Analysis of fundamental parameters for V477 Lyr

NASA Astrophysics Data System (ADS)

Shimansky, V. V.; Pozdnyakova, S. A.; Borisov, N. V.; Bikmaev, I. F.; Galeev, A. I.; Sakhibullin, N. A.; Spiridonova, O. I.

2008-06-01

We analyze the photometric and spectroscopic observations of the young pre-cataclysmic variable (pre-CV) V477 Lyr. The masses of both binary components have been corrected by analyzing their radial velocity curves. We show that agreement between the theoretical and observed light curves of the object is possible for several sets of its physical parameters corresponding to the chosen temperature of the primary component. The final parameters of V477 Lyr have been established by comparing observational data with evolutionary tracks for planetary nebula nuclei. The derived effective temperature of the O subdwarf is higher than that estimated by analyzing the object’s ultraviolet spectra by more than 10000 K. This is in agreement with the analogous results obtained previously for the young pre-CVs V664 Cas and UU Sge. The secondary component of V477 Lyr has been proven to have a more than 25-fold luminosity excess compared to main-sequence stars of similar mass. Comparison of the physical parameters for the cool stars in young pre-CVs indicates that their luminosities do not correlate with the masses of the objects. The observed luminosity excesses in such stars show a close correlation with the post-common-envelope lifetime of the systems and should be investigated within the framework of the theory of their relaxation to the state of main-sequence stars.

Mass loss from pre-main-sequence accretion disks. I - The accelerating wind of FU Orionis

NASA Technical Reports Server (NTRS)

Calvet, Nuria; Hartmann, Lee; Kenyon, Scott J.

1993-01-01

We present evidence that the wind of the pre-main-sequence object FU Orionis arises from the surface of the luminous accretion disk. A disk wind model calculated assuming radiative equilibrium explains the differential behavior of the observed asymmetric absorption-line profiles. The model predicts that strong lines should be asymmetric and blueshifted, while weak lines should be symmetric and double-peaked due to disk rotation, in agreement with observations. We propose that many blueshifted 'shell' absorption features are not produced in a true shell of material, but rather form in a differentially expanding wind that is rapidly rotating. The inference of rapid rotation supports the proposal that pre-main-sequence disk winds are rotationally driven.

Columbia/Einstein observations of galactic X-ray sources

NASA Technical Reports Server (NTRS)

Long, K. S.

1979-01-01

The imaging observations of galactic clusters are presented. These fall into three categories: pre-main-sequence stars in the Orion nebulae, isolated-main-and-post main-sequence stars, and supernova remnants SNR. In addition to SNR, approximately 30 sources were detected.

Pre-main Sequence Evolution and the Hydrogen-Burning Minimum Mass

NASA Astrophysics Data System (ADS)

Nakano, Takenori

There is a lower limit to the mass of the main-sequence stars (the hydrogen-burning minimum mass) below which the stars cannot replenish the energy lost from their surfaces with the energy released by the hydrogen burning in their cores. This is caused by the electron degeneracy in the stars which suppresses the increase of the central temperature with contraction. To find out the lower limit we need the accurate knowledge of the pre-main sequence evolution of very low-mass stars in which the effect of electron degeneracy is important. We review how Hayashi and Nakano (1963) carried out the first determination of this limit.

Microprocessor activity controls differential miRNA biogenesis In Vivo.

PubMed

Conrad, Thomas; Marsico, Annalisa; Gehre, Maja; Orom, Ulf Andersson

2014-10-23

In miRNA biogenesis, pri-miRNA transcripts are converted into pre-miRNA hairpins. The in vivo properties of this process remain enigmatic. Here, we determine in vivo transcriptome-wide pri-miRNA processing using next-generation sequencing of chromatin-associated pri-miRNAs. We identify a distinctive Microprocessor signature in the transcriptome profile from which efficiency of the endogenous processing event can be accurately quantified. This analysis reveals differential susceptibility to Microprocessor cleavage as a key regulatory step in miRNA biogenesis. Processing is highly variable among pri-miRNAs and a better predictor of miRNA abundance than primary transcription itself. Processing is also largely stable across three cell lines, suggesting a major contribution of sequence determinants. On the basis of differential processing efficiencies, we define functionality for short sequence features adjacent to the pre-miRNA hairpin. In conclusion, we identify Microprocessor as the main hub for diversified miRNA output and suggest a role for uncoupling miRNA biogenesis from host gene expression. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Activation and connectivity patterns of the presupplementary and dorsal premotor areas during free improvisation of melodies and rhythms.

PubMed

de Manzano, Örjan; Ullén, Fredrik

2012-10-15

Free, i.e. non-externally cued generation of movement sequences is fundamental to human behavior. We have earlier hypothesized that the dorsal premotor cortex (PMD), which has been consistently implicated in cognitive aspects of planning and selection of spatial motor sequences may be particularly important for the free generation of spatial movement sequences, whereas the pre-supplementary motor area (pre-SMA), which shows increased activation during perception, learning and reproduction of temporal sequences, may contribute more to the generation of temporal structures. Here we test this hypothesis using fMRI and musical improvisation in professional pianists as a model behavior. We employed a 2 × 2 factorial design with the factors Melody (Specified/Improvised) and Rhythm (Specified/Improvised). The main effect analyses partly confirmed our hypothesis: there was a main effect of Melody in the PMD; the pre-SMA was present in the main effect of Rhythm, as predicted, as well as in the main effect of Melody. A psychophysiological interaction analysis of functional connectivity demonstrated that the correlation in activity between the pre-SMA and cerebellum was higher during rhythmic improvisation than during the other conditions. In summary, there were only subtle differences in activity level between the pre-SMA and PMD during improvisation, regardless of condition. Consequently, the free generation of rhythmic and melodic structures, appears to be largely integrated processes but the functional connectivity between premotor areas and other regions may change during free generation in response to sequence-specific spatiotemporal demands. Copyright © 2012 Elsevier Inc. All rights reserved.

A search for pre-main sequence stars in the high-latitude molecular clouds. II - A survey of the Einstein database

NASA Technical Reports Server (NTRS)

Caillault, Jean-Pierre; Magnani, Loris

1990-01-01

The preliminary results are reported of a survey of every EINSTEIN image which overlaps any high-latitude molecular cloud in a search for X-ray emitting pre-main sequence stars. This survey, together with complementary KPNO and IRAS data, will allow the determination of how prevalent low mass star formation is in these clouds in general and, particularly, in the translucent molecular clouds.

Lithium abundances among solar-type pre-main-sequence stars

NASA Technical Reports Server (NTRS)

Strom, Karen M.; Wilkin, Francis P.; Strom, Stephen E.; Seaman, Robert L.

1989-01-01

Measurements of Li I 6707 A line strengths were carried out for two samples of pre-main-sequence (PMS) stars (L 1641 and Taurus-Auriga), and the Li abundances estimated for PMS stars are compared with those deduced from observations of Li line strengths for main-sequence stars in the Alpha Persei cluster. It was found that the maximum Li abundances among the PMS stars with solar mass values greater than 1.0 exceed the maximum abundances for Alpha Per stars by at least 0.3 dex. Some PMS stars, including few apparently young stars, showed large (greater than 1.0 dex) Li depletion, and some apparently old PMS stars showed little or no depletion.

High Contrast X-ray Flares In The Anchors Database

NASA Astrophysics Data System (ADS)

McCleary, Jacqueline; Wolk, S.

2010-01-01

The X-ray light curves of pre-main sequence stars can show variability in the form of flares altering a baseline characteristic activity level; the largest X-ray flares are characterized by a rapid rise to 10 or more times the characteristic count rate, followed by a slower quasi-exponential decay. Analysis of these high-contrast X-ray flares enables the study of the innermost magnetic fields of pre-main sequence stars. We have scanned the ANCHORS database of Chandra observations of star-forming regions to extend the study of flare events on pre-main sequence stars both in sky coverage and in volume. We developed a sample of 30 high-contrast flares out of the 14,000 stars available in ANCHORS at the time of our study. By not biasing our sample by cluster, age, or spectral type, we increased the number of X-ray flare events studied and subsequently the strength of any statements about their properties. Applying the generally accepted methods of time-resolved spectral analysis developed by Reale et al. (1997), we measured the temperatures, confining magnetic field strengths, and loop lengths of these large flares. The results of the flare analysis were compared to the 2MASS and Spitzer data available for the stars in our sample. We found that the longest flare loop lengths (of order several stellar radii) are only seen on stars whose IR data indicates the presence of disks, which suggests that the longest flares may stretch all the way to the disk. Such long flares tend to be more tenuous (rarified) than the other large flares studied. A wide range of loop lengths were observed, indicating that two types of flares may occur on disked young stellar objects: either compact and analogous to flares on evolved stars, or long and the result of star-disk magnetic connections.

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

DTIC Science & Technology

2012-06-25

reserved. Printed in the U.S.A. YSOVAR: SIX PRE-MAIN-SEQUENCE ECLIPSING BINARIES IN THE ORION NEBULA CLUSTER M. Morales-Calderón1,2, J. R. Stauffer1, K. G...multi-color light curves for∼2400 candidate Orion Nebula Cluster (ONC) members from our Warm Spitzer Exploration Science Program YSOVAR, we have...readable tables 1. INTRODUCTION The Orion Nebula Cluster (ONC) contains several thousand members, and since it is nearby, it provides an excellent em

Pre-main-sequence isochrones - II. Revising star and planet formation time-scales

NASA Astrophysics Data System (ADS)

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

2013-09-01

We have derived ages for 13 young (<30 Myr) star-forming regions and find that they are up to a factor of 2 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 confidence in the new age scale. This agreement is largely due to our adoption of empirical colour-Teff relations and bolometric corrections for pre-main-sequence stars cooler than 4000 K. The revised ages for the star-forming regions in our sample are: ˜2 Myr for NGC 6611 (Eagle Nebula; M 16), IC 5146 (Cocoon Nebula), NGC 6530 (Lagoon Nebula; M 8) and NGC 2244 (Rosette Nebula); ˜6 Myr for σ Ori, Cep OB3b and IC 348; ≃10 Myr for λ Ori (Collinder 69); ≃11 Myr for NGC 2169; ≃12 Myr for NGC 2362; ≃13 Myr for NGC 7160; ≃14 Myr for χ Per (NGC 884); and ≃20 Myr for NGC 1960 (M 36).

Pre-main sequence sun: a dynamic approach

DOE Office of Scientific and Technical Information (OSTI.GOV)

Newman, M.J.; Winkler, K.H.A.

1979-01-01

The classical pre-main sequence evolutionary behavior found by Hayashi and his coworkers for the Sun depends crucially on the choice of initial conditions. The Hayashi picture results from beginning the calculation with an already centrally condensed, highly Jeans unstable object not terribly far removed from the stellar state initially. The present calculation follows the work of Larson in investigating the hydrodynamic collapse and self-gravitational accretion of an initially uniform, just Jeans unstable interstellar gas-dust cloud. The resulting picture for the early history of the Sun is quite different from that found by Hayashi. A rather small (R approx. = 2more » R/sub sun/), low-luminosity (L greater than or equal to L/sub sun/) protostellar core develops. A fully convective stellar core, characteristic of Hayashi's work, is not found during the accretion process, and can only develop, if at all, in the subsequent pre-main sequence Kelvin-Helmholtz contraction of the core. 3 figures, 1 table.« less

The dot{M}-M_* relation of pre-main-sequence stars: a consequence of X-ray driven disc evolution

NASA Astrophysics Data System (ADS)

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

2014-03-01

We analyse current measurements of accretion rates on to pre-main-sequence stars as a function of stellar mass, and conclude that the steep dependence 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 dot{M}-M_* relation is found to be in the range of 1.6-1.9 for young stars with masses lower than 1 M⊙. 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 dot{M}-M_* relation in pre-main-sequence stars bears the signature of disc dispersal by X-ray photoevaporation, suggesting that the relation is a straightforward consequence of disc physics rather than an imprint of initial conditions.

THE SOLAR NEIGHBORHOOD. XXVI. AP Col: THE CLOSEST (8.4 pc) PRE-MAIN-SEQUENCE STAR

DOE Office of Scientific and Technical Information (OSTI.GOV)

Riedel, Adric R.; Henry, Todd J.; Jao, Wei-Chun

2011-10-15

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 0.9 m, from which we derive a proper motion of 342.0 {+-} 0.5 mas yr{sup -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{sup -1}), lithium equivalent width (EW) (0.28 {+-} 0.02 A), H{alpha} EW (-6.0 to -35 A), vsin i (11 {+-} 1more » km s{sup -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 {approx}40 Myr old Argus/IC 2391 Association.« less

YOUNG STELLAR CLUSTERS CONTAINING MASSIVE YOUNG STELLAR OBJECTS IN THE VVV SURVEY

DOE Office of Scientific and Technical Information (OSTI.GOV)

Borissova, J.; Alegría, S. Ramírez; Kurtev, R.

The purpose of this research is to study the connections of the global properties of eight young stellar clusters projected in the Vista Variables in the Via Lactea (VVV) ESO Large Public Survey disk area and their young stellar object (YSO) populations. The analysis is based on the combination of spectroscopic parallax-based reddening and distance determinations with main-sequence and pre-main-sequence ishochrone fitting to determine the basic parameters (reddening, age, distance) of the sample clusters. The lower mass limit estimations show that all clusters are low or intermediate mass (between 110 and 1800  M {sub ⊙}), the slope Γ of themore » obtained present-day mass functions of the clusters is close to the Kroupa initial mass function. The YSOs in the cluster’s surrounding fields are classified using low resolution spectra, spectral energy distribution fits with theoretical predictions, and variability, taking advantage of multi-epoch VVV observations. All spectroscopically confirmed YSOs (except one) are found to be massive (more than 8 M {sub ⊙}). Using VVV and GLIMPSE color–color cuts we have selected a large number of new YSO candidates, which are checked for variability and 57% are found to show at least low-amplitude variations. In few cases it was possible to distinguish between YSO and AGB classifications on the basis of light curves.« less

Investigating ChaMPlane X-Ray Sources in the Galactic Bulge with Magellan LDSS2 Spectra

NASA Astrophysics Data System (ADS)

Koenig, Xavier; Grindlay, Jonathan E.; van den Berg, Maureen; Laycock, Silas; Zhao, Ping; Hong, JaeSub; Schlegel, Eric M.

2008-09-01

We have carried out optical and X-ray spectral analyses on a sample of 136 candidate optical counterparts of X-ray sources found in five Galactic bulge fields included in our Chandra Multiwavelength Plane Survey. We use a combination of optical spectral fitting and quantile X-ray analysis to obtain the hydrogen column density toward each object, and a three-dimensional dust model of the Galaxy to estimate the most probable distance in each case. We present the discovery of a population of stellar coronal emission sources, likely consisting of pre-main-sequence, young main-sequence, and main-sequence stars, as well as a component of active binaries of RS CVn or BY Dra type. We identify one candidate quiescent low-mass X-ray binary with a subgiant companion; we note that this object may also be an RS CVn system. We report the discovery of three new X-ray-detected cataclysmic variables (CVs) in the direction of the Galactic center (at distances lesssim2 kpc). This number is in excess of predictions made with a simple CV model based on a local CV space density of lesssim10-5 pc-3, and a scale height ~200 pc. We discuss several possible reasons for this observed excess.

Evolution of Pre-Main Sequence Accretion Disks

NASA Technical Reports Server (NTRS)

Hartmann, Lee W.

2004-01-01

The aim of this project is to develop a comprehensive global picture of the physical conditions in, and evolutionary timescales of, pre-main sequence accretion disks. The results of this work will help constrain the initial conditions for planet formation. To this end we are developing much larger samples of 3-10 Myr-old stars to provide better empirical constraints on protoplanetary disk evolution; measuring disk accretion rates in these systems; and constructing detailed model disk structures consistent with observations to infer physical conditions such as grain growth in protoplanetary disks.

Evolution of Pre-Main Sequence Accretion Disks

NASA Technical Reports Server (NTRS)

Hartmann, Lee W.

2003-01-01

The aim of this project is to develop a comprehensive global picture of the physical conditions in, and evolutionary timescales of, pre-main sequence accretion disks. The results of this work will help constrain the initial conditions for planet formation. To this end we are developing much larger samples of 3-10 Myr-old stars to provide better empirical constraints on protoplanetary disk evolution; measuring disk accretion rates in these systems; and constructing detailed model disk structures consistent with observations to infer physical conditions such as grain growth in protoplanetary disks.

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

NASA Astrophysics Data System (ADS)

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 given photometric bandpass. This analysis shows that for Teff ≤ 4000 K the models systematically overestimate the flux by a factor of 2 at 0.5 μm, though this decreases with wavelength, becoming negligible at 2.2 μm. Thus before the pre-MS models are used to derive ages, a recalibration of the models is performed by incorporating an empirical colour-Teff relation and bolometric corrections based on the Ks-band luminosity of Pleiades members, with theoretical corrections for the dependence on the surface gravity (log g). The recalibrated pre-MS model isochrones are used to derive ages from the pre-MS populations of the SFRs. These ages are then compared with the MS derivations, thus providing a powerful diagnostic tool with which to discriminate between the different pre-MS age scales that arise from a much stronger model dependency in the pre-MS regime. The revised ages assigned to each of the 14 SFRs are up to a factor two older than previous derivations, a result with wide-ranging implications, including that circumstellar discs survive longer and that the average Class II lifetime is greater than currently believed.

Tidal dissipation in rotating low-mass stars and implications for the orbital evolution of close-in planets. I. From the PMS to the RGB at solar metallicity

NASA Astrophysics Data System (ADS)

Gallet, F.; Bolmont, E.; Mathis, S.; Charbonnel, C.; Amard, L.

2017-08-01

Context. Star-planet interactions must be taken into account in stellar models to understand the dynamical evolution of close-in planets. The dependence of the tidal interactions on the structural and rotational evolution of the star is of particular importance and should be correctly treated. Aims: We quantify how tidal dissipation in the convective envelope of rotating low-mass stars evolves from the pre-main sequence up to the red-giant branch depending on the initial stellar mass. We investigate the consequences of this evolution on planetary orbital evolution. Methods: We couple the tidal dissipation formalism previously described to the stellar evolution code STAREVOL and apply this coupling to rotating stars with masses between 0.3 and 1.4 M⊙. As a first step, this formalism assumes a simplified bi-layer stellar structure with corresponding averaged densities for the radiative core and the convective envelope. We use a frequency-averaged treatment of the dissipation of tidal inertial waves in the convection zone (but neglect the dissipation of tidal gravity waves in the radiation zone). In addition, we generalize a recent work by following the orbital evolution of close-in planets using the new tidal dissipation predictions for advanced phases of stellar evolution. Results: On the pre-main sequence the evolution of tidal dissipation is controlled by the evolution of the internal structure of the contracting star. On the main sequence it is strongly driven by the variation of surface rotation that is impacted by magnetized stellar winds braking. The main effect of taking into account the rotational evolution of the stars is to lower the tidal dissipation strength by about four orders of magnitude on the main sequence, compared to a normalized dissipation rate that only takes into account structural changes. Conclusions: The evolution of the dissipation strongly depends on the evolution of the internal structure and rotation of the star. From the pre-main sequence up to the tip of the red-giant branch, it varies by several orders of magnitude, with strong consequences for the orbital evolution of close-in massive planets. These effects are the strongest during the pre-main sequence, implying that the planets are mainly sensitive to the star's early history.

A search for pre-main-sequence stars in high-latitude molecular clouds. 3: A survey of the Einstein database

NASA Technical Reports Server (NTRS)

Caillault, Jean-Pierre; Magnani, Loris; Fryer, Chris

1995-01-01

In order to discern whether the high-latitude molecular clouds are regions of ongoing star formation, we have used X-ray emission as a tracer of youthful stars. The entire Einstein database yields 18 images which overlap 10 of the clouds mapped partially or completely in the CO (1-0) transition, providing a total of approximately 6 deg squared of overlap. Five previously unidentified X-ray sources were detected: one has an optical counterpart which is a pre-main-sequence (PMS) star, and two have normal main-sequence stellar counterparts, while the other two are probably extragalactic sources. The PMS star is located in a high Galactic latitude Lynds dark cloud, so this result is not too suprising. The translucent clouds, though, have yet to reveal any evidence of star formation.

Spectroscopy of the variable K-dwarf UNSW-V-760: is it a pre-main-sequence pulsator?

NASA Astrophysics Data System (ADS)

Koen, C.; Gray, R. O.; Kawaler, S.; Crawford, S. M.

2013-11-01

The star UNSW-V-760 is a known variable, showing both flares and two non-sinusoidal periodicities. Availability of high signal-to-noise spectra reported in this paper has enabled a revision of the spectral type of this star to K3 IV-Vk. The star is a very rapid rotator (v sin i ˜ 140 km s-1), and the abundance of lithium appears to be enhanced. 48 radial velocity measurements were obtained over the course of three successive nights. These may show the same two frequencies detected photometrically, but there is some uncertainty in the interpretation. Application of pulsation theory suggests that photometric frequencies could be explained as low ℓ pulsation modes, but an excitation mechanism remains to be found.

The Structure of the Star-forming Cluster RCW 38

NASA Astrophysics Data System (ADS)

Winston, E.; Wolk, S. J.; Bourke, T. L.; Megeath, S. T.; Gutermuth, R.; Spitzbart, B.

2011-12-01

We present a study of the structure of the high-mass star-forming region RCW 38 and the spatial distribution of its young stellar population. Spitzer Infrared Array Camera (IRAC) photometry (3-8 μm) is combined with Two Micron All Sky Survey near-IR data to identify young stellar objects (YSOs) by IR-excess emission from their circumstellar material. Chandra X-ray data are used to identify class III pre-main-sequence stars lacking circumstellar material. We identify 624 YSOs: 23 class 0/I and 90 flat spectrum protostars, 437 class II stars, and 74 class III stars. We also identify 29 (27 new) O star candidates over the IRAC field. Seventy-two stars exhibit IR-variability, including 7 class 0/I and 12 flat spectrum YSOs. A further 177 tentative candidates are identified by their location in the IRAC [3.6] versus [3.6]-[5.8] color-magnitude diagram. We find strong evidence of subclustering in the region. Three subclusters were identified surrounding the central cluster, with massive and variable stars in each subcluster. The central region shows evidence of distinct spatial distributions of the protostars and pre-main-sequence stars. A previously detected IR cluster, DB2001_Obj36, has been established as a subcluster of RCW 38. This suggests that star formation in RCW 38 occurs over a more extended area than previously thought. The gas-to-dust ratio is examined using the X-ray derived hydrogen column density, N H and the K-band extinction, and found to be consistent with the diffuse interstellar medium, in contrast with Serpens and NGC 1333. We posit that the high photoionizing flux of massive stars in RCW 38 affects the agglomeration of the dust grains.

VizieR Online Data Catalog: NGC 7129 pre-main sequence stars (Stelzer+, 2009)

NASA Astrophysics Data System (ADS)

Stelzer, B.; Scholz, A.

2010-09-01

We make use of X-ray and IR imaging observations to identify the pre-main sequence stars in NGC 7129. We define a sample of young stellar objects based on color-color diagrams composed from IR photometry between 1.6 and 8um, from 2MASS and Spitzer, and based on X-ray detected sources from a Chandra observation. A 22ks long Chandra observation targeting the Herbig star SVS 12 was carried out on Mar 11, 2006 (start of observation UT 14h29m18s). (5 data files).

Photometry and spectroscopy in the open cluster Alpha Persei, 2

NASA Technical Reports Server (NTRS)

Prosser, Charles F.

1993-01-01

Results from a combination of new spectroscopic and photometric observations in the lower main-sequence and pre-main sequence of the open cluster alpha Persei are presented. New echelle spectroscopy has provided radial and rotational velocity information for thirteen candidate members, three of which are nonmembers based on radial velocity, absence of a Li 6707A feature, and absence of H-alpha emission. A set of revised rotational velocity estimates for several slowly rotating candidates identified earlier is given, yielding rotational velocities as low as 7 km/s for two apparent cluster members. VRI photometry for several pre-main sequence members is given; the new (V,V-I(sub K)) photometry yields a more clearly defined pre-main sequence. A list of approximately 43 new faint candidate members based on the (V,V-I(sub K)) CCD photometry is presented in an effort to identify additional cluster members at very low masses. Low-dispersion spectra obtained for several of these candidates provide in some cases supporting evidence for cluster membership. The single brown dwarf candidate in this cluster is for the first time placed in a color-magnitude diagram with other cluster members, providing a better means for establishing its true status. Stars from among the list of new photometric candidates may provide the means for establishing a sequence of cluster members down to very faint magnitudes (V approximately 21) and consequently very low masses. New coordinate determinations for previous candidate members and finding charts for the new photometric candidates are provided in appendices.

Three years of ULTRASPEC at the Thai 2.4-m telescope: Capabilities and scientific highlights

NASA Astrophysics Data System (ADS)

Yadav, Ram Kesh; Richichi, Andrea; Irawati, Puji; Dhillon, Vikram Singh; Marsh, Thomas R.; Soonthornthum, Boonrucksar

2018-04-01

High temporal resolution observations enable the study of rapid phenomena such as the flux variations in binary system objects, e.g. cataclysmic variables, compact binary systems, the flux variations in young star clusters, stellar occultations and more. The 2.4-m Thai National Telescope (TNT) is ideally suited for this niche research, being the largest facility in Southeast Asia and being equipped with ULTRASPEC, a high-speed imager based on a low-noise frame transfer electron-multiplying CCD. In the sub-window mode, ULTRASPEC can record uninterrupted sequences with frame rates as fast as few milliseconds. We present some of the key results obtained in the area of high time resolution with ULTRASPEC. We also present the results of a recent worldwide campaign to observe the current series of lunar occultations of Aldebaran (α Tauri) carried out in close collaboration with the Devasthal facilities, the out-of-eclipse variations on the post common-envelope system J1021+1744, and pre-main-sequence variables in young open cluster Stock 8.

The evolution of the lithium abundances of solar-type stars. II - The Ursa Major Group

NASA Technical Reports Server (NTRS)

Soderblom, David R.; Pilachowski, Catherine A.; Fedele, Stephen B.; Jones, Burton F.

1993-01-01

We draw upon a recent study of the membership of the Ursa Major Group (UMaG) to examine lithium among 0.3 Gyr old solar-type stars. For most G and K dwarfs, Li confirms the conclusions about membership in UMaG reached on the basis of kinematics and chromospheric activity. G and K dwarfs in UMaG have less Li than comparable stars in the Pleiades. This indicates that G and K dwarfs undergo Li depletion while they are on the main sequence, in addition to any pre-main-sequence depletion they may have experienced. Moreover, the Li abundances of the Pleiades K dwarfs cannot be attributed to main-sequence depletion alone, demonstrating that pre-main-sequence depletion of Li also takes place. The sun's Li abundance implies that the main-sequence mechanism becomes less effective with age. The hottest stars in UMaG have Li abundances like those of hot stars in the Pleiades and Hyades and in T Tauris, and the two genuine UMaG members with temperatures near Boesgaard's Li chasm have Li abundances consistent with that chasm developing fully by 0.3 Gyr for stars with UMaG's metallicity. We see differences in the abundance of Li between UMaG members of the same spectral types, indicating that a real spread in the lithium abundance exists within this group.

From protostellar to pre-main-sequence evolution

NASA Astrophysics Data System (ADS)

D'Antona, F.

I summarize the status of pre-main-sequence evolutionary tracks starting from the first steps dating back to the concept of Hayashi track. Understanding of the dynamical protostellar phase in the vision of Palla & Stahler, who introduced the concept of the deuterium burning thermostat and of stellar birthline, provided for a long time a link between the dynamical and hydrostatic evolution. Disk accretion however changed considerably the view, but re-introducing some ambiguities which must still be solved. The limitations and uncertainties in the mass and age determination from models for young stellar objects are summarized, but the burning of light elements is still a powerful observational signature.

The sdA problem - I. Physical properties

NASA Astrophysics Data System (ADS)

Pelisoli, Ingrid; Kepler, S. O.; Koester, D.

2018-04-01

The so-called sdA stars are defined by having H-rich spectra and surface gravities similar to hot subdwarf stars, but effective temperature below the zero-age horizontal branch. Their evolutionary history is an enigma: their surface gravity is too high for main-sequence stars, but too low for single evolution white dwarfs. They are most likely byproducts of binary evolution, including blue-stragglers, extremely-low mass white dwarf stars (ELMs) and their precursors (pre-ELMs). A small number of ELMs with similar properties to sdAs is known. Other possibilities include metal-poor A/F dwarfs, second generation stars, or even stars accreted from dwarf galaxies. In this work, we analyse colours, proper motions, and spacial velocities of a sample of sdAs from the Sloan Digital Sky Survey to assess their nature and evolutionary origin. We define a probability of belonging to the main sequence and a probability of being a (pre-)ELM based on these properties. We find that 7 per cent of the sdAs are more likely to be (pre-)ELMs than main-sequence stars. However, the spacial velocity distribution suggests that over 35 per cent of them cannot be explained as single metal-poor A/F stars.

INTRINSIC COLORS, TEMPERATURES, AND BOLOMETRIC CORRECTIONS OF PRE-MAIN-SEQUENCE STARS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pecaut, Mark J.; Mamajek, Eric E.

2013-09-01

We present an analysis of the intrinsic colors and temperatures of 5-30 Myr old pre-main-sequence (pre-MS) stars using the F0- through M9-type members of nearby, negligibly reddened groups: the η Cha cluster, the TW Hydra Association, the β Pic Moving Group, and the Tucana-Horologium Association. To check the consistency of spectral types from the literature, we estimate new spectral types for 52 nearby pre-MS stars with spectral types F3 through M4 using optical spectra taken with the SMARTS 1.5 m telescope. Combining these new types with published spectral types and photometry from the literature (Johnson-Cousins BVI{sub C} , 2MASS JHK{submore » S} and WISE W1, W2, W3, and W4), we derive a new empirical spectral type-color sequence for 5-30 Myr old pre-MS stars. Colors for pre-MS stars match dwarf colors for some spectral types and colors, but for other spectral types and colors, deviations can exceed 0.3 mag. We estimate effective temperatures (T {sub eff}) and bolometric corrections (BCs) for our pre-MS star sample through comparing their photometry to synthetic photometry generated using the BT-Settl grid of model atmosphere spectra. We derive a new T {sub eff} and BC scale for pre-MS stars, which should be a more appropriate match for T Tauri stars than often-adopted dwarf star scales. While our new T {sub eff} scale for pre-MS stars is within ≅100 K of dwarfs at a given spectral type for stars« less

Social Cognitive Predictors of Pre-Service Teachers' Technology Integration Performance

ERIC Educational Resources Information Center

Perkmen, Serkan; Pamuk, Sonmez

2011-01-01

The main objective of the study was to examine interrelationships among social cognitive variables (self-efficacy, outcome expectations, and performance goals) and their role in predicting pre-service teachers' technology integration performance. Although researchers have examined the role of these variables in the teacher-education context, the…

Theory of winds in late-type evolved and pre-main-sequence stars

NASA Technical Reports Server (NTRS)

Macgregor, K. B.

1983-01-01

Recent observational results confirm that many of the physical processes which are known to occur in the Sun also occur among late-type stars in general. One such process is the continuous loss of mass from a star in the form of a wind. There now exists an abundance of either direct or circumstantial evidence which suggests that most (if not all) stars in the cool portion of the HR diagram possess winds. An attempt is made to assess the current state of theoretical understanding of mass loss from two distinctly different classes of late-type stars: the post-main-sequence giant/supergiant stars and the pre-main-sequence T Tauri stars. Toward this end, the observationally inferred properties of the wind associated with each of the two stellar classes under consideration are summarized and compared against the predictions of existing theoretical models. Although considerable progress has been made in attempting to identify the mechanisms responsible for mass loss from cool stars, many fundamental problems remain to be solved.

THE YOUNG OPEN CLUSTERS KING 12, NGC 7788, AND NGC 7790: PRE-MAIN-SEQUENCE STARS AND EXTENDED STELLAR HALOS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Davidge, T. J.

2012-12-20

The stellar contents of the open clusters King 12, NGC 7788, and NGC 7790 are investigated using MegaCam images. Comparisons with isochrones yield an age <20 Myr for King 12, 20-40 Myr for NGC 7788, and 60-80 Myr for NGC 7790 based on the properties of stars near the main-sequence turnoff (MSTO) in each cluster. The reddening of NGC 7788 is much larger than previously estimated. The luminosity functions (LFs) of King 12 and NGC 7788 show breaks that are attributed to the onset of pre-main-sequence (PMS) objects, and comparisons with models of PMS evolution yield ages that are consistentmore » with those measured from stars near the MSTO. In contrast, the r' LF of main-sequence stars in NGC 7790 is matched to r' = 20 by a model that is based on the solar neighborhood mass function. The structural properties of all three clusters are investigated by examining the two-point angular correlation function of blue main-sequence stars. King 12 and NGC 7788 are each surrounded by a stellar halo that extends out to a radius of 5 arcmin ({approx}3.4 pc). It is suggested that these halos form in response to large-scale mass ejection early in the evolution of the clusters, as predicted by models. In contrast, blue main-sequence stars in NGC 7790 are traced out to a radius of {approx}7.5 arcmin ({approx}5.5 pc), with no evidence of a halo. It is suggested that all three clusters may have originated in the same star-forming complex, but not in the same giant molecular cloud.« less

ASTEROSEISMIC ANALYSIS OF THE PRE-MAIN-SEQUENCE STARS IN NGC 2264

DOE Office of Scientific and Technical Information (OSTI.GOV)

Guenther, D. B.; Casey, M. P.; Kallinger, T.

2009-10-20

NGC 2264 is a young open cluster lying above the Galactic plane in which six variable stars have previously been identified as possible pre-main-sequence (PMS) pulsators. Their oscillation spectra are relatively sparse with each star having from 2 to 12 unambiguous frequency identifications based on Microvariability and Oscillations of Stars satellite and multi-site ground-based photometry. We describe our efforts to find classical PMS stellar models (i.e., models evolved from the Hayashi track) whose oscillation spectra match the observed frequencies. We find model eigenspectra that match the observed frequencies and are consistent with the stars' locations in the HR diagram formore » the three faintest of the six stars. Not all the frequencies found in spectra of the three brightest stars can be matched to classical PMS model spectra possibly because of effects not included in our PMS models such as chemical and angular momentum stratification in the outer layers of the star. All the oscillation spectra contain both radial and nonradial p-modes. We argue that the PMS pulsating stars divide into two groups depending on whether or not they have undergone complete mixing (i.e., have gone through a Hayashi phase). Lower mass stars that do evolve through a Hayashi phase have oscillation spectra predicted by classical PMS models, whereas more massive stars that do not, retain mass infall effects in their surface layers and are not well modeled by classical PMS models.« less

Stellar and Circumstellar Properties of the Pre-Main-Sequence Binary GV Tau from Infrared Spectroscopy

NASA Astrophysics Data System (ADS)

Doppmann, Greg W.; Najita, Joan R.; Carr, John S.

2008-09-01

We report spatially resolved spectroscopy of both components of the low-mass pre-main-sequence binary GV Tau. High-resolution spectroscopy in the K and L bands is used to characterize the stellar properties of the binary and to explore the nature of the circumstellar environment. We find that the southern component, GV Tau S, is a radial velocity variable, possibly as a result of an unseen low-mass companion. The strong warm gaseous HCN absorption reported previously by Gibb and coworkers toward GV Tau S was not present during the epoch of our observations. Instead, we detect warm (~500 K) molecular absorption with similar properties toward the northern infrared companion, GV Tau N. At the epoch of our observations, the absorbing gas toward GV Tau N was approximately at the radial velocity of the GV Tau molecular envelope, but it was redshifted with respect to the star by ~13 km s-1. One interpretation of our results is that GV Tau N is also a binary and that most of the warm molecular absorption arises in a circumbinary disk viewed close to edge-on. Data presented herein were obtained at the W. M. Keck Observatory from telescope time allocated to the National Aeronautics and Space Administration through the agency's scientific partnership with the California Institute of Technology and the University of California. The Observatory was made possible by the generous financial support of the W. M. Keck Foundation.

Delta Scuti Variables

NASA Astrophysics Data System (ADS)

Handler, Gerald

2009-09-01

We review recent research on Delta Scuti stars from an observer's viewpoint. First, some signposts helping to find the way through the Delta Scuti jungle are placed. Then, some problems in studying individual pulsators in the framework of asteroseismology are given before a view on how the study of these variables has benefited (or not) from past and present high-precision asteroseismic space missions is presented. Some possible pitfalls in the analysis of data with a large dynamical range in pulsational amplitudes are pointed out, and a strategy to optimize the outcome of asteroseismic studies of Delta Scuti stars is suggested. We continue with some views on ``hybrid'' pulsators and interesting individual High Amplitude Delta Scuti stars, and then take a look on Delta Scuti stars in stellar systems of several different kinds. Recent results on pre-main sequence Delta Scuti stars are discussed as are questions related to the instability strip of these variables. Finally, some remarkable new theoretical results are highlighted before, instead of a set of classical conclusions, questions to be solved in the future, are raised.

Evolution of Pre-Main Sequence Accretion Disks

NASA Technical Reports Server (NTRS)

Hartmann, Lee W.

2000-01-01

The aim of this project was to develop a comprehensive global picture of the physical conditions in, and evolutionary timescales of, pre-main sequence accretion disks. The results of this work will help constrain the initial conditions for planet formation. To this end we: (1) Developed detailed calculations of disk structure to study physical conditions and investigate the observational effects of grain growth in T Tauri disks; (2) Studied the dusty emission and accretion rates in older disk systems, with ages closer to the expected epoch of (giant) planet formation at 3-10 Myr, and (3) Began a project to develop much larger samples of 3-10 Myr-old stars to provide better empirical constraints on protoplanetary disk evolution.

ASCA X-ray observations of pre-main-sequence stars

NASA Technical Reports Server (NTRS)

Skinner, S. L.; Walter, F. M.; Yamauchi, S.

1996-01-01

The results of recent Advanced Satellite for Cosmology and Astrophysics (ASCA) X-ray observations of two pre-main sequence stars are presented: the weak emission line T Tauri star HD 142361, and the Herbig Ae star HD 104237. The solid state imaging spectrometer spectra for HD 142361 shows a clear emission line from H-like Mg 7, and spectral fits reveal a multiple temperature plasma with a hot component of at least 16 MK. The spectra of HD 104237 show a complex temperature structure with the hottest plasma at temperatures of greater than 30 MK. It is concluded that mechanisms that predict only soft X-ray emission can be dismissed for Herbig Ae stars.

High Resolution X-ray Spectroscopy and Star Formation: HETG Observations of the Pre-Main Sequence Stellar Cluster IC 348

NASA Astrophysics Data System (ADS)

Principe, David; Huenemoerder, David P.; Schulz, Norbert; Kastner, Joel H.; Weintraub, David; Preibisch, Thomas

2018-01-01

We present Chandra High Energy Transmission Grating (HETG) observations of the ∼3 Myr old pre-main sequence (pre-MS) stellar cluster IC 348. With 400-500 cluster members at a distance of ∼300 pc, IC 348 is an ideal target to observe a large number of X-ray sources in a single pointing and is thus an extremely efficient use of Chandra-HETG. High resolution X-ray spectroscopy offers a means to investigate detailed spectral characteristic of X-ray emitting plasmas and their surrounding environments. We present preliminary results where we compare X-ray spectral signatures (e.g., luminosity, temperature, column density, abundance) of the X-ray brightest pre-MS stars in IC 348 with spectral type, multiwavelength signatures of accretion, and the presence of circumstellar disks at multiple stages of pre-MS stellar evolution. Assuming all IC 348 members formed from the same primordial molecular cloud, any disparity between coronal abundances of individual members, as constrained by the identification and strength of emission lines, will constrain the source(s) of coronal chemical evolution at a stage of pre-MS evolution vital to the formation of planets.

No Evidence for Protoplanetary Disk Destruction By OB Stars in the MYStIX Sample

NASA Astrophysics Data System (ADS)

Richert, Alexander J. W.; Feigelson, Eric D.; Getman, Konstantin V.; Kuhn, Michael A.

2015-09-01

Hubble Space Telescope images of proplyds in the Orion Nebula, as well as submillimeter/radio measurements, show that the dominant O7 star {θ }1Ori C photoevaporates nearby disks around pre-main-sequence stars. Theory predicts that massive stars photoevaporate disks within distances of the order of 0.1 pc. These findings suggest that young, OB-dominated massive H ii regions are inhospitable to the survival of protoplanetary disks and, subsequently, to the formation and evolution of planets. In the current work, we test this hypothesis using large samples of pre-main-sequence stars in 20 massive star-forming regions selected with X-ray and infrared photometry in the MYStIX survey. Complete disk destruction would lead to a deficit of cluster members with an excess in JHKS and Spitzer/IRAC bands in the vicinity of O stars. In four MYStIX regions containing O stars and a sufficient surface density of disk-bearing sources to reliably test for spatial avoidance, we find no evidence for the depletion of inner disks around pre-main-sequence stars in the vicinity of O-type stars, even very luminous O2-O5 stars. These results suggest that massive star-forming regions are not very hostile to the survival of protoplanetary disks and, presumably, to the formation of planets.

Time Resolved X-Ray Spectral Analysis of Class II YSOs in NGC 2264 During Optical Dips and Bursts

NASA Astrophysics Data System (ADS)

Guarcello, Mario Giuseppe; Flaccomio, Ettore; Micela, Giuseppina; Argiroffi, Costanza; Venuti, Laura

2016-07-01

Pre-Main Sequence stars are variable sources. The main mechanisms responsible for their variability are variable extinction, unsteady accretion, and rotational modulation of both hot and dark photospheric spots and X-ray active regions. In stars with disks this variability is thus related to the morphology of the inner circumstellar region (<0.1 AU) and that of photosphere and corona, all impossible to be spatially resolved with present day techniques. This has been the main motivations of the Coordinated Synoptic Investigation of NGC2264, a set of simultaneous observations of NGC2264 with 15 different telescopes.We analyze the X-ray spectral properties of stars with disks extracted during optical bursts and dips in order to unveil the nature of these phenomena. Stars are analyzed in two different samples. In stars with variable extinction a simultaneous increase of optical extinction and X-ray absorption is searched during the optical dips; in stars with accretion bursts we search for soft X-ray emission and increasing X-ray absorption during the bursts. In 9/33 stars with variable extinction we observe simultaneous increase of X-ray absorption and optical extinction. In seven dips it is possible to calculate the NH/AV ratio in order to infer the composition of the obscuring material. In 5/27 stars with optical accretion bursts, we observe soft X-ray emission during the bursts that we associate to the emission of accreting gas. It is not surprising that these properties are not observed in all the stars with dips and bursts since favorable geometric configurations are required. The observed variable absorption during the dips is mainly due to dust-free material in accretion streams. In stars with accretion bursts we observe in average a larger soft X-ray spectral component not observed in non accreting stars. This indicates that this soft X-ray emission arises from the accretion shocks.

On the apparent positions of T Tauri stars in the H-R diagram

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kenyon, S.J.; Hartmann, L.W.

1990-01-01

The spread in apparent luminosities of T Tauri stars caused by occultation and emission from protostellar disks is investigated. A random distribution of disk inclination angles, coupled with a plausible range of accretion rates, introduces a significant scatter in apparent luminosities for intrinsically identical stars. The observed dispersion of luminosities for K7-M1 Hayashi track stars thought to have disks in Taurus-Auriga is similar to predictions of the simple accretion disk model, which suggets that age determinations form many pre-main-sequence stars are uncertain. The results also suggest that Stahler's birthline for convective track pre-main-sequence stars may be located at slightly lowermore » luminosities than previously thought. 38 refs.« less

Evolution of Pre-Main Sequence Accretion Disks

NASA Technical Reports Server (NTRS)

Hartmann, Lee W.

2002-01-01

The aim of this project is to develop a comprehensive global picture of the physical conditions in, and evolutionary timescales of, pre-main sequence accretion disks. The results of this work will help constrain the initial conditions for planet formation. To this end we plan to: (1) Develop much larger samples of 3-10 Myr-old stars to provide better empirical constraints on protoplanetary disk evolution; (2) Study the dusty emission and accretion rates in these systems, with ages closer to the expected epoch of (giant) planet formation at 3-10 Myr; and (3) Develop detailed model disk structures consistent with observations to infer physical conditions in protoplanetary disks and to constrain possible grain growth as the first stage of planetesimal formation.

A Rapidly Moving Shell in the Orion Nebula

NASA Technical Reports Server (NTRS)

Walter, Donald K.; O'Dell, C. R.; Hu, Xihai; Dufour, Reginald J.

1995-01-01

A well-resolved elliptical shell in the inner Orion Nebula has been investigated by monochromatic imaging plus high- and low-resolution spectroscopy. We find that it is of low ionization and the two bright ends are moving at -39 and -49 km/s with respect to OMC-1. There is no central object, even in the infrared J bandpass although H2 emission indicates a possible association with the nearby very young pre-main-sequence star J&W 352, which is one of the youngest pre-main-sequence stars in the inner Orion Nebula. Many of the characteristics of this object (low ionization, blue shift) are like those of the Herbig-Haro objects, although the symmetric form would make it an unusual member of that class.

International Ultraviolet Explorer (IUE) ultraviolet spectral atlas of selected astronomical objects

NASA Technical Reports Server (NTRS)

Wu, Chi-Chao; Reichert, Gail A.; Ake, Thomas B.; Boggess, Albert; Holm, Albert V.; Imhoff, Catherine L.; Kondo, Yoji; Mead, Jaylee M.; Shore, Steven N.

1992-01-01

The IUE Ultraviolet Spectral Atlas of Selected Astronomical Objects (or 'the Atlas'), is based on the data that were available in the IUE archive in 1986, and is intended to be a quick reference for the ultraviolet spectra of many categories of astronomical objects. It shows reflected sunlight from the Moon, planets, and asteroids, and also shows emission from comets. Comprehensive compilations of UV spectra for main sequence, subgiant, giant, bright giant, and supergiant stars are published elsewhere. This Atlas contains the spectra for objects occupying other areas of the Hertzsprung-Russell diagram: pre-main sequence stars, chemically peculiar stars, pulsating variables, subluminous stars, and Wolf-Rayet stars. This Atlas also presents phenomena such as the chromospheric and transition region emissions from late-type stars; composite spectra of stars, gas streams, accretion disks and gas envelopes of binary systems; the behavior of gas ejecta shortly after the outburst of novac and supernovac; and the H II regions, planetary nebulae, and supernova remnants. Population 2 stars, globular clusters, and luminous stars in the Magellanic Clouds, M31, and M33, are also included in this publication. Finally, the Atlas gives the ultraviolet spectra of galaxies of different Hubble types and of active galaxies.

Search for Variables in the Kepler Field on DASCH Plates

NASA Astrophysics Data System (ADS)

Tang, Sumin; Grindlay, J.; Los, E.; Servillat, M.

2011-01-01

The Digital Access to a Sky Century @ Harvard (DASCH) is a project to digitize the half a million glass photographic plates over the period 1880s-1980s. This 100 year coverage is a unique resource for studying temporal variations in the universe. Here we present our variable search algorithms and variable catalog in the Kepler fields based on 3000 scanned plates. We use the KIC spectral classifications to search for long-term variability of any main sequence stars, particularly M dwarfs. We apply a variability search technique developed for DASCH and set limits on the fraction of main sequence stars, by spectral type, which show detectable (>0.2mag) variability on timescales 10-100y. Such limits are of particular interest for M dwarfs given the recent discoveries of their planet systems.

Accretion dynamics in pre-main sequence binaries

NASA Astrophysics Data System (ADS)

Tofflemire, B.; Mathieu, R.; Herczeg, G.; Ardila, D.; Akeson, R.; Ciardi, D.; Johns-Krull, C.

Binary stars are a common outcome of star formation. Orbital resonances, especially in short-period systems, are capable of reshaping the distribution and flows of circumstellar material. Simulations of the binary-disk interaction predict a dynamically cleared gap around the central binary, accompanied by periodic ``pulsed'' accretion events that are driven by orbital motion. To place observational constraints on the binary-disk interaction, we have conducted a long-term monitoring program tracing the time-variable accretion behavior of 9 short-period binaries. In this proceeding we present two results from our campaign: 1) the detection of periodic pulsed accretion events in DQ Tau and TWA 3A, and 2) evidence that the TWA 3A primary is the dominant accretor in the system.

Revising Star and Planet Formation Timescales

NASA Astrophysics Data System (ADS)

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

2013-07-01

We have derived ages for 13 young (<30 Myr) star-forming regions and find that they are up to a factor of 2 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 confidence in the new age scale. This agreement is largely due to our adoption of empirical colour-Teff relations and bolometric corrections for pre-main-sequence stars cooler than 4000 K. The revised ages for the star-forming regions in our sample are: 2 Myr for NGC 6611 (Eagle Nebula; M 16), IC 5146 (Cocoon Nebula), NGC 6530 (Lagoon Nebula; M 8) and NGC 2244 (Rosette Nebula); 6 Myr for σ Ori, Cep OB3b and IC 348; ≃10 Myr for λ Ori (Collinder 69); ≃11 Myr for NGC 2169; ≃12 Myr for NGC 2362; ≃13 Myr for NGC 7160; ≃14 Myr for χ Per (NGC 884); and ≃20 Myr for NGC 1960 (M 36).

X-Raying the Coronae of HD 155555

NASA Technical Reports Server (NTRS)

Lalitha, S.; Singh, K.P.; Drake, S. A.; Kashyap, V.

2015-01-01

We present an analysis of the high-resolution Chandra observation of the multiple system, HD 155555 (an RS CVn type binary system, HD 155555 AB, and its spatially resolved low-mass companion HD 155555 C). This is an intriguing system which shows properties of both an active pre-main sequence star and a synchronised (main sequence) binary. We obtain the emission measure distribution, temperature structures, plasma densities, and abundances of this system and compare them with the coronal properties of other young/active stars. HD 155555 AB and HD 155555 C produce copious X-ray emission with log L(sub x) of 30.54 and 29.30, respectively, in the 0.3-6.0 kiloelectronvolt energy band. The light curves of individual stars show variability on timescales of few minutes to hours. We analyse the dispersed spectra and reconstruct the emission measure distribution using spectral line analysis. The resulting elemental abundances exhibit inverse first ionisation potential effect in both cases. An analysis of He-like triplets yields a range of coronal electron densities 1010 - 1013 per cubic centimeter. Since HD 155555 AB is classified both as an RS CVn and a PMS star, we compare our results with those of other slightly older active main-sequence stars and T Tauri stars, which indicates that the coronal properties of HD 155555 AB closely resemble that of an older RS CVn binary rather than a younger PMS star. Our results also suggests that the properties of HD 155555 C is very similar to those of other active M dwarfs.

An Unusual Massive Be Star HD 53367: Circumstellar Activity and Evidence for Binarity

NASA Astrophysics Data System (ADS)

Pogodin, M. A.; Malanushenko, V. P.; Kozlova, O. V.; Tarasova, T. N.; Franco, G. A. P.

2006-12-01

We present the results of high-resolution spectroscopy of the young B0e star HD 53367 obtained within the framework of a cooperative observing program in 1994--2005. We confirm that a long-term photometric variability of the object is indeed connected with the alternation of two states of the object when the gaseous circumstellar envelope disappears and arises again. Both these processes start near the star and then spread to remote parts of the envelope. We find that the radial velocities of He I and O II photospheric lines demonstrate a cyclic variability with the period P=183.7 days and the semi-amplitude K=19 km s-1. The radial velocity variation is interpreted in the framework of a model, in which the star is a companion of an eccentric binary system. An orbital solution is derived and the system's parameters are estimated. We find that the orbital eccentricity is e=0.28, the mean companion separation is 1.7 AU, and the secondary companion is most likely to be a 5 solar mass pre-main sequence object. The main part of circumstellar gas in the system is collected near the secondary companion.

The Winds of Main Sequence B Stars in NGC 6231, Evidence for Shocks in Weak Winds.

NASA Astrophysics Data System (ADS)

Massa, Derck

1996-07-01

Because the main sequence B stars in NGC 6231 have abnormallystrong C iv wind lines, they are the only main sequence Bstars with distinct edge velocities. Although the underlyingcause for the strong lines remains unknown, these stars doprovide an opportunity to test two important ideas concerningB star winds: 1) that the driving ions in the winds of starswith low mass loss rates decouple from the general flow, and;2) that shocks deep in the winds of main sequence B stars areresponsible for their observed X-rays. In both of thesemodels, the wind accelerates toward a terminal velocity,v_infty, far greater than the observed value, shocking ordecoupling well before it can attain the high v_infty. As aresult, the observable wind accelerates very rapidly, leadingto wind flushing times less than 30 minutes. If theseconjectures are correct, then the winds of main sequence Bstars should be highly variable on time scales of minutes.Model fitting of available IUE data are consistant with thegeneral notion of a rapidly accelerating wind, shocking wellbefore its actual v_infty. However, these are 5 hourexposures, so the fits are to ill-defined mean wind flows.The new GHRS observations will provide adequate spectral andtemporal resolution to observe the expected variability and,thereby, verify the existance of two important astrophysicalprocesses.

Sequence variability of the respiratory syncytial virus (RSV) fusion gene among contemporary and historical genotypes of RSV/A and RSV/B

PubMed Central

Hause, Anne M.; Henke, David M.; Avadhanula, Vasanthi; Shaw, Chad A.; Tapia, Lorena I.

2017-01-01

Background The fusion (F) protein of RSV is the major vaccine target. This protein undergoes a conformational change from pre-fusion to post-fusion. Both conformations share antigenic sites II and IV. Pre-fusion F has unique antigenic sites p27, ø, α2α3β3β4, and MPE8; whereas, post-fusion F has unique antigenic site I. Our objective was to determine the antigenic variability for RSV/A and RSV/B isolates from contemporary and historical genotypes compared to a historical RSV/A strain. Methods The F sequences of isolates from GenBank, Houston, and Chile (N = 1,090) were used for this analysis. Sequences were compared pair-wise to a reference sequence, a historical RSV/A Long strain. Variability (calculated as %) was defined as changes at each amino acid (aa) position when compared to the reference sequence. Only aa at antigenic sites with variability ≥5% were reported. Results A total of 1,090 sequences (822 RSV/A and 268 RSV/B) were analyzed. When compared to the reference F, those domains with the greatest number of non-synonymous changes included the signal peptide, p27, heptad repeat domain 2, antigenic site ø, and the transmembrane domain. RSV/A subgroup had 7 aa changes in the antigenic sites: site I (N = 1), II (N = 1), p27 (N = 4), α2α3β3β4(AM14) (N = 1), ranging in frequency from 7–91%. In comparison, RSV/B had 19 aa changes in antigenic sites: I (N = 3), II (N = 1), p27 (N = 9), ø (N = 4), α2α3β3β4(AM14) (N = 1), and MPE8 (N = 1), ranging in frequency from 79–100%. Discussion Although antigenic sites of RSV F are generally well conserved, differences are observed when comparing the two subgroups to the reference RSV/A Long strain. Further, these discrepancies are accented in the antigenic sites in pre-fusion F of RSV/B isolates, often occurring with a frequency of 100%. This could be of importance if a monovalent F protein from the historical GA1 genotype of RSV/A is used for vaccine development. PMID:28414749

Sequence variability of the respiratory syncytial virus (RSV) fusion gene among contemporary and historical genotypes of RSV/A and RSV/B.

PubMed

Hause, Anne M; Henke, David M; Avadhanula, Vasanthi; Shaw, Chad A; Tapia, Lorena I; Piedra, Pedro A

2017-01-01

The fusion (F) protein of RSV is the major vaccine target. This protein undergoes a conformational change from pre-fusion to post-fusion. Both conformations share antigenic sites II and IV. Pre-fusion F has unique antigenic sites p27, ø, α2α3β3β4, and MPE8; whereas, post-fusion F has unique antigenic site I. Our objective was to determine the antigenic variability for RSV/A and RSV/B isolates from contemporary and historical genotypes compared to a historical RSV/A strain. The F sequences of isolates from GenBank, Houston, and Chile (N = 1,090) were used for this analysis. Sequences were compared pair-wise to a reference sequence, a historical RSV/A Long strain. Variability (calculated as %) was defined as changes at each amino acid (aa) position when compared to the reference sequence. Only aa at antigenic sites with variability ≥5% were reported. A total of 1,090 sequences (822 RSV/A and 268 RSV/B) were analyzed. When compared to the reference F, those domains with the greatest number of non-synonymous changes included the signal peptide, p27, heptad repeat domain 2, antigenic site ø, and the transmembrane domain. RSV/A subgroup had 7 aa changes in the antigenic sites: site I (N = 1), II (N = 1), p27 (N = 4), α2α3β3β4(AM14) (N = 1), ranging in frequency from 7-91%. In comparison, RSV/B had 19 aa changes in antigenic sites: I (N = 3), II (N = 1), p27 (N = 9), ø (N = 4), α2α3β3β4(AM14) (N = 1), and MPE8 (N = 1), ranging in frequency from 79-100%. Although antigenic sites of RSV F are generally well conserved, differences are observed when comparing the two subgroups to the reference RSV/A Long strain. Further, these discrepancies are accented in the antigenic sites in pre-fusion F of RSV/B isolates, often occurring with a frequency of 100%. This could be of importance if a monovalent F protein from the historical GA1 genotype of RSV/A is used for vaccine development.

Cognitive ability and risk of post-traumatic stress disorder after military deployment: an observational cohort study

PubMed Central

Karstoft, Karen-Inge; Vedtofte, Mia S.; Nielsen, Anni B.S.; Osler, Merete; Mortensen, Erik L.; Christensen, Gunhild T.; Andersen, Søren B.

2017-01-01

Background Studies of the association between pre-deployment cognitive ability and post-deployment post-traumatic stress disorder (PTSD) have shown mixed results. Aims To study the influence of pre-deployment cognitive ability on PTSD symptoms 6–8 months post-deployment in a large population while controlling for pre-deployment education and deployment-related variables. Method Study linking prospective pre-deployment conscription board data with post-deployment self-reported data in 9695 Danish Army personnel deployed to different war zones in 1997–2013. The association between pre-deployment cognitive ability and post-deployment PTSD was investigated using repeated-measure logistic regression models. Two models with cognitive ability score as the main exposure variable were created (model 1 and model 2). Model 1 was only adjusted for pre-deployment variables, while model 2 was adjusted for both pre-deployment and deployment-related variables. Results When including only variables recorded pre-deployment (cognitive ability score and educational level) and gender (model 1), all variables predicted post-deployment PTSD. When deployment-related variables were added (model 2), this was no longer the case for cognitive ability score. However, when educational level was removed from the model adjusted for deployment-related variables, the association between cognitive ability and post-deployment PTSD became significant. Conclusions Pre-deployment lower cognitive ability did not predict post-deployment PTSD independently of educational level after adjustment for deployment-related variables. Declaration of interest None. Copyright and usage © The Royal College of Psychiatrists 2017. This is an open access article distributed under the terms of the Creative Commons Non-Commercial, No Derivatives (CC BY-NC-ND) license. PMID:29163983

Analysis of hepatitis B virus preS1 variability and prevalence of the rs2296651 polymorphism in a Spanish population

PubMed Central

Casillas, Rosario; Tabernero, David; Gregori, Josep; Belmonte, Irene; Cortese, Maria Francesca; González, Carolina; Riveiro-Barciela, Mar; López, Rosa Maria; Quer, Josep; Esteban, Rafael; Buti, Maria; Rodríguez-Frías, Francisco

2018-01-01

AIM To determine the variability/conservation of the domain of hepatitis B virus (HBV) preS1 region that interacts with sodium-taurocholate cotransporting polypeptide (hereafter, NTCP-interacting domain) and the prevalence of the rs2296651 polymorphism (S267F, NTCP variant) in a Spanish population. METHODS Serum samples from 246 individuals were included and divided into 3 groups: patients with chronic HBV infection (CHB) (n = 41, 73% Caucasians), patients with resolved HBV infection (n = 100, 100% Caucasians) and an HBV-uninfected control group (n = 105, 100% Caucasians). Variability/conservation of the amino acid (aa) sequences of the NTCP-interacting domain, (aa 2-48 in viral genotype D) and a highly conserved preS1 domain associated with virion morphogenesis (aa 92-103 in viral genotype D) were analyzed by next-generation sequencing and compared in 18 CHB patients with viremia > 4 log IU/mL. The rs2296651 polymorphism was determined in all individuals in all 3 groups using an in-house real-time PCR melting curve analysis. RESULTS The HBV preS1 NTCP-interacting domain showed a high degree of conservation among the examined viral genomes especially between aa 9 and 21 (in the genotype D consensus sequence). As compared with the virion morphogenesis domain, the NTCP-interacting domain had a smaller proportion of HBV genotype-unrelated changes comprising > 1% of the quasispecies (25.5% vs 31.8%), but a larger proportion of genotype-associated viral polymorphisms (34% vs 27.3%), according to consensus sequences from GenBank patterns of HBV genotypes A to H. Variation/conservation in both domains depended on viral genotype, with genotype C being the most highly conserved and genotype E the most variable (limited finding, only 2 genotype E included). Of note, proline residues were highly conserved in both domains, and serine residues showed changes only to threonine or tyrosine in the virion morphogenesis domain. The rs2296651 polymorphism was not detected in any participant. CONCLUSION In our CHB population, the NTCP-interacting domain was highly conserved, particularly the proline residues and essential amino acids related with the NTCP interaction, and the prevalence of rs2296651 was low/null. PMID:29456407

Optical photometric variable stars towards the Galactic H II region NGC 2282

NASA Astrophysics Data System (ADS)

Dutta, Somnath; Mondal, Soumen; Joshi, Santosh; Jose, Jessy; Das, Ramkrishna; Ghosh, Supriyo

2018-05-01

We report here CCD I-band time series photometry of a young (2-5 Myr) cluster NGC 2282, in order to identify and understand the variability of pre-main-sequence (PMS) stars. The I-band photometry, down to ˜20.5 mag, enables us to probe the variability towards the lower mass end (˜0.1 M⊙) of PMS stars. From the light curves of 1627 stars, we identified 62 new photometric variable candidates. Their association with the region was established from H α emission and infrared (IR) excess. Among 62 variables, 30 young variables exhibit H α emission, near-IR (NIR)/mid-IR (MIR) excess or both and are candidate members of the cluster. Out of 62 variables, 41 are periodic variables, with a rotation rate ranging from 0.2-7 d. The period distribution exhibits a median period at ˜1 d, as in many young clusters (e.g. NGC 2264, ONC, etc.), but it follows a unimodal distribution, unlike others that have bimodality, with slow rotators peaking at ˜6-8 d. To investigate the rotation-disc and variability-disc connection, we derived the NIR excess from Δ(I - K) and the MIR excess from Spitzer [3.6]-[4.5] μm data. No conclusive evidence of slow rotation with the presence of discs around stars and fast rotation for discless stars is obtained from our periodic variables. A clear increasing trend of the variability amplitude with IR excess is found for all variables.

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

NASA Technical Reports Server (NTRS)

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.

Extreme Radio Flares and Associated X-Ray Variability from Young Stellar Objects in the Orion Nebula Cluster

DOE Office of Scientific and Technical Information (OSTI.GOV)

Forbrich, Jan; Reid, Mark J.; Wolk, Scott J.

Young stellar objects are known to exhibit strong radio variability on timescales of weeks to months, and a few reports have documented extreme radio flares with at least an order of magnitude change in flux density on timescales of hours to days. However, there have been few constraints on the occurrence rate of such radio flares or on the correlation with pre-main sequence X-ray flares, although such correlations are known for the Sun and nearby active stars. Here we report simultaneous deep VLA radio and Chandra X-ray observations of the Orion Nebula Cluster, targeting hundreds of sources to look formore » the occurrence rate of extreme radio variability and potential correlation with the most extreme X-ray variability. We identify 13 radio sources with extreme radio variability, with some showing an order of magnitude change in flux density in less than 30 minutes. All of these sources show X-ray emission and variability, but we find clear correlations with extreme radio flaring only on timescales <1 hr. Strong X-ray variability does not predict the extreme radio sources and vice versa. Radio flares thus provide us with a new perspective on high-energy processes in YSOs and the irradiation of their protoplanetary disks. Finally, our results highlight implications for interferometric imaging of sources violating the constant-sky assumption.« less

Time Variability of the Dust Sublimation Zones in Pre-Main Sequence Disk Systems

NASA Technical Reports Server (NTRS)

Sitko, Michael L.; Carpenter, W. J.; Grady, C. A.; Russel, R. W.; Lynch, D. K.; Rudy, R. J.; Mazuk, S. M.; Venturini, C. C.; Kimes, R. L.; Beerman, L. C.;

A Multi-Fiber Spectroscopic Search for Low-mass Young Stars in Orion OB1

NASA Astrophysics Data System (ADS)

Loerincs, Jacqueline; Briceno, Cesar; Calvet, Nuria; Mateo, Mario L.; Hernandez, Jesus

2017-01-01

We present here results of a low resolution spectroscopic followup of candidate low-mass pre-main sequence stars in the Orion OB1 association. Our targets were selected from the CIDA Variability Survey of Orion (CVSO), and we used the Michigan/Magellan Fiber Spectrograph (M2FS) on the Magellan Clay 6.5m telescope to obtain spectra of 500 candidate T Tauri stars distributed in seven 0.5 deg diameter fields, adding to a total area of ~5.5 deg2. We identify young stars by looking at the distinctive Hα 6563 Å emission and Lithium Li I 6707 Å absorption features characteristic of young low mass pre-main sequence stars. Furthermore, by measuring the strength of their Hα emission lines, confirmed T Tauri stars can be classified as either Classical T Tauris (CTTS) or Weak-line T Tauris (WTTS), which give indication of whether the star is actively accreting material from a gas and dust disk surrounding the star, which may be the precursor of a planetary system. We confirm a total of 90 T Tauri stars, of which 50% are newly identified young members of Orion; out of the 49 new detections,15 are accreting CTTS, and of these all but one are found in the OB1b sub-region. This result is in line with our previous findings that this region is much younger than the more extended Orion OB1a sub-association. The M2FS results add to our growing census of young stars in Orion, that is allowing us to characterize in a systematic and consistent way the distribution of stellar ages across the entire complex, in order to building a complete picture of star formation in this, one of nearest most active sites of star birth.

A M2FS Spectroscopic Study of Low-mass Young Stars in Orion OB1

NASA Astrophysics Data System (ADS)

Kaleida, Catherine C.; Briceno, Cesar; Calvet, Nuria; Mateo, Mario L.; Hernandez, Jesus

2015-01-01

Surveys of pre-main sequence stars in the ~4-10 Myr range provide a window into the decline of the accretion phase of stars and the formation of planets. Nearby star clusters and stellar associations allow for the study of these young stellar populations all the way down to the lowest mass members. One of the best examples of nearby 4-10 Myr old stellar populations is the Orion OB1 association. The CIDA Variability Survey of Orion OB1 (CVSO - Briceño et al. 2001) has used the variability properties of low-mass pre-main-sequence (PMS) stars to identify hundreds of K and M-type stellar members of the Orion OB1 association, a number of them displaying IR-excess emission and thought to be representative of more evolved disk-bearing young stars. Characterizing these young, low-mass objects using spectroscopy is integral to understanding the accretion phase in young stars. We present preliminary results of a spectroscopic survey of candidate and confirmed Orion OB1 low-mass members taken during November 2014 and February 2014 using the Michigan/Magellan Fiber Spectrograph (M2FS), a PI instrument on the Magellan Clay Telescope (PI: M. Matteo). Target fields located in the off-cloud regions of Orion were identified in the CVSO, and observed using the low and high-resolution modes of M2FS. Both low and high-resolution spectra are needed in order to confirm membership and derive masses, ages, kinematics and accretion properties. Initial analysis of these spectra reveal many new K and M-type members of the Orion OB1 association in these low extinction, off-cloud areas. These are the more evolved siblings of the youngest stars still embedded in the molecular clouds, like those in the Orion Nebula Cluster. With membership and spectroscopic indicators of accretion we are building the most comprehensive stellar census of this association, enabling us to derive a robust estimate of the fraction of young stars still accreting at a various ages, a key constraint for the end of accretion and the formation of giant planets.

Accretion and Magnetic Reconnection in the Pre-Main Sequence Binary DQ Tau as Revealed through High-Cadence Optical Photometry

NASA Astrophysics Data System (ADS)

Tofflemire, Benjamin M.; Mathieu, Robert D.; Ardila, David R.; Akeson, Rachel L.; Ciardi, David R.; Herczeg, Gregory; Johns-Krull, Christopher M.; Vodniza, Alberto

2016-01-01

Protostellar disks are integral to the formation and evolution of low-mass stars and planets. A paradigm for the star-disk interaction has been extensively developed through theory and observation in the case of single stars. Most stars, however, form in binaries or higher order systems where the distribution of disk material and mass flows are more complex. Pre-main sequence (PMS) binary stars can have up to three accretion disks: two circumstellar disks and a circumbinary disk separated by a dynamically cleared gap. Theory suggests that mass may periodically flow in an accretion stream from a circumbinary disk across the gap onto circumstellar disks or stellar surfaces.The archetype for this theory is the eccentric, PMS binary DQ Tau. Moderate-cadence broadband photometry (~10 observations per orbital period) has shown pulsed brightening events near most periastron passages, just as numerical simulations would predict for a binary of similar orbital parameters. While this observed behavior supports the accretion stream theory, it is not exclusive to variable accretion rates. Magnetic reconnection events (flares) during the collision of stellar magnetospheres at periastron (when separated by 8 stellar radii) could produce the same periodic, broadband behavior when observed at a one-day cadence. Further evidence for magnetic activity comes from gyrosynchrotron, radio flares (typical of stellar flares) observed near multiple periastron passages. To reveal the physical mechanism seen in DQ Tau's moderate-cadence observations, we have obtained continuous, moderate-cadence, multi-band photometry over 10 orbital periods (LCOGT 1m network), supplemented with 32 nights of minute-cadence photometry centered on 4 separate periastron passages (WIYN 0.9m; APO ARCSAT). With detailed lightcurve morphologies we distinguish between the gradual rise and fall on multi-day time-scales predicted by the accretion stream theory and the hour time-scale, rapid-rise and exponential-decay typical of flares. While both are present, accretion dominates the observed variability providing evidence for the accretion stream theory and detailed mass accretion rates for comparison with numerical simulations.

Orbital motion in pre-main sequence binaries

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schaefer, G. H.; Prato, L.; Simon, M.

2014-06-01

We present results from our ongoing program to map the visual orbits of pre-main sequence (PMS) binaries in the Taurus star forming region using adaptive optics imaging at the Keck Observatory. We combine our results with measurements reported in the literature to analyze the orbital motion for each binary. We present preliminary orbits for DF Tau, T Tau S, ZZ Tau, and the Pleiades binary HBC 351. Seven additional binaries show curvature in their relative motion. Currently, we can place lower limits on the orbital periods for these systems; full solutions will be possible with more orbital coverage. Five othermore » binaries show motion that is indistinguishable from linear motion. We suspect that these systems are bound and might show curvature with additional measurements in the future. The observations reported herein lay critical groundwork toward the goal of measuring precise masses for low-mass PMS stars.« less

Star Formation in the Orion Nebula Cluster

NASA Astrophysics Data System (ADS)

Palla, Francesco; Stahler, Steven W.

1999-11-01

We study the record of star formation activity within the dense cluster associated with the Orion Nebula. The bolometric luminosity function of 900 visible members is well matched by a simplified theoretical model for cluster formation. This model assumes that stars are produced at a constant rate and distributed according to the field-star initial mass function. Our best-fit age for the system, within this framework, is 2×106 yr. To undertake a more detailed analysis, we present a new set of theoretical pre-main-sequence tracks. These cover all masses from 0.1 to 6.0 Msolar, and start from a realistic stellar birthline. The tracks end along a zero-age main-sequence that is in excellent agreement with the empirical one. As a further aid to cluster studies, we offer an heuristic procedure for the correction of pre-main-sequence luminosities and ages to account for the effects of unresolved binary companions. The Orion Nebula stars fall neatly between our birthline and zero-age main-sequence in the H-R diagram. All those more massive than about 8 Msolar lie close to the main sequence, as also predicted by theory. After accounting for the finite sensitivity of the underlying observations, we confirm that the population between 0.4 and 6.0 Msolar roughly follows a standard initial mass function. We see no evidence for a turnover at lower masses. We next use our tracks to compile stellar ages, also between 0.4 and 6.0 Msolar. Our age histogram reveals that star formation began at a low level some 107 yr ago and has gradually accelerated to the present epoch. The period of most active formation is indeed confined to a few×106 yr, and has recently ended with gas dispersal from the Trapezium. We argue that the acceleration in stellar births, which extends over a wide range in mass, reflects the gravitational contraction of the parent cloud spawning this cluster.

Prophylaxis against the systemic hypotension induced by propofol during rapid-sequence intubation.

PubMed

el-Beheiry, H; Kim, J; Milne, B; Seegobin, R

1995-10-01

The objective of this study was to determine the effectiveness of two prophylactic approaches against the anticipated hypotension induced by propofol during rapid-sequence intubation. Thirty-six male or female nonpremedicated ASA class I-II patients aged 21-60 yr undergoing elective outpatient surgery were included in the study. Patients were randomly allocated to receive pre-induction ephedrine sulphate (70 micrograms x kg(-1)iv), pre-induction volume loading (12 ml x kg(-1) Ringer's lactate) or no treatment. Rapid-sequence intubation with cricoid pressure was then performed with propofol (2.5 mg. x kg(-1)) and succinylcholine (1.5 mg x kg(-1). The lungs were subsequently ventilated with 0.25-0.5% isoflurane in a 2:1 N2O/O2 mixture. Vecuronium was given once neuromuscular function had recovered from the succinylcholine. Heart rate and systemic arterial blood pressure were measured non-invasively before induction, after propofol administration and every minute for ten minutes after intubation. Pre-induction volume loading prevented the hypotension observed before surgical stimulation in control and ephedrine groups. Moreover, pre-induction volume loading was not associated with increases in heart rate after intubation as was ephedrine administration. The intubating conditions were excellent to satisfactory in most patients and the overall incidence of adverse events during intubation was mainly due to pain during injection of propofol. The present study showed that preoperative volume loading is more efficacious than pre-induction administration of ephedrine sulphate in maintaining haemodynamic stability during rapid-sequence induction with propofol and succinylcholine. In addition, propofol in combination with succinylcholine provides excellent conditions for rapid-sequence intubation.

Age Spreads and the Temperature Dependence of Age Estimates in Upper Sco

NASA Astrophysics Data System (ADS)

Fang, Qiliang; Herczeg, Gregory J.; Rizzuto, Aaron

2017-06-01

Past estimates for the age of the Upper Sco Association are typically 11–13 Myr for intermediate-mass stars and 4–5 Myr for low-mass stars. In this study, we simulate populations of young stars to investigate whether this apparent dependence of estimated age on spectral type may be explained by the star formation history of the association. Solar and intermediate mass stars begin their pre-main sequence evolution on the Hayashi track, with fully convective interiors and cool photospheres. Intermediate-mass stars quickly heat up and transition onto the radiative Henyey track. As a consequence, for clusters in which star formation occurs on a timescale similar to that of the transition from a convective to a radiative interior, discrepancies in ages will arise when ages are calculated as a function of temperature instead of mass. Simple simulations of a cluster with constant star formation over several Myr may explain about half of the difference in inferred ages versus photospheric temperature; speculative constructions that consist of a constant star formation followed by a large supernova-driven burst could fully explain the differences, including those between F and G stars where evolutionary tracks may be more accurate. The age spreads of low-mass stars predicted from these prescriptions for star formation are consistent with the observed luminosity spread of Upper Sco. The conclusion that a lengthy star formation history will yield a temperature dependence in ages is expected from the basic physics of pre-main sequence evolution, and is qualitatively robust to the large uncertainties in pre-main sequence evolutionary models.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fang Qiliang; Herczeg, Gregory J.; Rizzuto, Aaron

Past estimates for the age of the Upper Sco Association are typically 11–13 Myr for intermediate-mass stars and 4–5 Myr for low-mass stars. In this study, we simulate populations of young stars to investigate whether this apparent dependence of estimated age on spectral type may be explained by the star formation history of the association. Solar and intermediate mass stars begin their pre-main sequence evolution on the Hayashi track, with fully convective interiors and cool photospheres. Intermediate-mass stars quickly heat up and transition onto the radiative Henyey track. As a consequence, for clusters in which star formation occurs on amore » timescale similar to that of the transition from a convective to a radiative interior, discrepancies in ages will arise when ages are calculated as a function of temperature instead of mass. Simple simulations of a cluster with constant star formation over several Myr may explain about half of the difference in inferred ages versus photospheric temperature; speculative constructions that consist of a constant star formation followed by a large supernova-driven burst could fully explain the differences, including those between F and G stars where evolutionary tracks may be more accurate. The age spreads of low-mass stars predicted from these prescriptions for star formation are consistent with the observed luminosity spread of Upper Sco. The conclusion that a lengthy star formation history will yield a temperature dependence in ages is expected from the basic physics of pre-main sequence evolution, and is qualitatively robust to the large uncertainties in pre-main sequence evolutionary models.« less

Evolutionary status of isolated B[e] stars

NASA Astrophysics Data System (ADS)

Lee, Chien-De; Chen, Wen-Ping; Liu, Sheng-Yuan

2016-08-01

Aims: We study a sample of eight B[e] stars with uncertain evolutionary status to shed light on the origin of their circumstellar dust. Methods: We performed a diagnostic analysis on the spectral energy distribution beyond infrared wavelengths, and conducted a census of neighboring region of each target to ascertain its evolutionary status. Results: In comparison to pre-main sequence Herbig stars, these B[e] stars show equally substantial excess emission in the near-infrared, indicative of existence of warm dust, but much reduced excess at longer wavelengths, so the dusty envelopes should be compact in size. Isolation from star-forming regions excludes the possibility of their pre-main sequence status. Six of our targets, including HD 50138, HD 45677, CD-24 5721, CD-49 3441, MWC 623, and HD 85567, have been previously considered as FS CMa stars, whereas HD 181615/6 and HD 98922 are added to the sample by this work. We argue that the circumstellar grains of these isolated B[e] stars, already evolved beyond the pre-main sequence phase, should be formed in situ. This is in contrast to Herbig stars, which inherit large grains from parental molecular clouds. It has been thought that HD 98922, in particular, is a Herbig star because of its large infrared excess, but we propose it being in a more evolved stage. Because dust condenses out of stellar mass loss in an inside-out manner, the dusty envelope is spatially confined, and anisotropic mass flows, or anomalous optical properties of tiny grains, lead to the generally low line-of-sight extinction toward these stars.

A NEAR-INFRARED STUDY OF THE STAR-FORMING REGION RCW 34

DOE Office of Scientific and Technical Information (OSTI.GOV)

Van der Walt, D. J.; De Villiers, H. M.; Czanik, R. J.

2012-07-15

We report the results of a near-infrared imaging study of a 7.8 Multiplication-Sign 7.8 arcmin{sup 2} region centered on the 6.7 GHz methanol maser associated with the RCW 34 star-forming region using the 1.4 m IRSF telescope at Sutherland. A total of 1283 objects were detected simultaneously in J, H, and K for an exposure time of 10,800 s. The J - H, H - K two-color diagram revealed a strong concentration of more than 700 objects with colors similar to what is expected of reddened classical T Tauri stars. The distribution of the objects on the K versus Jmore » - K color-magnitude diagram is also suggestive that a significant fraction of the 1283 objects is made up of lower mass pre-main-sequence stars. We also present the luminosity function for the subset of about 700 pre-main-sequence stars and show that it suggests ongoing star formation activity for about 10{sup 7} years. An examination of the spatial distribution of the pre-main-sequence stars shows that the fainter (older) part of the population is more dispersed over the observed region and the brighter (younger) subset is more concentrated around the position of the O8.5V star. This suggests that the physical effects of the O8.5V star and the two early B-type stars on the remainder of the cloud out of which they formed could have played a role in the onset of the more recent episode of star formation in RCW 34.« less

Mass loss from solar-type stars

NASA Technical Reports Server (NTRS)

Hartmann, L.

1985-01-01

The present picture of mass loss from solar-type (low-mass) stars is described, with special emphasis on winds from pre-main-sequence stars. Attention is given to winds from T Tauri stars and to angular momentum loss. Prospects are good for further advances in our understanding of the powerful mass loss observed from young stars; ultraviolet spectra obtainable with the Space Telescope should provide better estimates of mass loss rates and a clearer picture of physical conditions in the envelopes of these stars. To understand the mass ejection from old, slowly rotating main-sequence stars, we will have to study the sun.

Lithium in lower-main-sequence stars of the Alpha Persei cluster

NASA Technical Reports Server (NTRS)

Balachandran, Suchitra; Lambert, David L.; Stauffer, John R.

1988-01-01

Lithium abundances are presented for main-sequence stars of spectral types F, G, and K in the young open cluster Alpha Per. For 46 cluster members, a correlation between Li abundance and projected rotational velocity v sin i is found: all of the Li-poor stars are slow rotators. Two explanations are proposed to account for the correlation: (1) that the Li depletion is introduced following a rapid spin-down phase experienced by young low-mass stars, and that this episode of Li depletion may be the dominant one determining the spread of Li abundances among young low-mass main-sequence stars, and (2) that star formation has occurred over a finite period such that the older stars have undergone a spin-down and depletion of Li by a means that may or may not depend on rotation. The Li abundance in the warm and rapidly rotating stars appears to be undepleted, as is predicted by recent models of pre-main-sequence stars. The depletion observed in the cool stars exceeds the level predicted by these models.

The peculiar dipping events in the disc-bearing young-stellar object EPIC 204278916

NASA Astrophysics Data System (ADS)

Scaringi, S.; Manara, C. F.; Barenfeld, S. A.; Groot, P. J.; Isella, A.; Kenworthy, M. A.; Knigge, C.; Maccarone, T. J.; Ricci, L.; Ansdell, M.

2016-12-01

EPIC 204278916 has been serendipitously discovered from its K2 light curve that displays irregular dimmings of up to 65 per cent for ≈25 consecutive days out of 78.8 d of observations. For the remaining duration of the observations, the variability is highly periodic and attributed to stellar rotation. The star is a young, low-mass (M-type) pre-main-sequence star with clear evidence of a resolved tilted disc from Atacama Large Millimeter/submillimeter Array (ALMA) observations. We examine the K2 light curve in detail and hypothesize that the irregular dimmings are caused by either a warped inner disc edge or transiting cometary-like objects in either circular or eccentric orbits. The explanations discussed here are particularly relevant for other recently discovered young objects with similar absorption dips.

The Low-Mass Stellar Content of the Scorpius-Centaurus OB Association

NASA Technical Reports Server (NTRS)

Yorke, H.; Kunkel, M.; Brander, W.; Zinnecker, H.; Neuhauser, R.; Schmitt, J.; Mayor, M.; Udry, S.

2000-01-01

Based on ROSAT observations and data obtained with ground-based telescopes, we have carried out an extensive study of the low-mass pre-main-sequence population in Upper Scorpius, the youngest subgroup of the Scorpius-Centaurus OB association.

ASCA Observations of the T Tauri Star SU Aurigae and the Surrounding L1517 Dark Cloud

NASA Technical Reports Server (NTRS)

Skinner, Stephen L.; Walter, Frederick M.

1998-01-01

We present the results of a approximately equals 40 ks pointed Advanced Satellite for Cosmology and Astrophysics (ASCA) observation of the L1517 star-forming region, centered on the X-ray-bright T Tauri star SU Aurigae. This star has the highest X-ray luminosity of any classical T Tauri star in the Taurus-Auriga region, and its optical spectra show evidence for both mass inflow and outflow. Strong X-ray emission was detected from SU Aur (L(sub x) = 10(exp 30.9) ergs s(exp -1)) as well as weaker emission from five other pre-main-sequence stars. Although no large-amplitude flares were detected, the X-ray emission of SU Aur showed clear variability in the form of a slow decline in count rate during the 1.3 day observation. We provide the first direct comparison of the coronal differential emission measure (DEM) distribution of a classical T Tauri star with that of a young main-sequence star of similar spectral type. The DEM distributions of SU Aur (G2; age 3 Myr) and the young solar-like star EK Draconis (GO V; age 70 Myr) are qualitatively similar, with both showing a bimodal temperature distribution characterized by a cool plasma component peaking at approximately 8-9 MK and a hot component peaking at approximately 20-21 MK. However, there is a striking difference in the relative proportion of plasma at high temperatures in the two stars, with hot plasma (>20 MK) accounting for approximately equals 80% of the volume emission measure of SU Aur, compared to only approximately equals 40% in EK Dra. These results provide new insight into the changes that will occur in the corona of a T Tauri star as it descends onto the main sequence. A sharp decline in the fraction of coronal plasma at flarelike temperatures will occur during the late-T Tauri and post-T Tauri phases, and other recent X-ray studies have shown that this decline will continue after the young solar-like star reaches the main sequence.

Low emission internal combustion engine

DOEpatents

Karaba, Albert M.

1979-01-01

A low emission, internal combustion compression ignition engine having a cylinder, a piston movable in the cylinder and a pre-combustion chamber communicating with the cylinder near the top thereof and in which low emissions of NO.sub.x are achieved by constructing the pre-combustion chamber to have a volume of between 70% and 85% of the combined pre-chamber and main combustion chamber volume when the piston is at top dead center and by variably controlling the initiation of fuel injection into the pre-combustion chamber.

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

NASA Astrophysics Data System (ADS)

Jackson, R. J.; Jeffries, R. D.

2014-07-01

A polytropic model is used to investigate the effects of dark photospheric spots on the evolution and radii of magnetically active, low-mass (M < 0.5 M⊙), pre-main-sequence (PMS) stars. Spots slow the contraction along Hayashi tracks and inflate the radii of PMS stars by a factor of (1 - β)-N compared to unspotted stars of the same luminosity, where β is the equivalent covering fraction of dark starspots and N ≃ 0.45 ± 0.05. This is a much stronger inflation than predicted by Spruit & Weiss for main-sequence stars with the same β, where N ˜ 0.2-0.3. 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 zero-age main-sequence K-dwarfs have radii inflated by ˜10 per cent compared to an empirical radius-luminosity relation that is defined by magnetically inactive field dwarfs with interferometrically measured radii; low-mass M-type PMS stars, that are still on their Hayashi tracks, are inflated by up to ˜40 per cent. If this were attributable to starspots alone, we estimate that an effective spot coverage of 0.35 < β < 0.51 is required. Alternatively, global inhibition of convective flux transport by dynamo-generated fields may play a role. However, we find greater consistency with the starspot models when comparing the loci of active young stars and inactive field stars in colour-magnitude diagrams, particularly for the highly inflated PMS stars, where the large, uniform temperature reduction required in globally inhibited convection models would cause the stars to be much redder than observed.

Neural mechanisms of sequence generation in songbirds

NASA Astrophysics Data System (ADS)

Langford, Bruce

Animal models in research are useful for studying more complex behavior. For example, motor sequence generation of actions requiring good muscle coordination such as writing with a pen, playing an instrument, or speaking, may involve the interaction of many areas in the brain, each a complex system in itself; thus it can be difficult to determine causal relationships between neural behavior and the behavior being studied. Birdsong, however, provides an excellent model behavior for motor sequence learning, memory, and generation. The song consists of learned sequences of notes that are spectrographically stereotyped over multiple renditions of the song, similar to syllables in human speech. The main areas of the songbird brain involve in singing are known, however, the mechanisms by which these systems store and produce song are not well understood. We used a custom built, head-mounted, miniature motorized microdrive to chronically record the neural firing patterns of identified neurons in HVC, a pre-motor cortical nucleus which has been shown to be important in song timing. These were done in Bengalese finch which generate a song made up of stereotyped notes but variable note sequences. We observed song related bursting in neurons projecting to Area X, a homologue to basal ganglia, and tonic firing in HVC interneurons. Interneuron had firing rate patterns that were consistent over multiple renditions of the same note sequence. We also designed and built a light-weight, low-powered wireless programmable neural stimulator using Bluetooth Low Energy Protocol. It was able to generate perturbations in the song when current pulses were administered to RA, which projects to the brainstem nucleus responsible for syringeal muscle control.

Definition and empirical structure of the range of stellar chromospheres-coronae across the H-R diagram: Cool stars

NASA Technical Reports Server (NTRS)

Linsky, J. L.

1986-01-01

Major advances in our understanding of non-radiative heating and other activity in stars cooler than T sub eff = 10,000K has occured in the last few years. This observational evidence is reviewed and the trends that are now becoming apparent are discussed. The evidence for non-radiatively heated outer atmospheric layers (chromospheres, transition regions, and coronae) in dwarf stars cooler than spectral type A7, in F and G giants, pre-main sequence stars, and close bindary systems is unambiguous, as is the evidence for chromospheres in the K and M giants and supergiants. The existence of non-radiative heating in the outer layers of the A stars remains undetermined despite repeated searches at all wavelengths. Two important trends in the data are the decrease in plasma emission measure with age on the main sequence and decreasing rotational velocity. Variability and atmospheric inhomogeneity are commonly seen, and there is considerable evidence that magnetic fields define the geometry and control the energy balance in the outer atmospheric layers. In addition, the microwave observations imply that non-thermal electrons are confined in coronal magnetic flux tubes in at least the cool dwarfs and RS CVn systems. The chromospheres in the K and M giants and supergiants are geometrically extended, as are the coronae in the RS CVn systems and probably also in other stars.

Early-type objects in NGC 6611 and the Eagle Nebula

NASA Astrophysics Data System (ADS)

Martayan, C.; Floquet, M.; Hubert, A. M.; Neiner, C.; Frémat, Y.; Baade, D.; Fabregat, J.

2008-10-01

Aims: An important question about Be stars is whether they are born as such or whether they have become Be stars during their evolution. It is necessary to observe young clusters to answer this question. Methods: To this end, observations of stars in NGC 6611 and the star-formation region of Eagle Nebula were carried out with the ESO-WFI in slitless spectroscopic mode and at the VLT-GIRAFFE (R ≃ 6400-17 000). The targets for the GIRAFFE observations were pre-selected from the literature and our catalogue of emission-line stars based on the WFI study. GIRAFFE observations allowed us to study the population of the early-type stars accurately both with and without emission lines. For this study, we determined the fundamental parameters of OBA stars thanks to the GIRFIT code. We also studied the status of the objects (main sequence or pre-main sequence stars) by using IR data, membership probabilities, and location in HR diagrams. Results: The nature of the early-type stars with emission-line stars in NGC 6611 and its surrounding environment is derived. The slitless observations with the WFI clearly indicate a small number of emission-line stars in M16. We observed with GIRAFFE 101 OBA stars, among them 9 are emission-line stars with circumstellar emission in Hα. We found that W080 could be a new He-strong star, like W601. W301 is a possible classical Be star, W503 is a mass-transfer eclipsing binary with an accretion disk, and the other ones are possible Herbig Ae/Be stars. We also found that the rotational velocities of main sequence B stars are 18% lower than those of pre-main sequence B stars, in good agreement with theory about the evolution of rotational velocities. Combining adaptive optics, IR data, spectroscopy, and radial velocity indications, we found that 27% of the B-type stars are binaries. We also redetermined the age of NGC 6611 found equal to 1.2-1.8 Myears, in good agreement with the most recent determinations.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Somers, Garrett; Pinsonneault, Marc H., E-mail: somers@astronomy.ohio-state.edu, E-mail: pinsono@astronomy.ohio-state.edu

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 Limore » 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.« less

Analysis of human papillomavirus 16 E6, E7 genes and Long Control Region in cervical samples from Uruguayan women.

PubMed

Ramas, Viviana; Mirazo, Santiago; Bonilla, Sylvia; Ruchansky, Dora; Arbiza, Juan

2018-05-15

This study aims to investigate the HPV16 variant distribution by sequence analyses of E6, E7 oncogenes and the Long Control Region (LCR), from cervical cells collected from Uruguayan women, and to reconstruct the phylogenetic relationships among variants. Forty-seven HPV16 variants, obtained from women with HSIL, LSIL, ASCUS and NILM cytological classes were analyzed for LCR and 12 were further studied for E6 and E7. Detailed sequence comparison, genetic heterogeneity analyses and phylogenetic reconstruction were performed. A high variability was observed among LCR sequences, which were distributed in 18 different variants. E6 and E7 sequences exhibited novel non-synonymous substitutions. Uruguayan sequences mainly belonged to the European lineage, and only 5 sequences clustered in non-European branches; 3 of them in the Asian-American and North-American linage and 2 in an African branch. Additionally, 6 new variants from European and African clusters were identified. HPV16 isolates mainly belonged to the European lineage, though strains from African and Asian-American lineages were also identified. Herein is reported for the first time the distribution and molecular characterization of HPV16 variants from Uruguay, providing novel insights on the molecular epidemiology of this infectious disease in the South America. A high variability among HPV 16 isolates mainly belonged to European lineage, provides an extensive sequence dataset from a country with high burden of cervical cancer. Copyright © 2018 Elsevier B.V. All rights reserved.

Let-7 miRNA Precursors Co-express with LIN28B in Cervical Cells.

PubMed

Zamora-Contreras, Aida Margarita; Alvarez-Salas, Luis Marat

2018-01-01

The let-7 microRNAs (miRNAs) are frequently dysregulated in carcinogenic processes, including cervical cancer. LIN28 proteins regulate let-7 biogenesis by binding to conserved sequences within the pre-miRNA structure. Nevertheless, recent research has shown that some let-7 miRNAs may escape LIN28 regulation. Correlate pre-let-7 miRNAs and LIN28B levels in cervical cell lines with different malignancy and HPV content. Pre-let-7 levels were determined by RTqPCR. LIN28B and other let-7 targets were analyzed by immunoblot. In silico tools were used to correlate let-7 and LIN28B expression and to analyze prelet- 7 sequences and structures. Lin28B protein was detected in all tested cell lines although it was more expressed in tumor cell lines. High levels of pre-let-7c/f-1 and pre-miR-98 were present in almost all cell lines regardless malignancy and LIN28B expression. Pre-let-7g/i were mainly expressed in tumor cell lines, pre-let-7e and pre-let-7-a3 were absent in all cell lines and pre-let-7a-2 showed indistinct expression. LIN28B showed positive correlation with pre-let-7i/g/f-1 and pre-miR-98 in tumor cell lines, suggesting escape from regulation. Sequence alignment and analysis of pre-let-7 miRNAs showed distinctive structural features within the preE region that may influence the ideal pre-let-7 structuring for LIN28B interaction. Short preE-stems were present in pre-let-7 that may escape LIN28B regulation, but long preEstems were mostly associated with high-level pre-let-7 miRNAs. The observed differences of pre-let-7 levels in cervical cell lines may be the result of alternative preE structuring affecting interaction with LIN28B thus resulting in differential let-7 regulation. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

The CIDA-QUEST large-scale survey of Orion OB1: evidence for rapid disk dissipation in a dispersed stellar population.

PubMed

Briceño, C; Vivas, A K; Calvet, N; Hartmann, L; Pacheco, R; Herrera, D; Romero, L; Berlind, P; Sánchez, G; Snyder, J A; Andrews, P

2001-01-05

We are conducting a large-scale, multiepoch, optical photometric survey [Centro de Investigaciones de Astronomia-Quasar Equatorial Survey Team (CIDA-QUEST)] covering about 120 square degrees to identify the young low-mass stars in the Orion OB1 association. We present results for an area of 34 square degrees. Using photometric variability as our main selection criterion, as well as follow-up spectroscopy, we confirmed 168 previously unidentified pre-main sequence stars that are about 0.6 to 0.9 times the mass of the sun (Mo), with ages of about 1 million to 3 million years (Ori OB1b) and about 3 million to 10 million years (Ori OB1a). The low-mass stars are spatially coincident with the high-mass (at least 3 Mo) members of the associations. Indicators of disk accretion such as Halpha emission and near-infrared emission from dusty disks fall sharply from Ori OB1b to Ori OB1a, indicating that the time scale for disk dissipation and possibly the onset of planet formation is a few million years.

Substantial reservoirs of molecular hydrogen in the debris disks around young stars.

PubMed

Thi, W F; Blake, G A; van Dishoeck, E F; van Zadelhoff, G J; Horn, J M; Becklin, E E; Mannings, V; Sargent, A I; van Den Ancker, M E; Natta, A

2001-01-04

Circumstellar accretion disks transfer matter from molecular clouds to young stars and to the sites of planet formation. The disks observed around pre-main-sequence stars have properties consistent with those expected for the pre-solar nebula from which our own Solar System formed 4.5 Gyr ago. But the 'debris' disks that encircle more than 15% of nearby main-sequence stars appear to have very small amounts of gas, based on observations of the tracer molecule carbon monoxide: these observations have yielded gas/dust ratios much less than 0.1, whereas the interstellar value is about 100 (ref. 9). Here we report observations of the lowest rotational transitions of molecular hydrogen (H2) that reveal large quantities of gas in the debris disks around the stars beta Pictoris, 49 Ceti and HD135344. The gas masses calculated from the data are several hundreds to a thousand times greater than those estimated from the CO observations, and yield gas/dust ratios of the same order as the interstellar value.

IUE observations of pre-main-sequence stars. I - Mg II and Ca II resonance line fluxes for T Tauri stars

NASA Technical Reports Server (NTRS)

Giampapa n, M. S.

1981-01-01

IUE satellite and Lick 3 m reflector image tube scanner measurements of the Mg II and Ca II resonance lines in a sample of T Tauri stars are the basis of a discussion of the Mg II h and k line emission and the Ca II H and K line emission, within the context of stellar chromospheres. Corroborative evidence is presented for the chromospheric origin of these resonance lines, and chromospheric radiative loss rates in the Mg II and Ca II resonance lines are derived. It is found that the degree of nonradiative heating present in the outer atmospheres of T Tauri stars generally exceeds that of the RS CVn systems, as well as the dMe stars and other active chromospheric dwarfs, and it is inferred that the surfaces of such pre-main sequence stars are covered by regions similar to solar plages. The mean chromospheric electron density of T Tauri stars is determined as 10 to the 11th/cu cm.

Rates and delay times of Type Ia supernovae in the helium-enriched main-sequence donor scenario

NASA Astrophysics Data System (ADS)

Liu, Zheng-Wei; Stancliffe, Richard J.

2018-04-01

The nature of the progenitors of Type Ia supernovae (SNe Ia) remains a mystery. Comparing theoretical rates and delay-time distributions of SNe Ia with those inferred observationally can constrain their progenitor models. In this work, taking thermohaline mixing into account in the helium-enriched main-sequence (HEMS) donor scenario, we address rates and delay times of SNe Ia in this channel by combining the results of self-consistent binary evolution calculations with population synthesis models. We find that the Galactic SN Ia rate from the HEMS donor scenario is around 0.6-1.2 × 10-3 yr-1, which is about 30 per cent of the observed rate. Delay times of SNe Ia in this scenario cover a wide range of 0.1-1.0 Gyr. We also present the pre-explosion properties of companion stars in the HEMS donor scenario, which will be helpful for placing constraints on SN Ia progenitors through analysing their pre-explosion images.

Accretion in Close Pre-Main-Sequence Binaries

NASA Astrophysics Data System (ADS)

Ardila, David

2010-09-01

We propose to use COS to observe the circumbinary accretion flow in pre-main sequence binaries as a function of orbital phase. These observations will help us understand how the magnetosphere captures circumbinary gas, test model predictions regarding the importance of the mass ratio in directing the accretion flows, and study the kinematics of the gas filling the circumbinary gap. We will observe UZ Tau E {mass ratio q=0.3, e=0.33} and DQ Tau {q=1, e=0.58} in four phases, over three orbital periods, using G160M and G230L. The targets are Classical T Tauri stars for which the circumstellar disks are severely truncated. Our primary observables will be the CIV {1550 A} lines, formed at the footpoints of the accretion flow onto the star. We expect to observe the ebb and flow of the line shape, centroid, and flux as a function of orbital phase. The low-resolution NUV continuum observations will provide an independent measurement of the total accretion rate.

Second Language Idiom Learning: The Effects of Lexical Knowledge and Pedagogical Sequencing

ERIC Educational Resources Information Center

Zyzik, Eve

2011-01-01

This article examines the acquisition of Spanish idioms in a classroom setting that was supplemented with explicit instruction over a 10-week period. The research design manipulated two variables: prior lexical knowledge and idiom organization. Sixty-five second language (L2) learners completed pre- and posttests that measured their ability to…

Analysis of reflection effects in HS 2333+3927

NASA Astrophysics Data System (ADS)

Shimanskii, V. V.; Yakin, D. G.; Borisov, N. V.; Bikmaev, I. F.

2012-11-01

The results of photometric and spectroscopic observations of the pre-cataclysmic variable HS 2333+3927, which is a HW Vir binary system, are analyzed. The parameters of the sdB subdwarf companion ( T eff = 37 500 ± 500 K, log g = 5.7 ± 0.05) and the chemical composition of its atmosphere are refined using a spectrum of the binary system obtained at minimum brightness. Reflection effects can fully explain the observed brightness variations of HS 2333+3927, changes in the HI and HeI line profiles, and distortions of the radial-velocity curve of the primary star. A new method for determining the component-mass ratios in HW Vir binaries, based on their radial-velocity curves and models of irradiated atmospheres, is proposed. The set of parameters obtained for the binary components corresponds to models of horizontal-branch sdB subdwarfs and main-sequence stars.

VARIABILITY OF DISK EMISSION IN PRE-MAIN SEQUENCE AND RELATED STARS. III. EXPLORING STRUCTURAL CHANGES IN THE PRE-TRANSITIONAL DISK IN HD 169142

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wagner, Kevin R.; Sitko, Michael L.; Swearingen, Jeremy R.

We present near-IR (NIR) 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 μm over a maximum timescale of 10 yr. 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 β and Brmore » γ lines in our data we derive a mass accretion rate in 2013 May of M-dot ≈ (1.5-2.7) × 10{sup –9} M {sub ☉} yr{sup –1}. 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 yr of observations. We find that shifting the outer edge (r ≈ 0.3 AU) of the inner disk by 0.05 AU toward the star (in simulation of accretion and/or sculpting by forming planets) successfully reproduces the shift in NIR flux. We establish that the ∼40-70 AU dark ring imaged in the NIR by Quanz et al. and Momose et al. and at 7 mm by Osorio et al. may be reproduced with a 30% scaled density profile throughout the region, strengthening the link to this structure being dynamically cleared by one or more planetary mass bodies.« less

Introduced T cell receptor variable region gene segments recombine in pre-B cells: evidence that B and T cells use a common recombinase.

PubMed

Yancopoulos, G D; Blackwell, T K; Suh, H; Hood, L; Alt, F W

1986-01-31

We have recently proposed that a common recombinase performs all of the many variable region gene assembly events in B and T cells, and that the specificity of these joining events is mediated by regulating the "accessibility" of the involved gene segments. To test this possibility, we have introduced "accessible" T cell receptor (TCR) variable region gene segments into a pre-B cell line capable of recombining endogenous and transfected immunoglobulin (Ig) variable region gene segments. Although the corresponding "inaccessible" endogenous TCR gene segments do not rearrange in this line or in B cells in general, the introduced TCR gene segments join very frequently and, in fact, closely resemble introduced Ig gene segments in their recombination characteristics. These observations suggest a new role for conventional Ig transcriptional enhancers--recombinational enhancement. Our studies provide insight into additional aspects of the joining mechanism such as N region insertion, aberrant joining, and recombination-recognition sequence requirements for joining.

Massive pre-main-sequence stars in M17

NASA Astrophysics Data System (ADS)

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

Overview of Petroleum Settings in Deep Waters of the Brazilian South Atlantic Margin

NASA Astrophysics Data System (ADS)

Anjos, Sylvia; Penteado, Henrique; Oliveira, Carlos M. M.

2015-04-01

The objective of this work is to present an overall view of the tectonic and stratigraphic evolution of the western South Atlantic with focus on the Brazilian marginal basins. It includes the structural evolution, stratigraphic sequences, depositional environments and petroleum systems model along the Brazilian marginal basins. In addition, a description of the main petroleum provinces and selected plays including the pre-salt carbonates and post-salt turbidite reservoirs is presented. Source-rock ages and types, trap styles, main reservoir characteristics, petroleum compositions, and recent exploration results are discussed. Finally, an outlook and general assessment of the impact of the large pre-salt discoveries on the present-day and future production curves are given.

Genetic Characterization of the Fish Piaractus brachypomus by Microsatellites Derived from Transcriptome Sequencing.

PubMed

Jorge, Paulo H; Mastrochirico-Filho, Vito A; Hata, Milene E; Mendes, Natália J; Ariede, Raquel B; de Freitas, Milena Vieira; Vera, Manuel; Porto-Foresti, Fábio; Hashimoto, Diogo T

2018-01-01

The pirapitinga, Piaractus brachypomus (Characiformes, Serrasalmidae), is a fish from the Amazon basin and is considered to be one of the main native species used in aquaculture production in South America. The objectives of this study were: (1) to perform liver transcriptome sequencing of pirapitinga through NGS and then validate a set of microsatellite markers for this species; and (2) to use polymorphic microsatellites for analysis of genetic variability in farmed stocks. The transcriptome sequencing was carried out through the Roche/454 technology, which resulted in 3,696 non-redundant contigs. Of this total, 2,568 contigs had similarity in the non-redundant (nr) protein database (Genbank) and 2,075 sequences were characterized in the categories of Gene Ontology (GO). After the validation process of 30 microsatellite loci, eight markers showed polymorphism. The analysis of these polymorphic markers in farmed stocks revealed that fish farms from North Brazil had a higher genetic diversity than fish farms from Southeast Brazil. AMOVA demonstrated that the highest proportion of variation was presented within the populations. However, when comparing different groups (1: Wild; 2: North fish farms; 3: Southeast fish farms), a considerable variation between the groups was observed. The F ST values showed the occurrence of genetic structure among the broodstocks from different regions of Brazil. The transcriptome sequencing in pirapitinga provided important genetic resources for biological studies in this non-model species, and microsatellite data can be used as the framework for the genetic management of breeding stocks in Brazil, which might provide a basis for a genetic pre-breeding programme.

Stellar Variability at the Main-sequence Turnoff of the Intermediate-age LMC Cluster NGC 1846

NASA Astrophysics Data System (ADS)

Salinas, R.; Pajkos, M. A.; Vivas, A. K.; Strader, J.; Contreras Ramos, R.

2018-04-01

Intermediate-age (IA) star clusters in the Large Magellanic Cloud (LMC) present extended main-sequence turn-offs (MSTO) that have been attributed to either multiple stellar populations or an effect of stellar rotation. Recently it has been proposed that these extended main sequences can also be produced by ill-characterized stellar variability. Here we present Gemini-S/Gemini Multi-Object Spectrometer (GMOS) time series observations of the IA cluster NGC 1846. Using differential image analysis, we identified 73 new variable stars, with 55 of those being of the Delta Scuti type, that is, pulsating variables close the MSTO for the cluster age. Considering completeness and background contamination effects, we estimate the number of δ Sct belonging to the cluster between 40 and 60 members, although this number is based on the detection of a single δ Sct within the cluster half-light radius. This amount of variable stars at the MSTO level will not produce significant broadening of the MSTO, albeit higher-resolution imaging will be needed to rule out variable stars as a major contributor to the extended MSTO phenomenon. Though modest, this amount of δ Sct makes NGC 1846 the star cluster with the highest number of these variables ever discovered. Lastly, our results present a cautionary tale about the adequacy of shallow variability surveys in the LMC (like OGLE) to derive properties of its δ Sct population. Based on observations obtained at the Gemini Observatory, which is operated by the Association of Universities for Research in Astronomy, Inc., under a cooperative agreement with the NSF on behalf of the Gemini partnership: the National Science Foundation (United States), the National Research Council (Canada), CONICYT (Chile), Ministerio de Ciencia, Tecnología e Innovación Productiva (Argentina), and Ministério da Ciência, Tecnologia e Inovação (Brazil).

Variability of Disk Emission in Pre-Main Sequence and Related Stars. I. HD 31648 and HD 163296 - Isolated Herbig Ae Stars Driving Herbig-Haro Flows

NASA Technical Reports Server (NTRS)

Sitko, Michael L.; Carpenter, William J.; Kimes, Robin L.; Lynch, David K.; Russell, Ray W.; Rudy, Richard J.; Mazuk, Stephan M.; Venturini, Catherine C.; Puetter, Richard C.; Grady, Carol A.;

Variability of Disk Emission in Pre-Main-Sequence and Related Stars. I. HD 31648 and HD 163296: Isolated Herbig Ae Stars Driving Herbig-Haro Flows

NASA Astrophysics Data System (ADS)

Sitko, Michael L.; Carpenter, William J.; Kimes, Robin L.; Wilde, J. Leon; Lynch, David K.; Russell, Ray W.; Rudy, Richard J.; Mazuk, Stephan M.; Venturini, Catherine C.; Puetter, Richard C.; Grady, Carol A.; Polomski, Elisha F.; Wisnewski, John P.; Brafford, Suellen M.; Hammel, H. B.; Perry, R. Brad

2008-05-01

Infrared photometry and spectroscopy covering a time span of a quarter-century are presented for HD 31648 (MWC 480) and HD 163296 (MWC 275). Both are isolated Herbig Ae stars that exhibit signs of active accretion, including driving bipolar flows with embedded Herbig-Haro (HH) objects. HD 163296 was found to be relatively quiescent photometrically in its inner disk region, with the exception of a major increase in emitted flux in a broad wavelength region centered near 3 μm in 2002. In contrast, HD 31648 has exhibited sporadic changes in the entire 3-13 μm region throughout this span of time. In both stars, the changes in the 1-5 μm flux indicate structural changes in the region of the disk near the dust sublimation zone, possibly causing its distance from the star to vary with time. Repeated thermal cycling through this region will result in the preferential survival of large grains, and an increase in the degree of crystallinity. The variability observed in these objects has important consequences for the interpretation of other types of observations. For example, source variability will compromise models based on interferometry measurements unless the interferometry observations are accompanied by nearly simultaneous photometric data.

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

NASA Astrophysics Data System (ADS)

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.

A multi-wavelength study of pre-main sequence stars in the Taurus-Auriga star-forming region

NASA Astrophysics Data System (ADS)

Guenther, E. W.; Stelzer, B.; Neuhäuser, R.; Hillwig, T. C.; Durisen, R. H.; Menten, K. M.; Greimel, R.; Barwig, H.; Englhauser, J.; Robb, R. M.

2000-05-01

Although many lowmass pre-main sequence stars are strong X-ray sources, the origin of the X-ray emission is not well known. Since these objects are variable at all frequencies, simultaneous observations in X-rays and in other wavelengths are able to constrain the properties of the X-ray emitting regions. In this paper, we report quasi-simultaneous observations in X-rays, the optical, and the radio regime for classical and weak-line T Tauri stars from the Taurus-Auriga star-forming region. We find that all detected T Tauri stars show significant night-to-night variations of the X-ray emission. For three of the stars, FM Tau and CW Tau, both classical T Tauri stars, and V773 Tau, a weak-line T Tauri star, the variations are especially large. From observations taken simultaneously, we also find that there is some correspondence between the strength of Hα and the X-ray brightness in V773 Tau. The lack of a strong correlation leads us to conclude that the X-ray emission of V773 Tau is not a superposition of flares. However, we suggest that a weak correlation occurs because chromospherically active regions and regions of strong X-ray emission are generally related. V773 Tau was detected at 8.46 GHz as a weakly circularly polarised but highly variable source. We also find that the X-ray emission and the equivalent width of Hα remained unchanged, while large variations of the flux density in the radio regime were observed. This clearly indicates that the emitting regions are different. Using optical spectroscopy we detected a flare in Hα and event which showed a flare-like light-curve of the continuum brightness in FM Tau. However, ROSAT did not observe the field at the times of these flares. Nevertheless, an interesting X-ray event was observed in V773 Tau, during which the flux increased for about 8 hours and then decreased back to the same level in 5 hours. We interpret this as a long-duration event similar to those seen on the sun and other active stars. In the course of the observations, we discovered a new weak-line T Tauri star, GSC-1839-5674. Results are also presented for several other stars in the ROSAT field.

The complete mitochondrial genome sequence of the Tibetan red fox (Vulpes vulpes montana).

PubMed

Zhang, Jin; Zhang, Honghai; Zhao, Chao; Chen, Lei; Sha, Weilai; Liu, Guangshuai

2015-01-01

In this study, the complete mitochondrial genome of the Tibetan red fox (Vulpes Vulpes montana) was sequenced for the first time using blood samples obtained from a wild female red fox captured from Lhasa in Tibet, China. Qinghai--Tibet Plateau is the highest plateau in the world with an average elevation above 3500 m. Sequence analysis showed it contains 12S rRNA gene, 16S rRNA gene, 22 tRNA genes, 13 protein-coding genes and 1 control region (CR). The variable tandem repeats in CR is the main reason of the length variability of mitochondrial genome among canide animals.

Gene sequence variability of the three surface proteins of human respiratory syncytial virus (HRSV) in Texas.

PubMed

Tapia, Lorena I; Shaw, Chad A; Aideyan, Letisha O; Jewell, Alan M; Dawson, Brian C; Haq, Taha R; Piedra, Pedro A

2014-01-01

Human respiratory syncytial virus (HRSV) has three surface glycoproteins: small hydrophobic (SH), attachment (G) and fusion (F), encoded by three consecutive genes (SH-G-F). A 270-nt fragment of the G gene is used to genotype HRSV isolates. This study genotyped and investigated the variability of the gene and amino acid sequences of the three surface proteins of HRSV strains collected from 1987 to 2005 from one center. Sixty original clinical isolates and 5 prototype strains were analyzed. Sequences containing SH, F and G genes were generated, and multiple alignments and phylogenetic trees were analyzed. Genetic variability by protein domains comparing virus genotypes was assessed. Complete sequences of the SH-G-F genes were obtained for all 65 samples: HRSV-A = 35; HRSV-B = 30. In group A strains, genotypes GA5 and GA2 were predominant. For HRSV-B strains, the genotype GB4 was predominant from 1992 to 1994 and only genotype BA viruses were detected in 2004-2005. Different genetic variability at nucleotide level was detected between the genes, with G gene being the most variable and the highest variability detected in the 270-nt G fragment that is frequently used to genotype the virus. High variability (>10%) was also detected in the signal peptide and transmembrane domains of the F gene of HRSV A strains. Variability among the HRSV strains resulting in non-synonymous changes was detected in hypervariable domains of G protein, the signal peptide of the F protein, a not previously defined domain in the F protein, and the antigenic site Ø in the pre-fusion F. Divergent trends were observed between HRSV -A and -B groups for some functional domains. A diverse population of HRSV -A and -B genotypes circulated in Houston during an 18 year period. We hypothesize that diverse sequence variation of the surface protein genes provide HRSV strains a survival advantage in a partially immune-protected community.

Gene Sequence Variability of the Three Surface Proteins of Human Respiratory Syncytial Virus (HRSV) in Texas

PubMed Central

Tapia, Lorena I.; Shaw, Chad A.; Aideyan, Letisha O.; Jewell, Alan M.; Dawson, Brian C.; Haq, Taha R.; Piedra, Pedro A.

2014-01-01

Human respiratory syncytial virus (HRSV) has three surface glycoproteins: small hydrophobic (SH), attachment (G) and fusion (F), encoded by three consecutive genes (SH-G-F). A 270-nt fragment of the G gene is used to genotype HRSV isolates. This study genotyped and investigated the variability of the gene and amino acid sequences of the three surface proteins of HRSV strains collected from 1987 to 2005 from one center. Sixty original clinical isolates and 5 prototype strains were analyzed. Sequences containing SH, F and G genes were generated, and multiple alignments and phylogenetic trees were analyzed. Genetic variability by protein domains comparing virus genotypes was assessed. Complete sequences of the SH-G-F genes were obtained for all 65 samples: HRSV-A = 35; HRSV-B = 30. In group A strains, genotypes GA5 and GA2 were predominant. For HRSV-B strains, the genotype GB4 was predominant from 1992 to 1994 and only genotype BA viruses were detected in 2004–2005. Different genetic variability at nucleotide level was detected between the genes, with G gene being the most variable and the highest variability detected in the 270-nt G fragment that is frequently used to genotype the virus. High variability (>10%) was also detected in the signal peptide and transmembrane domains of the F gene of HRSV A strains. Variability among the HRSV strains resulting in non-synonymous changes was detected in hypervariable domains of G protein, the signal peptide of the F protein, a not previously defined domain in the F protein, and the antigenic site Ø in the pre-fusion F. Divergent trends were observed between HRSV -A and -B groups for some functional domains. A diverse population of HRSV -A and -B genotypes circulated in Houston during an 18 year period. We hypothesize that diverse sequence variation of the surface protein genes provide HRSV strains a survival advantage in a partially immune-protected community. PMID:24625544

Variability in Reading Ability Gains as a Function of Computer-Assisted Instruction Method of Presentation

ERIC Educational Resources Information Center

Johnson, Erin Phinney; Perry, Justin; Shamir, Haya

2010-01-01

This study examines the effects on early reading skills of three different methods of presenting material with computer-assisted instruction (CAI): (1) learner-controlled picture menu, which allows the student to choose activities, (2) linear sequencer, which progresses the students through lessons at a pre-specified pace, and (3) mastery-based…

Variability of Disk Emission in Pre-main-sequence and Related Stars. IV. Investigating the Structural Changes in the Inner Disk Region of MWC 480

NASA Astrophysics Data System (ADS)

Fernandes, Rachel B.; Long, Zachary C.; Pikhartova, Monika; Sitko, Michael L.; Grady, Carol A.; Russell, Ray W.; Luria, David M.; Tyler, Dakotah B.; Bayyari, Ammar; Danchi, William; Wisniewski, John P.

2018-04-01

We present five epochs of near-IR observations of the protoplanetary disk around MWC 480 (HD 31648) obtained with the SpeX spectrograph on NASA’s Infrared Telescope Facility between 2007 and 2013, inclusive. Using the measured line fluxes in the Pa β and Br γ lines, we found the mass accretion rates to be (1.26–2.30) × 10‑7 M ⊙ yr‑1 and (1.4–2.01) × 10‑7 M ⊙ yr‑1, respectively, but which varied by more than 50% from epoch to epoch. The spectral energy distribution reveals a variability of about 30% between 1.5 and 10 μm during this same period of time. We investigated the variability using of the continuum emission of the disk in using the Monte-Carlo Radiative Transfer Code HOCHUNK3D. We find that varying the height of the inner rim successfully produces a change in the NIR flux but lowers the far-IR emission to levels below all measured fluxes. Because the star exhibits bipolar flows, we utilized a structure that simulates an inner disk wind to model the variability in the near-IR, without producing flux levels in the far-IR that are inconsistent with existing data. For this object, variable near-IR emission due to such an outflow is more consistent with the data than changing the scale height of the inner rim of the disk.

Variable X-ray Emission from FU Orionis

NASA Astrophysics Data System (ADS)

Skinner, Steve L.; Guedel, M.; Briggs, K. R.; Lamzin, S. A.; Sokal, K. R.

2009-05-01

FU Orionis is the prototype of a small but remarkable class of pre-main sequence stars ('FUors') that have undergone large optical outbursts thought to be linked to episodic accretion. FU Ori increased in optical brightness by about 6 mag in 1936-37 and is still in slow decline. Because of their high accretion rates, FUors are good candidates for exploring potential effects of accretion on X-ray emission. A recently completed survey of FUors with XMM-Newton detected X-rays from FU Ori and V1735 Cyg. We present new results from a sensitive 99 ksec (1.15 day) follow-up X-ray observation of FU Ori with Chandra. The Chandra ACIS-S CCD spectrum confirms the presence of a cool plasma component (kT < 1 keV) viewed under moderate absorption and a much hotter component (kT > 3 keV), viewed under high absorption, in accord with previous XMM results. The uninterrupted Chandra light curve shows that the hot component is slowly variable on a timescale of one day, but no variability is detected in the cool component. The slow variability and high plasma temperature point to a magnetic origin for the hot component, but other mechanisms (including accretion) may be responsible for the cool non-variable component. We will discuss these new results in the context of what is known about FU Ori from previous observations, including XMM (Skinner et al. 2006, ApJ, 643, 995) and HST (Kravtsova et al. 2007, Ast. Ltrs., 33, 755).

Towards the Rational Design of a Candidate Vaccine against Pregnancy Associated Malaria: Conserved Sequences of the DBL6ε Domain of VAR2CSA

PubMed Central

Badaut, Cyril; Bertin, Gwladys; Rustico, Tatiana; Fievet, Nadine; Massougbodji, Achille; Gaye, Alioune; Deloron, Philippe

2010-01-01

Background Placental malaria is a disease linked to the sequestration of Plasmodium falciparum infected red blood cells (IRBC) in the placenta, leading to reduced materno-fetal exchanges and to local inflammation. One of the virulence factors of P. falciparum involved in cytoadherence to chondroitin sulfate A, its placental receptor, is the adhesive protein VAR2CSA. Its localisation on the surface of IRBC makes it accessible to the immune system. VAR2CSA contains six DBL domains. The DBL6ε domain is the most variable. High variability constitutes a means for the parasite to evade the host immune response. The DBL6ε domain could constitute a very attractive basis for a vaccine candidate but its reported variability necessitates, for antigenic characterisations, identifying and classifying commonalities across isolates. Methodology/Principal Findings Local alignment analysis of the DBL6ε domain had revealed that it is not as variable as previously described. Variability is concentrated in seven regions present on the surface of the DBL6ε domain. The main goal of our work is to classify and group variable sequences that will simplify further research to determine dominant epitopes. Firstly, variable sequences were grouped following their average percent pairwise identity (APPI). Groups comprising many variable sequences sharing low variability were found. Secondly, ELISA experiments following the IgG recognition of a recombinant DBL6ε domain, and of peptides mimicking its seven variable blocks, allowed to determine an APPI cut-off and to isolate groups represented by a single consensus sequence. Conclusions/Significance A new sequence approach is used to compare variable regions in sequences that have extensive segmental gene relationship. Using this approach, the VAR2CSA DBL6 domain is composed of 7 variable blocks with limited polymorphism. Each variable block is composed of a limited number of consensus types. Based on peptide based ELISA, variable blocks with 85% or greater sequence identity are expected to be recognized equally well by antibody and can be considered the same consensus type. Therefore, the analysis of the antibody response against the classified small number of sequences should be helpful to determine epitopes. PMID:20585655

Characterizing Intermediate-Mass, Pre-Main-Sequence Stars via X-Ray Emision

NASA Astrophysics Data System (ADS)

Haze Nunez, Evan; Povich, Matthew Samuel; Binder, Breanna Arlene; Broos, Patrick; Townsley, Leisa K.

2018-01-01

The X-ray emission from intermediate-mass, pre-main-sequence stars (IMPS) can provide useful constraints on the ages of very young (${<}5$~Myr) massive star forming regions. IMPS have masses between 2 and 8 $M_{\\odot}$ and are getting power from the gravitational contraction of the star. Main-sequence late-B and A-type stars are not expected to be strong X-ray emitters, because they lack the both strong winds of more massive stars and the magneto-coronal activity of lower-mass stars. There is, however, mounting evidence that IMPS are powerful intrinsic x-ray emitters during their convection-dominated early evolution, before the development and rapid growth of a radiation zone. We present our prime candidates for intrinsic, coronal X-ray emission from IMPS identified in the Chandra Carina Complex Project. The Carina massive star-forming complex is of special interest due to the wide variation of star formation stages within the region. Candidate IMPS were identified using infrared spectral energy distribution (SED) models. X-ray properties, including thermal plasma temperatures and absorption-corrected fluxes, were derived from XSPEC fits performed using absorption ($N_{H}$) constrained by the extinction values returned by the infrared SED fits. We find that IMPS have systematically higher X-ray luminosities compared to their lower-mass cousins, the TTauri stars.This work is supported by the National Science Foundation under grant CAREER-1454334 and by NASA through Chandra Award 18200040.

The detectability of radio emission from exoplanets

NASA Astrophysics Data System (ADS)

Lynch, C. R.; Murphy, Tara; Lenc, E.; Kaplan, D. L.

2018-05-01

Like the magnetised planets in our Solar System, magnetised exoplanets should emit strongly at radio wavelengths. Radio emission directly traces the planetary magnetic fields and radio detections can place constraints on the physical parameters of these features. Large comparative studies of predicted radio emission characteristics for the known population of exoplanets help to identify what physical parameters could be key for producing bright, observable radio emission. Since the last comparative study, many thousands of exoplanets have been discovered. We report new estimates for the radio flux densities and maximum emission frequencies for the current population of known exoplanets orbiting pre-main sequence and main-sequence stars with spectral types F-M. The set of exoplanets predicted to produce observable radio emission are Hot Jupiters orbiting young stars. The youth of these system predicts strong stellar magnetic fields and/or dense winds, which are key for producing bright, observable radio emission. We use a new all-sky circular polarisation Murchison Widefield Array survey to place sensitive limits on 200 MHz emission from exoplanets, with 3σ values ranging from 4.0 - 45.0 mJy. Using a targeted Giant Metre Wave Radio Telescope observing campaign, we also report a 3σ upper limit of 4.5 mJy on the radio emission from V830 Tau b, the first Hot Jupiter to be discovered orbiting a pre-main sequence star. Our limit is the first to be reported for the low-frequency radio emission from this source.

Evaluation of Quality Assessment Protocols for High Throughput Genome Resequencing Data

PubMed Central

Chiara, Matteo; Pavesi, Giulio

2017-01-01

Large-scale initiatives aiming to recover the complete sequence of thousands of human genomes are currently being undertaken worldwide, concurring to the generation of a comprehensive catalog of human genetic variation. The ultimate and most ambitious goal of human population scale genomics is the characterization of the so-called human “variome,” through the identification of causal mutations or haplotypes. Several research institutions worldwide currently use genotyping assays based on Next-Generation Sequencing (NGS) for diagnostics and clinical screenings, and the widespread application of such technologies promises major revolutions in medical science. Bioinformatic analysis of human resequencing data is one of the main factors limiting the effectiveness and general applicability of NGS for clinical studies. The requirement for multiple tools, to be combined in dedicated protocols in order to accommodate different types of data (gene panels, exomes, or whole genomes) and the high variability of the data makes difficult the establishment of a ultimate strategy of general use. While there already exist several studies comparing sensitivity and accuracy of bioinformatic pipelines for the identification of single nucleotide variants from resequencing data, little is known about the impact of quality assessment and reads pre-processing strategies. In this work we discuss major strengths and limitations of the various genome resequencing protocols are currently used in molecular diagnostics and for the discovery of novel disease-causing mutations. By taking advantage of publicly available data we devise and suggest a series of best practices for the pre-processing of the data that consistently improve the outcome of genotyping with minimal impacts on computational costs. PMID:28736571

The incidence of stellar mergers and mass gainers among massive stars

DOE Office of Scientific and Technical Information (OSTI.GOV)

De Mink, S. E.; Sana, H.; Langer, N.

2014-02-10

Because the majority of massive stars are born as members of close binary systems, populations of massive main-sequence stars contain stellar mergers and products of binary mass transfer. We simulate populations of massive stars accounting for all major binary evolution effects based on the most recent binary parameter statistics and extensively evaluate the effect of model uncertainties. Assuming constant star formation, we find that 8{sub −4}{sup +9}% of a sample of early-type stars are the products of a merger resulting from a close binary system. In total we find that 30{sub −15}{sup +10}% of massive main-sequence stars are the productsmore » of binary interaction. We show that the commonly adopted approach to minimize the effects of binaries on an observed sample by excluding systems detected as binaries through radial velocity campaigns can be counterproductive. Systems with significant radial velocity variations are mostly pre-interaction systems. Excluding them substantially enhances the relative incidence of mergers and binary products in the non-radial velocity variable sample. This poses a challenge for testing single stellar evolutionary models. It also raises the question of whether certain peculiar classes of stars, such as magnetic O stars, are the result of binary interaction and it emphasizes the need to further study the effect of binarity on the diagnostics that are used to derive the fundamental properties (star-formation history, initial mass function, mass-to-light ratio) of stellar populations nearby and at high redshift.« less

Depositional facies, environments and sequence stratigraphic interpretation of the Middle Triassic-Lower Cretaceous (pre-Late Albian) succession in Arif El-Naga anticline, northeast Sinai, Egypt

NASA Astrophysics Data System (ADS)

El-Azabi, M. H.; El-Araby, A.

2005-01-01

The Middle Triassic-Lower Cretaceous (pre-Late Albian) succession of Arif El-Naga anticline comprises various distinctive facies and environments that are connected with eustatic relative sea-level changes, local/regional tectonism, variable sediment influx and base-level changes. It displays six unconformity-bounded depositional sequences. The Triassic deposits are divided into a lower clastic facies (early Middle Triassic sequence) and an upper carbonate unit (late Middle- and latest Middle/early Late Triassic sequences). The early Middle Triassic sequence consists of sandstone with shale/mudstone interbeds that formed under variable regimes, ranging from braided fluvial, lower shoreface to beach foreshore. The marine part of this sequence marks retrogradational and progradational parasequences of transgressive- and highstand systems tract deposits respectively. Deposition has taken place under warm semi-arid climate and a steady supply of clastics. The late Middle- and latest Middle/early Late Triassic sequences are carbonate facies developed on an extensive shallow marine shelf under dry-warm climate. The late Middle Triassic sequence includes retrogradational shallow subtidal oyster rudstone and progradational lower intertidal lime-mudstone parasequences that define the transgressive- and highstand systems tracts respectively. It terminates with upper intertidal oncolitic packstone with bored upper surface. The next latest Middle/early Late Triassic sequence is marked by lime-mudstone, packstone/grainstone and algal stromatolitic bindstone with minor shale/mudstone. These lower intertidal/shallow subtidal deposits of a transgressive-systems tract are followed upward by progradational highstand lower intertidal lime-mudstone deposits. The overlying Jurassic deposits encompass two different sequences. The Lower Jurassic sequence is made up of intercalating lower intertidal lime-mudstone and wave-dominated beach foreshore sandstone which formed during a short period of rising sea-level with a relative increase in clastic supply. The Middle-Upper Jurassic sequence is represented by cycles of cross-bedded sandstone topped with thin mudstone that accumulated by northerly flowing braided-streams accompanying regional uplift of the Arabo-Nubian shield. It is succeeded by another regressive fluvial sequence of Early Cretaceous age due to a major eustatic sea-level fall. The Lower Cretaceous sequence is dominated by sandy braided-river deposits with minor overbank fines and basal debris flow conglomerate.

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

NASA Astrophysics Data System (ADS)

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

2008-11-01

Aims: 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 star-forming region. Methods: Fifty-seven candidate members were previously selected among the X-ray sources in the XEST survey, having a 2MASS counterpart compatible with a pre-main sequence 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 lithium absorption and to measure the Hα line and the radial and rotational velocities. Then, 18 low-resolution optical spectra obtained with the instrument DOLORES for other candidate members were used for spectral classification, for Hα measurements, and to assess membership together with IR color-color and color-magnitude diagrams and additional information from the X-ray data. Results: We found that 3 sources show lithium absorption, with equivalent widths (EWs) of 500 mÅ, broad spectral line profiles, indicating rotational velocities of 20{-}40 km s-1, radial velocities consistent with those for known members, and Hα emission. Two of them are classified as new weak-lined T Tauri stars, while the EW ( -9 Å) of the Hα line and its broad asymmetric profile clearly indicate that the third star (XEST-26-062) is a classical T Tauri star. Fourteen sources observed with DOLORES are M-type stars. Fifteen sources show Hα emission. Six of them have spectra that indicate surface gravity lower than in main sequence stars, and their de-reddened positions in IR color-magnitude diagrams are consistent with their derived spectral type and with pre-main sequence models at the distance of the TMC. The K-type star XEST-11-078 is confirmed as a new member on the basis of the strength of the Hα emission line. Overall, we confirm membership to the TMC for 10 out of 25 X-ray sources observed in the optical. Three sources remain uncertain. Based on data collected with the Italian Telescopio Nazionale Galileo (TNG) operated on the island of La Palma by the Centro Galileo Galilei of INAF (Istituto Nazionale di Astrofisica) at the Spanish Observatorio del Roque del los Muchachos of the Instituto de Astrofìsica de Canarias.

HUBBLE TARANTULA TREASURY PROJECT. V. THE STAR CLUSTER HODGE 301: THE OLD FACE OF 30 DORADUS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cignoni, M.; Sabbi, E.; Marel, R. P. van der

Based on color–magnitude diagrams (CMDs) from the Hubble Space Telescope  Hubble Tarantula Treasury Project (HTTP) survey, we present the star formation history of Hodge 301, the oldest star cluster in the Tarantula Nebula. The HTTP photometry extends faint enough to reach, for the first time, the cluster pre-main sequence (PMS) turn-on, where the PMS joins the main sequence. Using the location of this feature, along with synthetic CMDs generated with the latest PARSEC models, we find that Hodge 301 is older than previously thought, with an age between 26.5 and 31.5 Myr. From this age, we also estimate that between 38 andmore » 61 Type II supernovae exploded in the region. The same age is derived from the main sequence turn-off, whereas the age derived from the post-main sequence stars is younger and between 20 and 25 Myr. Other relevant parameters are a total stellar mass of ≈8800 ± 800  M {sub ⊙} and average reddening E ( B − V ) ≈ 0.22–0.24 mag, with a differential reddening δE ( B − V ) ≈ 0.04 mag.« less

Hubble Tarantula Treasury Project V. The Star Cluster Hodge 301: The Old Face of 30 Doradus

NASA Astrophysics Data System (ADS)

Cignoni, M.; Sabbi, E.; van der Marel, R. P.; Lennon, D. J.; Tosi, M.; Grebel, E. K.; Gallagher, J. S., III; Aloisi, A.; de Marchi, G.; Gouliermis, D. A.; Larsen, S.; Panagia, N.; Smith, L. J.

2016-12-01

Based on color-magnitude diagrams (CMDs) from the Hubble Space Telescope Hubble Tarantula Treasury Project (HTTP) survey, we present the star formation history of Hodge 301, the oldest star cluster in the Tarantula Nebula. The HTTP photometry extends faint enough to reach, for the first time, the cluster pre-main sequence (PMS) turn-on, where the PMS joins the main sequence. Using the location of this feature, along with synthetic CMDs generated with the latest PARSEC models, we find that Hodge 301 is older than previously thought, with an age between 26.5 and 31.5 Myr. From this age, we also estimate that between 38 and 61 Type II supernovae exploded in the region. The same age is derived from the main sequence turn-off, whereas the age derived from the post-main sequence stars is younger and between 20 and 25 Myr. Other relevant parameters are a total stellar mass of ≈8800 ± 800 M ⊙ and average reddening E(B - V) ≈ 0.22-0.24 mag, with a differential reddening δE(B - V) ≈ 0.04 mag. Based on observations with the NASA/ESA Hubble Space Telescope, obtained at the Space Telescope Science Institute, which is operated by AURA Inc., under NASA contract NAS 5-26555.

First results of the SONS survey: submillimetre detections of debris discs

NASA Astrophysics Data System (ADS)

Panić, O.; Holland, W. S.; Wyatt, M. C.; Kennedy, G. M.; Matthews, B. C.; Lestrade, J. F.; Sibthorpe, B.; Greaves, J. S.; Marshall, J. P.; Phillips, N. M.; Tottle, J.

2013-10-01

New detections of debris discs at submillimetre wavelengths present highly valuable complementary information to prior observations of these sources at shorter wavelengths. Characterization of discs through spectral energy distribution modelling including the submillimetre fluxes is essential for our basic understanding of disc mass and temperature, and presents a starting point for further studies using millimetre interferometric observations. In the framework of the ongoing SCUBA-2 Observations of Nearby Stars, the instrument SCUBA-2 on the James Clerk Maxwell Telescope was used to provide measurements of 450 and 850 μm fluxes towards a large sample of nearby main-sequence stars with debris discs detected previously at shorter wavelengths. We present the first results from the ongoing survey, concerning 850 μm detections and 450 μm upper limits towards 10 stars, the majority of which are detected at submillimetre wavelengths for the first time. One, or possibly two, of these new detections is likely a background source. We fit the spectral energy distributions of the star+disc systems with a blackbody emission approach and derive characteristic disc temperatures. We use these temperatures to convert the observed fluxes to disc masses. We obtain a range of disc masses from 0.001 to 0.1 M⊕, values similar to the prior dust mass measurements towards debris discs. There is no evidence for evolution in dust mass with age on the main sequence, and indeed the upper envelope remains relatively flat at ≈0.5 M⊕ at all ages. The inferred disc masses are lower than those from disc detections around pre-main-sequence stars, which may indicate a depletion of solid mass. This may also be due to a change in disc opacity, though limited sensitivity means that it is not yet known what fraction of pre-main-sequence stars have discs with dust masses similar to debris disc levels. New, high-sensitivity detections are a path towards investigating the trends in dust mass evolution.

FUV Spectroscopy Of Outflows And Disks Around The Intermediate Mass Pre-main-sequence Stars HD135344B And HD104237

NASA Astrophysics Data System (ADS)

Brown, Alexander; Herczeg, G.; Brown, J. M.; Walter, F. M.; Ayres, T. R.; DAOof TAU Team

2011-01-01

The intermediate-mass, pre-main-sequence (Herbig Ae/Fe) stars HD135344B (F4) and HD104237 (A8 IV-V) are both still surrounded by almost face-on circumstellar disks. The disk around HD135344B is a ``transitional'' disk with a 25 AU radius cleared inner hole but still with some gas and dust very close to the star. We have obtained FUV spectra of these stars using the HST COS and STIS spectrographs that show that both stars have dramatic high-velocity (terminal velocity = 300-400 km/s) outflows and rich fluorescently-excited molecular hydrogen emission, originating primarily from warm gas in their disks. We present these FUV spectra and outline the outflow and disk properties implied by the observed emission and absorption line profiles. The profiles and widths of the molecular hydrogen lines provide strong constraints on the location of the emitting regions. This work is supported by HST grants for GO projects 11828 and 11616, and Chandra grant GO9-0015X to the University of Colorado.

Discovery of Par 1802 as a Low-Mass, Pre-Main-Sequence Eclipsing Binary in the Orion Star-Forming Region

NASA Astrophysics Data System (ADS)

Cargile, P. A.; Stassun, K. G.; Mathieu, R. D.

2008-02-01

We report the discovery of a pre-main-sequence (PMS), low-mass, double-lined, spectroscopic, eclipsing binary in the Orion star-forming region. We present our observations, including radial velocities derived from optical high-resolution spectroscopy, and present an orbit solution that permits the determination of precise empirical masses for both components of the system. We find that Par 1802 is composed of two equal-mass (0.39 +/- 0.03, 0.40 +/- 0.03 M⊙) stars in a circular, 4.7 day orbit. There is strong evidence, such as the system exhibiting strong Li lines and a center-of-mass velocity consistent with cluster membership, that this system is a member of the Orion star-forming region and quite possibly the Orion Nebula Cluster, and therefore has an age of only a few million years. As there are currently only a few empirical mass and radius measurements for low-mass, PMS stars, this system presents an interesting test for the predictions of current theoretical models of PMS stellar evolution.

Lactobacillus delbrueckii subsp. bulgaricus CRL 454 cleaves allergenic peptides of β-lactoglobulin.

PubMed

Pescuma, Micaela; Hébert, Elvira M; Haertlé, Thomas; Chobert, Jean-Marc; Mozzi, Fernanda; Font de Valdez, Graciela

2015-03-01

Whey, a cheese by-product used as a food additive, is produced worldwide at 40.7 million tons per year. β-Lactoglobulin (BLG), the main whey protein, is poorly digested and is highly allergenic. We aimed to study the contribution of Lactobacillus delbrueckii subsp. bulgaricus CRL 454 to BLG digestion and to analyse its ability to degrade the main allergenic sequences of this protein. Pre-hydrolysis of BLG by L. delbrueckii subsp. bulgaricus CRL 454 increases digestion of BLG assayed by an in vitro simulated gastrointestinal system. Moreover, peptides from hydrolysis of the allergenic sequences V41-K60, Y102-R124, C121-L140 and L149-I162 were found when BLG was hydrolysed by this strain. Interestingly, peptides possessing antioxidant, ACE inhibitory, antimicrobial and immuno-modulating properties were found in BLG degraded by both the Lactobacillus strain and digestive enzymes. To conclude, pre-hydrolysis of BLG by L. delbrueckii subsp. bulgaricus CRL 454 has a positive effect on BLG digestion and could diminish allergenic reactions. Copyright © 2014 Elsevier Ltd. All rights reserved.

preAssemble: a tool for automatic sequencer trace data processing.

PubMed

Adzhubei, Alexei A; Laerdahl, Jon K; Vlasova, Anna V

2006-01-17

Trace or chromatogram files (raw data) are produced by automatic nucleic acid sequencing equipment or sequencers. Each file contains information which can be interpreted by specialised software to reveal the sequence (base calling). This is done by the sequencer proprietary software or publicly available programs. Depending on the size of a sequencing project the number of trace files can vary from just a few to thousands of files. Sequencing quality assessment on various criteria is important at the stage preceding clustering and contig assembly. Two major publicly available packages--Phred and Staden are used by preAssemble to perform sequence quality processing. The preAssemble pre-assembly sequence processing pipeline has been developed for small to large scale automatic processing of DNA sequencer chromatogram (trace) data. The Staden Package Pregap4 module and base-calling program Phred are utilized in the pipeline, which produces detailed and self-explanatory output that can be displayed with a web browser. preAssemble can be used successfully with very little previous experience, however options for parameter tuning are provided for advanced users. preAssemble runs under UNIX and LINUX operating systems. It is available for downloading and will run as stand-alone software. It can also be accessed on the Norwegian Salmon Genome Project web site where preAssemble jobs can be run on the project server. preAssemble is a tool allowing to perform quality assessment of sequences generated by automatic sequencing equipment. preAssemble is flexible since both interactive jobs on the preAssemble server and the stand alone downloadable version are available. Virtually no previous experience is necessary to run a default preAssemble job, on the other hand options for parameter tuning are provided. Consequently preAssemble can be used as efficiently for just several trace files as for large scale sequence processing.

SeqTrim: a high-throughput pipeline for pre-processing any type of sequence read

PubMed Central

2010-01-01

Background High-throughput automated sequencing has enabled an exponential growth rate of sequencing data. This requires increasing sequence quality and reliability in order to avoid database contamination with artefactual sequences. The arrival of pyrosequencing enhances this problem and necessitates customisable pre-processing algorithms. Results SeqTrim has been implemented both as a Web and as a standalone command line application. Already-published and newly-designed algorithms have been included to identify sequence inserts, to remove low quality, vector, adaptor, low complexity and contaminant sequences, and to detect chimeric reads. The availability of several input and output formats allows its inclusion in sequence processing workflows. Due to its specific algorithms, SeqTrim outperforms other pre-processors implemented as Web services or standalone applications. It performs equally well with sequences from EST libraries, SSH libraries, genomic DNA libraries and pyrosequencing reads and does not lead to over-trimming. Conclusions SeqTrim is an efficient pipeline designed for pre-processing of any type of sequence read, including next-generation sequencing. It is easily configurable and provides a friendly interface that allows users to know what happened with sequences at every pre-processing stage, and to verify pre-processing of an individual sequence if desired. The recommended pipeline reveals more information about each sequence than previously described pre-processors and can discard more sequencing or experimental artefacts. PMID:20089148

Molecular variability analysis of five new complete cacao swollen shoot virus genomic sequences.

PubMed

Muller, E; Sackey, S

2005-01-01

Cacao swollen shoot virus (CSSV), a member of the family Caulimovi-ridae, genus Badnavirus occurs in all the main cacao-growing areas of West Africa. We amplified, cloned and sequenced complete genomes of five new isolates, two originating from Togo and three originating from Ghana. The genome of these five newly sequenced isolates all contain the five putative open reading frames I, II, III, X and Y described for the first sequenced CSSV isolate, Agou1 originating from Togo. Their genomes have been aligned with the genome of Agou1. The nucleotide and amino acid sequence identities between isolates have been calculated and a phylogenetic analysis has been made including other pararetroviruses. Maximum nucleotide sequence variability between complete genomes of CSSV isolates was 29.4%. Geographical differentiation between isolates appears more important than differentiation between mild and severe isolates. ORF X differs greatly in size and sequence between the Togolese isolates Nyongbo2 and Agou1, and the four other isolates, its functional role is therefore clearly questionable.

Accreting Planets in the Habitable Zones of M-Stars Are Too Hot to Retain Liquid Water

NASA Astrophysics Data System (ADS)

Ramirez, R. M.; Kopparapu, R. K.; Kasting, J. F.

2014-12-01

Previous studies1,2 have shown that young accreting planets in the habitable zones (HZ) of pre-main sequence M-stars face major dynamical hurdles in both the retention and acquisition of volatiles. High collision rates with other bodies, short planetary formation timescales, and inefficient radial mixing are among the major problems encountered. However, another equally-important concern is the high temperatures predicted within the circumstellar disk, greatly hindering volatile delivery. We use a 1-D radiative-convective climate model to demonstrate that the fluxes received by accreting planets orbiting late K-M stars exceed the runaway greenhouse threshold. Given that M-stars are disproportionately brighter in their pre main-sequence lifetimes as compared to Sun-like stars (i.e. G-class insolation), planets orbiting M-stars are especially susceptible to the runaway, with intensity and duration increasing for cooler M-stars. Thus, accreting planetesimals in the HZs of M-stars could be too hot to maintain liquid water on their surfaces. In contrast, accreting planets located at Earth's distance (or farther) from a pre-main sequence solar analogue (i.e. G2 spectral class) receive stellar fluxes well below that of the runaway point. Our results suggest that future missions and surveys can improve their prospects of finding alien life by targeting HZ planets orbiting Sun-like stars. Moreover, our findings support recent claims that Venus may have lost its water during accretion3. REFERENCES1. Lissauer, Jack J. "Planets formed in habitable zones of M dwarf stars probably are deficient in volatiles." The Astrophysical Journal Letters 660.2 (2007): L149. 2. Raymond, Sean N., John Scalo, and Victoria S. Meadows. "A decreased probability of habitable planet formation around low-mass stars." The Astrophysical Journal 669.1 (2007): 606. 3. Hamano, Keiko, Yutaka Abe, and Hidenori Genda. "Emergence of two types of terrestrial planet on solidification of magma ocean." Nature 497.7451 (2013): 607-610.

High-Resolution Spectroscopy of some very Active Southern Stars

NASA Technical Reports Server (NTRS)

Soderblom, David R.; King, Jeremy R.; Henry, Todd J.

1998-01-01

We have obtained high-resolution echelle spectra of 18 solar-type stars that an earlier survey showed to have very high levels of Ca II H and K emission. Most of these stars belong to close binary systems, but five remain as probable single stars or well-separated binaries that are younger than the Pleiades on the basis of their lithium abundances and H.alpha emission. Three of these probable single stars also lie more than 1 mag above the main sequence in a color-magnitude diagram, and appear to have ages of 10 to 15 Myr. Two of them, HD 202917 and HD 222259, also appear to have a kinematic association with the pre-main-sequence multiple system HD 98800.

Observations of suspected low-mass post-T Tauri stars and their evolutionary status

NASA Technical Reports Server (NTRS)

Mundt, R.; Walter, F. M.; Feigelson, E. D.; Finkenzeller, U.; Herbig, G. H.; Odell, A. P.

1983-01-01

The results of a study of five X-ray discovered weak emission pre-main-sequence stars in the Taurus-Auriga star formation complex are presented. All are of spectral type K7-M0, and about 1-2 mag above the main sequence. One is a double-lined spectroscopic binary, the first spectroscopic binary PMS star to be confirmed. The ages, masses, and radii of these stars as determined by photometry and spectroscopy are discussed. The difference in emission strength between these and the T Tauri stars is investigated, and it is concluded that these 'post-T Tauri' stars do indeed appear more evolved than the T Tauri stars, although there is no evidence of any significant difference in ages.

Interactive neonatal gastrointestinal magnetic resonance imaging using fruit juice as an oral contrast media.

PubMed

Arthurs, Owen J; Graves, Martin J; Edwards, Andrea D; Joubert, Ilse; Set, Pat A K; Lomas, David J

2014-09-22

The objective was to evaluate the use of fruit juice with an interactive inversion recovery (IR) MR pulse sequence to visualise the gastrointestinal tract. We investigated the relaxation properties of 12 different natural fruit juices in vitro, to identify which could be used as oral contrast. We then describe our initial experience using an interactive MR pulse sequence to allow optimal visualisation after administering pineapple juice orally, and suppressing pre-existing bowel fluid contents, with variable TI in three adult and one child volunteer. Pineapple juice (PJ) had both the shortest T1 (243 ms) and shortest T2 (48 ms) of the fruit juices tested. Optimal signal differentiation between pre-existing bowel contents and oral PJ administration was obtained with TIs of between 900 and 1100 ms. The use of an inversion recovery preparation allowed long T1 pre-existing bowel contents to be suppressed whilst the short T1 of fruit juice acts as a positive contrast medium. Pineapple juice could be used as oral contrast agent for neonatal gastrointestinal magnetic resonance imaging.

On the non-variability of HR 7653 (15 Vul) based on BRITE data

NASA Astrophysics Data System (ADS)

Smalley, B.; Paunzen, E.; Lüftinger, T.; Moffat, A. F. J.; Pigulski, A.; Rucinski, S.; Sikora, J.; Wade, G. A.; Weiss, W.; BEST

2018-02-01

We present space-based BRITE photometric observations of the metallic line (CP1) star HR 7653 (15 Vul). This chemically peculiar star of the upper main sequence was suspected to show variability due to rotation and a magnetic field. Such a variability is quite unusual among the, in general, non-magnetic CP1 stars. We investigated the astrophysical parameters of HR 7653 placing it close to the terminal age main sequence or even in the subgiant phase. The longest BRITE data set has a time base of 18.01 d from which we conclude that there are no coherent long-period variations (>1 d) visible above 2.1 mmag in the red and 6.6 mmag in the blue. Furthermore, we searched for δ Scuti type pulsations. On the basis of a discrete Fourier analysis method, we find no peaks in the Fourier spectra above 0.5 mmag and 8.6 mmag, for the red and blue filters, respectively.

Evolution of Pre-Main Sequence Accretion Disks

NASA Technical Reports Server (NTRS)

Hartmann, Lee W.

2005-01-01

The aim of this project was to develop a comprehensive global picture of the physical conditions in, and evolutionary timescales of, premain sequence accretion disks. The results of this work will help constrain the initial conditions for planet formation. To this end we developed much larger samples of 3-10 Myr-old stars to provide better empirical constraints on protoplanetary disk evolution; measured disk accretion rates in these systems; and constructed detailed model disk structures consistent with observations to infer physical conditions such as grain growth in protoplanetary disks.

Comparing viral metagenomics methods using a highly multiplexed human viral pathogens reagent

PubMed Central

Li, Linlin; Deng, Xutao; Mee, Edward T.; Collot-Teixeira, Sophie; Anderson, Rob; Schepelmann, Silke; Minor, Philip D.; Delwart, Eric

2014-01-01

Unbiased metagenomic sequencing holds significant potential as a diagnostic tool for the simultaneous detection of any previously genetically described viral nucleic acids in clinical samples. Viral genome sequences can also inform on likely phenotypes including drug susceptibility or neutralization serotypes. In this study, different variables of the laboratory methods often used to generate viral metagenomics libraries on the efficiency of viral detection and virus genome coverage were compared. A biological reagent consisting of 25 different human RNA and DNA viral pathogens was used to estimate the effect of filtration and nuclease digestion, DNA/RNA extraction methods, pre-amplification and the use of different library preparation kits on the detection of viral nucleic acids. Filtration and nuclease treatment led to slight decreases in the percentage of viral sequence reads and number of viruses detected. For nucleic acid extractions silica spin columns improved viral sequence recovery relative to magnetic beads and Trizol extraction. Pre-amplification using random RT-PCR while generating more viral sequence reads resulted in detection of fewer viruses, more overlapping sequences, and lower genome coverage. The ScriptSeq library preparation method retrieved more viruses and a greater fraction of their genomes than the TruSeq and Nextera methods. Viral metagenomics sequencing was able to simultaneously detect up to 22 different viruses in the biological reagent analyzed including all those detected by qPCR. Further optimization will be required for the detection of viruses in biologically more complex samples such as tissues, blood, or feces. PMID:25497414

Hubble Tarantula Treasury Project - VI. Identification of Pre-Main-Sequence Stars using Machine Learning techniques

NASA Astrophysics Data System (ADS)

Ksoll, Victor F.; Gouliermis, Dimitrios A.; Klessen, Ralf S.; Grebel, Eva K.; Sabbi, Elena; Anderson, Jay; Lennon, Daniel J.; Cignoni, Michele; de Marchi, Guido; Smith, Linda J.; Tosi, Monica; van der Marel, Roeland P.

2018-05-01

The Hubble Tarantula Treasury Project (HTTP) has provided an unprecedented photometric coverage of the entire star-burst region of 30 Doradus down to the half Solar mass limit. We use the deep stellar catalogue of HTTP to identify all the pre-main-sequence (PMS) stars of the region, i.e., stars that have not started their lives on the main-sequence yet. The photometric distinction of these stars from the more evolved populations is not a trivial task due to several factors that alter their colour-magnitude diagram positions. The identification of PMS stars requires, thus, sophisticated statistical methods. We employ Machine Learning Classification techniques on the HTTP survey of more than 800,000 sources to identify the PMS stellar content of the observed field. Our methodology consists of 1) carefully selecting the most probable low-mass PMS stellar population of the star-forming cluster NGC2070, 2) using this sample to train classification algorithms to build a predictive model for PMS stars, and 3) applying this model in order to identify the most probable PMS content across the entire Tarantula Nebula. We employ Decision Tree, Random Forest and Support Vector Machine classifiers to categorise the stars as PMS and Non-PMS. The Random Forest and Support Vector Machine provided the most accurate models, predicting about 20,000 sources with a candidateship probability higher than 50 percent, and almost 10,000 PMS candidates with a probability higher than 95 percent. This is the richest and most accurate photometric catalogue of extragalactic PMS candidates across the extent of a whole star-forming complex.

Modeling the optical radiation of the precataclysmic variable SDSS J212531-010745

NASA Astrophysics Data System (ADS)

Shimansky, V. V.; Borisov, N. V.; Nurtdinova, D. N.; Solovyeva, Yu. N.; Sakhibullin, N. A.; Spiridonova, O. I.

2015-03-01

Optical observations are analyzed to derive a set of basic parameters for the precataclysmic variable star SDSS J212531-010745, whose primary is a PG1159-type star. Spectroscopic and multiband photometric observations of the star were performed in 2008-2011 with the 6-m telescope and the Zeiss-1000 telescope of the Special Astrophysical Observatory. The shape of the binary's orbital light curves is nearly sinusoidal, with the amplitude increasing with wavelength from Δ m = 0.40 m in the B band to Δ m = 0.73 m in the R band. The spectra contain absorption lines of HeII and neutral atoms, along with HI, HeI, CII, MgII, FeII emission lines, whose intensity increases synchronously with the brightness of the system. The optical radiation from SDSS J212531-010745 has a composite nature, corresponding to a model for a pre-cataclysmic variable with strong reflection effects. Cross-correlation techniques are used to measure the radial velocities and derive the component masses. Numerical modeling of the binary's light curves, radial velocities, and spectra is performed, and a complete set of parameters determined. Considerable abundance anomalies (to 1 dex) were detected for the secondary. The primary's characteristics correspond to the evolutionary predictions for DAO dwarfs with masses M ≈ 0.5 M ⊙, and the secondary's characteristics to low-mass, main-sequence stars with the solar metallicity.

Setting up a probe based, closed tube real-time PCR assay for focused detection of variable sequence alterations.

PubMed

Becságh, Péter; Szakács, Orsolya

2014-10-01

During diagnostic workflow when detecting sequence alterations, sometimes it is important to design an algorithm that includes screening and direct tests in combination. Normally the use of direct test, which is mainly sequencing, is limited. There is an increased need for effective screening tests, with "closed tube" during the whole process and therefore decreasing the risk of PCR product contamination. The aim of this study was to design such a closed tube, detection probe based screening assay to detect different kind of sequence alterations in the exon 11 of the human c-kit gene region. Inside this region there are variable possible deletions and single nucleotide changes. During assay setup, more probe chemistry formats were screened and tested. After some optimization steps the taqman probe format was selected.

Fault model of the 2014 Cephalonia seismic sequence - Evidence of spatiotemporal fault segmentation along the NW edge of Aegean Arc

NASA Astrophysics Data System (ADS)

Saltogianni, Vasso; Moschas, Fanis; Stiros, Stathis

2017-04-01

Finite fault models (FFM) are presented for the two main shocks of the 2014 Cephalonia (Ionian Sea, Greece) seismic sequence (M 6.0) which produced extreme peak ground accelerations ( 0.7g) in the west edge of the Aegean Arc, an area in which the poor coverage by seismological and GPS/INSAR data makes FFM a real challenge. Modeling was based on co-seismic GPS data and on the recently introduced TOPological INVersion algorithm. The latter is a novel uniform grid search-based technique in n-dimensional spaces, is based on the concept of stochastic variables and which can identify multiple unconstrained ("free") solutions in a specified search space. Derived FFMs for the 2014 earthquakes correspond to an essentially strike slip fault and of part of a shallow thrust, the surface projection of both of which run roughly along the west coast of Cephalonia. Both faults correlate with pre-existing faults. The 2014 faults, in combination with the faults of the 2003 and 2015 Leucas earthquakes farther NE, form a string of oblique slip, partly overlapping fault segments with variable geometric and kinematic characteristics along the NW edge of the Aegean Arc. This composite fault, usually regarded as the Cephalonia Transform Fault, accommodates shear along this part of the Arc. Because of the highly fragmented crust, dominated by major thrusts in this area, fault activity is associated with 20km long segments and magnitude 6.0-6.5 earthquakes recurring in intervals of a few seconds to 10 years.

Accretion-induced luminosity spreads in young clusters: evidence from stellar rotation

NASA Astrophysics Data System (ADS)

Littlefair, S. P.; Naylor, Tim; Mayne, N. J.; Saunders, Eric; Jeffries, R. D.

2011-05-01

We present an analysis of the rotation of young stars in the associations Cepheus OB3b, NGC 2264, 2362 and the Orion Nebula Cluster (ONC). We discover a correlation between rotation rate and position in a colour-magnitude diagram (CMD) such that stars which lie above an empirically determined median pre-main sequence rotate more rapidly than stars which lie below this sequence. The same correlation is seen, with a high degree of statistical significance, in each association studied here. If position within the CMD is interpreted as being due to genuine age spreads within a cluster, then the stars above the median pre-main sequence would be the youngest stars. This would in turn imply that the most rapidly rotating stars in an association are the youngest, and hence those with the largest moments of inertia and highest likelihood of ongoing accretion. Such a result does not fit naturally into the existing picture of angular momentum evolution in young stars, where the stars are braked effectively by their accretion discs until the disc disperses. Instead, we argue that, for a given association of young stars, position within the CMD is not primarily a function of age, but of accretion history. We show that this hypothesis could explain the correlation we observe between rotation rate and position within the CMD.

Hypersonic Vehicle Trajectory Optimization and Control

NASA Technical Reports Server (NTRS)

Balakrishnan, S. N.; Shen, J.; Grohs, J. R.

1997-01-01

Two classes of neural networks have been developed for the study of hypersonic vehicle trajectory optimization and control. The first one is called an 'adaptive critic'. The uniqueness and main features of this approach are that: (1) they need no external training; (2) they allow variability of initial conditions; and (3) they can serve as feedback control. This is used to solve a 'free final time' two-point boundary value problem that maximizes the mass at the rocket burn-out while satisfying the pre-specified burn-out conditions in velocity, flightpath angle, and altitude. The second neural network is a recurrent network. An interesting feature of this network formulation is that when its inputs are the coefficients of the dynamics and control matrices, the network outputs are the Kalman sequences (with a quadratic cost function); the same network is also used for identifying the coefficients of the dynamics and control matrices. Consequently, we can use it to control a system whose parameters are uncertain. Numerical results are presented which illustrate the potential of these methods.

A spectrum of the veiled T Tauri star CY Tau

NASA Technical Reports Server (NTRS)

Stuewe, J. A.; Schultz, R.

1994-01-01

We present a flux calibrated spectrum of the star listed as CY Tau in the `General Catalog of Variable Stars 4th ed.' in the spectral range 3700 A less than or equal to lambda less than or equal to 6400 A with a resolution of approximately equals 15 A showing the Balmer-Series from H(sub beta) to H(sub 10) as well as the CaII H (in blend with H(sub epsilon) and K lines in emission. Apart from the emission lines the spectrum is composed of a continuum equivalent to that of an ordinary pre-main sequence star (i.e. a `naked' T Tau) of spectral type M2 V with emission lines plus a `blue' veiling continuum that can be described as black body radiation of temperature T(sub BL) approximately equals 7000K due to accretion onto a boundary layer at a rate of M-dot(sub acc) greater than or approximately = 2.18 10(exp -8) solar mass/a.

Variability and molecular typing of the woody-tree infecting prunus necrotic ringspot ilarvirus.

PubMed

Vasková, D; Petrzik, K; Karesová, R

2000-01-01

The 3'-part of the movement protein gene, the intergenic region and the complete coat protein gene of sixteen isolates of Prunus necrotic ringspot virus (PNRSV) from five different host species from the Czech Republic were sequenced in order to search for the bases of extensive variability of viroses caused by this pathogen. According to phylogenetic analyses all the 46 isolates sequenced to date split into three main groups, which correlated to a certain extend with their geographic origin. Modelled serological properties showed that all the new isolates belong to one serotype.

Evolution models of helium white dwarf-main-sequence star merger remnants: the mass distribution of single low-mass white dwarfs

NASA Astrophysics Data System (ADS)

Zhang, Xianfei; Hall, Philip D.; Jeffery, C. Simon; Bi, Shaolan

2018-02-01

It is not known how single white dwarfs with masses less than 0.5Msolar -- low-mass white dwarfs -- are formed. One way in which such a white dwarf might be formed is after the merger of a helium-core white dwarf with a main-sequence star that produces a red giant branch star and fails to ignite helium. We use a stellar-evolution code to compute models of the remnants of these mergers and find a relation between the pre-merger masses and the final white dwarf mass. Combining our results with a model population, we predict that the mass distribution of single low-mass white dwarfs formed through this channel spans the range 0.37 to 0.5Msolar and peaks between 0.45 and 0.46Msolar. Helium white dwarf--main-sequence star mergers can also lead to the formation of single helium white dwarfs with masses up to 0.51Msolar. In our model the Galactic formation rate of single low-mass white dwarfs through this channel is about 8.7X10^-3yr^-1. Comparing our models with observations, we find that the majority of single low-mass white dwarfs (<0.5Msolar) are formed from helium white dwarf--main-sequence star mergers, at a rate which is about $2$ per cent of the total white dwarf formation rate.

Role of observation of live cases done by Japanese experts in the acquisition of ESD skills by a western endoscopist.

PubMed

Draganov, Peter V; Chang, Myron; Coman, Roxana M; Wagh, Mihir S; An, Qi; Gotoda, Takuji

2014-04-28

To evaluate the role of observation of experts performing endoscopic submucosal dissection (ESD) in the acquisition of ESD skills. This prospective study is documenting the learning curve of one Western endoscopist. The study consisted of three periods. In the first period (pre-observation), the trainee performed ESDs in animal models in his home institution in the United States. The second period (observation) consisted of visit to Japan and observation of live ESD cases done by experts. The observation of cases occurred over a 5-wk period. During the third period (post-observation), the trainee performed ESD in animal models in a similar fashion as in the first period. Three animal models were used: live 40-50 kg Yorkshire pig, explanted pig stomach model, and explanted pig rectum model. The outcomes from the ESDs done in the animal models before and after observation of live human cases (main study intervention) were compared. Statistical analysis of the data included: Fisher's exact test to compare distributions of a categorical variable, Wilcoxon rank sum test to compare distributions of a continuous variable between the two groups (pre-observation and post-observation), and Kruskal-Wallis test to evaluate the impact of lesion location and type of model (ex-vivo vs live pig) on lesion removal time. The trainee performed 38 ESDs in animal model (29 pre-observation/9 post-observation). The removal times post-observation were significantly shorter than those pre-observation (32.7 ± 15.0 min vs 63.5 ± 9.8 min, P < 0.001). To minimize the impact of improving physician skill, the 9 lesions post-observation were compared to the last 9 lesions pre-observation and the removal times remained significantly shorter (32.7 ± 15.0 min vs 61.0 ± 7.4 min, P = 0.0011). Regression analysis showed that ESD observation significantly reduced removal time when controlling for the sequence of lesion removal (P = 0.025). Furthermore, it was also noted a trend towards decrease in failure to remove lesions and decrease in complications after the period of observation. This study did not find a significant difference in the time needed to remove lesions in different animal models. This finding could have important implications in designing training programs due to the substantial difference in cost between live animal and explanted organ models. The main limitation of this study is that it reflects the experience of a single endoscopist. Observation of experts performing ESD over short period of time can significantly contribute to the acquisition of ESD skills.

[Standard algorithm of molecular typing of Yersinia pestis strains].

PubMed

Eroshenko, G A; Odinokov, G N; Kukleva, L M; Pavlova, A I; Krasnov, Ia M; Shavina, N Iu; Guseva, N P; Vinogradova, N A; Kutyrev, V V

2012-01-01

Development of the standard algorithm of molecular typing of Yersinia pestis that ensures establishing of subspecies, biovar and focus membership of the studied isolate. Determination of the characteristic strain genotypes of plague infectious agent of main and nonmain subspecies from various natural foci of plague of the Russian Federation and the near abroad. Genotyping of 192 natural Y. pestis strains of main and nonmain subspecies was performed by using PCR methods, multilocus sequencing and multilocus analysis of variable tandem repeat number. A standard algorithm of molecular typing of plague infectious agent including several stages of Yersinia pestis differentiation by membership: in main and nonmain subspecies, various biovars of the main subspecies, specific subspecies; natural foci and geographic territories was developed. The algorithm is based on 3 typing methods--PCR, multilocus sequence typing and multilocus analysis of variable tandem repeat number using standard DNA targets--life support genes (terC, ilvN, inv, glpD, napA, rhaS and araC) and 7 loci of variable tandem repeats (ms01, ms04, ms06, ms07, ms46, ms62, ms70). The effectiveness of the developed algorithm is shown on the large number of natural Y. pestis strains. Characteristic sequence types of Y. pestis strains of various subspecies and biovars as well as MLVA7 genotypes of strains from natural foci of plague of the Russian Federation and the near abroad were established. The application of the developed algorithm will increase the effectiveness of epidemiologic monitoring of plague infectious agent, and analysis of epidemics and outbreaks of plague with establishing the source of origin of the strain and routes of introduction of the infection.

Taxonomic and predicted metabolic profiles of the human gut microbiome in pre-Columbian mummies.

PubMed

Santiago-Rodriguez, Tasha M; Fornaciari, Gino; Luciani, Stefania; Dowd, Scot E; Toranzos, Gary A; Marota, Isolina; Cano, Raul J

2016-11-01

Characterization of naturally mummified human gut remains could potentially provide insights into the preservation and evolution of commensal and pathogenic microorganisms, and metabolic profiles. We characterized the gut microbiome of two pre-Columbian Andean mummies dating to the 10-15th centuries using 16S rRNA gene high-throughput sequencing and metagenomics, and compared them to a previously characterized gut microbiome of an 11th century AD pre-Columbian Andean mummy. Our previous study showed that the Clostridiales represented the majority of the bacterial communities in the mummified gut remains, but that other microbial communities were also preserved during the process of natural mummification, as shown with the metagenomics analyses. The gut microbiome of the other two mummies were mainly comprised by Clostridiales or Bacillales, as demonstrated with 16S rRNA gene amplicon sequencing, many of which are facultative anaerobes, possibly consistent with the process of natural mummification requiring low oxygen levels. Metagenome analyses showed the presence of other microbial groups that were positively or negatively correlated with specific metabolic profiles. The presence of sequences similar to both Trypanosoma cruzi and Leishmania donovani could suggest that these pathogens were prevalent in pre-Columbian individuals. Taxonomic and functional profiling of mummified human gut remains will aid in the understanding of the microbial ecology of the process of natural mummification. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

The Genetic Legacy of the Pre-Colonial Period in Contemporary Bolivians

PubMed Central

Vidal-Bralo, Laura; Gómez-Carballa, Alberto; Catelli, Laura; Pardo-Seco, Jacobo; Pastoriza, Ana; Carracedo, Ángel; Torres-Balanza, Antonio; Rocabado, Omar; Vullo, Carlos

2013-01-01

Only a few genetic studies have been carried out to date in Bolivia. However, some of the most important (pre)historical enclaves of South America were located in these territories. Thus, the (sub)-Andean region of Bolivia was part of the Inca Empire, the largest state in Pre-Columbian America. We have genotyped the first hypervariable region (HVS-I) of 720 samples representing the main regions in Bolivia, and these data have been analyzed in the context of other pan-American samples (>19,000 HVS-I mtDNAs). Entire mtDNA genome sequencing was also undertaken on selected Native American lineages. Additionally, a panel of 46 Ancestry Informative Markers (AIMs) was genotyped in a sub-set of samples. The vast majority of the Bolivian mtDNAs (98.4%) were found to belong to the main Native American haplogroups (A: 14.3%, B: 52.6%, C: 21.9%, D: 9.6%), with little indication of sub-Saharan and/or European lineages; however, marked patterns of haplogroup frequencies between main regions exist (e.g. haplogroup B: Andean [71%], Sub-Andean [61%], Llanos [32%]). Analysis of entire genomes unraveled the phylogenetic characteristics of three Native haplogroups: the pan-American haplogroup B2b (originated ∼21.4 thousand years ago [kya]), A2ah (∼5.2 kya), and B2o (∼2.6 kya). The data suggest that B2b could have arisen in North California (an origin even in the north most region of the American continent cannot be disregarded), moved southward following the Pacific coastline and crossed Meso-America. Then, it most likely spread into South America following two routes: the Pacific path towards Peru and Bolivia (arriving here at about ∼15.2 kya), and the Amazonian route of Venezuela and Brazil southwards. In contrast to the mtDNA, Ancestry Informative Markers (AIMs) reveal a higher (although geographically variable) European introgression in Bolivians (25%). Bolivia shows a decreasing autosomal molecular diversity pattern along the longitudinal axis, from the Altiplano to the lowlands. Both autosomes and mtDNA revealed a low impact (1–2%) of a sub-Saharan component in Bolivians. PMID:23527064

The genetic legacy of the pre-colonial period in contemporary Bolivians.

PubMed

Taboada-Echalar, Patricia; Alvarez-Iglesias, Vanesa; Heinz, Tanja; Vidal-Bralo, Laura; Gómez-Carballa, Alberto; Catelli, Laura; Pardo-Seco, Jacobo; Pastoriza, Ana; Carracedo, Angel; Torres-Balanza, Antonio; Rocabado, Omar; Vullo, Carlos; Salas, Antonio

2013-01-01

Only a few genetic studies have been carried out to date in Bolivia. However, some of the most important (pre)historical enclaves of South America were located in these territories. Thus, the (sub)-Andean region of Bolivia was part of the Inca Empire, the largest state in Pre-Columbian America. We have genotyped the first hypervariable region (HVS-I) of 720 samples representing the main regions in Bolivia, and these data have been analyzed in the context of other pan-American samples (>19,000 HVS-I mtDNAs). Entire mtDNA genome sequencing was also undertaken on selected Native American lineages. Additionally, a panel of 46 Ancestry Informative Markers (AIMs) was genotyped in a sub-set of samples. The vast majority of the Bolivian mtDNAs (98.4%) were found to belong to the main Native American haplogroups (A: 14.3%, B: 52.6%, C: 21.9%, D: 9.6%), with little indication of sub-Saharan and/or European lineages; however, marked patterns of haplogroup frequencies between main regions exist (e.g. haplogroup B: Andean [71%], Sub-Andean [61%], Llanos [32%]). Analysis of entire genomes unraveled the phylogenetic characteristics of three Native haplogroups: the pan-American haplogroup B2b (originated ∼21.4 thousand years ago [kya]), A2ah (∼5.2 kya), and B2o (∼2.6 kya). The data suggest that B2b could have arisen in North California (an origin even in the north most region of the American continent cannot be disregarded), moved southward following the Pacific coastline and crossed Meso-America. Then, it most likely spread into South America following two routes: the Pacific path towards Peru and Bolivia (arriving here at about ∼15.2 kya), and the Amazonian route of Venezuela and Brazil southwards. In contrast to the mtDNA, Ancestry Informative Markers (AIMs) reveal a higher (although geographically variable) European introgression in Bolivians (25%). Bolivia shows a decreasing autosomal molecular diversity pattern along the longitudinal axis, from the Altiplano to the lowlands. Both autosomes and mtDNA revealed a low impact (1-2%) of a sub-Saharan component in Bolivians.

Analysis of potential risks from the bacterial communities associated with air-contact surfaces from tilapia (Oreochromis niloticus) fish farming.

PubMed

Grande Burgos, Maria Jose; Romero, Jose Luis; Pérez Pulido, Rubén; Cobo Molinos, Antonio; Gálvez, Antonio; Lucas, Rosario

2018-01-01

Tilapia farming is a promising growing sector in aquaculture. Yet, there are limited studies on microbiological risks associated to tilapia farms. The aim of the present study was to analyse the bacterial communities from solid surfaces in contact with air in a tilapia farm in order to evaluate the presence of bacteria potentially toxinogenic or pathogenic to humans or animals. Samples from a local tilapia farm (tank wall, aerator, water outlets, sink and floor) were analyzed by high throughput sequencing technology. Sequences were assigned to operational taxonomic units (OTUs). Proteobacteria was the main phylum represented in most samples (except for one). Cyanobacteria were a relevant phylum in the inner wall from the fattening tank and the wet floor by the pre-fattening tank. Bacteroidetes were the second phylum in relative abundance for samples from the larval rearing tank and the pre-fattening tank and one sample from the fattening tank. Fusobacteria showed highest relative abundances in samples from the larval rearing tank and pre-fattening tank. Other phyla (Verrucomicrobia, Actinobacteria, Firmicutes, Planktomycetes, Acidobacteria, Chloroflexi, Chlorobi, Gemmatiomonadetes or Fibrobacters) had lower relative abundances. A large fraction of the reads (ranging from 43.67% to 72.25%) were assigned to uncultured bacteria. Genus Acinetobacter (mainly A. calcoaceticus/baumanni) was the predominant OTU in the aerator of the fattening tank and also in the nearby sink on the floor. The genera Cetobacterium and Bacteroides showed highest relative abundances in the samples from the larval rearing tank and the pre-fattening tank. Genera including fish pathogens (Fusobacterium, Aeromonas) were only detected at low relative abundances. Potential human pathogens other than Acinetobacter were either not detected or had very low relative abundances (< 0.01%). The results of the study suggest that the main risk factors to be monitored in tilapia farm are putative human pathogenic Acinetobacter and potential cyanotoxin-producing cyanobacteria. Copyright © 2017 Elsevier Inc. All rights reserved.

Statistical theory for protein combinatorial libraries. Packing interactions, backbone flexibility, and the sequence variability of a main-chain structure.

PubMed

Kono, H; Saven, J G

2001-02-23

Combinatorial experiments provide new ways to probe the determinants of protein folding and to identify novel folding amino acid sequences. These types of experiments, however, are complicated both by enormous conformational complexity and by large numbers of possible sequences. Therefore, a quantitative computational theory would be helpful in designing and interpreting these types of experiment. Here, we present and apply a statistically based, computational approach for identifying the properties of sequences compatible with a given main-chain structure. Protein side-chain conformations are included in an atom-based fashion. Calculations are performed for a variety of similar backbone structures to identify sequence properties that are robust with respect to minor changes in main-chain structure. Rather than specific sequences, the method yields the likelihood of each of the amino acids at preselected positions in a given protein structure. The theory may be used to quantify the characteristics of sequence space for a chosen structure without explicitly tabulating sequences. To account for hydrophobic effects, we introduce an environmental energy that it is consistent with other simple hydrophobicity scales and show that it is effective for side-chain modeling. We apply the method to calculate the identity probabilities of selected positions of the immunoglobulin light chain-binding domain of protein L, for which many variant folding sequences are available. The calculations compare favorably with the experimentally observed identity probabilities.

Factors associated with use of pre-operative chemoradiation therapy for rectal cancer in the Cancer Care Outcomes Research and Surveillance Consortium

PubMed Central

Charlton, Mary E.; Lin, Chi; Jiang, Dingfeng; Stitzenberg, Karyn B.; Halfdanarson, Thorvardur R.; Pendergast, Jane F.; Chrischilles, Elizabeth A.; Wallace, Robert B.

2012-01-01

Purpose Pre-operative (pre-op) chemoradiation therapy (CRT) improves local control and reduces toxicity more than post-operative (post-op) CRT for the treatment of stages II/III rectal cancer, but studies suggest many patients still receive post-op CRT. We examined patient beliefs, and clinical and provider characteristics associated with receipt of recommended therapy. Methods We identified stage II/III rectal cancer patients who had primary site resection and CRT among subjects in the Cancer Care Outcomes Research and Surveillance Consortium, a population- and health system-based prospective cohort of newly diagnosed colorectal cancer patients from 2003 to 2005. Patient surveys and abstracted medical records were used to construct variables and determine sequence of CRT and surgery. Logistic regression was used to model the association between predictors and receipt of pre-op CRT. Results Of the 201 patients, 66% received pre-op and 34% received post-op CRT. Those visiting a medical oncologist and/or radiation oncologist prior to a surgeon had a 96% (95% CI, 92% to 100%) predicted probability of receiving pre-op CRT, compared to 48% (95% CI, 41% to 55%) for those visiting a surgeon first. Among those visiting a surgeon first, documentation of recommended staging procedures was associated with receiving pre-op CRT. Conclusion Sequence of provider visits and documentation of recommended staging procedures were important predictors of receiving pre-op CRT. Initial multidisciplinary evaluation led to better adherence to CRT guidelines. Further evaluation of provider characteristics, referral patterns and related health system processes should be undertaken to inform targeted interventions to reduce variation from recommended care. PMID:22992624

A tailored e-learning program to improve handover in the chain of emergency care: a pre-test post-test study.

PubMed

Ebben, Remco H A; van Grunsven, Pierre M; Moors, Marie Louise; Aldenhoven, Peter; de Vaan, Jordan; van Hout, Roger; van Achterberg, Theo; Vloet, Lilian C M

2015-04-16

To standardize patient handover in the chain of emergency care a handover guideline was developed. The main guideline recommendation is to use the DeMIST model (Demographics, Mechanism of Injury/illness, Injury/Illness, Signs, Treatment given) to structure pre-hospital notification and handover. To benefit from the new guideline, guideline adherence is necessary. As adherence to guidelines in emergency care settings is variable, there is a need to systematically implement the new guideline. For implementation of the guideline we developed a e-learning program tailored to influencing factors. The aim of the study was to evaluate the effectiveness of this e-learning program to improve emergency care professionals' adherence to the handover guideline during pre-hospital notification and handover in the chain of emergency medical service (EMS), emergency medical dispatch (EMD), and emergency department (ED). A prospective pre-test post-test study was conducted. The intervention was a tailored e-learning program that was offered to ambulance crew and emergency medical dispatchers (n=88). Data on adherence included pre-hospital notifications and handovers and were collected through observations and audiotapes before and after the e-learning program. Data were analyzed using X(2)-tests and t-tests. In total, 78/88 (88.6%) professionals followed the e-learning program. During pre- and post-test, 146 and 169 handovers were observed respectively. After the e-learning program, no significant difference in the number of handovers with the DeMIST model (77.9% vs. 73.1%, p=.319) and the number of handovers with the correct sequence of the DeMIST model (69.9% vs. 70.5%, p=.159) existed. During the handover, the number of questions by ED staff and interruptions significantly increased from 49.0% to 68.9% and from 15.2% to 52.7% respectively (both p=.000). Most handovers were performed after patient transfer, this did not change after the intervention (p=.167). The number of handovers where information was documented during handover slightly increased from 26.9% to 29.3% (p=.632). The tailored e-learning program did not improve adherence to a handover guideline in the chain of emergency care. Results show a relatively high baseline adherence rate to usage and correct sequence of the DeMIST model. Improvements in the handover process can be made on the documentation of information during handover, the number of interruptions and questions, and the handover moment.

Stellar Clusters in the NGC 6334 Star-Forming Complex

NASA Astrophysics Data System (ADS)

Feigelson, Eric D.; Martin, Amanda L.; McNeill, Collin J.; Broos, Patrick S.; Garmire, Gordon P.

2009-07-01

The full stellar population of NGC 6334, one of the most spectacular regions of massive star formation in the nearby Galaxy, has not been well sampled in past studies. We analyze here a mosaic of two Chandra X-ray Observatory images of the region using sensitive data analysis methods, giving a list of 1607 faint X-ray sources with arcsecond positions and approximate line-of-sight absorption. About 95% of these are expected to be cluster members, most lower mass pre-main-sequence stars. Extrapolating to low X-ray levels, the total stellar population is estimated to be 20,000-30,000 pre-main-sequence stars. The X-ray sources show a complicated spatial pattern with ~10 distinct star clusters. The heavily obscured clusters are mostly associated with previously known far-infrared sources and radio H II regions. The lightly obscured clusters are mostly newly identified in the X-ray images. Dozens of likely OB stars are found, both in clusters and dispersed throughout the region, suggesting that star formation in the complex has proceeded over millions of years. A number of extraordinarily heavily absorbed X-ray sources are associated with the active regions of star formation.

Soft X-ray observations of pre-main sequence stars in the chamaeleon dark cloud

NASA Technical Reports Server (NTRS)

Feigelson, Eric D.; Kriss, Gerard A.

1987-01-01

Einstein IPC observations of the nearby Chamaeleon I star forming cloud show 22 well-resolved soft X-ray sources in a 1x2 deg region. Twelve are associated with H-alpha emission line pre-main sequence (PMS) stars, and four with optically selected PMS stars. Several X-ray sources have two or more PMS stars in their error circles. Optical spectra were obtained at CTIO of possible stellar counterparts of the remaining X-ray sources. They reveal 5 probable new cloud members, K7-MO stars with weak or absent emission lines. These naked X-ray selected PMS stars are similar to those found in the Taurus-Auriga cloud. The spatial distributions and H-R diagrams of the X-ray and optically selected PMS stars in the cloud are very similar. Luminosity functions indicate the Chamaeleon stars are on average approximately 5 times more X-ray luminous than Pleiad dwarfs. A significant correlation between L sub x and optical magnitude suggests this trend may continue within the PMS phase of stellar evolution. The relation of increasing X-ray luminosity with decreasing stellar ages is thus extended to stellar ages as young as 1 million years.

AK Sco, First Detection of a Highly Disturbed Atmosphere in a Pre-Main-Sequence Close Binary

NASA Astrophysics Data System (ADS)

Gómez de Castro, Ana I.

2009-06-01

AK Sco is a unique source: a ~10 Myr old pre-main-sequence (PMS) spectroscopic binary composed of two nearly equal F5 stars that at periastron are separated by barely 11 stellar radii, so the stellar magnetospheres fill the Roche lobe at periastron. The orbit is not yet circularized (e = 0.47) and very strong tides are expected. This makes AK Sco the ideal laboratory to study the effect of gravitational tides in the stellar magnetic field building up during PMS evolution. In this Letter, the detection of a highly disturbed (σ sime 100 km s-1) and very dense atmosphere (n e = 1.6 × 1010 cm-3) is reported. Significant line broadening blurs any signs of ion belts or bow shocks in the spectrum of the atmospheric plasma. The radiative losses cannot be accounted for solely by the dissipation of energy from the tidal wave propagating in the stellar atmosphere or by the accreting material. The release of internal energy from the star seems to be the most likely source of the plasma heating. This is the first clear indication of a highly disturbed atmosphere surrounding a PMS close binary.

Hot Jet Ignition Delay Characterization of Methane and Hydrogen at Elevated Temperatures

NASA Astrophysics Data System (ADS)

Tarraf Kojok, Ali

This study contributes to a better understanding of ignition by hot combustion gases which finds application in internal combustion chambers with pre-chamber ignition as well as in wave rotor engine applications. The experimental apparatus consists of two combustion chambers: a pre chamber that generates the transient hot jet of gas and a main chamber which contains the main fuel air blend under study. Variables considered are three fuel mixtures (Hydrogen, Methane, 50% Hydrogen-Methane), initial pressure in the pre-chamber ranging from 1 to 2 atm, equivalence ratio of the fuel air mixture in the main combustion chamber ranging from 0.4 to 1.5, and initial temperature of the main combustion chamber mixture ranging from 297 K to 500 K. Experimental data makes use of 4 pressure sensors with a recorded sampling rate up to 300 kHz, as well as high speed Schlieren imaging with a recorded frame rate up to 20,833 frame per seconds. Results shows an overall increase in ignition delay with increasing equivalence ratio. High temperature of the main chamber blend was found not to affect hot jet ignition delay considerably. Physical mixing effects, and density of the main chamber mixture have a greater effect on hot jet ignition delay.

Genetic variability of Echinococcus granulosus from the Tibetan plateau inferred by mitochondrial DNA sequences.

PubMed

Yan, Ning; Nie, Hua-Ming; Jiang, Zhong-Rong; Yang, Ai-Guo; Deng, Shi-Jin; Guo, Li; Yu, Hua; Yan, Yu-Bao; Tsering, Dawa; Kong, Wei-Shu; Wang, Ning; Wang, Jia-Hai; Xie, Yue; Fu, Yan; Yang, De-Ying; Wang, Shu-Xian; Gu, Xiao-Bin; Peng, Xue-Rong; Yang, Guang-You

2013-09-01

To analyse genetic variability and population structure, 84 isolates of Echinococcus granulosus (Cestoda: Taeniidae) collected from various host species at different sites of the Tibetan plateau in China were sequenced for the whole mitochondrial nad1 (894 bp) and atp6 (513 bp) genes. The vast majority were classified as G1 genotype (n=82), and two samples from human patients in Sichuan province were identified as G3 genotype. Based on the concatenated sequences of nad1+atp6, 28 different haplotypes (NA1-NA28) were identified. A parsimonious network of the concatenated sequence haplotypes showed star-like features in the overall population, with NA1 as the major haplotype in the population networks. By AMOVA it was shown that variation of E. granulosus within the overall population was the main pattern of the total genetic variability. Neutrality indexes of the concatenated sequence (nad1+atp6) were computed by Tajima's D and Fu's Fs tests and showed high negative values for E. granulosus, indicating significant deviations from neutrality. FST and Nm values suggested that the populations were not genetically differentiated. Copyright © 2013 Elsevier B.V. All rights reserved.

Inferring action structure and causal relationships in continuous sequences of human action.

PubMed

Buchsbaum, Daphna; Griffiths, Thomas L; Plunkett, Dillon; Gopnik, Alison; Baldwin, Dare

2015-02-01

In the real world, causal variables do not come pre-identified or occur in isolation, but instead are embedded within a continuous temporal stream of events. A challenge faced by both human learners and machine learning algorithms is identifying subsequences that correspond to the appropriate variables for causal inference. A specific instance of this problem is action segmentation: dividing a sequence of observed behavior into meaningful actions, and determining which of those actions lead to effects in the world. Here we present a Bayesian analysis of how statistical and causal cues to segmentation should optimally be combined, as well as four experiments investigating human action segmentation and causal inference. We find that both people and our model are sensitive to statistical regularities and causal structure in continuous action, and are able to combine these sources of information in order to correctly infer both causal relationships and segmentation boundaries. Copyright © 2014. Published by Elsevier Inc.

Intermediate to low-mass stellar content of Westerlund 1

NASA Astrophysics Data System (ADS)

Brandner, W.; Clark, J. S.; Stolte, A.; Waters, R.; Negueruela, I.; Goodwin, S. P.

2008-01-01

We have analysed near-infrared NTT/SofI observations of the starburst cluster Westerlund 1, which is among the most massive young clusters in the Milky Way. A comparison of colour-magnitude diagrams with theoretical main-sequence and pre-main sequence evolutionary tracks yields improved extinction and distance estimates of AKs = 1.13 ± 0.03 mag and d = 3.55 ± 0.17 kpc (DM = 12.75 ± 0.10 mag). The pre-main sequence population is best fit by a Palla & Stahler isochrone for an age of 3.2 Myr, while the main sequence population is in agreement with a cluster age of 3 to 5 Myr. An analysis of the structural parameters of the cluster yields that the half-mass radius of the cluster population increases towards lower mass, indicative of the presence of mass segregation. The cluster is clearly elongated with an eccentricity of 0.20 for stars with masses between 10 and 32 M_⊙, and 0.15 for stars with masses in the range 3 to 10 M_⊙. We derive the slope of the stellar mass function for stars with masses between 3.4 and 27 M_⊙. In an annulus with radii between 0.75 and 1.5 pc from the cluster centre, we obtain a slope of Γ = -1.3. Closer in, the mass function of Westerlund 1 is shallower with Γ = -0.6. The extrapolation of the mass function for stars with masses from 0.08 to 120 M_⊙ yields an initial total stellar mass of ≈52 000 M_⊙, and a present-day mass of 20 000 to 45 000 M_⊙ (about 10 times the stellar mass of the Orion nebula cluster, and 2 to 4 times the mass of the NGC 3603 young cluster), indicating that Westerlund 1 is the most massive starburst cluster identified to date in the Milky Way. Based on observations collected at the European Southern Observatory, La Silla, Chile, and retrieved from the ESO archive (Prog ID 67.C-0514).

Estudio de la población estelar de varios cúmulos en Carina

NASA Astrophysics Data System (ADS)

Molina-Lera, J. A.; Baume, G. L.; Carraro, G.; Costa, E.

2015-08-01

Based on deep photometric data in the bands, complemented with infrared 2MASS data, we conducted an analysis of the fundamental parameters of six open clusters located in the Carina region. To perform a systematic study we developed a specialized code. In particular, we investigated the behavior of the respective lower main sequences. Our analysis indicated the presence of a significant population of pre-sequence stars in several of the clusters. We therefore obtained estimated values of contraction ages. Furthermore, we have determined the slopes of the initial mass functions of the studied clusters.

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

NASA Astrophysics Data System (ADS)

Gregory, Scott G.; Adams, Fred C.; Davies, Claire L.

2016-04-01

Pre-main-sequence (PMS) stars of mass ≳0.35 M⊙ 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 analogue of the solar tachocline develops. We have combined archival X-ray, spectroscopic, and photometric data for ˜1000 PMS stars from five of the best studied star-forming regions: the Orion Nebula Cluster, NGC 2264, IC 348, NGC 2362, and NGC 6530. Using a modern, PMS calibrated, spectral type-to-effective temperature and intrinsic colour scale, we de-redden 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 (LX/L*) than those on Hayashi tracks, where this effect is driven by changes in LX. X-ray emission decays faster with age for higher mass PMS stars. There is a strong correlation between L* and LX for Hayashi track stars but no correlation for Henyey track stars. There is no correlation between LX and radiative core mass or radius. However, the longer stars have spent with radiative cores, the less X-ray luminous they become. The decay of coronal X-ray emission from young early K to late G-type PMS stars, the progenitors of main-sequence A-type stars, is consistent with the dearth of X-ray detections of the latter.

A review of blood sample handling and pre-processing for metabolomics studies.

PubMed

Hernandes, Vinicius Veri; Barbas, Coral; Dudzik, Danuta

2017-09-01

Metabolomics has been found to be applicable to a wide range of clinical studies, bringing a new era for improving clinical diagnostics, early disease detection, therapy prediction and treatment efficiency monitoring. A major challenge in metabolomics, particularly untargeted studies, is the extremely diverse and complex nature of biological specimens. Despite great advances in the field there still exist fundamental needs for considering pre-analytical variability that can introduce bias to the subsequent analytical process and decrease the reliability of the results and moreover confound final research outcomes. Many researchers are mainly focused on the instrumental aspects of the biomarker discovery process, and sample related variables sometimes seem to be overlooked. To bridge the gap, critical information and standardized protocols regarding experimental design and sample handling and pre-processing are highly desired. Characterization of a range variation among sample collection methods is necessary to prevent results misinterpretation and to ensure that observed differences are not due to an experimental bias caused by inconsistencies in sample processing. Herein, a systematic discussion of pre-analytical variables affecting metabolomics studies based on blood derived samples is performed. Furthermore, we provide a set of recommendations concerning experimental design, collection, pre-processing procedures and storage conditions as a practical review that can guide and serve for the standardization of protocols and reduction of undesirable variation. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Primary Hepatic Malignant Fibrous Histiocytoma on PET/CT.

PubMed

Liu, Yachao; Xu, Baixuan

2018-06-01

Malignant fibrous histiocytoma is mainly presented in extremities, less commonly in posterior peritoneum, but primary presented in liver is very rare and often with a poor prognosis because of its high aggression. The features of clinical presentations and images are variable and the pre-operative diagnosis is difficult. Here, we report a primary hepatic malignant fibrous histiocytoma patient with no distant metastasis showed on pre-operative F-FDG PET/CT, however with many metastases showed on the post-operative F-FDG PET/CT.

Occult HBV among Anti-HBc Alone: Mutation Analysis of an HBV Surface Gene and Pre-S Gene.

PubMed

Kim, Myeong Hee; Kang, So Young; Lee, Woo In

2017-05-01

The aim of this study is to investigate the molecular characteristics of occult hepatitis B virus (HBV) infection in 'anti-HBc alone' subjects. Twenty-four patients with 'anti-HBc alone' and 20 control patients diagnosed with HBV were analyzed regarding S and pre-S gene mutations. All specimens were analyzed for HBs Ag, anti-HBc, and anti-HBs. For specimens with an anti-HBc alone, quantitative analysis of HBV DNA, as well as sequencing and mutation analysis of S and pre-S genes, were performed. A total 24 were analyzed for the S gene, and 14 were analyzed for the pre-S gene through sequencing. A total of 20 control patients were analyzed for S and pre-S gene simultaneously. Nineteen point mutations of the major hydrophilic region were found in six of 24 patients. Among them, three mutations, S114T, P127S/T, M133T, were detected in common. Only one mutation was found in five subjects of the control group; this mutation was not found in the occult HBV infection group, however. Pre-S mutations were detected in 10 patients, and mutations of site aa58-aa100 were detected in 9 patients. A mutation on D114E was simultaneously detected. Although five mutations from the control group were found at the same location (aa58-aa100), no mutations of occult HBV infection were detected. The prevalence of occult HBV infection is not low among 'anti-HBc alone' subjects. Variable mutations in the S gene and pre-S gene were associated with the occurrence of occult HBV infection. Further larger scale studies are required to determine the significance of newly detected mutations. © Copyright: Yonsei University College of Medicine 2017

Absolute Transition Probabilities of Lines in the Spectra of Astrophysical Atoms, Molecules, and Ions

NASA Technical Reports Server (NTRS)

Parkinson, W. H.; Smith, P. L.; Yoshino, K.

1984-01-01

Progress in the investigation of absolute transition probabilities (A-values or F values) for ultraviolet lines is reported. A radio frequency ion trap was used for measurement of transition probabilities for intersystem lines seen in astronomical spectra. The intersystem line at 2670 A in Al II, which is seen in pre-main sequence stars and symbiotic stars, was studied.

Hiding in plain sight

NASA Astrophysics Data System (ADS)

Riedel, Adric Richard

2012-05-01

Since the first successful measurements of stellar trigonometric parallax in the 1830s, the study of nearby stars has focused on the highest proper motion stars (micro > 0.18″ yr-1). Those high proper motion stars have formed the backbone of the last 150 years of study of the Solar Neighborhood and the composition of the Galaxy. Statistically speaking, though, there is a population of stars that will have low proper motions when their space motions have been projected onto the sky. At the same time, over the last twenty years, populations of relatively young stars (less than ˜ 100 Myr), most of them with low proper motions, have been revealed near (< 100 pc) the Sun. This dissertation is the result of two related projects: A photometric search for nearby (< 25pc) southern-hemisphere M dwarf stars with low proper motions (micro < 0.18″ yr-1), and a search for nearby (< 100 pc) pre-main-sequence (< 125 Myr old) M dwarf systems. The projects rely on a variety of photometric, spectroscopic, and astrometric analyses (including parallaxes from our program) using data from telescopes at CTIO via the SMARTS Consortium and at Lowell Observatory. Within this dissertation, I describe the identification and confirmation of 23 new nearby low proper motion M dwarf systems within 25 pc, 8 of which are within 15 pc (50% of the anticipated low-proper-motion 15 pc sample). I also report photometric, spectroscopic, and astrometric parameters and identifications for a selection of 25 known and new candidate nearby young M dwarfs, including new low-mass members of the TW Hydra, beta Pictoris, Tucana-Horologium, Argus, and AB Doradus associations, following the methods of my Riedel et al. (2011) paper and its discovery of AP Col, the closest pre-main-sequence star to the Solar System. These low proper motion and nearby star discoveries are put into the context of the Solar Neighborhood as a whole by means of the new RECONS 25 pc Database, to which I have now added (including my Riedel et al. (2010) paper) 81 star systems (4% of the total). INDEX WORDS: Astronomy, Astrometry, Photometry, Spectroscopy, Kinematics, Proper motion, Parallax, Nearby stars, Low-mass stars, Young stars, Pre-main-sequence stars.

New direct measurement of the 10B(p,α)7Be reaction with the activation technique

NASA Astrophysics Data System (ADS)

Depalo, Rosanna; Caciolli, Antonio; Broggini, Carlo; La Cognata, Marco; Lamia, Livio; Menegazzo, Roberto; Mou, Liliana; Puglia, Sebastiana Maria Regina; Rigato, Valentino; Romano, Stefano; Alvarez, Carlos Rossi; Sergi, Maria Letizia; Spitaleri, Claudio; Tumino, Aurora

2018-01-01

Boron plays an important role in astrophysics and, together with lithium and beryllium, is a probe of stellar structure during the pre-main sequence and main-sequence phases. In this context, the 10B(p,α)7 Be reaction is of particular interest. The literature data show discrepancies in the energy range between 100 keV and 2 MeV. This also poses a normalization problem for indirect data obtained with the Trojan Horse Method. A new measurement of the 10B(p,α)7 Be reaction cross section was performed at Legnaro National Laboratories (LNL). At LNL, the cross section was determined with the activation technique by measuring the activated samples at a low-background counting facility. The analysis of that experiment is now complete and the results are here presented.

A Search for Pulsation in Young Brown Dwarfs and Very Low Mass Stars

NASA Astrophysics Data System (ADS)

Cody, Ann Marie

2012-05-01

In 2005, Palla and Baraffe proposed that brown dwarfs and very low mass stars (<0.1 solar masses) may be unstable to radial oscillations during the pre-main-sequence deuterium burning phase. With associated oscillation periods of 1--4 hours, this potentially new class of pulsation offers unprecedented opportunities to probe the interiors and evolution of low-mass objects in the 1--15 million year age range. Furthermore, several previous reports of short-period variability have suggested that deuterium-burning pulsation is in fact at work in young clusters. For my dissertation, I developed a photometric monitoring campaign to search for low-amplitude periodic variability in young brown dwarfs and very low mass stars using meter-class telescopes from both the ground and space. The resulting high-precision, high-cadence time-series photometry targeted four young clusters and achieved sensitivity to periodic oscillations with photometric amplitudes down to several millimagnitudes. This unprecedented variability census probed timescales ranging from minutes to weeks in a sample of 200 young, low-mass cluster members of IC 348, Sigma Orionis, Chamaeleon I, and Upper Scorpius. While I find a dearth of photometric periods under 10 hours, the campaign's high time resolution and precision have enabled detailed study of diverse light curve behavior in the clusters: rotational spot modulation, accretion signatures, and occultations by surrounding disk material. Analysis of the data has led to the establishment of a lower limit for the timescale of periodic photometric variability in young low-mass and substellar objects, an extension of the rotation period distribution to the brown dwarf regime, as well as insights into the connection between variability and circumstellar disks in the Sigma Orionis and Chamaeleon I clusters.

Microbial communities of biomethanization digesters fed with raw and heat pre-treated microalgae biomasses.

PubMed

Sanz, Jose Luis; Rojas, Patricia; Morato, Ana; Mendez, Lara; Ballesteros, Mercedes; González-Fernández, Cristina

2017-02-01

Microalgae biomasses are considered promising feedstocks for biofuel and methane productions. Two Continuously Stirred Tank Reactors (CSTR), fed with fresh (CSTR-C) and heat pre-treated (CSTR-T) Chlorella biomass were run in parallel in order to determine methane productions. The methane yield was 1.5 times higher in CSTR-T with regard to CSTR-C. Aiming to understand the microorganism roles within of the reactors, the sludge used as an inoculum (I), plus raw (CSTR-C) and heat pre-treated (CSTR-T) samples were analyzed by high-throughput pyrosequencing. The bacterial communities were dominated by Proteobacteria, Bacteroidetes, Chloroflexi and Firmicutes. Spirochaetae and Actinobacteria were only detected in sample I. Proteobacteria, mainly Alfaproteobacteria, were by far the dominant phylum within of the CSTR-C bioreactor. Many of the sequences retrieved were related to bacteria present in activated sludge treatment plants and they were absent after thermal pre-treatment. Most of the sequences affiliated to the Bacteroidetes were related to uncultured groups. Anaerolineaceae was the sole family found of the Chloroflexi phylum. All of the genera identified of the Firmicutes phylum carried out macromolecule hydrolysis and by-product fermentation. The proteolytic bacteria were prevalent over the saccharolytic microbes. The percentage of the proteolytic genera increased from the inoculum to the CSTR-T sample in a parallel fashion with an available protein increase owing to the high protein content of Chlorella. To relate the taxa identified by high-throughput sequencing to their functional roles remains a future challenge. Copyright © 2016 Elsevier Ltd. All rights reserved.

Synthesis, characterisation and analytical application of Fe₃O₄@SiO₂@polyaminoquinoline magnetic nanocomposite for the extraction and pre-concentration of Cd(II) and Pb(II) in food samples.

PubMed

Manoochehri, Mahboobeh; Asgharinezhad, Ali Akbar; Shekari, Nafiseh

2015-01-01

This work describes a novel Fe₃O₄@SiO₂@polyaminoquinoline magnetic nanocomposite and its application in the pre-concentration of Cd(II) and Pb(II) ions. The parameters affecting the pre-concentration procedure were optimised by a Box-Behnken design through response surface methodology. Three variables (extraction time, magnetic sorbent amount and pH) were selected as the main factors affecting the sorption step, while four variables (type, volume and concentration of the eluent, and elution time) were selected as main factors in the optimisation study of the elution step. Following the sorption and elution of analytes, the ions were quantified by flame atomic absorption spectrometry (FASS). The limits of detection were 0.1 and 0.7 ng ml(-1) for Cd(II) and Pb(II) ions, respectively. All the relative standard deviations were less than 7.6%. The sorption capacities of this new sorbent were 57 mg g(-)(1) for Cd(II) and 73 mg g(-1) for Pb(II). Ultimately, this nanocomposite was successfully applied to the rapid extraction of trace quantities of these heavy metal ions from seafood and agricultural samples and satisfactory results were obtained.

Tumour heterogeneity in glioblastoma assessed by MRI texture analysis: a potential marker of survival

PubMed Central

Pérez-Beteta, Julián; Luque, Belén; Arregui, Elena; Calvo, Manuel; Borrás, José M; López, Carlos; Martino, Juan; Velasquez, Carlos; Asenjo, Beatriz; Benavides, Manuel; Herruzo, Ismael; Martínez-González, Alicia; Pérez-Romasanta, Luis; Arana, Estanislao; Pérez-García, Víctor M

2016-01-01

Objective: The main objective of this retrospective work was the study of three-dimensional (3D) heterogeneity measures of post-contrast pre-operative MR images acquired with T1 weighted sequences of patients with glioblastoma (GBM) as predictors of clinical outcome. Methods: 79 patients from 3 hospitals were included in the study. 16 3D textural heterogeneity measures were computed including run-length matrix (RLM) features (regional heterogeneity) and co-occurrence matrix (CM) features (local heterogeneity). The significance of the results was studied using Kaplan–Meier curves and Cox proportional hazards analysis. Correlation between the variables of the study was assessed using the Spearman's correlation coefficient. Results: Kaplan–Meyer survival analysis showed that 4 of the 11 RLM features and 4 of the 5 CM features considered were robust predictors of survival. The median survival differences in the most significant cases were of over 6 months. Conclusion: Heterogeneity measures computed on the post-contrast pre-operative T1 weighted MR images of patients with GBM are predictors of survival. Advances in knowledge: Texture analysis to assess tumour heterogeneity has been widely studied. However, most works develop a two-dimensional analysis, focusing only on one MRI slice to state tumour heterogeneity. The study of fully 3D heterogeneity textural features as predictors of clinical outcome is more robust and is not dependent on the selected slice of the tumour. PMID:27319577

Tumour heterogeneity in glioblastoma assessed by MRI texture analysis: a potential marker of survival.

PubMed

Molina, David; Pérez-Beteta, Julián; Luque, Belén; Arregui, Elena; Calvo, Manuel; Borrás, José M; López, Carlos; Martino, Juan; Velasquez, Carlos; Asenjo, Beatriz; Benavides, Manuel; Herruzo, Ismael; Martínez-González, Alicia; Pérez-Romasanta, Luis; Arana, Estanislao; Pérez-García, Víctor M

2016-07-04

The main objective of this retrospective work was the study of three-dimensional (3D) heterogeneity measures of post-contrast pre-operative MR images acquired with T 1 weighted sequences of patients with glioblastoma (GBM) as predictors of clinical outcome. 79 patients from 3 hospitals were included in the study. 16 3D textural heterogeneity measures were computed including run-length matrix (RLM) features (regional heterogeneity) and co-occurrence matrix (CM) features (local heterogeneity). The significance of the results was studied using Kaplan-Meier curves and Cox proportional hazards analysis. Correlation between the variables of the study was assessed using the Spearman's correlation coefficient. Kaplan-Meyer survival analysis showed that 4 of the 11 RLM features and 4 of the 5 CM features considered were robust predictors of survival. The median survival differences in the most significant cases were of over 6 months. Heterogeneity measures computed on the post-contrast pre-operative T 1 weighted MR images of patients with GBM are predictors of survival. Texture analysis to assess tumour heterogeneity has been widely studied. However, most works develop a two-dimensional analysis, focusing only on one MRI slice to state tumour heterogeneity. The study of fully 3D heterogeneity textural features as predictors of clinical outcome is more robust and is not dependent on the selected slice of the tumour.

Comprehensive identification and clustering of CLV3/ESR-related (CLE) genes in plants finds groups with potentially shared function.

PubMed

Goad, David M; Zhu, Chuanmei; Kellogg, Elizabeth A

2017-10-01

CLV3/ESR (CLE) proteins are important signaling peptides in plants. The short CLE peptide (12-13 amino acids) is cleaved from a larger pre-propeptide and functions as an extracellular ligand. The CLE family is large and has resisted attempts at classification because the CLE domain is too short for reliable phylogenetic analysis and the pre-propeptide is too variable. We used a model-based search for CLE domains from 57 plant genomes and used the entire pre-propeptide for comprehensive clustering analysis. In total, 1628 CLE genes were identified in land plants, with none recognizable from green algae. These CLEs form 12 groups within which CLE domains are largely conserved and pre-propeptides can be aligned. Most clusters contain sequences from monocots, eudicots and Amborella trichopoda, with sequences from Picea abies, Selaginella moellendorffii and Physcomitrella patens scattered in some clusters. We easily identified previously known clusters involved in vascular differentiation and nodulation. In addition, we found a number of discrete groups whose function remains poorly characterized. Available data indicate that CLE proteins within a cluster are likely to share function, whereas those from different clusters play at least partially different roles. Our analysis provides a foundation for future evolutionary and functional studies. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

Structure and immune recognition of trimeric pre-fusion HIV-1 Env

DOE PAGES

Pancera, Marie; Zhou, Tongqing; Druz, Aliaksandr; ...

2014-10-08

The human immunodeficiency virus type 1 (HIV-1) envelope (Env) spike, comprising three gp120 and three gp41 subunits, is a conformational machine that facilitates HIV-1 entry by rearranging from a mature unliganded state, through receptor-bound intermediates, to a post-fusion state. As the sole viral antigen on the HIV-1 virion surface, Env is both the target of neutralizing antibodies and a focus of vaccine efforts. Here we report the structure at 3.5 Å resolution for an HIV-1 Env trimer captured in a mature closed state by antibodies PGT122 and 35O22. This structure reveals the pre-fusion conformation of gp41, indicates rearrangements needed formore » fusion activation, and defines parameters of immune evasion and immune recognition. Pre-fusion gp41 encircles amino- and carboxy-terminal strands of gp120 with four helices that form a membrane-proximal collar, fastened by insertion of a fusion peptide-proximal methionine into a gp41-tryptophan clasp. Spike rearrangements required for entry involve opening the clasp and expelling the termini. In conclusion, N-linked glycosylation and sequence-variable regions cover the pre-fusion closed spike; we used chronic cohorts to map the prevalence and location of effective HIV-1-neutralizing responses, which were distinguished by their recognition of N-linked glycan and tolerance for epitope-sequence variation.« less

Structure and immune recognition of trimeric pre-fusion HIV-1 Env

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pancera, Marie; Zhou, Tongqing; Druz, Aliaksandr

The human immunodeficiency virus type 1 (HIV-1) envelope (Env) spike, comprising three gp120 and three gp41 subunits, is a conformational machine that facilitates HIV-1 entry by rearranging from a mature unliganded state, through receptor-bound intermediates, to a post-fusion state. As the sole viral antigen on the HIV-1 virion surface, Env is both the target of neutralizing antibodies and a focus of vaccine efforts. Here we report the structure at 3.5 Å resolution for an HIV-1 Env trimer captured in a mature closed state by antibodies PGT122 and 35O22. This structure reveals the pre-fusion conformation of gp41, indicates rearrangements needed formore » fusion activation, and defines parameters of immune evasion and immune recognition. Pre-fusion gp41 encircles amino- and carboxy-terminal strands of gp120 with four helices that form a membrane-proximal collar, fastened by insertion of a fusion peptide-proximal methionine into a gp41-tryptophan clasp. Spike rearrangements required for entry involve opening the clasp and expelling the termini. In conclusion, N-linked glycosylation and sequence-variable regions cover the pre-fusion closed spike; we used chronic cohorts to map the prevalence and location of effective HIV-1-neutralizing responses, which were distinguished by their recognition of N-linked glycan and tolerance for epitope-sequence variation.« less

Quasispecies variant of pre-S/S gene in HBV-related hepatocellular carcinoma with HBs antigen positive and occult infection.

PubMed

Hatazawa, Yuri; Yano, Yoshihiko; Okada, Rina; Tanahashi, Toshihito; Hayashi, Hiroki; Hirano, Hirotaka; Minami, Akihiro; Kawano, Yuki; Tanaka, Motofumi; Fukumoto, Takumi; Murakami, Yoshiki; Yoshida, Masaru; Hayashi, Yoshitake

2018-01-01

Hepatocellular carcinoma (HCC) can develop in patients who are negative for the hepatitis B surface antigen (HBsAg) in serum but positive for hepatitis B virus (HBV) DNA in the liver, referred to as occult HBV infection (OBI). Previous reports showed that HBV variants in OBI-related HCC are different from those in HBsAg-positive HCC. In the present study, HBV quasispecies based on the pre-S/S gene in OBI-related HCC patients were examined by high throughput sequencing and compared with those in HBsAg-positive HCC. Nineteen tissue samples (9 OBI-related and 10 HBsAg-positive non-cancerous tissues) were collected at the time of surgery at Kobe University Hospital. The quasispecies with more than 1% variation in the pre-S/S region were isolated and analysed by ultra-deep sequencing. There were no significant differences in the major HBV populations, which exhibit more than 20% variation within the entire pre-S/S region, between OBI-related HCC and HBsAg-positive HCC. However, the prevalences of major populations with pre-S2 region mutations and of minor populations with polymerized human serum albumin-binding domain mutations were significantly higher in OBI-related HCC than in HBsAg-positive HCC. Moreover, the major variant populations associated with the B-cell epitope, located within the pre-S1 region, and the a determinant domain, located in the S region, were detected frequently in HBsAg-positive HCC. The minor populations of variants harbouring the W4R, L30S, Q118R/Stop, N123D and S124F/P mutations in the pre-S region and the L21F/S and L42F/S mutations in the S region were detected more frequently in OBI-related HCC than in HBsAg-positive HCC. Ultra-deep sequencing revealed that the B-cell epitope domain in the pre-S1 region and alpha determinant domain in the S region were variable in HBsAg-positive HCC, although the quasispecies associated with the pre-S2 region were highly prevalent in OBI-related HCC. Ref: R000034382/UMIN000030113; Retrospectively registered 25 November 2017.

Revolution evolution: tracing angular momentum during star and planetary system formation

NASA Astrophysics Data System (ADS)

Davies, Claire Louise

2015-04-01

Stars form via the gravitational collapse of molecular clouds during which time the protostellar object contracts by over seven orders of magnitude. If all the angular momentum present in the natal cloud was conserved during collapse, stars would approach rotational velocities rapid enough to tear themselves apart within just a few Myr. In contrast to this, observations of pre-main sequence rotation rates are relatively slow (∼ 1 - 15 days) indicating that significant quantities of angular momentum must be removed from the star. I use observations of fully convective pre-main sequence stars in two well-studied, nearby regions of star formation (namely the Orion Nebula Cluster and Taurus-Auriga) to determine the removal rate of stellar angular momentum. I find the accretion disc-hosting stars to be rotating at a slower rate and contain less specific angular momentum than the disc-less stars. I interpret this as indicating a period of accretion disc-regulated angular momentum evolution followed by near-constant rotational evolution following disc dispersal. Furthermore, assuming that the age spread inferred from the Hertzsprung-Russell diagram constructed for the star forming region is real, I find that the removal rate of angular momentum during the accretion-disc hosting phase to be more rapid than that expected from simple disc-locking theory whereby contraction occurs at a fixed rotation period. This indicates a more efficient process of angular momentum removal must operate, most likely in the form of an accretion-driven stellar wind or outflow emanating from the star-disc interaction. The initial circumstellar envelope that surrounds a protostellar object during the earliest stages of star formation is rotationally flattened into a disc as the star contracts. An effective viscosity, present within the disc, enables the disc to evolve: mass accretes inwards through the disc and onto the star while momentum migrates outwards, forcing the outer regions of the disc to expand. I used spatially resolved submillimetre detections of the dust and gas components of protoplanetary discs, gathered from the literature, to measure the radial extent of discs around low-mass pre-main sequence stars of ∼ 1-10 Myr and probe their viscous evolution. I find no clear observational evidence for the radial expansion of the dust component. However, I find tentative evidence for the expansion ofthe gas component. This suggests that the evolution of the gas and dust components of protoplanetary discs are likely governed by different astrophysical processes. Observations of jets and outflows emanating from protostars and pre-main sequence stars highlight that it may also be possible to remove angular momentum from the circumstellar material. Using the sample of spatially resolved protoplanetary discs, I find no evidence for angular momentum removal during disc evolution. I also use the spatially resolved debris discs from the Submillimetre Common-User Bolometer Array-2 Observations of Nearby Stars survey to constrain the amount of angular momentum retained within planetary systems. This sample is compared to the protoplanetary disc angular momenta and to the angular momentum contained within pre-stellar cores. I find that significant quantities of angular momentum must be removed during disc formation and disc dispersal. This likely occurs via magnetic braking during the formation of the disc, via the launching of a disc or photo-evaporative wind, and/or via ejection of planetary material following dynamical interactions.

Effect of pre-strain on precipitation and exfoliation corrosion resistance in an Al-Zn-Mg alloy

NASA Astrophysics Data System (ADS)

Lu, Xianghan; Du, Zhiwei; Han, Xiaolei; Li, Ting; Wang, Guojun; Lu, Liying; Bai, Xiaoxia; Zhou, Tietao

2017-12-01

To investigate the effect of pre-strain on behaviors in a specially developed Al-4.5Zn-1.2Mg alloy, transmission electron microscopy (TEM) bright field (BF) imaging combined with select area electron diffraction (SAED), Vickers-hardness tests and electrical conductivity tests was conducted for insight into precipitation in aluminum (Al) matrix during two step ageing, and standard exfoliation corrosion (EXCO) test combined with high-angle angular dark field scanning transmission electron microscopy (HAADF-STEM) and scanning electron microscopy (SEM) was carried out for corrosion behavior. Results showed that pre-strain accelerated precipitation during two step ageing as the sequence of: (i) supersaturated solid solution (SSS), GPI zones precipitations, GPI dissolution; (ii) SSS, fcc precipitates, η’ phases or η phases. And the precipitation hardening of the fcc precipitates was not effective as GPI zones. Pre-strain also accelerated EXCO developing, which was mainly attributed to the coverage ratio of η phases on high-angle grain boundaries (HAGBs) increasing as pre-strain increase.

Stress-based animal models of depression: Do we actually know what we are doing?

PubMed

Yin, Xin; Guven, Nuri; Dietis, Nikolas

2016-12-01

Depression is one of the leading causes of disability and a significant health-concern worldwide. Much of our current understanding on the pathogenesis of depression and the pharmacology of antidepressant drugs is based on pre-clinical models. Three of the most popular stress-based rodent models are the forced swimming test, the chronic mild stress paradigm and the learned helplessness model. Despite their recognizable advantages and limitations, they are associated with an immense variability due to the high number of design parameters that define them. Only few studies have reported how minor modifications of these parameters affect the model phenotype. Thus, the existing variability in how these models are used has been a strong barrier for drug development as well as benchmark and evaluation of these pre-clinical models of depression. It also has been the source of confusing variability in the experimental outcomes between research groups using the same models. In this review, we summarize the known variability in the experimental protocols, identify the main and relevant parameters for each model and describe the variable values using characteristic examples. Our view of depression and our efforts to discover novel and effective antidepressants is largely based on our detailed knowledge of these testing paradigms, and requires a sound understanding around the importance of individual parameters to optimize and improve these pre-clinical models. Copyright © 2016 Elsevier B.V. All rights reserved.

The Herbig B0e star HD 53367: circumstellar activity and evidence of binarity

NASA Astrophysics Data System (ADS)

Pogodin, M. A.; Malanushenko, V. P.; Kozlova, O. V.; Tarasova, T. N.; Franco, G. A. P.

2006-06-01

Aims.We investigate the spectroscopic behaviour of the young B0e star HD 53367 within a cooperative observing programme conducted from 1994 to 2005. Methods: .The data include more than 100 high-resolution spectra collected at the Crimean Astronomical Observatory (CrAO) near Hα, Hβ, He i λ 5876, 6678 Å, DNa i, and O ii λ 6641 Å lines. Two spectra obtained at the Observatório do Pico dos Dias (LNA), in the spectral bands λλ 4575-4725 Å and λλ 5625-5775 Å, were used for spectral classification of HD 53367. The temporal behaviour of the circumstellar lines Hα and Hβ as well as the photospheric lines O ii λ 6641 Å and He i λ 6678 Å were investigated during different stages of the photometric activity of this object. Results: .We confirm that the long-term photometric variability of HD 53367 is related to the alternation of two states of this object when the gaseous circumstellar envelope disappears and rises again. Both these processes start near the star and spread to the outlying parts of the envelope. We find that the radial velocities of He i and O ii photospheric lines demonstrate a cyclic variability with a period of P=183.7 days and semi-amplitude K=19 km s-1. The radial velocity change is interpreted in the framework of a model in which the star is a component of an eccentric binary system. An orbital solution is derived and the system's parameters estimated. We find that the orbital eccentricity is e=0.28, and the mean companion separation is 1.7 AU. Conclusions: .Based on the estimated parameters, we conclude that the system consists of a massive (~20 M_⊙) main sequence primary B0e star, and a secondary which is most likely a 5 solar mass pre-main sequence object. We found evidence that the main part of the circumstellar gas in this system is concentrated near the secondary companion. Although the young age of HD 53367, its evolved primary B0e star seems to have already became a classical Be star exhibiting a specific alternation of the B-Be stages.

Characterisation of monotreme caseins reveals lineage-specific expansion of an ancestral casein locus in mammals.

PubMed

Lefèvre, Christophe M; Sharp, Julie A; Nicholas, Kevin R

2009-01-01

Using a milk-cell cDNA sequencing approach we characterised milk-protein sequences from two monotreme species, platypus (Ornithorhynchus anatinus) and echidna (Tachyglossus aculeatus) and found a full set of caseins and casein variants. The genomic organisation of the platypus casein locus is compared with other mammalian genomes, including the marsupial opossum and several eutherians. Physical linkage of casein genes has been seen in the casein loci of all mammalian genomes examined and we confirm that this is also observed in platypus. However, we show that a recent duplication of beta-casein occurred in the monotreme lineage, as opposed to more ancient duplications of alpha-casein in the eutherian lineage, while marsupials possess only single copies of alpha- and beta-caseins. Despite this variability, the close proximity of the main alpha- and beta-casein genes in an inverted tail-tail orientation and the relative orientation of the more distant kappa-casein genes are similar in all mammalian genome sequences so far available. Overall, the conservation of the genomic organisation of the caseins indicates the early, pre-monotreme development of the fundamental role of caseins during lactation. In contrast, the lineage-specific gene duplications that have occurred within the casein locus of monotremes and eutherians but not marsupials, which may have lost part of the ancestral casein locus, emphasises the independent selection on milk provision strategies to the young, most likely linked to different developmental strategies. The monotremes therefore provide insight into the ancestral drivers for lactation and how these have adapted in different lineages.

Hydrothermal pre-treatment of rapeseed straw.

PubMed

Díaz, Manuel J; Cara, Cristóbal; Ruiz, Encarnación; Romero, Inmaculada; Moya, Manuel; Castro, Eulogio

2010-04-01

As a first step for ethanol production from alternative raw materials, rapeseed straw was studied for fermentable sugar production. Liquid hot water was used as a pre-treatment method and the influence of the main pre-treatment variables was assessed. Experimental design and response surface methodology were applied using pre-treatment temperature and process time as factors. The pretreated solids were further submitted to enzymatic hydrolysis and the corresponding yields were used as pre-treatment performance evaluation. Liquid fractions obtained from pre-treatment were also characterized in terms of sugars and no-sugar composition. A mathematical model describing pre-treatment effects is proposed. Results show that enzymatic hydrolysis yields near to 100% based on pretreated materials can be achieved at 210-220 degrees C for 30-50 min, equivalent to near 70% of glucose present in the raw material. According to the mathematical model, a softer pre-treatment at 193 degrees C for 27 min results in 65% of glucose and 39% of xylose available for fermentation. Copyright 2009 Elsevier Ltd. All rights reserved.

First insight into dead wood protistan diversity: a molecular sampling of bright-spored Myxomycetes (Amoebozoa, slime-moulds) in decaying beech logs.

PubMed

Clissmann, Fionn; Fiore-Donno, Anna Maria; Hoppe, Björn; Krüger, Dirk; Kahl, Tiemo; Unterseher, Martin; Schnittler, Martin

2015-06-01

Decaying wood hosts a large diversity of seldom investigated protists. Environmental sequencing offers novel insights into communities, but has rarely been applied to saproxylic protists. We investigated the diversity of bright-spored wood-inhabiting Myxomycetes by environmental sequencing. Myxomycetes have a complex life cycle culminating in the formation of mainly macroscopic fruiting bodies, highly variable in shape and colour that are often found on decaying logs. Our hypothesis was that diversity of bright-spored Myxomycetes would increase with decay. DNA was extracted from wood chips collected from 17 beech logs of varying decay stages from the Hainich-Dün region in Central Germany. We obtained 260 partial small subunit ribosomal RNA gene sequences of bright-spored Myxomycetes that were assembled into 29 OTUs, of which 65% were less than 98% similar to those in the existing database. The OTU richness revealed by molecular analysis surpassed that of a parallel inventory of fruiting bodies. We tested several environmental variables and identified pH, rather than decay stage, as the main structuring factor of myxomycete distribution. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

The Exoplant Migration Timescale from K2 Young Clusters

NASA Astrophysics Data System (ADS)

Rizzuto, Aaron C.; Mann, Andrew; Kraus, Adam L.; Ireland, Michael

2017-01-01

Planetary Migration models for close-in exoplanets(a < 0.1 AU, P < 20 days) can be loosely divided into three categories: Disk-driven migration, binary-star planet interaction, and planet-planet interaction. Disk migration, occurs over the lifetime of the protoplanetary disk (<5 Myr), while migration involving dynamical multi-body interactions operate on timescales of ~100’s of Myr to ~1Gyr, a lengthier process than disk migration. It is unclear which of these is the dominating mechanism.The K2 mission has measured planet formation timescales and migration pathways by sampling groups of stars at key pre-main-sequence ages: Over the past 10 campaigns, multiple groups of young stars have been observed by K2, ranging from the 10 Myr Upper Scorpius OB association, through the ˜120 Myr Pleiades, the ˜600-800 Myr Hyades and Praesepe moving groups, to the original Kepler Field. The frequency, orbital and compositional properties of the exoplanet population in these samples of different age, with careful treatment of detection completeness, will be sufficient to address the question of exoplanet migration as their host stars are settling onto the main sequence.We will present the initial results of a program to directly address the question of planet migration with a uniform injection-recovery tests on a new K2 detrending pipeline that is optimized for the particular case of young, rotationally variable stars in K2 to robustly measure the detectability of planets of differing size and orbit. Initial results point towards a migration timescale of 200-700 Myr, which is consistent with the slower planet-planet scattering or Kozai migration models.

Modeling of DNA local parameters predicts encrypted architectural motifs in Xenopus laevis ribosomal gene promoter.

PubMed

Roux-Rouquie, M; Marilley, M

2000-09-15

We have modeled local DNA sequence parameters to search for DNA architectural motifs involved in transcription regulation and promotion within the Xenopus laevis ribosomal gene promoter and the intergenic spacer (IGS) sequences. The IGS was found to be shaped into distinct topological domains. First, intrinsic bends split the IGS into domains of common but different helical features. Local parameters at inter-domain junctions exhibit a high variability with respect to intrinsic curvature, bendability and thermal stability. Secondly, the repeated sequence blocks of the IGS exhibit right-handed supercoiled structures which could be related to their enhancer properties. Thirdly, the gene promoter presents both inherent curvature and minor groove narrowing which may be viewed as motifs of a structural code for protein recognition and binding. Such pre-existing deformations could simply be remodeled during the binding of the transcription complex. Alternatively, these deformations could pre-shape the promoter in such a way that further remodeling is facilitated. Mutations shown to abolish promoter curvature as well as intrinsic minor groove narrowing, in a variant which maintained full transcriptional activity, bring circumstantial evidence for structurally-preorganized motifs in relation to transcription regulation and promotion. Using well documented X. laevis rDNA regulatory sequences we showed that computer modeling may be of invaluable assistance in assessing encrypted architectural motifs. The evidence of these DNA topological motifs with respect to the concept of structural code is discussed.

Parallel computation of genome-scale RNA secondary structure to detect structural constraints on human genome.

PubMed

Kawaguchi, Risa; Kiryu, Hisanori

2016-05-06

RNA secondary structure around splice sites is known to assist normal splicing by promoting spliceosome recognition. However, analyzing the structural properties of entire intronic regions or pre-mRNA sequences has been difficult hitherto, owing to serious experimental and computational limitations, such as low read coverage and numerical problems. Our novel software, "ParasoR", is designed to run on a computer cluster and enables the exact computation of various structural features of long RNA sequences under the constraint of maximal base-pairing distance. ParasoR divides dynamic programming (DP) matrices into smaller pieces, such that each piece can be computed by a separate computer node without losing the connectivity information between the pieces. ParasoR directly computes the ratios of DP variables to avoid the reduction of numerical precision caused by the cancellation of a large number of Boltzmann factors. The structural preferences of mRNAs computed by ParasoR shows a high concordance with those determined by high-throughput sequencing analyses. Using ParasoR, we investigated the global structural preferences of transcribed regions in the human genome. A genome-wide folding simulation indicated that transcribed regions are significantly more structural than intergenic regions after removing repeat sequences and k-mer frequency bias. In particular, we observed a highly significant preference for base pairing over entire intronic regions as compared to their antisense sequences, as well as to intergenic regions. A comparison between pre-mRNAs and mRNAs showed that coding regions become more accessible after splicing, indicating constraints for translational efficiency. Such changes are correlated with gene expression levels, as well as GC content, and are enriched among genes associated with cytoskeleton and kinase functions. We have shown that ParasoR is very useful for analyzing the structural properties of long RNA sequences such as mRNAs, pre-mRNAs, and long non-coding RNAs whose lengths can be more than a million bases in the human genome. In our analyses, transcribed regions including introns are indicated to be subject to various types of structural constraints that cannot be explained from simple sequence composition biases. ParasoR is freely available at https://github.com/carushi/ParasoR .

Effects of pre- and pro-sequence of thaumatin on the secretion by Pichia pastoris.

PubMed

Ide, Nobuyuki; Masuda, Tetsuya; Kitabatake, Naofumi

2007-11-23

Thaumatin is a 22-kDa sweet-tasting protein containing eight disulfide bonds. When thaumatin is expressed in Pichia pastoris using the thaumatin cDNA fused with both the alpha-factor signal sequence and the Kex2 protease cleavage site from Saccharomyces cerevisiae, the N-terminal sequence of the secreted thaumatin molecule is not processed correctly. To examine the role of the thaumatin cDNA-encoded N-terminal pre-sequence and C-terminal pro-sequence on the processing of thaumatin and efficiency of thaumatin production in P. pastoris, four expression plasmids with different pre-sequence and pro-sequence were constructed and transformed into P. pastoris. The transformants containing pre-thaumatin gene that has the native plant signal, secreted thaumatin molecules in the medium. The N-terminal amino acid sequence of the secreted thaumatin molecule was processed correctly. The production yield of thaumatin was not affected by the C-terminal pro-sequence, and the pro-sequence was not processed in P. pastoris, indicating that pro-sequence is not necessary for thaumatin synthesis.

Genomic Characterization of Vulvar (Pre)cancers Identifies Distinct Molecular Subtypes with Prognostic Significance.

PubMed

Nooij, Linda S; Ter Haar, Natalja T; Ruano, Dina; Rakislova, Natalia; van Wezel, Tom; Smit, Vincent T H B M; Trimbos, Baptist J B M Z; Ordi, Jaume; van Poelgeest, Mariette I E; Bosse, Tjalling

2017-11-15

Purpose: Vulvar cancer (VC) can be subclassified by human papillomavirus (HPV) status. HPV-negative VCs frequently harbor TP53 mutations; however, in-depth analysis of other potential molecular genetic alterations is lacking. We comprehensively assessed somatic mutations in a large series of vulvar (pre)cancers. Experimental Design: We performed targeted next-generation sequencing (17 genes), p53 immunohistochemistry and HPV testing on 36 VC and 82 precursors (sequencing cohort). Subsequently, the prognostic significance of the three subtypes identified in the sequencing cohort was assessed in a series of 236 VC patients (follow-up cohort). Results: Frequent recurrent mutations were identified in HPV-negative vulvar (pre)cancers in TP53 (42% and 68%), NOTCH1 (28% and 41%), and HRAS (20% and 31%). Mutation frequency in HPV-positive vulvar (pre)cancers was significantly lower ( P = 0.001). Furthermore, a substantial subset of the HPV-negative precursors (35/60, 58.3%) and VC (10/29, 34.5%) were TP53 wild-type (wt), suggesting a third, not-previously described, molecular subtype. Clinical outcomes in the three different subtypes (HPV + , HPV - /p53wt, HPV - /p53abn) were evaluated in a follow-up cohort consisting of 236 VC patients. Local recurrence rate was 5.3% for HPV + , 16.3% for HPV - /p53wt and 22.6% for HPV - /p53abn tumors ( P = 0.044). HPV positivity remained an independent prognostic factor for favorable outcome in the multivariable analysis ( P = 0.020). Conclusions: HPV - and HPV + vulvar (pre)cancers display striking differences in somatic mutation patterns. HPV - /p53wt VC appear to be a distinct clinicopathologic subgroup with frequent NOTCH1 mutations. HPV + VC have a significantly lower local recurrence rate, independent of clinicopathological variables, opening opportunities for reducing overtreatment in VC. Clin Cancer Res; 23(22); 6781-9. ©2017 AACR . ©2017 American Association for Cancer Research.

Constraints on pre-main-sequence evolution from stellar pulsations

NASA Astrophysics Data System (ADS)

Casey, M. P.; Zwintz, K.; Guenther, D. B.

2014-02-01

Pulsating pre-main-sequence (PMS) stars afford the earliest opportunity in the lifetime of a star to which the concepts of asteroseismology can be applied. PMS stars should be structurally simpler than their evolved counterparts, thus (hopefully!) making any asteroseismic analysis relatively easier. Unfortunately, this isn't necessarily the case. The majority of these stars (around 80) are δ Scuti pulsators, with a couple of γ Doradus, γ Doradus - δ Scuti hybrids, and slowly pulsating B stars thrown into the mix. The majority of these stars have only been discovered within the last ten years, with the community still uncovering the richness of phenomena associated with these stars, many of which defy traditional asteroseismic analysis. A systematic asteroseismic analysis of all of the δ Scuti PMS stars was performed in order to get a better handle on the properties of these stars as a group. Some strange results have been found, including one star pulsating up to the theoretical acoustic cut-off frequency of the star, and a number of stars in which the most basic asteroseismic analysis suggests problems with the stars' positions in the Hertzsprung-Russell diagram. From this we get an idea of the\\break constraints - or lack thereof - that these results can put on PMS stellar evolution.

Course 6: Star Formation

NASA Astrophysics Data System (ADS)

Natta, A.

Contents 1 Introduction 2 Collapse of molecular cores 2.1 Giant molecular clouds and cores 2.2 Conditions for collapse 2.3 Free-fall collapse 2.4 Collapse of an isothermal sphere of gas 2.5 Collapse of a slowly rotating core 3 Observable properties of protostars 3.1 Evidence of infall from molecular line profiles 3.2 SEDs of protostars 3.3 The line spectrumof a protostar 4 Protostellar and pre-main-sequence evolution 4.1 The protostellar phase 4.2 Pre-main-sequence evolution 4.3 The birthline 5 Circumstellar disks 5.1 Accretion disks 5.2 Properties of steady accretion disks 5.3 Reprocessing disks 5.4 Disk-star interaction 6 SEDs of disks 6.1 Power-law disks 6.2 Long-wavelength flux and disk mass 6.3 Comparison with TTS observations: Heating mechanism 7 Disk properties from observations 7.1 Mass accretion rate 7.2 Inner radius 7.3 Masses 7.4 Sizes 8 Disk lifetimes 8.1 Ground-based near and mid-infrared surveys 8.2 Mid-infrared ISOCAMsurveys 8.3 ISOPHOT 60 microm survey 8.4 Surveys at millimeter wavelengths 9 Disk evolution 9.1 Can we observe the early planet formation phase? 9.2 Evidence for grain growth 9.3 Evidence of planetesimals 9.4 Where is the diskmass? 10 Secondary or debris disks 11 Summary

V474 Car: A RARE HALO RS CVn BINARY IN RETROGRADE GALACTIC ORBIT

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bubar, Eric J.; Mamajek, Eric E.; Jensen, Eric L. N.

We report the discovery that the star V474 Car is an extremely active, high velocity halo RS CVn system. The star was originally identified as a possible pre-main-sequence star in Carina, given its enhanced stellar activity, rapid rotation (10.3 days), enhanced Li, and absolute magnitude which places it above the main sequence (MS). However, its extreme radial velocity (264 km s{sup -1}) suggested that this system was unlike any previously known pre-MS system. Our detailed spectroscopic analysis of echelle spectra taken with the CTIO 4 m finds that V474 Car is both a spectroscopic binary with an orbital period similarmore » to the photometric rotation period and metal-poor ([Fe/H] {approx_equal}-0.99). The star's Galactic orbit is extremely eccentric (e {approx_equal} 0.93) with a perigalacticon of only {approx}0.3 kpc of the Galactic center-and the eccentricity and smallness of its perigalacticon are surpassed by only {approx}0.05% of local F/G-type field stars. The observed characteristics are consistent with V474 Car being a high-velocity, metal-poor, tidally locked, chromospherically active binary, i.e., a halo RS CVn binary, and one of only a few such specimens known.« less

PEERING INTO THE GIANT-PLANET-FORMING REGION OF THE TW HYDRAE DISK WITH THE GEMINI PLANET IMAGER

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rapson, Valerie A.; Kastner, Joel H.; Millar-Blanchaer, Maxwell A.

2015-12-20

We present Gemini Planet Imager (GPI) adaptive optics near-infrared images of the giant-planet-forming regions of the protoplanetary disk orbiting the nearby (D = 54 pc), pre-main-sequence (classical T Tauri) star TW Hydrae. The GPI images, which were obtained in coronagraphic/polarimetric mode, exploit starlight scattered off small dust grains to elucidate the surface density structure of the TW Hya disk from ∼80 AU to within ∼10 AU of the star at ∼1.5 AU resolution. The GPI polarized intensity images unambiguously confirm the presence of a gap in the radial surface brightness distribution of the inner disk. The gap is centered near ∼23 AU,more » with a width of ∼5 AU and a depth of ∼50%. In the context of recent simulations of giant-planet formation in gaseous, dusty disks orbiting pre-main-sequence stars, these results indicate that at least one young planet with a mass ∼0.2 M{sub J} could be present in the TW Hya disk at an orbital semimajor axis similar to that of Uranus. If this (proto)planet is actively accreting gas from the disk, it may be readily detectable by GPI or a similarly sensitive, high-resolution infrared imaging system.« less

A VVWBO-BVO-based GM (1,1) and its parameter optimization by GRA-IGSA integration algorithm for annual power load forecasting

PubMed Central

Wang, Hongguang

2018-01-01

Annual power load forecasting is not only the premise of formulating reasonable macro power planning, but also an important guarantee for the safety and economic operation of power system. In view of the characteristics of annual power load forecasting, the grey model of GM (1,1) are widely applied. Introducing buffer operator into GM (1,1) to pre-process the historical annual power load data is an approach to improve the forecasting accuracy. To solve the problem of nonadjustable action intensity of traditional weakening buffer operator, variable-weight weakening buffer operator (VWWBO) and background value optimization (BVO) are used to dynamically pre-process the historical annual power load data and a VWWBO-BVO-based GM (1,1) is proposed. To find the optimal value of variable-weight buffer coefficient and background value weight generating coefficient of the proposed model, grey relational analysis (GRA) and improved gravitational search algorithm (IGSA) are integrated and a GRA-IGSA integration algorithm is constructed aiming to maximize the grey relativity between simulating value sequence and actual value sequence. By the adjustable action intensity of buffer operator, the proposed model optimized by GRA-IGSA integration algorithm can obtain a better forecasting accuracy which is demonstrated by the case studies and can provide an optimized solution for annual power load forecasting. PMID:29768450

Experimental Investigations on Subsequent Yield Surface of Pure Copper by Single-Sample and Multi-Sample Methods under Various Pre-Deformation.

PubMed

Liu, Gui-Long; Huang, Shi-Hong; Shi, Che-Si; Zeng, Bin; Zhang, Ke-Shi; Zhong, Xian-Ci

2018-02-10

Using copper thin-walled tubular specimens, the subsequent yield surfaces under pre-tension, pre-torsion and pre-combined tension-torsion are measured, where the single-sample and multi-sample methods are applied respectively to determine the yield stresses at specified offset strain. The rule and characteristics of the evolution of the subsequent yield surface are investigated. Under the conditions of different pre-strains, the influence of test point number, test sequence and specified offset strain on the measurement of subsequent yield surface and the concave phenomenon for measured yield surface are studied. Moreover, the feasibility and validity of the two methods are compared. The main conclusions are drawn as follows: (1) For the single or multi-sample method, the measured subsequent yield surfaces are remarkably different from cylindrical yield surfaces proposed by the classical plasticity theory; (2) there are apparent differences between the test results from the two kinds of methods: the multi-sample method is not influenced by the number of test points, test order and the cumulative effect of residual plastic strain resulting from the other test point, while those are very influential in the single-sample method; and (3) the measured subsequent yield surface may appear concave, which can be transformed to convex for single-sample method by changing the test sequence. However, for the multiple-sample method, the concave phenomenon will disappear when a larger offset strain is specified.

Targeted next-generation sequencing helps to decipher the genetic and phenotypic heterogeneity of hypertrophic cardiomyopathy

PubMed Central

Cecconi, Massimiliano; Parodi, Maria I.; Formisano, Francesco; Spirito, Paolo; Autore, Camillo; Musumeci, Maria B.; Favale, Stefano; Forleo, Cinzia; Rapezzi, Claudio; Biagini, Elena; Davì, Sabrina; Canepa, Elisabetta; Pennese, Loredana; Castagnetta, Mauro; Degiorgio, Dario; Coviello, Domenico A.

2016-01-01

Hypertrophic cardiomyopathy (HCM) is mainly associated with myosin, heavy chain 7 (MYH7) and myosin binding protein C, cardiac (MYBPC3) mutations. In order to better explain the clinical and genetic heterogeneity in HCM patients, in this study, we implemented a target-next generation sequencing (NGS) assay. An Ion AmpliSeq™ Custom Panel for the enrichment of 19 genes, of which 9 of these did not encode thick/intermediate and thin myofilament (TTm) proteins and, among them, 3 responsible of HCM phenocopy, was created. Ninety-two DNA samples were analyzed by the Ion Personal Genome Machine: 73 DNA samples (training set), previously genotyped in some of the genes by Sanger sequencing, were used to optimize the NGS strategy, whereas 19 DNA samples (discovery set) allowed the evaluation of NGS performance. In the training set, we identified 72 out of 73 expected mutations and 15 additional mutations: the molecular diagnosis was achieved in one patient with a previously wild-type status and the pre-excitation syndrome was explained in another. In the discovery set, we identified 20 mutations, 5 of which were in genes encoding non-TTm proteins, increasing the diagnostic yield by approximately 20%: a single mutation in genes encoding non-TTm proteins was identified in 2 out of 3 borderline HCM patients, whereas co-occuring mutations in genes encoding TTm and galactosidase alpha (GLA) altered proteins were characterized in a male with HCM and multiorgan dysfunction. Our combined targeted NGS-Sanger sequencing-based strategy allowed the molecular diagnosis of HCM with greater efficiency than using the conventional (Sanger) sequencing alone. Mutant alleles encoding non-TTm proteins may aid in the complete understanding of the genetic and phenotypic heterogeneity of HCM: co-occuring mutations of genes encoding TTm and non-TTm proteins could explain the wide variability of the HCM phenotype, whereas mutations in genes encoding only the non-TTm proteins are identifiable in patients with a milder HCM status. PMID:27600940

HII 2407: AN ECLIPSING BINARY REVEALED BY K2 OBSERVATIONS OF THE PLEIADES

DOE Office of Scientific and Technical Information (OSTI.GOV)

David, Trevor J.; Hillenbrand, Lynne A.; Zhang, Celia

2015-11-20

The star HII 2407 is a member of the relatively young Pleiades star cluster and was previously discovered to be a single-lined spectroscopic binary. It is newly identified here within Kepler/K2 photometric time series data as an eclipsing binary system. Mutual fitting of the radial velocity and photometric data leads to an orbital solution and constraints on fundamental stellar parameters. While the primary has arrived on the main sequence, the secondary is still pre-main sequence and we compare our results for the M/M{sub ⊙} and R/R{sub ⊙} values with stellar evolutionary models. We also demonstrate that the system is likelymore » to be tidally synchronized. Follow-up infrared spectroscopy is likely to reveal the lines of the secondary, allowing for dynamically measured masses and elevating the system to benchmark eclipsing binary status.« less

The Age Related Properties of Solar Type Stars

NASA Technical Reports Server (NTRS)

Soderblom, David

1999-01-01

The studies of lithium in solar-type stars in clusters of a wide range of ages has provided critical information on a tracer of convective processes, especially among very young stars. Our most recent work has been on a pre-main sequence cluster (NGC 2264) that took place after this grant expired, but was founded on it. The spread seen in Li in Zero-Age Main Sequence clusters like the Pleiades is huge and possibly related to rotation. No clear spread in seen in NGC 2264, so it does not have its origins in the conditions of formation but is instead a result of processes occurring during PMS evolution. Our observations of M67 were particularly interesting because this cluster is the same age as the Sun, i.e.,very old. Clear evidence was seen for a spread in Li there too, indicating that the spread seen in very young stars perpetuates itself into old age.

Pre-main-sequence stars in the young cluster IC 2391

NASA Technical Reports Server (NTRS)

Stauffer, John; Hartmann, Lee W.; Jones, Burton F.; Mcnamara, Brian R.

1989-01-01

Seven or eight new, late-type members of the poor open cluster IC 2391 are identified, and membership is confirmed for two other stars. The new members fall approximately along a 3 x 10 to the 7th yr isochrone, which is the age estimated for the cluster on the basis of it super main-seqence turnoff. Echelle spectra were obtained for the most probable cluster members. Most show H-alpha in emission and a strong Li 6707 A absorption line, and a few are rapid rotators. The Li abundances for cluster stars cooler than the sun are considerably less than the primordial Li abundance, providing the first direct evidence for substantial premain-sequence Li burning. The rotational velocities show a range from about 15 to 150 km/s, with a distribution of rotational velocities not significantly different from that observed for low-mass stars in the Pleiades.

10 micron Spectroscopy with OSCIR: Silicate Minerology and The Origins of Disks & Protoplanetesimals

NASA Astrophysics Data System (ADS)

Woodward, Chick; Wooden, Diane; Harker, David; Rodgers, Bernadette; Butner, Harold

1999-02-01

The analysis of the silicate mineralogy of pre-main sequence Herbig Ae/Be (HeAeBe) stars to main sequence (beta)-Pic systems, probes the chemical and physical conditions in these potentially planet-forming environments, the condensation of dust from the gas-disk, and the aggregation and accretion of these solids into planetesimals and comets. We propose to obtain 10 micron OSCIR spectra of a selected list of HeAeBe and (beta)-Pic like systems. Use of our ground-based data, combined with the ISO SWS database, and our extensive analytical modeling efforts will permit us to develop a fundamental understanding of connections between silicate mineralogy and the origins and evolution of disks and protoplanetesimals. This program will provide a framework to extend our understanding of planetary formation processes and the mineralogy of dust in differing circumstellar environs and comets to be studied with the NASA STARDUST and SIRTF missions.

The ancient sun: Fossil record in the earth, moon and meteorites; Proceedings of the Conference, Boulder, CO, October 16-19, 1979

NASA Technical Reports Server (NTRS)

Pepin, R. O. (Editor); Eddy, J. A.; Merrill, R. B.

1980-01-01

Papers are presented concerning theories of solar variability and their consequences for luminosity, particle emission and magnetic field changes within the past 4.5 billion years, and on the records of such solar behavior in lunar, meteoritic and terrestrial materials. Specific topics include the neutrino luminosity of the sun, the relation of sunspots to the terrestrial climate of the past 100 years, solar modulation of galactic cosmic rays, the historical record of solar activity, C-14 variations in terrestrial and marine reservoirs, and solar particle fluxes as indicated by track, thermoluminescence and solar wind measurements in lunar rocks. Attention is also given to the spin-down of the solar interior through circulation currents and fluid instabilities, grain surface exposure models in planetary regoliths, rare gases in the solar wind, nitrogen isotopic variations in the lunar regolith, the influence of solar UV radiation on climate, and the pre-main sequence evolution of the sun and evidence of the primordial solar wind in the electromagnetic induction heating of the asteroids and moon.

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

NASA Astrophysics Data System (ADS)

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.

Combining techniques for screening and evaluating interaction terms on high-dimensional time-to-event data.

PubMed

Sariyar, Murat; Hoffmann, Isabell; Binder, Harald

2014-02-26

Molecular data, e.g. arising from microarray technology, is often used for predicting survival probabilities of patients. For multivariate risk prediction models on such high-dimensional data, there are established techniques that combine parameter estimation and variable selection. One big challenge is to incorporate interactions into such prediction models. In this feasibility study, we present building blocks for evaluating and incorporating interactions terms in high-dimensional time-to-event settings, especially for settings in which it is computationally too expensive to check all possible interactions. We use a boosting technique for estimation of effects and the following building blocks for pre-selecting interactions: (1) resampling, (2) random forests and (3) orthogonalization as a data pre-processing step. In a simulation study, the strategy that uses all building blocks is able to detect true main effects and interactions with high sensitivity in different kinds of scenarios. The main challenge are interactions composed of variables that do not represent main effects, but our findings are also promising in this regard. Results on real world data illustrate that effect sizes of interactions frequently may not be large enough to improve prediction performance, even though the interactions are potentially of biological relevance. Screening interactions through random forests is feasible and useful, when one is interested in finding relevant two-way interactions. The other building blocks also contribute considerably to an enhanced pre-selection of interactions. We determined the limits of interaction detection in terms of necessary effect sizes. Our study emphasizes the importance of making full use of existing methods in addition to establishing new ones.

Mythical Maia, ultrashort and 53 PSC variables. Lecture 4

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cox, A.N.

1983-03-14

Moving down the main sequence from the ..beta.. Cephei variables, we come to later B-type stars. The suspicion of variability for these stars goes back to Vogel in 1891 who studied the radial velocities of Vega. Since that time there have been numerous studies of Vega (Wisniewski and Johnson 1979, Fernie 1981) and other B and early A stars which hint at variability in both radial velocity and light. Since Struve (1955) discussed these stars 28 years ago, they have been called the Maia stars after the Pleiades star that he thought was the prototype. The uncertainty in their actualmore » variability has led Breger (1980) to call them the mythical Maia variables.« less

Seismic stratigraphy of sedimentary cover in the southern Amerasia Basin between 140E and 170W

NASA Astrophysics Data System (ADS)

Poselov, V.; Butsenko, V.; Kaminskiy, V.; Kireev, A.; Grikurov, G.

2013-12-01

Seismic reflection data (MCS) acquired by Russian expeditions in 2007, 2009, 2011 and 2012 are correlated with earlier Polarstern (AWI-91090) and US (78AR_808) lines calibrated by drilling on the Lomonosov Ridge (LR) and in the Chukchi Sea (ACEX hole and POPCORN well, respectively). In the absence of direct intersections between those and Russian lines, the correlation is based on analysis of wave fields. Main seismic horizons and their intervening units are traced throughout the entire study area. The uppermost unconformity in both holes is related to pre-Miocene depositional hiatus at the base of essentially hemipelagic unit. Specific wave characteristics of both the unconformity and overlying sediments are persistently recorded on seismic lines. Hemipelagic drape is typically relatively thin (few hundred meters) but may thicken to ~1,500-2,000 m in some deepwater basins. Another major depositional hiatus spanning ~20 Ma is interpreted in the ACEX hole between the lowermost drilled Campanian and Upper Paleocene units. On seismic records it is recognized as post-Campanian unconformity (pCU) traced along the length of the near-Siberia segment of LR and in deep shelf/margin sedimentary basins of the East Siberian and western Chukchi Seas. Farther east pCU correlates with Mid-Brookian unconformity (MBU) separating the Lower and Upper Brookian terrigenous sequences. In Popcorn well the Upper Brookian is about 1,300 m thick; on the Russian margin a comparable thickness of equivalent Upper Paleocene-Eocene units sandwiched between pCU and pre-Miocene unconformity is observed only in structural lows. Older cover units on the Russian East Arctic margin are not sampled by drilling. Among them only one displays particular wave field features clearly comparable to those observed in the carbonate-dominated Carboniferous-Permian Lisburne Group (LG) of the US Chukchi Sea. This marker sequence is confidently recognized on seismic sections in the North Chukchi Trough (NCT) and the Vilkitsky Basin as relatively thick (1,500-3,000 m) unit whose much thinner (~300 m) continuation can also be traced over the southern Mendeleev Rise. A thick (~5000 m) well stratified sedimentary pile mapped in NCT between LG-type unit and the acoustic basement is likely to represent a counterpart of the D3-C1 base of the Lower Ellesmerian Sequence. Like in the US Chukchi Sea, the latter is also truncated here by Permian(?) unconformity and buried under 5,000-7,000 m of inferred Late Permian to Early Cretaceous strata probably corresponding to Upper Ellesmerian, 'Rift' and Lower Brookian Sequences and separated by respective (presumably Jurassic and Early Cretaceous) unconformities. The thickness of pre-Cenozoic units in NCT and the relief of intervening unconformities are highly variable suggesting syndepositional rifting.

HLA-E regulatory and coding region variability and haplotypes in a Brazilian population sample.

PubMed

Ramalho, Jaqueline; Veiga-Castelli, Luciana C; Donadi, Eduardo A; Mendes-Junior, Celso T; Castelli, Erick C

2017-11-01

The HLA-E gene is characterized by low but wide expression on different tissues. HLA-E is considered a conserved gene, being one of the least polymorphic class I HLA genes. The HLA-E molecule interacts with Natural Killer cell receptors and T lymphocytes receptors, and might activate or inhibit immune responses depending on the peptide associated with HLA-E and with which receptors HLA-E interacts to. Variable sites within the HLA-E regulatory and coding segments may influence the gene function by modifying its expression pattern or encoded molecule, thus, influencing its interaction with receptors and the peptide. Here we propose an approach to evaluate the gene structure, haplotype pattern and the complete HLA-E variability, including regulatory (promoter and 3'UTR) and coding segments (with introns), by using massively parallel sequencing. We investigated the variability of 420 samples from a very admixed population such as Brazilians by using this approach. Considering a segment of about 7kb, 63 variable sites were detected, arranged into 75 extended haplotypes. We detected 37 different promoter sequences (but few frequent ones), 27 different coding sequences (15 representing new HLA-E alleles) and 12 haplotypes at the 3'UTR segment, two of them presenting a summed frequency of 90%. Despite the number of coding alleles, they encode mainly two different full-length molecules, known as E*01:01 and E*01:03, which corresponds to about 90% of all. In addition, differently from what has been previously observed for other non classical HLA genes, the relationship among the HLA-E promoter, coding and 3'UTR haplotypes is not straightforward because the same promoter and 3'UTR haplotypes were many times associated with different HLA-E coding haplotypes. This data reinforces the presence of only two main full-length HLA-E molecules encoded by the many HLA-E alleles detected in our population sample. In addition, this data does indicate that the distal HLA-E promoter is by far the most variable segment. Further analyses involving the binding of transcription factors and non-coding RNAs, as well as the HLA-E expression in different tissues, are necessary to evaluate whether these variable sites at regulatory segments (or even at the coding sequence) may influence the gene expression profile. Copyright © 2017 Elsevier Ltd. All rights reserved.

The LANL hemorrhagic fever virus database, a new platform for analyzing biothreat viruses.

PubMed

Kuiken, Carla; Thurmond, Jim; Dimitrijevic, Mira; Yoon, Hyejin

2012-01-01

Hemorrhagic fever viruses (HFVs) are a diverse set of over 80 viral species, found in 10 different genera comprising five different families: arena-, bunya-, flavi-, filo- and togaviridae. All these viruses are highly variable and evolve rapidly, making them elusive targets for the immune system and for vaccine and drug design. About 55,000 HFV sequences exist in the public domain today. A central website that provides annotated sequences and analysis tools will be helpful to HFV researchers worldwide. The HFV sequence database collects and stores sequence data and provides a user-friendly search interface and a large number of sequence analysis tools, following the model of the highly regarded and widely used Los Alamos HIV database [Kuiken, C., B. Korber, and R.W. Shafer, HIV sequence databases. AIDS Rev, 2003. 5: p. 52-61]. The database uses an algorithm that aligns each sequence to a species-wide reference sequence. The NCBI RefSeq database [Sayers et al. (2011) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 39, D38-D51.] is used for this; if a reference sequence is not available, a Blast search finds the best candidate. Using this method, sequences in each genus can be retrieved pre-aligned. The HFV website can be accessed via http://hfv.lanl.gov.

Changes in tau phosphorylation in hibernating rodents.

PubMed

León-Espinosa, Gonzalo; García, Esther; García-Escudero, Vega; Hernández, Félix; Defelipe, Javier; Avila, Jesús

2013-07-01

Tau is a cytoskeletal protein present mainly in the neurons of vertebrates. By comparing the sequence of tau molecule among different vertebrates, it was found that the variability of the N-terminal sequence in tau protein is higher than that of the C-terminal region. The N-terminal region is involved mainly in the binding of tau to cellular membranes, whereas the C-terminal region of the tau molecule contains the microtubule-binding sites. We have compared the sequence of Syrian hamster tau with the sequences of other hibernating and nonhibernating rodents and investigated how differences in the N-terminal region of tau could affect the phosphorylation level and tau binding to cell membranes. We also describe a change, in tau phosphorylation, on a casein kinase 1 (ck1)-dependent site that is found only in hibernating rodents. This ck1 site seems to play an important role in the regulation of tau binding to membranes. Copyright © 2013 Wiley Periodicals, Inc.

Anodal transcranial direct current stimulation enhances the effects of motor imagery training in a finger tapping task.

PubMed

Saimpont, Arnaud; Mercier, Catherine; Malouin, Francine; Guillot, Aymeric; Collet, Christian; Doyon, Julien; Jackson, Philip L

2016-01-01

Motor imagery (MI) training and anodal transcranial direct current stimulation (tDCS) applied over the primary motor cortex can independently improve hand motor function. The main objective of this double-blind, sham-controlled study was to examine whether anodal tDCS over the primary motor cortex could enhance the effects of MI training on the learning of a finger tapping sequence. Thirty-six right-handed young human adults were assigned to one of three groups: (i) who performed MI training combined with anodal tDCS applied over the primary motor cortex; (ii) who performed MI training combined with sham tDCS; and (iii) who received tDCS while reading a book. The MI training consisted of mentally rehearsing an eight-item complex finger sequence for 13 min. Before (Pre-test), immediately after (Post-test 1), and at 90 min after (Post-test 2) MI training, the participants physically repeated the sequence as fast and as accurately as possible. An anova showed that the number of sequences correctly performed significantly increased between Pre-test and Post-test 1 and remained stable at Post-test 2 in the three groups (P < 0.001). Furthermore, the percentage increase in performance between Pre-test and Post-test 1 and Post-test 2 was significantly greater in the group that performed MI training combined with anodal tDCS compared with the other two groups (P < 0.05). As a potential physiological explanation, the synaptic strength within the primary motor cortex could have been reinforced by the association of MI training and tDCS compared with MI training alone and tDCS alone. © 2015 Federation of European Neuroscience Societies and John Wiley & Sons Ltd.

Deformation-based augmented reality for hepatic surgery.

PubMed

Haouchine, Nazim; Dequidt, Jérémie; Berger, Marie-Odile; Cotin, Stéphane

2013-01-01

In this paper we introduce a method for augmenting the laparoscopic view during hepatic tumor resection. Using augmented reality techniques, vessels, tumors and cutting planes computed from pre-operative data can be overlaid onto the laparoscopic video. Compared to current techniques, which are limited to a rigid registration of the pre-operative liver anatomy with the intra-operative image, we propose a real-time, physics-based, non-rigid registration. The main strength of our approach is that the deformable model can also be used to regularize the data extracted from the computer vision algorithms. We show preliminary results on a video sequence which clearly highlights the interest of using physics-based model for elastic registration.

Additives influence on spinning solution and nano web properties

NASA Astrophysics Data System (ADS)

Kukle, S.; Jegina, S.; Sutka, A.; Makovska, R.

2017-10-01

Needleless electrospinning operated as a one-stage process producing nanofibres webs from spinning solutions with the corresponding to the final use properties seems has a good future prospects. Complicated spinning solution designing started with the selection of composition and components proportion, pre-processing sequence and parameters establishing for every component and for their mixing. Spinning solution viscosity and electro conductivity together with the spinning distance and intensity of electromagnetic field are main parameters determined spin ability and properties of obtained nanofibers. Influence of some pre-processing parameters of components, combinations of organic and non-organic components and their concentration influence on spinning solution viscosity and conductivity, as well on fibres diameters are under discussion.

1961-2011: Fifty years of Hayashi tracks

NASA Astrophysics Data System (ADS)

Palla, Francesco

2012-09-01

Fifty years after the seminal paper by Prof. C. Hayashi, the field of pre-main sequence (PMS) evolution still plays a fundamental role in observational and theoretical astrophysics. In this contribution, I highlight the contribution made by Hayashi in establishing the theoretical foundation of early stellar evolution. Then, I discuss the changes of the classical theory introduced by the inclusion of protostellar evolution in PMS models and present selected results on young stars.

Study pre-earthquake features in the Earth atmosphere-ionosphere environment associated with 2016 Amatrice-Norcia (Central Italy) seismic sequence

NASA Astrophysics Data System (ADS)

Ouzounov, Dimitar; Pulinets, Sergey; Giuliani, Gioacchino; Hernández-Pajares, Manuel; García-Rigo, Alberto

2017-04-01

The 2016 Amatrice-Norcia (Central Italy) seismic sequence (M6.3, M6.1 and M6.5), became one of the unusual and important modern earthquake events. Recent studies indicate (including April 6th 2009 Abruzzo earthquake) an enhanced coupling between the atmospheric boundary layer and the ionosphere, which have been proposed to be related with large (>M6) earthquakes. This relationship has been studied for the 2016 Central Italy sequence using an integrated set of observations of five physical and environmental parameters. We present observational data from January to November 2016 of five physical parameters- radon, seismicity, temperature of the atmosphere boundary layer, outgoing earth infrared radiation and GPS/TEC and their temporal and spatial variations several days before the onset of the Amatrice-Norcia earthquake sequence. The Aug 24 M6.2 foreshock was situated about 70 kilometers from the 2 stations of radon near L'Aquila. These data show an increase prior to the main earthquake beginning in July-August this enhancement of radon coincides (with some delay) with an increase in the atmospheric chemical potential (Aug 11) measured near the epicentral area from satellite. And subsequently from Aug12 there was an association with the acceleration of outgoing infrared radiation observed on the top of the atmosphere from EOS satellite (Aug 16). The GPS/Total Electron Content data indicate an increase of electron concentration in ionosphere on August 22 and October 26, 1-2 days before the M6.2 foreshock and the M6.5 main shock on Oct 30, 2016. Both ground and satellite data have in common that they were evident in about the last ten days before the M6.2 foreshock of Aug 24 and continuously up to the main shock of Oct 30, although the radon variations started 2 months earlier. We examined the possible correlation between different pre-earthquake signals in the frame of a multidisciplinary investigation of Lithosphere -Atmosphere -Ionosphere coupling concept.

LONG-TERM LIGHT CURVE OF HIGHLY VARIABLE PROTOSTELLAR STAR GM CEP

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xiao Limin; Kroll, Peter; Henden, Arne A.

2010-04-15

We present data from the archival plates at Harvard College Observatory and Sonneberg Observatory showing the field of the solar-type pre-main-sequence star GM Cep. A total of 186 magnitudes of GM Cep have been measured on these archival plates, with 176 in blue sensitivity, six in visible, and four in red. We combine our data with data from the literature and from the American Association of Variable Star Observers to depict the long-term light curves of GM Cep in both B and V wavelengths. The light curves span from 1895 until now, with two densely sampled regions (1935-1945 in themore » B band, and 2006 until now in the V band). The long-term light curves do not show any fast rise behavior as predicted by an accretion mechanism. Both the light curves and the magnitude histograms confirm the conclusion that the light curves are dominated by dips (possibly from extinction) superposed on some quiescence state, instead of outbursts caused by accretion flares. Our result excludes the possibility of GM Cep being a FUor, EXor, or McNeil's Nebula-type star. Several special cases of T Tauri stars were checked, but none of these light curves were compatible with that of GM Cep. The lack of periodicity in the light curve excludes the possibility of GM Cep being a KH 15D system.« less

Differential rotation in magnetic chemically peculiar stars

NASA Astrophysics Data System (ADS)

Mikulášek, Z.; Krtička, J.; Paunzen, E.; Švanda, M.; Hummerich, S.; Bernhard, K.; Jagelka, M.; Janík, J.; Henry, G. W.; Shultz, M. E.

2018-01-01

Magnetic chemically peculiar (mCP) stars constitute about 10% of upper-main-sequence stars and are characterized by strong magnetic fields and abnormal photospheric abundances of some chemical elements. Most of them exhibit strictly periodic light, magnetic, radio, and spectral variations that can be fully explained by a rigidly rotating main-sequence star with persistent surface structures and a stable global magnetic field. Long-term observations of the phase curves of these variations enable us to investigate possible surface differential rotation with unprecedented accuracy and reliability. The analysis of the phase curves in the best-observed mCP stars indicates that the location and the contrast of photometric and spectroscopic spots as well as the geometry of the magnetic field remain constant for at least many decades. The strict periodicity of mCP variables supports the concept that the outer layers of upper-main-sequence stars do not rotate differentially. However, there is a small, inhomogeneous group consisting of a few mCP stars whose rotation periods vary on timescales of decades. The period oscillations may reflect real changes in the angular velocity of outer layers of the stars which are anchored by their global magnetic fields. In CU Vir, V901 Ori, and perhaps BS Cir, the rotational period variation indicates the presence of vertical differential rotation; however, its exact nature has remained elusive until now. The incidence of mCP stars with variable rotational periods is currently investigated using a sample of fifty newly identified Kepler mCP stars.

Automated segmentation of three-dimensional MR brain images

NASA Astrophysics Data System (ADS)

Park, Jonggeun; Baek, Byungjun; Ahn, Choong-Il; Ku, Kyo Bum; Jeong, Dong Kyun; Lee, Chulhee

2006-03-01

Brain segmentation is a challenging problem due to the complexity of the brain. In this paper, we propose an automated brain segmentation method for 3D magnetic resonance (MR) brain images which are represented as a sequence of 2D brain images. The proposed method consists of three steps: pre-processing, removal of non-brain regions (e.g., the skull, meninges, other organs, etc), and spinal cord restoration. In pre-processing, we perform adaptive thresholding which takes into account variable intensities of MR brain images corresponding to various image acquisition conditions. In segmentation process, we iteratively apply 2D morphological operations and masking for the sequences of 2D sagittal, coronal, and axial planes in order to remove non-brain tissues. Next, final 3D brain regions are obtained by applying OR operation for segmentation results of three planes. Finally we reconstruct the spinal cord truncated during the previous processes. Experiments are performed with fifteen 3D MR brain image sets with 8-bit gray-scale. Experiment results show the proposed algorithm is fast, and provides robust and satisfactory results.

Elastic Waves: Mental Models and Teaching/Learning Sequences

NASA Astrophysics Data System (ADS)

Tarantino, Giovanni

In last years many research studies have pointed out relevant student diff- culties in understanding the physics of mechanical waves. Moreover, it has been reported that these diffculties deal with some fundamental concepts as the role of the medium in wave propagation, the superposition principle and the mathematical description of waves involving the use of functions of two variables. In the context of pre-service courses for teacher preparation a teaching/learning (T/L) sequence based on using simple RTL experiments and interactive simulation environments aimed to show the effect of medium properties on the propagation speed of a wave pulse, has been experimented. Here, preliminary results of investigations carried out with a 120 traineeteacher (TT) group are reported and discussed.

Toward an Understanding of Changes in Diversity Associated with Fecal Microbiome Transplantation Based on 16S rRNA Gene Deep Sequencing

PubMed Central

Shahinas, Dea; Silverman, Michael; Sittler, Taylor; Chiu, Charles; Kim, Peter; Allen-Vercoe, Emma; Weese, Scott; Wong, Andrew; Low, Donald E.; Pillai, Dylan R.

2012-01-01

ABSTRACT Fecal microbiome transplantation by low-volume enema is an effective, safe, and inexpensive alternative to antibiotic therapy for patients with chronic relapsing Clostridium difficile infection (CDI). We explored the microbial diversity of pre- and posttransplant stool specimens from CDI patients (n = 6) using deep sequencing of the 16S rRNA gene. While interindividual variability in microbiota change occurs with fecal transplantation and vancomycin exposure, in this pilot study we note that clinical cure of CDI is associated with an increase in diversity and richness. Genus- and species-level analysis may reveal a cocktail of microorganisms or products thereof that will ultimately be used as a probiotic to treat CDI. PMID:23093385

Pre-supernova models for massive stars produced with large nuclear reaction network by MESA

NASA Astrophysics Data System (ADS)

Park, Byeongchan; Kwak, Kyujin

2018-04-01

Core-collapsed Supernova (CCSN) is one of violent phenomena in the universe. CCSN generates heavy elements and leaves a neutron star behind. It has been known that the physical properties of CCSN depend on those of pre-supernova such as mass, metallicities including distribution of elements, and the density and temperature profile which are obtained from the stellar evolution calculation. In particular, the production of heavy elements in CCSN is sensitive to the abundance profiles in the pre-supernova models. In this study, we evolve a massive main sequence star with 15Msun and solar metallicity to the pre-supernova stage by using two different networks, small and large. The large nuclear reaction network includes more than four times isotopes than the small network. Our calculations were done by MESA (Modules for Experiments in Stellar Astrophysics) which allowed us to use the large network containing about a hundred isotopes. We compare the results obtained with two networks.

Tidal dissipation in rotating low-mass stars and implications for the orbital evolution of close-in massive planets. II. Effect of stellar metallicity

NASA Astrophysics Data System (ADS)

Bolmont, E.; Gallet, F.; Mathis, S.; Charbonnel, C.; Amard, L.; Alibert, Y.

2017-08-01

Observations of hot-Jupiter exoplanets suggest that their orbital period distribution depends on the metallicity of the host stars. We investigate here whether the impact of the stellar metallicity on the evolution of the tidal dissipation inside the convective envelope of rotating stars and its resulting effect on the planetary migration might be a possible explanation for this observed statistical trend. We use a frequency-averaged tidal dissipation formalism coupled to an orbital evolution code and to rotating stellar evolution models in order to estimate the effect of a change of stellar metallicity on the evolution of close-in planets. We consider here two different stellar masses: 0.4 M⊙ and 1.0 M⊙ evolving from the early pre-main sequence phase up to the red-giant branch. We show that the metallicity of a star has a strong effect on the stellar parameters, which in turn strongly influence the tidal dissipation in the convective region. While on the pre-main sequence, the dissipation of a metal-poor Sun-like star is higher than the dissipation of a metal-rich Sun-like star; on the main sequence it is the opposite. However, for the 0.4 M⊙ star, the dependence of the dissipation with metallicity is much less visible. Using an orbital evolution model, we show that changing the metallicity leads to different orbital evolutions (e.g., planets migrate farther out from an initially fast-rotating metal-rich star). Using this model, we qualitatively reproduced the observational trends of the population of hot Jupiters with the metallicity of their host stars. However, more steps are needed to improve our model to try to quantitatively fit our results to the observations. Specifically, we need to improve the treatment of the rotation evolution in the orbital evolution model, and ultimately we need to consistently couple the orbital model to the stellar evolution model.

Modeling of DNA local parameters predicts encrypted architectural motifs in Xenopus laevis ribosomal gene promoter

PubMed Central

Roux-Rouquie, Magali; Marilley, Monique

2000-01-01

We have modeled local DNA sequence parameters to search for DNA architectural motifs involved in transcription regulation and promotion within the Xenopus laevis ribosomal gene promoter and the intergenic spacer (IGS) sequences. The IGS was found to be shaped into distinct topological domains. First, intrinsic bends split the IGS into domains of common but different helical features. Local parameters at inter-domain junctions exhibit a high variability with respect to intrinsic curvature, bendability and thermal stability. Secondly, the repeated sequence blocks of the IGS exhibit right-handed supercoiled structures which could be related to their enhancer properties. Thirdly, the gene promoter presents both inherent curvature and minor groove narrowing which may be viewed as motifs of a structural code for protein recognition and binding. Such pre-existing deformations could simply be remodeled during the binding of the transcription complex. Alternatively, these deformations could pre-shape the promoter in such a way that further remodeling is facilitated. Mutations shown to abolish promoter curvature as well as intrinsic minor groove narrowing, in a variant which maintained full transcriptional activity, bring circumstantial evidence for structurally-preorganized motifs in relation to transcription regulation and promotion. Using well documented X.laevis rDNA regulatory sequences we showed that computer modeling may be of invaluable assistance in assessing encrypted architectural motifs. The evidence of these DNA topological motifs with respect to the concept of structural code is discussed. PMID:10982860

Formulation development and optimization of a novel Cremophore EL-based nanoemulsion using ultrasound cavitation.

PubMed

Tang, Siah Ying; Manickam, Sivakumar; Wei, Tan Khang; Nashiru, Billa

2012-03-01

In the present study, response surface methodology (RSM) based on central composite design (CCD) was employed to investigate the influence of main emulsion composition variables, namely drug loading, oil content, emulsifier content as well as the effect of the ultrasonic operating parameters such as pre-mixing time, ultrasonic amplitude, and irradiation time on the properties of aspirin-loaded nanoemulsions. The two main emulsion properties studied as response variables were: mean droplet size and polydispersity index. The ultimate goal of the present work was to determine the optimum level of the six independent variables in which an optimal aspirin nanoemulsion with desirable properties could be produced. The response surface analysis results clearly showed that the variability of two responses could be depicted as a linear function of the content of main emulsion compositions and ultrasonic processing variables. In the present investigation, it is evidently shown that ultrasound cavitation is a powerful yet promising approach in the controlled production of aspirin nanoemulsions with smaller average droplet size in a range of 200-300 nm and with a polydispersity index (PDI) of about 0.30. This study proved that the use of low frequency ultrasound is of considerable importance in the controlled production of pharmaceutical nanoemulsions in the drug delivery system. Copyright © 2011 Elsevier B.V. All rights reserved.

Variability of FUV Emission Line in Classical T Tauri Stars as a Diagnostic for Disc Accretion

NASA Astrophysics Data System (ADS)

Ramkumar, B.; Johns-Krull, C. M.

2005-12-01

We present our results of FUV emission line variability studies done on four classical T Tauri stars. We have used the IUE Final Archive spectra of pre-main sequence stars to analyze the sample of four stars BP Tau, DR Tau, RU Lup and RY Tau where each of these low-resolution (R ˜6 Å) spectra was observed in the IUE short-wavelength band pass (1150--1980Å). Given a broad time line of multiple observations being available from the IUE Final archive, an intrinsic variability study has been possible with this sample. Our results indicate that the transition region lines \\ion{Si}{4} and \\ion{C}{4}, produced near the accretion shocks at ˜105 K, have a strong correlation between them in all four stars except DR Tau. We also observe a strong correlation between \\ion{C}{4} & \\ion{He}{2} on our entire sample with a correlation coefficient of 0.549 (false alarm probability = 7.9 x 10-2) or higher. In addition, \\ion{He}{2} correlates with the molecular hydrogen (1503Å) line in all but RU Lup. If the \\ion{He}{2} lines are produced because of X-ray ionization then the observed molecular hydrogen emission is indeed controlled by X-ray ionization and therefore \\ion{He}{2} could serve as an X-ray proxy for future studies. Also, our correlation results strengthen the fact that \\ion{C}{4} is a good predictor of \\ion{Si}{4} and have a common origin i.e. in accretion shocks in the star formation process.

The Gaia-ESO Survey: the present-day radial metallicity distribution of the Galactic disc probed by pre-main-sequence clusters

NASA Astrophysics Data System (ADS)

Spina, L.; Randich, S.; Magrini, L.; Jeffries, R. D.; Friel, E. D.; Sacco, G. G.; Pancino, E.; Bonito, R.; Bravi, L.; Franciosini, E.; Klutsch, A.; Montes, D.; Gilmore, G.; Vallenari, A.; Bensby, T.; Bragaglia, A.; Flaccomio, E.; Koposov, S. E.; Korn, A. J.; Lanzafame, A. C.; Smiljanic, R.; Bayo, A.; Carraro, G.; Casey, A. R.; Costado, M. T.; Damiani, F.; Donati, P.; Frasca, A.; Hourihane, A.; Jofré, P.; Lewis, J.; Lind, K.; Monaco, L.; Morbidelli, L.; Prisinzano, L.; Sousa, S. G.; Worley, C. C.; Zaggia, S.

2017-05-01

Context. The radial metallicity distribution in the Galactic thin disc represents a crucial constraint for modelling disc formation and evolution. Open star clusters allow us to derive both the radial metallicity distribution and its evolution over time. Aims: In this paper we perform the first investigation of the present-day radial metallicity distribution based on [Fe/H] determinations in late type members of pre-main-sequence clusters. Because of their youth, these clusters are therefore essential for tracing the current interstellar medium metallicity. Methods: We used the products of the Gaia-ESO Survey analysis of 12 young regions (age < 100 Myr), covering Galactocentric distances from 6.67 to 8.70 kpc. For the first time, we derived the metal content of star forming regions farther than 500 pc from the Sun. Median metallicities were determined through samples of reliable cluster members. For ten clusters the membership analysis is discussed in the present paper, while for other two clusters (I.e. Chamaeleon I and Gamma Velorum) we adopted the members identified in our previous works. Results: All the pre-main-sequence clusters considered in this paper have close-to-solar or slightly sub-solar metallicities. The radial metallicity distribution traced by these clusters is almost flat, with the innermost star forming regions having [Fe/H] values that are 0.10-0.15 dex lower than the majority of the older clusters located at similar Galactocentric radii. Conclusions: This homogeneous study of the present-day radial metallicity distribution in the Galactic thin disc favours models that predict a flattening of the radial gradient over time. On the other hand, the decrease of the average [Fe/H] at young ages is not easily explained by the models. Our results reveal a complex interplay of several processes (e.g. star formation activity, initial mass function, supernova yields, gas flows) that controlled the recent evolution of the Milky Way. Based on observations made with the ESO/VLT, at Paranal Observatory, under program 188.B-3002 (The Gaia-ESO Public Spectroscopic Survey).Full Table 1 is only 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/601/A70

Paleomagnetic and AMS study of Permian and Triassic rocks from the Hronic Nappe and Paleogene rocks from the Central Carpathian Paleogene Basin, Western Carpathians

NASA Astrophysics Data System (ADS)

Márton, Emö; Madzin, Jozef; Bučová, Jana; Grabowski, Jacek; Plašienka, Dušan; Aubrecht, Roman

2017-04-01

The Hronic (Choč) units form the highest cover nappe system of the Central Western Carpathians which was emplaced over the Fatric (Krížna) nappe system during the Late Cretaceous. The Permian (red beds and lava flows) and Triassic (sediments) rocks, the main targets of our study, were affected only by diagenetic or very low-grade, burial-related recrystallization and were tilted and transported together. The pre-late Cretaceous sequence is overlapped by Paleogene mainly flysch sequences. Three laboratories (Bratislava, Budapest and Warsaw) were involved in standard paleomagnetic processing and AMS measurements of the samples, while Curie-points were determined in Budapest. The site/locality mean paleomagnetic directions obtained were significantly different from the local direction of the present Earth magnetic field, indicating the long term stability of the paleomagnetic signal. The magnetic fabrics varied from un-oriented to dominantly schistose with well-defined lineations. The latter were normally subhorizontal, although subvertical maxima also occurred among the Triassic sediments. Shallow inclinations, after tilt corrections, suggest near-equatorial position for most of the Permian and Lower Triassic, while around 20°N for the Middle-Upper Triassic localities. The paleomagnetic declinations are interpreted in terms of CW tectonic rotations, which are normally larger for the Permian than for the Triassic samples, although there are some differences within the same age groups. This may be attributed to differential movements during nappe emplacement or subsequent tectonic disturbances. For two localities from the Paleogene cover sequence of the Hronic units, close to the main sampling area (Low Tatra Mts) of the present study documented fairly large CCW rotations, thus obtained additional evidence for the general CCW rotation of the Central Western Carpathians during the Cenozoic. Thus, we conclude that the Cenozoic CCW rotation was pre-dated by large CW rotations, probably connected to the nappe emplacement. In addition, a pre-Jurassic moderate CW rotation is inferred from the difference in declinations between Triassic and Permian palaeomagnetic declinations. Acknowledgement: This work was financially supported by the Slovak Research and Development Agency under the contract No. APVV-0212-12 and by the Hungarian Scientific Research Fund OTKA K105245.

The Barnes-Evans color-surface brightness relation: A preliminary theoretical interpretation

NASA Technical Reports Server (NTRS)

Shipman, H. L.

1980-01-01

Model atmosphere calculations are used to assess whether an empirically derived relation between V-R and surface brightness is independent of a variety of stellar paramters, including surface gravity. This relationship is used in a variety of applications, including the determination of the distances of Cepheid variables using a method based on the Beade-Wesselink method. It is concluded that the use of a main sequence relation between V-R color and surface brightness in determining radii of giant stars is subject to systematic errors that are smaller than 10% in the determination of a radius or distance for temperature cooler than 12,000 K. The error in white dwarf radii determined from a main sequence color surface brightness relation is roughly 10%.

Understanding young stars - A history

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stahler, S.W.

1988-12-01

The history of pre-main-sequence theory is briefly reviewed. The paper of Henyey et al. (1955) is seen as an important transitional work, one which abandoned previous simplifying assumptions yet failed to incorporate newer insights into the surface structure of late-type stars. The subsequent work of Hayashi and his contemporaries is outlined, with an emphasis on the underlying physical principles. Finally, the recent impact of protostar theory is discussed, and speculations are offered on future developments. 56 references.

Spitzer Spectroscopy of the Transition Object TW Hya

DTIC Science & Technology

2010-02-24

results bear on our understanding of the evolutionary state of the TW Hya disk . Subject headings: (stars:) circumstellar matter — (stars:) planetary systems... protoplanetary disks — stars: pre-main sequence — (stars: individual) TW Hya 1. Introduction Spectroscopy with the Spitzer Space Telescope has...region of the disk . (2) If a planet has formed with a mass sufficient to open a gap (∼ 1MJ), gas will be cleared in the vicinity of its orbit, but gap

Deciphering the X-ray Emission of the Nearest Herbig Ae Star

NASA Technical Reports Server (NTRS)

Skinner, Stephen L.

2004-01-01

In this research program, we obtained and analyzed an X-ray observation of the young nearby intermediate mass pre-main sequence star HD 104237 using the XMM-Newton space-based observatory. The observation was obtained on 17 Feb. 2002. This observation yielded high-quality X-ray images, spectra, and timing data which provided valuable information on the physical processes responsible for the X-ray emission. This star is a member of the group of so-called Herbig Ae/Be stars, which are young intermediate mass (approx. 2 - 4 solar masses) pre-main sequence (PMS) stars a few million years old that have not yet begun core hydrogen burning. The objective of the XMM-Newton observation was to obtain higher quality data than previously available in order to constrain possible X-ray emission mechanisms. The origin of the X-ray emission from Herbig Ae/Be stars is not yet known. These intermediate mass PMS stars lie on radiative tracks and are not expected to emit X-rays via solar-like magnetic processes, nor are their winds powerful enough to produce X-rays by radiative wind shocks as in more massive O-type stars. The emission could originate in unseen low-mass companions, or it may be intrinsic to the Herbig stars themselves if they still have primordial magnetic fields or can sustain magnetic activity via a nonsolar dynamo.

Astrophysical Impact of the Updated 9Be(p,α)6Li and 10B(p,α)7Be Reaction Rates As Deduced By THM

NASA Astrophysics Data System (ADS)

Lamia, L.; Spitaleri, C.; Tognelli, E.; Degl'Innocenti, S.; Pizzone, R. G.; Prada Moroni, P. G.

2015-10-01

The complete understanding of the stellar abundances of lithium, beryllium, and boron represents one of the most interesting open problems in astrophysics. These elements are largely used to probe stellar structure and mixing phenomena in different astrophysical scenarios, such as pre-main-sequence or main-sequence stars. Their different fragility against (p,α) burning reactions allows one to investigate different depths of the stellar interior. Such fusion mechanisms are triggered at temperatures between T ≈ (2-5) × {10}6 K, thus defining a corresponding Gamow energy between ≈ 3-10 keV, where S(E)-factor measurements need to be performed to get reliable reaction rate evaluations. The Trojan Horse Method is a well defined procedure to measure cross sections at Gamow energies overcoming the uncertainties due to low-energy S(E)-factor extrapolation as well as electron screening effects. Taking advantage of the {\\mathtt{THM}} measure of the 9Be(p,α)6Li and 10B(p,α)7Be cross sections, the corresponding reaction rates have been calculated and compared with the evaluations by the NACRE collaboration, widely used in the literature. The impact on surface abundances of the updated 9Be and 10B (p,α) burning rates is discussed for pre-MS stars.

The weak-line T Tauri star V410 Tau. I. A multi-wavelength study of variability

NASA Astrophysics Data System (ADS)

Stelzer, B.; Fernández, M.; Costa, V. M.; Gameiro, J. F.; Grankin, K.; Henden, A.; Guenther, E.; Mohanty, S.; Flaccomio, E.; Burwitz, V.; Jayawardhana, R.; Predehl, P.; Durisen, R. H.

2003-12-01

We present the results of an intensive coordinated monitoring campaign in the optical and X-ray wavelength ranges of the low-mass, pre-main sequence star V410 Tau carried out in November 2001. The aim of this project was to study the relation between various indicators for magnetic activity that probe different emitting regions and would allow us to obtain clues on the interplay of the different atmospheric layers: optical photometric star spot (rotation) cycle, chromospheric Hα emission, and coronal X-rays. Our optical photometric monitoring has allowed us to measure the time of the minimum of the lightcurve with high precision. Joining the result with previous data we provide a new estimate for the dominant periodicity of V410 Tau (1.871970 +/- 0.000010 d). This updated value removes systematic offsets of the time of minimum observed in data taken over the last decade. The recurrence of the minimum in the optical lightcurve over such a long timescale emphasizes the extraordinary stability of the largest spot. This is confirmed by radial velocity measurements: data from 1993 and 2001 fit almost exactly onto each other when folded with the new period. The combination of the new data from November 2001 with published measurements taken during the last decade allows us to examine long-term changes in the mean light level of the photometry of V410 Tau. A variation on the timescale of 5.4 yr is suggested. Assuming that this behavior is truly cyclic V410 Tau is the first pre-main sequence star on which an activity cycle is detected. Two X-ray pointings were carried out with the Chandra satellite simultaneously with the optical observations, and centered near the maximum and minimum levels of the optical lightcurve. A relation of their different count levels to the rotation period of the dominating spot is not confirmed by a third Chandra observation carried out some months later, during another minimum of the 1.87 d cycle. Similarly we find no indications for a correlation of the Hα emission with the spots' rotational phase. The lack of detected rotational modulation in two important activity diagnostics seems to argue against a direct association of chromospheric and coronal emission with the spot distribution.

Gradient waveform pre-emphasis based on the gradient system transfer function.

PubMed

Stich, Manuel; Wech, Tobias; Slawig, Anne; Ringler, Ralf; Dewdney, Andrew; Greiser, Andreas; Ruyters, Gudrun; Bley, Thorsten A; Köstler, Herbert

2018-02-25

The gradient system transfer function (GSTF) has been used to describe the distorted k-space trajectory for image reconstruction. The purpose of this work was to use the GSTF to determine the pre-emphasis for an undistorted gradient output and intended k-space trajectory. The GSTF of the MR system was determined using only standard MR hardware without special equipment such as field probes or a field camera. The GSTF was used for trajectory prediction in image reconstruction and for a gradient waveform pre-emphasis. As test sequences, a gradient-echo sequence with phase-encoding gradient modulation and a gradient-echo sequence with a spiral read-out trajectory were implemented and subsequently applied on a structural phantom and in vivo head measurements. Image artifacts were successfully suppressed by applying the GSTF-based pre-emphasis. Equivalent results are achieved with images acquired using GSTF-based post-correction of the trajectory as a part of image reconstruction. In contrast, the pre-emphasis approach allows reconstruction using the initially intended trajectory. The artifact suppression shown for two sequences demonstrates that the GSTF can serve for a novel pre-emphasis. A pre-emphasis based on the GSTF information can be applied to any arbitrary sequence type. © 2018 International Society for Magnetic Resonance in Medicine.

Molecular phylogenetics of the family Cyprinidae (Actinopterygii: Cypriniformes) as evidenced by sequence variation in the first intron of S7 ribosomal protein-coding gene: further evidence from a nuclear gene of the systematic chaos in the family.

PubMed

He, Shunping; Mayden, Richard L; Wang, Xuzheng; Wang, Wei; Tang, Kevin L; Chen, Wei-Jen; Chen, Yiyu

2008-03-01

The family Cyprinidae is the largest freshwater fish group in the world, including over 200 genera and 2100 species. The phylogenetic relationships of major clades within this family are simply poorly understood, largely because of the overwhelming diversity of the group; however, several investigators have advanced different hypotheses of relationships that pre- and post-date the use of shared-derived characters as advocated through phylogenetic systematics. As expected, most previous investigations used morphological characters. Recently, mitochondrial DNA (mtDNA) sequences and combined morphological and mtDNA investigations have been used to explore and advance our understanding of species relationships and test monophyletic groupings. Limitations of these studies include limited taxon sampling and a strict reliance upon maternally inherited mtDNA variation. The present study is the first endeavor to recover the phylogenetic relationships of the 12 previously recognized monophyletic subfamilies within the Cyprinidae using newly sequenced nuclear DNA (nDNA) for over 50 species representing members of the different previously hypothesized subfamily and family groupings within the Cyprinidae and from other cypriniform families as outgroup taxa. Hypothesized phylogenetic relationships are constructed using maximum parsimony and Basyesian analyses of 1042 sites, of which 971 sites were variable and 790 were phylogenetically informative. Using other appropriate cypriniform taxa of the families Catostomidae (Myxocyprinus asiaticus), Gyrinocheilidae (Gyrinocheilus aymonieri), and Balitoridae (Nemacheilus sp. and Beaufortia kweichowensis) as outgroups, the Cyprinidae is resolved as a monophyletic group. Within the family the genera Raiamas, Barilius, Danio, and Rasbora, representing many of the tropical cyprinids, represent basal members of the family. All other species can be classified into variably supported and resolved monophyletic lineages, depending upon analysis, that are consistent with or correspond to Barbini and Leuciscini. The Barbini includes taxa traditionally aligned with the subfamily Cyprininae sensu previous morphological revisionary studies by Howes (Barbinae, Labeoninae, Cyprininae and Schizothoracinae). The Leuciscini includes six other subfamilies that are mainly divided into three separate lineages. The relationships among genera and subfamilies are discussed as well as the possible origins of major lineages.

An Observational Study of Accretion Dynamics in Short-Period Pre-Main Sequence Binaries

NASA Astrophysics Data System (ADS)

Tofflemire, Benjamin; Mathieu, Robert; Herczeg, Greg; Johns-Krull, Christopher; Akeson, Rachel; Ciardi, David

2018-01-01

Over the past thirty years, a detailed picture of star formation has emerged that highlights the importance of the interaction between a pre-main sequence (pre-MS) star and its protoplanetary disk. The properties of an emergent star, the lifetime of a protoplanetary disk, and the formation of planets are all, in part, determined by this star-disk interaction. Many stars, however, form in binary or higher-order systems where orbital dynamics are capable of fundamentally altering this star-disk interaction. Orbital resonances, especially in short-period systems, are capable of clearing the central region of a protoplanetary disk, leaving the possibility for three stable accretion disks: a circumstellar disk around each star and a circumbinary disk. In this model, accretion onto the stars is predicted to proceed in periodic streams that form at the inner edge of the circumbinary disk, cross the dynamically cleared gap, and feed circumstellar disks or accrete directly onto the stars themselves. This pulsed-accretion paradigm predicts bursts of accretion that are periodic with the orbital period, where the duration, amplitude, location in orbital phase, and which star if preferentially fed, all depend on the orbital parameters. To test these predictions, we have carried out intensive observational campaigns combining time-series, optical and near-infrared photometry with time-series, optical spectroscopy. These data are capable of monitoring the stellar accretion rate, the properties of warm circumstellar dust, and the kinematics of accretion flows, all as a function of orbital phase. In our sample of 9 pre-MS binaries with diverse orbital parameters, we search for evidence of periodic accretion events and seek to determine the role orbital parameters have on the characteristics of accretion events. Two results from our campaign will be highlighted: 1) the detection of periodic pulsed accretion events in DQ Tau and TWA 3A, and 2) evidence that the TWA 3A primary is the dominant accretor in the system. We compare these findings to the results of numerical simulations and comment on the role of magnetospheric accretion in pre-MS binaries.

Exploring viral infection using single-cell sequencing.

PubMed

Rato, Sylvie; Golumbeanu, Monica; Telenti, Amalio; Ciuffi, Angela

2017-07-15

Single-cell sequencing (SCS) has emerged as a valuable tool to study cellular heterogeneity in diverse fields, including virology. By studying the viral and cellular genome and/or transcriptome, the dynamics of viral infection can be investigated at single cell level. Most studies have explored the impact of cell-to-cell variation on the viral life cycle from the point of view of the virus, by analyzing viral sequences, and from the point of view of the cell, mainly by analyzing the cellular host transcriptome. In this review, we will focus on recent studies that use single-cell sequencing to explore viral diversity and cell variability in response to viral replication. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

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

NASA Technical Reports Server (NTRS)

Sitko, Michael L.; Day, Amanda N.; Kimes, Robin L.; Beerman, Lori C.; Martus, Cameron; Lynch, David K.; Russell, Ray W.; Grady, Carol A.; Schneider, Glenn; Lisse, Carey M.;

Cognitive and neural foundations of discrete sequence skill: a TMS study.

PubMed

Ruitenberg, Marit F L; Verwey, Willem B; Schutter, Dennis J L G; Abrahamse, Elger L

2014-04-01

Executing discrete movement sequences typically involves a shift with practice from a relatively slow, stimulus-based mode to a fast mode in which performance is based on retrieving and executing entire motor chunks. The dual processor model explains the performance of (skilled) discrete key-press sequences in terms of an interplay between a cognitive processor and a motor system. In the present study, we tested and confirmed the core assumptions of this model at the behavioral level. In addition, we explored the involvement of the pre-supplementary motor area (pre-SMA) in discrete sequence skill by applying inhibitory 20 min 1-Hz off-line repetitive transcranial magnetic stimulation (rTMS). Based on previous work, we predicted pre-SMA involvement in the selection/initiation of motor chunks, and this was confirmed by our results. The pre-SMA was further observed to be more involved in more complex than in simpler sequences, while no evidence was found for pre-SMA involvement in direct stimulus-response translations or associative learning processes. In conclusion, support is provided for the dual processor model, and for pre-SMA involvement in the initiation of motor chunks. Copyright © 2014 Elsevier Ltd. All rights reserved.

Human action classification using procrustes shape theory

NASA Astrophysics Data System (ADS)

Cho, Wanhyun; Kim, Sangkyoon; Park, Soonyoung; Lee, Myungeun

2015-02-01

In this paper, we propose new method that can classify a human action using Procrustes shape theory. First, we extract a pre-shape configuration vector of landmarks from each frame of an image sequence representing an arbitrary human action, and then we have derived the Procrustes fit vector for pre-shape configuration vector. Second, we extract a set of pre-shape vectors from tanning sample stored at database, and we compute a Procrustes mean shape vector for these preshape vectors. Third, we extract a sequence of the pre-shape vectors from input video, and we project this sequence of pre-shape vectors on the tangent space with respect to the pole taking as a sequence of mean shape vectors corresponding with a target video. And we calculate the Procrustes distance between two sequences of the projection pre-shape vectors on the tangent space and the mean shape vectors. Finally, we classify the input video into the human action class with minimum Procrustes distance. We assess a performance of the proposed method using one public dataset, namely Weizmann human action dataset. Experimental results reveal that the proposed method performs very good on this dataset.

The LANL hemorrhagic fever virus database, a new platform for analyzing biothreat viruses

PubMed Central

Kuiken, Carla; Thurmond, Jim; Dimitrijevic, Mira; Yoon, Hyejin

2012-01-01

Hemorrhagic fever viruses (HFVs) are a diverse set of over 80 viral species, found in 10 different genera comprising five different families: arena-, bunya-, flavi-, filo- and togaviridae. All these viruses are highly variable and evolve rapidly, making them elusive targets for the immune system and for vaccine and drug design. About 55 000 HFV sequences exist in the public domain today. A central website that provides annotated sequences and analysis tools will be helpful to HFV researchers worldwide. The HFV sequence database collects and stores sequence data and provides a user-friendly search interface and a large number of sequence analysis tools, following the model of the highly regarded and widely used Los Alamos HIV database [Kuiken, C., B. Korber, and R.W. Shafer, HIV sequence databases. AIDS Rev, 2003. 5: p. 52–61]. The database uses an algorithm that aligns each sequence to a species-wide reference sequence. The NCBI RefSeq database [Sayers et al. (2011) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 39, D38–D51.] is used for this; if a reference sequence is not available, a Blast search finds the best candidate. Using this method, sequences in each genus can be retrieved pre-aligned. The HFV website can be accessed via http://hfv.lanl.gov. PMID:22064861

An RNAi in silico approach to find an optimal shRNA cocktail against HIV-1

PubMed Central

2010-01-01

Background HIV-1 can be inhibited by RNA interference in vitro through the expression of short hairpin RNAs (shRNAs) that target conserved genome sequences. In silico shRNA design for HIV has lacked a detailed study of virus variability constituting a possible breaking point in a clinical setting. We designed shRNAs against HIV-1 considering the variability observed in naïve and drug-resistant isolates available at public databases. Methods A Bioperl-based algorithm was developed to automatically scan multiple sequence alignments of HIV, while evaluating the possibility of identifying dominant and subdominant viral variants that could be used as efficient silencing molecules. Student t-test and Bonferroni Dunn correction test were used to assess statistical significance of our findings. Results Our in silico approach identified the most common viral variants within highly conserved genome regions, with a calculated free energy of ≥ -6.6 kcal/mol. This is crucial for strand loading to RISC complex and for a predicted silencing efficiency score, which could be used in combination for achieving over 90% silencing. Resistant and naïve isolate variability revealed that the most frequent shRNA per region targets a maximum of 85% of viral sequences. Adding more divergent sequences maintained this percentage. Specific sequence features that have been found to be related with higher silencing efficiency were hardly accomplished in conserved regions, even when lower entropy values correlated with better scores. We identified a conserved region among most HIV-1 genomes, which meets as many sequence features for efficient silencing. Conclusions HIV-1 variability is an obstacle to achieving absolute silencing using shRNAs designed against a consensus sequence, mainly because there are many functional viral variants. Our shRNA cocktail could be truly effective at silencing dominant and subdominant naïve viral variants. Additionally, resistant isolates might be targeted under specific antiretroviral selective pressure, but in both cases these should be tested exhaustively prior to clinical use. PMID:21172023

THE HOST GALAXY PROPERTIES OF VARIABILITY SELECTED AGN IN THE PAN-STARRS1 MEDIUM DEEP SURVEY

DOE Office of Scientific and Technical Information (OSTI.GOV)

Heinis, S.; Gezari, S.; Kumar, S.

2016-07-20

We study the properties of 975 active galactic nuclei (AGNs) selected by variability in the Pan-STARRS1 Medium deep Survey. Using complementary multi-wavelength data from the ultraviolet to the far-infrared, we use spectral energy distribution fitting to determine the AGN and host properties at z < 1 and compare to a well-matched control sample. We confirm the trend previously observed: that the variability amplitude decreases with AGN luminosity, but we also observe that the slope of this relation steepens with wavelength, resulting in a “redder when brighter” trend at low luminosities. Our results show that AGNs are hosted by more massivemore » hosts than control sample galaxies, while the rest frame dust-corrected NUV r color distribution of AGN hosts is similar to control galaxies. We find a positive correlation between the AGN luminosity and star formation rate (SFR), independent of redshift. AGN hosts populate the entire range of SFRs within and outside of the Main Sequence of star-forming galaxies. Comparing the distribution of AGN hosts and control galaxies, we show that AGN hosts are less likely to be hosted by quiescent galaxies and more likely to be hosted by Main Sequence or starburst galaxies.« less

Distribution of genotype network sizes in sequence-to-structure genotype-phenotype maps.

PubMed

Manrubia, Susanna; Cuesta, José A

2017-04-01

An essential quantity to ensure evolvability of populations is the navigability of the genotype space. Navigability, understood as the ease with which alternative phenotypes are reached, relies on the existence of sufficiently large and mutually attainable genotype networks. The size of genotype networks (e.g. the number of RNA sequences folding into a particular secondary structure or the number of DNA sequences coding for the same protein structure) is astronomically large in all functional molecules investigated: an exhaustive experimental or computational study of all RNA folds or all protein structures becomes impossible even for moderately long sequences. Here, we analytically derive the distribution of genotype network sizes for a hierarchy of models which successively incorporate features of increasingly realistic sequence-to-structure genotype-phenotype maps. The main feature of these models relies on the characterization of each phenotype through a prototypical sequence whose sites admit a variable fraction of letters of the alphabet. Our models interpolate between two limit distributions: a power-law distribution, when the ordering of sites in the prototypical sequence is strongly constrained, and a lognormal distribution, as suggested for RNA, when different orderings of the same set of sites yield different phenotypes. Our main result is the qualitative and quantitative identification of those features of sequence-to-structure maps that lead to different distributions of genotype network sizes. © 2017 The Author(s).

Cross-Specificities between cII-like Proteins and pRE-like Promoters of Lambdoid Bacteriophages

PubMed Central

Wulff, Daniel L.; Mahoney, Michael E.

1987-01-01

We have investigated the activation of transcription from the pRE promoters of phages λ, 21 and P22 by the λ and 21 cII proteins and the P22 c1 (cII-like) protein, using an in vivo system in which cII protein from a derepressed prophage activates transcription from a pRE DNA fragment on a multicopy plasmid. We find that each protein is highly specific for its own cognate pRE promoter, although measureable cross-reactions are observed. The primary recognition sequence for cII protein on λ pRE is a pair of TTGC repeat sequences in the sequence 5'-TTGCN 6TTGC-3' at the -35 region of the promoter. This same sequence is found in 21 pRE, while P22 pRE has the sequence 5'-TTGCN6TTGT-3', which is the same as that of λctr1, a pRE+ variant of λ. λctr1 pRE is half as active as λ + pRE when assayed with either the λ cII or the P22 c1 proteins. Therefore, the single base change in the P22 repeat sequence cannot explain why the P22 c1 protein is much more active with P22 pRE than λ p RE. The dya5 mutation, a G→A change at position -43 of pRE, makes pRE a stronger promoter when assayed with either the λ or 21 cII proteins or the P22 c1 protein. We conclude that efficient activation of a cII-dependent promoter by a cII protein requires sequence information in addition to the TTGC repeat sequences. We do not know the characteristics of the proteins which are responsible for the specificity of each protein for its own cognate promoter. However, λdya8, which has a Glu27→Lys alteration in the λ cII protein and a cII+ phenotype, results in a mutant cII protein that is much more highly specific than wild-type cII protein for its own cognate λ p RE promoter. This is especially remarkable because the dya8 amino acid alteration makes the helix-2 region (the region of the protein predicted to make contact with the phosphodiester backbone of the DNA) of λ cII protein conform exactly with the helix-2 region of the P22 c1 protein in both charge and charge distribution. PMID:2953649

Pre-rain green-up is ubiquitous across southern tropical Africa: implications for temporal niche separation and model representation.

PubMed

Ryan, Casey M; Williams, Mathew; Grace, John; Woollen, Emily; Lehmann, Caroline E R

2017-01-01

Tree phenology mediates land-atmosphere mass and energy exchange and is a determinant of ecosystem structure and function. In the dry tropics, including African savannas, many trees grow new leaves during the dry season - weeks or months before the rains typically start. This syndrome of pre-rain green-up has long been recognized at small scales, but the high spatial and interspecific variability in leaf phenology has precluded regional generalizations. We used remote sensing data to show that this precocious phenology is ubiquitous across the woodlands and savannas of southern tropical Africa. In 70% of the study area, green-up preceded rain onset by > 20 d (42% > 40 d). All the main vegetation formations exhibited pre-rain green-up, by as much as 53 ± 18 d (in the wet miombo). Green-up showed low interannual variability (SD between years = 11 d), and high spatial variability (> 100 d). These results are consistent with a high degree of local phenological adaptation, and an insolation trigger of green-up. Tree-tree competition and niche separation may explain the ubiquity of this precocious phenology. The ubiquity of pre-rain green-up described here challenges existing model representations and suggests resistance (but not necessarily resilience) to the delay in rain onset predicted under climate change. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

A Photometric Survey of the Open Clusters NGC 7789 and M67

NASA Astrophysics Data System (ADS)

Janes, Kenneth

2010-01-01

Although there is strong evidence that stellar activity declines as a star ages, beyond about the age of the Hyades (600 Myr) there is little direct confirmation of this decline in stars of known age. This report is an update of an earlier report (Hayes-Gehrke, et al., 2004, AJ, 128, 2862) of a long-term project to explore stellar activity in old open clusters. I have now accumulated 12 years of photometry of the old clusters NGC 7789 (about 1.8 Gyr) and M 67 (about 4 Gyr). An analysis of these data has revealed a substantial number of low-amplitude variable stars in both clusters, including a number of previously-discovered eclipsing binary stars, and several stars near the main sequence turnoff of both clusters that exhibit apparently erratic variations. Some of the M 67 erratics are known X-ray sources. On the main sequence, the large majority of stars show little or no evidence for variability at the 0.1% - 0.2% level, consistent with a regular systematic decline in activity level with age.

Fast selection of miRNA candidates based on large-scale pre-computed MFE sets of randomized sequences.

PubMed

Warris, Sven; Boymans, Sander; Muiser, Iwe; Noback, Michiel; Krijnen, Wim; Nap, Jan-Peter

2014-01-13

Small RNAs are important regulators of genome function, yet their prediction in genomes is still a major computational challenge. Statistical analyses of pre-miRNA sequences indicated that their 2D structure tends to have a minimal free energy (MFE) significantly lower than MFE values of equivalently randomized sequences with the same nucleotide composition, in contrast to other classes of non-coding RNA. The computation of many MFEs is, however, too intensive to allow for genome-wide screenings. Using a local grid infrastructure, MFE distributions of random sequences were pre-calculated on a large scale. These distributions follow a normal distribution and can be used to determine the MFE distribution for any given sequence composition by interpolation. It allows on-the-fly calculation of the normal distribution for any candidate sequence composition. The speedup achieved makes genome-wide screening with this characteristic of a pre-miRNA sequence practical. Although this particular property alone will not be able to distinguish miRNAs from other sequences sufficiently discriminative, the MFE-based P-value should be added to the parameters of choice to be included in the selection of potential miRNA candidates for experimental verification.

Ground penetrating radar documents short-term near-surface hydrological changes around Old Faithful Geyser, Yellowstone National Park, USA

NASA Astrophysics Data System (ADS)

Lynne, Bridget Y.; Heasler, Henry; Jaworowski, Cheryl; Smith, Gary J.; Smith, Isaac J.; Foley, Duncan

2018-04-01

In April 2015, Ground Penetrating Radar (GPR) was used to characterize the shallow subsurface (< 5 m depth) of the western sinter slope immediately adjacent to Old Faithful Geyser and near the north side of an inferred geyser cavity. A series of time-sequence images were collected between two eruptions of Old Faithful Geyser. Each set of time-sequence GPR recordings consisted of four transects aligned to provide coverage near the potential location of the inferred 15 m deep geyser chamber. However, the deepest penetration we could achieve with a 200 MHz GPR antennae was 5 m. Seven time-sequence events were collected over a 48-minute interval to image changes in the near-surface, during pre- and post-eruptive cycles. Time-sequence GPR images revealed a series of possible micro-fractures in a highly porous siliceous sinter in the near-surface that fill and drain repetitively, immediately after an eruption and during the recharge period prior to the next main eruptive event.

40 CFR 92.124 - Test sequence; general requirements.

Code of Federal Regulations, 2012 CFR

2012-07-01

.... (e) Pre-test engine measurements (e.g., idle and throttle notch speeds, fuel flows, etc.), pre-test engine performance checks (e.g., verification of engine power, etc.) and pre-test system calibrations (e... 40 Protection of Environment 21 2012-07-01 2012-07-01 false Test sequence; general requirements...

40 CFR 92.124 - Test sequence; general requirements.

Code of Federal Regulations, 2014 CFR

2014-07-01

.... (e) Pre-test engine measurements (e.g., idle and throttle notch speeds, fuel flows, etc.), pre-test engine performance checks (e.g., verification of engine power, etc.) and pre-test system calibrations (e... 40 Protection of Environment 20 2014-07-01 2013-07-01 true Test sequence; general requirements. 92...

40 CFR 92.124 - Test sequence; general requirements.

Code of Federal Regulations, 2010 CFR

2010-07-01

.... (e) Pre-test engine measurements (e.g., idle and throttle notch speeds, fuel flows, etc.), pre-test engine performance checks (e.g., verification of engine power, etc.) and pre-test system calibrations (e... 40 Protection of Environment 20 2010-07-01 2010-07-01 false Test sequence; general requirements...

40 CFR 92.124 - Test sequence; general requirements.

Code of Federal Regulations, 2013 CFR

2013-07-01

.... (e) Pre-test engine measurements (e.g., idle and throttle notch speeds, fuel flows, etc.), pre-test engine performance checks (e.g., verification of engine power, etc.) and pre-test system calibrations (e... 40 Protection of Environment 21 2013-07-01 2013-07-01 false Test sequence; general requirements...

40 CFR 92.124 - Test sequence; general requirements.

Code of Federal Regulations, 2011 CFR

2011-07-01

.... (e) Pre-test engine measurements (e.g., idle and throttle notch speeds, fuel flows, etc.), pre-test engine performance checks (e.g., verification of engine power, etc.) and pre-test system calibrations (e... 40 Protection of Environment 20 2011-07-01 2011-07-01 false Test sequence; general requirements...

Rapid and accurate synthesis of TALE genes from synthetic oligonucleotides.

PubMed

Wang, Fenghua; Zhang, Hefei; Gao, Jingxia; Chen, Fengjiao; Chen, Sijie; Zhang, Cuizhen; Peng, Gang

2016-01-01

Custom synthesis of transcription activator-like effector (TALE) genes has relied upon plasmid libraries of pre-fabricated TALE-repeat monomers or oligomers. Here we describe a novel synthesis method that directly incorporates annealed synthetic oligonucleotides into the TALE-repeat units. Our approach utilizes iterative sets of oligonucleotides and a translational frame check strategy to ensure the high efficiency and accuracy of TALE-gene synthesis. TALE arrays of more than 20 repeats can be constructed, and the majority of the synthesized constructs have perfect sequences. In addition, this novel oligonucleotide-based method can readily accommodate design changes to the TALE repeats. We demonstrated an increased gene targeting efficiency against a genomic site containing a potentially methylated cytosine by incorporating non-conventional repeat variable di-residue (RVD) sequences.

The Age-Related Properties of the HD 98800 System

NASA Technical Reports Server (NTRS)

Soderblom, David R.; Henry, Todd J.; Shetrone, Matthew D.; Jones, Burton F.; Saar, Steven H.

1996-01-01

We present optical spectroscopy of the field K star system HD 98800, which has been found to have significant infrared emission from circumstellar material. The lithium abundances of the stars in HD 98800 are well above those of Pleiades of similar color, but activity levels and rotation in these stars are at or below Pleiades level. Thus, it is not yet possible to say whether HD 98800 is or is not a pre-main-sequence system, and it is possible that its components are on or near the zero-age main sequence. However, the two visible objects that make up HD 98800 both have high levels of lithium and activity, strongly suggesting that they are physically related to one another. As shown by Torres and coworkers, having these stars physically tied implies that their relative orbit is highly eccentric and highly inclined to our line of sight, and it also means that we are viewing the HD 98800 system at an unusual time in its orbit.

Stress and Strain Rates from Faults Reconstructed by Earthquakes Relocalization

NASA Astrophysics Data System (ADS)

Morra, G.; Chiaraluce, L.; Di Stefano, R.; Michele, M.; Cambiotti, G.; Yuen, D. A.; Brunsvik, B.

2017-12-01

Recurrence of main earthquakes on the same fault depends on kinematic setting, hosting lithologies and fault geometry and population. Northern and central Italy transitioned from convergence to post-orogenic extension. This has produced a unique and very complex tectonic setting characterized by superimposed normal faults, crossing different geologic domains, that allows to investigate a variety of seismic manifestations. In the past twenty years three seismic sequences (1997 Colfiorito, 2009 L'Aquila and 2016-17 Amatrice-Norcia-Visso) activated a 150km long normal fault system located between the central and northern apennines and allowing the recordings of thousands of seismic events. Both the 1997 and the 2009 main shocks were preceded by a series of small pre-shocks occurring in proximity to the future largest events. It has been proposed and modelled that the seismicity pattern of the two foreshocks sequences was caused by active dilatancy phenomenon, due to fluid flow in the source area. Seismic activity has continued intensively until three events with 6.0

Pre-eclampsia and first-onset postpartum psychiatric episodes: a Danish population-based cohort study

PubMed Central

Bergink, V.; Laursen, T. M.; Johannsen, B. M. W.; Kushner, S. A.; Meltzer-Brody, S.; Munk-Olsen, T.

2016-01-01

Background Recent evidence suggests that postpartum psychiatric episodes may share similar etiological mechanisms with immune-related disorders. Pre-eclampsia is one of the most prevalent immune-related disorders of pregnancy. Multiple clinical features are shared between pre-eclampsia and postpartum psychiatric disorders, most prominently a strong link to first pregnancies. Therefore, we aimed to study if pre-eclampsia is a risk factor for first-onset postpartum psychiatric episodes. Method We conducted a cohort study using the Danish population registry, with a total of 400 717 primiparous women with a singleton delivery between 1995 and 2011. First-lifetime childbirth was the main exposure variable and the outcome of interest was first-onset postpartum psychiatric episodes. The main outcome measures were monthly incidence rate ratios (IRRs), with the period 11–12 months after birth as the reference category. Adjustments were made for age, calendar period, reproductive history, and perinatal maternal health including somatic and obstetric co-morbidity. Results Primiparous women were at particularly high risk of first-onset psychiatric episodes during the first month postpartum [IRR 2.93, 95% confidence interval (CI) 2.53–3.40] and pre-eclampsia added to that risk (IRR 4.21, 95% CI 2.89–6.13). Having both pre-eclampsia and a somatic co-morbidity resulted in the highest risk of psychiatric episodes during the 3-month period after childbirth (IRR 4.81, 95% CI 2.72–8.50). Conclusions We confirmed an association between pre-eclampsia and postpartum psychiatric episodes. The possible explanations for this association, which are not mutually exclusive, include the psychological impact of a serious medical condition such as pre-eclampsia and the neurobiological impact of pre-eclampsia-related vascular pathology and inflammation. PMID:26243040

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mello, M.R.; Soldan, A.L.; Maxwell, J.R.

A geochemical and biological marker investigation of a variety of oils from offshore Brazil and west Africa, ranging in age from Lower Cretaceous to Tertiary, has been done, with the following aims: (1) assessing the depositional environment of source rocks, (2) correlating the reservoired oils, (3) comparing the Brazilian oils with their west African counterparts. The approach was based in stable isotope data; bulk, elemental, and hydrous pyrolysis results; and molecular studies involving quantitative geological marker investigations of alkanes using GC-MS and GC-MS-MS. The results reveal similarities between groups of oils from each side of the Atlantic and suggest anmore » origin from source rocks deposited in five types of depositional environment: lacustrine fresh water, lacustrine saline water, marine evaporitic/carbonate, restricted marine anoxic, and marine deltaic. In west Africa, the Upper Cretaceous marine anoxic succession (Cenomanian-Santonian) appears to be a major oil producer, but in Brazil it is generally immature. The Brazilian offshore oils have arisen mainly from the pre-salt sequence, whereas the African oils show a balance between origins from the pre-salt and marine sequences. The integration of the geochemical and geological data indicate that new frontiers of hydrocarbon exploration in the west African basins must consider the Tertiary reservoirs in the offshore area of Niger Delta, the reservoirs of the rift sequences in the shallow-water areas of south Gabon, Congo, and Cuanza basins, and the reservoirs from the drift sequences (post-salt) in the deep-water areas of Gabon, Congo Cabinda, and Cuanza basins.« less

Trauma Exposures and Posttraumatic Stress among Zimbabwean refugees in South Africa.

PubMed

Idemudia, Erhabor S; Williams, John K; Madu, Sylvester N; Wyatt, Gail E

2013-09-25

Zimbabwean refugees can be considered a vulnerable group in terms of how they are displaced with many of them having lived through hardships on their way to South Africa and other African countries. Zimbabwe is known to be Africa's most extraordinary producer of migrants and the biggest producer of refugees in Southern Africa. It is estimated that 3.4 million Zimbabweans, a quarter of the country's population, have fled the country. Economic collapse, hunger and political repression have been blamed for the mass exodus. The present study examines the impact of trauma exposures (pre- and post-migration stressors and poor mental health) on posttraumatic stress disorder (PTSD) among homeless Zimbabwean refugees living in South Africa. Through a guided convenient sampling, in-depth interviews using questionnaires were collected from 125 homeless Zimbabwean refugees in Polokwane, Limpopo Province, South Africa. The study was anchored on the hypothesis that predictor variables (pre- and post- migration stressors, poor mental health) would significantly affect outcomes (PTSD). Participants were assessed on demographic variables, pre- and post-migration difficulties checklists, mental health using the General Health Questionnaire (GHQ-28) and the PTSD Checklist (Civilian Version (PCL). Participants ranged from 18 to 48 years with a mean age of 28.3 years (SD = 6.27). The majority of the sample had at least a secondary education (76.8%) and were employed as unskilled labourers (61.6%) in South Africa. Being married was reported by 54.4% in Zimbabwe but changed to only 19.2% in South Africa. Hierarchical multiple regression analyses showed that the overall model significantly predicted PTSD among homeless Zimbabweans (R 2 = 0.17, adjusted R 2 = 0.11, F (6, 124) = 2.960, p < .01). Thus, the entire set of pre- and post-migration variables (Post total stress, PreThreat to life, Presexabuse, PrePoverty, Postsexabuse, Postpoverty and two mental health symptoms (Anxiety and Insomnia, and Social dysfunction) explained 41.2 % of the total variance on PTSD. However, main significant predictors were Post total stress (t (125) = 2.571, P < .001); Postsexabuse (t (125) = 2.175, P < .003); Postpoverty (t (125) = 3.450, P < .001); Anxiety and Insomnia (t (125) = 2.000, P < .04) and Social dysfunction (t (125) = 2.113, P < .003). Of these variables in order of strong impact predictor is Post total stress ( β = 0.737) followed by Postpoverty ( β = 0.701), Postsexabuse ( β = 0.377) and Social dysfunction ( β = 0.196). The Dubin-Watson results (2.252) also showed that the assumption of independent errors was tenable and almost certainly met for this model. Variables excluded in the model were Pre total Stress, Post threat to life, Somatic complaints (GHQ A), Severe depression (GHQ D) and Total GHQ. Zimbabwean refugees constitute a particularly vulnerable group to poor mental health and PTSD. These findings have significant implications for refugees in South Africa and other places where integrating refugee treament in the main stream health system is undermined. As a migratory group, there is need to develop ways of using probability sampling methods in further research and increasing sample size. In addition, there is need to develop culturally relevant interventions to address the sequalaes of pre- and post-migration traumas and poor mental health.

Trauma Exposures and Posttraumatic Stress among Zimbabwean refugees in South Africa

PubMed Central

Idemudia, Erhabor S.; Williams, John K.; Madu, Sylvester N.; Wyatt, Gail E.

2014-01-01

Zimbabwean refugees can be considered a vulnerable group in terms of how they are displaced with many of them having lived through hardships on their way to South Africa and other African countries. Zimbabwe is known to be Africa’s most extraordinary producer of migrants and the biggest producer of refugees in Southern Africa. It is estimated that 3.4 million Zimbabweans, a quarter of the country’s population, have fled the country. Economic collapse, hunger and political repression have been blamed for the mass exodus. The present study examines the impact of trauma exposures (pre- and post-migration stressors and poor mental health) on posttraumatic stress disorder (PTSD) among homeless Zimbabwean refugees living in South Africa. Through a guided convenient sampling, in-depth interviews using questionnaires were collected from 125 homeless Zimbabwean refugees in Polokwane, Limpopo Province, South Africa. The study was anchored on the hypothesis that predictor variables (pre- and post- migration stressors, poor mental health) would significantly affect outcomes (PTSD). Participants were assessed on demographic variables, pre- and post-migration difficulties checklists, mental health using the General Health Questionnaire (GHQ-28) and the PTSD Checklist (Civilian Version (PCL). Participants ranged from 18 to 48 years with a mean age of 28.3 years (SD = 6.27). The majority of the sample had at least a secondary education (76.8%) and were employed as unskilled labourers (61.6%) in South Africa. Being married was reported by 54.4% in Zimbabwe but changed to only 19.2% in South Africa. Hierarchical multiple regression analyses showed that the overall model significantly predicted PTSD among homeless Zimbabweans (R2 = 0.17, adjusted R2 = 0.11, F (6, 124) = 2.960, p < .01). Thus, the entire set of pre- and post-migration variables (Post total stress, PreThreat to life, Presexabuse, PrePoverty, Postsexabuse, Postpoverty and two mental health symptoms (Anxiety and Insomnia, and Social dysfunction) explained 41.2 % of the total variance on PTSD. However, main significant predictors were Post total stress (t (125) = 2.571, P < .001); Postsexabuse (t (125) = 2.175, P < .003); Postpoverty (t (125) = 3.450, P < .001); Anxiety and Insomnia (t (125) = 2.000, P < .04) and Social dysfunction (t (125) = 2.113, P < .003). Of these variables in order of strong impact predictor is Post total stress (β = 0.737) followed by Postpoverty (β = 0.701), Postsexabuse (β = 0.377) and Social dysfunction (β = 0.196). The Dubin-Watson results (2.252) also showed that the assumption of independent errors was tenable and almost certainly met for this model. Variables excluded in the model were Pre total Stress, Post threat to life, Somatic complaints (GHQ A), Severe depression (GHQ D) and Total GHQ. Zimbabwean refugees constitute a particularly vulnerable group to poor mental health and PTSD. These findings have significant implications for refugees in South Africa and other places where integrating refugee treament in the main stream health system is undermined. As a migratory group, there is need to develop ways of using probability sampling methods in further research and increasing sample size. In addition, there is need to develop culturally relevant interventions to address the sequalaes of pre- and post-migration traumas and poor mental health. PMID:25382966

Software for pre-processing Illumina next-generation sequencing short read sequences

PubMed Central

2014-01-01

Background When compared to Sanger sequencing technology, next-generation sequencing (NGS) technologies are hindered by shorter sequence read length, higher base-call error rate, non-uniform coverage, and platform-specific sequencing artifacts. These characteristics lower the quality of their downstream analyses, e.g. de novo and reference-based assembly, by introducing sequencing artifacts and errors that may contribute to incorrect interpretation of data. Although many tools have been developed for quality control and pre-processing of NGS data, none of them provide flexible and comprehensive trimming options in conjunction with parallel processing to expedite pre-processing of large NGS datasets. Methods We developed ngsShoRT (next-generation sequencing Short Reads Trimmer), a flexible and comprehensive open-source software package written in Perl that provides a set of algorithms commonly used for pre-processing NGS short read sequences. We compared the features and performance of ngsShoRT with existing tools: CutAdapt, NGS QC Toolkit and Trimmomatic. We also compared the effects of using pre-processed short read sequences generated by different algorithms on de novo and reference-based assembly for three different genomes: Caenorhabditis elegans, Saccharomyces cerevisiae S288c, and Escherichia coli O157 H7. Results Several combinations of ngsShoRT algorithms were tested on publicly available Illumina GA II, HiSeq 2000, and MiSeq eukaryotic and bacteria genomic short read sequences with the focus on removing sequencing artifacts and low-quality reads and/or bases. Our results show that across three organisms and three sequencing platforms, trimming improved the mean quality scores of trimmed sequences. Using trimmed sequences for de novo and reference-based assembly improved assembly quality as well as assembler performance. In general, ngsShoRT outperformed comparable trimming tools in terms of trimming speed and improvement of de novo and reference-based assembly as measured by assembly contiguity and correctness. Conclusions Trimming of short read sequences can improve the quality of de novo and reference-based assembly and assembler performance. The parallel processing capability of ngsShoRT reduces trimming time and improves the memory efficiency when dealing with large datasets. We recommend combining sequencing artifacts removal, and quality score based read filtering and base trimming as the most consistent method for improving sequence quality and downstream assemblies. ngsShoRT source code, user guide and tutorial are available at http://research.bioinformatics.udel.edu/genomics/ngsShoRT/. ngsShoRT can be incorporated as a pre-processing step in genome and transcriptome assembly projects. PMID:24955109

Are Avellino (4365 cal BP) and Pompeii twin plinian eruptions? Pre-eruptive constraints and degassing history

NASA Astrophysics Data System (ADS)

Boudon, Georges; Balcone-Boissard, Hélène; Villemant, Benoît.; Ucciani, Guillaume; Cioni, Raffaello

2010-05-01

Somma-Vesuvius activity started 35 ky ago and is characterized by numerous eruptions of variable composition and eruptive style, sometimes interrupted by long periods of unrest. The main explosive eruptions are represented by four plinian eruptions: Pomici di Base eruption (22 cal ky), Mercato (~8900 cal BP), Avellino (4365 cal BP) and Pompeii (79 AD). The 79 AD eruption embodies the most famous eruption since it's responsible of the destruction of Pompeii and Herculanum and it's the first described eruption. The Avellino eruption represents the last plinian event that preceded the Pompeii eruption. The eruptive sequence is similar to the 79 AD plinian eruption, with an opening phase preceding a main plinian fallout activity which ended by a phreatomagmatic phase. The fallout deposit displays a sharp colour contrast from white to grey pumice, corresponding to a magma composition evolution. We focus our study on the main fallout deposit that we sampled in detail in the Traianello quarry, 9 km North-North East of the crater, to investigate the degassing processes during the eruption, using volatile content and textural observations. Density and vesicularity measurements were obtained on a minimum of 100 pumice clasts sampled in 10 stratigraphic levels in the fallout deposit. On the basis of the density distribution, bulk geochemical data, point analytical measurements on glasses (melt inclusions and residual glass) and textural observations were obtained simultaneously on a minimum of 5 pumice clasts per eruptive unit. The glass composition, in particular the Na/K ratio, evolves from Na-rich phonolite for white pumices to a more K-rich phonolite for grey pumices. The pre-eruptive conditions are constrained by systematic Cl measurements in melt inclusions and matrix glass of pumice clasts. The entire magma was saturated relative to sub-critical fluids (a Cl-rich H2O vapour phase and a brine), with a Cl melt content buffered at ~6000 ppm, and a mean pre-eruptive H2O content depending of the magma composition. Most of the pumices of the different eruptive units show that H2O degassing during the eruption followed a typical closed-system evolution as expected for plinian eruption. Contrary to H2O, Cl was not efficiently degassed during the plinian phase of the eruption: the matrix glass composition remains close to the pre-eruptive content. Compared to the 79AD eruption the degassing processes showed by the whole Avellino plinian phase is more homogeneous and similar to the white pumice phase of the Pompeii eruption whereas the open-system degassing mode identified from the grey pumices of the 79AD eruption is not represented during the Avellino eruption.

Is systematic training in opioid overdose prevention effective?

PubMed

Espelt, Albert; Bosque-Prous, Marina; Folch, Cinta; Sarasa-Renedo, Ana; Majó, Xavier; Casabona, Jordi; Brugal, M Teresa

2017-01-01

The objectives were to analyze the knowledge about overdose prevention, the use of naloxone, and the number of fatal overdoses after the implementation of Systematic Training in Overdose Prevention (STOOP) program. We conducted a quasi-experimental study, and held face-to-face interviews before (n = 725) and after (n = 722) implementation of systematic training in two different samples of people who injected opioids attending harm reduction centers. We asked participants to list the main causes of overdose and the main actions that should be taken when witnessing an overdose. We created two dependent variables, the number of (a) correct and (b) incorrect answers. The main independent variable was Study Group: Intervention Group (IG), Comparison Group (CG), Pre-Intervention Group With Sporadic Training in Overdose Prevention (PREIGS), or Pre-Intervention Group Without Training in Overdose Prevention (PREIGW). The relationship between the dependent and independent variables was assessed using a multivariate Poisson regression analysis. Finally, we conducted an interrupted time series analysis of monthly fatal overdoses before and after the implementation of systematic program during the period 2006-2015. Knowledge of overdose prevention increased after implementing systematic training program. Compared to the PREIGW, the IG gave more correct answers (IRR = 1.40;95%CI:1.33-1.47), and fewer incorrect answers (IRR = 0.33;95%CI:0.25-0.44). Forty percent of people who injected opioids who received a naloxone kit had used the kit in response to an overdose they witnessed. These courses increase knowledge of overdose prevention in people who use opioids, give them the necessary skills to use naloxone, and slightly diminish the number of fatal opioid overdoses in the city of Barcelona.

Is systematic training in opioid overdose prevention effective?

PubMed Central

Bosque-Prous, Marina; Folch, Cinta; Sarasa-Renedo, Ana; Majó, Xavier; Casabona, Jordi; Brugal, M. Teresa

2017-01-01

The objectives were to analyze the knowledge about overdose prevention, the use of naloxone, and the number of fatal overdoses after the implementation of Systematic Training in Overdose Prevention (STOOP) program. We conducted a quasi-experimental study, and held face-to-face interviews before (n = 725) and after (n = 722) implementation of systematic training in two different samples of people who injected opioids attending harm reduction centers. We asked participants to list the main causes of overdose and the main actions that should be taken when witnessing an overdose. We created two dependent variables, the number of (a) correct and (b) incorrect answers. The main independent variable was Study Group: Intervention Group (IG), Comparison Group (CG), Pre-Intervention Group With Sporadic Training in Overdose Prevention (PREIGS), or Pre-Intervention Group Without Training in Overdose Prevention (PREIGW). The relationship between the dependent and independent variables was assessed using a multivariate Poisson regression analysis. Finally, we conducted an interrupted time series analysis of monthly fatal overdoses before and after the implementation of systematic program during the period 2006–2015. Knowledge of overdose prevention increased after implementing systematic training program. Compared to the PREIGW, the IG gave more correct answers (IRR = 1.40;95%CI:1.33–1.47), and fewer incorrect answers (IRR = 0.33;95%CI:0.25–0.44). Forty percent of people who injected opioids who received a naloxone kit had used the kit in response to an overdose they witnessed. These courses increase knowledge of overdose prevention in people who use opioids, give them the necessary skills to use naloxone, and slightly diminish the number of fatal opioid overdoses in the city of Barcelona. PMID:29088247

Analysis of the complete genome of subgroup A' hepatitis B virus isolates from South Africa.

PubMed

Kramvis, Anna; Weitzmann, Louise; Owiredu, William K B A; Kew, Michael C

2002-04-01

A phylogenetic analysis is presented of six complete and seven pre-S1/S2/S gene sequences of hepatitis B virus (HBV) isolates from South Africa. Five of the full-length sequences and all of the pre-S2/S sequences have been previously reported. Four of the six complete genomes and three of the five incomplete sequences clustered with subgroup A', a unique segment of genotype A of HBV previously identified in 60% of South African isolates using analysis of the pre-S2/S region alone. This separation was also evident when the polymerase open reading frame was analysed, but not on analysis of either the X or pre-core/core genes. Amino acids were identified in the pre-S1 and polymerase regions specific to subgroup A'. In common with genotype D, 10 of 11 genotype A South African isolates had an 11 amino acid deletion in the amino end of the pre-S1 region. This deletion is also found in hepadnaviruses from non-human primates.

Contribution of genome-environment interaction to pre-eclampsia in a Havana Maternity Hospital.

PubMed

Lardoeyt, Roberto; Vargas, Gerardo; Lumpuy, Jairo; García, Ramón; Torres, Yuselis

2013-07-01

Pre-eclampsia is a major cause of morbidity and mortality during pregnancy worldwide and is among the leading causes of maternal mortality in Cuba. It is a complex, multifactoral disease, in which interaction of genetic and environmental factors should not be overlooked if the goal is proper risk assessment to support personalized preventive genetic counseling and more effective prenatal care to prevent pregnancy complications. Determine the contribution to pre-eclampsia of interaction between a predisposing genome and adverse environmental factors in pregnant women in a Havana maternity hospital. This was the exploratory phase of a hospital-based case-control study, using January 2007-December 2009 patient records from the Eusebio Hernández University Hospital, a provincial maternity hospital in Havana. Eighty pregnant women diagnosed with pre-eclampsia and 160 controls were studied. The main variables were age, parity, nutritional status (measured by BMI), alcohol use, tobacco use, and history of pre-eclampsia in relatives of the pregnant woman (proband) or of her partner. Pearson chi square and Fisher exact test were used to assess statistical significance of associations between variables and odds ratio as a measure of association strength. Familial aggregation was studied and a case-control design used to assess gene-environment interaction, using multiplicative and additive models. Among the environmental risk factors studied, alcohol showed the strongest effect on pre-eclampsia risk (OR 3.87, 95% CI 1.64-9.13). Familial pre-eclampsia clustering was observed; risk was increased for both first-degree (OR 2.43, 95% CI 1.62-3.73) and second-degree (OR 1.89, 95% CI 1.34-2.68) relatives as well as for husband's relatives (OR 2.32, 95% CI 1.40-3.86). There was evidence of interaction between alcohol consumption and family history. Familial aggregation of the disorder was demonstrated, the first Cuban epidemiological evidence of genetic and enviromental contributions to pre-eclampsia risk. Familial clustering among the husband's relatives demonstrates the fetal genome's importance in genesis of pre-eclampsia. The interaction of environmental risk factors with genetic ones produces increased pre-eclampsia risk, compared to expectations based on independent action of these variables. KEYWORDS Pre-eclampsia, toxemia of pregnancy, pregnancy outcome, environment, genetics, genome-environment interaction, genetic epidemiology, Cuba.

Discovery of magnetic A supergiants: the descendants of magnetic main-sequence B stars

NASA Astrophysics Data System (ADS)

Neiner, Coralie; Oksala, Mary E.; Georgy, Cyril; Przybilla, Norbert; Mathis, Stéphane; Wade, Gregg; Kondrak, Matthias; Fossati, Luca; Blazère, Aurore; Buysschaert, Bram; Grunhut, Jason

2017-10-01

In the context of the high resolution, high signal-to-noise ratio, high sensitivity, spectropolarimetric survey BritePol, which complements observations by the BRITE constellation of nanosatellites for asteroseismology, we are looking for and measuring the magnetic field of all stars brighter than V = 4. In this paper, we present circularly polarized spectra obtained with HarpsPol at ESO in La Silla (Chile) and ESPaDOnS at CFHT (Hawaii) for three hot evolved stars: ι Car, HR 3890 and ɛ CMa. We detected a magnetic field in all three stars. Each star has been observed several times to confirm the magnetic detections and check for variability. The stellar parameters of the three objects were determined and their evolutionary status was ascertained employing evolution models computed with the Geneva code. ɛ CMa was already known and is confirmed to be magnetic, but our modelling indicates that it is located near the end of the main sequence, I.e. it is still in a core hydrogen burning phase. ι Car and HR 3890 are the first discoveries of magnetic hot supergiants located well after the end of the main sequence on the Hertzsprung-Russell diagram. These stars are probably the descendants of main-sequence magnetic massive stars. Their current field strength (a few G) is compatible with magnetic flux conservation during stellar evolution. These results provide observational constraints for the development of future evolutionary models of hot stars including a fossil magnetic field.

Perceptions, intentions and behavioral norms that affect pre-license driving among Arab youth in Israel.

PubMed

Gesser-Edelsburg, Anat; Zemach, Mina; Lotan, Tsippy; Elias, Wafa; Grimberg, Einat

2018-02-01

The present study examines reported pre-license driving among youth from the population of Arab citizens of Israel. The purpose of the present study is to examine which sociodemographic variables, attitudes and perceptions about safe driving and individual and societal behavioral norms are associated with pre-license driving. The research distinguished between the factors that actually contribute to pre-license driving (reported behavior, peer norms, gender and parents' messages) and the factors that explain the intention (parental authority, social norms, parents' messages and fear of road crashes). Even though there was a significant partial overlap (84%) between those who intend to drive without a license and those who reported driving without a license, the main factors that distinguish pre-license driving groups are different from the factors that distinguish the intention to drive before receiving a license. What is unique about the findings is the identification of the context in which social norms are influential and that in which parental authority is influential. The study indicated that in the case of pre-license driving, the main motivating factor is subjective norms, whereas in the case of expecting to drive without a license, the main motivating factor is the interaction between parental authority and the messages that parents convey. While actual behavior pertains to the behavioral level, we argue that intended behavior pertains to the cognitive level. At this level, rational considerations arise, such as fear of parental punishment and fear of accidents. These considerations compete with the influence of friends and their norms, and may outweigh them. The findings suggest that it is important to safeguard youth against the influence of peer pressure as early as the stage of behavioral intentions. Follow-up studies can simulate situations of pre-license driving due to social pressure and identify the factors that might affect young people's decision-making. Moreover, providing parents with training before the accompaniment period is highly recommended. Copyright © 2017 Elsevier Ltd. All rights reserved.

Variable extinction in HD 45677 and the evolution of dust grains in pre-main-sequence disks

NASA Technical Reports Server (NTRS)

Sitko, Michael L.; Halbedel, Elaine M.; Lawrence, Geoffrey F.; Smith, J. Allyn; Yanow, Ken

1994-01-01

Changes in the UV extinction and IR emission were sought in the Herbig Ae/Be star candidate HD 45677 (= FS CMa) by comparing UV, optical, and IR observations made approximately 10 yr apart. HD 45677 varied significantly, becoming more than 50% brighter in the UV and optical than it was a decade ago. A comparison of the observations between epochs indicates that if the variations are due to changes in dust obscuration, the dust acts as a gray absorber into the near-IR and must be depleted in grains smaller than 1 micron. This is similar to the results obtained on the circumstellar disks of stars like Vega and Beta Pic, and suggests that radiation pressure may be responsible for the small-grain depletion. In addition, the total IR flux seems to have declined, indicating a decrease in the total mass of the dust envelope that contributes to the IR emission in this part of the spectrum. Due to the anomalous nature of the extinction, the use of normal extinction curves to deredden the spectral energy distributions of stars with circumstellar dust may lead to significant errors and should be used with great caution.

Investigating the long-term course of schizophrenia by sequence analysis.

PubMed

An der Heiden, Wolfram; Häfner, Heinz

2015-08-30

In the present study we set out to explore the long-term clinical course of schizophrenia in a holistic manner by adopting sequence analysis. Our aim was to identify course types of illness by means of cluster analysis. The study was based on course and outcome data for 107 patients followed up over 134 months after first admission in the ABC Schizophrenia Study. Focusing on the main syndromes (positive, negative, depressive and unspecific symptoms) and their combinations we looked for similarities in individual illness courses using the 'optimal matching' method. A cluster analysis performed on the resulting similarity matrix yielded two main groups (a 'improving' and a 'chronic' group), which comprised a total of six different types of illness course. The course types differed in both quantitative (frequency of syndromes and syndrome combinations) and qualitative terms (clinical presentation, sequence of syndromes). Cluster membership was only rarely, but clearly associated with sociodemographic characteristics, treatment data and other illness variables. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Fast selection of miRNA candidates based on large-scale pre-computed MFE sets of randomized sequences

PubMed Central

2014-01-01

Background Small RNAs are important regulators of genome function, yet their prediction in genomes is still a major computational challenge. Statistical analyses of pre-miRNA sequences indicated that their 2D structure tends to have a minimal free energy (MFE) significantly lower than MFE values of equivalently randomized sequences with the same nucleotide composition, in contrast to other classes of non-coding RNA. The computation of many MFEs is, however, too intensive to allow for genome-wide screenings. Results Using a local grid infrastructure, MFE distributions of random sequences were pre-calculated on a large scale. These distributions follow a normal distribution and can be used to determine the MFE distribution for any given sequence composition by interpolation. It allows on-the-fly calculation of the normal distribution for any candidate sequence composition. Conclusion The speedup achieved makes genome-wide screening with this characteristic of a pre-miRNA sequence practical. Although this particular property alone will not be able to distinguish miRNAs from other sequences sufficiently discriminative, the MFE-based P-value should be added to the parameters of choice to be included in the selection of potential miRNA candidates for experimental verification. PMID:24418292

EMG-based speech recognition using hidden markov models with global control variables.

PubMed

Lee, Ki-Seung

2008-03-01

It is well known that a strong relationship exists between human voices and the movement of articulatory facial muscles. In this paper, we utilize this knowledge to implement an automatic speech recognition scheme which uses solely surface electromyogram (EMG) signals. The sequence of EMG signals for each word is modelled by a hidden Markov model (HMM) framework. The main objective of the work involves building a model for state observation density when multichannel observation sequences are given. The proposed model reflects the dependencies between each of the EMG signals, which are described by introducing a global control variable. We also develop an efficient model training method, based on a maximum likelihood criterion. In a preliminary study, 60 isolated words were used as recognition variables. EMG signals were acquired from three articulatory facial muscles. The findings indicate that such a system may have the capacity to recognize speech signals with an accuracy of up to 87.07%, which is superior to the independent probabilistic model.

XII Multifrequency Behaviour of High Energy Cosmic Sources Workshop

NASA Astrophysics Data System (ADS)

2017-06-01

This is the twelfth edition of the series of Frascati Workshops on "Multifrequency Behaviour of High Energy Cosmic Sources" which is undoubtedly a largely accepted biennial meeting in which an updated experimental and theoretical panorama will be depicted. This edition comes at the 33rd anniversary of the first historical "multifrequency" workshop about "Multifrequency Behaviour of GalacticAccreting Sources", held in Vulcano in September 1984. This surely renders the Frascati Workshop Series the oldest among the many devoted to "Multifrequency Studies of Cosmic Sources". The study of the physics governing the cosmic sources will be the main goal of the workshop. A session devoted to the ongoing and next generation ground- and space-based experiments will give the actual prospects for the first decades of this millennium. The following items will be reviewed: Cosmology: Cosmic Background, Clusters of Galaxies Extragalactic Sources: Active Galaxies, Normal Galaxies Gamma-Rays Burst: Experiments versus Theories Galactic Sources: Pre-Main-Sequence and Main-Sequence Stars, Cataclysmic Variables and Novae, Supernovae and SNRs, X-Ray Binary Systems, Pulsars, Black Holes, Gamma-Ray Sources,Nucleosynthesis. The Astrophysics with the Ongoing and Future Experiments: Space-Based Experiments,Ground-Based Experiments. The workshop will include few 30-minute general review talks to introduce the current problems, and typically 20-minute talks discussing new experimental and theoretical results. A series of 20-minute talks will discuss the ongoing and planned ground- and space- based experiments. The cadence of the workshop is biennial. The participation will be only by invitation. All participants are kindly invited to attend the whole workshop. However, to keep alive the workshop it was decided that all presentations should be compulsorily given to the LOC, so that they can be inserted into the web page of the workshop. These presentations will form the basis for writing the papers to be published in the proceedings of the Frascati Workshop 2017 in electronic form by the Proceedings of Science (PoS-SISSA), after a peer referee process, and they will be freely available at once in the NASA- ADS. The editor of the proceedings will be Franco Giovannelli and Lola Sabau-Graziati.

AN OBJECTIVE DEFINITION FOR THE MAIN SEQUENCE OF STAR-FORMING GALAXIES

DOE Office of Scientific and Technical Information (OSTI.GOV)

Renzini, Alvio; Peng, Ying-jie, E-mail: alvio.renzini@oapd.inaf.it, E-mail: y.peng@mrao.cam.ac.uk

The main sequence (MS) of star-forming (SF) galaxies plays a fundamental role in driving galaxy evolution and our efforts to understand it. However, different studies find significant differences in the normalization, slope, and shape of the MS. These discrepancies arise mainly from the different selection criteria adopted to isolate SF galaxies, which may include or exclude galaxies with a specific star formation rate (SFR) substantially below the MS value. To obviate this limitation of all current criteria, we propose an objective definition of the MS that does not rely at all on a pre-selection of SF galaxies. Constructing the 3Dmore » SFR–mass–number plot, the MS is then defined as the ridge line of the SF peak, as illustrated with various figures. The advantages of such a definition are manifold. If generally adopted, it will facilitate the inter-comparison of results from different groups using the same SFR and stellar mass diagnostics, or it will highlight the relative systematics of different diagnostics. All of this could help to understand MS galaxies as systems in a quasi-steady state equilibrium and would also provide a more objective criterion for identifying quenching galaxies.« less

BP Piscium: its flaring disc imaged with SPHERE/ZIMPOL★

NASA Astrophysics Data System (ADS)

de Boer, J.; Girard, J. H.; Canovas, H.; Min, M.; Sitko, M.; Ginski, C.; Jeffers, S. V.; Mawet, D.; Milli, J.; Rodenhuis, M.; Snik, F.; Keller, C. U.

2017-03-01

Whether BP Piscium (BP Psc) is either a pre-main sequence T Tauri star at d ≈ 80 pc, or a post-main sequence G giant at d ≈ 300 pc is still not clear. As a first-ascent giant, it is the first to be observed with a molecular and dust disc. Alternatively, BP Psc would be among the nearest T Tauri stars with a protoplanetary disc (PPD). We investigate whether the disc geometry resembles typical PPDs, by comparing polarimetric images with radiative transfer models. Our Very Large Telescope/Spectro-Polarimetric High-contrast Exoplanet REsearch (SPHERE)/Zurich IMaging Polarimeter (ZIMPOL) observations allow us to perform polarimetric differential imaging, reference star differential imaging, and Richardson-Lucy deconvolution. We present the first visible light polarization and intensity images of the disc of BP Psc. Our deconvolution confirms the disc shape as detected before, mainly showing the southern side of the disc. In polarized intensity the disc is imaged at larger detail and also shows the northern side, giving it the typical shape of high-inclination flared discs. We explain the observed disc features by retrieving the large-scale geometry with MCMAX radiative transfer modelling, which yields a strongly flared model, atypical for discs of T Tauri stars.

Dust in circumstellar disks

NASA Astrophysics Data System (ADS)

Rodmann, Jens

2006-02-01

This thesis presents observational and theoretical studies of the size and spatial distribution of dust particles in circumstellar disks. Using millimetre interferometric observations of optically thick disks around T Tauri stars, I provide conclusive evidence for the presence of millimetre- to centimetre-sized dust aggregates. These findings demonstrate that dust grain growth to pebble-sized dust particles is completed within less than 1 Myr in the outer disks around low-mass pre-main-sequence stars. The modelling of the infrared spectral energy distributions of several solar-type main-sequence stars and their associated circumstellar debris disks reveals the ubiquity of inner gaps devoid of substantial amounts of dust among Vega-type infrared excess sources. It is argued that the absence of circumstellar material in the inner disks is most likely the result of the gravitational influence of a large planet and/or a lack of dust-producing minor bodies in the dust-free region. Finally, I describe a numerical model to simulate the dynamical evolution of dust particles in debris disks, taking into account the gravitational perturbations by planets, photon radiation pressure, and dissipative drag forces due to the Poynting-Robertson effect and stellar wind. The validity of the code it established by several tests and comparison to semi-analytic approximations. The debris disk model is applied to simulate the main structural features of a ring of circumstellar material around the main-sequence star HD 181327. The best agreement between model and observation is achieved for dust grains a few tens of microns in size locked in the 1:1 resonance with a Jupiter-mass planet (or above) on a circular orbit.

Mutually Exclusive Splicing of the Insect Dscam Pre-mRNA Directed by Competing Intronic RNA Secondary Structures

PubMed Central

Graveley, Brenton R.

2008-01-01

Summary Drosophila Dscam encodes 38,016 distinct axon guidance receptors through the mutually exclusive alternative splicing of 95 variable exons. Importantly, known mechanisms that ensure the mutually exclusive splicing of pairs of exons cannot explain this phenomenon in Dscam. I have identified two classes of conserved elements in the Dscam exon 6 cluster, which contains 48 alternative exons—the docking site, located in the intron downstream of constitutive exon 5, and the selector sequences, which are located upstream of each exon 6 variant. Strikingly, each selector sequence is complementary to a portion of the docking site, and this pairing juxtaposes one, and only one, alternative exon to the upstream constitutive exon. The mutually exclusive nature of the docking site:selector sequence interactions suggests that the formation of these competing RNA structures is a central component of the mechanism guaranteeing that only one exon 6 variant is included in each Dscam mRNA. PMID:16213213

A surprising dynamical mass for V773 Tau B

DOE PAGES

Boden, Andrew F.; Torres, Guillermo; Duchene, Gaspard; ...

2012-02-10

Here, we report on new high-resolution imaging and spectroscopy on the multiple T Tauri star system V773 Tau over the 2003-2009 period. With these data we derive relative astrometry, photometry between the A and B components, and radial velocity (RV) of the A-subsystem components. Combining these new data with previously published astrometry and RVs, we update the relative A-B orbit model. This updated orbit model, the known system distance, and A-subsystem parameters yield a dynamical mass for the B component for the first time. Remarkably, the derived B dynamical mass is in the range 1.7-3.0 M⊙. This is much highermore » than previous estimates and suggests that like A, B is also a multiple stellar system. Among these data, spatially resolved spectroscopy provides new insight into the nature of the B component. Similar to A, these near-IR spectra indicate that the dominant source in B is of mid-K spectral type. If B is in fact a multiple star system as suggested by the dynamical mass estimate, the simplest assumption is that B is composed of similar ~1.2 M ⊙ pre-main-sequence stars in a close (<1 AU) binary system. This inference is supported by line-shape changes in near-IR spectroscopy of B, tentatively interpreted as changing RV among components in V773 Tau B. Relative photometry indicates that B is highly variable in the near-IR. The most likely explanation for this variability is circum-B material resulting in variable line-of-sight extinction. The distribution of this material must be significantly affected by both the putative B multiplicity and the A-B orbit.« less

Common environmental factors explain both ectomycorrhizal species diversity and pine regeneration variability in a post-fire Mediterranean forest.

PubMed

Buscardo, Erika; Freitas, Helena; Pereira, João Santos; De Angelis, Paolo

2011-08-01

Natural seedling regeneration and establishment after stand replacing wildfires is influenced by a series of environmental and biological constraints. In this study, we characterized the diversity and structure of the ectomycorrhizal (ECM) fungal community associated with post-fire naturally regenerated maritime pine saplings, and individuate the environmental factors responsible for fungal species distribution. We also identify the main environmental factors responsible for maritime pine regeneration variability and assessed the relation between saplings performance and ECM fungal diversity indices. Fungal species were identified by direct sequencing of internal transcribed spacer regions. Five years after the disturbance event, a total of 30 taxa colonized the pine saplings. The ECM fungal community was dominated by ruderal species of the genus Rhizopogon (present in almost half of the samples). Almost one third of the identified ECM fungal species belonged to the family Thelephoraceae. Typical k-selected species like Amanita pantherina, Boletus aestivalis, Lactarius chrysorrheus, and Russula densifolia were found on pine saplings collected in proximity of unburnt pine trees, in correspondence with low erosion extents. Pine regeneration varied throughout the study areas and was enhanced at higher elevations, in correspondence with moderate slopes, shallower soils, and a reduced cover of ericaceous shrubs and bare ground. These conditions were found in close proximity to patches of pine trees that survived the disturbance event and were previously characterized by a higher pre-fire pine biomass. Even though no correlations were found between saplings performance and ECM fungal diversity indices, common environmental factors (i.e., ericaceous shrub cover, extent of erosion, slope, and soil depth) were responsible for shaping the ECM fungal distribution and for describing most of the explained regeneration variability.

G2LC: Resources Autoscaling for Real Time Bioinformatics Applications in IaaS.

PubMed

Hu, Rongdong; Liu, Guangming; Jiang, Jingfei; Wang, Lixin

2015-01-01

Cloud computing has started to change the way how bioinformatics research is being carried out. Researchers who have taken advantage of this technology can process larger amounts of data and speed up scientific discovery. The variability in data volume results in variable computing requirements. Therefore, bioinformatics researchers are pursuing more reliable and efficient methods for conducting sequencing analyses. This paper proposes an automated resource provisioning method, G2LC, for bioinformatics applications in IaaS. It enables application to output the results in a real time manner. Its main purpose is to guarantee applications performance, while improving resource utilization. Real sequence searching data of BLAST is used to evaluate the effectiveness of G2LC. Experimental results show that G2LC guarantees the application performance, while resource is saved up to 20.14%.

G2LC: Resources Autoscaling for Real Time Bioinformatics Applications in IaaS

PubMed Central

Hu, Rongdong; Liu, Guangming; Jiang, Jingfei; Wang, Lixin

2015-01-01

Cloud computing has started to change the way how bioinformatics research is being carried out. Researchers who have taken advantage of this technology can process larger amounts of data and speed up scientific discovery. The variability in data volume results in variable computing requirements. Therefore, bioinformatics researchers are pursuing more reliable and efficient methods for conducting sequencing analyses. This paper proposes an automated resource provisioning method, G2LC, for bioinformatics applications in IaaS. It enables application to output the results in a real time manner. Its main purpose is to guarantee applications performance, while improving resource utilization. Real sequence searching data of BLAST is used to evaluate the effectiveness of G2LC. Experimental results show that G2LC guarantees the application performance, while resource is saved up to 20.14%. PMID:26504488

Complete mitochondrial genome of Xingguo red carp (Cyprinus carpio var. singuonensis) and purse red carp (Cyprinus carpio var. wuyuanensis).

PubMed

Hu, Guang-Fu; Liu, Xiang-Jiang; Li, Zhong; Liang, Hong-Wei; Hu, Shao-Na; Zou, Gui-Wei

2016-01-01

The complete mitochondrial genomes of Xingguo red carp (Cyprinus carpio var. singuonensis) and purse red carp (Cyprinus carpio var. wuyuanensis) were sequenced. Comparison of these two mitochondrial genomes revealed that the mtDNAs of these two common carp varieties were remarkably similar in genome length, gene order and content, and AT content. However, size variation between these two mitochondrial genomes presented here showed 39 site differences in overall length. About 2 site differences were located in rRNAs, 3 in tRNAs, 3 in the control region, 31 in protein-coding genes. Thirty-one variable bases in the protein-coding regions between the two varieties mitochondrial sequences led to three variable amino acids, which were mainly located in the protein ND5 and ND4.

Discovery and Characterization of Eclipsing Binary Stars and Transiting Planets in Young Benchmark Clusters: The Pleiades and Hyades

NASA Astrophysics Data System (ADS)

Stassun, Keivan; David, Trevor J.; Conroy, Kyle E.; Hillenbrand, Lynne; Stauffer, John R.; Pepper, Joshua; Rebull, Luisa M.; Cody, Ann Marie

2016-06-01

Prior to K2, only one eclipsing binary in the Pleiades was known (HD 23642). We present the discovery and characterization of three additional eclipsing binaries (EBs) in this ~120 Myr old benchmark open cluster. Unlike HD 23642, all three of the new EBs are low mass (Mtot < 1 M⊙) and thus their components are still undergoing pre-main-sequence contraction at the Pleiades age. Low mass EBs are rare, especially in the pre-main-sequence phase, and thus these systems are valuable for constraining theoretical stellar evolution models. One of the three new EBs is single-lined with a K-type primary (HII 2407). The second (HCG 76) comprises two nearly equal-mass 0.3 M⊙ stars, with masses and radii measured with precisions of better than 3% and 5%, respectively. The third (MHO 9) has an M-type primary with a secondary that is possibly quite close to the hydrogen-burning limit, but needs additional follow-up observations to better constrain its parameters. We use the precise parameters of HCG 76 to test the predictions of stellar evolution models, and to derive an independent distance to the Pleiades of 132±5 pc. Finally, we present tentative evidence for differential rotation in the primary component of the newly discovered Pleiades EB HII 2407, and we also characterize a newly discovered transiting Neptune-sized planet orbiting an M-dwarf in the Hyades.

Photometric and spectroscopic study of low mass embedded star clusters in reflection nebulae

NASA Astrophysics Data System (ADS)

Soares, J. B.; Bica, E.; Ahumada, A. V.; Clariá, J. J.

2005-02-01

An analysis of the candidate embedded stellar systems in the reflection nebulae vdBH-RN 26, vdBH-RN} 38, vdBH-RN} 53a, GGD 20, ESO 95-RN 18 and NGC 6595 is presented. Optical spectroscopic data from CASLEO (Argentina) in conjunction with near infrared photometry from the 2MASS Point Source Catalogue were employed. The analysis is based on source surface density, colour-colour and colour-magnitude diagrams together with theoretical pre-main sequence isochrones. We take into account the field population affecting the analysis by carrying out a statistical subtraction. The fundamental parameters for the stellar systems were derived. The resulting ages are in the range 1-4 Myr and the objects are dominated by pre-main sequence stars. The observed masses locked in the clusters are less than 25 M⊙. The studied systems have no stars of spectral types earlier than B, indicating that star clusters do not necessarily evolve through an HII region phase. The relatively small locked mass combined with the fact that they are not numerous in catalogues suggests that these low mass clusters are not important donors of stars to the field populations. Based on observations made at Complejo Astronómico El Leoncito, which is operated under agreement between the Consejo Nacional de Investigaciones Científicas y Técnicas de la República Argentina and the National Universities of La Plata, Córdoba and San Juan, Argentina.

X-ray Emission from Pre-Main-Sequence Stars - Testing the Solar Analogy

NASA Technical Reports Server (NTRS)

Skinner, Stephen L.

2000-01-01

This LTSA award funded my research on the origin of stellar X-ray emission and the validity of the solar-stellar analogy. This research broadly addresses the relevance of our current understanding of solar X-ray physics to the interpretation of X-ray emission from stars in general. During the past five years the emphasis has been on space-based X-ray observations of very young stars in star-forming regions (T Tauri stars and protostars), cool solar-like G stars, and evolved high-mass Wolf-Rayet (WR) stars. These observations were carried out primarily with the ASCA and ROSAT space-based observatories (and most recently with Chandra), supplemented by ground-based observations. This research has focused on the identification of physical processes that are responsible for the high levels of X-ray emission seen in pre-main-sequence (PMS) stars, active cool stars, and WR stars. A related issue is how the X-ray emission of such stars changes over time, both on short timescales of days to years and on evolutionary timescales of millions of years. In the case of the Sun it is known that magnetic fields play a key role in the production of X-rays by confining the coronal plasma in loop-like structures where it is heated to temperatures of several million K. The extent to which the magnetically-confined corona interpretation can be applied to other X-ray emitting stars is the key issue that drives the research summarized here.

Effects of disc mid-plane evolution on CO snowline location

NASA Astrophysics Data System (ADS)

Panić, O.; Min, M.

2017-05-01

Temperature changes in the planet forming disc mid-planes carry important physico-chemical consequences, such as the effect on the locations of the condensation fronts of molecules - the snowlines. Snowlines impose major chemical gradients and possibly foster grain growth. The aim of this paper is to understand how disc mid-plane temperature changes with gas and dust evolution, and identify trends that may influence planet formation or allow to constrain disc evolution observationally. We calculate disc temperature, hydrostatic equilibrium and dust settling in a mutually consistent way from a grid of disc models at different stages of gas loss, grain growth and hole opening. We find that the CO snowline location depends very strongly on disc properties. The CO snowline location migrates closer to the star for increasing degrees of gas dispersal and dust growth. Around a typical A-type star, the snowline can be anywhere between several tens and a few hundred au, depending on the disc properties such as gas mass and grain size. In fact, gas loss is as efficient as dust evolution in settling discs, and flat discs may be gas-poor counterparts of flared discs. Our results, in the context of different pre-main-sequence evolution of the luminosity in low- and intermediate-mass stars suggest very different thermal (and hence chemical) histories in these two types of discs. Discs of T Tauri stars settle and cool down, while discs of Herbig Ae stars may remain rather warm throughout the pre-main sequence.

Measuring the Mass of a Pre-Main Sequence Binary Star Through the Orbit of TWA 5A

NASA Astrophysics Data System (ADS)

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

2005-12-01

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 5.55 ± 0.07 years and a semi-major axis of 0.063 arcsec ± 0.004 arcsec. Combining these results with a kinematic distance, we calculate a total mass of 0.70 ± 0.24 M⊙ for this system. This mass measurement, as well as the estimated age of this system, are in best agreement with the model predictions of Baraffe et al. (1998), but are also consistent to within 1.6σ of all other models considered. Our formal significance is low due to our proper accounting of correlated uncertainties; these correlations are important and generally not accounted for in comparisons of this kind. Nonetheless, with only a few more years of observation, these models will be easily distinguished. Support for this work was provided by the NASA Astrobiology Institute, the NSF Science & Technology Center for AO, managed by UCSC (AST-9876783), and the Packard Foundation.

Assembling in Sequence: A Saleable Work Skill. Occupation Simulation Packet. Grades 3rd-4th.

ERIC Educational Resources Information Center

Hueston, Jean

This teacher's guide for grades 3 and 4 contains simulated work experiences for students using the isolated skill concept - assembling in sequence. Teacher instructions include objectives, evaluation, and sequence of activities. The guide contains pre-tests and post-tests with instructions and answer keys. Three pre-skill activities are suggested,…

Inter-track interference mitigation with two-dimensional variable equalizer for bit patterned media recording

NASA Astrophysics Data System (ADS)

Wang, Yao; Vijaya Kumar, B. V. K.

2017-05-01

The increased track density in bit patterned media recording (BPMR) causes increased inter-track interference (ITI), which degrades the bit error rate (BER) performance. In order to mitigate the effect of the ITI, signals from multiple tracks can be equalized by a 2D equalizer with 1D target. Usually, the 2D fixed equalizer coefficients are obtained by using a pseudo-random bit sequence (PRBS) for training. In this study, a 2D variable equalizer is proposed, where various sets of 2D equalizer coefficients are predetermined and stored for different ITI patterns besides the usual PRBS training. For data detection, as the ITI patterns are unknown in the first global iteration, the main and adjacent tracks are equalized with the conventional 2D fixed equalizer, detected with Bahl-Cocke-Jelinek-Raviv (BCJR) detector and decoded with low-density parity-check (LDPC) decoder. Then using the estimated bit information from main and adjacent tracks, the ITI pattern for each island of the main track can be estimated and the corresponding 2D variable equalizers are used to better equalize the bits on the main track. This process is executed iteratively by feeding back the main track information. Simulation results indicate that for both single-track and two-track detection, the proposed 2D variable equalizer can achieve better BER and frame error rate (FER) compared to that with the 2D fixed equalizer.

Rotational evolution of slow-rotator sequence stars

NASA Astrophysics Data System (ADS)

Lanzafame, A. C.; Spada, F.

2015-12-01

Context. The observed relationship between mass, age and rotation in open clusters shows the progressive development of a slow-rotator sequence among stars possessing a radiative interior and a convective envelope during their pre-main sequence and main-sequence evolution. After 0.6 Gyr, most cluster members of this type have settled on this sequence. Aims: The observed clustering on this sequence suggests that it corresponds to some equilibrium or asymptotic condition that still lacks a complete theoretical interpretation, and which is crucial to our understanding of the stellar angular momentum evolution. Methods: We couple a rotational evolution model, which takes internal differential rotation into account, with classical and new proposals for the wind braking law, and fit models to the data using a Monte Carlo Markov chain (MCMC) method tailored to the problem at hand. We explore to what extent these models are able to reproduce the mass and time dependence of the stellar rotational evolution on the slow-rotator sequence. Results: The description of the evolution of the slow-rotator sequence requires taking the transfer of angular momentum from the radiative core to the convective envelope into account. We find that, in the mass range 0.85-1.10 M⊙, the core-envelope coupling timescale for stars in the slow-rotator sequence scales as M-7.28. Quasi-solid body rotation is achieved only after 1-2 Gyr, depending on stellar mass, which implies that observing small deviations from the Skumanich law (P ∝ √{t}) would require period data of older open clusters than is available to date. The observed evolution in the 0.1-2.5 Gyr age range and in the 0.85-1.10 M⊙ mass range is best reproduced by assuming an empirical mass dependence of the wind angular momentum loss proportional to the convective turnover timescale and to the stellar moment of inertia. Period isochrones based on our MCMC fit provide a tool for inferring stellar ages of solar-like main-sequence stars from their mass and rotation period that is largely independent of the wind braking model adopted. These effectively represent gyro-chronology relationships that take the physics of the two-zone model for the stellar angular momentum evolution into account.

A Photometric Search for Planets in the Open Cluster NGC 7086

NASA Astrophysics Data System (ADS)

Rosvick, Joanne M.; Robb, Russell

2006-12-01

In an attempt to discover short-period, Jupiter-mass planets orbiting solar-type stars in open clusters, we searched for planetary transits in the populous and relatively unstudied open cluster NGC 7086. A color-magnitude diagram constructed from new B and V photometry is presented, along with revised estimates of the cluster's color excess, distance modulus, and age. Several turnoff stars were observed spectroscopically in order to determine a color excess of E(B-V)=0.83+/-0.02. Empirically fitting the main sequences of two young open clusters and the semiempirical zero-age main sequence of Vandenberg and Poll yielded a distance modulus of (V-MV)=13.4+/-0.3 mag. This corresponds to a true distance modulus of (m-M)0=10.8 mag or a distance of 1.5 kpc to NGC 7086. These values were used with isochrones from the Padova group to obtain a cluster age of 100 Myr. Eleven nights of R-band photometry were used to search for planetary transits. Differential magnitudes were constructed for each star in the cluster. Light curves for each star were produced on a night-to-night basis and inspected for variability. No planetary transits were apparent; however, some interesting variable stars were discovered: a pulsating variable that appears to be a member of the γ Dor class and four possible eclipsing binary stars, one of which actually may be a multiple system.

An Experience Sampling Study of Physical Activity and Positive Affect: Investigating the Role of Situational Motivation and Perceived Intensity Across Time.

PubMed

Guérin, Eva; Fortier, Michelle S; Sweet, Shane N

2013-04-18

The nature of the association between physical activity and positive affect is complex, prompting experts to recommend continued examination of moderating variables. The main purpose of this 2-week field study was to examine the influence of situational motivational regulations from self-determination theory (SDT) on changes in positive affect from pre- to post- to 3-hours post-physical activity. Another purpose was to clarify the relationship between physical activity intensity [i.e., Ratings of Perceived Exertion (RPE)] and positive affect at the stated time points. This study employed an experience sampling design using electronic questionnaires. Sixty-six healthy and active, multiple-role women provided recurrent assessments of their physical activity, situational motivation, and positive affect in their everyday lives over a 14-day period. Specifically, measures were obtained at the three time points of interest (i.e., pre-, post-, 3-hours post-physical activity). The data were analyzed using multilevel modeling. Results showed that intrinsic motivation was related to post-physical activity positive affect while the influence of identified regulation appeared 3-hours post-physical activity. In addition, RPE, which was significantly predicted by levels of introjection, was more strongly associated with an increase in positive affect post-physical activity than three hours later. The theoretical implications of these findings vis-à vis SDT, namely in regards to a viable motivational sequence predicting the influence of physical activity on affective states, are discussed. The findings regarding the differential influences of RPE and motivational regulations carries applications for facilitating women's well-being.

Genomic V exons from whole genome shotgun data in reptiles.

PubMed

Olivieri, D N; von Haeften, B; Sánchez-Espinel, C; Faro, J; Gambón-Deza, F

2014-08-01

Reptiles and mammals diverged over 300 million years ago, creating two parallel evolutionary lineages amongst terrestrial vertebrates. In reptiles, two main evolutionary lines emerged: one gave rise to Squamata, while the other gave rise to Testudines, Crocodylia, and Aves. In this study, we determined the genomic variable (V) exons from whole genome shotgun sequencing (WGS) data in reptiles corresponding to the three main immunoglobulin (IG) loci and the four main T cell receptor (TR) loci. We show that Squamata lack the TRG and TRD genes, and snakes lack the IGKV genes. In representative species of Testudines and Crocodylia, the seven major IG and TR loci are maintained. As in mammals, genes of the IG loci can be grouped into well-defined IMGT clans through a multi-species phylogenetic analysis. We show that the reptilian IGHV and IGLV genes are distributed amongst the established mammalian clans, while their IGKV genes are found within a single clan, nearly exclusive from the mammalian sequences. The reptilian and mammalian TRAV genes cluster into six common evolutionary clades (since IMGT clans have not been defined for TR). In contrast, the reptilian TRBV genes cluster into three clades, which have few mammalian members. In this locus, the V exon sequences from mammals appear to have undergone different evolutionary diversification processes that occurred outside these shared reptilian clans. These sequences can be obtained in a freely available public repository (http://vgenerepertoire.org).

Rolling circle amplification-based analysis of Sri Lankan cassava mosaic virus isolates from Tamil Nadu, India, suggests a low level of genetic variability.

PubMed

Kushawaha, Akhilesh Kumar; Rabindran, Ramalingam; Dasgupta, Indranil

2018-03-01

Cassava mosaic disease is a widespread disease of cassava in south Asia and the African continent. In India, CMD is known to be caused by two single-stranded DNA viruses (geminiviruses), Indian cassava mosaic virus (ICMV) and Sri Lankan cassava mosdaic virus (SLCMV). Previously, the diversity of ICMV and SLCMV in India has been studied using PCR, a sequence-dependent method. To have a more in-depth study of the variability of the above viruses and to detect any novel geminiviruses associated with CMD, sequence-independent amplification using rolling circle amplification (RCA)-based methods were used. CMD affected cassava plants were sampled across eighty locations in nine districts of the southern Indian state of Tamil Nadu. Twelve complete sequence of coat protein genes of the resident geminiviruses, comprising 256 amino acid residues were generated from the above samples, which indicated changes at only six positions. RCA followed by RFLP of the 80 samples indicated that most samples (47) contained only SLCMV, followed by 8, which were infected jointly with ICMV and SLCMV. In 11 samples, the pattern did not match the expected patterns from either of the two viruses and hence, were variants. Sequence analysis of an average of 700 nucleotides from 31 RCA-generated fragments of the variants indicated identities of 97-99% with the sequence of a previously reported infectious clone of SLCMV. The evidence suggests low levels of genetic variability in the begomoviruses infecting cassava, mainly in the form of scattered single nucleotide changes.

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

NASA Astrophysics Data System (ADS)

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 University of California, and the National Aeronautics and Space Administration. The Observatory was made possible by the generous financial support of the W. M. Keck Foundation.

An Avian Basal Ganglia-Forebrain Circuit Contributes Differentially to Syllable Versus Sequence Variability of Adult Bengalese Finch Song

PubMed Central

Hampton, Cara M.; Sakata, Jon T.; Brainard, Michael S.

2009-01-01

Behavioral variability is important for motor skill learning but continues to be present and actively regulated even in well-learned behaviors. In adult songbirds, two types of song variability can persist and are modulated by social context: variability in syllable structure and variability in syllable sequencing. The degree to which the control of both types of adult variability is shared or distinct remains unknown. The output of a basal ganglia-forebrain circuit, LMAN (the lateral magnocellular nucleus of the anterior nidopallium), has been implicated in song variability. For example, in adult zebra finches, neurons in LMAN actively control the variability of syllable structure. It is unclear, however, whether LMAN contributes to variability in adult syllable sequencing because sequence variability in adult zebra finch song is minimal. In contrast, Bengalese finches retain variability in both syllable structure and syllable sequencing into adulthood. We analyzed the effects of LMAN lesions on the variability of syllable structure and sequencing and on the social modulation of these forms of variability in adult Bengalese finches. We found that lesions of LMAN significantly reduced the variability of syllable structure but not of syllable sequencing. We also found that LMAN lesions eliminated the social modulation of the variability of syllable structure but did not detect significant effects on the modulation of sequence variability. These results show that LMAN contributes differentially to syllable versus sequence variability of adult song and suggest that these forms of variability are regulated by distinct neural pathways. PMID:19357331

Analysis of the complete genome of the first Irkut virus isolate from China: comparison across the Lyssavirus genus.

PubMed

Liu, Ye; Li, Nan; Zhang, Shoufeng; Zhang, Fei; Lian, Hai; Wang, Ying; Zhang, Jinxia; Hu, Rongliang

2013-12-01

The genome of Irkut virus, isolate IRKV-THChina12, the first non-rabies lyssavirus from China (of bat origin), has been completely sequenced. In general, coding and non-coding regions of this viral genome are similar to those of other lyssaviruses. However, alignment of the deduced amino acid sequences of the structural proteins of IRKV-THChina12 with those of other lyssavirus representatives revealed significant variability between viral species. The nucleoprotein and matrix protein were found to be the most conserved, followed by the large protein, glycoprotein and phosphoprotein. Differences in the antigenic sites in glycoprotein may result in only partial protection of the available rabies biologics against Irkut virus, which is of particular concern for pre- and post-exposure rabies prophylaxis. Copyright © 2013 Elsevier Inc. All rights reserved.

CAN WE PREDICT THE GLOBAL MAGNETIC TOPOLOGY OF A PRE-MAIN-SEQUENCE STAR FROM ITS POSITION IN THE HERTZSPRUNG-RUSSELL DIAGRAM?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gregory, S. G.; Hillenbrand, L. A.; Donati, J.-F.

2012-08-20

Zeeman-Doppler imaging 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 (H-R) 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 arguemore » that the general characteristics of the global magnetic field of a PMS star can be determined from its position in the H-R diagram. Moving from hotter and more luminous to cooler and less luminous stars across the PMS of the H-R diagram, we present evidence for four distinct magnetic topology regimes. Stars with large radiative cores, empirically estimated to be those with a core mass in excess of {approx}40% of the stellar mass, host highly complex and dominantly non-axisymmetric magnetic fields, while those with smaller radiative cores host axisymmetric fields with field modes of higher order than the dipole dominant (typically, but not always, the octupole). Fully convective stars above {approx}> 0.5 M{sub Sun} appear to host dominantly axisymmetric fields with strong (kilo-Gauss) dipole components. Based on similarities between the magnetic properties of PMS stars and main-sequence M-dwarfs with similar internal structures, we speculate that a bistable dynamo process operates for lower mass stars ({approx}< 0.5 M{sub Sun} at an age of a few Myr) and that they will be found to host a variety of magnetic field topologies. If the magnetic topology trends across the H-R diagram are confirmed, they may provide a new method of constraining PMS stellar evolution models.« less

Evidence of the evolved nature of the B[e] star MWC 137

DOE Office of Scientific and Technical Information (OSTI.GOV)

Muratore, M. F.; Arias, M. L.; Cidale, L.

2015-01-01

The evolutionary phase of B[e] stars is difficult to establish due to the uncertainties in their fundamental parameters. For instance, possible classifications for the Galactic B[e] star MWC 137 include pre-main-sequence and post-main-sequence phases, with a large range in luminosity. Our goal is to clarify the evolutionary stage of this peculiar object, and to study the CO molecular component of its circumstellar medium. To this purpose, we modeled the CO molecular bands using high-resolution K-band spectra. We find that MWC 137 is surrounded by a detached cool (T=1900±100 K) and dense (N=(3±1)×10{sup 21} cm{sup −2}) ring of CO gas orbitingmore » the star with a rotational velocity, projected to the line of sight, of 84 ± 2 km s{sup −1}. We also find that the molecular gas is enriched in the isotope {sup 13}C, excluding the classification of the star as a Herbig Be. The observed isotopic abundance ratio ({sup 12}C/{sup 13}C = 25 ± 2) derived from our modeling is compatible with a proto-planetary nebula, main-sequence, or supergiant evolutionary phase. However, based on some observable characteristics of MWC 137, we propose that the supergiant scenario seems to be the most plausible. Hence, we suggest that MWC 137 could be in an extremely short-lived phase, evolving from a B[e] supergiant to a blue supergiant with a bipolar ring nebula.« less

[Methods, challenges and opportunities for big data analyses of microbiome].

PubMed

Sheng, Hua-Fang; Zhou, Hong-Wei

2015-07-01

Microbiome is a novel research field related with a variety of chronic inflamatory diseases. Technically, there are two major approaches to analysis of microbiome: metataxonome by sequencing the 16S rRNA variable tags, and metagenome by shot-gun sequencing of the total microbial (mainly bacterial) genome mixture. The 16S rRNA sequencing analyses pipeline includes sequence quality control, diversity analyses, taxonomy and statistics; metagenome analyses further includes gene annotation and functional analyses. With the development of the sequencing techniques, the cost of sequencing will decrease, and big data analyses will become the central task. Data standardization, accumulation, modeling and disease prediction are crucial for future exploit of these data. Meanwhile, the information property in these data, and the functional verification with culture-dependent and culture-independent experiments remain the focus in future research. Studies of human microbiome will bring a better understanding of the relations between the human body and the microbiome, especially in the context of disease diagnosis and therapy, which promise rich research opportunities.

Direct deposition of silver nanoplates on quartz surface by sequence pre-treatment hydroxylation and silanisation.

PubMed

Abu Bakar, Norhayati; Mat Salleh, Muhamad; Ali Umar, Akrajas; Shapter, Joseph George

2017-01-01

Silver nanoparticles deposited on quartz substrates are widely used as SERS substrates. The nanoparticles can be deposited directly from colloidal solution by dipping technique. However, the adhesion of the particles on the quartz surface is very poor. Normally the substrate is pre-treated with hydroxylation or silanisation process. In this paper, we have demonstrated that the application of the sequence pre-treatment hydroxylation and silanisation have improved the density of silver nanoplates desposited on the quartz surface. •Sequence hydroxylation and silanisation pre-treatment assists the deposition of the nanoplate on the surface.•Various immersion times of the quartz surface into the colloidal nanoplates determined size distributions and density surface of the nanoplates on the surface.

Discovery and characterization of 3000+ main-sequence binaries from APOGEE spectra

NASA Astrophysics Data System (ADS)

El-Badry, Kareem; Ting, Yuan-Sen; Rix, Hans-Walter; Quataert, Eliot; Weisz, Daniel R.; Cargile, Phillip; Conroy, Charlie; Hogg, David W.; Bergemann, Maria; Liu, Chao

2018-05-01

We develop a data-driven spectral model for identifying and characterizing spatially unresolved multiple-star systems and apply it to APOGEE DR13 spectra of main-sequence stars. Binaries and triples are identified as targets whose spectra can be significantly better fit by a superposition of two or three model spectra, drawn from the same isochrone, than any single-star model. From an initial sample of ˜20 000 main-sequence targets, we identify ˜2500 binaries in which both the primary and secondary stars contribute detectably to the spectrum, simultaneously fitting for the velocities and stellar parameters of both components. We additionally identify and fit ˜200 triple systems, as well as ˜700 velocity-variable systems in which the secondary does not contribute detectably to the spectrum. Our model simplifies the process of simultaneously fitting single- or multi-epoch spectra with composite models and does not depend on a velocity offset between the two components of a binary, making it sensitive to traditionally undetectable systems with periods of hundreds or thousands of years. In agreement with conventional expectations, almost all the spectrally identified binaries with measured parallaxes fall above the main sequence in the colour-magnitude diagram. We find excellent agreement between spectrally and dynamically inferred mass ratios for the ˜600 binaries in which a dynamical mass ratio can be measured from multi-epoch radial velocities. We obtain full orbital solutions for 64 systems, including 14 close binaries within hierarchical triples. We make available catalogues of stellar parameters, abundances, mass ratios, and orbital parameters.

Analysis of Post-Fire Vegetation Recovery in the Mediterranean Basin using MODIS Derived Vegetation Indices

NASA Astrophysics Data System (ADS)

Hawtree, Daniel; San Miguel, Jesus; Sedano, Fernando; Kempeneers, Pieter

2010-05-01

The Mediterranean basin region is highly susceptible to wildfire, with approximately 60,000 individual fires and half a million ha of natural vegetation burnt per year. Of particular concern in this region is the impact of repeated wildfires on the ability of natural lands to return to a pre-fire state, and of the possibility of desertification of semi-arid areas. Given these concerns, understanding the temporal patterns of vegetation recovery is important for the management of environmental resources in the region. A valuable tool for evaluating these recovery patterns are vegetation indices derived from remote sensing data. Previous research on post-fire vegetation recovery conducted in this region has found significant variability in recovery times across different study sites. It is unclear what the primary variables are affecting the differences in the rates of recovery, and if any geographic patterns of behavior exist across the Mediterranean basin. This research has primarily been conducted using indices derived from Landsat imagery. However, no extensive analysis of vegetation regeneration for large regions has been published, and assessment of vegetation recovery on the basis of medium-spatial resolution imagery such as that of MODIS has not yet been analyzed. This study examines the temporal pattern of vegetation recovery in a number of fire sites in the Mediterranean basin, using data derived from MODIS 16 -day composite vegetation indices. The intent is to develop a more complete picture of the temporal sequence of vegetation recovery, and to evaluate what additional factors impact variations in the recovery sequence. In addition, this study evaluates the utility of using MODIS derived vegetation indices for regeneration studies, and compares the findings to earlier studies which rely on Landsat data. Wildfires occurring between the years 2000 and 2004 were considered as potential study sites for this research. Using the EFFIS dataset, all wildfires covering an area of at least 1,000 ha were identified. The land-cover / land-use of these large fires sites were then evaluated using the CORINE land-cover data set, and the sites dominated primarily by natural vegetation were identified. Once these candidate sites were identified, a subset was selected across a range of locations and site characteristics for post-fire recovery analysis. To evaluate the post-fire recovery sequence in these locations, time-series of NDVI, EVI, and LAI were derived using 250 meter resolution MODIS data (MOD13Q). The vegetation index values were then compared to pre-fire values to determine recovery relative to the pre-fire vegetative state. The variability in rates of recovery are then considered with respect to moisture availability, vegetation type, and local site conditions to evaluate if any patterns of recovery can be determined.

Dynamical masses of pms stars in the taurus star formation region

NASA Astrophysics Data System (ADS)

Simon, M.

2013-02-01

Our preliminary orbital parameters for DF Tau, T Tau Sa-Sb, ZZ Tau and the Pleaides binary are presented in the paper Orbital Motion in Pre-Main Sequence Binaries by G.H. Schaefer, L. Prato, M. Simon, & J. Patience (2013, in prep. for AJ). In the few pages available here I present an overview of our motivation for this work and of our results. The slides and complete references for my talk at the Leuven conference are available at http://www.astro.sunysb.edu/msimon/public.

Studies of Circumstellar Disk Evolution

NASA Technical Reports Server (NTRS)

Hartmann, Lee W.

2005-01-01

The aim of this project is to develop a comprehensive global picture of the physical conditions in, and evolutionary timescales of, pre-main sequence accretion disks. The results of this work will help constrain the initial conditions for planet formation. To this end we are developing much larger samples of 3-10 Myr-old stars to provide better empirical constraints on protoplanetary disk evolution; measuring disk accretion rates in these systems; and constructing detailed model disk structures consistent with observations to infer physical conditions such as grain growth in protoplanetary disks.

Variable energy constant current accelerator structure

DOEpatents

Anderson, O.A.

1988-07-13

A variable energy, constant current ion beam accelerator structure is disclosed comprising an ion source capable of providing the desired ions, a pre-accelerator for establishing an initial energy level, a matching/pumping module having means for focusing means for maintaining the beam current, and at least one main accelerator module for continuing beam focus, with means capable of variably imparting acceleration to the beam so that a constant beam output current is maintained independent of the variable output energy. In a preferred embodiment, quadrupole electrodes are provided in both the matching/pumping module and the one or more accelerator modules, and are formed using four opposing cylinder electrodes which extend parallel to the beam axis and are spaced around the beam at 90/degree/ intervals with opposing electrodes maintained at the same potential. 12 figs., 3 tabs.

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

NASA Astrophysics Data System (ADS)

Rodríguez-Ledesma, M. V.; Mundt, R.; Ibrahimov, M.; Messina, S.; Parihar, P.; Hessman, F. V.; Alves de Oliveira, C.; Herbst, W.

2012-08-01

Aims: We have investigated the nature of the variability of CHS 7797, an unusual periodic variable in the Orion Nebula Cluster. Methods: An extensive I-band photometric data set of CHS 7797 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 CHS 7797 were performed in the I,J,Ks & IRAC 3.6 and 4.5 μm bands over a time interval of ≈40 d. Results: CHS 7797 shows an unusual large-amplitude variation of ≈1.7 mag in the R,I, and z' bands with a period 17.786 ± 0.03 d (FAP = 1 × 10-15%). 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 the seven different observing seasons shows minor changes and small-amplitude variations. Interestingly, there are no significant colour-flux correlations for λ ≲ 2 μm, while the object becomes redder when fainter at longer wavelengths. CHS 7797 has a spectral type of M 6 and an estimated mass between 0.04-0.1 M⊙. Conclusions: The analysis of the data suggests that the periodic variability of CHS 7797 is most probably caused by an orbital motion. Variability as a result of rotational brightness modulation by a hot spot is excluded by the lack of any colour-brightness correlation in the optical. The latter indicates that CHS 7797 is most probably occulted by circumstellar matter in which grains have grown from typical 0.1 μm to ≈1-2 μm sizes. We discuss two possible scenarios in which CHS 7797 is periodically eclipsed by structures in a disc, namely that CHS 7797 is a single object with a circumstellar disc, or that CHS 7797 is a binary system, similar to KH 15D, in which an inclined circumbinary disc is responsible of the variability. Possible reasons for the typical 0.3 mag variations in I-band at a given phase are discussed.

Stellar Evolution with Rotation: Mixing Processes in AGB Stars

NASA Astrophysics Data System (ADS)

Driebe, T.; Blöcker, T.

We included diffusive angular momentum transport and rotationally induced mixing processes in our stellar evolution code and studied the influence of rotation on the evolution of intermediate mass stars (M*=2dots6 Msolar) towards and along the asymptotic giant branch (AGB). The calculations start in the fully convective pre-main sequence phase and the initial angular momentu m was adjusted such that on the zero-age main sequence vrot=200 km/ s is achieved. The diffusion coefficients for the five rotational instabilities considered (dynamical shear, secular shear, Eddington-Sweet (ES) circulation, Solberg-Høiland-instability and Goldreich-Schubert-Fricke (GSF) instability) were adopted from Heger et al. (2000, ApJ 528, 368). Mixing efficiency and sensitivity of these processes against molecular weight gradients have been determined by calibration of the main sequence width. In this study we focus on the abundance evolution of carbon. On the one hand, the surface abundance ratios of 12C/13C a nd 12C/16O at the base of the AGB were found to be ≈ 7dots 10 and ≈ 0.1, resp., being a factor of two lower than in non-rotating models. This results from the slow but continuously operating rotationally induced mixing due to the ES-circulation and the GSF-instability during the long main sequence phase. On the other hand, 13C serves as neutron source for interior s-process nucleosynthesis in AGB stars vi a 13C(α,n)16O. Herwig et al. (1997, A&A 324, L81) found that a 13C pocket is forme d in the intershell region of 3 Msolar AGB star if diffusive overshoot is considered. Our calculations show, that mixing processes due to rotation open an alternative channel for the formation of a 13C pocket as found by Langer et al. (1999, A&A 346, L37). Again, ES-circulation and GSF-instability are the predominant rotational mixing processes.

Yucatan Subsurface Stratigraphy from Geophysical Data, Well Logs and Core Analyses in the Chicxulub Impact Crater and Implications for Target Heterogeneities

NASA Astrophysics Data System (ADS)

Canales, I.; Fucugauchi, J. U.; Perez-Cruz, L. L.; Camargo, A. Z.; Perez-Cruz, G.

2011-12-01

Asymmetries in the geophysical signature of Chicxulub crater are being evaluated to investigate on effects of impact angle and trajectory and pre-existing target structural controls for final crater form. Early studies interpreted asymmetries in the gravity anomaly in the offshore sector to propose oblique either northwest- and northeast-directed trajectories. An oblique impact was correlated to the global ejecta distribution and enhanced environmental disturbance. In contrast, recent studies using marine seismic data and computer modeling have shown that crater asymmetries correlate with pre-existing undulations of the Cretaceous continental shelf, suggesting a structural control of target heterogeneities. Documentation of Yucatan subsurface stratigraphy has been limited by lack of outcrops of pre-Paleogene rocks. The extensive cover of platform carbonate rocks has not been affected by faulting or deformation and with no rivers cutting the carbonates, information comes mainly from the drilling programs and geophysical surveys. Here we revisit the subsurface stratigraphy in the crater area from the well log data and cores retrieved in the drilling projects and marine seismic reflection profiles. Other source of information being exploited comes from the impact breccias, which contain a sampling of disrupted target sequences, including crystalline basement and Mesozoic sediments. We analyze gravity and seismic data from the various exploration surveys, including multiple Pemex profiles in the platform and the Chicxulub experiments. Analyses of well log data and seismic profiles identify contacts for Lower Cretaceous, Cretaceous/Jurassic and K/Pg boundaries. Results show that the Cretaceous continental shelf was shallower on the south and southwest than on the east, with emerged areas in Quintana Roo and Belize. Mesozoic and upper Paleozoic sediments show variable thickness, possibly reflecting the crystalline basement regional structure. Paleozoic and Precambrian basement outcrops are located farther to the southeast in Belize and northern Guatemala. Inferred shelf paleo-bathymetry supports existence of a sedimentary basin extending to the northeast, where crater rim and terrace zones are subdued in the seismic images.

Origin and distribution of Sporothrix globosa causing sapronoses in Asia.

PubMed

Moussa, Tarek A A; Kadasa, Naif M S; Al Zahrani, Hassan S; Ahmed, Sarah Abdallah; Feng, Peiying; Gerrits van den Ende, Albertus H G; Zhang, Yu; Kano, Rui; Li, Fuqiu; Li, Shanshan; Song, Yang; Dong, Bilin; Rossato, Luana; Dolatabadi, Somayeh; Hoog, Sybren de

2017-05-01

The aim of the study was to evaluate the main sources and epidemiological patterns and speculate on the evolutionary origin of Sporothrix globosa in Asia. Case and case series literature on sporotrichosis in Asia from January 2007 onwards were reviewed using meta-analysis. Phylogenetic analysis of relevant S. globosa was carried out on the basis of concatenated sequences of ITS, TEF3 and CAL. A haplotype network of CAL sequences of 281 Sporothrix isolates was analysed to determine the population structure of S. globosa. Nearly all cases of sporotrichosis caused by S. globosa in Asia were human. In contrast to the remaining pathogenic Sporothrix species, feline transmission was exceptional; nearly all regional cat-associated cases were caused by Sporothrix schenckii. While the latter species was highly variable and showed recombination, S. globosa seemed to be a clonal offshoot, as was Sporothrix brasiliensis. The origin of the segregants was located in an area of high variability in S. schenckii with a relatively high frequency of Asian strains. In Asia, S. globosa was the prevalent species. The low diversity of S. globosa suggested a recent divergence with a founder effect of low variability from the variable ancestral species, S. schenckii.

Effect of Sequencing Strength and Endurance Training in Young Male Soccer Players.

PubMed

Makhlouf, Issam; Castagna, Carlo; Manzi, Vincenzo; Laurencelle, Louis; Behm, David G; Chaouachi, Anis

2016-03-01

This study examined the effects of strength and endurance training sequence (strength before or after endurance) on relevant fitness variables in youth soccer players. Fifty-seven young elite-level male field soccer players (13.7 ± 0.5 years; 164 ± 8.3 cm; 53.5 ± 8.6 kg; body fat; 15.6 ± 3.9%) were randomly assigned to a control (n = 14, CG) and 3 experimental training groups (twice a week for 12 weeks) strength before (SE, n = 15), after (ES, n = 14) or on alternate days (ASE, n = 14) with endurance training. A significant (p = 0.001) intervention main effect was detected. There were only trivial training sequence differences (ES vs. SE) for all variables (p > 0.05). The CG showed large squat 1 repetition maximum (1RM) and medium sprint, change of direction ability, and jump improvements. ASE demonstrated a trivial difference in endurance performance with ES and SE (p > 0.05). Large to medium greater improvements for SE and ES were reported compared with ASE for sprinting over 10 and 30 m (p < 0.02). The SE squat 1RM was higher than in ASE (moderate, p < 0.02). Postintervention differences between ES and SE with CG fitness variables were small to medium (p ≤ 0.05) except for a large SE advantage with the Yo-Yo intermittent recovery test (p < 0.001, large). This study showed no effect of intrasession training sequence on soccer fitness-relevant variables. However, combining strength and endurance within a single training session provided superior results vs. training on alternate days. Concurrent training may be considered as an effective and safe training method for the development of the prospective soccer player.

MicroRNA categorization using sequence motifs and k-mers.

PubMed

Yousef, Malik; Khalifa, Waleed; Acar, İlhan Erkin; Allmer, Jens

2017-03-14

Post-transcriptional gene dysregulation can be a hallmark of diseases like cancer and microRNAs (miRNAs) play a key role in the modulation of translation efficiency. Known pre-miRNAs are listed in miRBase, and they have been discovered in a variety of organisms ranging from viruses and microbes to eukaryotic organisms. The computational detection of pre-miRNAs is of great interest, and such approaches usually employ machine learning to discriminate between miRNAs and other sequences. Many features have been proposed describing pre-miRNAs, and we have previously introduced the use of sequence motifs and k-mers as useful ones. There have been reports of xeno-miRNAs detected via next generation sequencing. However, they may be contaminations and to aid that important decision-making process, we aimed to establish a means to differentiate pre-miRNAs from different species. To achieve distinction into species, we used one species' pre-miRNAs as the positive and another species' pre-miRNAs as the negative training and test data for the establishment of machine learned models based on sequence motifs and k-mers as features. This approach resulted in higher accuracy values between distantly related species while species with closer relation produced lower accuracy values. We were able to differentiate among species with increasing success when the evolutionary distance increases. This conclusion is supported by previous reports of fast evolutionary changes in miRNAs since even in relatively closely related species a fairly good discrimination was possible.

Einstein X-ray survey of the Pleiades - The dependence of X-ray emission on stellar age

NASA Technical Reports Server (NTRS)

Micela, G.; Sciortino, S.; Serio, S.; Vaiana, G. S.; Bookbinder, J.; Golub, L.; Harnden, F. R., Jr.; Rosner, R.

1985-01-01

The data obtained with two pointed observations of 1 deg by 1 deg fields of the Pleiades region have been analyzed, and the results are presented. The maximum-likelihood X-ray luminosity functions for the Pleiades G and K stars in the cluster are derived, and it is shown that, for the G stars, the Pleiades X-ray luminosity function is significantly brighter than the corresponding function for Hyades G dwarf stars. This finding indicates a dependence of X-ray luminosity on stellar age, which is confirmed by comparison of the same data with median X-ray luminosities of pre-main sequence and local disk population dwarf G stars. It is suggested that the significantly larger number of bright X-ray sources associated with G stars than with K stars, the lack of detection of M stars, and the relatively rapid rotation of the Pleiades K stars can be explained in terms of the onset of internal differential rotation near the convective envelope-radidative core interface after the spin-up phase during evolution to the main sequence.

Dynamical Asteroseismology: towards improving the theories of stellar structure and (tidal) evolution

NASA Astrophysics Data System (ADS)

Tkachenko, Andrew

2017-10-01

The potential of the dynamical asteroseismology, the research area that builds upon the synergies between the asteroseismology and binary stars research fields, is discussed in this manuscript. We touch upon the following topics: i) the mass discrepancy observed in intermediate-to high-mass main-sequence and evolved binaries as well as in the low mass systems that are still in the pre-main sequence phase of their evolution; ii) the rotationally induced mixing in high-mass stars, in particular how the most recent theoretical predictions and spectroscopic findings compare to the results of asteroseismic investigations; iii) internal gravity waves and their potential role in the evolution of binary star systems and surface nitrogen enrichment in high-mass stars; iv) the tidal evolution theory, in particular how its predictions of spin-orbit synchronisation and orbital circularisation compare to the present-day high-quality observations; v) the tidally-induced pulsations and their role in the angular momentum transport within binary star systems; vi) the scaling relations between fundamental and seismic properties of stars across the entire HR-diagram.

Evolution Models of Helium White Dwarf–Main-sequence Star Merger Remnants

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Xianfei; Bi, Shaolan; Hall, Philip D.

It is predicted that orbital decay by gravitational-wave radiation and tidal interaction will cause some close binary stars to merge within a Hubble time. The merger of a helium-core white dwarf with a main-sequence (MS) star can produce a red giant branch star that has a low-mass hydrogen envelope when helium is ignited and thus become a hot subdwarf. Because detailed calculations have not been made, we compute post-merger models with a stellar evolution code. We find the evolutionary paths available to merger remnants and find the pre-merger conditions that lead to the formation of hot subdwarfs. We find thatmore » some such mergers result in the formation of stars with intermediate helium-rich surfaces. These stars later develop helium-poor surfaces owing to diffusion. Combining our results with a model population and comparing to observed stars, we find that some observed intermediate helium-rich hot subdwarfs can be explained as the remnants of the mergers of helium-core white dwarfs with low-mass MS stars.« less

Heart rate variability: Pre-deployment predictor of post-deployment PTSD symptoms

PubMed Central

Pyne, Jeffrey M.; Constans, Joseph I.; Wiederhold, Mark D.; Gibson, Douglas P.; Kimbrell, Timothy; Kramer, Teresa L.; Pitcock, Jeffery A.; Han, Xiaotong; Williams, D. Keith; Chartrand, Don; Gevirtz, Richard N.; Spira, James; Wiederhold, Brenda K.; McCraty, Rollin; McCune, Thomas R.

2017-01-01

Heart rate variability is a physiological measure associated with autonomic nervous system activity. This study hypothesized that lower pre-deployment HRV would be associated with higher post-deployment post-traumatic stress disorder (PTSD) symptoms. Three-hundred-forty-three Army National Guard soldiers enrolled in the Warriors Achieving Resilience (WAR) study were analyzed. The primary outcome was PTSD symptom severity using the PTSD Checklist – Military version (PCL) measured at baseline, 3- and 12-month post-deployment. Heart rate variability predictor variables included: high frequency power (HF) and standard deviation of the normal cardiac inter-beat interval (SDNN). Generalized linear mixed models revealed that the pre-deployment PCL*ln(HF) interaction term was significant (p < 0.0001). Pre-deployment SDNN was not a significant predictor of post-deployment PCL. Covariates included age, pre-deployment PCL, race/ethnicity, marital status, tobacco use, childhood abuse, pre-deployment traumatic brain injury, and previous combat zone deployment. Pre-deployment heart rate variability predicts post-deployment PTSD symptoms in the context of higher pre-deployment PCL scores. PMID:27773678

Phase field approaches of bone remodeling based on TIP

NASA Astrophysics Data System (ADS)

Ganghoffer, Jean-François; Rahouadj, Rachid; Boisse, Julien; Forest, Samuel

2016-01-01

The process of bone remodeling includes a cycle of repair, renewal, and optimization. This adaptation process, in response to variations in external loads and chemical driving factors, involves three main types of bone cells: osteoclasts, which remove the old pre-existing bone; osteoblasts, which form the new bone in a second phase; osteocytes, which are sensing cells embedded into the bone matrix, trigger the aforementioned sequence of events. The remodeling process involves mineralization of the bone in the diffuse interface separating the marrow, which contains all specialized cells, from the newly formed bone. The main objective advocated in this contribution is the setting up of a modeling and simulation framework relying on the phase field method to capture the evolution of the diffuse interface between the new bone and the marrow at the scale of individual trabeculae. The phase field describes the degree of mineralization of this diffuse interface; it varies continuously between the lower value (no mineral) and unity (fully mineralized phase, e.g. new bone), allowing the consideration of a diffuse moving interface. The modeling framework is the theory of continuous media, for which field equations for the mechanical, chemical, and interfacial phenomena are written, based on the thermodynamics of irreversible processes. Additional models for the cellular activity are formulated to describe the coupling of the cell activity responsible for bone production/resorption to the kinetics of the internal variables. Kinetic equations for the internal variables are obtained from a pseudo-potential of dissipation. The combination of the balance equations for the microforce associated to the phase field and the kinetic equations lead to the Ginzburg-Landau equation satisfied by the phase field with a source term accounting for the dissipative microforce. Simulations illustrating the proposed framework are performed in a one-dimensional situation showing the evolution of the diffuse interface separating new bone from marrow.

Description of HIV-1 Group M Molecular Epidemiology and Drug Resistance Prevalence in Equatorial Guinea from Migrants in Spain

PubMed Central

Yebra, Gonzalo; de Mulder, Miguel; Holguín, África

2013-01-01

Background The HIV epidemic is increasing in Equatorial Guinea (GQ), West Central Africa, but few studies have reported its HIV molecular epidemiology. We aimed to describe the HIV-1 group M (HIV-1M) variants and drug-resistance mutations in GQ using sequences sampled in this country and in Spain, a frequent destination of Equatoguinean migrants. Methods We collected 195 HIV-1M pol sequences from Equatoguinean subjects attending Spanish clinics during 1997-2011, and 83 additional sequences sampled in GQ in 1997 and 2008 from GenBank. All (n = 278) were re-classified using phylogeny and tested for drug-resistance mutations. To evaluate the origin of CRF02_AG in GQ, we analyzed 2,562 CRF02_AG sequences and applied Bayesian MCMC inference (BEAST program). Results Most Equatoguinean patients recruited in Spain were women (61.1%) or heterosexuals (87.7%). In the 278 sequences, the variants found were CRF02_AG (47.8%), A (13.7%), B (7.2%), C (5.8%), G (5.4%) and others (20.1%). We found 6 CRF02_AG clusters emerged from 1983.9 to 2002.5 with origin in GQ (5.5 sequences/cluster). Transmitted drug-resistance (TDR) rate among naïve patients attended in Spain (n = 144) was 4.7%: 3.4% for PI (all with M46IL), 1.8% for NRTI (all with M184V) and 0.9% for NNRTI (Y188L). Among pre-treated patients, 9/31 (29%) presented any resistance, mainly affecting NNRTI (27.8%). Conclusions We report a low (<5%) TDR rate among naïve, with PI as the most affected class. Pre-treated patients also showed a low drug-resistance prevalence (29%) maybe related to the insufficient treatment coverage in GQ. CRF02_AG was the prevalent HIV-1M variant and entered GQ through independent introductions at least since the early 1980s. PMID:23717585

MONET, HET and SALT and asteroseismological observations and theory in Göttingen

NASA Astrophysics Data System (ADS)

Schuh, S.; Hessman, F. V.; Dreizler, S.; Kollatschny, W.; Glatzel, W.

2007-06-01

The Göttingen stellar astrophysics group, headed by Stefan Dreizler, conducts research on extrasolar planets and their host stars, on lower-main sequence stars, and on evolved compact objects, in particular hot white dwarfs (including PG 1159 objects, magnetic WDs and cataclysmic variables), and subdwarf B stars. In addition to sophisticated NLTE spectral analyses of these stars, which draw on the extensive stellar atmosphere modelling experience of the group, we actively develop and apply a variety of photometric monitoring and time-resolved spectroscopic techniques to address time-dependent phenomena. With the new instrumentational developments described below, we plan to continue the study of variable white dwarfs (GW Vir, DB and ZZ Ceti variables) and in particular sdB EC 14026 and PG 1617 pulsators which already constitute a main focus, partly within the Whole Earth Telescope (WET/DARC), http://www.physics.udel.edu/~jlp/darc/) collaboration, on a new level. Additional interest is directed towards strange mode instabilities in Wolf Rayet stars.

Exploring bacterial diversity in hospital environments by GS-FLX Titanium pyrosequencing.

PubMed

Poza, Margarita; Gayoso, Carmen; Gómez, Manuel J; Rumbo-Feal, Soraya; Tomás, María; Aranda, Jesús; Fernández, Ana; Bou, Germán

2012-01-01

Understanding microbial populations in hospital environments is crucial for improving human health. Hospital-acquired infections are an increasing problem in intensive care units (ICU). In this work we present an exploration of bacterial diversity at inanimate surfaces of the ICU wards of the University Hospital A Coruña (Spain), as an example of confined hospital environment subjected to selective pressure, taking the entrance hall of the hospital, an open and crowded environment, as reference. Surface swab samples were collected from both locations and recovered DNA used as template to amplify a hypervariable region of the bacterial 16S rRNA gene. Sequencing of the amplicons was performed at the Roche 454 Sequencing Center using GS-FLX Titanium procedures. Reads were pre-processed and clustered into OTUs (operational taxonomic units), which were further classified. A total of 16 canonical bacterial phyla were detected in both locations. Members of the phyla Firmicutes (mainly Staphylococcus and Streptococcus) and Actinobacteria (mainly Micrococcaceae, Corynebacteriaceae and Brevibacteriaceae) were over-represented in the ICU with respect to the Hall. The phyllum Proteobacteria was also well represented in the ICU, mainly by members of the families Enterobacteriaceae, Methylobacteriaceae and Sphingomonadaceae. In the Hall sample, the phyla Proteobacteria, Bacteroidetes, Deinococcus-Thermus and Cyanobacteria were over-represented with respect to the ICU. Over-representation of Proteobacteria was mainly due to the high abundance of Enterobacteriaceae members. The presented results demonstrate that bacterial diversity differs at the ICU and entrance hall locations. Reduced diversity detected at ICU, relative to the entrance hall, can be explained by its confined character and by the existence of antimicrobial selective pressure. This is the first study using deep sequencing techniques made in hospital wards showing substantial hospital microbial diversity.

DIRECT N-BODY MODELING OF THE OLD OPEN CLUSTER NGC 188: A DETAILED COMPARISON OF THEORETICAL AND OBSERVED BINARY STAR AND BLUE STRAGGLER POPULATIONS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Geller, Aaron M.; Hurley, Jarrod R.; Mathieu, Robert D., E-mail: a-geller@northwestern.edu, E-mail: mathieu@astro.wisc.edu, E-mail: jhurley@astro.swin.edu.au

2013-01-01

Following on from a recently completed radial-velocity survey of the old (7 Gyr) open cluster NGC 188 in which we studied in detail the solar-type hard binaries and blue stragglers of the cluster, here we investigate the dynamical evolution of NGC 188 through a sophisticated N-body model. Importantly, we employ the observed binary properties of the young (180 Myr) open cluster M35, where possible, to guide our choices for parameters of the initial binary population. We apply pre-main-sequence tidal circularization and a substantial increase to the main-sequence tidal circularization rate, both of which are necessary to match the observed tidalmore » circularization periods in the literature, including that of NGC 188. At 7 Gyr the main-sequence solar-type hard-binary population in the model matches that of NGC 188 in both binary frequency and distributions of orbital parameters. This agreement between the model and observations is in a large part due to the similarities between the NGC 188 and M35 solar-type binaries. Indeed, among the 7 Gyr main-sequence binaries in the model, only those with P {approx}> 1000 days begin to show potentially observable evidence for modifications by dynamical encounters, even after 7 Gyr of evolution within the star cluster. This emphasizes the importance of defining accurate initial conditions for star cluster models, which we propose is best accomplished through comparisons with observations of young open clusters like M35. Furthermore, this finding suggests that observations of the present-day binaries in even old open clusters can provide valuable information on their primordial binary populations. However, despite the model's success at matching the observed solar-type main-sequence population, the model underproduces blue stragglers and produces an overabundance of long-period circular main-sequence-white-dwarf binaries as compared with the true cluster. We explore several potential solutions to the paucity of blue stragglers and conclude that the model dramatically underproduces blue stragglers through mass-transfer processes. We suggest that common-envelope evolution may have been incorrectly imposed on the progenitors of the spurious long-period circular main-sequence-white-dwarf binaries, which perhaps instead should have gone through stable mass transfer to create blue stragglers, thereby bringing both the number and binary frequency of the blue straggler population in the model into agreement with the true blue stragglers in NGC 188. Thus, improvements in the physics of mass transfer and common-envelope evolution employed in the model may in fact solve both discrepancies with the observations. This project highlights the unique accessibility of open clusters to both comprehensive observational surveys and full-scale N-body simulations, both of which have only recently matured sufficiently to enable such a project, and underscores the importance of open clusters to the study of star cluster dynamics.« less

Sequences downstream of AAUAAA signals affect pre-mRNA cleavage and polyadenylation in vitro both directly and indirectly.

PubMed Central

Ryner, L C; Takagaki, Y; Manley, J L

1989-01-01

To investigate the role of sequences lying downstream of the conserved AAUAAA hexanucleotide in pre-mRNA cleavage and polyadenylation, deletions or substitutions were constructed in polyadenylation signals from simian virus 40 and adenovirus, and their effects were assayed in both crude and fractionated HeLa cell nuclear extracts. As expected, these sequences influenced the efficiency of both cleavage and polyadenylation as well as the accuracy of the cleavage reaction. Sequences near or upstream of the actual site of poly(A) addition appeared to specify a unique cleavage site, since their deletion resulted, in some cases, in heterogeneous cleavage. Furthermore, the sequences that allowed the simian virus 40 late pre-RNA to be cleaved preferentially by partially purified cleavage activity were also those at the cleavage site itself. Interestingly, sequences downstream of the cleavage site interacted with factors not directly involved in catalyzing cleavage and polyadenylation, since the effects of deletions were substantially diminished when partially purified components were used in assays. In addition, these sequences contained elements that could affect 3'-end formation both positively and negatively. Images PMID:2566911

The first whole transcriptomic exploration of pre-oviposited early chicken embryos using single and bulked embryonic RNA-sequencing.

PubMed

Hwang, Young Sun; Seo, Minseok; Choi, Hee Jung; Kim, Sang Kyung; Kim, Heebal; Han, Jae Yong

2018-04-01

The chicken is a valuable model organism, especially in evolutionary and embryology research because its embryonic development occurs in the egg. However, despite its scientific importance, no transcriptome data have been generated for deciphering the early developmental stages of the chicken because of practical and technical constraints in accessing pre-oviposited embryos. Here, we determine the entire transcriptome of pre-oviposited avian embryos, including oocyte, zygote, and intrauterine embryos from Eyal-giladi and Kochav stage I (EGK.I) to EGK.X collected using a noninvasive approach for the first time. We also compare RNA-sequencing data obtained using a bulked embryo sequencing and single embryo/cell sequencing technique. The raw sequencing data were preprocessed with two genome builds, Galgal4 and Galgal5, and the expression of 17,108 and 26,102 genes was quantified in the respective builds. There were some differences between the two techniques, as well as between the two genome builds, and these were affected by the emergence of long intergenic noncoding RNA annotations. The first transcriptome datasets of pre-oviposited early chicken embryos based on bulked and single embryo sequencing techniques will serve as a valuable resource for investigating early avian embryogenesis, for comparative studies among vertebrates, and for novel gene annotation in the chicken genome.

Modelling the multiwavelength emission of Ultraluminous X-ray sources accreting above Eddington

NASA Astrophysics Data System (ADS)

Ambrosi, E.; Zampieri, L.

2017-10-01

Understanding ULXs requires a comprehensive modelling of their multiwavelength emission properties. We compute the optical-through-X-ray emission of ULXs assuming that they are binary systems with stellar-mass or massive-stellar Black Holes and considering the possibility that a non-standard disc sets in when the mass transfer rate (\\dot{M}) becomes highly super-Eddington. The emission model is applied to self-consistent simulations of ULX binaries. We compare our color-magnitude diagrams (CMDs) with those in the literature and find significant differences in the post main sequence evolution. When the donor is on the main-sequence and \\dot{M} is mildly super-Eddington, the behaviour of the system is similar to that found in previous investigations. However, when the donor star leaves the main-sequence and \\dot{M} becomes highly super-Eddington, the optical luminosity of the system is systematically larger and the colours show a markedly different evolution. The emission properties depend on the variable shielding of the outer disc and donor induced by the changing inner disc structure. We determine also the effects caused by the onset of a strong optically thick outflow. CMDs in various photometric systems are compared to the observed properties of the optical counterparts of several ULXs, obtaining updated constraints on their donor mass and accretion rate.

Spectroscopic observations of the optical counterpart of Centaurus X-4

NASA Technical Reports Server (NTRS)

Van Paradijs, J.; Verbunt, F.; Van Der Linden, T.; Pedersen, H.; Wamsteker, W.

1980-01-01

The optical spectrum of the transient X-ray burst source Centaurus X-4 was observed about 5 weeks after the source reached its maximum. The brightness of the optical counterpart had decreased to V = 18.2, and the star had become appreciably redder (B - V = 0.7) compared to its color at maximum. The spectrum of Centaurus X-4 is similar to that of cataclysmic variables showing strong emission lines of H-1 and weaker lines of He-1 and He-2. The N03 lambda 4640 line is not visible. The continuum energy distribution of Centaurus X-4 shows the presence of a main-sequence star in the system, with spectral type between K3 and K7. This is consistent with the orbital period of 8.2 hr proposed by Kaluzienski et al (1980), if the main-sequence star is close to filling its Roche lobe.

Analysis of surface structures of chemically peculiar stars with modern and future interferometers

NASA Astrophysics Data System (ADS)

Shulyak, D.; Perraut, K.; Paladini, Claudia; Li Causi, G.; Sacuto, Stephane; Kochukhov, O.

2014-07-01

Interferometry is a very powerful observational technique known in astronomy for many decades. Its application to main-sequence stars, however, is still limited to only brightest objects. In this work we aim to explore the application of interferometry to a special class of main-sequence stars known as chemically peculiar (CP) stars. These stars demonstrate surface chemical abundance inhomogeneities (spots) that usually cover a considerable part of the stellar surface and induce a pronounced spectral and photometric variability. Interferometry thus has a potential to naturally resolve such spots in single stars, providing unique complementary information about spots sizes and contrasts. By means of numerical experiments we derive the actual interferometric requirements essential for the CP stars research that can be addressed in future instrument development. The first comparison between theoretical predictions and already available observations will also be discussed.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sitko, Michael L.; Day, Amanda N.; Kimes, Robin L.

2012-01-20

We present 13 epochs of near-infrared (0.8-5 {mu}m) spectroscopic observations of the pre-transitional, 'gapped' disk system in SAO 206462 (=HD 135344B). In all, six gas emission lines (Br{alpha}, Br{gamma}, Pa{beta}, Pa{gamma}, Pa{delta}, Pa{epsilon}, and the 0.8446 {mu}m 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 Multiplication-Sign 10{sup -8} M{sub Sun} yr{sup -1} 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.more » The continuum also varied, but by only {approx}30%, and even decreased at a time when the gas emission was increasing. The H I line at 1.083 {mu}m 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 defining the inner edge of the gap, they could interact with the material on timescales commensurate with what is observed for the variations in the dust, while other disk instabilities (thermal, magnetorotational) would operate there on longer timescales than we observe for the inner dust belt. For SAO 206462, the orbital period would likely be 1-3 years. If the changes are being induced in the disk material closer to the star than the gap, a variety of mechanisms (disk instabilities, interactions via planets) might be responsible for the changes seen. The He I feature is most likely due to a wind whose orientation changes with respect to the observer on timescales of a day or less. To further constrain the origin of the gas and dust emission will require multiple spectroscopic and interferometric observations on both shorter and longer timescales that have been sampled so far.« less

CT imaging-based determination and classification of anatomic variations of left gastric vein.

PubMed

Wu, Yongyou; Chen, Guangqiang; Wu, Pengfei; Zhu, Jianbin; Peng, Wei; Xing, Chungen

2017-03-01

Precise determination and classification of left gastric vein (LGV) anatomy are helpful in planning for gastric surgery, in particular, for resection of gastric cancer. However, the anatomy of LGV is highly variable. A systematic classification of its variations is still to be proposed. We aimed to investigate the anatomical variations in LGV using CT imaging and develop a new nomenclature system. We reviewed CT images and tracked the course of LGV in 825 adults. The frequencies of common and variable LGV anatomical courses were recorded. Anatomic variations of LGV were proposed and classified into different types mainly based on its courses. The inflow sites of LGV into the portal system were also considered if common hepatic artery (CHA) or splenic artery (SA) could not be used as a frame of reference due to variations. Detailed anatomy and courses of LGV were depicted on CT images. Using CHA and SA as the frames of reference, the routes of LGV were divided into six types (i.e., PreS, RetroS, Mid, PreCH, RetroCH, and Supra). The inflow sites were classified into four types (i.e., PV, SV, PSV, and LPV). The new classification was mainly based on the courses of LGV, which was validated with MDCT in the 805 cases with an identifiable LGV, namely type I, RetroCH, 49.8 % (401/805); type II, PreS, 20.6 % (166/805); type III, Mid, 20.0 % (161/805); type IV, RetroS, 7.3 % (59/805); type V, Supra, 1.5 % (12/805); and type VI, PreCH, 0.7 % (6/805). Type VII, designated to the cases in which SA and CHA could not be used as frames of reference, was not observed in this series. Detailed depiction of the anatomy and courses of LGV on CT images allowed us to evaluate and develop a new classification and nomenclature system for the anatomical variations of LGV.

RoboOligo: software for mass spectrometry data to support manual and de novo sequencing of post-transcriptionally modified ribonucleic acids

PubMed Central

Sample, Paul J.; Gaston, Kirk W.; Alfonzo, Juan D.; Limbach, Patrick A.

2015-01-01

Ribosomal ribonucleic acid (RNA), transfer RNA and other biological or synthetic RNA polymers can contain nucleotides that have been modified by the addition of chemical groups. Traditional Sanger sequencing methods cannot establish the chemical nature and sequence of these modified-nucleotide containing oligomers. Mass spectrometry (MS) has become the conventional approach for determining the nucleotide composition, modification status and sequence of modified RNAs. Modified RNAs are analyzed by MS using collision-induced dissociation tandem mass spectrometry (CID MS/MS), which produces a complex dataset of oligomeric fragments that must be interpreted to identify and place modified nucleosides within the RNA sequence. Here we report the development of RoboOligo, an interactive software program for the robust analysis of data generated by CID MS/MS of RNA oligomers. There are three main functions of RoboOligo: (i) automated de novo sequencing via the local search paradigm. (ii) Manual sequencing with real-time spectrum labeling and cumulative intensity scoring. (iii) A hybrid approach, coined ‘variable sequencing’, which combines the user intuition of manual sequencing with the high-throughput sampling of automated de novo sequencing. PMID:25820423

Hematopoiesis In The Equine Fetal Liver Suggests Immune Preparedness

PubMed Central

Battista, JM; Tallmadge, RL; Stokol, T; Felippe, MJB

2014-01-01

We investigated how the equine fetus prepares its pre-immune humoral repertoire for an imminent exposure to pathogens in the neonatal period, particularly how the primary hematopoietic organs are equipped to support B cell hematopoiesis and immunoglobulin (Ig) diversity. We demonstrated that the liver and the bone marrow at approximately 100 days of gestation (DG) are active sites of hematopoiesis based on the expression of signature mRNA (c-KIT, CD34, IL7R, CXCL12, IRF8, PU.1, PAX5, NOTCH1, GATA1, CEBPA) and protein markers (CD34, CD19, IgM, CD3, CD4, CD5, CD8, CD11b, CD172A) of hematopoietic development and leukocyte differentiation molecules, respectively. To verify Ig diversity achieved during the production of B cells, V(D)J segments were sequenced in primary lymphoid organs of the equine fetus and adult horse, revealing that similar heavy chain VDJ segments and CDR3 lengths were most frequently used independent of life stage. In contrast, different lambda light chain segments were predominant in equine fetal compared to adult stage and, surprisingly, the fetus had less restricted use of variable gene segments to construct the lambda chain. Fetal Igs also contained elements of sequence diversity, albeit to a smaller degree than that of the adult horse. Our data suggest that the B cells produced in the liver and bone marrow of the equine fetus generate a wide repertoire of pre-immune Igs for protection, and the more diverse use of different lambda variable gene segments in fetal life may provide the neonate an opportunity to respond to a wider range of antigens at birth. PMID:25179685

The discovery of low-mass pre-main-sequence stars in Cepheus OB3b

NASA Astrophysics Data System (ADS)

Pozzo, M.; Naylor, T.; Jeffries, R. D.; Drew, J. E.

2003-05-01

We report the discovery of a low-mass pre-main-sequence (PMS) stellar population in the younger subgroup of the Cepheus OB3 association, Cep OB3b, using UBVI CCD photometry and follow-up spectroscopy. The optical survey covers approximately 1300 arcmin2 on the sky and gives a global photometric and astrometric catalogue for more than 7000 objects. The location of a PMS population is well defined in a V versus (V-I) colour-magnitude diagram. Multifibre spectroscopic results for optically selected PMS candidates confirm the T Tauri nature for 10 objects, with equal numbers of classical TTS (CTTS) and weak-line TTS (WTTS). There are six other objects that we classify as possible PMS stars. The newly discovered TTS stars have masses in the range ~0.9-3.0 Msolar and ages from <1 to nearly 10 Myr, based on the Siess, Dufour & Forestini isochrones. Their location close to the O and B stars of the association (especially the O7n star) demonstrates that low-mass star formation is indeed possible in such an apparently hostile environment dominated by early-type stars and that the latter must have been less effective in eroding the circumstellar discs of their lower-mass siblings compared with other OB associations (e.g. λ-Ori). We attribute this to the nature of the local environment, speculating that the bulk of molecular material, which shielded low-mass stars from the ionizing radiation of their early-type siblings, has only recently been removed.

On the Lack of Circumbinary Planets Orbiting Isolated Binary Stars

NASA Astrophysics Data System (ADS)

Fleming, David P.; Barnes, Rory; Graham, David E.; Luger, Rodrigo; Quinn, Thomas R.

2018-05-01

We outline a mechanism that explains the observed lack of circumbinary planets (CBPs) via coupled stellar–tidal evolution of isolated binary stars. Tidal forces between low-mass, short-period binary stars on the pre-main sequence slow the stellar rotations transferring rotational angular momentum to the orbit as the stars approach the tidally locked state. This transfer increases the binary orbital period, expanding the region of dynamical instability around the binary, and destabilizing CBPs that tend to preferentially orbit just beyond the initial dynamical stability limit. After the stars tidally lock, we find that angular momentum loss due to magnetic braking can significantly shrink the binary orbit, and hence the region of dynamical stability, over time, impacting where surviving CBPs are observed relative to the boundary. We perform simulations over a wide range of parameter space and find that the expansion of the instability region occurs for most plausible initial conditions and that, in some cases, the stability semimajor axis doubles from its initial value. We examine the dynamical and observable consequences of a CBP falling within the dynamical instability limit by running N-body simulations of circumbinary planetary systems and find that, typically, at least one planet is ejected from the system. We apply our theory to the shortest-period Kepler binary that possesses a CBP, Kepler-47, and find that its existence is consistent with our model. Under conservative assumptions, we find that coupled stellar–tidal evolution of pre-main sequence binary stars removes at least one close-in CBP in 87% of multi-planet circumbinary systems.

SEARCHING FOR YOUNG JUPITER ANALOGS AROUND AP COL: L-BAND HIGH-CONTRAST IMAGING OF THE CLOSEST PRE-MAIN-SEQUENCE STAR

DOE Office of Scientific and Technical Information (OSTI.GOV)

Quanz, Sascha P.; Avenhaus, Henning; Meyer, Michael R.

2012-08-01

The nearby M-dwarf AP Col was recently identified by Riedel et al. 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 {>=} 0.5-1 M{sub Jup} for projected separations a > 4.5 AU, and m {>=} 2more » M{sub 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 {approx}>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 around M-dwarfs, gravitational microlensing studies predict that 17{sup +6}{sub -9}% of these stars host massive planets with orbital separations of 1-10 AU. Sensitive high-contrast imaging observations, like those presented here, will help to validate results from complementary detection techniques by determining the frequency of gas giant planets on wide orbits around M-dwarfs.« less

A Constraint on the Formation Timescale of the Young Open Cluster NGC 2264: Lithium Abundance of Pre-main Sequence Stars

NASA Astrophysics Data System (ADS)

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

2016-11-01

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 to be 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\\lt {T}{eff}[{{K}}]≤slant 6500). Li abundance under the condition of local thermodynamic equilibrium (LTE) was derived using the conventional curve of growth method. After correction for non-LTE effects, we find that the initial Li abundance of NGC 2264 is A({Li})=3.2+/- 0.2. From the distribution of the Li abundances, the underlying age spread of the visible PMS stars is estimated to be about 3-4 Myr and this, together with the presence of embedded populations in NGC 2264, suggests that the cluster formed on a timescale shorter than 5 Myr.

SIMAP--a comprehensive database of pre-calculated protein sequence similarities, domains, annotations and clusters.

PubMed

Rattei, Thomas; Tischler, Patrick; Götz, Stefan; Jehl, Marc-André; Hoser, Jonathan; Arnold, Roland; Conesa, Ana; Mewes, Hans-Werner

2010-01-01

The prediction of protein function as well as the reconstruction of evolutionary genesis employing sequence comparison at large is still the most powerful tool in sequence analysis. Due to the exponential growth of the number of known protein sequences and the subsequent quadratic growth of the similarity matrix, the computation of the Similarity Matrix of Proteins (SIMAP) becomes a computational intensive task. The SIMAP database provides a comprehensive and up-to-date pre-calculation of the protein sequence similarity matrix, sequence-based features and sequence clusters. As of September 2009, SIMAP covers 48 million proteins and more than 23 million non-redundant sequences. Novel features of SIMAP include the expansion of the sequence space by including databases such as ENSEMBL as well as the integration of metagenomes based on their consistent processing and annotation. Furthermore, protein function predictions by Blast2GO are pre-calculated for all sequences in SIMAP and the data access and query functions have been improved. SIMAP assists biologists to query the up-to-date sequence space systematically and facilitates large-scale downstream projects in computational biology. Access to SIMAP is freely provided through the web portal for individuals (http://mips.gsf.de/simap/) and for programmatic access through DAS (http://webclu.bio.wzw.tum.de/das/) and Web-Service (http://mips.gsf.de/webservices/services/SimapService2.0?wsdl).

Asteroseismology of hybrid δ Scuti-γ Doradus pulsating stars

NASA Astrophysics Data System (ADS)

Sánchez Arias, J. P.; Córsico, A. H.; Althaus, L. G.

2017-01-01

Context. Hybrid δ Scuti-γ Doradus pulsating stars show acoustic (p) oscillation modes typical of δ Scuti variable stars, and gravity (g) pulsation modes characteristic of γ Doradus variable stars simultaneously excited. Observations from space missions such as MOST, CoRoT, and Kepler have revealed a large number of hybrid δ Scuti-γ Doradus pulsators, thus paving the way for an exciting new channel of asteroseismic studies. Aims: We perform detailed asteroseismological modelling of five hybrid δ Scuti-γ Doradus stars. Methods: A grid-based modeling approach was employed to sound the internal structure of the target stars using stellar models ranging from the zero-age main sequence to the terminal-age main sequence, varying parameters such as stellar mass, effective temperature, metallicity and core overshooting. Their adiabatic radial (ℓ = 0) and non-radial (ℓ = 1,2,3) p and g mode periods were computed. Two model-fitting procedures were used to search for asteroseismological models that best reproduce the observed pulsation spectra of each target star. Results: We derive the fundamental parameters and the evolutionary status of five hybrid δ Scuti-γ Doradus variable stars recently observed by the CoRoT and Kepler space missions: CoRoT 105733033, CoRoT 100866999, KIC 11145123, KIC 9244992, and HD 49434. The asteroseismological model for each star results from different criteria of model selection, in which we take full advantage of the richness of periods that characterises the pulsation spectra for this kind of star.

Quantitative assessment of prevalence of pre-analytical variables and their effect on coagulation assay. Can intervention improve patient safety?

PubMed

Bhushan, Ravi; Sen, Arijit

2017-04-01

Very few Indian studies exist on evaluation of pre-analytical variables affecting "Prothrombin Time" the commonest coagulation assay performed. The study was performed in an Indian tertiary care setting with an aim to assess quantitatively the prevalence of pre-analytical variables and their effects on the results (patient safety), for Prothrombin time test. The study also evaluated their effects on the result and whether intervention, did correct the results. The firstly evaluated the prevalence for various pre-analytical variables detected in samples sent for Prothrombin Time testing. These samples with the detected variables wherever possible were tested and result noted. The samples from the same patients were repeated and retested ensuring that no pre-analytical variable is present. The results were again noted to check for difference the intervention produced. The study evaluated 9989 samples received for PT/INR over a period of 18 months. The prevalence of different pre-analytical variables was found to be 862 (8.63%). The proportion of various pre-analytical variables detected were haemolysed samples 515 (5.16%), over filled vacutainers 62 (0.62%), under filled vacutainers 39 (0.39%), low values 205 (2.05%), clotted samples 11 (0.11%), wrong labeling 4 (0.04%), wrong vacutainer use 2 (0.02%), chylous samples 7 (0.07%) and samples with more than one variable 17 (0.17%). The comparison of percentage of samples showing errors were noted for the first variables since they could be tested with and without the variable in place. The reduction in error percentage was 91.5%, 69.2%, 81.5% and 95.4% post intervention for haemolysed, overfilled, under filled and samples collected with excess pressure at phlebotomy respectively. Correcting the variables did reduce the error percentage to a great extent in these four variables and hence the variables are found to affect "Prothrombin Time" testing and can hamper patient safety.

Solid Lipid Nanoparticle assemblies (SLNas) for an anti-TB inhalation treatment-A Design of Experiments approach to investigate the influence of pre-freezing conditions on the powder respirability.

PubMed

Maretti, Eleonora; Rustichelli, Cecilia; Romagnoli, Marcello; Balducci, Anna Giulia; Buttini, Francesca; Sacchetti, Francesca; Leo, Eliana; Iannuccelli, Valentina

2016-09-10

For direct intramacrophagic antitubercular therapy, pulmonary administration through Dry Powder Inhaler (DPI) devices is a reasonable option. For the achievement of efficacious aerosolisation, rifampicin-loaded Solid Lipid Nanoparticle assemblies (SLNas) were developed using the melt emulsifying technique followed by freeze-drying. Indeed, this drying method can cause freezing or drying stresses compromising powder respirability. It is the aim of this research to offer novel information regarding pre-freezing variables. These included type and concentration of cryoprotectants, pre-freezing temperature, and nanoparticle concentration in the suspension. In particular, the effects of such variables were observed at two main levels. First of all, on SLNas characteristics - i.e., size, polydispersity index, zeta-potential, circularity, density, and drug loading. Secondly, on powder respirability, taking into account aerodynamic diameter, emitted dose, and respirable fraction. Considering the complexity of the factors involved in a successful respirable powder, a Design of Experiments (DoE) approach was adopted as a statistical tool for evaluating the effect of pre-freezing conditions. Interestingly, the most favourable impact on powder respirability was exerted by quick-freezing combined with a certain grade of sample dilution before the pre-freezing step without the use of cryoprotectants. In such conditions, a very high SLNas respirable fraction (>50%) was achieved, along with acceptable yields in the final dry powder as well as a reduction of powder mass to be introduced into DPI capsules with benefits in terms of administered drug dose feasibility. Copyright © 2016 Elsevier B.V. All rights reserved.

Online health consultation: examining uses of an interactive cancer communication tool by low-income women with breast cancer.

PubMed

Lu, Hsueh-Yi; Shaw, Bret R; Gustafson, David H

2011-07-01

To examine how psychosocial variables predicted use of an online health consultation service among low-income breast cancer patients and in turn how using this service affected these same psychosocial outcomes. This retrospective study included 231 recently diagnosed, low-income (at or below 250% of the federal poverty level) breast cancer patients provided a free computer with 16 weeks of access to the Internet-based 'Ask an Expert' service offered as part of the Comprehensive Health Enhancement Support System (CHESS) "Living with Breast Cancer" program. The use activity included a total of 502 messages submitted to the online health consultation service. The data included five psychosocial variables: information seeking, social support, health self efficacy, participation in health care, and doctor-patient relationship, were collected at both the pre-test and 16-week post-test after using the service. Correlation tests were conducted to examine the relationship between pre- and post-test, and use activity. A multiple regression model was formed for each of five psychosocial variables to examine how use activity of the consultation service was associated with various psychosocial measurements. In total, 865 distinct consulting queries from 502 messages were identified as measurement of patients' use activities (3.74 consulting queries per participant). Use activity had significant negative relationships with pre-test scores across all five psychosocial variables. The regression models found significant positive main effects (use activity) associated with three of these psychosocial variables: health self efficacy, participation in health care and doctor-patient relationship. Use activity of the online consultation service did not have significant relationships with the dependent variables of information seeking and perceived social support. Low-income breast cancer patients sought out information from an online cancer information expert. Patients with more negative perceptions at pre-test tended to use the service more. Greater use of the service was associated with improvement in patients' perception of health self-efficacy, participation in health care and doctor-patient relationship. Moreover, use of online health consultation appears to level the differences, narrowing the gaps between those who were worse and better off at pre-test. These findings suggest that online health consultation can serve as an effective complement to other resources, which help low-income, breast cancer patients feel more confident to participate more actively in their health care, become more actively involved in making decisions about their treatments and enhance the relationship with their doctors. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

An ultra-sparse code underliesthe generation of neural sequences in a songbird

NASA Astrophysics Data System (ADS)

Hahnloser, Richard H. R.; Kozhevnikov, Alexay A.; Fee, Michale S.

2002-09-01

Sequences of motor activity are encoded in many vertebrate brains by complex spatio-temporal patterns of neural activity; however, the neural circuit mechanisms underlying the generation of these pre-motor patterns are poorly understood. In songbirds, one prominent site of pre-motor activity is the forebrain robust nucleus of the archistriatum (RA), which generates stereotyped sequences of spike bursts during song and recapitulates these sequences during sleep. We show that the stereotyped sequences in RA are driven from nucleus HVC (high vocal centre), the principal pre-motor input to RA. Recordings of identified HVC neurons in sleeping and singing birds show that individual HVC neurons projecting onto RA neurons produce bursts sparsely, at a single, precise time during the RA sequence. These HVC neurons burst sequentially with respect to one another. We suggest that at each time in the RA sequence, the ensemble of active RA neurons is driven by a subpopulation of RA-projecting HVC neurons that is active only at that time. As a population, these HVC neurons may form an explicit representation of time in the sequence. Such a sparse representation, a temporal analogue of the `grandmother cell' concept for object recognition, eliminates the problem of temporal interference during sequence generation and learning attributed to more distributed representations.

The evolution of massive stars and their spectra. I. A non-rotating 60 M⊙ star from the zero-age main sequence to the pre-supernova stage

NASA Astrophysics Data System (ADS)

Groh, Jose H.; Meynet, Georges; Ekström, Sylvia; Georgy, Cyril

2014-04-01

For the first time, the interior and spectroscopic evolution of a massive star is analyzed from the zero-age main sequence (ZAMS) to the pre-supernova (SN) stage. For this purpose, we combined stellar evolution models using the Geneva code and stellar atmospheric/wind models using CMFGEN. With our approach, we were able to produce observables, such as a synthetic high-resolution spectrum and photometry, thereby aiding the comparison between evolution models and observed data. Here we analyze the evolution of a non-rotating 60 M⊙ star and its spectrum throughout its lifetime. Interestingly, the star has a supergiant appearance (luminosity class I) even at the ZAMS. We find the following evolutionary sequence of spectral types: O3 I (at the ZAMS), O4 I (middle of the H-core burning phase), B supergiant (BSG), B hypergiant (BHG), hot luminous blue variable (LBV; end of H-core burning), cool LBV (H-shell burning through the beginning of the He-core burning phase), rapid evolution through late WN and early WN, early WC (middle of He-core burning), and WO (end of He-core burning until core collapse). We find the following spectroscopic phase lifetimes: 3.22 × 106 yr for the O-type, 0.34 × 105 yr (BSG), 0.79 × 105 yr (BHG), 2.35 × 105 yr (LBV), 1.05 × 105 yr (WN), 2.57 × 105 yr (WC), and 3.80 × 104 yr (WO). Compared to previous studies, we find a much longer (shorter) duration for the early WN (late WN) phase, as well as a long-lived LBV phase. We show that LBVs arise naturally in single-star evolution models at the end of the MS when the mass-loss rate increases as a consequence of crossing the bistability limit. We discuss the evolution of the spectra, magnitudes, colors, and ionizing flux across the star's lifetime, and the way they are related to the evolution of the interior. We find that the absolute magnitude of the star typically changes by ~6 mag in optical filters across the evolution, with the star becoming significantly fainter in optical filters at the end of the evolution, when it becomes a WO just a few 104 years before the SN explosion. We also discuss the origin of the different spectroscopic phases (i.e., O-type, LBV, WR) and how they are related to evolutionary phases (H-core burning, H-shell burning, He-core burning). Tables 1, 4 and 5 are available in electronic form at http://www.aanda.orgSynthetic spectra are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/564/A30

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hachisu, Izumi; Kato, Mariko, E-mail: hachisu@ea.c.u-tokyo.ac.jp, E-mail: mariko@educ.cc.keio.ac.jp

We identified a general course of classical nova outbursts in the B – V versus U – B color-color diagram. It is reported that novae show spectra similar to those of A-F supergiants near optical light maximum. However, they do not follow the supergiant sequence in the color-color diagram, neither the blackbody nor the main-sequence sequence. Instead, we found that novae evolve along a new sequence in the pre-maximum and near-maximum phases, which we call 'the nova-giant sequence'. This sequence is parallel to but Δ(U – B) ≈ –0.2 mag bluer than the supergiant sequence. This is because the massmore » of a nova envelope is much (∼10{sup –4} times) less than that of a normal supergiant. After optical maximum, its color quickly evolves back blueward along the same nova-giant sequence and reaches the point of free-free emission (B – V = –0.03, U – B = –0.97), which coincides with the intersection of the blackbody sequence and the nova-giant sequence, and remains there for a while. Then the color evolves leftward (blueward in B – V but almost constant in U – B), owing mainly to the development of strong emission lines. This is the general course of nova outbursts in the color-color diagram, which was deduced from eight well-observed novae in various speed classes. For a nova with unknown extinction, we can determine a reliable value of the color excess by matching the observed track of the target nova with this general course. This is a new and convenient method for obtaining the color excesses of classical novae. Using this method, we redetermined the color excesses of 20 well-observed novae. The obtained color excesses are in reasonable agreement with the previous results, which in turn support the idea of our general track of nova outbursts. Additionally, we estimated the absolute V magnitudes of about 30 novae using a method for time-stretching nova light curves to analyze the distance-reddening relations of the novae.« less

Humanoid assessing rehabilitative exercises.

PubMed

Simonov, M; Delconte, G

2015-01-01

This article is part of the Focus Theme of Methods of Information in Medicine on "New Methodologies for Patients Rehabilitation". The article presents the approach in which the rehabilitative exercise prepared by healthcare professional is encoded as formal knowledge and used by humanoid robot to assist patients without involving other care actors. The main objective is the use of humanoids in rehabilitative care. An example is pulmonary rehabilitation in COPD patients. Another goal is the automated judgment functionality to determine how the rehabilitation exercise matches the pre-programmed correct sequence. We use the Aldebaran Robotics' NAO humanoid to set up artificial cognitive application. Pre-programmed NAO induces elderly patient to undertake humanoid-driven rehabilitation exercise, but needs to evaluate the human actions against the correct template. Patient is observed using NAO's eyes. We use the Microsoft Kinect SDK to extract motion path from the humanoid's recorded video. We compare human- and humanoid-operated process sequences by using the Dynamic Time Warping (DTW) and test the prototype. This artificial cognitive software showcases the use of DTW algorithm to enable humanoids to judge in near real-time about the correctness of rehabilitative exercises performed by patients following the robot's indications. One could enable better sustainable rehabilitative care services in remote residential settings by combining intelligent applications piloting humanoids with the DTW pattern matching algorithm applied at run time to compare humanoid- and human-operated process sequences. In turn, it will lower the need of human care.

Advanced colorectal adenoma related gene expression signature may predict prognostic for colorectal cancer patients with adenoma-carcinoma sequence.

PubMed

Li, Bing; Shi, Xiao-Yu; Liao, Dai-Xiang; Cao, Bang-Rong; Luo, Cheng-Hua; Cheng, Shu-Jun

2015-01-01

There are still no absolute parameters predicting progression of adenoma into cancer. The present study aimed to characterize functional differences on the multistep carcinogenetic process from the adenoma-carcinoma sequence. All samples were collected and mRNA expression profiling was performed by using Agilent Microarray high-throughput gene-chip technology. Then, the characteristics of mRNA expression profiles of adenoma-carcinoma sequence were described with bioinformatics software, and we analyzed the relationship between gene expression profiles of adenoma-adenocarcinoma sequence and clinical prognosis of colorectal cancer. The mRNA expressions of adenoma-carcinoma sequence were significantly different between high-grade intraepithelial neoplasia group and adenocarcinoma group. The biological process of gene ontology function enrichment analysis on differentially expressed genes between high-grade intraepithelial neoplasia group and adenocarcinoma group showed that genes enriched in the extracellular structure organization, skeletal system development, biological adhesion and itself regulated growth regulation, with the P value after FDR correction of less than 0.05. In addition, IPR-related protein mainly focused on the insulin-like growth factor binding proteins. The variable trends of gene expression profiles for adenoma-carcinoma sequence were mainly concentrated in high-grade intraepithelial neoplasia and adenocarcinoma. The differentially expressed genes are significantly correlated between high-grade intraepithelial neoplasia group and adenocarcinoma group. Bioinformatics analysis is an effective way to study the gene expression profiles in the adenoma-carcinoma sequence, and may provide an effective tool to involve colorectal cancer research strategy into colorectal adenoma or advanced adenoma.

Investigating annually-resovled natural climate variability during MIS 11 using lacustrine records

NASA Astrophysics Data System (ADS)

Tye, G. J.; Palmer, A. P.; Candy, I.; Coxon, P.; Hardiman, M.

2012-04-01

Marine isotope stage 11 (MIS 11, ca 410,000 yrs BP) is considered to be one of the best analogues for current and future climate change due to the similarity of orbital forcing patterns during these two interglacials. Marine and ice-core records suggest that MIS 11 was a particularly long interglacial, characterised by stable climates. The investigation of high-resolution climate records from MIS 11 can, therefore, allow us to understand how the climate of a Holocene-like interglacial might evolve in the absence of anthropogenic modification. MIS 11 sediments preserved in the palaeolake basin at Marks Tey, eastern England, offer the potential for such a study as they are considered to be annually-laminated (varved) throughout a large part of the interglacial (Turner, 1970, 1975). The lamination sets appear to be comprised, primarily, of three regularly occurring laminae types; 1) authigenic carbonate, 2) diatom blooms, and 3) organic detritus, although there appears to be some variability in the microfacies of these laminations. The carbonate laminations are the key to the study of climate variability during MIS 11, as they represent authigenic carbonate precipitation, consistent with temperature/biologically driven changes in lake chemistry during the summer months. Oxygen isotopic analysis of the carbonate therefore gives a proxy for summer temperature. A period of key interest in the MIS 11 sequence at Marks Tey occurs during the early part of the interglacial, where there is a short-lived increase in grass pollen relative to tree pollen, termed the Non-Arboreal Pollen Zone (NAPZ). The cause of this shift in pollen has been subject to debate, with natural wildfire (Turner, 1970) or climatic deterioration (e.g. Kelly, 1964) being suggested as possible forcing mechanisms. In this study, as well as discussing the main characteristics of the MIS 11 sequence at Marks Tey, we will focus on the sedimentary, micromorphological and geochemical record of the NAPZ. In particular we discuss the potential role of abrupt, sub-Milankovitch, climate cooling in its genesis, whilst highlighting the complexity of ecological and landscape response that such a climatic event may generate. The study concludes by discussing the potential occurrence of 8.2ka-like events in pre-Holocene interglacials.

Infrared Observations of FS CMa Stars

NASA Astrophysics Data System (ADS)

Sitko, Michael L.; Russell, R. W.; Lynch, D. K.; Grady, C. A.; Hammel, H. B.; Beerman, L. C.; Day, A. N.; Huelsman, D.; Rudy, R. J.; Brafford, S. M.; Halbedel, E. M.

2009-01-01

A subset of non-supergiant B[e] stars has recently been recognized as forming a fairly unique class of objects with very strong emission lines, infrared excesses, and locations not associated with star formation. The exact evolutionary state of these stars, named for the prototype FS CMa, is uncertain, and they have often been classified as isolated Herbig AeBe stars. We present infrared observations of two of these stars, HD 45677 (FS CMa), HD 50138 (MWC 158), and the candidate FS CMa star HD 190073 (V1295 Aql) that span over a decade in time. All three exhibit an emission band at 10 microns due to amorphous silicates, confirming that much (if not all) of the infrared excess is due to dust. HD 50138 is found to exhibit 20% variability between 3-13 microns that resembles that found in pre-main sequence systems (HD 163296 and HD 31648). HD 45677, despite large changes at visual wavelengths, has remained relatively stable in the infrared. To date, no significant changes have been observed in HD 190073. This work is supported in part by NASA Origins of Solar Systems grant NAG5-9475, NASA Astrophysics Data Program contract NNH05CD30C, and the Independent Research and Development program at The Aerospace Corporation.

The evolution of angular momentum among zero-age main-sequence solar-type stars

NASA Technical Reports Server (NTRS)

Soderblom, David R.; Stauffer, John R.; Macgregor, Keith B.; Jones, Burton F.

1993-01-01

We consider a survey of rotation among F, G, and K dwarfs of the Pleiades in the context of other young clusters (Alpha Persei and the Hyades) and pre-main-sequence (PMS) stars (in Taurus-Auriga and Orion) in order to examine how the angular momentum of a star like the sun evolves during its early life on the main sequence. The rotation of PMS stars can be evolved into distributions like those seen in the young clusters if there is only modest, rotation-independent angular momentum loss prior to the ZAMS. Even then, the ultrafast rotators (UFRs, or ZAMS G and K dwarfs with v sin i equal to or greater than 30 km/s) must owe their extra angular momentum to their conditions of formation and to different angular momentum loss rates above a threshold velocity, for it is unlikely that these stars had angular momentum added as they neared the ZAMS, nor can a spread in ages within a cluster account for the range of rotation seen. Only a fraction of solar-type stars are thus capable of becoming UFRs, and it is not a phase that all stars experience. Simple scaling relations (like the Skumanich relation) applied to the observed surface rotation rates of young solar-type stars cannot reproduce the way in which the Pleiades evolve into the Hyades. We argue that invoking internal differential rotation in these ZAMS stars can explain several aspects of the observations and thus can provide a consistent picture of ZAMS angular momentum evolution.

On the determination of age and mass functions of stars in young open star clusters from the analysis of their luminosity functions

NASA Astrophysics Data System (ADS)

Piskunov, A. E.; Belikov, A. N.; Kharchenko, N. V.; Sagar, R.; Subramaniam, A.

2004-04-01

We construct the observed luminosity functions of the remote young open clusters NGC 2383, 2384, 4103, 4755, 7510 and Hogg 15 from CCD observations of them. The observed LFs are corrected for field star contamination determined with the help of a Galactic star count model. In the case of Hogg 15 and NGC 2383 we also consider the additional contamination from neighbouring clusters NGC 4609 and 2384, respectively. These corrections provide a realistic pattern of cluster LF in the vicinity of the main-sequence (MS) turn-on point and at fainter magnitudes reveal the so-called H-feature arising as a result of the transition of the pre-MS phase to the MS, which is dependent on the cluster age. The theoretical LFs are constructed representing a cluster population model with continuous star formation for a short time-scale and a power-law initial mass function (IMF), and these are fitted to the observed LF. As a result, we are able to determine for each cluster a set of parameters describing the cluster population (the age, duration of star formation, IMF slope and percentage of field star contamination). It is found that in spite of the non-monotonic behaviour of observed LFs, cluster IMFs can be described as power-law functions with slopes similar to Salpeter's value. The present main-sequence turn-on cluster ages are several times lower than those derived from the fitting of theoretical isochrones to the turn-off region of the upper main sequences.

VizieR Online Data Catalog: BI light curves of DDO210 pulsating variables (Ordonez+, 2016)

NASA Astrophysics Data System (ADS)

Ordonez, A. J.; Sarajedini, A.

2016-07-01

The data set used by Cole et al. (2014ApJ...794...64M) is very deep and covers a time baseline conducive to identifying short-period variable stars. These observations of DDO210 were originally intended for use in a detailed SFH analysis for this dwarf, and thus cover a significant portion of the galaxy while reaching photometric depths to the main-sequence turnoff. The observations consisting of 22920s in F475W and 33480s in F814W were taken with a cadence well suited for identifying short-period variable stars. We retrieved these images from the Mikulski Archive for Space Telescopes (MAST) for use in our study. (2 data files).

The provenance of Archean clastic metasediments in the Narryer Gneiss Complex, western Australia: Trace element geochemistry, Nd isotopes, and U-Pb ages for detrital zircons

DOE Office of Scientific and Technical Information (OSTI.GOV)

Maas, R.; McCulloch, M.T.

1991-07-01

Clastic metasedimentary rocks of mid-Archean age from the Mt. Narryer and Jack Hills metasedimentary belts have REE patterns resembling those of mid- to late-Archean pelitic-quartzitic cratonic sequences elsewhere, and post-Archean continental rocks in general. Detrital zircons in the metasediments range in age from ca. 3,000 to 3,700 Ma. This indicates a provenance from mature cratonic sources controlled by K-rich granitic rocks. Additional minor sediment sources were identified as older, mainly chemical sedimentary sequences, ultramafic rocks, and felsic rocks characterized by low HREE contents, perhaps of tonalitic affinity. Differences between sedimentary REE patterns and those in the surrounding 3.73-3.0 Ga orthogneissmore » terrain, and between detrital zircon ages and the age distribution in the gneisses, suggest that the present association of the metasedimentary belts with the orthogneiss terrain is of tectonic origin. The occurrence of detrital zircons with U-Pb ages > 4 Ga in certain quartzites and conglomerates of the Jack Hills and Mt. Narryer metasedimentary sequences indicates a further, most likely granitic, source. {epsilon}{sub Nd}(T{sub Dep}) values in Jack Hills metasediments vary widely (+5 to {minus}12) but have a smaller range in the Mt. Narryer belt ({minus}5 to {minus}9). The lowest {epsilon}{sub Nd} values of both sequences are interpreted to reflect the presence of detritus derived from 4.1-4.2 Ga old LREE-enriched continental crust in proportions considerably larger ({ge} 10%) than estimated previously from the abundance of pre-4 Ga detrital zircons ({approx}3%). This would imply the former existence of significant volumes of pre-4 Ga continental crust in the provenance of the Mt. Narryer and Jack Hills metasediments.« less

Changes in the influence of the western Pacific subtropical high on Asian summer monsoon rainfall in the late 1990s

NASA Astrophysics Data System (ADS)

Huang, Yanyan; Wang, Bin; Li, Xiaofan; Wang, Huijun

2017-10-01

The Year-to-year variability of the western Pacific subtropical high (WPSH) is primarily controlled by atmosphere-ocean interaction (AOI) between the WPSH and the Indo-Pacific warm pool dipole SST anomalies (AOI mode) and the anomalous SST forcing from the equatorial central Pacific (the CP forcing mode). In this study, we show that the impacts of the WPSH variability on Asian summer monsoon rainfall have changed after the late 1990s. Before the late 1990s (the PRE epoch), the WPSH primarily affects East Asian summer monsoon (EASM) and had little influence on Indian summer monsoon (ISM), whereas after the late 1990s (the POST epoch), the WPSH has strengthened its linkage to the ISM while weakened its relationship with the EASM. This epochal change is associated with a change in the leading circulation mode in the Asia-WP region. During the PRE (POST) epoch the WPSH variation is mainly controlled by the AOI (CP forcing) that mainly affects EASM (ISM). The epochal change of the leading mode may be attributed to the change of the ENSO properties in late 1990s: the CP types of El Nino become a leading ENSO mode in the POST epoch. This work provides a new perspective for understanding decadal changes of the ENSO-monsoon relationship through subtropical dynamics.

Implementation into earthquake sequence simulations of a rate- and state-dependent friction law incorporating pressure solution creep

NASA Astrophysics Data System (ADS)

Noda, H.

2016-05-01

Pressure solution creep (PSC) is an important elementary process in rock friction at high temperatures where solubilities of rock-forming minerals are significantly large. It significantly changes the frictional resistance and enhances time-dependent strengthening. A recent microphysical model for PSC-involved friction of clay-quartz mixtures, which can explain a transition between dilatant and non-dilatant deformation (d-nd transition), was modified here and implemented in dynamic earthquake sequence simulations. The original model resulted in essentially a kind of rate- and state-dependent friction (RSF) law, but assumed a constant friction coefficient for clay resulting in zero instantaneous rate dependency in the dilatant regime. In this study, an instantaneous rate dependency for the clay friction coefficient was introduced, consistent with experiments, resulting in a friction law suitable for earthquake sequence simulations. In addition, a term for time-dependent strengthening due to PSC was added which makes the friction law logarithmically rate-weakening in the dilatant regime. The width of the zone in which clasts overlap or, equivalently, the interface porosity involved in PSC plays a role as the state variable. Such a concrete physical meaning of the state variable is a great advantage in future modelling studies incorporating other physical processes such as hydraulic effects. Earthquake sequence simulations with different pore pressure distributions demonstrated that excess pore pressure at depth causes deeper rupture propagation with smaller slip per event and a shorter recurrence interval. The simulated ruptures were arrested a few kilometres below the point of pre-seismic peak stress at the d-nd transition and did not propagate spontaneously into the region of pre-seismic non-dilatant deformation. PSC weakens the fault against slow deformation and thus such a region cannot produce a dynamic stress drop. Dynamic rupture propagation further down to brittle-plastic transition, evidenced by geological observations, would require even smaller frictional resistance at coseismic slip rate, suggesting the importance of implementation of dynamic weakening activated at coseismic slip rates for more realistic simulation of earthquake sequences. The present models produced much smaller afterslip at deeper parts of arrested ruptures than those with logarithmic RSF laws because of a more significant rate-strengthening effect due to linearly viscous PSC. Detailed investigation of afterslip would give a clue to understand the deformation mechanism which controls shear resistance of the fault in a region of arrest of earthquake ruptures.

Demand characteristics, pre-test attitudes and time-on-task trends in the effects of chewing gum on attention and reported mood in healthy volunteers.

PubMed

Allen, A P; Smith, A P

2012-10-01

Previous research has indicated that chewing gum enhances reported alertness, but has variable effects on attention. Demand characteristics may explain these effects. The current study investigated the effects of gum and demand characteristics on attention and reported mood over time. Participants completed measures of mood and attention, with and without chewing gum. To manipulate demand characteristics, they were told that the hypothesised effect of gum was either positive or negative, or no hypothesis was mentioned. Attitudes towards gum were assessed pre- and post-manipulation. Gum increased reported alertness; this effect was only significant for positive and neutral demand characteristics. Vigilance accuracy was reduced for chewing gum, but only in the fourth minute of the task, and gum reduced focussed attention accuracy, but only for the first 64 trials. Demand characteristics did not moderate time-on-task effects. Gum improved selective attention. A positive effect on response organisation was observed; this was significant when demand characteristics and pre-test attitudes to gum were both negative. The results suggest that demand characteristics moderate effects on self-reported alertness and response organisation, but cannot explain time-on-task effects or variable main effects on other aspects of attention. Copyright © 2012 Elsevier Ltd. All rights reserved.

A comparative analysis of exome capture.

PubMed

Parla, Jennifer S; Iossifov, Ivan; Grabill, Ian; Spector, Mona S; Kramer, Melissa; McCombie, W Richard

2011-09-29

Human exome resequencing using commercial target capture kits has been and is being used for sequencing large numbers of individuals to search for variants associated with various human diseases. We rigorously evaluated the capabilities of two solution exome capture kits. These analyses help clarify the strengths and limitations of those data as well as systematically identify variables that should be considered in the use of those data. Each exome kit performed well at capturing the targets they were designed to capture, which mainly corresponds to the consensus coding sequences (CCDS) annotations of the human genome. In addition, based on their respective targets, each capture kit coupled with high coverage Illumina sequencing produced highly accurate nucleotide calls. However, other databases, such as the Reference Sequence collection (RefSeq), define the exome more broadly, and so not surprisingly, the exome kits did not capture these additional regions. Commercial exome capture kits provide a very efficient way to sequence select areas of the genome at very high accuracy. Here we provide the data to help guide critical analyses of sequencing data derived from these products.

GapFiller: a de novo assembly approach to fill the gap within paired reads

PubMed Central

2012-01-01

Background Next Generation Sequencing technologies are able to provide high genome coverages at a relatively low cost. However, due to limited reads' length (from 30 bp up to 200 bp), specific bioinformatics problems have become even more difficult to solve. De novo assembly with short reads, for example, is more complicated at least for two reasons: first, the overall amount of "noisy" data to cope with increased and, second, as the reads' length decreases the number of unsolvable repeats grows. Our work's aim is to go at the root of the problem by providing a pre-processing tool capable to produce (in-silico) longer and highly accurate sequences from a collection of Next Generation Sequencing reads. Results In this paper a seed-and-extend local assembler is presented. The kernel algorithm is a loop that, starting from a read used as seed, keeps extending it using heuristics whose main goal is to produce a collection of error-free and longer sequences. In particular, GapFiller carefully detects reliable overlaps and operates clustering similar reads in order to reconstruct the missing part between the two ends of the same insert. Our tool's output has been validated on 24 experiments using both simulated and real paired reads datasets. The output sequences are declared correct when the seed-mate is found. In the experiments performed, GapFiller was able to extend high percentages of the processed seeds and find their mates, with a false positives rate that turned out to be nearly negligible. Conclusions GapFiller, starting from a sufficiently high short reads coverage, is able to produce high coverages of accurate longer sequences (from 300 bp up to 3500 bp). The procedure to perform safe extensions, together with the mate-found check, turned out to be a powerful criterion to guarantee contigs' correctness. GapFiller has further potential, as it could be applied in a number of different scenarios, including the post-processing validation of insertions/deletions detection pipelines, pre-processing routines on datasets for de novo assembly pipelines, or in any hierarchical approach designed to assemble, analyse or validate pools of sequences. PMID:23095524

A Late Holocene explosive mafic eruption of Villarrica volcano, Southern Andes: The Chaimilla deposit

NASA Astrophysics Data System (ADS)

Costantini, L.; Pioli, L.; Bonadonna, C.; Clavero, J.; Longchamp, C.

2011-03-01

Villarrica (Chile) is one of the most active volcanoes in South America having erupted about 60 times in the last 460 years. Although its historical eruptive activity has been mainly effusive and weakly explosive, it had strong explosive behaviour in postglacial times. Chaimilla (< 3.1 ka) is one of the best exposed and widely dispersed pyroclastic deposits, related to both fall and flow activity. The deposit is dispersed over an area of 250 km 2 and consists of 8 units (A-H) which were grouped into four sequences. Stratigraphic data suggest that the eruption had a relatively short duration and evolved from i) an Opening phase, dispersing ash, lapilli clasts, accretionary lapilli, blocks and bombs, to ii) a Pulsatory phase, originating a series of magmatic explosions, to iii) a Collapsing phase, characterised by unstable plumes which emplaced a series of pyroclastic density currents intercalated with thin fallout layers and finally to iv) a Climactic phase forming a more sustained plume which eventually collapsed generating the final pyroclastic density currents. The deposit (fall and flow) has a minimum cumulative volume of 0.6 km 3, with the main sustained phase being associated with a VEI 4 and the flow units having a minimum estimated total volume of 0.04 km 3. The erupted material has a homogenous chemical composition but displays a remarkable variability in both textural and physical properties. The density distribution of juvenile products shows a clear bimodality characterised by two main populations: P1 and P2. Population P1 consists of highly vesicular clasts (modal density around 1000 kg m - 3 ) with mostly sub-spherical bubbles and moderately crystallised groundmass with large-sized microlites. Clasts from population P2 are poorly vesicular (modal density around 1600 kg m - 3 ) with irregular to collapsed bubbles and numerous smaller microlites. The variability of both vesicularity and microlite characteristics suggests the involvement of two magma batches with distinct pre-eruptive degassing and rising histories. Our eruption conceptual model implies the arrival of new magma (represented in the deposit by P1 clasts) into a small, outgassed magma body which was accumulated at shallow level (mainly represented by P2 clasts). A new Chaimilla-type eruption could significantly affect the communities that have recently developed around Villarrica volcano and subsist mainly on tourism and forestry. As a result, a better understanding of the dynamics and evolution of the Chaimilla eruption is necessary for the identification of potential hazard scenarios at Villarrica volcano and, ultimately, for the risk mitigation of this populated area of Southern Chile.

The 3of5 web application for complex and comprehensive pattern matching in protein sequences.

PubMed

Seiler, Markus; Mehrle, Alexander; Poustka, Annemarie; Wiemann, Stefan

2006-03-16

The identification of patterns in biological sequences is a key challenge in genome analysis and in proteomics. Frequently such patterns are complex and highly variable, especially in protein sequences. They are frequently described using terms of regular expressions (RegEx) because of the user-friendly terminology. Limitations arise for queries with the increasing complexity of patterns and are accompanied by requirements for enhanced capabilities. This is especially true for patterns containing ambiguous characters and positions and/or length ambiguities. We have implemented the 3of5 web application in order to enable complex pattern matching in protein sequences. 3of5 is named after a special use of its main feature, the novel n-of-m pattern type. This feature allows for an extensive specification of variable patterns where the individual elements may vary in their position, order, and content within a defined stretch of sequence. The number of distinct elements can be constrained by operators, and individual characters may be excluded. The n-of-m pattern type can be combined with common regular expression terms and thus also allows for a comprehensive description of complex patterns. 3of5 increases the fidelity of pattern matching and finds ALL possible solutions in protein sequences in cases of length-ambiguous patterns instead of simply reporting the longest or shortest hits. Grouping and combined search for patterns provides a hierarchical arrangement of larger patterns sets. The algorithm is implemented as internet application and freely accessible. The application is available at http://dkfz.de/mga2/3of5/3of5.html. The 3of5 application offers an extended vocabulary for the definition of search patterns and thus allows the user to comprehensively specify and identify peptide patterns with variable elements. The n-of-m pattern type offers an improved accuracy for pattern matching in combination with the ability to find all solutions, without compromising the user friendliness of regular expression terms.

The use of heart rate variability in assessing precompetitive stress in high-standard judo athletes.

PubMed

Morales, J; Garcia, V; García-Massó, X; Salvá, P; Escobar, R; Buscà, B

2013-02-01

The objective of this study is to examine the sensitivity to and changes in heart rate variability (HRV) in stressful situations before judo competitions and to observe the differences among judo athletes according to their competitive standards in both official and unofficial competitions. 24 (10 male and 14 female) national- and international-standard athletes were evaluated. Each participant answered the Revised Competitive State Anxiety Inventory (CSAI-2R) and their HRV was recorded both during an official and unofficial competition. The MANOVA showed significant main effects of the athlete's standard and the type of competition in CSAI-2R, in HRV time domain, in HRV frequency domain and in HRV nonlinear analysis (p<0.05). International-standard judo athletes have lower somatic anxiety, cognitive anxiety, heart rate and low-high frequency ratio than national-standard athletes (p<0.05). International-standard athletes have a higher confidence, mean RR interval, standard deviation of RR, square root of the mean squared difference of successive RR intervals, number of consecutive RR that differ by more than 5 ms, short-term variability, long-term variability, long-range scaling exponents and short-range scaling exponent than national-standard judo athletes. In conclusion, international-standard athletes show less pre-competitive anxiety than the national-standard athletes and HRV analysis is sensitive to changes in pre-competitive anxiety. © Georg Thieme Verlag KG Stuttgart · New York.

Microplates in liquid chromatography--new solution in clinical research? A review.

PubMed

Krcmova, Lenka; Solichova, Dagmar; Solich, Petr

2013-10-15

Microplates are routinely used in Radio- or Immuno-assays. Recently, microplates have found use not only in analytical but also in the pre-analytical phase in bioanalyses (sample storage, sample preparation). New connection of this technology to liquid chromatography could be economical, fast and simple solution for many routine laboratories handling large sequences of biological samples. This review summarises the application of microplates in bioanalytical laboratories. Different types of sorbents, materials and shapes of microplates are discussed, and the main advantages and disadvantages of microplates used in clinical research are presented. Copyright © 2013 Elsevier B.V. All rights reserved.

Stellar and Circumstellar Properties of the Pre-Main-Sequence Binary GV Tau From Infrared Spectroscopy

DTIC Science & Technology

2008-09-20

surface gravity . With ourL-band spectra in order 25 (3.0450Y3.0865m;Fig. 1e), we detect strong HCN absorption (10% deep) and weaker C2H2 absorption in...Doppmann et al. 2005). The absorption lines of Na i and Mg i are particularly gravity and temperature sensitive, but in the opposite sense from each...other. For example, at cool effective temperatures (3200Y4500 K) and subdwarf surface gravities (3:5 log g 4:5) Na andMg lines both grow stronger as

Lithium and age of pre-main sequence stars: the case of Parenago 1802

NASA Astrophysics Data System (ADS)

Giarrusso, M.; Tognelli, E.; Catanzaro, G.; Degl'Innocenti, S.; Dell'Omodarme, M.; Lamia, L.; Leone, F.; Pizzone, R. G.; Prada Moroni, P. G.; Romano, S.; Spitaleri, C.

2016-04-01

With the aim to test the present capability of the stellar surface lithium abundance in providing an estimation for the age of PMS stars, we analyze the case of the detached, double-lined, eclipsing binary system PAR 1802. For this system, the lithium age has been compared with the theoretical one, as estimated by applying a Bayesian analysis method on a large grid of stellar evolutionary models. The models have been computed for several values of chemical composition and mixing length, by means of the code FRANEC updated with the Trojan Horse reaction rates involving lithium burning.

Theoretical Modeling and Computer Simulations for the Origins and Evolution of Reproducing Molecular Systems and Complex Systems with Many Interactive Parts

NASA Technical Reports Server (NTRS)

Liang, Shoudan

2000-01-01

Our research effort has produced nine publications in peer-reviewed journals listed at the end of this report. The work reported here are in the following areas: (1) genetic network modeling; (2) autocatalytic model of pre-biotic evolution; (3) theoretical and computational studies of strongly correlated electron systems; (4) reducing thermal oscillations in atomic force microscope; (5) transcription termination mechanism in prokaryotic cells; and (6) the low glutamine usage in thennophiles obtained by studying completely sequenced genomes. We discuss the main accomplishments of these publications.

Nature vs. Nurture: The influence of OB star environments on proto-planetary disk evolution

NASA Astrophysics Data System (ADS)

Bouwman, Jeroen

2006-09-01

We propose a combined IRAC/IRS study of a large, well-defined and unbiased X-ray selected sample of pre-main-sequence stars in three OB associations: Pismis 24 in NGC 6357, NGC 2244 in the Rosette Nebula, and IC 1795 in the W3 complex. The samples are based on recent Chandra X-ray Observatory studies which reliably identify hundreds of cluster members and were carefully chosen to avoid high infrared nebular background. A new Chandra exposure of IC 1795 is requested, and an optical followup to characterise the host stars is planned.

Microwave pulse compression from a storage cavity with laser-induced switching

DOEpatents

Bolton, Paul R.

1992-01-01

A laser-induced switch and a multiple cavity configuration are disclosed for producing high power microwave pulses. The microwave pulses are well controlled in wavelength and timing, with a quick rise time and a variable shape and power of the pulse. In addition, a method of reducing pre-pulse leakage to a low level is disclosed. Microwave energy is directed coherently to one or more cavities that stores the energy in a single mode, represented as a standing wave pattern. In order to switch the stored microwave energy out of the main cavity and into the branch waveguide, a laser-actuated switch is provided for the cavity. The switch includes a laser, associated optics for delivering the beam into the main cavity, and a switching gas positioned at an antinode in the main cavity. When actuated, the switching gas ionizes, creating a plasma, which becomes reflective to the microwave energy, changing the resonance of the cavity, and as a result the stored microwave energy is abruptly switched out of the cavity. The laser may directly pre-ionize the switching gas, or it may pump an impurity in the switching gas to an energy level which switches when a pre-selected cavity field is attained. Timing of switching the cavities is controlled by varying the pathlength of the actuating laser beam. For example, the pathlengths may be adjusted to output a single pulse of high power, or a series of quick lower power pulses.

Pre-capture multiplexing improves efficiency and cost-effectiveness of targeted genomic enrichment.

PubMed

Shearer, A Eliot; Hildebrand, Michael S; Ravi, Harini; Joshi, Swati; Guiffre, Angelica C; Novak, Barbara; Happe, Scott; LeProust, Emily M; Smith, Richard J H

2012-11-14

Targeted genomic enrichment (TGE) is a widely used method for isolating and enriching specific genomic regions prior to massively parallel sequencing. To make effective use of sequencer output, barcoding and sample pooling (multiplexing) after TGE and prior to sequencing (post-capture multiplexing) has become routine. While previous reports have indicated that multiplexing prior to capture (pre-capture multiplexing) is feasible, no thorough examination of the effect of this method has been completed on a large number of samples. Here we compare standard post-capture TGE to two levels of pre-capture multiplexing: 12 or 16 samples per pool. We evaluated these methods using standard TGE metrics and determined the ability to identify several classes of genetic mutations in three sets of 96 samples, including 48 controls. Our overall goal was to maximize cost reduction and minimize experimental time while maintaining a high percentage of reads on target and a high depth of coverage at thresholds required for variant detection. We adapted the standard post-capture TGE method for pre-capture TGE with several protocol modifications, including redesign of blocking oligonucleotides and optimization of enzymatic and amplification steps. Pre-capture multiplexing reduced costs for TGE by at least 38% and significantly reduced hands-on time during the TGE protocol. We found that pre-capture multiplexing reduced capture efficiency by 23 or 31% for pre-capture pools of 12 and 16, respectively. However efficiency losses at this step can be compensated by reducing the number of simultaneously sequenced samples. Pre-capture multiplexing and post-capture TGE performed similarly with respect to variant detection of positive control mutations. In addition, we detected no instances of sample switching due to aberrant barcode identification. Pre-capture multiplexing improves efficiency of TGE experiments with respect to hands-on time and reagent use compared to standard post-capture TGE. A decrease in capture efficiency is observed when using pre-capture multiplexing; however, it does not negatively impact variant detection and can be accommodated by the experimental design.

Evolution of multi-drug resistant HCV clones from pre-existing resistant-associated variants during direct-acting antiviral therapy determined by third-generation sequencing

NASA Astrophysics Data System (ADS)

Takeda, Haruhiko; Ueda, Yoshihide; Inuzuka, Tadashi; Yamashita, Yukitaka; Osaki, Yukio; Nasu, Akihiro; Umeda, Makoto; Takemura, Ryo; Seno, Hiroshi; Sekine, Akihiro; Marusawa, Hiroyuki

2017-03-01

Resistance-associated variant (RAV) is one of the most significant clinical challenges in treating HCV-infected patients with direct-acting antivirals (DAAs). We investigated the viral dynamics in patients receiving DAAs using third-generation sequencing technology. Among 283 patients with genotype-1b HCV receiving daclatasvir + asunaprevir (DCV/ASV), 32 (11.3%) failed to achieve sustained virological response (SVR). Conventional ultra-deep sequencing of HCV genome was performed in 104 patients (32 non-SVR, 72 SVR), and detected representative RAVs in all non-SVR patients at baseline, including Y93H in 28 (87.5%). Long contiguous sequences spanning NS3 to NS5A regions of each viral clone in 12 sera from 6 representative non-SVR patients were determined by third-generation sequencing, and showed the concurrent presence of several synonymous mutations linked to resistance-associated substitutions in a subpopulation of pre-existing RAVs and dominant isolates at treatment failure. Phylogenetic analyses revealed close genetic distances between pre-existing RAVs and dominant RAVs at treatment failure. In addition, multiple drug-resistant mutations developed on pre-existing RAVs after DCV/ASV in all non-SVR cases. In conclusion, multi-drug resistant viral clones at treatment failure certainly originated from a subpopulation of pre-existing RAVs in HCV-infected patients. Those RAVs were selected for and became dominant with the acquisition of multiple resistance-associated substitutions under DAA treatment pressure.

Molecular and morphological discrimination of stipitate hydnoids in the genera Hydnellum and Phellodon.

PubMed

Parfitt, David; Martyn Ainsworth, A; Simpson, Deborah; Rogers, Hilary J; Boddy, Lynne

2007-07-01

Hydnellum and Phellodon species, generally considered ectomycorrhizal partners of a range of woody angiosperms and gymnosperms particularly within Fagaceae and Pinaceae, appear to be declining in continental Europe. They are listed as priority species in the UK Biodiversity Action Plan, but their UK conservation status remains uncertain. Interpretation of species distribution data is hampered by a lack of consensus regarding some key discriminatory morphological characters and difficulties with their interpretation. DNA sequencing of the ITS1 region of the ribosomal gene cluster discriminated between the known British species of Phellodon but revealed more terminal clusters than currently recognised taxa. Although the main focus within Hydnellum was on the very similar species pair H. concrescens and H. scrobiculatum, a few samples of H. caeruleum, H. ferrugineum, H. peckii, and H. spongiosipes were included in the study for reference. DNA sequencing of material identified on spore-based criteria as H. concrescens yielded two main groups, but samples received as H. scrobiculatum were generally more variable. Of these, two were reassigned and the remaining group, with very similar spores (although shorter than in published descriptions of H. scrobiculatum), had highly variable sequence data. The results and conservation importance of these fungi highlight the need for a taxonomic reassessment of P. melaleucus, P. niger, H. concrescens, and H. scrobiculatum collections from Britain and continental Europe using a combined molecular and morphological approach. Specific PCR primers were constructed to discriminate fruit bodies, mycelium, and mycorrhizal roots of P. niger and P. confluens from each other and from other stipitate hydnoids.

Sequence stratigraphy and high-frequency cycles: New aspects for a quantitative evaluation of the Gulf of Suez basin, Egypt

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nio, S.D.; Yang, C.S.; Tewfik, N.

1993-09-01

A new development in the application of sequence stratigraphic concepts in marine as well as continental basins is the recognition of high-frequency cyclic patterns in rock successions in the subsurface. Studies of six wells from the northern, central, and southern parts of the Gulf of Suez show the presence of well-preserved, high-frequency cycles with periodicities similar to the orbitally forced Malankovitch parameters. Subsurface rock successions, third-order sequences, and high-frequency cycles were compared with outcrops. After establishing the biostratigraphic framework for the above-mentioned wells, a sequence analysis was performed. Sequence boundaries and maximum flooding positions in each well were calibrated withmore » the occurrences and evaluation of the high-frequency cycles. It became obvious that there is an intimate relationship between these high-frequency Milankovitch cycles and sequence organization. In addition, a close relationship can be observed in the subsurface as well as in outcrops between high-frequency climatic changes (connected to the Milankovitch cycles) and (litho)facies variability. Quantitative evaluations of each sequence and/or systems tract can be computed with the International Geoservices' cyclicity analysis tool (MILABAR). The results are summarized in a well composite chart, rate (NAR), and ratio of preserved time. In correlations between the wells, an accuracy of 500-100 Ka can be obtained. The quantitative evaluation of the sequence and high-frequency cycle analysis gave some new aspects concerning the (litho)facies and geodynamic development during the pre- as well as the synrift stages of the Gulf of Suez Basin.« less

Comparison of whole-genome bisulfite sequencing library preparation strategies identifies sources of biases affecting DNA methylation data.

PubMed

Olova, Nelly; Krueger, Felix; Andrews, Simon; Oxley, David; Berrens, Rebecca V; Branco, Miguel R; Reik, Wolf

2018-03-15

Whole-genome bisulfite sequencing (WGBS) is becoming an increasingly accessible technique, used widely for both fundamental and disease-oriented research. Library preparation methods benefit from a variety of available kits, polymerases and bisulfite conversion protocols. Although some steps in the procedure, such as PCR amplification, are known to introduce biases, a systematic evaluation of biases in WGBS strategies is missing. We perform a comparative analysis of several commonly used pre- and post-bisulfite WGBS library preparation protocols for their performance and quality of sequencing outputs. Our results show that bisulfite conversion per se is the main trigger of pronounced sequencing biases, and PCR amplification builds on these underlying artefacts. The majority of standard library preparation methods yield a significantly biased sequence output and overestimate global methylation. Importantly, both absolute and relative methylation levels at specific genomic regions vary substantially between methods, with clear implications for DNA methylation studies. We show that amplification-free library preparation is the least biased approach for WGBS. In protocols with amplification, the choice of bisulfite conversion protocol or polymerase can significantly minimize artefacts. To aid with the quality assessment of existing WGBS datasets, we have integrated a bias diagnostic tool in the Bismark package and offer several approaches for consideration during the preparation and analysis of WGBS datasets.

A new model for approximating RNA folding trajectories and population kinetics

NASA Astrophysics Data System (ADS)

Kirkpatrick, Bonnie; Hajiaghayi, Monir; Condon, Anne

2013-01-01

RNA participates both in functional aspects of the cell and in gene regulation. The interactions of these molecules are mediated by their secondary structure which can be viewed as a planar circle graph with arcs for all the chemical bonds between pairs of bases in the RNA sequence. The problem of predicting RNA secondary structure, specifically the chemically most probable structure, has many useful and efficient algorithms. This leaves RNA folding, the problem of predicting the dynamic behavior of RNA structure over time, as the main open problem. RNA folding is important for functional understanding because some RNA molecules change secondary structure in response to interactions with the environment. The full RNA folding model on at most O(3n) secondary structures is the gold standard. We present a new subset approximation model for the full model, give methods to analyze its accuracy and discuss the relative merits of our model as compared with a pre-existing subset approximation. The main advantage of our model is that it generates Monte Carlo folding pathways with the same probabilities with which they are generated under the full model. The pre-existing subset approximation does not have this property.

Searches for electromagnetic signals from extraterrestrial beings

NASA Astrophysics Data System (ADS)

Zuckerman, B.

The techniques and rationale used in six radio-frequency surveys to detect possible signals from extraterrestrial beings (ETs) are reviewed. Reception attempts have been made by pointing antennas at the stars within 80 light years, toward F, G, K, andd M main sequence stars, and binary star systems with component separation less than one-third or more than three times the radius of the habitable zone around the main star. All of the searches explored narrow bandwidths, with attention given to rapid variability. Stars exhibiting variability were re-examined for longer periods, using the 21 cm bandwidth, which is not used for transmissions on earth. The best spectrum analyzer in operation for ET signal search purposes has a capacity of 200,000 channels. Further studies may be carried out at the 10 micron IR wavelength, which could detect planetary-size construction projects by ET civilizations.

The effects of differential and variable training on the quality parameters of a handball throw.

PubMed

Wagner, Herbert; Müller, Erich

2008-01-01

The aim of this study was to undertake a comprehensive temporal, effective, and practical training study (variable and differential learning) that would offer athletes the opportunity to increase their performance, and to analyse the effects by measuring kinematics and quality parameters. Two participants of differing standards--a player of the first Austrian League and an Olympic and World Champion--but of similar anthropometric characteristics were recruited. One of the participants (Austrian League) was tested on five different occasions (pre-test and four retests) to measure the effects of four different training phases using kinematic analysis. The results of the study indicate an increase in ball velocity within the differential training phases (first, second, and fourth phases), different proximal-to-distal sequences of the participants, and a change of movement pattern during training measured by the segment velocities and the angle-time courses.

HLA-E coding and 3' untranslated region variability determined by next-generation sequencing in two West-African population samples.

PubMed

Castelli, Erick C; Mendes-Junior, Celso T; Sabbagh, Audrey; Porto, Iane O P; Garcia, André; Ramalho, Jaqueline; Lima, Thálitta H A; Massaro, Juliana D; Dias, Fabrício C; Collares, Cristhianna V A; Jamonneau, Vincent; Bucheton, Bruno; Camara, Mamadou; Donadi, Eduardo A

2015-12-01

HLA-E is a non-classical Human Leucocyte Antigen class I gene with immunomodulatory properties. Whereas HLA-E expression usually occurs at low levels, it is widely distributed amongst human tissues, has the ability to bind self and non-self antigens and to interact with NK cells and T lymphocytes, being important for immunosurveillance and also for fighting against infections. HLA-E is usually the most conserved locus among all class I genes. However, most of the previous studies evaluating HLA-E variability sequenced only a few exons or genotyped known polymorphisms. Here we report a strategy to evaluate HLA-E variability by next-generation sequencing (NGS) that might be used to other HLA loci and present the HLA-E haplotype diversity considering the segment encoding the entire HLA-E mRNA (including 5'UTR, introns and the 3'UTR) in two African population samples, Susu from Guinea-Conakry and Lobi from Burkina Faso. Our results indicate that (a) the HLA-E gene is indeed conserved, encoding mainly two different protein molecules; (b) Africans do present several unknown HLA-E alleles presenting synonymous mutations; (c) the HLA-E 3'UTR is quite polymorphic and (d) haplotypes in the HLA-E 3'UTR are in close association with HLA-E coding alleles. NGS has proved to be an important tool on data generation for future studies evaluating variability in non-classical MHC genes. Copyright © 2015 American Society for Histocompatibility and Immunogenetics. Published by Elsevier Inc. All rights reserved.

Responses of woody species to spatial and temporal ground water changes in coastal sand dune systems

NASA Astrophysics Data System (ADS)

Máguas, C.; Rascher, K. G.; Martins-Loução, A.; Carvalho, P.; Pinho, P.; Ramos, M.; Correia, O.; Werner, C.

2011-12-01

In spite of the relative importance of groundwater in costal dune systems, studies concerning the responses of vegetation to ground water (GW) availability variations, particularly in Mediterranean regions, are scarce. Thus, the main purpose of this study is to compare the responses of co-occurring species possessing different functional traits, to changes in GW levels (i.e. the lowering of GW levels) in a sand dune ecosystem. For that, five sites were established within a 1 km2 area in a meso-mediterranean sand dune ecosystem dominated by a Pinus pinaster forest. Due to natural topographic variability and anthropogenic GW exploitation, substantial variability in depth to GW between sites was found. Under these conditions it was possible to identify the degree of usage and dependence on GW of different plant species (two deep-rooted trees, a drought adapted shrub, a phreatophyte and a non-native woody invader) and how GW dependence varied seasonally and between the heterogeneous sites. Results indicated that the plant species had differential responses to changes in GW depth according to specific functional traits (i.e. rooting depth, leaf morphology, and water use strategy). Species comparison revealed that variability in pre-dawn water potential (Ψpre) and bulk leaf δ13C was related to site differences in GW use in the deep-rooted (Pinus pinaster, Myrica faya) and phreatophyte (Salix repens) species. However, such variation was more evident during spring than during summer drought. The exotic invader, Acacia longifolia, which does not possess a very deep root system, presented the largest seasonal variability in Ψpre and bulk leaf δ13C. In contrast, the response of Corema album, an endemic understory drought-adapted shrub, seemed to be independent of water availability across seasons and sites. Thus, the susceptibility to lowering of GW due to anthropogenic exploitation, in plant species from sand dunes, is variable, being particularly relevant for deep rooted species and phreatophytes, which seem to depend heavily on access to GW.

[Hormonal regulation of metabolism in the human body in microgravity and during simulation of its physiological effects].

PubMed

Larina, I M

2003-01-01

The paper presents results of investigations into the effects of space flight and simulation experiments of various length on the hormonal regulation of metabolism in the human body. Microgravity was shown to instigate shifts on different levels of the hormonal regulation and consequent adjustment of metabolism to this new environment. For instance, adaptation occurs on the level of basal secretory activity resulting in altered metabolism and formation of a pool of hormones. Metabolism readaptation to the Earth's gravity is dependent on polymorphic processes in the system of hormonal regulation developing in the course of time. Trends in the hormonal regulation of water-electrolyte metabolism during early adaptation point to inequality of contributions of the antidiuretic hormone, natriuretic peptide, and the renin-angiotensin-aldosterone system. In the ground-based simulations responses of the hormonal regulation of water-electrolyte metabolism differ in intensity and types of hormones involved. Temperature variation can modify reactions of the comosis and volume regulating hormones at the beginning of adaptation. Physical-chemical regulation of calcium homeostasis in microgravity reveals itself by a rapid decline of the calcium-binding ability of blood buffers and, later on, degradation of the relative ability of extraplasmic structures to bind calcium. Qualitative and quantitative changes in the diurnal rhythm of the suprarenal steroidogenesis are indicative of modification of intensity of reactions of the main biosynthetic sequences. Countermeasures used by test-subjects in these investigations loosened significantly the aldosterone-secreting biosynthetic sequences but were favorable to the synthesis of testosterone and hydrocortisone. Some of the highly variable processes of hormonal regulation were mute to the diurnal rhythms in the pre-flight and preexperimental periods.

Monitoring of EPIC 204278916 requested

NASA Astrophysics Data System (ADS)

Waagen, Elizabeth O.

2017-04-01

Dr. Carlo Manara (ESA Science and Technology SCI-S, the Netherlands) and colleagues have requested AAVSO assistance in monitoring the young, disk-bearing low-mass (M type) pre-main-sequence star EPIC 204278916 (2MASS J16020757-2257467). Dr. Manara reports that this star showed "a very interesting dimming event in August-September 2014 which may be caused by transiting material (exo-comets like) (Scaringi et al., 2016MNRAS.463.2265S, https://ui.adsabs.harvard.edu/#abs/2016MNRAS.tmp.1267S/abstract). It would be very useful to know whether this event has any periodicity in order to constrain the possible scenario...The major dimming [up to 65%] we see is 1.2 mag in V, others are 0.5-0.8 mag" in V. He also notes that "the dimming event we saw lasted for some 25 days, although the most extreme event was 1 day long. Based on the noisy WASP data we have [there are] some suggestions that the event happens every 100 days, but we are not sure about it." Manara requests ongoing monitoring of this system to look for additional dimming events and to observe any that are seen, so that he and his colleagues may determine if periodicity exists in these events and to study its nature. Beginning now and continuing until further notice, nightly observations in V are requested. Weekly observations in B are also requested. If a dimming event occurs, observations in V and B at a higher cadence are requested. Finder charts with sequence may be created using the AAVSO Variable Star Plotter (https://www.aavso.org/vsp). Observations should be submitted to the AAVSO International Database. See full Alert Notice for more details.

DNA sequence templates adjacent nucleosome and ORC sites at gene amplification origins in Drosophila

PubMed Central

Liu, Jun; Zimmer, Kurt; Rusch, Douglas B.; Paranjape, Neha; Podicheti, Ram; Tang, Haixu; Calvi, Brian R.

2015-01-01

Eukaryotic origins of DNA replication are bound by the origin recognition complex (ORC), which scaffolds assembly of a pre-replicative complex (pre-RC) that is then activated to initiate replication. Both pre-RC assembly and activation are strongly influenced by developmental changes to the epigenome, but molecular mechanisms remain incompletely defined. We have been examining the activation of origins responsible for developmental gene amplification in Drosophila. At a specific time in oogenesis, somatic follicle cells transition from genomic replication to a locus-specific replication from six amplicon origins. Previous evidence indicated that these amplicon origins are activated by nucleosome acetylation, but how this affects origin chromatin is unknown. Here, we examine nucleosome position in follicle cells using micrococcal nuclease digestion with Ilumina sequencing. The results indicate that ORC binding sites and other essential origin sequences are nucleosome-depleted regions (NDRs). Nucleosome position at the amplicons was highly similar among developmental stages during which ORC is or is not bound, indicating that being an NDR is not sufficient to specify ORC binding. Importantly, the data suggest that nucleosomes and ORC have opposite preferences for DNA sequence and structure. We propose that nucleosome hyperacetylation promotes pre-RC assembly onto adjacent DNA sequences that are disfavored by nucleosomes but favored by ORC. PMID:26227968

The provenance of Archean clastic metasediments in the Narryer Gneiss Complex, Western Australia: Trace element geochemistry, Nd isotopes, and U-Pb ages for detrital zircons

NASA Astrophysics Data System (ADS)

Maas, Roland; McCulloch, Malcolm T.

1991-07-01

Clastic metasedimentary rocks of mid-Archean age from the Mt. Narryer and Jack Hills metasedimentary belts have REE patterns resembling those of mid- to late-Archean pelitic-quartzitic cratonic sequences elsewhere, and post-Archean continental rocks in general. Detrital zircons in the metasediments range in age from ca. 3000 to 3700 Ma. This indicates a provenance from mature cratonic sources controlled by K-rich granitic rocks. Additional minor sediment sources were identified as older, mainly chemical sedimentary sequences, ultramafic rocks, and felsic rocks characterized by low HREE contents, perhaps of tonalitic affinity. The association of the near-shore/fluviatile clastic association studied here with extensive turbiditic and chemical sedimentary sequences indicates these sources formed part of a (rifted ?) cratonic margin ca. 3 Ga ago. Differences between sedimentary REE patterns and those in the surrounding 3.73-3.0 Ga orthogneiss terrain, and between detrital zircon ages and the age distribution in the gneisses, suggest that the present association of the metasedimentary belts with the orthogneiss terrain is of tectonic origin. The occurrence of detrital zircons with U-Pb ages > 4 Ga in certain quartzites and conglomerates of the Jack Hills and Mt. Narryer metasedimentary sequences indicates a further, most likely granitic, source. ɛNd( TDep) values in Jack Hills metasediments vary widely (+5 to -12) but have a smaller range in the Mt. Narryer belt (-5 to -9). The lowest ɛNd values of both sequences are interpreted to reflect the presence of detritus derived from 4.1-4.2 Ga old LREE-enriched continental crust in proportions considerably larger (≥ 10%) than estimated previously from the abundance of pre-4 Ga detrital zircons (≈3%). This would imply the former existence of significant volumes of pre-4 Ga continental crust in the provenance of the Mt. Narryer and Jack Hills metasediments.

Monitoring solar-type stars for luminosity variations

NASA Technical Reports Server (NTRS)

Lockwood, G. W.; Skiff, B. A.

1988-01-01

Since 1984, researchers have made more than 1500 differential photometric b (471 nm) and y (551 nm) measurements of three dozen solar-like lower main sequence stars whose chromospheric activity was previosly studied by O. C. Wilson. Here, researchers describe their methodology and the statistical tests used to distinguish intrinsic stellar variability from observational and instrument errors. The incidence of detected variability among the program and comparison stars is summarized. Among the 100 plus pairs of stars measured differentially, only a dozen were found that were unusually constant, with peak-to-peak amplitudes of seasonal mean brightness smaller than 0.3 percent (0.003 mag) over a two-to-three-year interval.

Improved first-pass spiral myocardial perfusion imaging with variable density trajectories.

PubMed

Salerno, Michael; Sica, Christopher; Kramer, Christopher M; Meyer, Craig H

2013-11-01

To develop and evaluate variable-density spiral first-pass perfusion pulse sequences for improved efficiency and off-resonance performance and to demonstrate the utility of an apodizing density compensation function (DCF) to improve signal-to-noise ratio (SNR) and reduce dark-rim artifact caused by cardiac motion and Gibbs Ringing. Three variable density spiral trajectories were designed, simulated, and evaluated in 18 normal subjects, and in eight patients with cardiac pathology on a 1.5T scanner. By using a DCF, which intentionally apodizes the k-space data, the sidelobe amplitude of the theoretical point spread function (PSF) is reduced by 68%, with only a 13% increase in the full-width at half-maximum of the main-lobe when compared with the same data corrected with a conventional variable-density DCF, and has an 8% higher resolution than a uniform density spiral with the same number of interleaves and readout duration. Furthermore, this strategy results in a greater than 60% increase in measured SNR when compared with the same variable-density spiral data corrected with a conventional DCF (P < 0.01). Perfusion defects could be clearly visualized with minimal off-resonance and dark-rim artifacts. Variable-density spiral pulse sequences using an apodized DCF produce high-quality first-pass perfusion images with minimal dark-rim and off-resonance artifacts, high SNR and contrast-to-noise ratio, and good delineation of resting perfusion abnormalities. Copyright © 2012 Wiley Periodicals, Inc.

Coupled nature of evening-time ionospheric electrodynamics

NASA Astrophysics Data System (ADS)

Joshi, L. M.; Tsai, L. C.

2018-04-01

The F region evening electrodynamics in the equatorial region is characterized by a pre-reversal enhancement (PRE) in the zonal eastward electric field. Although the theoretical mechanisms for PRE are known, its variability, particularly day-to-day variability is not fully resolved. PRE is a large scale phenomenon driven by the F region dynamo after the sunset hours. This paper investigates whether the variability of the E region conductivity (particularly the one associated with the sporadic E, Es) has any influence on the F region dynamo and hence on the PRE of zonal electric field. Interestingly, ionosonde observations have indicated a higher occurrence of the blanketing type Es (Esb) over the low latitude on days with highly suppressed PRE of zonal electric field in comparison with the days with significantly larger PRE. Observational evidences presented in this paper suggests that the formation of the Esb in the evening hours is a sovereign process, not always controlled by the sheared F region vertical electric field of equatorial origin, mapping along the magnetic field line on to the low latitude E region. Model computations of the PRE suppression based on the measured Es densities have further substantiated the observational findings presented in this paper. These results clearly indicate that the low latitude Es has the potential to suppress the PRE of zonal electric field and possibly can play a vital role in explaining the PRE variability, particularly the day-to-day variability. Results have been discussed in light of earlier reports on PRE mechanisms and E-F region coupling processes.

IDENTIFICATION OF THE LITHIUM DEPLETION BOUNDARY AND AGE OF THE SOUTHERN OPEN CLUSTER BLANCO 1

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cargile, P. A.; James, D. J.; Jeffries, R. D., E-mail: p.cargile@vanderbilt.ed

2010-12-20

We present results from a spectroscopic study of the very low mass members of the Southern open cluster Blanco 1 using the Gemini-N telescope. We obtained intermediate resolution (R {approx} 4400) GMOS spectra for 15 cluster candidate members with I {approx} 14-20 mag, and employed a series of membership criteria-proximity to the cluster's sequence in an I/I - K{sub s} color-magnitude diagram (CMD), kinematics agreeing with the cluster systemic motion, magnetic activity as a youth indicator-to classify 10 of these objects as probable cluster members. For these objects, we searched for the presence of the Li I 6708 A featuremore » to identify the lithium depletion boundary (LDB) in Blanco 1. The I/I - K{sub s} CMD shows a clear mass segregation in the Li distribution along the cluster sequence; namely, all higher mass stars are found to be Li poor, while lower mass stars are found to be Li rich. The division between Li-poor and Li-rich (i.e., the LDB) in Blanco 1 is found at I = 18.78 {+-} 0.24 and I - K{sub s} = 3.05 {+-} 0.10. Using current pre-main-sequence evolutionary models, we determine an LDB age of 132 {+-} 24 Myr. Comparing our derived LDB age to upper-main-sequence isochrone ages for Blanco 1, as well as for other open clusters with identified LDBs, we find good chronometric consistency when using stellar evolution models that incorporate a moderate degree of convective core overshoot.« less

Pre-stack depth Migration imaging of the Hellenic Subduction Zone

NASA Astrophysics Data System (ADS)

Hussni, S. G.; Becel, A.; Schenini, L.; Laigle, M.; Dessa, J. X.; Galve, A.; Vitard, C.

2017-12-01

In 365 AD, a major M>8-tsunamignic earthquake occurred along the southwestern segment of the Hellenic subduction zone. Although this is the largest seismic event ever reported in Europe, some fundamental questions remain regarding the deep geometry of the interplate megathrust, as well as other faults within the overriding plate potentially connected to it. The main objective here is to image those deep structures, whose depths range between 15 and 45 km, using leading edge seismic reflection equipment. To this end, a 210-km-long multichannel seismic profile was acquired with the 8 km-long streamer and the 6600 cu.in source of R/V Marcus Langseth. This was realized at the end of 2015, during the SISMED cruise. This survey was made possible through a collective effort gathering labs (Géoazur, LDEO, ISTEP, ENS-Paris, EOST, LDO, Dpt. Geosciences of Pau Univ). A preliminary processing sequence has first been applied using Geovation software of CGG, which yielded a post-stack time migration of collected data, as well as pre-stack time migration obtained with a model derived from velocity analyses. Using Paradigm software, a pre-stack depth migration was subsequently carried out. This step required some tuning in the pre-processing sequence in order to improve multiple removal, noise suppression and to better reveal the true geometry of reflectors in depth. This iteration of pre-processing included, the use of parabolic Radon transform, FK filtering and time variant band pass filtering. An initial velocity model was built using depth-converted RMS velocities obtained from SISMED data for the sedimentary layer, complemented at depth with a smooth version of the tomographic velocities derived from coincident wide-angle data acquired during the 2012-ULYSSE survey. Then, we performed a Kirchhoff Pre-stack depth migration with traveltimes calculated using the Eikonal equation. Velocity model were then tuned through residual velocity analyses to flatten reflections in common reflection point gathers. These new results improve the imaging of deep reflectors and even reveal some new features. We will present this work, a comparison with our previously obtained post-stack time migration, as well as some insights into the new geological structures revealed by the depth imaging.

Investigation of New Morpholino Oligomers to Increase Survival Motor Neuron Protein Levels in Spinal Muscular Atrophy

PubMed Central

Ramirez, Agnese; Crisafulli, Sebastiano G.; Rizzuti, Mafalda; Bresolin, Nereo; Comi, Giacomo P.; Corti, Stefania

2018-01-01

Spinal muscular atrophy (SMA) is an autosomal-recessive childhood motor neuron disease and the main genetic cause of infant mortality. SMA is caused by deletions or mutations in the survival motor neuron 1 (SMN1) gene, which results in SMN protein deficiency. Only one approved drug has recently become available and allows for the correction of aberrant splicing of the paralogous SMN2 gene by antisense oligonucleotides (ASOs), leading to production of full-length SMN protein. We have already demonstrated that a sequence of an ASO variant, Morpholino (MO), is particularly suitable because of its safety and efficacy profile and is both able to increase SMN levels and rescue the murine SMA phenotype. Here, we optimized this strategy by testing the efficacy of four new MO sequences targeting SMN2. Two out of the four new MO sequences showed better efficacy in terms of SMN protein production both in SMA induced pluripotent stem cells (iPSCs) and SMAΔ7 mice. Further, the effect was enhanced when different MO sequences were administered in combination. Our data provide an important insight for MO-based treatment for SMA. Optimization of the target sequence and validation of a treatment based on a combination of different MO sequences could support further pre-clinical studies and the progression toward future clinical trials. PMID:29316633

Investigation of New Morpholino Oligomers to Increase Survival Motor Neuron Protein Levels in Spinal Muscular Atrophy.

PubMed

Ramirez, Agnese; Crisafulli, Sebastiano G; Rizzuti, Mafalda; Bresolin, Nereo; Comi, Giacomo P; Corti, Stefania; Nizzardo, Monica

2018-01-06

Spinal muscular atrophy (SMA) is an autosomal-recessive childhood motor neuron disease and the main genetic cause of infant mortality. SMA is caused by deletions or mutations in the survival motor neuron 1 ( SMN1 ) gene, which results in SMN protein deficiency. Only one approved drug has recently become available and allows for the correction of aberrant splicing of the paralogous SMN2 gene by antisense oligonucleotides (ASOs), leading to production of full-length SMN protein. We have already demonstrated that a sequence of an ASO variant, Morpholino (MO), is particularly suitable because of its safety and efficacy profile and is both able to increase SMN levels and rescue the murine SMA phenotype. Here, we optimized this strategy by testing the efficacy of four new MO sequences targeting SMN2 . Two out of the four new MO sequences showed better efficacy in terms of SMN protein production both in SMA induced pluripotent stem cells (iPSCs) and SMAΔ7 mice. Further, the effect was enhanced when different MO sequences were administered in combination. Our data provide an important insight for MO-based treatment for SMA. Optimization of the target sequence and validation of a treatment based on a combination of different MO sequences could support further pre-clinical studies and the progression toward future clinical trials.

The Australian electricity market's pre-dispatch process: Some observations on its efficiency using ordered probit model

NASA Astrophysics Data System (ADS)

Zainudin, Wan Nur Rahini Aznie; Becker, Ralf; Clements, Adam

2015-12-01

Many market participants in Australia Electricity Market had cast doubts on whether the pre-dispatch process in the electricity market is able to give them good and timely quantity and price information. In a study by [11], they observed a significant bias (mainly indicating that the pre-dispatch process tends to underestimate spot price outcomes), a seasonality features of the bias across seasons and/or trading periods and changes in bias across the years in our sample period (1999 to 2007). In a formal setting of an ordered probit model we establish that there are some exogenous variables that are able to explain increased probabilities of over- or under-predictions of the spot price. It transpires that meteorological data, expected pre-dispatch prices and information on past over- and under-predictions contribute significantly to explaining variation in the probabilities for over- and under-predictions. The results allow us to conjecture that some of the bids and re-bids provided by electricity generators are not made in good faith.

Prevalence of precore-defective mutant of hepatitis B virus in HBV carriers.

PubMed

Niitsuma, H; Ishii, M; Saito, Y; Miura, M; Kobayashi, K; Ohori, H; Toyota, T

1995-08-01

Two hundred and seventy-three serum specimens from hepatitis B virus (HBV) carriers were examined for the presence of a characteristic one point mutation at nucleotide (nt) 1896 from the EcoRI site of the HBV genome in the precore region (the preC mutant) using restriction fragment length polymorphism (RFLP) analysis. This assay approach could detect preC mutants or wild-type sequences when either form constituted more than 10% of the total sample. Overall, 65.5% (76/116) of HBeAg-positive carriers had only the preC wild-type. All HBeAg-positive asymptomatic carriers (n = 14) had only the preC wild-type. In patients with chronic hepatitis B and in anti-HBe-positive asymptomatic carriers, increased prevalence of the preC mutant was associated with the development of anti-HBe antibodies and normalization of the serum alanine aminotransferase concentration. Furthermore, 27 (29.0%) of 93 HBeAg-negative carriers had unexpectedly preC wild-type sequences only. Direct sequencing of the HBV precore region of HBV specimens from 24 patients revealed no mutation at nt 1896, supporting the specificity of the RFLP analysis. These results suggest that RFLP analysis was accurate for the detection of the preC mutation and that the absence of serum HBeAg cannot be explained solely by the dominance of the preC mutant.

A Double Whammy: Health Promotion Among Cancer Survivors with Pre-Existing Functional Limitations

PubMed Central

Volker, Deborah L.; Becker, Heather; Kang, Sook Jung; Kullberg, Vicki

2012-01-01

Purpose/Objectives To explore the experience of living with a cancer diagnosis within the context of a pre-existing functional disability and to identify strategies to promote health in this growing population of cancer survivors. Research Approach Qualitative descriptive Setting Four sites in the United States Participants 19 female cancer survivors with pre-existing disabling conditions Methodologic Approach Four focus groups were conducted. The audiotapes were transcribed and analyzed using content analysis techniques. Main Research Variables cancer survivor, disability, health promotion Findings Analytic categories included living with a cancer diagnosis, health promotion strategies, and wellness program development for survivors with pre-existing functional limitations. Participants described many challenges associated with managing a cancer diagnosis on top of living with a chronic disabling functional limitation. They identified strategies they used to maintain their health and topics to be included in health promotion programs tailored for this unique group of cancer survivors. Conclusions The “double whammy” of a cancer diagnosis for persons with pre-existing functional limitations requires modification of health promotion strategies and programs to promote wellness in this group of cancer survivors. Interpretation Nurses and other health care providers must attend to patients’ pre-existing conditions as well as the challenges of the physical, emotional, social, and economic sequelae of a cancer diagnosis. PMID:23269771

An outline of graphical Markov models in dentistry.

PubMed

Helfenstein, U; Steiner, M; Menghini, G

1999-12-01

In the usual multiple regression model there is one response variable and one block of several explanatory variables. In contrast, in reality there may be a block of several possibly interacting response variables one would like to explain. In addition, the explanatory variables may split into a sequence of several blocks, each block containing several interacting variables. The variables in the second block are explained by those in the first block; the variables in the third block by those in the first and the second block etc. During recent years methods have been developed allowing analysis of problems where the data set has the above complex structure. The models involved are called graphical models or graphical Markov models. The main result of an analysis is a picture, a conditional independence graph with precise statistical meaning, consisting of circles representing variables and lines or arrows representing significant conditional associations. The absence of a line between two circles signifies that the corresponding two variables are independent conditional on the presence of other variables in the model. An example from epidemiology is presented in order to demonstrate application and use of the models. The data set in the example has a complex structure consisting of successive blocks: the variable in the first block is year of investigation; the variables in the second block are age and gender; the variables in the third block are indices of calculus, gingivitis and mutans streptococci and the final response variables in the fourth block are different indices of caries. Since the statistical methods may not be easily accessible to dentists, this article presents them in an introductory form. Graphical models may be of great value to dentists in allowing analysis and visualisation of complex structured multivariate data sets consisting of a sequence of blocks of interacting variables and, in particular, several possibly interacting responses in the final block.

The usefulness of design of experimentation in defining the effect difficult airway factors and training have on simulator oral-tracheal intubation success rates in novice intubators.

PubMed

Thomas, Frank; Carpenter, Judi; Rhoades, Carol; Holleran, Renee; Snow, Gregory

2010-04-01

This exploratory study examined novice intubators and the effect difficult airway factors have on pre- and posttraining oral-tracheal simulation intubation success rates. Using a two-level, full-factorial design of experimentation (DOE) involving a combination of six airway factors (curved vs. straight laryngoscope blade, trismus, tongue edema, laryngeal spasm, pharyngeal obstruction, or cervical immobilization), 64 airway scenarios were prospectively randomized to 12 critical care nurses to evaluate pre- and posttraining first-pass intubation success rates on a simulator. Scenario variables and intubation outcomes were analyzed using a generalized linear mixed-effects model to determine two-way main and interactive effects. Interactive effects between the six study factors were nonsignificant (p = 0.69). For both pre- and posttraining, main effects showed the straight blade (p = 0.006), tongue edema (p = 0.0001), and laryngeal spasm (p = 0.004) significantly reduced success rates, while trismus (p = 0.358), pharyngeal obstruction (p = 0.078), and cervical immobilization did not significantly change the success rate. First-pass intubation success rate on the simulator significantly improved (p = 0.005) from pre- (19%) to posttraining (36%). Design of experimentation is useful in analyzing the effect difficult airway factors and training have on simulator intubation success rates. Future quality improvement DOE simulator research studies should be performed to help clarify the relationship between simulator factors and patient intubation rates.

The conserved CAAGAAAGA spacer sequence is an essential element for the formation of 3' termini of the sea urchin H3 histone mRNA by RNA processing.

PubMed Central

Georgiev, O; Birnstiel, M L

1985-01-01

Analysis of cDNA sequences obtained from the small nuclear RNA U7 has previously suggested specific contacts, by base pairing, between the conserved stem-loop structure and CAAGAAAGA sequence of the histone pre-mRNA and the 5'-terminal sequence of the U7 RNA during RNA processing. In order to test some aspects of the model we have created a series of linker scan, deletion and insertion mutants of the 3' terminus of a sea urchin H3 histone gene and have injected mutant DNAs or in vitro synthesized precursors into frog oocyte nuclei for interpretation. We find that, in addition to the stem-loop structure of the mRNA, the CAAGAAAGA spacer transcript within the histone pre-mRNA is required absolutely for RNA processing, as predicted from our model. Spacer sequences immediately downstream of the CAAGAAAGA motif are not complementary to U7 RNA. Nevertheless, they are necessary for obtaining a maximal rate of RNA processing, as is the ACCA sequence coding for the 3' terminus of the mature mRNA. An increase of distance between the mRNA palindrome and the CAAGAAAGA by as little as six nucleotides abolishes all processing. It may, therefore, be useful to regard both these sequence motifs as part of one and the same RNA processing signal with narrowly defined topologies. Interestingly, U7 RNA-dependent 3' processing of histone pre-mRNA can occur in RNA injection experiments only when the in vitro synthesized pre-mRNA contains sequence extensions well beyond the region of sequence complementarities to the U7 RNA. In addition to directing 3' processing the terminal mRNA sequences may have a role in histone mRNA stabilization in the cytoplasmic compartment. Images Fig. 3. Fig. 4. Fig. 5. Fig. 6. Fig. 7. PMID:2410259

The preS deletion of hepatitis B virus (HBV) is associated with liver fibrosis progression in patients with chronic HBV infection.

PubMed

Li, Fan; Li, Xiaodong; Yan, Tao; Liu, Yan; Cheng, Yongqian; Xu, Zhihui; Shao, Qing; Liao, Hao; Huang, Pengyu; Li, Jin; Chen, Guo-Feng; Xu, Dongping

2018-03-01

Limited data are available regarding the association of hepatitis B virus (HBV) mutations with liver fibrosis in HBV infection. The study aimed to clarify whether HBV preS deletion mutation is associated with liver fibrosis progression. A total of 469 patients were enrolled, including 324 with chronic hepatitis B (CHB), 28 with HBV-related compensated liver cirrhosis (LC), and 117 with HBV-related decompensated LC. All CHB and compensated LC patients received liver biopsy. Fibrosis grade was assessed using METAVIR score. HBV preS deletion was determined by direct sequencing and verified by clonal sequencing. Overall preS deletion was detected in 12.6% (59/469) patients, specifically, in 7.51% (13/173), 10.60% (16/151), and 20.69% (30/145) of patients with no-to-mild liver fibrosis (F0-1), moderate-to-severe liver fibrosis (F2-3), and cirrhosis (F4), respectively (p < 0.01). Patients with preS-deleted HBV had lower serum HBV DNA and albumin levels compared to patients with wild-type HBV. The median length of preS deletion was 39-base pairs (bp) (3-204 bp) and the deletion most frequently emerged in preS2 initial region. Multivariate analysis identified the preS2 deletion rather than preS1 deletion to be an independent risk factor of significant fibrosis, i.e., METAVIR F ≥ 2 (p = 0.007). In addition, preS-deleted viral sequences were detected in the pool of intrahepatic HBV covalently closed circular DNA. HBV preS deletion is positively associated with liver fibrosis progression in chronic HBV-infected patients. HBV preS2 deletion may serve as a warning indicator for liver fibrosis progression.

Aftershock decay, productivity, and stress rates in Hawaii: Indicators of temperature and stress from magma sources

USGS Publications Warehouse

Klein, Fred W.; Wright, Tom; Nakata, Jennifer

2006-01-01

We examined dozens of aftershock sequences in Hawaii in terms of Gutenberg-Richter and modified Omori law parameters. We studied p, the rate of aftershock decay; Ap, the aftershock productivity, defined as the observed divided by the expected number of aftershocks; and c, the time delay when aftershock rates begin to fall. We found that for earthquakes shallower than 20 km, p values >1.2 are near active magma centers. We associate this high decay rate with higher temperatures and faster stress relaxation near magma reservoirs. Deep earthquakes near Kilauea's inferred magma transport path show a range of p values, suggesting the absence of a large, deep magma reservoir. Aftershock productivity is >4.0 for flank earthquakes known to be triggered by intrusions but is normal (0.25 to 4.0) for isolated main shocks. We infer that continuing, post-main shock stress from the intrusion adds to the main shock's stress step and causes higher Ap. High Ap in other zones suggests less obvious intrusions and pulsing magma pressure near Kilauea's feeding conduit. We calculate stress rates and stress rate changes from pre-main shock and aftershock rates. Stress rate increased after many intrusions but decreased after large M7–8 earthquakes. Stress rates are highest in the seismically active volcano flanks and lowest in areas far from volcanic centers. We found sequences triggered by intrusions tend to have high Ap, high (>0.10 day) c values, a stress rate increase, and sometimes a peak in aftershock rate hours after the main shock. We interpret these values as indicating continuing intrusive stress after the main shock.

A VLT/NACO survey for triple and quadruple systems among visual pre-main sequence binaries

NASA Astrophysics Data System (ADS)

Correia, S.; Zinnecker, H.; Ratzka, Th.; Sterzik, M. F.

2006-12-01

Aims.This paper describes a systematic search for high-order multiplicity among wide visual Pre-Main Sequence (PMS) binaries. Methods: .We conducted an Adaptive Optics survey of a sample of 58 PMS wide binaries from various star-forming regions, which include 52 T Tauri systems with mostly K- and M-type primaries, with the NIR instrument NACO at the VLT. Results: .Of these 52 systems, 7 are found to be triple (2 new) and 7 quadruple (1 new). The new close companions are most likely physically bound based on their probability of chance projection and, for some of them, on their position on a color-color diagram. The corresponding degree of multiplicity among wide binaries (number of triples and quadruples divided by the number of systems) is 26.9 ± 7.2% in the projected separation range ~0.07 arcsec -12'', with the largest contribution from the Taurus-Auriga cloud. We also found that this degree of multiplicity is twice in Taurus compared to Ophiuchus and Chamaeleon for which the same number of sources are present in our sample. Considering a restricted sample composed of systems at distance 140-190 pc, the degree of multiplicity is 26.8 ± 8.1%, in the separation range 10/14 AU-1700/2300 AU (30 binaries, 5 triples, 6 quadruples). The observed frequency agrees with results from previous multiplicity surveys within the uncertainties, although a significant overabundance of quadruple systems compared to triple systems is apparent. Tentatively including the spectroscopic pairs in our restricted sample and comparing the multiplicity fractions to those measured for solar-type main-sequence stars in the solar neighborhood leads to the conclusion that both the ratio of triples to binaries and the ratio of quadruples to triples seems to be in excess among young stars. Most of the current numerical simulations of multiple star formation, and especially smoothed particles hydrodynamics simulations, over-predict the fraction of high-order multiplicity when compared to our results. The circumstellar properties around the individual components of our high-order multiple systems tend to favor mixed systems (i.e. systems including components of wTTS and cTTS type), which is in general agreement with previous studies of disks in binaries, with the exception of Taurus, where we find a preponderance of similar type of components among the multiples studied.

Pre-Service Teachers' Approaches to a Historical Problem in Mechanics

ERIC Educational Resources Information Center

Malgieri, Massimiliano; Onorato, Pasquale; Mascheretti, Paolo; De Ambrosis, Anna

2014-01-01

In this paper we report on an activity sequence with a group of 29 pre-service physics teachers based on the reconstruction and analysis of a thought experiment that was crucial for Huygens' derivation of the formula for the centre of oscillation of a physical pendulum. The sequence starts with student teachers approaching the historical…

A Statistical Test of Walrasian Equilibrium by Means of Complex Networks Theory

NASA Astrophysics Data System (ADS)

Bargigli, Leonardo; Viaggiu, Stefano; Lionetto, Andrea

2016-10-01

We represent an exchange economy in terms of statistical ensembles for complex networks by introducing the concept of market configuration. This is defined as a sequence of nonnegative discrete random variables {w_{ij}} describing the flow of a given commodity from agent i to agent j. This sequence can be arranged in a nonnegative matrix W which we can regard as the representation of a weighted and directed network or digraph G. Our main result consists in showing that general equilibrium theory imposes highly restrictive conditions upon market configurations, which are in most cases not fulfilled by real markets. An explicit example with reference to the e-MID interbank credit market is provided.

The Evolution of Cataclysmic Variables as Revealed by Their Donor Stars

NASA Astrophysics Data System (ADS)

Knigge, Christian; Baraffe, Isabelle; Patterson, Joseph

2011-06-01

We present an attempt to reconstruct the complete evolutionary path followed by cataclysmic variables (CVs), based on the observed mass-radius relationship of their donor stars. Along the way, we update the semi-empirical CV donor sequence presented previously by one of us, present a comprehensive review of the connection between CV evolution and the secondary stars in these systems, and reexamine most of the commonly used magnetic braking (MB) recipes, finding that even conceptually similar ones can differ greatly in both magnitude and functional form. The great advantage of using donor radii to infer mass-transfer and angular-momentum-loss (AML) rates is that they sample the longest accessible timescales and are most likely to represent the true secular (evolutionary average) rates. We show explicitly that if CVs exhibit long-term mass-transfer-rate fluctuations, as is often assumed, the expected variability timescales are so long that other tracers of the mass-transfer rate—including white dwarf (WD) temperatures—become unreliable. We carefully explore how much of the radius difference between CV donors and models of isolated main-sequence stars may be due to mechanisms other than mass loss. The tidal and rotational deformation of Roche-lobe-filling stars produces ~= 4.5% radius inflation below the period gap and ~= 7.9% above. A comparison of stellar models to mass-radius data for non-interacting stars suggests a real offset of ~= 1.5% for fully convective stars (i.e., donors below the gap) and ~= 4.9% for partially radiative ones (donors above the gap). We also show that donor bloating due to irradiation is probably smaller than, and at most comparable to, these effects. After calibrating our models to account for these issues, we fit self-consistent evolution sequences to our compilation of donor masses and radii. In the standard model of CV evolution, AMLs below the period gap are assumed to be driven solely by gravitational radiation (GR), while AMLs above the gap are usually described by an MB law first suggested by Rappaport et al. We adopt simple scaled versions of these AML recipes and find that these are able to match the data quite well. The optimal scaling factors turn out to be f GR = 2.47 ± 0.22 below the gap and f MB = 0.66 ± 0.05 above (the errors here are purely statistical, and the standard model corresponds to f GR = f MB = 1). This revised model describes the mass-radius data significantly better than the standard model. Some of the most important implications and applications of our results are as follows. (1) The revised evolution sequence yields correct locations for the minimum period and the upper edge of the period gap; the standard sequence does not. (2) The observed spectral types of CV donors are compatible with both standard and revised models. (3) A direct comparison of predicted and observed WD temperatures suggests an even higher value for f GR, but this comparison is sensitive to the assumed mean WD mass and the possible existence of mass-transfer-rate fluctuations. (4) The predicted absolute magnitudes of donor stars in the near-infrared form a lower envelope around the observed absolute magnitudes for systems with parallax distances. This is true for all of our sequences, so any of them can be used to set firm lower limits on (or obtain rough estimates of) the distances toward CVs based only on P orb and single epoch near-IR measurements. (5) Both standard and revised sequences predict that short-period CVs should be susceptible to dwarf nova (DN) eruptions, consistent with observations. However, both sequences also predict that the fraction of DNe among long-period CVs should decline with P orb above the period gap. Observations suggest the opposite behavior, and we discuss the possible explanations for this discrepancy. (6) Approximate orbital period distributions constructed from our evolution sequences suggest that the ratio of long-period CVs to short-period, pre-bounce CVs is about 3 × higher for the revised sequence than the standard one. This may resolve a long-standing problem in CV evolution. Tables describing our donor and evolution sequences are provided in electronically readable form.

The epistemic and aleatory uncertainties of the ETAS-type models: an application to the Central Italy seismicity.

PubMed

Lombardi, A M

2017-09-18

Stochastic models provide quantitative evaluations about the occurrence of earthquakes. A basic component of this type of models are the uncertainties in defining main features of an intrinsically random process. Even if, at a very basic level, any attempting to distinguish between types of uncertainty is questionable, an usual way to deal with this topic is to separate epistemic uncertainty, due to lack of knowledge, from aleatory variability, due to randomness. In the present study this problem is addressed in the narrow context of short-term modeling of earthquakes and, specifically, of ETAS modeling. By mean of an application of a specific version of the ETAS model to seismicity of Central Italy, recently struck by a sequence with a main event of Mw6.5, the aleatory and epistemic (parametric) uncertainty are separated and quantified. The main result of the paper is that the parametric uncertainty of the ETAS-type model, adopted here, is much lower than the aleatory variability in the process. This result points out two main aspects: an analyst has good chances to set the ETAS-type models, but he may retrospectively describe and forecast the earthquake occurrences with still limited precision and accuracy.

Stars of type MS with evidence of white dwarf companions. [IUE, Main Sequence (MS)

NASA Technical Reports Server (NTRS)

Peery, Benjamin F., Jr.

1986-01-01

A search for white dwarf companions of MS-type stars was conducted, using IUE. The overendowments of these stars in typical S-process nuclides suggest that they, like the Ba II stars, may owe their peculiar compositions to earlier mass transfer. Short-wavelength IUE spectra show striking emission line variability in HD35155, HD61913, and 4 Ori; HD35155 and 4 Ori show evidence of white dwarf companions.

Membership and Coronal Activity in the NGC 2232 and Cr 140 Open Clusters

NASA Technical Reports Server (NTRS)

Oliversen, Ronald J. (Technical Monitor); Patten, Brian M.

2004-01-01

Making use of eight archival ROSAT HRI images in the regions of the NGC 2232 and Cr 140, this project's primary focus is to identify X-ray sources and to extract net source counts for these sources in these two open clusters. These X-ray data would be combined with ground-based photometry and spectroscopy in order to identify G, K, and early-M type cluster members. Such membership data are important because, at present, no members later than spectral type approx. F5 are currently known for either cluster. With ages estimated to be approx. 25 Myr and at distances of just approx. 350 pc, the combined late-type membership of the NGC 2232 and Cr 140 clusters would yield an almost unique sample of solar-type stars in the post-T Tauri/pre-main sequence phase of evolution. These stars could be used to assess the level and dispersion of coronal activity levels, as a part of a probe of the importance of magnetic braking and the level of magnetic dynamo activity, for solar-type stars just before they reach the zero-age main sequence.

Designing experiments on thermal interactions by secondary-school students in a simulated laboratory environment

NASA Astrophysics Data System (ADS)

Lefkos, Ioannis; Psillos, Dimitris; Hatzikraniotis, Euripides

2011-07-01

Background and purpose: The aim of this study was to explore the effect of investigative activities with manipulations in a virtual laboratory on students' ability to design experiments. Sample Fourteen students in a lower secondary school in Greece attended a teaching sequence on thermal phenomena based on the use of information and communication technology, and specifically of the simulated virtual laboratory 'ThermoLab'. Design and methods A pre-post comparison was applied. Students' design of experiments was rated in eight dimensions; namely, hypothesis forming and verification, selection of variables, initial conditions, device settings, materials and devices used, process and phenomena description. A three-level ranking scheme was employed for the evaluation of students' answers in each dimension. Results A Wilcoxon signed-rank test revealed a statistically significant difference between the students' pre- and post-test scores. Additional analysis by comparing the pre- and post-test scores using the Hake gain showed high gains in all but one dimension, which suggests that this improvement was almost inclusive. Conclusions We consider that our findings support the statement that there was an improvement in students' ability to design experiments.

The Origin Of Cosmic Rays And The Stars Of Berkeley 87

NASA Astrophysics Data System (ADS)

Turner, David G.; Majaess, D. J.; Lane, D. J.; Balam, D. D.

2010-01-01

Spectroscopic observations and the results of photometric monitoring are presented for members of the heavily-reddened, young, 1.2 kpc-distant, open cluster Berkeley 87, which is spatially coincident with the strongest source of cosmic rays in the northern sky. Many cluster members exhibit evidence for extreme loss of mass over their lifetimes: the M3 Ia supergiant BC Cyg has an evolutionary mass half that of stars at the main-sequence turnoff, the B2 Iabe emission-line supergiant HDE 229059 also has an evolutionary mass smaller than that of the main-sequence turnoff, the WO2 star WR 142, the only example of an oxygen sequence Wolf-Rayet star in an open cluster, displays evidence for variable, high velocity winds in its spectrum, the curious object V439 Cyg (B0: Vnne) appears to be an example of a recent binary merger, and Vatican Emission Star VES 203 (B0.5 Ve) displays a strong P Cygni signature in its Balmer line emission. It appears that heavy mass loss is a common factor associated with cluster stars. Could that be associated with the location of a cosmic ray production factory from the vicinity of Berkeley 87?

Massive star formation by accretion. II. Rotation: how to circumvent the angular momentum barrier?

NASA Astrophysics Data System (ADS)

Haemmerlé, L.; Eggenberger, P.; Meynet, G.; Maeder, A.; Charbonnel, C.; Klessen, R. S.

2017-06-01

Context. Rotation plays a key role in the star-formation process, from pre-stellar cores to pre-main-sequence (PMS) objects. Understanding the formation of massive stars requires taking into account the accretion of angular momentum during their PMS phase. Aims: We study the PMS evolution of objects destined to become massive stars by accretion, focusing on the links between the physical conditions of the environment and the rotational properties of young stars. In particular, we look at the physical conditions that allow the production of massive stars by accretion. Methods: We present PMS models computed with a new version of the Geneva Stellar Evolution code self-consistently including accretion and rotation according to various accretion scenarios for mass and angular momentum. We describe the internal distribution of angular momentum in PMS stars accreting at high rates and we show how the various physical conditions impact their internal structures, evolutionary tracks, and rotation velocities during the PMS and the early main sequence. Results: We find that the smooth angular momentum accretion considered in previous studies leads to an angular momentum barrier and does not allow the formation of massive stars by accretion. A braking mechanism is needed in order to circumvent this angular momentum barrier. This mechanism has to be efficient enough to remove more than two thirds of the angular momentum from the inner accretion disc. Due to the weak efficiency of angular momentum transport by shear instability and meridional circulation during the accretion phase, the internal rotation profiles of accreting stars reflect essentially the angular momentum accretion history. As a consequence, careful choice of the angular momentum accretion history allows circumvention of any limitation in mass and velocity, and production of stars of any mass and velocity compatible with structure equations.

DETECTION OF A COOL, ACCRETION-SHOCK-GENERATED X-RAY PLASMA IN EX LUPI DURING THE 2008 OPTICAL ERUPTION

DOE Office of Scientific and Technical Information (OSTI.GOV)

Teets, William K.; Weintraub, David A.; Kastner, Joel H.

2012-11-20

EX Lupi is the prototype for a class of young, pre-main-sequence stars which are observed to undergo irregular, presumably accretion-generated, optical outbursts that result in a several magnitude rise of the optical flux. EX Lupi was observed to optically erupt in 2008 January, triggering Chandra ACIS Target of Opportunity observations shortly thereafter. We find very strong evidence that most of the X-ray emission in the first few months after the optical outburst is generated by accretion of circumstellar material onto the stellar photosphere. Specifically, we find a strong correlation between the decreasing optical and X-ray fluxes following the peak ofmore » the outburst in the optical, which suggests that these observed declines in both the optical and X-ray fluxes are the result of declining accretion rate. In addition, in our models of the X-ray spectrum, we find strong evidence for a {approx}0.4 keV plasma component, as expected for accretion shocks on low-mass, pre-main-sequence stars. From 2008 March through October, this cool plasma component appeared to fade as EX Lupi returned to its quiescent level in the optical, consistent with a decrease in the overall emission measure of accretion-shock-generated plasma. The overall small increase of the X-ray flux during the optical outburst of EX Lupi is similar to what was observed in previous X-ray observations of the 2005 optical outburst of the EX Lupi-type star V1118 Ori but contrasts with the large increase of the X-ray flux from the erupting young star V1647 Ori during its 2003 and 2008 optical outbursts.« less

The antenna transcriptome changes in mosquito Anopheles sinensis, pre- and post- blood meal.

PubMed

Chen, Qian; Pei, Di; Li, Jianyong; Jing, Chengyu; Wu, Wenjian; Man, Yahui

2017-01-01

Antenna is the main chemosensory organ in mosquitoes. Characterization of the transcriptional changes after blood meal, especially those related to chemoreception, may help to explain mosquito blood sucking behavior and to identify novel targets for mosquito control. Anopheles sinensis is an Asiatic mosquito species which transmits malaria and lymphatic filariasis. However, studies on chemosensory biology in female An. sinensis are quite lacking. Here we report a transcriptome analysis of An. sinensis female antennae pre- and post- blood meal. We created six An. sinensis antenna RNA-seq libraries, three from females without blood meal and three from females five hours after a blood meal. Illumina sequencing was conducted to analyze the transcriptome differences between the two groups. In total, the sequenced fragments created 21,643 genes, 1,828 of them were novel. 12,861 of these genes were considered to be expressed (FPKM >1.0) in at least one of the two groups, with 12,159 genes expressed in both groups. 548 genes were differentially expressed in the blood-fed group, with 331 genes up-regulated and 217 genes down-regulated. GO enrichment analysis of the differentially expressed genes suggested that there were no statistically over represented GO terms among down-regulated genes in blood-fed mosquitoes, while the enriched GO terms of the up-regulated genes occurred mainly in metabolic process. For the chemosensory gene families, a subtle distinction in the expression levels can be observed according to our statistical analysis. However, the firstly comprehensive identification of these chemosensory gene families in An. sinensis antennae will help to characterize the precise function of these proteins in odor recognition in mosquitoes. This study provides a first global view in the changes of transcript accumulation elicited by blood meal in An. sinensis female antennae.

Detection of a Cool, Accretion-Shock-Generated X-Ray Plasma in EX Lupi During the 2008 Optical Eruption

NASA Technical Reports Server (NTRS)

Teets, William K.; Weintraub, David A.; Kastner, Joel H.; Grosso, Nicholas; Hamaguchi, Kenji; Richmond, Michael

2012-01-01

EX Lupi is the prototype for a class of young, pre-main-sequence stars which are observed to undergo irregular, presumably accretion-generated, optical outbursts that result in a several magnitude rise of the optical flux. EX Lupi was observed to optically erupt in 2008 January, triggering Chandra ACIS Target of Opportunity observations shortly thereafter. We find very strong evidence that most of the X-ray emission in the first few months after the optical outburst is generated by accretion of circumstellar material onto the stellar photosphere. Specifically, we find a strong correlation between the decreasing optical and X-ray fluxes following the peak of the outburst in the optical, which suggests that these observed declines in both the optical and X-ray fluxes are the result of declining accretion rate. In addition, in our models of the X-ray spectrum, we find strong evidence for an approx 0.4 keV plasma component, as expected for accretion shocks on low-mass, pre-main-sequence stars. From 2008 March through October, this cool plasma component appeared to fade as EX Lupi returned to its quiescent level in the optical, consistent with a decrease in the overall emission measure of accretion-shock-generated plasma. The overall small increase of the X-ray flux during the optical outburst of EX Lupi is similar to what was observed in previous X-ray observations of the 2005 optical outburst of the EX Lupi-type star V1118 Ori but contrasts with the large increase of the X-ray flux from the erupting young star V1647 Ori during its 2003 and 2008 optical outbursts.

High Dispersion Line Profile Studies of TW HYA and Other Pre-Main Sequence Stars

NASA Astrophysics Data System (ADS)

Linsky, Jeffrey L.

1984-07-01

We propose to extend our study of line profiles in T Tauri stars by obtaining a 16 hour SWP-HI spectrum of TW Hya and 6-8 hour LWP-HI spectra of TW Hya, AK Sco, CoD -35 10525 and CoD -33 10685. High dispersion spectra of pre-main sequence (PMS) stars provide unique information on line widths, shifts, and asymmetries, as well as evidence for mass outflow, circumstellar absorption, and diagnostics for the temperature structure of the outer atmosphere layers of these complex yet incredibly important objects. We have previously obtained and studied line profiles in RU Lupi and the prototype star T Tau. RU Lupi has line profiles that are dominated by the wind expansion, for example the MgII and FeII multiplet UV1 profiles are unique in that they have a classical P Cygni shape, whereas T Tau has more symmetric emission profiles indicative of a chromosphere and hotter layers not dominated by expansion. TW Hya is different from these two previously studied stars in that it may be the brightest known example of a post-T Tauri star, and hence less active and older than the other PMS stars. We intend to compare its line profiles with those of RU Lupi and T Tauri in order to understand the differences in the non-thermal mass motions, wind expansion, and thermal structures of these three very different T Tau stars. The requested LWPHI spectra are to obtain MgII and FeII multiplet UV1. profiles of 4 different T Tauri objects so as to infer the expansion and thermal structure in their chromospheric layers.

RNA-seq mixology: designing realistic control experiments to compare protocols and analysis methods

PubMed Central

Holik, Aliaksei Z.; Law, Charity W.; Liu, Ruijie; Wang, Zeya; Wang, Wenyi; Ahn, Jaeil; Asselin-Labat, Marie-Liesse; Smyth, Gordon K.

2017-01-01

Abstract Carefully designed control experiments provide a gold standard for benchmarking different genomics research tools. A shortcoming of many gene expression control studies is that replication involves profiling the same reference RNA sample multiple times. This leads to low, pure technical noise that is atypical of regular studies. To achieve a more realistic noise structure, we generated a RNA-sequencing mixture experiment using two cell lines of the same cancer type. Variability was added by extracting RNA from independent cell cultures and degrading particular samples. The systematic gene expression changes induced by this design allowed benchmarking of different library preparation kits (standard poly-A versus total RNA with Ribozero depletion) and analysis pipelines. Data generated using the total RNA kit had more signal for introns and various RNA classes (ncRNA, snRNA, snoRNA) and less variability after degradation. For differential expression analysis, voom with quality weights marginally outperformed other popular methods, while for differential splicing, DEXSeq was simultaneously the most sensitive and the most inconsistent method. For sample deconvolution analysis, DeMix outperformed IsoPure convincingly. Our RNA-sequencing data set provides a valuable resource for benchmarking different protocols and data pre-processing workflows. The extra noise mimics routine lab experiments more closely, ensuring any conclusions are widely applicable. PMID:27899618

Rethinking Dental School Admission Criteria: Correlation Between Pre-Admission Variables and First-Year Performance for Six Classes at One Dental School.

PubMed

Rowland, Kevin C; Rieken, Susan

2018-04-01

Admissions committees in dental schools are charged with the responsibility of selecting candidates who will succeed in school and become successful members of the profession. Identifying students who will have academic difficulty is challenging. The aim of this study was to determine the predictive value of pre-admission variables for the first-year performance of six classes at one U.S. dental school. The authors hypothesized that the variables undergraduate grade point average (GPA), undergraduate science GPA (biology, chemistry, and physics), and Dental Admission Test (DAT) scores would predict the level of performance achieved in the first year of dental school, measured by year-end GPA. Data were collected in 2015 from school records for all 297 students in the six cohorts who completed the first year (Classes of 2007 through 2013). In the results, statistically significant correlations existed between all pre-admission variables and first-year GPA, but the associations were only weak to moderate. Lower performing students at the end of the first year (lowest 10% of GPA) had, on average, lower pre-admission variables than the other students, but the differences were small (≤10.8% in all categories). When all the pre-admission variables were considered together in a multiple regression analysis, a significant association was found between pre-admission variables and first-year GPA, but the association was weak (adjusted R 2 =0.238). This weak association suggests that these students' first-year dental school GPAs were mostly determined by factors other than the pre-admission variables studied and has resulted in the school's placing greater emphasis on other factors for admission decisions.

Leg pain and psychological variables predict outcome 2-3 years after lumbar fusion surgery.

PubMed

Abbott, Allan D; Tyni-Lenné, Raija; Hedlund, Rune

2011-10-01

Prediction studies testing a thorough range of psychological variables in addition to demographic, work-related and clinical variables are lacking in lumbar fusion surgery research. This prospective cohort study aimed at examining predictions of functional disability, back pain and health-related quality of life (HRQOL) 2-3 years after lumbar fusion by regressing nonlinear relations in a multivariate predictive model of pre-surgical variables. Before and 2-3 years after lumbar fusion surgery, patients completed measures investigating demographics, work-related variables, clinical variables, functional self-efficacy, outcome expectancy, fear of movement/(re)injury, mental health and pain coping. Categorical regression with optimal scaling transformation, elastic net regularization and bootstrapping were used to investigate predictor variables and address predictive model validity. The most parsimonious and stable subset of pre-surgical predictor variables explained 41.6, 36.0 and 25.6% of the variance in functional disability, back pain intensity and HRQOL 2-3 years after lumbar fusion. Pre-surgical control over pain significantly predicted functional disability and HRQOL. Pre-surgical catastrophizing and leg pain intensity significantly predicted functional disability and back pain while the pre-surgical straight leg raise significantly predicted back pain. Post-operative psychomotor therapy also significantly predicted functional disability while pre-surgical outcome expectations significantly predicted HRQOL. For the median dichotomised classification of functional disability, back pain intensity and HRQOL levels 2-3 years post-surgery, the discriminative ability of the prediction models was of good quality. The results demonstrate the importance of pre-surgical psychological factors, leg pain intensity, straight leg raise and post-operative psychomotor therapy in the predictions of functional disability, back pain and HRQOL-related outcomes.

Interferometric capability for the Magellan Project

NASA Astrophysics Data System (ADS)

Carleton, Nathaniel P.; Traub, Wesley A.; Angel, J. Roger P.

1998-07-01

The Magellan Project is building two 6.5-m telescopes, 60 m apart, at the Las Campanas Observatory in Chile. There are on-going plans to combine the beams of the two main telescopes, and of smaller auxiliary telescopes, for interferometric measurements. In this paper we consider the array of auxiliary telescopes as a stand-alone instrument, recognizing that it will operate as such for some large fraction of the time. Our interest is sharpened by the availability of six 1.8-m optical systems, retired from the Smithsonian-Arizona Multiple-Mirror Telescope in preparation for the installation of a single-mirror 6.5-m system. We have completed a design for a 1.8-m telescope, in which the MMT components are supported on a proven tripod mount. The optics-support uses steel for stiffness, and low-thermal- expansion rods for passive stability. This array will be a powerful tool for the investigation of stellar limb darkening, surface features, and changes of diameter in pulsations, as well as dust disks, shells, and binary companions. The 1.8-m telescopes on good sites such as Magellan's should be able to operate at full aperture for interferometry at 2.2 micrometers . They should therefore be able to reach to magnitude K equals 10 or so, and thus to cover substantial samples of both main-sequence and pre-main- sequence stars, and of fully evolved stars as well.

The kinetics of pre-mRNA splicing in the Drosophila genome and the influence of gene architecture.

PubMed

Pai, Athma A; Henriques, Telmo; McCue, Kayla; Burkholder, Adam; Adelman, Karen; Burge, Christopher B

2017-12-27

Production of most eukaryotic mRNAs requires splicing of introns from pre-mRNA. The splicing reaction requires definition of splice sites, which are initially recognized in either intron-spanning ('intron definition') or exon-spanning ('exon definition') pairs. To understand how exon and intron length and splice site recognition mode impact splicing, we measured splicing rates genome-wide in Drosophila , using metabolic labeling/RNA sequencing and new mathematical models to estimate rates. We found that the modal intron length range of 60-70 nt represents a local maximum of splicing rates, but that much longer exon-defined introns are spliced even faster and more accurately. We observed unexpectedly low variation in splicing rates across introns in the same gene, suggesting the presence of gene-level influences, and we identified multiple gene level variables associated with splicing rate. Together our data suggest that developmental and stress response genes may have preferentially evolved exon definition in order to enhance the rate or accuracy of splicing.

Genomic and phenotypic variation in epidemic-spanning Salmonella enterica serovar Enteritidis isolates

PubMed Central

2009-01-01

Background Salmonella enterica serovar Enteritidis (S. Enteritidis) has caused major epidemics of gastrointestinal infection in many different countries. In this study we investigate genome divergence and pathogenic potential in S. Enteritidis isolated before, during and after an epidemic in Uruguay. Results 266 S. Enteritidis isolates were genotyped using RAPD-PCR and a selection were subjected to PFGE analysis. From these, 29 isolates spanning different periods, genetic profiles and sources of isolation were assayed for their ability to infect human epithelial cells and subjected to comparative genomic hybridization using a Salmonella pan-array and the sequenced strain S. Enteritidis PT4 P125109 as reference. Six other isolates from distant countries were included as external comparators. Two hundred and thirty three chromosomal genes as well as the virulence plasmid were found as variable among S. Enteritidis isolates. Ten out of the 16 chromosomal regions that varied between different isolates correspond to phage-like regions. The 2 oldest pre-epidemic isolates lack phage SE20 and harbour other phage encoded genes that are absent in the sequenced strain. Besides variation in prophage, we found variation in genes involved in metabolism and bacterial fitness. Five epidemic strains lack the complete Salmonella virulence plasmid. Significantly, strains with indistinguishable genetic patterns still showed major differences in their ability to infect epithelial cells, indicating that the approach used was insufficient to detect the genetic basis of this differential behaviour. Conclusion The recent epidemic of S. Enteritidis infection in Uruguay has been driven by the introduction of closely related strains of phage type 4 lineage. Our results confirm previous reports demonstrating a high degree of genetic homogeneity among S. Enteritidis isolates. However, 10 of the regions of variability described here are for the first time reported as being variable in S. Enteritidis. In particular, the oldest pre-epidemic isolates carry phage-associated genetic regions not previously reported in S. Enteritidis. Overall, our results support the view that phages play a crucial role in the generation of genetic diversity in S. Enteritidis and that phage SE20 may be a key marker for the emergence of particular isolates capable of causing epidemics. PMID:19922635

Analysis of Pre-Analytic Factors Affecting the Success of Clinical Next-Generation Sequencing of Solid Organ Malignancies.

PubMed

Chen, Hui; Luthra, Rajyalakshmi; Goswami, Rashmi S; Singh, Rajesh R; Roy-Chowdhuri, Sinchita

2015-08-28

Application of next-generation sequencing (NGS) technology to routine clinical practice has enabled characterization of personalized cancer genomes to identify patients likely to have a response to targeted therapy. The proper selection of tumor sample for downstream NGS based mutational analysis is critical to generate accurate results and to guide therapeutic intervention. However, multiple pre-analytic factors come into play in determining the success of NGS testing. In this review, we discuss pre-analytic requirements for AmpliSeq PCR-based sequencing using Ion Torrent Personal Genome Machine (PGM) (Life Technologies), a NGS sequencing platform that is often used by clinical laboratories for sequencing solid tumors because of its low input DNA requirement from formalin fixed and paraffin embedded tissue. The success of NGS mutational analysis is affected not only by the input DNA quantity but also by several other factors, including the specimen type, the DNA quality, and the tumor cellularity. Here, we review tissue requirements for solid tumor NGS based mutational analysis, including procedure types, tissue types, tumor volume and fraction, decalcification, and treatment effects.

A contribution to regional stratigraphic correlations of the Afro-Brazilian depression - The Dom João Stage (Brotas Group and equivalent units - Late Jurassic) in Northeastern Brazilian sedimentary basins

NASA Astrophysics Data System (ADS)

Kuchle, Juliano; Scherer, Claiton Marlon dos Santos; Born, Christian Correa; Alvarenga, Renata dos Santos; Adegas, Felipe

2011-04-01

The Dom João Stage comprises an interval with variable thickness between 100 and 1200 m, composed of fluvial, eolian and lacustrine deposits of Late Jurassic age, based mainly on the lacustrine ostracod fauna (although the top deposits may extend into the Early Cretaceous). These deposits comprise the so-called Afro-Brazilian Depression, initially characterized as containing the Brotas Group of the Recôncavo Basin (which includes the Aliança and the Sergi Formations) and subsequently extended into the Tucano, Jatobá, Camamu, Almada, Sergipe, Alagoas and Araripe Basins in northeastern Brazil, encompassing the study area of this paper. The large occurrence area of the Dom João Stage gives rise to discussions about the depositional connectivity between the basins, and the real extension of sedimentation. In the first studies of this stratigraphic interval, the Dom João Stage was strictly associated with the rift phase, as an initial stage (decades of 1960-70), but subsequent analyses considered the Dom João as an intracratonic basin or pre-rift phase - without any relation to the active mechanics of a tectonic syn-rift phase (decades of 1980-2000). The present work developed an evolutionary stratigraphic and tectonic model, based on the characterization of depositional sequences, internal flooding surfaces, depositional systems arrangement and paleoflow directions. Several outcrops on the onshore basins were used to build composite sections of each basin, comprising facies, architectural elements, depositional systems, stratigraphic and lithostratigraphic frameworks, and paleocurrents. In addition to that, over a hundred onshore and offshore exploration wells were used (only 21 of which are showed) to map the depositional sequences and generate correlation sections. These show the characteristics and relations of the Dom João Stage in each studied basin, and they were also extended to the Gabon Basin. The results indicate that there were two main phases during the Dom João Stage, in which distinctive sedimentary environments were developed, reflecting depositional system arrangements, paleoflow directions were diverse, and continuous or compartmented basins were developed.

Implementing and Evaluating a Sequence of Instruction on Gaseous Pressure with Pre-Service Primary School Student Teachers.

ERIC Educational Resources Information Center

Taylor, Neil; Lucas, Keith B.

2000-01-01

Describes a teaching sequence on gaseous pressure implemented in a group of pre-service primary teachers in Fiji that provides subjects with a strong visual model of particle behavior which they then applied to a series of collaborative science activities for which they attempted to construct explanations. Suggests that this teaching sequence…

Petroleum source-rock potentials of the cretaceous transgressive-regressive sedimentary sequences of the Cauvery Basin

NASA Astrophysics Data System (ADS)

Chandra, Kuldeep; Philip, P. C.; Sridharan, P.; Chopra, V. S.; Rao, Brahmaji; Saha, P. K.

The present work is an attempt to contribute to knowledge on the petroleum source-rock potentials of the marine claystones and shales of basins associated with passive continental margins where the source-rock developments are known to have been associated with the anoxic events in the Mesozoic era. Data on three key exploratory wells from three major depressions Ariyallur-Pondicherry, Thanjavur and Nagapattinam of the Cauvery Basin are described and discussed. The average total organic carbon contents of the transgressive Pre-Albian-Cinomanian and Coniacian/Santonian claystones/shales range from 1.44 and 1.16%, respectively. The transgressive/regressive Campanian/Maastrichtian claystones contain average total organic carbon varying from 0.62 to 1.19%. The kerogens in all the studied stratigraphic sequences are classified as type-III with Rock-Eval hydrogen indices varying from 30 to 275. The nearness of land masses to the depositional basin and the mainly clastic sedimentation resulted in accumulation and preservation of dominantly type-III kerogens. The Pre-Albian to Cinomanian sequences of peak transgressive zone deposited in deep marine environments have kerogens with a relatively greater proportion of type-II components with likely greater contribution of planktonic organic matters. The global anoxic event associated with the Albian-Cinomanian marine transgression, like in many other parts of the world, has pervaded the Cauvery Basin and favoured development of good source-rocks with type-III kerogens. The Coniacian-Campanian-Maastrichtian transgressive/regressive phase is identified to be relatively of lesser significance for development of good quality source-rocks.

Structural diversity of domain superfamilies in the CATH database.

PubMed

Reeves, Gabrielle A; Dallman, Timothy J; Redfern, Oliver C; Akpor, Adrian; Orengo, Christine A

2006-07-14

The CATH database of domain structures has been used to explore the structural variation of homologous domains in 294 well populated domain structure superfamilies, each containing at least three sequence diverse relatives. Our analyses confirm some previously detected trends relating sequence divergence to structural variation but for a much larger dataset and in some superfamilies the new data reveal exceptional structural variation. Use of a new algorithm (2DSEC) to analyse variability in secondary structure compositions across a superfamily sheds new light on how structures evolve. 2DSEC detects inserted secondary structures that embellish the core of conserved secondary structures found throughout the superfamily. Analysis showed that for 56% of highly populated superfamilies (>9 sequence diverse relatives), there are twofold or more increases in the numbers of secondary structures in some relatives. In some families fivefold increases occur, sometimes modifying the fold of the domain. Manual inspection of secondary structure insertions or embellishments in 48 particularly variable superfamilies revealed that although these insertions were usually discontiguous in the sequence they were often co-located in 3D resulting in a larger structural motif that often modified the geometry of the active site or the surface conformation promoting diverse domain partnerships and protein interactions. These observations, supported by automatic analysis of all well populated CATH families, suggest that accretion of small secondary structure insertions may provide a simple mechanism for evolving new functions in diverse relatives. Some layered domain architectures (e.g. mainly-beta and alpha-beta sandwiches) that recur highly in the genomes more frequently exploit these types of embellishments to modify function. In these architectures, aggregation occurs most often at the edges, top or bottom of the beta-sheets. Information on structural variability across domain superfamilies has been made available through the CATH Dictionary of Homologous Structures (DHS).

THE FORMATION AND EVOLUTION OF YOUNG LOW-MASS STARS WITHIN HALOS WITH HIGH CONCENTRATION OF DARK MATTER PARTICLES

DOE Office of Scientific and Technical Information (OSTI.GOV)

Casanellas, Jordi; Lopes, IlIDio, E-mail: jordicasanellas@ist.utl.p, E-mail: ilidio.lopes@ist.utl.p

2009-11-01

The formation and evolution of low-mass stars within dense halos of dark matter (DM) leads to evolution scenarios quite different from the classical stellar evolution. As a result of our detailed numerical work, we describe these new scenarios for a range of DM densities on the host halo, for a range of scattering cross sections of the DM particles considered, and for stellar masses from 0.7 to 3 M {sub sun}. For the first time, we also computed the evolution of young low-mass stars in their Hayashi track in the pre-main-sequence phase and found that, for high DM densities, thesemore » stars stop their gravitational collapse before reaching the main sequence, in agreement with similar studies on first stars. Such stars remain indefinitely in an equilibrium state with lower effective temperatures (|DELTAT{sub eff}|>10{sup 3} K for a star of one solar mass), the annihilation of captured DM particles in their core being the only source of energy. In the case of lower DM densities, these protostars continue their collapse and progress through the main-sequence burning hydrogen at a lower rate. A star of 1 M{sub sun} will spend a time period greater than the current age of the universe consuming all the hydrogen in its core if it evolves in a halo with DM density rho{sub c}hi = 10{sup 9} GeV cm{sup -3}. We also show the strong dependence of the effective temperature and luminosity of these stars on the characteristics of the DM particles and how this can be used as an alternative method for DM research.« less

Chromospherically Active Stars in the RAVE Survey. II. Young Dwarfs in the Solar Neighborhood

NASA Astrophysics Data System (ADS)

Žerjal, M.; Zwitter, T.; Matijevič, G.; Grebel, E. K.; Kordopatis, G.; Munari, U.; Seabroke, G.; Steinmetz, M.; Wojno, J.; Bienaymé, O.; Bland-Hawthorn, J.; Conrad, C.; Freeman, K. C.; Gibson, B. K.; Gilmore, G.; Kunder, A.; Navarro, J.; Parker, Q. A.; Reid, W.; Siviero, A.; Watson, F. G.; Wyse, R. F. G.

2017-01-01

A large sample of over 38,000 chromospherically active candidate solar-like stars and cooler dwarfs from the RAVE survey is addressed in this paper. An improved activity identification with respect to the previous study was introduced to build a catalog of field stars in the solar neighborhood with an excess emission flux in the calcium infrared triplet wavelength region. The central result of this work is the calibration of the age-activity relation for main-sequence dwarfs in a range from a few 10 {Myr} up to a few Gyr. It enabled an order of magnitude age estimation of the entire active sample. Almost 15,000 stars are shown to be younger than 1 {Gyr} and ˜2000 younger than 100 {Myr}. The young age of the most active stars is confirmed by their position off the main sequence in the J - K versus {N}{UV}-V diagram showing strong ultraviolet excess, mid-infrared excess in the J - K versus {W}1-{W}2 diagram, and very cool temperatures (J-K> 0.7). They overlap with the reference pre-main-sequence RAVE stars often displaying X-ray emission. The activity level increasing with the color reveals their different nature from the solar-like stars and probably represents an underlying dynamo-generating magnetic fields in cool stars. Of the RAVE objects from DR5, 50% are found in the TGAS catalog and supplemented with accurate parallaxes and proper motions by Gaia. This makes the database of a large number of young stars in a combination with RAVE’s radial velocities directly useful as a tracer of the very recent large-scale star formation history in the solar neighborhood. The data are available online in the Vizier database.

The evolution of surface magnetic fields in young solar-type stars II: the early main sequence (250-650 Myr)

NASA Astrophysics Data System (ADS)

Folsom, C. P.; Bouvier, J.; Petit, P.; Lèbre, A.; Amard, L.; Palacios, A.; Morin, J.; Donati, J.-F.; Vidotto, A. A.

2018-03-01

There is a large change in surface rotation rates of sun-like stars on the pre-main sequence and early main sequence. Since these stars have dynamo-driven magnetic fields, this implies a strong evolution of their magnetic properties over this time period. The spin-down of these stars is controlled by interactions between stellar and magnetic fields, thus magnetic evolution in turn plays an important role in rotational evolution. We present here the second part of a study investigating the evolution of large-scale surface magnetic fields in this critical time period. We observed stars in open clusters and stellar associations with known ages between 120 and 650 Myr, and used spectropolarimetry and Zeeman Doppler Imaging to characterize their large-scale magnetic field strength and geometry. We report 15 stars with magnetic detections here. These stars have masses from 0.8 to 0.95 M⊙, rotation periods from 0.326 to 10.6 d, and we find large-scale magnetic field strengths from 8.5 to 195 G with a wide range of geometries. We find a clear trend towards decreasing magnetic field strength with age, and a power law decrease in magnetic field strength with Rossby number. There is some tentative evidence for saturation of the large-scale magnetic field strength at Rossby numbers below 0.1, although the saturation point is not yet well defined. Comparing to younger classical T Tauri stars, we support the hypothesis that differences in internal structure produce large differences in observed magnetic fields, however for weak-lined T Tauri stars this is less clear.

Oligo kernels for datamining on biological sequences: a case study on prokaryotic translation initiation sites

PubMed Central

Meinicke, Peter; Tech, Maike; Morgenstern, Burkhard; Merkl, Rainer

2004-01-01

Background Kernel-based learning algorithms are among the most advanced machine learning methods and have been successfully applied to a variety of sequence classification tasks within the field of bioinformatics. Conventional kernels utilized so far do not provide an easy interpretation of the learnt representations in terms of positional and compositional variability of the underlying biological signals. Results We propose a kernel-based approach to datamining on biological sequences. With our method it is possible to model and analyze positional variability of oligomers of any length in a natural way. On one hand this is achieved by mapping the sequences to an intuitive but high-dimensional feature space, well-suited for interpretation of the learnt models. On the other hand, by means of the kernel trick we can provide a general learning algorithm for that high-dimensional representation because all required statistics can be computed without performing an explicit feature space mapping of the sequences. By introducing a kernel parameter that controls the degree of position-dependency, our feature space representation can be tailored to the characteristics of the biological problem at hand. A regularized learning scheme enables application even to biological problems for which only small sets of example sequences are available. Our approach includes a visualization method for transparent representation of characteristic sequence features. Thereby importance of features can be measured in terms of discriminative strength with respect to classification of the underlying sequences. To demonstrate and validate our concept on a biochemically well-defined case, we analyze E. coli translation initiation sites in order to show that we can find biologically relevant signals. For that case, our results clearly show that the Shine-Dalgarno sequence is the most important signal upstream a start codon. The variability in position and composition we found for that signal is in accordance with previous biological knowledge. We also find evidence for signals downstream of the start codon, previously introduced as transcriptional enhancers. These signals are mainly characterized by occurrences of adenine in a region of about 4 nucleotides next to the start codon. Conclusions We showed that the oligo kernel can provide a valuable tool for the analysis of relevant signals in biological sequences. In the case of translation initiation sites we could clearly deduce the most discriminative motifs and their positional variation from example sequences. Attractive features of our approach are its flexibility with respect to oligomer length and position conservation. By means of these two parameters oligo kernels can easily be adapted to different biological problems. PMID:15511290

Relationship of goat milk flow emission variables with milking routine, milking parameters, milking machine characteristics and goat physiology.

PubMed

Romero, G; Panzalis, R; Ruegg, P

2017-11-01

The aim of this paper was to study the relationship between milk flow emission variables recorded during milking of dairy goats with variables related to milking routine, goat physiology, milking parameters and milking machine characteristics, to determine the variables affecting milking performance and help the goat industry pinpoint farm and milking practices that improve milking performance. In total, 19 farms were visited once during the evening milking. Milking parameters (vacuum level (VL), pulsation ratio and pulsation rate, vacuum drop), milk emission flow variables (milking time, milk yield, maximum milk flow (MMF), average milk flow (AVMF), time until 500 g/min milk flow is established (TS500)), doe characteristics of 8 to 10 goats/farm (breed, days in milk and parity), milking practices (overmilking, overstripping, pre-lag time) and milking machine characteristics (line height, presence of claw) were recorded on every farm. The relationships between recorded variables and farm were analysed by a one-way ANOVA analysis. The relationships of milk yield, MMF, milking time and TS500 with goat physiology, milking routine, milking parameters and milking machine design were analysed using a linear mixed model, considering the farm as the random effect. Farm was significant (P<0.05) in all the studied variables. Milk emission flow variables were similar to those recommended in scientific studies. Milking parameters were adequate in most of the farms, being similar to those recommended in scientific studies. Few milking parameters and milking machine characteristics affected the tested variables: average vacuum level only showed tendency on MMF, and milk pipeline height on TS500. Milk yield (MY) was mainly affected by parity, as the interaction of days in milk with parity was also significant. Milking time was mainly affected by milk yield and breed. Also significant were parity, the interaction of days in milk with parity and overstripping, whereas overmilking showed a slight tendency. We concluded that most of the studied variables were mainly related to goat physiology characteristics, as the effects of milking parameters and milking machine characteristics were scarce.

DNA Barcode Sequence Identification Incorporating Taxonomic Hierarchy and within Taxon Variability

PubMed Central

Little, Damon P.

2011-01-01

For DNA barcoding to succeed as a scientific endeavor an accurate and expeditious query sequence identification method is needed. Although a global multiple–sequence alignment can be generated for some barcoding markers (e.g. COI, rbcL), not all barcoding markers are as structurally conserved (e.g. matK). Thus, algorithms that depend on global multiple–sequence alignments are not universally applicable. Some sequence identification methods that use local pairwise alignments (e.g. BLAST) are unable to accurately differentiate between highly similar sequences and are not designed to cope with hierarchic phylogenetic relationships or within taxon variability. Here, I present a novel alignment–free sequence identification algorithm–BRONX–that accounts for observed within taxon variability and hierarchic relationships among taxa. BRONX identifies short variable segments and corresponding invariant flanking regions in reference sequences. These flanking regions are used to score variable regions in the query sequence without the production of a global multiple–sequence alignment. By incorporating observed within taxon variability into the scoring procedure, misidentifications arising from shared alleles/haplotypes are minimized. An explicit treatment of more inclusive terminals allows for separate identifications to be made for each taxonomic level and/or for user–defined terminals. BRONX performs better than all other methods when there is imperfect overlap between query and reference sequences (e.g. mini–barcode queries against a full–length barcode database). BRONX consistently produced better identifications at the genus–level for all query types. PMID:21857897

Selection of specific protein binders for pre-defined targets from an optimized library of artificial helicoidal repeat proteins (alphaRep).

PubMed

Guellouz, Asma; Valerio-Lepiniec, Marie; Urvoas, Agathe; Chevrel, Anne; Graille, Marc; Fourati-Kammoun, Zaineb; Desmadril, Michel; van Tilbeurgh, Herman; Minard, Philippe

2013-01-01

We previously designed a new family of artificial proteins named αRep based on a subgroup of thermostable helicoidal HEAT-like repeats. We have now assembled a large optimized αRep library. In this library, the side chains at each variable position are not fully randomized but instead encoded by a distribution of codons based on the natural frequency of side chains of the natural repeats family. The library construction is based on a polymerization of micro-genes and therefore results in a distribution of proteins with a variable number of repeats. We improved the library construction process using a "filtration" procedure to retain only fully coding modules that were recombined to recreate sequence diversity. The final library named Lib2.1 contains 1.7×10(9) independent clones. Here, we used phage display to select, from the previously described library or from the new library, new specific αRep proteins binding to four different non-related predefined protein targets. Specific binders were selected in each case. The results show that binders with various sizes are selected including relatively long sequences, with up to 7 repeats. ITC-measured affinities vary with Kd values ranging from micromolar to nanomolar ranges. The formation of complexes is associated with a significant thermal stabilization of the bound target protein. The crystal structures of two complexes between αRep and their cognate targets were solved and show that the new interfaces are established by the variable surfaces of the repeated modules, as well by the variable N-cap residues. These results suggest that αRep library is a new and versatile source of tight and specific binding proteins with favorable biophysical properties.

Selection of Specific Protein Binders for Pre-Defined Targets from an Optimized Library of Artificial Helicoidal Repeat Proteins (alphaRep)

PubMed Central

Chevrel, Anne; Graille, Marc; Fourati-Kammoun, Zaineb; Desmadril, Michel; van Tilbeurgh, Herman; Minard, Philippe

2013-01-01

We previously designed a new family of artificial proteins named αRep based on a subgroup of thermostable helicoidal HEAT-like repeats. We have now assembled a large optimized αRep library. In this library, the side chains at each variable position are not fully randomized but instead encoded by a distribution of codons based on the natural frequency of side chains of the natural repeats family. The library construction is based on a polymerization of micro-genes and therefore results in a distribution of proteins with a variable number of repeats. We improved the library construction process using a “filtration” procedure to retain only fully coding modules that were recombined to recreate sequence diversity. The final library named Lib2.1 contains 1.7×109 independent clones. Here, we used phage display to select, from the previously described library or from the new library, new specific αRep proteins binding to four different non-related predefined protein targets. Specific binders were selected in each case. The results show that binders with various sizes are selected including relatively long sequences, with up to 7 repeats. ITC-measured affinities vary with Kd values ranging from micromolar to nanomolar ranges. The formation of complexes is associated with a significant thermal stabilization of the bound target protein. The crystal structures of two complexes between αRep and their cognate targets were solved and show that the new interfaces are established by the variable surfaces of the repeated modules, as well by the variable N-cap residues. These results suggest that αRep library is a new and versatile source of tight and specific binding proteins with favorable biophysical properties. PMID:24014183

Mutations That Improve the pRE Promoter of Coliphage Lambda

PubMed Central

Mahoney, Michael E.; Wulff, Daniel L.

1987-01-01

The dya5 mutation, a C→T change at position -43 of the λ pRE promoter, results in a twofold increase in pRE activity in vivo. Smaller increases in pRE activity are found for the dya2 mutation, a T→C change at position -1 of pRE, and the dya3 mutation, an A→G change at +5 of pRE. The mutant p RE promoters retain complete dependence on cII protein for activity. These observations argue, at least for pRE-like promoters, that promoter activities are influenced by nucleotide sequences at least eight nucleotides to the 5'-side of the conventional -35 region consensus sequence, and by nucleotide sequences near the start-site of transcription. Although Hawley and McClure (1983) found A·T pairs more frequently than G·TC pairs in the region of -40 to -45 of prokaryotic promoters, other mutations that change a G·TC pair to an A·T pair at positions -41, -44 and -45 of pRE do not result in increased promoter activity. We also found that a T→C change at position -42 results in a mild decrease in promoter activity. These observations argue that Ts at positions -42 and -43 of pRE are required for maximum promoter activity, but do not support the hypothesis that As and Ts in the -40 to -45 region generally lead to higher promoter activities. PMID:2953648

Timing of terrane accretion in eastern and east-central Maine

NASA Astrophysics Data System (ADS)

Ludman, Allan

1986-05-01

The Norumbega fault zone is often cited as a post-Acadian suture between exotic blocks, even though stratigraphic, structural, and metamorphic data indicate that there is little offset of the Silurian-Devonian strata that the zone cuts in eastern Maine. Similarly, the Kingman fault zone has been shown by gravity and geochemical studies to separate distinct crustal blocks, whereas mapping shows that it lies entirely within a Silurian turbidite package. These conflicts are resolved if the two fault zones represent boundaries between Ordovician or older crustal blocks that had accreted to form a composite terrane prior to deposition of the cover sequences. The faults now mapped within these younger rocks formed by reactivation of the pre-Silurian boundaries during late Acadian time; movement continued until the late Carboniferous. Most of the accretionary history of Maine had thus ended before the Silurian. A complex composite terrane may have formed during Cambrian-Ordovician time that (1) interacted with cratonic North America during the Taconian orogeny and (2) became the “basement” upon which the Silurian and Lower Devonian strata of eastern Maine were deposited.

What Effects Do Didactic Interventions Have on Students' Attitudes Towards Science? A Meta-Analysis

NASA Astrophysics Data System (ADS)

Aguilera, David; Perales-Palacios, F. Javier

2018-03-01

Improving the attitudes of students towards science is one of the main challenges facing the teaching of the subject. The main objective of this study is to analyze the effect of students' attitudes towards science through different didactic interventions. The bibliographic search was carried out via the Web of Science database, specifically in the Education and Educational Research category, obtaining a population of 374 articles published between 2006 and 2016. We included studies with pre-experimental or quasi-experimental design that used pretest and posttest phases. Following the application of the inclusion criteria, 24 articles were selected with which a random effects meta-analysis was adopted, obtaining an average effect size of 0.54. Three moderating variables were analyzed, with a significant correlation between the type of teaching strategy and the effect of the attitude towards Science (Q = 23.17; df = 8; p < .01; R 2 = 0.05). The educational implications are mainly due to the importance of the teaching/learning strategy used in science education in the development of positive attitudes towards the subject, and the need to increase the number of Didactic Interventions that contemplate students' attitudes towards science as a study variable is also advocated.

[Deregulation of pre-messenger RNA splicing and rare diseases].

PubMed

de la Grange, Pierre

2016-12-01

Most of protein-coding human genes are subjected to alternative pre-mRNA splicing. This mechanism is highly regulated to precisely modulate detection of specific splice sites. This regulation is under control of the spliceosome and several splicing factors are also required to modulate the alternative usage of splice sites. Splicing factors and spliceosome components recognize splicing signals and regulatory sequences of the pre-mRNAs. These splicing sequences make splicing susceptible to polymorphisms and mutations. Examples of associations between human rare diseases and defects in pre-messenger RNA splicing are accumulating. Although many alterations are caused by mutations in splicing sequence (i.e., cis acting mutations), recent studies described the disruptive impact of mutations within spliceosome components or splicing factors (i.e., trans acting mutations). Following growing of knowledge regarding splicing regulation, several approaches have been developed to compensate for the effect of deleterious mutations and to restore sufficient amounts of functional protein. © 2016 médecine/sciences – Inserm.

An analysis of the uncertainty and bias in DCE-MRI measurements using the spoiled gradient-recalled echo pulse sequence.

PubMed

Subashi, Ergys; Choudhury, Kingshuk R; Johnson, G Allan

2014-03-01

The pharmacokinetic parameters derived from dynamic contrast-enhanced (DCE) MRI have been used in more than 100 phase I trials and investigator led studies. A comparison of the absolute values of these quantities requires an estimation of their respective probability distribution function (PDF). The statistical variation of the DCE-MRI measurement is analyzed by considering the fundamental sources of error in the MR signal intensity acquired with the spoiled gradient-echo (SPGR) pulse sequence. The variance in the SPGR signal intensity arises from quadrature detection and excitation flip angle inconsistency. The noise power was measured in 11 phantoms of contrast agent concentration in the range [0-1] mM (in steps of 0.1 mM) and in onein vivo acquisition of a tumor-bearing mouse. The distribution of the flip angle was determined in a uniform 10 mM CuSO4 phantom using the spin echo double angle method. The PDF of a wide range of T1 values measured with the varying flip angle (VFA) technique was estimated through numerical simulations of the SPGR equation. The resultant uncertainty in contrast agent concentration was incorporated in the most common model of tracer exchange kinetics and the PDF of the derived pharmacokinetic parameters was studied numerically. The VFA method is an unbiased technique for measuringT1 only in the absence of bias in excitation flip angle. The time-dependent concentration of the contrast agent measured in vivo is within the theoretically predicted uncertainty. The uncertainty in measuring K(trans) with SPGR pulse sequences is of the same order, but always higher than, the uncertainty in measuring the pre-injection longitudinal relaxation time (T10). The lowest achievable bias/uncertainty in estimating this parameter is approximately 20%-70% higher than the bias/uncertainty in the measurement of the pre-injection T1 map. The fractional volume parameters derived from the extended Tofts model were found to be extremely sensitive to the variance in signal intensity. The SNR of the pre-injection T1 map indicates the limiting precision with which K(trans) can be calculated. Current small-animal imaging systems and pulse sequences robust to motion artifacts have the capacity for reproducible quantitative acquisitions with DCE-MRI. In these circumstances, it is feasible to achieve a level of precision limited only by physiologic variability.

Characterization of hepatitis B virus surface antigen variability and impact on HBs antigen clearance under nucleos(t)ide analogue therapy.

PubMed

Velay, A; Jeulin, H; Eschlimann, M; Malvé, B; Goehringer, F; Bensenane, M; Frippiat, J-P; Abraham, P; Ismail, A M; Murray, J M; Combet, C; Zoulim, F; Bronowicki, J-P; Schvoerer, E

2016-05-01

For hepatitis B virus (HBV)-related chronic infection under treatment by nucleos(t)ide analogues (NUCs), HBsAg clearance is the ultimate therapeutic goal but very infrequent. We investigated how HBV envelope protein variability could lead to differential HBsAg clearance on NUCs. For 12 HBV genotype D patients receiving NUCs, six resolvers (HBsAg clearance) were compared to six matched nonresolvers (HBsAg persistence). PreS/S amino acid (aa) sequences were analysed with bioinformatics to predict HBV envelope antigenicity and aa covariance. To enrich our analyses on very rare resolvers, these were compared with other HBV genotype D strains in three characterized clinical cohorts including common chronically infected patients. The sT125M+sP127T combination was observed in four nonresolvers of six, corroborated by aa covariance analysis, associated with a lower predicted antigenicity than sT125T+sP127P. Concordant features within this HBV key functional domain, at positions 125 and 127, were reported from two of the three comparative cohorts. In our hands, a lower ELISA reactivity of HBV-vaccinated mice sera was observed against the sT125M mutant. In the S gene, 56 aa changes in minor variants were detected in non-resolvers, mainly in the major hydrophilic region, vs 28 aa changes in resolvers. Molecular features in patients showing HBsAg persistence on NUCs argue in favour of a different aa pattern in the HBV S gene compared to those showing HBsAg clearance. In nonresolvers, a decrease in HBs 'a' determinant antigenicity and more frequent mutations in the S gene suggest a role for the HBV envelope characteristics in HBsAg persistence. © 2016 John Wiley & Sons Ltd.

Heating the Primordial Soup: X-raying the Circumstellar Disk of T Cha

NASA Astrophysics Data System (ADS)

Principe, David; Huenemoerder, D.; Kastner, J. H.; Bessell, M. S.; Sacco, G.

2014-01-01

The classical T Tauri Star (cTTS) T Chamaeleontis (T Cha) presents a unique opportunity to probe pre-main sequence star-disk interactions and late-stage circumstellar disk evolution. T Cha is the only known example of a nearly edge-on, actively accreting star/disk system within ~110 pc, and furthermore may be orbited by a low-mass companion or massive planet that has cleared an inner hole in its disk. The star is characterized by strong variability in the optical 3 magnitudes in the V band) as well as large and variable extinction (AV in the range of 1-5). Like most cTTS, T Cha is also a luminous X-ray source. We present preliminary results of two observations (totaling 150 ks) of T Cha with Chandra’s HETGS. Our motivations are to (a) determine the intrinsic X-ray spectrum of T Cha, so as to establish whether its X-ray emission can be attributed to accretion shocks, coronal emission, or a combination; (b) investigate whether its X-ray flux exhibits modulation that may be related to the stellar rotational period 3.3 days); and (c) take advantage of the nearly-edge-on disk viewing geometry to model the spectrum of X-rays absorbed by the gaseous disk orbiting T Cha. These results will serve as much-needed input to models of magnetospheric accretion and irradiated, planet-forming disks. This research is supported via award number GO3-14022X to RIT issued by the Chandra X-ray Observatory Center, which is operated by the Smithsonian Astrophysical Observatory for and on behalf of NASA under contract NAS803060. Additional support is provided by National Science Foundation grant AST-1108950 to RIT.

A comparative analysis of serpin genes in the silkworm genome

PubMed Central

Zou, Zhen; Picheng, Zhao; Weng, Hua; Mita, Kazuei; Jiang, Haobo

2009-01-01

Serine protease inhibitors (serpins) are a superfamily of proteins, most of which control protease-mediated processes by inhibiting their cognate enzymes. Sequencing of the silkworm genome provides an opportunity to investigate serpin structure, function, and evolution at the genome level. There are thirty-four serpin genes in Bombyx mori. Six are highly similar to their Manduca sexta orthologs that regulate innate immunity. Three alternative exons in serpin1 gene and four in serpin28 encode a variable region including the reactive site loop. Splicing of serpin2 pre-mRNA yields variations in serpin2A, 2A′ and 2B. Sequence similarity and intron positions reveal the evolutionary pathway of seven serpin genes in group C. RT-PCR indicates an increase in the mRNA levels of serpin1, 3, 5, 6, 9, 12, 13, 25, 27, 32 and 34 in fat body and hemocytes of larvae injected with bacteria. These results suggest that the silkworm serpins play regulatory roles in defense responses. PMID:19150649

Climate change underlies global demographic, genetic, and cultural transitions in pre-Columbian southern Peru.

PubMed

Fehren-Schmitz, Lars; Haak, Wolfgang; Mächtle, Bertil; Masch, Florian; Llamas, Bastien; Cagigao, Elsa Tomasto; Sossna, Volker; Schittek, Karsten; Isla Cuadrado, Johny; Eitel, Bernhard; Reindel, Markus

2014-07-01

Several archaeological studies in the Central Andes have pointed at the temporal coincidence of climatic fluctuations (both long- and short-term) and episodes of cultural transition and changes of socioeconomic structures throughout the pre-Columbian period. Although most scholars explain the connection between environmental and cultural changes by the impact of climatic alterations on the capacities of the ecosystems inhabited by pre-Columbian cultures, direct evidence for assumed demographic consequences is missing so far. In this study, we address directly the impact of climatic changes on the spatial population dynamics of the Central Andes. We use a large dataset of pre-Columbian mitochondrial DNA sequences from the northern Rio Grande de Nasca drainage (RGND) in southern Peru, dating from ∼840 BC to 1450 AD. Alternative demographic scenarios are tested using Bayesian serial coalescent simulations in an approximate Bayesian computational framework. Our results indicate migrations from the lower coastal valleys of southern Peru into the Andean highlands coincident with increasing climate variability at the end of the Nasca culture at ∼640 AD. We also find support for a back-migration from the highlands to the coast coincident with droughts in the southeastern Andean highlands and improvement of climatic conditions on the coast after the decline of the Wari and Tiwanaku empires (∼1200 AD), leading to a genetic homogenization in the RGND and probably southern Peru as a whole.

Climate change underlies global demographic, genetic, and cultural transitions in pre-Columbian southern Peru

PubMed Central

Fehren-Schmitz, Lars; Haak, Wolfgang; Mächtle, Bertil; Masch, Florian; Llamas, Bastien; Tomasto Cagigao, Elsa; Sossna, Volker; Schittek, Karsten; Isla Cuadrado, Johny; Eitel, Bernhard; Reindel, Markus

2014-01-01

Several archaeological studies in the Central Andes have pointed at the temporal coincidence of climatic fluctuations (both long- and short-term) and episodes of cultural transition and changes of socioeconomic structures throughout the pre-Columbian period. Although most scholars explain the connection between environmental and cultural changes by the impact of climatic alterations on the capacities of the ecosystems inhabited by pre-Columbian cultures, direct evidence for assumed demographic consequences is missing so far. In this study, we address directly the impact of climatic changes on the spatial population dynamics of the Central Andes. We use a large dataset of pre-Columbian mitochondrial DNA sequences from the northern Rio Grande de Nasca drainage (RGND) in southern Peru, dating from ∼840 BC to 1450 AD. Alternative demographic scenarios are tested using Bayesian serial coalescent simulations in an approximate Bayesian computational framework. Our results indicate migrations from the lower coastal valleys of southern Peru into the Andean highlands coincident with increasing climate variability at the end of the Nasca culture at ∼640 AD. We also find support for a back-migration from the highlands to the coast coincident with droughts in the southeastern Andean highlands and improvement of climatic conditions on the coast after the decline of the Wari and Tiwanaku empires (∼1200 AD), leading to a genetic homogenization in the RGND and probably southern Peru as a whole. PMID:24979787

Inferring the expression variability of human transposable element-derived exons by linear model analysis of deep RNA sequencing data.

PubMed

Zhang, Wensheng; Edwards, Andrea; Fan, Wei; Fang, Zhide; Deininger, Prescott; Zhang, Kun

2013-08-28

The exonization of transposable elements (TEs) has proven to be a significant mechanism for the creation of novel exons. Existing knowledge of the retention patterns of TE exons in mRNAs were mainly established by the analysis of Expressed Sequence Tag (EST) data and microarray data. This study seeks to validate and extend previous studies on the expression of TE exons by an integrative statistical analysis of high throughput RNA sequencing data. We collected 26 RNA-seq datasets spanning multiple tissues and cancer types. The exon-level digital expressions (indicating retention rates in mRNAs) were quantified by a double normalized measure, called the rescaled RPKM (Reads Per Kilobase of exon model per Million mapped reads). We analyzed the distribution profiles and the variability (across samples and between tissue/disease groups) of TE exon expressions, and compared them with those of other constitutive or cassette exons. We inferred the effects of four genomic factors, including the location, length, cognate TE family and TE nucleotide proportion (RTE, see Methods section) of a TE exon, on the exons' expression level and expression variability. We also investigated the biological implications of an assembly of highly-expressed TE exons. Our analysis confirmed prior studies from the following four aspects. First, with relatively high expression variability, most TE exons in mRNAs, especially those without exact counterparts in the UCSC RefSeq (Reference Sequence) gene tables, demonstrate low but still detectable expression levels in most tissue samples. Second, the TE exons in coding DNA sequences (CDSs) are less highly expressed than those in 3' (5') untranslated regions (UTRs). Third, the exons derived from chronologically ancient repeat elements, such as MIRs, tend to be highly expressed in comparison with those derived from younger TEs. Fourth, the previously observed negative relationship between the lengths of exons and the inclusion levels in transcripts is also true for exonized TEs. Furthermore, our study resulted in several novel findings. They include: (1) for the TE exons with non-zero expression and as shown in most of the studied biological samples, a high TE nucleotide proportion leads to their lower retention rates in mRNAs; (2) the considered genomic features (i.e. a continuous variable such as the exon length or a category indicator such as 3'UTR) influence the expression level and the expression variability (CV) of TE exons in an inverse manner; (3) not only the exons derived from Alu elements but also the exons from the TEs of other families were preferentially established in zinc finger (ZNF) genes.

Modeling the vacuolar storage of malate shed lights on pre- and post-harvest fruit acidity.

PubMed

Etienne, Audrey; Génard, Michel; Lobit, Philippe; Bugaud, Christophe

2014-11-18

Malate is one of the most important organic acids in many fruits and its concentration plays a critical role in organoleptic properties. Several studies suggest that malate accumulation in fruit cells is controlled at the level of vacuolar storage. However, the regulation of vacuolar malate storage throughout fruit development, and the origins of the phenotypic variability of the malate concentration within fruit species remain to be clarified. In the present study, we adapted the mechanistic model of vacuolar storage proposed by Lobit et al. in order to study the accumulation of malate in pre and postharvest fruits. The main adaptation concerned the variation of the free energy of ATP hydrolysis during fruit development. Banana fruit was taken as a reference because it has the particularity of having separate growth and post-harvest ripening stages, during which malate concentration undergoes substantial changes. Moreover, the concentration of malate in banana pulp varies greatly among cultivars which make possible to use the model as a tool to analyze the genotypic variability. The model was calibrated and validated using data sets from three cultivars with contrasting malate accumulation, grown under different fruit loads and potassium supplies, and harvested at different stages. The model predicted the pre and post-harvest dynamics of malate concentration with fairly good accuracy for the three cultivars (mean RRMSE = 0.25-0.42). The sensitivity of the model to parameters and input variables was analyzed. According to the model, vacuolar composition, in particular potassium and organic acid concentrations, had an important effect on malate accumulation. The model suggested that rising temperatures depressed malate accumulation. The model also helped distinguish differences in malate concentration among the three cultivars and between the pre and post-harvest stages by highlighting the probable importance of proton pump activity and particularly of the free energy of ATP hydrolysis and vacuolar pH. This model appears to be an interesting tool to study malate accumulation in pre and postharvest fruits and to get insights into the ecophysiological determinants of fruit acidity, and thus may be useful for fruit quality improvement.

Interhemispheric gradient of atmospheric radiocarbon reveals natural variability of Southern Ocean winds

NASA Astrophysics Data System (ADS)

Rodgers, K. B.; Fletcher, S. E. M.; Bianchi, D.; Beaulieu, C.; Galbraith, E. D.; Gnanadesikan, A.; Hogg, A. G.; Iudicone, D.; Lintner, B.; Naegler, T.; Reimer, P. J.; Sarmiento, J. L.; Slater, R. D.

2011-01-01

Tree ring Δ14C data (Reimer et al., 2004; McCormac et al., 2004) indicate that atmospheric Δ14C varied on multi-decadal to centennial timescales, in both hemispheres, over the pre-industrial period AD 950-1830. Although the Northern and Southern Hemispheric Δ14C records display similar variability, it is difficult from these data alone to distinguish between variations driven by 14CO2 production in the upper atmosphere (Stuiver, 1980) and exchanges between carbon reservoirs (Siegenthaler, 1980). Here we consider rather the Interhemispheric Gradient in atmospheric Δ14C as revealing of the background pre-bomb air-sea Disequilbrium Flux between 14CO2 and CO2. As the global maximum of the Disequilibrium Flux is squarely centered in the open ocean regions of the Southern Ocean, relatively modest perturbations to the winds over this region drive significant perturbations to the Interhemispheric Gradient. The analysis presented here implies that changes to Southern Ocean windspeeds are likely a main driver of the observed variability in the Interhemispheric Gradient over 950-1830, and further, that this variability may be larger than the Southern Ocean wind trends that have been reported for recent decades (notably 1980-2004). This interpretation also implies a significant weakening of the winds over the Southern Ocean within a few decades of AD 1375, associated with the transition between the Medieval Climate Anomaly and the Little Ice Age. The driving forces that could have produced such a shift in the winds remain unkown.

Stellar magnetic cycles

NASA Astrophysics Data System (ADS)

Baliunas, S. L.

2004-05-01

Is hope for understanding the solar magnetic cycle to be found in stars? Observations of stars with significant sub-surface convective zones -- masses smaller than about 1.5 solar masses on the lower main sequence and many types of cool, post-main-sequence stars -- indicate the presence of surface and atmospheric inhomogeneities analogous to solar magnetic features, making stellar magnetic activity a cosmically widespread phenomenon. Observations have been made primarily in visible wavelengths, and important information has also been derived from the ultraviolet and x-ray spectrum regions. Interannual to interdecadal variability of spectrum indicators of stellar magnetic features is common, and in some cases similar in appearance to the 11-year sunspot cycle. Successful models of the physical processes responsible for stellar magnetic cycles, typically cast as a magnetohydrodynamic dynamo, require advances in understanding not only convection but also the magnetic field's interaction with it. The observed facts that underpin the hope for models will be summarized. Properties of stellar magnetic cycles will be compared and contrasted with those of the sun, including inferences from paleo-environmental reservoirs that contain information on solar century- to millennial-scale magnetic variability. Partial support of this research came from NASA NAG5-7635, NRC COBASE, CRDF 322, MIT-MSG 5710001241, JPL 1236821, AF 49620-02-1-0194, Richard Lounsberry Foundation, Langley-Abbot, Rollins, Scholarly Studies and James Arthur Funds (Smithsonian Institution) and several generous individuals.

User's guide to SEAWAT; a computer program for simulation of three-dimensional variable-density ground-water flow

USGS Publications Warehouse

Guo, Weixing; Langevin, C.D.

2002-01-01

This report documents a computer program (SEAWAT) that simulates variable-density, transient, ground-water flow in three dimensions. The source code for SEAWAT was developed by combining MODFLOW and MT3DMS into a single program that solves the coupled flow and solute-transport equations. The SEAWAT code follows a modular structure, and thus, new capabilities can be added with only minor modifications to the main program. SEAWAT reads and writes standard MODFLOW and MT3DMS data sets, although some extra input may be required for some SEAWAT simulations. This means that many of the existing pre- and post-processors can be used to create input data sets and analyze simulation results. Users familiar with MODFLOW and MT3DMS should have little difficulty applying SEAWAT to problems of variable-density ground-water flow.

X-ray and Optical Observations of NGC 1788

NASA Astrophysics Data System (ADS)

Alcalá, J. M.; Covino, E.; Wachter, S.; Hoard, D. W.; Sterzik, M. F.; Durisen, R. H.; Freyberg, M.; Cooksey, K.

We report on the results of ROSAT High Resolution Imager (HRI) X-ray observations and optical wide-field spectroscopy and imaging in the star forming region NGC 1788. Several new low mass pre-main sequence (PMS) stars have been found based on intermediate resolution spectroscopy. Many new PMS candidate members of NGC 1788 are selected using the spectroscopically confirmed PMS stars to define the PMS locus in color-magnitude diagrams. Some objects with very red colors detected just above the limiting magnitude of our images, are good candidates for young Brown Dwarfs (BDs). The BD nature of these objects need to be confirmed with subsequent IR observations.

The W Serpentis binaries with a few words on epsilon Aurigae

NASA Technical Reports Server (NTRS)

Plavec, M. J.

1982-01-01

The Algol systems, U-Cephei and V356 Sagittarii, which should be included among the W Serpentis stars, characterized by strong ultraviolet emission lines are discussed. The spectra of the W-Ser stars are similar to those of the T-Tauri stars, and a similarity of physical conditions is indicated. A model of W-Serpentis, a B-star embedded in a thick disk, may be relevant to other exotic eclipsing systems, possibly even to obliquity of ecliptic Aurigae. The obliquity of ecliptic and the relationship to Aur, BM Orionis is reviewed; the system probably contains a pre main sequence star highly flattened by differential rotation.

Advanced Stirling Convertor Dynamic Test Approach and Results

NASA Technical Reports Server (NTRS)

Meer, David W.; Hill, Dennis; Ursic, Joseph

2009-01-01

The U.S. Department of Energy (DOE), Lockheed Martin (LM), and NASA Glenn Research Center (GRC) have been developing the Advanced Stirling Radioisotope Generator (ASRG) for use as a power system for space science missions. As part of the extended operation testing of this power system, the Advanced Stirling Converters (ASC) at NASA John H. Glenn Research Center undergo a vibration test sequence intended to simulate the vibration history of an ASC used in an ASRG for a space mission. This sequence includes testing at Workmanship and Flight Acceptance levels interspersed with periods of extended operation to simulate pre and post fueling. The final step in the test sequence utilizes additional testing at Flight Acceptance levels to simulate launch. To better replicate the acceleration profile seen by an ASC incorporated into an ASRG, the input spectra used in testing the convertors was modified based on dynamic testing of the ASRG Engineering Unit ( ASRG-EU) at Lockheed Martin. This paper presents the vibration test plan for current and future ASC units, including the modified input spectra, and the results of recent tests using these spectra. The test results include data from several accelerometers mounted on the convertors as well as the piston position and output power variables.

A study of lateral fall-off (penumbra) optimisation for pencil beam scanning (PBS) proton therapy

NASA Astrophysics Data System (ADS)

Winterhalter, C.; Lomax, A.; Oxley, D.; Weber, D. C.; Safai, S.

2018-01-01

The lateral fall-off is crucial for sparing organs at risk in proton therapy. It is therefore of high importance to minimize the penumbra for pencil beam scanning (PBS). Three optimisation approaches are investigated: edge-collimated uniformly weighted spots (collimation), pencil beam optimisation of uncollimated pencil beams (edge-enhancement) and the optimisation of edge collimated pencil beams (collimated edge-enhancement). To deliver energies below 70 MeV, these strategies are evaluated in combination with the following pre-absorber methods: field specific fixed thickness pre-absorption (fixed), range specific, fixed thickness pre-absorption (automatic) and range specific, variable thickness pre-absorption (variable). All techniques are evaluated by Monte Carlo simulated square fields in a water tank. For a typical air gap of 10 cm, without pre-absorber collimation reduces the penumbra only for water equivalent ranges between 4-11 cm by up to 2.2 mm. The sharpest lateral fall-off is achieved through collimated edge-enhancement, which lowers the penumbra down to 2.8 mm. When using a pre-absorber, the sharpest fall-offs are obtained when combining collimated edge-enhancement with a variable pre-absorber. For edge-enhancement and large air gaps, it is crucial to minimize the amount of material in the beam. For small air gaps however, the superior phase space of higher energetic beams can be employed when more material is used. In conclusion, collimated edge-enhancement combined with the variable pre-absorber is the recommended setting to minimize the lateral penumbra for PBS. Without collimator, it would be favourable to use a variable pre-absorber for large air gaps and an automatic pre-absorber for small air gaps.

Genetic characterization of Strongyloides spp. from captive, semi-captive and wild Bornean orangutans (Pongo pygmaeus) in Central and East Kalimantan, Borneo, Indonesia.

PubMed

Labes, E M; Nurcahyo, W; Wijayanti, N; Deplazes, P; Mathis, A

2011-09-01

Orangutans (Pongo spp.), Asia's only great apes, are threatened in their survival due to habitat loss, hunting and infections. Nematodes of the genus Strongyloides may represent a severe cause of death in wild and captive individuals. In order to better understand which Strongyloides species/subspecies infect orangutans under different conditions, larvae were isolated from fecal material collected in Indonesia from 9 captive, 2 semi-captive and 9 wild individuals, 18 captive groups of Bornean orangutans and from 1 human working with wild orangutans. Genotyping was done at the genomic rDNA locus (part of the 18S rRNA gene and internal transcribed spacer 1, ITS1) by sequencing amplicons. Thirty isolates, including the one from the human, could be identified as S. fuelleborni fuelleborni with 18S rRNA gene identities of 98·5-100%, with a corresponding published sequence. The ITS1 sequences could be determined for 17 of these isolates revealing a huge variability and 2 main clusters without obvious pattern with regard to attributes of the hosts. The ITS1 amplicons of 2 isolates were cloned and sequenced, revealing considerable variability indicative of mixed infections. One isolate from a captive individual was identified as S. stercoralis (18S rRNA) and showed 99% identity (ITS1) with S. stercoralis sequences from geographically distinct locations and host species. The findings are significant with regard to the zoonotic nature of these parasites and might contribute to the conservation of remaining orangutan populations.

Fine Dissection of Human Mitochondrial DNA Haplogroup HV Lineages Reveals Paleolithic Signatures from European Glacial Refugia

PubMed Central

Sarno, Stefania; Sevini, Federica; Vianello, Dario; Tamm, Erika; Metspalu, Ene; van Oven, Mannis; Hübner, Alexander; Sazzini, Marco; Franceschi, Claudio; Pettener, Davide; Luiselli, Donata

2015-01-01

Genetic signatures from the Paleolithic inhabitants of Eurasia can be traced from the early divergent mitochondrial DNA lineages still present in contemporary human populations. Previous studies already suggested a pre-Neolithic diffusion of mitochondrial haplogroup HV*(xH,V) lineages, a relatively rare class of mtDNA types that includes parallel branches mainly distributed across Europe and West Asia with a certain degree of structure. Up till now, variation within haplogroup HV was addressed mainly by analyzing sequence data from the mtDNA control region, except for specific sub-branches, such as HV4 or the widely distributed haplogroups H and V. In this study, we present a revised HV topology based on full mtDNA genome data, and we include a comprehensive dataset consisting of 316 complete mtDNA sequences including 60 new samples from the Italian peninsula, a previously underrepresented geographic area. We highlight points of instability in the particular topology of this haplogroup, reconstructed with BEAST-generated trees and networks. We also confirm a major lineage expansion that probably followed the Late Glacial Maximum and preceded Neolithic population movements. We finally observe that Italy harbors a reservoir of mtDNA diversity, with deep-rooting HV lineages often related to sequences present in the Caucasus and the Middle East. The resulting hypothesis of a glacial refugium in Southern Italy has implications for the understanding of late Paleolithic population movements and is discussed within the archaeological cultural shifts occurred over the entire continent. PMID:26640946

Burial of thermally perturbed Lesser Himalayan mid-crust: Evidence from petrochemistry and P-T estimation of the western Arunachal Himalaya, India

NASA Astrophysics Data System (ADS)

Goswami-Banerjee, Sriparna; Bhowmik, Santanu Kumar; Dasgupta, Somnath; Pant, Naresh Chandra

2014-11-01

In this work, we establish a dual prograde P-T path of the Lesser Himalayan Sequence (LHS) rocks from the western Arunachal Himalaya (WAH). The investigated metagranites, garnet- and kyanite-zone metapelites of the LHS are part of an inverted metamorphic sequence (IMS) that is exposed on the footwall side of the Main Central Thrust (MCT). Integrated petrographic, mineral chemistry, geothermobarometric (conventional and isopleth intersection methods) and P-T pseudosection modeling studies reveal a near isobaric (at P ~ 8-9 kbar) peak Barrovian metamorphism with increase in TMax from ~ 560 °C in the metagranite through ~ 590-600 °C in the lower and middle garnet-zone to ~ 600-630 °C in the upper garnet- and kyanite-zone rocks. The metamorphic sequence of the LHS additionally records a pre-Barrovian near isobaric thermal gradient in the mid crust (at ~ 6 kbar) from ~ 515 °C (in the middle garnet zone) to ~ 560-580 °C (in the upper garnet- and kyanite zone, adjoining the Main Central Thrust). Further burial (along steep dP/dT gradient) to a uniform depth corresponding to ~ 8-9 kbar and prograde heating of the differentially heated LHS rocks led to the formation of near isobaric metamorphic field gradient in the Barrovian metamorphic zones of the WAH. A combined critical taper and channel flow model is presented to explain the inverted metamorphic zonation of the rocks of the WAH.

On the formation of TW Crv optical radiation

NASA Astrophysics Data System (ADS)

Shimansky, V. V.; Mitrofanova, A. A.; Borisov, N. V.; Fabrika, S. N.; Galeev, A. I.

2016-10-01

We present the analysis of the optical radiation of the young pre-cataclysmic variable TW Crv. Spectroscopic and photometric observations were obtained at the SAO RAS 6-m BTA telescope and at the Russian-Turkish RTT-150 telescope. The light curves of the system posses nearly sinusoidal shapes with the amplitudes of Δ m > 0.m7, what is typical for young pre-cataclysmic variables with sdO-subdwarfs and orbit inclinations of less than 45◦. The optical spectrum contains dominant radiation of the hot subdwarf with the HI and He II absorption lines and strong emission lines, which are formed in the atmosphere of the secondary owing to the reflection effects. Radial velocities of the cool star were measured by analyzing the λλ 4630-4650 Å Bowen blend, which for the first time allowed to determine the component masses. A numerical simulation of the light curves and spectra of TW Crv, obtaining a complete set of systems fundamental parameters was carried out. The hot star parameters prompt its belonging to the sdOsubdwarf class at the stage of transition to the cooling white dwarf sequence. The absence of its observable planetary nebula is caused by a long-lasting evolution of the system after the common envelope state. The secondary component has a luminosity excess, which is typical for other young sdO-subdwarf precataclysmic variables. Its position on the " age-luminosity excess" diagram points at the accuracy of the obtained set of TW Crv fundamental parameters and at the similarity of its evolutionary and physical conditions with that of other BE UMa-type objects.

High Class-Imbalance in pre-miRNA Prediction: A Novel Approach Based on deepSOM.

PubMed

Stegmayer, Georgina; Yones, Cristian; Kamenetzky, Laura; Milone, Diego H

2017-01-01

The computational prediction of novel microRNA within a full genome involves identifying sequences having the highest chance of being a miRNA precursor (pre-miRNA). These sequences are usually named candidates to miRNA. The well-known pre-miRNAs are usually only a few in comparison to the hundreds of thousands of potential candidates to miRNA that have to be analyzed, which makes this task a high class-imbalance classification problem. The classical way of approaching it has been training a binary classifier in a supervised manner, using well-known pre-miRNAs as positive class and artificially defining the negative class. However, although the selection of positive labeled examples is straightforward, it is very difficult to build a set of negative examples in order to obtain a good set of training samples for a supervised method. In this work, we propose a novel and effective way of approaching this problem using machine learning, without the definition of negative examples. The proposal is based on clustering unlabeled sequences of a genome together with well-known miRNA precursors for the organism under study, which allows for the quick identification of the best candidates to miRNA as those sequences clustered with known precursors. Furthermore, we propose a deep model to overcome the problem of having very few positive class labels. They are always maintained in the deep levels as positive class while less likely pre-miRNA sequences are filtered level after level. Our approach has been compared with other methods for pre-miRNAs prediction in several species, showing effective predictivity of novel miRNAs. Additionally, we will show that our approach has a lower training time and allows for a better graphical navegability and interpretation of the results. A web-demo interface to try deepSOM is available at http://fich.unl.edu.ar/sinc/web-demo/deepsom/.

Evidence for feedback and stellar-dynamically regulated bursty star cluster formation: the case of the Orion Nebula Cluster

NASA Astrophysics Data System (ADS)

Kroupa, Pavel; Jeřábková, Tereza; Dinnbier, František; Beccari, Giacomo; Yan, Zhiqiang

2018-04-01

A scenario for the formation of multiple co-eval populations separated in age by about 1 Myr in very young clusters (VYCs, ages less than 10 Myr) and with masses in the range 600-20 000 M⊙ is outlined. It rests upon a converging inflow of molecular gas building up a first population of pre-main sequence stars. The associated just-formed O stars ionise the inflow and suppress star formation in the embedded cluster. However, they typically eject each other out of the embedded cluster within 106 yr, that is before the molecular cloud filament can be ionised entirely. The inflow of molecular gas can then resume forming a second population. This sequence of events can be repeated maximally over the life-time of the molecular cloud (about 10 Myr), but is not likely to be possible in VYCs with mass <300 M⊙, because such populations are not likely to contain an O star. Stellar populations heavier than about 2000 M⊙ are likely to have too many O stars for all of these to eject each other from the embedded cluster before they disperse their natal cloud. VYCs with masses in the range 600-2000 M⊙ are likely to have such multi-age populations, while VYCs with masses in the range 2000-20 000 M⊙ can also be composed solely of co-eval, mono-age populations. More massive VYCs are not likely to host sub-populations with age differences of about 1 Myr. This model is applied to the Orion Nebula Cluster (ONC), in which three well-separated pre-main sequences in the colour-magnitude diagram of the cluster have recently been discovered. The mass-inflow history is constrained using this model and the number of OB stars ejected from each population are estimated for verification using Gaia data. As a further consequence of the proposed model, the three runaway O star systems, AE Aur, μ Col and ι Ori, are considered as significant observational evidence for stellar-dynamical ejections of massive stars from the oldest population in the ONC. Evidence for stellar-dynamical ejections of massive stars in the currently forming population is also discussed.

Chandra and HST Observations of the High Energy (X-ray/UV) Radiation Fields for an Evolutionary Sequence of Pre-Main-Sequence Stars

NASA Astrophysics Data System (ADS)

Brown, Alexander; Herczeg, G. J.; Brown, J. M.; Walter, F. M.; Valenti, J.; Ardila, D.; Hillenbrand, L. A.; Edwards, S.; Johns-Krull, C. M.; Alexander, R.; Bergin, E. A.; Calvet, N.; Bethell, T. J.; Ingleby, L.; Bary, J. S.; Audard, M.; Baldovin, C.; Roueff, E.; Abgrall, H.; Gregory, S. G.; Ayres, T. R.; Linsky, J. L.

2010-03-01

Pre-main-sequence (PMS) stars are strong X-ray and UV emitters and the high energy radiation from the central stars directly influences the physical and chemical processes in their protoplanetary disks. Gas and dust in protoplanetary systems are excited by these photons, which are the dominant ionization source for hundreds of AU around the star. X-rays penetrate deep into disks and power complex chemistry on grain surfaces. ``Transitional disks'' are an important short-lived evolutionary stage for PMS stars and protoplanetary systems. These disks have transformed most of the dust and gas in their inner regions into planetesimals or larger solid bodies. As dust disks disappear after ages of roughly 5 Myr high levels of stellar magnetic activity persist and continue to bathe the newly-forming protoplanetary systems with intense high energy radiation. We present new X-ray and UV spectra for a sample of PMS stars at a variety of evolutionary stages, including the classical T Tauri stars DE Tau and DK Tau, the transitional disk stars GM Aur and HD135344B, the Herbig Ae star HD104237, and the weak-lined T Tauri star LkCa4, the Eta Cha cluster [age 7 Myr] members RECX1, RECX-11, and RECX-15, and TW Hya association [age 8 Myr] member TWA-2. These include the first results from our 111 orbit HST Large project and associated X-ray data. New and archival Chandra, XMM, and Swift X-ray spectra and HST COS+STIS FUV spectra are being used to reconstruct the full high energy (X-ray/EUV/FUV/NUV) spectra of these stars, thus allowing detailed modeling of the physics and chemistry of their circumstellar environments. The UV spectra provide improved emission line profiles revealing details of the magnetically-heated plasma and accretion and outflow processes. This work is supported by Chandra grants GO8-9024X, GO9-0015X and GO9-0020B and proposal 11200754 and HST GO grants 11336, 11616, and 11828.

PreCisIon: PREdiction of CIS-regulatory elements improved by gene's positION.

PubMed

Elati, Mohamed; Nicolle, Rémy; Junier, Ivan; Fernández, David; Fekih, Rim; Font, Julio; Képès, François

2013-02-01

Conventional approaches to predict transcriptional regulatory interactions usually rely on the definition of a shared motif sequence on the target genes of a transcription factor (TF). These efforts have been frustrated by the limited availability and accuracy of TF binding site motifs, usually represented as position-specific scoring matrices, which may match large numbers of sites and produce an unreliable list of target genes. To improve the prediction of binding sites, we propose to additionally use the unrelated knowledge of the genome layout. Indeed, it has been shown that co-regulated genes tend to be either neighbors or periodically spaced along the whole chromosome. This study demonstrates that respective gene positioning carries significant information. This novel type of information is combined with traditional sequence information by a machine learning algorithm called PreCisIon. To optimize this combination, PreCisIon builds a strong gene target classifier by adaptively combining weak classifiers based on either local binding sequence or global gene position. This strategy generically paves the way to the optimized incorporation of any future advances in gene target prediction based on local sequence, genome layout or on novel criteria. With the current state of the art, PreCisIon consistently improves methods based on sequence information only. This is shown by implementing a cross-validation analysis of the 20 major TFs from two phylogenetically remote model organisms. For Bacillus subtilis and Escherichia coli, respectively, PreCisIon achieves on average an area under the receiver operating characteristic curve of 70 and 60%, a sensitivity of 80 and 70% and a specificity of 60 and 56%. The newly predicted gene targets are demonstrated to be functionally consistent with previously known targets, as assessed by analysis of Gene Ontology enrichment or of the relevant literature and databases.

A two-stage stochastic rule-based model to determine pre-assembly buffer content

NASA Astrophysics Data System (ADS)

Gunay, Elif Elcin; Kula, Ufuk

2018-01-01

This study considers instant decision-making needs of the automobile manufactures for resequencing vehicles before final assembly (FA). We propose a rule-based two-stage stochastic model to determine the number of spare vehicles that should be kept in the pre-assembly buffer to restore the altered sequence due to paint defects and upstream department constraints. First stage of the model decides the spare vehicle quantities, where the second stage model recovers the scrambled sequence respect to pre-defined rules. The problem is solved by sample average approximation (SAA) algorithm. We conduct a numerical study to compare the solutions of heuristic model with optimal ones and provide following insights: (i) as the mismatch between paint entrance and scheduled sequence decreases, the rule-based heuristic model recovers the scrambled sequence as good as the optimal resequencing model, (ii) the rule-based model is more sensitive to the mismatch between the paint entrance and scheduled sequences for recovering the scrambled sequence, (iii) as the defect rate increases, the difference in recovery effectiveness between rule-based heuristic and optimal solutions increases, (iv) as buffer capacity increases, the recovery effectiveness of the optimization model outperforms heuristic model, (v) as expected the rule-based model holds more inventory than the optimization model.

Effects of psychological priming, video, and music on anaerobic exercise performance.

PubMed

Loizou, G; Karageorghis, C I

2015-12-01

Peak performance videos accompanied by music can help athletes to optimize their pre-competition mindset and are often used. Priming techniques can be incorporated into such videos to influence athletes' motivational state. There has been limited empirical work investigating the combined effects of such stimuli on anaerobic performance. The present study examined the psychological and psychophysiological effects of video, music, and priming when used as a pre-performance intervention for an anaerobic endurance task. Psychological measures included the main axes of the circumplex model of affect and liking scores taken pre-task, and the Exercise-induced Feeling Inventory, which was administered post-task. Physiological measures comprised heart rate variability and heart rate recorded pre-task. Fifteen males (age = 26.3 ± 2.8 years) were exposed to four conditions prior to performing the Wingate Anaerobic Test: music-only, video and music, video with music and motivational primes, and a no-video/no-music control. Results indicate that the combined video, music, and primes condition was the most effective in terms of influencing participants' pre-task affect and subsequent anaerobic performance; this was followed by the music-only condition. The findings indicate the utility of such stimuli as a pre-performance technique to enhance athletes' or exercisers' psychological states. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Exploring Pre-Service Teachers' Perceived Teaching-Efficacy, Attitudes and Concerns about Inclusive Education in Bangladesh

ERIC Educational Resources Information Center

Ahsan, M. Tariq; Sharma, Umesh; Deppeler, Joanne M.

2012-01-01

This paper reports on pre-service teachers' preparedness for inclusive education in Bangladesh through measuring their perceived teaching-efficacy, concerns and attitudes towards inclusive education and identifying predictor variables that contribute to those three variables. Using two standardized scales with 1,623 pre-service teachers from 16…

[Study on ITS sequences of Aconitum vilmorinianum and its medicinal adulterant].

PubMed

Zhang, Xiao-nan; Du, Chun-hua; Fu, De-huan; Gao, Li; Zhou, Pei-jun; Wang, Li

2012-09-01

To analyze and compare the ITS sequences of Aconitum vilmorinianum and its medicinal adulterant Aconitum austroyunnanense. Total genomic DNA were extracted from sample materials by improved CTAB method, ITS sequences of samples were amplified using PCR systems, directly sequenced and analyzed using software DNAStar, ClustalX1.81 and MEGA 4.0. 299 consistent sites, 19 variable sites and 13 informative sites were found in ITS1 sequences, 162 consistent sites, 2 variable sites and 1 informative sites were found in 5.8S sequences, 217 consistent sites, 3 variable sites and 1 informative site were found in ITS2 sequences. Base transition and transversion was not found only in 5.8S sequences, 2 sites transition and 1 site transversion were found in ITS1 sequences, only 1 site transversion was found in ITS2 sequences comparting the ITS sequences data matrix. By analyzing the ITS sequences data matrix from 2 population of Aconitum vilmorinianum and 3 population of Aconitum austroyunnanense, we found a stable informative site at the 596th base in ITS2 sequences, in all the samples of Aconitum vilmorinianum the base was C, and in all the samples of Aconitum austroyunnanense the base was A. Aconitum vilmorinianum and Aconitum austroyunnanense can be identified by their characters of ITS sequences, and the variable sites in ITS1 sequences are more than in ITS2 sequences.

The Effect of a New Sodium Bicarbonate Loading Regimen on Anaerobic Capacity and Wrestling Performance.

PubMed

Durkalec-Michalski, Krzysztof; Zawieja, Emilia Ewa; Podgórski, Tomasz; Zawieja, Bogna Ewa; Michałowska, Patrycja; Łoniewski, Igor; Jeszka, Jan

2018-05-30

Gastrointestinal side effects are the main problem with sodium bicarbonate (SB) use in sports. Therefore, our study assessed the effect of a new SB loading regimen on anaerobic capacity and wrestling performance. Fifty-eight wrestlers were randomized to either a progressive-dose regimen of up to 100 mg∙kg -1 of SB or a placebo for 10 days. Before and after treatment, athletes completed an exercise protocol that comprised, in sequence, the first Wingate, dummy throw, and second Wingate tests. Blood samples were taken pre- and post-exercise. No gastrointestinal side effects were reported during the study. After SB treatment, there were no significant improvements in the outcomes of the Wingate and dummy throw tests. The only index that significantly improved with SB, compared to the placebo ( p = 0.0142), was the time-to-peak power in the second Wingate test, which decreased from 3.44 ± 1.98 to 2.35 ± 1.17 s. There were also no differences in blood lactate or glucose concentrations. In conclusion, although the new loading regimen eliminated gastrointestinal symptoms, the doses could have been too small to elicit additional improvements in anaerobic power and wrestling performance. However, shortening the time-to-peak power during fatigue may be particularly valuable and is one of the variables contributing to the final success of a combat sports athlete.

RNA-based analysis of two SMARCB1 mutations associated with familial schwannomatosis with meningiomas.

PubMed

Melean, German; Velasco, Ana; Hernández-Imaz, Elisabete; Rodríguez-Álvarez, Francisco Javier; Martín, Yolanda; Valero, Ana; Hernández-Chico, Concepción

2012-08-01

Germline mutations in the SMARCB1 gene cause familial schwannomatosis, a condition characterized by the presence of multiple schwannomas, although mutations in SMARCB1 have also been associated with rhadboid tumor predisposition syndrome 1 (RTPS1). Both schwannomatosis and RTPS1 are autosomal dominant conditions that predispose individuals to develop distinct types of tumors. We clinically and genetically characterized two families with schwannomatosis associated with SMARCB1 mutations. Eight affected members of these families developed different numbers of schwannomas and/or meningiomas at distinct ages, evidence that meningiomas are variably expressed in this condition. We identified two germline mutations in SMARCB1 associated with the familial disease, c.233-1G>A and the novel c.207_208dupTA mutation, which both proved to affect the main SMARCB1 isoforms at the RNA level distinctly. Interestingly, the c.207_208dupTA mutation had no effect on the coding sequence, pre-mRNA splicing or the level of expression of the SMARCB1 isoform 2. Furthermore, SMARCB1 isoforms harboring a premature termination codon were largely eliminated via the nonsense-mediated mRNA decay pathway. Our results highlight the importance of RNA-based studies to characterize SMARCB1 germline mutations in order to determine their impact on protein expression and gain further insight into the genetic basis of conditions associated with SMARCB1 mutations.

AmericaPlex26: A SNaPshot Multiplex System for Genotyping the Main Human Mitochondrial Founder Lineages of the Americas

PubMed Central

Coutinho, Alexandra; Valverde, Guido; Fehren-Schmitz, Lars; Cooper, Alan; Barreto Romero, Maria Inés; Espinoza, Isabel Flores; Llamas, Bastien; Haak, Wolfgang

2014-01-01

Phylogeographic studies have described a reduced genetic diversity in Native American populations, indicative of one or more bottleneck events during the peopling and prehistory of the Americas. Classical sequencing approaches targeting the mitochondrial diversity have reported the presence of five major haplogroups, namely A, B, C, D and X, whereas the advent of complete mitochondrial genome sequencing has recently refined the number of founder lineages within the given diversity to 15 sub-haplogroups. We developed and optimized a SNaPshot assay to study the mitochondrial diversity in pre-Columbian Native American populations by simultaneous typing of 26 single nucleotide polymorphisms (SNPs) characterising Native American sub-haplogroups. Our assay proved to be highly sensitive with respect to starting concentrations of target DNA and could be applied successfully to a range of ancient human skeletal material from South America from various time periods. The AmericaPlex26 is a powerful assay with enhanced phylogenetic resolution that allows time- and cost-efficient mitochondrial DNA sub-typing from valuable ancient specimens. It can be applied in addition or alternative to standard sequencing of the D-loop region in forensics, ancestry testing, and population studies, or where full-resolution mitochondrial genome sequencing is not feasible. PMID:24671218

AmericaPlex26: a SNaPshot multiplex system for genotyping the main human mitochondrial founder lineages of the Americas.

PubMed

Coutinho, Alexandra; Valverde, Guido; Fehren-Schmitz, Lars; Cooper, Alan; Barreto Romero, Maria Inés; Espinoza, Isabel Flores; Llamas, Bastien; Haak, Wolfgang

2014-01-01

Phylogeographic studies have described a reduced genetic diversity in Native American populations, indicative of one or more bottleneck events during the peopling and prehistory of the Americas. Classical sequencing approaches targeting the mitochondrial diversity have reported the presence of five major haplogroups, namely A, B, C, D and X, whereas the advent of complete mitochondrial genome sequencing has recently refined the number of founder lineages within the given diversity to 15 sub-haplogroups. We developed and optimized a SNaPshot assay to study the mitochondrial diversity in pre-Columbian Native American populations by simultaneous typing of 26 single nucleotide polymorphisms (SNPs) characterising Native American sub-haplogroups. Our assay proved to be highly sensitive with respect to starting concentrations of target DNA and could be applied successfully to a range of ancient human skeletal material from South America from various time periods. The AmericaPlex26 is a powerful assay with enhanced phylogenetic resolution that allows time- and cost-efficient mitochondrial DNA sub-typing from valuable ancient specimens. It can be applied in addition or alternative to standard sequencing of the D-loop region in forensics, ancestry testing, and population studies, or where full-resolution mitochondrial genome sequencing is not feasible.

Longitudinal study of religiosity and mental health of adolescents with psychiatric problems. The TRAILS study.

PubMed

van der Jagt-Jelsma, W; de Vries-Schot, M; Scheepers, P; van Deurzen, P A M; Klip, H; Buitelaar, J K

2017-09-01

This study used longitudinal data to examine the influence of the religiosity of pre-adolescents with psychiatric problems on the course of mental health during adolescence. In the TRAILS clinical cohort of 543 pre-adolescents (10-12 years), mental health problems were assessed using self-report at baseline, T2 (12-14 years), T3 (14-17 years), and T4 (17-21 years). The Youth Self Report (YSR) was used at baseline, T2, and T3, and the Adult Self Report (ASR) was used at T4. Religiosity was assessed at baseline using self-report and information from mothers and fathers, resulting in three categorical religiosity variables and six SOCON (Social Cultural Developments Questionnaire) religiosity scales that assess religiosity in greater detail. Repeated measure ANOVA analyses were performed for each independent religiosity variable with internalizing and externalizing problem behavior as dependent variables, gender as a factor and time (T1, T2, T3 and T4) as within factor. Results were adjusted for marital status of parents and socioeconomic status and corrected for multiple testing. There were main effects of the self-report SOCON scale "Humanistic beliefs" and gender and gender "by Humanistic beliefs" interaction effect on internalizing problems. Follow-up tests revealed that among females "high" scores on "Humanistic beliefs" were associated with increased internalizing problems. There were hardly any associations between religiosity and mental health in a clinical cohort of pre-adolescents up to adolescence. The exception being that among females strong humanistic beliefs were associated with internalizing problems. Implications of these findings are discussed. Copyright © 2017. Published by Elsevier Masson SAS.

Prediction of plant pre-microRNAs and their microRNAs in genome-scale sequences using structure-sequence features and support vector machine.

PubMed

Meng, Jun; Liu, Dong; Sun, Chao; Luan, Yushi

2014-12-30

MicroRNAs (miRNAs) are a family of non-coding RNAs approximately 21 nucleotides in length that play pivotal roles at the post-transcriptional level in animals, plants and viruses. These molecules silence their target genes by degrading transcription or suppressing translation. Studies have shown that miRNAs are involved in biological responses to a variety of biotic and abiotic stresses. Identification of these molecules and their targets can aid the understanding of regulatory processes. Recently, prediction methods based on machine learning have been widely used for miRNA prediction. However, most of these methods were designed for mammalian miRNA prediction, and few are available for predicting miRNAs in the pre-miRNAs of specific plant species. Although the complete Solanum lycopersicum genome has been published, only 77 Solanum lycopersicum miRNAs have been identified, far less than the estimated number. Therefore, it is essential to develop a prediction method based on machine learning to identify new plant miRNAs. A novel classification model based on a support vector machine (SVM) was trained to identify real and pseudo plant pre-miRNAs together with their miRNAs. An initial set of 152 novel features related to sequential structures was used to train the model. By applying feature selection, we obtained the best subset of 47 features for use with the Back Support Vector Machine-Recursive Feature Elimination (B-SVM-RFE) method for the classification of plant pre-miRNAs. Using this method, 63 features were obtained for plant miRNA classification. We then developed an integrated classification model, miPlantPreMat, which comprises MiPlantPre and MiPlantMat, to identify plant pre-miRNAs and their miRNAs. This model achieved approximately 90% accuracy using plant datasets from nine plant species, including Arabidopsis thaliana, Glycine max, Oryza sativa, Physcomitrella patens, Medicago truncatula, Sorghum bicolor, Arabidopsis lyrata, Zea mays and Solanum lycopersicum. Using miPlantPreMat, 522 Solanum lycopersicum miRNAs were identified in the Solanum lycopersicum genome sequence. We developed an integrated classification model, miPlantPreMat, based on structure-sequence features and SVM. MiPlantPreMat was used to identify both plant pre-miRNAs and the corresponding mature miRNAs. An improved feature selection method was proposed, resulting in high classification accuracy, sensitivity and specificity.

A study to compare traditional and constructivism-based instruction of a high school biology unit on biosystematics

NASA Astrophysics Data System (ADS)

Saigo, Barbara Woodworth

The researcher collaborated with four high school biology teachers who had been involved for 2-1/2 years in a constructivism-based professional development experience that emphasized teaching for conceptual change and using classroom-based inquiry as a basis for making instructional decisions. The researcher and teachers designed a five-day instructional unit on biosystematics using two contrasting approaches, comprising the treatment variable. The "traditional" unit emphasized lecture, written materials, and some laboratory activities. The "constructivist" unit emphasized a specific, inquiry-based, conceptual change strategy and collaborative learning. The study used a quasi-experimental, factorial design to explore impact of instructional approach (the treatment variable) on student performance (the dependent variable) on repeated measures (three) of a biology concept test. Additional independent variables considered were gender, cumulative GPA, and the section in which students were enrolled. Scores on the biology concept test were compiled for the 3 constructivist sections (N = 44) and the 3 traditional sections (N = 42). Analysis of Covariance (ANCOVA) was applied. The main findings in regard to the primary research question were that instructional approach did not have a significant relationship to immediate post test scores or gain, but that one month after instruction students in the constructivist group demonstrated less loss of gain than those in the traditional group; i.e., their longer-term retention was greater. Also, GPA*instructional approach effects were detected for post-post-test gain. GPA and gender were significantly associated with pre-test, post-test, and post-post scores; however, in terms of change (gain) from pre-test to post-test and pre-test to post-post-test, GPA and gender were not significant effects. Section was a significant effect for all three tests, in terms of both score and gain. Gender*section effects were detected for post-test gain and post-post-test scores.

Pre-vitamin D effective ultraviolet transmission through clothing during simulated wear.

PubMed

Parisi, A V; Wilson, C A

2005-12-01

Clothing is an important protective layer used to reduce ultraviolet (UV) exposures to the skin surface. However, not all UV exposure is linked to detrimental health effects with some exposure to UVB wavelengths below 316 nm required for the synthesis of pre-vitamin D(3). The aim of the current research was to investigate the effect of fabric type, color, fit, and wetness on the transmission of pre-vitamin D(3) effective UV through garments during simulated wear, in a high UV exposure environment. Dosimeters fabricated from polysulfone film were positioned at eight selected body sites on the skin surface and clothing surface of identically designed, loose and fitted, black and white T-shirts made up in two knitted fabric types and tested when both dry and when drying after initial wetting (n=3 replicates). The T-shirts were placed on manikins set to simulate humans in the sun between 09:30 and 12:30 Eastern Standard Time during the Southern Hemisphere summer period. The post-exposure absorbance was measured and the dosimeters were calibrated for biologically effective UV for pre-vitamin D(3) synthesis with a UV spectroradiometer. The effect of fit, fabric type, color, and wetness on pre-vitamin D(3) effective UV transmission during simulated wear was assessed. Irradiances varied among body sites with the highest erythemal exposures to a horizontal plane over the 3 h period reaching approximately 14.5 minimal erythema dose (MED) while the highest exposure under the garment was 0.22 MED which may not be above the threshold for pre-vitamin D(3) synthesis for the time period investigated. Fabric and fit were the main variables affecting transmission of pre-vitamin D(3) effective UV. Some interactions were identified between the fabric color and wetness and between fabric type and color; however, while significantly modifying transmission these effects were small. Transmission of pre-vitamin D(3) effective UV occurred through the high UPF knitted fabrics investigated. However, the length of exposure will influence whether the irradiances are sufficient to be above the threshold for pre-vitamin D(3) synthesis. The main effect on transmission of pre-vitamin D(3) effective UV was the fit of the T-shirt and its fabric type (probably structure) rather than color or degree of wetness.

Pre-design study for a modern four-bladed rotor for the Rotor System Research Aircraft (RSRA). [integrating the YAH-64 main rotor

NASA Technical Reports Server (NTRS)

Hughes, C. W.; Logan, A. H.

1981-01-01

Various candidate rotor systems were compared in an effort to select a modern four-bladed rotor for the RSRA. The YAH-64 rotor system was chosen as the candidate rotor system for further development for the RSRA. The process used to select the rotor system, studies conducted to mate the rotor with the RSRA and provide parametric variability, and the development plan which would be used to implement these studies are presented. Drawings are included.

Complete coding regions of the prototypes enterovirus B93 and C95: phylogenetic analyses of the P1 and P3 regions of EV-B and EV-C strains.

PubMed

Junttila, N; Lévêque, N; Magnius, L O; Kabue, J P; Muyembe-Tamfum, J J; Maslin, J; Lina, B; Norder, H

2015-03-01

Complete coding regions were sequenced for two new enterovirus genomes: EV-B93 previously identified by VP1 sequencing, derived from a child with acute flaccid paralysis in the Democratic Republic of Congo; and EV-C95 from a French soldier with acute gastroenteritis in Djibouti. The EV-B93 P1 had more than 30% nucleotide divergence from other EV-B types, with highest similarity to E-15 and EV-B80. The P1 nucleotide sequence of EV-C95 was most similar, 71%, to CV-A21. Complete coding regions for the new enteroviruses were compared with those of 135 EV-B and 176 EV-C strains representing all types available in GenBank. When strains from the same outbreak or strains isolated during the same year in the same geographical region were excluded, 27 of the 58 EV-B, and 16 of the 23 EV-C types were represented by more than one sequence. However, for EV-B the P3 sequences formed three clades mainly according to origin or time of isolation, irrespective of type, while for EV-C the P3 sequences segregated mainly according to disease manifestation, with most strains causing paralysis, including polioviruses, forming one clade, and strains causing respiratory illness forming another. There was no intermixing of types between these two clades, apart from two EV-C96 strains. The EV-B P3 sequences had lower inter-clade and higher intra-clade variability as compared to the EV-C sequences, which may explain why inter-clade recombinations are more frequent in EV-B. Further analysis of more isolates may shed light on the role of recombinations in the evolution of EV-B in geographical context. © 2014 Wiley Periodicals, Inc.

Pre-binding prior to full engagement improves loading conditions for front-row players in contested Rugby Union scrums.

PubMed

Preatoni, E; Cazzola, D; Stokes, K A; England, M; Trewartha, G

2016-12-01

We investigated the effect of a "PreBind" engagement protocol on the biomechanics of contested Rugby Union scrummaging at different playing levels. "PreBind" requires front-row props to take a bind on opposing players prior to the engagement, and to maintain the bind throughout the scrum duration. Twenty-seven teams from five different playing levels performed live scrums under realistic conditions. Video analysis, pressures sensors, and inertial measurement units measured biomechanical outcomes as teams scrummaged following different engagement protocols: the CTPE (referee calls "crouch-touch-pause-engage"), the CTS ("crouch-touch-set"), and the PreBind ("crouch-bind-set") variants. PreBind reduced the set-up distance between the packs (-27%) and the speed at which they came into contact by more than 20%. The peak biomechanical stresses acting on front rows during the engagement phase were decreased in PreBind by 14-25% with respect to CTPE and CTS, without reducing the capability to generate force in the subsequent sustained push. No relevant main effects were recorded for playing level due to within-group variability and there were no interaction effects between playing level and engagement protocol. Pre-binding reduced many mechanical quantities that have been indicated as possible factors for chronic and acute injury, and may lead to safer engagement conditions without affecting subsequent performance. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Diversity of tuco-tucos (Ctenomys, Rodentia) in the Northeastern wetlands from Argentina: mitochondrial phylogeny and chromosomal evolution.

PubMed

Caraballo, Diego A; Abruzzese, Giselle A; Rossi, María Susana

2012-06-01

Tuco-tucos (small subterranean rodents of the genus Ctenomys) that inhabit sandy soils of the area under the influence of the second largest wetland of South America, in Northeastern Argentina (Corrientes province), are a complex of species and forms whose taxonomic status were not defined, nor are the evolutionary relationships among them. The tuco-tuco populations of this area exhibit one of the most ample grades of chromosomal variability within the genus. In order to analyze evolutionary relationships within the Corrientes group and its chromosomal variability, we completed the missing karyotypic information and performed a phylogenetic analysis. We obtained partial sequences of three mitochondrial markers: D-loop, cytochrome b and cytochrome oxidase I. The Corrientes group was monophyletic and split into three main clades that grouped related karyomorphs. The phylogeny suggested an ancestral condition of the karyomorph with diploid number (2n) 70 and fundamental number (FN) 84 that has evolved mainly via reductions of the FN although amplifications occurred in certain lineages. We discuss the relationship between patterns of chromosomal variability and species and groups boundaries. From the three main clades the one named iberá exhibited a remarkable karyotypic homogeneity, and could be considered as an independent and cohesive evolutionary lineage. On the contrary, the former recognized species C. dorbignyi is a polyphyletic lineage and hence its systematic classification should be reviewed.

The 2016-2017 Central Italy Seismic Sequence: Source Complexity Inferred from Rupture Models.

NASA Astrophysics Data System (ADS)

Scognamiglio, L.; Tinti, E.; Casarotti, E.; Pucci, S.; Villani, F.; Cocco, M.; Magnoni, F.; Michelini, A.

2017-12-01

The Apennines have been struck by several seismic sequences in recent years, showing evidence of the activation of multiple segments of normal fault systems in a variable and, relatively short, time span, as in the case of the 1980 Irpinia earthquake (three shocks in 40 s), the 1997 Umbria-Marche sequence (four main shocks in 18 days) and the 2009 L'Aquila earthquake having three segments activated within a few weeks. The 2016-2017 central Apennines seismic sequence begin on August 24th with a MW 6.0 earthquake, which strike the region between Amatrice and Accumoli causing 299 fatalities. This earthquake ruptures a nearly 20 km long normal fault and shows a quite heterogeneous slip distribution. On October 26th, another main shock (MW 5.9) occurs near Visso extending the activated seismogenic area toward the NW. It is a double event rupturing contiguous patches on the fault segment of the normal fault system. Four days after the second main shock, on October 30th, a third earthquake (MW 6.5) occurs near Norcia, roughly midway between Accumoli and Visso. In this work we have inverted strong motion waveforms and GPS data to retrieve the source model of the MW 6.5 event with the aim of interpreting the rupture process in the framework of this complex sequence of moderate magnitude earthquakes. We noted that some preliminary attempts to model the slip distribution of the October 30th main shock using a single fault plane oriented along the Apennines did not provide convincing fits to the observed waveforms. In addition, the deformation pattern inferred from satellite observations suggested the activation of a multi-fault structure, that is coherent to the complexity and the extension of the geological surface deformation. We investigated the role of multi-fault ruptures and we found that this event revealed an extraordinary complexity of the rupture geometry and evolution: the coseismic rupture propagated almost simultaneously on a normal fault and on a blind fault, possibly inherited from compressional tectonics. These earthquakes raise serious concerns on our understanding of fault segmentation and seismicity evolution during sequences of normal faulting earthquakes. Finally, the retrieved rupture history has important implications on seismic hazard assessment and on the maximum expected magnitude in a given tectonic area.

Performance of aerobic nitrite granules treating an anaerobic pre-treated wastewater originating from the potato industry.

PubMed

Dobbeleers, Thomas; Daens, Dominique; Miele, Solange; D'aes, Jolien; Caluwé, Michel; Geuens, Luc; Dries, Jan

2017-02-01

In this study nitrogen removal via nitrite >80% was achieved after approximately 80days in a sequencing batch reactor (SBR) treating pre-treated industrial wastewater originating from the potato industry. Thereafter, SBR performance was investigated during the formation of aerobic nitrite granules (ANG). The first granules appeared after 26days leading to full granulation after 64days. ANG showed excellent settling properties, as the Sludge Volume Index (SVI) went down to 16mL/g and a SVI 10 /SVI 30 =1 was obtained. qPCR analysis showed that slow growing organisms, especially polyphosphate accumulating organisms (PAO) were stimulated by an anaerobic feeding strategy. The average nitrogen removal was 95.3% over the entire operational period, and it mainly followed the "nitrite-route". Moreover, with ANG also phosphorus removal efficiencies up to 65.7% could be achieved. However, it has to be mentioned that nitrous oxide was an important denitrification product, which implies some environmental concerns. Copyright © 2016 Elsevier Ltd. All rights reserved.

Evaluation of Metacognitive Competence of Pre-Service Music Teachers in Terms of Some Variables

ERIC Educational Resources Information Center

Hakan, Okay

2016-01-01

The purpose of the present research is to define pre-service music teachers' competence in using metacognitive activities in relation to academic achievement, gender, and class grade variables. The work-group consists of 131 pre-service music teachers, who study at Balikesir University Necatibey Faculty of Education, Programme of Music Teaching.…

Investigating Pre-Service Science Teachers' Critical Thinking Dispositions and Problem Solving Skills in Terms of Different Variables

ERIC Educational Resources Information Center

Yenice, Nilgun

2011-01-01

This study was conducted to examine pre-service science teachers' critical thinking dispositions and problem solving skills based on gender, grade level and graduated high school variables. Also relationship between pre-service science teachers' critical thinking dispositions and problem solving skills was examined based on gender, grade level and…

Translational initiation in Leishmania tarentolae and Phytomonas serpens (Kinetoplastida) is strongly influenced by pre-ATG triplet and its 5' sequence context.

PubMed

Lukes, Julius; Paris, Zdenek; Regmi, Sandesh; Breitling, Reinhard; Mureev, Sergey; Kushnir, Susanna; Pyatkov, Konstantin; Jirků, Milan; Alexandrov, Kirill A

2006-08-01

To investigate the influence of sequence context of translation initiation codon on translation efficiency in Kinetoplastida, we constructed a library of expression plasmids randomized in the three nucleotides prefacing ATG of a reporter gene encoding enhanced green fluorescent protein (EGFP). All 64 possible combinations of pre-ATG triplets were individually stably integrated into the rDNA locus of Leishmania tarentolae and the resulting cell lines were assessed for EGFP expression. The expression levels were quantified directly by measuring the fluorescence of EGFP protein in living cells and confirmed by Western blotting. We observed a strong influence of the pre-ATG triplet on the level of protein expression over a 20-fold range. To understand the degree of evolutionary conservation of the observed effect, we transformed Phytomonas serpens, a trypanosomatid parasite of plants, with a subset of the constructs. The pattern of translational efficiency mediated by individual pre-ATG triplets in this species was similar to that observed in L. tarentolae. However, the pattern of translational efficiency of two other proteins (red fluorescent protein and tetracycline repressor) containing selected pre-ATG triplets did not correlate with either EGFP or each other. Thus, we conclude that a conserved mechanism of translation initiation site selection exists in kinetoplastids that is strongly influenced not only by the pre-ATG sequences but also by the coding region of the gene.

125. Pre1911. Crew on main deck, starboard side at main ...

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

125. Pre-1911. Crew on main deck, starboard side at main hatch, looking aft. Note dark object in center of photo that may be original main deck capstan. Fred Heick collection. (K9.9571) - Ship BALCLUTHA, 2905 Hyde Street Pier, San Francisco, San Francisco County, CA

IDEPI: rapid prediction of HIV-1 antibody epitopes and other phenotypic features from sequence data using a flexible machine learning platform.

PubMed

Hepler, N Lance; Scheffler, Konrad; Weaver, Steven; Murrell, Ben; Richman, Douglas D; Burton, Dennis R; Poignard, Pascal; Smith, Davey M; Kosakovsky Pond, Sergei L

2014-09-01

Since its identification in 1983, HIV-1 has been the focus of a research effort unprecedented in scope and difficulty, whose ultimate goals--a cure and a vaccine--remain elusive. One of the fundamental challenges in accomplishing these goals is the tremendous genetic variability of the virus, with some genes differing at as many as 40% of nucleotide positions among circulating strains. Because of this, the genetic bases of many viral phenotypes, most notably the susceptibility to neutralization by a particular antibody, are difficult to identify computationally. Drawing upon open-source general-purpose machine learning algorithms and libraries, we have developed a software package IDEPI (IDentify EPItopes) for learning genotype-to-phenotype predictive models from sequences with known phenotypes. IDEPI can apply learned models to classify sequences of unknown phenotypes, and also identify specific sequence features which contribute to a particular phenotype. We demonstrate that IDEPI achieves performance similar to or better than that of previously published approaches on four well-studied problems: finding the epitopes of broadly neutralizing antibodies (bNab), determining coreceptor tropism of the virus, identifying compartment-specific genetic signatures of the virus, and deducing drug-resistance associated mutations. The cross-platform Python source code (released under the GPL 3.0 license), documentation, issue tracking, and a pre-configured virtual machine for IDEPI can be found at https://github.com/veg/idepi.

Movement variability in the golf swing.

PubMed

Langdown, Ben L; Bridge, Matt; Li, Francois-Xavier

2012-06-01

Traditionally, golf biomechanics has focused upon achieving consistency in swing kinematics and kinetics, whilst variability was considered to be noise and dysfunctional. There has been a growing argument that variability is an intrinsic aspect of skilled motor performance and plays a functional role. Two types of variability are described: 'strategic shot selection' and 'movement variability'. In 'strategic shot selection', the outcome remains consistent, but the swing kinematics/kinetics (resulting in the desired ball flight) are free to vary; 'movement variability' is the changes in swing kinematics and kinetics from trial to trial when the golfer attempts to hit the same shot. These changes will emerge due to constraints of the golfer's body, the environment, and the task. Biomechanical research has focused upon aspects of technique such as elite versus non-elite kinematics, kinetics, kinematic sequencing, peak angular velocities of body segments, wrist function, ground reaction forces, and electromyography, mainly in the search for greater distance and clubhead velocity. To date very little is known about the impact of variability on this complex motor skill, and it has yet to be fully researched to determine where the trade-off between functional and detrimental variability lies when in pursuit of enhanced performance outcomes.

Multicenter validation of cancer gene panel-based next-generation sequencing for translational research and molecular diagnostics.

PubMed

Hirsch, B; Endris, V; Lassmann, S; Weichert, W; Pfarr, N; Schirmacher, P; Kovaleva, V; Werner, M; Bonzheim, I; Fend, F; Sperveslage, J; Kaulich, K; Zacher, A; Reifenberger, G; Köhrer, K; Stepanow, S; Lerke, S; Mayr, T; Aust, D E; Baretton, G; Weidner, S; Jung, A; Kirchner, T; Hansmann, M L; Burbat, L; von der Wall, E; Dietel, M; Hummel, M

2018-04-01

The simultaneous detection of multiple somatic mutations in the context of molecular diagnostics of cancer is frequently performed by means of amplicon-based targeted next-generation sequencing (NGS). However, only few studies are available comparing multicenter testing of different NGS platforms and gene panels. Therefore, seven partner sites of the German Cancer Consortium (DKTK) performed a multicenter interlaboratory trial for targeted NGS using the same formalin-fixed, paraffin-embedded (FFPE) specimen of molecularly pre-characterized tumors (n = 15; each n = 5 cases of Breast, Lung, and Colon carcinoma) and a colorectal cancer cell line DNA dilution series. Detailed information regarding pre-characterized mutations was not disclosed to the partners. Commercially available and custom-designed cancer gene panels were used for library preparation and subsequent sequencing on several devices of two NGS different platforms. For every case, centrally extracted DNA and FFPE tissue sections for local processing were delivered to each partner site to be sequenced with the commercial gene panel and local bioinformatics. For cancer-specific panel-based sequencing, only centrally extracted DNA was analyzed at seven sequencing sites. Subsequently, local data were compiled and bioinformatics was performed centrally. We were able to demonstrate that all pre-characterized mutations were re-identified correctly, irrespective of NGS platform or gene panel used. However, locally processed FFPE tissue sections disclosed that the DNA extraction method can affect the detection of mutations with a trend in favor of magnetic bead-based DNA extraction methods. In conclusion, targeted NGS is a very robust method for simultaneous detection of various mutations in FFPE tissue specimens if certain pre-analytical conditions are carefully considered.

Calibration of ultrasonic power output in water, ethanol and sodium polytungstate

NASA Astrophysics Data System (ADS)

Mentler, Axel; Schomakers, Jasmin; Kloss, Stefanie; Zechmeister-Boltenstern, Sophie; Schuller, Reinhard; Mayer, Herwig

2017-10-01

Ultrasonic power is the main variable that forms the basis for many soil disaggregation experiments. Thus, a procedure for the rapid determination of this variable has been developed and is described in this article. Calorimetric experiments serve to measure specific heat capacity and ultrasonic power. Ultrasonic power is determined experimentally for deionised water, 30% ethanol and sodium polytungstate with a density of 1.6 g cm-3 and 1.8 g cm-3. All experiments are performed with a pre-selected ultrasonic probe vibration amplitude. Under these conditions, it was found that the emitted ultrasonic power was comparable in the four fluids. It is suggested, however, to perform calibration experiments prior to dispersion experiments, since the used fluid, as well as the employed ultrasonic equipment, may influence the power output.

Luminous blue variables and the fates of very massive stars

NASA Astrophysics Data System (ADS)

Smith, Nathan

2017-09-01

Luminous blue variables (LBVs) had long been considered massive stars in transition to the Wolf-Rayet (WR) phase, so their identification as progenitors of some peculiar supernovae (SNe) was surprising. More recently, environment statistics of LBVs show that most of them cannot be in transition to the WR phase after all, because LBVs are more isolated than allowed in this scenario. Additionally, the high-mass H shells around luminous SNe IIn require that some very massive stars above 40 M⊙ die without shedding their H envelopes, and the precursor outbursts are a challenge for understanding the final burning sequences leading to core collapse. Recent evidence suggests a clear continuum in pre-SN mass loss from super-luminous SNe IIn, to regular SNe IIn, to SNe II-L and II-P, whereas most stripped-envelope SNe seem to arise from a separate channel of lower-mass binary stars rather than massive WR stars. This article is part of the themed issue 'Bridging the gap: from massive stars to supernovae'.

Cognitive Stimulation of Elderly Residents in Social Protection Centers in Cartagena, 2014.

PubMed

Melguizo Herrera, Estela; Bertel De La Hoz, Anyel; Paternina Osorio, Diego; Felfle Fuentes, Yurani; Porto Osorio, Leidy

To determine the effectiveness of a program of cognitive stimulation of the elderly residents in Social Protection Centers in Cartagena, 2014. Quasi-experimental study with pre and post tests in control and experimental groups. A sample of 37 elderly residents in Social Protection Centers participated: 23 in the experimental group and 14 in the control group. A survey and a mental evaluation test (Pfeiffer) were applied. The experimental group participated in 10 sessions of cognitive stimulation. The paired t-test showed statistically significant differences in the Pfeiffer test, pre and post intervention, compared to the experimental group (P=.0005). The unpaired t-test showed statistically significant differences in Pfeiffer test results to the experimental and control groups (P=.0450). The analysis of the main components showed that more interrelated variables were: age, diseases, number of errors and test results; which were grouped around the disease variable, with a negative association. The intervention demonstrated a statistically significant improvement in cognitive functionality of the elderly. Nursing can lead this type of intervention. It should be studied further to strengthen and clarify these results. Copyright © 2016 Asociación Colombiana de Psiquiatría. Publicado por Elsevier España. All rights reserved.

ORBITAL SOLUTIONS FOR TWO YOUNG, LOW-MASS SPECTROSCOPIC BINARIES IN OPHIUCHUS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rosero, V.; Prato, L.; Wasserman, L. H.

2011-01-15

We report the orbital parameters for ROXR1 14 and RX J1622.7-2325Nw, two young, low-mass, and double-lined spectroscopic binaries recently discovered in the Ophiuchus star-forming region. Accurate orbital solutions were determined from over a dozen high-resolution spectra taken with the Keck II and Gemini South telescopes. These objects are T Tauri stars with mass ratios close to unity and periods of {approx}5 and {approx}3 days, respectively. In particular, RX J1622.7-2325Nw shows a non-circularized orbit with an eccentricity of 0.30, higher than any other short-period pre-main-sequence (PMS) spectroscopic binary known to date. We speculate that the orbit of RX J1622.7-2325Nw has notmore » yet circularized because of the perturbing action of a {approx}1'' companion, itself a close visual pair. A comparison of known young spectroscopic binaries (SBs) and main-sequence (MS) SBs in the eccentricity-period plane shows an indistinguishable distribution of the two populations, implying that orbital circularization occurs in the first 1 Myr of a star's lifetime. With the results presented in this paper we increase by {approx}4% the small sample of PMS spectroscopic binary stars with known orbital elements.« less

Using White Dwarf Companions of Blue Stragglers to Constrain Mass Transfer Physics

NASA Astrophysics Data System (ADS)

Gosnell, Natalie M.; Leiner, Emily; Geller, Aaron M.; Knigge, Christian; Mathieu, Robert D.; Sills, Alison; Leigh, Nathan

2018-06-01

Complete membership studies of old open clusters reveal that 25% of the evolved stars follow pathways in stellar evolution that are impacted by binary evolution. Recent studies show that the majority of blue straggler stars, traditionally defined to be stars brighter and bluer than the corresponding main sequence turnoff, are formed through mass transfer from a giant star onto a main sequence companion, resulting in a white dwarf in a binary system with a blue straggler. We will present constraints on the histories and mass transfer efficiencies for two blue straggler-white dwarf binaries in open cluster NGC 188. The constraints are a result of measuring white dwarf cooling temperatures and surface gravities with HST COS far-ultraviolet spectroscopy. This information sets both the timeline for mass transfer and the stellar masses in the pre-mass transfer binary, allowing us to constrain aspects of the mass transfer physics. One system is formed through Case C mass transfer, leaving a CO-core white dwarf, and provides an interesting test case for mass transfer from an asymptotic giant branch star in an eccentric system. The other system formed through Case B mass transfer, leaving a He-core white dwarf, and challenges our current understanding of the expected regimes for stable mass transfer from red giant branch stars.

Supernova SN 2011fe from an exploding carbon-oxygen white dwarf star.

PubMed

Nugent, Peter E; Sullivan, Mark; Cenko, S Bradley; Thomas, Rollin C; Kasen, Daniel; Howell, D Andrew; Bersier, David; Bloom, Joshua S; Kulkarni, S R; Kandrashoff, Michael T; Filippenko, Alexei V; Silverman, Jeffrey M; Marcy, Geoffrey W; Howard, Andrew W; Isaacson, Howard T; Maguire, Kate; Suzuki, Nao; Tarlton, James E; Pan, Yen-Chen; Bildsten, Lars; Fulton, Benjamin J; Parrent, Jerod T; Sand, David; Podsiadlowski, Philipp; Bianco, Federica B; Dilday, Benjamin; Graham, Melissa L; Lyman, Joe; James, Phil; Kasliwal, Mansi M; Law, Nicholas M; Quimby, Robert M; Hook, Isobel M; Walker, Emma S; Mazzali, Paolo; Pian, Elena; Ofek, Eran O; Gal-Yam, Avishay; Poznanski, Dovi

2011-12-14

Type Ia supernovae have been used empirically as 'standard candles' to demonstrate the acceleration of the expansion of the Universe even though fundamental details, such as the nature of their progenitor systems and how the stars explode, remain a mystery. There is consensus that a white dwarf star explodes after accreting matter in a binary system, but the secondary body could be anything from a main-sequence star to a red giant, or even another white dwarf. This uncertainty stems from the fact that no recent type Ia supernova has been discovered close enough to Earth to detect the stars before explosion. Here we report early observations of supernova SN 2011fe in the galaxy M101 at a distance from Earth of 6.4 megaparsecs. We find that the exploding star was probably a carbon-oxygen white dwarf, and from the lack of an early shock we conclude that the companion was probably a main-sequence star. Early spectroscopy shows high-velocity oxygen that slows rapidly, on a timescale of hours, and extensive mixing of newly synthesized intermediate-mass elements in the outermost layers of the supernova. A companion paper uses pre-explosion images to rule out luminous red giants and most helium stars as companions to the progenitor.

DNAAlignEditor: DNA alignment editor tool

PubMed Central

Sanchez-Villeda, Hector; Schroeder, Steven; Flint-Garcia, Sherry; Guill, Katherine E; Yamasaki, Masanori; McMullen, Michael D

2008-01-01

Background With advances in DNA re-sequencing methods and Next-Generation parallel sequencing approaches, there has been a large increase in genomic efforts to define and analyze the sequence variability present among individuals within a species. For very polymorphic species such as maize, this has lead to a need for intuitive, user-friendly software that aids the biologist, often with naïve programming capability, in tracking, editing, displaying, and exporting multiple individual sequence alignments. To fill this need we have developed a novel DNA alignment editor. Results We have generated a nucleotide sequence alignment editor (DNAAlignEditor) that provides an intuitive, user-friendly interface for manual editing of multiple sequence alignments with functions for input, editing, and output of sequence alignments. The color-coding of nucleotide identity and the display of associated quality score aids in the manual alignment editing process. DNAAlignEditor works as a client/server tool having two main components: a relational database that collects the processed alignments and a user interface connected to database through universal data access connectivity drivers. DNAAlignEditor can be used either as a stand-alone application or as a network application with multiple users concurrently connected. Conclusion We anticipate that this software will be of general interest to biologists and population genetics in editing DNA sequence alignments and analyzing natural sequence variation regardless of species, and will be particularly useful for manual alignment editing of sequences in species with high levels of polymorphism. PMID:18366684

Airborne fungal spores of Alternaria, meteorological parameters and predicting variables

NASA Astrophysics Data System (ADS)

Filali Ben Sidel, Farah; Bouziane, Hassan; del Mar Trigo, Maria; El Haskouri, Fatima; Bardei, Fadoua; Redouane, Abdelbari; Kadiri, Mohamed; Riadi, Hassane; Kazzaz, Mohamed

2015-03-01

Alternaria is frequently found as airborne fungal spores and is recognized as an important cause of respiratory allergies. The aerobiological monitoring of fungal spores was performed using a Burkard volumetric spore traps. To establish predicting variables for daily and weakly spore counts, a stepwise multiple regression between spore concentrations and independent variables (meteorological parameters and lagged values from the series of spore concentrations: previous day or week concentration (Alt t - 1) and mean concentration of the same day or week in other years ( C mean)) was made with data obtained during 2009-2011. Alternaria conidia are present throughout the year in the atmosphere of Tetouan, although they show important seasonal fluctuations. The highest levels of Alternaria spores were recorded during the spring and summer or autumn. Alternaria showed maximum daily values in April, May or October depending on year. When the spore variables of Alternaria, namely C mean and Alt t - 1, and meteorological parameters were included in the equation, the resulting R 2 satisfactorily predict future concentrations for 55.5 to 81.6 % during the main spore season and the pre-peak 2. In the predictive model using weekly values, the adjusted R 2 varied from 0.655 to 0.676. The Wilcoxon test was used to compare the results from the expected values and the pre-peak spore data or weekly values for 2012, indicating that there were no significant differences between series compared. This test showed the C mean, Alt t - 1, frequency of the wind third quadrant, maximum wind speed and minimum relative humidity as the most efficient independent variables to forecast the overall trend of this spore in the air.

On the evolutionary status and pulsations of the recently discovered blue large-amplitude pulsators (BLAPs)

NASA Astrophysics Data System (ADS)

Romero, Alejandra D.; Córsico, A. H.; Althaus, L. G.; Pelisoli, I.; Kepler, S. O.

2018-06-01

The blue large-amplitude pulsators (BLAPs) constitute a new class of pulsating stars. They are hot stars with effective temperatures of ˜30 000 K and surface gravities of log g ˜ 4.9, that pulsate with periods in the range 20-40 min. Until now, their origin and evolutionary state, as well as the nature of their pulsations, were not been unveiled. In this paper, we propose that the BLAPs are the hot counterpart of the already known pulsating pre-extremely low mass (pre-ELM) white dwarf (WD) stars, that are He-core low-mass stars resulting from interacting binary evolution. Using fully evolutionary sequences, we show that the BLAPs are well represented by pre-ELM WD models with high effective temperature and stellar masses ˜0.34 M⊙. From the analysis of their pulsational properties, we find that the observed variabilities can be explained by high-order non-radial g-mode pulsations or, in the case of the shortest periods, also by low-order radial modes, including the fundamental radial mode. The theoretical modes with periods in the observed range are unstable due to the κ mechanism associated with the Z-bump in the opacity at log T ˜ 5.25.

Pre-load on oral implants after screw tightening fixed full prostheses: an in vivo study.

PubMed

Duyck, J; Van Oosterwyck, H; Vander Sloten, J; De Cooman, M; Puers, R; Naert, I

2001-03-01

The fit of implant supported fixed prostheses is said to be of clinical concern because of the rigid fixation of an oral implant in its surrounding bone. The influence of the torque sequence of the set screws during fixation of implant supported fixed full prostheses on the final pre-load was investigated in vitro. No significant effect of the torque sequence of the set screws on the final pre-load was observed. The main objective of this study was to quantify and qualify the pre-load in vivo on implants supporting a fixed full prosthesis. This was performed when the prostheses were supported by all five or six implants and was repeated when the prostheses were supported by only four and three implants. A total of 13 patients with a fixed full implant supported prosthesis were selected. The existing abutments were changed for strain gauged abutments. After tightening the set screws with a torque of 10 N cm, the pre-load conditions were registered. The average (SEM) axial forces and bending moments in case of five or six, four and three supporting implants were 323 N (43 N), 346 N (59 N), 307 N (60 N) 21 N cm (3 N cm) and 21 N cm (2 N cm), 23 N cm (5 N cm), respectively. In addition, the pre-load was registered after fixation of a machined gold cylinder, as delivered by the manufacturer, on each of the supporting implants, representing the 'optimal fit' situation. The corresponding average (SEM) axial forces and bending moments in case of five or six, four and three supporting implants were 426 N (36 N), 405 N (40 N), 413 N (46 N) and 8 N cm (1 N cm), 8 N cm (1 N cm), 8 N cm (1 N cm), respectively. The induced axial forces after tightening the prostheses were significantly lower then after tightening the gold cylinder in case of five or six supporting implants (P < 0.02). The induced bending moments after tightening the prostheses were statistically significantly higher (P < 0.0001) then after tightening the gold cylinder in all test conditions (five or six, four or three supporting implants). This study underlines the static load present after screw tightening implant supported fixed full prostheses.