude of side maximums of autocorrelation function are measured. Modeling of ambiguity function. In this article, graphical results for modeling Kasami sequence ambiguity function are shown. These includes 3-dimensional plot of function body and its cross-sections by plane of equal ranges and planes of function level, equal to 0.9, 0.7, 0.5, 0.4, 0.3, 0.2 and 0.1 of its maximum. Were analyzed amplitude of side maximums, cross-section form and relative values of range and speed resolution. Conclusion. These articles contain analyses of characteristics of previously shown plots. These analyses include estimation of total value of side maximums of ambiguity function of Kasami sequence, ambiguity function cross-section form analysis and conclusion about ability of using these sequences as probe signal in radiolocation.

  1. Noise sequences of infinite matrices and their applications to the characterization of the canonical phase and box localization observables

    CERN Document Server

    Lahti, P J; Scheffold, E; Ylinen, K; Lahti, Pekka; Maczynski, Maciej J.; Scheffold, Egon; Ylinen, Kari

    2006-01-01

    Noise sequences of infinite matrices associated with covariant phase and box localization observables are defined and determined. The canonical observables are characterized within the relevant classes of observables as those with asymptotically minimal or minimal noise, i.e., the noise tending to 0 or having the value 0.

  2. Biodegradation of 4-nitrophenol in a two-phase sequencing batch reactor: concept demonstration, kinetics and modelling.

    Science.gov (United States)

    Tomei, M Concetta; Annesini, M Cristina; Rita, Sara; Daugulis, Andrew J

    2008-10-01

    The objectives of this work were to demonstrate the potential of a two-phase sequencing batch reactor in degrading xenobiotics and to evaluate the kinetic parameters leading to a mathematical model of the system. 4-Nitrophenol (4NP), a typical representative of substituted phenols, was selected as the target xenobiotic; this compound has never been remediated in a two-phase bioreactor before. Partition tests were conducted to determine the most appropriate partitioning solvent, and among the three investigated solvents (1-undecanol, 2-undecanone and oleyl alcohol), 2-undecanone was chosen because of its favourable partition coefficient and its negligible emulsion-forming tendencies. Moreover, the selected solvent showed satisfactory biocompatibility characteristics with respect to the biomass, with only minor effects on the intrinsic microbial kinetics. Kinetic tests were then performed in a sequencing batch reactor (2-l volume) operated in both conventional one- and two-phase configurations, with the two-phase system showing a significant improvement in the process kinetics in terms of reduced inhibition and increased maximum removal rate. The obtained kinetic parameters suggest that the two-phase sequencing batch system may find full-scale application, as the maximum removal rate k(max) (approximately 3 mg 4NP mgVSS(-1) day(-1)) is of the same order of magnitude of heterotrophic bacteria operating in wastewater treatment plants.

  3. Magnetic resonance visualization of conductive structures by sequence-triggered direct currents and spin-echo phase imaging

    Energy Technology Data Exchange (ETDEWEB)

    Eibofner, Frank; Wojtczyk, Hanne; Graf, Hansjörg, E-mail: hansjoerg.graf@med.uni-tuebingen.de, E-mail: drGraf@t-online.de [Section on Experimental Radiology, University Hospital Tübingen, Tübingen D-72076 (Germany); Clasen, Stephan [Department of Diagnostic and Interventional Radiology, University Hospital Tübingen, Tübingen D-72076 (Germany)

    2014-06-15

    Purpose: Instrument visualization in interventional magnetic resonance imaging (MRI) is commonly performed via susceptibility artifacts. Unfortunately, this approach suffers from limited conspicuity in inhomogeneous tissue and disturbed spatial encoding. Also, susceptibility artifacts are controllable only by sequence parameters. This work presents the basics of a new visualization method overcoming such problems by applying sequence-triggered direct current (DC) pulses in spin-echo (SE) imaging. SE phase images allow for background free current path localization. Methods: Application of a sequence-triggered DC pulse in SE imaging, e.g., during a time period between radiofrequency excitation and refocusing, results in transient field inhomogeneities. Dependent on the additional z-magnetic field from the DC, a phase offset results despite the refocusing pulse. False spatial encoding is avoided by DC application during periods when read-out or slice-encoding gradients are inactive. A water phantom containing a brass conductor (water equivalent susceptibility) and a titanium needle (serving as susceptibility source) was used to demonstrate the feasibility. Artifact dependence on current strength and orientation was examined. Results: Without DC, the brass conductor was only visible due to its water displacement. The titanium needle showed typical susceptibility artifacts. Applying triggered DC pulses, the phase offset of spins near the conductor appeared. Because SE phase images are homogenous also in regions of persistent field inhomogeneities, the position of the conductor could be determined with high reliability. Artifact characteristic could be easily controlled by amperage leaving sequence parameters unchanged. For an angle of 30° between current and static field visualization was still possible. Conclusions: SE phase images display the position of a conductor carrying pulsed DC free from artifacts caused by persistent field inhomogeneities. Magnitude and phase

  4. Delay enhancement patterns in apical hypertrophic cardiomyopathy by phase-sensitive inversion recovery sequence

    Institute of Scientific and Technical Information of China (English)

    Zi-Yi Guo; Jing Chen; Qi-Zhou Liang; Hai-Yan Liao; Shui-Xi Fu; Qian-Yu Tang; Cai-Xiang Chen; Xiang-Jun Han; Feng Gao

    2012-01-01

    Objective:Late gadolinium enhancement (LGE) patterns of cardiovascular magnetic resonance (CMR) relying on PSIR (phase-sensitive inversion recovery sequence) techniques had been used to determine the characteristics of LGE in apical hypertrophic cardiomyopathy (ApHCM). Methods:Forty patients pure ApHCM [age, (60.2±10.4) years, 31 men] were enrolled. LGE images were acquired using PSIR, and analyzed using a 17-segment model. Summing the LGE areas in all short axis slices yielded the total volume of late enhancement, which was subsequently presented as a proportion of total LV myocardium (%LGE). Results:Mean maximal apical wall thickness was (17.9±2.3) mm, and mean left ventricular (LV) ejection fraction was (67.7±8.0)%. LGE was detected in 130 segments of 30 patients (75.0%), occupying (4.9±5.5)%of LV myocardium. LGE was mainly detected at the junction between left and right ventricles in 12 (30%) and at the apex in 28 (70%), although LGE-positive areas were widely distributed, and not limited to the apex. Focal LGE at the non-hypertrophic LV segments was found in some ApHCM patients, even without LGE of hypertrophied apical segments. Conclusions: LGE was frequently observed not only in the thickened apex of the heart but also in other LV segments, irrespective of the presence or absence of hypertrophy. The simple presence of LGE on CMR was not representative of adverse prognosis in this population.

  5. A phase field method for joint denoising, edge detection, and motion estimation in image sequence processing

    NARCIS (Netherlands)

    Preusser, T.; Droske, M.; Garbe, C. S.; Telea, A.; Rumpf, M.

    2007-01-01

    The estimation of optical flow fields from image sequences is incorporated in a Mumford-Shah approach for image denoising and edge detection. Possibly noisy image sequences are considered as input and a piecewise smooth image intensity, a piecewise smooth motion field, and a joint discontinuity set

  6. De novo sequencing and comparative analysis of testicular transcriptome from different reproductive phases in freshwater spotted snakehead Channa punctatus

    Science.gov (United States)

    Roy, Alivia; Basak, Reetuparna

    2017-01-01

    The spotted snakehead Channa punctatus is a seasonally breeding teleost widely distributed in the Indian subcontinent and economically important due to high nutritional value. The declining population of C. punctatus prompted us to focus on genetic regulation of its reproduction. The present study carried out de novo testicular transcriptome sequencing during the four reproductive phases and correlated differential expression of transcripts with various testicular events in C. punctatus. The Illumina paired-end sequencing of testicular transcriptome from resting, preparatory, spawning and postspawning phases generated 41.94, 47.51, 61.81 and 44.45 million reads, and 105526, 105169, 122964 and 106544 transcripts, respectively. Transcripts annotated using Rattus norvegicus reference protein sequences and classified under various subcategories of biological process, molecular function and cellular component showed that the majority of the subcategories had highest number of transcripts during spawning phase. In addition, analysis of transcripts exhibiting differential expression during the four phases revealed an appreciable increase in upregulated transcripts of biological processes such as cell proliferation and differentiation, cytoskeleton organization, response to vitamin A, transcription and translation, regulation of angiogenesis and response to hypoxia during spermatogenically active phases. The study also identified significant differential expression of transcripts relevant to spermatogenesis (mgat3, nqo1, hes2, rgs4, cxcl2, alcam, agmat), steroidogenesis (star, tkt, gipc3), cell proliferation (eef1a2, btg3, pif1, myo16, grik3, trim39, plbd1), cytoskeletal organization (espn, wipf3, cd276), sperm development (klhl10, mast1, hspa1a, slc6a1, ros1, foxj1, hipk1), and sperm transport and motility (hint1, muc13). Analysis of functional annotation and differential expression of testicular transcripts depending on reproductive phases of C. punctatus helped in

  7. Reference genome-independent assessment of mutation density using restriction enzyme-phased sequencing

    Directory of Open Access Journals (Sweden)

    Monson-Miller Jennifer

    2012-02-01

    Full Text Available Abstract Background The availability of low cost sequencing has spurred its application to discovery and typing of variation, including variation induced by mutagenesis. Mutation discovery is challenging as it requires a substantial amount of sequencing and analysis to detect very rare changes and distinguish them from noise. Also challenging are the cases when the organism of interest has not been sequenced or is highly divergent from the reference. Results We describe the development of a simple method for reduced representation sequencing. Input DNA was digested with a single restriction enzyme and ligated to Y adapters modified to contain a sequence barcode and to provide a compatible overhang for ligation. We demonstrated the efficiency of this method at SNP discovery using rice and arabidopsis. To test its suitability for the discovery of very rare SNP, one control and three mutagenized rice individuals (1, 5 and 10 mM sodium azide were used to prepare genomic libraries for Illumina sequencers by ligating barcoded adapters to NlaIII restriction sites. For genome-dependent discovery 15-30 million of 80 base reads per individual were aligned to the reference sequence achieving individual sequencing coverage from 7 to 15×. We identified high-confidence base changes by comparing sequences across individuals and identified instances consistent with mutations, i.e. changes that were found in a single treated individual and were solely GC to AT transitions. For genome-independent discovery 70-mers were extracted from the sequence of the control individual and single-copy sequence was identified by comparing the 70-mers across samples to evaluate copy number and variation. This de novo "genome" was used to align the reads and identify mutations as above. Covering approximately 1/5 of the 380 Mb genome of rice we detected mutation densities ranging from 0.6 to 4 per Mb of diploid DNA depending on the mutagenic treatment. Conclusions The

  8. Quasi-Coherent Noise Jamming to LFM Radar Based on Pseudo-random Sequence Phase-modulation

    OpenAIRE

    2015-01-01

    A novel quasi-coherent noise jamming method is proposed against linear frequency modulation (LFM) signal and pulse compression radar. Based on the structure of digital radio frequency memory (DRFM), the jamming signal is acquired by the pseudo-random sequence phase-modulation of sampled radar signal. The characteristic of jamming signal in time domain and frequency domain is analyzed in detail. Results of ambiguity function indicate that the blanket jamming effect along the range direction wi...

  9. Sequencing and de novo analysis of Crassostrea angulata (Fujian oyster from 8 different developing phases using 454 GSFlx.

    Directory of Open Access Journals (Sweden)

    Ji Qin

    Full Text Available Research on the mechanism for early development of shellfish, such as body plan, shell formation, settlement and metamorphosis is currently an active research field. However, studies were still limited and not deep enough because of the lack of genomic resources such as genome or transcriptome sequences. In the present research, de novo transcriptome sequencing was performed for Crassostrea angulata, the most economically important cultured oyster species in China, at eight early developmental stages using the 454 sequencing technology. A total of 555,215 reads were produced with an average length of 309 nucleotides that were then assembled into 10,462 contigs. As determined by GO annotation and KEGG pathway mapping, functional annotation of the unigenes recovered diverse biological functions and processes. Six unique sequences related to settlement, metamorphosis and growth were subsequently analyzed by real-time PCR. Given the lack of whole genome information for oysters, transcriptome and de novo analysis of C. angulata from the eight different developing phases will provide important and useful information on early development mechanism and help genetic breeding of shellfish.

  10. Quasi-Coherent Noise Jamming to LFM Radar Based on Pseudo-random Sequence Phase-modulation

    Directory of Open Access Journals (Sweden)

    N. Tai

    2015-12-01

    Full Text Available A novel quasi-coherent noise jamming method is proposed against linear frequency modulation (LFM signal and pulse compression radar. Based on the structure of digital radio frequency memory (DRFM, the jamming signal is acquired by the pseudo-random sequence phase-modulation of sampled radar signal. The characteristic of jamming signal in time domain and frequency domain is analyzed in detail. Results of ambiguity function indicate that the blanket jamming effect along the range direction will be formed when jamming signal passes through the matched filter. By flexible controlling the parameters of interrupted-sampling pulse and pseudo-random sequence, different covering distances and jamming effects will be achieved. When the jamming power is equivalent, this jamming obtains higher process gain compared with non-coherent jamming. The jamming signal enhances the detection threshold and the real target avoids being detected. Simulation results and circuit engineering implementation validate that the jamming signal covers real target effectively.

  11. Detection of anthrax toxin genetic sequences by the solid phase oligo-probes

    Directory of Open Access Journals (Sweden)

    K C Addanki

    2011-01-01

    Full Text Available Purpose: There is an urgent need to detect a rapid field-based test to detect anthrax. We have developed a rapid, highly sensitive DNA-based method to detect the anthrax toxin lethal factor gene located in pXO1, which is necessary for the pathogenicity of Bacillus anthracis. Materials and Methods: We have adopted the enzyme-linked immunosorbent assay (ELISA so that instead of capturing antibodies we capture the DNA of the target sequence by a rapid oligo-based hybridization and then detect the captured DNA with another oligoprobe that binds to a different motif of the captured DNA sequences at a dissimilar location. We chose anthrax lethal factor endopeptidase sequences located in pXO1 and used complementary oligoprobe, conjugated with biotin, to detect the captured anthrax specific sequence by the streptavidin-peroxidase-based colorimetric assay. Result: Our system can detect picomoles (pMoles of anthrax (approximately 33 spores of anthrax and is >1000 times more sensitive than the current ELISA, which has a detection range of 0.1 to 1.0 ng/mL. False positive results can be minimized when various parameters and the colour development steps are optimized. Conclusion: Our results suggest that this assay can be adapted for the rapid detection of minuscule amounts of the anthrax spores that are aerosolized in the case of a bioterrorism attack. This detection system does not require polymerase chain reaction (PCR step and can be more specific than the antibody method. This method can also detect genetically engineered anthrax. Since, the antibody method is so specific to the protein epitope that bioengineered versions of anthrax may not be detected.

  12. Effect of Si additions on thermal stability and the phase transition sequence of sputtered amorphous alumina thin films

    Energy Technology Data Exchange (ETDEWEB)

    Bolvardi, H.; Baben, M. to; Nahif, F.; Music, D., E-mail: music@mch.rwth-aachen.de; Schnabel, V.; Shaha, K. P.; Mráz, S.; Schneider, J. M. [Materials Chemistry, RWTH Aachen University, Kopernikusstr. 10, D-52074 Aachen (Germany); Bednarcik, J.; Michalikova, J. [Deutsches Elektronen Synchrotron DESY, FS-PE group, Notkestrasse 85, D-22607 Hamburg (Germany)

    2015-01-14

    Si-alloyed amorphous alumina coatings having a silicon concentration of 0 to 2.7 at. % were deposited by combinatorial reactive pulsed DC magnetron sputtering of Al and Al-Si (90-10 at. %) split segments in Ar/O{sub 2} atmosphere. The effect of Si alloying on thermal stability of the as-deposited amorphous alumina thin films and the phase formation sequence was evaluated by using differential scanning calorimetry and X-ray diffraction. The thermal stability window of the amorphous phase containing 2.7 at. % of Si was increased by more than 100 °C compared to that of the unalloyed phase. A similar retarding effect of Si alloying was also observed for the α-Al{sub 2}O{sub 3} formation temperature, which increased by more than 120 °C. While for the latter retardation, the evidence for the presence of SiO{sub 2} at the grain boundaries was presented previously, this obviously cannot explain the stability enhancement reported here for the amorphous phase. Based on density functional theory molecular dynamics simulations and synchrotron X-ray diffraction experiments for amorphous Al{sub 2}O{sub 3} with and without Si incorporation, we suggest that the experimentally identified enhanced thermal stability of amorphous alumina with addition of Si is due to the formation of shorter and stronger Si–O bonds as compared to Al–O bonds.

  13. Anaerobic digestion of kitchen wastes in a single-phased anaerobic sequencing batch reactor(ASBR) with gas-phased absorb of CO2

    Institute of Scientific and Technical Information of China (English)

    ZHANG Bo; HE Zheng-guang; ZHANG Li-li; XU Jian-bo; SHI Hong-zhuan; CAI Wei-min

    2005-01-01

    The performance of the single-stage anaerobic digestion of kitchen wastes was investigated in an anaerobic sequencing batch reactor(ASBR) with gas-phased absorb of CO2. The ASBR was operated at four chemical oxygen demand(COD) loading rates, 2.8,respectively. The operation of the reactor with gas-phased absorb of CO2 was stable in spite of the low pH (2.6-3.9) and high concentration of TS(142 g/L) of input mixture. The output volatile fatty acid(VFA) concentration was between 2.7-4.7 g/L and had no inhibition on the methanogenic microorganism. The reactor without gas-phased absorb of CO2 became acidified when the total COD alkaline will be required to keep pH in the appropriate range for the methanogenic microorganism based on theoretical calculation. Gasphased absorb of CO2 effectively reduced the alkaline consumption, hence avoided excessive cation into the reactor.

  14. rTPPM: Towards Improving Solid-State NMR Two-Pulse Phase-Modulation Heteronuclear Dipolar Decoupling Sequence by Refocusing

    DEFF Research Database (Denmark)

    Equbal, Asif; Paul, Subhradip; Mithu, Venus Singh

    2014-01-01

    We present here a simple refocused modification, r TPPM, of the Two-Pulse Phase-Modulation (TPPM) heteronuclear decoupling method, which improves decoupling and makes the sequence much more robust with respect to essential experimental parameters. The modified sequence is compared with the establ...

  15. Analytic signal phase-based myocardial motion estimation in tagged MRI sequences by a bilinear model and motion compensation.

    Science.gov (United States)

    Wang, Liang; Basarab, Adrian; Girard, Patrick R; Croisille, Pierre; Clarysse, Patrick; Delachartre, Philippe

    2015-08-01

    Different mathematical tools, such as multidimensional analytic signals, allow for the calculation of 2D spatial phases of real-value images. The motion estimation method proposed in this paper is based on two spatial phases of the 2D analytic signal applied to cardiac sequences. By combining the information of these phases issued from analytic signals of two successive frames, we propose an analytical estimator for 2D local displacements. To improve the accuracy of the motion estimation, a local bilinear deformation model is used within an iterative estimation scheme. The main advantages of our method are: (1) The phase-based method allows the displacement to be estimated with subpixel accuracy and is robust to image intensity variation in time; (2) Preliminary filtering is not required due to the bilinear model. The proposed algorithm, integrating phase-based optical flow motion estimation and the combination of global motion compensation with local bilinear transform, allows spatio-temporal cardiac motion analysis, e.g. strain and dense trajectory estimation over the cardiac cycle. Results from 7 realistic simulated tagged magnetic resonance imaging (MRI) sequences show that our method is more accurate compared with state-of-the-art method for cardiac motion analysis and with another differential approach from the literature. The motion estimation errors (end point error) of the proposed method are reduced by about 33% compared with that of the two methods. In our work, the frame-to-frame displacements are further accumulated in time, to allow for the calculation of myocardial Lagrangian cardiac strains and point trajectories. Indeed, from the estimated trajectories in time on 11 in vivo data sets (9 patients and 2 healthy volunteers), the shape of myocardial point trajectories belonging to pathological regions are clearly reduced in magnitude compared with the ones from normal regions. Myocardial point trajectories, estimated from our phase-based analytic

  16. Strand specific RNA-sequencing and membrane lipid profiling reveals growth phase-dependent cold stress response mechanisms in Listeria monocytogenes

    DEFF Research Database (Denmark)

    Hingston, Patricia; Chen, Jessica; Allen, Kevin

    2017-01-01

    -supply-chain. This study utilized strand-specific RNA sequencing and whole cell fatty acid (FA) profiling to characterize the bacterium’s cold stress response. RNA and FAs were extracted from a cold-tolerant strain at five time points between early lag phase and late stationary-phase, both at 4°C and 20°C. Overall, more...

  17. Evaluation of a dedicated dual phased-array surface coil using a black-blood FSE sequence for high resolution MRI of the carotid vessel wall

    NARCIS (Netherlands)

    M. Ouhlous (Mohamed); F. Lethimonnier; D.W.J. Dippel (Diederik); M.R.H.M. van Sambeek (Marc); L.C.J. van Heerebeek (Lambertus C.); P.M.T. Pattynama (Peter); A. van der Lugt (Aad)

    2002-01-01

    textabstractPurpose: To investigate the ability of magnetic resonance imaging (MRI) to visualize the carotid vessel wall using a phased-array coil and a black-blood (BB) fast spin-echo (FSE) sequence. Materials and Methods: The phased-array coil was compared with a three-inch coil. Images from volun

  18. Controls on solid-phase inclusion during porphyroblast growth: insights from the Barrovian sequence (Scottish Dalradian)

    Science.gov (United States)

    Farber, Katja; Caddick, Mark J.; John, Timm

    2014-12-01

    A series of Barrovian sequence samples ranging from garnet to sillimanite zones were investigated to infer their porphyroblast-forming reactions and mineral inclusion histories. Quartz is overgrown and partly consumed during garnet formation and remains as inclusion-rich layers in porphyroblasts of the garnet zone. Staurolite crystals in the staurolite zone display sharp transitions between inclusion-rich and inclusion-free areas, suggesting two stages of growth with a different role of quartz in each. The inclusion-rich domains formed similarly to those in garnet by simple overgrowth and resorption of matrix minerals, with thermodynamic constraints suggesting that this staurolite-forming reaction required the presence of chloritoid that is now absent from the examined samples. The participation of garnet was limited in staurolite formation, with chloritoid breakdown supplying sufficient material to form the large amounts (c. 25 vol%) of staurolite found in the rock. This reaction produces an excess of SiO2, which leaves the crystal domain as SiO2aq and thus caused the formation of the inclusion-free areas in the staurolite and precipitation of quartz in the matrix. In the sillimanite zone, staurolite is consumed forming new garnet. The newly formed garnet has less quartz inclusions than its core due to a proportionally greater consumption of quartz by the second garnet-forming reaction than by the initial, garnet-grade reactions. Textural and thermodynamic data both suggest that inclusions in these porphyroblasts represent leftovers of a preferentially overgrown matrix than co-products of the porphyroblast-forming reaction.

  19. Comparison of the bacterial community composition in the granular and the suspended phase of sequencing batch reactors.

    Science.gov (United States)

    Szabó, Enikö; Liébana, Raquel; Hermansson, Malte; Modin, Oskar; Persson, Frank; Wilén, Britt-Marie

    2017-09-05

    Granulation of activated sludge is an increasingly important area within the field of wastewater treatment. Granulation is usually achieved by high hydraulic selection pressure, which results in the wash-out of slow settling particles. The effect of the harsh wash-out conditions on the granular sludge ecosystem is not yet fully understood, but different bacterial groups may be affected to varying degrees. In this study, we used high-throughput amplicon sequencing to follow the community composition in granular sludge reactors for 12 weeks, both in the granular phase and the suspended phase (effluent). The microbiome of the washed out biomass was similar but not identical to the microbiome of the granular biomass. Certain taxa (e.g. Flavobacterium spp. and Bdellovibrio spp.) had significantly (p Zooglea sp.) had significantly lower relative abundance in the granules compared to the effluent, and appeared to be mainly located on the surface of granules and therefore subject to erosion. Despite being washed out, these taxa were among the most abundant members of the granular sludge communities and were likely growing fast in the reactors. The ratio between relative abundance in the granular biomass and in the effluent did not predict temporal variation of the taxa in the reactors, but it did appear to predict the spatial location of the taxa in the granules.

  20. GRAIL-genQuest: A comprehensive computational system for DNA sequence analysis. Final report, DOE SBIR Phase II

    Energy Technology Data Exchange (ETDEWEB)

    Manning, Ruth Ann

    1999-01-05

    Recent advances in DNA sequencing and genome mapping technologies are making it possible, for the first time in history, to find genes in plants and animals and to elucidate their function. This means that diagnostics and therapeutics can be developed for human diseases such as cancer, obesity, hypertension, and cardiovascular problems. Crop and animal strains can be developed that are hardier, resistant to diseases, and produce higher yields. The challenge is to develop tools that will find the nucleotides in the DNA of a living organism that comprise a particular gene. In the human genome alone it is estimated that only about 51% of the approximately 3 billion pairs of nucleotides code for some 100,000 human genes. In this search for nucleotides within a genome which are active in the actual coding of proteins, efficient tools to locate and identify their function can be of significant value to mankind. Software tools such as ApoCom GRAIL{trademark} have assisted in this search. It can be used to analyze genome information, to identify exons (coding regions) and to construct gene models. Using a neural network approach, this software can ''learn'' sequence patterns and refine its ability to recognize a pattern as it is exposed to more and more examples of it. Since 1992 versions of GRAIL{trademark} have been publicly available over the Internet from Oak Ridge National Laboratory. Because of the potential for security and patent compromise, these Internet versions are not available to many researchers in pharmaceutical and biotechnology companies who cannot send proprietary sequences past their data-secure firewalls. ApoCom is making available commercial versions of the GRAIL{trademark} software to run self-contained over local area networks. As part of the commercialization effort, ApoCom has developed a new Java{trademark}-based graphical user interface, the ApoCom Client Tool for Genomics (ACTG){trademark}. Two products, ApoCom GRAIL

  1. Electrode Materials, Thermal Annealing Sequences, and Lateral/Vertical Phase Separation of Polymer Solar Cells from Multiscale Molecular Simulations

    KAUST Repository

    Lee, Cheng-Kuang

    2014-12-10

    © 2014 American Chemical Society. The nanomorphologies of the bulk heterojunction (BHJ) layer of polymer solar cells are extremely sensitive to the electrode materials and thermal annealing conditions. In this work, the correlations of electrode materials, thermal annealing sequences, and resultant BHJ nanomorphological details of P3HT:PCBM BHJ polymer solar cell are studied by a series of large-scale, coarse-grained (CG) molecular simulations of system comprised of PEDOT:PSS/P3HT:PCBM/Al layers. Simulations are performed for various configurations of electrode materials as well as processing temperature. The complex CG molecular data are characterized using a novel extension of our graph-based framework to quantify morphology and establish a link between morphology and processing conditions. Our analysis indicates that vertical phase segregation of P3HT:PCBM blend strongly depends on the electrode material and thermal annealing schedule. A thin P3HT-rich film is formed on the top, regardless of bottom electrode material, when the BHJ layer is exposed to the free surface during thermal annealing. In addition, preferential segregation of P3HT chains and PCBM molecules toward PEDOT:PSS and Al electrodes, respectively, is observed. Detailed morphology analysis indicated that, surprisingly, vertical phase segregation does not affect the connectivity of donor/acceptor domains with respective electrodes. However, the formation of P3HT/PCBM depletion zones next to the P3HT/PCBM-rich zones can be a potential bottleneck for electron/hole transport due to increase in transport pathway length. Analysis in terms of fraction of intra- and interchain charge transports revealed that processing schedule affects the average vertical orientation of polymer chains, which may be crucial for enhanced charge transport, nongeminate recombination, and charge collection. The present study establishes a more detailed link between processing and morphology by combining multiscale molecular

  2. Antithrombotic properties of rafigrelide: a phase 1, open-label, non-randomised, single-sequence, crossover study.

    Science.gov (United States)

    Balasubramaniam, K; Viswanathan, G; Dragone, J; Grose-Hodge, R; Martin, P; Troy, S; Preston, P; Zaman, A G

    2014-07-03

    Platelets play a central role in atherothrombotic events. We investigated the effect of a novel platelet-lowering agent, rafigrelide, on thrombus formation and characteristics. In this phase 1, open-label, non-randomised, single-sequence, crossover study, healthy male volunteers received rafigrelide for 14 days (Period 1). Following a ≥6-week washout period, they then received rafigrelide + acetylsalicylic acid (ASA) for 14 days (Period 2). Thrombus formation was assessed ex vivo using the Badimon perfusion chamber, and thrombus characteristics were assessed using thromboelastography. A total of 15 volunteers were enrolled in the study and were assigned to Panel A or Panel B, which had different schedules of assessments. In Panel A, after treatment with rafigrelide alone (Period 1), mean (± standard deviation) platelet count was reduced from 283 (± 17) × 10⁹/l at Day 1, to 125 (± 47) × 10⁹/l at Day 14 (n=6) and thrombus area reduced under high and low shear conditions. Reductions in thrombus area under high shear conditions correlated with reductions in platelet count (r²=0.11, p=0.022; n=12). Rafigrelide treatment prolonged clot formation time and reduced clot strength. The addition of ASA to rafigrelide (Period 2) had no additional effect on platelet count or thrombus area under high or low shear conditions. Similar results were seen in Panel B for all parameters. The most common adverse events (≥3 participants per period) were thrombocytopenia and headache. While confirming the platelet-lowering effects of rafigrelide, this early phase study also indicates that rafigrelide has antithrombotic properties under both high and low shear conditions.

  3. Crystal Structures and Phase Sequences of Metallocenium Salts with Fluorinated Anions: Effects of Molecular Size and Symmetry on Phase Transitions to Ionic Plastic Crystals.

    Science.gov (United States)

    Mochida, Tomoyuki; Funasako, Yusuke; Ishida, Mai; Saruta, Shingo; Kosone, Takashi; Kitazawa, Takafumi

    2016-10-24

    Sandwich compounds often exhibit various phase transitions, including those to plastic phases. To elucidate the general features of the phase transitions in metallocenium salts, the thermal properties and crystal structures of [Fe(C5 Me5 )2 ]X ([1]X), [Co(C5 Me5 )2 ]X ([2]X), and [Fe(C5 Me4 H)2 ]X ([3]X) have been investigated, where the counter anions (X) are Tf2 N (=(CF3 SO2 )2 N(-) ), OTf (=CF3 SO3(-) ), PF6 , and BF4 . The Tf2 N salts commonly undergo phase transitions from an ordered phase at low temperatures to an anion-disordered phase, followed by a plastic phase and finally melt at high temperatures. All these salts exhibit a phase transition to a plastic phase, and the transition temperature generally decreases with decreasing cation size and increasing anion size. The crystal structures of these salts comprise an alternating arrangement of cations and anions. About half of these salts exhibit phase transitions at low temperatures, which are mostly correlated with the order-disorder of the anion.

  4. A semi-Markov model for mitosis segmentation in time-lapse phase contrast microscopy image sequences of stem cell populations.

    Science.gov (United States)

    Liu, An-An; Li, Kang; Kanade, Takeo

    2012-02-01

    We propose a semi-Markov model trained in a max-margin learning framework for mitosis event segmentation in large-scale time-lapse phase contrast microscopy image sequences of stem cell populations. Our method consists of three steps. First, we apply a constrained optimization based microscopy image segmentation method that exploits phase contrast optics to extract candidate subsequences in the input image sequence that contains mitosis events. Then, we apply a max-margin hidden conditional random field (MM-HCRF) classifier learned from human-annotated mitotic and nonmitotic sequences to classify each candidate subsequence as a mitosis or not. Finally, a max-margin semi-Markov model (MM-SMM) trained on manually-segmented mitotic sequences is utilized to reinforce the mitosis classification results, and to further segment each mitosis into four predefined temporal stages. The proposed method outperforms the event-detection CRF model recently reported by Huh as well as several other competing methods in very challenging image sequences of multipolar-shaped C3H10T1/2 mesenchymal stem cells. For mitosis detection, an overall precision of 95.8% and a recall of 88.1% were achieved. For mitosis segmentation, the mean and standard deviation for the localization errors of the start and end points of all mitosis stages were well below 1 and 2 frames, respectively. In particular, an overall temporal location error of 0.73 ± 1.29 frames was achieved for locating daughter cell birth events.

  5. Phased genotyping-by-sequencing enhances analysis of genetic diversity and reveals divergent copy number variants in maize

    Science.gov (United States)

    High-throughput sequencing of reduced representation genomic libraries has ushered in an era of genotyping-by-sequencing (GBS), where genome-wide genotype data can be obtained for nearly any species. However, there remains a need for imputation-free GBS methods for genotyping large samples taken fr...

  6. Biological nutrient removal with low nitrous oxide generation by cancelling the anaerobic phase and extending the idle phase in a sequencing batch reactor.

    Science.gov (United States)

    Chen, Yinguang; Wang, Dongbo; Zheng, Xiong; Li, Xiang; Feng, Leiyu; Chen, Hong

    2014-08-01

    Although wastewater biological nutrient removal can be achieved by alternating the anaerobic-oxic-anoxic phases, significant amount of nitrous oxide (N2O) is generated in oxic phases, where ammonia-oxidizing bacteria (AOB) rather than heterotrophic denitrifiers are the main contributors. Here a new efficient strategy to remarkably reduce N2O generation was reported. It was found that by cancelling the anaerobic phase and extending the idle phase the N2O generation was reduced by 42% using synthetic wastewater, whereas the total nitrogen and phosphorus removals were unaffected. The mechanistic investigations revealed that the cancelling of anaerobic phase benefited heterotrophic denitrifiers instead of AOB to be responsible for nitrogen removal in the oxic phases, increased the ratio of total nitrogen removal driven by external carbon source, and decreased nitrite accumulation. Quantitative real-time polymerase chain reaction and fluorescence in situ hybridization analyses further showed that the new strategy increased the number of N2O reducing bacteria but decreased the abundance of glycogen accumulating organisms, with N2O as their primary denitrification product. It was also determined that the ratio of nitric oxide reductase activity to N2O reductase activity was significantly decreased after anaerobic phase was cancelled. All these observations were in accord with the reduction of N2O production. The feasibility of this strategy to minimize the generation of N2O was finally confirmed for a real municipal wastewater. The results reported in this paper provide a new viewpoint to reduce N2O generation from wastewater biological nutrient removal.

  7. Advanced DVR with Zero-Sequence Voltage Component and Voltage Harmonic Elimination for Three-Phase Three-Wire Distribution Systems

    Directory of Open Access Journals (Sweden)

    Margo P

    2009-11-01

    Full Text Available Dynamic Voltage Restorer (DVR is a power electronics device to protect sensitive load when voltage sag occurs. Commonly, sensitive loads are electronic-based devices which generate harmonics. The magnitude and phase of compensated voltage in DVR depend on grounding system and type of fault. If the system is floating, the zero sequence components do not appear on the load side. Meanwhile, in a neutral grounded system, voltage sag is extremely affected by zero sequence components. A blocking transformer is commonly installed in series with DVR to reduce the effect of zero sequence components. This paper proposes a new DVR control scheme that is capable of eliminating the blocking transformer and reducing harmonic distortion. The system uses fuzzy polar controller to replace the conventional PI or FL controller that is commonly used. By taking into account the zero sequence components in the controller design, the effects of zero sequence components can be compensated. Simulated results show the effectiveness of the proposed DVR controller

  8. Exact solution of the CPMG pulse sequence with phase variation down the echo train: application to R₂ measurements.

    Science.gov (United States)

    Bain, Alex D; Kumar Anand, Christopher; Nie, Zhenghua

    2011-04-01

    An implicit exact algebraic solution of CPMG experiments is presented and applied to fit experiments. Approximate solutions are also employed to explore oscillations and effective decay rates of CPMG experiments. The simplest algebraic approximate solution has illustrated that measured intensities will oscillate in the conventional CPMG experiments and that using even echoes can suppress errors of measurements of R₂ due to the imperfection of high-power pulses. To deal with low-power pulses with finite width, we adapt the effective field to calculate oscillations. An optimization model with the effective field approximation and dimensionless variables is proposed to quantify oscillations of measured intensities of CPMG experiments of different phases of the π pulses. We show, as was known using other methods, that repeating one group of four pulses with different phases in CPMG experiments, which we call phase variation, but others call phase alternation or phase cycling, can significantly smooth the dependence of measured intensities on frequency offset in the range of ±½γB₁. In this paper, a second-order expression with respect to the ratio of frequency offset to π-pulse amplitude is developed to describe the effective R₂ of CPMG experiments when using a group phase variation scheme. Experiments demonstrate that (1) the exact calculation of CPMG experiments can remarkably eliminate systematic errors in measured R₂s due to the effects of frequency offset, even in the absence of phase variation; (2) CPMG experiments with group phase variation can substantially remove oscillations and effects of the field inhomogeneity; (3) the second-order expression of the effective decay rate with phase variation is able to provide reliable estimates of R₂ when offsets are roughly within ±½γB₁; and, most significantly, (4) the more sophisticated optimization model using an exact solution of the discretized CPMG experiment extends, to ±γB₁, the range of

  9. Spinal imaging abnormality, low back and leg pain, and muscle tension--a five-phase hypothesis considering generative sequence and causal relationship.

    Science.gov (United States)

    Ishihara, Kiyoshi

    2009-11-01

    Although there are numerous studies examining the relationship between spinal imaging abnormality and low back and leg pain, the majority are only concerned with the correlation between these two. If we were to attempt to use the results of these studies as the basis for a treatment plan, it would be necessary to investigate the presence (or absence) of a causal relationship between the two. However, upon examination of previous studies we consider that this causal relationship has in fact either not been proven or has been refuted. To this end, we have conducted this study based on the hypothesis that spinal imaging abnormality and low back and leg pain possess a spurious relationship wherein muscle tension is the lurking variable. Furthermore, we propose a five-phase hypothesis considering the generative sequence of and causal relationship between spinal imaging abnormality, low back and leg pain, and muscle tension. Specifically, Phase I represents the healthy condition; Phase II indicates the occurrence of muscle tension only; Phase III indicates the occurrence of pain resulting from muscle tension; Phase IV represents the occurrence of both pain and imaging abnormality as a result of muscle tension; and Phase V indicates residual imaging abnormality despite amelioration of muscle tension. We believe that this hypothesis has the potential to facilitate pathological understanding and resolve the current confusion surrounding the diagnosis and treatment of spinal disorders.

  10. Pressure-induced phase-transition sequence in CoF2: An experimental and first-principles study on the crystal, vibrational, and electronic properties

    Science.gov (United States)

    Barreda-Argüeso, J. A.; López-Moreno, S.; Sanz-Ortiz, M. N.; Aguado, F.; Valiente, R.; González, J.; Rodríguez, F.; Romero, A. H.; Muñoz, A.; Nataf, L.; Baudelet, F.

    2013-12-01

    We report a complete structural study of CoF2 under pressure. Its crystal structure and vibrational and electronic properties have been studied both theoretically and experimentally using first-principles density functional theory (DFT) methods, x-ray diffraction, x-ray absorption at Co K-edge experiments, Raman spectroscopy, and optical absorption in the 0-80 GPa range. We have determined the structural phase-transition sequence in CoF2 and corresponding transition pressures. The results are similar to other transition-metal difluorides such as FeF2 but different to ZnF2 and MgF2, despite that the Co2+ size (ionic radius) is similar to Zn2+ and Mg2+. We found that the complete phase-transition sequence is tetragonal rutile (P42/mnm) → CaCl2 type (orthorhombic Pnnm) → distorted PdF2 (orthorhombic Pbca)+PdF2 (cubic Pa3¯) in coexistence → fluorite (cubic Fm3¯m) → cotunnite (orthorhombic Pnma). It was observed that the structural phase transition to the fluorite at 15 GPa involves a drastic change of coordination from sixfold octahedral to eightfold cubic with important modifications in the vibrational and electronic properties. We show that the stabilization of this high-pressure cubic phase is possible under nonhydrostatic conditions since ideal hydrostaticity would stabilize the distorted-fluorite structure (tetragonal I4/mmm) instead. Although the first rutile → CaCl2-type second-order phase transition is subtle by Raman spectroscopy, it was possible to define it through the broadening of the Eg Raman mode which is split in the CaCl2-type phase. First-principles DFT calculations are in fair agreement with the experimental Raman mode frequencies, thus providing an accurate description for all vibrational modes and elastic properties of CoF2 as a function of pressure.

  11. A planet in an 840-d orbit around a Kepler main-sequence A star found from phase modulation of its pulsations

    CERN Document Server

    Murphy, Simon J; Shibahashi, Hiromoto

    2016-01-01

    We have detected a 12 M$_{\\rm Jup}$ planet orbiting in or near the habitable zone of a main-sequence A star via the pulsational phase shifts induced by orbital motion. The planet has an orbital period of $840\\pm20$ d and an eccentricity of 0.15. All known planets orbiting main-sequence A stars have been found via the transit method or by direct imaging. The absence of astrometric or radial-velocity detections of planets around these hosts makes ours the first discovery using the orbital motion. It is also the first A star known to host a planet within 1$\\sigma$ of the habitable zone. We find evidence for planets in a large fraction of the parameter space where we are able to detect them. This supports the idea that A stars harbor high-mass planets in wide orbits.

  12. HIV sequence diversity during the early phase of infection is associated with HIV DNA reductions during antiretroviral therapy.

    Science.gov (United States)

    Wang, Nidan; Li, Yijia; Han, Yang; Xie, Jing; Li, Taisheng

    2017-06-01

    The association between baseline human immunodeficiency virus (HIV) sequence diversity and HIV DNA decay after the initiation of antiretroviral therapy (ART) remains uncharacterized during the early stages of HIV infection. Samples were obtained from a cohort of 17 patients with early HIV infection (HIV-1 envelope (env) gene was amplified via single genome amplification (SGA) to determine the peripheral plasma HIV quasispecies. We categorized HIV quasispecies into two groups according to baseline viral sequence genetic distance, which was determined by the Poisson-Fitter tool. Total HIV DNA in peripheral blood mononuclear cells (PBMCs), viral load, and T cell subsets were measured prior to and after the initiation of ART. The median SGA sequence number was 17 (range 6-28). At baseline, we identified 7 patients with homogeneous viral populations (designated the Homogeneous group) and 10 patients with heterogeneous viral populations (designated the Heterogeneous group) based on SGA sequences. Both groups exhibited similar HIV DNA decay rates during the first 6 months of ART (P > 0.99), but the Homogenous group experienced more prominent decay than the Heterogeneous group after 6 months (P = 0.037). The Heterogeneous group had higher CD4 cell counts after ART initiation; however, both groups had comparable recovery in terms of CD4/CD8 ratios and CD8 T cell activation levels. Viral population homogeneity upon the initiation of ART is associated with a decrease in HIV DNA levels during ART. J. Med. Virol. 89:982-988, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  13. 2'-Hydroxy protection of ribonucleosides as 2-cyano-2,2-dimethylethanimine-N-oxymethyl ethers in solid-phase synthesis of RNA sequences.

    Science.gov (United States)

    Cieślak, Jacek; Ausín, Cristina; Grajkowski, Andrzej; Beaucage, Serge L

    2013-10-08

    The reaction of 2'-O-aminooxymethylribonucleosides with 2-cyano-2-methyl propanal leads to the formation of stable and yet reversible 2'-O-(2-cyano-2,2-dimethylethanimine-N-oxymethyl)ribonucleosides in post-purification yields of 54% to 82%. Phenoxyacetylation of the exocyclic amino functions of these ribonucleosides proceeds in yields of 74% to 89%, and subsequent 5'-O-dimethoxytritylation and 3'-O-phosphitylation of the corresponding N-phenoxyacetylated ribonucleosides provide the fully protected ribonucleoside phosphoramidite monomers in isolated yields of 69% to 88%. These ribonucleoside phosphoramidites are employed in solid-phase synthesis of three chimeric RNA sequences, each differing in purine/pyrimidine content. The stepwise coupling efficiency of the ribonucleoside phosphoramidites (as 0.15 M solutions in acetonitrile) averages 99% over a coupling time of 180 s when 5-benzylthio-1H-tetrazole is used as an activator. Upon completion of RNA chain assembly, removal of the nucleobase- and phosphate-protecting groups and release of sequences from the solid support are carried out under standard basic conditions. Finally, the 2'-O-(2-cyano-2,2-dimethylethanimine-N-oxymethyl) protective groups are cleaved from the RNA sequences by treatment with 0.5 M tetra-n-butylammonium fluoride in dry DMSO for 24 to 48 hr at 55°C without releasing RNA-alkylating side-products. Characterization of the fully deprotected RNA sequences by PAGE, enzymatic hydrolysis, and MALDI-TOF mass spectrometry confirms the identity and high quality of these sequences.

  14. The 2-cyano-2,2-dimethylethanimine-N-oxymethyl group for the 2'-hydroxyl protection of ribonucleosides in the solid-phase synthesis of RNA sequences.

    Science.gov (United States)

    Cieślak, Jacek; Ausín, Cristina; Grajkowski, Andrzej; Beaucage, Serge L

    2013-04-02

    The reaction of 2-cyano-2-methyl propanal with 2'-O-aminooxymethylribonucleosides leads to stable and yet reversible 2'-O-(2-cyano-2,2-dimethylethanimine-N-oxymethyl)ribonucleosides. Following N-protection of the nucleobases, 5'-dimethoxytritylation and 3'-phosphitylation, the resulting 2'-protected ribonucleoside phosphoramidite monomers are employed in the solid-phase synthesis of three chimeric RNA sequences, each differing in their ratios of purine/pyrimidine. When the activation of phosphoramidite monomers is performed in the presence of 5-benzylthio-1H-tetrazole, coupling efficiencies averaging 99% are obtained within 180 s. Upon completion of the RNA-chain assemblies, removal of the nucleobase and phosphate protecting groups and release of the sequences from the solid support are carried out under standard basic conditions, whereas the cleavage of 2'-O-(2-cyano-2,2-dimethylethanimine-N-oxymethyl) protective groups is effected (without releasing RNA alkylating side-products) by treatment with tetra-n-butylammonium fluoride (0.5 M) in dry DMSO over a period of 24-48 h at 55 °C. Characterization of the fully deprotected RNA sequences by polyacrylamide gel electrophoresis (PAGE), enzymatic hydrolysis, and matrix-assisted laser desorption/ionization (MALDI) mass spectrometry confirmed the identity and quality of these sequences. Thus, the use of 2'-O-aminooxymethylribonucleosides in the design of new 2'-hydroxyl protecting groups is a powerful approach to the development of a straightforward, efficient, and cost-effective method for the chemical synthesis of high-quality RNA sequences in the framework of RNA interference applications.

  15. Strand specific RNA-sequencing and membrane lipid profiling reveals growth phase-dependent cold stress response mechanisms in Listeria monocytogenes

    Science.gov (United States)

    Hingston, Patricia; Chen, Jessica; Allen, Kevin; Truelstrup Hansen, Lisbeth

    2017-01-01

    The human pathogen Listeria monocytogenes continues to pose a challenge in the food industry, where it is known to contaminate ready-to-eat foods and grow during refrigerated storage. Increased knowledge of the cold-stress response of this pathogen will enhance the ability to control it in the food-supply-chain. This study utilized strand-specific RNA sequencing and whole cell fatty acid (FA) profiling to characterize the bacterium’s cold stress response. RNA and FAs were extracted from a cold-tolerant strain at five time points between early lag phase and late stationary-phase, both at 4°C and 20°C. Overall, more genes (1.3×) were suppressed than induced at 4°C. Late stationary-phase cells exhibited the greatest number (n = 1,431) and magnitude (>1,000-fold) of differentially expressed genes (>2-fold, pmonocytogenes, the growth-phase dependency of its cold-stress regulon, and the active roles of antisense transcripts in regulating its cold stress response. PMID:28662112

  16. Investigation of Proposed Process Sequence for the Array Automated Assembly Task, Phase 2. [low cost silicon solar array fabrication

    Science.gov (United States)

    Mardesich, N.; Garcia, A.; Bunyan, S.; Pepe, A.

    1979-01-01

    The technological readiness of the proposed process sequence was reviewed. Process steps evaluated include: (1) plasma etching to establish a standard surface; (2) forming junctions by diffusion from an N-type polymeric spray-on source; (3) forming a p+ back contact by firing a screen printed aluminum paste; (4) forming screen printed front contacts after cleaning the back aluminum and removing the diffusion oxide; (5) cleaning the junction by a laser scribe operation; (6) forming an antireflection coating by baking a polymeric spray-on film; (7) ultrasonically tin padding the cells; and (8) assembling cell strings into solar circuits using ethylene vinyl acetate as an encapsulant and laminating medium.

  17. A Pulse Width Modulation Scheme With Zero-sequence Voltage Injection for Single Phase Three-level NPC Rectifiers

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    A single phase three-level converter (shown in Fig. 1) has been widely applied in high-speed railway electrical traction drive systems. But the main technical drawback of the three-level converter is DC-link neutral point voltage drift. In order to solve this problem, it is important to understand the cause of DC-link neutral point voltage drift.

  18. Tuning the morphology, luminescence and magnetic properties of hexagonal-phase NaGdF4: Yb, Er nanocrystals via altering the addition sequence of the precursors

    Science.gov (United States)

    Zhao, Shuwen; Xia, Donglin; Zhao, Ruimin; Zhu, Hao; Zhu, Yiru; Xiong, Yuda; Wang, Youfa

    2017-01-01

    Hexagonal-phase NaGdF4: Yb, Er upconversion nanocrystals (UCNCs) with tunable morphology and properties were successfully prepared via a thermal decomposition method. The influences of the adding sequence of the precursors on the morphology, chemical composition, luminescence and magnetic properties were investigated by transmission electron microscopy (TEM), inductively coupled plasma-atomic emission spectrometry (ICP-AES), upconversion (UC) spectroscopy, and a vibrating sample magnetometer (VSM). It was found that the resulting nanocrystals, with different sizes ranging from 24 to 224 nm, are in the shape of spheres, hexagonal plates and flakes; moreover, the composition percentage of Yb3+-Er3+ and Gd3+ ions was found to vary in a regular pattern with the adding sequence. Furthermore, the intensity ratios of emission colors (f g/r, f g/p), and the magnetic mass susceptibility of hexagonal-phase NaGdF4: Yb, Er nanocrystals change along with the composition of the nanocrystals. A positive correlation between the susceptibility and f g/r of NaGdF4: Yb, Er was proposed. The decomposition processes of the precursors were investigated by a thermogravimetric (TG) analyzer. The result indicated that the decomposition of the resolved lanthanide trifluoroacetate is greatly different from lanthanide trifluoroacetate powder. It is of tremendous help to recognize the decomposition process of the precursors and to understand the related reaction mechanism.

  19. Three-dimensional phase-sensitive inversion recovery sequencing in the evaluation of left ventricular myocardial scars in ischemic and non-ischemic cardiomyopathy: Comparison to three-dimensional inversion recovery sequencing

    Energy Technology Data Exchange (ETDEWEB)

    Kido, Tomoyuki, E-mail: tomozo0421@gmail.com [Department of Radiology, Ehime University Graduate School of Medicine (Japan); Kido, Teruhito; Nakamura, Masashi; Kawaguchi, Naoto; Nishiyama, Yoshiko [Department of Radiology, Ehime University Graduate School of Medicine (Japan); Ogimoto, Akiyoshi [Department of Cardiovascular Internal Medicine, Ehime University Graduate School of Medicine (Japan); Miyagawa, Masao; Mochizuki, Teruhito [Department of Radiology, Ehime University Graduate School of Medicine (Japan)

    2014-12-15

    Highlights: • We evaluate 3D PSIR compared with 3D IR for the detection of myocardial scars. • In image quality, there was no significant difference between IR and PSIR. • A quantitative analysis of LGE volume shows a strong correlation between PSIR and IR. • PSIR detected greater LGE volume in non-ischemic cardiomyopathy patients than IR. • PSIR may have a specific role in scar evaluation of non-ischemic cardiomyopathy. - Abstract: Background: Late gadolinium enhancement (LGE) magnetic resonance imaging (MRI) is a useful technique for detecting myocardial fibrosis. LGE images are typically acquired using the inversion recovery (IR) method. Recently, phase-sensitive inversion recovery (PSIR) technology has been developed. The purpose of this study was to evaluate free-breathing 3D PSIR sequencing in comparison with breath-held 3D IR sequencing for the detection of myocardial fibrosis. Methods: One hundred twenty-three patients with suspected ischemic cardiac disease (n = 27) or non-ischemic cardiomyopathy (hypertrophic cardiomyopathy, n = 29; dilated cardiomyopathy, n = 22; sarcoidosis, n = 21; arrhythmia, n = 9; myocarditis, n = 4; amyloidosis, n = 3; and others, n = 8) were evaluated by LGE–MRI, which was performed first with the IR sequence and then with the PSIR sequence, using a 3 T MRI scanner. Image quality was scored by two independent readers using a four-point scale. The 3D LGE volume was analyzed quantitatively and compared between both sequencing methods. Results: There was no significant difference in overall image quality (p = 0.19). LGE was detected in 73 patients, who were evaluated visually. Ultimately, 58 patients with acceptable image quality were enrolled in further quantitative analyses (volume assessment). Although quantification of LGE volume revealed a strong correlation between both methods, larger LGE volumes were detected with PSIR compared to IR in patients suspected of non-ischemic cardiomyopathy (39.5 ± 25.9 cm{sup 3} for

  20. Microsequencing of proteins and peptides in the Knauer sequencer with and without covalent attachment to polyvinylidene difluoride membranes by the wet-phase degradation technique.

    Science.gov (United States)

    Herfurth, E; Pilling, U; Wittmann-Liebold, B

    1991-05-01

    Proteins and large peptides were degraded with phenylisothiocyanate (PITC) in the horizontal flow-through-reactor of the Modular Knauer Sequencer (Fischer, S., Reimann, F. & Wittmann-Liebold, B. (1989) in Methods in Protein Sequence Analysis (Wittmann-Liebold, B., ed.) Springer-Verlag, Berlin, pp. 98-107) by the wet-phase filter technique (Wittmann-Liebold, B. (1988) J. Prot. Chem. 7, 224-225) employing polyvinylidene difluoride (PVDF) membranes without polybrene. In order to prevent losses of small peptides during solvent washes at the degradation, 1.4-phenylene diisothiocyanate (DITC) derivatized PVDF support (MilliGen, Burlington, MA) was used to covalently attach the peptide via its lysine groups in situ within the cross-flow reaction chamber onto this membrane (Herfurth, E., Pilling, U. & Wittmann-Liebold, B. (1990) J. Prot. Chem. 9, 267). We found these membranes very suitable for peptide degradations in the Knauer sequencer. In almost all cases we were able to identify the amino-acid residues of the peptide up to its last covalent fixation point to the membrane.

  1. Unravelling the transcriptomic landscape of the major phase II UDP-glucuronosyltransferase drug metabolizing pathway using targeted RNA sequencing.

    Science.gov (United States)

    Tourancheau, A; Margaillan, G; Rouleau, M; Gilbert, I; Villeneuve, L; Lévesque, E; Droit, A; Guillemette, C

    2016-02-01

    A comprehensive view of the human UDP-glucuronosyltransferase (UGT) transcriptome is a prerequisite to the establishment of an individual's UGT metabolic glucuronidation signature. Here, we uncover the transcriptome landscape of the 10 human UGT gene loci in normal and tumoral metabolic tissues by targeted RNA next-generation sequencing. Alignment on the human hg19 reference genome identifies 234 novel exon-exon junctions. We recover all previously known UGT1 and UGT2 enzyme-coding transcripts and identify over 130 structurally and functionally diverse novel UGT variants. We further expose a revised genomic structure of UGT loci and provide a comprehensive repertoire of transcripts for each UGT gene. Data also uncover a remodelling of the UGT transcriptome occurring in a tissue- and tumor-specific manner. The complex alternative splicing program regulating UGT expression and protein functions is likely critical in determining detoxification capacity of an organ and stress-related responses, with significant impact on drug responses and diseases.

  2. Synthesis of oligodeoxyribonucleotides by solid phase phosphotriester method on a reduced scale; preparation of oligonucleotides for improved promoter sequence.

    Science.gov (United States)

    Naruto, M

    1982-01-01

    A small reaction vessel, composed of a balled sintered glass filter and a test tube with a stopcock, was designed for the solid phase phosphotriester synthesis of oligodeoxyribonucleotide. Operation of small scale synthesis (nucleoside on resin: 3-6 mumol, activated diester of dimer: 20-30 mumol) was performed under the atmosphere of argon. The yield of each coupling reaction was 60-100%. Twelve short oligonucleotides (6-16mer) were obtained in 19-78% overall yield by this method. These oligomers were prepared as a part of the control region of gene to increase the translation efficiency.

  3. Moon Phases

    Science.gov (United States)

    Riddle, Bob

    2010-01-01

    When teaching Moon phases, the focus seems to be on the sequence of Moon phases and, in some grade levels, how Moon phases occur. Either focus can sometimes be a challenge, especially without the use of models and observations of the Moon. In this month's column, the author describes some of the lessons that he uses to teach the phases of the Moon…

  4. Production of bio-hydrogen by mesophilic anaerobic fermentation in an acid-phase sequencing batch reactor.

    Science.gov (United States)

    Cheong, Dae-Yeol; Hansen, Conly L; Stevens, David K

    2007-02-15

    The pH and hydraulic retention time (HRT) of an anaerobic sequencing batch reactor (ASBR) were varied to optimize the conversion of carbohydrate-rich synthetic wastewater into bio-hydrogen. A full factorial design using evolutionary operation (EVOP) was used to determine the effect of the factors and to find the optimum condition of each factor required for high hydrogen production rate. Experimental results from 20 runs indicate that a maximum hydrogen production rate of 4,460-5,540 mL/L/day under the volumetric organic loading rate (VOLR) of 75 g-COD/L/day obtained at an observed design point of HRT = 8 h and pH = 5.7. The hydrogen production rate was strongly dependent on the HRT, and the effect was statistically significant (P 0.05) was found for the pH on the hydrogen production rate. When the ASBR conditions were set for a maximum hydrogen production rate, the hydrogen production yield and specific hydrogen production rate were 60-74 mL/g-COD and 330-360 mL/g-VSS/day, respectively. The hydrogen composition was 43-51%, and no methanogenesis was observed. Acetate, propionate, butyrate, valerate, caproate, and ethanol were major liquid intermediate metabolites during runs of this ASBR. The dominant fermentative types were butyrate-acetate or ethanol-acetate, representing the typical anaerobic pathway of Clostridium species. This hydrogen-producing ASBR had a higher hydrogen production rate, compared with that produced using continuous-flow stirred tank reactors (CSTRs). This study suggests that the hydrogen-producing ASBR is a promising bio-system for prolonged and stable hydrogen production.

  5. Infrared reflectivity investigation of the phase transition sequence in Pr0.5Ca0.5MnO3

    Science.gov (United States)

    Ribeiro, J. L.; Vieira, L. G.; Gomes, I. T.; Araújo, J. P.; Tavares, P.; Almeida, B. G.

    2016-06-01

    This work reports an infrared reflectivity study of the phase transition sequence observed in Pr0.5Ca0.5MnO3. The need to measure over an extended spectral range in order to properly take into account the effects of the high frequency polaronic absorption is circumvented by adopting a simple approximate method, based on the asymmetry present in the Kramers Kronig inversion of the phonon spectrum. The temperature dependence of the phonon optical conductivity is then investigated by monitoring the behavior of three relevant spectral moments of the optical conductivity. This combined methodology allows us to disclose subtle effects of the orbital, charge and magnetic orders on the lattice dynamics of the compound. The characteristic transition temperatures inferred from the spectroscopic measurements are compared and correlated with those obtained from the temperature dependence of the induced magnetization and electrical resistivity.

  6. A reference data set of 5.4 million phased human variants validated by genetic inheritance from sequencing a three-generation 17-member pedigree

    Science.gov (United States)

    Eberle, Michael A.; Fritzilas, Epameinondas; Krusche, Peter; Källberg, Morten; Moore, Benjamin L.; Bekritsky, Mitchell A.; Iqbal, Zamin; Chuang, Han-Yu; Humphray, Sean J.; Halpern, Aaron L.; Kruglyak, Semyon; Margulies, Elliott H.; McVean, Gil; Bentley, David R.

    2017-01-01

    Improvement of variant calling in next-generation sequence data requires a comprehensive, genome-wide catalog of high-confidence variants called in a set of genomes for use as a benchmark. We generated deep, whole-genome sequence data of 17 individuals in a three-generation pedigree and called variants in each genome using a range of currently available algorithms. We used haplotype transmission information to create a phased “Platinum” variant catalog of 4.7 million single-nucleotide variants (SNVs) plus 0.7 million small (1–50 bp) insertions and deletions (indels) that are consistent with the pattern of inheritance in the parents and 11 children of this pedigree. Platinum genotypes are highly concordant with the current catalog of the National Institute of Standards and Technology for both SNVs (>99.99%) and indels (99.92%) and add a validated truth catalog that has 26% more SNVs and 45% more indels. Analysis of 334,652 SNVs that were consistent between informatics pipelines yet inconsistent with haplotype transmission (“nonplatinum”) revealed that the majority of these variants are de novo and cell-line mutations or reside within previously unidentified duplications and deletions. The reference materials from this study are a resource for objective assessment of the accuracy of variant calls throughout genomes. PMID:27903644

  7. Sequencing of Sipuleucel-T and Androgen Deprivation Therapy in Men with Hormone-Sensitive Biochemically Recurrent Prostate Cancer: A Phase II Randomized Trial.

    Science.gov (United States)

    Antonarakis, Emmanuel S; Kibel, Adam S; Yu, Evan Y; Karsh, Lawrence I; Elfiky, Aymen; Shore, Neal D; Vogelzang, Nicholas J; Corman, John M; Millard, Frederick E; Maher, Johnathan C; Chang, Nancy N; DeVries, Todd; Sheikh, Nadeem A; Drake, Charles G

    2016-11-10

    Purpose: STAND, a randomized, phase II, open-label trial (NCT01431391), assessed sequencing of sipuleucel-T (an autologous cellular immunotherapy) with androgen deprivation therapy (ADT) in biochemically recurrent prostate cancer (BRPC) patients at high risk for metastasis.Experimental Design: Men with BRPC following prostatectomy and/or radiotherapy, a PSA doubling time ≤12 months, and no metastasis were enrolled. Patients were randomized (34/arm) to sipuleucel-T followed by ADT (started 2 weeks after sipuleucel-T completion), or ADT followed by sipuleucel-T (started 12 weeks after ADT initiation); ADT continued for 12 months in both arms. The primary endpoint was PA2024-specific T-cell response [enzyme-linked immunospot (ELISPOT)] over time.Results: PA2024-specific ELISPOT responses over time were similar between groups, except at week 6, where responses were higher with sipuleucel-T→ADT versus ADT→sipuleucel-T (P = 0.013). PA2024-specific T-cell proliferation responses, averaged across time points, were approximately 2-fold higher with sipuleucel-T→ADT versus ADT→sipuleucel-T (P = 0.001). PA2024-specific cellular and humoral responses and prostatic acid phosphatase-specific humoral responses increased significantly versus baseline (P Sipuleucel-T with ADT was generally well tolerated.Conclusions: Sipuleucel-T→ADT appears to induce greater antitumor immune responses than the reverse sequence. These results warrant further investigation to determine whether this sequence leads to improved clinical outcomes, as well as the independent contribution of ADT alone in terms of immune activation. Clin Cancer Res; 1-9. ©2016 AACR.

  8. Implication of respiratory syncytial virus (RSV) F transgene sequence heterogeneity observed in Phase 1 evaluation of MEDI-534, a live attenuated parainfluenza type 3 vectored RSV vaccine.

    Science.gov (United States)

    Yang, Chin-Fen; Wang, C Kathy; Malkin, Elissa; Schickli, Jeanne H; Shambaugh, Cindy; Zuo, Fengrong; Galinski, Mark S; Dubovsky, Filip; Tang, Roderick S

    2013-06-10

    MEDI-534 is the first live vectored RSV vaccine candidate to be evaluated in seronegative children. It consists of the bovine parainfluenza virus type 3 (PIV3) genome with substituted human PIV3 F and HN glycoproteins engineered to express RSV F protein. A Phase 1 study of 49 healthy RSV and PIV3 seronegative children 6 to <24 months of age demonstrated an acceptable safety profile at the following doses: 10(4), 10(5) and 10(6)TCID50. After 3 doses of MEDI-534 at 10(6)TCID50, administered at 0, 2 and 4 month intervals, 100% of subjects seroresponded to PIV3, whereas only 50% seroresponded to RSV. To investigate the discordance in seroresponse rates, the RSV F transgene and its flanking non-coding nucleotides were sequenced from shed virus recovered from the nasal washes of 24 MEDI-534-vaccinated children. Eleven out of 24 samples contained no nucleotide changes in the analyzed region. The other 13 samples contained mixtures of variant subpopulations. Fifty-five percent exhibited changes in the transcription termination poly A gene sequences of the upstream bPIV3N gene while 21% had variant subpopulations in the RSV F open reading frame that resulted in pre-mature stop codons. Both types of changes are expected to reduce RSV F expression. Evaluation of the administered vaccine by dual immunofluorescence staining showed ~2.5% variants with low or no RSV F expression while single nucleotide primer extension detected ~1% variation at nucleotide 2045 that resulted in a pre-mature translational termination at codon 85. An association between shedding of variants and lower RSV F serological response was observed but it was not possible to establish a definitive clinical significance due to the small number of subjects in this study.

  9. A Unified Approach to BER Analysis of Synchronous Downlink CDMA Systems with Random Signature Sequences in Fading Channels with Known Channel Phase

    Directory of Open Access Journals (Sweden)

    M. Deriche

    2008-02-01

    Full Text Available A detailed analysis of the multiple access interference (MAI for synchronous downlink CDMA systems is carried out for BPSK signals with random signature sequences in Nakagami-m fading environment with known channel phase. This analysis presents a unified approach as Nakagami-m fading is a general fading distribution that includes the Rayleigh, the one-sided Gaussian, the Nakagami-q, and the Rice distributions as special cases. Consequently, new explicit closed-form expressions for the probability density function (pdf of MAI and MAI plus noise are derived for Nakagami-m, Rayleigh, one-sided Gaussian, Nakagami-q, and Rician fading. Moreover, optimum coherent reception using maximum likelihood (ML criterion is investigated based on the derived statistics of MAI plus noise and expressions for probability of bit error are obtained for these fading environments. Furthermore, a standard Gaussian approximation (SGA is also developed for these fading environments to compare the performance of optimum receivers. Finally, extensive simulation work is carried out and shows that the theoretical predictions are very well substantiated.

  10. Synthesis of Mn-sensitized TiO{sub 2}nanoparticles: influence of sequence of reagents on phase composition and photocatalytic activity

    Energy Technology Data Exchange (ETDEWEB)

    Kuzmicheva, Galina M.; Savinkina, Elena V., E-mail: e.savinkina@mail.ru; Obolenskaya, Lubov N. [Lomonosov University of Fine Chemical Technology (Russian Federation); Zubavichus, Yan V.; Murzin, Vadim Y. [National Research Center “Kurchatov Institute” (Russian Federation); Podbelskiy, Vadim V. [National Research University Higher School of Economics (Russian Federation); Sadovskaya, Nataliya V. [Karpov Institute of Physical Chemistry (Russian Federation)

    2015-10-15

    A new approach has been developed to synthesize manganese-containing titanium dioxide materials by hydrolysis of titanyl sulfate. The samples were studied by a complex of methods (synchrotron radiation X-ray powder diffraction, high-resolution scanning electron microscopy with energy-dispersive X-ray spectroscopy, absorption spectroscopy). The sequence of the added reagents effects the phase composition (anatase or mixtures of anatase and “η-TiO{sub 2}”), size of crystallites, nanoparticles and agglomerates, manganese content, and oxidation state (Mn{sup 3+}, Mn{sup 2+}/Mn{sup 3+}, or Mn{sup 3+}/Mn{sup 4+}). The Mn-doped TiO{sub 2} samples have been proven to have high photocatalytic activity for methyl orange (MO) under visible light. The rate of MO degradation reached 0.0046 min{sup −1} (50 % in 150 min) for the sample containing a mixture of anatase (75 %) and “η-TiO{sub 2}” (25 %) with a high degree of amorphism; the sample is characterized by the smallest size of crystallites (44.3 Å), the largest size of nanoparticles (33 nm) and agglomerates (10 μm), and the lowest manganese content (0.3 at. %) with the ratio Mn{sup 3+}:Mn{sup 4+} = 1:1. The resultant Mn-doped titania has potential applications in photocatalysis and environmental protection.

  11. Comparison of 4D flow and 2D velocity-encoded phase contrast MRI sequences for the evaluation of aortic hemodynamics.

    Science.gov (United States)

    Bollache, Emilie; van Ooij, Pim; Powell, Alex; Carr, James; Markl, Michael; Barker, Alex J

    2016-10-01

    The purpose of this study was to compare aortic flow and velocity quantification using 4D flow MRI and 2D CINE phase-contrast (PC)-MRI with either one-directional (2D-1dir) or three-directional (2D-3dir) velocity encoding. 15 healthy volunteers (51 ± 19 years) underwent MRI including (1) breath-holding 2D-1dir and (2) free breathing 2D-3dir PC-MRI in planes orthogonal to the ascending (AA) and descending (DA) aorta, as well as (3) free breathing 4D flow MRI with full thoracic aorta coverage. Flow quantification included the co-registration of the 2D PC acquisition planes with 4D flow MRI data, AA and DA segmentation, and calculation of AA and DA peak systolic velocity, peak flow and net flow volume for all sequences. Additionally, the 2D-3dir velocity taking into account the through-plane component only was used to obtain results analogous to a free breathing 2D-1dir acquisition. Good agreement was found between 4D flow and 2D-3dir peak velocity (differences = -3 to 6 %), peak flow (-7 %) and net volume (-14 to -9 %). In contrast, breath-holding 2D-1dir measurements exhibited indices significantly lower than free breathing 2D-3dir and 2D-1dir (differences = -35 to -7 %, p < 0.05). Finally, high correlations (r ≥ 0.97) were obtained for indices estimated with or without eddy current correction, with the lowest correlation observed for net volume. 4D flow and 2D-3dir aortic hemodynamic indices were in concordance. However, differences between respiration state and 2D-1dir and 2D-3dir measurements indicate that reference values should be established according to the PC-MRI sequence, especially for the widely used net flow (e.g. stroke volume in the AA).

  12. Few Skewed Disks Found in First Closure-Phase Survey of Herbig Ae/Be stars

    CERN Document Server

    Monnier, J D; Millan-Gabet, R; Traub, W; Schloerb, F P; Pedretti, E; Benisty, M; Carleton, N P; Haguenauer, P; Kern, P; Labeye, P; Lacasse, M G; Malbet, F; Perraut, K; Pearlman, M; Zhao, M

    2006-01-01

    Using the 3-telescope IOTA interferometer on Mt. Hopkins, we report results from the first near-infrared (lambda=1.65 mu) closure-phase survey of Young Stellar Objects (YSOs). These closure phases allow us to unambiguously detect departures from centrosymmetry (i.e., skew) in the emission pattern from YSO disks on the scale of ~4 milliarcseconds, expected from generic ``flared disk'' models. Six of fourteen targets showed small, yet statistically-significant, non-zero closure phases, with largest values from the young binary system MWC 361-A and the (pre-main sequence?) Be star HD 45677. Our observations are quite sensitive to the vertical structure of the inner disk and we confront the predictions of the ``puffed-up inner wall'' models of Dullemond, Dominik, and Natta (DDN). Our data support disks models with curved inner rims because the expected emission appear symmetrically-distributed around the star over a wide range of inclination angles. In contrast, our results are incompatible with the models posses...

  13. 无功和三相负荷不平衡的序分量法补偿控制%Compensation control of reactive power and three-phase unbalance load based on the method of sequence component

    Institute of Scientific and Technical Information of China (English)

    辛业春; 李国庆; 王朝斌

    2014-01-01

    A static synchronous compensator (STATCOM) is used into distribution grid for compensating reactive power and three- phase unbalance load for the distribution grid. According to analyzing the positive sequence equivalent circuit and negative sequence equivalent circuit under the three-phase unbalance load of distribution grid, using the symmetrical component method and superposition principle, a new cascade loop control strategy of positive sequence current and negative sequence current is proposed. Usingδ-θ control, the positive sequence loop compensates reactive power of distribution grid and maintains stability of STATCOM DC voltage. Usingφ-θ control in the negative sequence loop can make STATCOM compensate negative-sequence current caused by three-phase load unbalance and keep distribution grid side three-phase load balanced. Simulation and experiment results are presented to verify the validity of the proposed control strategy. This work is supported by National Natural Science Foundation of China (No. 51377016).%将静止同步补偿器(Static Synchronous Compensator,STATCOM)并入电网来补偿无功功率和配电网三相负荷不平衡。通过对称分量法和叠加原理,对配电网三相负荷不平衡情况下正序、负序等效电路进行分析,提出一种新的正、负序补偿电流叠加补偿控制方法。正序控制环采用δ-θ控制,实现配电网无功功率补偿和保持STATCOM直流侧电压稳定;负序控制环采用φ-θ控制,实现STATCOM补偿三相负荷不平衡产生的负序电流,使电网侧三相负荷保持平衡。仿真和实验结果表明,该方法可以有效地补偿电网无功功率和三相负荷不平衡。

  14. Correction of phase errors in quantitative water-fat imaging using a monopolar time-interleaved multi-echo gradient echo sequence.

    Science.gov (United States)

    Ruschke, Stefan; Eggers, Holger; Kooijman, Hendrik; Diefenbach, Maximilian N; Baum, Thomas; Haase, Axel; Rummeny, Ernst J; Hu, Houchun H; Karampinos, Dimitrios C

    2017-09-01

    To propose a phase error correction scheme for monopolar time-interleaved multi-echo gradient echo water-fat imaging that allows accurate and robust complex-based quantification of the proton density fat fraction (PDFF). A three-step phase correction scheme is proposed to address a) a phase term induced by echo misalignments that can be measured with a reference scan using reversed readout polarity, b) a phase term induced by the concomitant gradient field that can be predicted from the gradient waveforms, and c) a phase offset between time-interleaved echo trains. Simulations were carried out to characterize the concomitant gradient field-induced PDFF bias and the performance estimating the phase offset between time-interleaved echo trains. Phantom experiments and in vivo liver and thigh imaging were performed to study the relevance of each of the three phase correction steps on PDFF accuracy and robustness. The simulation, phantom, and in vivo results showed in agreement with the theory an echo time-dependent PDFF bias introduced by the three phase error sources. The proposed phase correction scheme was found to provide accurate PDFF estimation independent of the employed echo time combination. Complex-based time-interleaved water-fat imaging was found to give accurate and robust PDFF measurements after applying the proposed phase error correction scheme. Magn Reson Med 78:984-996, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

  15. Automatic sequences

    CERN Document Server

    Haeseler, Friedrich

    2003-01-01

    Automatic sequences are sequences which are produced by a finite automaton. Although they are not random they may look as being random. They are complicated, in the sense of not being not ultimately periodic, they may look rather complicated, in the sense that it may not be easy to name the rule by which the sequence is generated, however there exists a rule which generates the sequence. The concept automatic sequences has special applications in algebra, number theory, finite automata and formal languages, combinatorics on words. The text deals with different aspects of automatic sequences, in particular:· a general introduction to automatic sequences· the basic (combinatorial) properties of automatic sequences· the algebraic approach to automatic sequences· geometric objects related to automatic sequences.

  16. Investigation of proposed process sequence for the array automated assembly task. Phase I and II. Final report, October 1, 1977-June 30, 1980

    Energy Technology Data Exchange (ETDEWEB)

    Mardesich, N.; Garcia, A.; Eskenas, K.

    1980-08-01

    A selected process sequence for the low cost fabrication of photovoltaic modules was defined during this contract. Each part of the process sequence was looked at regarding its contribution to the overall dollars per watt cost. During the course of the research done, some of the initially included processes were dropped due to technological deficiencies. The printed dielectric diffusion mask, codiffusion of the n+ and p+ regions, wraparound front contacts and retention of the diffusion oxide for use as an AR coating were all the processes that were removed for this reason. Other process steps were retained to achieve the desired overall cost and efficiency. Square wafers, a polymeric spin-on PX-10 diffusion source, a p+ back surface field and silver front contacts are all processes that have been recommended for use in this program. The printed silver solderable pad for making contact to the aluminum back was replaced by an ultrasonically applied tin-zinc pad. Also, the texturized front surface was dropped as inappropriate for the sheet silicon likely to be available in 1986. Progress has also been made on the process sequence for module fabrication. A shift from bonding with a conformal coating to laminating with ethylene vinyl acetate and a glass superstrate is recommended for further module fabrication. The finalized process sequence is described.

  17. Investigation of proposed process sequence for the array automated assembly task. Phase I and II. Final report, October 1, 1977-June 30, 1980

    Energy Technology Data Exchange (ETDEWEB)

    Mardesich, N.; Garcia, A.; Eskenas, K.

    1980-08-01

    A selected process sequence for the low cost fabrication of photovoltaic modules was defined during this contract. Each part of the process sequence was looked at regarding its contribution to the overall dollars per watt cost. During the course of the research done, some of the initially included processes were dropped due to technological deficiencies. The printed dielectric diffusion mask, codiffusion of the n+ and p+ regions, wraparound front contacts and retention of the diffusion oxide for use as an AR coating were all the processes that were removed for this reason. Other process steps were retained to achieve the desired overall cost and efficiency. Square wafers, a polymeric spin-on PX-10 diffusion source, a p+ back surface field and silver front contacts are all processes that have been recommended for use in this program. The printed silver solderable pad for making contact to the aluminum back was replaced by an ultrasonically applied tin-zinc pad. Also, the texturized front surface was dropped as inappropriate for the sheet silicon likely to be available in 1986. Progress has also been made on the process sequence for module fabrication. A shift from bonding with a conformal coating to laminating with ethylene vinyl acetate and a glass superstrate is recommended for further module fabrication. The finalized process sequence is described.

  18. Supressão das anomalias de fase e batimentos laterais em espectros de RMN 13c obtidos com a sequência de precessão livre no estado estacionário Suppression of phase anomalies and sidebands on 13c NMR spectra obtained with the steady-state free precession sequence

    Directory of Open Access Journals (Sweden)

    Poliana Macedo dos Santos

    2010-01-01

    Full Text Available The Steady-State Free Precession (SSFP sequence has been widely used in low-field and low-resolution imaging NMR experiments to increase the signal-to-noise ratio (s/n of the signals. Here, we analyzed the Scrambled Steady State - SSS and Unscrambled Steady State - USS sequences to suppress phase anomalies and sidebands of the 13C NMR spectrum acquired in the SSFP regime. The results showed that the application of the USS sequence allowed a uniform distribution of the time interval between pulses (Tp, in the established time range, allowing a greater suppression of phase anomalies and sidebands, when compared with the SSS sequence.

  19. The phase transition sequence and the location of the morphotropic phase boundary region in (1-x)[Pb (Mg sub 1 sub / sub 3 Nb sub 2 sub / sub 3)O sub 3 ]-xPbTiO sub 3 single crystal

    CERN Document Server

    Guo Yi Ping; Ling Di; Xu Hai Qing; He Tian Hou; Yin Zhi Wen

    2003-01-01

    Piezoelectric constant and temperature-dependent dielectric constant measurements have been performed on (110)-oriented (1-x)Pb (Mg sub 1 sub / sub 3 Nb sub 2 sub / sub 3)O sub 3 -xPbTiO sub 3 crystals with different compositions under different poling fields. The width of the morphotropic phase boundary region (0.30phase transition sequence was observed directly from the dielectric constant versus temperature results for (001)-poled rhombohedral crystals with compositions near the rhombohedral-monoclinic phase boundary. The structure of the morphotropic phase is shown to be monoclinic with space group P sub m. (letter to the editor)

  20. The influence of VKORC1 and CYP2C9 gene sequence variants on the stability of maintenance phase warfarin treatment

    DEFF Research Database (Denmark)

    Skov, Jane; Bladbjerg, Else-Marie; Leppin, Anja;

    2013-01-01

    INTRODUCTION: A substantial part of the inter-individual variation in vitamin K-antagonist dose can be explained by certain sequence variants in the genes CYP2C9 (NG_008385.1:g.8633C>T or *1/*2, NG_008385.1:g.47639A>C or *1/*3) and VKORC1 (NG_011564.1:g.6399C>T). Patients possessing these variant...

  1. Comprehensive screening of target molecules by next-generation sequencing in patients with malignant solid tumors: guiding entry into phase I clinical trials

    OpenAIRE

    Tanabe, Yuko; Ichikawa, Hitoshi; Kohno, Takashi; Yoshida, Hiroshi; Kubo, Takashi; Kato, Mamoru; Iwasa, Satoru; Ochiai, Atsushi; Yamamoto, Noboru; Fujiwara, Yasuhiro; Tamura, Kenji

    2016-01-01

    It is still controversial whether comprehensive genome screening of target molecules by next generation sequencing (NGS) is needed to increase clinical efficacy of investigational drugs or accelerate drug development, although several studies are being carried out. Therefore, we performed a prospective study to evaluate the feasibility of comprehensive gene screening in this setting. Our findings indicate that actionable alterations were identified in 45% of the analyzed patients, most freque...

  2. Whole genome sequence of Clostridium bornimense strain M2/40 isolated from a lab-scale mesophilic two-phase biogas reactor digesting maize silage and wheat straw.

    Science.gov (United States)

    Hahnke, Sarah; Wibberg, Daniel; Tomazetto, Geizecler; Pühler, Alfred; Klocke, Michael; Schlüter, Andreas

    2014-08-20

    The bacterium Clostridium bornimense M2/40 is a mesophilic, anaerobic bacterium isolated from a two-phase biogas reactor continuously fed with maize silage and 5% wheat straw. Grown on glucose, it produced H2, CO2, formiate, lactate and propionate as the main fermentation products, of which some compounds serve as substrates for methanogenic Archaea to form methane. Here, the whole genome sequence of the bacterium consisting of two circular replicons is reported. This genome information provides the basis for further studies addressing metabolic features of the isolate and its role in anaerobic biomass degradation.

  3. Sequence assembly

    DEFF Research Database (Denmark)

    Scheibye-Alsing, Karsten; Hoffmann, S.; Frankel, Annett Maria

    2009-01-01

    Despite the rapidly increasing number of sequenced and re-sequenced genomes, many issues regarding the computational assembly of large-scale sequencing data have remain unresolved. Computational assembly is crucial in large genome projects as well for the evolving high-throughput technologies...

  4. Characterizing and controlling intrinsic biases of lambda exonuclease in nascent strand sequencing reveals phasing between nucleosomes and G-quadruplex motifs around a subset of human replication origins

    DEFF Research Database (Denmark)

    Foulk, M. S.; Urban, J. M.; Casella, Cinzia;

    2015-01-01

    Nascent strand sequencing (NS-seq) is used to discover DNA replication origins genome-wide, allowing identification of features for their specification. NS-seq depends on the ability of lambda exonuclease (lambda-exo) to efficiently digest parental DNA while leaving RNA-primer protected nascent...... are not general determinants for origin specification but may play a role for a subset. Interestingly, we observed a periodic spacing of G4 motifs and nucleosomes around the peak summits, suggesting that G4s may position nucleosomes at this subset of origins. Finally, we demonstrate that use of Na+ instead of K...

  5. Solid‐Phase Synthesis of Structurally Diverse Heterocycles by an Amide–Ketone Condensation/N‐Acyliminium Pictet–Spengler Sequence

    DEFF Research Database (Denmark)

    Komnatnyy, Vitaly V.; Givskov, Michael Christian; Nielsen, Thomas Eiland

    2012-01-01

    An efficient approach for the solid‐phase synthesis of structurally diverse heterocyclic compounds is presented. Under acidic reaction conditions, peptidic levulinamides undergo intramolecular ketone–amide condensation reactions to form cyclic N‐acyliminium intermediates. In the presence of a tet......An efficient approach for the solid‐phase synthesis of structurally diverse heterocyclic compounds is presented. Under acidic reaction conditions, peptidic levulinamides undergo intramolecular ketone–amide condensation reactions to form cyclic N‐acyliminium intermediates. In the presence...... of a tethered nucleophile, a second cyclization reaction results in the formation of a fused bicyclic ring system. The scope of the methodology was demonstrated by several combinations of substituted ketones and nucleophiles, the latter conveniently originating from amino acids with functionalized side chains...

  6. Sphene and zircon in the Highland Range volcanic sequence (Miocene, southern Nevada, USA): Elemental partitioning, phase relations, and influence on evolution of silicic magma

    Science.gov (United States)

    Colombini, L.L.; Miller, C.F.; Gualda, G.A.R.; Wooden, J.L.; Miller, J.S.

    2011-01-01

    Sphene is prominent in Miocene plutonic rocks ranging from diorite to granite in southern Nevada, USA, but it is restricted to rhyolites in coeval volcanic sequences. In the Highland Range volcanic sequence, sphene appears as a phenocryst only in the most evolved rocks (72-77 mass% SiO2; matrix glass 77-78 mass% SiO2). Zr-in-sphene temperatures of crystallization are mostly restricted to 715 and 755??C, in contrast to zircon (710-920??C, Ti-in-zircon thermometry). Sphene rim/glass Kds for rare earth elements are extremely high (La 120, Sm 1200, Gd 1300, Lu 240). Rare earth elements, especially the middle REE (MREE), decrease from centers to rims of sphene phenocrysts along with Zr, demonstrating the effect of progressive sphene fractionation. Whole rocks and glasses have MREE-depleted, U-shaped REE patterns as a consequence of sphene fractionation. Within the co-genetic, sphene-rich Searchlight pluton, only evolved leucogranites show comparable MREE depletion. These results indicate that sphene saturation in intruded and extruded magmas occurred only in highly evolved melts: abundant sphene in less silicic plutonic rocks represents a late-stage 'bloom' in fractionated interstitial melt. ?? 2011 Springer-Verlag.

  7. A new multi-parametric climatological approach to the study of the earthquake preparatory phase: the 2016 Amatrice-Norcia (Central Italy) seismic sequence

    Science.gov (United States)

    Piscini, Alessandro; De Santis, Angelo; Marchetti, Dedalo; Cianchini, Gianfranco

    2017-04-01

    Based on observations prior to earthquakes, recent theoretical considerations suggest that some geophysical quantities reveal abnormal changes that anticipate moderate and strong earthquakes, within a defined spatial area (the so-called Dobrovolsky area) according to a Lithosphere-Atmosphere-Ionosphere coupling (LAIC) model. One of the possible pre-earthquake effects could be the appearance of some climatological anomalies in the epicentral region, weeks/months before the major earthquakes. An ESA-funded project, SAFE (Swarm for Earthquake study) was dedicated to investigate the LAIC from ground to satellite. In this work, the period of two months preceding the Amatrice-Norcia (Central Italy) earthquake sequence that started on 24 August 2016 with an M6 earthquake, and some months later produced other two major shocks, i.e. an M5.9 on 26 October and then an M6.5 on 30 October, was analyzed in terms of some climatological parameters. In particular, starting from a date preceding of about two months the first major shock, we applied a new approach based on the comparison of the thirty-seven year time series at the same seasonal time of three land/atmospheric parameters, i.e. skin temperature (skt), total column water vapour (tcwv) and total column of ozone (tco3), collected from European Center Medium Weather Forecast (ECMWF), and the year in which the earthquake sequence occurred. The originality of the method stands in the way the complete time series is reduced, where also the possible effect of global warming is properly removed. A confutation/confirmation analysis was undertaken where these parameters were successfully analyzed in the same months but considering two seismically "calm" years, when significant seismicity was not present, in order to validate the technique. We also extended the analysis to all available years to construct a confusion matrix comparing the climatological anomalies with the real seismicity. This latter analysis has confirmed the

  8. Characterizing and controlling intrinsic biases of lambda exonuclease in nascent strand sequencing reveals phasing between nucleosomes and G-quadruplex motifs around a subset of human replication origins.

    Science.gov (United States)

    Foulk, Michael S; Urban, John M; Casella, Cinzia; Gerbi, Susan A

    2015-05-01

    Nascent strand sequencing (NS-seq) is used to discover DNA replication origins genome-wide, allowing identification of features for their specification. NS-seq depends on the ability of lambda exonuclease (λ-exo) to efficiently digest parental DNA while leaving RNA-primer protected nascent strands intact. We used genomics and biochemical approaches to determine if λ-exo digests all parental DNA sequences equally. We report that λ-exo does not efficiently digest G-quadruplex (G4) structures in a plasmid. Moreover, λ-exo digestion of nonreplicating genomic DNA (LexoG0) enriches GC-rich DNA and G4 motifs genome-wide. We used LexoG0 data to control for nascent strand-independent λ-exo biases in NS-seq and validated this approach at the rDNA locus. The λ-exo-controlled NS-seq peaks are not GC-rich, and only 35.5% overlap with 6.8% of all G4s, suggesting that G4s are not general determinants for origin specification but may play a role for a subset. Interestingly, we observed a periodic spacing of G4 motifs and nucleosomes around the peak summits, suggesting that G4s may position nucleosomes at this subset of origins. Finally, we demonstrate that use of Na(+) instead of K(+) in the λ-exo digestion buffer reduced the effect of G4s on λ-exo digestion and discuss ways to increase both the sensitivity and specificity of NS-seq.

  9. Genome Sequencing

    DEFF Research Database (Denmark)

    Sato, Shusei; Andersen, Stig Uggerhøj

    2014-01-01

    The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based on transcr......The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based...

  10. A long-lasting quiescence phase of the eruptive variable V1118 Ori

    CERN Document Server

    Lorenzetti, D; Giannini, T; Harutyunyan, A; Arkharov, A A; Larionov, V M; Cusano, F; Di Paola, A; Causi, G Li; Nisini, B; Speziali, R; Vitali, F

    2015-01-01

    V1118 Ori is an eruptive variable belonging to the EXor class of Pre-Main Sequence stars whose episodic outbursts are attributed to disk accretion events. Since 2006, V1118 Ori is in the longest quiescence stage ever observed between two subsequent outbursts of its recent history. We present near-infrared photometry of V1118 Ori carried out during the last eight years, along with a complete spectroscopic coverage from 0.35 to 2.5 um. A longterm sampling of V1118 Ori in quiescence has never been done, hence we can benefit from the current circumstance to determine the lowest values (i.e. the zeroes) of the parameters to be used as a reference for evaluating the physical changes typical of more active phases. A quiescence mass accretion rate between 1--3 $\\times$ 10$^{-9}$ M$_{\\sun}$ yr$^{-1}$ can be derived and the difference with previous determinations is discussed. From line emission and IR colors analysis a visual extinction of 1-2 mag is consistently derived, confirming that V1118 Ori (at least in quiesce...

  11. Performance of simultaneous high temporal resolution quantitative perfusion imaging of bladder tumors and conventional multi-phase urography using a novel free-breathing continuously acquired radial compressed-sensing MRI sequence.

    Science.gov (United States)

    Parikh, Nainesh; Ream, Justin M; Zhang, Hoi Cheung; Block, Kai Tobias; Chandarana, Hersh; Rosenkrantz, Andrew B

    2016-06-01

    To investigate the feasibility of high temporal resolution quantitative perfusion imaging of bladder tumors performed simultaneously with conventional multi-phase MR urography (MRU) using a novel free-breathing continuously acquired radial MRI sequence with compressed-sensing reconstruction. 22 patients with bladder lesions underwent MRU using GRASP (Golden-angle RAdial Sparse Parallel) acquisition. Multi-phase contrast-enhanced abdominopelvic GRASP was performed during free-breathing (1.4×1.4×3.0mm(3) voxel size; 3:44min acquisition). Two dynamic datasets were retrospectively reconstructed by combining different numbers of sequentially acquired spokes into each dynamic frame: 110 spokes per frame for 25-s temporal resolution (serving as conventional MRU for clinical interpretation) and 8 spokes per frame for 1.7-s resolution. Using 1.7-s resolution images, ROIs were placed within bladder lesions and normal bladder wall, a femoral artery arterial input function was generated, and the Generalized Kinetic Model was applied. Biopsy/cystectomy demonstrated 16 bladder tumors (13 stage≥T2, 3 stage≤T1) and 6 benign lesions. All lesions were well visualized using 25-s clinical multi-phase images. Using 1.7-s resolution images, K(trans) was significantly higher in tumors (0.38±0.24) than normal bladder (0.12±0.02=8, pMRU examinations using only one contrast injection and without additional scan time. Copyright © 2016 Elsevier Inc. All rights reserved.

  12. Accurate measurement of heteronuclear dipolar couplings by phase-alternating R-symmetry (PARS) sequences in magic angle spinning NMR spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Hou, Guangjin, E-mail: hou@udel.edu, E-mail: tpolenov@udel.edu; Lu, Xingyu, E-mail: luxingyu@udel.edu, E-mail: lexvega@comcast.net; Vega, Alexander J., E-mail: luxingyu@udel.edu, E-mail: lexvega@comcast.net; Polenova, Tatyana, E-mail: hou@udel.edu, E-mail: tpolenov@udel.edu [Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA and Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, Pennsylvania 15261 (United States)

    2014-09-14

    We report a Phase-Alternating R-Symmetry (PARS) dipolar recoupling scheme for accurate measurement of heteronuclear {sup 1}H-X (X = {sup 13}C, {sup 15}N, {sup 31}P, etc.) dipolar couplings in MAS NMR experiments. It is an improvement of conventional C- and R-symmetry type DIPSHIFT experiments where, in addition to the dipolar interaction, the {sup 1}H CSA interaction persists and thereby introduces considerable errors in the dipolar measurements. In PARS, phase-shifted RN symmetry pulse blocks applied on the {sup 1}H spins combined with π pulses applied on the X spins at the end of each RN block efficiently suppress the effect from {sup 1}H chemical shift anisotropy, while keeping the {sup 1}H-X dipolar couplings intact. Another advantage over conventional DIPSHIFT experiments, which require the signal to be detected in the form of a reduced-intensity Hahn echo, is that the series of π pulses refocuses the X chemical shift and avoids the necessity of echo formation. PARS permits determination of accurate dipolar couplings in a single experiment; it is suitable for a wide range of MAS conditions including both slow and fast MAS frequencies; and it assures dipolar truncation from the remote protons. The performance of PARS is tested on two model systems, [{sup 15}N]-N-acetyl-valine and [U-{sup 13}C,{sup 15}N]-N-formyl-Met-Leu-Phe tripeptide. The application of PARS for site-resolved measurement of accurate {sup 1}H-{sup 15}N dipolar couplings in the context of 3D experiments is presented on U-{sup 13}C,{sup 15}N-enriched dynein light chain protein LC8.

  13. Accurate measurement of heteronuclear dipolar couplings by phase-alternating R-symmetry (PARS) sequences in magic angle spinning NMR spectroscopy.

    Science.gov (United States)

    Hou, Guangjin; Lu, Xingyu; Vega, Alexander J; Polenova, Tatyana

    2014-09-14

    We report a Phase-Alternating R-Symmetry (PARS) dipolar recoupling scheme for accurate measurement of heteronuclear (1)H-X (X = (13)C, (15)N, (31)P, etc.) dipolar couplings in MAS NMR experiments. It is an improvement of conventional C- and R-symmetry type DIPSHIFT experiments where, in addition to the dipolar interaction, the (1)H CSA interaction persists and thereby introduces considerable errors in the dipolar measurements. In PARS, phase-shifted RN symmetry pulse blocks applied on the (1)H spins combined with π pulses applied on the X spins at the end of each RN block efficiently suppress the effect from (1)H chemical shift anisotropy, while keeping the (1)H-X dipolar couplings intact. Another advantage over conventional DIPSHIFT experiments, which require the signal to be detected in the form of a reduced-intensity Hahn echo, is that the series of π pulses refocuses the X chemical shift and avoids the necessity of echo formation. PARS permits determination of accurate dipolar couplings in a single experiment; it is suitable for a wide range of MAS conditions including both slow and fast MAS frequencies; and it assures dipolar truncation from the remote protons. The performance of PARS is tested on two model systems, [(15)N]-N-acetyl-valine and [U-(13)C,(15)N]-N-formyl-Met-Leu-Phe tripeptide. The application of PARS for site-resolved measurement of accurate (1)H-(15)N dipolar couplings in the context of 3D experiments is presented on U-(13)C,(15)N-enriched dynein light chain protein LC8.

  14. The evolution of stellar metallicity gradients of the Milky Way disk from LSS-GAC main sequence turn-off stars: a two-phase disk formation history?

    CERN Document Server

    Xiang, M -S; Yuan, H -B; Huang, Y; Wang, C; Ren, J -J; Chen, B -Q; Sun, N -C; Zhang, H -W; Huo, Z -Y; Rebassa-Mansergas, A

    2015-01-01

    We use 297 042 main sequence turn-off stars selected from the LSS-GAC to determine the radial and vertical gradients of stellar metallicity of the Galactic disk in the anti-center direction. We determine ages of those turn-off stars by isochrone fitting and measure the temporal variations of metallicity gradients. Our results show that the gradients, both in the radial and vertical directions, exhibit significant spatial and temporal variations. The radial gradients yielded by stars of oldest ages (>11 Gyr) are essentially zero at all heights from the disk midplane, while those given by younger stars are always negative. The vertical gradients deduced from stars of oldest ages (>11Gyr) are negative and show only very weak variations with the Galactocentric distance in the disk plane, $R$, while those yielded by younger stars show strong variations with $R$. After being essentially flat at the earliest epochs of disk formation, the radial gradients steepen as age decreases, reaching a maxima (steepest) at age ...

  15. On the role of the post-starburst phase in the build-up of the red-sequence of intermediate redshift clusters

    CERN Document Server

    De Lucia, Gabriella; Halliday, Claire; Milvang-Jensen, Bo; Noll, Stefan; Smail, Ian; Zaritsky, Dennis

    2009-01-01

    We present new deep spectroscopic observations of 0.05--0.5 L_* galaxies in one cluster (cl1232.5-1250) drawn from the ESO Distant Cluster Survey (EDisCS) sample, at z = 0.54. The new data extend the spectroscopy already available for this cluster by about 1 magnitude. The cluster has a large fraction of passive galaxies and exhibits a well defined and relatively tight colour-magnitude relation. Among spectroscopic members, only six galaxies are classified as `post-starburst' (k+a). For another EDisCS cluster at similar redshift and with as deep spectroscopy, no member is found to have a k+a spectrum. The low measured numbers of post-starburst systems appear to be inadequate to explain the observed increase of faint red galaxies at lower redshift, even when accounting for the infall of new galaxies onto the cluster. Post-starburst galaxies represent a possible channel to move galaxies from the blue star-forming cloud to the red-sequence, but the available data suggest this is not the dominant channel in galax...

  16. A Positive and Negative Sequence Component Separation Method for Grid Voltage Based on the Phase Locked Loop With an Adaptive Notch Filter%基于ANF-PLL的电网电压基波正负序分离方法

    Institute of Scientific and Technical Information of China (English)

    杜雄; 郭宏达; 孙鹏菊; 周雒维

    2013-01-01

    为了满足并网变流器在电网电压不对称情况下的控制需求,需要快速准确地提取出基波正负序分量的幅值和相位。在电网电压不对称时,负序分量会在同步参考坐标系锁相环(phase locked loop based on synchronization reference frame,SRF-PLL)的 dq 轴分量中产生2倍工频波动,影响基波分量和相位的提取结果。该文通过将自适应陷波器(adaptive notch filter,ANF)加入到同步参考坐标系锁相环的结构中,提出了一种能够实现正负序分量分离的自适应陷波器锁相环(phase locked loop with ANF,ANF-PLL)方法。该方法利用ANF陷波器的2个相互正交的输出量分别抵消电网电压dq轴分量中由于负序分量造成的2倍工频波动,以此消除了电网电压不对称对同步信号检测的影响,并且可以同时提取出基波负序分量的幅值和相位。与其它方法相比,该方法无需进行正负序解耦或瞬时对称分量分离,在单同步参考坐标系下实现了基波正负序分量的分离提取,结构更加简单,减少了计算量。实验结果表明,文中提出的方法能够在电网电压不对称与频率变化的情况下准确提取出基波正负序分量的幅值与相位,并且具有良好的动态性能。%In order to meet the unbalanced control demand of the grid-connected power converters, the fast and accurate extraction of the fundamental positive and negative sequence components of the grid voltage is necessary. Under unbalanced grid voltage condition, the negative sequence component appears as the double frequency oscillations in the d-q axes components of the phase locked loop based on synchronization reference frame (SRF-PLL), which affects the extraction of the fundamental components and the phase angle signal. By applying the adaptive notch filter (ANF) to the structure of SRF-PLL, this paper proposed a grid voltage synchronization method based on phase locked loop with

  17. Code length limit in phase-sensitive OTDR using ultralong (>1M bits) pulse sequences due to fading induced by fiber optical path drifts

    Science.gov (United States)

    Martins, H. F.; Shi, K.; Thomsen, B. C.; Martin-Lopez, S.; Gonzalez-Herraez, M.; Savory, S. J.

    2017-04-01

    Recently, it has been demonstrated that by recovering the amplitude and phase of the backscattered optical signal, a ΦOTDR using pulse coding can be treated as a fully linear system in terms of trace coding/decoding, thus allowing for the use of tens of thousands of bits with a dramatic improvement of the system performance. In this communication, as a continuation of previous work by the same authors, a preliminary study aiming at characterizing the limits of the system in terms of maximum usable code length is presented. Using a code exceeding 1million bits over a duration of 0.26ms, it is observed that fiber optical path variations exceeding ≍π occurring over a time inferior to the pulse code length can lead to localized fading in the ΦOTDR trace. The occurrence, positions and form of the fading points along the ΦOTDR trace is observed to be strongly dependent on the type, frequency and amplitude of the perturbations applied to the fiber.

  18. Zero-sequence current decoupling control of three-phase four-wire active power filter%四桥臂有源滤波器零序电流解耦预测电流控制

    Institute of Scientific and Technical Information of China (English)

    王晓刚; 张杰

    2016-01-01

    针对应用于三相四线制系统中的三相四桥臂有源电力滤波器的特点,研究了一种基于零序电流解耦的预测电流控制方法,分析了零序电流解耦的原理,设计了控制系统。该方法有效地解除了第四桥臂和前三桥臂的耦合,对中线电流进行独立补偿,与三相三桥臂的控制方法兼容,简单易行,易于对三桥臂有源电力滤波器进行改造后应用于三相四线系统。仿真分析表明,与其他方法相比,基于零序电流解耦的预测电流控制可使有源电力滤波器获得更好的补偿性能,电源电流总谐波畸变率和中线电流正负峰值均达到最小。%Zero-sequence current decoupling based predictive current control of three-phase four-wire active power filter (APF)is studied based on the characteristics of three-phase four-leg APF.The principle of zero-se-quence decoupling is analyzed and the control system is designed.The control method eliminates the coupling between the first three legs and the fourth leg,and the neutral current is compensated independently.The meth-od is compatible with the control of three-phase three-leg APF and is simple to implement.It is easy to upgrade the three-leg APF to meet the three-phase four wire applications.Simulation analyses show that zero-sequence current decoupling based predictive current control achieves better compensation performance than other meth-ods,total harmonic distortion of supply currents and positive /negative amplitudes of neutral current are both with minimum.

  19. Optimum vector sequence for 3-phase AC/DC soft-switch converter control%三相AC/DC软开关变流器的最优矢量控制

    Institute of Scientific and Technical Information of China (English)

    孙孝峰; 刘裕华; 李长吾

    2001-01-01

    分析了矢量控制在三相变流器的应用,比较矢量圆的3种合成方式,得出了矢量控制的优化发波方式.考虑了开关信号中的谐振区间,以减小谐振环节对有效开关信号占空比丢失的影响.%This paper analysis the application of vector width pulse modulation in the paral- lel resonant DC link circuit control. Comparing three different synthesis methods of the vector circle, we have derived the optimum vector sequence for controlling the 3-phase AC/DC soft-switch converter, considering the resonant region in the switch signal to re- duce the influence of resonance to the lose of effective switch signal ratio.

  20. Dna Sequencing

    Science.gov (United States)

    Tabor, Stanley; Richardson, Charles C.

    1995-04-25

    A method for sequencing a strand of DNA, including the steps off: providing the strand of DNA; annealing the strand with a primer able to hybridize to the strand to give an annealed mixture; incubating the mixture with four deoxyribonucleoside triphosphates, a DNA polymerase, and at least three deoxyribonucleoside triphosphates in different amounts, under conditions in favoring primer extension to form nucleic acid fragments complementory to the DNA to be sequenced; labelling the nucleic and fragments; separating them and determining the position of the deoxyribonucleoside triphosphates by differences in the intensity of the labels, thereby to determine the DNA sequence.

  1. Visualization of acute focal lesions in rats with experimental autoimmune encephalomyelitis by magnetic nanoparticles, comparing different MRI sequences including phase imaging.

    Science.gov (United States)

    Hunger, Marcel; Budinger, Eike; Zhong, Kai; Angenstein, Frank

    2014-05-01

    To compare the sensitivity and specificity of phase imaging (PI) with other magnetic resonance imaging (MRI) methods in lesion detection in rats with experimental autoimmune encephalomyelitis (EAE), as an animal model for multiple sclerosis (MS). EAE was induced in rats (n = 14) by subcutaneous (s.c.) injection of myelin basic protein (MBP) and complete Freund's adjuvant (CFA). Control animals (n = 4) were given an s.c. injection of phosphate-buffered saline mixed with CFA. The development of local inflammatory processes, demyelinations, and blood-brain barrier (BBB) disruptions were monitored over 7 weeks in a 4.7T animal scanner by T1-, T2-, T2*-weighted images, magnetization transfer, and PI in the presence or absence of very small superparamagnetic iron oxide particles (VSOP) and confirmed by immunostaining using CD31, CD68, MBP, and albumin antibodies and Gallyas silver staining. EAE rats developed time-dependent local inflammations and BBB disruptions but no clear demyelinizations. In histological stainings these processes were trackable as accumulations of phagocytic monocytes and extravasal albumin. In MRI without application of VSOP inflammatory processes were not detectable. MRI in the presence of VSOP revealed inflammatory processes by the appearance of hypointense spots (hs). The specificity of PI to detect hs was similar to T1- and T2*-weighted images The calculated sensitivity was less than in corresponding T2*-weighted images. The diagnostic use of PI without VSOP as contrast agent to detect lesions is not recommended at field strength of 4.7T or lower. Copyright © 2013 Wiley Periodicals, Inc.

  2. Main: Sequences [KOME

    Lifescience Database Archive (English)

    Full Text Available Sequences Nucleotide Sequence Nucleotide sequence of full length cDNA (trimmed sequence) kome_ine_full_seq...uence_db.fasta.zip kome_ine_full_sequence_db.zip kome_ine_full_sequence_db ...

  3. The main sequences of NGC2808: constraints on the early disc accretion scenario

    CERN Document Server

    Cassisi, Santi

    2013-01-01

    [Abridged] A new scenario --early disc accretion-- has been proposed very recently to explain the origin of the multiple population phenomenon in Galactic globular clusters. It envisages the possibility that a fraction of low- and very low-mass cluster stars may accrete the ejecta of interacting massive binary (and possibly also fast rotating massive) stars during the fully convective, pre-main sequence stage, to reproduce the CN and ONa anticorrelations observed among stars in individual clusters. This scenario is assumed to be able to explain the presence (and properties) of the multiple populations in the majority of globular clusters in the Milky Way. Here we have considered the well studied cluster NGC 2808, which displays a triple main sequence with well defined and separate He abundances. Knowledge of these abundances allowed us to put strong constraints on the He mass fraction and amount of matter to be accreted by low-mass pre-main sequence stars. We find that the minimum He mass fraction in the accr...

  4. c2d Spitzer IRS Spectra of Disks around T Tauri Stars. III. [Ne II], [Fe I], and H_2 gas-phase lines

    CERN Document Server

    Lahuis, Fred; Blake, Geoffrey A; Evans, Neal J; Kessler-Silacci, Jacqueline E; Pontoppidan, Klaus M

    2007-01-01

    We present a survey of mid-infrared gas-phase lines toward a sample of 76 circumstellar disks around low mass pre-main sequence stars from the Spitzer "Cores to Disks" legacy program. We report the first detections of [Ne II] and [Fe I] toward classical T Tauri stars in ~20% respectively ~9% of our sources. The observed [Ne II] line fluxes and upper limits are consistent with [Ne II] excitation in an X-ray irradiated disk around stars with X-ray luminosities L_X=10^{29}-10^{31} erg s^{-1}. [Fe I] is detected at ~10^-5-10^-4 L_Sun, but no [S I] or [Fe II] is detected down to ~10^{-6} L_Sun. The [Fe I] detections indicate the presence of gas-rich disks with masses of >~0.1 M_J. No H_2 0-0 S(0) and S(1) disk emission is detected, except for S(1) toward one source. These data give upper limits on the warm (T~100-200K) gas mass of a few Jovian masses, consistent with recent T Tauri disk models which include gas heating by stellar radiation. Compact disk emission of hot (T>~500K) gas is observed through the H_2 0-0...

  5. 用对称映射ARMA模型的零极点研究子波相位对反射系数序列反演的影响%The research on the influence of wavelet phase on the inversion results of reflection coefficient sequences by using the ARMA model of symmetrical mapping Pole-Zeros

    Institute of Scientific and Technical Information of China (English)

    张亚南; 戴永寿; 陈健; 魏玉琴; 丁进杰; 张漫漫

    2013-01-01

    Abstract In order to research the influence of seismic wavelet phase on reflection coefficient sequences inversion,the autoregressive moving average (ARMA) model was used to describe the seismic wavelet,the wavelets with the same amplitude spectrum and different phase spectrums were constructed by symmetrical mapping Pole-Zeros of ARMA model in z domain,and spectrum division was used to implement reflection coefficient sequences inversion.The theoretical analysis shows that a pure-phase filter was remained after reflection coefficient sequences inversion in the condition of inaccurate seismic wavelet phase estimation,and the phase spectrum of the purephase filter was the phase spectrum difference between real wavelet and constructed wavelet.The real or accurate reflection coefficient sequences were identified in inversion results by the evaluation methods of Kurtosis and Variation.Simulation and actual seismic data processing results also verified the law of the wavelet phase influence on reflection coefficient sequences inversion and the effectiveness of the evaluation methods.Research interest for enhancing the precision of reflection coefficient sequences inversion results was indicated.%为研究地震子波相位对反射系数序列反演的影响,在自回归滑动平均(ARMA)模型描述子波的基础上,提出采用z域对称映射ARMA模型零极点的方法构造了一系列相同振幅谱、不同相位谱的地震子波,并结合谱除法对人工合成地震记录进行反射系数序列反演.理论分析表明,子波相位估计不准时反射系数序列反演结果中残留一个纯相位滤波器,该纯相位滤波器的相位谱为真实子波和构造子波的相位谱之差.采用丰度和变分作为评价方法,在反演结果中确定出真实的或准确的反射系数序列.仿真实验和实际数据处理结果也验证了子波相位对反射系数序列反演的影响规律和评价方法的有效性,为进一步提高反射系数

  6. Phases and Phase Transitions

    Science.gov (United States)

    Gitterman, Moshe

    2014-09-01

    In discussing phase transitions, the first thing that we have to do is to define a phase. This is a concept from thermodynamics and statistical mechanics, where a phase is defined as a homogeneous system. As a simple example, let us consider instant coffee. This consists of coffee powder dissolved in water, and after stirring it we have a homogeneous mixture, i.e., a single phase. If we add to a cup of coffee a spoonful of sugar and stir it well, we still have a single phase -- sweet coffee. However, if we add ten spoonfuls of sugar, then the contents of the cup will no longer be homogeneous, but rather a mixture of two homogeneous systems or phases, sweet liquid coffee on top and coffee-flavored wet sugar at the bottom...

  7. Single-phase to three-phase power conversion interface

    Science.gov (United States)

    Wu, Jinn-Chang; Wang, Yung-Shan; Jou, Hurng-Liahng; Lu, Wei-Tso

    2016-07-01

    This study proposes a single-phase to three-phase power conversion interface which converts the power from a single-phase utility to three-phase power for a three-phase load. The proposed single-phase to three-phase power conversion interface comprises a bridge-type switch set, a set of three-phase inductors, a transformer set and a set of three-phase capacitors. A current-mode control controls the switching of bridge-type switch set, to generate a set of nonzero-sequence (NZS) currents and a set of zero-sequence (ZS) currents. The transformer set is used to decouple the NZS currents and the ZS currents. The NZS currents are used to generate a high-quality three-phase voltage that supplies power to a three-phase load. The ZS currents flow to the single-phase utility so that the utility current is sinusoidal and in phase with the utility voltage. Accordingly, only a bridge-type switch set is used in the single-phase to three-phase power conversion interface to simply the power circuit. A prototype is developed and tested to verify the performance of the proposed single-phase to three-phase power conversion interface.

  8. Complex Variability of the H$\\alpha$ Emission Line Profile of the T Tauri Binary System KH 15D: The Influence of Orbital Phase, Occultation by the Circumbinary Disk, and Accretion Phenomenae

    CERN Document Server

    Hamilton, Catrina M; Mundt, Reinhard; Herbst, William; Winn, Joshua N

    2012-01-01

    We have obtained 48 high resolution echelle spectra of the pre-main sequence eclipsing binary system KH~15D (V582 Mon, P = 48.37 d, $e$ $\\sim$ 0.6, M$_{A}$ = 0.6 M$_{\\odot}$, M$_{B}$ = 0.7 M$_{\\odot}$). The eclipses are caused by a circumbinary disk seen nearly edge on, which at the epoch of these observations completely obscured the orbit of star B and a large portion of the orbit of star A. The spectra were obtained over five contiguous observing seasons from 2001/2002 to 2005/2006 while star A was fully visible, fully occulted, and during several ingress and egress events. The H$\\alpha$ line profile shows dramatic changes in these time series data over timescales ranging from days to years. A fraction of the variations are due to "edge effects" and depend only on the height of star A above or below the razor sharp edge of the occulting disk. Other observed variations depend on the orbital phase: the H$\\alpha$ emission line profile changes from an inverse P Cygni type profile during ingress to an enhanced d...

  9. Classifying Genomic Sequences by Sequence Feature Analysis

    Institute of Scientific and Technical Information of China (English)

    Zhi-Hua Liu; Dian Jiao; Xiao Sun

    2005-01-01

    Traditional sequence analysis depends on sequence alignment. In this study, we analyzed various functional regions of the human genome based on sequence features, including word frequency, dinucleotide relative abundance, and base-base correlation. We analyzed the human chromosome 22 and classified the upstream,exon, intron, downstream, and intergenic regions by principal component analysis and discriminant analysis of these features. The results show that we could classify the functional regions of genome based on sequence feature and discriminant analysis.

  10. Effects of an Additional Sequence of Color Stimuli on Visuomotor Sequence Learning

    Science.gov (United States)

    Tanaka, Kanji; Watanabe, Katsumi

    2017-01-01

    Through practice, people are able to integrate a secondary sequence (e.g., a stimulus-based sequence) into a primary sequence (e.g., a response-based sequence), but it is still controversial whether the integrated sequences lead to better learning than only the primary sequence. In the present study, we aimed to investigate the effects of a sequence that integrated space and color sequences on early and late learning phases (corresponding to effector-independent and effector-dependent learning, respectively) and how the effects differed in the integrated and primary sequences in each learning phase. In the task, the participants were required to learn a sequence of button presses using trial-and-error and to perform the sequence successfully for 20 trials (m × n task). First, in the baseline task, all participants learned a non-colored sequence, in which the response button always turned red. Then, in the learning task, the participants were assigned to two groups: a colored sequence group (i.e., space and color) or a non-colored sequence group (i.e., space). In the colored sequence, the response button turned a pre-determined color and the participants were instructed to attend to the sequences of both location and color as much as they could. The results showed that the participants who performed the colored sequence acquired the correct button presses of the sequence earlier, but showed a slower mean performance time than those who performed the non-colored sequence. Moreover, the slower performance time in the colored sequence group remained in a subsequent transfer task in which the spatial configurations of the buttons were vertically mirrored from the learning task. These results indicated that if participants explicitly attended to both the spatial response sequence and color stimulus sequence at the same time, they could develop their spatial representations of the sequence earlier (i.e., early development of the effector-independent learning), but might

  11. Main: Sequences [KOME

    Lifescience Database Archive (English)

    Full Text Available Sequences Amino Acid Sequence Amino Acid sequence of full length cDNA (Longest ORF) kome_ine_full_seq...uence_amino_db.fasta.zip kome_ine_full_sequence_amino_db.zip kome_ine_full_sequence_amino_db ...

  12. Shotgun protein sequencing.

    Energy Technology Data Exchange (ETDEWEB)

    Faulon, Jean-Loup Michel; Heffelfinger, Grant S.

    2009-06-01

    A novel experimental and computational technique based on multiple enzymatic digestion of a protein or protein mixture that reconstructs protein sequences from sequences of overlapping peptides is described in this SAND report. This approach, analogous to shotgun sequencing of DNA, is to be used to sequence alternative spliced proteins, to identify post-translational modifications, and to sequence genetically engineered proteins.

  13. Sequence Read Archive (SRA)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms including Roche 454 GS System®, Illumina Genome...

  14. Multimodal sequence learning.

    Science.gov (United States)

    Kemény, Ferenc; Meier, Beat

    2016-02-01

    While sequence learning research models complex phenomena, previous studies have mostly focused on unimodal sequences. The goal of the current experiment is to put implicit sequence learning into a multimodal context: to test whether it can operate across different modalities. We used the Task Sequence Learning paradigm to test whether sequence learning varies across modalities, and whether participants are able to learn multimodal sequences. Our results show that implicit sequence learning is very similar regardless of the source modality. However, the presence of correlated task and response sequences was required for learning to take place. The experiment provides new evidence for implicit sequence learning of abstract conceptual representations. In general, the results suggest that correlated sequences are necessary for implicit sequence learning to occur. Moreover, they show that elements from different modalities can be automatically integrated into one unitary multimodal sequence.

  15. Coordinate cytokine regulatory sequences

    Science.gov (United States)

    Frazer, Kelly A.; Rubin, Edward M.; Loots, Gabriela G.

    2005-05-10

    The present invention provides CNS sequences that regulate the cytokine gene expression, expression cassettes and vectors comprising or lacking the CNS sequences, host cells and non-human transgenic animals comprising the CNS sequences or lacking the CNS sequences. The present invention also provides methods for identifying compounds that modulate the functions of CNS sequences as well as methods for diagnosing defects in the CNS sequences of patients.

  16. 750kV同塔同窗同相序双回紧凑型线路的潜供电流和感应电压%Research on Secondary-Arc Currents and Induced Voltages for 750 kV Compact Double-Circuit Transmission Lines on the Same Tower With the Same Phase Sequence in the Same Tower Window

    Institute of Scientific and Technical Information of China (English)

    王晓彤; 班连庚; 朱普轩; 郑彬

    2011-01-01

    A model of 750kV compact double-circuit transmission lines on the same tower with the same phase sequence in the same tower window is built by use of electromagnetic transient program (EMTP). The problems of secondary-arc currents and recovery voltages, induced voltages and induced currents are studied when the structure of double-circuit compact transmission lines on the same tower with the same phase sequence in the same tower window are applied to full or partial length of the project. Research results show that in the viewpoint of suppressing secondary arc current, recovery voltage, induced voltage and induced current, it is not suitable to adopt such a line structure, i.e., double-circuit transmission lines on the same tower with the same phase sequence in the same tower window, to full length of the project while high voltage shunt reactors are configured. For this reason, following scheme that conventional type is used for the main part of this project and the structure of compact double-circuit transmission lines on the same tower with the same phase sequence in the same tower window is only applied in the sections where the land for line corridors is undersupplied. If the length of the section where the compact double-circuit transmission lines on the same tower with the same phase sequence in the same tower window is applied is short enough, the values of secondary arc current and induced voltages can be suppressed into a rational level. For short transmission lines where the high voltage shunt reactors are not to be configured, if the problem of switching-off induced currents can be solved, it is worthy of consideration to adopt the structure of compact double-circuit transmission lines on the same tower with the same phase sequence in the same tower window to the full lengths of transmission lines.%使用电磁暂态程序(electromagnetic transient program,EMTP),建立了750kV同塔同窗同相序双回紧凑型线路模型.研究了全线或部分采

  17. Sequence-dependent nucleosome positioning.

    Science.gov (United States)

    Chung, Ho-Ryun; Vingron, Martin

    2009-03-13

    Eukaryotic DNA is organized into a macromolecular structure called chromatin. The basic repeating unit of chromatin is the nucleosome, which consists of two copies of each of the four core histones and DNA. The nucleosomal organization and the positions of nucleosomes have profound effects on all DNA-dependent processes. Understanding the factors that influence nucleosome positioning is therefore of general interest. Among the many determinants of nucleosome positioning, the DNA sequence has been proposed to have a major role. Here, we analyzed more than 860,000 nucleosomal DNA sequences to identify sequence features that guide the formation of nucleosomes in vivo. We found that both a periodic enrichment of AT base pairs and an out-of-phase oscillating enrichment of GC base pairs as well as the overall preference for GC base pairs are determinants of nucleosome positioning. The preference for GC pairs can be related to a lower energetic cost required for deformation of the DNA to wrap around the histones. In line with this idea, we found that only incorporation of both signal components into a sequence model for nucleosome formation results in maximal predictive performance on a genome-wide scale. In this manner, one achieves greater predictive power than published approaches. Our results confirm the hypothesis that the DNA sequence has a major role in nucleosome positioning in vivo.

  18. FimE-catalyzed off-to-on inversion of the type 1 fimbrial phase switch and insertion sequence recruitment in an Escherichia coli K-12 fimB strain

    DEFF Research Database (Denmark)

    Stentebjerg-Olesen, Bodil; Chakraborty, Trinad; Klemm, Per

    2000-01-01

    We have investigated the capacity of a well-defined Escherichia coli fimB strain, AAEC350 (a derivative of MG1655), to express type 1 fimbriae under various growth conditions. The expression of type 1 fimbriae is phase-variable due to the inversion of a 314-bp DNA segment. Two tyrosine recombinases......, FimB and FimE, mediate the inversion of the phase switch. FimB can carry out recombination in both directions, whereas the current evidence suggests that FimE-catalyzed switching is on-to-off only. We show here that AAEC350 is in fact capable of off-to-on phase switching and type 1 fimbrial expression...

  19. DNA Sequence Determination by Hybridization: A Strategy for Efficient Large-Scale Sequencing

    Science.gov (United States)

    Drmanac, R.; Drmanac, S.; Strezoska, Z.; Paunesku, T.; Labat, I.; Zeremski, M.; Snoddy, J.; Funkhouser, W. K.; Koop, B.; Hood, L.; Crkvenjakov, R.

    1993-06-01

    The concept of sequencing by hybridization (SBH) makes use of an array of all possible n-nucleotide oligomers (n-mers) to identify n-mers present in an unknown DNA sequence. Computational approaches can then be used to assemble the complete sequence. As a validation of this concept, the sequences of three DNA fragments, 343 base pairs in length, were determined with octamer oligonucleotides. Possible applications of SBH include physical mapping (ordering) of overlapping DNA clones, sequence checking, DNA fingerprinting comparisons of normal and disease-causing genes, and the identification of DNA fragments with particular sequence motifs in complementary DNA and genomic libraries. The SBH techniques may accelerate the mapping and sequencing phases of the human genome project.

  20. Genome Sequence Databases (Overview): Sequencing and Assembly

    Energy Technology Data Exchange (ETDEWEB)

    Lapidus, Alla L.

    2009-01-01

    From the date its role in heredity was discovered, DNA has been generating interest among scientists from different fields of knowledge: physicists have studied the three dimensional structure of the DNA molecule, biologists tried to decode the secrets of life hidden within these long molecules, and technologists invent and improve methods of DNA analysis. The analysis of the nucleotide sequence of DNA occupies a special place among the methods developed. Thanks to the variety of sequencing technologies available, the process of decoding the sequence of genomic DNA (or whole genome sequencing) has become robust and inexpensive. Meanwhile the assembly of whole genome sequences remains a challenging task. In addition to the need to assemble millions of DNA fragments of different length (from 35 bp (Solexa) to 800 bp (Sanger)), great interest in analysis of microbial communities (metagenomes) of different complexities raises new problems and pushes some new requirements for sequence assembly tools to the forefront. The genome assembly process can be divided into two steps: draft assembly and assembly improvement (finishing). Despite the fact that automatically performed assembly (or draft assembly) is capable of covering up to 98% of the genome, in most cases, it still contains incorrectly assembled reads. The error rate of the consensus sequence produced at this stage is about 1/2000 bp. A finished genome represents the genome assembly of much higher accuracy (with no gaps or incorrectly assembled areas) and quality ({approx}1 error/10,000 bp), validated through a number of computer and laboratory experiments.

  1. Contamination of sequence databases with adaptor sequences

    Energy Technology Data Exchange (ETDEWEB)

    Yoshikawa, Takeo; Sanders, A.R.; Detera-Wadleigh, S.D. [National Institute of Mental Health, Bethesda, MD (United States)

    1997-02-01

    Because of the exponential increase in the amount of DNA sequences being added to the public databases on a daily basis, it has become imperative to identify sources of contamination rapidly. Previously, contaminations of sequence databases have been reported to alert the scientific community to the problem. These contaminations can be divided into two categories. The first category comprises host sequences that have been difficult for submitters to manage or control. Examples include anomalous sequences derived from Escherichia coli, which are inserted into the chromosomes (and plasmids) of the bacterial hosts. Insertion sequences are highly mobile and are capable of transposing themselves into plasmids during cloning manipulation. Another example of the first category is the infection with yeast genomic DNA or with bacterial DNA of some commercially available cDNA libraries from Clontech. The second category of database contamination is due to the inadvertent inclusion of nonhost sequences. This category includes incorporation of cloning-vector sequences and multicloning sites in the database submission. M13-derived artifacts have been common, since M13-based vectors have been widely used for subcloning DNA fragments. Recognizing this problem, the National Center for Biotechnology Information (NCBI) started to screen, in April 1994, all sequences directly submitted to GenBank, against a set of vector data retrieved from GenBank by use of key-word searches, such as {open_quotes}vector.{close_quotes} In this report, we present evidence for another sequence artifact that is widespread but that, to our knowledge, has not yet been reported. 11 refs., 1 tab.

  2. Automated DNA Sequencing System

    Energy Technology Data Exchange (ETDEWEB)

    Armstrong, G.A.; Ekkebus, C.P.; Hauser, L.J.; Kress, R.L.; Mural, R.J.

    1999-04-25

    Oak Ridge National Laboratory (ORNL) is developing a core DNA sequencing facility to support biological research endeavors at ORNL and to conduct basic sequencing automation research. This facility is novel because its development is based on existing standard biology laboratory equipment; thus, the development process is of interest to the many small laboratories trying to use automation to control costs and increase throughput. Before automation, biology Laboratory personnel purified DNA, completed cycle sequencing, and prepared 96-well sample plates with commercially available hardware designed specifically for each step in the process. Following purification and thermal cycling, an automated sequencing machine was used for the sequencing. A technician handled all movement of the 96-well sample plates between machines. To automate the process, ORNL is adding a CRS Robotics A- 465 arm, ABI 377 sequencing machine, automated centrifuge, automated refrigerator, and possibly an automated SpeedVac. The entire system will be integrated with one central controller that will direct each machine and the robot. The goal of this system is to completely automate the sequencing procedure from bacterial cell samples through ready-to-be-sequenced DNA and ultimately to completed sequence. The system will be flexible and will accommodate different chemistries than existing automated sequencing lines. The system will be expanded in the future to include colony picking and/or actual sequencing. This discrete event, DNA sequencing system will demonstrate that smaller sequencing labs can achieve cost-effective the laboratory grow.

  3. Single-primer fluorescent sequencing

    Energy Technology Data Exchange (ETDEWEB)

    Ruth, J.L.; Morgan, C.A.; Middendorf, L.R.; Grone, D.L.; Brumbaugh, J.A.

    1987-05-01

    Modified linker arm oligonucleotides complementary to standard M13 priming sites were synthesized, labelled with either one, two, or three fluoresceins, and purified by reverse-phase HPLC. When used as primers in standard dideoxy M13 sequencing with /sup 32/P-dNTPs, normal autoradiographic patterns were obtained. To eliminate the radioactivity, direct on-line fluorescence detection was achieved by the use of a scanning 10 mW Argon laser emitting 488 nm light. Fluorescent bands were detected directly in standard 0.2 or 0.35 mm thick polyacrylamide gels at a distance of 24 cm from the loading wells by a photomultiplier tube filtered at 520 nm. Horizontal and temporal location of each band was displayed by computer as a band in real time, providing visual appearance similar to normal 4-lane autoradiograms. Using a single primer labelled with two fluoresceins, sequences of between 500 and 600 bases have been read in a single loading with better than 98% accuracy; up to 400 bases can be read reproducibly with no errors. More than 50 sequences have been determined by this method. This approach requires only 1-2 ug of cloned template, and produces continuous sequence data at about one band per minute.

  4. Anomaly Detection in Sequences

    Data.gov (United States)

    National Aeronautics and Space Administration — We present a set of novel algorithms which we call sequenceMiner, that detect and characterize anomalies in large sets of high-dimensional symbol sequences that...

  5. DNA sequencing conference, 2

    Energy Technology Data Exchange (ETDEWEB)

    Cook-Deegan, R.M. [Georgetown Univ., Kennedy Inst. of Ethics, Washington, DC (United States); Venter, J.C. [National Inst. of Neurological Disorders and Strokes, Bethesda, MD (United States); Gilbert, W. [Harvard Univ., Cambridge, MA (United States); Mulligan, J. [Stanford Univ., CA (United States); Mansfield, B.K. [Oak Ridge National Lab., TN (United States)

    1991-06-19

    This conference focused on DNA sequencing, genetic linkage mapping, physical mapping, informatics and bioethics. Several were used to study this sequencing and mapping. This article also discusses computer hardware and software aiding in the mapping of genes.

  6. Roles of repetitive sequences

    Energy Technology Data Exchange (ETDEWEB)

    Bell, G.I.

    1991-12-31

    The DNA of higher eukaryotes contains many repetitive sequences. The study of repetitive sequences is important, not only because many have important biological function, but also because they provide information on genome organization, evolution and dynamics. In this paper, I will first discuss some generic effects that repetitive sequences will have upon genome dynamics and evolution. In particular, it will be shown that repetitive sequences foster recombination among, and turnover of, the elements of a genome. I will then consider some examples of repetitive sequences, notably minisatellite sequences and telomere sequences as examples of tandem repeats, without and with respectively known function, and Alu sequences as an example of interspersed repeats. Some other examples will also be considered in less detail.

  7. Roles of repetitive sequences

    Energy Technology Data Exchange (ETDEWEB)

    Bell, G.I.

    1991-12-31

    The DNA of higher eukaryotes contains many repetitive sequences. The study of repetitive sequences is important, not only because many have important biological function, but also because they provide information on genome organization, evolution and dynamics. In this paper, I will first discuss some generic effects that repetitive sequences will have upon genome dynamics and evolution. In particular, it will be shown that repetitive sequences foster recombination among, and turnover of, the elements of a genome. I will then consider some examples of repetitive sequences, notably minisatellite sequences and telomere sequences as examples of tandem repeats, without and with respectively known function, and Alu sequences as an example of interspersed repeats. Some other examples will also be considered in less detail.

  8. sequenceMiner algorithm

    Data.gov (United States)

    National Aeronautics and Space Administration — Detecting and describing anomalies in large repositories of discrete symbol sequences. sequenceMiner has been open-sourced! Download the file below to try it out....

  9. Enhanced virome sequencing using targeted sequence capture.

    Science.gov (United States)

    Wylie, Todd N; Wylie, Kristine M; Herter, Brandi N; Storch, Gregory A

    2015-12-01

    Metagenomic shotgun sequencing (MSS) is an important tool for characterizing viral populations. It is culture independent, requires no a priori knowledge of the viruses in the sample, and may provide useful genomic information. However, MSS can lack sensitivity and may yield insufficient data for detailed analysis. We have created a targeted sequence capture panel, ViroCap, designed to enrich nucleic acid from DNA and RNA viruses from 34 families that infect vertebrate hosts. A computational approach condensed ∼1 billion bp of viral reference sequence into <200 million bp of unique, representative sequence suitable for targeted sequence capture. We compared the effectiveness of detecting viruses in standard MSS versus MSS following targeted sequence capture. First, we analyzed two sets of samples, one derived from samples submitted to a diagnostic virology laboratory and one derived from samples collected in a study of fever in children. We detected 14 and 18 viruses in the two sets, comprising 19 genera from 10 families, with dramatic enhancement of genome representation following capture enrichment. The median fold-increases in percentage viral reads post-capture were 674 and 296. Median breadth of coverage increased from 2.1% to 83.2% post-capture in the first set and from 2.0% to 75.6% in the second set. Next, we analyzed samples containing a set of diverse anellovirus sequences and demonstrated that ViroCap could be used to detect viral sequences with up to 58% variation from the references used to select capture probes. ViroCap substantially enhances MSS for a comprehensive set of viruses and has utility for research and clinical applications.

  10. DNA sequences encoding erythropoietin

    Energy Technology Data Exchange (ETDEWEB)

    Lin, F.K.

    1987-10-27

    A purified and isolated DNA sequence is described consisting essentially of a DNA sequence encoding a polypeptide having an amino acid sequence sufficiently duplicative of that of erythropoietin to allow possession of the biological property of causing bone marrow cells to increase production of reticulocytes and red blood cells, and to increase hemoglobin synthesis or iron uptake.

  11. Low autocorrelation binary sequences

    Science.gov (United States)

    Packebusch, Tom; Mertens, Stephan

    2016-04-01

    Binary sequences with minimal autocorrelations have applications in communication engineering, mathematics and computer science. In statistical physics they appear as groundstates of the Bernasconi model. Finding these sequences is a notoriously hard problem, that so far can be solved only by exhaustive search. We review recent algorithms and present a new algorithm that finds optimal sequences of length N in time O(N {1.73}N). We computed all optimal sequences for N≤slant 66 and all optimal skewsymmetric sequences for N≤slant 119.

  12. Repdigits in -Lucas Sequences

    Indian Academy of Sciences (India)

    Jhon J J Bravo; Florian Luca

    2014-05-01

    For an integer ≥ 2, let $(L_n^{(k)})_n$ be the -Lucas sequence which starts with $0,\\ldots,0,2,1$ ( terms) and each term afterwards is the sum of the preceding terms. In 2000, Luca (Port. Math. 57(2) 2000 243-254) proved that 11 is the largest number with only one distinct digit (the so-called repdigit) in the sequence $(L_n^{(2)})_n$. In this paper, we address a similar problem in the family of -Lucas sequences. We also show that the -Lucas sequences have similar properties to those of -Fibonacci sequences and occur in formulae simultaneously with the latter.

  13. On Maximal Green Sequences

    CERN Document Server

    Brüstle, Thomas; Pérotin, Matthieu

    2012-01-01

    Maximal green sequences are particular sequences of quiver mutations which were introduced by Keller in the context of quantum dilogarithm identities and independently by Cecotti-Cordova-Vafa in the context of supersymmetric gauge theory. Our aim is to initiate a systematic study of these sequences from a combinatorial point of view. Interpreting maximal green sequences as paths in various natural posets arising in representation theory, we prove the finiteness of the number of maximal green sequences for cluster finite quivers, affine quivers and acyclic quivers with at most three vertices. We also give results concerning the possible numbers and lengths of these maximal green sequences. Finally we describe an algorithm for computing maximal green sequences for arbitrary valued quivers which we used to obtain numerous explicit examples that we present.

  14. Sequence of Quantum Phase Transitions in Bi2Sr2CaCu2O8 +δ Cuprates Revealed by In Situ Electrical Doping of One and the Same Sample

    Science.gov (United States)

    Jacobs, Th.; Simsek, Y.; Koval, Y.; Müller, P.; Krasnov, V. M.

    2016-02-01

    Our recently discovered electrical doping technique allows a broad-range variation of carrier concentration without changing the chemical composition. We show that it is possible to induce superconductivity in a nondoped insulating sample and to tune it reversibly all the way to an overdoped metallic state. This way, we can investigate the whole doping diagram of one and the same sample. Our study reveals two distinct critical points. The one at the overdoped side is associated with the onset of the pseudogap and with the metal-to-insulator transition in the c -axis transport. The other at optimal doping is associated with the appearance of a "dressed" electron energy. Our study confirms the existence of multiple phase transitions under the superconducting dome in cuprates.

  15. Arrested segregative phase separation in capillary tubes

    NARCIS (Netherlands)

    Tromp, R. Hans; Lindhoud, Saskia

    2006-01-01

    Phase separation in a capillary tube with one of the phases fully wetting the capillary wall is arrested when the typical size of the phase domains reaches the value of the diameter of the tube. The arrested state consists of an alternating sequence of concave-capped and convex-capped cylindrical

  16. Voltage Unbalance Compensation with Smart Three-phase Loads

    DEFF Research Database (Denmark)

    Douglass, Philip; Trintis, Ionut; Munk-Nielsen, Stig

    2016-01-01

    voltage, but it does not reduce the negative sequence voltage. The controller that uses phase-phase voltage as input eliminates negative sequence voltage, and reduces voltage deviations from the average to approximately half their initial value. Current unbalance is reduced when the voltage unbalance...... is caused by asymmetrical loads. These results suggest that the optimal algorithm to reduce system unbalance depends on which system parameter is most important: phase-neutral voltage unbalance, phase-phase voltage unbalance, or current unbalance....

  17. Direct Torque Control for Six-phase Permanent Magnet Synchronous Motor With Zero-sequence Current Self-adjust%具有零序电流自矫正的六相永磁同步电机直接转矩控制

    Institute of Scientific and Technical Information of China (English)

    周扬忠; 程明; 熊先云

    2015-01-01

    逆变器死区、功率管导通压降及开关过渡过程等非线性因素易导致直接转矩控制(direct torque control,DTC)多相永磁同步电机定子电流严重畸变。该文针对六相对称偏置60°定子绕组永磁同步电机提出一种DTC策略。首先,基于零序电流等于零思想进行电压矢量重构,并由此提出理想DTC;其次,基于死区补偿原理对实际电压矢量作用时间进行离散补偿;最后,利用 PI 调节器对电压矢量作用时间进行连续补偿,实现零序电流等于零目的。实验结果表明该文提出的驱动控制系统具有快速的转矩动态响应特性;同时零序电流基本等于零,定子电流总谐波含量较低。%There may be serious distortion in stator currents of multi-phase permanent magnet synchronous motor with direct torque control (DTC) because of the nonlinear factors such as inverter dead-zone, power switch voltage drop and switching transition. A novel DTC was proposed for six-phase symmetric winding phase-shifted by a 60 degree permanent magnet synchronous motor. Firstly, the synthesized voltage vectors were determined to achieve the zero-sequence current, and the ideal DTC strategy was proposed based on the synthesized vectors. Secondly, the factual voltage vector operating time was compensated according to the principle of dead-zone compensation. At last, the voltage vector operating time was regulated continuously by a proportion-integral controller aiming at zero zero-sequence current. The experimental results show that the presented DTC has fast response of torque and the total harmonics is very small due to very lower zero-sequence current.

  18. Automated Testing with Targeted Event Sequence Generation

    DEFF Research Database (Denmark)

    Jensen, Casper Svenning; Prasad, Mukul R.; Møller, Anders

    2013-01-01

    of the individual event handlers of the application. The second phase builds event sequences backward from the target, using the summaries together with a UI model of the application. Our experiments on a collection of open source Android applications show that this technique can successfully produce event...

  19. Automated Testing with Targeted Event Sequence Generation

    DEFF Research Database (Denmark)

    Jensen, Casper Svenning; Prasad, Mukul R.; Møller, Anders

    2013-01-01

    of the individual event handlers of the application. The second phase builds event sequences backward from the target, using the summaries together with a UI model of the application. Our experiments on a collection of open source Android applications show that this technique can successfully produce event...

  20. Next-generation sequencing

    DEFF Research Database (Denmark)

    Rieneck, Klaus; Bak, Mads; Jønson, Lars

    2013-01-01

    the feasibility of predicting the fetal KEL1 phenotype using next-generation sequencing (NGS) technology. STUDY DESIGN AND METHODS: The KEL1/2 single-nucleotide polymorphism was polymerase chain reaction (PCR) amplified with one adjoining base, and the PCR product was sequenced using a genome analyzer (GAIIx......, Illumina); several millions of PCR sequences were analyzed. RESULTS: The results demonstrated the feasibility of diagnosing the fetal KEL1 or KEL2 blood group from cell-free DNA purified from maternal plasma. CONCLUSION: This method requires only one primer pair, and the large amount of sequence...

  1. 单相重合时序对特高压交直流并联系统暂稳影响的机理分析%Mechanism Analysis of Single-Phase Reclosure Sequence's Influence on Ultra-High Voltage AC/DC Parallel System

    Institute of Scientific and Technical Information of China (English)

    孙士云; 束洪春; 于继来

    2009-01-01

    There is larger effect of single-phase reclosure sequence on ultra-high voltage AC/DC parallel system's transient stability. To discuss the inherent mechanism of this issue, single generator-ultra-high voltage AC/DC parallel transmission-infinite bus system is constructed, and equivalent AC impedance of DC system is derived based on switch function method and thus electromagnetic power expression is obtained. By analyzing the changing characteristic of power angle during the whole process that single-phase permanent fault is occurred, single-phase breaker is tripped, reclose to permanent fault and three phase breaker is tripped, influence of single-phase reclosure sequence on system's transient angle stability is described. Setting criterion of reclosure sequence to decrease acceleration area and enhance system's transient stability is proposed, i.e. to reclose on the terminal with smaller equivalent impedance of system. Correctness and effectiveness of the criterion is simulated in single generator-ultra-high voltage AC/DC parallel transmission-infinite bus system and south China power grid in 2010.%重合闸时序对特高压交直流并联系统暂态稳定性有较大的影响,为探讨其内在机理,构造了单机特高压交直流并联输电无穷大系统,采用开关函数法推导出直流系统的等值交流阻抗,得到了系统电磁功率的解析表达式.通过分析一回交流线路发生单相永久接地故障、故障相跳闸、故障相重合于永久故障、三相跳闸的整个过程中发电机的功角变化特性,利用等面积法则从机理上阐述了重合时序对系统功角稳定性的影响.提出了单相重合时序设置判据,即使系统等值阻抗较小的一侧首先重合,以期减小系统的加速面积,提高并联系统的暂态功角稳定性.在单机特高压交直流并联无穷大系统和2010年南方电网中,对该判据的正确性和有效性进行了仿真验证.

  2. Sequence Classification: 894897 [

    Lifescience Database Archive (English)

    Full Text Available ched-chain amino acid aminotransferase, homolog of murine ECA39; highly expressed during stationary phase and repressed during logari...thmic phase; Bat2p || http://www.ncbi.nlm.nih.gov/protein/6322608 ...

  3. Characterizing leader sequences of CRISPR loci

    DEFF Research Database (Denmark)

    Alkhnbashi, Omer; Shah, Shiraz Ali; Garrett, Roger Antony

    2016-01-01

    The CRISPR-Cas system is an adaptive immune system in many archaea and bacteria, which provides resistance against invading genetic elements. The first phase of CRISPR-Cas immunity is called adaptation, in which small DNA fragments are excised from genetic elements and are inserted into a CRISPR...... array generally adjacent to its so called leader sequence at one end of the array. It has been shown that transcription initiation and adaptation signals of the CRISPR array are located within the leader. However, apart from promoters, there is very little knowledge of sequence or structural motifs...... sequences by focusing on the consensus repeat of the adjacent CRISPR array and weak upstream conservation signals. We applied our tool to the analysis of a comprehensive genomic database and identified several characteristic properties of leader sequences specific to archaea and bacteria, ranging from...

  4. Hardware bitstream sequence recognizer

    OpenAIRE

    Karpin, Oleksandr; Sokil, Volodymyr

    2009-01-01

    This paper describes how to implement in hardware a bistream sequence recognizer using the PSoC Pseudo Random Sequence Generator (PRS) User Module. The PRS can be used in digital communication systems with the serial data interface for automatic preamble detection and extraction, control words selection, etc.

  5. Cosmetology: Scope and Sequence.

    Science.gov (United States)

    Nashville - Davidson County Metropolitan Public Schools, TN.

    This scope and sequence guide, developed for a cosmetology vocational education program, represents an initial step in the development of a systemwide articulated curriculum sequence for all vocational programs within the Metropolitan Nashville Public School System. It was developed as a result of needs expressed by teachers, parents, and the…

  6. DNA sequencing by CE.

    Science.gov (United States)

    Karger, Barry L; Guttman, András

    2009-06-01

    Sequencing of human and other genomes has been at the center of interest in the biomedical field over the past several decades and is now leading toward an era of personalized medicine. During this time, DNA-sequencing methods have evolved from the labor-intensive slab gel electrophoresis, through automated multiCE systems using fluorophore labeling with multispectral imaging, to the "next-generation" technologies of cyclic-array, hybridization based, nanopore and single molecule sequencing. Deciphering the genetic blueprint and follow-up confirmatory sequencing of Homo sapiens and other genomes were only possible with the advent of modern sequencing technologies that were a result of step-by-step advances with a contribution of academics, medical personnel and instrument companies. While next-generation sequencing is moving ahead at breakneck speed, the multicapillary electrophoretic systems played an essential role in the sequencing of the Human Genome, the foundation of the field of genomics. In this prospective, we wish to overview the role of CE in DNA sequencing based in part of several of our articles in this journal.

  7. Sequencing the maize genome.

    Science.gov (United States)

    Martienssen, Robert A; Rabinowicz, Pablo D; O'Shaughnessy, Andrew; McCombie, W Richard

    2004-04-01

    Sequencing of complex genomes can be accomplished by enriching shotgun libraries for genes. In maize, gene-enrichment by copy-number normalization (high C(0)t) and methylation filtration (MF) have been used to generate up to two-fold coverage of the gene-space with less than 1 million sequencing reads. Simulations using sequenced bacterial artificial chromosome (BAC) clones predict that 5x coverage of gene-rich regions, accompanied by less than 1x coverage of subclones from BAC contigs, will generate high-quality mapped sequence that meets the needs of geneticists while accommodating unusually high levels of structural polymorphism. By sequencing several inbred strains, we propose a strategy for capturing this polymorphism to investigate hybrid vigor or heterosis.

  8. RIKEN Integrated Sequence Analysis (RISA) System—384-Format Sequencing Pipeline with 384 Multicapillary Sequencer

    OpenAIRE

    Shibata, Kazuhiro; Itoh, Masayoshi; Aizawa, Katsunori; Nagaoka, Sumiharu; Sasaki, Nobuya; Carninci, Piero; Konno, Hideaki; AKIYAMA, Junichi; Nishi, Katsuo; Kitsunai, Tokuji; Tashiro, Hideo; Itoh, Mari; Sumi, Noriko; Ishii, Yoshiyuki; Nakamura, Shin

    2000-01-01

    The RIKEN high-throughput 384-format sequencing pipeline (RISA system) including a 384-multicapillary sequencer (the so-called RISA sequencer) was developed for the RIKEN mouse encyclopedia project. The RISA system consists of colony picking, template preparation, sequencing reaction, and the sequencing process. A novel high-throughput 384-format capillary sequencer system (RISA sequencer system) was developed for the sequencing process. This system consists of a 384-multicapillary auto seque...

  9. Post-Main Sequence Evolution of Debris Discs

    OpenAIRE

    Bonsor, Amy; Wyatt, Mark

    2010-01-01

    The population of debris discs on the main sequence is well constrained, however very little is known about debris discs around evolved stars. In this work we provide a theoretical framework that considers the effects of stellar evolution on debris discs; firstly considering the evolution of an individual disc from the main sequence through to the white dwarf phase, then extending this to the known population of debris discs around main sequence A stars. It is found that discs around evolved ...

  10. HIV Sequence Compendium 2015

    Energy Technology Data Exchange (ETDEWEB)

    Foley, Brian Thomas [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Leitner, Thomas Kenneth [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Apetrei, Cristian [Univ. of Pittsburgh, PA (United States); Hahn, Beatrice [Univ. of Pennsylvania, Philadelphia, PA (United States); Mizrachi, Ilene [National Center for Biotechnology Information, Bethesda, MD (United States); Mullins, James [Univ. of Washington, Seattle, WA (United States); Rambaut, Andrew [Univ. of Edinburgh, Scotland (United Kingdom); Wolinsky, Steven [Northwestern Univ., Evanston, IL (United States); Korber, Bette Tina Marie [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2015-10-05

    This compendium is an annual printed summary of the data contained in the HIV sequence database. We try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Each of the alignments attempts to display the genetic variability within the different species, groups and subtypes of the virus. This compendium contains sequences published before January 1, 2015. Hence, though it is published in 2015 and called the 2015 Compendium, its contents correspond to the 2014 curated alignments on our website. The number of sequences in the HIV database is still increasing. In total, at the end of 2014, there were 624,121 sequences in the HIV Sequence Database, an increase of 7% since the previous year. This is the first year that the number of new sequences added to the database has decreased compared to the previous year. The number of near complete genomes (>7000 nucleotides) increased to 5834 by end of 2014. However, as in previous years, the compendium alignments contain only a fraction of these. A more complete version of all alignments is available on our website, http://www.hiv.lanl.gov/ content/sequence/NEWALIGN/align.html As always, we are open to complaints and suggestions for improvement. Inquiries and comments regarding the compendium should be addressed to seq-info@lanl.gov.

  11. Phylogenetic Trees From Sequences

    Science.gov (United States)

    Ryvkin, Paul; Wang, Li-San

    In this chapter, we review important concepts and approaches for phylogeny reconstruction from sequence data.We first cover some basic definitions and properties of phylogenetics, and briefly explain how scientists model sequence evolution and measure sequence divergence. We then discuss three major approaches for phylogenetic reconstruction: distance-based phylogenetic reconstruction, maximum parsimony, and maximum likelihood. In the third part of the chapter, we review how multiple phylogenies are compared by consensus methods and how to assess confidence using bootstrapping. At the end of the chapter are two sections that list popular software packages and additional reading.

  12. MPS Editor - An Integrated Sequencing Environment

    Science.gov (United States)

    Streiffert, Barbara A.; O'Reilly, Taifun; Schrock, Mitchell; Catchen, Jaime

    2010-01-01

    In today's operations environment, the teams are smaller and need to be more efficient while still ensuring the safety and success of the mission. In addition, teams often begin working on a mission in its early development phases and continue on the team through actual operations. For these reasons the operations teams want to be presented with a software environment that integrates multiple needed software applications as well as providing them with context sensitive editing support for entering commands and sequences of commands. At Jet Propulsion Laboratory, the Multi-Mission Planning and Sequencing (MPS) Editor provided by the Multi-Mission Ground Systems and Services (MGSS) supports those operational needs.

  13. Calibrating for Ionospheric Phase Delays

    Science.gov (United States)

    Macdoran, P. F.

    1985-01-01

    Technique determines ionospheric phase delay on real-time universally applicable basis in terms of electrons per meter squared by coherently modulating two L-band carrier frequencies received from two Global Positioning System satelites. Two pseudorandom number sequences cross-correlated to derive delay time.

  14. Yeast genome sequencing:

    DEFF Research Database (Denmark)

    Piskur, Jure; Langkjær, Rikke Breinhold

    2004-01-01

    For decades, unicellular yeasts have been general models to help understand the eukaryotic cell and also our own biology. Recently, over a dozen yeast genomes have been sequenced, providing the basis to resolve several complex biological questions. Analysis of the novel sequence data has shown...... of closely related species helps in gene annotation and to answer how many genes there really are within the genomes. Analysis of non-coding regions among closely related species has provided an example of how to determine novel gene regulatory sequences, which were previously difficult to analyse because...... they are short and degenerate and occupy different positions. Comparative genomics helps to understand the origin of yeasts and points out crucial molecular events in yeast evolutionary history, such as whole-genome duplication and horizontal gene transfer(s). In addition, the accumulating sequence data provide...

  15. Scope and Sequence.

    Science.gov (United States)

    Callison, Daniel

    2002-01-01

    Discusses scope and sequence plans for curriculum coordination in elementary and secondary education related to school libraries. Highlights include library skills; levels of learning objectives; technology skills; media literacy skills; and information inquiry skills across disciplines by grade level. (LRW)

  16. Evolution of DNA sequencing

    National Research Council Canada - National Science Library

    Tipu, Hamid Nawaz; Shabbir, Ambreen

    2015-01-01

    Sanger and coworkers introduced DNA sequencing in 1970s for the first time. It principally relied on termination of growing nucleotide chain when a dideoxythymidine triphosphate (ddTTP) was inserted...

  17. Pierre Robin sequence

    Science.gov (United States)

    Pierre Robin syndrome; Pierre Robin complex; Pierre Robin anomaly ... The exact causes of Pierre Robin sequence are unknown. It may be part of many genetic syndromes. The lower jaw develops slowly before birth, but may grow ...

  18. In Favor of Sequencing?

    NARCIS (Netherlands)

    van der Borgh, G.J.C.

    2014-01-01

    This short article is a contribution to an online discussion about political sequencing and stability. It argues that despite all the risks of democratization in fragile states,a more gradual approach should be preferred.

  19. Gomphid DNA sequence data

    Data.gov (United States)

    U.S. Environmental Protection Agency — DNA sequence data for several genetic loci. This dataset is not publicly accessible because: It's already publicly available on GenBank. It can be accessed through...

  20. Text Mining: (Asynchronous Sequences

    Directory of Open Access Journals (Sweden)

    Sheema Khan

    2014-12-01

    Full Text Available In this paper we tried to correlate text sequences those provides common topics for semantic clues. We propose a two step method for asynchronous text mining. Step one check for the common topics in the sequences and isolates these with their timestamps. Step two takes the topic and tries to give the timestamp of the text document. After multiple repetitions of step two, we could give optimum result.

  1. Malaria Genome Sequencing Project

    Science.gov (United States)

    2004-01-01

    million cases and up to 2.7 million A whole chromosome shotgun sequencing strategy was used to deaths from malaria each year. The mortality levels are...deaths from malaria each year. The mortality levels are greatest in determine the genome sequence of P. falciparum clone 3D7. This sub-Saharan Africa...aminolevulinic acid dehydratase. Cura . Genet. 40, 391-398 (2002). 15. Lasonder, E. et al Analysis of the Plasmodium falciparum proteome by high-accuracy mass

  2. Biological sequence analysis

    DEFF Research Database (Denmark)

    Durbin, Richard; Eddy, Sean; Krogh, Anders Stærmose

    This book provides an up-to-date and tutorial-level overview of sequence analysis methods, with particular emphasis on probabilistic modelling. Discussed methods include pairwise alignment, hidden Markov models, multiple alignment, profile searches, RNA secondary structure analysis, and phylogene......This book provides an up-to-date and tutorial-level overview of sequence analysis methods, with particular emphasis on probabilistic modelling. Discussed methods include pairwise alignment, hidden Markov models, multiple alignment, profile searches, RNA secondary structure analysis...

  3. Genome sequencing conference II

    Energy Technology Data Exchange (ETDEWEB)

    1990-01-01

    Genome Sequencing Conference 2 was held September 30 to October 30, 1990. 26 speaker abstracts and 33 poster presentations were included in the program report. New and improved methods for DNA sequencing and genetic mapping were presented. Many of the papers were concerned with accuracy and speed of acquisition of data with computers and automation playing an increasing role. Individual papers have been processed separately for inclusion on the database.

  4. HIV Sequence Compendium 2010

    Energy Technology Data Exchange (ETDEWEB)

    Kuiken, Carla [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Foley, Brian [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Leitner, Thomas [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Apetrei, Christian [Univ. of Pittsburgh, PA (United States); Hahn, Beatrice [Univ. of Alabama, Tuscaloosa, AL (United States); Mizrachi, Ilene [National Center for Biotechnology Information, Bethesda, MD (United States); Mullins, James [Univ. of Washington, Seattle, WA (United States); Rambaut, Andrew [Univ. of Edinburgh, Scotland (United Kingdom); Wolinsky, Steven [Northwestern Univ., Evanston, IL (United States); Korber, Bette [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2010-12-31

    This compendium is an annual printed summary of the data contained in the HIV sequence database. In these compendia we try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Each of the alignments attempts to display the genetic variability within the different species, groups and subtypes of the virus. This compendium contains sequences published before January 1, 2010. Hence, though it is called the 2010 Compendium, its contents correspond to the 2009 curated alignments on our website. The number of sequences in the HIV database is still increasing exponentially. In total, at the time of printing, there were 339,306 sequences in the HIV Sequence Database, an increase of 45% since last year. The number of near complete genomes (>7000 nucleotides) increased to 2576 by end of 2009, reflecting a smaller increase than in previous years. However, as in previous years, the compendium alignments contain only a small fraction of these. Included in the alignments are a small number of sequences representing each of the subtypes and the more prevalent circulating recombinant forms (CRFs) such as 01 and 02, as well as a few outgroup sequences (group O and N and SIV-CPZ). Of the rarer CRFs we included one representative each. A more complete version of all alignments is available on our website, http://www.hiv.lanl.gov/content/sequence/NEWALIGN/align.html. Reprints are available from our website in the form of both HTML and PDF files. As always, we are open to complaints and suggestions for improvement. Inquiries and comments regarding the compendium should be addressed to seq-info@lanl.gov.

  5. Phase transitions

    CERN Document Server

    Solé, Ricard V

    2011-01-01

    Phase transitions--changes between different states of organization in a complex system--have long helped to explain physics concepts, such as why water freezes into a solid or boils to become a gas. How might phase transitions shed light on important problems in biological and ecological complex systems? Exploring the origins and implications of sudden changes in nature and society, Phase Transitions examines different dynamical behaviors in a broad range of complex systems. Using a compelling set of examples, from gene networks and ant colonies to human language and the degradation o

  6. Ion mixing and phase diagrams

    Science.gov (United States)

    Lau, S. S.; Liu, B. X.; Nicolet, M.-A.

    1983-05-01

    Interactions induced by ion irradiation are generally considered to be non-equilibrium processes, whereas phase diagrams are determined by phase equilibria. These two entities are seemingly unrelated. However, if one assumes that quasi-equilibrium conditions prevail after the prompt events, subsequent reactions are driven toward equilibrium by thermodynamical forces. Under this assumption, ion-induced reactions are related to equilibrium and therefore to phase diagrams. This relationship can be seen in the similarity that exists in thin films between reactions induced by ion irradiation and reactions induced by thermal annealing. In the latter case, phase diagrams have been used to predict the phase sequence of stable compound formation, notably so in cases of silicide formation. Ion-induced mixing not only can lead to stable compound formation, but also to metastable alloy formation. In some metal-metal systems, terminal solubilities can be greatly extended by ion mixing. In other cases, where the two constituents of the system have different crystal structures, extension of terminal solubility from both sides of the phase diagram eventually becomes structurally incompatible and a glassy (amorphous) mixture can form. The composition range where this bifurcation is likely to occur is in the two-phase regions of the phase diagram. These concepts are potentially useful guides in selecting metal pairs that from metallic glasses by ion mixing. In this report, phenomenological correlation between stable (and metastable) phase formation and phase diagram is discussed in terms of recent experimental data.

  7. Sequence-defined polymers via orthogonal allyl acrylamide building blocks.

    Science.gov (United States)

    Porel, Mintu; Alabi, Christopher A

    2014-09-24

    Biological systems have long recognized the importance of macromolecular diversity and have evolved efficient processes for the rapid synthesis of sequence-defined biopolymers. However, achieving sequence control via synthetic methods has proven to be a difficult challenge. Herein we describe efforts to circumvent this difficulty via the use of orthogonal allyl acrylamide building blocks and a liquid-phase fluorous support for the de novo design and synthesis of sequence-specific polymers. We demonstrate proof-of-concept via synthesis and characterization of two sequence-isomeric 10-mer polymers. (1)H NMR and LCMS were used to confirm their chemical structure while tandem MS was used to confirm sequence identity. Further validation of this methodology was provided via the successful synthesis of a sequence-specific 16-mer polymer incorporating nine different monomers. This strategy thus shows promise as an efficient approach for the assembly of sequence-specific functional polymers.

  8. Cognitive processing in new and practiced discrete keying sequences

    Directory of Open Access Journals (Sweden)

    Willem B Verwey

    2010-07-01

    Full Text Available This study addresses the role of cognitive control in the initiation and execution of familiar and unfamiliar movement sequences. To become familiar with two movement sequences participants first practiced two discrete key press sequences by responding to two fixed series of 6 key specific stimuli. In the ensuing test phase they executed these two familiar and also two unfamiliar keying sequences while there was a two-third chance a tone was presented together with one randomly selected key specific stimulus in each sequence. In the counting condition of the test phase participants counted the low pitched (i.e., target tones. By and large the results support the dual processor model in which the prime role of the cognitive processor shifts from executing to initiating sequences while the gradual development of motor chunks allows a motor processor to execute the sequences. Yet, the results extend this simple model by suggesting that with little practice sequence execution is based also on some non-cognitive (perhaps associative learning mechanism and, for some participants, on the use of explicit sequence knowledge. Also, after extensive practice the cognitive processor appears to still contribute to slower responses. The occurrence of long interkey intervals was replicated suggesting that fixed 6-key sequences include several motor chunks. Yet, no indication was found that the cognitive processor is responsible for concatenating these chunks.

  9. New cooling sequences for old white dwarfs

    CERN Document Server

    Renedo, Isabel; Bertolami, Marcelo M Miller; Romero, Alejandra D; Corsico, Alejandro H; Rohrmann, Rene D; Garcia-Berro, Enrique

    2010-01-01

    We present full evolutionary calculations appropriate for the study of hydrogen-rich DA white dwarfs. This is done by evolving white dwarf progenitors from the zero age main sequence, through the core hydrogen burning phase, the helium burning phase and the thermally pulsing asymptotic giant branch phase to the white dwarf stage. Complete evolutionary sequences are computed for a wide range of stellar masses and for two different metallicities: Z=0.01, which is representative of the solar neighborhood, and Z=0.001, which is appropriate for the study of old stellar systems, like globular clusters. During the white dwarf cooling stage we compute self-consistently the phase in which nuclear reactions are still important, the diffusive evolution of the elements in the outer layers and, finally, we also take into account all the relevant energy sources in the deep interior of the white dwarf, like the release of latent heat and the release of gravitational energy due to carbon-oxygen phase separation upon crystall...

  10. Sequence Classification: 893019 [

    Lifescience Database Archive (English)

    Full Text Available ptation prior to stationary phase entry; has similarity to Sps100p; Ygp1p || http://www.ncbi.nlm.nih.gov/protein/6324169 ... ...y glycoprotein; induced by nutrient deprivation-associated growth arrest and upon entry into stationary phase; may be involved in ada

  11. Estimation of visual motion in image sequences

    DEFF Research Database (Denmark)

    Larsen, Rasmus

    1994-01-01

    The problem of estimation of visual motion from sequences of images has been considered within a framework consisting of three stages of processing. First the extraction of motion invariants, secondly a local measurement of visual motion, and third integration of local measurements in conjunction...... with a priori knowledge. We have surveyed a series of attempts to extract motion invariants. Specifically we have illustrate the use of local Fourier phase. The Fourier phase is shown to define the local shape of the signal, thus accurately localizing an event. Different strategies for local measurement...... satellite images based on the estimated motion field is shown....

  12. Sequencing genes in silico using single nucleotide polymorphisms

    Directory of Open Access Journals (Sweden)

    Zhang Xinyi

    2012-01-01

    Full Text Available Abstract Background The advent of high throughput sequencing technology has enabled the 1000 Genomes Project Pilot 3 to generate complete sequence data for more than 906 genes and 8,140 exons representing 697 subjects. The 1000 Genomes database provides a critical opportunity for further interpreting disease associations with single nucleotide polymorphisms (SNPs discovered from genetic association studies. Currently, direct sequencing of candidate genes or regions on a large number of subjects remains both cost- and time-prohibitive. Results To accelerate the translation from discovery to functional studies, we propose an in silico gene sequencing method (ISS, which predicts phased sequences of intragenic regions, using SNPs. The key underlying idea of our method is to infer diploid sequences (a pair of phased sequences/alleles at every functional locus utilizing the deep sequencing data from the 1000 Genomes Project and SNP data from the HapMap Project, and to build prediction models using flanking SNPs. Using this method, we have developed a database of prediction models for 611 known genes. Sequence prediction accuracy for these genes is 96.26% on average (ranges 79%-100%. This database of prediction models can be enhanced and scaled up to include new genes as the 1000 Genomes Project sequences additional genes on additional individuals. Applying our predictive model for the KCNJ11 gene to the Wellcome Trust Case Control Consortium (WTCCC Type 2 diabetes cohort, we demonstrate how the prediction of phased sequences inferred from GWAS SNP genotype data can be used to facilitate interpretation and identify a probable functional mechanism such as protein changes. Conclusions Prior to the general availability of routine sequencing of all subjects, the ISS method proposed here provides a time- and cost-effective approach to broadening the characterization of disease associated SNPs and regions, and facilitating the prioritization of candidate

  13. Adaptive Processing for Sequence Alignment

    KAUST Repository

    Zidan, Mohammed Affan

    2012-01-26

    Disclosed are various embodiments for adaptive processing for sequence alignment. In one embodiment, among others, a method includes obtaining a query sequence and a plurality of database sequences. A first portion of the plurality of database sequences is distributed to a central processing unit (CPU) and a second portion of the plurality of database sequences is distributed to a graphical processing unit (GPU) based upon a predetermined splitting ratio associated with the plurality of database sequences, where the database sequences of the first portion are shorter than the database sequences of the second portion. A first alignment score for the query sequence is determined with the CPU based upon the first portion of the plurality of database sequences and a second alignment score for the query sequence is determined with the GPU based upon the second portion of the plurality of database sequences.

  14. High efficiency spreading spectrum modulation using double orthogonal complex sequences

    Institute of Scientific and Technical Information of China (English)

    Shi Xiaohong

    2012-01-01

    This paper presents a novel scheme of high efficiency spreading spectrum modulation using double orthogonal complex sequences (DoCS). In this scheme, input data bit-stream is split into many groups with length M. Each group is then mapped into a word of width M and then utihzed to select one sequence from 2u-2 DoCS sequences each with length L. After that, the selected sequence is modulated on carrier in quadrature phase shift keying (QPSK) mode. In addition, a new method named forward phase correction (FPC) is put forward for carrier recovery. Theoretical analysis and bit-error-ratio(BER) experiment results indicate that the proposed scheme has better performance than the conventional direct sequence spread spectrum(DSSS) scheme both in bandwidth efficiency and processing gain of the receiver.

  15. Controlled processing during sequencing.

    Science.gov (United States)

    Thothathiri, Malathi; Rattinger, Michelle

    2015-01-01

    Longstanding evidence has identified a role for the frontal cortex in sequencing within both linguistic and non-linguistic domains. More recently, neuropsychological studies have suggested a specific role for the left premotor-prefrontal junction (BA 44/6) in selection between competing alternatives during sequencing. In this study, we used neuroimaging with healthy adults to confirm and extend knowledge about the neural correlates of sequencing. Participants reproduced visually presented sequences of syllables and words using manual button presses. Items in the sequence were presented either consecutively or concurrently. Concurrent presentation is known to trigger the planning of multiple responses, which might compete with one another. Therefore, we hypothesized that regions involved in controlled processing would show greater recruitment during the concurrent than the consecutive condition. Whole-brain analysis showed concurrent > consecutive activation in sensory, motor and somatosensory cortices and notably also in rostral-dorsal anterior cingulate cortex. Region of interest analyses showed increased activation within left BA 44/6 and correlation between this region's activation and behavioral response times. Functional connectivity analysis revealed increased connectivity between left BA 44/6 and the posterior lobe of the cerebellum during the concurrent than the consecutive condition. These results corroborate recent evidence and demonstrate the involvement of BA 44/6 and other control regions when ordering co-activated representations.

  16. Controlled processing during sequencing

    Directory of Open Access Journals (Sweden)

    Malathi eThothathiri

    2015-10-01

    Full Text Available Longstanding evidence has identified a role for the frontal cortex in sequencing within both linguistic and non-linguistic domains. More recently, neuropsychological studies have suggested a specific role for the left premotor-prefrontal junction (BA 44/6 in selection between competing alternatives during sequencing. In this study, we used neuroimaging with healthy adults to confirm and extend knowledge about the neural correlates of sequencing. Participants reproduced visually presented sequences of syllables and words using manual button presses. Items in the sequence were presented either consecutively or concurrently. Concurrent presentation is known to trigger the planning of multiple responses, which might compete with one another. Therefore, we hypothesized that regions involved in controlled processing would show greater recruitment during the concurrent than the consecutive condition. Whole-brain analysis showed concurrent > consecutive activation in sensory, motor and somatosensory cortices and notably also in rostral-dorsal anterior cingulate cortex (ACC. Region of interest analyses showed increased activation within left BA 44/6 and correlation between this region’s activation and behavioral response times. Functional connectivity analysis revealed increased connectivity between left BA 44/6 and the posterior lobe of the cerebellum during the concurrent than the consecutive condition. These results corroborate recent evidence and demonstrate the involvement of BA 44/6 and other control regions when ordering co-activated representations.

  17. The sequence of learning cycle activities in high school chemistry

    Science.gov (United States)

    Abraham, Michael R.; Renner, John W.

    The sequence of the three phases of two high school learning cycles in chemistry was altered in order to: (I ) give insights into the factors which account for the success of the learning cycle, (2) serve as an indirect test of the association between Piaget's theory and the learning cycle, and (3) to compare the learning cycle with traditional instruction. Each of the six sequences (one n o d and five altered) was studied with content and atritudc measures. The outcomes of the study supported the contention that the normal learning cycle sequence is the optimum sequence for achievement of content knowledge.

  18. Program Synthesizes UML Sequence Diagrams

    Science.gov (United States)

    Barry, Matthew R.; Osborne, Richard N.

    2006-01-01

    A computer program called "Rational Sequence" generates Universal Modeling Language (UML) sequence diagrams of a target Java program running on a Java virtual machine (JVM). Rational Sequence thereby performs a reverse engineering function that aids in the design documentation of the target Java program. Whereas previously, the construction of sequence diagrams was a tedious manual process, Rational Sequence generates UML sequence diagrams automatically from the running Java code.

  19. Sequencing BPS Spectra

    CERN Document Server

    Gukov, Sergei; Saberi, Ingmar; Stosic, Marko; Sulkowski, Piotr

    2015-01-01

    This paper provides both a detailed study of color-dependence of link homologies, as realized in physics as certain spaces of BPS states, and a broad study of the behavior of BPS states in general. We consider how the spectrum of BPS states varies as continuous parameters of a theory are perturbed. This question can be posed in a wide variety of physical contexts, and we answer it by proposing that the relationship between unperturbed and perturbed BPS spectra is described by a spectral sequence. These general considerations unify previous applications of spectral sequence techniques to physics, and explain from a physical standpoint the appearance of many spectral sequences relating various link homology theories to one another. We also study structural properties of colored HOMFLY homology for links and evaluate Poincar\\'e polynomials in numerous examples. Among these structural properties is a novel "sliding" property, which can be explained by using (refined) modular $S$-matrix. This leads to the identifi...

  20. Next-generation sequencing

    DEFF Research Database (Denmark)

    Rieneck, Klaus; Bak, Mads; Jønson, Lars

    2013-01-01

    information obtained allows well for statistical analysis of the data. This general approach can be integrated into current laboratory practice and has numerous applications. Besides DNA-based predictions of blood group phenotypes, platelet phenotypes, or sickle cell anemia, and the determination of zygosity......, Illumina); several millions of PCR sequences were analyzed. RESULTS: The results demonstrated the feasibility of diagnosing the fetal KEL1 or KEL2 blood group from cell-free DNA purified from maternal plasma. CONCLUSION: This method requires only one primer pair, and the large amount of sequence...

  1. High-speed optical phase-shifting apparatus

    Energy Technology Data Exchange (ETDEWEB)

    Zortman, William A.

    2016-11-08

    An optical phase shifter includes an optical waveguide, a plurality of partial phase shifting elements arranged sequentially, and control circuitry electrically coupled to the partial phase shifting elements. The control circuitry is adapted to provide an activating signal to each of the N partial phase shifting elements such that the signal is delayed by a clock cycle between adjacent partial phase shifting elements in the sequence. The transit time for a guided optical pulse train between the input edges of consecutive partial phase shifting elements in the sequence is arranged to be equal to a clock cycle, thereby enabling pipelined processing of the optical pulses.

  2. 零序过流保护在单相接地故障选线中的应用探讨%Discussion on the Application of Zero Sequence Overcurrent Protection in Fault Line Selection for Single-phase-to-earth Faults

    Institute of Scientific and Technical Information of China (English)

    吴青军; 黄驾驾; 刘东红

    2016-01-01

    The 10 kV power system is a smal1 current earthing system, and the single-phase-to-earth of the power line is the commonest fault and power outage reason, which is quite risky and dangerous. At present, fault line selection modes in power grid operation are not accurate enough. By analyzing characteristics of fault line current in a fault condition, the paper suggests adopting zero sequence overcurrent protection for line selection more accurately; moreover, it tracks the practical application, which confirms the practicality of the scheme.%10 kV系统为小电流接地系统,线路单相接地是最常见的故障及停电诱因,其存在的危害和风险较大。目前电网运行实际中各类故障线路选判方式准确性不高,通过分析故障情况下故障线路电流的特点,提出利用零序过流保护进行较准确的选判方案,并通过对实际应用情况进行跟踪,确认了方案的实用性。

  3. Sequence Classification: 891582 [

    Lifescience Database Archive (English)

    Full Text Available its maintenance during G2 and M phases; also required for postreplicative double-strand break repair; interacts with Chl1p; Eco1p || http://www.ncbi.nlm.nih.gov/protein/14318550 ...

  4. Sequence Classification: 889621 [

    Lifescience Database Archive (English)

    Full Text Available activity is low in exponentially-growing cultures but expression is increased in post-diauxic and stationary-phase cultures; Gud1p || http://www.ncbi.nlm.nih.gov/protein/6319963 ...

  5. The magnetic strip(s) in the advanced phases of stellar evolution. Theoretical convective turnover timescale and Rossby number for low- and intermediate-mass stars up to the AGB at various metallicities

    Science.gov (United States)

    Charbonnel, C.; Decressin, T.; Lagarde, N.; Gallet, F.; Palacios, A.; Aurière, M.; Konstantinova-Antova, R.; Mathis, S.; Anderson, R. I.; Dintrans, B.

    2017-09-01

    Context. Recent spectropolarimetric observations of otherwise ordinary (in terms e.g. of surface rotation and chemical properties) G, K, and M giants have revealed localized magnetic strips in the Hertzsprung-Russell diagram coincident with the regions where the first dredge-up and core helium burning occur. Aims: We seek to understand the origin of magnetic fields in such late-type giant stars, which is currently unexplained. In analogy with late-type dwarf stars, we focus primarily on parameters known to influence the generation of magnetic fields in the outer convective envelope. Methods: We compute the classical dynamo parameters along the evolutionary tracks of low- and intermediate-mass stars at various metallicities using stellar models that have been extensively tested by spectroscopic and asteroseismic observations. Specifically, these include convective turnover timescales and convective Rossby numbers, computed from the pre-main sequence (PMS) to the tip of the red giant branch (RGB) or the early asymptotic giant branch (AGB) phase. To investigate the effects of the very extended outer convective envelope, we compute these parameters both for the entire convective envelope and locally, that is, at different depths within the envelope. We also compute the turnover timescales and corresponding Rossby numbers for the convective cores of intermediate-mass stars on the main sequence. Results: Our models show that the Rossby number of the convective envelope becomes lower than unity in the well-delimited locations of the Hertzsprung-Russell diagram where magnetic fields have indeed been detected. Conclusions: We show that α - Ω dynamo processes might not be continuously operating, but that they are favored in the stellar convective envelope at two specific moments along the evolution tracks, that is, during the first dredge-up at the base of the RGB and during central helium burning in the helium-burning phase and early-AGB. This general behavior can explain

  6. Family Sequencing and Cooperation

    NARCIS (Netherlands)

    Grundel, S.; Ciftci, B.B.; Borm, P.E.M.; Hamers, H.J.M.

    2012-01-01

    To analyze the allocation problem of the maximal cost savings of the whole group of jobs, we define and analyze a so-called corresponding cooperative family sequencing game which explicitly takes into account the maximal cost savings for any coalition of jobs. Using nonstandard techniques we prove t

  7. Twin anemia polycythemia sequence

    NARCIS (Netherlands)

    Slaghekke, Femke

    2014-01-01

    In this thesis we describe that Twin Anemia Polycythemia Sequence (TAPS) is a form of chronic feto-fetal transfusion in monochorionic (identical) twins based on a small amount of blood transfusion through very small anastomoses. For the antenatal diagnosis of TAPS, Middle Cerebral Artery – Peak Syst

  8. Twin anemia polycythemia sequence

    NARCIS (Netherlands)

    Slaghekke, Femke

    2014-01-01

    In this thesis we describe that Twin Anemia Polycythemia Sequence (TAPS) is a form of chronic feto-fetal transfusion in monochorionic (identical) twins based on a small amount of blood transfusion through very small anastomoses. For the antenatal diagnosis of TAPS, Middle Cerebral Artery – Peak

  9. Biological sequence analysis

    DEFF Research Database (Denmark)

    Durbin, Richard; Eddy, Sean; Krogh, Anders Stærmose

    This book provides an up-to-date and tutorial-level overview of sequence analysis methods, with particular emphasis on probabilistic modelling. Discussed methods include pairwise alignment, hidden Markov models, multiple alignment, profile searches, RNA secondary structure analysis, and phylogene...

  10. Phase Vocoder

    Directory of Open Access Journals (Sweden)

    J.L. Flanagan

    2013-08-01

    Full Text Available A vocoder technique is described in which speech signals are represented by their short-time phase and amplitude spectra. A complete transmission system utilizing this approach is simulated on a digital computer. The encoding method leads to an economy in transmission bandwidth and to a means for time compression and expansion of speech signals.

  11. Sequence analysis by iterated maps, a review.

    Science.gov (United States)

    Almeida, Jonas S

    2014-05-01

    Among alignment-free methods, Iterated Maps (IMs) are on a particular extreme: they are also scale free (order free). The use of IMs for sequence analysis is also distinct from other alignment-free methodologies in being rooted in statistical mechanics instead of computational linguistics. Both of these roots go back over two decades to the use of fractal geometry in the characterization of phase-space representations. The time series analysis origin of the field is betrayed by the title of the manuscript that started this alignment-free subdomain in 1990, 'Chaos Game Representation'. The clash between the analysis of sequences as continuous series and the better established use of Markovian approaches to discrete series was almost immediate, with a defining critique published in same journal 2 years later. The rest of that decade would go by before the scale-free nature of the IM space was uncovered. The ensuing decade saw this scalability generalized for non-genomic alphabets as well as an interest in its use for graphic representation of biological sequences. Finally, in the past couple of years, in step with the emergence of BigData and MapReduce as a new computational paradigm, there is a surprising third act in the IM story. Multiple reports have described gains in computational efficiency of multiple orders of magnitude over more conventional sequence analysis methodologies. The stage appears to be now set for a recasting of IMs with a central role in processing nextgen sequencing results.

  12. Probabilistic Sequence Learning in Mild Cognitive Impairment

    Directory of Open Access Journals (Sweden)

    Dezso eNemeth

    2013-07-01

    Full Text Available Mild Cognitive Impairment (MCI causes slight but noticeable disruption in cognitive systems, primarily executive and memory functions. However, it is not clear if the development of sequence learning is affected by an impaired cognitive system and, if so, how. The goal of our study was to investigate the development of probabilistic sequence learning, from the initial acquisition to consolidation, in MCI and healthy elderly control groups. We used the Alternating Serial Reaction Time task (ASRT to measure probabilistic sequence learning. Individuals with MCI showed weaker learning performance than the healthy elderly group. However, using the reaction times only from the second half of each learning block – after the reactivation phase - we found intact learning in MCI. Based on the assumption that the first part of each learning block is related to reactivation/recall processes, we suggest that these processes are affected in MCI. The 24-hour offline period showed no effect on sequence-specific learning in either group but did on general skill learning: the healthy elderly group showed offline improvement in general reaction times while individuals with MCI did not. Our findings deepen our understanding regarding the underlying mechanisms and time course of sequence acquisition and consolidation.

  13. Inverted temperature sequences: role of deformation partitioning

    Science.gov (United States)

    Grujic, D.; Ashley, K. T.; Coble, M. A.; Coutand, I.; Kellett, D.; Whynot, N.

    2015-12-01

    The inverted metamorphism associated with the Main Central thrust zone in the Himalaya has been historically attributed to a number of tectonic processes. Here we show that there is actually a composite peak and deformation temperature sequence that formed in succession via different tectonic processes. The deformation partitioning seems to the have played a key role, and the magnitude of each process has varied along strike of the orogen. To explain the formation of the inverted metamorphic sequence across the Lesser Himalayan Sequence (LHS) in eastern Bhutan, we used Raman spectroscopy of carbonaceous material (RSCM) to determine the peak metamorphic temperatures and Ti-in-quartz thermobarometry to determine the deformation temperatures combined with thermochronology including published apatite and zircon U-Th/He and fission-track data and new 40Ar/39Ar dating of muscovite. The dataset was inverted using 3D-thermal-kinematic modeling to constrain the ranges of geological parameters such as fault geometry and slip rates, location and rates of localized basal accretion, and thermal properties of the crust. RSCM results indicate that there are two peak temperature sequences separated by a major thrust within the LHS. The internal temperature sequence shows an inverted peak temperature gradient of 12 °C/km; in the external (southern) sequence, the peak temperatures are constant across the structural sequence. Thermo-kinematic modeling suggest that the thermochronologic and thermobarometric data are compatible with a two-stage scenario: an Early-Middle Miocene phase of fast overthrusting of a hot hanging wall over a downgoing footwall and inversion of the synkinematic isotherms, followed by the formation of the external duplex developed by dominant underthrusting and basal accretion. To reconcile our observations with the experimental data, we suggest that pervasive ductile deformation within the upper LHS and along the Main Central thrust zone at its top stopped at

  14. Allele Re-sequencing Technologies

    DEFF Research Database (Denmark)

    Byrne, Stephen; Farrell, Jacqueline Danielle; Asp, Torben

    2013-01-01

    The development of next-generation sequencing technologies has made sequencing an affordable approach for detection of genetic variations associated with various traits. However, the cost of whole genome re-sequencing still remains too high to be feasible for many plant species with large...... alternative to whole genome re-sequencing to identify causative genetic variations in plants. One challenge, however, will be efficient bioinformatics strategies for data handling and analysis from the increasing amount of sequence information....

  15. Rapid-Sequence Intubation

    Directory of Open Access Journals (Sweden)

    Evangelina Dávila Cabo de Villa

    2015-09-01

    Full Text Available In medical practice there are several situations that require immediate intervention of the airway in some patients, in order to ensure proper entrance and exit of gases into and out of the lungs and prevent aspiration. Rapid-sequence intubation has been considered as the administration of a hypnotic agent and a neuromuscular relaxant consecutively (virtually simultaneously to facilitate orotracheal intubation in critically ill patients and minimize the risk of aspiration. This paper aims to collect elements that promote a successful medical management according to the situation presented, since there is no single way of proceeding in case of rapid-sequence intubation. The elements to consider include: knowing the anatomy of the upper respiratory tract, having a group of drugs to choose from, receiving adequate training and having an alternative plan for the difficulties that may arise.

  16. Sequence Classification: 885394 [

    Lifescience Database Archive (English)

    Full Text Available 703); The expression pattern of this gene is described in PMID:12000842; possible frameshift detected when compared...Non-TMB TMH Non-TMB Non-TMB Non-TMB Non-TMB >gi|23619146|ref|NP_705108.1| Slight di...fference exist when compared to the published sequence of EBL-1 from Dd2 strain of P. falciparum (PMID:10613

  17. Sequencing of aromatase inhibitors

    OpenAIRE

    2005-01-01

    Since the development of the third-generation aromatase inhibitors (AIs), anastrozole, letrozole and exemestane, these agents have been the subject of intensive research to determine their optimal use in advanced breast cancer. Not only have they replaced progestins in second-line therapy and challenged the role of tamoxifen in first-line, but there is also evidence for a lack of cross-resistance between the steroidal and nonsteroidal AIs, meaning that they may be used in sequence to obtain p...

  18. Properties of Semijoin Sequences

    Institute of Scientific and Technical Information of China (English)

    BengC.Ooi; B.Srinivasan

    1989-01-01

    The problem of finding optimum semijoin sequ4ence of an arbitrary query under linear cost function for the transmission cost is NP.hard.Hence heuristic algorithms with desirable properties are explored.In this paper four properties of semijoin programs for distributed query processing are identified,The use of these properties in constructing semijoin sequence is justified.An existing algorithm is modified incorporating these properties.Empirical comparison with existing algorithms shows the superiority of the proposed algorithm.

  19. Learning Sequence Neighbourhood Metrics

    CERN Document Server

    Bayer, Justin; van der Smagt, Patrick

    2011-01-01

    Recurrent neural networks (RNNs) in combination with a pooling operator and the neighbourhood components analysis (NCA) objective function are able to detect the characterizing dynamics of sequences and embed them into a fixed-length vector space of arbitrary dimensionality. Subsequently, the resulting features are meaningful and can be used for visualization or nearest neighbour classification in linear time. This kind of metric learning for sequential data enables the use of algorithms tailored towards fixed length vector spaces such as R^n.

  20. Sequencing BPS spectra

    Science.gov (United States)

    Gukov, Sergei; Nawata, Satoshi; Saberi, Ingmar; Stošić, Marko; Sułkowski, Piotr

    2016-03-01

    This paper provides both a detailed study of color-dependence of link homologies, as realized in physics as certain spaces of BPS states, and a broad study of the behavior of BPS states in general. We consider how the spectrum of BPS states varies as continuous parameters of a theory are perturbed. This question can be posed in a wide variety of physical contexts, and we answer it by proposing that the relationship between unperturbed and perturbed BPS spectra is described by a spectral sequence. These general considerations unify previous applications of spectral sequence techniques to physics, and explain from a physical standpoint the appearance of many spectral sequences relating various link homology theories to one another. We also study structural properties of colored HOMFLY homology for links and evaluate Poincaré polynomials in numerous examples. Among these structural properties is a novel "sliding" property, which can be explained by using (refined) modular S-matrix. This leads to the identification of modular transformations in Chern-Simons theory and 3d {N}=2 theory via the 3d/3d correspondence. Lastly, we introduce the notion of associated varieties as classical limits of recursion relations of colored superpolynomials of links, and study their properties.

  1. Image sequence analysis

    CERN Document Server

    1981-01-01

    The processing of image sequences has a broad spectrum of important applica­ tions including target tracking, robot navigation, bandwidth compression of TV conferencing video signals, studying the motion of biological cells using microcinematography, cloud tracking, and highway traffic monitoring. Image sequence processing involves a large amount of data. However, because of the progress in computer, LSI, and VLSI technologies, we have now reached a stage when many useful processing tasks can be done in a reasonable amount of time. As a result, research and development activities in image sequence analysis have recently been growing at a rapid pace. An IEEE Computer Society Workshop on Computer Analysis of Time-Varying Imagery was held in Philadelphia, April 5-6, 1979. A related special issue of the IEEE Transactions on Pattern Anal­ ysis and Machine Intelligence was published in November 1980. The IEEE Com­ puter magazine has also published a special issue on the subject in 1981. The purpose of this book ...

  2. The Galaxy End Sequence

    Science.gov (United States)

    Eales, Stephen; de Vis, Pieter; Smith, Matthew W. L.; Appah, Kiran; Ciesla, Laure; Duffield, Chris; Schofield, Simon

    2017-03-01

    A common assumption is that galaxies fall in two distinct regions of a plot of specific star formation rate (SSFR) versus galaxy stellar mass: a star-forming galaxy main sequence (GMS) and a separate region of 'passive' or 'red and dead galaxies'. Starting from a volume-limited sample of nearby galaxies designed to contain most of the stellar mass in this volume, and thus representing the end-point of ≃12 billion years of galaxy evolution, we investigate the distribution of galaxies in this diagram today. We show that galaxies follow a strongly curved extended GMS with a steep negative slope at high galaxy stellar masses. There is a gradual change in the morphologies of the galaxies along this distribution, but there is no clear break between early-type and late-type galaxies. Examining the other evidence that there are two distinct populations, we argue that the 'red sequence' is the result of the colours of galaxies changing very little below a critical value of the SSFR, rather than implying a distinct population of galaxies. Herschel observations, which show at least half of early-type galaxies contain a cool interstellar medium, also imply continuity between early-type and late-type galaxies. This picture of a unitary population of galaxies requires more gradual evolutionary processes than the rapid quenching process needed to explain two distinct populations. We challenge theorists to predict quantitatively the properties of this 'Galaxy End Sequence'.

  3. Sequencing BPS spectra

    Energy Technology Data Exchange (ETDEWEB)

    Gukov, Sergei [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Max-Planck-Institut für Mathematik,Vivatsgasse 7, D-53111 Bonn (Germany); Nawata, Satoshi [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Centre for Quantum Geometry of Moduli Spaces, University of Aarhus,Nordre Ringgade 1, DK-8000 (Denmark); Saberi, Ingmar [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Stošić, Marko [CAMGSD, Departamento de Matemática, Instituto Superior Técnico,Av. Rovisco Pais, 1049-001 Lisbon (Portugal); Mathematical Institute SANU,Knez Mihajlova 36, 11000 Belgrade (Serbia); Sułkowski, Piotr [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Faculty of Physics, University of Warsaw,ul. Pasteura 5, 02-093 Warsaw (Poland)

    2016-03-02

    This paper provides both a detailed study of color-dependence of link homologies, as realized in physics as certain spaces of BPS states, and a broad study of the behavior of BPS states in general. We consider how the spectrum of BPS states varies as continuous parameters of a theory are perturbed. This question can be posed in a wide variety of physical contexts, and we answer it by proposing that the relationship between unperturbed and perturbed BPS spectra is described by a spectral sequence. These general considerations unify previous applications of spectral sequence techniques to physics, and explain from a physical standpoint the appearance of many spectral sequences relating various link homology theories to one another. We also study structural properties of colored HOMFLY homology for links and evaluate Poincaré polynomials in numerous examples. Among these structural properties is a novel “sliding” property, which can be explained by using (refined) modular S-matrix. This leads to the identification of modular transformations in Chern-Simons theory and 3d N=2 theory via the 3d/3d correspondence. Lastly, we introduce the notion of associated varieties as classical limits of recursion relations of colored superpolynomials of links, and study their properties.

  4. Information Theory of DNA Sequencing

    CERN Document Server

    Motahari, Abolfazl; Tse, David

    2012-01-01

    DNA sequencing is the basic workhorse of modern day biology and medicine. Shotgun sequencing is the dominant technique used: many randomly located short fragments called reads are extracted from the DNA sequence, and these reads are assembled to reconstruct the original sequence. By drawing an analogy between the DNA sequencing problem and the classic communication problem, we define an information theoretic notion of sequencing capacity. This is the maximum number of DNA base pairs that can be resolved reliably per read, and provides a fundamental limit to the performance that can be achieved by any assembly algorithm. We compute the sequencing capacity explicitly for a simple statistical model of the DNA sequence and the read process. Using this framework, we also study the impact of noise in the read process on the sequencing capacity.

  5. Critical behavior of marginal aperiodic sequences: a Monte Carlo study

    Science.gov (United States)

    Branco, Nilton

    2007-03-01

    We study layered marginal aperiodic sequences for the Ising and q=8 Potts model on a square lattice. The phase transition is continuous for the former and first-order for the latter. Using the Wolff algorithm we calculate critical exponents and the critical temperature for the Potts model when the interaction constant can assume two values, according to an aperiodic sequence: the period-doubling one for the Ising model and the Fibonacci one for the Potts model. These sequences and models chracterize marginal critical behavior, according to the Luck criterion and, therefore, interaction-dependent exponents are expected for a continuous transition. For first-order phase transitions, no study so far has been done on the influence of marginal sequences.

  6. Sequence Classification: 892960 [

    Lifescience Database Archive (English)

    Full Text Available pecific sites; mutation causes defects in fluid-phase endocytosis; Jjj1p || http://www.ncbi.nlm.nih.gov/protein/6324103 ... ...n that contains a 70 amino acid J-domain, may function as a co-chaperone to recruit Hsp70-like activity to s

  7. Sequence Classification: 892754 [

    Lifescience Database Archive (English)

    Full Text Available Non-TMB TMH Non-TMB Non-TMB Non-TMB Non-TMB >gi|6323393|ref|NP_013465.1| Putative phosphoesterase that funct...ions as a dosage-dependent positive regulator of the G1/S phase transition by contr

  8. Sequence Classification: 891115 [

    Lifescience Database Archive (English)

    Full Text Available involved in G1/S phase events such as bud site selection, bud emergence and cell cycle progression; similarity to Cup9p; Tos8p || http://www.ncbi.nlm.nih.gov/protein/6321342 ... ...omain-containing transcription factor; SBF regulated target gene that in turn regulates expression of genes

  9. Sequence Classification: 893259 [

    Lifescience Database Archive (English)

    Full Text Available required for ubiquitin-mediated protein degradation, forms complex with Cdc48p, plays a role in controlling cellular ubiquitin concen...tration; also promotes efficient NHEJ in postdiauxic/stationary phase; Doa1p || http://www.ncbi.nlm.nih.gov/protein/6322636 ...

  10. A vision for ubiquitous sequencing.

    Science.gov (United States)

    Erlich, Yaniv

    2015-10-01

    Genomics has recently celebrated reaching the $1000 genome milestone, making affordable DNA sequencing a reality. With this goal successfully completed, the next goal of the sequencing revolution can be sequencing sensors--miniaturized sequencing devices that are manufactured for real-time applications and deployed in large quantities at low costs. The first part of this manuscript envisions applications that will benefit from moving the sequencers to the samples in a range of domains. In the second part, the manuscript outlines the critical barriers that need to be addressed in order to reach the goal of ubiquitous sequencing sensors.

  11. Psychoacoustic Properties of Fibonacci Sequences

    Directory of Open Access Journals (Sweden)

    J. Sokoll

    2008-01-01

    Full Text Available 1202, Fibonacci set up one of the most interesting sequences in number theory. This sequence can be represented by so-called Fibonacci Numbers, and by a binary sequence of zeros and ones. If such a binary Fibonacci Sequence is played back as an audio file, a very dissonant sound results. This is caused by the “almost-periodic”, “self-similar” property of the binary sequence. The ratio of zeros and ones converges to the golden ratio, as do the primary and secondary spectral components intheir frequencies and amplitudes. These Fibonacci Sequences will be characterized using listening tests and psychoacoustic analyses. 

  12. Infinite sequences and series

    CERN Document Server

    Knopp, Konrad

    1956-01-01

    One of the finest expositors in the field of modern mathematics, Dr. Konrad Knopp here concentrates on a topic that is of particular interest to 20th-century mathematicians and students. He develops the theory of infinite sequences and series from its beginnings to a point where the reader will be in a position to investigate more advanced stages on his own. The foundations of the theory are therefore presented with special care, while the developmental aspects are limited by the scope and purpose of the book. All definitions are clearly stated; all theorems are proved with enough detail to ma

  13. Statistical mechanics of secondary structures formed by random RNA sequences.

    Science.gov (United States)

    Bundschuh, R; Hwa, T

    2002-03-01

    The formation of secondary structures by a random RNA sequence is studied as a model system for the sequence-structure problem omnipresent in biopolymers. Several toy energy models are introduced to allow detailed analytical and numerical studies. First, a two-replica calculation is performed. By mapping the two-replica problem to the denaturation of a single homogeneous RNA molecule in six-dimensional embedding space, we show that sequence disorder is perturbatively irrelevant, i.e., an RNA molecule with weak sequence disorder is in a molten phase where many secondary structures with comparable total energy coexist. A numerical study of various models at high temperature reproduces behaviors characteristic of the molten phase. On the other hand, a scaling argument based on the external statistics of rare regions can be constructed to show that the low-temperature phase is unstable to sequence disorder. We performed a detailed numerical study of the low-temperature phase using the droplet theory as a guide, and characterized the statistics of large-scale, low-energy excitations of the secondary structures from the ground state structure. We find the excitation energy to grow very slowly (i.e., logarithmically) with the length scale of the excitation, suggesting the existence of a marginal glass phase. The transition between the low-temperature glass phase and the high-temperature molten phase is also characterized numerically. It is revealed by a change in the coefficient of the logarithmic excitation energy, from being disorder dominated to being entropy dominated.

  14. Next-Generation Sequencing Platforms

    Science.gov (United States)

    Mardis, Elaine R.

    2013-06-01

    Automated DNA sequencing instruments embody an elegant interplay among chemistry, engineering, software, and molecular biology and have built upon Sanger's founding discovery of dideoxynucleotide sequencing to perform once-unfathomable tasks. Combined with innovative physical mapping approaches that helped to establish long-range relationships between cloned stretches of genomic DNA, fluorescent DNA sequencers produced reference genome sequences for model organisms and for the reference human genome. New types of sequencing instruments that permit amazing acceleration of data-collection rates for DNA sequencing have been developed. The ability to generate genome-scale data sets is now transforming the nature of biological inquiry. Here, I provide an historical perspective of the field, focusing on the fundamental developments that predated the advent of next-generation sequencing instruments and providing information about how these instruments work, their application to biological research, and the newest types of sequencers that can extract data from single DNA molecules.

  15. Spaces of Ideal Convergent Sequences

    Directory of Open Access Journals (Sweden)

    M. Mursaleen

    2014-01-01

    Full Text Available In the present paper, we introduce some sequence spaces using ideal convergence and Musielak-Orlicz function ℳ=Mk. We also examine some topological properties of the resulting sequence spaces.

  16. Precipitation of Icosahedral Quasicrystalline Phase, R-phase and Laves Phase in Ferritic Alloys

    Institute of Scientific and Technical Information of China (English)

    Keisuke Yamamoto; Yoshisato Kimura; Yoshinao Mishima

    2004-01-01

    Ferritic heat resistant steels involving precipitation of intermetallic phases have drawn a growing interest for the enhancement of creep strength, while the brittleness of the intermetallic phases may lower the toughness of the alloy.Therefore, it is necessary to optimize the dispersion characteristics of the intermetallics phase through microstructural control to minimize the trade-off between the strength and toughness. The effects of α-Fe matrix substructures on the precipitation sequence, morphology, dispersion characteristics, and the stability of the intermetallic phases are investigated in Fe-Cr-W-Co-Si system. The precipitates of the Si-free Fe-10Cr-1.4W-4.5Co (at%) alloy aged at 873K are the R-phase but those of the Si-added Fe-10Cr-1.4W-4.5Co-0.3Si (at%) alloy are the icosahedral quasicrystalline phase. The precipitates in both the Si-free and Si-added alloys aged at 973K are the Laves phase. Matrix of the alloys is controlled by heat treatments as to provide three types of matrix substructures; ferrite, ferrite/martensite mixture and martensite. The hardening behavior of the alloys depends on the matrix substructures and is independent of the kinds of precipitates. In the alloys with ferrite matrix, the peak of hardness during aging at 873K shifts to longer aging time in comparison with that in the alloys with lath martensite matrix which contain numbers of nucleation sites.

  17. Sequence Handling by Sequence Analysis Toolbox v1.0

    DEFF Research Database (Denmark)

    Ingrell, Christian Ravnsborg; Matthiesen, Rune; Jensen, Ole Nørregaard

    2006-01-01

    The fact that mass spectrometry have become a high-throughput method calls for bioinformatic tools for automated sequence handling and prediction. For efficient use of bioinformatic tools, it is important that these tools are integrated or interfaced with each other. The purpose of sequence...... analysis toolbox v1.0 was to have a general purpose sequence analyzing tool that can import sequences obtained by high-throughput sequencing methods. The program includes algorithms for calculation or prediction of isoelectric point, hydropathicity index, transmembrane segments, and glycosylphosphatidyl...

  18. The Galaxy End Sequence

    CERN Document Server

    Eales, Stephen; Smith, Matthew; Appah, Kiran; Ciesla, Laure; Duffield, Chris; Schofield, Simon

    2016-01-01

    A common assumption is that galaxies fall in two distinct regions on a plot of specific star-formation rate (SSFR) versus galaxy stellar mass: a star-forming Galaxy Main Sequence (GMS) and a separate region of `passive' or `red and dead galaxies'. Starting from a volume-limited sample of nearby galaxies designed to contain most of the stellar mass in this volume, and thus being a fair representation of the Universe at the end of 12 billion years of galaxy evolution, we investigate the distribution of galaxies in this diagram today. We show that galaxies follow a strongly curved extended GMS with a steep negative slope at high galaxy stellar masses. There is a gradual change in the morphologies of the galaxies along this distribution, but there is no clear break between early-type and late-type galaxies. Examining the other evidence that there are two distinct populations, we argue that the `red sequence' is the result of the colours of galaxies changing very little below a critical value of the SSFR, rather t...

  19. Rapid Polymer Sequencer

    Science.gov (United States)

    Stolc, Viktor (Inventor); Brock, Matthew W (Inventor)

    2013-01-01

    Method and system for rapid and accurate determination of each of a sequence of unknown polymer components, such as nucleic acid components. A self-assembling monolayer of a selected substance is optionally provided on an interior surface of a pipette tip, and the interior surface is immersed in a selected liquid. A selected electrical field is impressed in a longitudinal direction, or in a transverse direction, in the tip region, a polymer sequence is passed through the tip region, and a change in an electrical current signal is measured as each polymer component passes through the tip region. Each of the measured changes in electrical current signals is compared with a database of reference electrical change signals, with each reference signal corresponding to an identified polymer component, to identify the unknown polymer component with a reference polymer component. The nanopore preferably has a pore inner diameter of no more than about 40 nm and is prepared by heating and pulling a very small section of a glass tubing.

  20. Optimal filtering in multipulse sequences for nuclear quadrupole resonance detection

    Science.gov (United States)

    Osokin, D. Ya.; Khusnutdinov, R. R.; Mozzhukhin, G. V.; Rameev, B. Z.

    2014-05-01

    The application of the multipulse sequences in nuclear quadrupole resonance (NQR) detection of explosive and narcotic substances has been studied. Various approaches to increase the signal to noise ratio (SNR) of signal detection are considered. We discussed two modifications of the phase-alternated multiple-pulse sequence (PAMS): the 180° pulse sequence with a preparatory pulse and the 90° pulse sequence. The advantages of optimal filtering to detect NQR in the case of the coherent steady-state precession have been analyzed. It has been shown that this technique is effective in filtering high-frequency and low-frequency noise and increasing the reliability of NQR detection. Our analysis also shows the PAMS with 180° pulses is more effective than PSL sequence from point of view of the application of optimal filtering procedure to the steady-state NQR signal.

  1. Novel sequences propel familiar folds.

    Science.gov (United States)

    Jawad, Zahra; Paoli, Massimo

    2002-04-01

    Recent structure determinations have made new additions to a set of strikingly different sequences that give rise to the same topology. Proteins with a beta propeller fold are characterized by extreme sequence diversity despite the similarity in their three-dimensional structures. Several fold predictions, based in part on sequence repeats thought to match modular beta sheets, have been proved correct.

  2. Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria

    DEFF Research Database (Denmark)

    Larsen, Mette Voldby; Cosentino, Salvatore; Rasmussen, Simon

    2012-01-01

    Accurate strain identification is essential for anyone working with bacteria. For many species, multilocus sequence typing (MLST) is considered the "gold standard" of typing, but it is traditionally performed in an expensive and time-consuming manner. As the costs of whole-genome sequencing (WGS...... the MLST databases are downloaded monthly, and the best-matching MLST alleles of the specified MLST scheme are found using a BLAST-based ranking method. The sequence type is then determined by the combination of alleles identified. The method was tested on preassembled genomes from 336 isolates covering 56...... MLST schemes, on short sequence reads from 387 isolates covering 10 schemes, and on a small test set of short sequence reads from 29 isolates for which the sequence type had been determined by traditional methods. The method presented here enables investigators to determine the sequence types...

  3. 0,1 distribution in the highest level sequences of primitive sequences over Z2e

    Institute of Scientific and Technical Information of China (English)

    FAN; Shuqin(

    2003-01-01

    [1]Ward, M., The arithmetical theory of linear recurring sequences, Trans. Amer. Math. Soc, 1933, 35(6):600-628.[2]Dai Zongduo, Binary sequences derived from ML-sequences over rings I: Periods and minimal polynomials,Journal of Cryptology, 1992, 5: 193-207.[3]Dai, Z. D., Beth, T., Gollman, D., Lower bounds for the linear complexity of sequences over residue rings, Advances in Cryptology-Eurocrypt's 90, Spring-Verlag LNCS 19991, 473: 189-195.[4]Zeng Kencheng, Dai Zongduo, Huang Minqiang, Injectiveness of mappings from ring sequences to their sequences of the significant bits, Symposium on Theoretical Problems of Cryptology, State Key Laboratory of Information Security, Beijing, China, June 1995, 132-141.[5]Boztas, S., Hammons, A. R., Kumar, P. V., 4-phase sequences with near-optimum correlation properties, IEEE. Trans. Inform. Theory, 1992, 38: 1101-1113.[6]Kuzmin, A. S., Nechaev, A. A., A construction of noise stable codes using linear recurrents over Galois rings,Russian Math. Surveys, 1992, 47: 189-190.[7]Qi Wenfeng, Zhou Jinjun, Distribution of 0 and 1 in highest level of primitive sequences over Z2e, Science in China, Ser. A, 1997, 40(6): 606-611.[8]Qi Wenfeng, Zhou Jinjun, Distribution of 0 and 1 in highest level of primitive sequences over Z2e (Ц),Chinese Science Bulletin, 1998, 43(8): 633-635.[9]Zhu Fengxiang, Qi Wenfeng, Distribution of 0 and 1 in the highest level of primitive sequences over Z2e,Advances in Cryptology-CHINACRYPT' 2000, Beijing: Science Press, 2000, 1-5.[10]Kamlovski, O. V., Kuzmin, A. S., Distribution of elements on cycles of linear recurrents sequences over Galois rings, Russian Math. Surveys, 1998, 53(2): 392-393.[11]Kumar, P. V., Helleseth, T., Calderbank, A. R., An upper bound for Weil exponential sums over Galois rings and applications, IEEE. Trans. Infor. Theory, 1995, 41:456-468.

  4. Research of Hybrid Three-phase equilibrium Technology

    Science.gov (United States)

    Xu, K.; Liu, Z. Z.; Qi, G. Z.; Hou, Y. J.

    2016-08-01

    This paper puts forward a kind of managerial method based on the combination of PPF (passive power filter) and APF (active power filter) for the problem of three-phase current balance in three-phase four-wire system. This method uses two special reactors to filter zero- sequence current and uses APF to filter negative-sequence fundamental current, positive- sequence and negative-sequence harmonic current. It is more effective, reliable and economic. This paper proves feasibility of the method by the simulation results.

  5. Reading sequence-directed computational nucleosome maps.

    Science.gov (United States)

    Nibhani, Reshma; Trifonov, Edward N

    2015-01-01

    Recently developed latest version of the sequence-directed single-base resolution nucleosome mapping reveals existence of strong nucleosomes and chromatin columnar structures (columns). Broad application of this simple technique for further studies of chromatin and chromosome structure requires some basic understanding as to how it works and what information it affords. The paper provides such an introduction to the method. The oscillating maps of singular nucleosomes, of short and long oligonucleosome columns, are explained, as well as maps of chromatin on satellite DNA and occurrences of counter-phase (antiparallel) nucleosome neighbors.

  6. Protein comparative sequence analysis and computer modeling.

    Science.gov (United States)

    Hambly, Brett D; Oakley, Cecily E; Fajer, Piotr G

    2008-01-01

    A problem frequently encountered by the biological scientist is the identification of a previously unknown gene or protein sequence, where there are few or no clues as to the biochemical function, ligand specificity, gene regulation, protein-protein interactions, tissue specificity, cellular localization, developmental phase of activity, or biological role. Through the process of bioinformatics there are now many approaches for predicting answers to at least some of these questions, often then allowing the design of more insightful experiments to characterize more definitively the new protein.

  7. RIKEN Integrated Sequence Analysis (RISA) System—384-Format Sequencing Pipeline with 384 Multicapillary Sequencer

    Science.gov (United States)

    Shibata, Kazuhiro; Itoh, Masayoshi; Aizawa, Katsunori; Nagaoka, Sumiharu; Sasaki, Nobuya; Carninci, Piero; Konno, Hideaki; Akiyama, Junichi; Nishi, Katsuo; Kitsunai, Tokuji; Tashiro, Hideo; Itoh, Mari; Sumi, Noriko; Ishii, Yoshiyuki; Nakamura, Shin; Hazama, Makoto; Nishine, Tsutomu; Harada, Akira; Yamamoto, Rintaro; Matsumoto, Hiroyuki; Sakaguchi, Sumito; Ikegami, Takashi; Kashiwagi, Katsuya; Fujiwake, Syuji; Inoue, Kouji; Togawa, Yoshiyuki; Izawa, Masaki; Ohara, Eiji; Watahiki, Masanori; Yoneda, Yuko; Ishikawa, Tomokazu; Ozawa, Kaori; Tanaka, Takumi; Matsuura, Shuji; Kawai, Jun; Okazaki, Yasushi; Muramatsu, Masami; Inoue, Yorinao; Kira, Akira; Hayashizaki, Yoshihide

    2000-01-01

    The RIKEN high-throughput 384-format sequencing pipeline (RISA system) including a 384-multicapillary sequencer (the so-called RISA sequencer) was developed for the RIKEN mouse encyclopedia project. The RISA system consists of colony picking, template preparation, sequencing reaction, and the sequencing process. A novel high-throughput 384-format capillary sequencer system (RISA sequencer system) was developed for the sequencing process. This system consists of a 384-multicapillary auto sequencer (RISA sequencer), a 384-multicapillary array assembler (CAS), and a 384-multicapillary casting device. The RISA sequencer can simultaneously analyze 384 independent sequencing products. The optical system is a scanning system chosen after careful comparison with an image detection system for the simultaneous detection of the 384-capillary array. This scanning system can be used with any fluorescent-labeled sequencing reaction (chain termination reaction), including transcriptional sequencing based on RNA polymerase, which was originally developed by us, and cycle sequencing based on thermostable DNA polymerase. For long-read sequencing, 380 out of 384 sequences (99.2%) were successfully analyzed and the average read length, with more than 99% accuracy, was 654.4 bp. A single RISA sequencer can analyze 216 kb with >99% accuracy in 2.7 h (90 kb/h). For short-read sequencing to cluster the 3′ end and 5′ end sequencing by reading 350 bp, 384 samples can be analyzed in 1.5 h. We have also developed a RISA inoculator, RISA filtrator and densitometer, RISA plasmid preparator which can handle throughput of 40,000 samples in 17.5 h, and a high-throughput RISA thermal cycler which has four 384-well sites. The combination of these technologies allowed us to construct the RISA system consisting of 16 RISA sequencers, which can process 50,000 DNA samples per day. One haploid genome shotgun sequence of a higher organism, such as human, mouse, rat, domestic animals, and plants, can

  8. RIKEN integrated sequence analysis (RISA) system--384-format sequencing pipeline with 384 multicapillary sequencer.

    Science.gov (United States)

    Shibata, K; Itoh, M; Aizawa, K; Nagaoka, S; Sasaki, N; Carninci, P; Konno, H; Akiyama, J; Nishi, K; Kitsunai, T; Tashiro, H; Itoh, M; Sumi, N; Ishii, Y; Nakamura, S; Hazama, M; Nishine, T; Harada, A; Yamamoto, R; Matsumoto, H; Sakaguchi, S; Ikegami, T; Kashiwagi, K; Fujiwake, S; Inoue, K; Togawa, Y

    2000-11-01

    The RIKEN high-throughput 384-format sequencing pipeline (RISA system) including a 384-multicapillary sequencer (the so-called RISA sequencer) was developed for the RIKEN mouse encyclopedia project. The RISA system consists of colony picking, template preparation, sequencing reaction, and the sequencing process. A novel high-throughput 384-format capillary sequencer system (RISA sequencer system) was developed for the sequencing process. This system consists of a 384-multicapillary auto sequencer (RISA sequencer), a 384-multicapillary array assembler (CAS), and a 384-multicapillary casting device. The RISA sequencer can simultaneously analyze 384 independent sequencing products. The optical system is a scanning system chosen after careful comparison with an image detection system for the simultaneous detection of the 384-capillary array. This scanning system can be used with any fluorescent-labeled sequencing reaction (chain termination reaction), including transcriptional sequencing based on RNA polymerase, which was originally developed by us, and cycle sequencing based on thermostable DNA polymerase. For long-read sequencing, 380 out of 384 sequences (99.2%) were successfully analyzed and the average read length, with more than 99% accuracy, was 654.4 bp. A single RISA sequencer can analyze 216 kb with >99% accuracy in 2.7 h (90 kb/h). For short-read sequencing to cluster the 3' end and 5' end sequencing by reading 350 bp, 384 samples can be analyzed in 1.5 h. We have also developed a RISA inoculator, RISA filtrator and densitometer, RISA plasmid preparator which can handle throughput of 40,000 samples in 17.5 h, and a high-throughput RISA thermal cycler which has four 384-well sites. The combination of these technologies allowed us to construct the RISA system consisting of 16 RISA sequencers, which can process 50,000 DNA samples per day. One haploid genome shotgun sequence of a higher organism, such as human, mouse, rat, domestic animals, and plants, can be

  9. 基于相空间重构的风电功率波动特性分析及其对预测误差影响%Volatility of Wind Power Sequence and Its Influence on Prediction Error Based on Phase Space Reconstruction

    Institute of Scientific and Technical Information of China (English)

    杨茂; 齐玥

    2015-01-01

    The accurate prediction of wind power is important to guarantee the security and stability of any power system containing a large contribution from wind energy. To improve the accuracy of predictions of wind power generation, many new prediction methods have emerged. However, the accuracy of wind power prediction is not only related to the prediction methods, but also associated with the volatility of wind power. Regardless of the method adopted, it is not possible to guarantee accurate and error-free prediction. The necessity of the volatility in the wind power sequence was explained. To depict the probability of the occurrence of a new volatility mode, based on phase space reconstruction, a recurrence plot, and the recurrence rate was proposed to qualitatively and quantitatively depict the volatility. The changing rules of the recurrence plot and recurrence rate at different spatial scales were discussed. Based on this, a method to analyze the relationship between the volatility of a wind power sequence and prediction error was established. Finally a fair method for evaluating predictions accuracy was provided based on the recurrence rate. The study further illustrates the effectiveness of the method.%精确的风电功率预测是保证含大规模风电电力系统安全稳定运行的重要基础.为提高风电功率预测精度,已开展了诸多研究,新的预测方法不断涌现.但任何方法都无法保证无差预报,究其原因,风电功率的预测精度不但和预测方法有关,还与风电功率波动特性有关.该文阐述了评价风电功率波动特性的必要性;在相空间重构基础上,利用递归图和递归率对风电功率时间序列波动特性分别进行了定性和定量的刻画,以表征风电功率波动新模态产生的机率;分析了不同空间尺度下递归率的变化规律,建立了分析风电功率时间序列波动特性与预测误差关系的方法,最后给出了利用递归率为风电场管理机构

  10. Musical Sequences in Comics

    Directory of Open Access Journals (Sweden)

    Kieron Michael Brown

    2013-11-01

    Full Text Available Critical attention paid to the media of music and comics has historically focused on parallels between the temporal rhythm and pacing of music and the implied rhythm and temporality of comics (Eisner 2008, Godek 2007. Recent attention has begun to focus on both comics’ potential to represent the character of music (Whitted 2011 and the effects of musical images and themes on comics’ narratology (Peters 2013.    I suggest that analyses of comics that combine the traditional interplay of image and word with the use of elements of musical notation are able to shed further light on each of these areas, via the connotations and conventions of symbols pulled exclusively from the realms of music, and their integration with the other elements of the page in sequence.

  11. Phases of Kaluza-Klein Black Holes

    DEFF Research Database (Denmark)

    Harmark, Troels; Obers, N. A.

    2005-01-01

    We review the latest progress in understanding the phase structure of static and neutral Kaluza-Klein black holes, i.e. static and neutral solutions of pure gravity with an event horizon that asymptote to a d-dimensional Minkowski-space times a circle. We start by reviewing the (mu,n) phase diagram...... and the split-up of the phase structure into solutions with an internal SO(d-1) symmetry and solutions with Kaluza-Klein bubbles. We then discuss the uniform black string, non-uniform black string and localized black hole phases, and how those three phases are connected, involving issues such as classical...... instability and horizon-topology changing transitions. Finally, we review the bubble-black hole sequences, their place in the phase structure and interesting aspects such as the continuously infinite non-uniqueness of solutions for a given mass and relative tension....

  12. Optimization of micropillar sequences for fluid flow sculpting

    Energy Technology Data Exchange (ETDEWEB)

    Stoecklein, Daniel; Ganapathysubramanian, Baskar [Department of Mechanical Engineering, Iowa State University, Ames, Iowa 50011 (United States); Wu, Chueh-Yu; Kim, Donghyuk; Di Carlo, Dino [Department of Bioengineering, University of California at Los Angeles, Los Angeles, California 90095 (United States)

    2016-01-15

    Inertial fluid flow deformation around pillars in a microchannel is a new method for controlling fluid flow. Sequences of pillars have been shown to produce a rich phase space with a wide variety of flow transformations. Previous work has successfully demonstrated manual design of pillar sequences to achieve desired transformations of the flow cross section, with experimental validation. However, such a method is not ideal for seeking out complex sculpted shapes as the search space quickly becomes too large for efficient manual discovery. We explore fast, automated optimization methods to solve this problem. We formulate the inertial flow physics in microchannels with different micropillar configurations as a set of state transition matrix operations. These state transition matrices are constructed from experimentally validated streamtraces for a fixed channel length per pillar. This facilitates modeling the effect of a sequence of micropillars as nested matrix-matrix products, which have very efficient numerical implementations. With this new forward model, arbitrary micropillar sequences can be rapidly simulated with various inlet configurations, allowing optimization routines quick access to a large search space. We integrate this framework with the genetic algorithm and showcase its applicability by designing micropillar sequences for various useful transformations. We computationally discover micropillar sequences for complex transformations that are substantially shorter than manually designed sequences. We also determine sequences for novel transformations that were difficult to manually design. Finally, we experimentally validate these computational designs by fabricating devices and comparing predictions with the results from confocal microscopy.

  13. Optimization of micropillar sequences for fluid flow sculpting

    Science.gov (United States)

    Stoecklein, Daniel; Wu, Chueh-Yu; Kim, Donghyuk; Di Carlo, Dino; Ganapathysubramanian, Baskar

    2016-01-01

    Inertial fluid flow deformation around pillars in a microchannel is a new method for controlling fluid flow. Sequences of pillars have been shown to produce a rich phase space with a wide variety of flow transformations. Previous work has successfully demonstrated manual design of pillar sequences to achieve desired transformations of the flow cross section, with experimental validation. However, such a method is not ideal for seeking out complex sculpted shapes as the search space quickly becomes too large for efficient manual discovery. We explore fast, automated optimization methods to solve this problem. We formulate the inertial flow physics in microchannels with different micropillar configurations as a set of state transition matrix operations. These state transition matrices are constructed from experimentally validated streamtraces for a fixed channel length per pillar. This facilitates modeling the effect of a sequence of micropillars as nested matrix-matrix products, which have very efficient numerical implementations. With this new forward model, arbitrary micropillar sequences can be rapidly simulated with various inlet configurations, allowing optimization routines quick access to a large search space. We integrate this framework with the genetic algorithm and showcase its applicability by designing micropillar sequences for various useful transformations. We computationally discover micropillar sequences for complex transformations that are substantially shorter than manually designed sequences. We also determine sequences for novel transformations that were difficult to manually design. Finally, we experimentally validate these computational designs by fabricating devices and comparing predictions with the results from confocal microscopy.

  14. 40 CFR 86.1773-99 - Test sequence; general requirements.

    Science.gov (United States)

    2010-07-01

    ... required for fuel-flexible and dual-fuel vehicles when operating on gasoline. Natural gas, hybrid electric and diesel-fueled vehicles shall also be exempt from 50 °F testing. (3) The following schedule... vehicle shall be approximately level during all phases of the test sequence to prevent abnormal fuel...

  15. Pulse Sequence Shaper For Radiospectroscopy And Relaxation Methods In NQR

    Directory of Open Access Journals (Sweden)

    Bobalo Yuriy

    2015-09-01

    Full Text Available A pulse sequence shaper for the pursuance of the research using a wide spectrum of radiospectroscopy and relaxation methods in NQR is proposed. The distinctive feature of this product is its implementation with the application of a multi-functional programmable frequency synthesizer suitable for high-speed amplitude and phase manipulations.

  16. Mixed phases during the phase transitions

    CERN Document Server

    Tatsumi, Toshitaka; Maruyama, Toshiki

    2011-01-01

    Quest for a new form of matter inside compact stars compels us to examine the thermodynamical properties of the phase transitions. We closely consider the first-order phase transitions and the phase equilibrium on the basis of the Gibbs conditions, taking the liquid-gas phase transition in asymmetric nuclear matter as an example. Characteristic features of the mixed phase are figured out by solving the coupled equations for mean-fields and densities of constituent particles self-consistently within the Thomas-Fermi approximation. The mixed phase is inhomogeneous matter composed of two phases in equilibrium; it takes a crystalline structure with a unit of various geometrical shapes, inside of which one phase with a characteristic shape, called "pasta", is embedded in another phase by some volume fraction. This framework enables us to properly take into account the Coulomb interaction and the interface energy, and thereby sometimes we see the mechanical instability of the geometric structures of the mixed phase...

  17. Graphene nanodevices for DNA sequencing

    Science.gov (United States)

    Heerema, Stephanie J.; Dekker, Cees

    2016-02-01

    Fast, cheap, and reliable DNA sequencing could be one of the most disruptive innovations of this decade, as it will pave the way for personalized medicine. In pursuit of such technology, a variety of nanotechnology-based approaches have been explored and established, including sequencing with nanopores. Owing to its unique structure and properties, graphene provides interesting opportunities for the development of a new sequencing technology. In recent years, a wide range of creative ideas for graphene sequencers have been theoretically proposed and the first experimental demonstrations have begun to appear. Here, we review the different approaches to using graphene nanodevices for DNA sequencing, which involve DNA passing through graphene nanopores, nanogaps, and nanoribbons, and the physisorption of DNA on graphene nanostructures. We discuss the advantages and problems of each of these key techniques, and provide a perspective on the use of graphene in future DNA sequencing technology.

  18. Endocrine pancreatic tumours: which are the most useful MRI sequences?

    Energy Technology Data Exchange (ETDEWEB)

    Caramella, C.; Dromain, C; Baere, T. de; Boulet, B.; Schlumberger, M.; Ducreux, M.; Baudin, E. [Institut Gustave-Roussy, Department of Radiology, Villejuif Cedex (France)

    2010-11-15

    To determine magnetic resonance imaging (MRI) signal and enhancement characteristics of endocrine pancreatic tumours (ETPs) and which MR sequences show them most consistently. Fifty-five consecutive patients with 68 ETPs underwent 1.5-T abdominal MRI comprising T2-weighted, unenhanced T1-weighted and dynamic T1-weighted after injection of gadopentetate dimeglumine sequences. Twenty-one patients underwent diffusion-weighted imaging (DWI). Two radiologists identified the number, location, size, signal and enhancement patterns of ETPs, and determined a confidence scale indicating the presence of tumours on DWI. The results were compared with echo-endoscopy (endoscopic ultrasound) findings. The detection sensitivity was 95%, similar to that of echo-endoscopy. T2-weighted and T1-weighted sequences at the arterial phase had the highest contrast-to-noise ratio (CNR) median value. On DWI, the mean sensitivity was 65%. The mean apparent diffusion coefficient (ADC) value of ETP was significantly lower than in the normal parenchyma. In suspected ETP, MRI is a sensitive method, similar to echo-endoscopy and could be recommended as the first imaging technique. T2-weighted sequences and T1-weighted sequences in the arterial phase are the optimal pulse sequences. The quantitative assessment of ADC values is a promising tool for the characterisation of pancreatic lesions. (orig.)

  19. Code domains in tandem repetitive DNA sequence structures.

    Science.gov (United States)

    Vogt, P

    1992-10-01

    Traditionally, many people doing research in molecular biology attribute coding properties to a given DNA sequence if this sequence contains an open reading frame for translation into a sequence of amino acids. This protein coding capability of DNA was detected about 30 years ago. The underlying genetic code is highly conserved and present in every biological species studied so far. Today, it is obvious that DNA has a much larger coding potential for other important tasks. Apart from coding for specific RNA molecules such as rRNA, snRNA and tRNA molecules, specific structural and sequence patterns of the DNA chain itself express distinct codes for the regulation and expression of its genetic activity. A chromatin code has been defined for phasing of the histone-octamer protein complex in the nucleosome. A translation frame code has been shown to exist that determines correct triplet counting at the ribosome during protein synthesis. A loop code seems to organize the single stranded interaction of the nascent RNA chain with proteins during the splicing process, and a splicing code phases successive 5' and 3' splicing sites. Most of these DNA codes are not exclusively based on the primary DNA sequence itself, but also seem to include specific features of the corresponding higher order structures. Based on the view that these various DNA codes are genetically instructive for specific molecular interactions or processes, important in the nucleus during interphase and during cell division, the coding capability of tandem repetitive DNA sequences has recently been reconsidered.

  20. Short sequence motifs, overrepresented in mammalian conservednon-coding sequences

    Energy Technology Data Exchange (ETDEWEB)

    Minovitsky, Simon; Stegmaier, Philip; Kel, Alexander; Kondrashov,Alexey S.; Dubchak, Inna

    2007-02-21

    Background: A substantial fraction of non-coding DNAsequences of multicellular eukaryotes is under selective constraint. Inparticular, ~;5 percent of the human genome consists of conservednon-coding sequences (CNSs). CNSs differ from other genomic sequences intheir nucleotide composition and must play important functional roles,which mostly remain obscure.Results: We investigated relative abundancesof short sequence motifs in all human CNSs present in the human/mousewhole-genome alignments vs. three background sets of sequences: (i)weakly conserved or unconserved non-coding sequences (non-CNSs); (ii)near-promoter sequences (located between nucleotides -500 and -1500,relative to a start of transcription); and (iii) random sequences withthe same nucleotide composition as that of CNSs. When compared tonon-CNSs and near-promoter sequences, CNSs possess an excess of AT-richmotifs, often containing runs of identical nucleotides. In contrast, whencompared to random sequences, CNSs contain an excess of GC-rich motifswhich, however, lack CpG dinucleotides. Thus, abundance of short sequencemotifs in human CNSs, taken as a whole, is mostly determined by theiroverall compositional properties and not by overrepresentation of anyspecific short motifs. These properties are: (i) high AT-content of CNSs,(ii) a tendency, probably due to context-dependent mutation, of A's andT's to clump, (iii) presence of short GC-rich regions, and (iv) avoidanceof CpG contexts, due to their hypermutability. Only a small number ofshort motifs, overrepresented in all human CNSs are similar to bindingsites of transcription factors from the FOX family.Conclusion: Human CNSsas a whole appear to be too broad a class of sequences to possess strongfootprints of any short sequence-specific functions. Such footprintsshould be studied at the level of functional subclasses of CNSs, such asthose which flank genes with a particular pattern of expression. Overallproperties of CNSs are affected by

  1. Nonlinear analysis of biological sequences

    Energy Technology Data Exchange (ETDEWEB)

    Torney, D.C.; Bruno, W.; Detours, V. [and others

    1998-11-01

    This is the final report of a three-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). The main objectives of this project involved deriving new capabilities for analyzing biological sequences. The authors focused on tabulating the statistical properties exhibited by Human coding DNA sequences and on techniques of inferring the phylogenetic relationships among protein sequences related by descent.

  2. Biosensors for DNA sequence detection

    Science.gov (United States)

    Vercoutere, Wenonah; Akeson, Mark

    2002-01-01

    DNA biosensors are being developed as alternatives to conventional DNA microarrays. These devices couple signal transduction directly to sequence recognition. Some of the most sensitive and functional technologies use fibre optics or electrochemical sensors in combination with DNA hybridization. In a shift from sequence recognition by hybridization, two emerging single-molecule techniques read sequence composition using zero-mode waveguides or electrical impedance in nanoscale pores.

  3. Blazar Sequence in Fermi Era

    Indian Academy of Sciences (India)

    Liang Chen

    2014-09-01

    In this paper, we review the latest research results on the topic of blazar sequence. It seems that the blazar sequence is phenomenally ruled out, while the theoretical blazar sequence still holds. We point out that black hole mass is a dominated parameter accounting for high-power-high-synchrotron-peaked and low-power-low-sychrotron-peaked blazars. Because most blazars have similar size of emission region, theoretical blazar sequence implies that the break of Spectral Energy Distribution (SED) is a cooling break in nature.

  4. ABS: Sequence alignment by scanning

    KAUST Repository

    Bonny, Mohamed Talal

    2011-08-01

    Sequence alignment is an essential tool in almost any computational biology research. It processes large database sequences and considered to be high consumers of computation time. Heuristic algorithms are used to get approximate but fast results. We introduce fast alignment algorithm, called Alignment By Scanning (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the well-known alignment algorithms, the FASTA (which is heuristic) and the \\'Needleman-Wunsch\\' (which is optimal). The proposed algorithm achieves up to 76% enhancement in alignment score when it is compared with the FASTA Algorithm. The evaluations are conducted using different lengths of DNA sequences. © 2011 IEEE.

  5. Assembly sequencing with toleranced parts

    Energy Technology Data Exchange (ETDEWEB)

    Latombe, J.C. [Stanford Univ., CA (United States). Robotics Lab.; Wilson, R.H. [Sandia National Labs., Albuquerque, NM (United States). Intelligent Systems and Robotics Center

    1995-02-21

    The goal of assembly sequencing is to plan a feasible series of operations to construct a product from its individual parts. Previous research has thoroughly investigated assembly sequencing under the assumption that parts have nominal geometry. This paper considers the case where parts have toleranced geometry. Its main contribution is an efficient procedure that decides if a product admits an assembly sequence with infinite translations that is feasible for all possible instances of the components within the specified tolerances. If the product admits one such sequence, the procedure can also generate it. For the cases where there exists no such assembly sequence, another procedure is proposed which generates assembly sequences that are feasible only for some values of the toleranced dimensions. If this procedure produces no such sequence, then no instance of the product is assemblable. Finally, this paper analyzes the relation between assembly and disassembly sequences in the presence of toleranced parts. This work assumes a simple, but non-trivial tolerance language that falls short of capturing all imperfections of a manufacturing process. Hence, it is only one step toward assembly sequencing with toleranced parts.

  6. The ontology of biological sequences

    Directory of Open Access Journals (Sweden)

    Kelso Janet

    2009-11-01

    Full Text Available Abstract Background Biological sequences play a major role in molecular and computational biology. They are studied as information-bearing entities that make up DNA, RNA or proteins. The Sequence Ontology, which is part of the OBO Foundry, contains descriptions and definitions of sequences and their properties. Yet the most basic question about sequences remains unanswered: what kind of entity is a biological sequence? An answer to this question benefits formal ontologies that use the notion of biological sequences and analyses in computational biology alike. Results We provide both an ontological analysis of biological sequences and a formal representation that can be used in knowledge-based applications and other ontologies. We distinguish three distinct kinds of entities that can be referred to as "biological sequence": chains of molecules, syntactic representations such as those in biological databases, and the abstract information-bearing entities. For use in knowledge-based applications and inclusion in biomedical ontologies, we implemented the developed axiom system for use in automated theorem proving. Conclusion Axioms are necessary to achieve the main goal of ontologies: to formally specify the meaning of terms used within a domain. The axiom system for the ontology of biological sequences is the first elaborate axiom system for an OBO Foundry ontology and can serve as starting point for the development of more formal ontologies and ultimately of knowledge-based applications.

  7. Fast global sequence alignment technique

    KAUST Repository

    Bonny, Mohamed Talal

    2011-11-01

    Bioinformatics database is growing exponentially in size. Processing these large amount of data may take hours of time even if super computers are used. One of the most important processing tool in Bioinformatics is sequence alignment. We introduce fast alignment algorithm, called \\'Alignment By Scanning\\' (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the wellknown sequence alignment algorithms, the \\'GAP\\' (which is heuristic) and the \\'Needleman-Wunsch\\' (which is optimal). The proposed algorithm achieves up to 51% enhancement in alignment score when it is compared with the GAP Algorithm. The evaluations are conducted using different lengths of DNA sequences. © 2011 IEEE.

  8. Revised sequence components power system models for unbalanced power system studies

    Energy Technology Data Exchange (ETDEWEB)

    Abdel-Akher, M. [Tunku Abdul Rahman Univ., Kuala Lumpur (Malaysia); Nor, K.-M. [Univ. of Technology Malaysia, Johor (Malaysia); Rashid, A.H.A. [Univ. of Malaya, Kuala Lumpur (Malaysia)

    2007-07-01

    The principle method of analysis using positive, negative, and zero-sequence networks has been used to examine the balanced power system under both balanced and unbalanced loading conditions. The significant advantage of the sequence networks is that the sequence networks become entirely uncoupled in the case of balanced three-phase power systems. The uncoupled sequence networks then can be solved in independent way such as in fault calculation programs. However, the hypothesis of balanced power systems cannot be considered in many cases due to untransposed transmission lines; multiphase line segments in a distribution power system; or transformer phase shifts which cannot be incorporated in the existing models. A revised sequence decoupled power system models for analyzing unbalanced power systems based on symmetrical networks was presented in this paper. These models included synchronous machines, transformers, transmission lines, and voltage regulators. The models were derived from their counterpart's models in phase coordinates frame of reference. In these models, the three sequence networks were fully decoupled with a three-phase coordinates features such as transformer phase shifts and transmission line coupling. The proposed models were used to develop an unbalanced power-flow program for analyzing both balanced and unbalanced networks. The power flow solution was identical to results obtained from a full phase coordinate three-phase power-flow program. 11 refs., 3 tabs.

  9. Sequence Algebra, Sequence Decision Diagrams and Dynamic Fault Trees

    Energy Technology Data Exchange (ETDEWEB)

    Rauzy, Antoine B., E-mail: Antoine.Rauzy@lix.polytechnique.f [LIX-CNRS, Computer Science, Ecole Polytechnique, 91128 Palaiseau Cedex (France)

    2011-07-15

    A large attention has been focused on the Dynamic Fault Trees in the past few years. By adding new gates to static (regular) Fault Trees, Dynamic Fault Trees aim to take into account dependencies among events. Merle et al. proposed recently an algebraic framework to give a formal interpretation to these gates. In this article, we extend Merle et al.'s work by adopting a slightly different perspective. We introduce Sequence Algebras that can be seen as Algebras of Basic Events, representing failures of non-repairable components. We show how to interpret Dynamic Fault Trees within this framework. Finally, we propose a new data structure to encode sets of sequences of Basic Events: Sequence Decision Diagrams. Sequence Decision Diagrams are very much inspired from Minato's Zero-Suppressed Binary Decision Diagrams. We show that all operations of Sequence Algebras can be performed on this data structure.

  10. Statistical approaches to use a model organism for regulatory sequences annotation of newly sequenced species.

    Directory of Open Access Journals (Sweden)

    Pietro Liò

    Full Text Available A major goal of bioinformatics is the characterization of transcription factors and the transcriptional programs they regulate. Given the speed of genome sequencing, we would like to quickly annotate regulatory sequences in newly-sequenced genomes. In such cases, it would be helpful to predict sequence motifs by using experimental data from closely related model organism. Here we present a general algorithm that allow to identify transcription factor binding sites in one newly sequenced species by performing Bayesian regression on the annotated species. First we set the rationale of our method by applying it within the same species, then we extend it to use data available in closely related species. Finally, we generalise the method to handle the case when a certain number of experiments, from several species close to the species on which to make inference, are available. In order to show the performance of the method, we analyse three functionally related networks in the Ascomycota. Two gene network case studies are related to the G2/M phase of the Ascomycota cell cycle; the third is related to morphogenesis. We also compared the method with MatrixReduce and discuss other types of validation and tests. The first network is well known and provides a biological validation test of the method. The two cell cycle case studies, where the gene network size is conserved, demonstrate an effective utility in annotating new species sequences using all the available replicas from model species. The third case, where the gene network size varies among species, shows that the combination of information is less powerful but is still informative. Our methodology is quite general and could be extended to integrate other high-throughput data from model organisms.

  11. Three-Distance Sequences with Three Symbols

    OpenAIRE

    SAKAMOTO, Kuniko

    2003-01-01

    We will show that every $3$ dimensional cutting sequence is a three-distance sequence, and there are uncountable many periodic or aperiodic three-distance sequences (with $3$-symbols) which are not $3$ dimensional cutting sequences.

  12. NSIT: novel sequence identification tool.

    Directory of Open Access Journals (Sweden)

    Benjarath Pupacdi

    Full Text Available Novel sequences are DNA sequences present in an individual's genome but absent in the human reference assembly. They are predicted to be biologically important, both individual and population specific, and consistent with the known human migration paths. Recent works have shown that an average person harbors 2-5 Mb of such sequences and estimated that the human pan-genome contains as high as 19-40 Mb of novel sequences. To identify them in a de novo genome assembly, some existing sequence aligners have been used but no computational method has been specifically proposed for this task. In this work, we developed NSIT (Novel Sequence Identification Tool, a software that can accurately and efficiently identify novel sequences in an individual's de novo whole genome assembly. We identified and characterized 1.1 Mb, 1.2 Mb, and 1.0 Mb of novel sequences in NA18507 (African, YH (Asian, and NA12878 (European de novo genome assemblies, respectively. Our results show very high concordance with the previous work using the respective reference assembly. In addition, our results using the latest human reference assembly suggest that the amount of novel sequences per individual may not be as high as previously reported. We additionally developed a graphical viewer for comparisons of novel sequence contents. The viewer also helped in identifying sequence contamination; we found 130 kb of Epstein-Barr virus sequence in the previously published NA18507 novel sequences as well as 287 kb of zebrafish repeats in NA12878 de novo assembly. NSIT requires [Formula: see text]2GB of RAM and 1.5-2 hrs on a commodity desktop. The program is applicable to input assemblies with varying contig/scaffold sizes, ranging from 100 bp to as high as 50 Mb. It works in both 32-bit and 64-bit systems and outperforms, by large margins, other fast sequence aligners previously applied to this task. To our knowledge, NSIT is the first software designed specifically for novel sequence

  13. Haplotype-resolved genome sequencing of a Gujarati Indian individual.

    Science.gov (United States)

    Kitzman, Jacob O; Mackenzie, Alexandra P; Adey, Andrew; Hiatt, Joseph B; Patwardhan, Rupali P; Sudmant, Peter H; Ng, Sarah B; Alkan, Can; Qiu, Ruolan; Eichler, Evan E; Shendure, Jay

    2011-01-01

    Haplotype information is essential to the complete description and interpretation of genomes, genetic diversity and genetic ancestry. Although individual human genome sequencing is increasingly routine, nearly all such genomes are unresolved with respect to haplotype. Here we combine the throughput of massively parallel sequencing with the contiguity information provided by large-insert cloning to experimentally determine the haplotype-resolved genome of a South Asian individual. A single fosmid library was split into a modest number of pools, each providing ∼3% physical coverage of the diploid genome. Sequencing of each pool yielded reads overwhelmingly derived from only one homologous chromosome at any given location. These data were combined with whole-genome shotgun sequence to directly phase 94% of ascertained heterozygous single nucleotide polymorphisms (SNPs) into long haplotype blocks (N50 of 386 kilobases (kbp)). This method also facilitates the analysis of structural variation, for example, to anchor novel insertions to specific locations and haplotypes.

  14. HIV-1 quasispecies delineation by tag linkage deep sequencing.

    Science.gov (United States)

    Wu, Nicholas C; De La Cruz, Justin; Al-Mawsawi, Laith Q; Olson, C Anders; Qi, Hangfei; Luan, Harding H; Nguyen, Nguyen; Du, Yushen; Le, Shuai; Wu, Ting-Ting; Li, Xinmin; Lewis, Martha J; Yang, Otto O; Sun, Ren

    2014-01-01

    Trade-offs between throughput, read length, and error rates in high-throughput sequencing limit certain applications such as monitoring viral quasispecies. Here, we describe a molecular-based tag linkage method that allows assemblage of short sequence reads into long DNA fragments. It enables haplotype phasing with high accuracy and sensitivity to interrogate individual viral sequences in a quasispecies. This approach is demonstrated to deduce ∼ 2000 unique 1.3 kb viral sequences from HIV-1 quasispecies in vivo and after passaging ex vivo with a detection limit of ∼ 0.005% to ∼ 0.001%. Reproducibility of the method is validated quantitatively and qualitatively by a technical replicate. This approach can improve monitoring of the genetic architecture and evolution dynamics in any quasispecies population.

  15. Post-Main Sequence Evolution of Debris Discs

    CERN Document Server

    Bonsor, Amy

    2010-01-01

    The population of debris discs on the main sequence is well constrained, however very little is known about debris discs around evolved stars. In this work we provide a theoretical framework that considers the effects of stellar evolution on debris discs; firstly considering the evolution of an individual disc from the main sequence through to the white dwarf phase, then extending this to the known population of debris discs around main sequence A stars. It is found that discs around evolved stars are harder to detect than on the main sequence. In the context of our models discs should be detectable with Herschel or Alma on the giant branch, subject to the uncertain effect of sublimation on the discs. The best chances are for hot young white dwarfs, fitting nicely with the observations e.g the helix nebula (Su et al. 2007) and 9 systems presented by Chu & Bilikova.

  16. Phase shifting in the spatial frequency domain

    Science.gov (United States)

    Yazdani, Roghayeh; Petsch, Sebastian; Fallah, Hamidreza; Hajimahmoodzadeh, Morteza; Zappe, Hans

    2016-03-01

    We present a simple mathematical method for phase shifting that overcomes some phase shift errors and limitations of commonly used methods. The method is used to generate a sequence of phase-shifted interferograms from a single interferogram. The generated interferograms are employed to reconstruct the wavefront aberrations, as an application. The approach yields results with only very small deviations compared to both simulated wavefront aberrations, including the first 25 Zernike polynomials (0.05%) and those measured with a Shack-Hartmann sensor (0.5%).

  17. Zero-field nuclear magnetic resonance in high field by modulated rf sequences.

    Science.gov (United States)

    Nishiyama, Yusuke; Yamazaki, Toshio

    2007-04-07

    The authors propose a novel approach to design and evaluate sequences for zero-field NMR spectra in high field (ZFHF) by using amplitude and phase modulated rf sequences. ZFHF provide sharp peaks for the dipolar interaction between two nuclear spins even if the orientation of the molecules is distributed. The internuclear distance r can be directly obtained from the peak position which is proportional to r-3. Numerous ZFHF sequences are obtained. A sequence is selected from them by the systematic evaluation of the sequences. The new ZFHF sequence is less affected by chemical shift anisotropy (CSA) than the previous sequences; the sequence can be used for systems with large CSA such as a dipolar coupled 13C-pair system under realistically high field. 13C ZFHF spectra of 13C2 diammonium succinate and 13C2 diammonium oxalate were observed under the 9.4 T field.

  18. Liaison concatenation – A method to obtain feasible assembly sequences from 3D-CAD product

    Indian Academy of Sciences (India)

    M V A Raju Bahubalendruni; Bibhuti Bhusan Biswal

    2016-01-01

    Selection of optimized assembly sequence from the available feasible assembly sequences is significantly essential to achieve cost-effective manufacturing process. To achieve this, at the outset, generation of feasible assembly sequences with topological, geometrical, precedence and stability conditions should be generated. The increase of part count in a product results huge number of assembly sequences, the Liaison matrix/Liaison graph generated based on the connections between the assembly components eliminates nonpossible assembly sequences at the initial phase. There exist methods namely cut-set method to eliminate the non-possible assembly sequences using liaison graph. In this paper a new approach to eliminate the non-possible assembly sequences based on liaisons is described and the correctness of the methodology is illustrated with an example. The methodology to obtain the feasible assembly sequences is also briefly described and presented. An algorithm to interface with the CAD environment is described briefly.

  19. Phase diagram for the Eigen quasispecies theory with a truncated fitness landscape

    Science.gov (United States)

    Saakian, David B.; Biebricher, Christof K.; Hu, Chin-Kun

    2009-04-01

    Using methods of statistical physics, we present rigorous theoretical calculations of Eigen’s quasispecies theory with the truncated fitness landscape which dramatically limits the available sequence space of information carriers. As the mutation rate is increased from small values to large values, one can observe three phases: the first (I) selective (also known as ferromagnetic) phase, the second (II) intermediate phase with some residual order, and the third (III) completely randomized (also known as paramagnetic) phase. We calculate the phase diagram for these phases and the concentration of information carriers in the master sequence (also known as peak configuration) x0 and other classes of information carriers. As the phase point moves across the boundary between phase I and phase II, x0 changes continuously; as the phase point moves across the boundary between phase II and phase III, x0 has a large change. Our results are applicable for the general case of a fitness landscape.

  20. Sequence stratigraphy of the last filling phase of an intra continental rift: a model based on the Lower Barremian of the Reconcavo Basin; Estratigrafia de sequencias da fase final de preenchimento de um rifte intracontinental: um modelo com base no Barremiano Inferior da Bacia do Reconcavo

    Energy Technology Data Exchange (ETDEWEB)

    Santos, Clovis Francisco [PETROBRAS S.A., Campos dos Goytacases, RJ (Brazil). E e P.], E-mail: cfsantos@petrobras.com.br

    2005-05-15

    The sedimentary deposits of the Buracica Stage (Lower Barremian) of the Reconcavo Basin are characterized by a cyclic succession of fluvial, deltaic and lacustrine sediments, included in the Sao Sebastiao Formation. Outcrop, core and well log studies supported the proposal of a model that explains the architecture of the stratigraphic sequences and its subdivision in six third order sequences and twenty fourth order sequences. The lowstand lake-level systems tract (LLST) is characterized by a broad fluviodeltaic progradation, whereas the transgressive lake-level systems tract (TLST) is characterized by a retrogradational architecture, mainly in the distal areas of the basin. An aggradational pattern can occur in the proximal areas, where the sedimentation rate equals the rate of creation of accommodation space. The high stand lake level systems tract (HLST) is predominantly characterized by a lacustrine pelitic sedimentation, which is a continuation of the sedimentation of the TLST pelites. The broad deltaic progradation anticipated by the Sequence Stratigraphy for the high stand systems tract of the marine sequences does not apply to the studied interval. The forced-regression systems tract (FRST) is represented by thin sandstone beds. The identification of this systems tract is hard since its deposits can be easily eroded. In the proposed model, the sequence boundaries are erosive surfaces produced during falling lake-level periods, which are climatically controlled. The position of transgressive and maximum flooding surfaces are related to the rate of coarse-grained sediment influx, which is dependent upon the water influx. The sequences are deposited and preserved by the accommodation space created by subsidence. (author)

  1. MR phase imaging with bipolar acquisition.

    Science.gov (United States)

    Dagher, Joseph; Nael, Kambiz

    2017-04-01

    We have previously proposed a novel magnetic resonance (MR) phase imaging framework (MAGPI) based on a three-echo sequence that demonstrated substantial gains in phase signal-to-noise ratio (SNR). We improve upon the performance of MAGPI by extending the formulation to handle (i) an alternating gradient polarity (bipolar) readout scheme and (ii) an arbitrary number of echoes. We formulate the phase-imaging problem using maximum-likelihood (ML) estimation. The acquisition uses an optimized multi-echo gradient echo (MEGE) sequence. The tissue-phase estimation algorithm is a voxel-per-voxel approach, which requires no reference scans, no phase unwrapping and no spatial denoising. Unlike other methods, our bipolar readout model is general and does not make simplifying assumptions about the even-odd echo phase errors. The results show that (a) our proposed bipolar MAGPI approach improves on the phase SNR gains achieved with monopolar MAGPI and (b) the phase SNR converges with the number of echoes more rapidly with bipolar MAGPI. Importantly, bipolar MAGPI enables phase imaging in severely SNR-constrained scenarios, where monopolar MAGPI is unable to find solutions. The substantial phase SNR gains achieved with our framework are used here to (a) accelerate acquisitions (full brain 0.89 mm in-plane resolution in 2 min 30 sec) and (b) enable high-contrast high-resolution phase imaging (310 µm in-plane resolution) at clinical field strengths. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  2. Sequence to Medical Phenotypes: A Framework for Interpretation of Human Whole Genome DNA Sequence Data.

    Directory of Open Access Journals (Sweden)

    Frederick E Dewey

    2015-10-01

    Full Text Available High throughput sequencing has facilitated a precipitous drop in the cost of genomic sequencing, prompting predictions of a revolution in medicine via genetic personalization of diagnostic and therapeutic strategies. There are significant barriers to realizing this goal that are related to the difficult task of interpreting personal genetic variation. A comprehensive, widely accessible application for interpretation of whole genome sequence data is needed. Here, we present a series of methods for identification of genetic variants and genotypes with clinical associations, phasing genetic data and using Mendelian inheritance for quality control, and providing predictive genetic information about risk for rare disease phenotypes and response to pharmacological therapy in single individuals and father-mother-child trios. We demonstrate application of these methods for disease and drug response prognostication in whole genome sequence data from twelve unrelated adults, and for disease gene discovery in one father-mother-child trio with apparently simplex congenital ventricular arrhythmia. In doing so we identify clinically actionable inherited disease risk and drug response genotypes in pre-symptomatic individuals. We also nominate a new candidate gene in congenital arrhythmia, ATP2B4, and provide experimental evidence of a regulatory role for variants discovered using this framework.

  3. PERIODIC COMPLEMENTARY BINARY SEQUENCE PAIRS

    Institute of Scientific and Technical Information of China (English)

    XuChengqian; ZhaoXiaoqun

    2002-01-01

    A new set of binary sequences-Periodic Complementary Binary Sequence Pair (PCSP)is proposed .A new class of block design-Difference Family Pair (DFP)is also proposed .The relationship between PCSP and DFP,the properties and exising conditions of PCSP and the recursive constructions for PCSP are given.

  4. PERIODIC COMPLEMENTARY BINARY SEQUENCE PAIRS

    Institute of Scientific and Technical Information of China (English)

    Xu Chengqian; Zhao Xiaoqun

    2002-01-01

    A new set of binary sequences-Periodic Complementary Binary Sequence Pair (PCSP) is proposed. A new class of block design-Difference Family Pair (DFP) is also proposed.The relationship between PCSP and DFP, the properties and existing conditions of PCSP and the recursive constructions for PCSP are given.

  5. DNA Sequencing Sensors: An Overview

    Directory of Open Access Journals (Sweden)

    Jose Antonio Garrido-Cardenas

    2017-03-01

    Full Text Available The first sequencing of a complete genome was published forty years ago by the double Nobel Prize in Chemistry winner Frederick Sanger. That corresponded to the small sized genome of a bacteriophage, but since then there have been many complex organisms whose DNA have been sequenced. This was possible thanks to continuous advances in the fields of biochemistry and molecular genetics, but also in other areas such as nanotechnology and computing. Nowadays, sequencing sensors based on genetic material have little to do with those used by Sanger. The emergence of mass sequencing sensors, or new generation sequencing (NGS meant a quantitative leap both in the volume of genetic material that was able to be sequenced in each trial, as well as in the time per run and its cost. One can envisage that incoming technologies, already known as fourth generation sequencing, will continue to cheapen the trials by increasing DNA reading lengths in each run. All of this would be impossible without sensors and detection systems becoming smaller and more precise. This article provides a comprehensive overview on sensors for DNA sequencing developed within the last 40 years.

  6. Gambling strategies for random sequences

    OpenAIRE

    George Davie

    2010-01-01

    There is a general consensus that it is not possible to gamble successfully against a random se-quence. This consensus is based on results from probability theory that all gambling systems arein some sense futile and the idea that at any stage of the sequence, the next outcome is entirelyunpredictable.

  7. Sequence conserved for subcellular localization

    Science.gov (United States)

    Nair, Rajesh; Rost, Burkhard

    2002-01-01

    The more proteins diverged in sequence, the more difficult it becomes for bioinformatics to infer similarities of protein function and structure from sequence. The precise thresholds used in automated genome annotations depend on the particular aspect of protein function transferred by homology. Here, we presented the first large-scale analysis of the relation between sequence similarity and identity in subcellular localization. Three results stood out: (1) The subcellular compartment is generally more conserved than what might have been expected given that short sequence motifs like nuclear localization signals can alter the native compartment; (2) the sequence conservation of localization is similar between different compartments; and (3) it is similar to the conservation of structure and enzymatic activity. In particular, we found the transition between the regions of conserved and nonconserved localization to be very sharp, although the thresholds for conservation were less well defined than for structure and enzymatic activity. We found that a simple measure for sequence similarity accounting for pairwise sequence identity and alignment length, the HSSP distance, distinguished accurately between protein pairs of identical and different localizations. In fact, BLAST expectation values outperformed the HSSP distance only for alignments in the subtwilight zone. We succeeded in slightly improving the accuracy of inferring localization through homology by fine tuning the thresholds. Finally, we applied our results to the entire SWISS-PROT database and five entirely sequenced eukaryotes. PMID:12441382

  8. Bayesian analysis of binary sequences

    Science.gov (United States)

    Torney, David C.

    2005-03-01

    This manuscript details Bayesian methodology for "learning by example", with binary n-sequences encoding the objects under consideration. Priors prove influential; conformable priors are described. Laplace approximation of Bayes integrals yields posterior likelihoods for all n-sequences. This involves the optimization of a definite function over a convex domain--efficiently effectuated by the sequential application of the quadratic program.

  9. Chameleon sequences in neurodegenerative diseases

    Energy Technology Data Exchange (ETDEWEB)

    Bahramali, Golnaz [Institute of Biochemistry and Biophysics, University of Tehran, Tehran (Iran, Islamic Republic of); Goliaei, Bahram, E-mail: goliaei@ut.ac.ir [Institute of Biochemistry and Biophysics, University of Tehran, Tehran (Iran, Islamic Republic of); Minuchehr, Zarrin, E-mail: minuchehr@nigeb.ac.ir [Department of Systems Biotechnology, National Institute of Genetic Engineering and Biotechnology, (NIGEB), Tehran (Iran, Islamic Republic of); Salari, Ali [Department of Systems Biotechnology, National Institute of Genetic Engineering and Biotechnology, (NIGEB), Tehran (Iran, Islamic Republic of)

    2016-03-25

    Chameleon sequences can adopt either alpha helix sheet or a coil conformation. Defining chameleon sequences in PDB (Protein Data Bank) may yield to an insight on defining peptides and proteins responsible in neurodegeneration. In this research, we benefitted from the large PDB and performed a sequence analysis on Chameleons, where we developed an algorithm to extract peptide segments with identical sequences, but different structures. In order to find new chameleon sequences, we extracted a set of 8315 non-redundant protein sequences from the PDB with an identity less than 25%. Our data was classified to “helix to strand (HE)”, “helix to coil (HC)” and “strand to coil (CE)” alterations. We also analyzed the occurrence of singlet and doublet amino acids and the solvent accessibility in the chameleon sequences; we then sorted out the proteins with the most number of chameleon sequences and named them Chameleon Flexible Proteins (CFPs) in our dataset. Our data revealed that Gly, Val, Ile, Tyr and Phe, are the major amino acids in Chameleons. We also found that there are proteins such as Insulin Degrading Enzyme IDE and GTP-binding nuclear protein Ran (RAN) with the most number of chameleons (640 and 405 respectively). These proteins have known roles in neurodegenerative diseases. Therefore it can be inferred that other CFP's can serve as key proteins in neurodegeneration, and a study on them can shed light on curing and preventing neurodegenerative diseases.

  10. Generalisation of new sequence knowledge depends on response modality.

    Directory of Open Access Journals (Sweden)

    Clive R Rosenthal

    Full Text Available New visuomotor skills can guide behaviour in novel situations. Prior studies indicate that learning a visuospatial sequence via responses based on manual key presses leads to effector- and response-independent knowledge. Little is known, however, about the extent to which new sequence knowledge can generalise, and, thereby guide behaviour, outside of the manual response modality. Here, we examined whether learning a visuospatial sequence either via manual (key presses, without eye movements, oculomotor (obligatory eye movements, or perceptual (covert reorienting of visuospatial attention responses supported generalisation to direct and indirect tests administered either in the same (baseline conditions or a novel response modality (transfer conditions with respect to initial study. Direct tests measured the use of conscious knowledge about the studied sequence, whereas the indirect tests did not ostensibly draw on the study phase and measured response priming. Oculomotor learning supported the use of conscious knowledge on the manual direct tests, whereas manual learning supported generalisation to the oculomotor direct tests but did not support the conscious use of knowledge. Sequence knowledge acquired via perceptual responses did not generalise onto any of the manual tests. Manual, oculomotor, and perceptual sequence learning all supported generalisation in the baseline conditions. Notably, the manual baseline condition and the manual to oculomotor transfer condition differed in the magnitude of general skill acquired during the study phase; however, general skill did not predict performance on the post-study tests. The results demonstrated that generalisation was only affected by the responses used to initially code the visuospatial sequence when new knowledge was applied to a novel response modality. We interpret these results in terms of response-effect distinctiveness, the availability of integrated effector- and motor-plan based

  11. Phase contrast image synthesis

    DEFF Research Database (Denmark)

    Glückstad, J.

    1996-01-01

    A new method is presented for synthesizing arbitrary intensity patterns based on phase contrast imaging. The concept is grounded on an extension of the Zernike phase contrast method into the domain of full range [0; 2 pi] phase modulation. By controlling the average value of the input phase...... function and by choosing appropriate phase retardation at the phase contrast filter, a pure phase to intensity imaging is accomplished. The method presented is also directly applicable in dark field image synthesis....

  12. Rapid Diagnostics of Onboard Sequences

    Science.gov (United States)

    Starbird, Thomas W.; Morris, John R.; Shams, Khawaja S.; Maimone, Mark W.

    2012-01-01

    Keeping track of sequences onboard a spacecraft is challenging. When reviewing Event Verification Records (EVRs) of sequence executions on the Mars Exploration Rover (MER), operators often found themselves wondering which version of a named sequence the EVR corresponded to. The lack of this information drastically impacts the operators diagnostic capabilities as well as their situational awareness with respect to the commands the spacecraft has executed, since the EVRs do not provide argument values or explanatory comments. Having this information immediately available can be instrumental in diagnosing critical events and can significantly enhance the overall safety of the spacecraft. This software provides auditing capability that can eliminate that uncertainty while diagnosing critical conditions. Furthermore, the Restful interface provides a simple way for sequencing tools to automatically retrieve binary compiled sequence SCMFs (Space Command Message Files) on demand. It also enables developers to change the underlying database, while maintaining the same interface to the existing applications. The logging capabilities are also beneficial to operators when they are trying to recall how they solved a similar problem many days ago: this software enables automatic recovery of SCMF and RML (Robot Markup Language) sequence files directly from the command EVRs, eliminating the need for people to find and validate the corresponding sequences. To address the lack of auditing capability for sequences onboard a spacecraft during earlier missions, extensive logging support was added on the Mars Science Laboratory (MSL) sequencing server. This server is responsible for generating all MSL binary SCMFs from RML input sequences. The sequencing server logs every SCMF it generates into a MySQL database, as well as the high-level RML file and dictionary name inputs used to create the SCMF. The SCMF is then indexed by a hash value that is automatically included in all command

  13. Spatiotemporal correlations of aftershock sequences

    CERN Document Server

    Peixoto, Tiago P; Davidsen, Jörn

    2010-01-01

    Aftershock sequences are of particular interest in seismic research since they may condition seismic activity in a given region over long time spans. While they are typically identified with periods of enhanced seismic activity after a large earthquake as characterized by the Omori law, our knowledge of the spatiotemporal correlations between events in an aftershock sequence is limited. Here, we study the spatiotemporal correlations of two aftershock sequences form California (Parkfield and Hector Mine) using the recently introduced concept of "recurrent" events. We find that both sequences have very similar properties and that most of them are captured by the space-time epidemic-type aftershock sequence (ETAS) model if one takes into account catalog incompleteness. However, the stochastic model does not capture the spatiotemporal correlations leading to the observed structure of seismicity on small spatial scales.

  14. Quantum Exchangeable Sequences of Algebras

    CERN Document Server

    Curran, Stephen

    2008-01-01

    We extend the notion of quantum exchangeability, introduced by K\\"ostler and Speicher in arXiv:0807.0677, to sequences (\\rho_1,\\rho_2,...c) of homomorphisms from an algebra C into a noncommutative probability space (A,\\phi), and prove a free de Finetti theorem: an infinite quantum exchangeable sequence (\\rho_1,\\rho_2,...c) is freely independent and identically distributed with respect to a conditional expectation. As a corollary we obtain a free analogue of the Hewitt Savage zero-one law. As in the classical case, the theorem fails for finite sequences. We give a characterization of finite quantum exchangeable sequences, which can be viewed as a noncommutative analogue of sampling without replacement. We then give an approximation to how far a finite quantum exchangeable sequence is from being freely independent with amalgamation.

  15. PSSRdb: a relational database of polymorphic simple sequence repeats extracted from prokaryotic genomes

    OpenAIRE

    Kumar, Pankaj; Chaitanya, Pasumarthy S.; Nagarajaram, Hampapathalu A

    2010-01-01

    PSSRdb (Polymorphic Simple Sequence Repeats database) (http://www.cdfd.org.in/PSSRdb/) is a relational database of polymorphic simple sequence repeats (PSSRs) extracted from 85 different species of prokaryotes. Simple sequence repeats (SSRs) are the tandem repeats of nucleotide motifs of the sizes 1–6 bp and are highly polymorphic. SSR mutations in and around coding regions affect transcription and translation of genes. Such changes underpin phase variations and antigenic variations seen in s...

  16. Spectral-temporal encoding and decoding of the femtosecond pulses sequences with a THz repetition rate

    Science.gov (United States)

    Tcypkin, A. N.; Putilin, S. E.

    2017-01-01

    Experimental and numerical modeling techniques demonstrated the possibilities of the spectral-time encoding and decoding for time division multiplexing sequence of femtosecond subpulses with a repetition rate of up to 6.4 THz. The sequence was formed as a result of the interference of two phase-modulated pulses. We report the limits of the application of the developed method of controlling formed sequence at the spectral-temporal coding.

  17. Ossification sequence heterochrony among amphibians.

    Science.gov (United States)

    Harrington, Sean M; Harrison, Luke B; Sheil, Christopher A

    2013-01-01

    Heterochrony is an important mechanism in the evolution of amphibians. Although studies have centered on the relationship between size and shape and the rates of development, ossification sequence heterochrony also may have been important. Rigorous, phylogenetic methods for assessing sequence heterochrony are relatively new, and a comprehensive study of the relative timing of ossification of skeletal elements has not been used to identify instances of sequence heterochrony across Amphibia. In this study, a new version of the program Parsimov-based genetic inference (PGi) was used to identify shifts in ossification sequences across all extant orders of amphibians, for all major structural units of the skeleton. PGi identified a number of heterochronic sequence shifts in all analyses, the most interesting of which seem to be tied to differences in metamorphic patterns among major clades. Early ossification of the vomer, premaxilla, and dentary is retained by Apateon caducus and members of Gymnophiona and Urodela, which lack the strongly biphasic development seen in anurans. In contrast, bones associated with the jaws and face were identified as shifting late in the ancestor of Anura. The bones that do not shift late, and thereby occupy the earliest positions in the anuran cranial sequence, are those in regions of the skull that undergo the least restructuring throughout anuran metamorphosis. Additionally, within Anura, bones of the hind limb and pelvic girdle were also identified as shifting early in the sequence of ossification, which may be a result of functional constraints imposed by the drastic metamorphosis of most anurans.

  18. The consolidation of implicit sequence memory in obstructive sleep apnea.

    Directory of Open Access Journals (Sweden)

    Eszter Csabi

    Full Text Available Obstructive Sleep Apnea (OSA Syndrome is a relatively frequent sleep disorder characterized by disrupted sleep patterns. It is a well-established fact that sleep has beneficial effect on memory consolidation by enhancing neural plasticity. Implicit sequence learning is a prominent component of skill learning. However, the formation and consolidation of this fundamental learning mechanism remains poorly understood in OSA. In the present study we examined the consolidation of different aspects of implicit sequence learning in patients with OSA. We used the Alternating Serial Reaction Time task to measure general skill learning and sequence-specific learning. There were two sessions: a learning phase and a testing phase, separated by a 10-hour offline period with sleep. Our data showed differences in offline changes of general skill learning between the OSA and control group. The control group demonstrated offline improvement from evening to morning, while the OSA group did not. In contrast, we did not observe differences between the groups in offline changes in sequence-specific learning. Our findings suggest that disrupted sleep in OSA differently affects neural circuits involved in the consolidation of sequence learning.

  19. A Criterion for Regular Sequences

    Indian Academy of Sciences (India)

    D P Patil; U Storch; J Stückrad

    2004-05-01

    Let be a commutative noetherian ring and $f_1,\\ldots,f_r \\in R$. In this article we give (cf. the Theorem in $\\mathcal{x}$2) a criterion for $f_1,\\ldots,f_r$ to be regular sequence for a finitely generated module over which strengthens and generalises a result in [2]. As an immediate consequence we deduce that if $V(g_1,\\ldots,g_r) \\subseteq V(f_1,\\ldots,f_r)$ in Spec and if $f_1,\\ldots,f_r$ is a regular sequence in , then $g_1,\\ldots,g_r$ is also a regular sequence in .

  20. Weak disorder in Fibonacci sequences

    Energy Technology Data Exchange (ETDEWEB)

    Ben-Naim, E [Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); Krapivsky, P L [Department of Physics and Center for Molecular Cybernetics, Boston University, Boston, MA 02215 (United States)

    2006-05-19

    We study how weak disorder affects the growth of the Fibonacci series. We introduce a family of stochastic sequences that grow by the normal Fibonacci recursion with probability 1 - {epsilon}, but follow a different recursion rule with a small probability {epsilon}. We focus on the weak disorder limit and obtain the Lyapunov exponent that characterizes the typical growth of the sequence elements, using perturbation theory. The limiting distribution for the ratio of consecutive sequence elements is obtained as well. A number of variations to the basic Fibonacci recursion including shift, doubling and copying are considered. (letter to the editor)

  1. Microbial Dark Matter Phase II: Stepping deeper into unknown territory

    Energy Technology Data Exchange (ETDEWEB)

    Jarett, Jessica; Dunfield, Peter; Peura, Sari; Wielen, Paul van der; Hedlund, Brian; Elshahed, Mostafa; Kormas, Konstantinos; Stott, Andreas Teske8, Matt; Birkeland, Nils-Kare; Zhang, Chuanlun; Rengefors, Karin; Lindemann, Stephen; Ravin, Nikolai V.; Spear, John; Hallam, Steven; Crowe, Sean; Steele, Jillian; Goudeau, Danielle; Malmstrom, Rex; Kyrpides, Nikos; Stepanauskas, Ramunas; Woyke, Tanja

    2014-10-27

    Currently available microbial genomes are of limited phylogenetic breadth due to our historical inability to cultivate most microorganisms in the laboratory. The first phase of the Microbial Dark Matter project used single-cell genomics to sequence 201 single cells from uncultivated lineages, and was able to resolve new superphyla and reveal novel metabolic features in bacteria and archaea. However, many fundamental questions about the evolution and function of microbes remain unanswered, and many candidate phyla remain uncharacterized. Phase II of the Microbial Dark Matter project will target candidate phyla with no sequenced representatives at a variety of new sites using a combination of single-cell sequencing and shotgun metagenomics approaches.

  2. Industrial applications of multi-functional, multi-phase reactors

    NARCIS (Netherlands)

    Harmsen, G.J.; Chewter, L.A.

    1999-01-01

    To reveal trends in the design and operation of multi-functional, multi-phase reactors, this paper describes, in historical sequence, three industrial applications of multi-functional, multi-phase reactors developed and operated by Shell Chemicals during the last five decades. For each case, we desc

  3. Sequences of gluing bifurcations in an analog electronic circuit

    Energy Technology Data Exchange (ETDEWEB)

    Akhtanov, Sayat N.; Zhanabaev, Zeinulla Zh. [Physico-Technical Department, Al Farabi Kazakh National University, Al Farabi Av. 71, Almaty, 050038 Kazakhstan (Kazakhstan); Zaks, Michael A., E-mail: zaks@math.hu-berlin.de [Institute of Mathematics, Humboldt University, Rudower Chaussee 25, D-12489 Berlin (Germany)

    2013-10-01

    We report on the experimental investigation of gluing bifurcations in the analog electronic circuit which models a dynamical system of the third order: Lorenz equations with an additional quadratic nonlinearity. Variation of one of the resistances in the circuit changes the coefficient at this nonlinearity and replaces the Lorenz route to chaos by a different scenario which leads, through the sequence of homoclinic bifurcations, from periodic oscillations of the voltage to the irregular ones. Every single bifurcation “glues” in the phase space two stable periodic orbits and creates a new one, with the doubled length: a sequence of such bifurcations results in the birth of the chaotic attractor.

  4. Phase equilibrium engineering

    CERN Document Server

    Brignole, Esteban Alberto

    2013-01-01

    Traditionally, the teaching of phase equilibria emphasizes the relationships between the thermodynamic variables of each phase in equilibrium rather than its engineering applications. This book changes the focus from the use of thermodynamics relationships to compute phase equilibria to the design and control of the phase conditions that a process needs. Phase Equilibrium Engineering presents a systematic study and application of phase equilibrium tools to the development of chemical processes. The thermodynamic modeling of mixtures for process development, synthesis, simulation, design and

  5. Phase Statistics of Soliton

    OpenAIRE

    Ho, Keang-Po

    2003-01-01

    The characteristic function of soliton phase jitter is found analytically when the soliton is perturbed by amplifier noise. In additional to that from amplitude jitter, the nonlinear phase noise due to frequency and timing jitter is also analyzed. Because the nonlinear phase noise is not Gaussian distributed, the overall phase jitter is also non-Gaussian. For a fixed mean nonlinear phase shift, the contribution of nonlinear phase noise from frequency and timing jitter decreases with distance ...

  6. ISIS Individualized Support In Sequencing

    NARCIS (Netherlands)

    Drachsler, Hendrik; Hummel, Hans

    2007-01-01

    Drachsler, H., & Hummel, H. G. K. (2007). ISIS Individualized Support In Sequencing. Presentation given during the PIP meeting on March 22, 2007. Open University of the Netherlands: Heerlen, The Netherlands.

  7. Molecular beacon sequence design algorithm.

    Science.gov (United States)

    Monroe, W Todd; Haselton, Frederick R

    2003-01-01

    A method based on Web-based tools is presented to design optimally functioning molecular beacons. Molecular beacons, fluorogenic hybridization probes, are a powerful tool for the rapid and specific detection of a particular nucleic acid sequence. However, their synthesis costs can be considerable. Since molecular beacon performance is based on its sequence, it is imperative to rationally design an optimal sequence before synthesis. The algorithm presented here uses simple Microsoft Excel formulas and macros to rank candidate sequences. This analysis is carried out using mfold structural predictions along with other free Web-based tools. For smaller laboratories where molecular beacons are not the focus of research, the public domain algorithm described here may be usefully employed to aid in molecular beacon design.

  8. Classification of Base Sequences (+1,

    Directory of Open Access Journals (Sweden)

    Dragomir Ž. Ðoković

    2010-01-01

    Full Text Available Base sequences BS(+1, are quadruples of {±1}-sequences (;;;, with A and B of length +1 and C and D of length n, such that the sum of their nonperiodic autocor-relation functions is a -function. The base sequence conjecture, asserting that BS(+1, exist for all n, is stronger than the famous Hadamard matrix conjecture. We introduce a new definition of equivalence for base sequences BS(+1, and construct a canonical form. By using this canonical form, we have enumerated the equivalence classes of BS(+1, for ≤30. As the number of equivalence classes grows rapidly (but not monotonically with n, the tables in the paper cover only the cases ≤13.

  9. DNA Sequencing Using capillary Electrophoresis

    Energy Technology Data Exchange (ETDEWEB)

    Dr. Barry Karger

    2011-05-09

    The overall goal of this program was to develop capillary electrophoresis as the tool to be used to sequence for the first time the Human Genome. Our program was part of the Human Genome Project. In this work, we were highly successful and the replaceable polymer we developed, linear polyacrylamide, was used by the DOE sequencing lab in California to sequence a significant portion of the human genome using the MegaBase multiple capillary array electrophoresis instrument. In this final report, we summarize our efforts and success. We began our work by separating by capillary electrophoresis double strand oligonucleotides using cross-linked polyacrylamide gels in fused silica capillaries. This work showed the potential of the methodology. However, preparation of such cross-linked gel capillaries was difficult with poor reproducibility, and even more important, the columns were not very stable. We improved stability by using non-cross linked linear polyacrylamide. Here, the entangled linear chains could move when osmotic pressure (e.g. sample injection) was imposed on the polymer matrix. This relaxation of the polymer dissipated the stress in the column. Our next advance was to use significantly lower concentrations of the linear polyacrylamide that the polymer could be automatically blown out after each run and replaced with fresh linear polymer solution. In this way, a new column was available for each analytical run. Finally, while testing many linear polymers, we selected linear polyacrylamide as the best matrix as it was the most hydrophilic polymer available. Under our DOE program, we demonstrated initially the success of the linear polyacrylamide to separate double strand DNA. We note that the method is used even today to assay purity of double stranded DNA fragments. Our focus, of course, was on the separation of single stranded DNA for sequencing purposes. In one paper, we demonstrated the success of our approach in sequencing up to 500 bases. Other

  10. Pythagorean Triples from Harmonic Sequences.

    Science.gov (United States)

    DiDomenico, Angelo S.; Tanner, Randy J.

    2001-01-01

    Shows how all primitive Pythagorean triples can be generated from harmonic sequences. Use inductive and deductive reasoning to explore how Pythagorean triples are connected with another area of mathematics. (KHR)

  11. Overview of Sequence Data Formats.

    Science.gov (United States)

    Zhang, Hongen

    2016-01-01

    Next-generation sequencing experiment can generate billions of short reads for each sample and processing of the raw reads will add more information. Various file formats have been introduced/developed in order to store and manipulate this information. This chapter presents an overview of the file formats including FASTQ, FASTA, SAM/BAM, GFF/GTF, BED, and VCF that are commonly used in analysis of next-generation sequencing data.

  12. Structural Complexity of DNA Sequence

    Directory of Open Access Journals (Sweden)

    Cheng-Yuan Liou

    2013-01-01

    Full Text Available In modern bioinformatics, finding an efficient way to allocate sequence fragments with biological functions is an important issue. This paper presents a structural approach based on context-free grammars extracted from original DNA or protein sequences. This approach is radically different from all those statistical methods. Furthermore, this approach is compared with a topological entropy-based method for consistency and difference of the complexity results.

  13. Nanogrid rolling circle DNA sequencing

    Energy Technology Data Exchange (ETDEWEB)

    Church, George M.; Porreca, Gregory J.; Shendure, Jay; Rosenbaum, Abraham Meir

    2017-04-18

    The present invention relates to methods for sequencing a polynucleotide immobilized on an array having a plurality of specific regions each having a defined diameter size, including synthesizing a concatemer of a polynucleotide by rolling circle amplification, wherein the concatemer has a cross-sectional diameter greater than the diameter of a specific region, immobilizing the concatemer to the specific region to make an immobilized concatemer, and sequencing the immobilized concatemer.

  14. Replacement collision sequence studies in iron

    CERN Document Server

    Hou, M; Becquart, C S

    2002-01-01

    The properties of replacement collision sequences (RCS) in iron and their contribution to radiation damage are studied as they are generated in atomic collision cascades with the binary collision approximation Marlowe. Length distributions of RCS in collision cascades generated by primaries with a couple of ten keV kinetic energies are predicted short. Whatever the interatomic potential employed, at least 90% of the generated RCS have a length of no more than three successive collisions, whatever the directions. This property was found for all the known phases of iron at standard pressure (bcc and fcc). The RCS length distributions are not significantly influenced by the temperature nor by the accurate form of the model describing the energy loss in RCS. Close to 50% of the stable Frenkel pairs (FP) created result from RCS that are shorter than the vacancy-interstitial recombination distance estimated on the basis of molecular dynamics calculations. The other half results from longer RCS (about five successiv...

  15. Solid phase syntheses of oligoureas

    Energy Technology Data Exchange (ETDEWEB)

    Burgess, K.; Linthicum, D.S.; Russell, D.H.; Shin, H.; Shitangkoon, A.; Totani, R.; Zhang, A.J.; Ibarzo, J. [Texas A& M Univ., College Station, TX (United States)

    1997-02-19

    Isocyanates 7 were formed from monoprotected diamines 3 or 6, which in turn can be easily prepared from commercially available N-BOC- or N-FMOC-protected amino acid derivatives. Isocyanates 7, formed in situ, could be coupled directly to a solid support functionalized with amine groups or to amino acids anchored on resins using CH{sub 2}Cl{sub 2} as solvent and an 11 h coupling time at 25 {degree}C. Such couplings afforded peptidomimetics with an N-phthaloyl group at the N-terminus. The optimal conditions identified for removal of the N-phthaloyl group were to use 60% hydrazine in DMF for 1-3 h. Several sequences of amino acids coupled to ureas (`peptidic ureas`) and of sequential urea units (`oligoureas`) were prepared via solid phase syntheses and isolated by HPLC. Partition coefficients were measured for two of these peptidomimetics, and their water solubilities were found to be similar to the corresponding peptides. A small library of 160 analogues of the YGGFL-amide sequence was prepared via Houghten`s tea bag methodology. This library was tested for binding to the anti-{beta}-endorphin monoclonal antibody. Overall, this paper describes methodology for solid phase syntheses of oligourea derivatives with side chains corresponding to some of the protein amino acids. The chemistry involved is ideal for high-throughput syntheses and screening operations. 51 refs., 3 figs., 2 tabs.

  16. Quantitative imaging of complex samples by spiral phase contrast microscopy.

    Science.gov (United States)

    Bernet, Stefan; Jesacher, Alexander; Fürhapter, Severin; Maurer, Christian; Ritsch-Marte, Monika

    2006-05-01

    Recently a spatial spiral phase filter in a Fourier plane of a microscopic imaging setup has been demonstrated to produce edge enhancement and relief-like shadow formation of amplitude and phase samples. Here we demonstrate that a sequence of at least 3 spatially filtered images, which are recorded with different rotational orientations of the spiral phase plate, can be used to obtain a quantitative reconstruction of both, amplitude and phase information of a complex microscopic sample, i.e. an object consisting of mixed absorptive and refractive components. The method is demonstrated using a calibrated phase sample, and an epithelial cheek cell.

  17. Pig genome sequence - analysis and publication strategy

    NARCIS (Netherlands)

    Archibald, A.L.; Bolund, L.; Churcher, C.; Fredholm, M.; Groenen, M.A.M.; Harlizius, B.

    2010-01-01

    Background - The pig genome is being sequenced and characterised under the auspices of the Swine Genome Sequencing Consortium. The sequencing strategy followed a hybrid approach combining hierarchical shotgun sequencing of BAC clones and whole genome shotgun sequencing. Results - Assemblies of the B

  18. Long-range barcode labeling-sequencing

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Feng; Zhang, Tao; Singh, Kanwar K.; Pennacchio, Len A.; Froula, Jeff L.; Eng, Kevin S.

    2016-10-18

    Methods for sequencing single large DNA molecules by clonal multiple displacement amplification using barcoded primers. Sequences are binned based on barcode sequences and sequenced using a microdroplet-based method for sequencing large polynucleotide templates to enable assembly of haplotype-resolved complex genomes and metagenomes.

  19. Sequencing and comparative analysis of the gorilla MHC genomic sequence.

    Science.gov (United States)

    Wilming, Laurens G; Hart, Elizabeth A; Coggill, Penny C; Horton, Roger; Gilbert, James G R; Clee, Chris; Jones, Matt; Lloyd, Christine; Palmer, Sophie; Sims, Sarah; Whitehead, Siobhan; Wiley, David; Beck, Stephan; Harrow, Jennifer L

    2013-01-01

    Major histocompatibility complex (MHC) genes play a critical role in vertebrate immune response and because the MHC is linked to a significant number of auto-immune and other diseases it is of great medical interest. Here we describe the clone-based sequencing and subsequent annotation of the MHC region of the gorilla genome. Because the MHC is subject to extensive variation, both structural and sequence-wise, it is not readily amenable to study in whole genome shotgun sequence such as the recently published gorilla genome. The variation of the MHC also makes it of evolutionary interest and therefore we analyse the sequence in the context of human and chimpanzee. In our comparisons with human and re-annotated chimpanzee MHC sequence we find that gorilla has a trimodular RCCX cluster, versus the reference human bimodular cluster, and additional copies of Class I (pseudo)genes between Gogo-K and Gogo-A (the orthologues of HLA-K and -A). We also find that Gogo-H (and Patr-H) is coding versus the HLA-H pseudogene and, conversely, there is a Gogo-DQB2 pseudogene versus the HLA-DQB2 coding gene. Our analysis, which is freely available through the VEGA genome browser, provides the research community with a comprehensive dataset for comparative and evolutionary research of the MHC.

  20. Accurate Location of the Yao'an Earthquake Sequence and the Yongsheng Earthquake Sequence

    Institute of Scientific and Technical Information of China (English)

    Wang Xinling; Liu Jie; Zhang Guomin; Zhao Cuiping

    2006-01-01

    The Yao'an Ms6.5 earthquake occurred on Jan. 15, 2000 and the Yongsheng Ms6.0 earthquake occurred on Oct. 27, 2001 in Yunnan Province, China. They are both located in the middle of the Dian block. Their epicenters are close to each other, the tectonic and strain characters of the earthquakes were similar, and there were many aftershocks after the two main shocks. In order to further study the spatial-temporal distributions and fault rupture characters of the main shocks and aftershocks, the latter are located using the Geiger earthquake location algorithm (Geiger) and the double difference earthquake location algorithm (DD) based on the seismic phase data of the two earthquake sequences. They were recorded by two Near Source Digital Seismic Networks (YNSSN and YSNSSN) deployed by the Yunnan Seismological Bureau (YNSB). Then, two main shock parameters were relocated using DD based on the data of larger magnitude aftershocks and the two main shocks that were recorded by the Kunming Regional Digital Seismic Network (KMSN). Combining the spatialtemporal distributions of the two earthquake sequences, the tectonic and strain characters of earthquakes, the rupture processes of the two aftershock sequences along faults are analyzed and discussed contrastively.

  1. Use of the Frank sequence in pulsed EPR

    DEFF Research Database (Denmark)

    Tseitlin, Mark; Quine, Richard W.; Eaton, Sandra S.;

    2011-01-01

    The Frank polyphase sequence has been applied to pulsed EPR of triarylmethyl radicals at 256MHz (9.1mT magnetic field), using 256 phase pulses. In EPR, as in NMR, use of a Frank sequence of phase steps permits pulsed FID signal acquisition with very low power microwave/RF pulses (ca. 1.5m......W in the application reported here) relative to standard pulsed EPR. A 0.2mM aqueous solution of a triarylmethyl radical was studied using a 16mm diameter cross-loop resonator to isolate the EPR signal detection system from the incident pulses. Keyword: Correlation spectroscopy,Multi-pulse EPR,Low power pulses...

  2. Comparison between open phase fault of arc suppression coil and single phase to earth fault in coal mine distribution network

    Institute of Scientific and Technical Information of China (English)

    LI Xiao-bo; WANG Chong-lin

    2008-01-01

    When, in a coal mine distribution network whose neutral point is grounded by an arc suppression coil (ASC), a fault occurs in the ASC, compensation cannot be properly realized. Furthermore, it can damage the safe and reliable run of the network.We first introduce a three-phase five-column arc suppression coil (TPFCASC) and discuss its autotracking compensation theory.Then we compare the single phase to ground fault of the coal mine distribution network with an open phase fault at the TPFCASC using the Thévenin theory, the symmetrical-component method and the complex sequence network respectively. The results show that, in both types of faults, zero-sequence voltage of the network will appear and the maximum magnitude of this zero-sequence voltage is different in both faults. Based on this situation, a protection for the open phase fault at the TPFCASC should be estab-lished.

  3. ARC Code TI: sequenceMiner

    Data.gov (United States)

    National Aeronautics and Space Administration — The sequenceMiner was developed to address the problem of detecting and describing anomalies in large sets of high-dimensional symbol sequences. sequenceMiner works...

  4. Sequencing Needs for Viral Diagnostics

    Energy Technology Data Exchange (ETDEWEB)

    Gardner, S N; Lam, M; Mulakken, N J; Torres, C L; Smith, J R; Slezak, T

    2004-01-26

    We built a system to guide decisions regarding the amount of genomic sequencing required to develop diagnostic DNA signatures, which are short sequences that are sufficient to uniquely identify a viral species. We used our existing DNA diagnostic signature prediction pipeline, which selects regions of a target species genome that are conserved among strains of the target (for reliability, to prevent false negatives) and unique relative to other species (for specificity, to avoid false positives). We performed simulations, based on existing sequence data, to assess the number of genome sequences of a target species and of close phylogenetic relatives (''near neighbors'') that are required to predict diagnostic signature regions that are conserved among strains of the target species and unique relative to other bacterial and viral species. For DNA viruses such as variola (smallpox), three target genomes provide sufficient guidance for selecting species-wide signatures. Three near neighbor genomes are critical for species specificity. In contrast, most RNA viruses require four target genomes and no near neighbor genomes, since lack of conservation among strains is more limiting than uniqueness. SARS and Ebola Zaire are exceptional, as additional target genomes currently do not improve predictions, but near neighbor sequences are urgently needed. Our results also indicate that double stranded DNA viruses are more conserved among strains than are RNA viruses, since in most cases there was at least one conserved signature candidate for the DNA viruses and zero conserved signature candidates for the RNA viruses.

  5. A self-tuning phase-shifting algorithm for interferometry.

    Science.gov (United States)

    Estrada, Julio C; Servin, Manuel; Quiroga, Juan A

    2010-02-01

    In Phase Stepping Interferometry (PSI) an interferogram sequence having a known, and constant phase shift between the interferograms is required. Here we take the case where this constant phase shift is unknown and the only assumption is that the interferograms do have a temporal carrier. To recover the modulating phase from the interferograms, we propose a self-tuning phase-shifting algorithm. Our algorithm estimates the temporal frequency first, and then this knowledge is used to estimate the interesting modulating phase. There are several well known iterative schemes published before, but our approach has the unique advantage of being very fast. Our new temporal carrier, and phase estimator is capable of obtaining a very good approximation of their temporal carrier in a single iteration. Numerical experiments are given to show the performance of this simple yet powerful self-tuning phase shifting algorithm.

  6. Optimization of micropillar sequences for fluid flow sculpting

    CERN Document Server

    Stoecklein, Daniel; Kim, Dongyuk; Di Carlo, Dino; Ganapathysubramanian, Baskar

    2015-01-01

    Inertial fluid flow deformation around pillars in a microchannel is a new method for controlling fluid flow. Sequences of pillars have been shown to produce a rich phase space with a wide variety of flow transformations. Previous work has successfully demonstrated manual design of pillar sequences to achieve desired transformations of the flow cross-section, with experimental validation. However, such a method is not ideal for seeking out complex sculpted shapes as the search space quickly becomes too large for efficient manual discovery. We explore fast, automated optimization methods to solve this problem. We formulate the inertial flow physics in microchannels with different micropillar configurations as a set of state transition matrix operations. These state transition matrices are constructed from experimentally validated streamtraces. This facilitates modeling the effect of a sequence of micropillars as nested matrix-matrix products, which have very efficient numerical implementations. With this new fo...

  7. On-Demand Indexing for Referential Compression of DNA Sequences.

    Directory of Open Access Journals (Sweden)

    Fernando Alves

    Full Text Available The decreasing costs of genome sequencing is creating a demand for scalable storage and processing tools and techniques to deal with the large amounts of generated data. Referential compression is one of these techniques, in which the similarity between the DNA of organisms of the same or an evolutionary close species is exploited to reduce the storage demands of genome sequences up to 700 times. The general idea is to store in the compressed file only the differences between the to-be-compressed and a well-known reference sequence. In this paper, we propose a method for improving the performance of referential compression by removing the most costly phase of the process, the complete reference indexing. Our approach, called On-Demand Indexing (ODI compresses human chromosomes five to ten times faster than other state-of-the-art tools (on average, while achieving similar compression ratios.

  8. Selective detection of ordered sodium signals by a jump-and-return pulse sequence

    Science.gov (United States)

    Lee, Jae-Seung; Regatte, Ravinder R.; Jerschow, Alexej

    2009-09-01

    A simple pulse sequence, derived from the shaped pulse optimally exciting the central transition of a spin 3/2, can be used to selectively detect ordered sodium with a given quadrupolar coupling. The pulse sequence consists of two pulses with opposite phases and separated by a delay, called a quadrupolar jump-and-return (QJR) sequence. This QJR sequence is tested with a phantom made of sodium ions in bacteriophage and in aqueous solution and its feasibility for contrast modification based on the quadrupolar coupling is demonstrated.

  9. Identification of errors introduced during high throughput sequencing of the T cell receptor repertoire

    Directory of Open Access Journals (Sweden)

    Cheng Cheng

    2011-02-01

    Full Text Available Abstract Background Recent advances in massively parallel sequencing have increased the depth at which T cell receptor (TCR repertoires can be probed by >3log10, allowing for saturation sequencing of immune repertoires. The resolution of this sequencing is dependent on its accuracy, and direct assessments of the errors formed during high throughput repertoire analyses are limited. Results We analyzed 3 monoclonal TCR from TCR transgenic, Rag-/- mice using Illumina® sequencing. A total of 27 sequencing reactions were performed for each TCR using a trifurcating design in which samples were divided into 3 at significant processing junctures. More than 20 million complementarity determining region (CDR 3 sequences were analyzed. Filtering for lower quality sequences diminished but did not eliminate sequence errors, which occurred within 1-6% of sequences. Erroneous sequences were pre-dominantly of correct length and contained single nucleotide substitutions. Rates of specific substitutions varied dramatically in a position-dependent manner. Four substitutions, all purine-pyrimidine transversions, predominated. Solid phase amplification and sequencing rather than liquid sample amplification and preparation appeared to be the primary sources of error. Analysis of polyclonal repertoires demonstrated the impact of error accumulation on data parameters. Conclusions Caution is needed in interpreting repertoire data due to potential contamination with mis-sequence reads. However, a high association of errors with phred score, high relatedness of erroneous sequences with the parental sequence, dominance of specific nt substitutions, and skewed ratio of forward to reverse reads among erroneous sequences indicate approaches to filter erroneous sequences from repertoire data sets.

  10. Explaining the harmonic sequence paradox.

    Science.gov (United States)

    Schmidt, Ulrich; Zimper, Alexander

    2012-05-01

    According to the harmonic sequence paradox, an expected utility decision maker's willingness to pay for a gamble whose expected payoffs evolve according to the harmonic series is finite if and only if his marginal utility of additional income becomes zero for rather low payoff levels. Since the assumption of zero marginal utility is implausible for finite payoff levels, expected utility theory - as well as its standard generalizations such as cumulative prospect theory - are apparently unable to explain a finite willingness to pay. This paper presents first an experimental study of the harmonic sequence paradox. Additionally, it demonstrates that the theoretical argument of the harmonic sequence paradox only applies to time-patient decision makers, whereas the paradox is easily avoided if time-impatience is introduced.

  11. Transgressive Surface as Sequence Boundary

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Analysis of the four cases of the sequence boundary (SB)-transgressive surface (TS) relation in nature shows that applying transgressive surfaces as sequence boundaries has the following merits: it improves the methodology of stratigraphic subdivision; the position of transgressive surface in a sea level curve is relatively fixed; the transgressive surface is a transforming surface of the stratal structure; in platforms or ramps, the transgressive surface is the only choice for determining the sequence boundary; the transgressive surface is a readily recognized physical surface reflected by seismic records in seismostratigraphy. The paper reaches a conclusion that to delineate a SB in terms of the TS is theoretically and practically better than to delineate it between highstand and lowstand sediments as has been done traditionally.

  12. On the base sequence conjecture

    CERN Document Server

    Djokovic, Dragomir Z

    2010-01-01

    Let BS(m,n) denote the set of base sequences (A;B;C;D), with A and B of length m and C and D of length n. The base sequence conjecture (BSC) asserts that BS(n+1,n) exist (i.e., are non-empty) for all n. This is known to be true for n <= 36 and when n is a Golay number. We show that it is also true for n=37 and n=38. It is worth pointing out that BSC is stronger than the famous Hadamard matrix conjecture. In order to demonstrate the abundance of base sequences, we have previously attached to BS(n+1,n) a graph Gamma_n and computed the Gamma_n for n <= 27. We now extend these computations and determine the Gamma_n for n=28,...,35. We also propose a conjecture describing these graphs in general.

  13. Nomenclature of magnetic, incommensurate, composition-changed morphotropic, polytype, transient-structural and quasicrystalline phases undergoing phase transitions. II. Report of an IUCr Working Group on Phase Transition Nomenclature.

    Science.gov (United States)

    Tolédano, J C; Berry, R S; Brown, P J; Glazer, A M; Metselaar, R; Pandey, D; Perez-Mato, J M; Roth, R S; Abrahams, S C

    2001-09-01

    A general nomenclature applicable to the phases that form in any sequence of transitions in the solid state has been recommended by an IUCr Working Group [Acta Cryst. (1998). A54, 1028-1033]. The six-field notation of the first Report, hereafter I, was applied to the case of structural phase transitions, i.e. to transformations resulting from temperature and/or pressure changes between two crystalline (strictly periodic) phases involving modifications to the atomic arrangement. Extensive examples that illustrate the recommendations were provided. This second Report considers, within the framework of a similar six-field notation, the more complex nomenclature of transitions involving magnetic phases, incommensurate phases and transitions that occur as a function of composition change. Extension of the nomenclature to the case of phases with less clearly established relevance to standard schemes of transition in equilibrium systems, namely polytype phases, radiation-induced and other transient phases, quasicrystalline phases and their transitions is recommended more tentatively. A uniform notation for the translational periodicity, propagation vector or wavevector for magnetic and/or incommensurate substances is specified. The notation adopted for incommensurate phases, relying partly on the existence of an average structure, is also consistent with that for commensurate phases in a sequence. The sixth field of the nomenclature is used to emphasize the special features of polytypes and transient phases. As in I, illustrative examples are provided for each category of phase sequence.

  14. Comparative analysis of sequences from PT 2013

    DEFF Research Database (Denmark)

    Mikkelsen, Susie Sommer

    . All but one sequence mapped to the MCP gene while the last sequence mapped to the Neurofilament gene. Approx. half of the sequences contained no errors while the rest differed with 88-99 percent similarity with most having 99% similarity. One sequence, when BLASTed, showed most similarity to European...... Sheatfish and not EHNV. Generally, mistakes occurred at the ends of the sequences. This can be due to several factors. One is that the sequence has not been trimmed of the sequence primer sites. Another is the lack of quality control of the chromatogram. Finally, sequencing in just one direction can result...

  15. Sequence Patterns of Identity Authentication Protocols

    Institute of Scientific and Technical Information of China (English)

    Tao Hongcai; He Dake

    2006-01-01

    From the viewpoint of protocol sequence, analyses are made of the sequence patterns of possible identity authentication protocol under two cases: with or without the trusted third party (TTP). Ten feasible sequence patterns of authentication protocol with TTP and 5 sequence patterns without TTP are gained. These gained sequence patterns meet the requirements for identity authentication,and basically cover almost all the authentication protocols with TTP and without TTP at present. All of the sequence patterns gained are classified into unilateral or bilateral authentication. Then , according to the sequence symmetry, several good sequence patterns with TTP are evaluated. The accompolished results can provide a reference to design of new identity authentication protocols.

  16. Phase diagram of elastic spheres.

    Science.gov (United States)

    Athanasopoulou, L; Ziherl, P

    2017-02-15

    Experiments show that polymeric nanoparticles often self-assemble into several non-close-packed lattices in addition to the face-centered cubic lattice. Here, we explore theoretically the possibility that the observed phase sequences may be associated with the softness of the particles, which are modeled as elastic spheres interacting upon contact. The spheres are described by two finite-deformation theories of elasticity, the modified Saint-Venant-Kirchhoff model and the neo-Hookean model. We determine the range of indentations where the repulsion between the spheres is pairwise additive and agrees with the Hertz theory. By computing the elastic energies of nine trial crystal lattices at densities far beyond the Hertzian range, we construct the phase diagram and find the face- and body-centered cubic lattices as well as the A15 lattice and the simple hexagonal lattice, with the last two being stable at large densities where the spheres are completely faceted. These results are qualitatively consistent with observations, suggesting that deformability may indeed be viewed as a generic property that determines the phase behavior in nanocolloidal suspensions.

  17. KERNEL WORDS AND GAP SEQUENCE OF THE TRIBONACCI SEQUENCE

    Institute of Scientific and Technical Information of China (English)

    Yuke HUANG; Zhiying WEN

    2016-01-01

    In this paper, we investigate the factor properties and gap sequence of the Tri-bonacci sequence, the fixed point of the substitution σ(a, b, c) = (ab, ac, a). Let ωp be the p-th occurrence of ω and Gp(ω) be the gap between ωp and ωp+1. We introduce a notion of kernel for each factor ω, and then give the decomposition of the factor ω with respect to its kernel. Using the kernel and the decomposition, we prove the main result of this paper:for each factorω, the gap sequence{Gp(ω)}p≥1 is the Tribonacci sequence over the alphabet{G1(ω), G2(ω), G4(ω)}, and the expressions of gaps are determined completely. As an appli-cation, for each factorω and p∈N, we determine the position ofωp. Finally we introduce a notion of spectrum for studying some typical combinatorial properties, such as power, overlap and separate of factors.

  18. Sequences and series involving the sequence of composite numbers

    Directory of Open Access Journals (Sweden)

    Panayiotis Vlamos

    2002-01-01

    Full Text Available Denoting by pn and cn the nth prime number and the nth composite number, respectively, we prove that both the sequence (xnn≥1, defined by xn=∑k=1n (ck+1−ck / k−pn / n, and the series ∑n=1∞ (pcn−cpn / npn are convergent.

  19. Integrated sequence analysis. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Andersson, K.; Pyy, P

    1998-02-01

    The NKS/RAK subprojet 3 `integrated sequence analysis` (ISA) was formulated with the overall objective to develop and to test integrated methodologies in order to evaluate event sequences with significant human action contribution. The term `methodology` denotes not only technical tools but also methods for integration of different scientific disciplines. In this report, we first discuss the background of ISA and the surveys made to map methods in different application fields, such as man machine system simulation software, human reliability analysis (HRA) and expert judgement. Specific event sequences were, after the surveys, selected for application and testing of a number of ISA methods. The event sequences discussed in the report were cold overpressure of BWR, shutdown LOCA of BWR, steam generator tube rupture of a PWR and BWR disturbed signal view in the control room after an external event. Different teams analysed these sequences by using different ISA and HRA methods. Two kinds of results were obtained from the ISA project: sequence specific and more general findings. The sequence specific results are discussed together with each sequence description. The general lessons are discussed under a separate chapter by using comparisons of different case studies. These lessons include areas ranging from plant safety management (design, procedures, instrumentation, operations, maintenance and safety practices) to methodological findings (ISA methodology, PSA,HRA, physical analyses, behavioural analyses and uncertainty assessment). Finally follows a discussion about the project and conclusions are presented. An interdisciplinary study of complex phenomena is a natural way to produce valuable and innovative results. This project came up with structured ways to perform ISA and managed to apply the in practice. The project also highlighted some areas where more work is needed. In the HRA work, development is required for the use of simulators and expert judgement as

  20. Network motifs in music sequences

    CERN Document Server

    Zanette, Damian H

    2010-01-01

    In this note, I summarize ongoing research on motif distribution in networks built up out of symbolic sequences of Western musical origin. Their motif significance profiles exhibit remarkable consistency over different styles and periods, and define a class that cannot be identified with any of the four "superfamilies" to which most real networks seem to belong. Networks from music sequences possess an unusual abundance of bidirectional connections, due to the inherent reversibility of short musical note patterns. This property contributes to motif significance from both local and large-scale features of musical structure.