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Sample records for pre-main sequence pms

  1. Orbital motion in pre-main sequence binaries

    Energy Technology Data Exchange (ETDEWEB)

    Schaefer, G. H. [The CHARA Array of Georgia State University, Mount Wilson Observatory, Mount Wilson, CA 91023 (United States); Prato, L. [Lowell Observatory, 1400 West Mars Hill Road, Flagstaff, AZ 86001 (United States); Simon, M. [Department of Physics and Astronomy, Stony Brook University, Stony Brook, NY 11794 (United States); Patience, J., E-mail: schaefer@chara-array.org [Astrophysics Group, School of Physics, University of Exeter, Exeter, EX4 4QL (United Kingdom)

    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 other 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.

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

    Science.gov (United States)

    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.

  3. Relation of chromospheric activity to convection, rotation, and pre-main-sequence evolution

    International Nuclear Information System (INIS)

    Gilliland, R.L.

    1986-01-01

    Pre-main-sequence, or T Tauri, stars are characterized by much larger fluxes of nonradiative origin than their main-sequence counterparts. As a class, the T Tauri stars have only moderate rotation rates, making an explanation of their chromospheric properties based on rapid rotation problematic. The recent success of correlating nonradiative fluxes to the Rossby number, Ro = P/sub rot//tau/sub conv/, a central parameter of simple dynamo theories of magnetic field generation, has led to the suggestion that the same relation might be of use in explaining the pre-main-sequence (PMS) stars if tau/sub conv/ is very large. We show that tau/sub conv/ does depend strongly on evolutionary effects above the main sequence (MS), but that this dependence alone cannot account for the high observed nonradiative fluxes. The acoustic flux is also strongly dependent on PMS evolutionary state, and when coupled to the parameterization of magnetic activity based on Ro, these two mechanisms seem capable of explaining the high observed level of chromospheric activity in T Tauri stars. The moment of inertia decreases by two to three order of magnitude during PMS evolution. Since young MS stars do not rotate two to three orders of magnitude faster than PMS stars, rapid loss or redistribution of angular momentum must occur

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2012-07-10

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

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

    International Nuclear Information System (INIS)

    Morales-Calderón, M.; Stauffer, J. R.; Rebull, L. M.; Stassun, K. G.; Vrba, F. J.; Prato, L.; Hillenbrand, L. A.; Carpenter, J. M.; Terebey, S.; Angione, J.; Covey, K. R.; Terndrup, D. M.; Gutermuth, R.; Song, I.; Plavchan, P.; Marchis, F.; García, E. V.; Margheim, S.; Luhman, K. L.; Irwin, J. M.

    2012-01-01

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

  6. Photometric monitoring of pre-main sequence stars - 2

    International Nuclear Information System (INIS)

    Evans, A.; Davies, J.K.; Kilkenny, D.; Bode, M.F.

    1989-01-01

    A discussion is presented of the infrared and optical photometric variability of the pre-main sequence stars BF Ori and UX Ori. In the former case, the reddening that occurs during decline, at both optical and infrared wavelengths, is consistent with variable extinction by circumstellar grains having an interstellar-like reddening law. While in the case of UX Ori, the data suggest variability due to starspots. In both cases, a study of the polarimetric variability would be valuable to confirm these conclusions. (author)

  7. Pre-main sequence sun: a dynamic approach

    International Nuclear Information System (INIS)

    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. = 2 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

  8. Additional measurements of pre-main-sequence stellar rotation

    International Nuclear Information System (INIS)

    Hartmann, L.; Stauffer, J.R.

    1989-01-01

    New rotational-velocity measurements for pre-main-sequence stars in the Taurus-Auriga molecular cloud are reported. Rotational velocities or upper limits of 10 km/s are now available for 90 percent of the T Tauri stars with V less than 14.7 in the catalog of Cohen and Kuhi. Measurements of 'continuum emission' stars, thought to be accreting high-angular-momentum material from a circumstellar disk, show that these objects are not especially rapid rotators. The results confirm earlier findings that angular-momentum loss proceeds very efficiently in the earliest stages of star formation, and suggest that stars older than about one million yr contract to the main sequence at nearly constant angular momentum. The slow rotation of T Tauri stars probably requires substantial angular-momentum loss via a magnetically coupled wind. 35 references

  9. Pre-main-sequence disk accretion in Z Canis Majoris

    International Nuclear Information System (INIS)

    Hartmann, L.; Kenyon, S.J.; Hewett, R.; Edwards, S.; Strom, K.M.; Strom, S.E.; Stauffer, J.R.

    1989-01-01

    It is suggested that the pre-main-sequence object Z CMa is a luminous accretion disk, similar in many respects to the FU Orionis variables. Z CMa shows the broad, doubled optical absorption lines expected from a rapidly rotating accretion disk. The first overtone CO absorption detected in Z CMa is blue-shifted, suggesting line formation in a disk wind. Accretion at rates about 0.001 solar mass/yr over 100 yr is required to explain the luminosity of Z CMa. The large amount of material accreted (0.1 solar mass/yr) indicates that Z CMa is in a very early stage of stellar evolution, possibly in an initial phase of massive disk accretion. 41 references

  10. Pre-main-sequence disk accretion in Z Canis Majoris

    Science.gov (United States)

    Hartmann, L.; Kenyon, S. J.; Hewett, R.; Edwards, S.; Strom, K. M.; Strom, S. E.; Stauffer, J. R.

    1989-01-01

    It is suggested that the pre-main-sequence object Z CMa is a luminous accretion disk, similar in many respects to the FU Orionis variables. Z CMa shows the broad, doubled optical absorption lines expected from a rapidly rotating accretion disk. The first overtone CO absorption detected in Z CMa is blue-shifted, suggesting line formation in a disk wind. Accretion at rates about 0.001 solar mass/yr over 100 yr is required to explain the luminosity of Z CMa. The large amount of material accreted (0.1 solar mass/yr) indicates that Z CMa is in a very early stage of stellar evolution, possibly in an initial phase of massive disk accretion.

  11. Globules, dark clouds, and low mass pre-main sequence stars

    International Nuclear Information System (INIS)

    Hyland, A.R.

    1981-01-01

    The current observational and theoretical literature on Bok globules and their relationship to star formation is reviewed. Recent observations of globules at optical, infrared, and far infrared wavelengths are shown to provide important constraints on their structure and evolutionary status, and the suggestion that many globules are gravitationally unstable is seriously questioned. Dark clouds associated with T associations are well-known sites of recent and continuing star formation. In recent years molecular observations and far infrared surveys have provided maps of such regions from which possible sites of star formation may be identified. Optical (Hα) and near infrared surveys have enabled a clear identification of pre-main sequence (PMS) objects within the clouds. Methods of distinguishing these from background objects and the nature of their infrared excesses are examined in the light of recent observations in the near and far infrared. The perennial question as to the existence of anomalous reddening within dark clouds is also investigated. (Auth.)

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

    Science.gov (United States)

    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.; hide

    2007-01-01

    The dust sublimation zone (DSZ) is the region of pre-main sequence (PMS) disks where dust grains most easily anneal, sublime, and condense out of the gas. Because of this, it is a location where crystalline material may be enhanced and redistributed throughout the rest of the disk. A decade-long program to monitor the thermal emission of the grains located in this region demonstrates that large changes in emitted flux occur in many systems. Changes in the thermal emission between 3 and 13.5 microns were observed in HD 31648 (MWC 480), HD 163296 (MWC 275), and DG Tau. This emission is consistent with it being produced at the DSZ, where the transition from a disk of gas to one of gas+dust occurs. In the case of DG Tau, the outbursts were accompanied by increased emission on the 10 micron silicate band on one occasion, while on another occasion it went into absorption. This requires lofting of the material above the disk into the line of sight. Such changes will affect the determination of the inner disk structure obtained through interferometry measurements, and this has been confirmed in the case of HD 163296. Cyclic variations in the heating of the DSZ will lead to the annealing of large grains, the sublimation of smaller grains, possibly followed by re-condensation as the zone enters a cooling phase. Lofting of dust above the disk plane, and outward acceleration by stellar winds and radiation pressure, can re-distribute the processed material to cooler regions of the disk, where cometesimals form. This processing is consistent with the detection of the preferential concentration of large crystalline grains in the inner few AU of PMS disks using interferometric spectroscopy with the VLTI.

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

    International Nuclear Information System (INIS)

    Torres, Guillermo; Latham, David W.; Ruíz-Rodríguez, Dary; Prato, L.; Wasserman, Lawrence H.; Badenas, Mariona; Schaefer, G. H.; Mathieu, Robert D.

    2013-01-01

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

  14. Pre-main-sequence evolution of the sun

    International Nuclear Information System (INIS)

    Gough, D.

    1980-01-01

    The phase of solar evolution after the dynamical collapse is considered. The physics of the Kelvin-Helmholtz phase of gravitational collapse is described, attention being given to the early stages of the star when it was completely convective. It is noted that subsequently, a radiative core developed and evolution was controlled by the rate at which heat can diffuse through it by radiative transfer. Since the study of the Kelvin-Helmholtz contraction alone does not give enough information regarding the state of the sun when it first settled down to approximate hydrostatic equilibrium, other stars are studied, and information on the sun is obtained by analogy. Many young solar-type stars, such as the T Tauri stars, are not in the completely convective Hayashi (1961) phase hence it is proposed that the sun was completely mixed soon after its formation, which has some bearing on the sun's chemical structure. It is suggested that the surface of the sun was very nonuniform compared with the photosphere of today. The simple solar evolution model presented gives a good guide to the general way in which the sun contracted to the main sequence

  15. Empirical tests of pre-main-sequence stellar evolution models with eclipsing binaries

    Science.gov (United States)

    Stassun, Keivan G.; Feiden, Gregory A.; Torres, Guillermo

    2014-06-01

    We examine the performance of standard pre-main-sequence (PMS) stellar evolution models against the accurately measured properties of a benchmark sample of 26 PMS stars in 13 eclipsing binary (EB) systems having masses 0.04-4.0 M⊙ and nominal ages ≈1-20 Myr. We provide a definitive compilation of all fundamental properties for the EBs, with a careful and consistent reassessment of observational uncertainties. We also provide a definitive compilation of the various PMS model sets, including physical ingredients and limits of applicability. No set of model isochrones is able to successfully reproduce all of the measured properties of all of the EBs. In the H-R diagram, the masses inferred for the individual stars by the models are accurate to better than 10% at ≳1 M⊙, but below 1 M⊙ they are discrepant by 50-100%. Adjusting the observed radii and temperatures using empirical relations for the effects of magnetic activity helps to resolve the discrepancies in a few cases, but fails as a general solution. We find evidence that the failure of the models to match the data is linked to the triples in the EB sample; at least half of the EBs possess tertiary companions. Excluding the triples, the models reproduce the stellar masses to better than ∼10% in the H-R diagram, down to 0.5 M⊙, below which the current sample is fully contaminated by tertiaries. We consider several mechanisms by which a tertiary might cause changes in the EB properties and thus corrupt the agreement with stellar model predictions. We show that the energies of the tertiary orbits are comparable to that needed to potentially explain the scatter in the EB properties through injection of heat, perhaps involving tidal interaction. It seems from the evidence at hand that this mechanism, however it operates in detail, has more influence on the surface properties of the stars than on their internal structure, as the lithium abundances are broadly in good agreement with model predictions. The

  16. AK SCO, FIRST DETECTION OF A HIGHLY DISTURBED ATMOSPHERE IN A PRE-MAIN-SEQUENCE CLOSE BINARY

    International Nuclear Information System (INIS)

    Gomez de Castro, Ana I.

    2009-01-01

    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 ≅ 100 km s -1 ) and very dense atmosphere (n e = 1.6 x 10 10 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.

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

    Science.gov (United States)

    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.

  18. MASS LOSS IN PRE-MAIN-SEQUENCE STARS VIA CORONAL MASS EJECTIONS AND IMPLICATIONS FOR ANGULAR MOMENTUM LOSS

    Energy Technology Data Exchange (ETDEWEB)

    Aarnio, Alicia N. [Astronomy Department, University of Michigan, 830 Dennison Building, 500 Church Street, Ann Arbor, MI 48109 (United States); Matt, Sean P. [Laboratoire AIM Paris-Saclay, CEA/Irfu Universite Paris-Diderot CNRS/INSU, F-91191 Gif-sur-Yvette (France); Stassun, Keivan G., E-mail: aarnio@umich.edu [Department of Physics and Astronomy, Vanderbilt University, Nashville, TN 37235 (United States)

    2012-11-20

    We develop an empirical model to estimate mass-loss rates via coronal mass ejections (CMEs) for solar-type pre-main-sequence (PMS) stars. Our method estimates the CME mass-loss rate from the observed energies of PMS X-ray flares, using our empirically determined relationship between solar X-ray flare energy and CME mass: log (M {sub CME}[g]) = 0.63 Multiplication-Sign log (E {sub flare}[erg]) - 2.57. Using masses determined for the largest flaring magnetic structures observed on PMS stars, we suggest that this solar-calibrated relationship may hold over 10 orders of magnitude in flare energy and 7 orders of magnitude in CME mass. The total CME mass-loss rate we calculate for typical solar-type PMS stars is in the range 10{sup -12}-10{sup -9} M {sub Sun} yr{sup -1}. We then use these CME mass-loss rate estimates to infer the attendant angular momentum loss leading up to the main sequence. Assuming that the CME outflow rate for a typical {approx}1 M {sub Sun} T Tauri star is <10{sup -10} M {sub Sun} yr{sup -1}, the resulting spin-down torque is too small during the first {approx}1 Myr to counteract the stellar spin-up due to contraction and accretion. However, if the CME mass-loss rate is {approx}> 10{sup -10} M {sub Sun} yr{sup -1}, as permitted by our calculations, then the CME spin-down torque may influence the stellar spin evolution after an age of a few Myr.

  19. A near-infrared survey for pre-main sequence stars in Taurus

    Science.gov (United States)

    Gomez, Mercedes; Kenyon, Scott J.; Hartmann, Lee

    1994-01-01

    We present a near-infrared survey of approximately 2 sq deg covering parts of L1537, L1538, and Heiles cloud 2 in the Taurus-Auriga molecular cloud. Although this study is more sensitive than previous attempts to identify pre-main sequence stars in Taurus-Auriga, our survey regions contain only one new optically visible, young star. We did find several candidate embedded protostars; additional 10 micrometer photometry is necessary to verify the pre-main sequence nature of these sources. Our results--combined with those of previous surveys--show that the L1537/L1538 clouds contain no pre-main sequence stars. These two clouds are less dense than the active star formation sites in Taurus-Auriga, which suggests a cloud must achieve a threshold density to form stars.

  20. A catalog of pre-main-sequence emission-line stars with IRAS source associations

    International Nuclear Information System (INIS)

    Weintraub, D.A.

    1990-01-01

    To aid in finding premain-sequence (PMS) emission-line stars that might have dusty circumstellar environments, 361 PMS stars that are associated with 304 separate IRAS sources were identified. These stars include 200 classical T Tauri stars, 25 weak-lined (naked) T Tauri stars, 56 Herbig Ae/Be stars, six FU Orionis stars, and two SU Aurigae stars. All six of the FU Orionis stars surveyed by IRAS were detected. Of the PMS-IRAS Point Source Catalog (PSC) associations, 90 are new and are not noted in the PSC. The other 271 entries include 104 that are correctly identified in the PSC but have not yet appeared in the literature, 56 more that can be found in both the PSC and in the published and unpublished iterature, and 111 that are in the literature but not in the PSC. Spectral slope diagrams constructed from the 12-, 25-, and 60-micron flux densities reveal unique distributions for the different PMS subclasses; these diagrams may help identify the best candidate PMS stars for observations of circumstellar dust. 30 refs

  1. AK Sco: a tidally induced atmospheric dynamo in a pre-main sequence binary?

    Science.gov (United States)

    Gómez de Castro, A. I.

    2009-02-01

    AK Sco is a unique source: a 10-30 Myrs old pre-main sequence spectroscopic binary composed by two nearly equal F5 stars that at periastron are separated by barely eleven 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 of AK Sco, the ideal laboratory to study the effect of gravitational tides in the stellar magnetic field building up during pre-main sequence evolution. Evidence of this effect is reported in this contribution.

  2. PRE-MAIN-SEQUENCE TURN-ON AS A CHRONOMETER FOR YOUNG CLUSTERS: NGC 346 AS A BENCHMARK

    International Nuclear Information System (INIS)

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

    2010-01-01

    We present a novel approach to deriving the age of very young star clusters, by using the Turn-On (TOn). The TOn is the point in the color-magnitude diagram (CMD) where the pre-main sequence (PMS) joins the main sequence (MS). In the MS luminosity function (LF) of the cluster, the TOn is identified as a peak followed by a dip. We propose that by combining the CMD analysis with the monitoring of the spatial distribution of MS stars it is possible to reliably identify the TOn in extragalactic star-forming regions. Compared to alternative methods, this technique is complementary to the turnoff dating and avoids the systematic biases affecting the PMS phase. We describe the method and its uncertainties and apply it to the star-forming region NGC 346, which has been extensively imaged with the Hubble Space Telescope (HST). This study extends the LF approach in crowded extragalactic regions and opens the way for future studies with HST/WFC3, the James Webb Space Telescope and from the ground with adaptive optics.

  3. Lithium evolution in metal-poor stars: from Pre-Main Sequence to the Spite plateau

    OpenAIRE

    Fu, Xiaoting; Bressan, Alessandro; Molaro, Paolo; Marigo, Paola

    2015-01-01

    Lithium abundance derived in metal-poor main sequence stars is about three times lower than the value of primordial Li predicted by the standard Big Bang nucleosynthesis when the baryon density is taken from the CMB or the deuterium measurements. This disagreement is generally referred as the lithium problem. We here reconsider the stellar Li evolution from the pre-main sequence to the end of the main sequence phase by introducing the effects of convective overshooting and residual mass accre...

  4. IRAS IDENTIFICATION OF PRE-MAIN-SEQUENCE STARS IN THE CHAMELEON-II ASSOCIATION

    NARCIS (Netherlands)

    PRUSTI, T; WHITTET, DCB; ASSENDORP, R; WESSELIUS, PR

    We report the results of a search for new pre-main sequence candidates in the Chamaeleon II dark cloud based on three IRAS catalogues (the Point Source Catalog, the Serendipitous Survey Catalog and the Faint Source Survey). A total of 30 sources were selected. Twelve of these display IRAS colours

  5. Pre-main sequence masses and the age spread in the Orion cluster

    International Nuclear Information System (INIS)

    McNamara, B.J.

    1975-01-01

    The spread in formation times for stars earlier than GO in the Orion cluster is investigated. The range of stellar ages in this cluster is found to extend from at least 10 6 years to about 10 7 years. On the basis of this evidence and the similarity of the color--magnitude diagrams of other young clusters to the Orion cluster, it is suggested that the current method of dating these clusters (from the point at which the most massive stars just reach the zero-age main sequence) might not be valid. The masses of forty-one pre-main sequence stars within the ranges 4.05 less than or equal to log(Te) less than or equal to 3.77 and 0.6 less than or equal to log (L/L/sub sun/) less than or equal to 2.1 are determined from observed effective temperatures, luminosities, and gravities. These masses were then compared with those expected from Iben's (1965) pre-main sequence evolutionary calculations. In most cases, the agreement between these values was found to be within the observational errors. Finally, the pre-main sequence stars possessing infrared excesses are found to be apparently among the most massive and youngest stars still contracting toward the zero-age main sequence

  6. Radio emission from pre-main-sequence stars in Corona Australis

    International Nuclear Information System (INIS)

    Brown, A.

    1987-01-01

    The central region of the Corona Australis molecular cloud surrounding the stars R and TY CrA has been studied using the VLA at 6 cm. Eleven radio sources are detected including five associated with pre-main-sequence objects. The most striking is associated with the near-IR source IRS 7 and shows a complex structure comprising two strong pointlike sources positioned either side of the deeply embedded IR source and two extended lobes of radio emission. The IRS 7 radio source appears to be similar to that associated with Lynds 1551 IRS 5 but has a considerably larger angular size. The other detected sources include the massive pre-main-sequence star TY CrA, the near-IR sources IRS 1 and IRS 5, and the Herbig-Haro object HH 101. The stars R and T CrA were not detected. 35 references

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

    Science.gov (United States)

    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.

  8. 13-colour photometry of pre-main sequence stars: preliminary report and results

    Energy Technology Data Exchange (ETDEWEB)

    Chavarria-K, C; de Lara, E [Universidad Nacional Autonoma de Mexico, Mexico City. Inst. de Astronomia

    1981-01-01

    Broad (UBVRI) and intermediate (13-colour) band photometry of 160 stars selected mainly from the Herbig Rao catalogue are being carried on currently, mainly to complement the published data of these stars in the optical window (for example shortward of the Balmer and longward of the Paschen discontinuities). The 13-colour photometric system and its applications to pre-main sequences stars are briefly discussed. First results are presented.

  9. Tracing early stellar evolution with asteroseismology: pre-main sequence stars in NGC 2264

    Directory of Open Access Journals (Sweden)

    Zwintz Konstanze

    2015-01-01

    Full Text Available Asteroseismology has been proven to be a successful tool to unravel details of the internal structure for different types of stars in various stages of their main sequence and post-main sequence evolution. Recently, we found a relation between the detected pulsation properties in a sample of 34 pre-main sequence (pre-MS δ Scuti stars and the relative phase in their pre-MS evolution. With this we are able to demonstrate that asteroseismology is similarly powerful if applied to stars in the earliest stages of evolution before the onset of hydrogen core burning.

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

    Science.gov (United States)

    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.

  11. Discovery of three x-ray luminous pre-main-sequence stars

    International Nuclear Information System (INIS)

    Feigelson, E.D.; Kriss, G.A.

    1981-01-01

    Three X-ray sources found serendipitously in Einstein images of the Taurus-Auriga cloud complex were observed at the McGraw-Hill Observatory and are found to be associated with approx.12 mag stars with weak Hα emission. The stars lie on the edges of dark clouds and are spectroscopically similar to the least active emission-line pre-main-sequence stars. Although they lie well above the ZAMS in the H-R diagram, they do not exhibit ultraviolet excess, strong optical variability, or evidence for mass outflow/inflow characteristics of the more active T Tauri stars. Their only unusual property is high X-ray luminosity (approx.10 30 ergs s1). It is suggested that the X-ray emission from pre-main-sequence stars is not closely linked to the conditions giving rise to their unusual spectroscopic properties. The emission may instead represent an enhanced form of the coronal activity producing X-rays observed in late-type main-sequence stars

  12. Rotation in moderate-mass pre-main-sequence radiative track G stars

    International Nuclear Information System (INIS)

    Mcnamara, B.

    1990-01-01

    Recent studies suggest that the observed high-mass radiative track velocity histograms for pre-main-sequence stars differ significantly. In the Vogel and Kuhi (1981) study, these stars were found to possess a rather broad distribution of rotational velocities with a moderate peak at low velocities. In contrast, Smith et al. (1983), found a very sharply peaked distribution located at low values of v sin i. The difference in these velocity distributions is shown to be due to inadequate allowance for field stars in the Smith, et al., work. Once these stars are removed, the high-mass velocity distributions of the two regions are remarkably similar. This result suggests that a unique velocity distribution might be used in modeling very young stars. Assuming that the Orion Ic proto-F stars continue to contract in a homologous fashion, their average current rotational velocity is in agreement with that expected for zero-age main sequence F stars. 27 refs

  13. A Constraint on the Formation Timescale of the Young Open Cluster NGC 2264: Lithium Abundance of Pre-main Sequence Stars

    Science.gov (United States)

    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.

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

    Science.gov (United States)

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

    1990-01-01

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

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

    International Nuclear Information System (INIS)

    Skinner, S.L.; Brown, A.; Linsky, J.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. 32 refs

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

    International Nuclear Information System (INIS)

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

    2012-01-01

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

  17. ABSOLUTE PROPERTIES OF THE PRE-MAIN-SEQUENCE ECLIPSING BINARY STAR NP PERSEI

    Energy Technology Data Exchange (ETDEWEB)

    Lacy, Claud H. Sandberg [Physics Department, University of Arkansas, Fayetteville, AR 72701 (United States); Fekel, Francis C.; Muterspaugh, Matthew W. [Center of Excellence in Information Systems, Tennessee State University, Nashville, TN 37209 (United States); Pavlovski, Krešimir [Department of Physics, Faculty of Science, University of Zagreb, Bijenička cesta 32, 10000 Zagreb (Croatia); Torres, Guillermo, E-mail: clacy@uark.edu, E-mail: fekel@evans.tsuniv.edu, E-mail: pavlovski@phy.hr, E-mail: gtorres@cfa.harvard.edu, E-mail: matthew1@coe.tsuniv.edu [Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138 (United States)

    2016-07-01

    NP Per is a well-detached, 2.2 day eclipsing binary whose components are both pre-main-sequence stars that are still contracting toward the main-sequence phase of evolution. We report extensive photometric and spectroscopic observations with which we have determined their properties accurately. Their surface temperatures are quite different: 6420 ± 90 K for the larger F5 primary star and 4540 ± 160 K for the smaller K5e star. Their masses and radii are 1.3207 ± 0.0087 solar masses and 1.372 ± 0.013 solar radii for the primary, and 1.0456 ± 0.0046 solar masses and 1.229 ± 0.013 solar radii for the secondary. The orbital period is variable over long periods of time. A comparison of the observations with current stellar evolution models from MESA indicates that the stars cannot be fit at a single age: the secondary appears significantly younger than the primary. If the stars are assumed to be coeval and to have the age of the primary (17 Myr), then the secondary is larger and cooler than predicted by current models. The H α spectral line of the secondary component is completely filled by, presumably, chromospheric emission due to a magnetic activity cycle.

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

    Science.gov (United States)

    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 (${getting power from the gravitational contraction of the star. Main-sequence late-B and A-type stars are not expected to be strong X-ray emitters, because they lack the both strong winds of more massive stars and the magneto-coronal activity of lower-mass stars. There is, however, mounting evidence that IMPS are powerful intrinsic x-ray emitters during their convection-dominated early evolution, before the development and rapid growth of a radiation zone. We present our prime candidates for intrinsic, coronal X-ray emission from IMPS identified in the Chandra Carina Complex Project. The Carina massive star-forming complex is of special interest due to the wide variation of star formation stages within the region. Candidate IMPS were identified using infrared spectral energy distribution (SED) models. X-ray properties, including thermal plasma temperatures and absorption-corrected fluxes, were derived from XSPEC fits performed using absorption ($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.

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

    Science.gov (United States)

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

    2017-09-01

    Context. Studies of the formation and evolution of young stars and their disks rely on knowledge of the stellar parameters of the young stars. The derivation of these parameters is commonly based on comparison with photospheric template spectra. Furthermore, chromospheric emission in young active stars impacts the measurement of mass accretion rates, a key quantity for studying disk evolution. Aims: Here we derive stellar properties of low-mass (M⋆≲ 2 M⊙) pre-main sequence stars without disks, which represent ideal photospheric templates for studies of young stars. We also use these spectra to constrain the impact of chromospheric emission on the measurements of mass accretion rates. The spectra are reduced, flux-calibrated, and corrected for telluric absorption, and are made available to the community. Methods: We derive the spectral type for our targets by analyzing the photospheric molecular features present in their VLT/X-shooter spectra by means of spectral indices and comparison of the relative strength of photospheric absorption features. We also measure effective temperature, gravity, projected rotational velocity, and radial velocity from our spectra by fitting them with synthetic spectra with the ROTFIT tool. The targets have negligible extinction (AVpresented in our previous publication. We perform synthetic photometry on the spectra to derive the typical colors of young stars in different filters. We measure the luminosity of the emission lines present in the spectra and estimate the noise due to chromospheric emission in the measurements of accretion luminosity in accreting stars. Results: We provide a calibration of the photospheric colors of young pre-main sequence stars as a function of their spectral type in a set of standard broad-band optical and near-infrared filters. The logarithm of the noise on the accretion luminosity normalized to the stellar luminosity is roughly constant and equal to -2.3 for targets with masses larger than 1 solar

  20. THE MULTIPLE PRE-MAIN-SEQUENCE SYSTEM HBC 515 IN L1622

    International Nuclear Information System (INIS)

    Reipurth, Bo; Aspin, Colin; Herbig, George

    2010-01-01

    The bright pre-main-sequence star HBC 515 (HD 288313) located in the L1622 cometary cloud in Orion has been studied extensively with optical/infrared imaging and ultraviolet/optical/infrared spectroscopy. The spectra indicate that HBC 515 is a weakline T Tauri star (TTS) of spectral type K2V. Adaptive optics imaging in the K band reveals that HBC 515 is a binary with two equally bright components separated by 0.''5. A very faint third component is found 5'' to the northwest. Spitzer IRAC and MIPS observations show that at mid-infrared wavelengths this third source dominates the system, suggesting that it is a protostar still embedded in the nascent cloud of HBC 515. The close association of a weakline TTS with a newborn protostar in a multiple system is noteworthy. Two nearby TTSs are likely associated with the HBC 515 multiple system, and the dynamical evolution of the complex that would lead to such a configuration is considered.

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

    Energy Technology Data Exchange (ETDEWEB)

    Pecaut, Mark J.; Mamajek, Eric E. [University of Rochester, Department of Physics and Astronomy, Rochester, NY 14627-0171 (United States)

    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{sub 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 sequence for O9V-M9V MS stars based on an extensive literature survey, (2) a revised Q-method relation for dereddening UBV photometry of OB-type stars, and (3) introduce two candidate spectral standard stars as representatives of spectral types K8V and K9V.

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

    Science.gov (United States)

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

    2017-09-01

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

  3. Pre-main-sequence depletion of Li-6 and Li-7

    International Nuclear Information System (INIS)

    Proffitt, C.R.; Michaud, G.

    1989-01-01

    Depletion of Li-6 and Li-7 during premain-sequence contraction has been calculated for several evolutionary sequences. Slightly greater Li-7 depletion was found than by other recent workers. On the premain sequence, Li-6 is depleted by a factor of at least 10 in the present models for stars with T(eff) lower than 6800 K on the main sequence. Because of the shorter destruction time scale for Li-6 as compared to Li-7, the determination of the abundances of these two isotopes would place strict constraints on the structure of premain-sequence stars. 39 refs

  4. On precise ZAMSs, the solar color, and pre-main-sequence lithium depletion

    International Nuclear Information System (INIS)

    Vandenberg, D.A.; Poll, H.E.

    1989-01-01

    This paper describes a semiempirical main-sequence-fitting method for the determination of distances to stellar systems, which uses a ZAMS locus carefully normalized to the sun, and whose shape is defined by a quartic over the color range for (B-V)0 values between 0.2 and 1.0 such that the morphology of the Pleiades C-M diagram is accurately reproduced. Using this technique, distances were derived for a number of star clusters. It was found that the observed depletion of lithium among cool main-sequence stars in the Hyades and Pleiades can be matched quite well by the present models. Calculations also show that the depletion of Li at a fixed T(eff) along the main sequence is a sensitive function of Fe/H. 98 refs

  5. ULTRAVIOLET-SELECTED FIELD AND PRE-MAIN-SEQUENCE STARS TOWARD TAURUS AND UPPER SCORPIUS

    International Nuclear Information System (INIS)

    Findeisen, K.; Hillenbrand, L.

    2010-01-01

    We have carried out a Galaxy Evolution Explorer (GALEX) Cycle 1 guest investigator program covering 56 deg 2 near the Taurus T association and 12 deg 2 along the northern edge of the Upper Scorpius OB association. We combined photometry in the GALEX far-ultraviolet and near-ultraviolet bands with data from the Two Micron All Sky Survey to identify candidate young (∼<100 Myr old) stars as those with an ultraviolet excess relative to older main-sequence stars. Follow-up spectroscopy of a partial sample of these candidates suggests five new members of Taurus, with 8-20 expected from additional observations, and five new members of Upper Scorpius, with three to six expected from additional observations. These candidate new members appear to represent a distributed, non-clustered population in either region, although our sample statistics are as of yet too poor to constrain the nature or extent of this population. Rather, our study demonstrates the ability of GALEX observations to identify young stellar populations distributed over a wide area of the sky. We also highlight the necessity of a better understanding of the Galactic ultraviolet source population to support similar investigations. In particular, we report a large population of stars with an ultraviolet excess but no optical indicators of stellar activity or accretion, and briefly argue against several interpretations of these sources.

  6. Radio-emission of pre-main sequence stars of the Rho Ophiuchi cloud: observations and interpretation

    International Nuclear Information System (INIS)

    Andre, P.

    1987-11-01

    Observations of the radio continuum emission of a young star population have been made at VLA on the whole molecular cloud Rho Ophiuchi, one of the closest site of star formation. A dozen of stellar sources have been detected. Radio emission of some identified objects seems to have a magnetic nature and be produced by gyrosynchrotron mechanism. In particular, one of the sources shows a radio radiation circularly polarized; two other stars have a radiation strongly variable probably due to magnetic eruptions more important than those detected in X radiation. More generally, radio observations select probably a specific population of young stars characterized by magnetic field presence extended on several stellar radii and by absence of dense circumstellar environment. Spatial distribution of these objects suggest, they are younger than most of the pre-main sequence stars [fr

  7. X-ray sources in regions of star formation. II. The pre-main-sequence G star HDE 283572

    International Nuclear Information System (INIS)

    Walter, F.M.; Brown, A.; Linsky, J.L.; Rydgren, A.E.; Vrba, F.; Joint Institute for Laboratory Astrophysics, Boulder, CO; Computer Sciences Corp., El Segundo, CA; Naval Observatory, Flagstaff, AZ)

    1987-01-01

    This paper reports the detection of HDE 283572, a ninth-magnitude G star 8 arcmin south of RY Tau, as a bright X-ray source. The observations reveal this object to be a fairly massive (about 2 solar masses) pre-main-sequence star associated with the Taurus-Auriga star formation complex. It exhibits few of the characteristics of the classical T Tauri stars and is a good example of a naked T Tauri star. The star is a mid-G subgiant, of about three solar radii and rotates with a period of 1.5 d. The coronal and chromospheric surface fluxes are similar to those of the most active late type stars (excluding T Tauri stars). The X-ray and UV lines most likely arise in different atmospheric structures. Radiative losses are some 1000 times the quiet solar value and compare favorably with those of T Tauri stars. 49 references

  8. ON THE RELIABILITY OF STELLAR AGES AND AGE SPREADS INFERRED FROM PRE-MAIN-SEQUENCE EVOLUTIONARY MODELS

    International Nuclear Information System (INIS)

    Hosokawa, Takashi; Offner, Stella S. R.; Krumholz, Mark R.

    2011-01-01

    We revisit the problem of low-mass pre-main-sequence stellar evolution and its observational consequences for where stars fall on the Hertzsprung-Russell diagram (HRD). In contrast to most previous work, our models follow stars as they grow from small masses via accretion, and we perform a systematic study of how the stars' HRD evolution is influenced by their initial radius, by the radiative properties of the accretion flow, and by the accretion history, using both simple idealized accretion histories and histories taken from numerical simulations of star cluster formation. We compare our numerical results to both non-accreting isochrones and to the positions of observed stars in the HRD, with a goal of determining whether both the absolute ages and the age dispersions inferred from non-accreting isochrones are reliable. We show that non-accreting isochrones can sometimes overestimate stellar ages for more massive stars (those with effective temperatures above ∼3500 K), thereby explaining why non-accreting isochrones often suggest a systematic age difference between more and less massive stars in the same cluster. However, we also find the only way to produce a similar overestimate for the ages of cooler stars is if these stars grow from ∼0.01 M sun seed protostars that are an order of magnitude smaller than predicted by current theoretical models, and if the size of the seed protostar correlates systematically with the final stellar mass at the end of accretion. We therefore conclude that, unless both of these conditions are met, inferred ages and age spreads for cool stars are reliable, at least to the extent that the observed bolometric luminosities and temperatures are accurate. Finally, we note that the time dependence of the mass accretion rate has remarkably little effect on low-mass stars' evolution on the HRD, and that such time dependence may be neglected for all stars except those with effective temperatures above ∼4000 K.

  9. EXTENDED MAGNETOSPHERES IN PRE-MAIN-SEQUENCE EVOLUTION: FROM T TAURI STARS TO THE BROWN DWARF LIMIT

    Energy Technology Data Exchange (ETDEWEB)

    Gomez de Castro, Ana I.; Marcos-Arenal, Pablo [Grupo de Investigacion Complutense AEGORA, Universidad Complutense de Madrid, 28040 Madrid (Spain)

    2012-04-20

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

  10. Quantification of sequence exchange events between PMS2 and PMS2CL provides a basis for improved mutation scanning of Lynch syndrome patients.

    NARCIS (Netherlands)

    Klift, H.M. van der; Tops, C.M.; Bik, E.C.; Boogaard, M.W.; Borgstein, A.M.; Hansson, K.B.; Ausems, M.G.E.M.; Gomez Garcia, E.; Green, A.; Hes, F.J.; Izatt, L.; Hest, L.P. van; Alonso, A.M.; Vriends, A.H.; Wagner, A.; Zelst-Stams, W.A.G. van; Vasen, H.F.; Morreau, H.; Devilee, P.; Wijnen, J.T.

    2010-01-01

    Heterozygous mutations in PMS2 are involved in Lynch syndrome, whereas biallelic mutations are found in Constitutional mismatch repair-deficiency syndrome patients. Mutation detection is complicated by the occurrence of sequence exchange events between the duplicated regions of PMS2 and PMS2CL. We

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

    Science.gov (United States)

    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.

  12. Quantification of sequence exchange events between PMS2 and PMS2CL provides a basis for improved mutation scanning of Lynch syndrome patients.

    Science.gov (United States)

    van der Klift, Heleen M; Tops, Carli M J; Bik, Elsa C; Boogaard, Merel W; Borgstein, Anne-Marijke; Hansson, Kerstin B M; Ausems, Margreet G E M; Gomez Garcia, Encarna; Green, Andrew; Hes, Frederik J; Izatt, Louise; van Hest, Liselotte P; Alonso, Angel M; Vriends, Annette H J T; Wagner, Anja; van Zelst-Stams, Wendy A G; Vasen, Hans F A; Morreau, Hans; Devilee, Peter; Wijnen, Juul T

    2010-05-01

    Heterozygous mutations in PMS2 are involved in Lynch syndrome, whereas biallelic mutations are found in Constitutional mismatch repair-deficiency syndrome patients. Mutation detection is complicated by the occurrence of sequence exchange events between the duplicated regions of PMS2 and PMS2CL. We investigated the frequency of such events with a nonspecific polymerase chain reaction (PCR) strategy, co-amplifying both PMS2 and PMS2CL sequences. This allowed us to score ratios between gene and pseudogene-specific nucleotides at 29 PSV sites from exon 11 to the end of the gene. We found sequence transfer at all investigated PSVs from intron 12 to the 3' end of the gene in 4 to 52% of DNA samples. Overall, sequence exchange between PMS2 and PMS2CL was observed in 69% (83/120) of individuals. We demonstrate that mutation scanning with PMS2-specific PCR primers and MLPA probes, designed on PSVs, in the 3' duplicated region is unreliable, and present an RNA-based mutation detection strategy to improve reliability. Using this strategy, we found 19 different putative pathogenic PMS2 mutations. Four of these (21%) are lying in the region with frequent sequence transfer and are missed or called incorrectly as homozygous with several PSV-based mutation detection methods. (c) 2010 Wiley-Liss, Inc.

  13. PMS2 gene mutational analysis: direct cDNA sequencing to circumvent pseudogene interference.

    Science.gov (United States)

    Wimmer, Katharina; Wernstedt, Annekatrin

    2014-01-01

    The presence of highly homologous pseudocopies can compromise the mutation analysis of a gene of interest. In particular, when using PCR-based strategies, pseudogene co-amplification has to be effectively prevented. This is often achieved by using primers designed to be parental gene specific according to the reference sequence and by applying stringent PCR conditions. However, there are cases in which this approach is of limited utility. For example, it has been shown that the PMS2 gene exchanges sequences with one of its pseudogenes, named PMS2CL. This results in functional PMS2 alleles containing pseudogene-derived sequences at their 3'-end and in nonfunctional PMS2CL pseudogene alleles that contain gene-derived sequences. Hence, the paralogues cannot be distinguished according to the reference sequence. This shortcoming can be effectively circumvented by using direct cDNA sequencing. This approach is based on the selective amplification of PMS2 transcripts in two overlapping 1.6-kb RT-PCR products. In addition to avoiding pseudogene co-amplification and allele dropout, this method has also the advantage that it allows to effectively identify deletions, splice mutations, and de novo retrotransposon insertions that escape the detection of most DNA-based mutation analysis protocols.

  14. Hydrodynamic ejection of bipolar flows from objects undergoing disk accretion: T Tauri stars, massive pre-main-sequence objects, and cataclysmic variables

    International Nuclear Information System (INIS)

    Torbett, M.V.

    1984-01-01

    A general mechanism is presented for generating pressure-driven winds that are intrinsically bipolar from objects undergoing disk accretion. The energy librated in a boundary layer shock as the disk matter impacts the central object is shown to be sufficient to eject a fraction βapprox.10 -2 to 10 -3 of the accreted mass. These winds are driven by a mechanism that accelerates the flow perpendicular to the plane of the disk and can therefore account for the bipolar geometry of the mass loss observed near young stars. The mass loss contained in these winds is comparable to that inferred for young stars. Thus, disk accretion-driven winds may constitute the T Tauri phase of stellar evolution. This mechanism is generally applicable, and thus massive pre-main-sequence objects as well as cataclysmic variables at times of enhanced accretion are predicted to eject bipolar outflows as well. Unmagnetized accreting neutron stas are also expected to eject bipolar flows. Since this mechanism requires stellar surfaces, however, it will not operate in disk accretion onto black holes

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

    Science.gov (United States)

    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 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

  16. EFFECT OF METALLICITY ON THE EVOLUTION OF THE HABITABLE ZONE FROM THE PRE-MAIN SEQUENCE TO THE ASYMPTOTIC GIANT BRANCH AND THE SEARCH FOR LIFE

    Energy Technology Data Exchange (ETDEWEB)

    Danchi, William C. [Exoplanets and Stellar Astrophysics Laboratory, NASA Goddard Space Flight Center, Code 667, Greenbelt, MD 20771 (United States); Lopez, Bruno, E-mail: william.c.danchi@nasa.gov, E-mail: bruno.lopez@oca.eu [Observatoire de la Cote d' Azur, Laboratoire Lagrange UMR 7293, BP 4229, F-06034 Nice Cedex 4 (France)

    2013-05-20

    During the course of stellar evolution, the location and width of the habitable zone changes as the luminosity and radius of the star evolves. The duration of habitability for a planet located at a given distance from a star is greatly affected by the characteristics of the host star. A quantification of these effects can be used observationally in the search for life around nearby stars. The longer the duration of habitability, the more likely it is that life has evolved. The preparation of observational techniques aimed at detecting life would benefit from the scientific requirements deduced from the evolution of the habitable zone. We present a study of the evolution of the habitable zone around stars of 1.0, 1.5, and 2.0 M{sub Sun} for metallicities ranging from Z = 0.0001 to Z = 0.070. We also consider the evolution of the habitable zone from the pre-main sequence until the asymptotic giant branch is reached. We find that metallicity strongly affects the duration of the habitable zone for a planet as well as the distance from the host star where the duration is maximized. For a 1.0 M{sub Sun} star with near solar metallicity, Z = 0.017, the duration of the habitable zone is >10 Gyr at distances 1.2-2.0 AU from the star, whereas the duration is >20 Gyr for high-metallicity stars (Z = 0.070) at distances of 0.7-1.8 AU, and {approx}4 Gyr at distances of 1.8-3.3 AU for low-metallicity stars (Z = 0.0001). Corresponding results have been obtained for stars of 1.5 and 2.0 solar masses.

  17. EFFECT OF METALLICITY ON THE EVOLUTION OF THE HABITABLE ZONE FROM THE PRE-MAIN SEQUENCE TO THE ASYMPTOTIC GIANT BRANCH AND THE SEARCH FOR LIFE

    International Nuclear Information System (INIS)

    Danchi, William C.; Lopez, Bruno

    2013-01-01

    During the course of stellar evolution, the location and width of the habitable zone changes as the luminosity and radius of the star evolves. The duration of habitability for a planet located at a given distance from a star is greatly affected by the characteristics of the host star. A quantification of these effects can be used observationally in the search for life around nearby stars. The longer the duration of habitability, the more likely it is that life has evolved. The preparation of observational techniques aimed at detecting life would benefit from the scientific requirements deduced from the evolution of the habitable zone. We present a study of the evolution of the habitable zone around stars of 1.0, 1.5, and 2.0 M ☉ for metallicities ranging from Z = 0.0001 to Z = 0.070. We also consider the evolution of the habitable zone from the pre-main sequence until the asymptotic giant branch is reached. We find that metallicity strongly affects the duration of the habitable zone for a planet as well as the distance from the host star where the duration is maximized. For a 1.0 M ☉ star with near solar metallicity, Z = 0.017, the duration of the habitable zone is >10 Gyr at distances 1.2-2.0 AU from the star, whereas the duration is >20 Gyr for high-metallicity stars (Z = 0.070) at distances of 0.7-1.8 AU, and ∼4 Gyr at distances of 1.8-3.3 AU for low-metallicity stars (Z = 0.0001). Corresponding results have been obtained for stars of 1.5 and 2.0 solar masses.

  18. qPMS7: a fast algorithm for finding (ℓ, d-motifs in DNA and protein sequences.

    Directory of Open Access Journals (Sweden)

    Hieu Dinh

    Full Text Available Detection of rare events happening in a set of DNA/protein sequences could lead to new biological discoveries. One kind of such rare events is the presence of patterns called motifs in DNA/protein sequences. Finding motifs is a challenging problem since the general version of motif search has been proven to be intractable. Motifs discovery is an important problem in biology. For example, it is useful in the detection of transcription factor binding sites and transcriptional regulatory elements that are very crucial in understanding gene function, human disease, drug design, etc. Many versions of the motif search problem have been proposed in the literature. One such is the (ℓ, d-motif search (or Planted Motif Search (PMS. A generalized version of the PMS problem, namely, Quorum Planted Motif Search (qPMS, is shown to accurately model motifs in real data. However, solving the qPMS problem is an extremely difficult task because a special case of it, the PMS Problem, is already NP-hard, which means that any algorithm solving it can be expected to take exponential time in the worse case scenario. In this paper, we propose a novel algorithm named qPMS7 that tackles the qPMS problem on real data as well as challenging instances. Experimental results show that our Algorithm qPMS7 is on an average 5 times faster than the state-of-art algorithm. The executable program of Algorithm qPMS7 is freely available on the web at http://pms.engr.uconn.edu/downloads/qPMS7.zip. Our online motif discovery tools that use Algorithm qPMS7 are freely available at http://pms.engr.uconn.edu or http://motifsearch.com.

  19. Pms2 suppresses large expansions of the (GAA·TTCn sequence in neuronal tissues.

    Directory of Open Access Journals (Sweden)

    Rebecka L Bourn

    Full Text Available Expanded trinucleotide repeat sequences are the cause of several inherited neurodegenerative diseases. Disease pathogenesis is correlated with several features of somatic instability of these sequences, including further large expansions in postmitotic tissues. The presence of somatic expansions in postmitotic tissues is consistent with DNA repair being a major determinant of somatic instability. Indeed, proteins in the mismatch repair (MMR pathway are required for instability of the expanded (CAG·CTG(n sequence, likely via recognition of intrastrand hairpins by MutSβ. It is not clear if or how MMR would affect instability of disease-causing expanded trinucleotide repeat sequences that adopt secondary structures other than hairpins, such as the triplex/R-loop forming (GAA·TTC(n sequence that causes Friedreich ataxia. We analyzed somatic instability in transgenic mice that carry an expanded (GAA·TTC(n sequence in the context of the human FXN locus and lack the individual MMR proteins Msh2, Msh6 or Pms2. The absence of Msh2 or Msh6 resulted in a dramatic reduction in somatic mutations, indicating that mammalian MMR promotes instability of the (GAA·TTC(n sequence via MutSα. The absence of Pms2 resulted in increased accumulation of large expansions in the nervous system (cerebellum, cerebrum, and dorsal root ganglia but not in non-neuronal tissues (heart and kidney, without affecting the prevalence of contractions. Pms2 suppressed large expansions specifically in tissues showing MutSα-dependent somatic instability, suggesting that they may act on the same lesion or structure associated with the expanded (GAA·TTC(n sequence. We conclude that Pms2 specifically suppresses large expansions of a pathogenic trinucleotide repeat sequence in neuronal tissues, possibly acting independently of the canonical MMR pathway.

  20. Pms2 suppresses large expansions of the (GAA·TTC)n sequence in neuronal tissues.

    Science.gov (United States)

    Bourn, Rebecka L; De Biase, Irene; Pinto, Ricardo Mouro; Sandi, Chiranjeevi; Al-Mahdawi, Sahar; Pook, Mark A; Bidichandani, Sanjay I

    2012-01-01

    Expanded trinucleotide repeat sequences are the cause of several inherited neurodegenerative diseases. Disease pathogenesis is correlated with several features of somatic instability of these sequences, including further large expansions in postmitotic tissues. The presence of somatic expansions in postmitotic tissues is consistent with DNA repair being a major determinant of somatic instability. Indeed, proteins in the mismatch repair (MMR) pathway are required for instability of the expanded (CAG·CTG)(n) sequence, likely via recognition of intrastrand hairpins by MutSβ. It is not clear if or how MMR would affect instability of disease-causing expanded trinucleotide repeat sequences that adopt secondary structures other than hairpins, such as the triplex/R-loop forming (GAA·TTC)(n) sequence that causes Friedreich ataxia. We analyzed somatic instability in transgenic mice that carry an expanded (GAA·TTC)(n) sequence in the context of the human FXN locus and lack the individual MMR proteins Msh2, Msh6 or Pms2. The absence of Msh2 or Msh6 resulted in a dramatic reduction in somatic mutations, indicating that mammalian MMR promotes instability of the (GAA·TTC)(n) sequence via MutSα. The absence of Pms2 resulted in increased accumulation of large expansions in the nervous system (cerebellum, cerebrum, and dorsal root ganglia) but not in non-neuronal tissues (heart and kidney), without affecting the prevalence of contractions. Pms2 suppressed large expansions specifically in tissues showing MutSα-dependent somatic instability, suggesting that they may act on the same lesion or structure associated with the expanded (GAA·TTC)(n) sequence. We conclude that Pms2 specifically suppresses large expansions of a pathogenic trinucleotide repeat sequence in neuronal tissues, possibly acting independently of the canonical MMR pathway.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-03-20

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

  2. The Pisa pre-main sequence tracks and isochrones. A database covering a wide range of Z, Y, mass, and age values

    Science.gov (United States)

    Tognelli, E.; Prada Moroni, P. G.; Degl'Innocenti, S.

    2011-09-01

    Context. In recent years new observations of pre-main sequence stars (pre-MS) with Z ≤ Z⊙ have been made available. To take full advantage of the continuously growing amount of data of pre-MS stars in different environments, we need to develop updated pre-MS models for a wide range of metallicity to assign reliable ages and masses to the observed stars. Aims: We present updated evolutionary pre-MS models and isochrones for a fine grid of mass, age, metallicity, and helium values. Methods: We use a standard and well-tested stellar evolutionary code (i.e. FRANEC), that adopts outer boundary conditions from detailed and realistic atmosphere models. In this code, we incorporate additional improvements to the physical inputs related to the equation of state and the low temperature radiative opacities essential to computing low-mass stellar models. Results: We make available via internet a large database of pre-MS tracks and isochrones for a wide range of chemical compositions (Z = 0.0002-0.03), masses (M = 0.2-7.0 M⊙), and ages (1-100 Myr) for a solar-calibrated mixing length parameter α (i.e. 1.68). For each chemical composition, additional models were computed with two different mixing length values, namely α = 1.2 and 1.9. Moreover, for Z ≥ 0.008, we also provided models with two different initial deuterium abundances. The characteristics of the models have been discussed in detail and compared with other work in the literature. The main uncertainties affecting theoretical predictions have been critically discussed. Comparisons with selected data indicate that there is close agreement between theory and observation. Tracks and isochrones are available on the web at the http://astro.df.unipi.it/stellar-models/Tracks and isochrones are also available in electronic form at the CDS via anonymous ftp to cdsarc.u-strasbg.fr (130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/533/A109

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-07-20

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

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

    International Nuclear Information System (INIS)

    Somers, Garrett; Pinsonneault, Marc H.

    2014-01-01

    We investigate lithium depletion in standard stellar models (SSMs) and main sequence (MS) open clusters, and explore the origin of the Li dispersion in young, cool stars of equal mass, age, and composition. We first demonstrate that SSMs accurately predict the Li abundances of solar analogs at the zero-age main sequence (ZAMS) within theoretical uncertainties. We then measure the rate of MS Li depletion by removing the [Fe/H]-dependent ZAMS Li pattern from three well-studied clusters, and comparing the detrended data. MS depletion is found to be mass-dependent, in the sense of more depletion at low mass. A dispersion in Li abundance at fixed T 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.

  5. Switch junction sequences in PMS2-deficient mice reveal a microhomology-mediated mechanism of Ig class switch recombination

    Science.gov (United States)

    Ehrenstein, Michael R.; Rada, Cristina; Jones, Anne-Marie; Milstein, César; Neuberger, Michael S.

    2001-01-01

    Isotype switching involves a region-specific, nonhomologous recombinational deletion that has been suggested to occur by nonhomologous joining of broken DNA ends. Here, we find increased donor/acceptor homology at switch junctions from PMS2-deficient mice and propose that class switching can occur by microhomology-mediated end-joining. Interestingly, although isotype switching and somatic hypermutation show many parallels, we confirm that PMS2 deficiency has no major effect on the pattern of nucleotide substitutions generated during somatic hypermutation. This finding is in contrast to MSH2 deficiency. With MSH2, the altered pattern of switch recombination and hypermutation suggests parallels in the mechanics of the two processes, whereas the fact that PMS2 deficiency affects only switch recombination may reflect differences in the pathways of break resolution. PMID:11717399

  6. Improved multiplex ligation-dependent probe amplification analysis identifies a deleterious PMS2 allele generated by recombination with crossover between PMS2 and PMS2CL.

    Science.gov (United States)

    Wernstedt, Annekatrin; Valtorta, Emanuele; Armelao, Franco; Togni, Roberto; Girlando, Salvatore; Baudis, Michael; Heinimann, Karl; Messiaen, Ludwine; Staehli, Noemie; Zschocke, Johannes; Marra, Giancarlo; Wimmer, Katharina

    2012-09-01

    Heterozygous PMS2 germline mutations are associated with Lynch syndrome. Up to one third of these mutations are genomic deletions. Their detection is complicated by a pseudogene (PMS2CL), which--owing to extensive interparalog sequence exchange--closely resembles PMS2 downstream of exon 12. A recently redesigned multiplex ligation-dependent probe amplification (MLPA) assay identifies PMS2 copy number alterations with improved reliability when used with reference DNAs containing equal numbers of PMS2- and PMS2CL-specific sequences. We selected eight such reference samples--all publicly available--and used them with this assay to study 13 patients with PMS2-defective colorectal tumors. Three presented deleterious alterations: an Alu-mediated exon deletion; a 125-kb deletion encompassing PMS2 and four additional genes (two with tumor-suppressing functions); and a novel deleterious hybrid PMS2 allele produced by recombination with crossover between PMS2 and PMS2CL, with the breakpoint in intron 10 (the most 5' breakpoint of its kind reported thus far). We discuss mechanisms that might generate this allele in different chromosomal configurations (and their diagnostic implications) and describe an allele-specific PCR assay that facilitates its detection. Our data indicate that the redesigned PMS2 MLPA assay is a valid first-line option. In our series, it identified roughly a quarter of all PMS2 mutations. Copyright © 2012 Wiley Periodicals, Inc.

  7. Improved multiplex ligation-dependent probe amplification analysis identifies a deleterious PMS2 allele generated by recombination with crossover between PMS2 and PMS2CL

    OpenAIRE

    Wernstedt, Annekatrin; Valtorta, Emanuele; Armelao, Franco; Togni, Roberto; Girlando, Salvatore; Baudis, Michael; Heinimann, Karl; Messiaen, Ludwine; Staehli, Noemie; Zschocke, Johannes; Marra, Giancarlo; Wimmer, Katharina

    2012-01-01

    Heterozygous PMS2 germline mutations are associated with Lynch syndrome. Up to one third of these mutations are genomic deletions. Their detection is complicated by a pseudogene (PMS2CL), which – owing to extensive interparalog sequence exchange – closely resembles PMS2 downstream of exon 12. A recently redesigned multiplex ligation-dependent probe amplification (MLPA) assay identifies PMS2 copy number alterations with improved reliability when used with reference DNAs containing equal number...

  8. Premenstrual Syndrome (PMS) FAQ

    Science.gov (United States)

    ... relationships, you may have premenstrual dysphoric disorder (PMDD). PMDD is a severe type of PMS that affects a small percentage of women. Drugs ... selective serotonin reuptake inhibitors (SSRIs) can help treat PMDD in some women. ... depression. Can PMS be treated? If your symptoms are mild to ...

  9. [PMS and PMDD].

    Science.gov (United States)

    Leminen, Henri; Paavonen, Jorma

    2013-01-01

    The symptoms of premenstrual syndrome (PMS) and premenstrual dysphoric disorder (PMDD) significantly impair daily functioning. Symptoms occur in the late luteal phase. There must be a symptom-free interval between the end of menstruation and the time of ovulation. A two-month daily rating of symptoms is required for the diagnosis. The etiology is not well-known. Premenstrual disorders do not occur in anovulatory states. Hormonal therapy suppressing ovulation and selective serotonin reuptake inhibitors (SSRIs) are effective treatments. PMS and PMDD can be successfully managed in general practice.

  10. PMS2 involvement in patients suspected of Lynch syndrome.

    Science.gov (United States)

    Niessen, Renée C; Kleibeuker, Jan H; Westers, Helga; Jager, Paul O J; Rozeveld, Dennie; Bos, Krista K; Boersma-van Ek, Wytske; Hollema, Harry; Sijmons, Rolf H; Hofstra, Robert M W

    2009-04-01

    It is well-established that germline mutations in the mismatch repair genes MLH1, MSH2, and MSH6 cause Lynch syndrome. However, mutations in these three genes do not account for all Lynch syndrome (suspected) families. Recently, it was shown that germline mutations in another mismatch repair gene, PMS2, play a far more important role in Lynch syndrome than initially thought. To explore this further, we determined the prevalence of pathogenic germline PMS2 mutations in a series of Lynch syndrome-suspected patients. Ninety-seven patients who had early-onset microsatellite instable colorectal or endometrial cancer, or multiple Lynch syndrome-associated tumors and/or were from an Amsterdam Criteria II-positive family were selected for this study. These patients carried no pathogenic germline mutation in MLH1, MSH2, or MSH6. When available, tumors were investigated for immunohistochemical staining (IHC) for PMS2. PMS2 was screened in all patients by exon-by-exon sequencing. We identified four patients with a pathogenic PMS2 mutation (4%) among the 97 patients we selected. IHC of PMS2 was informative in one of the mutation carriers, and in this case, the tumor showed loss of PMS2 expression. In conclusion, our study confirms the finding of previous studies that PMS2 is more frequently involved in Lynch syndrome than originally expected.

  11. Premenstrual Dysphoric Disorder (PMDD): Different from PMS?

    Science.gov (United States)

    ... between premenstrual dysphoric disorder (PMDD) and premenstrual syndrome (PMS)? How is PMDD treated? Answers from Jacqueline M. Thielen, M.D. ... disabling extension of premenstrual syndrome (PMS). Although regular PMS and PMDD both have physical and emotional symptoms, PMDD causes ...

  12. Avoidance of pseudogene interference in the detection of 3' deletions in PMS2.

    Science.gov (United States)

    Vaughn, Cecily P; Hart, Kimberly J; Samowitz, Wade S; Swensen, Jeffrey J

    2011-09-01

    Lynch syndrome is characterized by mutations in the mismatch repair genes MLH1, MSH2, MSH6, and PMS2. In PMS2, detection of mutations is confounded by numerous pseudogenes. Detection of 3' deletions is particularly complicated by the pseudogene PMS2CL, which has strong similarity to PMS2 exons 9 and 11-15, due to extensive gene conversion. A newly designed multiplex ligation-dependent probe amplification (MLPA) kit incorporates probes for variants found in both PMS2 and PMS2CL. This provides detection of deletions, but does not allow localization of deletions to the gene or pseudogene. To address this, we have developed a methodology incorporating reference samples with known copy numbers of variants, and paired MLPA results with sequencing of PMS2 and PMS2CL. We tested a subset of clinically indicated samples for which mutations were either unidentified or not fully characterized using existing methods. We identified eight unrelated patients with deletions encompassing exons 9-15, 11-15, 13-15, 14-15, and 15. By incorporating specific, characterized reference samples and sequencing the gene and pseudogene it is possible to identify deletions in this region of PMS2 and provide clinically relevant results. This methodology represents a significant advance in the diagnosis of patients with Lynch syndrome caused by PMS2 mutations. © 2011 Wiley-Liss, Inc.

  13. Extensive gene conversion at the PMS2 DNA mismatch repair locus.

    Science.gov (United States)

    Hayward, Bruce E; De Vos, Michel; Valleley, Elizabeth M A; Charlton, Ruth S; Taylor, Graham R; Sheridan, Eamonn; Bonthron, David T

    2007-05-01

    Mutations of the PMS2 DNA repair gene predispose to a characteristic range of malignancies, with either childhood onset (when both alleles are mutated) or a partially penetrant adult onset (if heterozygous). These mutations have been difficult to detect, due to interference from a family of pseudogenes located on chromosome 7. One of these, the PMS2CL pseudogene, lies within a 100-kb inverted duplication (inv dup), 700 kb centromeric to PMS2 itself on 7p22. Here, we show that the reference genomic sequences cannot be relied upon to distinguish PMS2 from PMS2CL, because of sequence transfer between the two loci. The 7p22 inv dup occurred prior to the divergence of modern ape species (15 million years ago [Mya]), but has undergone extensive sequence homogenization. This process appears to be ongoing, since there is considerable allelic diversity within the duplicated region, much of it derived from sequence exchange between PMS2 and PMS2CL. This sequence diversity can result in both false-positive and false-negative mutation analysis at this locus. Great caution is still needed in the design and interpretation of PMS2 mutation screens. 2007 Wiley-Liss, Inc.

  14. VizieR Online Data Catalog: Pisa pre-main sequence tracks and isochrones (Tognelli+, 2011)

    Science.gov (United States)

    Tognelli, E.; Prada Moroni, P. G.; Degl'Innocenti, S.

    2011-07-01

    Evolutionary tracks and Isochrones in the log L vs log Te plane, for the following chemical compositions: Z Y Y Y 2.00E-04 0.230 0.249 0.250 1.00E-03 0.232 0.251 0.254 2.00E-03 0.234 0.253 0.259 3.00E-03 0.236 0.254 0.263 4.00E-03 0.238 0.256 0.269 5.00E-03 0.240 0.258 0.273 6.00E-03 0.242 0.260 0.279 7.00E-03 0.244 0.262 0.283 8.00E-03 0.246 0.265 0.289 9.00E-03 0.248 0.267 0.294 1.00E-02 0.250 0.268 0.299 1.25E-02 0.255 0.274 0.311 1.50E-02 0.260 0.278 0.323 1.75E-02 0.265 0.284 0.336 2.00E-02 0.270 0.288 0.349 2.25E-02 0.275 0.294 0.361 2.50E-02 0.280 0.299 0.374 2.75E-02 0.285 0.304 0.386 3.00E-02 0.290 0.308 0.398 Each model is calculated with an initial Deuterium abundance XD=4.0E-05. For Z>=0.008, models with XD=2.0E-05 are available, too. Each model is calculated with three different values of the mixing length parameter alpha = 1.20, 1.68 (solar calibrated), 1.90. There is also a dataset for our Standard Solar Model parameters (Z=0.01377, Y=0.2533, alpha=1.68, XD=2.0E-05). (5 data files).

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

    Science.gov (United States)

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

    2017-08-01

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

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

    Science.gov (United States)

    2012-06-25

    ISOY J053446.01−044922.1i V1448 Ori 17.43c 15.61c 13.88 13.26 12.95 12.73 12.66 12.91 . . . K5c 0.5424125 ISOY J053605.95−050041.2i 2MASS J05360595...identified 12 EB candidates. Four of them, 2MASS 05352184−0546085 (Stassun et al. 2006), V1174 Ori (Stassun et al. 2004), Par1802 (Cargile et al. 2008...Zero points for the photometry were established by reference to data for non-variable stars in our FOV from the Two Micron All Sky Survey ( 2MASS

  17. Excitation of Solar-like Oscillations: From PMS to MS Stellar Models ...

    Indian Academy of Sciences (India)

    excited modes in pre-main sequence stars are also discussed. Key words. Turbulence—convection—oscillations—excitation—sun, stars: α Cen A—stars: main and pre-main sequence stars. 1. Introduction. In the past approximately five years, solar-like oscillations have been detected in several intermediate massive stars ...

  18. A Comprehensive Strategy for Accurate Mutation Detection of the Highly Homologous PMS2.

    Science.gov (United States)

    Li, Jianli; Dai, Hongzheng; Feng, Yanming; Tang, Jia; Chen, Stella; Tian, Xia; Gorman, Elizabeth; Schmitt, Eric S; Hansen, Terah A A; Wang, Jing; Plon, Sharon E; Zhang, Victor Wei; Wong, Lee-Jun C

    2015-09-01

    Germline mutations in the DNA mismatch repair gene PMS2 underlie the cancer susceptibility syndrome, Lynch syndrome. However, accurate molecular testing of PMS2 is complicated by a large number of highly homologous sequences. To establish a comprehensive approach for mutation detection of PMS2, we have designed a strategy combining targeted capture next-generation sequencing (NGS), multiplex ligation-dependent probe amplification, and long-range PCR followed by NGS to simultaneously detect point mutations and copy number changes of PMS2. Exonic deletions (E2 to E9, E5 to E9, E8, E10, E14, and E1 to E15), duplications (E11 to E12), and a nonsense mutation, p.S22*, were identified. Traditional multiplex ligation-dependent probe amplification and Sanger sequencing approaches cannot differentiate the origin of the exonic deletions in the 3' region when PMS2 and PMS2CL share identical sequences as a result of gene conversion. Our approach allows unambiguous identification of mutations in the active gene with a straightforward long-range-PCR/NGS method. Breakpoint analysis of multiple samples revealed that recurrent exon 14 deletions are mediated by homologous Alu sequences. Our comprehensive approach provides a reliable tool for accurate molecular analysis of genes containing multiple copies of highly homologous sequences and should improve PMS2 molecular analysis for patients with Lynch syndrome. Copyright © 2015 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

  19. Long-range PCR facilitates the identification of PMS2-specific mutations.

    Science.gov (United States)

    Clendenning, Mark; Hampel, Heather; LaJeunesse, Jennifer; Lindblom, Annika; Lockman, Jan; Nilbert, Mef; Senter, Leigha; Sotamaa, Kaisa; de la Chapelle, Albert

    2006-05-01

    Mutations within the DNA mismatch repair gene, "postmeiotic segregation increased 2" (PMS2), have been associated with a predisposition to hereditary nonpolyposis colorectal cancer (HNPCC; Lynch syndrome). The presence of a large family of highly homologous PMS2 pseudogenes has made previous attempts to sequence PMS2 very difficult. Here, we describe a novel method that utilizes long-range PCR as a way to preferentially amplify PMS2 and not the pseudogenes. A second, exon-specific, amplification from diluted long-range products enables us to obtain a clean sequence that shows no evidence of pseudogene contamination. This method has been used to screen a cohort of patients whose tumors were negative for the PMS2 protein by immunohistochemistry and had not shown any mutations within the MLH1 gene. Sequencing of the PMS2 gene from 30 colorectal and 11 endometrial cancer patients identified 10 novel sequence changes as well as 17 sequence changes that had previously been identified. In total, putative pathologic mutations were detected in 11 of the 41 families. Among these were five novel mutations, c.705+1G>T, c.736_741del6ins11, c.862_863del, c.1688G>T, and c.2007-1G>A. We conclude that PMS2 mutation detection in selected Lynch syndrome and Lynch syndrome-like patients is both feasible and desirable. Published 2006 Wiley-Liss, Inc.

  20. A frame-shift mutation of PMS2 is a widespread cause of Lynch syndrome

    DEFF Research Database (Denmark)

    Clendenning, Mark; Senter, Leigha; Hampel, Heather

    2008-01-01

    BACKGROUND: When compared to the other mismatch repair genes involved in Lynch syndrome, the identification of mutations within PMS2 has been limited (Lynch syndrome cases...... on immunohistochemical analysis. RESULTS: We have identified a frequently occurring frame-shift mutation (c.736_741del6ins11) in 12 ostensibly unrelated Lynch syndrome patients (20% of patients we have identified with a deleterious mutation in PMS2, n=61). These individuals all display the rare allele (population...... are caused by PMS2. This disparity is primarily due to complications in the study of this gene caused by interference from pseudogene sequences. METHODS: Using a recently developed method for detecting PMS2 specific mutations, we have screened 99 patients who are likely candidates for PMS2 mutations based...

  1. Novel PMS2 Pseudogenes Can Conceal Recessive Mutations Causing a Distinctive Childhood Cancer Syndrome

    OpenAIRE

    De Vos, Michel; Hayward, Bruce E.; Picton, Susan; Sheridan, Eamonn; Bonthron, David T.

    2004-01-01

    We investigated a family with an autosomal recessive syndrome of café-au-lait patches and childhood malignancy, notably supratentorial primitive neuroectodermal tumor. There was no cancer predisposition in heterozygotes; nor was there bowel cancer in any individual. However, autozygosity mapping indicated linkage to a region of 7p22 surrounding the PMS2 mismatch-repair gene. Sequencing of genomic PCR products initially failed to identify a PMS2 mutation. Genome searches then revealed a previo...

  2. 23 CFR 500.106 - PMS.

    Science.gov (United States)

    2010-04-01

    ... the “AASHTO Guidelines for Pavement Management Systems.” 1 1 AASHTO Guidelines for Pavement Management... ADMINISTRATION, DEPARTMENT OF TRANSPORTATION TRANSPORTATION INFRASTRUCTURE MANAGEMENT MANAGEMENT AND MONITORING SYSTEMS Management Systems § 500.106 PMS. An effective PMS for Federal-aid highways is a systematic...

  3. Germline mutations in PMS2 and MLH1 in individuals with solitary loss of PMS2 expression in colorectal carcinomas from the Colon Cancer Family Registry Cohort.

    Science.gov (United States)

    Rosty, Christophe; Clendenning, Mark; Walsh, Michael D; Eriksen, Stine V; Southey, Melissa C; Winship, Ingrid M; Macrae, Finlay A; Boussioutas, Alex; Poplawski, Nicola K; Parry, Susan; Arnold, Julie; Young, Joanne P; Casey, Graham; Haile, Robert W; Gallinger, Steven; Le Marchand, Loïc; Newcomb, Polly A; Potter, John D; DeRycke, Melissa; Lindor, Noralane M; Thibodeau, Stephen N; Baron, John A; Win, Aung Ko; Hopper, John L; Jenkins, Mark A; Buchanan, Daniel D

    2016-02-19

    Immunohistochemistry for DNA mismatch repair proteins is used to screen for Lynch syndrome in individuals with colorectal carcinoma (CRC). Although solitary loss of PMS2 expression is indicative of carrying a germline mutation in PMS2, previous studies reported MLH1 mutation in some cases. We determined the prevalence of MLH1 germline mutations in a large cohort of individuals with a CRC demonstrating solitary loss of PMS2 expression. This cohort study included 88 individuals affected with a PMS2-deficient CRC from the Colon Cancer Family Registry Cohort. Germline PMS2 mutation analysis (long-range PCR and multiplex ligation-dependent probe amplification) was followed by MLH1 mutation testing (Sanger sequencing and multiplex ligation-dependent probe amplification). Of the 66 individuals with complete mutation screening, we identified a pathogenic PMS2 mutation in 49 (74%), a pathogenic MLH1 mutation in 8 (12%) and a MLH1 variant of uncertain clinical significance predicted to be damaging by in silico analysis in 3 (4%); 6 (9%) carried variants likely to have no clinical significance. Missense point mutations accounted for most alterations (83%; 9/11) in MLH1. The MLH1 c.113A> G p.Asn38Ser mutation was found in 2 related individuals. One individual who carried the MLH1 intronic mutation c.677+3A>G p.Gln197Argfs*8 leading to the skipping of exon 8, developed 2 tumours, both of which retained MLH1 expression. A substantial proportion of CRCs with solitary loss of PMS2 expression are associated with a deleterious MLH1 germline mutation supporting the screening for MLH1 in individuals with tumours of this immunophenotype, when no PMS2 mutation has been identified. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

  4. Premenstrual syndrome (PMS among high school students

    Directory of Open Access Journals (Sweden)

    Buddhabunyakan N

    2017-07-01

    Full Text Available Nattapong Buddhabunyakan, Srinaree Kaewrudee, Chompilas Chongsomchai, Sukree Soontrapa, Woraluk Somboonporn, Jen Sothornwit Department of Obstetrics and Gynaecology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand Background: Premenstrual syndrome (PMS is a common health problem among adolescents.Objective: To assess the prevalence of PMS in Thai high school students.Materials and methods: This was a prospective study conducted among menstruating high school students in Khon Kaen, Thailand, from September to December, 2015. Participants were asked to prospectively complete an anonymous questionnaire, which included information about demographic data, menstrual patterns, and symptoms to be recorded on a daily calendar of premenstrual experiences according to the diagnostic criteria proposed by the American College of Obstetricians and Gynecologists. All of the data were prospectively recorded for 90 consecutive days.Results: Of the 399 participants, 289 (72.4% completed the self-report questionnaire. Eighty-six participants (29.8%; 95% CI, 24.5%–35.4% reported having PMS. The most common somatic and affective symptoms among participants with PMS were breast tenderness (74.4% and angry outbursts (97.7%. There were significant differences between the PMS and non-PMS groups, and PMS was associated with various problems related to educational activities, including lack of concentration and motivation, poor individual work performance, poor collaborative work performance, and low scores. However, there were no significant differences regarding interpersonal relationships between the PMS and non-PMS groups.Conclusions: PMS is a common menstrual disorder among Thai high school students. The most common symptoms reported in this study were angry outbursts and breast tenderness. Keywords: premenstrual symptoms, prevalence, association, high school students

  5. The frequency of previously undetectable deletions involving 3' Exons of the PMS2 gene.

    Science.gov (United States)

    Vaughn, Cecily P; Baker, Christine L; Samowitz, Wade S; Swensen, Jeffrey J

    2013-01-01

    Lynch syndrome is characterized by mutations in one of four mismatch repair genes, MLH1, MSH2, MSH6, or PMS2. Clinical mutation analysis of these genes includes sequencing of exonic regions and deletion/duplication analysis. However, detection of deletions and duplications in PMS2 has previously been confined to Exons 1-11 due to gene conversion between PMS2 and the pseudogene PMS2CL in the remaining 3' exons (Exons 12-15). We have recently described an MLPA-based method that permits detection of deletions of PMS2 Exons 12-15; however, the frequency of such deletions has not yet been determined. To address this question, we tested for 3' deletions in 58 samples that were reported to be negative for PMS2 mutations using previously available methods. All samples were from individuals whose tumors exhibited loss of PMS2 immunohistochemical staining without concomitant loss of MLH1 immunostaining. We identified seven samples in this cohort with deletions in the 3' region of PMS2, including three previously reported samples with deletions of Exons 13-15 (two samples) and Exons 14-15. Also detected were deletions of Exons 12-15, Exon 13, and Exon 14 (two samples). Breakpoint analysis of the intragenic deletions suggests they occurred through Alu-mediated recombination. Our results indicate that ∼12% of samples suspected of harboring a PMS2 mutation based on immunohistochemical staining, for which mutations have not yet been identified, would benefit from testing using the new methodology. Copyright © 2012 Wiley Periodicals, Inc.

  6. Germline PMS2 mutation screened by mismatch repair protein immunohistochemistry of colorectal cancer in Japan.

    Science.gov (United States)

    Sugano, Kokichi; Nakajima, Takeshi; Sekine, Shigeki; Taniguchi, Hirokazu; Saito, Shinya; Takahashi, Masahiro; Ushiama, Mineko; Sakamoto, Hiromi; Yoshida, Teruhiko

    2016-11-01

    Germline PMS2 gene mutations were detected by RT-PCR/direct sequencing of total RNA extracted from puromycin-treated peripheral blood lymphocytes (PBL) and multiplex ligation-dependent probe amplification (MLPA) analyses of Japanese patients with colorectal cancer (CRC) fulfilling either the revised Bethesda Guidelines or being an age at disease onset of younger than 70 years, and screened by mismatch repair protein immunohistochemistry of formalin-fixed paraffin embedded sections. Of the 501 subjects examined, 7 (1.40%) showed the downregulated expression of the PMS2 protein alone and were referred to the genetic counseling clinic. Germline PMS2 mutations were detected in 6 (85.7%), including 3 nonsense and 1 frameshift mutations by RT-PCR/direct sequencing and 2 genomic deletions by MLPA. No mutations were identified in the other MMR genes (i.e. MSH2, MLH1 and MSH6). The prevalence of the downregulated expression of the PMS2 protein alone was 1.40% among the subjects examined and IHC results predicted the presence of PMS2 germline mutations. RT-PCR from puromycin-treated PBL and MLPA may be employed as the first screening step to detect PMS2 mutations without pseudogene interference, followed by the long-range PCR/nested PCR validation using genomic DNA. © 2016 The Authors. Cancer Science published by John Wiley & Sons Australia, Ltd on behalf of Japanese Cancer Association.

  7. PMS2 mutations in childhood cancer.

    Science.gov (United States)

    De Vos, Michel; Hayward, Bruce E; Charlton, Ruth; Taylor, Graham R; Glaser, Adam W; Picton, Susan; Cole, Trevor R; Maher, Eamonn R; McKeown, Carole M E; Mann, Jill R; Yates, John R; Baralle, Diana; Rankin, Julia; Bonthron, David T; Sheridan, Eamonn

    2006-03-01

    Until recently, the PMS2 DNA mismatch repair gene has only rarely been implicated as a cancer susceptibility locus. New studies have shown, however, that earlier analyses of this gene have had technical limitations and also that the genetic behavior of mutant PMS2 alleles is unusual, in that, unlike MLH1 or MSH2 mutations, PMS2 mutations show low heterozygote penetrance. As a result, a dominantly inherited cancer predisposition has not been a feature reported in families with PMS2 mutations. Such families have instead been ascertained through childhood-onset cancers in homozygotes or through apparently sporadic colorectal cancer in heterozygotes. We present further information on the phenotype associated with homozygous PMS2 deficiency in 13 patients from six families of Pakistani origin living in the United Kingdom. This syndrome is characterized by café-au-lait skin pigmentation and a characteristic tumor spectrum, including leukemias, lymphomas, cerebral malignancies (such as supratentorial primitive neuroectodermal tumors, astrocytomas, and glioblastomas), and colorectal neoplasia with an onset in early adult life. We present evidence for a founder effect in five families, all of which carried the same R802-->X mutation (i.e., arginine-802 to stop) in PMS2. This cancer syndrome can be mistaken for neurofibromatosis type 1, with important management implications including the risk of the disorder occurring in siblings and the likelihood of tumor development in affected individuals.

  8. Functional PMS2 hybrid alleles containing a pseudogene-specific missense variant trace back to a single ancient intrachromosomal recombination event.

    Science.gov (United States)

    Ganster, Christina; Wernstedt, Annekatrin; Kehrer-Sawatzki, Hildegard; Messiaen, Ludwine; Schmidt, Konrad; Rahner, Nils; Heinimann, Karl; Fonatsch, Christa; Zschocke, Johannes; Wimmer, Katharina

    2010-05-01

    Sequence exchange between PMS2 and its pseudogene PMS2CL, embedded in an inverted duplication on chromosome 7p22, has been reported to be an ongoing process that leads to functional PMS2 hybrid alleles containing PMS2- and PMS2CL-specific sequence variants at the 5'-and the 3'-end, respectively. The frequency of PMS2 hybrid alleles, their biological significance, and the mechanisms underlying their formation are largely unknown. Here we show that overall hybrid alleles account for one-third of 384 PMS2 alleles analyzed in individuals of different ethnic backgrounds. Depending on the population, 14-60% of hybrid alleles carry PMS2CL-specific sequences in exons 13-15, the remainder only in exon 15. We show that exons 13-15 hybrid alleles, named H1 hybrid alleles, constitute different haplotypes but trace back to a single ancient intrachromosomal recombination event with crossover. Taking advantage of an ancestral sequence variant specific for all H1 alleles we developed a simple gDNA-based polymerase chain reaction (PCR) assay that can be used to identify H1-allele carriers with high sensitivity and specificity (100 and 99%, respectively). Because H1 hybrid alleles harbor missense variant p.N775S of so far unknown functional significance, we assessed the H1-carrier frequency in 164 colorectal cancer patients. So far, we found no indication that the variant plays a major role with regard to cancer susceptibility. (c) 2010 Wiley-Liss, Inc.

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

    Science.gov (United States)

    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.

  10. Explaining the luminosity spread in young clusters: proto and pre-main sequence stellar evolution in a molecular cloud environment

    Science.gov (United States)

    Jensen, Sigurd S.; Haugbølle, Troels

    2018-02-01

    Hertzsprung-Russell diagrams of star-forming regions show a large luminosity spread. This is incompatible with well-defined isochrones based on classic non-accreting protostellar evolution models. Protostars do not evolve in isolation of their environment, but grow through accretion of gas. In addition, while an age can be defined for a star-forming region, the ages of individual stars in the region will vary. We show how the combined effect of a protostellar age spread, a consequence of sustained star formation in the molecular cloud, and time-varying protostellar accretion for individual protostars can explain the observed luminosity spread. We use a global magnetohydrodynamic simulation including a sub-scale sink particle model of a star-forming region to follow the accretion process of each star. The accretion profiles are used to compute stellar evolution models for each star, incorporating a model of how the accretion energy is distributed to the disc, radiated away at the accretion shock, or incorporated into the outer layers of the protostar. Using a modelled cluster age of 5 Myr, we naturally reproduce the luminosity spread and find good agreement with observations of the Collinder 69 cluster, and the Orion Nebular Cluster. It is shown how stars in binary and multiple systems can be externally forced creating recurrent episodic accretion events. We find that in a realistic global molecular cloud model massive stars build up mass over relatively long time-scales. This leads to an important conceptual change compared to the classic picture of non-accreting stellar evolution segmented into low-mass Hayashi tracks and high-mass Henyey tracks.

  11. Efficient Detection of Copy Number Mutations in PMS2 Exons with a Close Homolog.

    Science.gov (United States)

    Herman, Daniel S; Smith, Christina; Liu, Chang; Vaughn, Cecily P; Palaniappan, Selvi; Pritchard, Colin C; Shirts, Brian H

    2018-07-01

    Detection of 3' PMS2 copy-number mutations that cause Lynch syndrome is difficult because of highly homologous pseudogenes. To improve the accuracy and efficiency of clinical screening for these mutations, we developed a new method to analyze standard capture-based, next-generation sequencing data to identify deletions and duplications in PMS2 exons 9 to 15. The approach captures sequences using PMS2 targets, maps sequences randomly among regions with equal mapping quality, counts reads aligned to homologous exons and introns, and flags read count ratios outside of empirically derived reference ranges. The method was trained on 1352 samples, including 8 known positives, and tested on 719 samples, including 17 known positives. Clinical implementation of the first version of this method detected new mutations in the training (N = 7) and test (N = 2) sets that had not been identified by our initial clinical testing pipeline. The described final method showed complete sensitivity in both sample sets and false-positive rates of 5% (training) and 7% (test), dramatically decreasing the number of cases needing additional mutation evaluation. This approach leveraged the differences between gene and pseudogene to distinguish between PMS2 and PMS2CL copy-number mutations. These methods enable efficient and sensitive Lynch syndrome screening for 3' PMS2 copy-number mutations and may be applied similarly to other genomic regions with highly homologous pseudogenes. Copyright © 2018 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

  12. On the orbit calculation of visual binaries with a very short arc: application to the PMS binary system, FW Tau AB

    Science.gov (United States)

    Docobo, J. A.; Tamazian, V. S.; Campo, P. P.

    2018-05-01

    In the vast majority of cases when available astrometric measurements of a visual binary cover a very short orbital arc, it is practically impossible to calculate a good quality orbit. It is especially important for systems with pre-main-sequence components where standard mass-spectrum calibrations cannot be applied nor can a dynamical parallax be calculated. We have shown that the analytical method of Docobo allows us to put certain constraints on the most likely orbital solutions, using an available realistic estimate of the global mass of the system. As an example, we studied the interesting PMS binary, FW Tau AB, located in the Taurus-Auriga as well as investigated a range of its possible orbital solutions combined with an assumed distance between 120 and 160 pc. To maintain the total mass of FW Tau AB in a realistic range between 0.2 and 0.6M_{⊙}, minimal orbital periods should begin at 105, 150, 335, and 2300 yr for distances of 120, 130, 140, and 150 pc, respectively (no plausible orbits were found assuming a distance of 160 pc). An original criterion to establish the upper limit of the orbital period is applied. When the position angle in some astrometric measurements was flipped by 180°, orbits with periods close to 45 yr are also plausible. Three example orbits with periods of 44.6, 180, and 310 yr are presented.

  13. A frame-shift mutation of PMS2 is a widespread cause of Lynch syndrome.

    Science.gov (United States)

    Clendenning, M; Senter, L; Hampel, H; Robinson, K Lagerstedt; Sun, S; Buchanan, D; Walsh, M D; Nilbert, M; Green, J; Potter, J; Lindblom, A; de la Chapelle, A

    2008-06-01

    When compared to the other mismatch repair genes involved in Lynch syndrome, the identification of mutations within PMS2 has been limited (PMS2. This disparity is primarily due to complications in the study of this gene caused by interference from pseudogene sequences. Using a recently developed method for detecting PMS2 specific mutations, we have screened 99 patients who are likely candidates for PMS2 mutations based on immunohistochemical analysis. We have identified a frequently occurring frame-shift mutation (c.736_741del6ins11) in 12 ostensibly unrelated Lynch syndrome patients (20% of patients we have identified with a deleterious mutation in PMS2, n = 61). These individuals all display the rare allele (population frequency 10 000 carriers of this mutation in the USA alone. The identification of both the mutation and the common haplotype in one Swedish control sample (n = 225), along with evidence that Lynch syndrome associated cancers are rarer than expected in the probands' families, would suggest that this is a prevalent mutation with reduced penetrance.

  14. Nuclear import of human MLH1, PMS2, and MutLalpha: redundancy is the key.

    Science.gov (United States)

    Leong, Vivian; Lorenowicz, Jessica; Kozij, Natalie; Guarné, Alba

    2009-08-01

    DNA mismatch repair maintains genomic stability by correcting errors that have escaped polymerase proofreading. Defects on mismatch repair genes lead to an increased mutation rate, microsatellite instability and predisposition to human non-polyposis colorectal cancer (HNPCC). Human MutLalpha is a heterodimer formed by the interaction of MLH1 and PMS2 that coordinates a series of key events in mismatch repair. It has been proposed that nuclear import of MutLalpha may be the first regulatory step on the activation of the mismatch repair pathway. Using confocal microscopy and mismatch repair deficient cells, we have identified the sequence determinants that drive nuclear import of human MLH1, PMS2, and MutLalpha. Transient transfection of the individual proteins reveals that MLH1 has a bipartite and PMS2 has a single monopartite nuclear localization signal. Although dimerization is not required for nuclear localization, the MutLalpha heterodimer is imported more efficiently than the MLH1 or PMS2 monomers. Interestingly, the bipartite localization signal of MLH1 can direct import of MutLalpha even when PMS2 encompasses a mutated localization signal. Hence we conclude that the presence of redundant nuclear localization signals guarantees nuclear transport of MutLalpha and, consequently, efficient mismatch repair.

  15. Detection of large scale 3' deletions in the PMS2 gene amongst Colon-CFR participants: have we been missing anything?

    Science.gov (United States)

    Clendenning, Mark; Walsh, Michael D; Gelpi, Judith Balmana; Thibodeau, Stephen N; Lindor, Noralane; Potter, John D; Newcomb, Polly; LeMarchand, Loic; Haile, Robert; Gallinger, Steve; Hopper, John L; Jenkins, Mark A; Rosty, Christophe; Young, Joanne P; Buchanan, Daniel D

    2013-09-01

    Current screening practices have been able to identify PMS2 mutations in 78 % of cases of colorectal cancer from the Colorectal Cancer Family Registry (Colon CFR) which showed solitary loss of the PMS2 protein. However the detection of large-scale deletions in the 3' end of the PMS2 gene has not been possible due to technical difficulties associated with pseudogene sequences. Here, we utilised a recently described MLPA/long-range PCR-based approach to screen the remaining 22 % (n = 16) of CRC-affected probands for mutations in the 3' end of the PMS2 gene. No deletions encompassing any or all of exons 12 through 15 were identified; therefore, our results suggest that 3' deletions in PMS2 are not a frequent occurrence in such families.

  16. Detection of large scale 3′ deletions in the PMS2 gene amongst Colon-CFR participants – have we been missing anything?

    Science.gov (United States)

    Clendenning, Mark; Walsh, Michael D; Gelpi, Judith Balmana; Thibodeau, Stephen N.; Lindor, Noralane; Potter, John D.; Newcomb, Polly; LeMarchand, Loic; Haile, Robert; Gallinger, Steve; Hopper, John L.; Jenkins, Mark A.; Rosty, Christophe; Young, Joanne P.; Buchanan, Daniel D.

    2013-01-01

    Current screening practices have been able to identify PMS2 mutations in 78% of cases of colorectal cancer from the Colorectal Cancer Family Registry (Colon CFR) which showed solitary loss of the PMS2 protein. However the detection of large-scale deletions in the 3′ end of the PMS2 gene has not been possible due to technical difficulties associated with pseudogene sequences. Here, we utilised a recently described MLPA/long-range PCR-based approach to screen the remaining 22% (n = 16) of CRC-affected probands for mutations in the 3′ end of the PMS2 gene. No deletions encompassing any or all of exons 12 through 15 were identified; therefore, our results suggest that 3′ deletions in PMS2 are not a frequent occurrence in such families. PMID:23288611

  17. Top Performing PMs: How DAU Develops Them

    Science.gov (United States)

    2015-12-01

    online, while intermediate courses feature a combination of online prerequisites followed by classroom training. Advanced PM courses use teams of...hours of online instruction and 27.5 classroom days. For major acquisition PMs, 70 additional classroom days of specialized training (PMT 401 and...training and experience is that creative , informed thought is necessary to optimize the structure of a program. DAU embeds principles of critical

  18. Correlations between the stellar and disc properties of Taurus PMS stars in the GASPS sample

    NARCIS (Netherlands)

    Alonso-Martínez, Miguel; Riviere-Marichalar, Pablo; Pascual, Natalia; Montesinos, Benjamín; Howard, Christian D.; Sandell, Göran; Meeus, Gwendolyn; Eiroa, Carlos; Dent, Bill

    The Herschel Open Time Key Programme GASPS (P.I. B. Dent) has observed a large number of pre-main sequence TTauri stars in Taurus with PACS (photometry and spectroscopy). In addition, we have also carried out new ground-based optical and near-IR observations (photometry and spectroscopy) of most of

  19. PMS2 expression in epithelial ovarian cancer is posttranslationally regulated by Akt and essential for platinum-induced apoptosis.

    Science.gov (United States)

    Jia, Jinghui; Wang, Zehua; Cai, Jing; Zhang, Yuan

    2016-03-01

    Epithelial ovarian cancer (EOC) is the most lethal of the gynecologic malignancies, mainly due to the advanced stage at diagnosis and development of cisplatin resistance. The sensitivity of tumor cells to cisplatin is frequently affected by defect in DNA mismatch repair (MMR), which repairs mispaired DNA sequences and regulates DNA-damage-induced apoptosis. However, the role of postmeiotic segregation increased 2 (PMS2), a member of MMR protein family, in cisplatin resistance remains elusive. In the present study, we demonstrated the frequent deficiency of PMS2 and phosphorylation of Akt in EOC cell lines and tissues. Results of complex immunoprecipitation (co-IP) and protein stability assay indicated that activated Akt could directly bind to PMS2 and cause degradation of PMS2 in EOC cells. In addition, functional experiments revealed that PMS2 was required for cisplatin-induced apoptosis and cell cycle arrest in G2/M phase. These findings provide a novel insight into molecular mechanisms linking MMR with chemoresistance and suggest that stabilization of PMS2 expression may be useful in overcoming the cisplatin resistance in EOC.

  20. RNA-based mutation analysis identifies an unusual MSH6 splicing defect and circumvents PMS2 pseudogene interference.

    Science.gov (United States)

    Etzler, J; Peyrl, A; Zatkova, A; Schildhaus, H-U; Ficek, A; Merkelbach-Bruse, S; Kratz, C P; Attarbaschi, A; Hainfellner, J A; Yao, S; Messiaen, L; Slavc, I; Wimmer, K

    2008-02-01

    Heterozygous germline mutations in one of the mismatch repair (MMR) genes MLH1, MSH2, MSH6, and PMS2 cause hereditary nonpolyposis colorectal cancer (HNPCC) or Lynch syndrome, a dominantly inherited cancer susceptibility syndrome. Recent reports provide evidence for a novel recessively inherited cancer syndrome with constitutive MMR deficiency due to biallelic germline mutations in one of the MMR genes. MMR-deficiency (MMR-D) syndrome is characterized by childhood brain tumors, hematological and/or gastrointestinal malignancies, and signs of neurofibromatosis type 1 (NF1). We established an RNA-based mutation detection assay for the four MMR genes, since 1) a number of splicing defects may escape detection by the analysis of genomic DNA, and 2) DNA-based mutation detection in the PMS2 gene is severely hampered by the presence of multiple highly similar pseudogenes, including PMS2CL. Using this assay, which is based on direct cDNA sequencing of RT-PCR products, we investigated two families with children suspected to suffer from MMR-D syndrome. We identified a homozygous complex MSH6 splicing alteration in the index patients of the first family and a novel homozygous PMS2 mutation (c.182delA) in the index patient of the second family. Furthermore, we demonstrate, by the analysis of a PMS2/PMS2CL "hybrid" allele carrier, that RNA-based PMS2 testing effectively avoids the caveats of genomic DNA amplification approaches; i.e., pseudogene coamplification as well as allelic dropout, and will, thus, allow more sensitive mutation analysis in MMR deficiency and in HNPCC patients with PMS2 defects. (c) 2007 Wiley-Liss, Inc.

  1. Army Personnel Management System Study (PMS2). Volume II. Appendices.

    Science.gov (United States)

    1979-11-06

    demonstrated desirability, some functions would be facilitated, costs need further study, and mobilization capabilities should be emphasized. PMS2 is basis for current reorganization planning within ODCSPER.

  2. Epitope-positive truncating MLH1 mutation and loss of PMS2: implications for IHC-directed genetic testing for Lynch syndrome.

    Science.gov (United States)

    Zighelboim, Israel; Powell, Matthew A; Babb, Sheri A; Whelan, Alison J; Schmidt, Amy P; Clendenning, Mark; Senter, Leigha; Thibodeau, Stephen N; de la Chapelle, Albert; Goodfellow, Paul J

    2009-01-01

    We assessed mismatch repair by immunohistochemistry (IHC) and microsatellite instability (MSI) analysis in an early onset endometrial cancer and a sister's colon cancer. We demonstrated high-level MSI and normal expression for MLH1, MSH2 and MSH6. PMS2 failed to stain in both tumors, strongly implicating a PMS2 defect. This family did not meet clinical criteria for Lynch syndrome. However, early onset endometrial cancers in the proband and her sister, a metachronous colorectal cancer in the sister as well as MSI in endometrial and colonic tumors suggested a heritable mismatch repair defect. PCR-based direct exonic sequencing and multiplex ligation-dependent probe amplification (MLPA) were undertaken to search for PMS2 mutations in the germline DNA from the proband and her sister. No mutation was identified in the PMS2 gene. However, PMS2 exons 3, 4, 13, 14, 15 were not evaluated by MLPA and as such, rearrangements involving those exons cannot be excluded. Clinical testing for MLH1 and MSH2 mutation revealed a germline deletion of MLH1 exons 14 and 15. This MLH1 germline deletion leads to an immunodetectable stable C-terminal truncated MLH1 protein which based on the IHC staining must abrogate PMS2 stabilization. To the best of our knowledge, loss of PMS2 in MLH1 truncating mutation carriers that express MLH1 in their tumors has not been previously reported. This family points to a potential limitation of IHC-directed gene testing for suspected Lynch syndrome and the need to consider comprehensive MLH1 testing for individuals whose tumors lack PMS2 but for whom PMS2 mutations are not identified.

  3. PMS2 monoallelic mutation carriers: the known unknown.

    Science.gov (United States)

    Goodenberger, McKinsey L; Thomas, Brittany C; Riegert-Johnson, Douglas; Boland, C Richard; Plon, Sharon E; Clendenning, Mark; Win, Aung Ko; Senter, Leigha; Lipkin, Steven M; Stadler, Zsofia K; Macrae, Finlay A; Lynch, Henry T; Weitzel, Jeffrey N; de la Chapelle, Albert; Syngal, Sapna; Lynch, Patrick; Parry, Susan; Jenkins, Mark A; Gallinger, Steven; Holter, Spring; Aronson, Melyssa; Newcomb, Polly A; Burnett, Terrilea; Le Marchand, Loïc; Pichurin, Pavel; Hampel, Heather; Terdiman, Jonathan P; Lu, Karen H; Thibodeau, Stephen; Lindor, Noralane M

    2016-01-01

    Germ-line mutations in MLH1, MSH2, MSH6, and PMS2 have been shown to cause Lynch syndrome. The penetrance of the cancer and tumor spectrum has been repeatedly studied, and multiple professional societies have proposed clinical management guidelines for affected individuals. Several studies have demonstrated a reduced penetrance for monoallelic carriers of PMS2 mutations compared with the other mismatch repair (MMR) genes, but clinical management guidelines have largely proposed the same screening recommendations for all MMR gene carriers. The authors considered whether enough evidence existed to propose new screening guidelines specific to PMS2 mutation carriers with regard to age at onset and frequency of colonic screening. Published reports of PMS2 germ-line mutations were combined with unpublished cases from the authors' research registries and clinical practices, and a discussion of potential modification of cancer screening guidelines was pursued. A total of 234 monoallelic PMS2 mutation carriers from 170 families were included. Approximately 8% of those with colorectal cancer (CRC) were diagnosed before age 30, and each of these tumors presented on the left side of the colon. As it is currently unknown what causes the early onset of CRC in some families with monoallelic PMS2 germline mutations, the authors recommend against reducing cancer surveillance guidelines in families found having monoallelic PMS2 mutations in spite of the reduced penetrance.Genet Med 18 1, 13-19.

  4. Dominant mutations in S. cerevisiae PMS1 identify the Mlh1-Pms1 endonuclease active site and an exonuclease 1-independent mismatch repair pathway.

    Directory of Open Access Journals (Sweden)

    Catherine E Smith

    2013-10-01

    Full Text Available Lynch syndrome (hereditary nonpolypsis colorectal cancer or HNPCC is a common cancer predisposition syndrome. Predisposition to cancer in this syndrome results from increased accumulation of mutations due to defective mismatch repair (MMR caused by a mutation in one of the mismatch repair genes MLH1, MSH2, MSH6 or PMS2/scPMS1. To better understand the function of Mlh1-Pms1 in MMR, we used Saccharomyces cerevisiae to identify six pms1 mutations (pms1-G683E, pms1-C817R, pms1-C848S, pms1-H850R, pms1-H703A and pms1-E707A that were weakly dominant in wild-type cells, which surprisingly caused a strong MMR defect when present on low copy plasmids in an exo1Δ mutant. Molecular modeling showed these mutations caused amino acid substitutions in the metal coordination pocket of the Pms1 endonuclease active site and biochemical studies showed that they inactivated the endonuclease activity. This model of Mlh1-Pms1 suggested that the Mlh1-FERC motif contributes to the endonuclease active site. Consistent with this, the mlh1-E767stp mutation caused both MMR and endonuclease defects similar to those caused by the dominant pms1 mutations whereas mutations affecting the predicted metal coordinating residue Mlh1-C769 had no effect. These studies establish that the Mlh1-Pms1 endonuclease is required for MMR in a previously uncharacterized Exo1-independent MMR pathway.

  5. Dominant mutations in S. cerevisiae PMS1 identify the Mlh1-Pms1 endonuclease active site and an exonuclease 1-independent mismatch repair pathway.

    Science.gov (United States)

    Smith, Catherine E; Mendillo, Marc L; Bowen, Nikki; Hombauer, Hans; Campbell, Christopher S; Desai, Arshad; Putnam, Christopher D; Kolodner, Richard D

    2013-10-01

    Lynch syndrome (hereditary nonpolypsis colorectal cancer or HNPCC) is a common cancer predisposition syndrome. Predisposition to cancer in this syndrome results from increased accumulation of mutations due to defective mismatch repair (MMR) caused by a mutation in one of the mismatch repair genes MLH1, MSH2, MSH6 or PMS2/scPMS1. To better understand the function of Mlh1-Pms1 in MMR, we used Saccharomyces cerevisiae to identify six pms1 mutations (pms1-G683E, pms1-C817R, pms1-C848S, pms1-H850R, pms1-H703A and pms1-E707A) that were weakly dominant in wild-type cells, which surprisingly caused a strong MMR defect when present on low copy plasmids in an exo1Δ mutant. Molecular modeling showed these mutations caused amino acid substitutions in the metal coordination pocket of the Pms1 endonuclease active site and biochemical studies showed that they inactivated the endonuclease activity. This model of Mlh1-Pms1 suggested that the Mlh1-FERC motif contributes to the endonuclease active site. Consistent with this, the mlh1-E767stp mutation caused both MMR and endonuclease defects similar to those caused by the dominant pms1 mutations whereas mutations affecting the predicted metal coordinating residue Mlh1-C769 had no effect. These studies establish that the Mlh1-Pms1 endonuclease is required for MMR in a previously uncharacterized Exo1-independent MMR pathway.

  6. DNA mismatch repair proteins MLH1 and PMS2 can be imported to the nucleus by a classical nuclear import pathway.

    Science.gov (United States)

    de Barros, Andrea C; Takeda, Agnes A S; Dreyer, Thiago R; Velazquez-Campoy, Adrian; Kobe, Boštjan; Fontes, Marcos R M

    2018-03-01

    MLH1 and PMS2 proteins form the MutLα heterodimer, which plays a major role in DNA mismatch repair (MMR) in humans. Mutations in MMR-related proteins are associated with cancer, especially with colon cancer. The N-terminal region of MutLα comprises the N-termini of PMS2 and MLH1 and, similarly, the C-terminal region of MutLα is composed by the C-termini of PMS2 and MLH1, and the two are connected by linker region. The nuclear localization sequences (NLSs) necessary for the nuclear transport of the two proteins are found in this linker region. However, the exact NLS sequences have been controversial, with different sequences reported, particularly for MLH1. The individual components are not imported efficiently, presumably due to their C-termini masking their NLSs. In order to gain insights into the nuclear transport of these proteins, we solved the crystal structures of importin-α bound to peptides corresponding to the supposed NLSs of MLH1 and PMS2 and performed isothermal titration calorimetry to study their binding affinities. Both putative MLH1 and PMS2 NLSs can bind to importin-α as monopartite NLSs, which is in agreement with some previous studies. However, MLH1-NLS has the highest affinity measured by a natural NLS peptide, suggesting a major role of MLH1 protein in nuclear import compared to PMS2. Finally, the role of MLH1 and PMS2 in the nuclear transport of the MutLα heterodimer is discussed. Copyright © 2017 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.

  7. Lynch Syndrome Caused by Germline PMS2 Mutations

    DEFF Research Database (Denmark)

    Ten Broeke, Sanne W; Brohet, Richard M; Tops, Carli M

    2015-01-01

    PURPOSE: The clinical consequences of PMS2 germline mutations are poorly understood compared with other Lynch-associated mismatch repair gene (MMR) mutations. The aim of this European cohort study was to define the cancer risk faced by PMS2 mutation carriers. METHODS: Data were collected from 98...... PMS2 families ascertained from family cancer clinics that included a total of 2,548 family members and 377 proven mutation carriers. To adjust for potential ascertainment bias, a modified segregation analysis model was used to calculate colorectal cancer (CRC) and endometrial cancer (EC) risks....... Standardized incidence ratios (SIRs) were calculated to estimate risks for other Lynch syndrome-associated cancers. RESULTS: The cumulative risk (CR) of CRC for male mutation carriers by age 70 years was 19%. The CR among female carriers was 11% for CRC and 12% for EC. The mean age of CRC development was 52...

  8. High Power Wind Generator Designs with Less or No PMs

    DEFF Research Database (Denmark)

    Boldea, Ion; Tutelea, Lucian; Blaabjerg, Frede

    2014-01-01

    synchronous generators, by doubly-fed (wound rotor) induction and cage induction generators and by introducing new topologies with pertinent costs for high power (MW range) wind energy conversion units. The present overview attempts, based on recent grid specifications, an evaluation of commercial and novel...... considering the interaction with the PWM converter in terms of power/speed range, losses, kVA, and costs) rather than on the control issues which abound in literature, will be of use for future R&D efforts in wind energy conversion, storage and use.......The recent steep increase in high energy permanent magnet (PM) price (above 130$/kg and more) triggered already strong R&D efforts to develop wind generators with less PMs (less weight in NdFeB magnets/kW or the use of ferrite PMs) or fully without PMs. All these by optimizing existing dc excited...

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

    Energy Technology Data Exchange (ETDEWEB)

    Wagner, Kevin R.; Sitko, Michael L.; Swearingen, Jeremy R.; Champney, Elizabeth H.; Johnson, Alexa N.; Werren, Chelsea [Department of Physics, University of Cincinnati, Cincinnati, OH 45221 (United States); Grady, Carol A. [Eureka Scientific, 2452 Delmer, Suite 100, Oakland, CA 96002 (United States); Whitney, Barbara A. [Department of Astronomy, University of Wisconsin, 475 North CharterStreet, Madison, WI 53706-1582 (United States); Russell, Ray W. [The Aerospace Corporation, Los Angeles, CA 90009 (United States); Schneider, Glenn H. [Steward Observatory, 933 North Cherry Avenue, University of Arizona, Tucson, AZ 85721 (United States); Momose, Munetake [Ibaraki University, 310-0056 Ibaraki, Mito, Bunkyo, 11 (Japan); Muto, Takayuki [Kogakuin University, 1-24-2 Nishishinjuku, Shinjuku, Tokyo 163-8677 (Japan); Inoue, Akio K. [Osaka Sangyo University, College of General Education, 3-1-1 Nakagaito, Daito, Osaka 574-8530 (Japan); Lauroesch, James T.; Hornbeck, Jeremy [University of Louisville Research Foundation, Inc., 2301 South 3rd Street, Louisville, KY 40292 (United States); Brown, Alexander [Center for Astrophysics and Space Astronomy, Astrophysics Research Laboratory, 593 UCB, University of Colorado, Boulder, CO 80309-0593 (United States); Fukagawa, Misato [Department of Earth and Space Science, Graduate School of Science, Osaka University, 1-1, Machikaneyama, Toyonaka, Osaka 560-0043 (Japan); Currie, Thayne M. [Oak Ridge Associated Universities, 100 ORAU Way, Oak Ridge, TN 37830-6218 (United States); Wisniewski, John P. [University of Oklahoma, 660 Parrington Oval, Norman, OK 73019 (United States); Woodgate, Bruce E., E-mail: wagnekr@mail.uc.edu, E-mail: sitkoml@ucmail.uc.edu, E-mail: swearijr@mail.uc.edu, E-mail: ehchampney@gmail.com, E-mail: astefank@andrew.cmu.edu, E-mail: ccwerren@yahoo.com, E-mail: carol.a.grady@nasa.gov, E-mail: bwhitney@astro.wisc.edu, E-mail: Ray.W.Russell@aero.org [NASA Goddard Space Flight Center, 8800 Greenbelt Road, Greenbelt, MD 20771 (United States)

    2015-01-10

    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 Br 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.

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

    International Nuclear Information System (INIS)

    Gómez Maqueo Chew, Yilen; Stassun, Keivan G.; Hebb, Leslie; Prša, Andrej; Stempels, Eric; Barnes, Rory; Heller, René; Mathieu, Robert D.

    2012-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2012-01-20

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

  12. 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

    Science.gov (United States)

    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.; hide

    2011-01-01

    We present thirteen epochs of near-infrared (0.8-5 microns) 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(delta), Pa(epsilon), and the 0.8446 microns line of O I) along with continuum measurements made near the standard J, H, K, and L photometric bands were measured. A mass accretion rate of approximately 2 x 10(exp 8)Solar Mass/yr was derived from the Br(gamma) and Pa(beta) lines. However, the fluxes of these lines varied by a factor of over two during the course of a few months. The continuum also varied, but by only approx.30%, and even decreased at a time when the gas emission was increasing. The H I line at 1.083 microns was also found to vary in a manner inconsistent with that of either the hydrogen lines or the dust. Both the gas and dust variabilities indicate significant changes in the region of the inner gas and the inner dust belt that may be common to many young disk systems. If planets are responsible for defining the inner edge of the gap, they could interact with the material on time scales commensurate with what is observed for the variations in the dust, while other disk instabilities (thermal, magneto-rotational) would operate there on longer time scales 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 time scales 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 time scales that have been sampled so far.

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

    Science.gov (United States)

    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.

  14. A CENSUS OF ROTATION AND VARIABILITY IN L1495: A UNIFORM ANALYSIS OF TRANS-ATLANTIC EXOPLANET SURVEY LIGHT CURVES FOR PRE-MAIN-SEQUENCE STARS IN TAURUS

    International Nuclear Information System (INIS)

    Xiao Hongyu; Covey, Kevin R.; Lloyd, James P.; Rebull, Luisa; Charbonneau, David; Mandushev, Georgi; O'Donovan, Francis; Slesnick, Catherine

    2012-01-01

    We analyze light curves obtained by the Trans-atlantic Exoplanet Survey (TrES) for a field centered on the L1495 dark cloud in Taurus. The Spitzer Taurus Legacy Survey catalog identifies 179 bona fide Taurus members within the TrES field; 48 of the known Taurus members are detected by TrES, as well as 26 candidate members identified by the Spitzer Legacy team. We quantify the variability of each star in our sample using the ratio of the standard deviation of the original light curve (σ orig. ) to the standard deviation of a light curve that has been smoothed by 9 or 1001 epochs (σ 9 and σ 1001 , respectively). Known Taurus members typically demonstrate (σ orig. /σ 9 ) orig. /σ 1001 ) orig. /σ 9 ) ∼ 3.0 and (σ orig. /σ 1001 ) ∼ 10, as expected for light curves dominated by unstructured white noise. Of the 74 Taurus members/candidates with TrES light curves, we detect significant variability in 49 sources. Adapting a quantitative metric originally developed to assess the reliability of transit detections, we measure the amount of red and white noise in each light curve and identify 18 known or candidate Taurus members with highly significant period measurements. These appear to be the first periods measured for four of these sources (HD 282276, CX Tau, FP Tau, TrES J042423+265008), and in two other cases, the first non-aliased periods (LkCa 21 and DK Tau AB). For the remainder, the TrES measurements typically agree very well (δP < 1%) with previously reported values. Including periods measured at lower confidence for 15 additional sources, we report periods for 11 objects where no previous periods were found, including 8 confirmed Taurus members. We also identify 10 of the 26 candidate Taurus members that demonstrate variability levels consistent with being bona fide T Tauri stars. A Kolomgorov-Smirnov (K-S) test confirms that these new periods confirm the distinction between the rotation period distributions of stars with and without circumstellar disks, with only a 10% probability of the two populations sharing the same parent period distribution. K-S tests do suggest, however, that the updated Taurus period distribution now more closely resembles those measured in other young star-forming clusters (i.e., NGC 2264, NGC 6530, and the ONC). This improved agreement may reflect the exclusion of long rotation periods which are detected in Taurus at lower significance, and which may be beyond the limits of detectability in more distant star-forming regions.

  15. IN-SYNC. II. VIRIAL STARS FROM SUBVIRIAL CORES—THE VELOCITY DISPERSION OF EMBEDDED PRE-MAIN-SEQUENCE STARS IN NGC 1333

    International Nuclear Information System (INIS)

    Foster, Jonathan B.; Cottaar, Michiel; Meyer, Michael R.; Covey, Kevin R.; Arce, Héctor G.; Nidever, David L.; Stassun, Keivan G.; Tan, Jonathan C.; Da Rio, Nicola; Chojnowski, S. Drew; Majewski, Steven R.; Skrutskie, Michael; Wilson, John C.; Flaherty, Kevin M.; Rebull, Luisa; Frinchaboy, Peter M.; Zasowski, Gail

    2015-01-01

    The initial velocity dispersion of newborn stars is a major unconstrained aspect of star formation theory. Using near-infrared spectra obtained with the APOGEE spectrograph, we show that the velocity dispersion of young (1-2 Myr) stars in NGC 1333 is 0.92 ± 0.12 km s –1 after correcting for measurement uncertainties and the effect of binaries. This velocity dispersion is consistent with the virial velocity of the region and the diffuse gas velocity dispersion, but significantly larger than the velocity dispersion of the dense, star-forming cores, which have a subvirial velocity dispersion of 0.5 km s –1 . Since the NGC 1333 cluster is dynamically young and deeply embedded, this measurement provides a strong constraint on the initial velocity dispersion of newly formed stars. We propose that the difference in velocity dispersion between stars and dense cores may be due to the influence of a 70 μG magnetic field acting on the dense cores or be the signature of a cluster with initial substructure undergoing global collapse

  16. IN-SYNC I: Homogeneous stellar parameters from high-resolution apogee spectra for thousands of pre-main sequence stars

    International Nuclear Information System (INIS)

    Cottaar, Michiel; Meyer, Michael R.; Covey, Kevin R.; Nidever, David L.; Stassun, Keivan G.; Foster, Jonathan B.; Tan, Jonathan C.; Da Rio, Nicola; Chojnowski, S. Drew; Skrutskie, Michael; Majewski, Steven R.; Wilson, John C.; Zasowski, Gail; Flaherty, Kevin M.; Frinchaboy, Peter M.

    2014-01-01

    Over two years, 8859 high-resolution H-band spectra of 3493 young (1-10 Myr) stars were gathered by the multi-object spectrograph of the APOGEE project as part of the IN-SYNC ancillary program of the SDSS-III survey. Here we present the forward modeling approach used to derive effective temperatures, surface gravities, radial velocities, rotational velocities, and H-band veiling from these near-infrared spectra. We discuss in detail the statistical and systematic uncertainties in these stellar parameters. In addition, we present accurate extinctions by measuring the E(J – H) of these young stars with respect to the single-star photometric locus in the Pleiades. Finally, we identify an intrinsic stellar radius spread of about 25% for late-type stars in IC 348 using three (nearly) independent measures of stellar radius, namely, the extinction-corrected J-band magnitude, the surface gravity, and the Rsin i from the rotational velocities and literature rotation periods. We exclude that this spread is caused by uncertainties in the stellar parameters by showing that the three estimators of stellar radius are correlated, so that brighter stars tend to have lower surface gravities and larger Rsin i than fainter stars at the same effective temperature. Tables providing the spectral and photometric parameters for the Pleiades and IC 348 have been provided online.

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

    International Nuclear Information System (INIS)

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

    2015-01-01

    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 Br γ lines in our data we derive a mass accretion rate in 2013 May of M-dot ≈ (1.5-2.7) × 10 –9 M ☉ yr –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

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

    International Nuclear Information System (INIS)

    Henderson, Calen B.; Stassun, Keivan G.

    2012-01-01

    We have conducted a long-term, wide-field, high-cadence photometric monitoring survey of ∼50,000 stars in the Lagoon Nebula H II region. This first paper presents rotation periods for 290 low-mass stars in NGC 6530, the young cluster illuminating the nebula, and for which we assemble a catalog of infrared and spectroscopic disk indicators, estimated masses and ages, and X-ray luminosities. The distribution of rotation periods we measure is broadly uniform for 0.5 days X /L bol ≈ –3.3). However, we find a significant positive correlation between L X /L bol and corotation radius, suggesting that the observed X-ray luminosities are regulated by centrifugal stripping of the stellar coronae. The period-mass relationship in NGC 6530 is broadly similar to that of the Orion Nebula Cluster (ONC), but the slope of the relationship among the slowest rotators differs from that in the ONC and other young clusters. We show that the slope of the period-mass relationship for the slowest rotators can be used as a proxy for the age of a young cluster, and we argue that NGC 6530 may be slightly younger than the ONC, making it a particularly important touchstone for models of angular momentum evolution in young, low-mass stars.

  19. Recurrent and founder mutations in the PMS2 gene.

    Science.gov (United States)

    Tomsic, J; Senter, L; Liyanarachchi, S; Clendenning, M; Vaughn, C P; Jenkins, M A; Hopper, J L; Young, J; Samowitz, W; de la Chapelle, A

    2013-03-01

    Germline mutations in PMS2 are associated with Lynch syndrome (LS), the most common known cause of hereditary colorectal cancer. Mutation detection in PMS2 has been difficult due to the presence of several pseudogenes, but a custom-designed long-range PCR strategy now allows adequate mutation detection. Many mutations are unique. However, some mutations are observed repeatedly across individuals not known to be related due to the mutation being either recurrent, arising multiple times de novo at hot spots for mutations, or of founder origin, having occurred once in an ancestor. Previously, we observed 36 distinct mutations in a sample of 61 independently ascertained Caucasian probands of mixed European background with PMS2 mutations. Eleven of these mutations were detected in more than one individual not known to be related and of these, six were detected more than twice. These six mutations accounted for 31 (51%) ostensibly unrelated probands. Here, we performed genotyping and haplotype analysis in four mutations observed in multiple probands and found two (c.137G>T and exon 10 deletion) to be founder mutations and one (c.903G>T) a probable founder. One (c.1A>G) could not be evaluated for founder mutation status. We discuss possible explanations for the frequent occurrence of founder mutations in PMS2. © 2012 John Wiley & Sons A/S.

  20. LADOTD pavement management system (PMS) for project level applications.

    Science.gov (United States)

    2011-06-01

    To fully address the research needs described in the problem statement, the primary objective of this project is to develop guidelines that provide information on how network level PMS data can be used at a project level in activities of pavement eng...

  1. PMS2 gene mutation results in DNA mismatch repair system failure in a case of adult granulosa cell tumor.

    Science.gov (United States)

    Wang, Wen-Chung; Lee, Ya-Ting; Lai, Yen-Chein

    2017-03-27

    Granulosa cell tumors are rare ovarian malignancies. Their characteristics include unpredictable indolent growth with malignant potential and late recurrence. Approximately 95% are of adult type. Recent molecular studies have characterized the FOXL2 402C > G mutation in adult granulosa cell tumor. Our previous case report showed that unique FOXL2 402C > G mutation and defective DNA mismatch repair system are associated with the development of adult granulosa cell tumor. In this study, the DNA sequences of four genes, MSH2, MLH1, MSH6, and PMS2, in the DNA mismatch repair system were determined via direct sequencing to elucidate the exact mechanism for the development of this granulosa cell tumor. The results showed that two missense germline mutations, T485K and N775L, inactivate the PMS2 gene. The results of this case study indicated that although FOXL2 402C > G mutation determines the development of granulosa cell tumor, PMS2 mutation may be the initial driver of carcinogenesis. Immunohistochemistry-based tumor testing for mismatch repair gene expression may be necessary for granulosa cell tumors to determine their malignant potential or if they are part of Lynch syndrome.

  2. Lynch Syndrome Caused by Germline PMS2 Mutations: Delineating the Cancer Risk

    NARCIS (Netherlands)

    ten Broeke, Sanne W.; Brohet, Richard M.; Tops, Carli M.; van der Klift, Heleen M.; Velthuizen, Mary E.; Bernstein, Inge; Capellá Munar, Gabriel; Gomez Garcia, Encarna; Hoogerbrugge, Nicoline; Letteboer, Tom G. W.; Menko, Fred H.; Lindblom, Annika; Mensenkamp, Arjen R.; Moller, Pal; van Os, Theo A.; Rahner, Nils; Redeker, Bert J. W.; Sijmons, Rolf H.; Spruijt, Liesbeth; Suerink, Manon; Vos, Yvonne J.; Wagner, Anja; Hes, Frederik J.; Vasen, Hans F.; Nielsen, Maartje; Wijnen, Juul T.

    2015-01-01

    Purpose The clinical consequences of PMS2 germline mutations are poorly understood compared with other Lynch-associated mismatch repair gene (MMR) mutations. The aim of this European cohort study was to define the cancer risk faced by PMS2 mutation carriers. Methods Data were collected from 98 PMS2

  3. Lynch Syndrome Caused by Germline PMS2 Mutations : Delineating the Cancer Risk

    NARCIS (Netherlands)

    ten Broeke, Sanne W.; Brohet, Richard M.; Tops, Carli M.; van der Klift, Heleen M.; Velthuizen, Mary E.; Bernstein, Inge; Capella Munar, Gabriel; Garcia, Encarna Gomez; Hoogerbrugge, Nicoline; Letteboer, Tom G. W.; Menko, Fred H.; Lindblom, Annika; Mensenkamp, Arjen R.; Moller, Pal; Van Os, Theo A.; Rahner, Nils; Redeker, Bert J. W.; Sijmons, Rolf H.; Spruijt, Liesbeth; Suerink, Manon; Vos, Yvonne J.; Wagner, Anja; Hes, Frederik J.; Vasen, Hans F.; Nielsen, Maartje; Wijnen, Juul T.

    2015-01-01

    Purpose The clinical consequences of PMS2 germline mutations are poorly understood compared with other Lynch-associated mismatch repair gene (MMR) mutations. The aim of this European cohort study was to define the cancer risk faced by PMS2 mutation carriers. Methods Data were collected from 98 PMS2

  4. Imaging with SiPMs in noble-gas detectors

    International Nuclear Information System (INIS)

    Yahlali, N; González, K; Fernandes, L M P; Garcia, A N C; Soriano, A

    2013-01-01

    Silicon photomultipliers (SiPMs) are photosensors widely used for imaging in a variety of high energy and nuclear physics experiments. In noble-gas detectors for double-beta decay and dark matter experiments, SiPMs are attractive photosensors for imaging. However they are insensitive to the VUV scintillation emitted by the noble gases (xenon and argon). This difficulty is overcome in the NEXT experiment by coating the SiPMs with tetraphenyl butadiene (TPB) to convert the VUV light into visible light. TPB requires stringent storage and operational conditions to prevent its degradation by environmental agents. The development of UV sensitive SiPMs is thus of utmost interest for experiments using electroluminescence of noble-gas detectors. It is in particular an important issue for a robust and background free ββ0ν experiment with xenon gas aimed by NEXT. The photon detection efficiency (PDE) of UV-enhanced SiPMs provided by Hamamatsu was determined for light in the range 250–500 nm. The PDE of standard SiPMs of the same model (S10362-33-50C), coated and non-coated with TPB, was also determined for comparison. In the UV range 250–350 nm, the PDE of the standard SiPM is shown to decrease strongly, down to about 3%. The UV-enhanced SiPM without window is shown to have the maximum PDE of 44% at 325 nm and 30% at 250 nm. The PDE of the UV-enhanced SiPM with silicon resin window has a similar trend in the UV range, although it is about 30% lower. The TPB-coated SiPM has shown to have about 6 times higher PDE than the non-coated SiPM in the range 250–315 nm. This is however below the performance of the UV-enhanced prototypes in the same wavelength range. Imaging in noble-gas detectors using UV-enhanced SiPMs is discussed.

  5. A Fe(II)/citrate/UV/PMS process for carbamazepine degradation at a very low Fe(II)/PMS ratio and neutral pH: The mechanisms.

    Science.gov (United States)

    Ling, Li; Zhang, Dapeng; Fan, Chihhao; Shang, Chii

    2017-11-01

    A novel Fe(II)/citrate/UV/PMS process for degrading a model micropollutant, carbamazepine (CBZ), at a low Fe(II)/PMS ratio and neutral pH has been proposed in this study, and the mechanisms of radical generation in the system was explored. With a UV dose of 302.4 mJ/cm 2 , an initial pH of 7, and CBZ, PMS, Fe(II) and citrate at initial concentrations of 10, 100, 12 and 26 μM, respectively, the CBZ degradation efficiency reached 71% in 20 min in the Fe(II)/citrate/UV/PMS process, which was 4.7 times higher than that in either the citrate/UV/PMS or Fe(II)/citrate/PMS process. The enhanced CBZ degradation in the Fe(II)/citrate/UV/PMS process was mainly attributed to the continuous activation of PMS by the UV-catalyzed regenerated Fe(II) from a Fe(III)-citrate complex, [Fe 3 O(cit) 3 H 3 ] 2- , which not only maintained Fe(III) soluble at neutral pH, but also increased 6.6 and 2.6 times of its molar absorbance and quantum yield as compared to those of ionic Fe(III), respectively. In the Fe(II)/citrate/UV/PMS process, the SO 4 •- produced from the fast reaction between PMS and the initially-added Fe(II) contributed 11% of CBZ degradation. The PMS activation by the UV radiation and regenerated Fe(II) contributed additional 14% and 46% of CBZ removal, respectively. The low iron and citrate doses and the fast radical generation at neutral pH make the Fe(II)/citrate/UV/PMS process suitable for degrading recalcitrant organic compounds in potable water. Copyright © 2017 Elsevier Ltd. All rights reserved.

  6. PMS2 endonuclease activity has distinct biological functions and is essential for genome maintenance.

    Science.gov (United States)

    van Oers, Johanna M M; Roa, Sergio; Werling, Uwe; Liu, Yiyong; Genschel, Jochen; Hou, Harry; Sellers, Rani S; Modrich, Paul; Scharff, Matthew D; Edelmann, Winfried

    2010-07-27

    The DNA mismatch repair protein PMS2 was recently found to encode a novel endonuclease activity. To determine the biological functions of this activity in mammals, we generated endonuclease-deficient Pms2E702K knock-in mice. Pms2EK/EK mice displayed increased genomic mutation rates and a strong cancer predisposition. In addition, class switch recombination, but not somatic hypermutation, was impaired in Pms2EK/EK B cells, indicating a specific role in Ig diversity. In contrast to Pms2-/- mice, Pms2EK/EK male mice were fertile, indicating that this activity is dispensable in spermatogenesis. Therefore, the PMS2 endonuclease activity has distinct biological functions and is essential for genome maintenance and tumor suppression.

  7. An intact Pms2 ATPase domain is not essential for male fertility.

    Science.gov (United States)

    Fischer, Jared M; Dudley, Sandra; Miller, Ashleigh J; Liskay, R Michael

    2016-03-01

    The DNA mismatch repair (MMR) machinery in mammals plays critical roles in both mutation avoidance and spermatogenesis. Meiotic analysis of knockout mice of two different MMR genes, Mlh1 and Mlh3, revealed both male and female infertility associated with a defect in meiotic crossing over. In contrast, another MMR gene knockout, Pms2 (Pms2(ko/ko)), which contained a deletion of a portion of the ATPase domain, produced animals that were male sterile but female fertile. However, the meiotic phenotype of Pms2(ko/ko) males was less clear-cut than for Mlh1- or Mlh3-deficient meiosis. More recently, we generated a different Pms2 mutant allele (Pms2(cre)), which results in deletion of the same portion of the ATPase domain. Surprisingly, Pms2(cre/cre) male mice were completely fertile, suggesting that the ATPase domain of Pms2 is not required for male fertility. To explore the difference in male fertility, we examined the Pms2 RNA and found that alternative splicing of the Pms2(cre) allele results in a predicted Pms2 containing the C-terminus, which contains the Mlh1-interaction domain, a possible candidate for stabilizing Mlh1 levels. To study further the basis of male fertility, we examined Mlh1 levels in testes and found that whereas Pms2 loss in Pms2(ko/ko) mice results in severely reduced levels of Mlh1 expression in the testes, Mlh1 levels in Pms2(cre/cre) testes were reduced to a lesser extent. Thus, we propose that a primary function of Pms2 during spermatogenesis is to stabilize Mlh1 levels prior to its critical crossing over function with Mlh3. Copyright © 2015 Elsevier B.V. All rights reserved.

  8. SNP association study in PMS2-associated Lynch syndrome.

    Science.gov (United States)

    Ten Broeke, Sanne W; Elsayed, Fadwa A; Pagan, Lisa; Olderode-Berends, Maran J W; Garcia, Encarna Gomez; Gille, Hans J P; van Hest, Liselot P; Letteboer, Tom G W; van der Kolk, Lizet E; Mensenkamp, Arjen R; van Os, Theo A; Spruijt, Liesbeth; Redeker, Bert J W; Suerink, Manon; Vos, Yvonne J; Wagner, Anja; Wijnen, Juul T; Steyerberg, E W; Tops, Carli M J; van Wezel, Tom; Nielsen, Maartje

    2017-11-17

    Lynch syndrome (LS) patients are at high risk of developing colorectal cancer (CRC). Phenotypic variability might in part be explained by common susceptibility loci identified in Genome Wide Association Studies (GWAS). Previous studies focused mostly on MLH1, MSH2 and MSH6 carriers, with conflicting results. We aimed to determine the role of GWAS SNPs in PMS2 mutation carriers. A cohort study was performed in 507 PMS2 carriers (124 CRC cases), genotyped for 24 GWAS SNPs, including SNPs at 11q23.1 and 8q23.3. Hazard ratios (HRs) were calculated using a weighted Cox regression analysis to correct for ascertainment bias. Discrimination was assessed with a concordance statistic in a bootstrap cross-validation procedure. Individual SNPs only had non-significant associations with CRC occurrence with HRs lower than 2, although male carriers of allele A at rs1321311 (6p21.31) may have increased risk of CRC (HR = 2.1, 95% CI 1.2-3.0). A polygenic risk score (PRS) based on 24 HRs had an HR of 2.6 (95% CI 1.5-4.6) for the highest compared to the lowest quartile, but had no discriminative ability (c statistic 0.52). Previously suggested SNPs do not modify CRC risk in PMS2 carriers. Future large studies are needed for improved risk stratification among Lynch syndrome patients.

  9. Clinical analysis of PMS2: mutation detection and avoidance of pseudogenes.

    Science.gov (United States)

    Vaughn, Cecily P; Robles, Jorge; Swensen, Jeffrey J; Miller, Christine E; Lyon, Elaine; Mao, Rong; Bayrak-Toydemir, Pinar; Samowitz, Wade S

    2010-05-01

    Germline mutation detection in PMS2, one of four mismatch repair genes associated with Lynch syndrome, is greatly complicated by the presence of numerous pseudogenes. We used a modification of a long-range PCR method to evaluate PMS2 in 145 clinical samples. This modification avoids potential interference from the pseudogene PMS2CL by utilizing a long-range product spanning exons 11-15, with the forward primer anchored in exon 10, an exon not shared by PMS2CL. Large deletions were identified by MLPA. Pathogenic PMS2 mutations were identified in 22 of 59 patients whose tumors showed isolated loss of PMS2 by immunohistochemistry (IHC), the IHC profile most commonly associated with a germline PMS2 mutation. Three additional patients with pathogenic mutations were identified from 53 samples without IHC data. Thirty-seven percent of the identified mutations were large deletions encompassing one or more exons. In 27 patients whose tumors showed absence of either another protein or combination of proteins, no pathogenic mutations were identified. We conclude that modified long-range PCR can be used to preferentially amplify the PMS2 gene and avoid pseudogene interference, thus providing a clinically useful germline analysis of PMS2. Our data also support the use of IHC screening to direct germline testing of PMS2. (c) 2010 Wiley-Liss, Inc.

  10. Phosphorylation-dependent signaling controls degradation of DNA mismatch repair protein PMS2.

    Science.gov (United States)

    Hinrichsen, Inga; Weßbecher, Isabel M; Huhn, Meik; Passmann, Sandra; Zeuzem, Stefan; Plotz, Guido; Biondi, Ricardo M; Brieger, Angela

    2017-12-01

    MutLα, a heterodimer consisting of MLH1 and PMS2, plays an important role in DNA mismatch repair and has been shown to be additionally involved in several other important cellular mechanisms. Previous work indicated that AKT could modulate PMS2 stability by phosphorylation. Still, the mechanisms of regulation of MutLα remain unclear. The stability of MutLα subunits was investigated by transiently overexpression of wild type and mutant forms of MLH1 and PMS2 using immunoblotting for measuring the protein levels after treatment. We found that treatment with the cell-permeable serine/threonine phosphatase inhibitor, Calyculin, leads to degradation of PMS2 when MLH1 or its C-terminal domain is missing or if amino acids of MLH1 essential for PMS2 interaction are mutated. In addition, we discovered that the C-terminal tail of PMS2 is relevant for this Calyculin-dependent degradation. A direct involvement of AKT, which was previously described to be responsible for PMS2 degradation, could not be detected. The multi-kinase inhibitor Sorafenib, in contrast, was able to avoid the degradation of PMS2 which postulates that cellular phosphorylation is involved in this process. Together, we show that pharmacologically induced phosphorylation by Calyculin can induce the selective proteasome-dependent degradation of PMS2 but not of MLH1 and that the PMS2 degradation could be blocked by Sorafenib treatment. Curiously, the C-terminal Lynch Syndrome-variants MLH1 L749P and MLH1 Y750X make PMS2 prone to Calyculin induced degradation. Therefore, we conclude that the specific degradation of PMS2 may represent a new mechanism to regulate MutLα. © 2017 Wiley Periodicals, Inc.

  11. Meiotic gene conversion mutants in Saccharomyces cerevisiae. I. Isolation and characterization of PMS1-1 and PMS1-2

    International Nuclear Information System (INIS)

    Williamson, M.S.; Game, J.C.; Fogel, S.

    1985-01-01

    The PMS1 mutants, isolated on the basis of sharply elevated meiotic prototroph frequencies for two closely linked HIS4 alleles, display pleiotropic phenotypes in meiotic and mitotic cells. Two isolates carrying recessive mutations in PMS1 were characterized. They identify a function required to maintain low postmeiotic segregation (PMS) frequencies at many heterozygous sites. In addition, they are mitotic mutators. In mutant diploids, spore viability is reduced, and among survivors, gene conversion and postmeiotic segregation frequencies are increased, but reciprocal exchange frequencies are not affected. The conversion event pattern is also dramatically changed in multiply marked regions in PMS1 homozygotes. The PMS1 locus maps near MET4 on chromosome XIV. The PMS1 gene may identify an excision-resynthesis long patch mismatch correction function or a function that facilitates correction tract elongation. The PMS1 gene product may also play an important role in spontaneous mitotic mutation avoidance and correction of mismatches in heteroduplex DNA formed during spontaneous and UV-induced mitotic recombination. Based on meiotic recombination models emphasizing mismatch correction in heteroduplex DNA intermediates, this interpretation is favored, but alternative interpretations involving longer recombination intermediates in the mutants are also considered

  12. A case of early onset rectal cancer of Lynch syndrome with a novel deleterious PMS2 mutation.

    Science.gov (United States)

    Nomura, Sachio; Fujimoto, Yoshiya; Yamamoto, Noriko; Sato, Yuri; Ashihara, Yuumi; Kita, Mizuho; Yamaguchi, Junya; Ishikawa, Yuichi; Ueno, Masashi; Arai, Masami

    2015-10-01

    Heterozygous deleterious mutation of the PMS2 gene is a cause of Lynch syndrome, an autosomal dominant cancer disease. However, the frequency of PMS2 mutation is rare compared with that of the other causative genes; MSH2, MLH1 and MSH6. PMS2 mutation has so far only been reported once from a Japanese facility. Detection of PMS2 mutation is relatively complicated due to the existence of 15 highly homologous pseudogenes, and its gene conversion event with the pseudogene PMS2CL. Therefore, for PMS2 mutation analysis, it is crucial to clearly distinguish PMS2 from its pseudogenes. We report here a novel deleterious 11 bp deletion mutation of exon 11 of PMS2 distinguished from PMS2CL in a 34-year-old Japanese female with rectal cancer. PMS2 mutated at c.1492del11 results in a truncated 500 amino acid protein rather than the wild-type protein of 862 amino acids. This is supported by the fact that, although there is usually concordance between MLH1 and PMS2 expression, cells were immunohistochemically positive for MLH1, whereas PMS2 could not be immunohistochemically stained using an anti-C-terminal PMS2 antibody, or effective PMS2 mRNA degradation with NMD caused by the frameshift mutation. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  13. Army Personnel Management System Study (PMS2). Volume I. Main Report.

    Science.gov (United States)

    1979-11-06

    demonstrated desirability, some functions would be facilitated, costs need further study, and mobilization capabilities should be emphasized. PMS2 is basis for current reorganization planning within ODCSPER.

  14. Lynch syndrome caused by germline PMS2 mutations: delineating the cancer risk

    NARCIS (Netherlands)

    Broeke, S.W. ten; Brohet, R.M.; Tops, C.M.; Klift, H.M. van der; Velthuizen, M.E.; Bernstein, I.; Capella Munar, G.; Garcia, E.; Hoogerbrugge, N.; Letteboer, T.G.; Menko, F.H.; Lindblom, A.; Mensenkamp, A.R.; Moller, P.; Os, T.A. van; Rahner, N.; Redeker, B.J.; Sijmons, R.H.; Spruijt, L.; Suerink, M.; Vos, Y.J.; Wagner, A.; Hes, F.J.; Vasen, H.F.A.; Nielsen, M.; Wijnen, J.T.

    2015-01-01

    PURPOSE: The clinical consequences of PMS2 germline mutations are poorly understood compared with other Lynch-associated mismatch repair gene (MMR) mutations. The aim of this European cohort study was to define the cancer risk faced by PMS2 mutation carriers. METHODS: Data were collected from 98

  15. Parameters of the preproduction series SiPMs for the CMS HCAL phase I upgrade

    Energy Technology Data Exchange (ETDEWEB)

    Heering, A., E-mail: Adriaan.Heering@cern.ch [University of Notre Dame, Notre Dame, IN 46556 (United States); Musienko, Yu., E-mail: Iouri.Musienko@cern.ch [University of Notre Dame, Notre Dame, IN 46556 (United States); Institute for Nuclear Research RAS, pr. 60-letiya Oktyabrya 7a, 117312 Moscow (Russian Federation); Ruchti, R.; Wayne, M. [University of Notre Dame, Notre Dame, IN 46556 (United States); Karneyeu, A.; Postoev, V. [Institute for Nuclear Research RAS, pr. 60-letiya Oktyabrya 7a, 117312 Moscow (Russian Federation)

    2016-07-11

    In 2012 the HCAL SiPM photo sensor upgrade was approved for the increased luminosity (5*10{sup 34}) of SLHC. The upgrade will replace the current hybrid photodiodes (HPDs) with multi-pixel Geiger-mode avalanche photodiodes, also known as silicon photomultipliers (SiPMs). A key aspect of the upgrade to SiPMs is to add longitudinal segmentation and improve signal to noise to compensate for scintillator radiation damage. After 5 years of R&D with multiple companies we developed custom large dynamic range SiPMs with large PDE and small ENC. To ensure good mechanical alignment and easy handling of the large number of production channels (>20,000) we have developed a custom ceramic package with a very thin 0.3 mm quartz window with Kyocera. Each package holds 8 channels of SiPMs. Here we report on the final SiPM parameters of the 2014 preproduction run from Hamamatsu (HPK) who has produced a series of 175 arrays with a total of 1400 SiPMs. An overview of our QA results and measurements of the photon detection efficiency, spectral response, crosstalk and cell recovery time will be discussed. - Highlights: • Uniformity of large scale SiPM production. • Small cell size SiPMs with high photo detection efficiency. • Fast recovery time SiPMs. • Custom packaging of SiPMs in High Energy Physics experiments.

  16. 23 CFR 973.208 - Indian lands pavement management system (PMS).

    Science.gov (United States)

    2010-04-01

    ... 23 Highways 1 2010-04-01 2010-04-01 false Indian lands pavement management system (PMS). 973.208... PROGRAM Bureau of Indian Affairs Management Systems § 973.208 Indian lands pavement management system (PMS... concepts described in the AASHTO's “Pavement Management Guide.” 1 1 “Pavement Management Guide,” AASHTO...

  17. One More Look at PMS: Implications for Women of a New Focus on an Old Problem.

    Science.gov (United States)

    Ames, Natalie

    1988-01-01

    This article surveys research and opinion on Premenstrual Syndrome (PMS), its causes, symptoms, and treatment and the implications of each for women. Researchers and medical service providers are urged to consider all factors--physical, social, and emotional--which play a role in causing PMS before diagnosing and treating the disorder. (JL)

  18. 23 CFR 972.208 - Federal lands pavement management system (PMS).

    Science.gov (United States)

    2010-04-01

    ..., as a basic framework for a PMS: (1) A database and an ongoing program for the collection and maintenance of the inventory, inspection, cost, and supplemental data needed to support the PMS. The minimum... life (performance and remaining service life to be developed with time); and (iii) An investment...

  19. 23 CFR 970.208 - Federal lands pavement management system (PMS).

    Science.gov (United States)

    2010-04-01

    ... goals, policies, criteria, and needs using the following components, at a minimum, as a basic framework..., inspection, cost, and supplemental data needed to support the PMS. The minimum PMS database shall include: (i... life (performance and remaining service life to be developed with time); and (iii) An investment...

  20. [Inactivation of PMS2 gene by promoter methylation in nasopharyngeal carcinoma].

    Science.gov (United States)

    Ni, H F; Jiang, B; Zhou, Z; Li, Y; Yuan, X Y; Cao, X L; Huang, G W

    2016-11-23

    Objective: To investigate the inactivation of PMS2 gene mediated by promoter methylation and its regulatory mechanism in nasopharyngeal carcinoma (NPC). Methods: Fifty-four NPC tissues, 16 normal nasopharyngeal epithelia (NNE), 5 NPC cell lines (CNE1, CNE2, TWO3, HNE1 and HONE1) and 1 normal nasopharyngeal epithelial cell line (NP69) were collected.Methylation-specific PCR (MSP) was used to detect the PMS2 promoter methylation, semi-quantitative reverse transcription PCR (qRT-PCR) was applied to determine its mRNA expression, and immunohistochemistry (IHC) was used to detect the protein expression of PMS2. The expressions of PMS2 mRNA in CNE1 and CNE2 cells before and after treated with methyltransferase inhibitor 5-aza-2-deoxycytidine were analyzed by qRT-PCR. The impact of methylation and demethylation on the mRNA expression of PMS2, and the association of mRNA and protein expression of PMS2 with clinicopathological features of nasopharyngeal cancer were analyzed. Results: Methylation of PMS2 gene was detected in all of the five NPC cell lines, but not in normal nasopharyngeal epithelial NP69 cells. The methylation rate of PMS2 gene in NPC tissues was 63% (34/54), significantly higher than that of the normal nasopharyngeal epithelia (0/16, P PMS2 mRNA and protein were significantly down-regulated in the 54 NPC tissues when compared with those in the 16 NNE tissues ( P PMS2 mRNA was restored in the CNE1 and CNE2 cells.However, the expressions of PMS2 mRNA and protein were not significantly correlated with patients' age, gender, TNM stage, histopathologic type or lymph node metastasis ( P >0.05 for all). Conclusions: Promoter methylation-mediated inactivation of PMS2 gene participates in carcinogenesis and development of NPC. PMS2 may be a candidate tumor suppressor in the treatment for patients with inactivation of PMS2 promoter methylation.

  1. Effects of compositions and Nb-doping on microstructure and piezoelectric properties of PMS-PZ-PT system

    Energy Technology Data Exchange (ETDEWEB)

    Jiwen, Long; Haiyan, Chen; Zhongyan, Meng

    2003-05-25

    Sr-substituted (2 mol%) xPMS-(1-x)(PZ-PT) compositions were investigated systematically as a function of PMS concentrations as well as Niobium (Nb) contents. X-ray diffraction (XRD) patterns show that phases shift from tetragonal phase to rhombohedral phase with the increase of PMS concentrations and with the increase of Nb-doping contents in PMS2. The compositions with x=0.05 (PMS2) was found to have superior piezoelectric properties. The properties of the PMS2 compositions were optimized by the Nb-doping contents of 0.1 mol% (d{sub 33}=450 pC N{sup -1}, K{sub p}=0.65, Q{sub m}=1210). The compositions of PMS2 and 0.1 mol% Nb-doped compositions of PMS2 are practically suitable for ultrasonic motor (USM) applications.

  2. Artefactual punctate MLH1 staining can lead to erroneous reporting of isolated PMS2 loss.

    Science.gov (United States)

    Niu, Bonnie T; Hammond, Rory F L; Leen, Sarah L S; Faruqi, Asma Z; Trevisan, Giorgia; Gilks, C Blake; Singh, Naveena

    2018-05-31

    Germline mutations in the PMS2 gene are an uncommon cause of Lynch Syndrome (LS), present in PMS2 immunohistochemical expression, with retained MLH1 expression, triggers referral to genetics services due to the significant risk of LS 3 . As detection of PMS2 germline mutations is problematic 4 , this may result in patients being labeled as "Lynch-like", with implications for future surveillance 5 . A recent study suggested that some cases of isolated PMS2 loss result from MLH1 promoter methylation and are sporadic rather than likely LS 6 ; they therefore recommended MLH1 promoter methylation testing in all cases of isolated PMS2 loss 6 . This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  3. The Implementation of Performance Measurement System (PMS: Malaysian Facilities Management (FM Industry

    Directory of Open Access Journals (Sweden)

    Myeda N.E.

    2014-01-01

    Full Text Available Performance Measurement System (PMS is an effective performance measurement tool and technique that is being widely implemented in the global industries. Literature has suggested the significant contributions of its implementation in enhancing the strategic service delivery and performance. However, there is little study undertaken to explore the PMS implementation in Facilities Management (FM industry, particularly focusing on Malaysia. This study explores the PMS practice among FM practitioners and their knowledge in Performance Measurement (PM generally. Findings from this study also proposed the 20 contributing factors that the FM practitioners believed are the barriers in implementing PMS. This research also suggests the future research opportunities in developing a PMS framework that can be used as guidance for FM service delivery in Malaysia.

  4. The clinical phenotype of Lynch syndrome due to germline PMS2 mutations

    Science.gov (United States)

    Senter, Leigha; Clendenning, Mark; Sotamaa, Kaisa; Hampel, Heather; Green, Jane; Potter, John D.; Lindblom, Annika; Lagerstedt, Kristina; Thibodeau, Stephen N.; Lindor, Noralane M.; Young, Joanne; Winship, Ingrid; Dowty, James G.; White, Darren M.; Hopper, John L.; Baglietto, Laura; Jenkins, Mark A.; de la Chapelle, Albert

    2009-01-01

    Background and Aims Although the clinical phenotype of Lynch syndrome (also known as Hereditary Nonpolyposis Colorectal Cancer) has been well described, little is known about disease in PMS2 mutation carriers. Now that mutation detection methods can discern mutations in PMS2 from mutations in its pseudogenes, more mutation carriers have been identified. Information about the clinical significance of PMS2 mutations is crucial for appropriate counseling. Here, we report the clinical characteristics of a large series of PMS2 mutation carriers. Methods We performed PMS2 mutation analysis using long range PCR and MLPA for 99 probands diagnosed with Lynch syndrome-associated tumors showing isolated loss of PMS2 by immunohistochemistry. Penetrance was calculated using a modified segregation analysis adjusting for ascertainment. Results Germline PMS2 mutations were detected in 62% of probands (n = 55 monoallelic; 6 biallelic). Among families with monoallelic PMS2 mutations, 65.5% met revised Bethesda guidelines. Compared with the general population, in mutation carriers, the incidence of colorectal cancer was 5.2 fold higher and the incidence of endometrial cancer was 7.5 fold higher. In North America, this translates to a cumulative cancer risk to age 70 of 15–20% for colorectal cancer, 15% for endometrial cancer, and 25–32% for any Lynch syndrome-associated cancer. No elevated risk for non-Lynch syndrome-associated cancers was observed. Conclusions PMS2 mutations contribute significantly to Lynch syndrome but the penetrance for monoallelic mutation carriers appears to be lower than that for the other mismatch repair genes. Modified counseling and cancer surveillance guidelines for PMS2 mutation carriers are proposed. PMID:18602922

  5. The clinical phenotype of Lynch syndrome due to germ-line PMS2 mutations.

    Science.gov (United States)

    Senter, Leigha; Clendenning, Mark; Sotamaa, Kaisa; Hampel, Heather; Green, Jane; Potter, John D; Lindblom, Annika; Lagerstedt, Kristina; Thibodeau, Stephen N; Lindor, Noralane M; Young, Joanne; Winship, Ingrid; Dowty, James G; White, Darren M; Hopper, John L; Baglietto, Laura; Jenkins, Mark A; de la Chapelle, Albert

    2008-08-01

    Although the clinical phenotype of Lynch syndrome (also known as hereditary nonpolyposis colorectal cancer) has been well described, little is known about disease in PMS2 mutation carriers. Now that mutation detection methods can discern mutations in PMS2 from mutations in its pseudogenes, more mutation carriers have been identified. Information about the clinical significance of PMS2 mutations is crucial for appropriate counseling. Here, we report the clinical characteristics of a large series of PMS2 mutation carriers. We performed PMS2 mutation analysis using long-range polymerase chain reaction and multiplex ligation-dependent probe amplification for 99 probands diagnosed with Lynch syndrome-associated tumors showing isolated loss of PMS2 by immunohistochemistry. Penetrance was calculated using a modified segregation analysis adjusting for ascertainment. Germ-line PMS2 mutations were detected in 62% of probands (n = 55 monoallelic; 6 biallelic). Among families with monoallelic PMS2 mutations, 65.5% met revised Bethesda guidelines. Compared with the general population, in mutation carriers, the incidence of colorectal cancer was 5.2-fold higher, and the incidence of endometrial cancer was 7.5-fold higher. In North America, this translates to a cumulative cancer risk to age 70 years of 15%-20% for colorectal cancer, 15% for endometrial cancer, and 25%-32% for any Lynch syndrome-associated cancer. No elevated risk for non-Lynch syndrome-associated cancers was observed. PMS2 mutations contribute significantly to Lynch syndrome, but the penetrance for monoallelic mutation carriers appears to be lower than that for the other mismatch repair genes. Modified counseling and cancer surveillance guidelines for PMS2 mutation carriers are proposed.

  6. Advances in digital SiPMs and their application in biomedical imaging

    Energy Technology Data Exchange (ETDEWEB)

    Schaart, Dennis R., E-mail: d.r.schaart@tudelft.nl [Delft University of Technology, Faculty of Applied Sciences, Radiation Science and Technology, Mekelweg 15, 2629 JB Delft (Netherlands); Charbon, Edoardo [Delft University of Technology, Faculty of Electrical Engineering, Circuits and Systems, Mekelweg 4, 2628 CD Delft (Netherlands); Frach, Thomas [Philips Digital Photon Counting, Pauwelsstraße 17, 52074 Aachen (Germany); Schulz, Volkmar [Department for Physics of Molecular Imaging Systems, Institute for Experimental Molecular Imaging, RWTH Aachen University, Germany and Philips Research Europe, Aachen (Germany)

    2016-02-11

    Similar to analog silicon photomultipliers (SiPMs), digital SiPMs (dSiPMs) essentially consist of an array of single-photon avalanche photodiodes (SPADs). Instead of a passive quench resistor, however, an active quenching circuit is locally integrated with each SPAD, making the sensor response faster and less sensitive to the gains of the individual SPADs. Moreover, additional circuits for the fully digital acquisition, processing, and readout of optical signals are integrated within the sensor. As a result, dSiPMs offer high photo-detection efficiency, high single-photon time resolution (SPTR), and high uniformity, as well as many practical advantages, such as a very compact form factor, low voltage operation, magnetic field compatibility, high stability of operation, low gain drift, and a high degree of scalability. At the same time, dSiPMs represent a new paradigm in low-level light sensing technology. That is, their fully digital operation makes them true photon counting devices, preserving at least partly the discrete spatio-temporal structure of the information embedded in the optical signal. This means that the operation of dSiPMs can be fully understood only in statistical terms, but also opens up novel possibilities for extracting information from the measured data. So far, the main driver behind the development of dSiPMs has been the detection of scintillation pulses in detectors for time-of-flight (TOF) positron emission tomography (PET). Several types of dSiPM have been developed in recent years. Moreover, first imaging devices based on dSiPMs have been realized by various groups. This review summarizes the main dSiPM concepts and technologies currently under development, provides an overview of the results obtained recently with dSiPMs-based PET and SPECT devices, and presents a critical outlook on the challenges and chances for dSiPMs in future radiomolecular imaging systems.

  7. Four novel germline mutations in the MLH1 and PMS2 mismatch repair genes in patients with hereditary nonpolyposis colorectal cancer.

    Science.gov (United States)

    Montazer Haghighi, Mahdi; Radpour, Ramin; Aghajani, Katayoun; Zali, Narges; Molaei, Mahsa; Zali, Mohammad Reza

    2009-08-01

    Hereditary nonpolyposis colorectal cancer (HNPCC) is the most common cause of early onset hereditary colorectal cancer. In the majority of HNPCC families, microsatellite instability (MSI) and germline mutation in one of the DNA mismatch repair (MMR) genes are found. The entire coding sequence of MMR genes (MLH1, MLH2, MLH6, and PMS2) was analyzed using direct sequencing. Also, tumor tests were done as MSI and immunohistochemistry testing. We were able to find three novel MLH1 and one novel PMS2 germline mutations in three Iranian HNPCC patients. The first was a transversion mutation c.346A>C (T116P) and happened in the highly conserved HATPase-c region of MLH1 protein. The second was a transversion mutation c.736A>T (I246L), which caused an amino acid change of isoleucine to leucine. The third mutation (c.2145,6 delTG) was frameshift and resulted in an immature stop codon in five codons downstream. All of these three mutations were detected in the MLH1 gene. The other mutation was a transition mutation, c.676G>A (G207E), which has been found in exon six of the PMS2 gene and caused an amino acid change of glycine to glutamic acid. MSI assay revealed high instability in microsatellite for two patients and microsatellite stable for one patient. In all patients, an abnormal expression of the MMR proteins in HNPCC was related to the above novel mutations.

  8. Electrical characterization and simulation of SiPMs

    Energy Technology Data Exchange (ETDEWEB)

    Scheuch, Florian, E-mail: scheuch@physik.rwth-aachen.de; Führen, Daniel; Hebbeker, Thomas; Heidemann, Carsten; Merschmeyer, Markus

    2015-07-01

    Silicon Photomultipliers (SiPMs) are versatile and sensitive photon detectors that experience a fast growing variety of use in particle physics and related fields of application. These photo detectors have a very promising photon detection efficiency and are therefore interesting for very low light flux applications such as scintillation and fluorescence light detection. As a semiconductor device the SiPM's gain and time response strongly depend on the operating temperature and voltage. Thus they have to be understood for a proper use of the SiPM. Therefore, accurate electrical simulations of the SiPM's behavior involving electrical readout and front-end electronics help to improve the design of experimental setups, since several different designs can be tested and simulated with a manageable amount of effort. To perform these simulations, a detailed equivalent circuit of the SiPM has to be used containing a set of well-defined parameters. For this purpose, SPICE simulations of SiPMs and readout electronics have been performed. These simulations utilize an improved SiPM model consisting of resistors, capacitances and inductances. The SiPM parameters for these simulations have been determined by measuring the impedance over a wide frequency range while applying a DC voltage in forward direction and various DC voltages from zero up to the SiPM breakdown voltage in order to determine the behavior under operating conditions. The impedance measurements, the electrical model and the resulting simulations are presented. The impact of different setups and the electrical properties of the SiPM is discussed.

  9. Functional role of DNA mismatch repair gene PMS2 in prostate cancer cells.

    Science.gov (United States)

    Fukuhara, Shinichiro; Chang, Inik; Mitsui, Yozo; Chiyomaru, Takeshi; Yamamura, Soichiro; Majid, Shahana; Saini, Sharanjot; Deng, Guoren; Gill, Ankurpreet; Wong, Darryn K; Shiina, Hiroaki; Nonomura, Norio; Lau, Yun-Fai C; Dahiya, Rajvir; Tanaka, Yuichiro

    2015-06-30

    DNA mismatch repair (MMR) enzymes act as proofreading complexes that maintains genomic integrity and MMR-deficient cells show an increased mutation rate. MMR has also been shown to influence cell signaling and the regulation of tumor development. MMR consists of various genes and includes post-meiotic segregation (PMS) 2 which is a vital component of mutL-alpha. In prostate, the functional role of this gene has never been reported and in this study, our aim was to investigate the effect of PMS2 on growth properties of prostate cancer (PCa) cells. Previous studies have shown PMS2 to be deficient in DU145 cells and this lack of expression was confirmed by Western blotting whereas normal prostatic PWR-1E and RWPE-1 cells expressed this gene. PMS2 effects on various growth properties of DU145 were then determined by creating stable gene transfectants. Interestingly, PMS2 caused decreased cell proliferation, migration, invasion, and in vivo growth; and increased apoptosis as compared to vector control. We further analyzed genes affected by PMS2 expression and observe the apoptosis-related TMS1 gene to be significantly upregulated whereas anti-apoptotic BCL2A1 was downregulated. These results demonstrate a functional role for PMS2 to protect against PCa progression by enhancing apoptosis of PCa cells.

  10. Colorectal Carcinomas With Isolated Loss of PMS2 Staining by Immunohistochemistry.

    Science.gov (United States)

    Alpert, Lindsay; Pai, Reetesh K; Srivastava, Amitabh; McKinnon, Wendy; Wilcox, Rebecca; Yantiss, Rhonda K; Arcega, Ramir; Wang, Hanlin L; Robert, Marie E; Liu, Xiuli; Pai, Rish K; Zhao, Lei; Westerhoff, Maria; Hampel, Heather; Kupfer, Sonia; Setia, Namrata; Xiao, Shu-Yuan; Hart, John; Frankel, Wendy L

    2018-04-01

    - Isolated loss of PMS2 staining is an uncommon immunophenotype in colorectal carcinomas, accounting for approximately 4% of tumors with microsatellite instability. Limited information regarding these tumors is available in the literature. - To compare the clinicopathologic features of colorectal carcinomas with isolated PMS2 loss by immunohistochemistry to those with other forms of mismatch repair deficiency. - Ninety-three colorectal carcinomas with isolated PMS2 loss by immunohistochemistry and 193 with other forms of mismatch repair deficiency were identified. Forty (43%) of the isolated PMS2 loss cases and 35 control cases (18%) had a known germline mutation or a clinical diagnosis of Lynch syndrome. - Overall, isolated PMS2-loss tumors occurred in significantly younger patients ( P PMS2-loss group also exhibited increased odds of disease-specific death (odds ratio [OR], 3.09; 95% CI, 1.41-6.85; P = .007). When the analysis was restricted to germline mutation/Lynch syndrome cases and controls, no significant differences were detected for age, sex, tumor location, tumor grade, histologic features, or distant metastases, although a trend toward increased odds of disease-specific death in the isolated PMS2-loss group was evident (OR, 3.87; 95% CI, 0.89-27.04; P = .10). - Unusual clinicopathologic features observed in colorectal carcinomas with isolated PMS2 loss are likely related to the high proportion of cases caused by germline mutations. Isolated PMS2-loss tumors may demonstrate more aggressive behavior than other tumors with microsatellite instability, but larger studies are needed to investigate that possibility further.

  11. Activation of Saccharomyces cerevisiae Mlh1-Pms1 Endonuclease in a Reconstituted Mismatch Repair System*

    Science.gov (United States)

    Smith, Catherine E.; Bowen, Nikki; Graham, William J.; Goellner, Eva M.; Srivatsan, Anjana; Kolodner, Richard D.

    2015-01-01

    Previous studies reported the reconstitution of an Mlh1-Pms1-independent 5′ nick-directed mismatch repair (MMR) reaction using Saccharomyces cerevisiae proteins. Here we describe the reconstitution of a mispair-dependent Mlh1-Pms1 endonuclease activation reaction requiring Msh2-Msh6 (or Msh2-Msh3), proliferating cell nuclear antigen (PCNA), and replication factor C (RFC) and a reconstituted Mlh1-Pms1-dependent 3′ nick-directed MMR reaction requiring Msh2-Msh6 (or Msh2-Msh3), exonuclease 1 (Exo1), replication protein A (RPA), RFC, PCNA, and DNA polymerase δ. Both reactions required Mg2+ and Mn2+ for optimal activity. The MMR reaction also required two reaction stages in which the first stage required incubation of Mlh1-Pms1 with substrate DNA, with or without Msh2-Msh6 (or Msh2-Msh3), PCNA, and RFC but did not require nicking of the substrate, followed by a second stage in which other proteins were added. Analysis of different mutant proteins demonstrated that both reactions required a functional Mlh1-Pms1 endonuclease active site, as well as mispair recognition and Mlh1-Pms1 recruitment by Msh2-Msh6 but not sliding clamp formation. Mutant Mlh1-Pms1 and PCNA proteins that were defective for Exo1-independent but not Exo1-dependent MMR in vivo were partially defective in the Mlh1-Pms1 endonuclease and MMR reactions, suggesting that both reactions reflect the activation of Mlh1-Pms1 seen in Exo1-independent MMR in vivo. The availability of this reconstituted MMR reaction should now make it possible to better study both Exo1-independent and Exo1-dependent MMR. PMID:26170454

  12. Activation of Saccharomyces cerevisiae Mlh1-Pms1 Endonuclease in a Reconstituted Mismatch Repair System.

    Science.gov (United States)

    Smith, Catherine E; Bowen, Nikki; Graham, William J; Goellner, Eva M; Srivatsan, Anjana; Kolodner, Richard D

    2015-08-28

    Previous studies reported the reconstitution of an Mlh1-Pms1-independent 5' nick-directed mismatch repair (MMR) reaction using Saccharomyces cerevisiae proteins. Here we describe the reconstitution of a mispair-dependent Mlh1-Pms1 endonuclease activation reaction requiring Msh2-Msh6 (or Msh2-Msh3), proliferating cell nuclear antigen (PCNA), and replication factor C (RFC) and a reconstituted Mlh1-Pms1-dependent 3' nick-directed MMR reaction requiring Msh2-Msh6 (or Msh2-Msh3), exonuclease 1 (Exo1), replication protein A (RPA), RFC, PCNA, and DNA polymerase δ. Both reactions required Mg(2+) and Mn(2+) for optimal activity. The MMR reaction also required two reaction stages in which the first stage required incubation of Mlh1-Pms1 with substrate DNA, with or without Msh2-Msh6 (or Msh2-Msh3), PCNA, and RFC but did not require nicking of the substrate, followed by a second stage in which other proteins were added. Analysis of different mutant proteins demonstrated that both reactions required a functional Mlh1-Pms1 endonuclease active site, as well as mispair recognition and Mlh1-Pms1 recruitment by Msh2-Msh6 but not sliding clamp formation. Mutant Mlh1-Pms1 and PCNA proteins that were defective for Exo1-independent but not Exo1-dependent MMR in vivo were partially defective in the Mlh1-Pms1 endonuclease and MMR reactions, suggesting that both reactions reflect the activation of Mlh1-Pms1 seen in Exo1-independent MMR in vivo. The availability of this reconstituted MMR reaction should now make it possible to better study both Exo1-independent and Exo1-dependent MMR. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  13. Comprehensive population-wide analysis of Lynch syndrome in Iceland reveals founder mutations in MSH6 and PMS2

    Science.gov (United States)

    Haraldsdottir, Sigurdis; Rafnar, Thorunn; Frankel, Wendy L.; Einarsdottir, Sylvia; Sigurdsson, Asgeir; Hampel, Heather; Snaebjornsson, Petur; Masson, Gisli; Weng, Daniel; Arngrimsson, Reynir; Kehr, Birte; Yilmaz, Ahmet; Haraldsson, Stefan; Sulem, Patrick; Stefansson, Tryggvi; Shields, Peter G.; Sigurdsson, Fridbjorn; Bekaii-Saab, Tanios; Moller, Pall H.; Steinarsdottir, Margret; Alexiusdottir, Kristin; Hitchins, Megan; Pritchard, Colin C.; de la Chapelle, Albert; Jonasson, Jon G.; Goldberg, Richard M.; Stefansson, Kari

    2017-01-01

    Lynch syndrome, caused by germline mutations in the mismatch repair genes, is associated with increased cancer risk. Here using a large whole-genome sequencing data bank, cancer registry and colorectal tumour bank we determine the prevalence of Lynch syndrome, associated cancer risks and pathogenicity of several variants in the Icelandic population. We use colorectal cancer samples from 1,182 patients diagnosed between 2000–2009. One-hundred and thirty-two (11.2%) tumours are mismatch repair deficient per immunohistochemistry. Twenty-one (1.8%) have Lynch syndrome while 106 (9.0%) have somatic hypermethylation or mutations in the mismatch repair genes. The population prevalence of Lynch syndrome is 0.442%. We discover a translocation disrupting MLH1 and three mutations in MSH6 and PMS2 that increase endometrial, colorectal, brain and ovarian cancer risk. We find thirteen mismatch repair variants of uncertain significance that are not associated with cancer risk. We find that founder mutations in MSH6 and PMS2 prevail in Iceland unlike most other populations. PMID:28466842

  14. Insertion of an SVA element, a nonautonomous retrotransposon, in PMS2 intron 7 as a novel cause of Lynch syndrome.

    Science.gov (United States)

    van der Klift, Heleen M; Tops, Carli M; Hes, Frederik J; Devilee, Peter; Wijnen, Juul T

    2012-07-01

    Heterozygous germline mutations in the mismatch repair gene PMS2 predispose carriers for Lynch syndrome, an autosomal dominant predisposition to cancer. Here, we present a LINE-1-mediated retrotranspositional insertion in PMS2 as a novel mutation type for Lynch syndrome. This insertion, detected with Southern blot analysis in the genomic DNA of the patient, is characterized as a 2.2 kb long 5' truncated SVA_F element. The insertion is not detectable by current diagnostic testing limited to MLPA and direct Sanger sequencing on genomic DNA. The molecular nature of this insertion could only be resolved in RNA from cultured lymphocytes in which nonsense-mediated RNA decay was inhibited. Our report illustrates the technical problems encountered in the detection of this mutation type. Especially large heterozygous insertions will remain unnoticed because of preferential amplification of the smaller wild-type allele in genomic DNA, and are probably underreported in the mutation spectra of autosomal dominant disorders. © 2012 Wiley Periodicals, Inc.

  15. Comprehensive population-wide analysis of Lynch syndrome in Iceland reveals founder mutations in MSH6 and PMS2.

    Science.gov (United States)

    Haraldsdottir, Sigurdis; Rafnar, Thorunn; Frankel, Wendy L; Einarsdottir, Sylvia; Sigurdsson, Asgeir; Hampel, Heather; Snaebjornsson, Petur; Masson, Gisli; Weng, Daniel; Arngrimsson, Reynir; Kehr, Birte; Yilmaz, Ahmet; Haraldsson, Stefan; Sulem, Patrick; Stefansson, Tryggvi; Shields, Peter G; Sigurdsson, Fridbjorn; Bekaii-Saab, Tanios; Moller, Pall H; Steinarsdottir, Margret; Alexiusdottir, Kristin; Hitchins, Megan; Pritchard, Colin C; de la Chapelle, Albert; Jonasson, Jon G; Goldberg, Richard M; Stefansson, Kari

    2017-05-03

    Lynch syndrome, caused by germline mutations in the mismatch repair genes, is associated with increased cancer risk. Here using a large whole-genome sequencing data bank, cancer registry and colorectal tumour bank we determine the prevalence of Lynch syndrome, associated cancer risks and pathogenicity of several variants in the Icelandic population. We use colorectal cancer samples from 1,182 patients diagnosed between 2000-2009. One-hundred and thirty-two (11.2%) tumours are mismatch repair deficient per immunohistochemistry. Twenty-one (1.8%) have Lynch syndrome while 106 (9.0%) have somatic hypermethylation or mutations in the mismatch repair genes. The population prevalence of Lynch syndrome is 0.442%. We discover a translocation disrupting MLH1 and three mutations in MSH6 and PMS2 that increase endometrial, colorectal, brain and ovarian cancer risk. We find thirteen mismatch repair variants of uncertain significance that are not associated with cancer risk. We find that founder mutations in MSH6 and PMS2 prevail in Iceland unlike most other populations.

  16. A homozygote splice site PMS2 mutation as cause of Turcot syndrome gives rise to two different abnormal transcripts.

    Science.gov (United States)

    Sjursen, Wenche; Bjørnevoll, Inga; Engebretsen, Lars F; Fjelland, Kristine; Halvorsen, Tore; Myrvold, Helge E

    2009-01-01

    Turcot syndrome is a rare, inherited disease predisposing of tumours in the central nerve system and in the colorectal system. This report describes a Turcot patient with an extraordinary clinical history. The patient is still alive at the age of 43. She was operated at the age of 10 by brain tumour and at the age of 16 by colorectal cancer. She has since then been treated for multiple cancers (gastrointestinal, endometrial, basal cell carcinomas), and removal of adenomatous polyps at several occasions. The aim of this work was to investigate if there was any specific genotype that explains her remarkable clinical history. Microsatellite instability and immunohistochemistry analysis for four DNA mismatch repair proteins were performed. DNA mutation analysis was done for genes involved in polyposis and mismatch repair by denaturing high performance liquid chromatography and sequencing. cDNA analysis was carried out for the mismatch repair gene PMS2. The patients genotype was found to be a homozygous splice site mutation in the PMS2 gene, c.989-1G

  17. Two co-existing germline mutations P53 V157D and PMS2 R20Q promote tumorigenesis in a familial cancer syndrome.

    Science.gov (United States)

    Wang, Zuoyun; Sun, Yihua; Gao, Bin; Lu, Yi; Fang, Rong; Gao, Yijun; Xiao, Tian; Liu, Xin-Yuan; Pao, William; Zhao, Yun; Chen, Haiquan; Ji, Hongbin

    2014-01-01

    Germline mutations are responsible for familial cancer syndromes which account for approximately 5-10% of all types of cancers. These mutations mainly occur at tumor suppressor genes or genome stability genes, such as DNA repair genes. Here we have identified a cancer predisposition family, in which eight members were inflicted with a wide spectrum of cancer including one diagnosed with lung cancer at 22years old. Sequencing analysis of tumor samples as well as histologically normal specimens identified two germline mutations co-existing in the familial cancer syndrome, the mutation of tumor suppressor gene P53 V157D and mismatch repair gene PMS2 R20Q. We further demonstrate that P53 V157D and/or PMS2 R20Q mutant promotes lung cancer cell proliferation. These two mutants are capable of promoting colony formation in soft agar as well as tumor formation in transgenic drosophila system. Collectively, these data have uncovered the important role of co-existing germline P53 and PMS2 mutations in the familial cancer syndrome development. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  18. Characterization of FBK SiPMs under illumination with very fast light pulses

    Energy Technology Data Exchange (ETDEWEB)

    Tarolli, A., E-mail: tarolli@fbk.e [Fondazione Bruno Kessler (FBK), Trento (Italy); Dalla Betta, G.-F. [University of Trento and INFN, Trento (Italy); Melchiorri, M.; Piazza, A.; Pancheri, L.; Piemonte, C.; Zorzi, N. [Fondazione Bruno Kessler (FBK), Trento (Italy)

    2010-05-21

    A characterization of the response of SiPMs and SPADs produced at FBK-IRST Trento stimulated with fast laser pulses is presented. The tests were aimed at studying both the intrinsic timing proprieties (of SiPMs and SPADs) using the time-correlated single-photon counting technique and the dynamic range (of SiPMs). Measurements were carried out on devices with different cell size, namely, from 40x40 to 100x100 {mu}m{sup 2}. Concerning the timing resolution, all the devices exhibit a value less than 150 psec FWHM. The dynamic range of SiPMs shows a response linearity which is in line with the theory describing these devices.

  19. Characterization of FBK SiPMs under illumination with very fast light pulses

    International Nuclear Information System (INIS)

    Tarolli, A.; Dalla Betta, G.-F.; Melchiorri, M.; Piazza, A.; Pancheri, L.; Piemonte, C.; Zorzi, N.

    2010-01-01

    A characterization of the response of SiPMs and SPADs produced at FBK-IRST Trento stimulated with fast laser pulses is presented. The tests were aimed at studying both the intrinsic timing proprieties (of SiPMs and SPADs) using the time-correlated single-photon counting technique and the dynamic range (of SiPMs). Measurements were carried out on devices with different cell size, namely, from 40x40 to 100x100 μm 2 . Concerning the timing resolution, all the devices exhibit a value less than 150 psec FWHM. The dynamic range of SiPMs shows a response linearity which is in line with the theory describing these devices.

  20. An intact Pms2 ATPase domain is not essential for male fertility

    OpenAIRE

    Fischer, Jared M; Dudley, Sandra; Miller, Ashleigh J; Liskay, R Michael

    2015-01-01

    The DNA mismatch repair (MMR) machinery in mammals plays critical roles in both mutation avoidance and spermatogenesis. Meiotic analysis of knockout mice of two different MMR genes, Mlh1 and Mlh3, revealed both male and female infertility associated with a defect in meiotic crossing over. In contrast, another MMR gene knockout, Pms2 (Pms2ko/ko), which contained a deletion of a portion of the ATPase domain, produced animals that were male sterile but female fertile. However, the meiotic phenot...

  1. High incidence of large deletions in the PMS2 gene in Spanish Lynch syndrome families.

    Science.gov (United States)

    Brea-Fernández, A J; Cameselle-Teijeiro, J M; Alenda, C; Fernández-Rozadilla, C; Cubiella, J; Clofent, J; Reñé, J M; Anido, U; Milá, M; Balaguer, F; Castells, A; Castellvi-Bel, S; Jover, R; Carracedo, A; Ruiz-Ponte, C

    2014-06-01

    Lynch syndrome (LS) is caused by germline mutations in one of the four mismatch repair (MMR) genes. Defects in this pathway lead to microsatellite instability (MSI) in DNA tumors, which constitutes the molecular hallmark of this disease. Selection of patients for genetic testing in LS is usually based on fulfillment of diagnostic clinical criteria (i.e. Amsterdam criteria or the revised Bethesda guidelines). However, following these criteria PMS2 mutations have probably been underestimated as their penetrances appear to be lower than those of the other MMR genes. The use of universal MMR study-based strategies, using MSI testing and immunohistochemical (IHC) staining, is being one proposed alternative. Besides, germline mutation detection in PMS2 is complicated by the presence of highly homologous pseudogenes. Nevertheless, specific amplification of PMS2 by long-range polymerase chain reaction (PCR) and the improvement of the analysis of large deletions/duplications by multiplex ligation-dependent probe amplification (MLPA) overcome this difficulty. By using both approaches, we analyzed 19 PMS2-suspected carriers who have been selected by clinical or universal strategies and found five large deletions and one frameshift mutation in PMS2 in six patients (31%). Owing to the high incidence of large deletions found in our cohort, we recommend MLPA analysis as the first-line method for searching germline mutations in PMS2. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  2. Effectiveness of Group Cognitive-Behavioral Therapy on Symptoms of Premenstrual Syndrome (PMS) ‎.

    Science.gov (United States)

    Maddineshat, Maryam; Keyvanloo, Sodabe; Lashkardoost, Hossein; Arki, Mina; Tabatabaeichehr, Mahbubeh

    2016-01-01

    Standards of care and treatment of premenstrual syndrome (PMS) vary. Non-drug ‎psychosocial intervention therapy is recommended for women with any kind of ‎discomfort or distress caused by PMS. The current study examined the effectiveness of ‎group cognitive-behavioral therapy on the symptoms of PMS at a girls' dormitory of ‎North Khorasan University of Medical Sciences. In this quasi-experimental study, 32 female students with PMS who were majoring in ‎nursing and midwifery and residing in the dormitory were selected using the ‎convenience sampling method and were assigned to experimental and control groups. ‎The Standardized Premenstrual Symptoms Screening Tool was used as the research ‎tool. Eight sessions of cognitive-behavioral group therapy were held for the students Results: There was a significant difference in psychological symptoms before and after ‎cognitive-behavioral therapy (p=0.012). Furthermore, cognitive-behavioral therapy was ‎effective on social interferences caused by PMS symptoms (p=0.012).‎ Group cognitive-behavioral therapy effectively alleviates PMS symptoms in female ‎college students.‎.

  3. Examination of chromosome 7p22 candidate genes RBaK, PMS2 and GNA12 in familial hyperaldosteronism type II.

    Science.gov (United States)

    Jeske, Y W A; So, A; Kelemen, L; Sukor, N; Willys, C; Bulmer, B; Gordon, R D; Duffy, D; Stowasser, M

    2008-04-01

    1. There are two types of familial hyperaldosteronism (FH): FH-I and FH-II. FH-I is caused by a hybrid CYP11B1/CYP11B2 gene mutation. The genetic cause of FH-II, which is more common, is unknown. Adrenal hyperplasia and adenomas are features. We previously reported linkage of FH-II to a approximately 5 Mb region on chromosome 7p22. We subsequently reported finding no causative mutations in the retinoblastoma-associated Kruppel-associated box gene (RBaK), a candidate at 7p22 involved in tumorigenesis and cell cycle control. 2. In the current study we investigated RBaK regulatory regions and two other candidate genes: postmeiotic segregation increased 2 (PMS2, involved in DNA mismatch repair and tumour predisposition) and guanine nucleotide-binding protein alpha-12 (GNA12, a transforming oncogene). 3. The GNA12 and PMS2 genes were examined in two affected (A1, A2) and two unaffected (U1, U2) subjects from a large 7p22-linked FH-II family (family 1). No mutations were found. 4. The RBaK and PMS2 distal promoters were sequenced to -2150 bp from the transcription start site for RBaK and-2800 bp for PMS2. Five unreported single nucleotide polymorphisms (SNPs) were found in subjects A1, A2 but not in U1 or U2; A(-2031 bp)T, T(-2030 bp)G, G(-834 bp)C, C(-821 bp)G in RBaK and A(-876 bp)G in PMS2. Additional affected and unaffected subjects from family 1 and from two other 7p22-linked FH-II families and 58 unrelated normotensive control subjects were genotyped for these SNPs. 5. The five novel SNPs were found to be present in a significant proportion of normotensive controls. The four RBaK promoter SNPs were found to be in linkage disequilibrium in the normal population. The RBaK promoter (-)2031T/2030G/834C/821T allele was found to be in linkage disequilibrium with the causative mutation in FH-II family 1, but not in families 2 and 3. The PMS2 promoter (-)876G allele was also found to be linked to affected phenotypes in family 1. 6. The RBaK and PMS2 promoter SNPs alter the

  4. Implementation of the Performance Management System (PMS) in Senior Secondary Schools in Botswana: An Investigation of Senior Management Team's Expected Benefits of the PMS

    Science.gov (United States)

    Bulawa, Philip

    2012-01-01

    Different forms of the performance management system have been implemented in many countries for some years. As in other countries, in 1999 the government of Botswana took a decision to implement a performance management system (PMS) across the entire public service including schools. The government explained the purpose for which this reform was…

  5. PMS2 inactivation by a complex rearrangement involving an HERV retroelement and the inverted 100-kb duplicon on 7p22.1.

    Science.gov (United States)

    Vogt, Julia; Wernstedt, Annekatrin; Ripperger, Tim; Pabst, Brigitte; Zschocke, Johannes; Kratz, Christian; Wimmer, Katharina

    2016-11-01

    Biallelic PMS2 mutations are responsible for more than half of all cases of constitutional mismatch repair deficiency (CMMRD), a recessively inherited childhood cancer predisposition syndrome. The mismatch repair gene PMS2 is partly embedded within one copy of an inverted 100-kb low-copy repeat (LCR) on 7p22.1. In an individual with CMMRD syndrome, PMS2 was found to be homozygously inactivated by a complex chromosomal rearrangement, which separates the 5'-part from the 3'-part of the gene. The rearrangement involves sequences of the inverted 100-kb LCR and a human endogenous retrovirus element and may be associated with an inversion that is indistinguishable from the known inversion polymorphism affecting the ~0.7-Mb sequence intervening the LCR. Its formation is best explained by a replication-based mechanism (RBM) such as fork stalling and template switching/microhomology-mediated break-induced replication (FoSTeS/MMBIR). This finding supports the hypothesis that the inverted LCR can not only facilitate the formation of the non-allelic homologous recombination-mediated inversion polymorphism but it also promotes the occurrence of more complex rearrangements that can be associated with a large inversion, as well, but are mediated by a RBM. This further suggests that among the inversion polymorphism on 7p22.1, more complex rearrangements might be hidden. Furthermore, as the locus is embedded in a common fragile site (CFS) region, this rearrangement also supports the recently raised hypothesis that CFS sequence motifs may facilitate replication-based rearrangement mechanisms.

  6. Increased sensitivity of p53-deficient cells to anticancer agents due to loss of Pms2

    Science.gov (United States)

    Fedier, A; Ruefenacht, U B; Schwarz, V A; Haller, U; Fink, D

    2002-01-01

    A large fraction of human tumours carries mutations in the p53 gene. p53 plays a central role in controlling cell cycle checkpoint regulation, DNA repair, transcription, and apoptosis upon genotoxic stress. Lack of p53 function impairs these cellular processes, and this may be the basis of resistance to chemotherapeutic regimens. By virtue of the involvement of DNA mismatch repair in modulating cytotoxic pathways in response to DNA damaging agents, we investigated the effects of loss of Pms2 on the sensitivity to a panel of widely used anticancer agents in E1A/Ha-Ras-transformed p53-null mouse fibroblasts either proficient or deficient in Pms2. We report that lack of the Pms2 gene is associated with an increased sensitivity, ranging from 2–6-fold, to some types of anticancer agents including the topoisomerase II poisons doxorubicin, etoposide and mitoxantrone, the platinum compounds cisplatin and oxaliplatin, the taxanes docetaxel and paclitaxel, and the antimetabolite gemcitabine. In contrast, no change in sensitivity was found after treatment with 5-fluorouracil. Cell cycle analysis revealed that both, Pms2-deficient and -proficient cells, retain the ability to arrest at the G2/M upon cisplatin treatment. The data indicate that the concomitant loss of Pms2 function chemosensitises p53-deficient cells to some types of anticancer agents, that Pms2 positively modulates cell survival by mechanisms independent of p53, and that increased cytotoxicity is paralleled by increased apoptosis. Tumour-targeted functional inhibition of Pms2 may be a valuable strategy for increasing the efficacy of anticancer agents in the treatment of p53-mutant cancers. British Journal of Cancer (2002) 87, 1027–1033. doi:10.1038/sj.bjc.6600599 www.bjcancer.com © 2002 Cancer Research UK PMID:12434296

  7. Chronic periodontitis as an etiology of sleep disturbances and premenstrual syndrome (PMS

    Directory of Open Access Journals (Sweden)

    Haryono Utomo

    2007-03-01

    Full Text Available It is obvious that sleep disturbances may induced by acute pulpal or periodontal pain. Other causes of sleep disturbances which also termed as sleep dysfunction, or insomnia, according to the patient has to be treated by physician. Nevertheless, in a case report, surprisingly, periodontal treatment relieved sleep disturbances and premenstrual syndrome (PMS. Coincidentally, women also more vulnerable to sleep disturbances and periodontal disease. It is also interesting that the exact etiology of PMS is still unknown, and 80% women who suffered from PMS also experience sleep disturbances. Recently, there has been increasing numbers of literatures and evidence-based cases linking periodontal disease to systemic diseases. However, systemic effects of periodontal disease that lead to PMS which associated with sleep disturbances are rarely discussed. Several mechanisms had been proposed to involve in these symptoms: female sexual hormonal imbalance, stimulation of the hypothalamic-pituitary-adrenal axis (HPA-axis and neurogenic switching mechanism. In addition, as estrogen makes women more susceptible to stress, it worsen the symptoms. The glucocorticoid hormones synthesized upon stimulation of the HPA-axis, either by stress or pro-inflammatory cytokines, may disrupt the sleep-wake cycle; and also create estrogen dominance. The aim of this study is to propose the etiopathogenesis of PMS which associated with sleep disturbances that may be related to chronic periodontitis. Since in this case report scaling and curettage resulted in the disappearing of PMS and sleep disturbances; the conclusion is that chronic periodontal disease may act as one of the etiologies of PMS and sleep disturbance.

  8. Refining the role of PMS2 in Lynch syndrome: germline mutational analysis improved by comprehensive assessment of variants.

    Science.gov (United States)

    Borràs, Ester; Pineda, Marta; Cadiñanos, Juan; Del Valle, Jesús; Brieger, Angela; Hinrichsen, Inga; Cabanillas, Ruben; Navarro, Matilde; Brunet, Joan; Sanjuan, Xavier; Musulen, Eva; van der Klift, Helen; Lázaro, Conxi; Plotz, Guido; Blanco, Ignacio; Capellá, Gabriel

    2013-08-01

    The majority of mismatch repair (MMR) gene mutations causing Lynch syndrome (LS) occur either in MLH1 or MSH2. However, the relative contribution of PMS2 is less well defined. The aim of this study was to evaluate the role of PMS2 in LS by assessing the pathogenicity of variants of unknown significance (VUS) detected in the mutational analysis of PMS2 in a series of Spanish patients. From a cohort of 202 LS suspected patients, 13 patients showing loss of PMS2 expression in tumours were screened for germline mutations in PMS2, using a long range PCR based strategy and multiplex ligation dependent probe amplification (MLPA). Pathogenicity assessment of PMS2 VUS was performed evaluating clinicopathological data, frequency in control population and in silico and in vitro analyses at the RNA and protein level. Overall 25 different PMS2 DNA variants were detected. Fourteen were classified as polymorphisms. Nine variants were classified as pathogenic: seven alterations based on their molecular nature and two after demonstrating a functional defect (c.538-3C>G affected mRNA processing and c.137G>T impaired MMR activity). The c.1569C>G variant was classified as likely neutral while the c.384G>A remained as a VUS. We have also shown that the polymorphic variant c.59G>A is MMR proficient. Pathogenic PMS2 mutations were detected in 69% of patients harbouring LS associated tumours with loss of PMS2 expression. In all, PMS2 mutations account for 6% of the LS cases identified. The comprehensive functional analysis shown here has been useful in the classification of PMS2 VUS and contributes to refining the role of PMS2 in LS.

  9. Apoptotic function of human PMS2 compromised by the nonsynonymous single-nucleotide polymorphic variant R20Q.

    Science.gov (United States)

    Marinovic-Terzic, Ivana; Yoshioka-Yamashita, Atsuko; Shimodaira, Hideki; Avdievich, Elena; Hunton, Irina C; Kolodner, Richard D; Edelmann, Winfried; Wang, Jean Y J

    2008-09-16

    Mismatch repair (MMR) corrects replication errors during DNA synthesis. The mammalian MMR proteins also activate cell cycle checkpoints and apoptosis in response to persistent DNA damage. MMR-deficient cells are resistant to cisplatin, a DNA cross-linking agent used in chemotherapy, because of impaired activation of apoptotic pathways. It is shown that postmeiotic segregation 2 (PMS2), an MMR protein, is required for cisplatin-induced activation of p73, a member of the p53 family of transcription factors with proapoptotic activity. The human PMS2 is highly polymorphic, with at least 12 known nonsynonymous codon changes identified. We show here that the PMS2(R20Q) variant is defective in activating p73-dependent apoptotic response to cisplatin. When expressed in Pms2-deficient mouse fibroblasts, human PMS2(R20Q) but not PMS2 interfered with the apoptotic response to cisplatin. Correspondingly, PMS2 but not PMS2(R20Q) enhanced the cytotoxic effect of cisplatin measured by clonogenic survival. Because PMS2(R20Q) lacks proapoptotic activity, this polymorphic allele may modulate tumor responses to cisplatin among cancer patients.

  10. Origin and Evolution of Magnetic Field in PMS Stars: Influence of Rotation and Structural Changes

    Energy Technology Data Exchange (ETDEWEB)

    Emeriau-Viard, Constance; Brun, Allan Sacha, E-mail: constance.emeriau@cea.fr, E-mail: sacha.brun@cea.fr [Laboratoire AIM Paris-Saclay CEA/DSM—CNRS—Université Paris Diderot, IRFU/DAp CEA Paris-Saclay, F-91191 Gif-sur-Yvette Cedex (France)

    2017-09-01

    During stellar evolution, especially in the pre-main-sequence phase, stellar structure and rotation evolve significantly, causing major changes in the dynamics and global flows of the star. We wish to assess the consequences of these changes on stellar dynamo, internal magnetic field topology, and activity level. To do so, we have performed a series of 3D HD and MHD simulations with the ASH code. We choose five different models characterized by the radius of their radiative zone following an evolutionary track computed by a 1D stellar evolution code. These models characterized stellar evolution from 1 to 50 Myr. By introducing a seed magnetic field in the fully convective model and spreading its evolved state through all four remaining cases, we observe systematic variations in the dynamical properties and magnetic field amplitude and topology of the models. The five MHD simulations develop a strong dynamo field that can reach an equipartition state between the kinetic and magnetic energies and even superequipartition levels in the faster-rotating cases. We find that the magnetic field amplitude increases as it evolves toward the zero-age main sequence. Moreover, the magnetic field topology becomes more complex, with a decreasing axisymmetric component and a nonaxisymmetric one becoming predominant. The dipolar components decrease as the rotation rate and the size of the radiative core increase. The magnetic fields possess a mixed poloidal-toroidal topology with no obvious dominant component. Moreover, the relaxation of the vestige dynamo magnetic field within the radiative core is found to satisfy MHD stability criteria. Hence, it does not experience a global reconfiguration but slowly relaxes by retaining its mixed stable poloidal-toroidal topology.

  11. Elevated levels of the mismatch repair protein PMS2 are associated with prostate cancer.

    Science.gov (United States)

    Norris, Alixanna M; Woodruff, R D; D'Agostino, Ralph B; Clodfelter, Jill E; Scarpinato, Karin Drotschmann

    2007-02-01

    Defects in mismatch repair (MMR) proteins have been identified in various types of cancer. However, an association with prostate cancer has been controversial. Defective MMR results in genome instability with detrimental consequences that significantly contribute to tumorigenesis. This study determined alterations in key MMR protein levels in prostate cancer with the goal to identify prognostic markers. Prostatectomy samples were immunohistochemically stained and the relative presence or absence of key proteins MSH2, MLH1, and PMS2 determined. Cancer tissue of distinct grades was compared with the normal surrounding tissue. Microsatellite instability (MSI) in altered tissues was determined according to NCI guidelines. In contrast to reports that associate a lack of individual MMR proteins with tumorigenesis, a significant increase in PMS2 levels was identified in PIN lesions and prostate cancer tissue. This elevation in PMS2 was independent of changes in levels in its heterodimeric partner, MLH1. Prostate tumors with elevated levels of PMS2 were genetically unstable, which was corrected by MLH1 co-elevation. This is the first documentation of detrimental consequences associated with the increase in a MMR protein in human cancer. This study recognizes PMS2 elevation as a prognostic marker in pre-neoplastic and prostate cancer lesions. This result has significant implications for future diagnostic and treatment measures. (c) 2006 Wiley-Liss, Inc.

  12. Lynch syndrome caused by germline PMS2 mutations: delineating the cancer risk.

    Science.gov (United States)

    ten Broeke, Sanne W; Brohet, Richard M; Tops, Carli M; van der Klift, Heleen M; Velthuizen, Mary E; Bernstein, Inge; Capellá Munar, Gabriel; Gomez Garcia, Encarna; Hoogerbrugge, Nicoline; Letteboer, Tom G W; Menko, Fred H; Lindblom, Annika; Mensenkamp, Arjen R; Moller, Pal; van Os, Theo A; Rahner, Nils; Redeker, Bert J W; Sijmons, Rolf H; Spruijt, Liesbeth; Suerink, Manon; Vos, Yvonne J; Wagner, Anja; Hes, Frederik J; Vasen, Hans F; Nielsen, Maartje; Wijnen, Juul T

    2015-02-01

    The clinical consequences of PMS2 germline mutations are poorly understood compared with other Lynch-associated mismatch repair gene (MMR) mutations. The aim of this European cohort study was to define the cancer risk faced by PMS2 mutation carriers. Data were collected from 98 PMS2 families ascertained from family cancer clinics that included a total of 2,548 family members and 377 proven mutation carriers. To adjust for potential ascertainment bias, a modified segregation analysis model was used to calculate colorectal cancer (CRC) and endometrial cancer (EC) risks. Standardized incidence ratios (SIRs) were calculated to estimate risks for other Lynch syndrome-associated cancers. The cumulative risk (CR) of CRC for male mutation carriers by age 70 years was 19%. The CR among female carriers was 11% for CRC and 12% for EC. The mean age of CRC development was 52 years, and there was a significant difference in mean age of CRC between the probands (mean, 47 years; range, 26 to 68 years) and other family members with a PMS2 mutation (mean, 58 years; range, 31 to 86 years; P PMS2 mutation, and it should be noted that we observed a substantial variation in cancer phenotype within and between families, suggesting the influence of genetic modifiers and lifestyle factors on cancer risks. © 2014 by American Society of Clinical Oncology.

  13. Overexpression of the DNA mismatch repair factor, PMS2, confers hypermutability and DNA damage tolerance.

    Science.gov (United States)

    Gibson, Shannon L; Narayanan, Latha; Hegan, Denise Campisi; Buermeyer, Andrew B; Liskay, R Michael; Glazer, Peter M

    2006-12-08

    Inherited defects in genes associated with DNA mismatch repair (MMR) have been linked to familial colorectal cancer. Cells deficient in MMR are genetically unstable and demonstrate a tolerance phenotype in response to certain classes of DNA damage. Some sporadic human cancers also show abnormalities in MMR gene function, typically due to diminished expression of one of the MutL homologs, MLH1. Here, we report that overexpression of the MutL homolog, human PMS2, can also cause a disruption of the MMR pathway in mammalian cells, resulting in hypermutability and DNA damage tolerance. A mouse fibroblast cell line carrying a recoverable lambda phage shuttle vector for mutation detection was transfected with either a vector designed to express hPMS2 or with an empty vector control. Cells overexpressing hPMS2 were found to have elevated spontaneous mutation frequencies at the cII reporter gene locus. They also showed an increase in the level of mutations induced by the alkylating agent, methynitrosourea (MNU). Clonogenic survival assays demonstrated increased survival of the PMS2-overexpressing cells following exposure to MNU, consistent with the induction of a damage tolerance phenotype. Similar results were seen in cells expressing a mutant PMS2 gene, containing a premature stop codon at position 134 and representing a variant found in an individual with familial colon cancer. These results show that dysregulation of PMS2 gene expression can disrupt MMR function in mammalian cells and establish an additional carcinogenic mechanism by which cells can develop genetic instability and acquire resistance to cytotoxic cancer therapies.

  14. Comprehensive Mutation Analysis of PMS2 in a Large Cohort of Probands Suspected of Lynch Syndrome or Constitutional Mismatch Repair Deficiency Syndrome.

    Science.gov (United States)

    van der Klift, Heleen M; Mensenkamp, Arjen R; Drost, Mark; Bik, Elsa C; Vos, Yvonne J; Gille, Hans J J P; Redeker, Bert E J W; Tiersma, Yvonne; Zonneveld, José B M; García, Encarna Gómez; Letteboer, Tom G W; Olderode-Berends, Maran J W; van Hest, Liselotte P; van Os, Theo A; Verhoef, Senno; Wagner, Anja; van Asperen, Christi J; Ten Broeke, Sanne W; Hes, Frederik J; de Wind, Niels; Nielsen, Maartje; Devilee, Peter; Ligtenberg, Marjolijn J L; Wijnen, Juul T; Tops, Carli M J

    2016-11-01

    Monoallelic PMS2 germline mutations cause 5%-15% of Lynch syndrome, a midlife cancer predisposition, whereas biallelic PMS2 mutations cause approximately 60% of constitutional mismatch repair deficiency (CMMRD), a rare childhood cancer syndrome. Recently improved DNA- and RNA-based strategies are applied to overcome problematic PMS2 mutation analysis due to the presence of pseudogenes and frequent gene conversion events. Here, we determined PMS2 mutation detection yield and mutation spectrum in a nationwide cohort of 396 probands. Furthermore, we studied concordance between tumor IHC/MSI (immunohistochemistry/microsatellite instability) profile and mutation carrier state. Overall, we found 52 different pathogenic PMS2 variants explaining 121 Lynch syndrome and nine CMMRD patients. In vitro mismatch repair assays suggested pathogenicity for three missense variants. Ninety-one PMS2 mutation carriers (70%) showed isolated loss of PMS2 in their tumors, for 31 (24%) no or inconclusive IHC was available, and eight carriers (6%) showed discordant IHC (presence of PMS2 or loss of both MLH1 and PMS2). Ten cases with isolated PMS2 loss (10%; 10/97) harbored MLH1 mutations. We confirmed that recently improved mutation analysis provides a high yield of PMS2 mutations in patients with isolated loss of PMS2 expression. Application of universal tumor prescreening methods will however miss some PMS2 germline mutation carriers. © 2016 WILEY PERIODICALS, INC.

  15. Inactivation of DNA mismatch repair by variants of uncertain significance in the PMS2 gene.

    Science.gov (United States)

    Drost, Mark; Koppejan, Hester; de Wind, Niels

    2013-11-01

    Lynch syndrome (LS) is a common cancer predisposition caused by an inactivating mutation in one of four DNA mismatch repair (MMR) genes. Frequently a variant of uncertain significance (VUS), rather than an obviously pathogenic mutation, is identified in one of these genes. The inability to define pathogenicity of such variants precludes targeted healthcare. Here, we have modified a cell-free assay to test VUS in the MMR gene PMS2 for functional activity. We have analyzed nearly all VUS in PMS2 found thus far and describe loss of MMR activity for five, suggesting the applicability of the assay for diagnosis of LS. © 2013 WILEY PERIODICALS, INC.

  16. Novel biallelic mutations in MSH6 and PMS2 genes: gene conversion as a likely cause of PMS2 gene inactivation.

    Science.gov (United States)

    Auclair, Jessie; Leroux, Dominique; Desseigne, Françoise; Lasset, Christine; Saurin, Jean Christophe; Joly, Marie Odile; Pinson, Stéphane; Xu, Xiao Li; Montmain, Gilles; Ruano, Eric; Navarro, Claudine; Puisieux, Alain; Wang, Qing

    2007-11-01

    Since the first report by our group in 1999, more than 20 unrelated biallelic mutations in DNA mismatch repair genes (MMR) have been identified. In the present report, we describe two novel cases: one carrying compound heterozygous mutations in the MSH6 gene; and the other, compound heterozygous mutations in the PMS2 gene. Interestingly, the inactivation of one PMS2 allele was likely caused by gene conversion. Although gene conversion has been suggested to be a mutation mechanism underlying PMS2 inactivation, this is the first report of its involvement in a pathogenic mutation. The clinical features of biallelic mutation carriers were similar to other previously described patients, with the presence of café-au-lait spots (CALS), early onset of brain tumors, and colorectal neoplasia. Our data provide further evidence of the existence, although rare, of a distinct recessively inherited syndrome on the basis of MMR constitutional inactivation. The identification of this syndrome should be useful for genetic counseling, especially in families with atypical hereditary nonpolyposis colon cancer (HNPCC) associated with childhood cancers, and for the clinical surveillance of these mutation carriers. 2007 Wiley-Liss, Inc.

  17. Evaluation of current prediction models for Lynch syndrome: updating the PREMM5 model to identify PMS2 mutation carriers

    NARCIS (Netherlands)

    A. Goverde (Anne); M.C.W. Spaander (Manon); D. Nieboer (Daan); A.M.W. van den Ouweland (Ans); W.N.M. Dinjens (Winand); H.J. Dubbink (Erik Jan); C. Tops (Cmj); S.W. Ten Broeke (Sanne W.); M.J. Bruno (Marco); R.M.W. Hofstra (Robert); E.W. Steyerberg (Ewout); A. Wagner (Anja)

    2017-01-01

    textabstractUntil recently, no prediction models for Lynch syndrome (LS) had been validated for PMS2 mutation carriers. We aimed to evaluate MMRpredict and PREMM5 in a clinical cohort and for PMS2 mutation carriers specifically. In a retrospective, clinic-based cohort we calculated predictions for

  18. Isolated Loss of PMS2 Immunohistochemical Expression is Frequently Caused by Heterogenous MLH1 Promoter Hypermethylation in Lynch Syndrome Screening for Endometrial Cancer Patients.

    Science.gov (United States)

    Kato, Aya; Sato, Naoki; Sugawara, Tae; Takahashi, Kazue; Kito, Masahiko; Makino, Kenichi; Sato, Toshiharu; Shimizu, Dai; Shirasawa, Hiromistu; Miura, Hiroshi; Sato, Wataru; Kumazawa, Yukiyo; Sato, Akira; Kumagai, Jin; Terada, Yukihiro

    2016-06-01

    Lynch syndrome (LS) is an autosomal-dominant inherited disorder mainly caused by a germline mutation in the DNA mismatch repair (MMR) genes (MLH1, MSH2, MSH6, and PMS2) and is associated with increased risk for various cancers, particularly colorectal cancer and endometrial cancer (EC). Women with LS account for 2% to 6% of EC patients; it is clinically important to identify LS in such individuals for predicting and/or preventing additional LS-associated cancers. PMS2 germline mutation (PMS2-LS) is the rarest contribution to LS etiology among the 4 LS-associated MMR germline mutations, and its detection is complicated. Therefore, prudent screening for PMS2-LS is important as it leads to an efficient LS identification strategy. Immunohistochemistry is recommended as a screening method for LS in EC. Isolated loss of PMS2 (IL-PMS2) expression is caused not only by PMS2-LS but also by MLH1 germline mutation or MLH1 promoter hypermethylation (MLH-PHM). This study aimed to determine the association between MLH1-PHM and IL-PMS2 to avoid inappropriate genetic analysis. We performed MLH1 methylation analysis and MLH1/PMS2 germline mutation testing on the IL-PMS2 cases. By performing MMR-immunohistochemistry on 360 unselected ECs, we could select 8 (2.2%) cases as IL-PMS2. Heterogenous MLH1 staining and MLH1-PHM were detected in 4 of 8 (50%) IL-PMS2 tumors. Of the 5 IL-PMS2 patients who underwent genetic analysis, 1 had PMS2 germline mutation with normal MLH1 expression (without MLH1-PHM), and no MLH1 germline mutation was detected. We suggest that MLH1 promoter methylation analysis for IL-PMS2 EC should be performed to exclude sporadic cases before further PMS2 genetic testing.

  19. The changing landscape of Lynch syndrome due to PMS2 mutations.

    Science.gov (United States)

    Blount, J; Prakash, A

    2018-07-01

    DNA repair pathways are essential for cellular survival as our DNA is constantly under assault from both exogenous and endogenous DNA damaging agents. Five major mammalian DNA repair pathways exist within a cell to maintain genomic integrity. Of these, the DNA mismatch repair (MMR) pathway is highly conserved among species and is well documented in bacteria. In humans, the importance of MMR is underscored by the discovery that a single mutation in any 1 of 4 genes within the MMR pathway (MLH1, MSH2, MSH6 and PMS2) results in Lynch syndrome (LS). LS is a autosomal dominant condition that predisposes individuals to a higher incidence of many malignancies including colorectal, endometrial, ovarian, and gastric cancers. In this review, we discuss the role of PMS2 in the MMR pathway, the evolving testing criteria used to identify variants in the PMS2 gene, the LS phenotype as well as the autosomal recessive condition called constitutional mismatch repair deficiency syndrome, and current methods used to elucidate the clinical impact of PMS2 mutations. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  20. Development of high performance readout ASICs for silicon photomultipliers (SiPMs)

    International Nuclear Information System (INIS)

    Shen, Wei

    2012-01-01

    Silicon Photomultipliers (SiPMs) are novel kind of solid state photon detectors with extremely high photon detection resolution. They are composed of hundreds or thousands of avalanche photon diode pixels connected in parallel. These avalanche photon diodes are operated in Geiger Mode. SiPMs have the same magnitude of multiplication gain compared to the conventional photomultipliers (PMTs). Moreover, they have a lot of advantages such as compactness, relatively low bias voltage and magnetic field immunity etc. Special readout electronics are required to preserve the high performance of the detector. KLauS and STiC are two CMOS ASIC chips designed in particular for SiPMs. KLauS is used for SiPM charge readout applications. Since SiPMs have a much larger detector capacitance compared to other solid state photon detectors such as PIN diodes and APDs, a few special techniques are used inside the chip to make sure a descent signal to noise ratio for pixel charge signal can be obtained. STiC is a chip dedicated to SiPM time-of-flight applications. High bandwidth and low jitter design schemes are mandatory for such applications where time jitter less than tens of picoseconds is required. Design schemes and error analysis as well as measurement results are presented in the thesis.

  1. 23 CFR 971.208 - Federal lands pavement management system (PMS).

    Science.gov (United States)

    2010-04-01

    ... components, at a minimum, as a basic framework for a PMS: (1) A database and an ongoing program for the collection and maintenance of the inventory, inspection, cost, and supplemental data needed to support the... estimate of the remaining service life. Performance and remaining service life may be developed with time...

  2. Stabilization of mismatch repair gene PMS2 by glycogen synthase kinase 3beta is implicated in the treatment of cervical carcinoma.

    Science.gov (United States)

    Zhang, Yuan; Shu, Yi Min; Wang, Shu Fang; Da, Bang Hong; Wang, Ze Hua; Li, Hua Bin

    2010-02-23

    PMS2 expression loss was reported in a variety of human. However, its importance has not been fully understood in cervical carcinoma. The aim of this study was to determine the expression of PMS2 in cervical carcinoma and evaluate the significance of mismatch repair gene PMS2 regulated by glycogen synthase kinase 3beta (GSK-3beta) in chemosensitivity. We examined PMS2 and phosphorylated GSK-3beta(s9) expression in cervical carcinoma tissues using immunohistochemical staining. Furthermore, we detected PMS2 expression in HeLa cells and evaluate the interaction with GSK-3beta after transfection with GSK-3beta by small interference RNA (siRNA), co-immunoprecipitation and immunoblotting. We also evaluated the effect of PMS2 transfection on HeLa cells' chemosensitivity to cisplatin treatment. We found significant downregulation of PMS2 in cervical carcinoma, which was negatively associated with phosphorylated GSK-3beta (s9). Furthermore, we demonstrated GSK-3beta transfection was able to interact with PMS2 and enhance PMS2 production in HeLa cells, and increased PMS2 production was responsible for enhanced chemosensitivity. Our results provide the evidence that stabilization of PMS2 production by GSK-3beta was important to improve chemosensitization, indicating the significance of GSK-3beta-related PMS2 downregulation in the development of cervical carcinoma and in developing a potential strategy for chemotherapy.

  3. Stabilization of mismatch repair gene PMS2 by glycogen synthase kinase 3β is implicated in the treatment of cervical carcinoma

    Directory of Open Access Journals (Sweden)

    Wang Ze

    2010-02-01

    Full Text Available Abstract Background PMS2 expression loss was reported in a variety of human. However, its importance has not been fully understood in cervical carcinoma. The aim of this study was to determine the expression of PMS2 in cervical carcinoma and evaluate the significance of mismatch repair gene PMS2 regulated by glycogen synthase kinase 3β (GSK-3β in chemosensitivity. Methods We examined PMS2 and phosphorylated GSK-3β(s9 expression in cervical carcinoma tissues using immunohistochemical staining. Furthermore, we detected PMS2 expression in HeLa cells and evaluate the interaction with GSK-3β after transfection with GSK-3β by small interference RNA (siRNA, co-immunoprecipitation and immunoblotting. We also evaluated the effect of PMS2 transfection on HeLa cells' chemosensitivity to cisplatin treatment. Results We found significant downregulation of PMS2 in cervical carcinoma, which was negatively associated with phosphorylated GSK-3β (s9. Furthermore, we demonstrated GSK-3β transfection was able to interact with PMS2 and enhance PMS2 production in HeLa cells, and increased PMS2 production was responsible for enhanced chemosensitivity. Conclusions Our results provide the evidence that stabilization of PMS2 production by GSK-3β was important to improve chemosensitization, indicating the significance of GSK-3β-related PMS2 downregulation in the development of cervical carcinoma and in developing a potential strategy for chemotherapy.

  4. Stabilization of mismatch repair gene PMS2 by glycogen synthase kinase 3β is implicated in the treatment of cervical carcinoma

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Yuan [Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022 (China); Shu, Yi Min [Allergy and Cancer Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080 (China); Wang, Shu Fang [Department of Pathology, Baylor College of Medicine, Houston, TX 77030 (United States); Da, Bang Hong; Wang, Ze Hua [Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022 (China); Li, Hua Bin [Allergy and Cancer Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080 (China); Department of Medicine, Feinberg Medical School, Northwestern University, Chicago, IL 60611 (United States)

    2010-02-23

    PMS2 expression loss was reported in a variety of human. However, its importance has not been fully understood in cervical carcinoma. The aim of this study was to determine the expression of PMS2 in cervical carcinoma and evaluate the significance of mismatch repair gene PMS2 regulated by glycogen synthase kinase 3β (GSK-3β) in chemosensitivity. We examined PMS2 and phosphorylated GSK-3β(s9) expression in cervical carcinoma tissues using immunohistochemical staining. Furthermore, we detected PMS2 expression in HeLa cells and evaluate the interaction with GSK-3β after transfection with GSK-3β by small interference RNA (siRNA), co-immunoprecipitation and immunoblotting. We also evaluated the effect of PMS2 transfection on HeLa cells' chemosensitivity to cisplatin treatment. We found significant downregulation of PMS2 in cervical carcinoma, which was negatively associated with phosphorylated GSK-3β (s9). Furthermore, we demonstrated GSK-3β transfection was able to interact with PMS2 and enhance PMS2 production in HeLa cells, and increased PMS2 production was responsible for enhanced chemosensitivity. Our results provide the evidence that stabilization of PMS2 production by GSK-3β was important to improve chemosensitization, indicating the significance of GSK-3β-related PMS2 downregulation in the development of cervical carcinoma and in developing a potential strategy for chemotherapy.

  5. Stabilization of mismatch repair gene PMS2 by glycogen synthase kinase 3β is implicated in the treatment of cervical carcinoma

    Science.gov (United States)

    2010-01-01

    Background PMS2 expression loss was reported in a variety of human. However, its importance has not been fully understood in cervical carcinoma. The aim of this study was to determine the expression of PMS2 in cervical carcinoma and evaluate the significance of mismatch repair gene PMS2 regulated by glycogen synthase kinase 3β (GSK-3β) in chemosensitivity. Methods We examined PMS2 and phosphorylated GSK-3β(s9) expression in cervical carcinoma tissues using immunohistochemical staining. Furthermore, we detected PMS2 expression in HeLa cells and evaluate the interaction with GSK-3β after transfection with GSK-3β by small interference RNA (siRNA), co-immunoprecipitation and immunoblotting. We also evaluated the effect of PMS2 transfection on HeLa cells' chemosensitivity to cisplatin treatment. Results We found significant downregulation of PMS2 in cervical carcinoma, which was negatively associated with phosphorylated GSK-3β (s9). Furthermore, we demonstrated GSK-3β transfection was able to interact with PMS2 and enhance PMS2 production in HeLa cells, and increased PMS2 production was responsible for enhanced chemosensitivity. Conclusions Our results provide the evidence that stabilization of PMS2 production by GSK-3β was important to improve chemosensitization, indicating the significance of GSK-3β-related PMS2 downregulation in the development of cervical carcinoma and in developing a potential strategy for chemotherapy. PMID:20178594

  6. Stabilization of mismatch repair gene PMS2 by glycogen synthase kinase 3β is implicated in the treatment of cervical carcinoma

    International Nuclear Information System (INIS)

    Zhang, Yuan; Shu, Yi Min; Wang, Shu Fang; Da, Bang Hong; Wang, Ze Hua; Li, Hua Bin

    2010-01-01

    PMS2 expression loss was reported in a variety of human. However, its importance has not been fully understood in cervical carcinoma. The aim of this study was to determine the expression of PMS2 in cervical carcinoma and evaluate the significance of mismatch repair gene PMS2 regulated by glycogen synthase kinase 3β (GSK-3β) in chemosensitivity. We examined PMS2 and phosphorylated GSK-3β(s9) expression in cervical carcinoma tissues using immunohistochemical staining. Furthermore, we detected PMS2 expression in HeLa cells and evaluate the interaction with GSK-3β after transfection with GSK-3β by small interference RNA (siRNA), co-immunoprecipitation and immunoblotting. We also evaluated the effect of PMS2 transfection on HeLa cells' chemosensitivity to cisplatin treatment. We found significant downregulation of PMS2 in cervical carcinoma, which was negatively associated with phosphorylated GSK-3β (s9). Furthermore, we demonstrated GSK-3β transfection was able to interact with PMS2 and enhance PMS2 production in HeLa cells, and increased PMS2 production was responsible for enhanced chemosensitivity. Our results provide the evidence that stabilization of PMS2 production by GSK-3β was important to improve chemosensitization, indicating the significance of GSK-3β-related PMS2 downregulation in the development of cervical carcinoma and in developing a potential strategy for chemotherapy

  7. A homozygous PMS2 founder mutation with an attenuated constitutional mismatch repair deficiency phenotype.

    Science.gov (United States)

    Li, Lili; Hamel, Nancy; Baker, Kristi; McGuffin, Michael J; Couillard, Martin; Gologan, Adrian; Marcus, Victoria A; Chodirker, Bernard; Chudley, Albert; Stefanovici, Camelia; Durandy, Anne; Hegele, Robert A; Feng, Bing-Jian; Goldgar, David E; Zhu, Jun; De Rosa, Marina; Gruber, Stephen B; Wimmer, Katharina; Young, Barbara; Chong, George; Tischkowitz, Marc D; Foulkes, William D

    2015-05-01

    Inherited mutations in DNA mismatch repair genes predispose to different cancer syndromes depending on whether they are mono-allelic or bi-allelic. This supports a causal relationship between expression level in the germline and phenotype variation. As a model to study this relationship, our study aimed to define the pathogenic characteristics of a recurrent homozygous coding variant in PMS2 displaying an attenuated phenotype identified by clinical genetic testing in seven Inuit families from Northern Quebec. Pathogenic characteristics of the PMS2 mutation NM_000535.5:c.2002A>G were studied using genotype-phenotype correlation, single-molecule expression detection and single genome microsatellite instability analysis. This PMS2 mutation generates a de novo splice site that competes with the authentic site. In homozygotes, expression of the full-length protein is reduced to a level barely detectable by conventional diagnostics. Median age at primary cancer diagnosis is 22 years among 13 NM_000535.5:c.2002A>G homozygotes, versus 8 years in individuals carrying bi-allelic truncating mutations. Residual expression of full-length PMS2 transcript was detected in normal tissues from homozygotes with cancers in their 20s. Our genotype-phenotype study of c.2002A>G illustrates that an extremely low level of PMS2 expression likely delays cancer onset, a feature that could be exploited in cancer preventive intervention. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

  8. Extended object-oriented Petri net model for mission reliability simulation of repairable PMS with common cause failures

    International Nuclear Information System (INIS)

    Wu, Xin-yang; Wu, Xiao-Yue

    2015-01-01

    Phased Mission Systems (PMS) have several phases with different success criteria. Generally, traditional analytical methods need to make some assumptions when they are applied for reliability evaluation and analysis of complex PMS, for example, the components are non-repairable or components are not subjected to common cause failures (CCF). However, the evaluation and analysis results may be inapplicable when the assumptions do not agree with practical situation. In this article, we propose an extended object-oriented Petri net (EOOPN) model for mission reliability simulation of repairable PMS with CCFs. Based on object-oriented Petri net (OOPN), EOOPN defines four reusable sub-models to depict PMS at system, phase, or component levels respectively, logic transitions to depict complex components reliability logics in a more readable form, and broadcast place to transmit shared information among components synchronously. After extension, EOOPN could deal with repairable PMS with both external and internal CCFs conveniently. The mission reliability modelling, simulation and analysis using EOOPN are illustrated by a PMS example. The results demonstrate that the proposed EOOPN model is effective. - Highlights: • EOOPN model was effective in reliability simulation for repairable PMS with CCFs. • EOOPN had modular and hierarchical structure. • New elements of EOOPN made the modelling process more convenient and friendlier. • EOOPN had better model reusability and readability than other PNs

  9. Effects of a combination of Hypericum perforatum and Vitex agnus-castus on PMS-like symptoms in late-perimenopausal women: findings from a subpopulation analysis.

    Science.gov (United States)

    van Die, Margaret Diana; Bone, Kerry M; Burger, Henry G; Reece, John E; Teede, Helena J

    2009-09-01

    It has been suggested that some of the symptoms typically attributed to menopause may be more related to premenstrual syndrome (PMS) than menopause, as perimenopausal women appear to be more prone to PMS-like symptoms, or at least to tolerate them less well. The objective of this study was to evaluate the effectiveness of a phytotherapeutic intervention comprising a combination of Hypericum perforatum (St. John's wort) and Vitex agnus-castus (chaste tree/berry) in the management of PMS-like symptoms in perimenopausal women. A double-blind, randomized, placebo-controlled parallel trial was conducted over 16 weeks on menopause-related symptoms. Data on PMS-like symptoms were collected at 4-weekly intervals from a small subgroup of late-perimenopausal women (n = 14) participating in this study. The primary endpoint was PMS scores measured on the Abrahams Menstrual Symptoms Questionnaire, comprising the subclusters of PMS-A (anxiety), PMS-D (depression), PMS-H (hydration), and PMS-C (cravings). Herbal combination therapy or placebo tablets were administered twice daily. At the end of the 16-week treatment phase, analyses of covariance showed the herbal combination to be superior to placebo for total PMS-like scores (p = 0.02), PMS-D (p = 0.006), and PMS-C clusters (p = 0.027). The active treatment group also showed significant reductions in the anxiety (p = 0.003) and hydration (p = 0.002) clusters, using paired-samples t tests. Results of trend analyses showed significant treatment group effects across the five phases for total PMS and all subscales, all in the clinically expected direction. No significant trends were evident in the placebo group. These results suggest a potentially significant clinical application for this phytotherapeutic combination in PMS-like symptoms among perimenopausal women. Further research is warranted through a randomized, controlled trial dedicated to investigation of these symptoms.

  10. SiPMs coated with TPB: coating protocol and characterization for NEXT

    International Nuclear Information System (INIS)

    Álvarez, V; Agramunt, J; Ball, M; Bayarri, J; Cárcel, S; Cervera, A; Díaz, J; Batallé, M; Borges, F I G; Conde, C A N; Dias, T H V T; Bolink, H; Brine, H; Carmona, J M; Castel, J; Cebrián, S; Dafni, T; Catalá, J M; Esteve, R; Chan, D

    2012-01-01

    Silicon photomultipliers (SiPM) are the photon detectors chosen for the tracking readout in NEXT, a neutrinoless ββ decay experiment which uses a high pressure gaseous xenon time projection chamber (TPC). The reconstruction of event track and topology in this gaseous detector is a key handle for background rejection. Among the commercially available sensors that can be used for tracking, SiPMs offer important advantages, mainly high gain, ruggedness, cost-effectiveness and radio-purity. Their main drawback, however, is their non sensitivity in the emission spectrum of the xenon scintillation (peak at 175 nm). This is overcome by coating these sensors with the organic wavelength shifter tetraphenyl butadiene (TPB). In this paper we describe the protocol developed for coating the SiPMs with TPB and the measurements performed for characterizing the coatings as well as the performance of the coated sensors in the UV-VUV range.

  11. A frame-shift mutation of PMS2 is a widespread cause of Lynch syndrome

    DEFF Research Database (Denmark)

    Clendenning, Mark; Senter, Leigha; Hampel, Heather

    2008-01-01

    BACKGROUND: When compared to the other mismatch repair genes involved in Lynch syndrome, the identification of mutations within PMS2 has been limited (Lynch syndrome cases...... on immunohistochemical analysis. RESULTS: We have identified a frequently occurring frame-shift mutation (c.736_741del6ins11) in 12 ostensibly unrelated Lynch syndrome patients (20% of patients we have identified with a deleterious mutation in PMS2, n=61). These individuals all display the rare allele (population...... and Swedish ancestry. We estimate that there are >10,000 carriers of this mutation in the United States alone. The identification of both the mutation and the common haplotype in one Swedish control sample (n = 225), along with evidence that Lynch syndrome associated cancers are rarer than expected...

  12. Radiation hardness tests of SiPMs for the JLab Hall D Barrel calorimeter

    International Nuclear Information System (INIS)

    Qiang, Yi; Zorn, Carl; Barbosa, Fernando; Smith, Elton

    2013-01-01

    We report on the measurement of the neutron radiation hardness of silicon photomultipliers (SiPMs) manufactured by Hamamatsu Corporation in Japan and SensL in Ireland. Samples from both companies were irradiated by neutrons created by a 1 GeV electron beam hitting a thin lead target at Jefferson Lab Hall A. More tests regarding the temperature dependence of the neutron radiation damage and self-annealing were performed on Hamamatsu SiPMs using a calibrated Am–Be neutron source from the Jefferson Lab Radiation Control group. As the result of irradiation both dark current and dark rate increase linearly as a function of the 1 MeV equivalent neutron fluence and a temperature dependent self-annealing effect is observed.

  13. Reduction of MLH1 and PMS2 confers temozolomide resistance and is associated with recurrence of glioblastoma.

    Science.gov (United States)

    Shinsato, Yoshinari; Furukawa, Tatsuhiko; Yunoue, Shunji; Yonezawa, Hajime; Minami, Kentarou; Nishizawa, Yukihiko; Ikeda, Ryuji; Kawahara, Kohichi; Yamamoto, Masatatsu; Hirano, Hirofumi; Tokimura, Hiroshi; Arita, Kazunori

    2013-12-01

    Although there is a relationship between DNA repair deficiency and temozolomide (TMZ) resistance in glioblastoma (GBM), it remains unclear which molecule is associated with GBM recurrence. We isolated three TMZ-resistant human GBM cell lines and examined the expression of O6-methylguanine-DNA methyltransferase (MGMT) and mismatch repair (MMR) components. We used immunohistochemical analysis to compare MutL homolog 1 (MLH1), postmeiotic segregation increased 2 (PMS2) and MGMT expression in primary and recurrent GBM specimens obtained from GBM patients during TMZ treatment. We found a reduction in MLH1 expression and a subsequent reduction in PMS2 protein levels in TMZ-resistant cells. Furthermore, MLH1 or PMS2 knockdown confered TMZ resistance. In recurrent GBM tumours, the expression of MLH1 and PMS2 was reduced when compared to primary tumours.

  14. Evaluation of current Louisiana flexible pavement structures using PMS data and new M-E pavement design guide.

    Science.gov (United States)

    2010-10-01

    The proposed study uses the new MEPDG together with data available from LADOTDs Pavement Management System (PMS) and other data sources from LADOTDs main frame to evaluate typical flexible pavement structures currently used and to make changes ...

  15. Development of adaptive core emulator for PMS-XRBP of CE type plant

    International Nuclear Information System (INIS)

    Song, Jae Seung; Zee, Sung Quun; Lee, Chung Chan; Lee, Ki Bog; Rhy, Hyo Sang; Chang, Jong Hwa; Lee, Young Ouk; Baek, Seung Min; Seo, Ho Joon.

    1996-12-01

    The purpose of this report is to develop ONED-based adaptive core emulator (ACE) for Korean Standard Nuclear Power Plant. This report is first year report and includes 1) augmentation of ONED94 I/O system 2) non-equilibrium xenon initialization for core transient simulation 3) ONED94 verification via plant measurements 4) automatic data link system from PMS and personal computer. (author). 4 tabs., 4 figs., 8 refs

  16. Homozygous PMS2 deletion causes a severe colorectal cancer and multiple adenoma phenotype without extraintestinal cancer.

    Science.gov (United States)

    Will, Olivia; Carvajal-Carmona, Luis G; Gorman, Patricia; Howarth, Kimberley M; Jones, Angela M; Polanco-Echeverry, Guadalupe M; Chinaleong, Jo-Anne; Günther, Thomas; Silver, Andrew; Clark, Susan K; Tomlinson, Ian

    2007-02-01

    We report a patient of Indian descent with parental consanguinity, who developed 10 carcinomas and 35 adenomatous polyps at age 23 and duodenal adenocarcinoma at age 25. He also had dysmorphic features, mental retardation, and café-au-lait spots but no brain tumor. We aimed to establish his molecular diagnosis. Germ-line screening for APC and MYH/MUTYH mutations was normal as was immunohistochemistry for MLH1 and MSH2 proteins. Investigation by array-comparative genomic hybridization revealed deletion of a small region on chromosome 7. Using polymerase chain reaction, this region was refined to a 400-kilobase deletion, which included exons 9-15 of the PMS2 gene, and all coding regions of oncomodulin, TRIAD3, and FSCN1. The deletion was confirmed as homozygous, and both parents were carriers. Immunohistochemistry showed absent PMS2 expression in all tumors and normal tissue. Most tumors showed microsatellite instability, more marked at dinucleotide than mononucleotide repeats. The tumors harbored no somatic mutations in APC, BRAF, AXIN2, or beta-catenin, but KRAS2 and TGFBR2 mutations were found. Our patient represents a novel phenotype for homozygous PMS2 mutation and perhaps the most severe colorectal cancer phenotype-in terms of numbers of malignancies at an early age-described to date. PMS2 mutations-and perhaps other homozygous mismatch repair mutations-should be considered in any patient presenting with multiple gastrointestinal tumors, since our patient could not be distinguished clinically from cases with attenuated familial adenomatous polyposis or MUTYH-associated polyposis.

  17. Development of adaptive core emulator for PMS-XRBP of CE type plant

    Energy Technology Data Exchange (ETDEWEB)

    Song, Jae Seung; Zee, Sung Quun; Lee, Chung Chan; Lee, Ki Bog; Rhy, Hyo Sang; Chang, Jong Hwa; Lee, Young Ouk; Baek, Seung Min; Seo, Ho Joon

    1996-12-01

    The purpose of this report is to develop ONED-based adaptive core emulator (ACE) for Korean Standard Nuclear Power Plant. This report is first year report and includes (1) augmentation of ONED94 I/O system (2) non-equilibrium xenon initialization for core transient simulation (3) ONED94 verification via plant measurements (4) automatic data link system from PMS and personal computer. (author). 4 tabs., 4 figs., 8 refs.

  18. Oxidation of Refractory Benzothiazoles with PMS/CuFe2O4: Kinetics and Transformation Intermediates

    KAUST Repository

    Zhang, Tao

    2016-05-04

    Benzothiazole (BTH) and its derivatives, 2-(methylthio)bezothiazole (MTBT), 2-benzothiazolsulfonate (BTSA) and 2-hydroxybenzothiazole (OHBT), are refractory pollutants ubiquitously existing in urban runoff at relatively high concentrations. Here, we report their oxidation by CuFe2O4-activated peroxomonosulfate (PMS/CuFe2O4), focusing on kinetics and transformation intermediates. These benzothiazoles can be efficiently degraded by this oxidation process which is confirmed to generate mainly sulfate radicals (with negligible hydroxyl-radical formation) under slightly acidic to neutral pH conditions. The molar exposure ratio of sulfate radical to residual PMS (i.e. Rct) of this process is a constant which is related to reaction condition and can be easily determined. Reaction rate constants of these benzothiazoles towards sulfate radical are (3.3 ± 0.3) × 109, (1.4 ± 0.3) × 109, (1.5 ± 0.1) × 109 and (4.7 ± 0.5) × 109 M-1s-1, respectively (pH 7 and 20 oC). Based on Rct and these rate constants, their degradation in the presence of organic matter can be well predicted. A number of transformation products were detected and tentatively identified using triple-quadruple/linear ion trap MS/MS and high-resolution MS. It appears that sulfate radicals attack BTH, MTBT and BTSA on their benzo ring via electron transfer, generating multiple hydroxylated intermediates which are reactive towards common oxidants. For OHBT oxidation, it prefers to break down the thiazole ring. Due to competitions of the transformation intermediates, a minimum PMS/pollutant molar ratio of 10-20 is required for effective degradation. The flexible PMS/CuFe2O4 could be a useful process to remove the benzothiazoles from low DOC waters like urban runoff or polluted groundwater.

  19. Oxidation of Refractory Benzothiazoles with PMS/CuFe2O4: Kinetics and Transformation Intermediates

    KAUST Repository

    Zhang, Tao; Chen, Yin; Leiknes, TorOve

    2016-01-01

    Benzothiazole (BTH) and its derivatives, 2-(methylthio)bezothiazole (MTBT), 2-benzothiazolsulfonate (BTSA) and 2-hydroxybenzothiazole (OHBT), are refractory pollutants ubiquitously existing in urban runoff at relatively high concentrations. Here, we report their oxidation by CuFe2O4-activated peroxomonosulfate (PMS/CuFe2O4), focusing on kinetics and transformation intermediates. These benzothiazoles can be efficiently degraded by this oxidation process which is confirmed to generate mainly sulfate radicals (with negligible hydroxyl-radical formation) under slightly acidic to neutral pH conditions. The molar exposure ratio of sulfate radical to residual PMS (i.e. Rct) of this process is a constant which is related to reaction condition and can be easily determined. Reaction rate constants of these benzothiazoles towards sulfate radical are (3.3 ± 0.3) × 109, (1.4 ± 0.3) × 109, (1.5 ± 0.1) × 109 and (4.7 ± 0.5) × 109 M-1s-1, respectively (pH 7 and 20 oC). Based on Rct and these rate constants, their degradation in the presence of organic matter can be well predicted. A number of transformation products were detected and tentatively identified using triple-quadruple/linear ion trap MS/MS and high-resolution MS. It appears that sulfate radicals attack BTH, MTBT and BTSA on their benzo ring via electron transfer, generating multiple hydroxylated intermediates which are reactive towards common oxidants. For OHBT oxidation, it prefers to break down the thiazole ring. Due to competitions of the transformation intermediates, a minimum PMS/pollutant molar ratio of 10-20 is required for effective degradation. The flexible PMS/CuFe2O4 could be a useful process to remove the benzothiazoles from low DOC waters like urban runoff or polluted groundwater.

  20. 2. All-Polish Seminar: Monitoring of Radioactive Environment Contamination Using ASS-500 and PMS Stations

    International Nuclear Information System (INIS)

    1998-01-01

    During last 10 years the modern system of radiological pollution monitoring has been developed in Poland. At the beginning it was composed of ASS-500 stations. At the end of 1995 five automatic PMS stations have been installed as the result of the collaboration between Polish and Danish governments. Several stations of both types were include later. The system is coordinated by Central Laboratory for Radiological Protection. The report reviews the meeting dedicated to problems and future developments of the system

  1. The PM/S module and the BIO/TSR requirements comparison report summary

    International Nuclear Information System (INIS)

    PEERY, B.Q.

    1999-01-01

    This report summarizes the comparison between the Preventive Maintenance/Surveillance System (PM/S) database and the requirements identified in the Tank Waste Remediation Systems Basis for Interim Operation (BIO) (HNF-SD-WM-BIO-001); the Technical Safety Requirements (TSR's) (HNF-SD-WM-TSR-006); The Tank Farms Administrative Controls Manual, (HNF-IP-1266); and The TWRS Facility Safety Equipment List, (HNF-SD-WM-SEL-0404). Corrective actions identified are completed or in process

  2. SiPMs characterization and selection for the DUNE far detector photon detection system

    Science.gov (United States)

    Sun, Y.; Maricic, J.

    2016-01-01

    The Deep Underground Neutrino Experiment (DUNE) together with the Long Baseline Neutrino Facility (LBNF) hosted at the Fermilab will provide a unique, world-leading program for the exploration of key questions at the forefront of neutrino physics and astrophysics. CP violation in neutrino flavor mixing is one of its most important potential discoveries. Additionally, the experiment will determine the neutrino mass hierarchy and precisely measure the neutrino mixing parameters which may potentially reveal new fundamental symmetries of nature. Moreover, the DUNE is also designed for the observation of nucleon decay and supernova burst neutrinos. The photon detection (PD) system in the DUNE far detector provides trigger for cosmic backgrounds, enhances supernova burst trigger efficiency and improves the energy resolution of the detector. The DUNE adopts the technology of liquid argon time projection chamber (LArTPC) that requires the PD sensors, silicon photomultipliers (SiPM), to be carefully chosen to not only work properly in LAr temperature, but also meet certain specifications for the life of the experiment. A comprehensive testing of SiPMs in cryostat is necessary since the datasheet provided by the manufactures in the market does not cover this temperature regime. This paper gives the detailed characterization results of SenSL C-Series 60035 SiPMs, including gain, dark count rate (DCR), cross-talk and after-pulse rate. Characteristic studies on SiPMs from other vendors are also discussed in order to avoid any potential problems associated with using a single source. Moreover, the results of the ongoing mechanical durability tests are shown for the current candidate, SenSL B/C-Series 60035 SiPMs.

  3. JST Thesaurus Headwords and Synonyms: PMS [MeCab user dictionary for science technology term[Archive

    Lifescience Database Archive (English)

    Full Text Available MeCab user dictionary for science technology term PMS 名詞 一般 * * * * 医薬品市販後調査 イヤクヒンシハンゴチョウサ イヤクヒンシハンゴチョーサ Thesaurus2015 200906079217411060 C LS41 UNKNOWN_1 PMS

  4. Evaluation of current prediction models for Lynch syndrome: updating the PREMM5 model to identify PMS2 mutation carriers.

    Science.gov (United States)

    Goverde, A; Spaander, M C W; Nieboer, D; van den Ouweland, A M W; Dinjens, W N M; Dubbink, H J; Tops, C J; Ten Broeke, S W; Bruno, M J; Hofstra, R M W; Steyerberg, E W; Wagner, A

    2018-07-01

    Until recently, no prediction models for Lynch syndrome (LS) had been validated for PMS2 mutation carriers. We aimed to evaluate MMRpredict and PREMM5 in a clinical cohort and for PMS2 mutation carriers specifically. In a retrospective, clinic-based cohort we calculated predictions for LS according to MMRpredict and PREMM5. The area under the operator receiving characteristic curve (AUC) was compared between MMRpredict and PREMM5 for LS patients in general and for different LS genes specifically. Of 734 index patients, 83 (11%) were diagnosed with LS; 23 MLH1, 17 MSH2, 31 MSH6 and 12 PMS2 mutation carriers. Both prediction models performed well for MLH1 and MSH2 (AUC 0.80 and 0.83 for PREMM5 and 0.79 for MMRpredict) and fair for MSH6 mutation carriers (0.69 for PREMM5 and 0.66 for MMRpredict). MMRpredict performed fair for PMS2 mutation carriers (AUC 0.72), while PREMM5 failed to discriminate PMS2 mutation carriers from non-mutation carriers (AUC 0.51). The only statistically significant difference between PMS2 mutation carriers and non-mutation carriers was proximal location of colorectal cancer (77 vs. 28%, p PMS2 mutation carriers (AUC 0.77) and overall (AUC 0.81 vs. 0.72). We validated these results in an external cohort of 376 colorectal cancer patients, including 158 LS patients. MMRpredict and PREMM5 cannot adequately identify PMS2 mutation carriers. Adding location of colorectal cancer to PREMM5 may improve the performance of this model, which should be validated in larger cohorts.

  5. Molecular Background of Colorectal Tumors From Patients with Lynch Syndrome Associated With Germline Variants in PMS2.

    Science.gov (United States)

    Ten Broeke, S W; van Bavel, T C; Jansen, A M L; Gómez-García, E; Hes, F J; van Hest, L P; Letteboer, T G W; Olderode-Berends, M J W; Ruano, D; Spruijt, L; Suerink, M; Tops, C M; van Eijk, R; Morreau, H; van Wezel, T; Nielsen, M

    2018-05-11

    Germline variants in the mismatch repair genes MLH1, MSH2 (EPCAM), MSH6, or PMS2 cause Lynch syndrome. Patients with these variants have an increased risk of developing colorectal cancers (CRCs) that differ from sporadic CRCs in genetic and histologic features. It has been a challenge to study CRCs associated with PMS2 variants (PMS2-associated CRCs) because these develop less frequently and in patients of older ages than colorectal tumors with variants in the other mismatch repair genes. We analyzed 20 CRCs associated with germline variants in PMS2, 22 sporadic CRCs, 18 CRCs with germline variants in MSH2, and 24 CRCs from patients with germline variants in MLH1. Tumor tissue blocks were collected from Dutch pathology departments in 2017. After extraction of tumor DNA, we used a platform designed to detect approximately 3000 somatic hotspot variants in 55 genes (including KRAS, APC, CTNNB1, and TP53). Somatic variant frequencies were compared using the Fisher's exact test. None of the PMS2-associated CRCs contained any somatic variants in the catenin beta 1 gene (CTNNB1), which encodes β-catenin, whereas 14/24 MLH1-associated CRCs (58%) contained variants in CTNNB1. Half of PMS2-associated CRCs contained KRAS variants, but only 20% of these were in hotspots that encoded G12D or G13D. These hotspot variants occurred more frequently in CRCs associated with variants in MLH1 (37.5%, P=.44) and MSH2 (and 71.4%, P=.035) than with variants in PMS2. In a genetic analysis of 84 colorectal tumors, we found tumors from patients with PMS2-associated Lynch syndrome to be distinct from colorectal tumors associated with defects in other mismatch repair genes. This might account for differences in development and less frequent occurrence. Copyright © 2018 AGA Institute. Published by Elsevier Inc. All rights reserved.

  6. The prevalence, impairment, impact, and burden of premenstrual dysphoric disorder (PMS/PMDD).

    Science.gov (United States)

    Halbreich, Uriel; Borenstein, Jeff; Pearlstein, Terry; Kahn, Linda S

    2003-08-01

    Currently it is estimated that 3-8% of women of reproductive age meet strict criteria for premenstrual dysphoric disorder (PMDD). Assessment of published reports demonstrate that the prevalence of clinically relevant dysphoric premenstrual disorder is probably higher. 13-18% of women of reproductive age may have premenstrual dysphoric symptoms severe enough to induce impairment and distress, though the number of symptoms may not meet the arbitrary count of 5 symptoms on the PMDD list. The impairment and lowered quality of life for PMDD is similar to that of dysthymic disorder and is not much lower than major depressive disorder. Nevertheless, PMS/PMDD is still under-recognized in large published epidemiological studies, as well as assessments of burden of disease. It is demonstrated here that the burden of PMS/PMDD as well as the disability adjusted life years (DALY) lost due to this repeated-cyclic disorder is in the same magnitude as major recognized disorders. Appropriate recognition of the disorder and its impact should lead to treatment of more women with PMS/PMDD. Efficacious treatments are available. They should reduce individual suffering and impact on family, society, and economy.

  7. Improved equivalent magnetic network modeling for analyzing working points of PMs in interior permanent magnet machine

    Science.gov (United States)

    Guo, Liyan; Xia, Changliang; Wang, Huimin; Wang, Zhiqiang; Shi, Tingna

    2018-05-01

    As is well known, the armature current will be ahead of the back electromotive force (back-EMF) under load condition of the interior permanent magnet (PM) machine. This kind of advanced armature current will produce a demagnetizing field, which may make irreversible demagnetization appeared in PMs easily. To estimate the working points of PMs more accurately and take demagnetization under consideration in the early design stage of a machine, an improved equivalent magnetic network model is established in this paper. Each PM under each magnetic pole is segmented, and the networks in the rotor pole shoe are refined, which makes a more precise model of the flux path in the rotor pole shoe possible. The working point of each PM under each magnetic pole can be calculated accurately by the established improved equivalent magnetic network model. Meanwhile, the calculated results are compared with those calculated by FEM. And the effects of d-axis component and q-axis component of armature current, air-gap length and flux barrier size on working points of PMs are analyzed by the improved equivalent magnetic network model.

  8. Simultaneous removal of NO and SO2 using vacuum ultraviolet light (VUV)/heat/peroxymonosulfate (PMS).

    Science.gov (United States)

    Liu, Yangxian; Wang, Yan; Wang, Qian; Pan, Jianfeng; Zhang, Jun

    2018-01-01

    Simultaneous removal process of SO 2 and NO from flue gas using vacuum ultraviolet light (VUV)/heat/peroxymonosulfate (PMS) in a VUV spraying reactor was proposed. The key influencing factors, active species, reaction products and mechanism of SO 2 and NO simultaneous removal were investigated. The results show that vacuum ultraviolet light (185 nm) achieves the highest NO removal efficiency and yield of and under the same test conditions. NO removal is enhanced at higher PMS concentration, light intensity and oxygen concentration, and is inhibited at higher NO concentration, SO 2 concentration and solution pH. Solution temperature has a double impact on NO removal. CO 2 concentration has no obvious effect on NO removal. and produced from VUV-activation of PMS play a leading role in NO removal. O 3 and ·O produced from VUV-activation of O 2 also play an important role in NO removal. SO 2 achieves complete removal under all experimental conditions due to its very high solubility in water and good reactivity. The highest simultaneous removal efficiency of SO 2 and NO reaches 100% and 91.3%, respectively. Copyright © 2017 Elsevier Ltd. All rights reserved.

  9. Effectiveness of group cognitive-behavioral therapy ‎on ‎symptoms of premenstrual syndrome (PMS

    Directory of Open Access Journals (Sweden)

    Maryam Maddineshat

    2016-02-01

    Full Text Available Objective: Standards of care and treatment of premenstrual syndrome (PMS vary. Non-drug ‎psychosocial intervention therapy is recommended for women with any kind of ‎discomfort or distress caused by PMS. The current study examined the effectiveness of ‎group cognitive-behavioral therapy on the symptoms of PMS at a girls’ dormitory of ‎North Khorasan University of Medical Sciences.Method: In this quasi-experimental study, 32 female students with PMS who were majoring in ‎nursing and midwifery and residing in the dormitory were selected using the ‎convenience sampling method and were assigned to experimental and control groups. ‎The Standardized Premenstrual Symptoms Screening Tool was used as the research ‎tool. Eight sessions of cognitive-behavioral group therapy were held for the studentsResults: There was a significant difference in psychological symptoms before and after ‎cognitive-behavioral therapy (p=0.012. Furthermore, cognitive-behavioral therapy was ‎effective on social interferences caused by PMS symptoms (p=0.012.‎Conclusion: Group cognitive-behavioral therapy effectively alleviates PMS symptoms in female ‎college students.‎

  10. Homozygous germ-line mutation of the PMS2 mismatch repair gene: a unique case report of constitutional mismatch repair deficiency (CMMRD).

    Science.gov (United States)

    Ramchander, N C; Ryan, N A J; Crosbie, E J; Evans, D G

    2017-04-05

    Constitutional mismatch repair deficiency syndrome results from bi-allelic inheritance of mutations affecting the key DNA mismatch repair genes: MLH1, MSH2, MSH6 or PMS2. Individuals with bi-allelic mutations have a dysfunctional mismatch repair system from birth; as a result, constitutional mismatch repair deficiency syndrome is characterised by early onset malignancies. Fewer than 150 cases have been reported in the literature over the past 20 years. This is the first report of the founder PMS2 mutation - NM_000535.5:c.1500del (p.Val501TrpfsTer94) in exon 11 and its associated cancers in this family. The proband is 30 years old and is alive today. She is of Pakistani ethnic origin and a product of consanguinity. She initially presented aged 24 with painless bleeding per-rectum from colorectal polyps and was referred to clinical genetics. Clinical examination revealed two café-au-lait lesions, lichen planus, and a dermoid cyst. Her sister had been diagnosed in childhood with an aggressive brain tumour followed by colorectal cancer. During follow up, the proband developed 37 colorectal adenomatous polyps, synchronous ovarian and endometrial adenocarcinomas, and ultimately a metachronous gastric adenocarcinoma. DNA sequencing of peripheral lymphocytes revealed a bi-allelic inheritance of the PMS2 mutation NM_000535.5:c.1500del (p.Val501TrpfsTer94) in exon 11. Ovarian tumour tissue demonstrated low microsatellite instability. To date, she has had a total abdominal hysterectomy, bilateral salpingo-oophorectomy, and a total gastrectomy. Aspirin and oestrogen-only hormone replacement therapy provide some chemoprophylaxis and manage postmenopausal symptoms, respectively. An 18-monthly colonoscopy surveillance programme has led to the excision of three high-grade dysplastic colorectal tubular adenomatous polyps. The proband's family pedigree displays multiple relatives with cancers including a likely case of 'true' Turcot syndrome. Constitutional mismatch repair

  11. Germline PMS2 and somatic POLE exonuclease mutations cause hypermutability of the leading DNA strand in biallelic mismatch repair deficiency syndrome brain tumours.

    Science.gov (United States)

    Andrianova, Maria A; Chetan, Ghati Kasturirangan; Sibin, Madathan Kandi; Mckee, Thomas; Merkler, Doron; Narasinga, Rao Kvl; Ribaux, Pascale; Blouin, Jean-Louis; Makrythanasis, Periklis; Seplyarskiy, Vladimir B; Antonarakis, Stylianos E; Nikolaev, Sergey I

    2017-11-01

    Biallelic mismatch repair deficiency (bMMRD) in tumours is frequently associated with somatic mutations in the exonuclease domains of DNA polymerases POLE or POLD1, and results in a characteristic mutational profile. In this article, we describe the genetic basis of ultramutated high-grade brain tumours in the context of bMMRD. We performed exome sequencing of two second-cousin patients from a large consanguineous family of Indian origin with early onset of high-grade glioblastoma and astrocytoma. We identified a germline homozygous nonsense variant, p.R802*, in the PMS2 gene. Additionally, by genome sequencing of these tumours, we found extremely high somatic mutation rates (237/Mb and 123/Mb), as well as somatic mutations in the proofreading domain of POLE polymerase (p.P436H and p.L424V), which replicates the leading DNA strand. Most interestingly, we found, in both cancers, that the vast majority of mutations were consistent with the signature of POLE exo - , i.e. an abundance of C>A and C>T mutations, particularly in special contexts, on the leading strand. We showed that the fraction of mutations under positive selection among mutations in tumour suppressor genes is more than two-fold lower in ultramutated tumours than in other glioblastomas. Genetic analyses enabled the diagnosis of the two consanguineous childhood brain tumours as being due to a combination of PMS2 germline and POLE somatic variants, and confirmed them as bMMRD/POLE exo - disorders. Copyright © 2017 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd. Copyright © 2017 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

  12. Peritumoral granulomatous reaction in endometrial carcinoma: association with DNA mismatch repair protein deficiency, particularly loss of PMS2 expression.

    Science.gov (United States)

    Stewart, Colin J R; Pearn, Amy; Pachter, Nicholas; Tan, Adeline

    2018-04-30

    The observation of peritumoral granulomatous reactions (PGRs) in two endometrial carcinomas (ECs) with a PMS2-deficient/MLH1-intact expression pattern led us to investigate whether PGRs in EC were specifically associated with DNA mismatch repair (MMR) protein deficiency, particularly PMS2 loss. Hysterectomy specimens from 22 MMR protein-intact and 54 MMR protein-deficient ECs were reviewed with specific attention to the presence of a PGR and a tumour-associated lymphoid reaction [including tumour-infiltrating lymphocytes (TILs) and stromal lymphoid infiltrates]. The MMR protein-deficient ECs included 22 cases with combined MLH1/PMS2 loss, 11 with combined MSH2/MSH6 loss, 11 with isolated MSH6 loss, and 10 with PMS2 loss but intact MLH1 staining (including the two 'index' cases). Overall, PGRs were identified in seven of 54 (13%) MMR protein-deficient ECs, five of which showed a PMS2-deficient/MLH1-intact immunophenotype; three of these patients had germline PMS2 mutations and one additional patient had a germline MSH6 mutation. None of the MMR protein-intact tumours showed a PGR. Although five of the seven PGR-positive ECs had a high-grade histological component, six were stage I. Most ECs with PGRs also showed TILs and stromal lymphoid reactions, similarly to MMR protein-deficient ECs in general. MMR protein-deficient ECs, particularly those with PMS2 loss, occasionally show PGRs in addition to stromal lymphoid infiltrates and TILs. Therefore, PGRs could be considered to constitute a histological prompt for consideration of Lynch syndrome. The potential prognostic significance of PGRs in EC requires further study. © 2018 John Wiley & Sons Ltd.

  13. Reduced Pms2 expression in non-neoplastic flat mucosa from patients with colon cancer correlates with reduced apoptosis competence.

    Science.gov (United States)

    Bernstein, Harris; Prasad, Anil; Holubec, Hana; Bernstein, Carol; Payne, Claire M; Ramsey, Lois; Dvorakova, Katerina; Wilson, Megan; Warneke, James A; Garewal, Harinder

    2006-06-01

    Pms2 protein is a component of the DNA mismatch repair complex responsible both for post-replication correction of DNA nucleotide mispairs and for early steps in apoptosis. Germline mutations in DNA mismatch repair genes give rise to hereditary non-polyposis colon cancer, which accounts for about 4% of colon cancers. However, little is known about the expression of mismatch repair proteins in relation to sporadic colon cancer, which accounts for the great majority of colon cancers. Multiple samples were taken from the non-neoplastic flat mucosa of colon resections from patients with no colonic neoplasia, a tubulovillous adenoma, or an adenocarcinoma. Expression of Pms2 was assessed using semiquantitative immunohistochemistry. Apoptosis was assessed in polychrome-stained epoxy sections using morphologic criteria. Samples from patients without colonic neoplasia had moderate to strong staining for Pms2 in cell nuclei at the base of crypts, while samples from 2 of the 3 colons with a tubulovillous adenoma, and from 6 of the 10 colons with adenocarcinomas, showed reduced Pms2 expression. Samples from patients with an adenocarcinoma that had reduced Pms2 expression also exhibited reduced apoptosis capability in nearby tissue samples, evidenced when this paired tissue was stressed ex vivo with bile acid. Reduced Pms2 expression in the colonic mucosa may be an early step in progression to colon cancer. This reduction may cause decreased mismatch repair, increased genetic instability, and/or reduced apoptotic capability. Immunohistochemical determination of reduced Pms2 expression, upon further testing, may prove to be a promising early biomarker of risk of progression to malignancy.

  14. Café-au-lait macules and pediatric malignancy caused by biallelic mutations in the DNA mismatch repair (MMR) gene PMS2.

    Science.gov (United States)

    Jackson, Carl-Christian; Holter, Spring; Pollett, Aaron; Clendenning, Mark; Chou, Shirley; Senter, Leigha; Ramphal, Raveena; Gallinger, Steven; Boycott, Kym

    2008-06-01

    A 14-year-old male presented with a T4 sigmoid adenocarcinoma, PMS2 protein and high frequency microsatellite instability. Germline analysis identified biallelic PMS2 missense mutations. A new cancer syndrome caused by biallelic mutations in the mismatch repair genes, including PMS2, is now emerging and is characterized by café-au-lait macules, colonic polyps and a distinctive tumor spectrum. (c) 2007 Wiley-Liss, Inc.

  15. Higher frequency of isolated PMS2 loss in colorectal tumors in Colombian population: preliminary results

    Directory of Open Access Journals (Sweden)

    Shamekh R

    2016-08-01

    Full Text Available Rania Shamekh,1 Mauro Cives,2 Jaime Mejia,3 Domenico Coppola,4 1Department of Pathology, University of South Florida, 2Department of Gastrointestinal Oncology, Moffitt Cancer Center, Tampa, FL, USA; 3Department of Pathology, Institutode Patologia Mejia Jimenez, Cali, Colombia; 4Department of Anatomic Pathology, Moffitt Cancer Center, Tampa, FL, USA Abstract: Colorectal cancer (CRC is the third most common cancer and the fourth most common cause of death worldwide. It accounts for >9% of all cancers. One of the pathogenic factors of CRC is germline mutation, leading to alteration and inactivation in the mismatch repair (MMR genes. The aim of the study is to compare the frequency of alterations in MMR protein expression in Caucasian CRC patients with Colombian CRC patients. A total of 45 Colombians and 48 Caucasians with CRC were studied. The microsatellite instability status of tumors was determined in primary CRC by immunohistochemistry using the automated Ventana Ultra. The combined loss of MLH1 and PMS2 was the most common alteration in both Colombian (11%, five out of 45 and Caucasian (12%, six out of 48 CRC patients. Interestingly, the loss of PMS2 expression in the presence of intact MLH1 was the second most common alteration in Colombians (8%, four out of 45, which was never seen in the Caucasian cohort (P=0.05. The loss of MLH1 alone and the combined loss of MSH6 and PMS2 expression were only observed in one out of 45 (2% Colombians but not in Caucasians. The combined loss of MSH2 and MSH6 was not observed in any of the patients studied. The preliminary findings support a significant difference in alterations of MMR protein expression in Colombian CRC patients compared with Caucasian CRC patients. These findings are novel and warrant further studies in larger cohorts. Keywords: colon cancer, MSI, MMR, immunohistochemistry

  16. Detector block based on arrays of 144 SiPMs and monolithic scintillators: A performance study

    International Nuclear Information System (INIS)

    González, A.J.; Conde, P.; Iborra, A.; Aguilar, A.; Bellido, P.; García-Olcina, R.; Hernández, L.; Moliner, L.; Rigla, J.P.; Rodríguez-Álvarez, M.J.; Sánchez, F.; Seimetz, M.; Soriano, A.; Torres, J.; Vidal, L.F.; Benlloch, J.M.

    2015-01-01

    We have developed a detector block composed by a monolithic LYSO scintillator coupled to a custom made 12×12 SiPMs array. The design is mainly focused to applications such as Positron Emission Tomography. The readout electronics is based on 3 identical and scalable Application Specific Integrated Circuits (ASIC). We have determined the main performance of the detector block namely spatial, energy, and time resolution but also the system capability to determine the photon depth of interaction, for different crystal surface treatments. Intrinsic detector spatial resolution values as good as 1.7 mm FWHM and energies of 15% for black painted crystals were measured

  17. Double-blind, placebo-controlled pilot study of adjunctive quetiapine SR in the treatment of PMS/PMDD.

    Science.gov (United States)

    Jackson, Christine; Pearson, Brenda; Girdler, Susan; Johnson, Jacqueline; Hamer, Robert M; Killenberg, Susan; Meltzer-Brody, Samantha

    2015-11-01

    Premenstrual dysphoric disorder (PMDD), a more severe form of premenstrual syndrome (PMS), afflicts 5-8% of reproductive age women and results in significant functional impairment. We conducted a double-blind, placebo-controlled trial of adjunctive quetiapine in patients with PMS/PMDD who had inadequate response to selective serotonin reuptake inhibitor/serotonin-norepinephrine reuptake inhibitor therapy for their symptoms. A PMS/PMDD diagnosis was confirmed by 2-month prospective diagnostic assessment of PMS/PMDD using the Prospective Record of the Impact and Severity of Premenstrual Symptoms (PRISM) calendar. Women were randomized equally to receive quetiapine sustained-release (SR) or placebo (25-mg starting dose) during the luteal phase for 3 months. Outcome variables included the Hamilton Depression and Anxiety Scales, Clinical Global Impression Scale, and PRISM. Twenty women were enrolled in the treatment phase. Although the study was underpowered, greater reductions in luteal phase mood ratings were observed in the quetiapine group on the 17-item Hamilton Depression Rating Scale, Clinical Global Impression improvement rating, and PRISM daily score. The quetiapine group showed most improvement in symptoms of mood lability, anxiety, and irritability. This small double-blind study suggests that adjunctive treatment with quetiapine SR may be a useful addition to selective serotonin reuptake inhibitor therapy in women with PMS/PMDD by reducing symptoms and improving quality of life. Copyright © 2015 John Wiley & Sons, Ltd.

  18. Comparing the Effects of Vitamin B1 and Calcium on Premenstrual Syndrome (PMS among Female Students, Ilam- Iran

    Directory of Open Access Journals (Sweden)

    Soheila Samieipour

    2016-09-01

    Full Text Available Background Premenstrual syndrome (PMS is a combination of physical, psychological and emotional symptoms that occur periodically before menstruation and disappear with the onset of menstruation. There are some therapeutic methods mostly according to the clinical trials that reduce the prevalence and intensity of symptoms of PMS by unknown mechanisms. This study aimed to investigate the effects of Calcium and vitamin B1 on Premenstrual syndrome among female students. Materials and Methods: This is a triple-blind clinical trial conducted on 210 female students living in dormitories of Ilam University of Medical Sciences who had PMS. PMS symptoms questionnaire was used to investigate the symptoms. Participants were assigned in 3 groups of 70 people with the following regimen: group 1 received one pill containing 100 milligrams vitamin B1, group 2 received Calcium pills and group 3 received placebo. The participants in all groups took medicines for 2 months and then reported the intensity of their symptoms by the questionnaire. The collected data was analyzed by descriptive and inferential statistics, using SPSS-16. Results: In groups receiving vitamin B1, Calcium and placebo, the intensity of physical and psychological symptoms as well as general symptoms of PMS had a remarkable reduction (P

  19. Vicarious absolute radiometric calibration of GF-2 PMS2 sensor using permanent artificial targets in China

    Science.gov (United States)

    Liu, Yaokai; Li, Chuanrong; Ma, Lingling; Wang, Ning; Qian, Yonggang; Tang, Lingli

    2016-10-01

    GF-2, launched on August 19 2014, is one of the high-resolution land resource observing satellite of the China GF series satellites plan. The radiometric performance evaluation of the onboard optical pan and multispectral (PMS2) sensor of GF-2 satellite is very important for the further application of the data. And, the vicarious absolute radiometric calibration approach is one of the most useful way to monitor the radiometric performance of the onboard optical sensors. In this study, the traditional reflectance-based method is used to vicarious radiometrically calibrate the onboard PMS2 sensor of GF-2 satellite using three black, gray and white reflected permanent artificial targets located in the AOE Baotou site in China. Vicarious field calibration campaign were carried out in the AOE-Baotou calibration site on 22 April 2016. And, the absolute radiometric calibration coefficients were determined with in situ measured atmospheric parameters and surface reflectance of the permanent artificial calibration targets. The predicted TOA radiance of a selected desert area with our determined calibrated coefficients were compared with the official distributed calibration coefficients. Comparison results show a good consistent and the mean relative difference of the multispectral channels is less than 5%. Uncertainty analysis was also carried out and a total uncertainty with 3.87% is determined of the TOA radiance.

  20. Reevaluation of the PMS alarm set-points in OPR1000

    International Nuclear Information System (INIS)

    Roh, Kyung Ho; Yang, Sung Tae; Jung, Sung In

    2011-01-01

    In Optimized Power Reactor 1000 (OPR1000), the common alarm of the plant monitoring system (PMS), which is related to the channel-to-channel core protection calculator (CPC), experiences frequent deviations in the departure from nucleate boiling ratio (DNBR) and the local power density (LPD) between the middle of the cycle and the end of the cycle. Because the channel-to-channel CPC causes deviations in the values of the DNBR and LPD, the increase in the CPC input variables exceeds the alarm set-points. The CPC DNBR and LPD are defined as follows: Deviation = the average of four CPC channels of the LPD and DNBR minus the value of each CPC channel LPD and DNBR. In this paper, we report on a review by the Korea Hydro and Nuclear Power Co., Ltd. (KHNP) regarding the suitability of the alarm set-points for the channel-tochannel deviations of the CPC DNBR and LPD. The set-points were revaluated in light of operational experience and the case of Palo Verde (which is the reference model of OPR1000). The KHNP consequently revised the relevant procedures, as well as and the PMS alarm set-points, as part of its follow-up action

  1. FORMULASI MINUMAN SUPLEMEN DAUN TORBANGUN (Coleus amboinicus Lour. UNTUK WANITA YANG MENDERITA PMS (PREMENSTRUAL SYNDROME

    Directory of Open Access Journals (Sweden)

    Pramadya Alfitra

    2012-03-01

    Full Text Available 800x600 Normal 0 false false false IN X-NONE X-NONE MicrosoftInternetExplorer4 Torbangun (Coleus amboinicus Lour is one of Labiatae family containing a lot of micronutrients and active components. The plant is used as traditional medicine for relieving premenstrual syndromes (PMS. Based on the results of previous studies, a capsule containing 750 mg of dried Torbangun leaves can relieve PMS as well as commercial herbal, and better than placebo. Capsule supplement form seems less acceptable because it tastes like taking a drug. Therefore, it requires development for Torbangun supplement product in other forms, and one of them is a supplement drink. The study is aimed to formulate  a supplement drink from Torbangun leaves as the basic ingredients. Supplement drink formulation is made in trial and error by combining extract of torbangun leaves, sucrose, and lemon, obtaining three formulas: DT1 contains 10 g extract of torbangun leaves and 16 g sucrose, DT2 contains 10 g extract of torbangun leaves, 2 g lemon, 22 g sucrose, and DT3 contains 10 g extract of torbangun leaves, 4 g lemon, and 28 g sucrose. These formulas are then tested by organoleptic, physical, and chemical. The results show that the formula DT3 has the highest average score. Blanching treatment improves organoleptic properties of supplement drinks. Mean scores in color, aroma, and taste of the blanched supplement drink are different (p Key words: Torbangun leaves, premenstrual syndrome, supplement drink, blanching.

  2. Evaluation of PMS-PCR technology for detection of Mycobacterium avium subsp. paratuberculosis directly from bovine fecal specimens.

    Science.gov (United States)

    Salgado, M; Steuer, P; Troncoso, E; Collins, M T

    2013-12-27

    Mycobacterium avium subsp. paratuberculosis (MAP) causes paratuberculosis, or Johne's disease, in animals. Diagnosis of MAP infection is challenging because of the pathogen's fastidious in vitro growth requirements and low-level intermittent shedding in feces during the preclinical phase of the infection. Detection of these "low-shedders" is important for effective control of paratuberculosis as these animals serve as sources of infection for susceptible calves. Magnetic separation technology, used in combination with culture or molecular methods for the isolation and detection of pathogenic bacteria, enhances the analytical sensitivity and specificity of detection methods. The aim of the present study was to evaluate peptide-mediated magnetic separation (PMS) capture technology coupled with IS900 PCR using the Roche real-time PCR system (PMS-PCR), in comparison with fecal culture using BACTEC-MGIT 960 system, for detection of MAP in bovine fecal samples. Among the 351 fecal samples 74.9% (263/351) were PMS-PCR positive while only 12.3% (43/351) were MGIT culture-positive (p=0.0001). All 43 MGIT culture-positive samples were also positive by PMS-PCR. Mean PMS-PCR crossing-point (Cp) values for the 13 fecal samples with the highest number of MAP, based on time to detection, (26.3) were significantly lower than for the 17 fecal samples with technology provided results in a shorter time and yielded a higher number of positive results than MGIT culture. Earlier and faster detection of animals shedding MAP by PMS-PCR should significantly strengthen control efforts for MAP-infected cattle herds by helping to limit infection transmission at earlier stages of the infection. Copyright © 2013 Elsevier B.V. All rights reserved.

  3. The unstructured linker arms of Mlh1-Pms1 are important for interactions with DNA during mismatch repair

    Science.gov (United States)

    Plys, Aaron J.; Rogacheva, Maria V.; Greene, Eric C.; Alani, Eric

    2012-01-01

    DNA mismatch repair (MMR) models have proposed that MSH proteins identify DNA polymerase errors while interacting with the DNA replication fork. MLH proteins (primarily Mlh1-Pms1 in baker’s yeast) then survey the genome for lesion-bound MSH proteins. The resulting MSH-MLH complex formed at a DNA lesion initiates downstream steps in repair. MLH proteins act as dimers and contain long (20 – 30 nanometers) unstructured arms that connect two terminal globular domains. These arms can vary between 100 to 300 amino acids in length, are highly divergent between organisms, and are resistant to amino acid substitutions. To test the roles of the linker arms in MMR, we engineered a protease cleavage site into the Mlh1 linker arm domain of baker’s yeast Mlh1-Pms1. Cleavage of the Mlh1 linker arm in vitro resulted in a defect in Mlh1-Pms1 DNA binding activity, and in vivo proteolytic cleavage resulted in a complete defect in MMR. We then generated a series of truncation mutants bearing Mlh1 and Pms1 linker arms of varying lengths. This work revealed that MMR is greatly compromised when portions of the Mlh1 linker are removed, whereas repair is less sensitive to truncation of the Pms1 linker arm. Purified complexes containing truncations in Mlh1 and Pms1 linker arms were analyzed and found to have differential defects in DNA binding that also correlated with the ability to form a ternary complex with Msh2-Msh6 and mismatch DNA. These observations are consistent with the unstructured linker domains of MLH proteins providing distinct interactions with DNA during MMR. PMID:22659005

  4. Studies on surface-mounted SiPMs in 2015 testbeam of a highly granular hadron calorimeter

    Energy Technology Data Exchange (ETDEWEB)

    Krause, Sascha [Institut fuer Physik, Johannes Gutenberg-Universitaet Mainz, Mainz (Germany); Collaboration: CALICE-D-Collaboration

    2016-07-01

    To achieve excellent jet energy resolution, a highly granular hadronic calorimeter is being developed within the CALICE collaboration. Therefore, about 8 million detector units consisting of scintillator tiles and silicon photomultipliers (SiPMs) will be installed in the final HCAL design. The usage of surface-mounted (SMD) SiPMs allows an automated mass assembly. During CERN SPS testbeam 2015, data for a prototype consisting of up to 11 layers of HCAL base units (HBU) was collected using electron, muon and pion beams. One of the layers was equipped with the first SMD HBU. Results and performance, especially of the SMD HBU are presented.

  5. Comprehensive Mutation Analysis of PMS2 in a Large Cohort of Probands Suspected of Lynch Syndrome or Constitutional Mismatch Repair Deficiency Syndrome

    NARCIS (Netherlands)

    Klift, H.M. van der; Mensenkamp, A.R.; Drost, M.; Bik, E.C.; Vos, Y.J.; Gille, H.J.; Redeker, B.E.; Tiersma, Y.; Zonneveld, J.B.; Garcia, E.G.; Letteboer, T.G.; Olderode-Berends, M.J.; Hest, L.P. van; Os, T.A. van; Verhoef, S.; Wagner, A.; Asperen, C.J. van; Broeke, S.W. ten; Hes, F.J.; Wind, N. de; Nielsen, M.; Devilee, P.; Ligtenberg, M.J.L.; Wijnen, J.T.; Tops, C.M.

    2016-01-01

    Monoallelic PMS2 germline mutations cause 5%-15% of Lynch syndrome, a midlife cancer predisposition, whereas biallelic PMS2 mutations cause approximately 60% of constitutional mismatch repair deficiency (CMMRD), a rare childhood cancer syndrome. Recently improved DNA- and RNA-based strategies are

  6. Comprehensive Mutation Analysis of PMS2 in a Large Cohort of Probands Suspected of Lynch Syndrome or Constitutional Mismatch Repair Deficiency Syndrome

    NARCIS (Netherlands)

    van der Klift, Heleen M.; Mensenkamp, Arjen R.; Drost, Mark; Bik, Elsa C.; Vos, Yvonne J.; Gille, Hans J. J. P.; Redeker, Bert E. J. W.; Tiersma, Yvonne; Zonneveld, Jose B. M.; Garcia, Encarna Gomez; Letteboer, Tom G. W.; Olderode-Berends, Maran J. W.; van Hest, Liselotte P.; van Os, Theo A.; Verhoef, Senno; Wagner, Anja; van Asperen, Christi J.; ten Broeke, Sanne W.; Hes, Frederik J.; de Wind, Niels; Nielsen, Maartje; Devilee, Peter; Ligtenberg, Marjolijn J. L.; Wijnen, Juul T.; Tops, Carli M. J.

    Monoallelic PMS2 germline mutations cause 5%-15% of Lynch syndrome, a midlife cancer predisposition, whereas biallelic PMS2 mutations cause approximately 60% of constitutional mismatch repair deficiency (CMMRD), a rare childhood cancer syndrome. Recently improved DNA- and RNA-based strategies are

  7. Comprehensive Mutation Analysis of PMS2 in a Large Cohort of Probands Suspected of Lynch Syndrome or Constitutional Mismatch Repair Deficiency (CMMRD) Syndrome

    NARCIS (Netherlands)

    van der Klift, Heleen M; Mensenkamp, Arjen R; Drost, Mark; Bik, Elsa C; Vos, Yvonne J; Gille, Hans J J P; Redeker, Bert E J W; Tiersma, Yvonne; Zonneveld, José B M; García, Encarna Gómez; Letteboer, Tom G W; Olderode-Berends, Maran J W; van Hest, Liselotte P; van Os, Theo A; Verhoef, Senno; Wagner, Anja; van Asperen, Christi J; Ten Broeke, Sanne W; Hes, Frederik J; de Wind, Niels; Nielsen, Maartje; Devilee, Peter; Ligtenberg, Marjolijn J L; Wijnen, Juul T; Tops, Carli M J

    2016-01-01

    Monoallelic PMS2 germline mutations cause 5-15% of Lynch syndrome, a midlife cancer predisposition, whereas biallelic PMS2 mutations cause approximately 60% of constitutional MMR deficiency (CMMRD), a rare childhood cancer syndrome. Recently improved DNA and RNA-based strategies are applied to

  8. Expression of mismatch repair gene PMS2 in nasopharyngeal carcinoma and regulation by glycogen synthase kinase-3β in vivo and in vitro.

    Science.gov (United States)

    Fang, Jugao; Lei, Wenbin; Huang, Xiaoming; Li, Pingdong; Chen, Xiaohong; Zhu, Xiaolin; Wen, Weiping; Li, Huabin

    2012-02-01

    To evaluate the expression of mismatch repair gene PMS2 in human nasopharyngeal carcinoma (NPC) tissues and evaluate the effect of glycogen synthase kinase (GSK)-3β on PMS2 production in vivo and in vitro. The expression of PMS2 and inactivated phosphorylated GSK-3β(s9) was examined by immunohistochemical staining in 25 NPC tissues and the relation was determined by correlation analysis. The effect of GSK-3β transfection in CNE-2 cells on PMS2 production as well as cell apoptosis and chemosensitization were evaluated using small interference RNA (siRNA), immunoblotting and flow cytometric analysis in vitro. The expression of inactivated phosphorylated GSK-3β(s9) was found to negative correlated with PMS2 in vivo. And transfected GSK-3β was found to be able to enhance PMS2 production, and increase cell apoptosis in CNE-2 cells in combination with cisplatin administration in vitro. Inactivation of GSK-3β might be important for NPC tumorgenesis through negatively regulating PMS2 production, and enhanced PMS2 production by GSK-3β is beneficial for understanding the NPC tumorgenesis and developing potential strategy for future therapy. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

  9. Germline MLH1 Mutations Are Frequently Identified in Lynch Syndrome Patients With Colorectal and Endometrial Carcinoma Demonstrating Isolated Loss of PMS2 Immunohistochemical Expression.

    Science.gov (United States)

    Dudley, Beth; Brand, Randall E; Thull, Darcy; Bahary, Nathan; Nikiforova, Marina N; Pai, Reetesh K

    2015-08-01

    Current guidelines on germline mutation testing for patients suspected of having Lynch syndrome are not entirely clear in patients with tumors demonstrating isolated loss of PMS2 immunohistochemical expression. We analyzed the clinical and pathologic features of patients with tumors demonstrating isolated loss of PMS2 expression in an attempt to (1) determine the frequency of germline MLH1 and PMS2 mutations and (2) correlate mismatch-repair protein immunohistochemistry and tumor histology with germline mutation results. A total of 3213 consecutive colorectal carcinomas and 215 consecutive endometrial carcinomas were prospectively analyzed for DNA mismatch-repair protein expression by immunohistochemistry. In total, 32 tumors from 31 patients demonstrated isolated loss of PMS2 immunohistochemical expression, including 16 colorectal carcinomas and 16 endometrial carcinomas. Microsatellite instability (MSI) polymerase chain reaction was performed in 29 tumors from 28 patients with the following results: 28 tumors demonstrated high-level MSI, and 1 tumor demonstrated low-level MSI. Twenty of 31 (65%) patients in the study group had tumors demonstrating histopathology associated with high-level MSI. Seventeen patients underwent germline mutation analysis with the following results: 24% with MLH1 mutations, 35% with PMS2 mutations, 12% with PMS2 variants of undetermined significance, and 29% with no mutations in either MLH1 or PMS2. Three of the 4 patients with MLH1 germline mutations had a mutation that results in decreased stability and quantity of the MLH1 protein that compromises the MLH1-PMS2 protein complex, helping to explain the presence of immunogenic but functionally inactive MLH1 protein within the tumor. The high frequency of MLH1 germline mutations identified in our study has important implications for testing strategies in patients suspected of having Lynch syndrome and indicates that patients with tumors demonstrating isolated loss of PMS2 expression

  10. Screening for germline mutations of MLH1, MSH2, MSH6 and PMS2 genes in Slovenian colorectal cancer patients: implications for a population specific detection strategy of Lynch syndrome.

    Science.gov (United States)

    Berginc, Gasper; Bracko, Matej; Ravnik-Glavac, Metka; Glavac, Damjan

    2009-01-01

    Microsatellite instability (MSI) is present in more than 90% of colorectal cancers of patients with Lynch syndrome, and is therefore a feasible marker for the disease. Mutations in MLH1, MSH2, MSH6 and PMS2, which are one of the main causes of deficient mismatch repair and subsequent MSI, have been linked to the disease. In order to establish the role of each of the 4 genes in Slovenian Lynch syndrome patients, we performed MSI analysis on 593 unselected CRC patients and subsequently searched for the presence of point mutations, larger genomic rearrangements and MLH1 promoter hypermethylation in patients with MSI-high tumours. We detected 43 (7.3%) patients with MSI-H tumours, of which 7 patients (1.3%) harboured germline defects: 2 in MLH1, 4 in MSH2, 1 in PMS2 and none in MSH6. Twenty-nine germline sequence variations of unknown significance and 17 deleterious somatic mutations were found. MLH1 promoter methylation was detected in 56% of patients without detected germline defects and in 1 (14%) suspected Lynch syndrome. Due to the minor role of germline MSH6 mutations, we adapted the Lynch syndrome detection strategy for the Slovenian population of CRC patients, whereby germline alterations should be first sought in MLH1 and MSH2 followed by a search for larger genomic rearrangements in these two genes. When no germline mutations are found tumors should be further tested for the presence of germline defects in PMS2 and MSH6. The choice about which gene should be tested first can be guided more accurately by the immunohistochemical analysis. Our study demonstrates that the incidence of MMR mutations in a population should be known prior to the application of one of several suggested strategies for detection of Lynch syndrome.

  11. Simultaneous colonic adenocarcinoma and medulloblastoma in a 12-year-old with biallelic deletions in PMS2.

    Science.gov (United States)

    Lindsay, Holly; Jubran, Rima F; Wang, Larry; Kipp, Benjamin R; May, William A

    2013-08-01

    We describe a 12-year-old girl, simultaneously presenting with colonic adenocarcinoma and medulloblastoma from bialleic deletions in the mismatch repair gene PMS2. Her distinctive physical and clinical findings are characteristic of constitutional mismatch repair deficiency syndrome. Earlier recognition of such findings may permit better screening and more effective treatment. Copyright © 2013 Mosby, Inc. All rights reserved.

  12. Low-cost RFID-based palm oil monitoring system (PMS): First prototype

    International Nuclear Information System (INIS)

    Kiama, J W; Patrick, T H H; Raman, V

    2014-01-01

    Under collaboration with our local oil palm plantation enterprise, our research focuses on producing proof-of-concept by using RFID technology to monitor palm oil productivity. Passive RFID tags are used in the plantation field to uniquely identify each palm oil tree and their Fresh Fruit Bunches (FFB) production is collected and monitored by scanning the passive RFID tags using high frequency RFID scanners. This technology aims to convert the harvest data into digital information which can be processed and analyzed by PMS system and presented as informative outputs such as dynamic charts. This analyzed information is further used as input to a proprietary GIS system where it is mapped as color-coded spatial data which enables an accurate evaluation and monitoring of the overall plantation productivity

  13. Diagnosis and analysis for PMS model implementation in a footwear industry

    Directory of Open Access Journals (Sweden)

    Marcia Athayde Moreira

    2017-08-01

    Full Text Available One of the options that the literature suggests assisting challenges in performance evaluation comes from studies of management control systems, which have been an important mechanism to assist in business performance evaluation. Given this fact, this study aims to analyze what are the difficulties and the possible benefits that the implementation of performance management systems - PMS model developed by Ferreira and Otley (2009 could help an evaluation of strategic and operational performance. So, we did a case study in a large Brazilian shoe industry. The results indicate that the main difficulties were: identification of key success factors; identification of key performance measures; creation of a reward or sanction policy for the results. As for the expected benefits, the results showed that the implementation would promote: greater integration between strategy and operations; creating more consistent business strategies; correct measurement of performance; and better fit with the objectives outlined.

  14. Deficient Pms2, ERCC1, Ku86, CcOI in field defects during progression to colon cancer.

    Science.gov (United States)

    Nguyen, Huy; Loustaunau, Cristy; Facista, Alexander; Ramsey, Lois; Hassounah, Nadia; Taylor, Hilary; Krouse, Robert; Payne, Claire M; Tsikitis, V Liana; Goldschmid, Steve; Banerjee, Bhaskar; Perini, Rafael F; Bernstein, Carol

    2010-07-28

    In carcinogenesis, the "field defect" is recognized clinically because of the high propensity of survivors of certain cancers to develop other malignancies of the same tissue type, often in a nearby location. Such field defects have been indicated in colon cancer. The molecular abnormalities that are responsible for a field defect in the colon should be detectable at high frequency in the histologically normal tissue surrounding a colonic adenocarcinoma or surrounding an adenoma with advanced neoplasia (well on the way to a colon cancer), but at low frequency in the colonic mucosa from patients without colonic neoplasia. Using immunohistochemistry, entire crypts within 10 cm on each side of colonic adenocarcinomas or advanced colonic neoplasias were found to be frequently reduced or absent in expression for two DNA repair proteins, Pms2 and/or ERCC1. Pms2 is a dual role protein, active in DNA mismatch repair as well as needed in apoptosis of cells with excess DNA damage. ERCC1 is active in DNA nucleotide excision repair. The reduced or absent expression of both ERCC1 and Pms2 would create cells with both increased ability to survive (apoptosis resistance) and increased level of mutability. The reduced or absent expression of both ERCC1 and Pms2 is likely an early step in progression to colon cancer. DNA repair gene Ku86 (active in DNA non-homologous end joining) and Cytochrome c Oxidase Subunit I (involved in apoptosis) had each been reported to be decreased in expression in mucosal areas close to colon cancers. However, immunohistochemical evaluation of their levels of expression showed only low to modest frequencies of crypts to be deficient in their expression in a field defect surrounding colon cancer or surrounding advanced colonic neoplasia. We show, here, our method of evaluation of crypts for expression of ERCC1, Pms2, Ku86 and CcOI. We show that frequency of entire crypts deficient for Pms2 and ERCC1 is often as great as 70% to 95% in 20 cm long areas

  15. Levels of H-ras codon 61 CAA to AAA mutation: response to 4-ABP-treatment and Pms2-deficiency.

    Science.gov (United States)

    Parsons, Barbara L; Delongchamp, Robert R; Beland, Frederick A; Heflich, Robert H

    2006-01-01

    DNA mismatch repair (MMR) deficiencies result in increased frequencies of spontaneous mutation and tumor formation. In the present study, we tested the hypothesis that a chemically-induced mutational response would be greater in a mouse with an MMR-deficiency than in the MMR-proficient mouse models commonly used to assay for chemical carcinogenicity. To accomplish this, the induction of H-ras codon 61 CAA-->AAA mutation was examined in Pms2 knockout mice (Pms2-/-, C57BL/6 background) and sibling wild-type mice (Pms2+/+). Groups of five or six neonatal male mice were treated with 0.3 micromol 4-aminobiphenyl (4-ABP) or the vehicle control, dimethylsulfoxide. Eight months after treatment, liver DNAs were isolated and analysed for levels of H-ras codon 61 CAA-->AAA mutation using allele-specific competitive blocker-PCR. In Pms2-proficient and Pms2-deficient mice, 4-ABP treatment caused an increase in mutant fraction (MF) from 1.65x10(-5) to 2.91x10(-5) and from 3.40x10(-5) to 4.70x10(-5), respectively. Pooling data from 4-ABP-treated and control mice, the approximately 2-fold increase in MF observed in Pms2-deficient as compared with Pms2-proficient mice was statistically significant (P=0.0207) and consistent with what has been reported previously in terms of induction of G:C-->T:A mutation in a Pms2-deficient background. Pooling data from both genotypes, the increase in H-ras MF in 4-ABP-treated mice, as compared with control mice, did not reach the 95% confidence level of statistical significance (P=0.0606). The 4-ABP treatment caused a 1.76-fold and 1.38-fold increase in average H-ras MF in Pms2-proficient and Pms2-deficient mice, respectively. Furthermore, the levels of induced mutation in Pms2-proficient and Pms2-deficient mice were nearly identical (1.26x10(-5) and 1.30x10(-5), respectively). We conclude that Pms2-deficiency does not result in an amplification of the H-ras codon 61 CAA-->AAA mutational response induced by 4-ABP.

  16. Abrupt loss of MLH1 and PMS2 expression in endometrial carcinoma: molecular and morphologic analysis of 6 cases.

    Science.gov (United States)

    Pai, Rish K; Plesec, Thomas P; Abdul-Karim, Fadi W; Yang, Bin; Marquard, Jessica; Shadrach, Bonnie; Roma, Andres R

    2015-07-01

    Given that endometrial cancer (EC) is often the sentinel cancer for female Lynch syndrome patients, we have successfully implemented universal screening of ECs and have previously shown that this is the preferred method to identify these patients. However, during the course of universal screening of EC, we encountered 6 cases with an unusual pattern of mismatch-repair protein immunohistochemistry that has not been previously described in this setting. In these 6 cases, there was an abrupt loss of MLH1 and PMS2 expression in a portion of the tumor. In 3 cases, marked histologic differences were identified between the areas of the tumor with retained expression and areas with loss of expression. In 2 cases, the areas with loss of expression were of higher grade (1 demonstrated solid growth and the other demonstrated increased nuclear atypia with diffuse p53 expression). In 4 tumors, histologic features associated with microsatellite instability (MSI) were present, including increased intraepithelial lymphocytes. The areas with loss of and retained MLH1/PMS2 expression were separately microdissected and assessed for MSI and MLH1 promoter methylation. The areas with loss of MLH1 and PMS2 more commonly demonstrated MSI compared with the areas with intact expression (83% vs. 33%). MLH1 promoter methylation analysis demonstrated heterogenous hypermethylation, as all areas with loss of MLH1/PMS2 expression had more extensive methylation of MLH1 compared with those areas with retained expression. In summary, we describe the histologic and molecular features of 6 cases of EC with abrupt loss of MLH1 and PMS2 expression and demonstrate that heterogenous methylation of the MLH1 promoter results in this distinct and unusual pattern of immunohistochemical expression.

  17. WIYN Open Cluster Study: Tidal Interactions in Solar type Binaries

    OpenAIRE

    Meibom, S.; Mathieu, R. D.

    2003-01-01

    We present an ongoing study on tidal interactions in late-type close binary stars. New results on tidal circularization are combined with existing data to test and constrain theoretical predictions of tidal circularization in the pre-main-sequence (PMS) phase and throughout the main-sequence phase of stellar evolution. Current data suggest that tidal circularization during the PMS phase sets the tidal cutoff period for binary populations younger than ~1 Gyr. Binary populations older than ~1 G...

  18. MSH6 and PMS2 mutation positive Australian Lynch syndrome families: novel mutations, cancer risk and age of diagnosis of colorectal cancer.

    Science.gov (United States)

    Talseth-Palmer, Bente A; McPhillips, Mary; Groombridge, Claire; Spigelman, Allan; Scott, Rodney J

    2010-05-21

    Approximately 10% of Lynch syndrome families have a mutation in MSH6 and fewer families have a mutation in PMS2. It is assumed that the cancer incidence is the same in families with mutations in MSH6 as in families with mutations in MLH1/MSH2 but that the disease tends to occur later in life, little is known about families with PMS2 mutations. This study reports on our findings on mutation type, cancer risk and age of diagnosis in MSH6 and PMS2 families. A total of 78 participants (from 29 families) with a mutation in MSH6 and 7 participants (from 6 families) with a mutation in PMS2 were included in the current study. A database of de-identified patient information was analysed to extract all relevant information such as mutation type, cancer incidence, age of diagnosis and cancer type in this Lynch syndrome cohort. Cumulative lifetime risk was calculated utilising Kaplan-Meier survival analysis. MSH6 and PMS2 mutations represent 10.3% and 1.9%, respectively, of the pathogenic mutations in our Australian Lynch syndrome families. We identified 26 different MSH6 and 4 different PMS2 mutations in the 35 families studied. We report 15 novel MSH6 and 1 novel PMS2 mutations. The estimated cumulative risk of CRC at age 70 years was 61% (similar in males and females) and 65% for endometrial cancer in MSH6 mutation carriers. The risk of developing CRC is different between males and females at age 50 years, which is 34% for males and 21% for females. Novel MSH6 and PMS2 mutations are being reported and submitted to the current databases for identified Lynch syndrome mutations. Our data provides additional information to add to the genotype-phenotype spectrum for both MSH6 and PMS2 mutations.

  19. MSH6 and PMS2 mutation positive Australian Lynch syndrome families: novel mutations, cancer risk and age of diagnosis of colorectal cancer

    Directory of Open Access Journals (Sweden)

    Talseth-Palmer Bente A

    2010-05-01

    Full Text Available Abstract Background Approximately 10% of Lynch syndrome families have a mutation in MSH6 and fewer families have a mutation in PMS2. It is assumed that the cancer incidence is the same in families with mutations in MSH6 as in families with mutations in MLH1/MSH2 but that the disease tends to occur later in life, little is known about families with PMS2 mutations. This study reports on our findings on mutation type, cancer risk and age of diagnosis in MSH6 and PMS2 families. Methods A total of 78 participants (from 29 families with a mutation in MSH6 and 7 participants (from 6 families with a mutation in PMS2 were included in the current study. A database of de-identified patient information was analysed to extract all relevant information such as mutation type, cancer incidence, age of diagnosis and cancer type in this Lynch syndrome cohort. Cumulative lifetime risk was calculated utilising Kaplan-Meier survival analysis. Results MSH6 and PMS2 mutations represent 10.3% and 1.9%, respectively, of the pathogenic mutations in our Australian Lynch syndrome families. We identified 26 different MSH6 and 4 different PMS2 mutations in the 35 families studied. We report 15 novel MSH6 and 1 novel PMS2 mutations. The estimated cumulative risk of CRC at age 70 years was 61% (similar in males and females and 65% for endometrial cancer in MSH6 mutation carriers. The risk of developing CRC is different between males and females at age 50 years, which is 34% for males and 21% for females. Conclusion Novel MSH6 and PMS2 mutations are being reported and submitted to the current databases for identified Lynch syndrome mutations. Our data provides additional information to add to the genotype-phenotype spectrum for both MSH6 and PMS2 mutations.

  20. The Premenstrual Symptoms Screening Tool revised for adolescents (PSST-A): prevalence of severe PMS and premenstrual dysphoric disorder in adolescents.

    Science.gov (United States)

    Steiner, Meir; Peer, Miki; Palova, Eva; Freeman, Ellen W; Macdougall, Mary; Soares, Claudio N

    2011-02-01

    The Premenstrual Symptoms Screening Tool was modified for use in adolescents and piloted in 578 girls at three international sites. Nearly one third (29.6%) reported experiencing severe PMS or PMDD, with irritability being the most commonly reported symptom. Rates of menstrual-related pain were high, particularly in those with severe PMS or PMDD. Severe PMS and PMDD present with similar rates and symptoms in adolescents as in adults, and the Premenstrual Symptoms Screening Tool modified for adolescents is a fast, reliable tool to screen for these syndromes in adolescents.

  1. Application of large area SiPMs for the readout of a plastic scintillator based timing detector

    Science.gov (United States)

    Betancourt, C.; Blondel, A.; Brundler, R.; Dätwyler, A.; Favre, Y.; Gascon, D.; Gomez, S.; Korzenev, A.; Mermod, P.; Noah, E.; Serra, N.; Sgalaberna, D.; Storaci, B.

    2017-11-01

    In this study an array of eight 6 mm × 6 mm area SiPMs was coupled to the end of a long plastic scintillator counter which was exposed to a 2.5 GeV/c muon beam at the CERN PS. Timing characteristics of bars with dimensions 150 cm × 6 cm × 1 cm and 120 cm × 11 cm × 2.5 cm have been studied. An 8-channel SiPM anode readout ASIC (MUSIC R1) based on a novel low input impedance current conveyor has been used to read out and amplify SiPMs independently and sum the signals at the end. Prospects for applications in large-scale particle physics detectors with timing resolution below 100 ps are provided in light of the results.

  2. arXiv Application of large area SiPMs for the readout of a plastic scintillator based timing detector

    CERN Document Server

    Betancourt, C.; Brundler, R.; Dätwyler, A.; Favre, Y.; Gascon, D.; Gomez, S.; Korzenev, Alexander; Mermod, P.; Noah, E.; Serra, N.; Sgalaberna, D.; Storaci, B.

    2017-11-27

    In this study an array of eight 6 mm × 6 mm area SiPMs was coupled to the end of a long plastic scintillator counter which was exposed to a 2.5 GeV/c muon beam at the CERN PS. Timing characteristics of bars with dimensions 150 cm × 6 cm × 1 cm and 120 cm × 11 cm × 2.5 cm have been studied. An 8-channel SiPM anode readout ASIC (MUSIC R1) based on a novel low input impedance current conveyor has been used to read out and amplify SiPMs independently and sum the signals at the end. Prospects for applications in large-scale particle physics detectors with timing resolution below 100 ps are provided in light of the results.

  3. Apoptotic function of human PMS2 compromised by the nonsynonymous single-nucleotide polymorphic variant R20Q

    OpenAIRE

    Marinovic-Terzic, Ivana; Yoshioka-Yamashita, Atsuko; Shimodaira, Hideki; Avdievich, Elena; Hunton, Irina C.; Kolodner, Richard D.; Edelmann, Winfried; Wang, Jean Y. J.

    2008-01-01

    Mismatch repair (MMR) corrects replication errors during DNA synthesis. The mammalian MMR proteins also activate cell cycle checkpoints and apoptosis in response to persistent DNA damage. MMR-deficient cells are resistant to cisplatin, a DNA cross-linking agent used in chemotherapy, because of impaired activation of apoptotic pathways. It is shown that postmeiotic segregation 2 (PMS2), an MMR protein, is required for cisplatin-induced activation of p73, a member of the p53 family of transcrip...

  4. Pitfalls in molecular analysis for mismatch repair deficiency in a family with biallelic pms2 germline mutations.

    Science.gov (United States)

    Leenen, C H M; Geurts-Giele, W R R; Dubbink, H J; Reddingius, R; van den Ouweland, A M; Tops, C M J; van de Klift, H M; Kuipers, E J; van Leerdam, M E; Dinjens, W N M; Wagner, A

    2011-12-01

    Heterozygous germline mutations in the mismatch repair (MMR) genes MLH1, MSH2, MSH6 and PMS2 cause Lynch syndrome. Biallelic mutations in the MMR genes are associated with a childhood cancer syndrome [constitutional mismatch repair deficiency (CMMR-D)]. This is predominantly characterized by hematological malignancies and tumors of the bowel and brain, often associated with signs of neurofibromatosis type 1 (NF1). Diagnostic strategies for selection of patients for MMR gene analysis include analysis of microsatellite instability (MSI) and immunohistochemical (IHC) analysis of MMR proteins in tumor tissue. We report the clinical characterization and molecular analyses of tumor specimens from a family with biallelic PMS2 germline mutations. This illustrates the pitfalls of present molecular screening strategies. Tumor tissues of five family members were analyzed for MSI and IHC. MSI was observed in only one of the analyzed tissues. However, IHC analysis of brain tumor tissue of the index patient and his sister showed absence of PMS2 expression, and germline mutation analyses showed biallelic mutations in PMS2: p.Ser46IIe and p.Pro246fs. The same heterozygous mutations were confirmed in the father and mother, respectively. These data support the conclusion that in case of a clinical phenotype of CMMR-D, it is advisable to routinely combine MSI analysis with IHC analysis for the expression of MMR proteins. With inconclusive or conflicting results, germline mutation analysis of the MMR genes should be considered after thorough counselling of the patients and/or their relatives. © 2011 John Wiley & Sons A/S.

  5. Characterization of UV-enhanced SiPMs for Imaging in High Pressure Xenon Electroluminescent TPC

    International Nuclear Information System (INIS)

    Yahlali, Nadia; Lorca, David; Fernandes, L.M.P.

    2013-06-01

    The possibility of recording charged particle tracks in an electro-luminescent xenon gas TPC is investigated using a SiPM-based tracking system, operated in the demonstrator prototype of the NEXT-100 ββ decay experiment. The tracks of the ββ0ν events from the decay of the 136 Xe isotope have a distinctive topology, which allows their discrimination against single-electron events from the natural radioactivity that populates the region of interest of the neutrinoless decay in the ββ energy spectrum. Combined to the near-intrinsic energy resolution of the gaseous detector, this tracking capability provides a powerful background rejection tool for the search of the neutrinoless ββ decay aimed by the experiment. The NEXT-100 detector concepts and sensitivity and the first results of its demonstrator prototype are presented. The characterization studies relevant for the operation of UV-enhanced SiPMs used for imaging in an electro-luminescent TPC are reviewed. (authors)

  6. Development of a Gamma Spectrometer using a Large NaI Scintillator and SiPMs

    International Nuclear Information System (INIS)

    Kim, Chankyu; Yoo, Hyunjun; Kim, Yewon and others

    2014-01-01

    A typical scintillation gamma spectrometer is composed of a NaI(Tl) scintillation crystal and a PM tube. From last years, a Silicon Photomultiplier (SiPM) is being developed and expanding its application area as a substitute of PM tube due to its advantages like low operating voltage, small volume, and cheap production cost, MR compatibility. This approach could make gamma spectrometer smaller, cheaper, easier to use, and these advantage are quite suitable to original purpose of scintillation gamma spectrometer. Gamma spectrometry and gamma spectrometer is used to analyze gamma source in nuclear science, geochemistry, and astrophysics. In this research, gamma spectrometer which uses SiPMs instead of PM tube is proposed. The proposed gamma spectrometer has advantages of low cost, small volume, low operation voltage; but it has disadvantages of performances. To reduce this loss in performances, a light guide of effective structure is required. (Material, reflection type, tapering angle) For design of the light guide, DETECT simulation was performed. And through DETECT simulation, the characteristics of light guide could be prospected. Actual light guide was manufactured on the basis of this simulation result. Using the light guide, gamma spectrometer system was composed and tested. In the test result, gamma spectrometer using SiPM shows degraded energy resolution. The reason of this degradation is being analyzed and the test system is under modification

  7. Ultrafast detection in particle physics and positron emission tomography using SiPMs

    Science.gov (United States)

    Dolenec, R.; Korpar, S.; Križan, P.; Pestotnik, R.

    2017-12-01

    Silicon photomultiplier (SiPM) photodetectors perform well in many particle and medical physics applications, especially where good efficiency, insensitivity to magnetic field and precise timing are required. In Cherenkov time-of-flight positron emission tomography the requirements for photodetector performance are especially high. On average only a couple of photons are available for detection and the best possible timing resolution is needed. Using SiPMs as photodetectors enables good detection efficiency, but the large sensitive area devices needed have somewhat limited time resolution for single photons. We have observed an additional degradation of the timing at very low light intensities due to delayed events in distribution of signals resulting from multiple fired micro cells. In this work we present the timing properties of AdvanSiD ASD-NUV3S-P-40 SiPM at single photon level picosecond laser illumination and a simple modification of the time-walk correction algorithm, that resulted in reduced degradation of timing resolution due to the delayed events.

  8. Oral contraceptives positively affect mood in healthy PMS-free women: A longitudinal study.

    Science.gov (United States)

    Hamstra, Danielle A; de Kloet, E Ronald; de Rover, Mischa; Van der Does, Willem

    2017-12-01

    Menstrual cycle phase and oral contraceptives (OC) use influence mood and cognition and these effects may be moderated by the mineralocorticoid receptor (MR) genotype. The effect of menstrual cycle phase on mood may be increased if participants know that this is the focus of study. We assessed aspects associated with reproductive depression such as mood, interpersonal sensitivity, affect lability and depressive cognitions in MR-genotyped OC-users and naturally cycling (NC) women in a carefully masked design. A homogenous sample of healthy, PMS-free, pre-menopausal MR-genotyped women (n=92) completed online questionnaires eight times during two consecutive cycles. The masking of the research question was successful. OC-users did not differ significantly from NC women in positive and negative affect at the time of assessment, personality characteristics (e.g. neuroticism) or mental and physical health. Both groups reported more shifts in anger in the first cycle week (pemotional blunting effect, which is in line with previous reports on affect-stabilizing effects of OC. Limitations were loss of cases due to irregularities in the menstrual cycle length and possible confounding by the 'survivor effect', since almost all OC-users took OC for more than a year. Copyright © 2017 Elsevier Inc. All rights reserved.

  9. Isolated loss of PMS2 immunohistochemical expression is frequently caused by heterogeneous MLH1 promoter hypermethylation in Lynch syndrome screening for endometrial cancer patients

    OpenAIRE

    Kato, Aya; Sato, Naoki; Sugawara, Tae; Takahashi, Kazue; Kito, Masahiko; Makino, Kenichi; Sato, Toshiharu; Shimizu, Dai; Shirasawa, Hiromitu; Miura, Hiroshi; Sato, Wataru; Kumazawa, Yukiyo; Sato, Akira; Kumagai, Jin; Terada, Yukihiro

    2016-01-01

    Lynch syndrome (LS) is an autosomal dominant inherited disorder mainly caused by a germline mutation in the DNA mismatch repair (MMR) genes (MLH1, MSH2, MSH6, PMS2) and is associated with increased risk of various cancers, particularly colorectal cancer and endometrial cancer (EC). Women with LS account for 2–6% of EC patients; it is clinically important to identify LS in such individuals for predicting and/or preventing additional LS-associated cancers. PMS2 germline mutation ...

  10. Identification of Lynch syndrome mutations in the MLH1-PMS2 interface that disturb dimerization and mismatch repair.

    Science.gov (United States)

    Kosinski, Jan; Hinrichsen, Inga; Bujnicki, Janusz M; Friedhoff, Peter; Plotz, Guido

    2010-08-01

    Missense alterations of the mismatch repair gene MLH1 have been identified in a significant proportion of individuals suspected of having Lynch syndrome, a hereditary syndrome that predisposes for cancer of colon and endometrium. The pathogenicity of many of these alterations, however, is unclear. A number of MLH1 alterations are located in the C-terminal domain (CTD) of MLH1, which is responsible for constitutive dimerization with PMS2. We analyzed which alterations may result in pathogenic effects due to interference with dimerization. We used a structural model of CTD of MLH1-PMS2 heterodimer to select 19 MLH1 alterations located inside and outside two candidate dimerization interfaces in the MLH1-CTD. Three alterations (p.Gln542Leu, p.Leu749Pro, p.Tyr750X) caused decreased coexpression of PMS2, which is unstable in the absence of interaction with MLH1, suggesting that these alterations interfere with dimerization. All three alterations are located within the dimerization interface suggested by our model. They also compromised mismatch repair, suggesting that defects in dimerization abrogate repair and confirming that all three alterations are pathogenic. Additionally, we provided biochemical evidence that four alterations with uncertain pathogenicity (p.Ala586Pro, p.Leu636Pro, p.Thr662Pro, and p.Arg755Trp) are deleterious because of poor expression or poor repair efficiency, and confirm the deleterious effect of eight further alterations.

  11. Radioimmunological oestrogen and progesterone measurement in the serum and ovaries of pseudogravid female rats after PMS and HCG treatment

    International Nuclear Information System (INIS)

    Hauck, P.

    1978-01-01

    Infantile female rats were made pseudogravid with PMS-HCG (according to Karg). Two bioassays were employed to investigate the effects of HCG on the ovaries; the HCG was injected subactaneously in the back of the animals in varying doses and at various intervals after the initial PMS administration. As specific parameters, oestrogen and progesterone levels in serum and ovary homogenate were determined radioimmunologically. The first animal experiment showed that the ovaries of pseudogravid animals had reached maximum sensitivity for corpus luteum production after HCG administration between 50 and 70 hours after PMS administration. In the second animal experiment with repeated HCG stimulus in the luteal phase, it was found that the corpus luteum of the rat ovary is apparently unable to synthesize oestrogens. In contrast, progesteron synthesis received maximum stimulation already with the lowest dose administered (3 IE HCG). The experiments clearly showed a dependence on HCG dose and the time which the test substance is allowed to take effect. (orig./AJ) 891 AJ/orig.- 892 KN [de

  12. Paediatric intestinal cancer and polyposis due to bi-allelic PMS2 mutations: case series, review and follow-up guidelines.

    Science.gov (United States)

    Herkert, Johanna C; Niessen, Renée C; Olderode-Berends, Maria J W; Veenstra-Knol, Hermine E; Vos, Yvonne J; van der Klift, Heleen M; Scheenstra, Rene; Tops, Carli M J; Karrenbeld, Arend; Peters, Frans T M; Hofstra, Robert M W; Kleibeuker, Jan H; Sijmons, Rolf H

    2011-05-01

    Bi-allelic germline mutations of one of the DNA mismatch repair genes, so far predominantly found in PMS2, cause constitutional MMR-deficiency syndrome. This rare disorder is characterised by paediatric intestinal cancer and other malignancies. We report the clinical, immunohistochemical and genetic characterisation of four families with bi-allelic germline PMS2 mutations. We present an overview of the published gastrointestinal manifestations of CMMR-D syndrome and propose recommendations for gastro-intestinal screening. The first proband developed a cerebral angiosarcoma at age 2 and two colorectal adenomas at age 7. Genetic testing identified a complete PMS2 gene deletion and a frameshift c.736_741delinsTGTGTGTGAAG (p.Pro246CysfsX3) mutation. In the second family, both the proband and her brother had multiple intestinal adenomas, initially wrongly diagnosed as familial adenomatous polyposis. A splice site c.2174+1G>A, and a missense c.137G>T (p.Ser46Ile) mutation in PMS2 were identified. The third patient was diagnosed with multiple colorectal adenomas at age 11; he developed a high-grade dysplastic colorectal adenocarcinoma at age 21. Two intragenic PMS2 deletions were found. The fourth proband developed a cerebral anaplastic ganglioma at age 9 and a high-grade colerectal dysplastic adenoma at age 10 and carries a homozygous c.2174+1G>A mutation. Tumours of all patients showed microsatellite instability and/or loss of PMS2 expression. Our findings show the association between bi-allelic germline PMS2 mutations and severe childhood-onset gastrointestinal manifestations, and support the notion that patients with early-onset gastrointestinal adenomas and cancer should be investigated for CMMR-D syndrome. We recommend yearly follow-up with colonoscopy from age 6 and simultaneous video-capsule small bowel enteroscopy from age 8. Copyright © 2011 Elsevier Ltd. All rights reserved.

  13. Assessing pathogenicity of MLH1 variants by co-expression of human MLH1 and PMS2 genes in yeast

    Energy Technology Data Exchange (ETDEWEB)

    Vogelsang, Matjaz; Comino, Aleksandra; Zupanec, Neja [Department for Biosynthesis and Biotransformation, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana (Slovenia); Hudler, Petra [Medical Center for Molecular Biology, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, SI-1000 Ljubljana (Slovenia); Komel, Radovan [Department for Biosynthesis and Biotransformation, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana (Slovenia); Medical Center for Molecular Biology, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, SI-1000 Ljubljana (Slovenia)

    2009-10-28

    Loss of DNA mismatch repair (MMR) in humans, mainly due to mutations in the hMLH1 gene, is linked to hereditary nonpolyposis colorectal cancer (HNPCC). Because not all MLH1 alterations result in loss of MMR function, accurate characterization of variants and their classification in terms of their effect on MMR function is essential for reliable genetic testing and effective treatment. To date, in vivo assays for functional characterization of MLH1 mutations performed in various model systems have used episomal expression of the modified MMR genes. We describe here a novel approach to determine accurately the functional significance of hMLH1 mutations in vivo, based on co-expression of human MLH1 and PMS2 in yeast cells. Yeast MLH1 and PMS1 genes, whose protein products form the MutLα complex, were replaced by human orthologs directly on yeast chromosomes by homologous recombination, and the resulting MMR activity was tested. The yeast strain co-expressing hMLH1 and hPMS2 exhibited the same mutation rate as the wild-type. Eight cancer-related MLH1 variants were introduced, using the same approach, into the prepared yeast model, and their effect on MMR function was determined. Five variants (A92P, S93G, I219V, K618R and K618T) were classified as non-pathogenic, whereas variants T117M, Y646C and R659Q were characterized as pathogenic. Results of our in vivo yeast-based approach correlate well with clinical data in five out of seven hMLH1 variants and the described model was thus shown to be useful for functional characterization of MLH1 variants in cancer patients found throughout the entire coding region of the gene.

  14. MSH6 and PMS2 germ-line pathogenic variants implicated in Lynch syndrome are associated with breast cancer.

    Science.gov (United States)

    Roberts, Maegan E; Jackson, Sarah A; Susswein, Lisa R; Zeinomar, Nur; Ma, Xinran; Marshall, Megan L; Stettner, Amy R; Milewski, Becky; Xu, Zhixiong; Solomon, Benjamin D; Terry, Mary Beth; Hruska, Kathleen S; Klein, Rachel T; Chung, Wendy K

    2018-01-18

    PurposeAn association of Lynch syndrome (LS) with breast cancer has been long suspected; however, there have been insufficient data to address this question for each of the LS genes individually.MethodsWe conducted a retrospective review of personal and family history in 423 women with pathogenic or likely pathogenic germ-line variants in MLH1 (N = 65), MSH2 (N = 94), MSH6 (N = 140), or PMS2 (N = 124) identified via clinical multigene hereditary cancer testing. Standard incidence ratios (SIRs) of breast cancer were calculated by comparing breast cancer frequencies in our study population with those in the general population (Surveillance, Epidemiology, and End Results 18 data).ResultsWhen evaluating by gene, the age-standardized breast cancer risks for MSH6 (SIR = 2.11; 95% confidence interval (CI), 1.56-2.86) and PMS2 (SIR = 2.92; 95% CI, 2.17-3.92) were associated with a statistically significant risk for breast cancer whereas no association was observed for MLH1 (SIR = 0.87; 95% CI, 0.42-1.83) or MSH2 (SIR = 1.22; 95% CI, 0.72-2.06).ConclusionOur data demonstrate that two LS genes, MSH6 and PMS2, are associated with an increased risk for breast cancer and should be considered when ordering genetic testing for individuals who have a personal and/or family history of breast cancer.GENETICS in MEDICINE advance online publication, 18 January 2018; doi:10.1038/gim.2017.254.

  15. Assessing pathogenicity of MLH1 variants by co-expression of human MLH1 and PMS2 genes in yeast

    Directory of Open Access Journals (Sweden)

    Hudler Petra

    2009-10-01

    Full Text Available Abstract Background Loss of DNA mismatch repair (MMR in humans, mainly due to mutations in the hMLH1 gene, is linked to hereditary nonpolyposis colorectal cancer (HNPCC. Because not all MLH1 alterations result in loss of MMR function, accurate characterization of variants and their classification in terms of their effect on MMR function is essential for reliable genetic testing and effective treatment. To date, in vivo assays for functional characterization of MLH1 mutations performed in various model systems have used episomal expression of the modified MMR genes. We describe here a novel approach to determine accurately the functional significance of hMLH1 mutations in vivo, based on co-expression of human MLH1 and PMS2 in yeast cells. Methods Yeast MLH1 and PMS1 genes, whose protein products form the MutLα complex, were replaced by human orthologs directly on yeast chromosomes by homologous recombination, and the resulting MMR activity was tested. Results The yeast strain co-expressing hMLH1 and hPMS2 exhibited the same mutation rate as the wild-type. Eight cancer-related MLH1 variants were introduced, using the same approach, into the prepared yeast model, and their effect on MMR function was determined. Five variants (A92P, S93G, I219V, K618R and K618T were classified as non-pathogenic, whereas variants T117M, Y646C and R659Q were characterized as pathogenic. Conclusion Results of our in vivo yeast-based approach correlate well with clinical data in five out of seven hMLH1 variants and the described model was thus shown to be useful for functional characterization of MLH1 variants in cancer patients found throughout the entire coding region of the gene.

  16. Assessing pathogenicity of MLH1 variants by co-expression of human MLH1 and PMS2 genes in yeast

    International Nuclear Information System (INIS)

    Vogelsang, Matjaz; Comino, Aleksandra; Zupanec, Neja; Hudler, Petra; Komel, Radovan

    2009-01-01

    Loss of DNA mismatch repair (MMR) in humans, mainly due to mutations in the hMLH1 gene, is linked to hereditary nonpolyposis colorectal cancer (HNPCC). Because not all MLH1 alterations result in loss of MMR function, accurate characterization of variants and their classification in terms of their effect on MMR function is essential for reliable genetic testing and effective treatment. To date, in vivo assays for functional characterization of MLH1 mutations performed in various model systems have used episomal expression of the modified MMR genes. We describe here a novel approach to determine accurately the functional significance of hMLH1 mutations in vivo, based on co-expression of human MLH1 and PMS2 in yeast cells. Yeast MLH1 and PMS1 genes, whose protein products form the MutLα complex, were replaced by human orthologs directly on yeast chromosomes by homologous recombination, and the resulting MMR activity was tested. The yeast strain co-expressing hMLH1 and hPMS2 exhibited the same mutation rate as the wild-type. Eight cancer-related MLH1 variants were introduced, using the same approach, into the prepared yeast model, and their effect on MMR function was determined. Five variants (A92P, S93G, I219V, K618R and K618T) were classified as non-pathogenic, whereas variants T117M, Y646C and R659Q were characterized as pathogenic. Results of our in vivo yeast-based approach correlate well with clinical data in five out of seven hMLH1 variants and the described model was thus shown to be useful for functional characterization of MLH1 variants in cancer patients found throughout the entire coding region of the gene

  17. Assessing interactions of binary mixtures of Penicillium mycotoxins (PMs) by using a bovine macrophage cell line (BoMacs)

    Energy Technology Data Exchange (ETDEWEB)

    Oh, Se-Young, E-mail: ohs@uoguelph.ca [Department of Animal Biosciences, Ontario Agriculture College (OAC), University of Guelph, Guelph, ON N1G 2W1 (Canada); Cedergreen, Nina [Department of Life Sciences, University of Copenhagen, Frederiksberg (Denmark); Yiannikouris, Alexandros [Alltech Inc., Nicholasville, KY (United States); Swamy, H.V.L.N. [Trouw Nutrition Pvt. Ltd. India, Karnataka State 560065 (India); Karrow, Niel A., E-mail: nkarrow@uoguelph.ca [Department of Animal Biosciences, Ontario Agriculture College (OAC), University of Guelph, Guelph, ON N1G 2W1 (Canada)

    2017-03-01

    Penicillium mycotoxins (PMs) are toxic contaminants commonly found as mixtures in animal feed. Therefore, it is important to investigate potential joint toxicity of PM mixtures. In the present study, we assessed the joint effect of binary combinations of the following PMs: citrinin (CIT), ochratoxin A (OTA), patulin (PAT), mycophenolic acid (MPA) and penicillic acid (PA) using independent action (IA) and concentration addition (CA) concepts. Previously published toxicity data (i.e. IC25; PM concentration that inhibited bovine macrophage (BoMacs) proliferation by 25%) were initially analyzed, and both concepts agreed that OTA + PA demonstrated synergism (p < 0.05), while PAT + PA showed antagonism (p < 0.05). When a follow-up dilution study was carried out using binary combinations of PMs at three different dilution levels (i.e. IC25, 0.5 ∗ IC25, 0.25 ∗ IC25), only the mixture of CIT + OTA at 0.5 ∗ IC25 was determined to have synergism by both IA and CA concepts with Model Deviation Ratios (MDRs; the ratio of predicted versus observed effect concentrations) of 1.4 and 1.7, respectively. The joint effect of OTA + MPA, OTA + PA and CIT + PAT complied with the IA concept, while CIT + PA, PAT + MPA and PAT + PA were better predicted with the CA over the IA concept. The present study suggests to test both IA and CA concepts using multiple doses when assessing risk of mycotoxin mixtures if the mode of action is unknown. In addition, the study showed that the tested PMs could be predicted by IA or CA within an approximate two-fold certainty, raising the possibility for a joint risk assessment of mycotoxins in food and feed. - Highlights: • We investigated the potential joint toxicity of Penicillium mycotoxin (PM) mixtures. • Independent action (IA) and concentration addition (CA) concepts were used. • 7 out of 10 mixtures followed joint toxicity described by IA or CA concepts. • Both concepts agreed that CIT + OTA mixture had synergistic interaction.

  18. Assessing interactions of binary mixtures of Penicillium mycotoxins (PMs) by using a bovine macrophage cell line (BoMacs)

    International Nuclear Information System (INIS)

    Oh, Se-Young; Cedergreen, Nina; Yiannikouris, Alexandros; Swamy, H.V.L.N.; Karrow, Niel A.

    2017-01-01

    Penicillium mycotoxins (PMs) are toxic contaminants commonly found as mixtures in animal feed. Therefore, it is important to investigate potential joint toxicity of PM mixtures. In the present study, we assessed the joint effect of binary combinations of the following PMs: citrinin (CIT), ochratoxin A (OTA), patulin (PAT), mycophenolic acid (MPA) and penicillic acid (PA) using independent action (IA) and concentration addition (CA) concepts. Previously published toxicity data (i.e. IC25; PM concentration that inhibited bovine macrophage (BoMacs) proliferation by 25%) were initially analyzed, and both concepts agreed that OTA + PA demonstrated synergism (p < 0.05), while PAT + PA showed antagonism (p < 0.05). When a follow-up dilution study was carried out using binary combinations of PMs at three different dilution levels (i.e. IC25, 0.5 ∗ IC25, 0.25 ∗ IC25), only the mixture of CIT + OTA at 0.5 ∗ IC25 was determined to have synergism by both IA and CA concepts with Model Deviation Ratios (MDRs; the ratio of predicted versus observed effect concentrations) of 1.4 and 1.7, respectively. The joint effect of OTA + MPA, OTA + PA and CIT + PAT complied with the IA concept, while CIT + PA, PAT + MPA and PAT + PA were better predicted with the CA over the IA concept. The present study suggests to test both IA and CA concepts using multiple doses when assessing risk of mycotoxin mixtures if the mode of action is unknown. In addition, the study showed that the tested PMs could be predicted by IA or CA within an approximate two-fold certainty, raising the possibility for a joint risk assessment of mycotoxins in food and feed. - Highlights: • We investigated the potential joint toxicity of Penicillium mycotoxin (PM) mixtures. • Independent action (IA) and concentration addition (CA) concepts were used. • 7 out of 10 mixtures followed joint toxicity described by IA or CA concepts. • Both concepts agreed that CIT + OTA mixture had synergistic interaction.

  19. Interaction of proliferating cell nuclear antigen with PMS2 is required for MutLα activation and function in mismatch repair.

    Science.gov (United States)

    Genschel, Jochen; Kadyrova, Lyudmila Y; Iyer, Ravi R; Dahal, Basanta K; Kadyrov, Farid A; Modrich, Paul

    2017-05-09

    Eukaryotic MutLα (mammalian MLH1-PMS2 heterodimer; MLH1-PMS1 in yeast) functions in early steps of mismatch repair as a latent endonuclease that requires a mismatch, MutSα/β, and DNA-loaded proliferating cell nuclear antigen (PCNA) for activation. We show here that human PCNA and MutLα interact specifically but weakly in solution to form a complex of approximately 1:1 stoichiometry that depends on PCNA interaction with the C-terminal endonuclease domain of the MutLα PMS2 subunit. Amino acid substitution mutations within a PMS2 C-terminal 721 QRLIAP motif attenuate or abolish human MutLα interaction with PCNA, as well as PCNA-dependent activation of MutLα endonuclease, PCNA- and DNA-dependent activation of MutLα ATPase, and MutLα function in in vitro mismatch repair. Amino acid substitution mutations within the corresponding yeast PMS1 motif ( 723 QKLIIP) reduce or abolish mismatch repair in vivo. Coupling of a weak allele within this motif ( 723 AKLIIP) with an exo1 Δ null mutation, which individually confer only weak mutator phenotypes, inactivates mismatch repair in the yeast cell.

  20. Identification of a novel PMS2 alteration c.505C>G (R169G) in trans with a PMS2 pathogenic mutation in a patient with constitutional mismatch repair deficiency.

    Science.gov (United States)

    Mork, Maureen E; Borras, Ester; Taggart, Melissa W; Cuddy, Amanda; Bannon, Sarah A; You, Y Nancy; Lynch, Patrick M; Ramirez, Pedro T; Rodriguez-Bigas, Miguel A; Vilar, Eduardo

    2016-10-01

    Constitutional mismatch repair deficiency syndrome (CMMRD) is a rare autosomal recessive predisposition to colorectal polyposis and other malignancies, often childhood-onset, that is caused by biallelic inheritance of mutations in the same mismatch repair gene. Here, we describe a patient with a clinical diagnosis of CMMRD based on colorectal polyposis and young-onset endometrial cancer who was identified to have two alterations in trans in PMS2: one known pathogenic mutation (c.1831insA; p.Ile611Asnfs*2) and one novel variant of uncertain significance (c.505C>G; p.Arg169Glu), a missense alteration. We describe the clinical and molecular features in the patient harboring this novel alteration c.505C>G, who meets clinical criteria for CMMRD and exhibits molecular evidence supporting a diagnosis of CMMRD. Although experimental validation is needed to confirm its pathogenicity, PMS2 c.505C>G likely has functional consequences that contributes to our patient's phenotype based on the patient's clinical presentation, tumor studies, and bioinformatics analysis.

  1. Elucidating the clinical significance of two PMS2 missense variants coexisting in a family fulfilling hereditary cancer criteria.

    Science.gov (United States)

    González-Acosta, Maribel; Del Valle, Jesús; Navarro, Matilde; Thompson, Bryony A; Iglesias, Sílvia; Sanjuan, Xavier; Paúles, María José; Padilla, Natàlia; Fernández, Anna; Cuesta, Raquel; Teulé, Àlex; Plotz, Guido; Cadiñanos, Juan; de la Cruz, Xavier; Balaguer, Francesc; Lázaro, Conxi; Pineda, Marta; Capellá, Gabriel

    2017-10-01

    The clinical spectrum of germline mismatch repair (MMR) gene variants continues increasing, encompassing Lynch syndrome, Constitutional MMR Deficiency (CMMRD), and the recently reported MSH3-associated polyposis. Genetic diagnosis of these hereditary cancer syndromes is often hampered by the presence of variants of unknown significance (VUS) and overlapping phenotypes. Two PMS2 VUS, c.2149G>A (p.V717M) and c.2444C>T (p.S815L), were identified in trans in one individual diagnosed with early-onset colorectal cancer (CRC) who belonged to a family fulfilling clinical criteria for hereditary cancer. Clinico-pathological data, multifactorial likelihood calculations and functional analyses were used to refine their clinical significance. Likelihood analysis based on cosegregation and tumor data classified the c.2444C>T variant as pathogenic, which was supported by impaired MMR activity associated with diminished protein expression in functional assays. Conversely, the c.2149G>A variant displayed MMR proficiency and protein stability. These results, in addition to the conserved PMS2 expression in normal tissues and the absence of germline microsatellite instability (gMSI) in the biallelic carrier ruled out a CMMRD diagnosis. The use of comprehensive strategies, including functional and clinico-pathological information, is mandatory to improve the clinical interpretation of naturally occurring MMR variants. This is critical for appropriate clinical management of cancer syndromes associated to MMR gene mutations.

  2. IMMUNOHISTOCHEMICAL STUDY OF MSH2, MSH6, PMS2, MLH1 IN EVALUATION OF DIFFERENTIATION GRADE OF COLON ADENOCARCINOMA

    Directory of Open Access Journals (Sweden)

    G. A. Raskin

    2015-01-01

    Full Text Available Microsatellite instability is associated with dysfunction of the MSH2, MLH1, PMS2 and MSH6 genes, which participate in the repair of unpaired nucleotides of DNA. It is known that microsatellite instability is an independent prognostic factor in determining the differentiation grade of colon cancer. The use of immunohistochemistry to study the repair system of unpaired nucleotides has its own characteristics and limitations. Materials and methods. The study included 39 patients with colon adenocarcinoma. Moderately-differentiated colon adenocarcinoma was the most common histological type (72 %. There were 8 % of well-differentiated and 12 % poorly-differentiated carcinomas. Immunohistochemical analysis of SH2, MSH6, PMS2 and MLH1 proteins was done according to the standard protocol. Results. Out of 39 cases, 6 (15 % had loss of expression of at least one of the studied proteins. Out of these 6 cases with indirect signs of MSI-H, 3 were poorlydifferentiated, 1 was mucinous and 2 were moderately differentiated adenocarcinomas. Conclusion. Thus, immunohistochemical analysis of DNA repair genes can be used to determine the histological differentiation of colon adenocarcinoma.

  3. How to measure the impact of premenstrual symptoms? Development and validation of the German PMS-Impact Questionnaire.

    Science.gov (United States)

    Kues, Johanna N; Janda, Carolyn; Kleinstäuber, Maria; Weise, Cornelia

    2016-10-01

    With 75% of women of reproductive age affected, premenstrual symptoms are very common, ranging from emotional and cognitive to physical symptoms. Premenstrual Syndrome and Premenstrual Dysphoric Disorder can lead to substantial functional interference and psychological distress comparable to that of dysthymic disorders. The assessment of this impact is required as a part of the diagnostic procedure in the DSM-5. In the absence of a specific measure, the authors developed the PMS-Impact Questionnaire. A sample of 101 women reporting severe premenstrual complaints was assessed with the twenty-two items in the questionnaire during their premenstrual phase in an ongoing intervention study at the Philipps-University Marburg from August 2013 until January 2015. An exploratory factor analysis revealed a two-factor solution (labeled Psychological Impact and Functional Impact) with 18 items. A Cronbach's alpha of 0.90 for Psychological Impact and of 0.90 for Functional Impact indicated good reliability. Convergent construct validity was demonstrated by moderate to high correlations with the Pain Disability Index. Low correlations with the Big Five Inventory-10 indicated good divergent validity. The PMS-Impact Questionnaire was found to be a valid, reliable, and an economic measure to assess the impact of premenstrual symptoms. In future research, cross validations and confirmatory factor analyses should be conducted.

  4. A design of scintillator tiles read out by surface-mounted SiPMs for a future hadron calorimeter

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Yong; Bauss, Bruno; Buescher, Volker; Caudron, Julien; Chau, Phi; Degele, Reinhold; Geib, Karl-Heinrich; Masetti, Lucia; Schaefer, Ulrich; Tapprogge, Stefan; Wanke, Rainer [Institut fuer Physik and PRISMA Detector Lab, Johannes Gutenberg-Universitaet Mainz (Germany)

    2015-07-01

    Precision calorimetry using highly granular sampling calorimeters is being developed based on the particle flow concept within the CALICE collaboration. One design option of a hadron calorimeter is based on silicon photomultipliers (SiPMs) to detect photons generated in plastic scintillator tiles. Driven by the need of automated mass assembly of around ten millions of channels stringently required by the high granularity, we developed a design of scintillator tiles directly coupled with surface-mounted SiPMs. A cavity is created in the center of the bottom surface of each tile to provide enough room for the whole SiPM package and to improve collection of the light produced by incident particles penetrating the tile at different positions. The cavity design has been optimized using a GEANT4-based full simulation model to achieve high response to Minimum Ionizing Particles (MIPs) and also good areal uniformity. Cosmic-ray measurements confirms high 1-MIP response for scintillator tiles with an optimized cavity design. Uniformity measurements by scanning the tile area using focused electrons from a beta source show excellent response uniformity. This optimized design is well beyond the requirements for a precision hadron calorimeter.

  5. Efficacy of Vitex agnus castus L. extract Ze 440 in patients with pre-menstrual syndrome (PMS).

    Science.gov (United States)

    Berger, D; Schaffner, W; Schrader, E; Meier, B; Brattström, A

    2000-11-01

    In a prospective, multicentre trial the efficacy of an Vitex agnus castus L extract Ze 440 was investigated in 50 patients with pre-menstrual syndrome (PMS). The patients were treated daily with one tablet (20 mg native extract) during three menstrual cycles. 43 patients completed the study protocol which encompassed 8 menstrual cycles (2 baseline, 3 treatment and 3 post-treatment). 13/43 patients were receiving concomitant oral contraceptives. 6 patients did not complete the study for reasons not related to study medication, and one patient complained of fatigue possibly related to study medication. All evaluated patients took at least 85% of the prescribed medication. The main effect parameter was the validated Moos' menstrual distress questionnaire (MMDQ), and secondary parameters were a visual analogue scale (VAS; self-assessment) and a global impression scale (GI, self-assessment). The study population was homogenous in age (31.3+/-7.7 years) weight (58.9+/-6.9 kg) and cycle length (28.4+/-0.3 d). The diagnosis was according to DMS-III. At the end of the study, PMS-related symptoms were reduced by treatment. There was a significant score reduction (42.5%) of the MMDQ as the main effect parameter (pVitex agnus-castus extract Ze 440, as indicated by clear improvement in the main effect parameter during treatment and the gradual return after cessation of treatment. The main response to treatment seems related to symptomatic relief rather than to the duration of the syndrome.

  6. Immunohistochemistry for PMS2 and MSH6 alone can replace a four antibody panel for mismatch repair deficiency screening in colorectal adenocarcinoma.

    Science.gov (United States)

    Hall, Geoffrey; Clarkson, Adele; Shi, Amanda; Langford, Eileen; Leung, Helen; Eckstein, Robert P; Gill, Anthony J

    2010-01-01

    Currently, testing for mismatch repair deficiency in colorectal cancers is initiated by performing immunohistochemistry with four antibodies (MLH1, PMS2, MSH2 and MSH6). If any one of these stains is negative the tumour is considered microsatellite unstable and, if clinical circumstances warrant it, the patient is offered genetic testing for Lynch's syndrome. Due to the binding properties of the mismatch repair heterodimer complexes, gene mutation and loss of MLH1 and MSH2 invariably result in the degradation of PMS2 and MSH6, respectively, but the converse is not true. We propose that staining for PMS2 and MSH6 alone will be sufficient to detect all cases of mismatch repair deficiency and should replace routine screening with all four antibodies. The electronic database of the department of Anatomical Pathology, Royal North Shore Hospital, Sydney, Australia, was searched for all colorectal carcinomas on which a four panel immunohistochemical microsatellite instability screen was performed. An audit of the slides for concordant loss of MLH1-PMS2 and MSH2-MSH6 was then undertaken. Unusual or discordant cases were reviewed and, in some cases, re-stained to confirm the staining pattern. Of 344 cases of colorectal cancer which underwent four antibody immunohistochemistry, 104 displayed loss of at least one mismatch repair protein. Of these, 100 showed concordant mismatch repair loss (i.e., loss of MLH1 and PMS2 or loss of MSH2 and MSH6). The four discordant cases comprised two single negative cases (1 MSH6 negative/MSH2 positive case, 1 PMS2 negative/MLH1 positive) and two triple negative (both MLH1/PMS2/MSH6 negative). The microsatellite instability (MSI) group showed a relatively high median age (69.3 years) due to the departmental policy of testing all cases with possible MSI morphology regardless of age. The sensitivity and specificity of a two panel test comprised of PMS2 and MSH6, compared to a four panel test, is 100%. No false negatives or positives were

  7. Mass test of AdvanSiD model ASD-NUV3S-P SiliconPMs for the Pixel Timing Counter of the MEG II experiment

    Science.gov (United States)

    Rossella, M.; Bariani, S.; Barnaba, O.; Cattaneo, P. W.; Cervi, T.; Menegolli, A.; Nardò, R.; Prata, M. C.; Romano, E.; Scagliotti, C.; Simonetta, M.; Vercellati, F.

    2017-02-01

    The MEG II Timing Counter will measure the positron time of arrival with a resolution of 30 ps relying on two arrays of scintillator pixels read out by 6144 Silicon Photomultipliers (SiPMs) from AdvanSiD. They must be characterized, measuring their breakdown voltage, to assure that the gains of the SiPMs of each pixel are as uniform as possible, to maximize the pixel resolution. To do this an automatic test system that can measure sequentially the parameters of 32 devices has been developed.

  8. Journal of Astrophysics and Astronomy | Indian Academy of Sciences

    Indian Academy of Sciences (India)

    2016-01-27

    Jan 27, 2016 ... The probable cluster memberships of the X-ray sources have been established on the basis of multi-wavelength archival data, and samples of 152 pre-main sequence (PMS) low mass ( 10⊙) stars have been generated. X-ray spectral analyses ...

  9. Influences of donor dopants on the properties of PZT-PMS-PZN piezoelectric ceramics sintered at low temperatures

    International Nuclear Information System (INIS)

    Yoon, Seokjin; Choi, Jiwon; Choi, Jooyoung; Wan, Dandan; Li, Qian; Yang, Ying

    2010-01-01

    0.90Pb(Zr 0.48 Ti 0.52 )O 3 -0.05Pb(Mn 1/3 Sb 2/3 )O 3 -0.05Pb(Zn 1/3 Nb 2/3 )O 3 quaternary piezoelectric ceramics with CuO added were synthesized by using a conventional method at low sintering temperatures. CuO additive, 1.0 wt%, significantly improves the sinterability of 0.90PZT-0.05PMS-0.05PZN ceramics, lowering the sintering temperature to 900 .deg. C and showing moderate electrical properties: d 33 = 306 pC/N, Q m = 997, k p = 53.6%, tanδ = 0.50%, and ε T 33 = 1351. To obtain more optimal piezoelectric properties, we selected Bi 2 O 3 and Nb 2 O 5 as donor dopants to introduce a softening effect. The crystal structure, micro-morphology and electrical properties were studied in terms of the Bi 2 O 3 and the Nb 2 O 5 contents. Our study demonstrates that Bi 2 O 3 is very effective in improving the piezoelectric properties, causing a significant enhancement in d 33 and k p values. Particularly, 0.75-wt%-Bi 2 O 3 -added 0.90PZT-0.05PMS-0.05PZN + 1.0 wt% CuO ceramics show excellent electrical properties: d 33 = 363 pC/N, Q m = 851, k p = 59.3%, tanδ = 0.38%, and ε T 33 = 1596. On the other hand, the effect of Nb 2 O 5 on the piezoelectric properties is very complicated, 0.50 wt% Nb 2 O 5 doped 0.90PZT-0.05PMS-0.05PZN + 1.0 wt% CuO ceramics have a remarkable improvement in k p value and maintain good electrical properties: d 33 = 300 pC/N, Q m = 971, k p = 58.4%, tanδ = 0.36%, and ε T 33 = 1332.

  10. The effect of genotypes and parent of origin on cancer risk and age of cancer development in PMS2 mutation carriers

    NARCIS (Netherlands)

    Suerink, Manon; van der Klift, Heleen M.; ten Broeke, Sanne W.; Dekkers, Olaf M.; Bernstein, Inge; Capella Munar, Gabriel; Gomez Garcia, Encarna; Hoogerbrugge, Nicoline; Letteboer, Tom G. W.; Menko, Fred H.; Lindblom, Annika; Mensenkamp, Arjen; Moller, Pal; van Os, Theo A.; Rahner, Nils; Redeker, Bert J. W.; Olderode, Maran; Spruijt, Liesbeth; Vos, Yvonne J.; Wagner, Anja; Morreau, Hans; Hes, Frederik J.; Vasen, Hans F. A.; Tops, Carli M.; Wijnen, Juul T.; Nielsen, Maartje

    Purpose: Lynch syndrome (LS), a heritable disorder with an increased risk of primarily colorectal cancer (CRC) and endometrial cancer (EC), can be caused by mutations in the PMS2 gene. We wished to establish whether genotype and/or parent-of-origin effects (POE) explain (part of) the reported

  11. Paediatric intestinal cancer and polyposis due to bi-allelic PMS2 mutations : Case series, review and follow-up guidelines

    NARCIS (Netherlands)

    Herkert, Johanna C; Niessen, Renée C; Olderode-Berends, Maria J W; Veenstra-Knol, Hermine E; Vos, Yvonne J; van der Klift, Heleen M; Scheenstra, Rene; Tops, Carli M J; Karrenbeld, Arend; Peters, Frans T M; Hofstra, Robert M W; Kleibeuker, Jan H; Sijmons, Rolf H

    BACKGROUND: Bi-allelic germline mutations of one of the DNA mismatch repair genes, so far predominantly found in PMS2, cause constitutional MMR-deficiency syndrome. This rare disorder is characterised by paediatric intestinal cancer and other malignancies. We report the clinical, immunohistochemical

  12. The effect of genotypes and parent of origin on cancer risk and age of cancer development in PMS2 mutation carriers

    NARCIS (Netherlands)

    Suerink, Manon; van der Klift, Heleen M; Ten Broeke, Sanne W; Dekkers, Olaf M; Bernstein, Inge; Capellá Munar, Gabriel; Gomez Garcia, Encarna; Hoogerbrugge, Nicoline; Letteboer, Tom G W; Menko, Fred H; Lindblom, Annika; Mensenkamp, Arjen; Moller, Pal; van Os, Theo A; Rahner, Nils; Redeker, Bert J W; Olderode, Maran; Spruijt, Liesbeth; Vos, Yvonne J; Wagner, Anja; Morreau, Hans; Hes, Frederik J; Vasen, Hans F A; Tops, Carli M; Wijnen, Juul T; Nielsen, Maartje

    PURPOSE: Lynch syndrome (LS), a heritable disorder with an increased risk of primarily colorectal cancer (CRC) and endometrial cancer (EC), can be caused by mutations in the PMS2 gene. We wished to establish whether genotype and/or parent-of-origin effects (POE) explain (part of) the reported

  13. The effect of genotypes and parent of origin on cancer risk and age of cancer development in PMS2 mutation carriers

    NARCIS (Netherlands)

    Suerink, Manon; van der Klift, Heleen M.; ten Broeke, Sanne W.; Dekkers, Olaf M.; Bernstein, Inge; Capellá Munar, Gabriel; Gomez Garcia, Encarna; Hoogerbrugge, Nicoline; Letteboer, Tom G. W.; Menko, Fred H.; Lindblom, Annika; Mensenkamp, Arjen; Moller, Pal; van Os, Theo A.; Rahner, Nils; Redeker, Bert J. W.; Olderode-Berends, M. J. W.; Olderode, Maran; Spruijt, Liesbeth; Vos, Yvonne J.; Wagner, Anja; Morreau, Hans; Hes, Frederik J.; Vasen, Hans F. A.; Tops, Carli M.; Wijnen, Juul T.; Nielsen, Maartje

    2016-01-01

    Lynch syndrome (LS), a heritable disorder with an increased risk of primarily colorectal cancer (CRC) and endometrial cancer (EC), can be caused by mutations in the PMS2 gene. We wished to establish whether genotype and/or parent-of-origin effects (POE) explain (part of) the reported variability in

  14. The effect of genotypes and parent of origin on cancer risk and age of cancer development in PMS2 mutation carriers

    NARCIS (Netherlands)

    Suerink, M.; Klift, H.M. van der; Broeke, S.W. ten; Dekkers, O.M.; Bernstein, I.; Capella Munar, G.; Garcia, E.; Hoogerbrugge, N.; Letteboer, T.G.; Menko, F.H.; Lindblom, A.; Mensenkamp, A.; Moller, P.; Os, T.A. van; Rahner, N.; Redeker, B.J.; Olderode-Berends, M.J.; Spruijt, L.; Vos, Y.J.; Wagner, A.; Morreau, H.; Hes, F.J.; Vasen, H.F.A.; Tops, C.M.; Wijnen, J.T.; Nielsen, M.

    2016-01-01

    PURPOSE: Lynch syndrome (LS), a heritable disorder with an increased risk of primarily colorectal cancer (CRC) and endometrial cancer (EC), can be caused by mutations in the PMS2 gene. We wished to establish whether genotype and/or parent-of-origin effects (POE) explain (part of) the reported

  15. Comparison of the effect of omega-3 fatty acids and perforan (Hypericum perforatum on severity of premenstrual syndrome (PMS: a randomized trial

    Directory of Open Access Journals (Sweden)

    Masoomeh kheirkhah

    2016-11-01

    Full Text Available Premenstrual syndrome (PMS encompasses a wide variety of cyclic and recurrent physical, emotional, and behavioral symptoms that occur before menstruation and has negative impact on activities of daily living, social activities, sexual functioning and quality of life. The aim of the present study was to compare the effect of omega-3 fatty acid and perforan (Hypericum perforatum on severity of premenstrual syndrome (PMS. This study is a triple-blind clinical trial that was carried out across three groups with 150 students after considering inclusion and exclusion criteria. The subjects of this study were randomly divided into three groups include omega-3 fatty acid group, perforan group and control (placebo group. Every subject in this study took drugs during three subsequent cycles so they took capsules daily in the first cycle for one month and in the second and third cycles they took them from eight days before menstruation to two days after and recorded the severity of premenstrual syndrome questionnaire. Statistical analyses were performed using SPSS version 17. The repeated measures ANOVA, chi-square and Wilcoxon tests were used to compare mean differences in three groups. The data showed that there were no significant differences between 3 groups before the intervention but 1, 2 and 3 months after consumption of perforan and omega-3 capsules, the severity of PMS was significantly lower than that in control group (p<0.001. perforan and omega-3 significantly reduce the severity of PMS.

  16. Promoter methylation of MLH1, PMS2, MSH2 and p16 is a phenomenon of advanced-stage HCCs.

    Science.gov (United States)

    Hinrichsen, Inga; Kemp, Matthias; Peveling-Oberhag, Jan; Passmann, Sandra; Plotz, Guido; Zeuzem, Stefan; Brieger, Angela

    2014-01-01

    Epigenetic silencing of tumour suppressor genes has been observed in various cancers. Looking at hepatocellular carcinoma (HCC) specific protein silencing was previously demonstrated to be associated with the Hepatitis C virus (HCV). However, the proposed HCV dependent promoter methylation of DNA mismatch repair (MMR) genes and thereby enhanced progression of hepatocarcinogenesis has been the subject of controversial discussion. We investigated promoter methylation pattern of the MMR genes MLH1, MSH2 and PMS2 as well as the cyclin-dependent kinase inhibitor 2A gene (p16) in 61 well characterized patients with HCCs associated with HCV, Hepatitis B virus infection or alcoholic liver disease. DNA was isolated from formalin-fixed, paraffin-embedded tumour and non-tumour adjacent tissue and analysed by methylation-specific PCR. Moreover, microsatellite analysis was performed in tissues showing methylation in MMR gene promoters. Our data demonstrated that promoter methylation of MLH1, MSH2, PMS2 and p16 is present among all considered HCCs. Hereby, promoter silencing was detectable more frequently in advanced-stage HCCs than in low-stage ones. However, there was no significant correlation between aberrant DNA methylation of MMR genes or p16 and HCV infection in related HCC specimens. In summary, we show that promoter methylation of essential MMR genes and p16 is detectable in HCCs most dominantly in pT3 stage tumour cases. Since loss of MMR proteins was previously described to be not only responsible for tumour development but also for chemotherapy resistance, the knowledge of mechanisms jointly responsible for HCC progression might enable significant improvement of individual HCC therapy in the future.

  17. Promoter methylation of MLH1, PMS2, MSH2 and p16 is a phenomenon of advanced-stage HCCs.

    Directory of Open Access Journals (Sweden)

    Inga Hinrichsen

    Full Text Available Epigenetic silencing of tumour suppressor genes has been observed in various cancers. Looking at hepatocellular carcinoma (HCC specific protein silencing was previously demonstrated to be associated with the Hepatitis C virus (HCV. However, the proposed HCV dependent promoter methylation of DNA mismatch repair (MMR genes and thereby enhanced progression of hepatocarcinogenesis has been the subject of controversial discussion. We investigated promoter methylation pattern of the MMR genes MLH1, MSH2 and PMS2 as well as the cyclin-dependent kinase inhibitor 2A gene (p16 in 61 well characterized patients with HCCs associated with HCV, Hepatitis B virus infection or alcoholic liver disease. DNA was isolated from formalin-fixed, paraffin-embedded tumour and non-tumour adjacent tissue and analysed by methylation-specific PCR. Moreover, microsatellite analysis was performed in tissues showing methylation in MMR gene promoters. Our data demonstrated that promoter methylation of MLH1, MSH2, PMS2 and p16 is present among all considered HCCs. Hereby, promoter silencing was detectable more frequently in advanced-stage HCCs than in low-stage ones. However, there was no significant correlation between aberrant DNA methylation of MMR genes or p16 and HCV infection in related HCC specimens. In summary, we show that promoter methylation of essential MMR genes and p16 is detectable in HCCs most dominantly in pT3 stage tumour cases. Since loss of MMR proteins was previously described to be not only responsible for tumour development but also for chemotherapy resistance, the knowledge of mechanisms jointly responsible for HCC progression might enable significant improvement of individual HCC therapy in the future.

  18. Activation of the mu-opiate receptor by Vitex agnus-castus methanol extracts: implication for its use in PMS.

    Science.gov (United States)

    Webster, D E; Lu, J; Chen, S-N; Farnsworth, N R; Wang, Z Jim

    2006-06-30

    The dried ripe fruit of Vitex agnus-castus L. (VAC) is widely used for the treatment of premenstrual syndrome (PMS). A previous study reported that extracts of VAC showed affinity to opiate receptors; however, functional activity was not determined. We tested two different VAC extracts in receptor binding and functional assays. Our objectives were: (1) to confirm the opiate affinity; (2) to rule out interference by free fatty acids (FFA); (3) to determine the mode of action of VAC at the mu-opiate receptor. Methanol extracts of VAC were prepared either before (VAC-M1) or after (VAC-M2) extraction with petroleum ether to remove fatty acids. Both extracts showed significant affinities to the mu-opiate receptor, as indicated by the concentration-dependent displacement of [3H]DAMGO binding in Chinese hamster ovary (CHO)-human mu-opiate receptor (hMOR) cells. The IC50 values were estimated to be 159.8 microg/ml (VAC-M1) and 69.5 microg/ml (VAC-M2). Since the defatted extract not only retained, but exhibited a higher affinity (p<0.001), it argued against significant interference by fatty acids. In an assay to determine receptor activation, VAC-M1 and VAC-M2 stimulated [35S]GTPgammaS binding by 41 and 61% (p<0.001), respectively. These results suggested for the first time that VAC acted as an agonist at the mu-opiate receptor, supporting its beneficial action in PMS.

  19. Secondary mutation in a coding mononucleotide tract in MSH6 causes loss of immunoexpression of MSH6 in colorectal carcinomas with MLH1/PMS2 deficiency.

    Science.gov (United States)

    Shia, Jinru; Zhang, Liying; Shike, Moshe; Guo, Min; Stadler, Zsofia; Xiong, Xiaoling; Tang, Laura H; Vakiani, Efsevia; Katabi, Nora; Wang, Hangjun; Bacares, Ruben; Ruggeri, Jeanine; Boland, C Richard; Ladanyi, Marc; Klimstra, David S

    2013-01-01

    Immunohistochemical staining for DNA mismatch repair proteins may be affected by various biological and technical factors. Staining variations that could potentially lead to erroneous interpretations have been recognized. A recently recognized staining variation is the significant reduction of staining for MSH6 in some colorectal carcinomas. The frequency and specific characteristics of this aberrant MSH6 staining pattern, however, have not been well analyzed. In this study of 420 colorectal carcinoma samples obtained from patients fulfilling the Revised Bethesda Guidelines, we detected 9 tumors (2%) showing extremely limited staining for MSH6 with positive staining present in PMS2 protein-deficient carcinomas (n=5, including 1 with a pathogenic mutation in PMS2); and (2) MLH1, PMS2 and MSH2 normal but with chemotherapy or chemoradiation therapy before surgery (n=4). To test our hypothesis that somatic mutation in the coding region microsatellite of the MSH6 gene might be a potential underlying mechanism for such limited MSH6 staining, we evaluated frameshift mutation in a (C)(8) tract in exon 5 of the MSH6 gene in seven tumors that had sufficient DNA for analysis, and detected mutation in four; all four tumors belonged to the MLH1/PMS2-deficient group. In conclusion, our data outline the main scenarios where significant reduction of MSH6 staining is more likely to occur in colorectal carcinoma, and suggest that somatic mutations of the coding region microsatellites of the MSH6 gene is an underlying mechanism for this staining phenomenon in MLH1/PMS2-deficient carcinomas.

  20. A lecithin phosphatidylserine and phosphatidic acid complex (PAS) reduces symptoms of the premenstrual syndrome (PMS): Results of a randomized, placebo-controlled, double-blind clinical trial.

    Science.gov (United States)

    Schmidt, Katja; Weber, Nicole; Steiner, Meir; Meyer, Nadin; Dubberke, Anne; Rutenberg, David; Hellhammer, Juliane

    2018-04-01

    Many women experience emotional and physical symptoms around the time of ovulation and more so before menstruation interfering with their daily normal life also known as premenstrual syndrome (PMS). Recent observational data suggest that supplementation with Lipogen's phosphatidylserine (PS) and phosphatidic acid (PA) complex (PAS) alleviates these PMS symptoms. The aim of this study was to confirm these observations on the effects of PAS on PMS symptom severity within a controlled clinical trial setting. Forty women aged 18-45 years with a diagnosis of PMS were assigned to either take PAS (containing 400 mg PS & 400 mg PA per day) or a matching placebo. The study comprised 5 on-site visits including 1 baseline menstrual cycle followed by 3 treatment cycles. Treatment intake was controlled for by using an electronic device, the Medication Event Monitoring System (MEMS ® ). Primary outcome of the study was the PMS symptoms severity as assessed by using the Daily Record of Severity of Problems (DRSP). Further, SIPS questionnaire (a German version of the Premenstrual Symptoms Screening Tool (PSST)), salivary hormone levels (cortisol awakening response (CAR) and evening cortisol levels) as well as serum levels (cortisol, estradiol, progesterone and corticosteroid binding globulin (CBG)) were assessed. PMS symptoms as assessed by the DRSP Total score showed a significantly better improvement (p = 0.001) over a 3 cycles PAS intake as compared to placebo. In addition, PAS treated women reported a greater improvement in physical (p = 0.002) and depressive symptoms (p = 0.068). They also reported a lower reduction of productivity (p = 0.052) and a stronger decrease in interference with relationships with others (p = 0.099) compared to the placebo group. No other DRSP scale or item showed significant results. Likewise, the reduction in the number of subjects fulfilling PMS or premenstrual dysphoric disorder (PMDD) criteria as classified by the SIPS did not

  1. MSH6- or PMS2-deficiency causes re-replication in DT40 B cells, but it has little effect on immunoglobulin gene conversion or on repair of AID-generated uracils

    Science.gov (United States)

    Campo, Vanina A.; Patenaude, Anne-Marie; Kaden, Svenja; Horb, Lori; Firka, Daniel; Jiricny, Josef; Di Noia, Javier M.

    2013-01-01

    The mammalian antibody repertoire is shaped by somatic hypermutation (SHM) and class switch recombination (CSR) of the immunoglobulin (Ig) loci of B lymphocytes. SHM and CSR are triggered by non-canonical, error-prone processing of G/U mismatches generated by activation-induced deaminase (AID). In birds, AID does not trigger SHM, but it triggers Ig gene conversion (GC), a ‘homeologous’ recombination process involving the Ig variable region and proximal pseudogenes. Because recombination fidelity is controlled by the mismatch repair (MMR) system, we investigated whether MMR affects GC in the chicken B cell line DT40. We show here that Msh6−/− and Pms2−/− DT40 cells display cell cycle defects, including genomic re-replication. However, although IgVλ GC tracts in MMR-deficient cells were slightly longer than in normal cells, Ig GC frequency, donor choice or the number of mutations per sequence remained unaltered. The finding that the avian MMR system, unlike that of mammals, does not seem to contribute towards the processing of G/U mismatches in vitro could explain why MMR is unable to initiate Ig GC in this species, despite initiating SHM and CSR in mammalian cells. Moreover, as MMR does not counteract or govern Ig GC, we report a rare example of ‘homeologous’ recombination insensitive to MMR. PMID:23314153

  2. Sequence assembly

    DEFF Research Database (Denmark)

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

    2009-01-01

    Despite the rapidly increasing number of sequenced and re-sequenced genomes, many issues regarding the computational assembly of large-scale sequencing data have remain unresolved. Computational assembly is crucial in large genome projects as well for the evolving high-throughput technologies and...... in genomic DNA, highly expressed genes and alternative transcripts in EST sequences. We summarize existing comparisons of different assemblers and provide a detailed descriptions and directions for download of assembly programs at: http://genome.ku.dk/resources/assembly/methods.html....

  3. Genome Sequencing

    DEFF Research Database (Denmark)

    Sato, Shusei; Andersen, Stig Uggerhøj

    2014-01-01

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

  4. Biallelic PMS2 Mutation and Heterozygous DICER1 Mutation Presenting as Constitutional Mismatch Repair Deficiency With Corpus Callosum Agenesis: Case Report and Review of Literature.

    Science.gov (United States)

    Cheyuo, Cletus; Radwan, Walid; Ahn, Janice; Gyure, Kymberly; Qaiser, Rabia; Tomboc, Patrick

    2017-10-01

    Constitutional mismatch repair deficiency syndrome is a cancer predisposition syndrome caused by autosomal recessive biallelic (homozygous) germline mutations in the mismatch repair genes (MLH1, MSH2, MSH6, and PMS2). The clinical spectrum includes neoplastic and non-neoplastic manifestations. We present the case of a 7-year-old boy who presented with T-lymphoblastic lymphoma and glioblastoma, together with non-neoplastic manifestations including corpus callosum agenesis, arachnoid cyst, developmental venous anomaly, and hydrocephalus. Gene mutation analysis revealed pathogenic biallelic mutations of PMS2 and heterozygous DICER1 variant predicted to be pathogenic. This report is the first to allude to a possible interaction of the mismatch repair system with DICER1 to cause corpus callosum agenesis.

  5. Homozygous germ-line mutation of the PMS2 mismatch repair gene: a unique case report of constitutional mismatch repair deficiency (CMMRD)

    OpenAIRE

    Ramchander, N. C.; Ryan, N. A. J.; Crosbie, E. J.; Evans, D. G.

    2017-01-01

    BackgroundConstitutional mismatch repair deficiency syndrome results from bi-allelic inheritance of mutations affecting the key DNA mismatch repair genes: MLH1, MSH2, MSH6 or PMS2. Individuals with bi-allelic mutations have a dysfunctional mismatch repair system from birth; as a result, constitutional mismatch repair deficiency syndrome is characterised by early onset malignancies. Fewer than 150 cases have been reported in the literature over the past 20 years. This is the first report of th...

  6. A massive parallel sequencing workflow for diagnostic genetic testing of mismatch repair genes

    Science.gov (United States)

    Hansen, Maren F; Neckmann, Ulrike; Lavik, Liss A S; Vold, Trine; Gilde, Bodil; Toft, Ragnhild K; Sjursen, Wenche

    2014-01-01

    The purpose of this study was to develop a massive parallel sequencing (MPS) workflow for diagnostic analysis of mismatch repair (MMR) genes using the GS Junior system (Roche). A pathogenic variant in one of four MMR genes, (MLH1, PMS2, MSH6, and MSH2), is the cause of Lynch Syndrome (LS), which mainly predispose to colorectal cancer. We used an amplicon-based sequencing method allowing specific and preferential amplification of the MMR genes including PMS2, of which several pseudogenes exist. The amplicons were pooled at different ratios to obtain coverage uniformity and maximize the throughput of a single-GS Junior run. In total, 60 previously identified and distinct variants (substitutions and indels), were sequenced by MPS and successfully detected. The heterozygote detection range was from 19% to 63% and dependent on sequence context and coverage. We were able to distinguish between false-positive and true-positive calls in homopolymeric regions by cross-sample comparison and evaluation of flow signal distributions. In addition, we filtered variants according to a predefined status, which facilitated variant annotation. Our study shows that implementation of MPS in routine diagnostics of LS can accelerate sample throughput and reduce costs without compromising sensitivity, compared to Sanger sequencing. PMID:24689082

  7. VizieR Online Data Catalog: Photmetry and spectroscopy of PMS stars in NGC 2264 (Lim+, 2016)

    Science.gov (United States)

    Lim, B.; Sung, H.; Kim, J. S.; Bessell, M. S.; Hwang, N.; Park, B.-G.

    2018-04-01

    Queue scheduled observations were carried out on 2015 April 1 and November 24 with the multi-object high resolution echelle spectrograph Hectochelle attached to the 6.5m telescope of the MMT observatory. The resolving power of the spectrograph (R~34,000) is high enough to detect the LiI λ6708 resonance doublet with little blending from adjacent metallic lines. The multi-object capability allowed us to simultaneously obtain 240 target and sky spectra in a single observation. The OB 26 filter transmits the wavelength range 6530-6715Å, and therefore the useful spectral features Hα λ6563 and HeI λ6678 could also be observed along with the LiI λ6708 line. The spectra of a total of 134 PMS stars were taken in two sets of exposure times -8 minutes x3 for bright stars (V<13.6mag) and 30 minutes x3 for fainter stars. Offset sky spectra were also obtained to correct for the contributions of locally variable nebula emission lines to the spectra of the faint stars. Calibration frames, such as dome flat and comparison spectra, were also acquired, just before and after the target exposure. (1 data file).

  8. The cross-talk problem in SiPMs and their use as light sensors for imaging atmospheric Cherenkov telescopes

    International Nuclear Information System (INIS)

    Buzhan, P.; Dolgoshein, B.; Ilyin, A.; Kaplin, V.; Klemin, S.; Mirzoyan, R.; Popova, E.; Teshima, M.

    2009-01-01

    One of the major drawbacks of a SiPM is due to the so-called cross-talk effect. Often, one single photon in a chain reaction can generate more photons and thus can fire more than one micro-cell of a SiPM. This can be considered as a noise in the signal multiplication process and this degrades the signal/noise ratio. In self-trigger schemes this noise can be so high that it can make operating them difficult at low threshold settings. For the past few years, we have dwelt on this effect aiming to suppress it at the design stage. One can use (a) trenches around the micro-cells for suppressing the direct photon 'communication' channel and (b) the so-called double p-n junction for suppressing photon-induced charge 'communication' in neighbor pixels. The low cross-talk is mandatory, for example, for producing SiPM-based light sensor modules for the Imaging Atmospheric Cherenkov Technique projects for ground-based gamma-ray astrophysics. We produced and tested a few modules consisting of 4 SiPMs, each with a size of 5 mmx5 mm of custom production type. We report here on the main parameters of these units.

  9. Deoxyinosine triphosphate induces MLH1/PMS2- and p53-dependent cell growth arrest and DNA instability in mammalian cells

    Science.gov (United States)

    Yoneshima, Yasuto; Abolhassani, Nona; Iyama, Teruaki; Sakumi, Kunihiko; Shiomi, Naoko; Mori, Masahiko; Shiomi, Tadahiro; Noda, Tetsuo; Tsuchimoto, Daisuke; Nakabeppu, Yusaku

    2016-01-01

    Deoxyinosine (dI) occurs in DNA either by oxidative deamination of a previously incorporated deoxyadenosine residue or by misincorporation of deoxyinosine triphosphate (dITP) from the nucleotide pool during replication. To exclude dITP from the pool, mammals possess specific hydrolysing enzymes, such as inosine triphosphatase (ITPA). Previous studies have shown that deficiency in ITPA results in cell growth suppression and DNA instability. To explore the mechanisms of these phenotypes, we analysed ITPA-deficient human and mouse cells. We found that both growth suppression and accumulation of single-strand breaks in nuclear DNA of ITPA-deficient cells depended on MLH1/PMS2. The cell growth suppression of ITPA-deficient cells also depended on p53, but not on MPG, ENDOV or MSH2. ITPA deficiency significantly increased the levels of p53 protein and p21 mRNA/protein, a well-known target of p53, in an MLH1-dependent manner. Furthermore, MLH1 may also contribute to cell growth arrest by increasing the basal level of p53 activity. PMID:27618981

  10. The effect of genotypes and parent of origin on cancer risk and age of cancer development in PMS2 mutation carriers.

    Science.gov (United States)

    Suerink, Manon; van der Klift, Heleen M; Ten Broeke, Sanne W; Dekkers, Olaf M; Bernstein, Inge; Capellá Munar, Gabriel; Gomez Garcia, Encarna; Hoogerbrugge, Nicoline; Letteboer, Tom G W; Menko, Fred H; Lindblom, Annika; Mensenkamp, Arjen; Moller, Pal; van Os, Theo A; Rahner, Nils; Redeker, Bert J W; Olderode-Berends, M J W; Olderode, Maran; Spruijt, Liesbeth; Vos, Yvonne J; Wagner, Anja; Morreau, Hans; Hes, Frederik J; Vasen, Hans F A; Tops, Carli M; Wijnen, Juul T; Nielsen, Maartje

    2016-04-01

    Lynch syndrome (LS), a heritable disorder with an increased risk of primarily colorectal cancer (CRC) and endometrial cancer (EC), can be caused by mutations in the PMS2 gene. We wished to establish whether genotype and/or parent-of-origin effects (POE) explain (part of) the reported variability in severity of the phenotype. European PMS2 mutation carriers (n = 381) were grouped and compared based on RNA expression and whether the mutation was inherited paternally or maternally. Mutation carriers with loss of RNA expression (group 1) had a significantly lower age at CRC diagnosis (51.1 years vs. 60.0 years, P = 0.035) and a lower age at EC diagnosis (55.8 years vs. 61.0 years, P = 0.2, nonsignificant) compared with group 2 (retention of RNA expression). Furthermore, group 1 showed slightly higher, but nonsignificant, hazard ratios (HRs) for both CRC (HR: 1.31, P = 0.38) and EC (HR: 1.22, P = 0.72). No evidence for a significant parent-of-origin effect was found for either CRC or EC. PMS2 mutation carriers with retention of RNA expression developed CRC 9 years later than those with loss of RNA expression. If confirmed, this finding would justify a delay in surveillance for these cases. Cancer risk was not influenced by a parent-of-origin effect.Genet Med 18 4, 405-409.

  11. Pms2 and uracil-DNA glycosylases act jointly in the mismatch repair pathway to generate Ig gene mutations at A-T base pairs.

    Science.gov (United States)

    Girelli Zubani, Giulia; Zivojnovic, Marija; De Smet, Annie; Albagli-Curiel, Olivier; Huetz, François; Weill, Jean-Claude; Reynaud, Claude-Agnès; Storck, Sébastien

    2017-04-03

    During somatic hypermutation (SHM) of immunoglobulin genes, uracils introduced by activation-induced cytidine deaminase are processed by uracil-DNA glycosylase (UNG) and mismatch repair (MMR) pathways to generate mutations at G-C and A-T base pairs, respectively. Paradoxically, the MMR-nicking complex Pms2/Mlh1 is apparently dispensable for A-T mutagenesis. Thus, how detection of U:G mismatches is translated into the single-strand nick required for error-prone synthesis is an open question. One model proposed that UNG could cooperate with MMR by excising a second uracil in the vicinity of the U:G mismatch, but it failed to explain the low impact of UNG inactivation on A-T mutagenesis. In this study, we show that uracils generated in the G1 phase in B cells can generate equal proportions of A-T and G-C mutations, which suggests that UNG and MMR can operate within the same time frame during SHM. Furthermore, we show that Ung -/- Pms2 -/- mice display a 50% reduction in mutations at A-T base pairs and that most remaining mutations at A-T bases depend on two additional uracil glycosylases, thymine-DNA glycosylase and SMUG1. These results demonstrate that Pms2/Mlh1 and multiple uracil glycosylases act jointly, each one with a distinct strand bias, to enlarge the immunoglobulin gene mutation spectrum from G-C to A-T bases. © 2017 Girelli Zubani et al.

  12. Disposable self-support paper-based multi-anode microbial fuel cell (PMMFC) integrated with power management system (PMS) as the real time "shock" biosensor for wastewater.

    Science.gov (United States)

    Xu, Zhiheng; Liu, Yucheng; Williams, Isaiah; Li, Yan; Qian, Fengyu; Zhang, Hui; Cai, Dingyi; Wang, Lei; Li, Baikun

    2016-11-15

    A paper-based multi-anode microbial fuel cell (PMMFC) integrated with power management system (PMS) was developed as a disposable self-support real-time "shock" biosensor for wastewater. PMMFCs were examined at three types of shocks (chromium, hypochlorite and acetate) in a batch-mode chamber, and exhibited various responses to shock types and concentrations. The power output of PMMFC sensor was four times as the carbon cloth (CC)-based MFCs, indicating the advantage of paper-based anode for bacterial adhesion. The power output was more sensitive than the voltage output under shocks, and thus preventing the false signals. The simulation of power harvest using PMS indicated that PMMFC could accomplish more frequent data transmission than single-anode MFCs (PSMFC) and CC anode MFCs (CCMMFC), making the self-support wastewater monitor and data transmission possible. Compared with traditional MFC sensors, PMMFCs integrated with PMS exhibit the distinct advantages of tight paper-packed structure, short acclimation period, high power output, and high sensitivity to a wide range of shocks, posing a great potential as "disposable self-support shock sensor" for real time in situ monitoring of wastewater quality. Copyright © 2016 Elsevier B.V. All rights reserved.

  13. Protostellar formation in rotating interstellar clouds. I. Numerical methods and tests

    International Nuclear Information System (INIS)

    Boss, A.P.

    1980-01-01

    The details of how dense interstellar clouds collapse to form protostars are obscured from observation by the very clouds in which the condensation takes place, leaving an observational gap between the clouds and pre--main-sequence (PMS) stars. There is also a gap of roughly four orders of magnitude between the specific spin angular momentum of such clouds and that of PMS stars. Thus in order to fully understand the sequence of events in stellar formation, we must construct theoretical models of the collapse and fragmentation of rotating interstellar clouds into single or multiple protostellar systems

  14. Exposure to atmospheric pms, pahs, pcdd/fs and metals near an open air waste burning site in Beirut

    Directory of Open Access Journals (Sweden)

    Rima Baalbaki

    2016-12-01

    Full Text Available Baalbaki, R., El Hage, R., Nassar, J., Gerard, J., Saliba, N.B., Zaarour, R., Abboud, M., Wehbeh, F., Khalaf, L.K., Shihadeh, A.L., Saliba, N.A. 2016. Exposure to atmospheric PMS, PAHS, PCDD/FS and metals near an open air waste burning site in Beirut. Lebanese Science Journal, 17(2: 91-103. Since July 2015, Lebanon has experienced the worst solid waste management crisis in its history. Consequently, open-air waste burning in the vicinity of highly populated areas in Beirut has become a common practice. This study evaluates the effects of open-air dumping and burning on local air quality and public health. The levels of particulate matter (PM10, PM2.5, gaseous and particle-bound polycyclic aromatic hydrocarbons (PAHs, polychlorinated dibenzo-dioxins and furans (PCDD/Fs, and particle-bound metals at a residence close to waste burning are reported. Concentrations, determined between October 2 and December 2, 2015, were compared either to previous measurements or to measurements taken away from a nearby burning incident, and after it had rained. Subsequently, the cancer risk due to exposure to these chemicals was assessed. Results showed alarming increases in pollutant concentrations which was translated into an increase in short-term cancer risk from about 1 to 20 people per million on the days when waste was being burned. Findings were shared with the public to warn the community against the dangers of waste mismanagement, and underline the obvious need for solid waste management at the governmental and municipal levels.

  15. Premenstrual Syndrome (PMS)

    Science.gov (United States)

    ... Physical signs and symptoms Joint or muscle pain Headache Fatigue Weight gain related to fluid retention Abdominal bloating Breast tenderness Acne flare-ups Constipation or diarrhea Alcohol intolerance For some, the physical pain and emotional stress are severe enough to affect their daily lives. ...

  16. Premenstrual Syndrome (PMS)

    Science.gov (United States)

    ... federal government website managed by the Office on Women's Health in the Office of the Assistant Secretary for Health at the U.S. Department of Health and Human Services . 200 Independence Avenue, S.W., Washington, DC 20201 1-800-994- ...

  17. Promoter methylation and expression of MGMT and the DNA mismatch repair genes MLH1, MSH2, MSH6 and PMS2 in paired primary and recurrent glioblastomas.

    Science.gov (United States)

    Felsberg, Jörg; Thon, Niklas; Eigenbrod, Sabina; Hentschel, Bettina; Sabel, Michael C; Westphal, Manfred; Schackert, Gabriele; Kreth, Friedrich Wilhelm; Pietsch, Torsten; Löffler, Markus; Weller, Michael; Reifenberger, Guido; Tonn, Jörg C

    2011-08-01

    Epigenetic silencing of the O(6) -methylguanine-DNA methyltransferase (MGMT) gene promoter is associated with prolonged survival in glioblastoma patients treated with temozolomide (TMZ). We investigated whether glioblastoma recurrence is associated with changes in the promoter methylation status and the expression of MGMT and the DNA mismatch repair (MMR) genes MLH1, MSH2, MSH6 and PMS2 in pairs of primary and recurrent glioblastomas of 80 patients, including 64 patients treated with radiotherapy and TMZ after the first operation. Among the primary tumors, the MGMT promoter was methylated in 31 patients and unmethylated in 49 patients. In 71 patients (89%), the MGMT promoter methylation status of the primary tumor was retained at recurrence. MGMT promoter methylation, but not MGMT protein expression, was associated with longer progression-free survival, overall survival and postrecurrence survival (PRS). Moreover, PRS was increased under salvage chemotherapy. Investigation of primary and recurrent glioblastomas of 43 patients did not identify promoter methylation in any of the four MMR genes. However, recurrent glioblastomas demonstrated significantly lower MSH2, MSH6 and PMS2 protein expression as detected by immunohistochemistry. In conclusion, reduced expression of MMR proteins, but not changes in MGMT promoter methylation, is characteristic of glioblastomas recurring after the current standards of care. Copyright © 2011 UICC.

  18. Ovarian metastasis from uveal melanoma with MLH1/PMS2 protein loss in a patient with germline MLH1 mutated Lynch syndrome: consequence or coincidence?

    Science.gov (United States)

    Lobo, João; Pinto, Carla; Freitas, Micaela; Pinheiro, Manuela; Vizcaino, Rámon; Oliva, Esther; Teixeira, Manuel R; Jerónimo, Carmen; Bartosch, Carla

    2017-03-01

    Currently, uveal melanoma is not considered within the Lynch syndrome tumor spectrum. However, there are studies suggesting a contribution of microsatellite instability in sporadic uveal melanoma tumorigenesis. We report a 45-year-old woman who was referred for genetic counseling due to a family history of Lynch syndrome caused by a MLH1 mutation. She originally underwent enucleation of the right eye secondary to a uveal spindle cell melanoma diagnosed at age 25. The tumor recurred 22 years later presenting as an ovarian metastasis and concurrently a microscopic endometrial endometrioid carcinoma, grade 1/3 was diagnosed. Subsequent studies highlighted that the uveal melanoma showed high microsatellite instability and loss of MLH1 and PMS2 protein expression, with no MLH1 promoter methylation or BRAF mutation. Additionally, a GNAQ mutation was found. We conclude that our patient's uveal melanoma is most likely related to MLH1 germline mutation and thus Lynch syndrome related. To the best of our knowledge, this is the first report of uveal melanoma showing MLH1/PMS2 protein loss in the context of Lynch syndrome.

  19. SUPLEMENTASI DAUN TORBANGUN (COLEUS AMBOINICUS LOUR UNTUK MENURUNKAN KELUHAN SINDROM PRAMENSTRUASI PADA REMAJA PUTRI (SUPPLEMENTATION OF TORBANGUN LEAVES [COLEUS AMBOINICUS LOUR] IN REDUCING THE COMPLAINST OF PRE-MENSTRUAL SYNDROME [PMS] AMONG TEENAGE G

    Directory of Open Access Journals (Sweden)

    Mazarina Devi

    2013-07-01

    Full Text Available ABSTRACT Background: Torbangun leaves (Coleus ambonicus Lour is one of type of species from Labiatae family which contains a lot of micronutrient and active element which have been examined as beneficial for human health and quality of life. The plants containing iridoid and flavonoid as well as phytochemical which deal with reproduction hormone is applicable to traditional medication toward PMS cases. Methods: The present study was aimed to assess the efficacy of CAL leaves in the management of PMS. An experimental clinical trial was conducted in 35 teenagers with PMS. Three intervention groups were defined: CAL leaves; commercial preparation; and placebo. Participants were followed-up individually for 1 month. Result: The results showed average menarche occurred around age 13 years, with menstruation lasting 5 days. During each successive treatment cycle, participants experienced a lower pain intensity score. Chi Square test, after adjusting each cycle for baseline pain, treatment compliance and other variables, showed that the group receiving CAL extract had significantly reduced pain intensity (p<0.05 compared with commercial preparation and placebo. Conclusion: The torbangun leaves supplement can be used as treatment to relief symptoms of the premenstrual syndrome. [Penel Gizi Makan 2010, 33(2:180-194]   Keywords: Torbangun leaves (Coleus amboinicus Lour, pre-menstrual syndrome (PMS, teenage girls

  20. [Immunohistochemical examination of MSH2, PMS2, MLH1, MSH6 compared with the analysis of microsatellite instability in colon adenocarcinoma].

    Science.gov (United States)

    Raskin, G A; Ianus, G A; Kornilov, A V; Orlova, R V; Petrov, S V; Protasova, A É; Pozharisskiĭ, K M; Imianitov, E N

    2014-01-01

    Adenocarcinoma of the colon in 10-20% is associated with microsatellite instability, which can occur both in sporadic cancers and in hereditary nonpolyposis colon cancer. Our analysis of 195 cases of adenocarcinoma of the colon showed that microsatellite instability (MSI-H) was found only in 1.5% of patients. Subsequent choice of patients with suspected hereditary Lynch syndrome led to the identification of additional 17 patients with microsatellite instability. They passed an analysis of genes of repair system of unpaired nucleotides of DNA. The study showed that immunohistochemical staining of MSH2, MSH6, MLH1, PMS2 could effectively conduct a preliminary screening of the Lynch syndrome but was unable to divide cases of sporadic and hereditary MSI-H colon cancer.

  1. A new approach for improved time and position measurements for TOF-PET: Time-stamping of the photo-electrons using analogue SiPMs

    Energy Technology Data Exchange (ETDEWEB)

    Doroud, K., E-mail: Katayoun.Doroud@cern.ch [CERN Geneva (Switzerland); Williams, M.C.S. [CERN Geneva (Switzerland); INFN, Bologna (Italy)

    2017-03-21

    Measurement of the Time-of-Flight (TOF) of the 511 keV gammas brings an important reduction of statistical noise in the PET image, with higher precision time measurements producing clearer images. The common method of coupling a photodetector to scintillating crystals is to have two matching matrices, with a one-to-one coupling between the crystal and the photodetector. We propose a new geometry based on analogue strip SiPMs reading out a scintillator cut into slabs. This technique allows the time stamping of individual photo-electrons and extracts the best time resolution using a specific algorithm. Here we present the results from the first ‘slab module’ test.

  2. A new approach for improved time and position measurements for TOF-PET: Time-stamping of the photo-electrons using analogue SiPMs

    CERN Document Server

    Doroud, K

    2017-01-01

    Measurement of the Time-of-Flight (TOF) of the 511 keV gammas brings an important reduction of statistical noise in the PET image, with higher precision time measurements producing clearer images. The common method of coupling a photodetector to scintillating crystals is to have two matching matrices, with a one-to-one coupling between the crystal and the photodetector. We propose a new geometry based on analogue strip SiPMs reading out a scintillator cut into slabs. This technique allows the time stamping of individual photo-electrons and extracts the best time resolution using a specific algorithm. Here we present the results from the first ‘slab module’ test.

  3. Influence of the active area size and read-out method on the timing performance of SiPMs coupled to LYSO scintillators

    Energy Technology Data Exchange (ETDEWEB)

    Tarolli, Alessandro, E-mail: tarolli@fbk.eu [Fondazione Bruno Kessler (FBK), Trento (Italy); Gola, Alberto; Ferri, Alessandro; Pro, Tiziana; Serra, Nicola; Zorzi, Nicola; Piemonte, Claudio [Fondazione Bruno Kessler (FBK), Trento (Italy)

    2013-02-21

    In this work we report on the coincidence resolving time performance of SiPMs with different sizes, produced at FBK, coupled to the same LYSO scintillators. The measurements are performed both with and without the differential leading edge discriminator at three different temperatures, 20 °C, 0 °C and −20 °C. The photo-detectors feature an active area of 2×2 mm{sup 2} and 4×4 mm{sup 2}. The scintillators have a cross-section of 1.8×1.8 mm{sup 2} and height of 10 mm. The measurements show that, once we eliminate the effect of noise on the timing measurements, we obtain similar coincidence resolving times for the two SiPM sizes considered. This means that the SiPM capacitance, at least up to 4×4 mm{sup 2}, is not a limiting factor.

  4. Influence of the active area size and read-out method on the timing performance of SiPMs coupled to LYSO scintillators

    International Nuclear Information System (INIS)

    Tarolli, Alessandro; Gola, Alberto; Ferri, Alessandro; Pro, Tiziana; Serra, Nicola; Zorzi, Nicola; Piemonte, Claudio

    2013-01-01

    In this work we report on the coincidence resolving time performance of SiPMs with different sizes, produced at FBK, coupled to the same LYSO scintillators. The measurements are performed both with and without the differential leading edge discriminator at three different temperatures, 20 °C, 0 °C and −20 °C. The photo-detectors feature an active area of 2×2 mm 2 and 4×4 mm 2 . The scintillators have a cross-section of 1.8×1.8 mm 2 and height of 10 mm. The measurements show that, once we eliminate the effect of noise on the timing measurements, we obtain similar coincidence resolving times for the two SiPM sizes considered. This means that the SiPM capacitance, at least up to 4×4 mm 2 , is not a limiting factor

  5. The Norwegian PMS2 founder mutation c.989-1G > T shows high penetrance of microsatellite instable cancers with normal immunohistochemistry.

    Science.gov (United States)

    Grindedal, Eli Marie; Aarset, Harald; Bjørnevoll, Inga; Røyset, Elin; Mæhle, Lovise; Stormorken, Astrid; Heramb, Cecilie; Medvik, Heidi; Møller, Pål; Sjursen, Wenche

    2014-01-01

    Using immunohistochemistry (IHC) to select cases for mismatch repair (MMR) genetic testing, we failed to identify a large kindred with the deleterious PMS2 mutation c.989-1G > T. The purpose of the study was to examine the sensitivity of IHC and microsatellite instability-analysis (MSI) to identify carriers of the mutation, and to estimate its penetrance and expressions. All carriers and obligate carriers of the mutation were identified. All cancer diagnoses were confirmed. IHC and MSI-analysis were performed on available tumours. Penetrances of cancers included in the Amsterdam and the Bethesda Criteria, for MSI-high tumours and MSI-high and low tumours were calculated by the Kaplan-Meier algorithm. Probability for co-segregation of the mutation and cancers by chance was 0.000004. Fifty-six carriers or obligate carriers were identified. There was normal staining for PMS2 in 15/18 (83.3%) of tumours included in the AMS1/AMS2/Bethesda criteria. MSI-analysis showed that 15/21 (71.4%) of tumours were MSI-high and 4/21 (19.0%) were MSI-low. Penetrance at 70 years was 30.6% for AMS1 cancers (colorectal cancers), 42.8% for AMS2 cancers, 47.2% for Bethesda cancers, 55.6% for MSI-high and MSI-low cancers and 52.2% for MSI-high cancers. The mutation met class 5 criteria for pathogenicity. IHC was insensitive in detecting tumours caused by the mutation. Penetrance of cancers that displayed MSI was 56% at 70 years. Besides colorectal cancers, the most frequent expressions were carcinoma of the endometrium and breast in females and stomach and prostate in males.

  6. Shotgun protein sequencing.

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-06-01

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

  7. Multimodal sequence learning.

    Science.gov (United States)

    Kemény, Ferenc; Meier, Beat

    2016-02-01

    While sequence learning research models complex phenomena, previous studies have mostly focused on unimodal sequences. The goal of the current experiment is to put implicit sequence learning into a multimodal context: to test whether it can operate across different modalities. We used the Task Sequence Learning paradigm to test whether sequence learning varies across modalities, and whether participants are able to learn multimodal sequences. Our results show that implicit sequence learning is very similar regardless of the source modality. However, the presence of correlated task and response sequences was required for learning to take place. The experiment provides new evidence for implicit sequence learning of abstract conceptual representations. In general, the results suggest that correlated sequences are necessary for implicit sequence learning to occur. Moreover, they show that elements from different modalities can be automatically integrated into one unitary multimodal sequence. Copyright © 2015 Elsevier B.V. All rights reserved.

  8. Sequence Read Archive (SRA)

    Data.gov (United States)

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

  9. PROGRESSIVE STAR FORMATION IN THE YOUNG GALACTIC SUPER STAR CLUSTER NGC 3603

    International Nuclear Information System (INIS)

    Beccari, Giacomo; Spezzi, Loredana; De Marchi, Guido; Andersen, Morten; Paresce, Francesco; Young, Erick; Panagia, Nino; Bond, Howard; Balick, Bruce; Calzetti, Daniela; Carollo, C. Marcella; Disney, Michael J.; Dopita, Michael A.; Frogel, Jay A.; Hall, Donald N. B.; Holtzman, Jon A.; Kimble, Randy A.; McCarthy, Patrick J.; O'Connell, Robert W.; Saha, Abhijit

    2010-01-01

    Early Release Science observations of the cluster NGC 3603 with the WFC3 on the refurbished Hubble Space Telescope allow us to study its recent star formation history. Our analysis focuses on stars with Hα excess emission, a robust indicator of their pre-main sequence (PMS) accreting status. The comparison with theoretical PMS isochrones shows that 2/3 of the objects with Hα excess emission have ages from 1 to 10 Myr, with a median value of 3 Myr, while a surprising 1/3 of them are older than 10 Myr. The study of the spatial distribution of these PMS stars allows us to confirm their cluster membership and to statistically separate them from field stars. This result establishes unambiguously for the first time that star formation in and around the cluster has been ongoing for at least 10-20 Myr, at an apparently increasing rate.

  10. Suplementasi Daun Torbangun (Coleus Amboinicus Lour) Untuk Menurunkan Keluhan Sindrom Pramenstruasi Pada Remaja Putri (Supplementation of Torbangun Leaves [Coleus Amboinicus Lour] in Reducing the Complainst of Pre-menstrual Syndrome [Pms] Among Teenage G

    OpenAIRE

    Devi, Mazarina; Syarief, Hidayat; Damanik, Rizal; Sulaeman, Ahmad; Setiawan, Budi; Dewi, Rousmala

    2010-01-01

    ABSTRACT Background: Torbangun leaves (Coleus ambonicus Lour) is one of type of species from Labiatae family which contains a lot of micronutrient and active element which have been examined as beneficial for human health and quality of life. The plants containing iridoid and flavonoid as well as phytochemical which deal with reproduction hormone is applicable to traditional medication toward PMS cases. Methods: The present study was aimed to assess the efficacy of CAL leaves in the managemen...

  11. Mismatch Repair Proteins and Microsatellite Instability in Colorectal Carcinoma (MLH1, MSH2, MSH6 and PMS2): Histopathological and Immunohistochemical Study.

    Science.gov (United States)

    Ismael, Nour El Hoda S; El Sheikh, Samar A; Talaat, Suzan M; Salem, Eman M

    2017-03-15

    Colorectal cancer (CRC) is one of the most common cancers worldwide. Microsatellite instability (MSI) is detected in about 15% of all colorectal cancers. CRC with MSI has particular characteristics such as improved survival rates and better prognosis. They also have a distinct sensitivity to the action of chemotherapy. The aim of the study was to detect microsatellite instability in a cohort of colorectal cancer Egyptian patients using the immunohistochemical expression of mismatch repair proteins (MLH1, MSH2, MSH6 and PMS2). Cases were divided into Microsatellite stable (MSS), Microsatellite unstable low (MSI-L) and Microsatellite unstable high (MSI-H). This Microsatellite stability status was correlated with different clinicopathological parameters. There was a statistically significant correlation between the age of cases, tumor site & grade and the microsatellite stability status. There was no statistically significant correlation between the gender of patients, tumor subtype, stage, mucoid change, necrosis, tumor borders, lymphocytic response, lymphovascular emboli and the microsatellite stability status. Testing for MSI should be done for all colorectal cancer patients, especially those younger than 50 years old, right sided and high-grade CRCs.

  12. Unique mutational profile associated with a loss of TDG expression in the rectal cancer of a patient with a constitutional PMS2 deficiency.

    Science.gov (United States)

    Vasovcak, P; Krepelova, A; Menigatti, M; Puchmajerova, A; Skapa, P; Augustinakova, A; Amann, G; Wernstedt, A; Jiricny, J; Marra, G; Wimmer, K

    2012-07-01

    Cells with DNA repair defects have increased genomic instability and are more likely to acquire secondary mutations that bring about cellular transformation. We describe the frequency and spectrum of somatic mutations involving several tumor suppressor genes in the rectal carcinoma of a 13-year-old girl harboring biallelic, germline mutations in the DNA mismatch repair gene PMS2. Apart from microsatellite instability, the tumor DNA contained a number of C:G→T:A or G:C→A:T transitions in CpG dinucleotides, which often result through spontaneous deamination of cytosine or 5-methylcytosine. Four DNA glycosylases, UNG2, SMUG1, MBD4 and TDG, are involved in the repair of these deamination events. We identified a heterozygous missense mutation in TDG, which was associated with TDG protein loss in the tumor. The CpGs mutated in this patient's tumor are generally methylated in normal colonic mucosa. Thus, it is highly likely that loss of TDG contributed to the supermutator phenotype and that most of the point mutations were caused by deamination of 5-methylcytosine to thymine, which remained uncorrected owing to the TDG deficiency. This case provides the first in vivo evidence of the key role of TDG in protecting the human genome against the deleterious effects of 5-methylcytosine deamination. Copyright © 2012 Elsevier B.V. All rights reserved.

  13. Nonparametric combinatorial sequence models.

    Science.gov (United States)

    Wauthier, Fabian L; Jordan, Michael I; Jojic, Nebojsa

    2011-11-01

    This work considers biological sequences that exhibit combinatorial structures in their composition: groups of positions of the aligned sequences are "linked" and covary as one unit across sequences. If multiple such groups exist, complex interactions can emerge between them. Sequences of this kind arise frequently in biology but methodologies for analyzing them are still being developed. This article presents a nonparametric prior on sequences which allows combinatorial structures to emerge and which induces a posterior distribution over factorized sequence representations. We carry out experiments on three biological sequence families which indicate that combinatorial structures are indeed present and that combinatorial sequence models can more succinctly describe them than simpler mixture models. We conclude with an application to MHC binding prediction which highlights the utility of the posterior distribution over sequence representations induced by the prior. By integrating out the posterior, our method compares favorably to leading binding predictors.

  14. Tissue expression of MLH1, PMS2, MSH2, and MSH6 proteins and prognostic value of microsatellite instability in Wilms tumor: experience of 45 cases.

    Science.gov (United States)

    Diniz, Gulden; Aktas, Safiye; Cubuk, Cankut; Ortac, Ragip; Vergin, Canan; Olgun, Nur

    2013-05-01

    Although the importance of microsatellite instability (MSI) and mismatch repair genes (MMR) is strongly established in colorectal cancer seen in the Lynch syndrome, its significance has not been fully established in Wilms tumor (WT). The aim of this study was to determine the prognostic value of MSI and MMR proteins in WT. This study included 45 pediatric cases with nephroblastoma. Protein expression was analyzed by immunohistochemistry of archival tissue sections. Real-time PCR melting analysis and fluorescence capillary electrophoresis (FCE) were performed to evaluate the MSI markers BAT25, BAT26, NR21, NR24, MONO27, penta D, and penta C in DNA extracted from tumor and normal tissues. Lower levels of MSI were observed in six cases (13.3%). There were no statistically significant correlations between MSI and some clinical prognostic factors such as stage of the tumors, and survival rates. Nineteen tumors (42.2%) showed loss of protein expression of MLH1, PMS2, MSH2, or MSH6. MMR protein defects were correlated with size (P = .021), and stage (P = .019) of the tumor, and survival rates (P < .01).Similarly MSI was also correlated with the size of the tumor (P = .046). This study showed that a small proportion of WT might be associated with the presence of MSI, as is the case with defects of DNA mismatch repair genes in the pathogenesis of WT. However, there was no concordance with the frequency of tissue expression of MMR proteins and MSI. These findings suggest that MMR genes may play an important role in the development of WT via different pathways.

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

    Energy Technology Data Exchange (ETDEWEB)

    Lapidus, Alla L.

    2009-01-01

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

  16. Identification of IncA/C Plasmid Replication and Maintenance Genes and Development of a Plasmid Multilocus Sequence Typing Scheme.

    Science.gov (United States)

    Hancock, Steven J; Phan, Minh-Duy; Peters, Kate M; Forde, Brian M; Chong, Teik Min; Yin, Wai-Fong; Chan, Kok-Gan; Paterson, David L; Walsh, Timothy R; Beatson, Scott A; Schembri, Mark A

    2017-02-01

    Plasmids of incompatibility group A/C (IncA/C) are becoming increasingly prevalent within pathogenic Enterobacteriaceae They are associated with the dissemination of multiple clinically relevant resistance genes, including bla CMY and bla NDM Current typing methods for IncA/C plasmids offer limited resolution. In this study, we present the complete sequence of a bla NDM-1 -positive IncA/C plasmid, pMS6198A, isolated from a multidrug-resistant uropathogenic Escherichia coli strain. Hypersaturated transposon mutagenesis, coupled with transposon-directed insertion site sequencing (TraDIS), was employed to identify conserved genetic elements required for replication and maintenance of pMS6198A. Our analysis of TraDIS data identified roles for the replicon, including repA, a toxin-antitoxin system; two putative partitioning genes, parAB; and a putative gene, 053 Construction of mini-IncA/C plasmids and examination of their stability within E. coli confirmed that the region encompassing 053 contributes to the stable maintenance of IncA/C plasmids. Subsequently, the four major maintenance genes (repA, parAB, and 053) were used to construct a new plasmid multilocus sequence typing (PMLST) scheme for IncA/C plasmids. Application of this scheme to a database of 82 IncA/C plasmids identified 11 unique sequence types (STs), with two dominant STs. The majority of bla NDM -positive plasmids examined (15/17; 88%) fall into ST1, suggesting acquisition and subsequent expansion of this bla NDM -containing plasmid lineage. The IncA/C PMLST scheme represents a standardized tool to identify, track, and analyze the dissemination of important IncA/C plasmid lineages, particularly in the context of epidemiological studies. Copyright © 2017 American Society for Microbiology.

  17. Long sequence correlation coprocessor

    Science.gov (United States)

    Gage, Douglas W.

    1994-09-01

    A long sequence correlation coprocessor (LSCC) accelerates the bitwise correlation of arbitrarily long digital sequences by calculating in parallel the correlation score for 16, for example, adjacent bit alignments between two binary sequences. The LSCC integrated circuit is incorporated into a computer system with memory storage buffers and a separate general purpose computer processor which serves as its controller. Each of the LSCC's set of sequential counters simultaneously tallies a separate correlation coefficient. During each LSCC clock cycle, computer enable logic associated with each counter compares one bit of a first sequence with one bit of a second sequence to increment the counter if the bits are the same. A shift register assures that the same bit of the first sequence is simultaneously compared to different bits of the second sequence to simultaneously calculate the correlation coefficient by the different counters to represent different alignments of the two sequences.

  18. Roles of repetitive sequences

    Energy Technology Data Exchange (ETDEWEB)

    Bell, G.I.

    1991-12-31

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

  19. Anomaly Detection in Sequences

    Data.gov (United States)

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

  20. DNA sequencing conference, 2

    Energy Technology Data Exchange (ETDEWEB)

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

    1991-06-19

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

  1. sequenceMiner algorithm

    Data.gov (United States)

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

  2. The 116G > A MSH6 and IVS1-1121C > T PMS2 Genes Polymorphisms Modulate the Risk of the Sporadic Colorectal Cancer Development in Polish Population.

    Science.gov (United States)

    Zelga, Piotr; Przybyłowska-Sygut, Karolina; Zelga, Marta; Dziki, Adam; Majsterek, Ireneusz

    2018-04-01

    Colorectal cancer (CRC) is one of the most common cancers worldwide. DNA mismatch repair (MMR) is an evolutionarily conserved process that corrects mismatches generated during DNA replication. MMR defects were found to be associated with hereditary non-polyposis colorectal cancer (HNPCC) and a subset of sporadic colon cancers. The inheritance of common variations in MMR genes may influences individual susceptibility to the development of colorectal cancer. The purpose of the study was to evaluate the association between gene polymorphisms Glu39Gly (c.116G > A) of MSH6 gene and IVS1-1121C > T of PMS2 gene and sporadic colorectal cancer risk, in a case-control study comprising 200 patients and 200 controls origination from polish population. DNA was isolated from peripheral blood lymphocytes of enrolled patients, and gene polymorphisms were analysed by restriction fragment length polymorphism-polymerase chain reaction (RFLP-PCR) for MSH6 and TaqMan for PMS2. G/A variant of Glu39Gly (c.116G > A) genotype was associated with an increased risk of colorectal cancer (OR 1,65 95%CI:1,01-2,69 p = 0.44). Presence of A allele was also significantly higher in patient with CRC (OR 1,57 95% CI: 1,04-2,38 p = 0.032). Prevalence of this genotype was also markedly higher in females and patients above 60 years in CRC group (OR 2.25 95%CI: 1.22-4.14 p = 0.0098 and OR 2.74 95% CI: 1.27-5.93 p = 0.0097 respectively). None of such correlations was observed for genotype variants of IVS1-1121C > T PMS2. In conclusion, our data suggests thatMSH6 Glu39Gly polymorphism is associated with the risk of developing sporadic colorectal cancer in polish population. Linkage to the female gender, onset above 60 years old and further increase of risk when combined with wild-type allele of PMS2 IVS1-1121C > T polymorphism indicates defective mismatch repair system.

  3. A 16-ch module for thermal neutron detection using ZnS:{sup 6}LiF scintillator with embedded WLS fibers coupled to SiPMs and its dedicated readout electronics

    Energy Technology Data Exchange (ETDEWEB)

    Mosset, J.-B., E-mail: jean-baptiste.mosset@psi.ch; Stoykov, A.; Greuter, U.; Gromov, A.; Hildebrandt, M.; Panzner, T.; Schlumpf, N.

    2017-02-11

    A scalable 16-ch thermal neutron detection system has been developed in the framework of the upgrade of a neutron diffractometer. The detector is based on a ZnS:{sup 6}LiF scintillator with embedded WLS fibers which are read out with SiPMs. In this paper, we present the 16-ch module, the dedicated readout electronics, a direct comparison between the performance of the diffractometer obtained with the current {sup 3}He detector and with the 16-ch detection module, and the channel-to-channel uniformity.

  4. A 16-ch module for thermal neutron detection using ZnS:6LiF scintillator with embedded WLS fibers coupled to SiPMs and its dedicated readout electronics

    Science.gov (United States)

    Mosset, J.-B.; Stoykov, A.; Greuter, U.; Gromov, A.; Hildebrandt, M.; Panzner, T.; Schlumpf, N.

    2017-02-01

    A scalable 16-ch thermal neutron detection system has been developed in the framework of the upgrade of a neutron diffractometer. The detector is based on a ZnS:6LiF scintillator with embedded WLS fibers which are read out with SiPMs. In this paper, we present the 16-ch module, the dedicated readout electronics, a direct comparison between the performance of the diffractometer obtained with the current 3He detector and with the 16-ch detection module, and the channel-to-channel uniformity.

  5. Sequences for Student Investigation

    Science.gov (United States)

    Barton, Jeffrey; Feil, David; Lartigue, David; Mullins, Bernadette

    2004-01-01

    We describe two classes of sequences that give rise to accessible problems for undergraduate research. These problems may be understood with virtually no prerequisites and are well suited for computer-aided investigation. The first sequence is a variation of one introduced by Stephen Wolfram in connection with his study of cellular automata. The…

  6. Sequence History Update Tool

    Science.gov (United States)

    Khanampompan, Teerapat; Gladden, Roy; Fisher, Forest; DelGuercio, Chris

    2008-01-01

    The Sequence History Update Tool performs Web-based sequence statistics archiving for Mars Reconnaissance Orbiter (MRO). Using a single UNIX command, the software takes advantage of sequencing conventions to automatically extract the needed statistics from multiple files. This information is then used to populate a PHP database, which is then seamlessly formatted into a dynamic Web page. This tool replaces a previous tedious and error-prone process of manually editing HTML code to construct a Web-based table. Because the tool manages all of the statistics gathering and file delivery to and from multiple data sources spread across multiple servers, there is also a considerable time and effort savings. With the use of The Sequence History Update Tool what previously took minutes is now done in less than 30 seconds, and now provides a more accurate archival record of the sequence commanding for MRO.

  7. HIV Sequence Compendium 2015

    Energy Technology Data Exchange (ETDEWEB)

    Foley, Brian Thomas [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Leitner, Thomas Kenneth [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Apetrei, Cristian [Univ. of Pittsburgh, PA (United States); Hahn, Beatrice [Univ. of Pennsylvania, Philadelphia, PA (United States); Mizrachi, Ilene [National Center for Biotechnology Information, Bethesda, MD (United States); Mullins, James [Univ. of Washington, Seattle, WA (United States); Rambaut, Andrew [Univ. of Edinburgh, Scotland (United Kingdom); Wolinsky, Steven [Northwestern Univ., Evanston, IL (United States); Korber, Bette Tina Marie [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2015-10-05

    This compendium is an annual printed summary of the data contained in the HIV sequence database. We try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Each of the alignments attempts to display the genetic variability within the different species, groups and subtypes of the virus. This compendium contains sequences published before January 1, 2015. Hence, though it is published in 2015 and called the 2015 Compendium, its contents correspond to the 2014 curated alignments on our website. The number of sequences in the HIV database is still increasing. In total, at the end of 2014, there were 624,121 sequences in the HIV Sequence Database, an increase of 7% since the previous year. This is the first year that the number of new sequences added to the database has decreased compared to the previous year. The number of near complete genomes (>7000 nucleotides) increased to 5834 by end of 2014. However, as in previous years, the compendium alignments contain only a fraction of these. A more complete version of all alignments is available on our website, http://www.hiv.lanl.gov/ content/sequence/NEWALIGN/align.html As always, we are open to complaints and suggestions for improvement. Inquiries and comments regarding the compendium should be addressed to seq-info@lanl.gov.

  8. Mapping sequences by parts

    Directory of Open Access Journals (Sweden)

    Guziolowski Carito

    2007-09-01

    Full Text Available Abstract Background: We present the N-map method, a pairwise and asymmetrical approach which allows us to compare sequences by taking into account evolutionary events that produce shuffled, reversed or repeated elements. Basically, the optimal N-map of a sequence s over a sequence t is the best way of partitioning the first sequence into N parts and placing them, possibly complementary reversed, over the second sequence in order to maximize the sum of their gapless alignment scores. Results: We introduce an algorithm computing an optimal N-map with time complexity O (|s| × |t| × N using O (|s| × |t| × N memory space. Among all the numbers of parts taken in a reasonable range, we select the value N for which the optimal N-map has the most significant score. To evaluate this significance, we study the empirical distributions of the scores of optimal N-maps and show that they can be approximated by normal distributions with a reasonable accuracy. We test the functionality of the approach over random sequences on which we apply artificial evolutionary events. Practical Application: The method is illustrated with four case studies of pairs of sequences involving non-standard evolutionary events.

  9. The Colliding Beams Sequencer

    International Nuclear Information System (INIS)

    Johnson, D.E.; Johnson, R.P.

    1989-01-01

    The Colliding Beam Sequencer (CBS) is a computer program used to operate the pbar-p Collider by synchronizing the applications programs and simulating the activities of the accelerator operators during filling and storage. The Sequencer acts as a meta-program, running otherwise stand alone applications programs, to do the set-up, beam transfers, acceleration, low beta turn on, and diagnostics for the transfers and storage. The Sequencer and its operational performance will be described along with its special features which include a periodic scheduler and command logger. 14 refs., 3 figs

  10. Phylogenetic Trees From Sequences

    Science.gov (United States)

    Ryvkin, Paul; Wang, Li-San

    In this chapter, we review important concepts and approaches for phylogeny reconstruction from sequence data.We first cover some basic definitions and properties of phylogenetics, and briefly explain how scientists model sequence evolution and measure sequence divergence. We then discuss three major approaches for phylogenetic reconstruction: distance-based phylogenetic reconstruction, maximum parsimony, and maximum likelihood. In the third part of the chapter, we review how multiple phylogenies are compared by consensus methods and how to assess confidence using bootstrapping. At the end of the chapter are two sections that list popular software packages and additional reading.

  11. Gomphid DNA sequence data

    Data.gov (United States)

    U.S. Environmental Protection Agency — DNA sequence data for several genetic loci. This dataset is not publicly accessible because: It's already publicly available on GenBank. It can be accessed through...

  12. Yeast genome sequencing:

    DEFF Research Database (Denmark)

    Piskur, Jure; Langkjær, Rikke Breinhold

    2004-01-01

    For decades, unicellular yeasts have been general models to help understand the eukaryotic cell and also our own biology. Recently, over a dozen yeast genomes have been sequenced, providing the basis to resolve several complex biological questions. Analysis of the novel sequence data has shown...... of closely related species helps in gene annotation and to answer how many genes there really are within the genomes. Analysis of non-coding regions among closely related species has provided an example of how to determine novel gene regulatory sequences, which were previously difficult to analyse because...... they are short and degenerate and occupy different positions. Comparative genomics helps to understand the origin of yeasts and points out crucial molecular events in yeast evolutionary history, such as whole-genome duplication and horizontal gene transfer(s). In addition, the accumulating sequence data provide...

  13. Dynamic Sequence Assignment.

    Science.gov (United States)

    1983-12-01

    D-136 548 DYNAMIIC SEQUENCE ASSIGNMENT(U) ADVANCED INFORMATION AND 1/2 DECISION SYSTEMS MOUNTAIN YIELW CA C A 0 REILLY ET AL. UNCLSSIIED DEC 83 AI/DS...I ADVANCED INFORMATION & DECISION SYSTEMS Mountain View. CA 94040 84 u ,53 V,..’. Unclassified _____ SCURITY CLASSIFICATION OF THIS PAGE REPORT...reviews some important heuristic algorithms developed for fas- ter solution of the sequence assignment problem. 3.1. DINAMIC MOGRAMUNIG FORMULATION FOR

  14. HIV Sequence Compendium 2010

    Energy Technology Data Exchange (ETDEWEB)

    Kuiken, Carla [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Foley, Brian [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Leitner, Thomas [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Apetrei, Christian [Univ. of Pittsburgh, PA (United States); Hahn, Beatrice [Univ. of Alabama, Tuscaloosa, AL (United States); Mizrachi, Ilene [National Center for Biotechnology Information, Bethesda, MD (United States); Mullins, James [Univ. of Washington, Seattle, WA (United States); Rambaut, Andrew [Univ. of Edinburgh, Scotland (United Kingdom); Wolinsky, Steven [Northwestern Univ., Evanston, IL (United States); Korber, Bette [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2010-12-31

    This compendium is an annual printed summary of the data contained in the HIV sequence database. In these compendia we try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Each of the alignments attempts to display the genetic variability within the different species, groups and subtypes of the virus. This compendium contains sequences published before January 1, 2010. Hence, though it is called the 2010 Compendium, its contents correspond to the 2009 curated alignments on our website. The number of sequences in the HIV database is still increasing exponentially. In total, at the time of printing, there were 339,306 sequences in the HIV Sequence Database, an increase of 45% since last year. The number of near complete genomes (>7000 nucleotides) increased to 2576 by end of 2009, reflecting a smaller increase than in previous years. However, as in previous years, the compendium alignments contain only a small fraction of these. Included in the alignments are a small number of sequences representing each of the subtypes and the more prevalent circulating recombinant forms (CRFs) such as 01 and 02, as well as a few outgroup sequences (group O and N and SIV-CPZ). Of the rarer CRFs we included one representative each. A more complete version of all alignments is available on our website, http://www.hiv.lanl.gov/content/sequence/NEWALIGN/align.html. Reprints are available from our website in the form of both HTML and PDF files. As always, we are open to complaints and suggestions for improvement. Inquiries and comments regarding the compendium should be addressed to seq-info@lanl.gov.

  15. General LTE Sequence

    OpenAIRE

    Billal, Masum

    2015-01-01

    In this paper,we have characterized sequences which maintain the same property described in Lifting the Exponent Lemma. Lifting the Exponent Lemma is a very powerful tool in olympiad number theory and recently it has become very popular. We generalize it to all sequences that maintain a property like it i.e. if p^{\\alpha}||a_k and p^\\b{eta}||n, then p^{{\\alpha}+\\b{eta}}||a_{nk}.

  16. Pairwise Sequence Alignment Library

    Energy Technology Data Exchange (ETDEWEB)

    2015-05-20

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

  17. Digital signal processing for a thermal neutron detector using ZnS(Ag):{sup 6}LiF scintillating layers read out with WLS fibers and SiPMs

    Energy Technology Data Exchange (ETDEWEB)

    Mosset, J.-B., E-mail: jean-baptiste.mosset@psi.ch; Stoykov, A.; Greuter, U.; Hildebrandt, M.; Schlumpf, N.

    2016-07-11

    We present a digital signal processing system based on a photon counting approach which we developed for a thermal neutron detector consisting of ZnS(Ag):{sup 6}LiF scintillating layers read out with WLS fibers and SiPMs. Three digital filters have been evaluated: a moving sum, a moving sum after differentiation and a digital CR-RC{sup 4} filter. The performances of the detector with these filters are presented. A full analog signal processing using a CR-RC{sup 4} filter has been emulated digitally. The detector performance obtained with this analog approach is compared with the one obtained with the best performing digital approach. - Highlights: • Application of digital signal processing for a SiPM-based ZnS:6LiF neutron detector. • Optimisation of detector performances with 3 different digital filters. • Comparison with detector performances with a full analog signal processing.

  18. Adaptive Processing for Sequence Alignment

    KAUST Repository

    Zidan, Mohammed A.; Bonny, Talal; Salama, Khaled N.

    2012-01-01

    Disclosed are various embodiments for adaptive processing for sequence alignment. In one embodiment, among others, a method includes obtaining a query sequence and a plurality of database sequences. A first portion of the plurality of database sequences is distributed to a central processing unit (CPU) and a second portion of the plurality of database sequences is distributed to a graphical processing unit (GPU) based upon a predetermined splitting ratio associated with the plurality of database sequences, where the database sequences of the first portion are shorter than the database sequences of the second portion. A first alignment score for the query sequence is determined with the CPU based upon the first portion of the plurality of database sequences and a second alignment score for the query sequence is determined with the GPU based upon the second portion of the plurality of database sequences.

  19. Adaptive Processing for Sequence Alignment

    KAUST Repository

    Zidan, Mohammed A.

    2012-01-26

    Disclosed are various embodiments for adaptive processing for sequence alignment. In one embodiment, among others, a method includes obtaining a query sequence and a plurality of database sequences. A first portion of the plurality of database sequences is distributed to a central processing unit (CPU) and a second portion of the plurality of database sequences is distributed to a graphical processing unit (GPU) based upon a predetermined splitting ratio associated with the plurality of database sequences, where the database sequences of the first portion are shorter than the database sequences of the second portion. A first alignment score for the query sequence is determined with the CPU based upon the first portion of the plurality of database sequences and a second alignment score for the query sequence is determined with the GPU based upon the second portion of the plurality of database sequences.

  20. Up-regulation of mismatch repair genes MSH6, PMS2 and MLH1 parallels development of genetic instability and is linked to tumor aggressiveness and early PSA recurrence in prostate cancer.

    Science.gov (United States)

    Wilczak, Waldemar; Rashed, Semin; Hube-Magg, Claudia; Kluth, Martina; Simon, Ronald; Büscheck, Franziska; Clauditz, Till Sebastian; Grupp, Katharina; Minner, Sarah; Tsourlakis, Maria Christina; Möller-Koop, Christina; Graefen, Markus; Adam, Meike; Haese, Alexander; Wittmer, Corinna; Sauter, Guido; Izbicki, Jakob Robert; Huland, Hartwig; Schlomm, Thorsten; Steurer, Stefan; Krech, Till; Lebok, Patrick

    2017-01-01

    DNA mismatch repair (MMR) is integral to the maintenance of genetic stability. We aimed to evaluate the clinical impact of MMR gene expression in prostate cancer. The MMR genes MSH6, MLH1 and PMS2 were analyzed by immunohistochemistry on a tissue microarray containing 11152 prostate cancer specimens. Results were compared with ETS-related gene status and deletions of PTEN, 3p13, 5q21 and 6q15. MSH6, MLH1 and PMS2 expression was detectable in 89.5%, 85.4% and 85.0% of cancers and was particularly strong in cancers with advanced pathological tumor stage (P < 0.0001 each), high Gleason grade (P < 0.0001 each), nodal metastasis (P ≤ 0.0083) and early biochemical recurrence (P < 0.0001). High levels of MMR gene expression paralleled features of genetic instability, such as the number of genomic deletions per cancer; strong expression of all three MMR genes was found in 24%, 29%, 30%, 33% and 42% of cancers with no, one, two, three or four to five deletions (P < 0.0001). The prognostic value of the analyzed MMR genes was largely driven by the subset of cancers lacking ERG fusion (P < 0.0001), while the prognostic impact of MMR gene overexpression was only marginal in ERG-positive cancers. Multivariate analyses suggested an independent prognostic relevance of MMR genes in ERG-negative prostate cancers when compared with prognostic parameters available at the time of initial biopsy. In conclusion, MMR overexpression is common in prostate cancer and is linked to poor outcome as well as features indicating genetic instability. ERG fusion should be analyzed along with MMR gene expression in potential clinical tests. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  1. Main sequence mass loss

    International Nuclear Information System (INIS)

    Brunish, W.M.; Guzik, J.A.; Willson, L.A.; Bowen, G.

    1987-01-01

    It has been hypothesized that variable stars may experience mass loss, driven, at least in part, by oscillations. The class of stars we are discussing here are the δ Scuti variables. These are variable stars with masses between about 1.2 and 2.25 M/sub θ/, lying on or very near the main sequence. According to this theory, high rotation rates enhance the rate of mass loss, so main sequence stars born in this mass range would have a range of mass loss rates, depending on their initial rotation velocity and the amplitude of the oscillations. The stars would evolve rapidly down the main sequence until (at about 1.25 M/sub θ/) a surface convection zone began to form. The presence of this convective region would slow the rotation, perhaps allowing magnetic braking to occur, and thus sharply reduce the mass loss rate. 7 refs

  2. Massive star formation by accretion. II. Rotation: how to circumvent the angular momentum barrier?

    Science.gov (United States)

    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.

  3. Electricity sequence control

    International Nuclear Information System (INIS)

    Shin, Heung Ryeol

    2010-03-01

    The contents of the book are introduction of control system, like classification and control signal, introduction of electricity power switch, such as push-button and detection switch sensor for induction type and capacitance type machinery for control, solenoid valve, expression of sequence and type of electricity circuit about using diagram, time chart, marking and term, logic circuit like Yes, No, and, or and equivalence logic, basic electricity circuit, electricity sequence control, added condition, special program control about choice and jump of program, motor control, extra circuit on repeat circuit, pause circuit in a conveyer, safety regulations and rule about classification of electricity disaster and protective device for insulation.

  4. Next-generation sequencing

    DEFF Research Database (Denmark)

    Rieneck, Klaus; Bak, Mads; Jønson, Lars

    2013-01-01

    , Illumina); several millions of PCR sequences were analyzed. RESULTS: The results demonstrated the feasibility of diagnosing the fetal KEL1 or KEL2 blood group from cell-free DNA purified from maternal plasma. CONCLUSION: This method requires only one primer pair, and the large amount of sequence...... information obtained allows well for statistical analysis of the data. This general approach can be integrated into current laboratory practice and has numerous applications. Besides DNA-based predictions of blood group phenotypes, platelet phenotypes, or sickle cell anemia, and the determination of zygosity...

  5. Biological sequence analysis

    DEFF Research Database (Denmark)

    Durbin, Richard; Eddy, Sean; Krogh, Anders Stærmose

    This book provides an up-to-date and tutorial-level overview of sequence analysis methods, with particular emphasis on probabilistic modelling. Discussed methods include pairwise alignment, hidden Markov models, multiple alignment, profile searches, RNA secondary structure analysis, and phylogene...

  6. THE RHIC SEQUENCER

    International Nuclear Information System (INIS)

    VAN ZEIJTS, J.; DOTTAVIO, T.; FRAK, B.; MICHNOFF, R.

    2001-01-01

    The Relativistic Heavy Ion Collider (RHIC) has a high level asynchronous time-line driven by a controlling program called the ''Sequencer''. Most high-level magnet and beam related issues are orchestrated by this system. The system also plays an important task in coordinated data acquisition and saving. We present the program, operator interface, operational impact and experience

  7. Twin anemia polycythemia sequence

    NARCIS (Netherlands)

    Slaghekke, Femke

    2014-01-01

    In this thesis we describe that Twin Anemia Polycythemia Sequence (TAPS) is a form of chronic feto-fetal transfusion in monochorionic (identical) twins based on a small amount of blood transfusion through very small anastomoses. For the antenatal diagnosis of TAPS, Middle Cerebral Artery – Peak

  8. simple sequence repeat (SSR)

    African Journals Online (AJOL)

    In the present study, 78 mapped simple sequence repeat (SSR) markers representing 11 linkage groups of adzuki bean were evaluated for transferability to mungbean and related Vigna spp. 41 markers amplified characteristic bands in at least one Vigna species. The transferability percentage across the genotypes ranged ...

  9. Targeted sequencing of plant genomes

    Science.gov (United States)

    Mark D. Huynh

    2014-01-01

    Next-generation sequencing (NGS) has revolutionized the field of genetics by providing a means for fast and relatively affordable sequencing. With the advancement of NGS, wholegenome sequencing (WGS) has become more commonplace. However, sequencing an entire genome is still not cost effective or even beneficial in all cases. In studies that do not require a whole-...

  10. Almost convergence of triple sequences

    OpenAIRE

    Ayhan Esi; M.Necdet Catalbas

    2013-01-01

    In this paper we introduce and study the concepts of almost convergence and almost Cauchy for triple sequences. Weshow that the set of almost convergent triple sequences of 0's and 1's is of the first category and also almost everytriple sequence of 0's and 1's is not almost convergent.Keywords: almost convergence, P-convergent, triple sequence.

  11. A few Smarandache Integer Sequences

    OpenAIRE

    Ibstedt, Henry

    2010-01-01

    This paper deals with the analysis of a few Smarandache Integer Sequences which first appeared in Properties or the Numbers, F. Smarandache, University or Craiova Archives, 1975. The first four sequences are recurrence generated sequences while the last three are concatenation sequences.

  12. Allele Re-sequencing Technologies

    DEFF Research Database (Denmark)

    Byrne, Stephen; Farrell, Jacqueline Danielle; Asp, Torben

    2013-01-01

    The development of next-generation sequencing technologies has made sequencing an affordable approach for detection of genetic variations associated with various traits. However, the cost of whole genome re-sequencing still remains too high to be feasible for many plant species with large...... alternative to whole genome re-sequencing to identify causative genetic variations in plants. One challenge, however, will be efficient bioinformatics strategies for data handling and analysis from the increasing amount of sequence information....

  13. Multilocus Sequence Typing

    OpenAIRE

    Belén, Ana; Pavón, Ibarz; Maiden, Martin C.J.

    2009-01-01

    Multilocus sequence typing (MLST) was first proposed in 1998 as a typing approach that enables the unambiguous characterization of bacterial isolates in a standardized, reproducible, and portable manner using the human pathogen Neisseria meningitidis as the exemplar organism. Since then, the approach has been applied to a large and growing number of organisms by public health laboratories and research institutions. MLST data, shared by investigators over the world via the Internet, have been ...

  14. Achalasia Carcinoma Sequence

    OpenAIRE

    Makmun, Dadang

    2001-01-01

    We report a case of carcinoma of the esophagus in a 58 years old woman with achalasia, who has been diagnosed since 30 years ago, which initiated by surgical treatment (myotomy) and the symptoms recurred since 3 years ago. According to the progress of the disease, Malignancy was strongly suspected due to prolonged stasis and mucosal irritation caused by achalasia (achalasia carcinoma sequence). Because of these contributing factors for the development of serious complications such as Malignan...

  15. Sequencing BPS spectra

    Energy Technology Data Exchange (ETDEWEB)

    Gukov, Sergei [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Max-Planck-Institut für Mathematik,Vivatsgasse 7, D-53111 Bonn (Germany); Nawata, Satoshi [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Centre for Quantum Geometry of Moduli Spaces, University of Aarhus,Nordre Ringgade 1, DK-8000 (Denmark); Saberi, Ingmar [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Stošić, Marko [CAMGSD, Departamento de Matemática, Instituto Superior Técnico,Av. Rovisco Pais, 1049-001 Lisbon (Portugal); Mathematical Institute SANU,Knez Mihajlova 36, 11000 Belgrade (Serbia); Sułkowski, Piotr [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Faculty of Physics, University of Warsaw,ul. Pasteura 5, 02-093 Warsaw (Poland)

    2016-03-02

    This paper provides both a detailed study of color-dependence of link homologies, as realized in physics as certain spaces of BPS states, and a broad study of the behavior of BPS states in general. We consider how the spectrum of BPS states varies as continuous parameters of a theory are perturbed. This question can be posed in a wide variety of physical contexts, and we answer it by proposing that the relationship between unperturbed and perturbed BPS spectra is described by a spectral sequence. These general considerations unify previous applications of spectral sequence techniques to physics, and explain from a physical standpoint the appearance of many spectral sequences relating various link homology theories to one another. We also study structural properties of colored HOMFLY homology for links and evaluate Poincaré polynomials in numerous examples. Among these structural properties is a novel “sliding” property, which can be explained by using (refined) modular S-matrix. This leads to the identification of modular transformations in Chern-Simons theory and 3d N=2 theory via the 3d/3d correspondence. Lastly, we introduce the notion of associated varieties as classical limits of recursion relations of colored superpolynomials of links, and study their properties.

  16. Sequencing BPS spectra

    International Nuclear Information System (INIS)

    Gukov, Sergei; Nawata, Satoshi; Saberi, Ingmar; Stošić, Marko; Sułkowski, Piotr

    2016-01-01

    This paper provides both a detailed study of color-dependence of link homologies, as realized in physics as certain spaces of BPS states, and a broad study of the behavior of BPS states in general. We consider how the spectrum of BPS states varies as continuous parameters of a theory are perturbed. This question can be posed in a wide variety of physical contexts, and we answer it by proposing that the relationship between unperturbed and perturbed BPS spectra is described by a spectral sequence. These general considerations unify previous applications of spectral sequence techniques to physics, and explain from a physical standpoint the appearance of many spectral sequences relating various link homology theories to one another. We also study structural properties of colored HOMFLY homology for links and evaluate Poincaré polynomials in numerous examples. Among these structural properties is a novel “sliding” property, which can be explained by using (refined) modular S-matrix. This leads to the identification of modular transformations in Chern-Simons theory and 3d N=2 theory via the 3d/3d correspondence. Lastly, we introduce the notion of associated varieties as classical limits of recursion relations of colored superpolynomials of links, and study their properties.

  17. Image sequence analysis

    CERN Document Server

    1981-01-01

    The processing of image sequences has a broad spectrum of important applica­ tions including target tracking, robot navigation, bandwidth compression of TV conferencing video signals, studying the motion of biological cells using microcinematography, cloud tracking, and highway traffic monitoring. Image sequence processing involves a large amount of data. However, because of the progress in computer, LSI, and VLSI technologies, we have now reached a stage when many useful processing tasks can be done in a reasonable amount of time. As a result, research and development activities in image sequence analysis have recently been growing at a rapid pace. An IEEE Computer Society Workshop on Computer Analysis of Time-Varying Imagery was held in Philadelphia, April 5-6, 1979. A related special issue of the IEEE Transactions on Pattern Anal­ ysis and Machine Intelligence was published in November 1980. The IEEE Com­ puter magazine has also published a special issue on the subject in 1981. The purpose of this book ...

  18. IN-SYNC. VII. Evidence for a Decreasing Spectroscopic Binary Fraction (from 1 to 100 Myr) within the IN-SYNC Sample

    Science.gov (United States)

    Jaehnig, Karl; Bird, Jonathan C.; Stassun, Keivan G.; Da Rio, Nicola; Tan, Jonathan C.; Cotaar, Michiel; Somers, Garrett

    2017-12-01

    We study the occurrence of spectroscopic binaries in young star-forming regions using the INfrared Spectroscopy of Young Nebulous Clusters (IN-SYNC) survey, carried out in SDSS-III with the APOGEE spectrograph. Multi-epoch observations of thousands of low-mass stars in Orion A, NGC 2264, NGC 1333, IC 348, and the Pleiades have been carried out, yielding H-band spectra with a nominal resolution of R = 22,500 for sources with H factor of 3-4, from the age of our pre-main-sequence (PMS) sample to the Pleiades age . The significance of this decline is weakened if spot-induced radial-velocity jitter is strong in the sample, and is only marginally significant when comparing any one of the PMS clusters against the Pleiades. However, the same decline in both sense and magnitude is found for each of the five PMS clusters, and the decline reaches a statistical significance of greater than 95% confidence when considering the PMS clusters jointly. Our results suggest that dynamical processes disrupt the widest spectroscopic binaries ({P}{orb}≈ {10}3{--}{10}4 days) as clusters age, indicating that this occurs early in the stars’ evolution, while they still reside within their nascent clusters.

  19. Foundations of Sequence-to-Sequence Modeling for Time Series

    OpenAIRE

    Kuznetsov, Vitaly; Mariet, Zelda

    2018-01-01

    The availability of large amounts of time series data, paired with the performance of deep-learning algorithms on a broad class of problems, has recently led to significant interest in the use of sequence-to-sequence models for time series forecasting. We provide the first theoretical analysis of this time series forecasting framework. We include a comparison of sequence-to-sequence modeling to classical time series models, and as such our theory can serve as a quantitative guide for practiti...

  20. Novel expressed sequence tag- simple sequence repeats (EST ...

    African Journals Online (AJOL)

    Using different bioinformatic criteria, the SUCEST database was used to mine for simple sequence repeat (SSR) markers. Among 42,189 clusters, 1,425 expressed sequence tag- simple sequence repeats (EST-SSRs) were identified in silico. Trinucleotide repeats were the most abundant SSRs detected. Of 212 primer pairs ...

  1. Infinite sequences and series

    CERN Document Server

    Knopp, Konrad

    1956-01-01

    One of the finest expositors in the field of modern mathematics, Dr. Konrad Knopp here concentrates on a topic that is of particular interest to 20th-century mathematicians and students. He develops the theory of infinite sequences and series from its beginnings to a point where the reader will be in a position to investigate more advanced stages on his own. The foundations of the theory are therefore presented with special care, while the developmental aspects are limited by the scope and purpose of the book. All definitions are clearly stated; all theorems are proved with enough detail to ma

  2. Fast global sequence alignment technique

    KAUST Repository

    Bonny, Mohamed Talal; Salama, Khaled N.

    2011-01-01

    fast alignment algorithm, called 'Alignment By Scanning' (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the wellknown sequence alignment algorithms, the 'GAP' (which is heuristic) and the 'Needleman

  3. Next-Generation Sequencing Platforms

    Science.gov (United States)

    Mardis, Elaine R.

    2013-06-01

    Automated DNA sequencing instruments embody an elegant interplay among chemistry, engineering, software, and molecular biology and have built upon Sanger's founding discovery of dideoxynucleotide sequencing to perform once-unfathomable tasks. Combined with innovative physical mapping approaches that helped to establish long-range relationships between cloned stretches of genomic DNA, fluorescent DNA sequencers produced reference genome sequences for model organisms and for the reference human genome. New types of sequencing instruments that permit amazing acceleration of data-collection rates for DNA sequencing have been developed. The ability to generate genome-scale data sets is now transforming the nature of biological inquiry. Here, I provide an historical perspective of the field, focusing on the fundamental developments that predated the advent of next-generation sequencing instruments and providing information about how these instruments work, their application to biological research, and the newest types of sequencers that can extract data from single DNA molecules.

  4. Rapid Polymer Sequencer

    Science.gov (United States)

    Stolc, Viktor (Inventor); Brock, Matthew W (Inventor)

    2013-01-01

    Method and system for rapid and accurate determination of each of a sequence of unknown polymer components, such as nucleic acid components. A self-assembling monolayer of a selected substance is optionally provided on an interior surface of a pipette tip, and the interior surface is immersed in a selected liquid. A selected electrical field is impressed in a longitudinal direction, or in a transverse direction, in the tip region, a polymer sequence is passed through the tip region, and a change in an electrical current signal is measured as each polymer component passes through the tip region. Each of the measured changes in electrical current signals is compared with a database of reference electrical change signals, with each reference signal corresponding to an identified polymer component, to identify the unknown polymer component with a reference polymer component. The nanopore preferably has a pore inner diameter of no more than about 40 nm and is prepared by heating and pulling a very small section of a glass tubing.

  5. The advantages of SMRT sequencing

    OpenAIRE

    Roberts, Richard J; Carneiro, Mauricio O; Schatz, Michael C

    2013-01-01

    Of the current next-generation sequencing technologies, SMRT sequencing is sometimes overlooked. However, attributes such as long reads, modified base detection and high accuracy make SMRT a useful technology and an ideal approach to the complete sequencing of small genomes.

  6. Putting instruction sequences into effect

    NARCIS (Netherlands)

    Bergstra, J.A.

    2011-01-01

    An attempt is made to define the concept of execution of an instruction sequence. It is found to be a special case of directly putting into effect of an instruction sequence. Directly putting into effect of an instruction sequences comprises interpretation as well as execution. Directly putting into

  7. Region segmentation along image sequence

    International Nuclear Information System (INIS)

    Monchal, L.; Aubry, P.

    1995-01-01

    A method to extract regions in sequence of images is proposed. Regions are not matched from one image to the following one. The result of a region segmentation is used as an initialization to segment the following and image to track the region along the sequence. The image sequence is exploited as a spatio-temporal event. (authors). 12 refs., 8 figs

  8. Exomic sequencing of immune-related genes reveals novel candidate variants associated with alopecia universalis.

    Directory of Open Access Journals (Sweden)

    Seungbok Lee

    Full Text Available Alopecia areata (AA is a common autoimmune disorder mostly presented as round patches of hair loss and subclassified into alopecia totalis/alopecia universalis (AT/AU based on the area of alopecia. Although AA is relatively common, only 5% of AA patients progress to AT/AU, which affect the whole scalp and whole body respectively. To determine genetic determinants of this orphan disease, we undertook whole-exome sequencing of 6 samples from AU patients, and 26 variants in immune-related genes were selected as candidates. When an additional 14 AU samples were genotyped for these candidates, 6 of them remained at the level of significance in comparison with 155 Asian controls (p<1.92×10(-3. Linkage disequilibrium was observed between some of the most significant SNPs, including rs41559420 of HLA-DRB5 (p<0.001, OR 44.57 and rs28362679 of BTNL2 (p<0.001, OR 30.21. While BTNL2 was reported as a general susceptibility gene of AA previously, HLA-DRB5 has not been implicated in AA. In addition, we found several genetic variants in novel genes (HLA-DMB, TLR1, and PMS2 and discovered an additional locus on HLA-A, a known susceptibility gene of AA. This study provides further evidence for the association of previously reported genes with AA and novel findings such as HLA-DRB5, which might represent a hidden culprit gene for AU.

  9. State of the art timing in TOF-PET detectors with LuAG, GAGG and L(Y)SO scintillators of various sizes coupled to FBK-SiPMs

    CERN Document Server

    Gundacker, S.; Auffray, E.; Ferri, A.; Gola, A.; Nemallapudi, M.V.; Paternoster, G.; Piemonte, C.; Lecoq, P.

    2016-01-01

    Time of flight (TOF) in positron emission tomography (PET) has experienced a revival of interest after its first introduction in the eighties. This is due to a significant progress in solid state photodetectors (SiPMs) and newly developed scintillators (LSO and its derivatives). Latest developments at Fondazione Bruno Kessler (FBK) lead to the NUV-HD SiPM with a very high photon detection efficiency of around 55%. Despite the large area of 4×4 mm2 it achieves a good single photon time resolution (SPTR) of 180±5ps FWHM. Coincidence time resolution (CTR) measurements using LSO:Ce codoped with Ca scintillators yield best values of 73±2ps FWHM for 2×2×3 mm3 and 117±3ps for 2×2×20 mm3 crystal sizes. Increasing the crystal cross-section from 2×2 mm2 to 3×3 mm2 a non negligible CTR deterioration of approximately 7ps FWHM is observed. Measurements with LSO:Ce codoped Ca and LYSO:Ce scintillators with various cross-sections (1×1 mm2 - 4×4 mm2) and lengths (3mm - 30mm) will be a basis for discussing on how ...

  10. Log-balanced combinatorial sequences

    Directory of Open Access Journals (Sweden)

    Tomislav Došlic

    2005-01-01

    Full Text Available We consider log-convex sequences that satisfy an additional constraint imposed on their rate of growth. We call such sequences log-balanced. It is shown that all such sequences satisfy a pair of double inequalities. Sufficient conditions for log-balancedness are given for the case when the sequence satisfies a two- (or more- term linear recurrence. It is shown that many combinatorially interesting sequences belong to this class, and, as a consequence, that the above-mentioned double inequalities are valid for all of them.

  11. New MR pulse sequence

    International Nuclear Information System (INIS)

    Harms, S.E.; Flamig, D.P.; Griffey, R.H.

    1990-01-01

    This paper describes a method for fat suppression for three-dimensional MR imaging. The FATS (fat-suppressed acquisition with echo time shortened) sequence employs a pair of opposing adiabatic half-passage RF pulses tuned on fat resonance. The imaging parameters are as follows: TR, 20 msec; TE, 21.7-3.2 msec; 1,024 x 128 x 128 acquired matrix; imaging time, approximately 11 minutes. A series of 54 examinations were performed. Excellent fat suppression with water excitation is achieved in all cases. The orbital images demonstrate superior resolution of small orbital lesions. The high signal-to-noise ratio (SNR) in cranial studies demonstrates excellent petrous bone and internal auditory canal anatomy

  12. Quantum-Sequencing: Fast electronic single DNA molecule sequencing

    Science.gov (United States)

    Casamada Ribot, Josep; Chatterjee, Anushree; Nagpal, Prashant

    2014-03-01

    A major goal of third-generation sequencing technologies is to develop a fast, reliable, enzyme-free, high-throughput and cost-effective, single-molecule sequencing method. Here, we present the first demonstration of unique ``electronic fingerprint'' of all nucleotides (A, G, T, C), with single-molecule DNA sequencing, using Quantum-tunneling Sequencing (Q-Seq) at room temperature. We show that the electronic state of the nucleobases shift depending on the pH, with most distinct states identified at acidic pH. We also demonstrate identification of single nucleotide modifications (methylation here). Using these unique electronic fingerprints (or tunneling data), we report a partial sequence of beta lactamase (bla) gene, which encodes resistance to beta-lactam antibiotics, with over 95% success rate. These results highlight the potential of Q-Seq as a robust technique for next-generation sequencing.

  13. Universal sequence map (USM of arbitrary discrete sequences

    Directory of Open Access Journals (Sweden)

    Almeida Jonas S

    2002-02-01

    Full Text Available Abstract Background For over a decade the idea of representing biological sequences in a continuous coordinate space has maintained its appeal but not been fully realized. The basic idea is that any sequence of symbols may define trajectories in the continuous space conserving all its statistical properties. Ideally, such a representation would allow scale independent sequence analysis – without the context of fixed memory length. A simple example would consist on being able to infer the homology between two sequences solely by comparing the coordinates of any two homologous units. Results We have successfully identified such an iterative function for bijective mappingψ of discrete sequences into objects of continuous state space that enable scale-independent sequence analysis. The technique, named Universal Sequence Mapping (USM, is applicable to sequences with an arbitrary length and arbitrary number of unique units and generates a representation where map distance estimates sequence similarity. The novel USM procedure is based on earlier work by these and other authors on the properties of Chaos Game Representation (CGR. The latter enables the representation of 4 unit type sequences (like DNA as an order free Markov Chain transition table. The properties of USM are illustrated with test data and can be verified for other data by using the accompanying web-based tool:http://bioinformatics.musc.edu/~jonas/usm/. Conclusions USM is shown to enable a statistical mechanics approach to sequence analysis. The scale independent representation frees sequence analysis from the need to assume a memory length in the investigation of syntactic rules.

  14. Short sequence motifs, overrepresented in mammalian conservednon-coding sequences

    Energy Technology Data Exchange (ETDEWEB)

    Minovitsky, Simon; Stegmaier, Philip; Kel, Alexander; Kondrashov,Alexey S.; Dubchak, Inna

    2007-02-21

    Background: A substantial fraction of non-coding DNAsequences of multicellular eukaryotes is under selective constraint. Inparticular, ~;5 percent of the human genome consists of conservednon-coding sequences (CNSs). CNSs differ from other genomic sequences intheir nucleotide composition and must play important functional roles,which mostly remain obscure.Results: We investigated relative abundancesof short sequence motifs in all human CNSs present in the human/mousewhole-genome alignments vs. three background sets of sequences: (i)weakly conserved or unconserved non-coding sequences (non-CNSs); (ii)near-promoter sequences (located between nucleotides -500 and -1500,relative to a start of transcription); and (iii) random sequences withthe same nucleotide composition as that of CNSs. When compared tonon-CNSs and near-promoter sequences, CNSs possess an excess of AT-richmotifs, often containing runs of identical nucleotides. In contrast, whencompared to random sequences, CNSs contain an excess of GC-rich motifswhich, however, lack CpG dinucleotides. Thus, abundance of short sequencemotifs in human CNSs, taken as a whole, is mostly determined by theiroverall compositional properties and not by overrepresentation of anyspecific short motifs. These properties are: (i) high AT-content of CNSs,(ii) a tendency, probably due to context-dependent mutation, of A's andT's to clump, (iii) presence of short GC-rich regions, and (iv) avoidanceof CpG contexts, due to their hypermutability. Only a small number ofshort motifs, overrepresented in all human CNSs are similar to bindingsites of transcription factors from the FOX family.Conclusion: Human CNSsas a whole appear to be too broad a class of sequences to possess strongfootprints of any short sequence-specific functions. Such footprintsshould be studied at the level of functional subclasses of CNSs, such asthose which flank genes with a particular pattern of expression. Overallproperties of CNSs are affected by

  15. Genomic sequencing in clinical trials

    OpenAIRE

    Mestan, Karen K; Ilkhanoff, Leonard; Mouli, Samdeep; Lin, Simon

    2011-01-01

    Abstract Human genome sequencing is the process by which the exact order of nucleic acid base pairs in the 24 human chromosomes is determined. Since the completion of the Human Genome Project in 2003, genomic sequencing is rapidly becoming a major part of our translational research efforts to understand and improve human health and disease. This article reviews the current and future directions of clinical research with respect to genomic sequencing, a technology that is just beginning to fin...

  16. Biosensors for DNA sequence detection

    Science.gov (United States)

    Vercoutere, Wenonah; Akeson, Mark

    2002-01-01

    DNA biosensors are being developed as alternatives to conventional DNA microarrays. These devices couple signal transduction directly to sequence recognition. Some of the most sensitive and functional technologies use fibre optics or electrochemical sensors in combination with DNA hybridization. In a shift from sequence recognition by hybridization, two emerging single-molecule techniques read sequence composition using zero-mode waveguides or electrical impedance in nanoscale pores.

  17. ABS: Sequence alignment by scanning

    KAUST Repository

    Bonny, Mohamed Talal

    2011-08-01

    Sequence alignment is an essential tool in almost any computational biology research. It processes large database sequences and considered to be high consumers of computation time. Heuristic algorithms are used to get approximate but fast results. We introduce fast alignment algorithm, called Alignment By Scanning (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the well-known alignment algorithms, the FASTA (which is heuristic) and the \\'Needleman-Wunsch\\' (which is optimal). The proposed algorithm achieves up to 76% enhancement in alignment score when it is compared with the FASTA Algorithm. The evaluations are conducted using different lengths of DNA sequences. © 2011 IEEE.

  18. ABS: Sequence alignment by scanning

    KAUST Repository

    Bonny, Mohamed Talal; Salama, Khaled N.

    2011-01-01

    Sequence alignment is an essential tool in almost any computational biology research. It processes large database sequences and considered to be high consumers of computation time. Heuristic algorithms are used to get approximate but fast results. We introduce fast alignment algorithm, called Alignment By Scanning (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the well-known alignment algorithms, the FASTA (which is heuristic) and the 'Needleman-Wunsch' (which is optimal). The proposed algorithm achieves up to 76% enhancement in alignment score when it is compared with the FASTA Algorithm. The evaluations are conducted using different lengths of DNA sequences. © 2011 IEEE.

  19. Fast global sequence alignment technique

    KAUST Repository

    Bonny, Mohamed Talal

    2011-11-01

    Bioinformatics database is growing exponentially in size. Processing these large amount of data may take hours of time even if super computers are used. One of the most important processing tool in Bioinformatics is sequence alignment. We introduce fast alignment algorithm, called \\'Alignment By Scanning\\' (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the wellknown sequence alignment algorithms, the \\'GAP\\' (which is heuristic) and the \\'Needleman-Wunsch\\' (which is optimal). The proposed algorithm achieves up to 51% enhancement in alignment score when it is compared with the GAP Algorithm. The evaluations are conducted using different lengths of DNA sequences. © 2011 IEEE.

  20. Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria

    DEFF Research Database (Denmark)

    Larsen, Mette Voldby; Cosentino, Salvatore; Rasmussen, Simon

    2012-01-01

    Accurate strain identification is essential for anyone working with bacteria. For many species, multilocus sequence typing (MLST) is considered the "gold standard" of typing, but it is traditionally performed in an expensive and time-consuming manner. As the costs of whole-genome sequencing (WGS...

  1. Dog Y chromosomal DNA sequence: identification, sequencing and SNP discovery

    Directory of Open Access Journals (Sweden)

    Kirkness Ewen

    2006-10-01

    Full Text Available Abstract Background Population genetic studies of dogs have so far mainly been based on analysis of mitochondrial DNA, describing only the history of female dogs. To get a picture of the male history, as well as a second independent marker, there is a need for studies of biallelic Y-chromosome polymorphisms. However, there are no biallelic polymorphisms reported, and only 3200 bp of non-repetitive dog Y-chromosome sequence deposited in GenBank, necessitating the identification of dog Y chromosome sequence and the search for polymorphisms therein. The genome has been only partially sequenced for one male dog, disallowing mapping of the sequence into specific chromosomes. However, by comparing the male genome sequence to the complete female dog genome sequence, candidate Y-chromosome sequence may be identified by exclusion. Results The male dog genome sequence was analysed by Blast search against the human genome to identify sequences with a best match to the human Y chromosome and to the female dog genome to identify those absent in the female genome. Candidate sequences were then tested for male specificity by PCR of five male and five female dogs. 32 sequences from the male genome, with a total length of 24 kbp, were identified as male specific, based on a match to the human Y chromosome, absence in the female dog genome and male specific PCR results. 14437 bp were then sequenced for 10 male dogs originating from Europe, Southwest Asia, Siberia, East Asia, Africa and America. Nine haplotypes were found, which were defined by 14 substitutions. The genetic distance between the haplotypes indicates that they originate from at least five wolf haplotypes. There was no obvious trend in the geographic distribution of the haplotypes. Conclusion We have identified 24159 bp of dog Y-chromosome sequence to be used for population genetic studies. We sequenced 14437 bp in a worldwide collection of dogs, identifying 14 SNPs for future SNP analyses, and

  2. SVX Sequencer Board

    International Nuclear Information System (INIS)

    Utes, M.

    1997-01-01

    The SVX Sequencer boards are 9U by 280mm circuit boards that reside in slots 2 through 21 of each of eight Eurocard crates in the D0 Detector Platform. The basic purpose is to control the SVX chips for data acquisition and when a trigger occurs, to gather the SVX data and relay the data to the VRB boards in the Movable Counting House. Functions and features are as follows: (1) Initialization of eight SVX chip strings using the MIL-STD-1553 data bus; (2) Real time manipulation of the SVX control lines to effect data acquisition, digitization, and readout based on the NRZ/Clock signals from the Controller; (3) Conversion of 8-bit electrical SVX readout data to an optical signal operating at 1.062 Gbit/sec, sent to the VRB. Eight HDIs will be serviced per board; (4) Built-in logic analyzer which can record the most important control and data lines during a data acquisition cycle and put this recorded information onto the 1553 bus; (5) Identification header and end of data trailer tacked onto data stream; (6) 1553 register which can read the current values of the control and data lines; (7) 1553 register which can test the optical link; (8) 1553 registers for crossing pulse width, calibration pulse voltage, and calibration pipeline select; (9) 1553 register for reading the optical drivers status link; (10) 1553 register for power control of SVX chips and ignoring bad SVX strings; (11) Front panel displays and LEDs show the board status at a glance; (12) In-system programmable EPLDs are programmed via 1553 or Altera's 'Bitblaster'; (13) Automatic readout abort after 45us; (14) Supplies BUSY signal back to Trigger Framework; (15) Supports a heartbeat system to prevent excessive SVX current draw; and (16) Supports a SVX power trip feature if heartbeat failure occurs.

  3. Sequence Algebra, Sequence Decision Diagrams and Dynamic Fault Trees

    International Nuclear Information System (INIS)

    Rauzy, Antoine B.

    2011-01-01

    A large attention has been focused on the Dynamic Fault Trees in the past few years. By adding new gates to static (regular) Fault Trees, Dynamic Fault Trees aim to take into account dependencies among events. Merle et al. proposed recently an algebraic framework to give a formal interpretation to these gates. In this article, we extend Merle et al.'s work by adopting a slightly different perspective. We introduce Sequence Algebras that can be seen as Algebras of Basic Events, representing failures of non-repairable components. We show how to interpret Dynamic Fault Trees within this framework. Finally, we propose a new data structure to encode sets of sequences of Basic Events: Sequence Decision Diagrams. Sequence Decision Diagrams are very much inspired from Minato's Zero-Suppressed Binary Decision Diagrams. We show that all operations of Sequence Algebras can be performed on this data structure.

  4. Chameleon sequences in neurodegenerative diseases

    International Nuclear Information System (INIS)

    Bahramali, Golnaz; Goliaei, Bahram; Minuchehr, Zarrin; Salari, Ali

    2016-01-01

    Chameleon sequences can adopt either alpha helix sheet or a coil conformation. Defining chameleon sequences in PDB (Protein Data Bank) may yield to an insight on defining peptides and proteins responsible in neurodegeneration. In this research, we benefitted from the large PDB and performed a sequence analysis on Chameleons, where we developed an algorithm to extract peptide segments with identical sequences, but different structures. In order to find new chameleon sequences, we extracted a set of 8315 non-redundant protein sequences from the PDB with an identity less than 25%. Our data was classified to “helix to strand (HE)”, “helix to coil (HC)” and “strand to coil (CE)” alterations. We also analyzed the occurrence of singlet and doublet amino acids and the solvent accessibility in the chameleon sequences; we then sorted out the proteins with the most number of chameleon sequences and named them Chameleon Flexible Proteins (CFPs) in our dataset. Our data revealed that Gly, Val, Ile, Tyr and Phe, are the major amino acids in Chameleons. We also found that there are proteins such as Insulin Degrading Enzyme IDE and GTP-binding nuclear protein Ran (RAN) with the most number of chameleons (640 and 405 respectively). These proteins have known roles in neurodegenerative diseases. Therefore it can be inferred that other CFP's can serve as key proteins in neurodegeneration, and a study on them can shed light on curing and preventing neurodegenerative diseases.

  5. Direct, rapid RNA sequence analysis

    International Nuclear Information System (INIS)

    Peattie, D.A.

    1987-01-01

    The original methods of RNA sequence analysis were based on enzymatic production and chromatographic separation of overlapping oligonucleotide fragments from within an RNA molecule followed by identification of the mononucleotides comprising the oligomer. Over the past decade the field of nucleic acid sequencing has changed dramatically, however, and RNA molecules now can be sequenced in a variety of more streamlined fashions. Most of the more recent advances in RNA sequencing have involved one-dimensional electrophoretic separation of 32 P-end-labeled oligoribonucleotides on polyacrylamide gels. In this chapter the author discusses two of these methods for determining the nucleotide sequences of RNA molecules rapidly: the chemical method and the enzymatic method. Both methods are direct and degradative, i.e., they rely on fragmatic and chemical approaches should be utilized. The single-strand-specific ribonucleases (A, T 1 , T 2 , and S 1 ) provide an efficient means to locate double-helical regions rapidly, and the chemical reactions provide a means to determine the RNA sequence within these regions. In addition, the chemical reactions allow one to assign interactions to specific atoms and to distinguish secondary interactions from tertiary ones. If the RNA molecule is small enough to be sequenced directly by the enzymatic or chemical method, the probing reactions can be done easily at the same time as sequencing reactions

  6. Chameleon sequences in neurodegenerative diseases.

    Science.gov (United States)

    Bahramali, Golnaz; Goliaei, Bahram; Minuchehr, Zarrin; Salari, Ali

    2016-03-25

    Chameleon sequences can adopt either alpha helix sheet or a coil conformation. Defining chameleon sequences in PDB (Protein Data Bank) may yield to an insight on defining peptides and proteins responsible in neurodegeneration. In this research, we benefitted from the large PDB and performed a sequence analysis on Chameleons, where we developed an algorithm to extract peptide segments with identical sequences, but different structures. In order to find new chameleon sequences, we extracted a set of 8315 non-redundant protein sequences from the PDB with an identity less than 25%. Our data was classified to "helix to strand (HE)", "helix to coil (HC)" and "strand to coil (CE)" alterations. We also analyzed the occurrence of singlet and doublet amino acids and the solvent accessibility in the chameleon sequences; we then sorted out the proteins with the most number of chameleon sequences and named them Chameleon Flexible Proteins (CFPs) in our dataset. Our data revealed that Gly, Val, Ile, Tyr and Phe, are the major amino acids in Chameleons. We also found that there are proteins such as Insulin Degrading Enzyme IDE and GTP-binding nuclear protein Ran (RAN) with the most number of chameleons (640 and 405 respectively). These proteins have known roles in neurodegenerative diseases. Therefore it can be inferred that other CFP's can serve as key proteins in neurodegeneration, and a study on them can shed light on curing and preventing neurodegenerative diseases. Copyright © 2016 Elsevier Inc. All rights reserved.

  7. Farey sequences and resistor networks

    Indian Academy of Sciences (India)

    Green's function, while the perturbation of a network is investigated in [3]. ... In Theorem 1 below, we employ the Farey sequence to establish a strict .... We next show that the Farey sequence method is applicable for circuits with n or fewer.

  8. DNA Sequencing by Capillary Electrophoresis

    Science.gov (United States)

    Karger, Barry L.; Guttman, Andras

    2009-01-01

    Sequencing of human and other genomes has been at the center of interest in the biomedical field over the past several decades and is now leading toward an era of personalized medicine. During this time, DNA sequencing methods have evolved from the labor intensive slab gel electrophoresis, through automated multicapillary electrophoresis systems using fluorophore labeling with multispectral imaging, to the “next generation” technologies of cyclic array, hybridization based, nanopore and single molecule sequencing. Deciphering the genetic blueprint and follow-up confirmatory sequencing of Homo sapiens and other genomes was only possible by the advent of modern sequencing technologies that was a result of step by step advances with a contribution of academics, medical personnel and instrument companies. While next generation sequencing is moving ahead at break-neck speed, the multicapillary electrophoretic systems played an essential role in the sequencing of the Human Genome, the foundation of the field of genomics. In this prospective, we wish to overview the role of capillary electrophoresis in DNA sequencing based in part of several of our articles in this journal. PMID:19517496

  9. Graphene nanodevices for DNA sequencing

    NARCIS (Netherlands)

    Heerema, S.J.; Dekker, C.

    2016-01-01

    Fast, cheap, and reliable DNA sequencing could be one of the most disruptive innovations of this decade, as it will pave the way for personalized medicine. In pursuit of such technology, a variety of nanotechnology-based approaches have been explored and established, including sequencing with

  10. Chameleon sequences in neurodegenerative diseases

    Energy Technology Data Exchange (ETDEWEB)

    Bahramali, Golnaz [Institute of Biochemistry and Biophysics, University of Tehran, Tehran (Iran, Islamic Republic of); Goliaei, Bahram, E-mail: goliaei@ut.ac.ir [Institute of Biochemistry and Biophysics, University of Tehran, Tehran (Iran, Islamic Republic of); Minuchehr, Zarrin, E-mail: minuchehr@nigeb.ac.ir [Department of Systems Biotechnology, National Institute of Genetic Engineering and Biotechnology, (NIGEB), Tehran (Iran, Islamic Republic of); Salari, Ali [Department of Systems Biotechnology, National Institute of Genetic Engineering and Biotechnology, (NIGEB), Tehran (Iran, Islamic Republic of)

    2016-03-25

    Chameleon sequences can adopt either alpha helix sheet or a coil conformation. Defining chameleon sequences in PDB (Protein Data Bank) may yield to an insight on defining peptides and proteins responsible in neurodegeneration. In this research, we benefitted from the large PDB and performed a sequence analysis on Chameleons, where we developed an algorithm to extract peptide segments with identical sequences, but different structures. In order to find new chameleon sequences, we extracted a set of 8315 non-redundant protein sequences from the PDB with an identity less than 25%. Our data was classified to “helix to strand (HE)”, “helix to coil (HC)” and “strand to coil (CE)” alterations. We also analyzed the occurrence of singlet and doublet amino acids and the solvent accessibility in the chameleon sequences; we then sorted out the proteins with the most number of chameleon sequences and named them Chameleon Flexible Proteins (CFPs) in our dataset. Our data revealed that Gly, Val, Ile, Tyr and Phe, are the major amino acids in Chameleons. We also found that there are proteins such as Insulin Degrading Enzyme IDE and GTP-binding nuclear protein Ran (RAN) with the most number of chameleons (640 and 405 respectively). These proteins have known roles in neurodegenerative diseases. Therefore it can be inferred that other CFP's can serve as key proteins in neurodegeneration, and a study on them can shed light on curing and preventing neurodegenerative diseases.

  11. Commercial Art: Scope and Sequence.

    Science.gov (United States)

    Nashville - Davidson County Metropolitan Public Schools, TN.

    This scope and sequence guide, developed for a commercial art vocational education program, represents an initial step in the development of a systemwide articulated curriculum sequence for all vocational programs within the Metropolitan Nashville Public School System. It was developed as a result of needs expressed by teachers, parents, and the…

  12. Rapid Diagnostics of Onboard Sequences

    Science.gov (United States)

    Starbird, Thomas W.; Morris, John R.; Shams, Khawaja S.; Maimone, Mark W.

    2012-01-01

    Keeping track of sequences onboard a spacecraft is challenging. When reviewing Event Verification Records (EVRs) of sequence executions on the Mars Exploration Rover (MER), operators often found themselves wondering which version of a named sequence the EVR corresponded to. The lack of this information drastically impacts the operators diagnostic capabilities as well as their situational awareness with respect to the commands the spacecraft has executed, since the EVRs do not provide argument values or explanatory comments. Having this information immediately available can be instrumental in diagnosing critical events and can significantly enhance the overall safety of the spacecraft. This software provides auditing capability that can eliminate that uncertainty while diagnosing critical conditions. Furthermore, the Restful interface provides a simple way for sequencing tools to automatically retrieve binary compiled sequence SCMFs (Space Command Message Files) on demand. It also enables developers to change the underlying database, while maintaining the same interface to the existing applications. The logging capabilities are also beneficial to operators when they are trying to recall how they solved a similar problem many days ago: this software enables automatic recovery of SCMF and RML (Robot Markup Language) sequence files directly from the command EVRs, eliminating the need for people to find and validate the corresponding sequences. To address the lack of auditing capability for sequences onboard a spacecraft during earlier missions, extensive logging support was added on the Mars Science Laboratory (MSL) sequencing server. This server is responsible for generating all MSL binary SCMFs from RML input sequences. The sequencing server logs every SCMF it generates into a MySQL database, as well as the high-level RML file and dictionary name inputs used to create the SCMF. The SCMF is then indexed by a hash value that is automatically included in all command

  13. Accident sequence quantification with KIRAP

    International Nuclear Information System (INIS)

    Kim, Tae Un; Han, Sang Hoon; Kim, Kil You; Yang, Jun Eon; Jeong, Won Dae; Chang, Seung Cheol; Sung, Tae Yong; Kang, Dae Il; Park, Jin Hee; Lee, Yoon Hwan; Hwang, Mi Jeong.

    1997-01-01

    The tasks of probabilistic safety assessment(PSA) consists of the identification of initiating events, the construction of event tree for each initiating event, construction of fault trees for event tree logics, the analysis of reliability data and finally the accident sequence quantification. In the PSA, the accident sequence quantification is to calculate the core damage frequency, importance analysis and uncertainty analysis. Accident sequence quantification requires to understand the whole model of the PSA because it has to combine all event tree and fault tree models, and requires the excellent computer code because it takes long computation time. Advanced Research Group of Korea Atomic Energy Research Institute(KAERI) has developed PSA workstation KIRAP(Korea Integrated Reliability Analysis Code Package) for the PSA work. This report describes the procedures to perform accident sequence quantification, the method to use KIRAP's cut set generator, and method to perform the accident sequence quantification with KIRAP. (author). 6 refs

  14. Accident sequence quantification with KIRAP

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Tae Un; Han, Sang Hoon; Kim, Kil You; Yang, Jun Eon; Jeong, Won Dae; Chang, Seung Cheol; Sung, Tae Yong; Kang, Dae Il; Park, Jin Hee; Lee, Yoon Hwan; Hwang, Mi Jeong

    1997-01-01

    The tasks of probabilistic safety assessment(PSA) consists of the identification of initiating events, the construction of event tree for each initiating event, construction of fault trees for event tree logics, the analysis of reliability data and finally the accident sequence quantification. In the PSA, the accident sequence quantification is to calculate the core damage frequency, importance analysis and uncertainty analysis. Accident sequence quantification requires to understand the whole model of the PSA because it has to combine all event tree and fault tree models, and requires the excellent computer code because it takes long computation time. Advanced Research Group of Korea Atomic Energy Research Institute(KAERI) has developed PSA workstation KIRAP(Korea Integrated Reliability Analysis Code Package) for the PSA work. This report describes the procedures to perform accident sequence quantification, the method to use KIRAP`s cut set generator, and method to perform the accident sequence quantification with KIRAP. (author). 6 refs.

  15. Repeated DNA sequences in fungi

    Energy Technology Data Exchange (ETDEWEB)

    Dutta, S K

    1974-11-01

    Several fungal species, representatives of all broad groups like basidiomycetes, ascomycetes and phycomycetes, were examined for the nature of repeated DNA sequences by DNA:DNA reassociation studies using hydroxyapatite chromatography. All of the fungal species tested contained 10 to 20 percent repeated DNA sequences. There are approximately 100 to 110 copies of repeated DNA sequences of approximately 4 x 10/sup 7/ daltons piece size of each. Repeated DNA sequence homoduplexes showed on average 5/sup 0/C difference of T/sub e/50 (temperature at which 50 percent duplexes dissociate) values from the corresponding homoduplexes of unfractionated whole DNA. It is suggested that a part of repetitive sequences in fungi constitutes mitochondrial DNA and a part of it constitutes nuclear DNA. (auth)

  16. [Complete genome sequencing and sequence analysis of BCG Tice].

    Science.gov (United States)

    Wang, Zhiming; Pan, Yuanlong; Wu, Jun; Zhu, Baoli

    2012-10-04

    The objective of this study is to obtain the complete genome sequence of Bacillus Calmette-Guerin Tice (BCG Tice), in order to provide more information about the molecular biology of BCG Tice and design more reasonable vaccines to prevent tuberculosis. We assembled the data from high-throughput sequencing with SOAPdenovo software, with many contigs and scaffolds obtained. There are many sequence gaps and physical gaps remained as a result of regional low coverage and low quality. We designed primers at the end of contigs and performed PCR amplification in order to link these contigs and scaffolds. With various enzymes to perform PCR amplification, adjustment of PCR reaction conditions, and combined with clone construction to sequence, all the gaps were finished. We obtained the complete genome sequence of BCG Tice and submitted it to GenBank of National Center for Biotechnology Information (NCBI). The genome of BCG Tice is 4334064 base pairs in length, with GC content 65.65%. The problems and strategies during the finishing step of BCG Tice sequencing are illuminated here, with the hope of affording some experience to those who are involved in the finishing step of genome sequencing. The microarray data were verified by our results.

  17. GROUPING WEB ACCESS SEQUENCES uSING SEQUENCE ALIGNMENT METHOD

    OpenAIRE

    BHUPENDRA S CHORDIA; KRISHNAKANT P ADHIYA

    2011-01-01

    In web usage mining grouping of web access sequences can be used to determine the behavior or intent of a set of users. Grouping websessions is how to measure the similarity between web sessions. There are many shortcomings in traditional measurement methods. The taskof grouping web sessions based on similarity and consists of maximizing the intra-group similarity while minimizing the inter-groupsimilarity is done using sequence alignment method. This paper introduces a new method to group we...

  18. LPTAU, Quasi Random Sequence Generator

    International Nuclear Information System (INIS)

    Sobol, Ilya M.

    1993-01-01

    1 - Description of program or function: LPTAU generates quasi random sequences. These are uniformly distributed sets of L=M N points in the N-dimensional unit cube: I N =[0,1]x...x[0,1]. These sequences are used as nodes for multidimensional integration; as searching points in global optimization; as trial points in multi-criteria decision making; as quasi-random points for quasi Monte Carlo algorithms. 2 - Method of solution: Uses LP-TAU sequence generation (see references). 3 - Restrictions on the complexity of the problem: The number of points that can be generated is L 30 . The dimension of the space cannot exceed 51

  19. Weak disorder in Fibonacci sequences

    Energy Technology Data Exchange (ETDEWEB)

    Ben-Naim, E [Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); Krapivsky, P L [Department of Physics and Center for Molecular Cybernetics, Boston University, Boston, MA 02215 (United States)

    2006-05-19

    We study how weak disorder affects the growth of the Fibonacci series. We introduce a family of stochastic sequences that grow by the normal Fibonacci recursion with probability 1 - {epsilon}, but follow a different recursion rule with a small probability {epsilon}. We focus on the weak disorder limit and obtain the Lyapunov exponent that characterizes the typical growth of the sequence elements, using perturbation theory. The limiting distribution for the ratio of consecutive sequence elements is obtained as well. A number of variations to the basic Fibonacci recursion including shift, doubling and copying are considered. (letter to the editor)

  20. Circumstellar Disk Lifetimes In Numerous Galactic Young Stellar Clusters

    Science.gov (United States)

    Richert, A. J. W.; Getman, K. V.; Feigelson, E. D.; Kuhn, M. A.; Broos, P. S.; Povich, M. S.; Bate, M. R.; Garmire, G. P.

    2018-04-01

    Photometric detections of dust circumstellar disks around pre-main sequence (PMS) stars, coupled with estimates of stellar ages, provide constraints on the time available for planet formation. Most previous studies on disk longevity, starting with Haisch, Lada & Lada (2001), use star samples from PMS clusters but do not consider datasets with homogeneous photometric sensitivities and/or ages placed on a uniform timescale. Here we conduct the largest study to date of the longevity of inner dust disks using X-ray and 1-8 {μ m} infrared photometry from the MYStIX and SFiNCs projects for 69 young clusters in 32 nearby star-forming regions with ages t ≤ 5 Myr. Cluster ages are derived by combining the empirical AgeJX method with PMS evolutionary models, which treat dynamo-generated magnetic fields in different ways. Leveraging X-ray data to identify disk-free objects, we impose similar stellar mass sensitivity limits for disk-bearing and disk-free YSOs while extending the analysis to stellar masses as low as M ˜ 0.1 M⊙. We find that the disk longevity estimates are strongly affected by the choice of PMS evolutionary model. Assuming a disk fraction of 100% at zero age, the inferred disk half-life changes significantly, from t1/2 ˜ 1.3 - 2 Myr to t1/2 ˜ 3.5 Myr when switching from non-magnetic to magnetic PMS models. In addition, we find no statistically significant evidence that disk fraction varies with stellar mass within the first few Myr of life for stars with masses <2 M⊙, but our samples may not be complete for more massive stars. The effects of initial disk fraction and star-forming environment are also explored.

  1. Sequence analysis of Leukemia DNA

    Science.gov (United States)

    Nacong, Nasria; Lusiyanti, Desy; Irawan, Muhammad. Isa

    2018-03-01

    Cancer is a very deadly disease, one of which is leukemia disease or better known as blood cancer. The cancer cell can be detected by taking DNA in laboratory test. This study focused on local alignment of leukemia and non leukemia data resulting from NCBI in the form of DNA sequences by using Smith-Waterman algorithm. SmithWaterman algorithm was invented by TF Smith and MS Waterman in 1981. These algorithms try to find as much as possible similarity of a pair of sequences, by giving a negative value to the unequal base pair (mismatch), and positive values on the same base pair (match). So that will obtain the maximum positive value as the end of the alignment, and the minimum value as the initial alignment. This study will use sequences of leukemia and 3 sequences of non leukemia.

  2. Integrated sequence analysis. Final report

    International Nuclear Information System (INIS)

    Andersson, K.; Pyy, P.

    1998-02-01

    The NKS/RAK subprojet 3 'integrated sequence analysis' (ISA) was formulated with the overall objective to develop and to test integrated methodologies in order to evaluate event sequences with significant human action contribution. The term 'methodology' denotes not only technical tools but also methods for integration of different scientific disciplines. In this report, we first discuss the background of ISA and the surveys made to map methods in different application fields, such as man machine system simulation software, human reliability analysis (HRA) and expert judgement. Specific event sequences were, after the surveys, selected for application and testing of a number of ISA methods. The event sequences discussed in the report were cold overpressure of BWR, shutdown LOCA of BWR, steam generator tube rupture of a PWR and BWR disturbed signal view in the control room after an external event. Different teams analysed these sequences by using different ISA and HRA methods. Two kinds of results were obtained from the ISA project: sequence specific and more general findings. The sequence specific results are discussed together with each sequence description. The general lessons are discussed under a separate chapter by using comparisons of different case studies. These lessons include areas ranging from plant safety management (design, procedures, instrumentation, operations, maintenance and safety practices) to methodological findings (ISA methodology, PSA,HRA, physical analyses, behavioural analyses and uncertainty assessment). Finally follows a discussion about the project and conclusions are presented. An interdisciplinary study of complex phenomena is a natural way to produce valuable and innovative results. This project came up with structured ways to perform ISA and managed to apply the in practice. The project also highlighted some areas where more work is needed. In the HRA work, development is required for the use of simulators and expert judgement as

  3. Optimization of sequence alignment for simple sequence repeat regions

    Directory of Open Access Journals (Sweden)

    Ogbonnaya Francis C

    2011-07-01

    Full Text Available Abstract Background Microsatellites, or simple sequence repeats (SSRs, are tandemly repeated DNA sequences, including tandem copies of specific sequences no longer than six bases, that are distributed in the genome. SSR has been used as a molecular marker because it is easy to detect and is used in a range of applications, including genetic diversity, genome mapping, and marker assisted selection. It is also very mutable because of slipping in the DNA polymerase during DNA replication. This unique mutation increases the insertion/deletion (INDELs mutation frequency to a high ratio - more than other types of molecular markers such as single nucleotide polymorphism (SNPs. SNPs are more frequent than INDELs. Therefore, all designed algorithms for sequence alignment fit the vast majority of the genomic sequence without considering microsatellite regions, as unique sequences that require special consideration. The old algorithm is limited in its application because there are many overlaps between different repeat units which result in false evolutionary relationships. Findings To overcome the limitation of the aligning algorithm when dealing with SSR loci, a new algorithm was developed using PERL script with a Tk graphical interface. This program is based on aligning sequences after determining the repeated units first, and the last SSR nucleotides positions. This results in a shifting process according to the inserted repeated unit type. When studying the phylogenic relations before and after applying the new algorithm, many differences in the trees were obtained by increasing the SSR length and complexity. However, less distance between different linage had been observed after applying the new algorithm. Conclusions The new algorithm produces better estimates for aligning SSR loci because it reflects more reliable evolutionary relations between different linages. It reduces overlapping during SSR alignment, which results in a more realistic

  4. ADDRESS SEQUENCES FOR MULTI RUN RAM TESTING

    Directory of Open Access Journals (Sweden)

    V. N. Yarmolik

    2014-01-01

    Full Text Available A universal approach for generation of address sequences with specified properties is proposed and analyzed. A modified version of the Antonov and Saleev algorithm for Sobol sequences genera-tion is chosen as a mathematical description of the proposed method. Within the framework of the proposed universal approach, the Sobol sequences form a subset of the address sequences. Other sub-sets are also formed, which are Gray sequences, anti-Gray sequences, counter sequences and sequenc-es with specified properties.

  5. Baltic PMs urge support for EU

    Index Scriptorium Estoniae

    2003-01-01

    Eesti peaministri Juhan Partsi, Läti peaministri Einars Repshe ja Leedu peaministri Algirdas Brazauskase ühisavaldusest Eestile ning Lätile järgimaks Leedu eeskuju referendumil EL-i poolt hääletamises

  6. Fast and secure retrieval of DNA sequences

    NARCIS (Netherlands)

    2014-01-01

    Sequence models are retrieved from a sequences index. The sequence models model DNA or RNA sequences stored in a database, and each comprises a finite memory tree source model and parameters for the finite memory tree source model. One or more DNA or RNA sequences stored in the database are

  7. Decidability of uniform recurrence of morphic sequences

    OpenAIRE

    Durand , Fabien

    2012-01-01

    We prove that the uniform recurrence of morphic sequences is decidable. For this we show that the number of derived sequences of uniformly recurrent morphic sequences is bounded. As a corollary we obtain that uniformly recurrent morphic sequences are primitive substitutive sequences.

  8. Sequence Factorization with Multiple References.

    Directory of Open Access Journals (Sweden)

    Sebastian Wandelt

    Full Text Available The success of high-throughput sequencing has lead to an increasing number of projects which sequence large populations of a species. Storage and analysis of sequence data is a key challenge in these projects, because of the sheer size of the datasets. Compression is one simple technology to deal with this challenge. Referential factorization and compression schemes, which store only the differences between input sequence and a reference sequence, gained lots of interest in this field. Highly-similar sequences, e.g., Human genomes, can be compressed with a compression ratio of 1,000:1 and more, up to two orders of magnitude better than with standard compression techniques. Recently, it was shown that the compression against multiple references from the same species can boost the compression ratio up to 4,000:1. However, a detailed analysis of using multiple references is lacking, e.g., for main memory consumption and optimality. In this paper, we describe one key technique for the referential compression against multiple references: The factorization of sequences. Based on the notion of an optimal factorization, we propose optimization heuristics and identify parameter settings which greatly influence 1 the size of the factorization, 2 the time for factorization, and 3 the required amount of main memory. We evaluate a total of 30 setups with a varying number of references on data from three different species. Our results show a wide range of factorization sizes (optimal to an overhead of up to 300%, factorization speed (0.01 MB/s to more than 600 MB/s, and main memory usage (few dozen MB to dozens of GB. Based on our evaluation, we identify the best configurations for common use cases. Our evaluation shows that multi-reference factorization is much better than single-reference factorization.

  9. Analysis of Pteridium ribosomal RNA sequences by rapid direct sequencing.

    Science.gov (United States)

    Tan, M K

    1991-08-01

    A total of 864 bases from 5 regions interspersed in the 18S and 26S rRNA molecules from various clones of Pteridium covering the general geographical distribution of the genus was analysed using a rapid rRNA sequencing technique. No base difference has been detected amongst the three major lineages, two of which apparently separated before the breakup of the ancient supercontinent, Pangaea. These regions of the rRNA sequences have thus been conserved for at least 160 million years and are here compared with other eukaryotic, especially plant rRNAs.

  10. Genome Sequences of Oryza Species

    KAUST Repository

    Kumagai, Masahiko; Tanaka, Tsuyoshi; Ohyanagi, Hajime; Hsing, Yue-Ie C.; Itoh, Takeshi

    2018-01-01

    This chapter summarizes recent data obtained from genome sequencing, annotation projects, and studies on the genome diversity of Oryza sativa and related Oryza species. O. sativa, commonly known as Asian rice, is the first monocot species whose complete genome sequence was deciphered based on physical mapping by an international collaborative effort. This genome, along with its accurate and comprehensive annotation, has become an indispensable foundation for crop genomics and breeding. With the development of innovative sequencing technologies, genomic studies of O. sativa have dramatically increased; in particular, a large number of cultivars and wild accessions have been sequenced and compared with the reference rice genome. Since de novo genome sequencing has become cost-effective, the genome of African cultivated rice, O. glaberrima, has also been determined. Comparative genomic studies have highlighted the independent domestication processes of different rice species, but it also turned out that Asian and African rice share a common gene set that has experienced similar artificial selection. An international project aimed at constructing reference genomes and examining the genome diversity of wild Oryza species is currently underway, and the genomes of some species are publicly available. This project provides a platform for investigations such as the evolution, development, polyploidization, and improvement of crops. Studies on the genomic diversity of Oryza species, including wild species, should provide new insights to solve the problem of growing food demands in the face of rapid climatic changes.

  11. Genome Sequences of Oryza Species

    KAUST Repository

    Kumagai, Masahiko

    2018-02-14

    This chapter summarizes recent data obtained from genome sequencing, annotation projects, and studies on the genome diversity of Oryza sativa and related Oryza species. O. sativa, commonly known as Asian rice, is the first monocot species whose complete genome sequence was deciphered based on physical mapping by an international collaborative effort. This genome, along with its accurate and comprehensive annotation, has become an indispensable foundation for crop genomics and breeding. With the development of innovative sequencing technologies, genomic studies of O. sativa have dramatically increased; in particular, a large number of cultivars and wild accessions have been sequenced and compared with the reference rice genome. Since de novo genome sequencing has become cost-effective, the genome of African cultivated rice, O. glaberrima, has also been determined. Comparative genomic studies have highlighted the independent domestication processes of different rice species, but it also turned out that Asian and African rice share a common gene set that has experienced similar artificial selection. An international project aimed at constructing reference genomes and examining the genome diversity of wild Oryza species is currently underway, and the genomes of some species are publicly available. This project provides a platform for investigations such as the evolution, development, polyploidization, and improvement of crops. Studies on the genomic diversity of Oryza species, including wild species, should provide new insights to solve the problem of growing food demands in the face of rapid climatic changes.

  12. Transformed composite sequences for improved qubit addressing

    Science.gov (United States)

    Merrill, J. True; Doret, S. Charles; Vittorini, Grahame; Addison, J. P.; Brown, Kenneth R.

    2014-10-01

    Selective laser addressing of a single atom or atomic ion qubit can be improved using narrow-band composite pulse sequences. We describe a Lie-algebraic technique to generalize known narrow-band sequences and introduce sequences related by dilation and rotation of sequence generators. Our method improves known narrow-band sequences by decreasing both the pulse time and the residual error. Finally, we experimentally demonstrate these composite sequences using 40Ca+ ions trapped in a surface-electrode ion trap.

  13. Sequences, groups, and number theory

    CERN Document Server

    Rigo, Michel

    2018-01-01

    This collaborative book presents recent trends on the study of sequences, including combinatorics on words and symbolic dynamics, and new interdisciplinary links to group theory and number theory. Other chapters branch out from those areas into subfields of theoretical computer science, such as complexity theory and theory of automata. The book is built around four general themes: number theory and sequences, word combinatorics, normal numbers, and group theory. Those topics are rounded out by investigations into automatic and regular sequences, tilings and theory of computation, discrete dynamical systems, ergodic theory, numeration systems, automaton semigroups, and amenable groups.  This volume is intended for use by graduate students or research mathematicians, as well as computer scientists who are working in automata theory and formal language theory. With its organization around unified themes, it would also be appropriate as a supplemental text for graduate level courses.

  14. Explaining the harmonic sequence paradox.

    Science.gov (United States)

    Schmidt, Ulrich; Zimper, Alexander

    2012-05-01

    According to the harmonic sequence paradox, an expected utility decision maker's willingness to pay for a gamble whose expected payoffs evolve according to the harmonic series is finite if and only if his marginal utility of additional income becomes zero for rather low payoff levels. Since the assumption of zero marginal utility is implausible for finite payoff levels, expected utility theory - as well as its standard generalizations such as cumulative prospect theory - are apparently unable to explain a finite willingness to pay. This paper presents first an experimental study of the harmonic sequence paradox. Additionally, it demonstrates that the theoretical argument of the harmonic sequence paradox only applies to time-patient decision makers, whereas the paradox is easily avoided if time-impatience is introduced. ©2011 The British Psychological Society.

  15. X-Ray Flare Oscillations Track Plasma Sloshing along Star-disk Magnetic Tubes in the Orion Star-forming Region

    Science.gov (United States)

    Reale, Fabio; Lopez-Santiago, Javier; Flaccomio, Ettore; Petralia, Antonino; Sciortino, Salvatore

    2018-03-01

    Pulsing X-ray emission tracks the plasma “echo” traveling in an extremely long magnetic tube that flares in an Orion pre-main sequence (PMS) star. On the Sun, flares last from minutes to a few hours and the longest-lasting ones typically involve arcades of closed magnetic tubes. Long-lasting X-ray flares are observed in PMS stars. Large-amplitude (∼20%), long-period (∼3 hr) pulsations are detected in the light curve of day-long flares observed by the Advanced CCD Imaging Spectrometer on-board Chandra from PMS stars in the Orion cluster. Detailed hydrodynamic modeling of two flares observed on V772 Ori and OW Ori shows that these pulsations may track the sloshing of plasma along a single long magnetic tube, triggered by a sufficiently short (∼1 hr) heat pulse. These magnetic tubes are ≥20 solar radii long, enough to connect the star with the surrounding disk.

  16. Integrated sequence analysis. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Andersson, K.; Pyy, P

    1998-02-01

    The NKS/RAK subprojet 3 `integrated sequence analysis` (ISA) was formulated with the overall objective to develop and to test integrated methodologies in order to evaluate event sequences with significant human action contribution. The term `methodology` denotes not only technical tools but also methods for integration of different scientific disciplines. In this report, we first discuss the background of ISA and the surveys made to map methods in different application fields, such as man machine system simulation software, human reliability analysis (HRA) and expert judgement. Specific event sequences were, after the surveys, selected for application and testing of a number of ISA methods. The event sequences discussed in the report were cold overpressure of BWR, shutdown LOCA of BWR, steam generator tube rupture of a PWR and BWR disturbed signal view in the control room after an external event. Different teams analysed these sequences by using different ISA and HRA methods. Two kinds of results were obtained from the ISA project: sequence specific and more general findings. The sequence specific results are discussed together with each sequence description. The general lessons are discussed under a separate chapter by using comparisons of different case studies. These lessons include areas ranging from plant safety management (design, procedures, instrumentation, operations, maintenance and safety practices) to methodological findings (ISA methodology, PSA,HRA, physical analyses, behavioural analyses and uncertainty assessment). Finally follows a discussion about the project and conclusions are presented. An interdisciplinary study of complex phenomena is a natural way to produce valuable and innovative results. This project came up with structured ways to perform ISA and managed to apply the in practice. The project also highlighted some areas where more work is needed. In the HRA work, development is required for the use of simulators and expert judgement as

  17. Matrix transformations and sequence spaces

    International Nuclear Information System (INIS)

    Nanda, S.

    1983-06-01

    In most cases the most general linear operator from one sequence space into another is actually given by an infinite matrix and therefore the theory of matrix transformations has always been of great interest in the study of sequence spaces. The study of general theory of matrix transformations was motivated by the special results in summability theory. This paper is a review article which gives almost all known results on matrix transformations. This also suggests a number of open problems for further study and will be very useful for research workers. (author)

  18. Green's theorem and Gorenstein sequences

    OpenAIRE

    Ahn, Jeaman; Migliore, Juan C.; Shin, Yong-Su

    2016-01-01

    We study consequences, for a standard graded algebra, of extremal behavior in Green's Hyperplane Restriction Theorem. First, we extend his Theorem 4 from the case of a plane curve to the case of a hypersurface in a linear space. Second, assuming a certain Lefschetz condition, we give a connection to extremal behavior in Macaulay's theorem. We apply these results to show that $(1,19,17,19,1)$ is not a Gorenstein sequence, and as a result we classify the sequences of the form $(1,a,a-2,a,1)$ th...

  19. Sequences in language and text

    CERN Document Server

    Mikros, George K

    2015-01-01

    The aim of this volume is to present the diverse but highly interesting area of the quantitative analysis of the sequence of various linguistic structures. The collected articles present a wide spectrum of quantitative analyses of linguistic syntagmatic structures and explore novel sequential linguistic entities. This volume will be interesting to all researchers studying linguistics using quantitative methods.

  20. Probabilistic studies of accident sequences

    International Nuclear Information System (INIS)

    Villemeur, A.; Berger, J.P.

    1986-01-01

    For several years, Electricite de France has carried out probabilistic assessment of accident sequences for nuclear power plants. In the framework of this program many methods were developed. As the interest in these studies was increasing and as adapted methods were developed, Electricite de France has undertaken a probabilistic safety assessment of a nuclear power plant [fr

  1. MRI sequences and their parameters

    International Nuclear Information System (INIS)

    Teissier, J.M.

    1993-01-01

    Listing basic sequences and their present variants makes a synthetic classification of the various acquisition modes possible. The knowledge of the advantages of each of them, as well as of their disadvantages and restraints, seems to be an essential prerequisite to an optimal utilization of each magnetic resonance imaging system. (author)

  2. Degree sequence in message transfer

    Science.gov (United States)

    Yamuna, M.

    2017-11-01

    Message encryption is always an issue in current communication scenario. Methods are being devised using various domains. Graphs satisfy numerous unique properties which can be used for message transfer. In this paper, I propose a message encryption method based on degree sequence of graphs.

  3. Fractals in DNA sequence analysis

    Institute of Scientific and Technical Information of China (English)

    Yu Zu-Guo(喻祖国); Vo Anh; Gong Zhi-Min(龚志民); Long Shun-Chao(龙顺潮)

    2002-01-01

    Fractal methods have been successfully used to study many problems in physics, mathematics, engineering, finance,and even in biology. There has been an increasing interest in unravelling the mysteries of DNA; for example, how can we distinguish coding and noncoding sequences, and the problems of classification and evolution relationship of organisms are key problems in bioinformatics. Although much research has been carried out by taking into consideration the long-range correlations in DNA sequences, and the global fractal dimension has been used in these works by other people, the models and methods are somewhat rough and the results are not satisfactory. In recent years, our group has introduced a time series model (statistical point of view) and a visual representation (geometrical point of view)to DNA sequence analysis. We have also used fractal dimension, correlation dimension, the Hurst exponent and the dimension spectrum (multifractal analysis) to discuss problems in this field. In this paper, we introduce these fractal models and methods and the results of DNA sequence analysis.

  4. On primes in Lucas sequences

    Czech Academy of Sciences Publication Activity Database

    Křížek, Michal; Somer, L.

    2015-01-01

    Roč. 53, č. 1 (2015), s. 2-23 ISSN 0015-0517 R&D Projects: GA ČR GA14-02067S Institutional support: RVO:67985840 Keywords : Lucas sequence * primes Subject RIV: BA - General Mathematics http://www.fq.math.ca/Abstracts/53-1/somer.pdf

  5. Is sequence awareness mandatory for perceptual sequence learning: An assessment using a pure perceptual sequence learning design.

    Science.gov (United States)

    Deroost, Natacha; Coomans, Daphné

    2018-02-01

    We examined the role of sequence awareness in a pure perceptual sequence learning design. Participants had to react to the target's colour that changed according to a perceptual sequence. By varying the mapping of the target's colour onto the response keys, motor responses changed randomly. The effect of sequence awareness on perceptual sequence learning was determined by manipulating the learning instructions (explicit versus implicit) and assessing the amount of sequence awareness after the experiment. In the explicit instruction condition (n = 15), participants were instructed to intentionally search for the colour sequence, whereas in the implicit instruction condition (n = 15), they were left uninformed about the sequenced nature of the task. Sequence awareness after the sequence learning task was tested by means of a questionnaire and the process-dissociation-procedure. The results showed that the instruction manipulation had no effect on the amount of perceptual sequence learning. Based on their report to have actively applied their sequence knowledge during the experiment, participants were subsequently regrouped in a sequence strategy group (n = 14, of which 4 participants from the implicit instruction condition and 10 participants from the explicit instruction condition) and a no-sequence strategy group (n = 16, of which 11 participants from the implicit instruction condition and 5 participants from the explicit instruction condition). Only participants of the sequence strategy group showed reliable perceptual sequence learning and sequence awareness. These results indicate that perceptual sequence learning depends upon the continuous employment of strategic cognitive control processes on sequence knowledge. Sequence awareness is suggested to be a necessary but not sufficient condition for perceptual learning to take place. Copyright © 2018 Elsevier B.V. All rights reserved.

  6. STAR FORMATION IN 30 DORADUS

    International Nuclear Information System (INIS)

    De Marchi, Guido; Spezzi, Loredana; Sirianni, Marco; Andersen, Morten; Paresce, Francesco; Panagia, Nino; Mutchler, Max; Whitmore, Bradley C.; Bond, Howard; Beccari, Giacomo; Balick, Bruce; Dopita, Michael A.; Frogel, Jay A.; Calzetti, Daniela; Marcella Carollo, C.; Disney, Michael J.; Hall, Donald N. B.; Holtzman, Jon A.; Kimble, Randy A.; McCarthy, Patrick J.

    2011-01-01

    Using observations obtained with the Wide-Field Camera 3 on board the Hubble Space Telescope, we have studied the properties of the stellar populations in the central regions of 30 Dor in the Large Magellanic Cloud. The observations clearly reveal the presence of considerable differential extinction across the field. We characterize and quantify this effect using young massive main-sequence stars to derive a statistical reddening correction for most objects in the field. We then search for pre-main-sequence (PMS) stars by looking for objects with a strong (>4σ) Hα excess emission and find about 1150 of them over the entire field. Comparison of their location in the Hertzsprung-Russell diagram with theoretical PMS evolutionary tracks for the appropriate metallicity reveals that about one-third of these objects are younger than ∼4 Myr, compatible with the age of the massive stars in the central ionizing cluster R 136, whereas the rest have ages up to ∼30 Myr, with a median age of ∼12 Myr. This indicates that star formation has proceeded over an extended period of time, although we cannot discriminate between an extended episode and a series of short and frequent bursts that are not resolved in time. While the younger PMS population preferentially occupies the central regions of the cluster, older PMS objects are more uniformly distributed across the field and are remarkably few at the very center of the cluster. We attribute this latter effect to photo-evaporation of the older circumstellar disks caused by the massive ionizing members of R 136.

  7. Teaching Task Sequencing via Verbal Mediation.

    Science.gov (United States)

    Rusch, Frank R.; And Others

    1987-01-01

    Verbal sequence training was used to teach a moderately mentally retarded woman to sequence job-related tasks. Learning to say the tasks in the proper sequence resulted in the employee performing her tasks in that sequence, and the employee was capable of mediating her own work behavior when scheduled changes occurred. (Author/JDD)

  8. Repdigits in k-Lucas sequences

    Indian Academy of Sciences (India)

    57(2) 2000 243-254) proved that 11 is the largest number with only one distinct digit (the so-called repdigit) in the sequence ( L n ( 2 ) ) n . In this paper, we address a similar problem in the family of -Lucas sequences. We also show that the -Lucas sequences have similar properties to those of -Fibonacci sequences ...

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

    Energy Technology Data Exchange (ETDEWEB)

    Cignoni, M. [Department of Physics—University of Pisa, Largo Pontecorvo, 3 Pisa, I-56127 (Italy); Sabbi, E.; Marel, R. P. van der; Aloisi, A.; Panagia, N. [Space Telescope Science Institute, 3700 San Martin Drive, Baltimore, MD, 21218 (United States); Lennon, D. J. [European Space Astronomy Centre, Apdo. de Correo 78, E-28691 Villanueva de la Canada, Madrid (Spain); Tosi, M. [INAF-Osservatorio Astronomico di Bologna, Via Ranzani 1, I-40127 Bologna (Italy); Grebel, E. K. [Astronomisches Rechen-Institut, Zentrum für Astronomie der Universität Heidelberg, Mönchhofstr. 12-14, D-69120 Heidelberg (Germany); Gallagher, J. S. III [Department of Astronomy, University of Wisconsin-Madison, WI 53706 (United States); Marchi, G. de [European Space Research and Technology Centre, Keplerlaan 1, NL-2200 AG Noordwijk (Netherlands); Gouliermis, D. A. [Zentrum für Astronomie der Universität Heidelberg, Institut für Theoretische Astrophysik, Albert-Ueberle-Str. 2, D-69120 Heidelberg (Germany); Larsen, S. [Department of Astrophysics, Radboud University, P.O. Box 9010, NL-6500 GL Nijmegen (Netherlands); Smith, L. J., E-mail: michele.cignoni@unipi.it [European Space Agency and Space Telescope Science Institute, 3700 San Martin Drive, Baltimore, MD 21218 (United States)

    2016-12-20

    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 {sub ⊙} and average reddening E ( B − V ) ≈ 0.22–0.24 mag, with a differential reddening δE ( B − V ) ≈ 0.04 mag.

  10. Nonparametric Inference for Periodic Sequences

    KAUST Repository

    Sun, Ying

    2012-02-01

    This article proposes a nonparametric method for estimating the period and values of a periodic sequence when the data are evenly spaced in time. The period is estimated by a "leave-out-one-cycle" version of cross-validation (CV) and complements the periodogram, a widely used tool for period estimation. The CV method is computationally simple and implicitly penalizes multiples of the smallest period, leading to a "virtually" consistent estimator of integer periods. This estimator is investigated both theoretically and by simulation.We also propose a nonparametric test of the null hypothesis that the data have constantmean against the alternative that the sequence of means is periodic. Finally, our methodology is demonstrated on three well-known time series: the sunspots and lynx trapping data, and the El Niño series of sea surface temperatures. © 2012 American Statistical Association and the American Society for Quality.

  11. Multi-qubit compensation sequences

    International Nuclear Information System (INIS)

    Tomita, Y; Merrill, J T; Brown, K R

    2010-01-01

    The Hamiltonian control of n qubits requires precision control of both the strength and timing of interactions. Compensation pulses relax the precision requirements by reducing unknown but systematic errors. Using composite pulse techniques designed for single qubits, we show that systematic errors for n-qubit systems can be corrected to arbitrary accuracy given either two non-commuting control Hamiltonians with identical systematic errors or one error-free control Hamiltonian. We also examine composite pulses in the context of quantum computers controlled by two-qubit interactions. For quantum computers based on the XY interaction, single-qubit composite pulse sequences naturally correct systematic errors. For quantum computers based on the Heisenberg or exchange interaction, the composite pulse sequences reduce the logical single-qubit gate errors but increase the errors for logical two-qubit gates.

  12. Cassini Mission Sequence Subsystem (MSS)

    Science.gov (United States)

    Alland, Robert

    2011-01-01

    This paper describes my work with the Cassini Mission Sequence Subsystem (MSS) team during the summer of 2011. It gives some background on the motivation for this project and describes the expected benefit to the Cassini program. It then introduces the two tasks that I worked on - an automatic system auditing tool and a series of corrections to the Cassini Sequence Generator (SEQ_GEN) - and the specific objectives these tasks were to accomplish. Next, it details the approach I took to meet these objectives and the results of this approach, followed by a discussion of how the outcome of the project compares with my initial expectations. The paper concludes with a summary of my experience working on this project, lists what the next steps are, and acknowledges the help of my Cassini colleagues.

  13. Sequence complexity and work extraction

    International Nuclear Information System (INIS)

    Merhav, Neri

    2015-01-01

    We consider a simplified version of a solvable model by Mandal and Jarzynski, which constructively demonstrates the interplay between work extraction and the increase of the Shannon entropy of an information reservoir which is in contact with a physical system. We extend Mandal and Jarzynski’s main findings in several directions: first, we allow sequences of correlated bits rather than just independent bits. Secondly, at least for the case of binary information, we show that, in fact, the Shannon entropy is only one measure of complexity of the information that must increase in order for work to be extracted. The extracted work can also be upper bounded in terms of the increase in other quantities that measure complexity, like the predictability of future bits from past ones. Third, we provide an extension to the case of non-binary information (i.e. a larger alphabet), and finally, we extend the scope to the case where the incoming bits (before the interaction) form an individual sequence, rather than a random one. In this case, the entropy before the interaction can be replaced by the Lempel–Ziv (LZ) complexity of the incoming sequence, a fact that gives rise to an entropic meaning of the LZ complexity, not only in information theory, but also in physics. (paper)

  14. Entropic fluctuations in DNA sequences

    Science.gov (United States)

    Thanos, Dimitrios; Li, Wentian; Provata, Astero

    2018-03-01

    The Local Shannon Entropy (LSE) in blocks is used as a complexity measure to study the information fluctuations along DNA sequences. The LSE of a DNA block maps the local base arrangement information to a single numerical value. It is shown that despite this reduction of information, LSE allows to extract meaningful information related to the detection of repetitive sequences in whole chromosomes and is useful in finding evolutionary differences between organisms. More specifically, large regions of tandem repeats, such as centromeres, can be detected based on their low LSE fluctuations along the chromosome. Furthermore, an empirical investigation of the appropriate block sizes is provided and the relationship of LSE properties with the structure of the underlying repetitive units is revealed by using both computational and mathematical methods. Sequence similarity between the genomic DNA of closely related species also leads to similar LSE values at the orthologous regions. As an application, the LSE covariance function is used to measure the evolutionary distance between several primate genomes.

  15. Method and apparatus for biological sequence comparison

    Science.gov (United States)

    Marr, T.G.; Chang, W.I.

    1997-12-23

    A method and apparatus are disclosed for comparing biological sequences from a known source of sequences, with a subject (query) sequence. The apparatus takes as input a set of target similarity levels (such as evolutionary distances in units of PAM), and finds all fragments of known sequences that are similar to the subject sequence at each target similarity level, and are long enough to be statistically significant. The invention device filters out fragments from the known sequences that are too short, or have a lower average similarity to the subject sequence than is required by each target similarity level. The subject sequence is then compared only to the remaining known sequences to find the best matches. The filtering member divides the subject sequence into overlapping blocks, each block being sufficiently large to contain a minimum-length alignment from a known sequence. For each block, the filter member compares the block with every possible short fragment in the known sequences and determines a best match for each comparison. The determined set of short fragment best matches for the block provide an upper threshold on alignment values. Regions of a certain length from the known sequences that have a mean alignment value upper threshold greater than a target unit score are concatenated to form a union. The current block is compared to the union and provides an indication of best local alignment with the subject sequence. 5 figs.

  16. Memory and learning with rapid audiovisual sequences

    Science.gov (United States)

    Keller, Arielle S.; Sekuler, Robert

    2015-01-01

    We examined short-term memory for sequences of visual stimuli embedded in varying multisensory contexts. In two experiments, subjects judged the structure of the visual sequences while disregarding concurrent, but task-irrelevant auditory sequences. Stimuli were eight-item sequences in which varying luminances and frequencies were presented concurrently and rapidly (at 8 Hz). Subjects judged whether the final four items in a visual sequence identically replicated the first four items. Luminances and frequencies in each sequence were either perceptually correlated (Congruent) or were unrelated to one another (Incongruent). Experiment 1 showed that, despite encouragement to ignore the auditory stream, subjects' categorization of visual sequences was strongly influenced by the accompanying auditory sequences. Moreover, this influence tracked the similarity between a stimulus's separate audio and visual sequences, demonstrating that task-irrelevant auditory sequences underwent a considerable degree of processing. Using a variant of Hebb's repetition design, Experiment 2 compared musically trained subjects and subjects who had little or no musical training on the same task as used in Experiment 1. Test sequences included some that intermittently and randomly recurred, which produced better performance than sequences that were generated anew for each trial. The auditory component of a recurring audiovisual sequence influenced musically trained subjects more than it did other subjects. This result demonstrates that stimulus-selective, task-irrelevant learning of sequences can occur even when such learning is an incidental by-product of the task being performed. PMID:26575193

  17. Memory and learning with rapid audiovisual sequences.

    Science.gov (United States)

    Keller, Arielle S; Sekuler, Robert

    2015-01-01

    We examined short-term memory for sequences of visual stimuli embedded in varying multisensory contexts. In two experiments, subjects judged the structure of the visual sequences while disregarding concurrent, but task-irrelevant auditory sequences. Stimuli were eight-item sequences in which varying luminances and frequencies were presented concurrently and rapidly (at 8 Hz). Subjects judged whether the final four items in a visual sequence identically replicated the first four items. Luminances and frequencies in each sequence were either perceptually correlated (Congruent) or were unrelated to one another (Incongruent). Experiment 1 showed that, despite encouragement to ignore the auditory stream, subjects' categorization of visual sequences was strongly influenced by the accompanying auditory sequences. Moreover, this influence tracked the similarity between a stimulus's separate audio and visual sequences, demonstrating that task-irrelevant auditory sequences underwent a considerable degree of processing. Using a variant of Hebb's repetition design, Experiment 2 compared musically trained subjects and subjects who had little or no musical training on the same task as used in Experiment 1. Test sequences included some that intermittently and randomly recurred, which produced better performance than sequences that were generated anew for each trial. The auditory component of a recurring audiovisual sequence influenced musically trained subjects more than it did other subjects. This result demonstrates that stimulus-selective, task-irrelevant learning of sequences can occur even when such learning is an incidental by-product of the task being performed.

  18. Multineuronal Spike Sequences Repeat with Millisecond Precision

    Directory of Open Access Journals (Sweden)

    Koki eMatsumoto

    2013-06-01

    Full Text Available Cortical microcircuits are nonrandomly wired by neurons. As a natural consequence, spikes emitted by microcircuits are also nonrandomly patterned in time and space. One of the prominent spike organizations is a repetition of fixed patterns of spike series across multiple neurons. However, several questions remain unsolved, including how precisely spike sequences repeat, how the sequences are spatially organized, how many neurons participate in sequences, and how different sequences are functionally linked. To address these questions, we monitored spontaneous spikes of hippocampal CA3 neurons ex vivo using a high-speed functional multineuron calcium imaging technique that allowed us to monitor spikes with millisecond resolution and to record the location of spiking and nonspiking neurons. Multineuronal spike sequences were overrepresented in spontaneous activity compared to the statistical chance level. Approximately 75% of neurons participated in at least one sequence during our observation period. The participants were sparsely dispersed and did not show specific spatial organization. The number of sequences relative to the chance level decreased when larger time frames were used to detect sequences. Thus, sequences were precise at the millisecond level. Sequences often shared common spikes with other sequences; parts of sequences were subsequently relayed by following sequences, generating complex chains of multiple sequences.

  19. Static multiplicities in heterogeneous azeotropic distillation sequences

    DEFF Research Database (Denmark)

    Esbjerg, Klavs; Andersen, Torben Ravn; Jørgensen, Sten Bay

    1998-01-01

    In this paper the results of a bifurcation analysis on heterogeneous azeotropic distillation sequences are given. Two sequences suitable for ethanol dehydration are compared: The 'direct' and the 'indirect' sequence. It is shown, that the two sequences, despite their similarities, exhibit very...... different static behavior. The method of Petlyuk and Avet'yan (1971), Bekiaris et al. (1993), which assumes infinite reflux and infinite number of stages, is extended to and applied on heterogeneous azeotropic distillation sequences. The predictions are substantiated through simulations. The static sequence...

  20. Blind sequence-length estimation of low-SNR cyclostationary sequences

    CSIR Research Space (South Africa)

    Vlok, JD

    2014-06-01

    Full Text Available Several existing direct-sequence spread spectrum (DSSS) detection and estimation algorithms assume prior knowledge of the symbol period or sequence length, although very few sequence-length estimation techniques are available in the literature...

  1. The Secrets of the Nearest Starburst Cluster. I. Very Large Telescope/ISAAC Photometry of NGC 3603

    Science.gov (United States)

    Stolte, Andrea; Brandner, Wolfgang; Brandl, Bernhard; Zinnecker, Hans; Grebel, Eva K.

    2004-08-01

    VLT/ISAAC JHKL photometry with subarcsecond resolution of the dense, massive starburst cluster NGC 3603 YC forming the core of the NGC 3603 giant molecular cloud is analyzed to reveal characteristics of the stellar population in unprecedented detail. The color-magnitude plane features a strong pre-main-sequence/main-sequence (PMS/MS) transition region, including the PMS/MS transition point, and reveals a secondary sequence for the first time in a nearby young starburst cluster. Arguments for a possible binary nature of this sequence are given. The resolved PMS/MS transition region allows isochrone fitting below the hydrogen-burning turn-on in NGC 3603 YC, yielding an independent estimate of global cluster parameters. A distance modulus of 13.9 mag, equivalent to d=6.0+/-0.3 kpc, is derived, as well as a line-of-sight extinction of AV=4.5+/-0.6 toward PMS stars in the cluster center. The interpretation of a binary candidate sequence suggests a single age of 1 Myr for NGC 3603 YC, providing evidence for a single burst of star formation without the need to employ an age spread in the PMS population, as argued for in earlier studies. Disk fractions are derived from L-band excesses, indicating a radial increase in the disk frequency from 20% to 40% from the core to the cluster outskirts. The low disk fraction in the cluster core, as compared to the 42% L-band excess fraction found for massive stars in the Trapezium cluster of a comparably young age, indicates strong photoevaporation in the cluster center. The estimated binary fraction of 30%, as well as the low disk fraction, suggest strong impacts on low-mass star formation due to stellar interactions in the dense starburst. The significant differences between NGC 3603 YC and less dense and massive young star clusters in the Milky Way reveal the importance of using local starbursts as templates for massive extragalactic star formation. Based on observations obtained at the ESO VLT on Paranal, Chile, under programs 63.I

  2. Infinite matrices and sequence spaces

    CERN Document Server

    Cooke, Richard G

    2014-01-01

    This clear and correct summation of basic results from a specialized field focuses on the behavior of infinite matrices in general, rather than on properties of special matrices. Three introductory chapters guide students to the manipulation of infinite matrices, covering definitions and preliminary ideas, reciprocals of infinite matrices, and linear equations involving infinite matrices.From the fourth chapter onward, the author treats the application of infinite matrices to the summability of divergent sequences and series from various points of view. Topics include consistency, mutual consi

  3. Parallel motif extraction from very long sequences

    KAUST Repository

    Sahli, Majed; Mansour, Essam; Kalnis, Panos

    2013-01-01

    Motifs are frequent patterns used to identify biological functionality in genomic sequences, periodicity in time series, or user trends in web logs. In contrast to a lot of existing work that focuses on collections of many short sequences, modern

  4. Computational analysis of sequence selection mechanisms.

    Science.gov (United States)

    Meyerguz, Leonid; Grasso, Catherine; Kleinberg, Jon; Elber, Ron

    2004-04-01

    Mechanisms leading to gene variations are responsible for the diversity of species and are important components of the theory of evolution. One constraint on gene evolution is that of protein foldability; the three-dimensional shapes of proteins must be thermodynamically stable. We explore the impact of this constraint and calculate properties of foldable sequences using 3660 structures from the Protein Data Bank. We seek a selection function that receives sequences as input, and outputs survival probability based on sequence fitness to structure. We compute the number of sequences that match a particular protein structure with energy lower than the native sequence, the density of the number of sequences, the entropy, and the "selection" temperature. The mechanism of structure selection for sequences longer than 200 amino acids is approximately universal. For shorter sequences, it is not. We speculate on concrete evolutionary mechanisms that show this behavior.

  5. The recurrence sequences via Sylvester matrices

    Science.gov (United States)

    Karaduman, Erdal; Deveci, Ömür

    2017-07-01

    In this work, we define the Pell-Jacobsthal-Slyvester sequence and the Jacobsthal-Pell-Slyvester sequence by using the Slyvester matrices which are obtained from the characteristic polynomials of the Pell and Jacobsthal sequences and then, we study the sequences defined modulo m. Also, we obtain the cyclic groups and the semigroups from the generating matrices of these sequences when read modulo m and then, we derive the relationships among the orders of the cyclic groups and the periods of the sequences. Furthermore, we redefine Pell-Jacobsthal-Slyvester sequence and the Jacobsthal-Pell-Slyvester sequence by means of the elements of the groups and then, we examine them in the finite groups.

  6. ON SOME RECURRENCE TYPE SMARANDACHE SEQUENCES

    OpenAIRE

    MAJUMDAR, A.A.K.; GUNARTO, H.

    2000-01-01

    In this paper, we study some properties of ten recurrence type Smarandache sequences, namely, the Smarandache odd, even, prime product, square product, higher-power product, permutation, consecutive, reverse, symmetric, and pierced chain sequences.

  7. "First generation" automated DNA sequencing technology.

    Science.gov (United States)

    Slatko, Barton E; Kieleczawa, Jan; Ju, Jingyue; Gardner, Andrew F; Hendrickson, Cynthia L; Ausubel, Frederick M

    2011-10-01

    Beginning in the 1980s, automation of DNA sequencing has greatly increased throughput, reduced costs, and enabled large projects to be completed more easily. The development of automation technology paralleled the development of other aspects of DNA sequencing: better enzymes and chemistry, separation and imaging technology, sequencing protocols, robotics, and computational advancements (including base-calling algorithms with quality scores, database developments, and sequence analysis programs). Despite the emergence of high-throughput sequencing platforms, automated Sanger sequencing technology remains useful for many applications. This unit provides background and a description of the "First-Generation" automated DNA sequencing technology. It also includes protocols for using the current Applied Biosystems (ABI) automated DNA sequencing machines. © 2011 by John Wiley & Sons, Inc.

  8. Comparative analysis of sequences from PT 2013

    DEFF Research Database (Denmark)

    Mikkelsen, Susie Sommer

    Sheatfish and not EHNV. Generally, mistakes occurred at the ends of the sequences. This can be due to several factors. One is that the sequence has not been trimmed of the sequence primer sites. Another is the lack of quality control of the chromatogram. Finally, sequencing in just one direction can result...... diseases in Europe. As part of the EURL proficiency test for fish diseases it is required to sequence any RANA virus isolates found in any of the samples. It is also highly recommended to sequence the ISA virus to determine whether it be HPRΔ or HPR0. Furthermore, it is recommended that any VHSV and IHNV...... isolates be genotyped. As part of the evaluation of the proficiency results it was decided this year to look into the quality and similarity of the sequence results for selected viruses. Ampoule III in the proficiency test 2013 contained an EHNV isolate. The EURL received 43 sequences from 41 laboratories...

  9. Perfect sequences over the real quaternions

    OpenAIRE

    Kuznetsov, Oleg

    2017-01-01

    In this Thesis, perfect sequences over the real quaternions are first considered. Definitions for the right and left periodic autocorrelation functions are given, and right and left perfect sequences introduced. It is shown that the right (left) perfection of any sequence implies the left (right) perfection, so concepts of right and left perfect sequences over the real quaternions are equivalent. Unitary transformations of the quaternion space ℍ are then considered. Using the equivalence of t...

  10. Information decomposition method to analyze symbolical sequences

    International Nuclear Information System (INIS)

    Korotkov, E.V.; Korotkova, M.A.; Kudryashov, N.A.

    2003-01-01

    The information decomposition (ID) method to analyze symbolical sequences is presented. This method allows us to reveal a latent periodicity of any symbolical sequence. The ID method is shown to have advantages in comparison with application of the Fourier transformation, the wavelet transform and the dynamic programming method to look for latent periodicity. Examples of the latent periods for poetic texts, DNA sequences and amino acids are presented. Possible origin of a latent periodicity for different symbolical sequences is discussed

  11. Parallel sequencing lives, or what makes large sequencing projects successful.

    Science.gov (United States)

    Quilez, Javier; Vidal, Enrique; Dily, François Le; Serra, François; Cuartero, Yasmina; Stadhouders, Ralph; Graf, Thomas; Marti-Renom, Marc A; Beato, Miguel; Filion, Guillaume

    2017-11-01

    T47D_rep2 and b1913e6c1_51720e9cf were 2 Hi-C samples. They were born and processed at the same time, yet their fates were very different. The life of b1913e6c1_51720e9cf was simple and fruitful, while that of T47D_rep2 was full of accidents and sorrow. At the heart of these differences lies the fact that b1913e6c1_51720e9cf was born under a lab culture of Documentation, Automation, Traceability, and Autonomy and compliance with the FAIR Principles. Their lives are a lesson for those who wish to embark on the journey of managing high-throughput sequencing data. © The Author 2017. Published by Oxford University Press.

  12. MatrixPlot: visualizing sequence constraints

    DEFF Research Database (Denmark)

    Gorodkin, Jan; Stærfeldt, Hans Henrik; Lund, Ole

    1999-01-01

    MatrixPlot: visualizing sequence constraints. Sub-title Abstract Summary : MatrixPlot is a program for making high-quality matrix plots, such as mutual information plots of sequence alignments and distance matrices of sequences with known three-dimensional coordinates. The user can add information...

  13. Comparative genomics beyond sequence-based alignments

    DEFF Research Database (Denmark)

    Þórarinsson, Elfar; Yao, Zizhen; Wiklund, Eric D.

    2008-01-01

    Recent computational scans for non-coding RNAs (ncRNAs) in multiple organisms have relied on existing multiple sequence alignments. However, as sequence similarity drops, a key signal of RNA structure--frequent compensating base changes--is increasingly likely to cause sequence-based alignment me...

  14. DNA sequence modeling based on context trees

    NARCIS (Netherlands)

    Kusters, C.J.; Ignatenko, T.; Roland, J.; Horlin, F.

    2015-01-01

    Genomic sequences contain instructions for protein and cell production. Therefore understanding and identification of biologically and functionally meaningful patterns in DNA sequences is of paramount importance. Modeling of DNA sequences in its turn can help to better understand and identify such

  15. Compact flow diagrams for state sequences

    NARCIS (Netherlands)

    Buchin, K.A.; Buchin, M.E.; Gudmundsson, J.; Horton, M.J.; Sijben, S.

    2016-01-01

    We introduce the concept of compactly representing a large number of state sequences, e.g., sequences of activities, as a flow diagram. We argue that the flow diagram representation gives an intuitive summary that allows the user to detect patterns among large sets of state sequences. Simplified,

  16. Blazar Sequence in Fermi Era Liang Chen

    Indian Academy of Sciences (India)

    Abstract. In this paper, we review the latest research results on the topic of blazar sequence. It seems that the blazar sequence is phenomenally ruled out, while the theoretical blazar sequence still holds. We point out that black hole mass is a dominated parameter accounting for high-power- high-synchrotron-peaked and ...

  17. Tidying up international nucleotide sequence databases: ecological, geographical and sequence quality annotation of its sequences of mycorrhizal fungi.

    Science.gov (United States)

    Tedersoo, Leho; Abarenkov, Kessy; Nilsson, R Henrik; Schüssler, Arthur; Grelet, Gwen-Aëlle; Kohout, Petr; Oja, Jane; Bonito, Gregory M; Veldre, Vilmar; Jairus, Teele; Ryberg, Martin; Larsson, Karl-Henrik; Kõljalg, Urmas

    2011-01-01

    Sequence analysis of the ribosomal RNA operon, particularly the internal transcribed spacer (ITS) region, provides a powerful tool for identification of mycorrhizal fungi. The sequence data deposited in the International Nucleotide Sequence Databases (INSD) are, however, unfiltered for quality and are often poorly annotated with metadata. To detect chimeric and low-quality sequences and assign the ectomycorrhizal fungi to phylogenetic lineages, fungal ITS sequences were downloaded from INSD, aligned within family-level groups, and examined through phylogenetic analyses and BLAST searches. By combining the fungal sequence database UNITE and the annotation and search tool PlutoF, we also added metadata from the literature to these accessions. Altogether 35,632 sequences belonged to mycorrhizal fungi or originated from ericoid and orchid mycorrhizal roots. Of these sequences, 677 were considered chimeric and 2,174 of low read quality. Information detailing country of collection, geographical coordinates, interacting taxon and isolation source were supplemented to cover 78.0%, 33.0%, 41.7% and 96.4% of the sequences, respectively. These annotated sequences are publicly available via UNITE (http://unite.ut.ee/) for downstream biogeographic, ecological and taxonomic analyses. In European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena/), the annotated sequences have a special link-out to UNITE. We intend to expand the data annotation to additional genes and all taxonomic groups and functional guilds of fungi.

  18. Permutation Entropy for Random Binary Sequences

    Directory of Open Access Journals (Sweden)

    Lingfeng Liu

    2015-12-01

    Full Text Available In this paper, we generalize the permutation entropy (PE measure to binary sequences, which is based on Shannon’s entropy, and theoretically analyze this measure for random binary sequences. We deduce the theoretical value of PE for random binary sequences, which can be used to measure the randomness of binary sequences. We also reveal the relationship between this PE measure with other randomness measures, such as Shannon’s entropy and Lempel–Ziv complexity. The results show that PE is consistent with these two measures. Furthermore, we use PE as one of the randomness measures to evaluate the randomness of chaotic binary sequences.

  19. The 2016 Kumamoto earthquake sequence.

    Science.gov (United States)

    Kato, Aitaro; Nakamura, Kouji; Hiyama, Yohei

    2016-01-01

    Beginning in April 2016, a series of shallow, moderate to large earthquakes with associated strong aftershocks struck the Kumamoto area of Kyushu, SW Japan. An M j 7.3 mainshock occurred on 16 April 2016, close to the epicenter of an M j 6.5 foreshock that occurred about 28 hours earlier. The intense seismicity released the accumulated elastic energy by right-lateral strike slip, mainly along two known, active faults. The mainshock rupture propagated along multiple fault segments with different geometries. The faulting style is reasonably consistent with regional deformation observed on geologic timescales and with the stress field estimated from seismic observations. One striking feature of this sequence is intense seismic activity, including a dynamically triggered earthquake in the Oita region. Following the mainshock rupture, postseismic deformation has been observed, as well as expansion of the seismicity front toward the southwest and northwest.

  20. Data selector group sequencer interface

    International Nuclear Information System (INIS)

    Zizka, G.; Turko, B.

    1984-01-01

    A CAMAC-based module for high rate data selection and transfer to Tracor Northern TN-1700 multichannel analysis system is described. The module can select any group of 4096 consecutive addresses of events, in the range of 24 bits. This module solves the problem of connecting a number of time digitizing systems to the memory of a multichannel analyzer. Continuous processing rate up to 200,000 events per second along with the live display make the testing of the above systems very efficient and relatively inexpensive. The module also can be programmed for storing the preset group of addresses into more than one section of the memory. The events are analyzed in each section of the memory during the preset time. Multiple spectra can thus be taken automatically in a sequence

  1. A main sequence for quasars

    Science.gov (United States)

    Marziani, Paola; Dultzin, Deborah; Sulentic, Jack W.; Del Olmo, Ascensión; Negrete, C. A.; Martínez-Aldama, Mary L.; D'Onofrio, Mauro; Bon, Edi; Bon, Natasa; Stirpe, Giovanna M.

    2018-03-01

    The last 25 years saw a major step forward in the analysis of optical and UV spectroscopic data of large quasar samples. Multivariate statistical approaches have led to the definition of systematic trends in observational properties that are the basis of physical and dynamical modeling of quasar structure. We discuss the empirical correlates of the so-called “main sequence” associated with the quasar Eigenvector 1, its governing physical parameters and several implications on our view of the quasar structure, as well as some luminosity effects associated with the virialized component of the line emitting regions. We also briefly discuss quasars in a segment of the main sequence that includes the strongest FeII emitters. These sources show a small dispersion around a well-defined Eddington ratio value, a property which makes them potential Eddington standard candles.

  2. The 2016 Kumamoto earthquake sequence

    Science.gov (United States)

    KATO, Aitaro; NAKAMURA, Kouji; HIYAMA, Yohei

    2016-01-01

    Beginning in April 2016, a series of shallow, moderate to large earthquakes with associated strong aftershocks struck the Kumamoto area of Kyushu, SW Japan. An Mj 7.3 mainshock occurred on 16 April 2016, close to the epicenter of an Mj 6.5 foreshock that occurred about 28 hours earlier. The intense seismicity released the accumulated elastic energy by right-lateral strike slip, mainly along two known, active faults. The mainshock rupture propagated along multiple fault segments with different geometries. The faulting style is reasonably consistent with regional deformation observed on geologic timescales and with the stress field estimated from seismic observations. One striking feature of this sequence is intense seismic activity, including a dynamically triggered earthquake in the Oita region. Following the mainshock rupture, postseismic deformation has been observed, as well as expansion of the seismicity front toward the southwest and northwest. PMID:27725474

  3. A Main Sequence for Quasars

    Directory of Open Access Journals (Sweden)

    Paola Marziani

    2018-03-01

    Full Text Available The last 25 years saw a major step forward in the analysis of optical and UV spectroscopic data of large quasar samples. Multivariate statistical approaches have led to the definition of systematic trends in observational properties that are the basis of physical and dynamical modeling of quasar structure. We discuss the empirical correlates of the so-called “main sequence” associated with the quasar Eigenvector 1, its governing physical parameters and several implications on our view of the quasar structure, as well as some luminosity effects associated with the virialized component of the line emitting regions. We also briefly discuss quasars in a segment of the main sequence that includes the strongest FeII emitters. These sources show a small dispersion around a well-defined Eddington ratio value, a property which makes them potential Eddington standard candles.

  4. RANDNA: a random DNA sequence generator.

    Science.gov (United States)

    Piva, Francesco; Principato, Giovanni

    2006-01-01

    Monte Carlo simulations are useful to verify the significance of data. Genomic regularities, such as the nucleotide correlations or the not uniform distribution of the motifs throughout genomic or mature mRNA sequences, exist and their significance can be checked by means of the Monte Carlo test. The test needs good quality random sequences in order to work, moreover they should have the same nucleotide distribution as the sequences in which the regularities have been found. Random DNA sequences are also useful to estimate the background score of an alignment, that is a threshold below which the resulting score is merely due to chance. We have developed RANDNA, a free software which allows to produce random DNA or RNA sequences setting both their length and the percentage of nucleotide composition. Sequences having the same nucleotide distribution of exonic, intronic or intergenic sequences can be generated. Its graphic interface makes it possible to easily set the parameters that characterize the sequences being produced and saved in a text format file. The pseudo-random number generator function of Borland Delphi 6 is used, since it guarantees a good randomness, a long cycle length and a high speed. We have checked the quality of sequences generated by the software, by means of well-known tests, both by themselves and versus genuine random sequences. We show the good quality of the generated sequences. The software, complete with examples and documentation, is freely available to users from: http://www.introni.it/en/software.

  5. Locomotor sequence learning in visually guided walking

    DEFF Research Database (Denmark)

    Choi, Julia T; Jensen, Peter; Nielsen, Jens Bo

    2016-01-01

    walking. In addition, we determined how age (i.e., healthy young adults vs. children) and biomechanical factors (i.e., walking speed) affected the rate and magnitude of locomotor sequence learning. The results showed that healthy young adults (age 24 ± 5 years, N = 20) could learn a specific sequence...... of step lengths over 300 training steps. Younger children (age 6-10 years, N = 8) have lower baseline performance, but their magnitude and rate of sequence learning was the same compared to older children (11-16 years, N = 10) and healthy adults. In addition, learning capacity may be more limited...... to modify step length from one trial to the next. Our sequence learning paradigm is derived from the serial reaction-time (SRT) task that has been used in upper limb studies. Both random and ordered sequences of step lengths were used to measure sequence-specific and sequence non-specific learning during...

  6. The RNA world, automatic sequences and oncogenetics

    Energy Technology Data Exchange (ETDEWEB)

    Tahir Shah, K

    1993-04-01

    We construct a model of the RNA world in terms of naturally evolving nucleotide sequences assuming only Crick-Watson base pairing and self-cleaving/splicing capability. These sequences have the following properties. (1) They are recognizable by an automation (or automata). That is, to each k-sequence, there exist a k-automation which accepts, recognizes or generates the k-sequence. These are known as automatic sequences. Fibonacci and Morse-Thue sequences are the most natural outcome of pre-biotic chemical conditions. (2) Infinite (resp. large) sequences are self-similar (resp. nearly self-similar) under certain rewrite rules and consequently give rise to fractal (resp.fractal-like) structures. Computationally, such sequences can also be generated by their corresponding deterministic parallel re-write system, known as a DOL system. The self-similar sequences are fixed points of their respective rewrite rules. Some of these automatic sequences have the capability that they can read or ``accept`` other sequences while others can detect errors and trigger error-correcting mechanisms. They can be enlarged and have block and/or palindrome structure. Linear recurring sequences such as Fibonacci sequence are simply Feed-back Shift Registers, a well know model of information processing machines. We show that a mutation of any rewrite rule can cause a combinatorial explosion of error and relates this to oncogenetical behavior. On the other hand, a mutation of sequences that are not rewrite rules, leads to normal evolutionary change. Known experimental results support our hypothesis. (author). Refs.

  7. The RNA world, automatic sequences and oncogenetics

    International Nuclear Information System (INIS)

    Tahir Shah, K.

    1993-04-01

    We construct a model of the RNA world in terms of naturally evolving nucleotide sequences assuming only Crick-Watson base pairing and self-cleaving/splicing capability. These sequences have the following properties. 1) They are recognizable by an automation (or automata). That is, to each k-sequence, there exist a k-automation which accepts, recognizes or generates the k-sequence. These are known as automatic sequences. Fibonacci and Morse-Thue sequences are the most natural outcome of pre-biotic chemical conditions. 2) Infinite (resp. large) sequences are self-similar (resp. nearly self-similar) under certain rewrite rules and consequently give rise to fractal (resp.fractal-like) structures. Computationally, such sequences can also be generated by their corresponding deterministic parallel re-write system, known as a DOL system. The self-similar sequences are fixed points of their respective rewrite rules. Some of these automatic sequences have the capability that they can read or 'accept' other sequences while others can detect errors and trigger error-correcting mechanisms. They can be enlarged and have block and/or palindrome structure. Linear recurring sequences such as Fibonacci sequence are simply Feed-back Shift Registers, a well know model of information processing machines. We show that a mutation of any rewrite rule can cause a combinatorial explosion of error and relates this to oncogenetical behavior. On the other hand, a mutation of sequences that are not rewrite rules, leads to normal evolutionary change. Known experimental results support our hypothesis. (author). Refs

  8. Targeted assembly of short sequence reads.

    Directory of Open Access Journals (Sweden)

    René L Warren

    Full Text Available As next-generation sequence (NGS production continues to increase, analysis is becoming a significant bottleneck. However, in situations where information is required only for specific sequence variants, it is not necessary to assemble or align whole genome data sets in their entirety. Rather, NGS data sets can be mined for the presence of sequence variants of interest by localized assembly, which is a faster, easier, and more accurate approach. We present TASR, a streamlined assembler that interrogates very large NGS data sets for the presence of specific variants by only considering reads within the sequence space of input target sequences provided by the user. The NGS data set is searched for reads with an exact match to all possible short words within the target sequence, and these reads are then assembled stringently to generate a consensus of the target and flanking sequence. Typically, variants of a particular locus are provided as different target sequences, and the presence of the variant in the data set being interrogated is revealed by a successful assembly outcome. However, TASR can also be used to find unknown sequences that flank a given target. We demonstrate that TASR has utility in finding or confirming genomic mutations, polymorphisms, fusions and integration events. Targeted assembly is a powerful method for interrogating large data sets for the presence of sequence variants of interest. TASR is a fast, flexible and easy to use tool for targeted assembly.

  9. Pareto optimal pairwise sequence alignment.

    Science.gov (United States)

    DeRonne, Kevin W; Karypis, George

    2013-01-01

    Sequence alignment using evolutionary profiles is a commonly employed tool when investigating a protein. Many profile-profile scoring functions have been developed for use in such alignments, but there has not yet been a comprehensive study of Pareto optimal pairwise alignments for combining multiple such functions. We show that the problem of generating Pareto optimal pairwise alignments has an optimal substructure property, and develop an efficient algorithm for generating Pareto optimal frontiers of pairwise alignments. All possible sets of two, three, and four profile scoring functions are used from a pool of 11 functions and applied to 588 pairs of proteins in the ce_ref data set. The performance of the best objective combinations on ce_ref is also evaluated on an independent set of 913 protein pairs extracted from the BAliBASE RV11 data set. Our dynamic-programming-based heuristic approach produces approximated Pareto optimal frontiers of pairwise alignments that contain comparable alignments to those on the exact frontier, but on average in less than 1/58th the time in the case of four objectives. Our results show that the Pareto frontiers contain alignments whose quality is better than the alignments obtained by single objectives. However, the task of identifying a single high-quality alignment among those in the Pareto frontier remains challenging.

  10. Hierarchically nested river landform sequences

    Science.gov (United States)

    Pasternack, G. B.; Weber, M. D.; Brown, R. A.; Baig, D.

    2017-12-01

    River corridors exhibit landforms nested within landforms repeatedly down spatial scales. In this study we developed, tested, and implemented a new way to create river classifications by mapping domains of fluvial processes with respect to the hierarchical organization of topographic complexity that drives fluvial dynamism. We tested this approach on flow convergence routing, a morphodynamic mechanism with different states depending on the structure of nondimensional topographic variability. Five nondimensional landform types with unique functionality (nozzle, wide bar, normal channel, constricted pool, and oversized) represent this process at any flow. When this typology is nested at base flow, bankfull, and floodprone scales it creates a system with up to 125 functional types. This shows how a single mechanism produces complex dynamism via nesting. Given the classification, we answered nine specific scientific questions to investigate the abundance, sequencing, and hierarchical nesting of these new landform types using a 35-km gravel/cobble river segment of the Yuba River in California. The nested structure of flow convergence routing landforms found in this study revealed that bankfull landforms are nested within specific floodprone valley landform types, and these types control bankfull morphodynamics during moderate to large floods. As a result, this study calls into question the prevailing theory that the bankfull channel of a gravel/cobble river is controlled by in-channel, bankfull, and/or small flood flows. Such flows are too small to initiate widespread sediment transport in a gravel/cobble river with topographic complexity.

  11. Sequencing intractable DNA to close microbial genomes.

    Directory of Open Access Journals (Sweden)

    Richard A Hurt

    Full Text Available Advancement in high throughput DNA sequencing technologies has supported a rapid proliferation of microbial genome sequencing projects, providing the genetic blueprint for in-depth studies. Oftentimes, difficult to sequence regions in microbial genomes are ruled "intractable" resulting in a growing number of genomes with sequence gaps deposited in databases. A procedure was developed to sequence such problematic regions in the "non-contiguous finished" Desulfovibrio desulfuricans ND132 genome (6 intractable gaps and the Desulfovibrio africanus genome (1 intractable gap. The polynucleotides surrounding each gap formed GC rich secondary structures making the regions refractory to amplification and sequencing. Strand-displacing DNA polymerases used in concert with a novel ramped PCR extension cycle supported amplification and closure of all gap regions in both genomes. The developed procedures support accurate gene annotation, and provide a step-wise method that reduces the effort required for genome finishing.

  12. Sequencing Intractable DNA to Close Microbial Genomes

    Energy Technology Data Exchange (ETDEWEB)

    Hurt, Jr., Richard Ashley [ORNL; Brown, Steven D [ORNL; Podar, Mircea [ORNL; Palumbo, Anthony Vito [ORNL; Elias, Dwayne A [ORNL

    2012-01-01

    Advancement in high throughput DNA sequencing technologies has supported a rapid proliferation of microbial genome sequencing projects, providing the genetic blueprint for for in-depth studies. Oftentimes, difficult to sequence regions in microbial genomes are ruled intractable resulting in a growing number of genomes with sequence gaps deposited in databases. A procedure was developed to sequence such difficult regions in the non-contiguous finished Desulfovibrio desulfuricans ND132 genome (6 intractable gaps) and the Desulfovibrio africanus genome (1 intractable gap). The polynucleotides surrounding each gap formed GC rich secondary structures making the regions refractory to amplification and sequencing. Strand-displacing DNA polymerases used in concert with a novel ramped PCR extension cycle supported amplification and closure of all gap regions in both genomes. These developed procedures support accurate gene annotation, and provide a step-wise method that reduces the effort required for genome finishing.

  13. Identification of human chromosome 22 transcribed sequences with ORF expressed sequence tags

    Science.gov (United States)

    de Souza, Sandro J.; Camargo, Anamaria A.; Briones, Marcelo R. S.; Costa, Fernando F.; Nagai, Maria Aparecida; Verjovski-Almeida, Sergio; Zago, Marco A.; Andrade, Luis Eduardo C.; Carrer, Helaine; El-Dorry, Hamza F. A.; Espreafico, Enilza M.; Habr-Gama, Angelita; Giannella-Neto, Daniel; Goldman, Gustavo H.; Gruber, Arthur; Hackel, Christine; Kimura, Edna T.; Maciel, Rui M. B.; Marie, Suely K. N.; Martins, Elizabeth A. L.; Nóbrega, Marina P.; Paçó-Larson, Maria Luisa; Pardini, Maria Inês M. C.; Pereira, Gonçalo G.; Pesquero, João Bosco; Rodrigues, Vanderlei; Rogatto, Silvia R.; da Silva, Ismael D. C. G.; Sogayar, Mari C.; de Fátima Sonati, Maria; Tajara, Eloiza H.; Valentini, Sandro R.; Acencio, Marcio; Alberto, Fernando L.; Amaral, Maria Elisabete J.; Aneas, Ivy; Bengtson, Mário Henrique; Carraro, Dirce M.; Carvalho, Alex F.; Carvalho, Lúcia Helena; Cerutti, Janete M.; Corrêa, Maria Lucia C.; Costa, Maria Cristina R.; Curcio, Cyntia; Gushiken, Tsieko; Ho, Paulo L.; Kimura, Elza; Leite, Luciana C. C.; Maia, Gustavo; Majumder, Paromita; Marins, Mozart; Matsukuma, Adriana; Melo, Analy S. A.; Mestriner, Carlos Alberto; Miracca, Elisabete C.; Miranda, Daniela C.; Nascimento, Ana Lucia T. O.; Nóbrega, Francisco G.; Ojopi, Élida P. B.; Pandolfi, José Rodrigo C.; Pessoa, Luciana Gilbert; Rahal, Paula; Rainho, Claudia A.; da Ro's, Nancy; de Sá, Renata G.; Sales, Magaly M.; da Silva, Neusa P.; Silva, Tereza C.; da Silva, Wilson; Simão, Daniel F.; Sousa, Josane F.; Stecconi, Daniella; Tsukumo, Fernando; Valente, Valéria; Zalcberg, Heloisa; Brentani, Ricardo R.; Reis, Luis F. L.; Dias-Neto, Emmanuel; Simpson, Andrew J. G.

    2000-01-01

    Transcribed sequences in the human genome can be identified with confidence only by alignment with sequences derived from cDNAs synthesized from naturally occurring mRNAs. We constructed a set of 250,000 cDNAs that represent partial expressed gene sequences and that are biased toward the central coding regions of the resulting transcripts. They are termed ORF expressed sequence tags (ORESTES). The 250,000 ORESTES were assembled into 81,429 contigs. Of these, 1,181 (1.45%) were found to match sequences in chromosome 22 with at least one ORESTES contig for 162 (65.6%) of the 247 known genes, for 67 (44.6%) of the 150 related genes, and for 45 of the 148 (30.4%) EST-predicted genes on this chromosome. Using a set of stringent criteria to validate our sequences, we identified a further 219 previously unannotated transcribed sequences on chromosome 22. Of these, 171 were in fact also defined by EST or full length cDNA sequences available in GenBank but not utilized in the initial annotation of the first human chromosome sequence. Thus despite representing less than 15% of all expressed human sequences in the public databases at the time of the present analysis, ORESTES sequences defined 48 transcribed sequences on chromosome 22 not defined by other sequences. All of the transcribed sequences defined by ORESTES coincided with DNA regions predicted as encoding exons by genscan. (http://genes.mit.edu/GENSCAN.html). PMID:11070084

  14. cis sequence effects on gene expression

    Directory of Open Access Journals (Sweden)

    Jacobs Kevin

    2007-08-01

    Full Text Available Abstract Background Sequence and transcriptional variability within and between individuals are typically studied independently. The joint analysis of sequence and gene expression variation (genetical genomics provides insight into the role of linked sequence variation in the regulation of gene expression. We investigated the role of sequence variation in cis on gene expression (cis sequence effects in a group of genes commonly studied in cancer research in lymphoblastoid cell lines. We estimated the proportion of genes exhibiting cis sequence effects and the proportion of gene expression variation explained by cis sequence effects using three different analytical approaches, and compared our results to the literature. Results We generated gene expression profiling data at N = 697 candidate genes from N = 30 lymphoblastoid cell lines for this study and used available candidate gene resequencing data at N = 552 candidate genes to identify N = 30 candidate genes with sufficient variance in both datasets for the investigation of cis sequence effects. We used two additive models and the haplotype phylogeny scanning approach of Templeton (Tree Scanning to evaluate association between individual SNPs, all SNPs at a gene, and diplotypes, with log-transformed gene expression. SNPs and diplotypes at eight candidate genes exhibited statistically significant (p cis sequence effects in our study, respectively. Conclusion Based on analysis of our results and the extant literature, one in four genes exhibits significant cis sequence effects, and for these genes, about 30% of gene expression variation is accounted for by cis sequence variation. Despite diverse experimental approaches, the presence or absence of significant cis sequence effects is largely supported by previously published studies.

  15. Multiple tag labeling method for DNA sequencing

    Science.gov (United States)

    Mathies, R.A.; Huang, X.C.; Quesada, M.A.

    1995-07-25

    A DNA sequencing method is described which uses single lane or channel electrophoresis. Sequencing fragments are separated in the lane and detected using a laser-excited, confocal fluorescence scanner. Each set of DNA sequencing fragments is separated in the same lane and then distinguished using a binary coding scheme employing only two different fluorescent labels. Also described is a method of using radioisotope labels. 5 figs.

  16. Exome sequencing and genetic testing for MODY.

    Directory of Open Access Journals (Sweden)

    Stefan Johansson

    Full Text Available Genetic testing for monogenic diabetes is important for patient care. Given the extensive genetic and clinical heterogeneity of diabetes, exome sequencing might provide additional diagnostic potential when standard Sanger sequencing-based diagnostics is inconclusive.The aim of the study was to examine the performance of exome sequencing for a molecular diagnosis of MODY in patients who have undergone conventional diagnostic sequencing of candidate genes with negative results.We performed exome enrichment followed by high-throughput sequencing in nine patients with suspected MODY. They were Sanger sequencing-negative for mutations in the HNF1A, HNF4A, GCK, HNF1B and INS genes. We excluded common, non-coding and synonymous gene variants, and performed in-depth analysis on filtered sequence variants in a pre-defined set of 111 genes implicated in glucose metabolism.On average, we obtained 45 X median coverage of the entire targeted exome and found 199 rare coding variants per individual. We identified 0-4 rare non-synonymous and nonsense variants per individual in our a priori list of 111 candidate genes. Three of the variants were considered pathogenic (in ABCC8, HNF4A and PPARG, respectively, thus exome sequencing led to a genetic diagnosis in at least three of the nine patients. Approximately 91% of known heterozygous SNPs in the target exomes were detected, but we also found low coverage in some key diabetes genes using our current exome sequencing approach. Novel variants in the genes ARAP1, GLIS3, MADD, NOTCH2 and WFS1 need further investigation to reveal their possible role in diabetes.Our results demonstrate that exome sequencing can improve molecular diagnostics of MODY when used as a complement to Sanger sequencing. However, improvements will be needed, especially concerning coverage, before the full potential of exome sequencing can be realized.

  17. Identifying driver mutations in sequenced cancer genomes

    DEFF Research Database (Denmark)

    Raphael, Benjamin J; Dobson, Jason R; Oesper, Layla

    2014-01-01

    High-throughput DNA sequencing is revolutionizing the study of cancer and enabling the measurement of the somatic mutations that drive cancer development. However, the resulting sequencing datasets are large and complex, obscuring the clinically important mutations in a background of errors, nois...... patterns of mutual exclusivity. These techniques, coupled with advances in high-throughput DNA sequencing, are enabling precision medicine approaches to the diagnosis and treatment of cancer....

  18. EGNAS: an exhaustive DNA sequence design algorithm

    Directory of Open Access Journals (Sweden)

    Kick Alfred

    2012-06-01

    Full Text Available Abstract Background The molecular recognition based on the complementary base pairing of deoxyribonucleic acid (DNA is the fundamental principle in the fields of genetics, DNA nanotechnology and DNA computing. We present an exhaustive DNA sequence design algorithm that allows to generate sets containing a maximum number of sequences with defined properties. EGNAS (Exhaustive Generation of Nucleic Acid Sequences offers the possibility of controlling both interstrand and intrastrand properties. The guanine-cytosine content can be adjusted. Sequences can be forced to start and end with guanine or cytosine. This option reduces the risk of “fraying” of DNA strands. It is possible to limit cross hybridizations of a defined length, and to adjust the uniqueness of sequences. Self-complementarity and hairpin structures of certain length can be avoided. Sequences and subsequences can optionally be forbidden. Furthermore, sequences can be designed to have minimum interactions with predefined strands and neighboring sequences. Results The algorithm is realized in a C++ program. TAG sequences can be generated and combined with primers for single-base extension reactions, which were described for multiplexed genotyping of single nucleotide polymorphisms. Thereby, possible foldback through intrastrand interaction of TAG-primer pairs can be limited. The design of sequences for specific attachment of molecular constructs to DNA origami is presented. Conclusions We developed a new software tool called EGNAS for the design of unique nucleic acid sequences. The presented exhaustive algorithm allows to generate greater sets of sequences than with previous software and equal constraints. EGNAS is freely available for noncommercial use at http://www.chm.tu-dresden.de/pc6/EGNAS.

  19. Genome Sequencing and Analysis Conference IV

    Energy Technology Data Exchange (ETDEWEB)

    1993-12-31

    J. Craig Venter and C. Thomas Caskey co-chaired Genome Sequencing and Analysis Conference IV held at Hilton Head, South Carolina from September 26--30, 1992. Venter opened the conference by noting that approximately 400 researchers from 16 nations were present four times as many participants as at Genome Sequencing Conference I in 1989. Venter also introduced the Data Fair, a new component of the conference allowing exchange and on-site computer analysis of unpublished sequence data.

  20. FRESCO: Referential compression of highly similar sequences.

    Science.gov (United States)

    Wandelt, Sebastian; Leser, Ulf

    2013-01-01

    In many applications, sets of similar texts or sequences are of high importance. Prominent examples are revision histories of documents or genomic sequences. Modern high-throughput sequencing technologies are able to generate DNA sequences at an ever-increasing rate. In parallel to the decreasing experimental time and cost necessary to produce DNA sequences, computational requirements for analysis and storage of the sequences are steeply increasing. Compression is a key technology to deal with this challenge. Recently, referential compression schemes, storing only the differences between a to-be-compressed input and a known reference sequence, gained a lot of interest in this field. In this paper, we propose a general open-source framework to compress large amounts of biological sequence data called Framework for REferential Sequence COmpression (FRESCO). Our basic compression algorithm is shown to be one to two orders of magnitudes faster than comparable related work, while achieving similar compression ratios. We also propose several techniques to further increase compression ratios, while still retaining the advantage in speed: 1) selecting a good reference sequence; and 2) rewriting a reference sequence to allow for better compression. In addition,we propose a new way of further boosting the compression ratios by applying referential compression to already referentially compressed files (second-order compression). This technique allows for compression ratios way beyond state of the art, for instance,4,000:1 and higher for human genomes. We evaluate our algorithms on a large data set from three different species (more than 1,000 genomes, more than 3 TB) and on a collection of versions of Wikipedia pages. Our results show that real-time compression of highly similar sequences at high compression ratios is possible on modern hardware.

  1. Mesa Isochrones and Stellar Tracks (MIST). I. Solar-scaled Models

    Science.gov (United States)

    Choi, Jieun; Dotter, Aaron; Conroy, Charlie; Cantiello, Matteo; Paxton, Bill; Johnson, Benjamin D.

    2016-06-01

    This is the first of a series of papers presenting the Modules for Experiments in Stellar Astrophysics (MESA) Isochrones and Stellar Tracks (MIST) project, a new comprehensive set of stellar evolutionary tracks and isochrones computed using MESA, a state-of-the-art open-source 1D stellar evolution package. In this work, we present models with solar-scaled abundance ratios covering a wide range of ages (5≤slant {log}({Age}) [{year}]≤slant 10.3), masses (0.1≤slant M/{M}⊙ ≤slant 300), and metallicities (-2.0≤slant [{{Z}}/{{H}}]≤slant 0.5). The models are self-consistently and continuously evolved from the pre-main sequence (PMS) to the end of hydrogen burning, the white dwarf cooling sequence, or the end of carbon burning, depending on the initial mass. We also provide a grid of models evolved from the PMS to the end of core helium burning for -4.0≤slant [{{Z}}/{{H}}]\\lt -2.0. We showcase extensive comparisons with observational constraints as well as with some of the most widely used existing models in the literature. The evolutionary tracks and isochrones can be downloaded from the project website at http://waps.cfa.harvard.edu/MIST/.

  2. Magnetic fields driven by tidal mixing in radiative stars

    Science.gov (United States)

    Vidal, Jérémie; Cébron, David; Schaeffer, Nathanaël; Hollerbach, Rainer

    2018-04-01

    Stellar magnetism plays an important role in stellar evolution theory. Approximatively 10 per cent of observed main sequence (MS) and pre-main-sequence (PMS) radiative stars exhibit surface magnetic fields above the detection limit, raising the question of their origin. These stars host outer radiative envelopes, which are stably stratified. Therefore, they are assumed to be motionless in standard models of stellar structure and evolution. We focus on rapidly rotating, radiative stars which may be prone to the tidal instability, due to an orbital companion. Using direct numerical simulations in a sphere, we study the interplay between a stable stratification and the tidal instability, and assess its dynamo capability. We show that the tidal instability is triggered regardless of the strength of the stratification (Brunt-Väisälä frequency). Furthermore, the tidal instability can lead to both mixing and self-induced magnetic fields in stably stratified layers (provided that the Brunt-Väisälä frequency does not exceed the stellar spin rate in the simulations too much). The application to stars suggests that the resulting magnetic fields could be observable at the stellar surfaces. Indeed, we expect magnetic field strengths up to several Gauss. Consequently, tidally driven dynamos should be considered as a (complementary) dynamo mechanism, possibly operating in radiative MS and PMS stars hosting orbital companions. In particular, tidally driven dynamos may explain the observed magnetism of tidally deformed and rapidly rotating Vega-like stars.

  3. Robustness analysis of chiller sequencing control

    International Nuclear Information System (INIS)

    Liao, Yundan; Sun, Yongjun; Huang, Gongsheng

    2015-01-01

    Highlights: • Uncertainties with chiller sequencing control were systematically quantified. • Robustness of chiller sequencing control was systematically analyzed. • Different sequencing control strategies were sensitive to different uncertainties. • A numerical method was developed for easy selection of chiller sequencing control. - Abstract: Multiple-chiller plant is commonly employed in the heating, ventilating and air-conditioning system to increase operational feasibility and energy-efficiency under part load condition. In a multiple-chiller plant, chiller sequencing control plays a key role in achieving overall energy efficiency while not sacrifices the cooling sufficiency for indoor thermal comfort. Various sequencing control strategies have been developed and implemented in practice. Based on the observation that (i) uncertainty, which cannot be avoided in chiller sequencing control, has a significant impact on the control performance and may cause the control fail to achieve the expected control and/or energy performance; and (ii) in current literature few studies have systematically addressed this issue, this paper therefore presents a study on robustness analysis of chiller sequencing control in order to understand the robustness of various chiller sequencing control strategies under different types of uncertainty. Based on the robustness analysis, a simple and applicable method is developed to select the most robust control strategy for a given chiller plant in the presence of uncertainties, which will be verified using case studies

  4. Multiplexed microsatellite recovery using massively parallel sequencing

    Science.gov (United States)

    Jennings, T.N.; Knaus, B.J.; Mullins, T.D.; Haig, S.M.; Cronn, R.C.

    2011-01-01

    Conservation and management of natural populations requires accurate and inexpensive genotyping methods. Traditional microsatellite, or simple sequence repeat (SSR), marker analysis remains a popular genotyping method because of the comparatively low cost of marker development, ease of analysis and high power of genotype discrimination. With the availability of massively parallel sequencing (MPS), it is now possible to sequence microsatellite-enriched genomic libraries in multiplex pools. To test this approach, we prepared seven microsatellite-enriched, barcoded genomic libraries from diverse taxa (two conifer trees, five birds) and sequenced these on one lane of the Illumina Genome Analyzer using paired-end 80-bp reads. In this experiment, we screened 6.1 million sequences and identified 356958 unique microreads that contained di- or trinucleotide microsatellites. Examination of four species shows that our conversion rate from raw sequences to polymorphic markers compares favourably to Sanger- and 454-based methods. The advantage of multiplexed MPS is that the staggering capacity of modern microread sequencing is spread across many libraries; this reduces sample preparation and sequencing costs to less than $400 (USD) per species. This price is sufficiently low that microsatellite libraries could be prepared and sequenced for all 1373 organisms listed as 'threatened' and 'endangered' in the United States for under $0.5M (USD).

  5. Digital Recovery Sequencer - Advanced Concept Ejection Seats

    National Research Council Canada - National Science Library

    Ross, David A; Cotter, Lee; Culhane, David; Press, Matthew J

    2005-01-01

    .... Continued usage of the Analog Sequencer is undesirable due to limitations with respect to its installed life, electronic component obsolescence, flexibility to accommodate seat safety improvements...

  6. Quantitative phenotyping via deep barcode sequencing.

    Science.gov (United States)

    Smith, Andrew M; Heisler, Lawrence E; Mellor, Joseph; Kaper, Fiona; Thompson, Michael J; Chee, Mark; Roth, Frederick P; Giaever, Guri; Nislow, Corey

    2009-10-01

    Next-generation DNA sequencing technologies have revolutionized diverse genomics applications, including de novo genome sequencing, SNP detection, chromatin immunoprecipitation, and transcriptome analysis. Here we apply deep sequencing to genome-scale fitness profiling to evaluate yeast strain collections in parallel. This method, Barcode analysis by Sequencing, or "Bar-seq," outperforms the current benchmark barcode microarray assay in terms of both dynamic range and throughput. When applied to a complex chemogenomic assay, Bar-seq quantitatively identifies drug targets, with performance superior to the benchmark microarray assay. We also show that Bar-seq is well-suited for a multiplex format. We completely re-sequenced and re-annotated the yeast deletion collection using deep sequencing, found that approximately 20% of the barcodes and common priming sequences varied from expectation, and used this revised list of barcode sequences to improve data quality. Together, this new assay and analysis routine provide a deep-sequencing-based toolkit for identifying gene-environment interactions on a genome-wide scale.

  7. Hardware Accelerated Sequence Alignment with Traceback

    Directory of Open Access Journals (Sweden)

    Scott Lloyd

    2009-01-01

    in a timely manner. Known methods to accelerate alignment on reconfigurable hardware only address sequence comparison, limit the sequence length, or exhibit memory and I/O bottlenecks. A space-efficient, global sequence alignment algorithm and architecture is presented that accelerates the forward scan and traceback in hardware without memory and I/O limitations. With 256 processing elements in FPGA technology, a performance gain over 300 times that of a desktop computer is demonstrated on sequence lengths of 16000. For greater performance, the architecture is scalable to more processing elements.

  8. Multipliers on Generalized Mixed Norm Sequence Spaces

    Directory of Open Access Journals (Sweden)

    Oscar Blasco

    2014-01-01

    Full Text Available Given 1≤p,q≤∞ and sequences of integers (nkk and (nk′k such that nk≤nk′≤nk+1, the generalized mixed norm space ℓℐ(p,q is defined as those sequences (ajj such that ((∑j∈Ik‍|aj|p1/pk∈ℓq where Ik={j∈ℕ0 s.t. nk≤jsequence λ=(λjj to belong to the space of multipliers (ℓℐ(r,s,ℓ(u,v, for different sequences ℐ and of intervals in ℕ0, are determined.

  9. Recursive sequences in first-year calculus

    Science.gov (United States)

    Krainer, Thomas

    2016-02-01

    This article provides ready-to-use supplementary material on recursive sequences for a second-semester calculus class. It equips first-year calculus students with a basic methodical procedure based on which they can conduct a rigorous convergence or divergence analysis of many simple recursive sequences on their own without the need to invoke inductive arguments as is typically required in calculus textbooks. The sequences that are accessible to this kind of analysis are predominantly (eventually) monotonic, but also certain recursive sequences that alternate around their limit point as they converge can be considered.

  10. A measurement of disorder in binary sequences

    Science.gov (United States)

    Gong, Longyan; Wang, Haihong; Cheng, Weiwen; Zhao, Shengmei

    2015-03-01

    We propose a complex quantity, AL, to characterize the degree of disorder of L-length binary symbolic sequences. As examples, we respectively apply it to typical random and deterministic sequences. One kind of random sequences is generated from a periodic binary sequence and the other is generated from the logistic map. The deterministic sequences are the Fibonacci and Thue-Morse sequences. In these analyzed sequences, we find that the modulus of AL, denoted by |AL | , is a (statistically) equivalent quantity to the Boltzmann entropy, the metric entropy, the conditional block entropy and/or other quantities, so it is a useful quantitative measure of disorder. It can be as a fruitful index to discern which sequence is more disordered. Moreover, there is one and only one value of |AL | for the overall disorder characteristics. It needs extremely low computational costs. It can be easily experimentally realized. From all these mentioned, we believe that the proposed measure of disorder is a valuable complement to existing ones in symbolic sequences.

  11. Polynomial sequences generated by infinite Hessenberg matrices

    Directory of Open Access Journals (Sweden)

    Verde-Star Luis

    2017-01-01

    Full Text Available We show that an infinite lower Hessenberg matrix generates polynomial sequences that correspond to the rows of infinite lower triangular invertible matrices. Orthogonal polynomial sequences are obtained when the Hessenberg matrix is tridiagonal. We study properties of the polynomial sequences and their corresponding matrices which are related to recurrence relations, companion matrices, matrix similarity, construction algorithms, and generating functions. When the Hessenberg matrix is also Toeplitz the polynomial sequences turn out to be of interpolatory type and we obtain additional results. For example, we show that every nonderogative finite square matrix is similar to a unique Toeplitz-Hessenberg matrix.

  12. Genomic sequencing of Pleistocene cave bears

    Energy Technology Data Exchange (ETDEWEB)

    Noonan, James P.; Hofreiter, Michael; Smith, Doug; Priest, JamesR.; Rohland, Nadin; Rabeder, Gernot; Krause, Johannes; Detter, J. Chris; Paabo, Svante; Rubin, Edward M.

    2005-04-01

    Despite the information content of genomic DNA, ancient DNA studies to date have largely been limited to amplification of mitochondrial DNA due to technical hurdles such as contamination and degradation of ancient DNAs. In this study, we describe two metagenomic libraries constructed using unamplified DNA extracted from the bones of two 40,000-year-old extinct cave bears. Analysis of {approx}1 Mb of sequence from each library showed that, despite significant microbial contamination, 5.8 percent and 1.1 percent of clones in the libraries contain cave bear inserts, yielding 26,861 bp of cave bear genome sequence. Alignment of this sequence to the dog genome, the closest sequenced genome to cave bear in terms of evolutionary distance, revealed roughly the expected ratio of cave bear exons, repeats and conserved noncoding sequences. Only 0.04 percent of all clones sequenced were derived from contamination with modern human DNA. Comparison of cave bear with orthologous sequences from several modern bear species revealed the evolutionary relationship of these lineages. Using the metagenomic approach described here, we have recovered substantial quantities of mammalian genomic sequence more than twice as old as any previously reported, establishing the feasibility of ancient DNA genomic sequencing programs.

  13. Design of Long Period Pseudo-Random Sequences from the Addition of -Sequences over

    Directory of Open Access Journals (Sweden)

    Ren Jian

    2004-01-01

    Full Text Available Pseudo-random sequence with good correlation property and large linear span is widely used in code division multiple access (CDMA communication systems and cryptology for reliable and secure information transmission. In this paper, sequences with long period, large complexity, balance statistics, and low cross-correlation property are constructed from the addition of -sequences with pairwise-prime linear spans (AMPLS. Using -sequences as building blocks, the proposed method proved to be an efficient and flexible approach to construct long period pseudo-random sequences with desirable properties from short period sequences. Applying the proposed method to , a signal set is constructed.

  14. Compressing DNA sequence databases with coil

    Directory of Open Access Journals (Sweden)

    Hendy Michael D

    2008-05-01

    Full Text Available Abstract Background Publicly available DNA sequence databases such as GenBank are large, and are growing at an exponential rate. The sheer volume of data being dealt with presents serious storage and data communications problems. Currently, sequence data is usually kept in large "flat files," which are then compressed using standard Lempel-Ziv (gzip compression – an approach which rarely achieves good compression ratios. While much research has been done on compressing individual DNA sequences, surprisingly little has focused on the compression of entire databases of such sequences. In this study we introduce the sequence database compression software coil. Results We have designed and implemented a portable software package, coil, for compressing and decompressing DNA sequence databases based on the idea of edit-tree coding. coil is geared towards achieving high compression ratios at the expense of execution time and memory usage during compression – the compression time represents a "one-off investment" whose cost is quickly amortised if the resulting compressed file is transmitted many times. Decompression requires little memory and is extremely fast. We demonstrate a 5% improvement in compression ratio over state-of-the-art general-purpose compression tools for a large GenBank database file containing Expressed Sequence Tag (EST data. Finally, coil can efficiently encode incremental additions to a sequence database. Conclusion coil presents a compelling alternative to conventional compression of flat files for the storage and distribution of DNA sequence databases having a narrow distribution of sequence lengths, such as EST data. Increasing compression levels for databases having a wide distribution of sequence lengths is a direction for future work.

  15. Direct chloroplast sequencing: comparison of sequencing platforms and analysis tools for whole chloroplast barcoding.

    Directory of Open Access Journals (Sweden)

    Marta Brozynska

    Full Text Available Direct sequencing of total plant DNA using next generation sequencing technologies generates a whole chloroplast genome sequence that has the potential to provide a barcode for use in plant and food identification. Advances in DNA sequencing platforms may make this an attractive approach for routine plant identification. The HiSeq (Illumina and Ion Torrent (Life Technology sequencing platforms were used to sequence total DNA from rice to identify polymorphisms in the whole chloroplast genome sequence of a wild rice plant relative to cultivated rice (cv. Nipponbare. Consensus chloroplast sequences were produced by mapping sequence reads to the reference rice chloroplast genome or by de novo assembly and mapping of the resulting contigs to the reference sequence. A total of 122 polymorphisms (SNPs and indels between the wild and cultivated rice chloroplasts were predicted by these different sequencing and analysis methods. Of these, a total of 102 polymorphisms including 90 SNPs were predicted by both platforms. Indels were more variable with different sequencing methods, with almost all discrepancies found in homopolymers. The Ion Torrent platform gave no apparent false SNP but was less reliable for indels. The methods should be suitable for routine barcoding using appropriate combinations of sequencing platform and data analysis.

  16. Step out - Step in Sequencing Games

    NARCIS (Netherlands)

    Musegaas, M.; Borm, P.E.M.; Quant, M.

    2014-01-01

    In this paper a new class of relaxed sequencing games is introduced: the class of Step out - Step in sequencing games. In this relaxation any player within a coalition is allowed to step out from his position in the processing order and to step in at any position later in the processing order.

  17. Step out-step in sequencing games

    NARCIS (Netherlands)

    Musegaas, Marieke; Borm, Peter; Quant, Marieke

    2015-01-01

    In this paper a new class of relaxed sequencing games is introduced: the class of Step out–Step in sequencing games. In this relaxation any player within a coalition is allowed to step out from his position in the processing order and to step in at any position later in the processing order. First,

  18. Enhanced throughput for infrared automated DNA sequencing

    Science.gov (United States)

    Middendorf, Lyle R.; Gartside, Bill O.; Humphrey, Pat G.; Roemer, Stephen C.; Sorensen, David R.; Steffens, David L.; Sutter, Scott L.

    1995-04-01

    Several enhancements have been developed and applied to infrared automated DNA sequencing resulting in significantly higher throughput. A 41 cm sequencing gel (31 cm well- to-read distance) combines high resolution of DNA sequencing fragments with optimized run times yielding two runs per day of 500 bases per sample. A 66 cm sequencing gel (56 cm well-to-read distance) produces sequence read lengths of up to 1000 bases for ds and ss templates using either T7 polymerase or cycle-sequencing protocols. Using a multichannel syringe to load 64 lanes allows 16 samples (compatible with 96-well format) to be visualized for each run. The 41 cm gel configuration allows 16,000 bases per day (16 samples X 500 bases/sample X 2 ten hour runs/day) to be sequenced with the advantages of infrared technology. Enhancements to internal labeling techniques using an infrared-labeled dATP molecule (Boehringer Mannheim GmbH, Penzberg, Germany; Sequenase (U.S. Biochemical) have also been made. The inclusion of glycerol in the sequencing reactions yields greatly improved results for some primer and template combinations. The inclusion of (alpha) -Thio-dNTP's in the labeling reaction increases signal intensity two- to three-fold.

  19. Thread extraction for polyadic instruction sequences

    NARCIS (Netherlands)

    Bergstra, J.; Middelburg, C.

    2011-01-01

    In this paper, we study the phenomenon that instruction sequences are split into fragments which somehow produce a joint behaviour. In order to bring this phenomenon better into the picture, we formalize a simple mechanism by which several instruction sequence fragments can produce a joint

  20. Genome sequence of Lactobacillus rhamnosus ATCC 8530.

    Science.gov (United States)

    Pittet, Vanessa; Ewen, Emily; Bushell, Barry R; Ziola, Barry

    2012-02-01

    Lactobacillus rhamnosus is found in the human gastrointestinal tract and is important for probiotics. We became interested in L. rhamnosus isolate ATCC 8530 in relation to beer spoilage and hops resistance. We report here the genome sequence of this isolate, along with a brief comparison to other available L. rhamnosus genome sequences.