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Sample records for repeated 14co2 pulse-labelling

  1. Influence of atmospheric circulation on regional 14CO2 differences

    NASA Astrophysics Data System (ADS)

    Hua, Quan; Barbetti, Mike

    2007-10-01

    Detailed analyses of published 14C data from tree rings and atmospheric CO2 samples for the northern tropics in Asia (India, Thailand, and Vietnam) and Africa (Ethiopia) have been performed for the heavily bomb-influenced period 1963-1967 A.D. The results show that the Asian summer monsoon and Intertropical Convergence Zone (ITCZ) position influenced atmospheric 14CO2 over the study area. Similar analyses of atmospheric records for northern and western Europe, northwestern Africa, and the northeastern United States and tree ring data for east Asia show that the Northern Hemisphere distribution of bomb 14C for 1963-1967 depended on atmospheric circulation controlled by the seasonal positions of Hadley cell boundaries and the ITCZ. The distribution of 14C did not have a simple latitudinal dependence. This work shows that the seasonal atmospheric circulation patterns are crucial for the description of atmospheric 14C gradients during the bomb peak period. These principles can be applied to the interpretation of the small intrahemispheric 14C offsets of the remote past.

  2. Regional 14CO2 offsets in the troposphere: magnitude, mechanisms, and consequences.

    PubMed

    Kromer, B; Manning, S W; Kuniholm, P I; Newton, M W; Spurk, M; Levin, I

    2001-12-21

    Radiocarbon dating methods typically assume that there are no significant tropospheric (14)CO(2) gradients within the low- to mid-latitude zone of the Northern Hemisphere. Comparison of tree ring (14)C data from southern Germany and Anatolia supports this assumption in general but also documents episodes of significant short-term regional (14)CO(2) offsets. We suggest that the offset is caused by an enhanced seasonal (14)CO(2) cycle, with seasonally peaked flux of stratospheric (14)C into the troposphere during periods of low solar magnetic activity, coinciding with substantial atmospheric cooling. Short-term episodes of regional (14)CO(2) offsets are important to palaeoclimate studies and to high-resolution archaeological dating.

  3. Optical Measurements of 14CO2 Using Cavity Ring-Down Spectroscopy

    NASA Astrophysics Data System (ADS)

    Long, David A.; Fleisher, Adam J.; Liu, Qingnan; Hodges, Joseph T.

    2016-06-01

    Measurements of radiocarbon (14C) provide a unique platform in order to determine the age of a material or alternatively for source attribution between biogenic and petrochemical sources. We describe a cavity ring-down spectrometer which uses an infrared quantum cascade laser to probe the fundamental of 14CO2. This instrument offers one of the highest sensitivities which has been reported in the mid-infrared and has fully automated spectral scanning for continuous data acquisition. Despite the ultra-low abundance of 14CO2 in the atmosphere (1.2 pmol/mol relative to 12CO2) we have been able to rapidly record the 14CO2 transition and determine the origin of carbon dioxide samples. Our experimental approach and future improvements to the instrument will be discussed as well as selected measurement targets.

  4. Constraining the Stratosphere-Troposphere Exchange of Radiocarbon using AirCore 14CO2 Measurements

    NASA Astrophysics Data System (ADS)

    Chen, H.

    2016-12-01

    Radiocarbon (14C) plays an important role in the carbon cycle studies to understand both natural and anthropogenic carbon fluxes, but also in atmospheric chemistry to constrain hydroxyl radical (OH) concentrations in the atmosphere. Apart from the enormous 14C emissions from nuclear bomb testing in the 1950s and 1960s, radiocarbon is primarily produced in the upper atmosphere due to reactions of nitrogen nuclei with thermal neutrons that are induced by cosmic rays. 14C is quickly oxidized to 14CO, which is then further oxidized to 14CO2 by OH. To this end, better understanding the radiocarbon source is very useful to advance the use of radiocarbon for these applications. However, upper atmospheric 14C observations have been very sparse to constrain the magnitude and the location of the 14C production as well as the transport of radiocarbon from the stratosphere to the troposphere. Recently we have successfully made stratospheric 14CO2 measurements using AirCore samples from Sodankylä, Northern Finland, along with regular AirCore profiles of CO2, CH4, and CO since 2013. In this study, we calculate the stratosphere-troposphere exchange of 14C using the correlation between 14CO2 and N2O, and the estimated N2O loss rate. Besides this, we assess the impact of the mean age of air on 14CO2 profiles. Furthermore, we will evaluate the influence of different cosmogenic 14C production scenarios and the uncertainties in the OH field on the seasonal cycles of radiocarbon and on the stratosphere-troposphere exchange.

  5. Vertical Distribution of 14CO2 in the Free Troposphere and Stratosphere

    NASA Astrophysics Data System (ADS)

    Garofalo, L.; Guilderson, T. P.; Atlas, E. L.; Blake, D. R.; Pfister, L.; Boering, K. A.

    2016-12-01

    The radiocarbon (14C) content of CO2 has long been used to quantify inventories, residence times and gross fluxes of carbon in and between the atmosphere, biosphere, and oceans, and can also be used to study large-scale atmospheric transport, as we have recently shown in Kanu et al. [2016]. Here, we present new measurements of the vertical distribution of Δ14C-CO2 from whole air samples collected aboard NASA aircraft (ER-2, DC-8, WB-57) in flight campaigns in 1997, 2000, 2004, 2012, and 2013 and have used them to estimate the net 14CO2 flux between the stratosphere and the troposphere. To within the uncertainties of the current set of measurements, we do not detect a trend in the net 14CO2 flux nor a dependence on the solar cycle in 14C production, which may further suggest that there has not been a change in stratospheric residence times over this time period. For the new vertical profiles of 14CO2 from the DC3 (2012) and SEAC4RS (2013) missions that extend into the lower troposphere from the stratosphere, the 14CO2 content generally increases with increasing altitude, as expected for a tracer with a stratospheric source (cosmogenic production in the upper troposphere/lower stratosphere) combined with a 14C-depleted source of CO2 at the surface (fossil fuel combustion). However, in several vertical profiles from the SEAC4RS mission, low ozone was measured at 410K (several kilometers above the tropopause), for which very low 14CO2 was also observed. These and other tracers, along with back-trajectory calculations, suggest that this air did not enter the stratosphere by local or regional convective input into the stratosphere, but rather by long-range influences from the Asian monsoon. Kanu, A. M., L. L. Comfort, T. P. Guilderson, P. J. Cameron-Smith, D. J. Bergmann, E. L. Atlas, S. Schauffler, K. A. Boering, "Measurements and modeling of contemporary radiocarbon in the stratosphere," Geophys. Res. Lett. 43, 1399-1406, 2016.

  6. Observations of 14CO2 in ecosystem respiration from a temperate deciduous forest in Northern Wisconsin

    NASA Astrophysics Data System (ADS)

    Phillips, Claire L.; McFarlane, Karis J.; LaFranchi, Brian; Desai, Ankur R.; Miller, John B.; Lehman, Scott J.

    2015-04-01

    The 14CO2 composition of plant and soil respiration can be used to determine the residence time of photosynthetically fixed carbon before it is released back to the atmosphere. To estimate the residence time of actively cycled carbon in a temperate forest, we employed two approaches for estimating the Δ14CO2 of ecosystem respiration (Δ14C-Reco) at the Willow Creek AmeriFlux site in Northern Wisconsin, USA. Our first approach was to construct nighttime Keeling plots from subcanopy profiles of Δ14CO2 and CO2, providing estimates of Δ14C-Reco of 121.7‰ in June and 42.0‰ in August 2012. These measurements are likely dominated by soil fluxes due to proximity to the ground level. Our second approach utilized samples taken over 20 months within the forest canopy and from 396 m above ground level at the nearby LEF NOAA tall tower site (Park Falls, WI). In this canopy-minus-background approach we employed a mixing model described by Miller and Tans (2003) for estimating isotopic sources by subtracting time-varying background conditions. For the period from May 2011 to December 2012 the estimated Δ14C-Reco using the Miller-Tans model was 76.8‰. Together, these Δ14C-Reco values represent mean Reco carbon ages of approximately 1-19 years. We also found that heterotrophic soil-respired Δ 14C at Willow Creek was 5-38‰ higher (i.e., 1-10 years older) than predicted by the Carnegie-Ames-Stanford Approach global biosphere carbon model for the 1 × 1 pixel nearest to the site. This study provides much needed observational constraints of ecosystem carbon residence times, which are a major source of uncertainty in terrestrial carbon cycle models.

  7. 14CO2 processing using an improved and robust molecular sieve cartridge

    NASA Astrophysics Data System (ADS)

    Wotte, Anja; Wordell-Dietrich, Patrick; Wacker, Lukas; Don, Axel; Rethemeyer, Janet

    2017-06-01

    Radiocarbon (14C) analysis on CO2 can provide valuable information on the carbon cycle as different carbon pools differ in their 14C signature. While fresh, biogenic carbon shows atmospheric 14C concentrations, fossil carbon is 14C free. As shown in previous studies, CO2 can be collected for 14C analysis using molecular sieve cartridges (MSC). These devices have previously been made of plastic and glass, which can easily be damaged during transport. We thus constructed a robust MSC suitable for field application under tough conditions or in remote areas, which is entirely made of stainless steel. The new MSC should also be tight over several months to allow long sampling campaigns and transport times, which was proven by a one year storage test. The reliability of the 14CO2 results obtained with the MSC was evaluated by detailed tests of different procedures to clean the molecular sieve (zeolite type 13X) and for the adsorption and desorption of CO2 from the zeolite using a vacuum rig. We show that the 14CO2 results are not affected by any contamination of modern or fossil origin, cross contamination from previous samples, and by carbon isotopic fractionation. In addition, we evaluated the direct CO2 transfer from the MSC into the automatic graphitization equipment AGE with the subsequent 14C AMS analysis as graphite. This semi-automatic approach can be fully automated in the future, which would allow a high sample throughput. We obtained very promising, low blank values between 0.0018 and 0.0028 F14C (equivalent to 50,800 and 47,200 yrs BP), which are within the analytical background and lower than results obtained in previous studies.

  8. First observations of 14CO2 at the Boulder Atmospheric Observatory (BAO)

    NASA Astrophysics Data System (ADS)

    Lafranchi, B. W.; Petron, G.; Andrews, A. E.; Miller, J. B.; Lehman, S. J.; Montzka, S. A.; Miller, B. R.; Guilderson, T. P.

    2010-12-01

    Atmospheric radiocarbon (14C) represents an important observational constraint on emissions of fossil-fuel derived carbon into the atmosphere due to the near absence of 14C in fossil fuel reservoirs. The high sensitivity and precision that accelerator mass spectrometry (AMS) affords in atmospheric 14C analysis has greatly increased the potential for using such measurements to facilitate carbon cycle studies and the validation of greenhouse gas emissions inventories. Here we report on the first ever 14CO2 observations from the Boulder Atmospheric Observatory (BAO), located 35 km north of Denver, CO. The BAO tower is one of 8 tall towers in the NOAA/ESRL greenhouse gas flask sampling network that has recently begun sampling for atmospheric 14C, as well as other trace gases. We will present observations of Δ14C in whole air samples collected between June 2009 and March 2010 at BAO (300 m a.g.l.). Values ranged from -10‰ to +46 ‰ corresponding to estimated fossil fuel CO2 (CO2ff) mixing ratios as high as 10 ppm above the background. Strong correlations between [CO2] and Δ14C suggest that much of the day-to-day variability in [CO2] is driven primarily by changes in [CO2ff] reaching the site. This variability is expected to be a function of the fossil fuel emission strength, regional transport, and boundary layer height. An analysis of differences in Δ14C with day of week provides a simple means to disentangle changes in the emission source strength of CO2ff from natural meteorological variability. Performing this analysis, we find that on average the site experiences slightly less fossil fuel emissions on weekends than on weekdays, presumably due to changes in anthropogenic emission patterns. Lastly, we will examine the correlations of Δ14C with traces gases, such as benzene, CO, and acetylene, in order to better assess the potential for using these relationships to interpolate [CO2ff] to faster time-scales, to extrapolate over a longer observational period, and

  9. Climate Change to the Nuclear Fuel Cycle: Expanding the spectral (14)CO(2) database for non-AMS Field Measurement Systems

    NASA Astrophysics Data System (ADS)

    Marino, B. D. V.; Odonnell, R. G.; Tolliver, D. E.

    2014-06-01

    Accelerator Mass Spectrometry (AMS) is well known and universally employed for radiocarbon analysis but is not adaptable to in-situ field measurements limiting applications. 14CO2 is a key tracer for fossil fuel CO2 as well as for release of enriched 14CO2 characteristic of the nuclear fuel cycle with ∆14CO2 values ranging from -1000 to ˜+500 per mil. However, to exploit the full value of in situ 14CO2 data in diverse climate change and nuclear fuel cycle applications, high data rate temporal and spatial field measurement sensors and systems are required. The development of non-AMS methods based on quantum cascade laser, cavity ring down and optogalvanic spectroscopy are emerging applications but not fully developed for field use or widely accepted. Spectral data for lasing transitions for 14CO2 are lacking in contrast to HITRAN data available for 12CO2 (626) and 13CO2 (636) (among other isotopologues 628, 638, etc.) in the spectral databases limiting development and innovation in non-AMS 14CO2 sensors and systems. We review the corpus of 14CO2 spectral data available in the literature and document grating tuned isotopic lasers (e.g., Freed 19901; Bradley et al., 19862), well suited for expanded spectral studies of 14CO2 and inclusion in the HITRAN database. Non-AMS 14CO2 approaches are reviewed with suggestions for future work to support field systems for 14CO2 measurements. Available isotopic lasers for 14CO2 collaborative studies are described.

  10. Carbon-14 Distribution in Carbohydrates of Immature Zea mays. Kernels Following 14CO2 Treatment of Intact Plants 1

    PubMed Central

    Shannon, Jack C.

    1968-01-01

    Shortly after Zea mays L. plants were exposed to 14CO2, most of the radioactivity in the kernel occurred in the free monosaccharides, glucose and fructose. Later the proportion of 14C in sucrose increased and that in the monosaccharides declined. These data have been interpreted as showing that the translocated sugar is hydrolyzed prior to or during its movement into the storage cells of the endosperm. This hydrolysis appears to occur in the “pedicel region” of the kernel. After entry into the endosperm tissue, sucrose was rapidly resynthesized from the monosaccharides prior to its utilization in starch synthesis. PMID:16656904

  11. A Synthesized Model-Observation Approach to Constraining Gross Urban CO2 Fluxes Using 14CO2 and carbonyl sulfide

    NASA Astrophysics Data System (ADS)

    LaFranchi, B. W.; Campbell, J. E.; Cameron-Smith, P. J.; Bambha, R.; Michelsen, H. A.

    2013-12-01

    Urbanized regions are responsible for a disproportionately large percentage (30-40%) of global anthropogenic greenhouse gas (GHG) emissions, despite covering only 2% of the Earth's surface area [Satterthwaite, 2008]. As a result, policies enacted at the local level in these urban areas can, in aggregate, have a large global impact, both positive and negative. In order to address the scientific questions that are required to drive these policy decisions, methods are needed that resolve gross CO2 flux components from the net flux. Recent work suggests that the critical knowledge gaps in CO2 surface fluxes could be addressed through the combined analysis of atmospheric carbonyl sulfide (COS) and radiocarbon in atmospheric CO2 (14CO2) [e.g. Campbell et al., 2008; Graven et al., 2009]. The 14CO2 approach relies on mass balance assumptions about atmospheric CO2 and the large differences in 14CO2 abundance between fossil and natural sources of CO2 [Levin et al., 2003]. COS, meanwhile, is a potentially transformative tracer of photosynthesis because its variability in the atmosphere has been found to be influenced primarily by vegetative uptake, scaling linearly will gross primary production (GPP) [Kettle et al., 20027]. Taken together, these two observations provide constraints on two of the three main components of the CO2 budget at the urban scale: photosynthesis and fossil fuel emissions. The third component, respiration, can then be determined by difference if the net flux is known. Here we present a general overview of our synthesized model-observation approach for improving surface flux estimates of CO2 for the upwind fetch of a ~30m tower located in Livermore, CA, USA, a suburb (pop. ~80,000) at the eastern edge of the San Francisco Bay Area. Additionally, we will present initial results from a one week observational intensive, which includes continuous CO2, CH4, CO, SO2, NOx, and O3 observations in addition to measurements of 14CO2 and COS from air samples

  12. Estimation of 14CO2 flux at soil-atmosphere interface and distribution of 14C in forest ecosystem.

    PubMed

    Koarashi, Jun; Amano, Hikaru; Andoh, Mariko; Iida, Takao; Moriizumi, Jun

    2002-01-01

    To realize the dynamical behavior of 14C among exchangeable carbon reservoirs in terrestrial environment, a method for in situ determination of 14CO2 flux at soil-atmosphere interface and a high flow rate CO2 sampler were developed. This method allowed us to collect integrated quantity of CO2 for determining 14C activity over an extended time period under environmental conditions with minimal site disturbance. The 14CO2 flux from ground surface was estimated to be 1.59 x 10(-5) Bq m (-2) S (-1) in a forest floor with the method. The specific activities of 14C in environmental materials such as some biological and air samples were also determined in the vicinity of the place, where the flux measurement was made, to discuss the behavior of 14C in the forest ecosystem. The results indicated that fresh pine needles had a similar 14C specific activity to the atmospheric CO2 at the same height due to its fairly rapid equilibrium, 14C specific activity in the atmospheric CO2 has a concentration gradient near the ground surface and, at least in this site, CO2 with high 14C specific activity was generated by decomposition of soil organic matter which may be accumulated in soil as a result of former nuclear weapons tests.

  13. Atmospheric 14CO2 Over the mid Pacific Ocean and at Point Barrow, Alaska, USA From 2002 to 2004

    NASA Astrophysics Data System (ADS)

    Xu, X.; Trumbore, S.; Ajie, H.; Tyler, S.; Randerson, J.; Krakauer, N.

    2004-12-01

    14CO2 is a useful tracer for studying the carbon cycle, in terms of determining residence times and fluxes between different carbon reservoirs, and understanding the various underlying processes. Knowledge of the regional and global distribution of atmospheric 14CO2 is essential for many of these applications. We have recently begun measuring atmospheric 14CO2 in the mid-Pacific and at stations in the US to add to the sparse available data for atmospheric 14C distribution. Our samples represent air collected over the time span of a few minutes from flasks. All of our samples were analyzed for Δ 14C at the Keck AMS facility at UC Irvine. Atmospheric CO2 samples were collected on a shipboard transect over the Pacific Ocean between Los Angeles (34° N, 118° W) and Auckland, New Zealand (34° N, 177° W) from fall 2002 to spring 2004. These samples were also measured for C-trace gas abundance (CO, CH4 in addition to CO2, and their stable isotopes). The 2002 transect (collected from Sept. 23 to Oct. 4, 2002) terminated in Manzanillo, Mexico (16° N, 109° W) instead of from Los Angeles. The 2002 transect showed that Δ 14C in atmospheric CO2 in this latitude range was relatively uniform spatially during the collection period. The average Δ 14C value of all 24 samples was 79.9±2.3‰ (1σ ). The spread of the data was comparable to our analytical error estimated by standard measurements. There was a slight decreasing trend in Δ 14C of air CO2 northward of 6° N, consistent with an increase in fossil fuel inputs to air in the northern hemisphere. The 2003 transect (from July 2003 to Aug. 2003) was similar to that of 2002 transect, in terms of the latitudinal distribution. It gave an average Δ 14C value of 75.4±2.7‰ (1σ ), indicating a decrease of approximately 4.5‰ per year. Samples from a coastal mid-latitude sites (Montaña de Oro State Park, CA (35° N, 121° W) show a similar average Δ 14C value of 76.1±6.5‰ from January 10, 2003 to April 27, 2003

  14. Influence of exogenous urea on photosynthetic pigments, (14)CO 2 uptake, and urease activity in Elodea densa-environmental implications.

    PubMed

    Maleva, Maria; Borisova, Galina; Chukina, Nadezda; Nekrasova, Galina; Prasad, M N V

    2013-09-01

    This paper analyzes the effect of exogenous urea in increased concentration gradient (0, 100, 500 and 1,000 mg L(-1)) on photosynthetic pigments (measured spectrophotometrically), uptake of (14)CO2 (using radioisotope), and urease activity (by measuring ammonia with Nessler's reagent) in leaves of Elodea densa Planch. We have observed that low concentration of urea (100 mg L(-1)) stimulates the accumulation of photosynthetic pigments and intensifies photosynthesis in E. densa, whereas high concentration (1,000 mg L(-1)) suppresses these processes. Urease activity increased by approximately 2.7 and 8 fold when exogenous urea concentrations were 100 and 500 mg L(-1), respectively. However, exogenous urea in high concentration (1,000 mg L(-1)) decreased urease activity by 1.5 fold compared to the control. The necessity of mitigating urea and other nitrogen-containing compounds (NH3 from urea) in water bodies has been discussed with emphasis on the potential for phytoremediation of urea using common water weed viz. E. densa.

  15. Inferring high-resolution fossil fuel CO2 records at continental sites from combined 14CO2 and CO observations

    NASA Astrophysics Data System (ADS)

    Levin, Ingeborg; Karstens, Ute

    2007-04-01

    An uncertainty estimate of a purely observational approach to derive hourly regional fossil fuel CO2 offsets (ΔCO2(foss)) at continental CO2 monitoring sites is presented. Weekly mean 14C-based fossil fuel CO2 mixing ratios and corresponding regional CO offsets (ΔCO) are proposed to determine weekly mean ΔCO/ΔCO2(foss) ratios in order to derive hourly ΔCO2(foss) mixing ratios from hourly ΔCO measurements. Respective regional model estimates of CO and CO2(foss) are applied to test this approach and obtain root mean square errors of the correspondingly determined regional hourly fossil fuel CO2 component. The method is further validated with campaign-based observations in Heidelberg. The uncertainty of the proposed method turns out to increase with decreasing fossil fuel CO2 fraction ranging from about 15% up to 40% for continental Europe. Together with the uncertainty of the ΔCO/ΔCO2(foss) ratio, which is determined by the precision of the 14CO2 measurement, this method is still more accurate and precise than any model-based approach.

  16. The apparent absence of a pathway for synthesis of acetyl coenzyme A in pea chloroplasts: Lack of (14)CO 2 incorporation into lipids by the isolated organelle.

    PubMed

    Sherratt, D; Givan, C V

    1973-03-01

    We have examined the extent to which isotopic lable derived from photosynthetically fixed (14)CO2 can be transferred to lipids by aqueously isolated chloroplasts of Pisum sativum. Although photosynthetically active, chloroplast preparations incubated with (14)CO2 showed little or no accumulation of label in lipids under any condition tested. Under identical conditions the chloroplasts were readily able to incorporate [(14)C]acetate into the lipid fraction; a fatty-acid synthesizing system was therefore operative in these chloroplasts.The essential failure of the isolated chloroplasts to incorporate label from fixed (14)CO2 into fatty acids supports the view that the organelle itself does not possess a self-contained pathway for the synthesis of acetyl coenzyme A, and favours the possibility that a shuttle mechanism involving the participation of extra-chloroplastic enzymes may be responsible for supplying the chloroplast with acetyl coenzyme A in vivo.

  17. Breath /sup 14/CO2 after intravenous administration of (/sup 14/C)aminopyrine in liver diseases

    SciTech Connect

    Pauwels, S.; Geubel, A.P.; Dive, C.; Beckers, C.

    1982-01-01

    The determination of of /sup 14/CO2 in breath after oral administration of (/sup 14/C)aminopyrine has been proposed as a quantitative liver function test. In order to shorten the procedure and avoid misinterpretations related to variable rates of intestinal absorption, the (/sup 14/C)aminopyrine breath test (ABT) was performed after intravenous administration of (/sup 14/C)aminopyrine in 21 controls and 89 patients with biopsy-proven liver disease. The specific activity of the first hour sample corrected for body weight (SA1) was the most discriminant expression of breath data. The SA1 value, expressed as the percentage of the administered dose, was 0.86 +/- 0.1% (mean +/- SD) in controls and significantly less in patients (0.46 +/- 0.31%). Low values were observed in patients with untreated chronic active hepatitis (0.16 +/- 0.13%), alcoholic cirrhosis (0.2 +/ 0.15%0, and untreated postnecrotic cirrhosis (0.47 +/- 0.17%). In contrast, normal values were obtained in chronic persistent hepatitis (0.86 +/- 0.13%) and 58% of noncirrhotic alcoholic liver diseases (0.83 +/- 0.27%). The results of duplicate studies were reproducible and SA1 correlated with other conventional liver function tests, including 45-min BSP retention. Among these, ABT was the most sensitive screening test for the presence of cirrhosis, especially in alcoholic patients, where it allowed a sharp distinction between cirrhotic and noncirrhotic cases. The results obtained in chronic hepatitis suggested that ABT may provide a reliable index of the activity of the disease. In our hands, intravenous ABT, performed over a 1-hr period, was a fast, sensitive, and discriminant liver function test.

  18. Linking emissions of fossil fuel CO2 and other anthropogenic trace gases using atmospheric 14CO2

    NASA Astrophysics Data System (ADS)

    Miller, John B.; Lehman, Scott J.; Montzka, Stephen A.; Sweeney, Colm; Miller, Benjamin R.; Karion, Anna; Wolak, Chad; Dlugokencky, Ed J.; Southon, John; Turnbull, Jocelyn C.; Tans, Pieter P.

    2012-04-01

    Atmospheric CO2 gradients are usually dominated by the signal from net terrestrial biological fluxes, despite the fact that fossil fuel combustion fluxes are larger in the annual mean. Here, we use a six year long series of 14CO2 and CO2 measurements obtained from vertical profiles at two northeast U.S. aircraft sampling sites to partition lower troposphere CO2 enhancements (and depletions) into terrestrial biological and fossil fuel components (Cbio and Cff). Mean Cff is 1.5 ppm, and 2.4 ppm when we consider only planetary boundary layer samples. However, we find that the contribution of Cbio to CO2 enhancements is large throughout the year, and averages 60% in winter. Paired observations of Cff and the lower troposphere enhancements (Δgas) of 22 other anthropogenic gases (CH4, CO, halo- and hydrocarbons and others) measured in the same samples are used to determine apparent emission ratios for each gas. We then scale these ratios by the well known U.S. fossil fuel CO2 emissions to provide observationally based estimates of national emissions for each gas and compare these to "bottom up" estimates from inventories. Correlations of Δgas with Cff for almost all gases are statistically significant with median r2for winter, summer and the entire year of 0.59, 0.45, and 0.42, respectively. Many gases exhibit statistically significant winter:summer differences in ratios that indicate seasonality of emissions or chemical destruction. The variability of ratios in a given season is not readily attributable to meteorological or geographic variables and instead most likely reflects real, short-term spatiotemporal variability of emissions.

  19. Observations of Atmospheric Δ(14)CO2 at the Global and Regional Background Sites in China: Implication for Fossil Fuel CO2 Inputs.

    PubMed

    Niu, Zhenchuan; Zhou, Weijian; Cheng, Peng; Wu, Shugang; Lu, Xuefeng; Xiong, Xiaohu; Du, Hua; Fu, Yunchong

    2016-11-15

    Six months to more than one year of atmospheric Δ(14)CO2 were measured in 2014-2015 at one global background site in Waliguan (WLG) and four regional background sites at Shangdianzi (SDZ), Lin'an (LAN), Longfengshan (LFS) and Luhuitou (LHT), China. The objectives of the study are to document the Δ(14)CO2 levels at each site and to trace the variations in fossil fuel CO2 (CO2ff) inputs at regional background sites. Δ(14)CO2 at WLG varied from 7.1 ± 2.9‰ to 32.0 ± 3.2‰ (average 17.1 ± 6.8‰) in 2015, with high values generally in autumn/summer and low values in winter/spring. During the same period, Δ(14)CO2 values at the regional background sites were found to be significantly (p < 0.05) lower than those at WLG, indicating different levels of CO2ff inputs at those sites. CO2ff concentrations at LAN (12.7 ± 9.6 ppm) and SDZ (11.5 ± 8.2 ppm) were significantly (p < 0.05) higher than those at LHT (4.6 ± 4.3 ppm) in 2015. There were no significant (p > 0.05) seasonal differences in CO2ff concentrations for the regional sites. Regional sources contributed in part to the CO2ff inputs at LAN and SDZ, while local sources dominated the trend observed at LHT. These data provide a preliminary understanding of atmospheric Δ(14)CO2 and CO2ff inputs for a range of Chinese background sites.

  20. Instantaneous and continuous measurement of /sup 14/C-labeled substrate oxidation to /sup 14/CO2 by minute tissue specimens: an ionization chamber method

    SciTech Connect

    Davidson, W.D.; Klein, K.L.; Kurokawa, K.; Soll, A.H.

    1981-06-01

    The vibrating reed electrometer and ionization chamber have been adapted for the instantaneous and continuous measurement of /sup 14/C-labeled substrate oxidation to /sup 14/CO2 by minute quantities of isolated tissues. This modified technique, utilizing a ''closed'' circulation incubation system, is 10-50 times as sensitive as the previously described ''open'' circulation techniques. Substrate oxidation curves are described for human erythrocytes and polymorphonuclear leucocytes, canine parietal cells and isolated segments of the rat nephron. This apparatus should prove to be a useful tool for metabolic studies of small quantities of isolated tissue.

  1. How old is the carbon that forests respire? Seasonal patterns in soil and ecosystem 14CO2 from a hardwood forest in Northern Wisconsin

    NASA Astrophysics Data System (ADS)

    Phillips, C. L.; McFarlane, K. J.; Desai, A. R.

    2012-12-01

    While radiocarbon (14C) abundance in soil organic matter is often used to assess long-term soil C turnover rates, little is known about fluctuations in the activity of different soil C pools at seasonal to annual timescales. Working at Willow Creek AmeriFlux site in Northern Wisconsin, we used 14C measurements of soil-respired CO2 to detect fluctuations in the relative activity of slow- and fast-turnover C pools, the former of which is comparatively enriched in "bomb" 14C. We also characterized 14CO2 above the forest canopy to determine whether 14C-enriched soil sources could be detected in the atmosphere. Over 2012, we found heterotrophic soil respiration (from a root-exclusion plot) had a seasonal range in Δ14C exceeding 40‰, with more bomb-C respired at higher soil temperatures. Compared to respired Δ14C in laboratory soil incubations, in situ measurements showed little vertical variation in Δ14C through the soil profile, suggesting important transport processes are missed in laboratory experiments. In bulk soil profiles, seasonal patterns in 14CO2 were less clear due to root contributions. During the summer, roots contributed approximately 50% of total soil respiration, and reduced respired Δ14C by about 20‰. Although soil-respired Δ14C was generally 20-60‰ higher than the background atmosphere, soil contributions were difficult to detect in atmospheric measurements, because theoretical Δ14C enhancements were close to our analytical resolution. Additionally, canopy atmospheric Δ14CO2 may have been influenced by variability in 14C at higher atmospheric levels, relating to fossil-C contributions. In conclusion, we observed large seasonal fluctuations in Δ14C that were related to root contributions as well as changes in the activity of organic C pools; however, analytical sensitivity was not high enough to detect these fluctuations in atmospheric measurements. This work was performed under the auspices of the U.S. Department of Energy by Lawrence

  2. Separation of biospheric and fossil fuel fluxes of CO2 by atmospheric inversion of CO2 and 14CO2 measurements: Observation System Simulations

    NASA Astrophysics Data System (ADS)

    Basu, Sourish; Bharat Miller, John; Lehman, Scott

    2016-05-01

    National annual total CO2 emissions from combustion of fossil fuels are likely known to within 5-10 % for most developed countries. However, uncertainties are inevitably larger (by unknown amounts) for emission estimates at regional and monthly scales, or for developing countries. Given recent international efforts to establish emission reduction targets, independent determination and verification of regional and national scale fossil fuel CO2 emissions are likely to become increasingly important. Here, we take advantage of the fact that precise measurements of 14C in CO2 provide a largely unbiased tracer for recently added fossil-fuel-derived CO2 in the atmosphere and present an atmospheric inversion technique to jointly assimilate observations of CO2 and 14CO2 in order to simultaneously estimate fossil fuel emissions and biospheric exchange fluxes of CO2. Using this method in a set of Observation System Simulation Experiments (OSSEs), we show that given the coverage of 14CO2 measurements available in 2010 (969 over North America, 1063 globally), we can recover the US national total fossil fuel emission to better than 1 % for the year and to within 5 % for most months. Increasing the number of 14CO2 observations to ˜ 5000 per year over North America, as recently recommended by the National Academy of Science (NAS) (Pacala et al., 2010), we recover monthly emissions to within 5 % for all months for the US as a whole and also for smaller, highly emissive regions over which the specified data coverage is relatively dense, such as for the New England states or the NY-NJ-PA tri-state area. This result suggests that, given continued improvement in state-of-the art transport models, a measurement program similar in scale to that recommended by the NAS can provide for independent verification of bottom-up inventories of fossil fuel CO2 at the regional and national scale. In addition, we show that the dual tracer inversion framework can detect and minimize biases in

  3. Nutrient Availability and Carbon Cycling in a Subarctic Wetland - a Pulse Labeling Experiment

    NASA Astrophysics Data System (ADS)

    Lund, M.; Mastepanov, M.; Christensen, T. R.; Ström, L.

    2008-12-01

    Northern wetlands are important ecosystems in the context of biospheric feedbacks to climate change, due to the large storage of organic C in their soils. Nitrogen deposition and increased nutrient availability in soils following climate warming may cause changes in these ecosystems affecting greenhouse gas exchange. We have studied C cycling under controlled laboratory conditions using whole ecosystem monoliths with intact surface vegetation from a fertilization experiment in a north Swedish subarctic wetland. The experimental site has been fertilized with N and P since 2006, and during autumn 2007, three monoliths from fertilized plots and three monoliths from control plots were collected. The monoliths were installed in a growth chamber where temperature and radiation could be controlled to simulate natural conditions. The monoliths were isolated from the surroundings using transparent chambers connected to tubing with a constant inflow of atmospheric air. The outflowing air from all six chambers and a reference chamber were analyzed for CO2 and CH4. Each monolith was exposed to 14CO2 during an hour under daytime irradiation conditions allowing vegetation to assimilate labeled CO2. During more than 70 days after labeling, we monitored the amount of 14CO2 and 14CH4 in outflowing air, as well as the amount of 14C in soil water. Above and belowground plant biomass were analyzed for 14C after the experiment was terminated. We hypothesize that fertilization will lower 14C root to shoot ratio compared to control. This in turn will lead to decreased 14C root exudation rates in fertilized monoliths, which may lower substrate availability for methanogenesis. The results from this experiment will be presented and discussed at the conference.

  4. Pulse labelling for carbon turnover measurements with a CRDS for wetlands - challenges and solutions

    NASA Astrophysics Data System (ADS)

    Strozecki, Marcin; Samson, Mateusz; Chojnicki, Bogdan H.; Leśny, Jacek; Moni, Christophe; Urbaniak, Marek; Olejnik, Janusz; Juszczak, Radosław; Silvennoinnen, Hanna

    2016-04-01

    Carbon turnover in peatlands has commonly been studied by estimating carbon allocation and decomposition rates by litterbags, assessing changes in carbon stocks and by measuring the biosphere-atmosphere exchange of carbon gases with various chamber methods or by eddy covariance. In addition, C turnover rates have been measured with pulse labelling methods using 13C and 14C (e.g. Bahn et al. 2009). Pulse labeling (PL) studies in wetlands are, however, sparse (e.g. Gao et al. 2015), presumably as descriptive high water table levels and relatively low productivity render successful tracing difficult. Quite low cost fast-gas-analyzers (Cavity Ring Down Spectrometry, CRDS) make PL experiments more cost-worthy, but their applicability at wetland field and further for measuring elevated 13C - levels is challenging. We carried out a PL as a pre-experiment for a larger labelling campaign of the Wetman-project at Rzecin wetland in Poland. We aimed at defining 1) The optimum labeling for the peatland site, 2) The importance of dissolved 13CO2 both for the loss of the pulse label and for the potential bias to respiratory flux, 3) The reliability of the 13CO2 and 13CH4 measurements when using dynamic closed chambers with a factory calibrated CRDS. We labelled the study area by a transparent chamber combined to Picarro CRDS G2201-i (C input during labelling 4.9 μg 13C). After labelling, we monitored the respiratory 13CO2 flux and the 13CO2 content in the peat water over a 10d- period. In addition, we measured the vegetation13C before labelling and 10 days after. Plants assimilated 2.1 μg C of the added 13C. Half of the recovered 13CO2 (3.6 μg C) originated from respiration. Nearly one third of added 13CO2 immediately dissolved in the water, which at the end of the experiment retained 0.5 μg 13C. Finally, 127 % of the added label was recovered. The high recovery was mainly caused by overestimation in the δ13C. The results of our pre-experiment indicate that 1) Measuring

  5. Belowground carbon allocation dynamics in changing environments: insights from in situ pulse labeling studies

    NASA Astrophysics Data System (ADS)

    Bahn, M.

    2012-12-01

    Belowground carbon (C) allocation is a key process in ecosystems: it plays an important role for plant C storage, fuels root metabolism and provides substrates for soil microorganisms, with strong implications for microbial community composition and activity and thus soil organic matter turnover. Belowground C allocation has been well studied in young plants and mesocosms, and as long-term patterns in ecosystems. Much less is known on the short-term dynamics of C allocation in mature plants and ecosystems, which reflect more closely the actual processes underlying observed C allocation patterns and the mechanisms determining responses to changing environmental conditions. C allocation dynamics can best be analyzed with isotopic pulse labeling experiments, which permit a tracing of recently photo-assimilated C to carbohydrate pools, microbial communities and respiratory fluxes. This overview talk will highlight the potential and limitations of in situ isotopic tracer experiments for assessing belowground C allocation dynamics in changing environments, summarize some major recent findings and point towards emerging research questions.

  6. Interaction between rhizosphere microorganisms and plant roots: 13C fluxes in the rhizosphere after pulse labeling

    NASA Astrophysics Data System (ADS)

    Yevdokimov, I. V.; Ruser, R.; Buegger, F.; Marx, M.; Munch, J. C.

    2007-07-01

    The input dynamics of labeled C into pools of soil organic matter and CO2 fluxes from soil were studied in a pot experiment with the pulse labeling of oats and corn under a 13CO2 atmosphere, and the contribution of the root and microbial respiration to the emission of CO2 from the soil was determined from the fluxes of labeled C in the microbial biomass and the evolved carbon dioxide. A considerable amount of 13C (up to 96% of the total amount of the label found in the rhizosphere soil) was incorporated into the biomass of the rhizosphere microorganisms. The diurnal fluctuations of the labeled C pools in the microbial biomass, dissolved organic carbon, and CO2 released in the rhizosphere of oats and corn were related to the day/night changes, i.e., to the on and off periods of the photosynthetic activity of the plants. The average contribution of the corn root respiration (70% of the total CO2 emission from the soil surface) was higher than that of the oats roots (44%), which was related to the lower incorporation of rhizodeposit carbon into the microbial biomass in the soil under the corn plants than in the soil under the oats plants.

  7. Δ(14)CO2 from dark respiration in plants and its impact on the estimation of atmospheric fossil fuel CO2.

    PubMed

    Xiong, Xiaohu; Zhou, Weijian; Cheng, Peng; Wu, Shugang; Niu, Zhenchuan; Du, Hua; Lu, Xuefeng; Fu, Yunchong; Burr, George S

    2017-04-01

    Radiocarbon ((14)C) has been widely used for quantification of fossil fuel CO2 (CO2ff) in the atmosphere and for ecosystem source partitioning studies. The strength of the technique lies in the intrinsic differences between the (14)C signature of fossil fuels and other sources. In past studies, the (14)C content of CO2 derived from plants has been equated with the (14)C content of the atmosphere. Carbon isotopic fractionation mechanisms vary among plants however, and experimental study on fractionation associated with dark respiration is lacking. Here we present accelerator mass spectrometry (AMS) radiocarbon results of CO2 respired from 21 plants using a lab-incubation method and associated bulk organic matter. From the respired CO2 we determine Δ(14)Cres values, and from the bulk organic matter we determine Δ(14)Cbom values. A significant difference between Δ(14)Cres and Δ(14)Cbom (P < 0.01) was observed for all investigated plants, ranging from -42.3‰ to 10.1‰. The results show that Δ(14)Cres values are in agreement with mean atmospheric Δ(14)CO2 for several days leading up to the sampling date, but are significantly different from corresponding bulk organic Δ(14)C values. We find that although dark respiration is unlikely to significantly influence the estimation of CO2ff, an additional bias associated with the respiration rate during a plant's growth period should be considered when using Δ(14)C in plants to quantify atmospheric CO2ff. Copyright © 2017 Elsevier Ltd. All rights reserved.

  8. Biosphere-atmosphere gross carbon exchange flux and the δ13CO2 and Δ14CO2 disequilibria constrained by the biospheric excess radiocarbon inventory

    NASA Astrophysics Data System (ADS)

    Naegler, Tobias; Levin, Ingeborg

    2009-09-01

    Estimates of the global biospheric excess 14C inventory IB14,E from Naegler and Levin (2009) were used to constrain the age distribution a(τ) in heterotrophically respired CO2 with a simple (radio)carbon model of the global biosphere. Subsequently, a(τ) could be used to estimate the global gross carbon exchange FeqC (net primary productivity, NPP, and heterotrophic respiration) between atmosphere and biosphere as well as both the δ13C and Δ14C signatures in heterotrophically respired CO2 (δ13CRH and Δ14CRH, respectively). Our estimates of FeqC range from 41 to 64 petagrams carbon per year (Pg C a-1), with a best estimate of 55 Pg C a-1. The uncertainty of this value is dominated by the uncertainties of IB14,E and of the net biospheric uptake of anthropogenic CO2. Limitations intrinsic to our approach as well as uncertainties in effective global average atmospheric Δ14CO2 add an uncertainty of ±3 Pg C a-1. The δ13CRH of heterotrophically respired CO2 lags the δ13C of assimilated CO2 by ˜10-17 years. This leads to a somewhat smaller estimate of the biospheric 13CO2 disequilibrium flux than previously assumed. Δ14CRH increased from ˜-20‰ in the early 1950s to maximum values of 300-325‰ in the late 1960s/early 1970s. In the 1980s, when the maximum IB14,E occurred, Δ14CRH was in a transient equilibrium with the atmosphere. The Δ14C disequilibrium between atmosphere and biosphere increased to Δ14CDIS = 20-50‰ in the mid-1990s, before it dropped to 15-40‰ in 2005.

  9. Using annual plants as atmospheric 14CO2 samplers for regional fossil fuel emissions estimates: crop modeling and intensive sampling approaches

    NASA Astrophysics Data System (ADS)

    Bozhinova, D.; Peters, W.; Combe, M.; Palstra, S. W.; Meijer, H. A.; Krol, M. C.

    2010-12-01

    Using radiocarbon (14C) as a tracer for fossil fuel emissions is promising, even as sampling atmospheric 14CO2 for long periods of time is demanding and expensive. An alternative is to use plants to record the atmospheric carbon isotopic abundances, as plants naturally integrate carbon during their growing period by photosynthesis. A main uncertainty in this approach, however, is the unknown time period in which the uptake of CO2 has taken place. How plants “sample” the atmospheric carbon and transport it to their different parts depends strongly on their growth and developmental pattern. We use the Weather Research and Forecast model (WRF) together with a mechanistic crop growth model to quantify the representativeness of plant sampled atmospheric 14C mixing ratios on a regional scale. We compare our modeled results to measured 14C in maize and wheat samples from a region in the north of the Netherlands, affected by urban CO2 plumes as well as a local power plant. We find based on the modeled results that even in the absence of spatial fossil fuel gradients in the atmosphere, differences in plant growth rates can introduce Δ14C gradients of up to 3.5‰ over plants in the Netherlands. We furthermore use the simulated plant growth rates to narrow the period for which a plant sample can be used as a proxy, which will help to lower the uncertainty on estimated fossil fuel emissions. Our work provides first steps towards quantitatively using plant 14C sampling for verification of regional fossil fuel emissions. Map of Δ14C signature (in ‰) of spring wheat at flowering day, with grid resolution of 4x4 km. Plant growth is simulated by mechanistic crop growth model (SUCROS 2) with weather data over the growing season provided by WRF model. The temporal evolution of the 14C signature of the atmosphere is spatially uniform over the domain. The figure shows that differences in daily growth can introduce Δ14C gradients of up to 3.5‰ even in the absence of spatial

  10. Constraints on emissions of carbon monoxide, methane, and a suite of hydrocarbons in the Colorado Front Range using observations of 14CO2

    NASA Astrophysics Data System (ADS)

    LaFranchi, B. W.; Pétron, G.; Miller, J. B.; Lehman, S. J.; Andrews, A. E.; Dlugokencky, E. J.; Hall, B.; Miller, B. R.; Montzka, S. A.; Neff, W.; Novelli, P. C.; Sweeney, C.; Turnbull, J. C.; Wolfe, D. E.; Tans, P. P.; Gurney, K. R.; Guilderson, T. P.

    2013-11-01

    Atmospheric radiocarbon (14C) represents an important observational constraint on emissions of fossil-fuel derived carbon into the atmosphere due to the absence of 14C in fossil fuel reservoirs. The high sensitivity and precision that accelerator mass spectrometry (AMS) affords in atmospheric 14C analysis has greatly increased the potential for using such measurements to evaluate bottom-up emissions inventories of fossil fuel CO2 (CO2ff), as well as those for other co-emitted species. Here we use observations of 14CO2 and a series of primary hydrocarbons and combustion tracers from discrete air samples collected between June 2009 and September 2010 at the National Oceanic and Atmospheric Administration Boulder Atmospheric Observatory (BAO; Lat: 40.050° N, Lon: 105.004° W) to derive emission ratios of each species with respect to CO2ff. The BAO tower is situated at the boundary of the Denver metropolitan area to the south and a large industrial and agricultural region to the north and east, making it an ideal location to study the contrasting mix of emissions from the activities in each region. The species considered in this analysis are carbon monoxide (CO), methane (CH4), acetylene (C2H2), benzene (C6H6), and C3-C5 alkanes. We estimate emissions for a subset of these species by using the Vulcan high resolution CO2ff emission data product as a reference. We find that CO is overestimated in the 2008 National Emissions Inventory (NEI08) by a factor of ~2. A close evaluation of the inventory suggests that the ratio of CO emitted per unit fuel burned from on-road gasoline vehicles is likely over-estimated by a factor of 2.5. Using a wind-directional analysis of the data, we find enhanced concentrations of CH4, relative to CO2ff, in air influenced by emissions to the north and east of the BAO tower when compared to air influenced by emissions in the Denver metro region to the south. Along with enhanced CH4, the strongest enhancements of the C3-C5 alkanes are also

  11. Constraints on emissions of hydrocarbons and combustion tracers in the Colorado Front Range using observations of 14CO2 at the Boulder Atmospheric Observatory (BAO)

    NASA Astrophysics Data System (ADS)

    LaFranchi, B. W.; Petron, G.; Miller, J. B.; Lehman, S. J.; Andrews, A. E.; Dlugokencky, E. J.; Miller, B. R.; Montzka, S. A.; Turnbull, J. C.; Tans, P. P.; Guilderson, T. P.

    2011-12-01

    Bottom-up inventories of trace gases formed as a byproduct of fossil fuel combustion have significant uncertainty associated with them because of the difficulty in quantifying the relationship between the mass of fuel consumed and the mass emitted; this is in contrast to the near stoichiometric production of CO2 from the combustion of hydrocarbons. Emissions of species such as CO, CH4, acetylene, and benzene depend greatly on a number of variables including fuel type, combustion temperature, oxidant-to-fuel ratio, and post-combustion tail-pipe or flue-stack "scrubbing". Given the impact of many of these combustion by-products on air quality, human health, and climate, atmospheric observations are necessary in order to critically evaluate bottom-up emissions estimates. Atmospheric radiocarbon (14C) represents an important observational constraint on emissions of fossil-fuel derived carbon into the atmosphere due to the near absence of 14C in fossil fuel reservoirs. The high sensitivity and precision that accelerator mass spectrometry (AMS) affords in atmospheric 14C analysis has greatly increased the potential for using such measurements to verify bottom-up emissions inventories of fossil fuel CO2 (CO2ff), as well as other co-emitted species. Here we use observations of 14CO2 and a series of hydrocarbons and combustion tracers from the Boulder Atmospheric Observatory (BAO; Lat: 40.050o, Lon: -105.004o) to derive emission ratios of each species to CO2. From these emission ratios, we estimate absolute emission fluxes of these species by using an existing CO2ff inventory. Among the species considered are CO, CH4, acetylene (C2H2), benzene (C6H6), and C3-C5 alkanes. Comparisons of top-down emissions estimates are made to existing inventories of these species for the region, where available, as well as to previous efforts to estimate emissions from atmospheric observations in the Colorado Front Range.We find that CO is overestimated in the NEI 2008 by a factor of ~2; a

  12. Carbon allocation belowground in Pinus pinaster using stable carbon isotope pulse labeling technique

    NASA Astrophysics Data System (ADS)

    Dannoura, M.; Bosc, A.; Chipeaux, C.; Sartore, M.; Lambrot, C.; Trichet, P.; Bakker, M.; Loustau, D.; Epron, D.

    2010-12-01

    Carbon allocation belowground competes with aboveground growth and biomass production. In the other hand, it contributes to resource acquisition such as nutrient, water and carbon sequestration in soil. Thus, a better characterization of carbon flow from plant to soil and its residence time within each compartment is an important issue for understanding and modeling forest ecosystem carbon budget. 13C pulse labeling of whole crown was conducted at 4 seasons to study the fate of assimilated carbon by photosynthesis into the root on 12 year old Pinus pinaster planted in the INRA domain of Pierroton. Maritime pine is the most widely planted species in South-West Europe. Stem, root and soil CO2 effluxes and their isotope composition were measured continuously by tunable diode laser absorption spectroscopy with a trace gas analyzer (TGA 100A; Campbell Scientific) coupled to flow-through chambers. 13CO2 recovery and peak were observed in respiration of each compartment after labeling. It appeared sequentially from top of stem to bottom, and to coarse root. The maximum velocity of carbon transfer was calculated as the difference in time lag of recovery between two positions on the trunk or on the root. It ranged between 0.08-0.2 m h-1 in stem and between 0.04-0.12 m h-1 in coarse root. This velocity was higher in warmer season, and the difference between time lag of recovery and peak increased after first frost. Photosynthates arrived underground 1.5 to 5 days after labeling, at similar time in soil CO2 effluxes and coarse root respiration. 0.08-1.4 g of carbon was respired per tree during first 20 days following labeling. It presented 0.6 -10% of 13C used for labeling and it is strongly related to seasons. The isotope signal was detected in fine root organs and microbial biomass by periodical core sampling. The peak was observed 6 days after labeling in early summer while it was delayed more than 10 days in autumn and winter with less amount of carbon allocated

  13. Soil matrix tracer contamination and canopy recycling did not impair ¹³CO₂ plant-soil pulse labelling experiments.

    PubMed

    Barthel, Matthias; Sturm, Patrick; Knohl, Alexander

    2011-09-01

    When conducting (13)CO(2) plant-soil pulse labelling experiments, tracer material might cause unwanted side effects which potentially affect δ(13)C measurements of soil respiration (δ(13)C(SR)) and the subsequent data interpretation. First, when the soil matrix is not isolated from the atmosphere, contamination of the soil matrix with tracer material occurs leading to a physical back-diffusion from soil pores. Second, when using canopy chambers continuously, (13)CO(2) is permanently re-introduced into the atmosphere due to leaf respiration which then aids re-assimilation of tracer material by the canopy. Accordingly, two climate chamber experiments on European beech saplings (Fagus sylvatica L.) were conducted to evaluate the influence of soil matrix (13)CO(2) contamination and canopy recycling on soil (13)CO(2) efflux during (13)CO(2) plant-soil pulse labelling experiments. For this purpose, a combined soil/canopy chamber system was developed which separates soil and canopy compartments in order to (a) prevent diffusion of (13)C tracer into the soil chamber during a (13)CO(2) canopy pulse labelling and (b) study stable isotope processes in soil and canopy individually and independently. In combination with laser spectrometry measuring CO(2) isotopologue mixing ratios at a rate of 1 Hz, we were able to measure δ(13)C in canopy and soil at very high temporal resolution. For the soil matrix contamination experiment, (13)CO(2) was applied to bare soil, canopy only or, simultaneously, to soil and canopy of the beech trees. The obtained δ(13)C(SR) fluxes from the different treatments were then compared with respect to label re-appearance, first peak time and magnitude. By determining the δ(13)C(SR) decay of physical (13)CO(2) back-diffusion from bare soils (contamination), it was possible to separate biological and physical components in δ(13)C(SR) of a combined flux of both. A second pulse labelling experiment, with chambers permanently enclosing the canopy

  14. Pulse-labelling trees to study carbon allocation dynamics: a review of methods, current knowledge and future prospects.

    PubMed

    Epron, Daniel; Bahn, Michael; Derrien, Delphine; Lattanzi, Fernando Alfredo; Pumpanen, Jukka; Gessler, Arthur; Högberg, Peter; Maillard, Pascale; Dannoura, Masako; Gérant, Dominique; Buchmann, Nina

    2012-06-01

    Pulse-labelling of trees with stable or radioactive carbon (C) isotopes offers the unique opportunity to trace the fate of labelled CO(2) into the tree and its release to the soil and the atmosphere. Thus, pulse-labelling enables the quantification of C partitioning in forests and the assessment of the role of partitioning in tree growth, resource acquisition and C sequestration. However, this is associated with challenges as regards the choice of a tracer, the methods of tracing labelled C in tree and soil compartments and the quantitative analysis of C dynamics. Based on data from 47 studies, the rate of transfer differs between broadleaved and coniferous species and decreases as temperature and soil water content decrease. Labelled C is rapidly transferred belowground-within a few days or less-and this transfer is slowed down by drought. Half-lives of labelled C in phloem sap (transfer pool) and in mature leaves (source organs) are short, while those of sink organs (growing tissues, seasonal storage) are longer. (13)C measurements in respiratory efflux at high temporal resolution provide the best estimate of the mean residence times of C in respiratory substrate pools, and the best basis for compartmental modelling. Seasonal C dynamics and allocation patterns indicate that sink strength variations are important drivers for C fluxes. We propose a conceptual model for temperate and boreal trees, which considers the use of recently assimilated C versus stored C. We recommend best practices for designing and analysing pulse-labelling experiments, and identify several topics which we consider of prime importance for future research on C allocation in trees: (i) whole-tree C source-sink relations, (ii) C allocation to secondary metabolism, (iii) responses to environmental change, (iv) effects of seasonality versus phenology in and across biomes, and (v) carbon-nitrogen interactions. Substantial progress is expected from emerging technologies, but the largest challenge

  15. Quantifying the Length and Variance of the Eukaryotic Cell Cycle Phases by a Stochastic Model and Dual Nucleoside Pulse Labelling

    PubMed Central

    Weber, Tom Serge; Jaehnert, Irene; Schichor, Christian; Or-Guil, Michal; Carneiro, Jorge

    2014-01-01

    A fundamental property of cell populations is their growth rate as well as the time needed for cell division and its variance. The eukaryotic cell cycle progresses in an ordered sequence through the phases and and is regulated by environmental cues and by intracellular checkpoints. Reflecting this regulatory complexity, the length of each phase varies considerably in different kinds of cells but also among genetically and morphologically indistinguishable cells. This article addresses the question of how to describe and quantify the mean and variance of the cell cycle phase lengths. A phase-resolved cell cycle model is introduced assuming that phase completion times are distributed as delayed exponential functions, capturing the observations that each realization of a cycle phase is variable in length and requires a minimal time. In this model, the total cell cycle length is distributed as a delayed hypoexponential function that closely reproduces empirical distributions. Analytic solutions are derived for the proportions of cells in each cycle phase in a population growing under balanced growth and under specific non-stationary conditions. These solutions are then adapted to describe conventional cell cycle kinetic assays based on pulse labelling with nucleoside analogs. The model fits well to data obtained with two distinct proliferating cell lines labelled with a single bromodeoxiuridine pulse. However, whereas mean lengths are precisely estimated for all phases, the respective variances remain uncertain. To overcome this limitation, a redesigned experimental protocol is derived and validated in silico. The novelty is the timing of two consecutive pulses with distinct nucleosides that enables accurate and precise estimation of both the mean and the variance of the length of all phases. The proposed methodology to quantify the phase length distributions gives results potentially equivalent to those obtained with modern phase-specific biosensor-based fluorescent

  16. Seasonal variations of belowground carbon transfer assessed by in situ 13CO2 pulse labelling of trees

    NASA Astrophysics Data System (ADS)

    Epron, D.; Ngao, J.; Dannoura, M.; Bakker, M. R.; Zeller, B.; Bazot, S.; Bosc, A.; Plain, C.; Lata, J. C.; Priault, P.; Barthes, L.; Loustau, D.

    2011-02-01

    Soil CO2 efflux is the main source of CO2 from forest ecosystems and it is tightly coupled to the transfer of recent photosynthetic assimilates belowground and their metabolism in roots, mycorrhiza and rhizosphere microorganisms feeding on root-derived exudates. The objectives of our study were to assess patterns of belowground carbon allocation among tree species and along seasons. Pure 13CO2 pulse labelling of the entire crown of three different tree species (beech, oak and pine) was carried out at distinct phenological stages. Excess 13C in soil CO2 efflux was tracked using tunable diode laser absorption spectrometry to determine time lags between the start of the labelling and the appearance of 13C in soil CO2 efflux and the amount of 13C allocated to soil CO2 efflux. Isotope composition (δ13C) of CO2 respired by fine roots and soil microbes was measured at several occasions after labelling, together with δ13C of bulk root tissue and microbial carbon. Time lags ranged from 0.5 to 1.3 days in beech and oak and were longer in pine (1.6-2.7 days during the active growing season, more than 4 days during the resting season), and the transfer of C to the microbial biomass was as fast as to the fine roots. The amount of 13C allocated to soil CO2 efflux was estimated from a compartment model. Seasonal patterns of carbon allocation to soil CO2 efflux differed markedly between species, with pronounced seasonal variations in pine and beech. In beech, it may reflect competition with other sinks (aboveground growth in late spring and storage in late summer) that were not observed in oak.

  17. Carbon assimilation and turnover in grassland vegetation using an in situ (13)CO(2) pulse labelling system.

    PubMed

    Ostle, N; Ineson, P; Benham, D; Sleep, D

    2000-01-01

    A mobile laboratory was developed to administer a controlled flow of (13)C labelled CO(2) at ambient concentrations ( approximately 350 ppm) in the field. The stable isotope delivery (SID) system consists of an isotope-mixing unit with flow control to a series of 12 independent labelling chambers. In-line CPU controlled infrared gas analysers allow automated measurement of chamber CO(2) concentrations and gas flow management. A preliminary experiment was established on an upland pasture located at the NERC Soil Biodiversity experimental site, Sourhope, UK, in August 1999. The objective of this investigation was to determine the magnitude of pulse-derived C incorporation into a typical upland plant community. To achieve this, the SID system was deployed to pulse-label vegetation with CO(2) enriched with (13)C (50 atom %) at ambient concentrations ( approximately 350 ppm) on two consecutive days in August 1999. Samples of headspace CO(2), shoot and root were taken on four occasions over a period of 28 days after (13)C labelling. These materials were then prepared for (13)C/(12)C ratio determination by continuous-flow/combustion/isotope ratio mass spectrometry (CF-C-IRMS). Results showed that pulse derived CO(2)-C was assimilated at a rate of 128 +/- 32 microg g shoot-C hour(-1). Dynamic samplings showed that pulse-derived (13)C concentrations in the labelled plant tissues declined by 77.4 +/- 6% after 48 hours. The rapid decline in (13)C concentrations in plant matter was the result of C loss from the plant in the form of respired CO(2) and root exudates, and dilution by subsequent unlabelled C assimilates. This novel system offers considerable potential for in situ tracer investigations.

  18. Seasonal variations of belowground carbon transfer assessed by in situ 13CO2 pulse labelling of trees

    NASA Astrophysics Data System (ADS)

    Epron, D.; Ngao, J.; Dannoura, M.; Bakker, M. R.; Zeller, B.; Bazot, S.; Bosc, A.; Plain, C.; Lata, J. C.; Priault, P.; Barthes, L.; Loustau, D.

    2011-05-01

    Soil CO2 efflux is the main source of CO2 from forest ecosystems and it is tightly coupled to the transfer of recent photosynthetic assimilates belowground and their metabolism in roots, mycorrhiza and rhizosphere microorganisms feeding on root-derived exudates. The objective of our study was to assess patterns of belowground carbon allocation among tree species and along seasons. Pure 13CO2 pulse labelling of the entire crown of three different tree species (beech, oak and pine) was carried out at distinct phenological stages. Excess 13C in soil CO2 efflux was tracked using tuneable diode laser absorption spectrometry to determine time lags between the start of the labelling and the appearance of 13C in soil CO2 efflux and the amount of 13C allocated to soil CO2 efflux. Isotope composition (δ13C) of CO2 respired by fine roots and soil microbes was measured at several occasions after labelling, together with δ13C of bulk root tissue and microbial carbon. Time lags ranged from 0.5 to 1.3 days in beech and oak and were longer in pine (1.6-2.7 days during the active growing season, more than 4 days during the resting season), and the transfer of C to the microbial biomass was as fast as to the fine roots. The amount of 13C allocated to soil CO2 efflux was estimated from a compartment model. It varied between 1 and 21 % of the amount of 13CO2 taken up by the crown, depending on the species and the season. While rainfall exclusion that moderately decreased soil water content did not affect the pattern of carbon allocation to soil CO2 efflux in beech, seasonal patterns of carbon allocation belowground differed markedly between species, with pronounced seasonal variations in pine and beech. In beech, it may reflect competition with the strength of other sinks (aboveground growth in late spring and storage in late summer) that were not observed in oak. We report a fast transfer of recent photosynthates to the mycorhizosphere and we conclude that the patterns of carbon

  19. Whole Ecosystem Low-level 14C Pulse Labeling and CO2 Flux Measurements in a Boreal Forest

    NASA Astrophysics Data System (ADS)

    Carbone, M.; Trumbore, S.; Czimczik, C.; McDuffee, K.; McMillan, A.

    2004-12-01

    We developed a large volume, low level, 14C pulse-chase, field labeling method to determine the timing and contribution of recent photosynthetic products to total ecosystem respiration in a poorly drained black spruce forest stand in Manitoba, Canada. The site is part of a chronosequence of black spruce stands located in the BOREAS Northern Study Area (55N, 98W), and time since fire is 40 years. The radiocarbon addition was designed to produce a 14C signature of ~1500 times Modern for CO2 at ambient levels inside the ~37,000 L volume light chamber. At this level of labeling, the radioactivity in our 14C source (acidified sodium bicarbonate solution with specific activity of ~30 nCi/g) and in the chamber were well below levels that are regulated. We labeled two chambers in August 2004. The vegetation inside the first (37,000 L) chamber included black spruce trees (ranging from seedlings to 4 m tall) with feather moss and shrub understory. A second 14CO2 label was applied in a smaller chamber (500 L) containing only feather mosses. Both chambers were constructed from polyethylene plastic that allowed for 70 percent transmission of PAR. For seven days following the label, we measured the quantity and 14C content of soil respiration with small (10 L) dark chambers, above-ground respiration with branch bags, and total ecosystem respiration with a dark chamber. Live root and moss 14C content were measured by field incubations. Additionally, soil gas 14C content at two depths within the moss/organic layer was measured. Radiocarbon measurements are made using Accelerator Mass Spectrometry, which allows us to easily distinguish the presence of the label in small amounts (mg) of material. We will report the radiocarbon (delta 14C) signature of individual respiration sources. Preliminary results show that we can use these isotopic signatures to follow the labeled contribution of respiration from individual sources (moss, root/root exudates, and needle) to total ecosystem

  20. BrdU pulse labelling in vivo to characterise cell proliferation during regeneration and repair following injury to the airway wall in sheep.

    PubMed

    Yahaya, B; McLachlan, G; Collie, D D S

    2013-01-01

    The response of S-phase cells labelled with bromodeoxyuridine (BrdU) in sheep airways undergoing repair in response to endobronchial brush biopsy was investigated in this study. Separate sites within the airway tree of anaesthetised sheep were biopsied at intervals prior to pulse labelling with BrdU, which was administered one hour prior to euthanasia. Both brushed and spatially disparate unbrushed (control) sites were carefully mapped, dissected, and processed to facilitate histological analysis of BrdU labelling. Our study indicated that the number and location of BrdU-labelled cells varied according to the age of the repairing injury. There was little evidence of cell proliferation in either control airway tissues or airway tissues examined six hours after injury. However, by days 1 and 3, BrdU-labelled cells were increased in number in the airway wall, both at the damaged site and in the regions flanking either side of the injury. Thereafter, cell proliferative activity largely declined by day 7 after injury, when consistent evidence of remodelling in the airway wall could be appreciated. This study successfully demonstrated the effectiveness of in vivo pulse labelling in tracking cell proliferation during repair which has a potential value in exploring the therapeutic utility of stem cell approaches in relevant lung disease models.

  1. BrdU Pulse Labelling In Vivo to Characterise Cell Proliferation during Regeneration and Repair following Injury to the Airway Wall in Sheep

    PubMed Central

    Yahaya, B.; McLachlan, G.; Collie, D. D. S.

    2013-01-01

    The response of S-phase cells labelled with bromodeoxyuridine (BrdU) in sheep airways undergoing repair in response to endobronchial brush biopsy was investigated in this study. Separate sites within the airway tree of anaesthetised sheep were biopsied at intervals prior to pulse labelling with BrdU, which was administered one hour prior to euthanasia. Both brushed and spatially disparate unbrushed (control) sites were carefully mapped, dissected, and processed to facilitate histological analysis of BrdU labelling. Our study indicated that the number and location of BrdU-labelled cells varied according to the age of the repairing injury. There was little evidence of cell proliferation in either control airway tissues or airway tissues examined six hours after injury. However, by days 1 and 3, BrdU-labelled cells were increased in number in the airway wall, both at the damaged site and in the regions flanking either side of the injury. Thereafter, cell proliferative activity largely declined by day 7 after injury, when consistent evidence of remodelling in the airway wall could be appreciated. This study successfully demonstrated the effectiveness of in vivo pulse labelling in tracking cell proliferation during repair which has a potential value in exploring the therapeutic utility of stem cell approaches in relevant lung disease models. PMID:23533365

  2. In situ assessment of the velocity of carbon transfer by tracing 13 C in trunk CO2 efflux after pulse labelling: variations among tree species and seasons.

    PubMed

    Dannoura, Masako; Maillard, Pascale; Fresneau, Chantal; Plain, Caroline; Berveiller, Daniel; Gerant, Dominique; Chipeaux, Christophe; Bosc, Alexandre; Ngao, Jérôme; Damesin, Claire; Loustau, Denis; Epron, Daniel

    2011-04-01

    Phloem is the main pathway for transferring photosynthates belowground. In situ(13) C pulse labelling of trees 8-10 m tall was conducted in the field on 10 beech (Fagus sylvatica) trees, six sessile oak (Quercus petraea) trees and 10 maritime pine (Pinus pinaster) trees throughout the growing season. Respired (13) CO2 from trunks was tracked at different heights using tunable diode laser absorption spectrometry to determine time lags and the velocity of carbon transfer (V). The isotope composition of phloem extracts was measured on several occasions after labelling and used to estimate the rate constant of phloem sap outflux (kP ). Pulse labelling together with high-frequency measurement of the isotope composition of trunk CO2 efflux is a promising tool for studying phloem transport in the field. Seasonal variability in V was predicted in pine and oak by bivariate linear regressions with air temperature and soil water content. V differed among the three species consistently with known differences in phloem anatomy between broadleaf and coniferous trees. V increased with tree diameter in oak and beech, reflecting a nonlinear increase in volumetric flow with increasing bark cross-sectional area, which suggests changes in allocation pattern with tree diameter in broadleaf species. Discrepancies between V and kP indicate vertical changes in functional phloem properties.

  3. Effects of season and nitrogen supply on the partitioning of recently fixed carbon in understory vegetation using a 13CO2 pulse labeling technique

    NASA Astrophysics Data System (ADS)

    Hasselquist, Niles; Metcalfe, Daniel; Högberg, Peter

    2013-04-01

    Vegetation research in boreal forests has traditionally been focused on trees, with little attention given to understory vegetation. However, understory vegetation has been identified as a key driver for the functioning of boreal forests and may play an important role in the amount of carbon (C) that is entering and leaving these forested ecosystems. We conducted a large-scale 13C pulse labeling experiment to better understand how recently fixed C is allocated in the understory vegetation characteristic of boreal forests. We used transparent plastic chambers to pulse label the understory vegetation with enriched 13CO2 in the early (June) and late (August) growing seasons. This study was also replicated across a nitrogen (N) fertilization treatment to better understand the effects of N availability on C allocation patterns. We present data on the amount of 13C label found in different components of the understory vegetation (i.e. leaves, stems, lichens, mosses, rhizomes and fine roots) as well as CO2 efflux. Additionally, we provide estimates of C residence time (MRT) among the different components and examine how MRT of C is affected by seasonality and N availability. Seasonality had a large effect on how recently fixed C is allocated in understory vegetation, whereas N fertilization influenced the MRT of C in the different components of ericaceous vegetation. Moreover, there was a general trend that N additions increased the amount of 13C in CO2 efflux compared to the amount of 13C in biomass, suggesting that N fertilization may lead to an increase in the utilization of recently fixed C, whereas N-limitation promotes the storage of recently fixed C.

  4. Applicability of a "Multi-Stage Pulse Labeling" (15)N Approach to Phenotype N Dynamics in Maize Plant Components during the Growing Season.

    PubMed

    de Oliveira Silva, Amanda; Camberato, James J; Coram, Tristan; Filley, Timothy; Vyn, Tony J

    2017-01-01

    Highlights This work utilizes "multi-stage pulse labeling" (15)N applications, primarily during reproductive growth stages, as a phenotyping strategy to identify maize hybrids with superior N use efficiency (NUE) under low N conditions. Research using labeled isotopic N ((15)N) can precisely quantify fertilizer nitrogen (N) uptake and organ-specific N allocation in field crops such as maize (Zea mays L.). The overall research objective was to study plant N uptake patterns potentially correlated with N use efficiency (NUE) in field-grown maize hybrids using a "multi-stage pulse labeling" (15)N phenotyping strategy with an emphasis on the reproductive period. Five hybrids varying in NUE were compared under zero N fertilizer application (0N) plus a moderate rate of 112 kg N ha(-1) (112N) in 2013 (2 locations) and 2014 growing seasons. The equivalent of 3.2 (2013) to 2.1 (2014) kg of (15)N ha(-1), as labeled Ca((15)NO3)2, was injected into soil on both sides of consecutive plants at multiple stages between V14 and R5. Aboveground plant biomass was primarily collected in short-term intervals (4-6 days after each (15)N application) in both years, and following a single long-term interval (at R6 after (15)N injection at R1) in 2014. Averaged across hybrids and site-years, the moderate N rate (112N) increased absolute (15)N uptake at all stages; however, plants in the 0N treatment allocated proportionally more (15)N to reproductive organs. Before flowering, short-term recovery of (15)N ((15)Nrec) totaled ~0.30 or 0.40 kg kg(-1) of the (15)N applied, and ~50% of that accumulated (15)Nu was found in leaves and 40% in stems. After flowering, plant (15)Nrec totaled ~0.30 kg kg(-1) of (15)N applied, and an average 30% of accumulated (15)Nu was present in leaves, 17% in stems, and the remainder-usually the majority-in ears. At the R5 stage, despite a declining overall rate of (15)N uptake per GDD thermal unit, plant (15)Nrec represented ~0.25 kg kg(-1) of (15)N applied, of which

  5. Field 13CO2 pulse labeling reveals differential partitioning patterns of photoassimilated carbon in response to livestock exclosure in a Kobresia meadow

    NASA Astrophysics Data System (ADS)

    Zou, J.; Zhao, L.; Xu, S.; Xu, X.; Chen, D.; Li, Q.; Zhao, N.; Luo, C.; Zhao, X.

    2014-08-01

    Livestock exclosure has been widely used as an approach for grassland restoration. However, the effects of exclosures on grasslands are controversial and can depend on many factors, such as the grassland ecosystem types, evolutionary history and so on. In this study, we conduct field experiments to investigate the variations of the ecosystem function in response to livestock exclosure in a Kobresia humilis meadow with 6 years of grazing exclosure on the Qinghai-Tibetan Plateau. We focused on two ecosystem functions: plant community structure and ecosystem carbon cycling. The plant aboveground productivity, plant diversity and the composition of plant functional groups of the meadow were addressed as the indicators of the plant community structure. The 13C isotope pulse labeling technique was applied to evaluate the alterations of ecosystem carbon cycling during a short term. The results showed that the plant community structure was changed after being fenced in for 6 years, with significantly decreased aboveground productivity, species loss and varied composition of the four plant functional groups (grasses, sedges, legumes and forbs). Using the pulse labeling technique, we found a lower cycling rate of 13C in the plant-soil system of the fenced plots compared with the grazed sites during the first 24 h after labeling. A higher proportion of recovered 13C in the plant-soil system migrated into the soil as root exudates immediately after labeling at both fenced and control grazed sites, with a significantly lower proportion in the fenced site, coinciding with the lower proportion of 13C lost from soil respiration. Thirty-two days after labeling, 37% of the recovered 13C remained in the soil of the fenced plots, with significant differences compared to in the grazed plots (47%). In addition, less 13C (5 vs. 7%) was lost by soil respiration in the fenced plots during the chase period of 32 days. Overall, our study suggests that livestock exclosures have negative

  6. Allocation of freshly assimilated carbon into primary and secondary metabolites after in situ ¹³C pulse labelling of Norway spruce (Picea abies).

    PubMed

    Heinrich, Steffen; Dippold, Michaela A; Werner, Christiane; Wiesenberg, Guido L B; Kuzyakov, Yakov; Glaser, Bruno

    2015-11-01

    Plants allocate carbon (C) to sink tissues depending on phenological, physiological or environmental factors. We still have little knowledge on C partitioning into various cellular compounds and metabolic pathways at various ecophysiological stages. We used compound-specific stable isotope analysis to investigate C partitioning of freshly assimilated C into tree compartments (needles, branches and stem) as well as into needle water-soluble organic C (WSOC), non-hydrolysable structural organic C (stOC) and individual chemical compound classes (amino acids, hemicellulose sugars, fatty acids and alkanes) of Norway spruce (Picea abies) following in situ (13)C pulse labelling 15 days after bud break. The (13)C allocation within the above-ground tree biomass demonstrated needles as a major C sink, accounting for 86% of the freshly assimilated C 6 h after labelling. In needles, the highest allocation occurred not only into the WSOC pool (44.1% of recovered needle (13)C) but also into stOC (33.9%). Needle growth, however, also caused high (13)C allocation into pathways not involved in the formation of structural compounds: (i) pathways in secondary metabolism, (ii) C-1 metabolism and (iii) amino acid synthesis from photorespiration. These pathways could be identified by a high (13)C enrichment of their key amino acids. In addition, (13)C was strongly allocated into the n-alkyl lipid fraction (0.3% of recovered (13)C), whereby (13)C allocation into cellular and cuticular exceeded that of epicuticular fatty acids. (13)C allocation decreased along the lipid transformation and translocation pathways: the allocation was highest for precursor fatty acids, lower for elongated fatty acids and lowest for the decarbonylated n-alkanes. The combination of (13)C pulse labelling with compound-specific (13)C analysis of key metabolites enabled tracing relevant C allocation pathways under field conditions. Besides the primary metabolism synthesizing structural cell compounds, a complex

  7. Effects of waterlogging on carbon assimilate partitioning in the Zoigê alpine wetlands revealed by 13CO2 pulse labeling.

    PubMed

    Gao, Jun-Qin; Gao, Ju-Juan; Zhang, Xue-Wen; Xu, Xing-Liang; Deng, Zhao-Heng; Yu, Fei-Hai

    2015-03-23

    Waterlogging has been suggested to affect carbon (C) turnover in wetlands, but how it affects C allocation and stocks remains unclear in alpine wetlands. Using in situ (13)CO2 pulse labelling, we investigated C allocation in both waterlogged and non-waterlogged sites in the Zoigê wetlands on the Tibetan Plateau in August 2011. More than 50% of total (13)C fixed by photosynthesis was lost via shoot respiration. Shoots recovered about 19% of total (13)C fixed by photosynthesis at both sites. Only about 26% of total fixed (13)C was translocated into the belowground pools. Soil organic C pool accounted for 19% and roots recovered about 5-7% of total fixed (13)C at both sites. Waterlogging significantly reduced soil respiration and very little (13)C was lost via soil respiration in the alpine wetlands compared to that in grasslands. We conclude that waterlogging did not significantly alter C allocations among the C pools except the (13)CO2 efflux derived from soil respiration and that shoots made similar contributions to C sequestration as the belowground parts in the Zoigê alpine wetlands. Therefore, changes in waterlogging due to climate change will not affect C assimilate partitioning but soil C efflux.

  8. Simultaneous extension of both basic microstructural components in scleractinian coral skeleton during night and daytime, visualized by in situ 86Sr pulse labeling.

    PubMed

    Domart-Coulon, I; Stolarski, J; Brahmi, C; Gutner-Hoch, E; Janiszewska, K; Shemesh, A; Meibom, A

    2014-01-01

    Using in situ (12 h) pulse-labeling of scleractinian coral aragonitic skeleton with stable 86Sr isotope, the diel pattern of skeletal extension was investigated in the massive Porites lobata species, grown at 5 m depth in the Gulf of Eilat. Several microstructural aspects of coral biomineralization were elucidated, among which the most significant is simultaneous extension of the two basic microstructural components Rapid Accretion Deposits (RAD; also called Centers of Calcification) and Thickening Deposits (TD; also called fibers), both at night and during daytime. Increased thickness of the 86Sr-labeled growth-front in the RADs compared to the adjacent TDs revealed that in this species RADs extend on average twice as fast as TDs. At the level of the individual corallite, skeletal extension is spatially highly heterogeneous, with sporadic slowing or cessation depending on growth directions and skeletal structure morphology. Daytime photosynthesis by symbiotic dinoflagellates is widely acknowledged to substantially increase calcification rates at the colony and the corallite level in reef-building corals. However, in our study, the average night-time extension rate (visualized in three successive 12 h pulses) was similar to the average daytime extension (visualized in the initial 12 h pulse), in all growth directions and skeletal structures. This research provides a platform for further investigations into the temporal calibration of coral skeletal extension via cyclic growth increment deposition, which is a hallmark of coral biomineralization.

  9. Carbon pools and fluxes in a Tibetan alpine Kobresia pygmaea pasture partitioned by coupled eddy-covariance measurements and ¹³CO₂ pulse labeling.

    PubMed

    Ingrisch, Johannes; Biermann, Tobias; Seeber, Elke; Leipold, Thomas; Li, Maoshan; Ma, Yaoming; Xu, Xingliang; Miehe, Georg; Guggenberger, Georg; Foken, Thomas; Kuzyakov, Yakov

    2015-02-01

    The Tibetan highlands host the largest alpine grassland ecosystems worldwide, bearing soils that store substantial stocks of carbon (C) that are very sensitive to land use changes. This study focuses on the cycling of photoassimilated C within a Kobresia pygmaea pasture, the dominating ecosystems on the Tibetan highlands. We investigated short-term effects of grazing cessation and the role of the characteristic Kobresia root turf on C fluxes and belowground C turnover. By combining eddy-covariance measurements with (13)CO₂ pulse labeling we applied a powerful new approach to measure absolute fluxes of assimilates within and between various pools of the plant-soil-atmosphere system. The roots and soil each store roughly 50% of the overall C in the system (76 Mg C ha(-1)), with only a minor contribution from shoots, which is also expressed in the root:shoot ratio of 90. During June and July the pasture acted as a weak C sink with a strong uptake of approximately 2 g C m(-2) d(-1) in the first half of July. The root turf was the main compartment for the turnover of photoassimilates, with a subset of highly dynamic roots (mean residence time 20 days), and plays a key role for the C cycling and C storage in this ecosystem. The short-term grazing cessation only affected aboveground biomass but not ecosystem scale C exchange or assimilate allocation into roots and soil.

  10. Short-term Fate of Carbon in two Woody Species Under Contrasting Resources Availability: Insights From a 13CO2 Pulse Labeling Approach

    NASA Astrophysics Data System (ADS)

    Mambelli, S.; Dawson, T. E.; Bird, J. A.; Torn, M. S.; Gaudinski, J. B.

    2003-12-01

    In response to the environment, plants adjust allocation patterns to maintain a functional balance between the activities of roots and shoots such that belowground resources are acquired in approximate balance with aboveground resources. Changes in allocation driven by changes in environmental conditions may affect the amount of carbon stored in plant tissues, released by the root system, and ultimately sequestered into the soil. The aim of this study was to quantify the allocation belowground of recently fixed carbon in contrasting species and resources availability. We tested the hypothesis that carbon limitation and high nitrogen supply both negatively affect carbon transport to roots, causing a reduction of the carbon flow into the soil rhizosphere. Two woody species, a conifer (Pinus Ponderosa) and a deciduous tree (Acer Rubrum) were grown in a greenhouse under a factorial of light and nitrogen regimes (full light/shade and limited/excess nitrogen). At the stage of full leaf expansion plants were pulse-labeled by addition of 13CO2 and harvested after 0, 7 and 30 days. During the experiment the treatments affected the pattern of plant biomass allocation. Shade negatively influenced belowground growth and Maple showed a more conservative response than Pine. High supply of nitrogen also reduced allocation to roots but only when plants were grown under light. Preliminary results show that the initial amount of recently fixed carbon into the rhizosphere was in general higher under Pine. However, after 7 and 30 days, the new soil carbon pool increased only in the rhizosphere of carbon limited Pine seedlings. These findings suggest that belowground respiration was negatively affected or, alternatively, that the exudates released were less easily decomposable

  11. The effect of elevated atmospheric CO2 concentration on gross nitrogen and carbon dynamics in a permanent grassland: A field pulse-labeling study

    NASA Astrophysics Data System (ADS)

    Moser, Gerald; Gorenflo, André; Keidel, Lisa; Brenzinger, Kristof; Elias, Dafydd; McNamara, Niall; Maček, Irena; Vodnik, Dominik; Braker, Gesche; Schimmelpfennig, Sonja; Gerstner, Judith; Müller, Christoph

    2014-05-01

    To predict ecosystem reactions to elevated atmospheric CO2 (eCO2) it is essential to understand the interactions between plant carbon input, microbial community composition and activity and associated nutrient dynamics. Long-term observations (> 14 years) within the Giessen Free Air Carbon dioxide Enrichment (Giessen FACE) study on permanent grassland showed next to an enhanced biomass production an unexpected strong positive feedback effect on ecosystem respiration and nitrous oxide (N2O) production. The overall goal of this study is to understand the long-term effects of eCO2 and carbon input on microbial community composition and activity as well as the associated nitrogen dynamics, N2O production and plant N uptake in the Giessen FACE study on permanent grassland. A combination of 13CO2 pulse labelling with 15N tracing of 15NH4+ and 15NO3- was carried out in situ. Different fractions of soil organic matter (recalcitrant, labile SOM) and the various mineral N pools in the soil (NH4+, NO3-), gross N transformation rates, pool size dependent N2O and N2 emissions as well as N species dependent plant N uptake rates and the origin of the CO2 respiration have been quantified. Microbial analyses include exploring changes in the composition of microbial communities involved in the turnover of NH4+, NO3-, N2O and N2, i.e. ammonia oxidizing, denitrifying, and microbial communities involved in dissimilatory nitrate reduction to ammonia (DNRA). mRNA based analyses will be employed to comparably evaluate the long-term effects of eCO2 on the structure and abundance of these communities, while transcripts of these genes will be used to target the fractions of the communities which actively contribute to N transformations. We quantified the contribution of mycorrhizae on N2O emissions and observed the phenological development of the mycorrhizae after the labeling.

  12. In situ 13CO2 pulse labelling of field-grown eucalypt trees revealed the effects of potassium nutrition and throughfall exclusion on phloem transport of photosynthetic carbon.

    PubMed

    Epron, Daniel; Cabral, Osvaldo Machado Rodrigues; Laclau, Jean-Paul; Dannoura, Masako; Packer, Ana Paula; Plain, Caroline; Battie-Laclau, Patricia; Moreira, Marcelo Zacharias; Trivelin, Paulo Cesar Ocheuze; Bouillet, Jean-Pierre; Gérant, Dominique; Nouvellon, Yann

    2016-01-01

    Potassium (K) is an important limiting factor of tree growth, but little is known of the effects of K supply on the long-distance transport of photosynthetic carbon (C) in the phloem and of the interaction between K fertilization and drought. We pulse-labelled 2-year-old Eucalyptus grandis L. trees grown in a field trial combining K fertilization (+K and -K) and throughfall exclusion (+W and -W), and we estimated the velocity of C transfer by comparing time lags between the uptake of (13)CO2 and its recovery in trunk CO2 efflux recorded at different heights. We also analysed the dynamics of the labelled photosynthates recovered in the foliage and in the phloem sap (inner bark extract). The mean residence time of labelled C in the foliage was short (21-31 h). The time series of (13)C in excess in the foliage was affected by the level of fertilization, whereas the effect of throughfall exclusion was not significant. The velocity of C transfer in the trunk (0.20-0.82 m h(-1)) was twice as high in +K trees than in -K trees, with no significant effect of throughfall exclusion except for one +K -W tree labelled in the middle of the drought season that was exposed to a more pronounced water stress (midday leaf water potential of -2.2 MPa). Our results suggest that besides reductions in photosynthetic C supply and in C demand by sink organs, the lower velocity under K deficiency is due to a lower cross-sectional area of the sieve tubes, whereas an increase in phloem sap viscosity is more likely limiting phloem transport under drought. In all treatments, 10 times less (13)C was recovered in inner bark extracts at the bottom of the trunk when compared with the base of the crown, suggesting that a large part of the labelled assimilates has been exported out of the phloem and replaced by unlabelled C. This supports the 'leakage-retrieval mechanism' that may play a role in maintaining the pressure gradient between source and sink organs required to sustain high

  13. Seasonal variations of the amount of carbon allocated to respiration after in situ 13CO2 pulse labelling of trees (Invited)

    NASA Astrophysics Data System (ADS)

    Epron, D.; Dannoura, M.; Ngao, J.; Plain, C.; Berveller, D.; Chipeaux, C.; Gerant, D.; Bosc, A.; Maillard, P.; Loustau, D.; Damesin, C.; Cats Project (Anr-07-Blan-0109)

    2010-12-01

    , Maillard P, Dannoura M, Dong Y, Zeller B, Priault P, Parent F, Epron D. 2009. Tracing of recently assimilated carbon in respiration at high temporal resolution in the field with a tuneable diode laser absorption spectrometer after in situ 13CO2 pulse labelling of 20-year-old beech trees. Tree Physiology 29: 1433-1447.

  14. Does the time of the sampling matter in 13C pulse labeling and chasing experiments? A case study on beech seedlings

    NASA Astrophysics Data System (ADS)

    Gavrichkova, Olga; Thoms, Ronny; Muhr, Jan; Karlowsky, Stefan; Keitel, Claudia; Kayler, Zachary; Calfapietra, Carlo; Gessler, Arthur; Brugnoli, Enrico; Gleixner, Gerd

    2016-04-01

    13C pulse labeling and chasing is a valuable and very popular tool for determination of the fate and turnover rates of C in plant-soil systems. Continuous isoflux measurements became an accessible reality allowing to cover completely the diurnal variation in label assimilation and respiration fluxes. Label turnover in multiple pools, especially of those located belowground, is more often assessed instead by isolated day-time samplings. By increasing the sampling frequency of belowground compartments we aimed to catch the short-term diurnal variations in label allocation and to link these processes with label dynamics in the aboveground biomass. For these purposes we labeled 3-m height soil-grown European beech seedlings with 13C enriched CO2 and traced the flow of 13C within belowground plant-soil continuum. Continuous soil isoflux measurements were accompanied by a 3-h-frequency sampling of root and soil material during the first 48 h, followed by a daily sampling in the successive 5 days. The amount of label found in microbial biomass depended partially on the amount of roots in the sample. Microbial biomass C (MBC) and microbial respiration showed very strong correlation, suggesting the possibility to use one as a proxy of the other. MBC enrichment showed a clear diurnal pattern with night-time and early morning peaks. These peaks were similar in shape and shifted by one sampling when compared to root sugars enrichment. Soil respiration showed instead a single bell-shape peak in 13C, likely due to a sequence of peaks of root and microbial origin. 13C flow into soil microbial functional groups was assessed less frequently through phospholipid fatty acid analyses (PLFA). The microorganisms were separated into two distinct groups by the time of the appearance of the label in the single PLFAs. The first group was characterized by a fast appearance of the label and higher enrichment and was composed of Gram negative bacteria and saprotrophic fungi likely living in

  15. Unsaturated zone 14CO2: implications for groundwater dating

    NASA Astrophysics Data System (ADS)

    Wood, C.; Cook, P. G.; Harrington, G. A.; Meredith, K.; Kipfer, R.

    2013-12-01

    Quantitative interpretation of the carbon-14 activity (14C) of dissolved inorganic carbon (DIC) in groundwater requires an understanding of the various chemical and physical processes that can vary the initial 14C activity from that of the original atmospheric source (carbon dioxide, CO2). Such processes include radioactive decay, carbonate mineral dissolution, isotope exchange, decay of organic matter and molecular diffusion. Many geochemical correction models exist to account for some of these processes (e.g., Fontes and Garnier, 1979). However in most existing correction schemes, it is assumed that the 14C activity of CO2 in the unsaturated zone is in equilibrium with the atmosphere (i.e., 14C:12C is the same as the atmospheric ratio). This assumption is rarely tested and in several cases has been found to be inappropriate (eg. Bacon and Keller, 1998; Walvoord et al., 2005). Not accounting for the influence of unsaturated zone processes on 14C may lead to problems in determining residence time and estimating fluxes from measured 14C data in groundwater. In this study we examined carbon isotope processes in deep unsaturated zone profiles (up to 30m in depth) in arid central Australia. At five sites, multi-level samples of unsaturated zone gas and groundwater were collected for 14C analysis. Chlorofluorocarbon (CFC-11 and CFC-12) samples were also collected in unsaturated zone gas. At all sites we observed a decrease in the 14C activity of unsaturated zone gas with depth, from approximately 107 pmC near the ground surface to 50 - 80 pmC immediately above the water table. The measured 14C data was reproduced in a one-dimensional model using Hydrus, with CFC concentrations used to help constrain the gas transport parameters. Modelling showed that the decrease in 14C could be explained by CO2 production from different sources at different depths in the unsaturated zone (e.g. plant root respiration at shallower depths, oxidation of dead organic matter at greater depths). Several scenarios have been run to assess the effect of changes in recharge rate and watertable depth on unsaturated zone 14C. This helps us understand under what hydrogeological conditions the influence of unsaturated zone processes on 14C becomes significant, which has important implications for using 14C in groundwater dating projects. The results of this work are particularly important in arid environments where groundwater residence time is typically long (>1,000 years old), recharge is low and unsaturated zones may be deep (>10m).

  16. Repeated nightmares

    MedlinePlus

    ... different from night terrors . Alternative Names Nightmares - repeated; Dream anxiety disorder References American Academy of Family Physicians. Information from your family doctor. Nightmares and night terrors in children. ...

  17. Rates and quantities of carbon flux to ectomycorrhizal mycelium following 14C pulse labeling of Pinus sylvestris seedlings: effects of litter patches and interaction with a wood-decomposer fungus.

    PubMed

    Leake, J R; Donnelly, D P; Saunders, E M; Boddy, L; Read, D J

    2001-02-01

    We used a novel digital autoradiographic technique that enabled, for the first time, simultaneous visualization and quantification of spatial and temporal changes in carbon allocation patterns in ectomycorrhizal mycelia. Mycorrhizal plants of Pinus sylvestris L. were grown in microcosms containing non-sterile peat. The time course and spatial distribution of carbon allocation by P. sylvestris to mycelia of its mycorrhizal partners, Paxillus involutus (Batsch) Fr. and Suillus bovinus (L.): Kuntze, were quantified following 14C pulse labeling of the plants. Litter patches were used to investigate the effects of nutrient resource quality on carbon allocation. The wood-decomposer fungus Phanerochaete velutina (D.C.: Pers.) Parmasto was introduced to evaluate competitive and territorial interactions between its mycelial cords and the mycelial system of S. bovinus. Growth of ectomycorrhizal mycelium was stimulated in the litter patches. Nearly 60% of the C transferred from host plant to external mycorrhizal mycelium (> 2 mm from root surfaces) was allocated to mycelium in the patches, which comprised only 12% of the soil area available for mycelial colonization. Mycelia in the litter patch most recently colonized by mycorrhizal mycelium received the largest investment of carbon, amounting to 27 to 50% of the total 14C in external mycorrhizal mycelium. The amount of C transfer to external mycelium of S. bovinus following pulse labeling was reduced from a maximum of 167 nmol in systems with no saprotroph to a maximum of 61 nmol in systems interacting with P. velutina. The 14C content of S. bovinus mycelium reached a maximum 24-36 h after labeling in control microcosms, but allocation did not reach a peak until 56 h after labeling, when S. bovinus interacted with mycelium of P. velutina. The mycelium of S. bovinus contained 9% of the total 14C in the plants (including mycorrhizae) at the end of the experiment, but this was reduced to 4% in the presence of P. velutina. The

  18. A Repeat Look at Repeating Patterns

    ERIC Educational Resources Information Center

    Markworth, Kimberly A.

    2016-01-01

    A "repeating pattern" is a cyclical repetition of an identifiable core. Children in the primary grades usually begin pattern work with fairly simple patterns, such as AB, ABC, or ABB patterns. The unique letters represent unique elements, whereas the sequence of letters represents the core that is repeated. Based on color, shape,…

  19. Optical Detection and Quantification of Radiocarbon Dioxide (^{14}CO_{2}) at and Below Ambient Levels

    NASA Astrophysics Data System (ADS)

    Long, David A.; Fleisher, Adam J.; Liu, Qingnan; Hodges, Joseph T.

    2017-06-01

    Due to their age, fossil fuels and their byproducts are almost entirely depleted in radiocarbon (^{14}C). As a result, measurements of radiocarbon provide a unique tracer for determining the origin of products and emissions. Recent efforts at NIST have applied mid-infrared cavity ring-down spectroscopy to measurements of radiocarbon dioxide to allow for more rapid and less expensive measurements than are possible with traditional techniques such as accelerator mass spectrometry. I will discuss our present measurement detection limits and precision as well as discuss limiting noise sources and plans to further improve the instrument's stability and reproducibility.

  20. Materials Data on Li14Co2S9 (SG:147) by Materials Project

    SciTech Connect

    Kristin Persson

    2016-02-04

    Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

  1. Materials Data on Na14Co2O9 (SG:147) by Materials Project

    SciTech Connect

    Kristin Persson

    2016-04-22

    Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations

  2. Developing a passive trap for diffusive atmospheric 14CO2 sampling

    NASA Astrophysics Data System (ADS)

    Walker, Jennifer C.; Xu, Xiaomei; Fahrni, Simon M.; Lupascu, Massimo; Czimczik, Claudia I.

    2015-10-01

    14C-CO2 measurement is an unique tool to quantify source-based emissions of CO2 for both the urban and natural environments. Acquiring a sample that temporally integrates the atmospheric 14C-CO2 signature that allows for precise 14C analysis is often necessary, but can require complex sampling devices, which can be difficult to deploy and maintain, especially for multiple locations. Here we describe our progress in developing a diffusive atmospheric CO2 molecular sieve trap, which requires no power to operate. We present results from various cleaning procedures, and rigorously tested for blank and memory effects. Traps were tested in the environment along-side conventional sampling flasks for accuracy. Results show that blank and memory effects can be minimized with thorough cleaning and by avoiding overheating, and that diffusively collected air samples agree well with traditionally canister-sampled air.

  3. Repeating the Past

    NASA Astrophysics Data System (ADS)

    Moore, John W.

    1998-05-01

    As part of the celebration of the Journal 's 75th year, we are scanning each Journal issue from 25, 50, and 74 years ago. Many of the ideas and practices described are so similar to present-day "innovations" that George Santayana's adage (1) "Those who cannot remember the past are condemned to repeat it" comes to mind. But perhaps "condemned" is too strong - sometimes it may be valuable to repeat something that was done long ago. One example comes from the earliest days of the Division of Chemical Education and of the Journal.

  4. Slit Wheel Repeatability

    NASA Astrophysics Data System (ADS)

    DiFelice, Audrey

    2013-10-01

    Test the repeatibility of the slit wheel by taking a sequence of comparison lamp spectra with grating G230MB {2697} and the three smallest long slits {52X0.2, 52X0.1, and 52X0.05}. This is a clone of Cycle 20 Program 13140.

  5. Slit Wheel Repeatability

    NASA Astrophysics Data System (ADS)

    Long, Chris

    2011-10-01

    Test the repeatibility of the slit wheel by taking a sequence of comparison lamp spectra with grating G230MB {2697} and the three smallest long slits {52X0.2, 52X0.1, and 52X0.05}. This is a clone of Cycle 18 Program 12410.

  6. Slit Wheel Repeatability

    NASA Astrophysics Data System (ADS)

    DiFelice, Audrey

    2012-10-01

    Test the repeatibility of the slit wheel by taking a sequence of comparison lamp spectra with grating G230MB {2697} and the three smallest long slits {52X0.2, 52X0.1, and 52X0.05}. This is a clone of Cycle 19 Program 12771.

  7. Repeated Causal Decision Making

    ERIC Educational Resources Information Center

    Hagmayer, York; Meder, Bjorn

    2013-01-01

    Many of our decisions refer to actions that have a causal impact on the external environment. Such actions may not only allow for the mere learning of expected values or utilities but also for acquiring knowledge about the causal structure of our world. We used a repeated decision-making paradigm to examine what kind of knowledge people acquire in…

  8. A Novel Splice Variant of Pmel17 Expressed by Human Melanocytes and Melanoma Cells Lacking Some of the Internal Repeats

    PubMed Central

    Nichols, Sarah E.; Harper, Dawn C.; Berson, Joanne F.; Marks, Michael S.

    2009-01-01

    Pmel17 is a ≈100 kDa pigment cell specific glycoprotein that plays a crucial part in the morphogenesis of melanosome precursors. Anti-Pmel17 immunoprecipitates from metabolically pulse labeled melanoma cells and melanocytes contain, in addition to full-length Pmel17, a glycoprotein that migrates with a lower relative molecular weight. Here we show that this glycoprotein is encoded by an mRNA that results from alternative splicing of the human Pmel17 gene from which a cryptic intron is excised. Immunoprecipitation recapture experiments showed that this glycoprotein contained both the N- and C-termini of full-length Pmel17. Sequence analysis of cDNA corresponding to the alternatively spliced form reveals the loss of three of 10 imperfect direct repeats from the central region of the lumenal domain. The product of the splice variant is processed with similar kinetics to full-length Pmel17, and localizes similarly to late endosomes when expressed ectopically in nonpigment cells. We speculate that truncation of the repeat region within Pmel17 alters either fibrillogenic activity or the interaction of Pmel17 with melanin intermediates. The expression of an alternatively spliced product may furthermore affect the cohort of peptides generated for recognition of melanoma cells by tumor-directed T lymphocytes. PMID:14632201

  9. Duct Leakage Repeatability Testing

    SciTech Connect

    Walker, Iain; Sherman, Max

    2014-01-01

    Duct leakage often needs to be measured to demonstrate compliance with requirements or to determine energy or Indoor Air Quality (IAQ) impacts. Testing is often done using standards such as ASTM E1554 (ASTM 2013) or California Title 24 (California Energy Commission 2013 & 2013b), but there are several choices of methods available within the accepted standards. Determining which method to use or not use requires an evaluation of those methods in the context of the particular needs. Three factors that are important considerations are the cost of the measurement, the accuracy of the measurement and the repeatability of the measurement. The purpose of this report is to evaluate the repeatability of the three most significant measurement techniques using data from the literature and recently obtained field data. We will also briefly discuss the first two factors. The main question to be answered by this study is to determine if differences in the repeatability of these tests methods is sufficient to indicate that any of these methods is so poor that it should be excluded from consideration as an allowed procedure in codes and standards.

  10. Accumulate repeat accumulate codes

    NASA Technical Reports Server (NTRS)

    Abbasfar, Aliazam; Divsalar, Dariush; Yao, Kung

    2004-01-01

    In this paper we propose an innovative channel coding scheme called 'Accumulate Repeat Accumulate codes' (ARA). This class of codes can be viewed as serial turbo-like codes, or as a subclass of Low Density Parity Check (LDPC) codes, thus belief propagation can be used for iterative decoding of ARA codes on a graph. The structure of encoder for this class can be viewed as precoded Repeat Accumulate (RA) code or as precoded Irregular Repeat Accumulate (IRA) code, where simply an accumulator is chosen as a precoder. Thus ARA codes have simple, and very fast encoder structure when they representing LDPC codes. Based on density evolution for LDPC codes through some examples for ARA codes, we show that for maximum variable node degree 5 a minimum bit SNR as low as 0.08 dB from channel capacity for rate 1/2 can be achieved as the block size goes to infinity. Thus based on fixed low maximum variable node degree, its threshold outperforms not only the RA and IRA codes but also the best known LDPC codes with the dame maximum node degree. Furthermore by puncturing the accumulators any desired high rate codes close to code rate 1 can be obtained with thresholds that stay close to the channel capacity thresholds uniformly. Iterative decoding simulation results are provided. The ARA codes also have projected graph or protograph representation that allows for high speed decoder implementation.

  11. Repeatability of Cryogenic Multilayer Insulation

    NASA Technical Reports Server (NTRS)

    Johnson, W. L.; Vanderlaan, M.; Wood, J. J.; Rhys, N. O.; Guo, W.; Van Sciver, S.; Chato, D. J.

    2017-01-01

    Due to the variety of requirements across aerospace platforms, and one off projects, the repeatability of cryogenic multilayer insulation has never been fully established. The objective of this test program is to provide a more basic understanding of the thermal performance repeatability of MLI systems that are applicable to large scale tanks. There are several different types of repeatability that can be accounted for: these include repeatability between multiple identical blankets, repeatability of installation of the same blanket, and repeatability of a test apparatus. The focus of the work in this report is on the first two types of repeatability. Statistically, repeatability can mean many different things. In simplest form, it refers to the range of performance that a population exhibits and the average of the population. However, as more and more identical components are made (i.e. the population of concern grows), the simple range morphs into a standard deviation from an average performance. Initial repeatability testing on MLI blankets has been completed at Florida State University. Repeatability of five GRC provided coupons with 25 layers was shown to be +/- 8.4 whereas repeatability of repeatedly installing a single coupon was shown to be +/- 8.0. A second group of 10 coupons have been fabricated by Yetispace and tested by Florida State University, through the first 4 tests, the repeatability has been shown to be +/- 16. Based on detailed statistical analysis, the data has been shown to be statistically significant.

  12. Duct Leakage Repeatability Testing

    SciTech Connect

    Walker, Iain; Sherman, Max

    2014-08-01

    The purpose of this report is to evaluate the repeatability of the three most significant measurement techniques for duct leakage using data from the literature and recently obtained field data. We will also briefly discuss the first two factors. The main question to be answered by this study is to determine if differences in the repeatability of these tests methods is sufficient to indicate that any of these methods is so poor that it should be excluded from consideration as an allowed procedure in codes and standards. The three duct leak measurement methods assessed in this report are the two duct pressurization methods that are commonly used by many practitioners and the DeltaQ technique. These are methods B, C and A, respectively of the ASTM E1554 standard. Although it would be useful to evaluate other duct leak test methods, this study focused on those test methods that are commonly used and are required in various test standards, such as BPI (2010), RESNET (2014), ASHRAE 62.2 (2013), California Title 24 (CEC 2012), DOE Weatherization and many other energy efficiency programs.

  13. 78 FR 65594 - Vehicular Repeaters

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-11-01

    ... changes, and on whether current mobile repeater filter technologies can support reduced frequency... feasibility of adapting SAW filters, or other filter technology, for mobile repeater use. We particularly... mobile repeaters by public safety licensees on certain frequencies in the VHF band. DATES:...

  14. Repeat Customer Success in Extension

    ERIC Educational Resources Information Center

    Bess, Melissa M.; Traub, Sarah M.

    2013-01-01

    Four multi-session research-based programs were offered by two Extension specialist in one rural Missouri county. Eleven participants who came to multiple Extension programs could be called "repeat customers." Based on the total number of participants for all four programs, 25% could be deemed as repeat customers. Repeat customers had…

  15. Repeat Customer Success in Extension

    ERIC Educational Resources Information Center

    Bess, Melissa M.; Traub, Sarah M.

    2013-01-01

    Four multi-session research-based programs were offered by two Extension specialist in one rural Missouri county. Eleven participants who came to multiple Extension programs could be called "repeat customers." Based on the total number of participants for all four programs, 25% could be deemed as repeat customers. Repeat customers had…

  16. RepeatsDB: a database of tandem repeat protein structures

    PubMed Central

    Di Domenico, Tomás; Potenza, Emilio; Walsh, Ian; Gonzalo Parra, R.; Giollo, Manuel; Minervini, Giovanni; Piovesan, Damiano; Ihsan, Awais; Ferrari, Carlo; Kajava, Andrey V.; Tosatto, Silvio C.E.

    2014-01-01

    RepeatsDB (http://repeatsdb.bio.unipd.it/) is a database of annotated tandem repeat protein structures. Tandem repeats pose a difficult problem for the analysis of protein structures, as the underlying sequence can be highly degenerate. Several repeat types haven been studied over the years, but their annotation was done in a case-by-case basis, thus making large-scale analysis difficult. We developed RepeatsDB to fill this gap. Using state-of-the-art repeat detection methods and manual curation, we systematically annotated the Protein Data Bank, predicting 10 745 repeat structures. In all, 2797 structures were classified according to a recently proposed classification schema, which was expanded to accommodate new findings. In addition, detailed annotations were performed in a subset of 321 proteins. These annotations feature information on start and end positions for the repeat regions and units. RepeatsDB is an ongoing effort to systematically classify and annotate structural protein repeats in a consistent way. It provides users with the possibility to access and download high-quality datasets either interactively or programmatically through web services. PMID:24311564

  17. Persistence and accumulation of micronucleated hepatocytes in liver of rats after repeated administration of diethylnitrosamine.

    PubMed

    Narumi, Kazunori; Ashizawa, Koji; Fujiishi, Yohei; Tochinai, Ryota; Okada, Emiko; Tsuzuki, Yasuhiro; Tatemoto, Hideki; Hamada, Shuichi; Kaneko, Kimiyuki; Ohyama, Wakako

    2013-08-15

    A repeat-dose micronucleus assay in adult rat liver was recently developed [Mutat. Res. 747 (2012) 234-239]. This assay demonstrated a high detectability of hepatocarcinogens at relatively low doses, as indicated by dose-dependent micronucleus induction. Because the adult rat liver is known to have a long life-span, this desirable property of the assay will be an advantage in detecting micronucleated hepatocytes (MNHEPs) that have persisted for long periods in the liver following repeated dosing. However, no data directly supporting the underlying mechanisms have been published to date. In the present study, we verified the mechanisms by means of pulse-labeling of micronucleated hepatocytes with the thymidine analog 5-ethynyl-2'-deoxyuridine (EdU). The rodent hepatocarcinogen diethylnitrosamine (DEN) was repeatedly administered orally to male Crl:CD (SD) rats (6 weeks old) for up to 2 weeks, and EdU was injected intraperitoneally on days 1, 7, or 14. Hepatocytes were isolated by use of a non-perfusion technique at 24h, 1 week, or 2 weeks after EdU injection and analyzed for EdU incorporation and micronucleus formation. The results of our study confirmed that MNHEPs labeled with EdU on the first day of DEN administration persisted until 2 weeks post-administration in the rat livers. However, the frequency of MHNEPs among EdU-labeled hepatocytes decreased over time. In addition, the number of terminal deoxynucleotidyl transferase-mediated nick end-labeling (TUNEL)-positive cells in the liver tissue increased, suggesting selective removal of micronucleated cells. Theoretical calculation of the cumulative MNHEP frequency on each of the days on which DEN was administered, taking into account the rate of loss, came out closer to the actual value observed in the liver micronucleus test. Taken together, these results indicate that although micronucleated cells induced in rat livers by administration of the genotoxic hepatocarcinogen DEN undergo selective removal, they

  18. To Repeat or Not to Repeat a Course

    ERIC Educational Resources Information Center

    Armstrong, Michael J.; Biktimirov, Ernest N.

    2013-01-01

    The difficult transition from high school to university means that many students need to repeat (retake) 1 or more of their university courses. The authors examine the performance of students repeating first-year core courses in an undergraduate business program. They used data from university records for 116 students who took a total of 232…

  19. To Repeat or Not to Repeat a Course

    ERIC Educational Resources Information Center

    Armstrong, Michael J.; Biktimirov, Ernest N.

    2013-01-01

    The difficult transition from high school to university means that many students need to repeat (retake) 1 or more of their university courses. The authors examine the performance of students repeating first-year core courses in an undergraduate business program. They used data from university records for 116 students who took a total of 232…

  20. Nifty Nines and Repeating Decimals

    ERIC Educational Resources Information Center

    Brown, Scott A.

    2016-01-01

    The traditional technique for converting repeating decimals to common fractions can be found in nearly every algebra textbook that has been published, as well as in many precalculus texts. However, students generally encounter repeating decimal numerals earlier than high school when they study rational numbers in prealgebra classes. Therefore, how…

  1. Nifty Nines and Repeating Decimals

    ERIC Educational Resources Information Center

    Brown, Scott A.

    2016-01-01

    The traditional technique for converting repeating decimals to common fractions can be found in nearly every algebra textbook that has been published, as well as in many precalculus texts. However, students generally encounter repeating decimal numerals earlier than high school when they study rational numbers in prealgebra classes. Therefore, how…

  2. Repeated Prescribed Burning in Aspen

    Treesearch

    Donald A. Perala

    1974-01-01

    Infrequent burning weather, low flammability of the aspen-hardwood association, and prolific sprouting and seeding of shrubs and hardwoods made repeated dormant season burning a poor tool to convert good site aspen to conifers. Repeat fall burns for wildlife habitat maintenance is workable if species composition changes are not important.

  3. All-photonic quantum repeaters

    NASA Astrophysics Data System (ADS)

    Azuma, Koji; Tamaki, Kiyoshi; Lo, Hoi-Kwong

    2015-04-01

    Quantum communication holds promise for unconditionally secure transmission of secret messages and faithful transfer of unknown quantum states. Photons appear to be the medium of choice for quantum communication. Owing to photon losses, robust quantum communication over long lossy channels requires quantum repeaters. It is widely believed that a necessary and highly demanding requirement for quantum repeaters is the existence of matter quantum memories. Here we show that such a requirement is, in fact, unnecessary by introducing the concept of all-photonic quantum repeaters based on flying qubits. In particular, we present a protocol based on photonic cluster-state machine guns and a loss-tolerant measurement equipped with local high-speed active feedforwards. We show that, with such all-photonic quantum repeaters, the communication efficiency scales polynomially with the channel distance. Our result paves a new route towards quantum repeaters with efficient single-photon sources rather than matter quantum memories.

  4. All-photonic quantum repeaters

    PubMed Central

    Azuma, Koji; Tamaki, Kiyoshi; Lo, Hoi-Kwong

    2015-01-01

    Quantum communication holds promise for unconditionally secure transmission of secret messages and faithful transfer of unknown quantum states. Photons appear to be the medium of choice for quantum communication. Owing to photon losses, robust quantum communication over long lossy channels requires quantum repeaters. It is widely believed that a necessary and highly demanding requirement for quantum repeaters is the existence of matter quantum memories. Here we show that such a requirement is, in fact, unnecessary by introducing the concept of all-photonic quantum repeaters based on flying qubits. In particular, we present a protocol based on photonic cluster-state machine guns and a loss-tolerant measurement equipped with local high-speed active feedforwards. We show that, with such all-photonic quantum repeaters, the communication efficiency scales polynomially with the channel distance. Our result paves a new route towards quantum repeaters with efficient single-photon sources rather than matter quantum memories. PMID:25873153

  5. All-photonic quantum repeaters.

    PubMed

    Azuma, Koji; Tamaki, Kiyoshi; Lo, Hoi-Kwong

    2015-04-15

    Quantum communication holds promise for unconditionally secure transmission of secret messages and faithful transfer of unknown quantum states. Photons appear to be the medium of choice for quantum communication. Owing to photon losses, robust quantum communication over long lossy channels requires quantum repeaters. It is widely believed that a necessary and highly demanding requirement for quantum repeaters is the existence of matter quantum memories. Here we show that such a requirement is, in fact, unnecessary by introducing the concept of all-photonic quantum repeaters based on flying qubits. In particular, we present a protocol based on photonic cluster-state machine guns and a loss-tolerant measurement equipped with local high-speed active feedforwards. We show that, with such all-photonic quantum repeaters, the communication efficiency scales polynomially with the channel distance. Our result paves a new route towards quantum repeaters with efficient single-photon sources rather than matter quantum memories.

  6. Quantum repeaters: fundamental and future

    NASA Astrophysics Data System (ADS)

    Li, Yue; Hua, Sha; Liu, Yu; Ye, Jun; Zhou, Quan

    2007-04-01

    An overview of the Quantum Repeater techniques based on Entanglement Distillation and Swapping is provided. Beginning with a brief history and the basic concepts of the quantum repeaters, the article primarily focuses on the communication model based on the quantum repeater techniques, which mainly consists of two fundamental modules --- the Entanglement Distillation module and the Swapping module. The realizations of Entanglement Distillation are discussed, including the Bernstein's Procrustean method, the Entanglement Concentration and the CNOT-purification method, etc. The schemes of implementing Swapping, which include the Swapping based on Bell-state measurement and the Swapping in Cavity QED, are also introduced. Then a comparison between these realizations and evaluations on them are presented. At last, the article discusses the experimental schemes of quantum repeaters at present, documents some remaining problems and emerging trends in this field.

  7. Repeatability in redundant manipulator systems

    NASA Astrophysics Data System (ADS)

    Mukherjee, Ranjan

    1994-02-01

    Terrestrial manipulators with more DOF than the dimension of the workspace and space manipulators with as many manipulator DOF as the dimension of the workspace are both redundant systems. An interesting problem of such redundant systems has been the repeatability problem due to the presence of nonholonomic constraints. We show, contrary to the existing belief, that integrability of the nonholonomic constraints is not a necessary condition for the repeatability of the configuration variables. There exist certain trajectories in the independent configuration variable space that are like 'holonomic loops' along which the redundant manipulators exhibit repeatable motion. We present a simple method based on optimization techniques for designing repeatable trajectories for free-flying space manipulators and terrestrial manipulators under pseudoinverse control.

  8. Protein Repeats from First Principles.

    PubMed

    Turjanski, Pablo; Parra, R Gonzalo; Espada, Rocío; Becher, Verónica; Ferreiro, Diego U

    2016-04-05

    Some natural proteins display recurrent structural patterns. Despite being highly similar at the tertiary structure level, repeating patterns within a single repeat protein can be extremely variable at the sequence level. We use a mathematical definition of a repetition and investigate the occurrences of these in sequences of different protein families. We found that long stretches of perfect repetitions are infrequent in individual natural proteins, even for those which are known to fold into structures of recurrent structural motifs. We found that natural repeat proteins are indeed repetitive in their families, exhibiting abundant stretches of 6 amino acids or longer that are perfect repetitions in the reference family. We provide a systematic quantification for this repetitiveness. We show that this form of repetitiveness is not exclusive of repeat proteins, but also occurs in globular domains. A by-product of this work is a fast quantification of the likelihood of a protein to belong to a family.

  9. Protein Repeats from First Principles

    PubMed Central

    Turjanski, Pablo; Parra, R. Gonzalo; Espada, Rocío; Becher, Verónica; Ferreiro, Diego U.

    2016-01-01

    Some natural proteins display recurrent structural patterns. Despite being highly similar at the tertiary structure level, repeating patterns within a single repeat protein can be extremely variable at the sequence level. We use a mathematical definition of a repetition and investigate the occurrences of these in sequences of different protein families. We found that long stretches of perfect repetitions are infrequent in individual natural proteins, even for those which are known to fold into structures of recurrent structural motifs. We found that natural repeat proteins are indeed repetitive in their families, exhibiting abundant stretches of 6 amino acids or longer that are perfect repetitions in the reference family. We provide a systematic quantification for this repetitiveness. We show that this form of repetitiveness is not exclusive of repeat proteins, but also occurs in globular domains. A by-product of this work is a fast quantification of the likelihood of a protein to belong to a family. PMID:27044676

  10. Nanospring behaviour of ankyrin repeats.

    PubMed

    Lee, Gwangrog; Abdi, Khadar; Jiang, Yong; Michaely, Peter; Bennett, Vann; Marszalek, Piotr E

    2006-03-09

    Ankyrin repeats are an amino-acid motif believed to function in protein recognition; they are present in tandem copies in diverse proteins in nearly all phyla. Ankyrin repeats contain antiparallel alpha-helices that can stack to form a superhelical spiral. Visual inspection of the extrapolated structure of 24 ankyrin-R repeats indicates the possibility of spring-like behaviour of the putative superhelix. Moreover, stacks of 17-29 ankyrin repeats in the cytoplasmic domains of transient receptor potential (TRP) channels have been identified as candidates for a spring that gates mechanoreceptors in hair cells as well as in Drosophila bristles. Here we report that tandem ankyrin repeats exhibit tertiary-structure-based elasticity and behave as a linear and fully reversible spring in single-molecule measurements by atomic force microscopy. We also observe an unexpected ability of unfolded repeats to generate force during refolding, and report the first direct measurement of the refolding force of a protein domain. Thus, we show that one of the most common amino-acid motifs has spring properties that could be important in mechanotransduction and in the design of nanodevices.

  11. Towards constraining the stratosphere-troposphere exchange of radiocarbon: strategies of stratospheric 14CO2 measurements using AirCore

    NASA Astrophysics Data System (ADS)

    Chen, Huilin; Paul, Dipayan; Meijer, Harro; Miller, John; Kivi, Rigel; Krol, Maarten

    2016-04-01

    Radiocarbon (14C) plays an important role in the carbon cycle studies to understand both natural and anthropogenic carbon fluxes, but also in atmospheric chemistry to constrain hydroxyl radical (OH) concentrations in the atmosphere. Apart from the enormous 14C emissions from nuclear bomb testing in the 1950s and 1960s, radiocarbon is primarily produced in the stratosphere due to the cosmogenic production. To this end, better understanding the stratospheric radiocarbon source is very useful to advance the use of radiocarbon for these applications. However, stratospheric 14C observations have been very limited so that there are large uncertainties on the magnitude and the location of the 14C production as well as the transport of radiocarbon from the stratosphere to the troposphere. Recently we have successfully made stratospheric 14C measurements using AirCore samples from Sodankylä, Northern Finland. AirCore is an innovative atmospheric sampling system, which passively collects atmospheric air samples into a long piece of coiled stainless steel tubing during the descent of a balloon flight. Due to the relatively low cost of the consumables, there is a potential to make such AirCore profiling in other parts of the world on a regular basis. In this study, we simulate the 14C in the atmosphere and assess the stratosphere-troposphere exchange of radiocarbon using the TM5 model. The Sodankylä radiocarbon measurements will be used to verify the performance of the model at high latitude. Besides this, we will also evaluate the influence of different cosmogenic 14C production scenarios and the uncertainties in the OH field on the seasonal cycles of radiocarbon and on the stratosphere-troposphere exchange, and based on the results design a strategy to set up a 14C measurement program using AirCore.

  12. Limitations on quantum key repeaters

    NASA Astrophysics Data System (ADS)

    Bäuml, Stefan; Christandl, Matthias; Horodecki, Karol; Winter, Andreas

    2015-04-01

    A major application of quantum communication is the distribution of entangled particles for use in quantum key distribution. Owing to noise in the communication line, quantum key distribution is, in practice, limited to a distance of a few hundred kilometres, and can only be extended to longer distances by use of a quantum repeater, a device that performs entanglement distillation and quantum teleportation. The existence of noisy entangled states that are undistillable but nevertheless useful for quantum key distribution raises the question of the feasibility of a quantum key repeater, which would work beyond the limits of entanglement distillation, hence possibly tolerating higher noise levels than existing protocols. Here we exhibit fundamental limits on such a device in the form of bounds on the rate at which it may extract secure key. As a consequence, we give examples of states suitable for quantum key distribution but unsuitable for the most general quantum key repeater protocol.

  13. Limitations on quantum key repeaters.

    PubMed

    Bäuml, Stefan; Christandl, Matthias; Horodecki, Karol; Winter, Andreas

    2015-04-23

    A major application of quantum communication is the distribution of entangled particles for use in quantum key distribution. Owing to noise in the communication line, quantum key distribution is, in practice, limited to a distance of a few hundred kilometres, and can only be extended to longer distances by use of a quantum repeater, a device that performs entanglement distillation and quantum teleportation. The existence of noisy entangled states that are undistillable but nevertheless useful for quantum key distribution raises the question of the feasibility of a quantum key repeater, which would work beyond the limits of entanglement distillation, hence possibly tolerating higher noise levels than existing protocols. Here we exhibit fundamental limits on such a device in the form of bounds on the rate at which it may extract secure key. As a consequence, we give examples of states suitable for quantum key distribution but unsuitable for the most general quantum key repeater protocol.

  14. Repeated DNA in Pneumocystis carinii.

    PubMed Central

    Stringer, S L; Hong, S T; Giuntoli, D; Stringer, J R

    1991-01-01

    A 16-kb DNA fragment designated Rp3-1 and cloned from the genome of rat-derived Pneumocystis carinii was found to contain sequences that were repeated approximately 70 times per genome. The repeated sequences in Rp3-1 spanned at least 10.4 kb. Sequences in Rp3-1 were present on each of the 16 P. carinii chromosomes resolved by field inversion gel electrophoresis. Most of the P. carinii genomic sequences homologous to those in the Rp3-1 clone appeared to be as long as those in the Rp3-1 clone but were highly polymorphic with respect to restriction enzyme cleavage sites. The Rp3-1 DNA fragment appears to be a member of a family of large, degenerate, dispersed repeats. Images PMID:1677941

  15. Magnetars as soft gamma repeaters

    NASA Astrophysics Data System (ADS)

    O'Meara, Karen

    1999-05-01

    The source of non-periodic, repeating, gamma-ray bursts located within our galaxy and near supernova remnants has been a mystery. A new theory by Christopher Thompson and Robert Duncan, postulating the existence of young neutron stars with intense magnetic fields (1E14 Gauss or more) offers an explanation. The intense magnetic fields of these "magnetars" suffice to create the phenomena detected from soft gamma-ray repeaters. The poles of a magnetar are hot enough to emit steady, low level x-ray emissions. Stresses on the star's crust due to the drifting of the magnetic field through the superfluid core create seismic activity and "starquakes," which release enormous bursts of energy. Data collected from recent soft gamma-ray repeater bursts appear to be strong evidence in support of this exciting new theory.

  16. Hysteresis of magnetostructural transitions: Repeatable and non-repeatable processes

    NASA Astrophysics Data System (ADS)

    Provenzano, Virgil; Della Torre, Edward; Bennett, Lawrence H.; ElBidweihy, Hatem

    2014-02-01

    The Gd5Ge2Si2 alloy and the off-stoichiometric Ni50Mn35In15 Heusler alloy belong to a special class of metallic materials that exhibit first-order magnetostructural transitions near room temperature. The magnetic properties of this class of materials have been extensively studied due to their interesting magnetic behavior and their potential for a number of technological applications such as refrigerants for near-room-temperature magnetic refrigeration. The thermally driven first-order transitions in these materials can be field-induced in the reverse order by applying a strong enough field. The field-induced transitions are typically accompanied by the presence of large magnetic hysteresis, the characteristics of which are a complicated function of temperature, field, and magneto-thermal history. In this study we show that the virgin curve, the major loop, and sequentially measured MH loops are the results of both repeatable and non-repeatable processes, in which the starting magnetostructural state, prior to the cycling of field, plays a major role. Using the Gd5Ge2Si2 and Ni50Mn35In15 alloys, as model materials, we show that a starting single phase state results in fully repeatable processes and large magnetic hysteresis, whereas a mixed phase starting state results in non-repeatable processes and smaller hysteresis.

  17. Do Twelfths Terminate or Repeat?

    ERIC Educational Resources Information Center

    Ambrose, Rebecca; Burnison, Erica

    2015-01-01

    When finding the decimal equivalent of a fraction with 12 in the denominator, will it terminate or repeat? This question came from a seventh grader in author Erica Burnison's class as the student was pondering a poster generated by one of her classmates. Not only was the question intriguing, but it also affirmed the belief in the power of…

  18. Mechanical Anisotropy of Ankyrin Repeats

    PubMed Central

    Lee, Whasil; Zeng, Xiancheng; Rotolo, Kristina; Yang, Ming; Schofield, Christopher J.; Bennett, Vann; Yang, Weitao; Marszalek, Piotr E.

    2012-01-01

    Red blood cells are frequently deformed and their cytoskeletal proteins such as spectrin and ankyrin-R are repeatedly subjected to mechanical forces. While the mechanics of spectrin was thoroughly investigated in vitro and in vivo, little is known about the mechanical behavior of ankyrin-R. In this study, we combine coarse-grained steered molecular dynamics simulations and atomic force spectroscopy to examine the mechanical response of ankyrin repeats (ARs) in a model synthetic AR protein NI6C, and in the D34 fragment of native ankyrin-R when these proteins are subjected to various stretching geometry conditions. Our steered molecular dynamics results, supported by AFM measurements, reveal an unusual mechanical anisotropy of ARs: their mechanical stability is greater when their unfolding is forced to propagate from the N-terminus toward the C-terminus (repeats unfold at ∼60 pN), as compared to the unfolding in the opposite direction (unfolding force ∼ 30 pN). This anisotropy is also reflected in the complex refolding behavior of ARs. The origin of this unfolding and refolding anisotropy is in the various numbers of native contacts that are broken and formed at the interfaces between neighboring repeats depending on the unfolding/refolding propagation directions. Finally, we discuss how these complex mechanical properties of ARs in D34 may affect its behavior in vivo. PMID:22404934

  19. Do Twelfths Terminate or Repeat?

    ERIC Educational Resources Information Center

    Ambrose, Rebecca; Burnison, Erica

    2015-01-01

    When finding the decimal equivalent of a fraction with 12 in the denominator, will it terminate or repeat? This question came from a seventh grader in author Erica Burnison's class as the student was pondering a poster generated by one of her classmates. Not only was the question intriguing, but it also affirmed the belief in the power of…

  20. Pentapeptide Repeat Proteins and Cyanobacteria

    SciTech Connect

    Buchko, Garry W.

    2009-10-16

    Cyanobacteria are unique in many ways and one unusual feature is the presence of a suite of proteins that contain at least one domain with a minimum of eight tandem repeated five-residues (Rfr) of the general consensus sequence A[N/D]LXX. The function of such pentapeptide repeat proteins (PRPs) are still unknown, however, their prevalence in cyanobacteria suggests that they may play some role in the unique biological activities of cyanobacteria. As part of an inter-disciplinary Membrane Biology Grand Challenge at the Environmental Molecular Sciences Laboratory (Pacific Northwest National Laboratory) and Washington University in St. Louis, the genome of Cyanothece 51142 was sequenced and its molecular biology studied with relation to circadian rhythms. The genome of Cyanothece encodes for 35 proteins that contain at least one PRP domain. These proteins range in size from 105 (Cce_3102) to 930 (Cce_2929) kDa with the PRP domains ranging in predicted size from 12 (Cce_1545) to 62 (cce_3979) tandem pentapeptide repeats. Transcriptomic studies with 29 out of the 35 genes showed that at least three of the PRPs in Cyanothece 51142 (cce_0029, cce_3083, and cce_3272) oscillated with repeated periods of light and dark, further supporting a biological function for PRPs. Using X-ray diffraction crystallography, the structure for two pentapeptide repeat proteins from Cyanothece 51142 were determined, cce_1272 (aka Rfr32) and cce_4529 (aka Rfr23). Analysis of their molecular structures suggests that all PRP may share the same structural motif, a novel type of right-handed quadrilateral β-helix, or Rfr-fold, reminiscent of a square tower with four distinct faces. Each pentapeptide repeat occupies one face of the Rfr-fold with four consecutive pentapeptide repeats completing a coil that, in turn, stack upon each other to form “protein skyscrapers”. Details of the structural features of the Rfr-fold are reviewed here together with a discussion for the possible role of end

  1. Measurement of Bremsstrahlung radiation for in vivo monitoring of 14C tracer distribution between fruit and roots of kiwifruit (Actinidia arguta) cuttings.

    PubMed

    Black, Marykate Z; Minchin, Peter E H; Gould, Nick; Patterson, Kevin J; Clearwater, Michael J

    2012-10-01

    In vivo measurements of (14)C tracer distribution have usually involved monitoring the β(-) particles produced as (14)C decays. These particles are only detectable over short distances, limiting the use of this technique to thin plant material. In the present experiments, X-ray detectors were used to monitor the Bremsstrahlung radiation emitted since β(-) particles were absorbed in plant tissues. Bremsstrahlung radiation is detectable through larger tissue depths. The aim of these experiments was to demonstrate the Bremsstrahlung method by monitoring in vivo tracer-labelled photosynthate partitioning in small kiwifruit (Actinidia arguta (Siebold & Zucc.) Planch. ex Miq.) plants in response to root pruning. A source shoot, consisting of four leaves, was pulse labelled with (14)CO(2). Detectors monitored import into a fruit and the root system, and export from a source leaf. Repeat pulse labelling enabled the comparison of pre- and post-treatment observations within an individual plant. Diurnal trends were observed in the distribution of tracer, with leaf export reduced at night. Tracer accumulated in the roots declined after approximately 48 h, which may have resulted from export of (14)C from the roots in carbon skeletons. Cutting off half the roots did not affect tracer distribution to the remaining half. Tracer distribution to the fruit was increased after root pruning, demonstrating the higher competitive strength of the fruit than the roots for carbohydrate supply. Increased partitioning to the fruit following root pruning has also been demonstrated in kiwifruit field trials.

  2. Dominant short repeated sequences in bacterial genomes.

    PubMed

    Avershina, Ekaterina; Rudi, Knut

    2015-03-01

    We use a novel multidimensional searching approach to present the first exhaustive search for all possible repeated sequences in 166 genomes selected to cover the bacterial domain. We found an overrepresentation of repeated sequences in all but one of the genomes. The most prevalent repeats by far were related to interspaced short palindromic repeats (CRISPRs)—conferring bacterial adaptive immunity. We identified a deep branching clade of thermophilic Firmicutes containing the highest number of CRISPR repeats. We also identified a high prevalence of tandem repeated heptamers. In addition, we identified GC-rich repeats that could potentially be involved in recombination events. Finally, we identified repeats in a 16322 amino acid mega protein (involved in biofilm formation) and inverted repeats flanking miniature transposable elements (MITEs). In conclusion, the exhaustive search for repeated sequences identified new elements and distribution of these, which has implications for understanding both the ecology and evolution of bacteria.

  3. Observations of Soft Gamma Repeaters

    NASA Technical Reports Server (NTRS)

    Kouveliotou, Chryssa

    2004-01-01

    Magnetars (Soft Gamma Repeaters and Anomalous X-ray Pulsars) are a subclass of neutron stars characterized by their recurrent X-ray bursts. While in an active (bursting) state (lasting anywhere between days and years), they are emit&ng hundreds of predominantly soft (kT=30 kev), short (0.1-100 ms long) events. Their quiescent source x-ray light ewes exhibit puhlions rotational period rate changes (spin-down) indicate that their magnetic fields are extremely high, of the order of 10^14- 10^l5 G. Such high B-field objects, dubbed "magnetars", had been predicted to exist in 1992, but the first concrete observational evidence were obtained in 1998 for two of these sources. I will discuss here the history of Soft Gamma Repeaters, and their spectral, timing and flux characteristics both in the persistent and their burst emission.

  4. A repeating fast radio burst.

    PubMed

    Spitler, L G; Scholz, P; Hessels, J W T; Bogdanov, S; Brazier, A; Camilo, F; Chatterjee, S; Cordes, J M; Crawford, F; Deneva, J; Ferdman, R D; Freire, P C C; Kaspi, V M; Lazarus, P; Lynch, R; Madsen, E C; McLaughlin, M A; Patel, C; Ransom, S M; Seymour, A; Stairs, I H; Stappers, B W; van Leeuwen, J; Zhu, W W

    2016-03-10

    Fast radio bursts are millisecond-duration astronomical radio pulses of unknown physical origin that appear to come from extragalactic distances. Previous follow-up observations have failed to find additional bursts at the same dispersion measure (that is, the integrated column density of free electrons between source and telescope) and sky position as the original detections. The apparent non-repeating nature of these bursts has led to the suggestion that they originate in cataclysmic events. Here we report observations of ten additional bursts from the direction of the fast radio burst FRB 121102. These bursts have dispersion measures and sky positions consistent with the original burst. This unambiguously identifies FRB 121102 as repeating and demonstrates that its source survives the energetic events that cause the bursts. Additionally, the bursts from FRB 121102 show a wide range of spectral shapes that appear to be predominantly intrinsic to the source and which vary on timescales of minutes or less. Although there may be multiple physical origins for the population of fast radio bursts, these repeat bursts with high dispersion measure and variable spectra specifically seen from the direction of FRB 121102 support an origin in a young, highly magnetized, extragalactic neutron star.

  5. A repeating fast radio burst

    NASA Astrophysics Data System (ADS)

    Spitler, L. G.; Scholz, P.; Hessels, J. W. T.; Bogdanov, S.; Brazier, A.; Camilo, F.; Chatterjee, S.; Cordes, J. M.; Crawford, F.; Deneva, J.; Ferdman, R. D.; Freire, P. C. C.; Kaspi, V. M.; Lazarus, P.; Lynch, R.; Madsen, E. C.; McLaughlin, M. A.; Patel, C.; Ransom, S. M.; Seymour, A.; Stairs, I. H.; Stappers, B. W.; van Leeuwen, J.; Zhu, W. W.

    2016-03-01

    Fast radio bursts are millisecond-duration astronomical radio pulses of unknown physical origin that appear to come from extragalactic distances. Previous follow-up observations have failed to find additional bursts at the same dispersion measure (that is, the integrated column density of free electrons between source and telescope) and sky position as the original detections. The apparent non-repeating nature of these bursts has led to the suggestion that they originate in cataclysmic events. Here we report observations of ten additional bursts from the direction of the fast radio burst FRB 121102. These bursts have dispersion measures and sky positions consistent with the original burst. This unambiguously identifies FRB 121102 as repeating and demonstrates that its source survives the energetic events that cause the bursts. Additionally, the bursts from FRB 121102 show a wide range of spectral shapes that appear to be predominantly intrinsic to the source and which vary on timescales of minutes or less. Although there may be multiple physical origins for the population of fast radio bursts, these repeat bursts with high dispersion measure and variable spectra specifically seen from the direction of FRB 121102 support an origin in a young, highly magnetized, extragalactic neutron star.

  6. Accumulate Repeat Accumulate Coded Modulation

    NASA Technical Reports Server (NTRS)

    Abbasfar, Aliazam; Divsalar, Dariush; Yao, Kung

    2004-01-01

    In this paper we propose an innovative coded modulation scheme called 'Accumulate Repeat Accumulate Coded Modulation' (ARA coded modulation). This class of codes can be viewed as serial turbo-like codes, or as a subclass of Low Density Parity Check (LDPC) codes that are combined with high level modulation. Thus at the decoder belief propagation can be used for iterative decoding of ARA coded modulation on a graph, provided a demapper transforms the received in-phase and quadrature samples to reliability of the bits.

  7. Crowding by a repeating pattern

    PubMed Central

    Rosen, Sarah; Pelli, Denis G.

    2015-01-01

    Theinability to recognize a peripheral target among flankers is called crowding. For a foveal target, crowding can be distinguished from overlap masking by its sparing of detection, linear scaling with eccentricity, and invariance with target size.Crowding depends on the proximity and similarity of the flankers to the target. Flankers that are far from or dissimilar to the target do not crowd it. On a gray page, text whose neighboring letters have different colors, alternately black and white, has enough dissimilarity that it might escape crowding. Since reading speed is normally limited by crowding, escape from crowding should allow faster reading. Yet reading speed is unchanged (Chung & Mansfield, 2009). Why? A recent vernier study found that using alternating-color flankers produces strong crowding (Manassi, Sayim, & Herzog, 2012). Might that effect occur with letters and reading? Critical spacing is the minimum center-to-center target–flanker spacing needed to correctly identify the target. We measure it for a target letter surrounded by several equidistant flanker letters of the same polarity, opposite polarity, or mixed polarity: alternately white and black. We find strong crowding in the alternating condition, even though each flanker letter is beyond its own critical spacing (as measured in a separate condition). Thus a periodic repeating pattern can produce crowding even when the individual elements do not. Further, in all conditions we find that, once a periodic pattern repeats (two cycles), further repetition does not affect critical spacing of the innermost flanker. PMID:26024457

  8. Crowding by a repeating pattern.

    PubMed

    Rosen, Sarah; Pelli, Denis G

    2015-01-01

    Theinability to recognize a peripheral target among flankers is called crowding. For a foveal target, crowding can be distinguished from overlap masking by its sparing of detection, linear scaling with eccentricity, and invariance with target size.Crowding depends on the proximity and similarity of the flankers to the target. Flankers that are far from or dissimilar to the target do not crowd it. On a gray page, text whose neighboring letters have different colors, alternately black and white, has enough dissimilarity that it might escape crowding. Since reading speed is normally limited by crowding, escape from crowding should allow faster reading. Yet reading speed is unchanged (Chung & Mansfield, 2009). Why? A recent vernier study found that using alternating-color flankers produces strong crowding (Manassi, Sayim, & Herzog, 2012). Might that effect occur with letters and reading? Critical spacing is the minimum center-to-center target-flanker spacing needed to correctly identify the target. We measure it for a target letter surrounded by several equidistant flanker letters of the same polarity, opposite polarity, or mixed polarity: alternately white and black. We find strong crowding in the alternating condition, even though each flanker letter is beyond its own critical spacing (as measured in a separate condition). Thus a periodic repeating pattern can produce crowding even when the individual elements do not. Further, in all conditions we find that, once a periodic pattern repeats (two cycles), further repetition does not affect critical spacing of the innermost flanker.

  9. CDC Vital Signs: Preventing Repeat Teen Births

    MedlinePlus

    ... file Error processing SSI file Preventing Repeat Teen Births Recommend on Facebook Tweet Share Compartir On this ... Too many teens, ages 15–19, have repeat births. Nearly 1 in 5 births to teens, ages ...

  10. Repeated Reading. What Works Clearinghouse Intervention Report

    ERIC Educational Resources Information Center

    What Works Clearinghouse, 2014

    2014-01-01

    "Repeated reading" is an academic practice that aims to increase oral reading fluency. "Repeated reading" can be used with students who have developed initial word reading skills but demonstrate inadequate reading fluency for their grade level. During "repeated reading," a student sits in a quiet location with a…

  11. Evolution of Protein Domain Repeats in Metazoa

    PubMed Central

    Schüler, Andreas; Bornberg-Bauer, Erich

    2016-01-01

    Repeats are ubiquitous elements of proteins and they play important roles for cellular function and during evolution. Repeats are, however, also notoriously difficult to capture computationally and large scale studies so far had difficulties in linking genetic causes, structural properties and evolutionary trajectories of protein repeats. Here we apply recently developed methods for repeat detection and analysis to a large dataset comprising over hundred metazoan genomes. We find that repeats in larger protein families experience generally very few insertions or deletions (indels) of repeat units but there is also a significant fraction of noteworthy volatile outliers with very high indel rates. Analysis of structural data indicates that repeats with an open structure and independently folding units are more volatile and more likely to be intrinsically disordered. Such disordered repeats are also significantly enriched in sites with a high functional potential such as linear motifs. Furthermore, the most volatile repeats have a high sequence similarity between their units. Since many volatile repeats also show signs of recombination, we conclude they are often shaped by concerted evolution. Intriguingly, many of these conserved yet volatile repeats are involved in host-pathogen interactions where they might foster fast but subtle adaptation in biological arms races. Key Words: protein evolution, domain rearrangements, protein repeats, concerted evolution. PMID:27671125

  12. Two-dimensional quantum repeaters

    NASA Astrophysics Data System (ADS)

    Wallnöfer, J.; Zwerger, M.; Muschik, C.; Sangouard, N.; Dür, W.

    2016-11-01

    The endeavor to develop quantum networks gave rise to a rapidly developing field with far-reaching applications such as secure communication and the realization of distributed computing tasks. This ultimately calls for the creation of flexible multiuser structures that allow for quantum communication between arbitrary pairs of parties in the network and facilitate also multiuser applications. To address this challenge, we propose a two-dimensional quantum repeater architecture to establish long-distance entanglement shared between multiple communication partners in the presence of channel noise and imperfect local control operations. The scheme is based on the creation of self-similar multiqubit entanglement structures at growing scale, where variants of entanglement swapping and multiparty entanglement purification are combined to create high-fidelity entangled states. We show how such networks can be implemented using trapped ions in cavities.

  13. Linear Synchronous Motor Repeatability Tests

    SciTech Connect

    Ward, C.R.

    2002-10-18

    A cart system using linear synchronous motors was being considered for the Plutonium Immobilization Plant (PIP). One of the applications in the PIP was the movement of a stack of furnace trays, filled with the waste form (pucks) from a stacking/unstacking station to several bottom loaded furnaces. A system was ordered to perform this function in the PIP Ceramic Prototype Test Facility (CPTF). This system was installed and started up in SRTC prior to being installed in the CPTF. The PIP was suspended and then canceled after the linear synchronous motor system was started up. This system was used to determine repeatability of a linear synchronous motor cart system for the Modern Pit Facility.

  14. Repeated episodes of endosulfan poisoning.

    PubMed

    Dewan, Aruna; Bhatnagar, Vijay K; Mathur, Murli L; Chakma, Tapas; Kashyap, Rekha; Sadhu, Harsiddha G; Sinha, Sukesh N; Saiyed, Habibullah N

    2004-01-01

    A number of families in a rural area of Jabalpur District (Madhya Pradesh), India, were affected by repeated episodes of convulsive illness over a period of three weeks. The aim of this investigation was to determine the cause of the illness. The investigation included a house-to-house survey, interviews of affected families, discussions with treating physicians, and examination of hospital records. Endosulfan poisoning was suspected as many villagers were using empty pesticide containers for food storage. To confirm this, our team collected blood and food samples, which were transported to the laboratory and analyzed with GC-ECD. Thirty-six persons of all age groups had illness of varying severity over a period of three weeks. In the first week, due to superstitions and lack of treatment, three children died. In the second week, symptomatic treatment of affected persons in a district hospital led to recovery but recurrence of convulsive episodes occurred after the return home. In the third week, 10 people were again hospitalized in a teaching hospital. Investigations carried out in this hospital ruled out infective etiology but no facilities were available for chemical analysis. All persons responded to symptomatic treatment. The blood and food samples analyzed by our team showed presence of endosulfan, which was confirmed by GCMS. One of the food items (Laddu) prepared from wheat flour was found to contain 676 ppm of alpha-endosulfan. Contamination of wheat grains or flour with endosulfan and its consumption over a period of time was the most likely cause of repeated episodes of convulsions, but the exact reason for this contamination could not be determined. This report highlights the unsafe disposal of pesticide containers by illiterate farm workers, superstitions leading to delay in treatment, and susceptibility of children to endosulfan.

  15. Learning in repeated visual search

    PubMed Central

    Hout, Michael C.; Goldinger, Stephen D.

    2014-01-01

    Visual search (e.g., finding a specific object in an array of other objects) is performed most effectively when people are able to ignore distracting nontargets. In repeated search, however, incidental learning of object identities may facilitate performance. In three experiments, with over 1,100 participants, we examined the extent to which search could be facilitated by object memory and by memory for spatial layouts. Participants searched for new targets (real-world, nameable objects) embedded among repeated distractors. To make the task more challenging, some participants performed search for multiple targets, increasing demands on visual working memory (WM). Following search, memory for search distractors was assessed using a surprise two-alternative forced choice recognition memory test with semantically matched foils. Search performance was facilitated by distractor object learning and by spatial memory; it was most robust when object identity was consistently tied to spatial locations and weakest (or absent) when object identities were inconsistent across trials. Incidental memory for distractors was better among participants who searched under high WM load, relative to low WM load. These results were observed when visual search included exhaustive-search trials (Experiment 1) or when all trials were self-terminating (Experiment 2). In Experiment 3, stimulus exposure was equated across WM load groups by presenting objects in a single-object stream; recognition accuracy was similar to that in Experiments 1 and 2. Together, the results suggest that people incidentally generate memory for nontarget objects encountered during search and that such memory can facilitate search performance. PMID:20601709

  16. Repeat instability: mechanisms of dynamic mutations.

    PubMed

    Pearson, Christopher E; Nichol Edamura, Kerrie; Cleary, John D

    2005-10-01

    Disease-causing repeat instability is an important and unique form of mutation that is linked to more than 40 neurological, neurodegenerative and neuromuscular disorders. DNA repeat expansion mutations are dynamic and ongoing within tissues and across generations. The patterns of inherited and tissue-specific instability are determined by both gene-specific cis-elements and trans-acting DNA metabolic proteins. Repeat instability probably involves the formation of unusual DNA structures during DNA replication, repair and recombination. Experimental advances towards explaining the mechanisms of repeat instability have broadened our understanding of this mutational process. They have revealed surprising ways in which metabolic pathways can drive or protect from repeat instability.

  17. Unfolding a linker between helical repeats.

    PubMed

    Ortiz, Vanessa; Nielsen, Steven O; Klein, Michael L; Discher, Dennis E

    2005-06-10

    In many multi-repeat proteins, linkers between repeats have little secondary structure and place few constraints on folding or unfolding. However, the large family of spectrin-like proteins, including alpha-actinin, spectrin, and dystrophin, share three-helix bundle, spectrin repeats that appear in crystal structures to be linked by long helices. All of these proteins are regularly subjected to mechanical stress. Recent single molecule atomic force microscopy (AFM) experiments demonstrate not only forced unfolding but also simultaneous unfolding of tandem repeats at finite frequency, which suggests that the contiguous helix between spectrin repeats can propagate a cooperative helix-to-coil transition. Here, we address what happens atomistically to the linker under stress by steered molecular dynamics simulations of tandem spectrin repeats in explicit water. The results for alpha-actinin repeats reveal rate-dependent pathways, with one pathway showing that the linker between repeats unfolds, which may explain the single-repeat unfolding pathway observed in AFM experiments. A second pathway preserves the structural integrity of the linker, which explains the tandem-repeat unfolding event. Unfolding of the linker begins with a splay distortion of proximal loops away from hydrophobic contacts with the linker. This is followed by linker destabilization and unwinding with increased hydration of the backbone. The end result is an unfolded helix that mechanically decouples tandem repeats. Molecularly detailed insights obtained here aid in understanding the mechanical coupling of domain stability in spectrin family proteins.

  18. A Semiparametric Bayesian Model for Repeatedly Repeated Binary Outcomes

    PubMed Central

    Quintana, Fernando A.; Müller, Peter; Rosner, Gary L.; Relling, Mary V.

    2009-01-01

    Summary We discuss the analysis of data from single nucleotide polymorphism (SNP) arrays comparing tumor and normal tissues. The data consist of sequences of indicators for loss of heterozygosity (LOH) and involve three nested levels of repetition: chromosomes for a given patient, regions within chromosomes, and SNPs nested within regions. We propose to analyze these data using a semiparametric model for multi-level repeated binary data. At the top level of the hierarchy we assume a sampling model for the observed binary LOH sequences that arises from a partial exchangeability argument. This implies a mixture of Markov chains model. The mixture is defined with respect to the Markov transition probabilities. We assume a nonparametric prior for the random mixing measure. The resulting model takes the form of a semiparametric random effects model with the matrix of transition probabilities being the random effects. The model includes appropriate dependence assumptions for the two remaining levels of the hierarchy, i.e., for regions within chromosomes and for chromosomes within patient. We use the model to identify regions of increased LOH in a dataset coming from a study of treatment-related leukemia in children with an initial cancer diagnostic. The model successfully identifies the desired regions and performs well compared to other available alternatives. PMID:19746193

  19. Modeling Repeatedly Flaring δ Sunspots.

    PubMed

    Chatterjee, Piyali; Hansteen, Viggo; Carlsson, Mats

    2016-03-11

    Active regions (ARs) appearing on the surface of the Sun are classified into α, β, γ, and δ by the rules of the Mount Wilson Observatory, California on the basis of their topological complexity. Amongst these, the δ sunspots are known to be superactive and produce the most x-ray flares. Here, we present results from a simulation of the Sun by mimicking the upper layers and the corona, but starting at a more primitive stage than any earlier treatment. We find that this initial state consisting of only a thin subphotospheric magnetic sheet breaks into multiple flux tubes which evolve into a colliding-merging system of spots of opposite polarity upon surface emergence, similar to those often seen on the Sun. The simulation goes on to produce many exotic δ sunspot associated phenomena: repeated flaring in the range of typical solar flare energy release and ejective helical flux ropes with embedded cool-dense plasma filaments resembling solar coronal mass ejections.

  20. Modeling Repeatedly Flaring δ Sunspots

    NASA Astrophysics Data System (ADS)

    Chatterjee, Piyali; Hansteen, Viggo; Carlsson, Mats

    2016-03-01

    Active regions (ARs) appearing on the surface of the Sun are classified into α , β , γ , and δ by the rules of the Mount Wilson Observatory, California on the basis of their topological complexity. Amongst these, the δ sunspots are known to be superactive and produce the most x-ray flares. Here, we present results from a simulation of the Sun by mimicking the upper layers and the corona, but starting at a more primitive stage than any earlier treatment. We find that this initial state consisting of only a thin subphotospheric magnetic sheet breaks into multiple flux tubes which evolve into a colliding-merging system of spots of opposite polarity upon surface emergence, similar to those often seen on the Sun. The simulation goes on to produce many exotic δ sunspot associated phenomena: repeated flaring in the range of typical solar flare energy release and ejective helical flux ropes with embedded cool-dense plasma filaments resembling solar coronal mass ejections.

  1. Trinucleotide Repeats: A Structural Perspective

    PubMed Central

    Almeida, Bruno; Fernandes, Sara; Abreu, Isabel A.; Macedo-Ribeiro, Sandra

    2013-01-01

    Trinucleotide repeat (TNR) expansions are present in a wide range of genes involved in several neurological disorders, being directly involved in the molecular mechanisms underlying pathogenesis through modulation of gene expression and/or the function of the RNA or protein it encodes. Structural and functional information on the role of TNR sequences in RNA and protein is crucial to understand the effect of TNR expansions in neurodegeneration. Therefore, this review intends to provide to the reader a structural and functional view of TNR and encoded homopeptide expansions, with a particular emphasis on polyQ expansions and its role at inducing the self-assembly, aggregation and functional alterations of the carrier protein, which culminates in neuronal toxicity and cell death. Detail will be given to the Machado-Joseph Disease-causative and polyQ-containing protein, ataxin-3, providing clues for the impact of polyQ expansion and its flanking regions in the modulation of ataxin-3 molecular interactions, function, and aggregation. PMID:23801983

  2. TRDB—The Tandem Repeats Database

    PubMed Central

    Gelfand, Yevgeniy; Rodriguez, Alfredo; Benson, Gary

    2007-01-01

    Tandem repeats in DNA have been under intensive study for many years, first, as a consequence of their usefulness as genomic markers and DNA fingerprints and more recently as their role in human disease and regulatory processes has become apparent. The Tandem Repeats Database (TRDB) is a public repository of information on tandem repeats in genomic DNA. It contains a variety of tools for repeat analysis, including the Tandem Repeats Finder program, query and filtering capabilities, repeat clustering, polymorphism prediction, PCR primer selection, data visualization and data download in a variety of formats. In addition, TRDB serves as a centralized research workbench. It provides user storage space and permits collaborators to privately share their data and analysis. TRDB is available at . PMID:17175540

  3. Short Tandem Repeat DNA Internet Database

    National Institute of Standards and Technology Data Gateway

    SRD 130 Short Tandem Repeat DNA Internet Database (Web, free access)   Short Tandem Repeat DNA Internet Database is intended to benefit research and application of short tandem repeat DNA markers for human identity testing. Facts and sequence information on each STR system, population data, commonly used multiplex STR systems, PCR primers and conditions, and a review of various technologies for analysis of STR alleles have been included.

  4. Understanding and identifying amino acid repeats

    PubMed Central

    Nijveen, Harm

    2014-01-01

    Amino acid repeats (AARs) are abundant in protein sequences. They have particular roles in protein function and evolution. Simple repeat patterns generated by DNA slippage tend to introduce length variations and point mutations in repeat regions. Loss of normal and gain of abnormal function owing to their variable length are potential risks leading to diseases. Repeats with complex patterns mostly refer to the functional domain repeats, such as the well-known leucine-rich repeat and WD repeat, which are frequently involved in protein–protein interaction. They are mainly derived from internal gene duplication events and stabilized by ‘gate-keeper’ residues, which play crucial roles in preventing inter-domain aggregation. AARs are widely distributed in different proteomes across a variety of taxonomic ranges, and especially abundant in eukaryotic proteins. However, their specific evolutionary and functional scenarios are still poorly understood. Identifying AARs in protein sequences is the first step for the further investigation of their biological function and evolutionary mechanism. In principle, this is an NP-hard problem, as most of the repeat fragments are shaped by a series of sophisticated evolutionary events and become latent periodical patterns. It is not possible to define a uniform criterion for detecting and verifying various repeat patterns. Instead, different algorithms based on different strategies have been developed to cope with different repeat patterns. In this review, we attempt to describe the amino acid repeat-detection algorithms currently available and compare their strategies based on an in-depth analysis of the biological significance of protein repeats. PMID:23418055

  5. Visual Scan Adaptation During Repeated Visual Search

    DTIC Science & Technology

    2010-01-01

    repeated distractor –target configurations both require environmental stability. For stable distractor – target configurations, Chun and Jiang (1998) have...demon- strated search time savings from repeating distractor –target configurations, and Song and Jiang (2005) demonstrated that as little as 25% of the...search environment (i.e., two distractor locations and the target location out of 12 total locations per trial) repeated from trial to trial resulted

  6. Repeat Concussions in the National Football League

    PubMed Central

    Casson, Ira R.; Viano, David C.; Powell, John W.; Pellman, Elliot J.

    2011-01-01

    Background: Repeat concussion is an important issue in the National Football League (NFL). An initial description of repeat injuries was published for 6 years (1996-2001). Hypothesis: The characteristics and frequency of repeat concussion in the NFL have not changed in the subsequent 6 years (2002-2007). Study Design: Case control. Methods: From 1996 to 2007, concussions were reported using a standardized form documenting signs and symptoms, loss of consciousness and medical action taken. Data on repeat concussions were analyzed for the 12 years and compared between the 2 periods. Results: In 2002-2007, 152 players had repeat concussions (vs 160 in 1996-2001); 44 had 3+ head injuries (vs 52). The positions most often associated with repeat concussion in 2002-2007 were the defensive secondary, kick unit, running back, and linebacker. The odds for repeat concussion were elevated for wide receivers, tight ends, and linebackers but lower than in the earlier period. During 2002-2007, over half of players with repeat concussion were removed from play, and fewer immediately returned (vs 1996-2001). The average duration between concussions was 1.25 years for 2002-2007 and 1.65 years for the 12-year period. Over 12 years, 7.6% of all repeat concussions occurred within 2 weeks of the prior concussion. Conclusions: The defensive secondary, kick unit, running back, and linebacker have the highest incidence of repeat concussion. During 2002-2007, more than half of players with repeat concussion were removed from play, and only a fraction immediately returned. Although concussion was managed more conservatively by team physicians in the recent 6 years, repeat concussions occurred at similar rates during both periods. PMID:23015986

  7. Repeat concussions in the national football league.

    PubMed

    Casson, Ira R; Viano, David C; Powell, John W; Pellman, Elliot J

    2011-01-01

    Repeat concussion is an important issue in the National Football League (NFL). An initial description of repeat injuries was published for 6 years (1996-2001). The characteristics and frequency of repeat concussion in the NFL have not changed in the subsequent 6 years (2002-2007). Case control. From 1996 to 2007, concussions were reported using a standardized form documenting signs and symptoms, loss of consciousness and medical action taken. Data on repeat concussions were analyzed for the 12 years and compared between the 2 periods. In 2002-2007, 152 players had repeat concussions (vs 160 in 1996-2001); 44 had 3+ head injuries (vs 52). The positions most often associated with repeat concussion in 2002-2007 were the defensive secondary, kick unit, running back, and linebacker. The odds for repeat concussion were elevated for wide receivers, tight ends, and linebackers but lower than in the earlier period. During 2002-2007, over half of players with repeat concussion were removed from play, and fewer immediately returned (vs 1996-2001). The average duration between concussions was 1.25 years for 2002-2007 and 1.65 years for the 12-year period. Over 12 years, 7.6% of all repeat concussions occurred within 2 weeks of the prior concussion. The defensive secondary, kick unit, running back, and linebacker have the highest incidence of repeat concussion. During 2002-2007, more than half of players with repeat concussion were removed from play, and only a fraction immediately returned. Although concussion was managed more conservatively by team physicians in the recent 6 years, repeat concussions occurred at similar rates during both periods.

  8. Lambda Exonuclease Digestion of CGG Trinucleotide Repeats

    PubMed Central

    Conroy, R.S.; Koretsky, A.P.; Moreland, J.

    2011-01-01

    Fragile X syndrome and other triplet repeat diseases are characterized by an elongation of a repeating DNA triplet. The ensemble-averaged lambda exonuclease digestion rate of different substrates, including one with an elongated FMR1 gene containing 120 CGG repeats, was measured using absorption and fluorescence spectroscopy. Using magnetic tweezers sequence-dependent digestion rates and pausing was measured for individual lambda exonucleases. Within the triplet repeats a lower average and narrower distribution of rates and a higher frequency of pausing was observed. PMID:19562332

  9. An improved selective-repeat ARQ strategy

    NASA Astrophysics Data System (ADS)

    Weldon, E. J., Jr.

    1982-03-01

    ARQ is the term used for an automatic system which provides error correction by utilizing a constant ratio code and a closed loop to request retransmission of mutilated characters. A selective repeat strategy was described by Stuart (1963). In a selective-repeat ARQ system, blocks are numbered and ACKed (acknowledged) or NACKed by number. Practical selective-repeat ARQ procedures fall far short of channel capacity when the error probability is high. The present investigation is concerned with a new selective-repeat ARQ strategy, which is shown to be superior, with respect to its throughput, to earlier techniques.

  10. Identifying tandem Ankyrin repeats in protein structures.

    PubMed

    Chakrabarty, Broto; Parekh, Nita

    2014-12-30

    Tandem repetition of structural motifs in proteins is frequently observed across all forms of life. Topology of repeating unit and its frequency of occurrence are associated to a wide range of structural and functional roles in diverse proteins, and defects in repeat proteins have been associated with a number of diseases. It is thus desirable to accurately identify specific repeat type and its copy number. Weak evolutionary constraints on repeat units and insertions/deletions between them make their identification difficult at the sequence level and structure based approaches are desired. The proposed graph spectral approach is based on protein structure represented as a graph for detecting one of the most frequently observed structural repeats, Ankyrin repeat. It has been shown in a large number of studies that 3-dimensional topology of a protein structure is well captured by a graph, making it possible to analyze a complex protein structure as a mathematical entity. In this study we show that eigen spectra profile of a protein structure graph exhibits a unique repetitive profile for contiguous repeating units enabling the detection of the repeat region and the repeat type. The proposed approach uses a non-redundant set of 58 Ankyrin proteins to define rules for the detection of Ankyrin repeat motifs. It is evaluated on a set of 370 proteins comprising 125 known Ankyrin proteins and remaining non-solenoid proteins and the prediction compared with UniProt annotation, sequence-based approach, RADAR, and structure-based approach, ConSole. To show the efficacy of the approach, we analyzed the complete PDB structural database and identified 641 previously unrecognized Ankyrin repeat proteins. We observe a unique eigen spectra profile for different repeat types and show that the method can be easily extended to detect other repeat types. It is implemented as a web server, AnkPred. It is freely available at 'bioinf.iiit.ac.in/AnkPred'. AnkPred provides an elegant and

  11. All repeats are not equal: a module-based approach to guide repeat protein design.

    PubMed

    Sawyer, Nicholas; Chen, Jieming; Regan, Lynne

    2013-05-27

    Repeat proteins composed of tandem arrays of a short structural motif often mediate protein-protein interactions. Past efforts to design repeat protein-based molecular recognition tools have focused on the creation of templates from the consensus of individual repeats, regardless of their natural context. Such an approach assumes that all repeats are essentially equivalent. In this study, we present the results of a "module-based" approach in which modules composed of tandem repeats are aligned to identify repeat-specific features. Using this approach to analyze tetratricopeptide repeat modules that contain three tandem repeats (3TPRs), we identify two classes of 3TPR modules with distinct structural signatures that are correlated with different sets of functional residues. Our analyses also reveal a high degree of correlation between positions across the entire ligand-binding surface, indicative of a coordinated, coevolving binding surface. Extension of our analyses to different repeat protein modules reveals more examples of repeat-specific features, especially in armadillo repeat modules. In summary, the module-based analyses that we present effectively capture key repeat-specific features that will be important to include in future repeat protein design templates.

  12. Trinucleotide repeats associated with human disease.

    PubMed Central

    Mitas, M

    1997-01-01

    Triplet repeat expansion diseases (TREDs) are characterized by the coincidence of disease manifestation with amplification of d(CAG. CTG), d(CGG.CCG) or d(GAA.TTC) repeats contained within specific genes. Amplification of triplet repeats continues in offspring of affected individuals, which generally results in progressive severity of the disease and/or an earlier age of onset, phenomena clinically referred to as 'anticipation'. Recent biophysical and biochemical studies reveal that five of the six [d(CGG)n, d(CCG)n, (CAG)n, d(CTG)n and d(GAA)n] complementary sequences that are associated with human disease form stable hairpin structures. Although the triplet repeat sequences d(GAC)n and d(GTC)n also form hairpins, repeats of the double-stranded forms of these sequences are conspicuously absent from DNA sequence databases and are not anticipated to be associated with human disease. With the exception of d(GAG)n and d(GTG)n, the remaining triplet repeat sequences are unlikely to form hairpin structures at physiological salt and temperature. The details of hairpin structures containing trinucleotide repeats are summarized and discussed with respect to potential mechanisms of triplet repeat expansion and d(CGG.CCG) n methylation/demethylation. PMID:9171073

  13. Reward modulation of contextual cueing: Repeated context overshadows repeated target location.

    PubMed

    Sharifian, Fariba; Contier, Oliver; Preuschhof, Claudia; Pollmann, Stefan

    2017-08-07

    Contextual cueing can be enhanced by reward. However, there is a debate if reward is associated with the repeated target-distractor configurations or with the repeated target locations that occur in both repeated and new displays. Based on neuroimaging evidence, we hypothesized that reward becomes associated with the target location only in new displays, but not in repeated displays, where the repeated target location is overshadowed by the more salient repeated target-distractor configuration. To test this hypothesis, we varied the reward value associated with the same target location in repeated and new displays. The results confirmed the overshadowing hypothesis in that search facilitation in repeated target-distractor configurations was modulated by the variable value associated with the target location. This effect was observed mainly in early learning.

  14. Repeated Testing Produces Superior Transfer of Learning Relative to Repeated Studying

    ERIC Educational Resources Information Center

    Butler, Andrew C.

    2010-01-01

    The present research investigated whether test-enhanced learning can be used to promote transfer. More specifically, 4 experiments examined how repeated testing and repeated studying affected retention and transfer of facts and concepts. Subjects studied prose passages and then either repeatedly restudied or took tests on the material. One week…

  15. A Comparison of DWI Repeaters and Non-repeaters Who Attended a Level I Rehabilitation Program.

    ERIC Educational Resources Information Center

    Landrum, James W.; Windham, Gerald O.

    1981-01-01

    Compares behavioral and demographic characteristics of drunk drivers with repeated arrests and drivers not having repeated arrests, after attending an alcohol education program. Previous public drunkeness and previous drunk driving arrests were strong predictors of repeat arrests and were judged useful in screening offenders for rehabilitation…

  16. A Comparison of DWI Repeaters and Non-repeaters Who Attended a Level I Rehabilitation Program.

    ERIC Educational Resources Information Center

    Landrum, James W.; Windham, Gerald O.

    1981-01-01

    Compares behavioral and demographic characteristics of drunk drivers with repeated arrests and drivers not having repeated arrests, after attending an alcohol education program. Previous public drunkeness and previous drunk driving arrests were strong predictors of repeat arrests and were judged useful in screening offenders for rehabilitation…

  17. Metazoan evolution of the armadillo repeat superfamily.

    PubMed

    Gul, Ismail Sahin; Hulpiau, Paco; Saeys, Yvan; van Roy, Frans

    2017-02-01

    The superfamily of armadillo repeat proteins is a fascinating archetype of modular-binding proteins involved in various fundamental cellular processes, including cell-cell adhesion, cytoskeletal organization, nuclear import, and molecular signaling. Despite their diverse functions, they all share tandem armadillo (ARM) repeats, which stack together to form a conserved three-dimensional structure. This superhelical armadillo structure enables them to interact with distinct partners by wrapping around them. Despite the important functional roles of this superfamily, a comprehensive analysis of the composition, classification, and phylogeny of this protein superfamily has not been reported. Furthermore, relatively little is known about a subset of ARM proteins, and some of the current annotations of armadillo repeats are incomplete or incorrect, often due to high similarity with HEAT repeats. We identified the entire armadillo repeat superfamily repertoire in the human genome, annotated each armadillo repeat, and performed an extensive evolutionary analysis of the armadillo repeat proteins in both metazoan and premetazoan species. Phylogenetic analyses of the superfamily classified them into several discrete branches with members showing significant sequence homology, and often also related functions. Interestingly, the phylogenetic structure of the superfamily revealed that about 30 % of the members predate metazoans and represent an ancient subset, which is gradually evolving to acquire complex and highly diverse functions.

  18. Epigenetics and Triplet-Repeat Neurological Diseases.

    PubMed

    Nageshwaran, Sathiji; Festenstein, Richard

    2015-01-01

    The term "junk DNA" has been reconsidered following the delineation of the functional significance of repetitive DNA regions. Typically associated with centromeres and telomeres, DNA repeats are found in nearly all organisms throughout their genomes. Repetitive regions are frequently heterochromatinized resulting in silencing of intrinsic and nearby genes. However, this is not a uniform rule, with several genes known to require such an environment to permit transcription. Repetitive regions frequently exist as dinucleotide, trinucleotide, and tetranucleotide repeats. The association between repetitive regions and disease was emphasized following the discovery of abnormal trinucleotide repeats underlying spinal and bulbar muscular atrophy (Kennedy's disease) and fragile X syndrome of mental retardation (FRAXA) in 1991. In this review, we provide a brief overview of epigenetic mechanisms and then focus on several diseases caused by DNA triplet-repeat expansions, which exhibit diverse epigenetic effects. It is clear that the emerging field of epigenetics is already generating novel potential therapeutic avenues for this group of largely incurable diseases.

  19. The telomere repeat motif of basal Metazoa.

    PubMed

    Traut, Walther; Szczepanowski, Monika; Vítková, Magda; Opitz, Christian; Marec, Frantisek; Zrzavý, Jan

    2007-01-01

    In most eukaryotes the telomeres consist of short DNA tandem repeats and associated proteins. Telomeric repeats are added to the chromosome ends by telomerase, a specialized reverse transcriptase. We examined telomerase activity and telomere repeat sequences in representatives of basal metazoan groups. Our results show that the 'vertebrate' telomere motif (TTAGGG)( n ) is present in all basal metazoan groups, i.e. sponges, Cnidaria, Ctenophora, and Placozoa, and also in the unicellular metazoan sister group, the Choanozoa. Thus it can be considered the ancestral telomere repeat motif of Metazoa. It has been conserved from the metazoan radiation in most animal phylogenetic lineages, and replaced by other motifs-according to our present knowledge-only in two major lineages, Arthropoda and Nematoda.

  20. DNA Triplet Repeat Expansion and Mismatch Repair

    PubMed Central

    Iyer, Ravi R.; Pluciennik, Anna; Napierala, Marek; Wells, Robert D.

    2016-01-01

    DNA mismatch repair is a conserved antimutagenic pathway that maintains genomic stability through rectification of DNA replication errors and attenuation of chromosomal rearrangements. Paradoxically, mutagenic action of mismatch repair has been implicated as a cause of triplet repeat expansions that cause neurological diseases such as Huntington disease and myotonic dystrophy. This mutagenic process requires the mismatch recognition factor MutSβ and the MutLα (and/or possibly MutLγ) endonuclease, and is thought to be triggered by the transient formation of unusual DNA structures within the expanded triplet repeat element. This review summarizes the current knowledge of DNA mismatch repair involvement in triplet repeat expansion, which encompasses in vitro biochemical findings, cellular studies, and various in vivo transgenic animal model experiments. We present current mechanistic hypotheses regarding mismatch repair protein function in mediating triplet repeat expansions and discuss potential therapeutic approaches targeting the mismatch repair pathway. PMID:25580529

  1. Newly arisen DNA repeats in primate phylogeny.

    PubMed

    Ryan, S C; Dugaiczyk, A

    1989-12-01

    We discovered the presence of an Alu and an Xba repetitive DNA element within introns 4 and 7, respectively, of the human alpha-fetoprotein (AFP) gene; these elements are absent from the same gene in the gorilla. The Alu element is flanked by 12-base-pair direct repeats, AGGATGTTGTGG ... (Alu) ... AGGATGTTGTGG, which presumably arose by way of duplication of the intronic target site AGGATGTTGTGG at the time of the Alu insertion. In the gorilla, only a single copy of the unoccupied target site is present, which is identical to the terminal repeat flanking the human Alu element. There are two copies of an Xba repeat in the human AFP gene, apparently the only two in the genome. Xba1 and Xba2, located within introns 8 and 7, respectively, differ from each other at 3 of 303 positions. Xba1 is referred to as the old (ancestral) repeat because it lacks direct repeats. The new (derived) Xba2 is flanked by direct repeats, TTTCTTTTT ... (Xba) ... TTTCTTCTT, and is thought to have arisen as a result of transposition of Xba1. The ancestral Xba1 and a single copy of the Xba2 target site are present at orthologous positions in the gorilla, but the new Xba2 is absent. We conclude that the Alu and Xba DNA repeats emerged in the human genome at a time postdating the human-gorilla divergence and became established as genetic novelties in the human lineage. We submit that the chronology of divergence of primate lines of evolution can be correlated with the timing of insertion of new DNA repeats into the genomes of those primates.

  2. Cumulative Effect of Repeated Brief Cerebral Ischemia

    DTIC Science & Technology

    1993-05-31

    KL, Pohost GM and Conger KA, Correlating EEG and Lactate Kinetics During Repeated Brief Cerebral Ischemia, Proceedings of the American Heart Association 1993...Cornelating EEG and Lactate Kinetics During Repeated Brief Cerebral Ischemia, Proceedings of the American Heart Association 1993. 4) HP Hetherington...thes Bernhard Foundation. ass- 134 󈧑&.1 n5. 9# American Heart Association 026085 66th Scientific Sessions Abstract Form Medical Research Nursing

  3. Repeat radiosurgery for cerebral arteriovenous malformations.

    PubMed

    Awad, Ahmed J; Walcott, Brian P; Stapleton, Christopher J; Ding, Dale; Leed, Cheng-Chia; Loeffler, Jay S

    2015-06-01

    We perform a systematic review of repeat radiosurgery for cerebral arteriovenous malformations (AVM) with an emphasis on lesion obliteration rates and complications. Radiosurgery is an accepted treatment modality for AVM located in eloquent cortex or deep brain structures. For residual or persistent lesions, repeat radiosurgery can be considered if sufficient time has passed to allow for a full appreciation of treatment effects, usually at least 3years. A systematic review was performed in accordance with Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. References for this review were identified by searches of MEDLINE, Web of Science and Google Scholar databases. A total of 14 studies comprising 733 patients met the review criteria and were included. For series that reported target dose at both first and repeat treatments, the weighted means were 19.42Gy and 19.06Gy, respectively. The mean and median obliteration rate for the repeat radiosurgery treatments were 61% (95% confidence interval 51.9-71.7%) and 61.5%, respectively. The median follow up following radiosurgery ranged from 19.5 to 80months. Time to complete obliteration after the repeat treatment ranged from 21 to 40.8months. The most common complications of repeat radiosurgery for AVM included hemorrhage (7.6%) and radiation-induced changes (7.4%). Repeat radiosurgery can be used to treat incompletely obliterated AVM with an obliteration rate of 61%. Complications are related to treatment effect latency (hemorrhage risk) as well as radiation-induced changes. Repeat radiosurgery can be performed at 3 years following the initial treatment, allowing for full realization of effects from the initial treatment prior to commencing therapy. Copyright © 2015 Elsevier Ltd. All rights reserved.

  4. Repeat radiosurgery for cerebral arteriovenous malformations

    PubMed Central

    Stapleton, Christopher J.; Ding, Dale; Leed, Cheng-Chia; Loeffler, Jay S.

    2015-01-01

    We perform a systematic review of repeated radiosurgery for cerebral arteriovenous malformations (AVM) with an emphasis on lesion obliteration rates and complications. Radiosurgery is an accepted treatment modality for AVM located in eloquent cortex or deep brain structures. For residual or persistent lesions, repeated radiosurgery can be considered if sufficient time has passed to allow for a full appreciation of treatment effects, usually at least 3 years. A systematic review was performed in accordance with Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. References for this review were identified by searches of MEDLINE, Web of Science and Google Scholar databases. A total of 14 studies comprising 733 patients met the review criteria and were included. For series that reported target dose at both first and repeat treatments, the weighted means were 19.42 Gy and 19.06 Gy, respectively. The mean and median obliteration rate for the repeat radiosurgery treatments were 61% (95% confidence interval 51.9–71.7%) and 61.5%, respectively. The median follow up following radiosurgery ranged from 19.5 to 80 months. Time to complete obliteration after the repeat treatment ranged from 21 to 40.8 months. The most common complications of repeated radiosurgery for AVM included hemorrhage (7.6%) and radiation-induced changes (7.4%). Repeat radiosurgery can be used to treat incompletely obliterated AVM with an obliteration rate of 61%. Complications are related to treatment effect latency (hemorrhage risk) as well as radiation-induced changes. Repeat radiosurgery can be performed at three years following the initial treatment, allowing for full realization of effects from the initial treatment prior to commencing therapy. PMID:25913746

  5. Security of Quantum Repeater Network Operation

    DTIC Science & Technology

    2016-10-03

    can disrupt operation of the network. Our work produced a first-of-its-kind taxonomy of potential attacks on quantum repeater network operations...behaving node, or a small number of them, can disrupt operation of the network. Our work produced a first-of-its-kind taxonomy of potential attacks on...created a taxonomy of possible attacks on repeater nodes, published in SENT 2015 (Suzuki & Van Meter, 2015). We modeled our taxonomy after security

  6. Monitoring plant phenology using digital repeat photography.

    PubMed

    Crimmins, Michael A; Crimmins, Theresa M

    2008-06-01

    Repeated observations of plant phenology have been shown to be important indicators of global change. However, capturing the exact date of key events requires daily observations during the growing season, making phenologic observations relatively labor intensive and costly to collect. One alternative to daily observations for capturing the dates of key phenologic events is repeat photography. In this study, we explored the utility of repeat digital photography for monitoring phenologic events in plants. We provide an illustration of this approach and its utility by placing observations made using repeat digital imagery in context with local meteorologic and edaphic variables. We found that repeat photography provides a reliable, consistent measurement of phenophase. In addition, digital photography offers advantages in that it can be mathematically manipulated to detect and enhance patterns; it can classify objects; and digital photographs can be archived for future analysis. In this study, an estimate of greenness and counts of individual flowers were extracted by way of mathematic algorithms from the photo time series. These metrics were interpreted using meteorologic measurements collected at the study site. We conclude that repeat photography, coupled with site-specific meteorologic measurements, could greatly enhance our understanding environmental triggers of phenologic events. In addition, the methods described could easily be adopted by citizen scientists and the general public as well as professionals in the field.

  7. Digital repeat analysis; setup and operation.

    PubMed

    Nol, J; Isouard, G; Mirecki, J

    2006-06-01

    Since the emergence of digital imaging, there have been questions about the necessity of continuing reject analysis programs in imaging departments to evaluate performance and quality. As a marketing strategy, most suppliers of digital technology focus on the supremacy of the technology and its ability to reduce the number of repeats, resulting in less radiation doses given to patients and increased productivity in the department. On the other hand, quality assurance radiographers and radiologists believe that repeats are mainly related to positioning skills, and repeat analysis is the main tool to plan training needs to up-skill radiographers. A comparative study between conventional and digital imaging was undertaken to compare outcomes and evaluate the need for reject analysis. However, digital technology still being at its early development stages, setting a credible reject analysis program became the major task of the study. It took the department, with the help of the suppliers of the computed radiography reader and the picture archiving and communication system, over 2 years of software enhancement to build a reliable digital repeat analysis system. The results were supportive of both philosophies; the number of repeats as a result of exposure factors was reduced dramatically; however, the percentage of repeats as a result of positioning skills was slightly on the increase for the simple reason that some rejects in the conventional system qualifying for both exposure and positioning errors were classified as exposure error. The ability of digitally adjusting dark or light images reclassified some of those images as positioning errors.

  8. Remarkable selective constraints on exonic dinucleotide repeats.

    PubMed

    Haasl, Ryan J; Payseur, Bret A

    2014-09-01

    Long dinucleotide repeats found in exons present a substantial mutational hazard: mutations at these loci occur often and generate frameshifts. Here, we provide clear and compelling evidence that exonic dinucleotides experience strong selective constraint. In humans, only 18 exonic dinucleotides have repeat lengths greater than six, which contrasts sharply with the genome-wide distribution of dinucleotides. We genotyped each of these dinucleotides in 200 humans from eight 1000 Genomes Project populations and found a near-absence of polymorphism. More remarkably, divergence data demonstrate that repeat lengths have been conserved across the primate phylogeny in spite of what is likely considerable mutational pressure. Coalescent simulations show that even a very low mutation rate at these loci fails to explain the anomalous patterns of polymorphism and divergence. Our data support two related selective constraints on the evolution of exonic dinucleotides: a short-term intolerance for any change to repeat length and a long-term prevention of increases to repeat length. In general, our results implicate purifying selection as the force that eliminates new, deleterious mutants at exonic dinucleotides. We briefly discuss the evolution of the longest exonic dinucleotide in the human genome--a 10 x CA repeat in fibroblast growth factor receptor-like 1 (FGFRL1)--that should possess a considerably greater mutation rate than any other exonic dinucleotide and therefore generate a large number of deleterious variants. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

  9. Dynamic combinatorial libraries of artificial repeat proteins.

    PubMed

    Eisenberg, Margarita; Shumacher, Inbal; Cohen-Luria, Rivka; Ashkenasy, Gonen

    2013-06-15

    Repeat proteins are found in almost all cellular systems, where they are involved in diverse molecular recognition processes. Recent studies have suggested that de novo designed repeat proteins may serve as universal binders, and might potentially be used as practical alternative to antibodies. We describe here a novel chemical methodology for producing small libraries of repeat proteins, and screening in parallel the ligand binding of library members. The first stage of this research involved the total synthesis of a consensus-based three-repeat tetratricopeptide (TPR) protein (~14 kDa), via sequential attachment of the respective peptides. Despite the effectiveness of the synthesis and ligation steps, this method was found to be too demanding for the production of proteins containing variable number of repeats. Additionally, the analysis of binding of the individual proteins was time consuming. Therefore, we designed and prepared novel dynamic combinatorial libraries (DCLs), and show that their equilibration can facilitate the formation of TPR proteins containing up to eight repeating units. Interestingly, equilibration of the library building blocks in the presence of the biologically relevant ligands, Hsp90 and Hsp70, induced their oligomerization into forming more of the proteins with large recognition surfaces. We suggest that this work presents a novel simple and rapid tool for the simultaneous screening of protein mixtures with variable binding surfaces, and for identifying new binders for ligands of interest.

  10. Proliferating cell nuclear antigen prevents trinucleotide repeat expansions by promoting repeat deletion and hairpin removal

    PubMed Central

    Beaver, Jill M.; Lai, Yanhao; Rolle, Shantell J.; Liu, Yuan

    2017-01-01

    DNA base lesions and base excision repair (BER) within trinucleotide repeat (TNR) tracts modulate repeat instability through the coordination among the key BER enzymes DNA polymerase β, flap endonuclease 1 (FEN1) and DNA ligase I (LIG I). However, it remains unknown whether BER cofactors can also alter TNR stability. In this study, we discovered that proliferating cell nuclear antigen (PCNA), a cofactor of BER, promoted CAG repeat deletion and removal of a CAG repeat hairpin during BER in a duplex CAG repeat tract and CAG hairpin loop, respectively. We showed that PCNA stimulated LIG I activity on a nick across a small template loop during BER in a duplex (CAG)20 repeat tract promoting small repeat deletions. Surprisingly, we found that during BER in a hairpin loop, PCNA promoted reannealing of the upstream flap of a double-flap intermediate, thereby facilitating the formation of a downstream flap and stimulating FEN1 cleavage activity and hairpin removal. Our results indicate that PCNA plays a critical role in preventing CAG repeat expansions by modulating the structures of dynamic DNA via cooperation with BER enzymes. We provide the first evidence that PCNA prevents CAG repeat expansions during BER by promoting CAG repeat deletion and removal of a TNR hairpin. PMID:27793507

  11. Automated genotyping of dinucleotide repeat markers

    SciTech Connect

    Perlin, M.W.; Hoffman, E.P. |

    1994-09-01

    The dinucleotide repeats (i.e., microsatellites) such as CA-repeats are a highly polymorphic, highly abundant class of PCR-amplifiable markers that have greatly streamlined genetic mapping experimentation. It is expected that over 30,000 such markers (including tri- and tetranucleotide repeats) will be characterized for routine use in the next few years. Since only size determination, and not sequencing, is required to determine alleles, in principle, dinucleotide repeat genotyping is easily performed on electrophoretic gels, and can be automated using DNA sequencers. Unfortunately, PCR stuttering with these markers generates not one band for each allele, but a pattern of bands. Since closely spaced alleles must be disambiguated by human scoring, this poses a key obstacle to full automation. We have developed methods that overcome this obstacle. Our model is that the observed data is generated by arithmetic superposition (i.e., convolution) of multiple allele patterns. By quantitatively measuring the size of each component band, and exploiting the unique stutter pattern associated with each marker, closely spaced alleles can be deconvolved; this unambiguously reconstructs the {open_quotes}true{close_quotes} allele bands, with stutter artifact removed. We used this approach in a system for automated diagnosis of (X-linked) Duchenne muscular dystrophy; four multiplexed CA-repeats within the dystrophin gene were assayed on a DNA sequencer. Our method accurately detected small variations in gel migration that shifted the allele size estimate. In 167 nonmutated alleles, 89% (149/167) showed no size variation, 9% (15/167) showed 1 bp variation, and 2% (3/167) showed 2 bp variation. We are currently developing a library of dinucleotide repeat patterns; together with our deconvolution methods, this library will enable fully automated genotyping of dinucleotide repeats from sizing data.

  12. Role of memory errors in quantum repeaters

    NASA Astrophysics Data System (ADS)

    Hartmann, L.; Kraus, B.; Briegel, H.-J.; Dür, W.

    2007-03-01

    We investigate the influence of memory errors in the quantum repeater scheme for long-range quantum communication. We show that the communication distance is limited in standard operation mode due to memory errors resulting from unavoidable waiting times for classical signals. We show how to overcome these limitations by (i) improving local memory and (ii) introducing two operational modes of the quantum repeater. In both operational modes, the repeater is run blindly, i.e., without waiting for classical signals to arrive. In the first scheme, entanglement purification protocols based on one-way classical communication are used allowing to communicate over arbitrary distances. However, the error thresholds for noise in local control operations are very stringent. The second scheme makes use of entanglement purification protocols with two-way classical communication and inherits the favorable error thresholds of the repeater run in standard mode. One can increase the possible communication distance by an order of magnitude with reasonable overhead in physical resources. We outline the architecture of a quantum repeater that can possibly ensure intercontinental quantum communication.

  13. Spectrin repeat proteins in the nucleus.

    PubMed

    Young, Kevin G; Kothary, Rashmi

    2005-02-01

    Spectrin repeat sequences are among the more common repeat elements identified in proteins, typically occurring in large structural proteins. Examples of spectrin repeat-containing proteins include dystrophin, alpha-actinin and spectrin itself--all proteins with well-demonstrated roles of establishing and maintaining cell structure. Over the past decade, it has become clear that, although these proteins display a cytoplasmic and plasma membrane distribution, several are also found both at the nuclear envelope, and within the intranuclear space. In this review, we provide an overview of recent work regarding various spectrin repeat-containing structural proteins in the nucleus. As well, we hypothesize about the regulation of their nuclear localization and possible nuclear functions based on domain architecture, known interacting proteins and evolutionary relationships. Given their large size, and their potential for interacting with multiple proteins and with chromatin, spectrin repeat-containing proteins represent strong candidates for important organizational proteins within the nucleus. Supplementary material for this article can be found on the BioEssays website (http://www.interscience.wiley.com/jpages/0265-9247/suppmat/index.html).

  14. Efficacy and safety of repeated oral sucrose for repeated procedural pain in neonates: A systematic review.

    PubMed

    Gao, Haixia; Gao, Honglian; Xu, Guihua; Li, Mei; Du, Shizheng; Li, Fang; Zhang, Hua; Wang, Danwen

    2016-10-01

    Although sucrose is most extensively examined for its analgesia effect on a single procedural pain, neonates in neonatal intensive care units can be exposed to numerous painful procedures every day requiring multiple doses of sucrose. Some experiments have been performed to examine the efficacy and safety of repeated sucrose administration for repeated procedural pain; however, a systematic review of this topic has not yet been carried out. To identify and assess the evidence demonstrating the efficacy and safety of repeated sucrose for repeated procedural pain in neonates. A systematic review was conducted using the Cochrane methodology. Pubmed, Cochrane Library, Web of Science, CINAHL (Cumulative Index to Nursing and Allied Health Literature), CBMdisc, CNKI, VIP, and Wanfang databases were searched through December 2015. All related abstracts were reviewed and the full texts of relevant articles were studied. Randomized controlled trials (RCTs) were included. Risk of bias was assessed for RCTs using quality critical appraisal criteria recommended by Cochrane Handbook. A standardised data form was used to extract information. Eight RCTs met our inclusion criteria. Different study designs were used in the included RCTs, which did not allow us to carry out a meta-analysis. The findings from this review indicated that repeated sucrose was effective in reducing both behavioral pain response and composite pain scores during repeated procedural pain. However, as for physiological pain response, one trial found less variability in physiological pain response for term neonates in the sucrose group than the sterile water group, while two trials demonstrated repeated sucrose was inefficacious for preterm neonates. Regarding the clinical outcomes, no study reported adverse effects related to the repeated sucrose administration. Regarding the neurobehavioral development, two trials reported repeated sucrose for repeated procedural pain would not lead to poor neurologic

  15. Some characteristics of repeated sickness absence

    PubMed Central

    Ferguson, David

    1972-01-01

    Ferguson, D. (1972).Brit. J. industr. Med.,29, 420-431. Some characteristics of repeated sickness absence. Several studies have shown that frequency of absence attributed to sickness is not distributed randomly but tends to follow the negative binomial distribution, and this has been taken to support the concept of `proneness' to such absence. Thus, the distribution of sickness absence resembles that of minor injury at work demonstrated over 50 years ago. Because the investigation of proneness to absence does not appear to have been reported by others in Australia, the opportunity was taken, during a wider study of health among telegraphists in a large communications undertaking, to analyse some characteristics of repeated sickness absence. The records of medically certified and uncertified sickness absence of all 769 telegraphists continuously employed in all State capitals over a two-and-a-half-year period were compared with those of 411 clerks and 415 mechanics and, in Sydney, 380 mail sorters and 80 of their supervisors. All telegraphists in Sydney, Melbourne, and Brisbane, and all mail sorters in Sydney, who were available and willing were later medically examined. From their absence pattern repeaters (employees who had had eight or more certified absences in two and a half years) were separated into three types based on a presumptive origin in chance, recurrent disease and symptomatic non-specific disorder. The observed distribution of individual frequency of certified absence over the full two-and-a-half-year period of study followed that expected from the univariate negative binomial, using maximum likelihood estimators, rather than the poisson distribution, in three of the four occupational groups in Sydney. Limited correlational and bivariate analysis supported the interpretation of proneness ascribed to the univariate fit. In the two groups studied, frequency of uncertified absence could not be fitted by the negative binomial, although the numbers of

  16. Rate analysis for a hybrid quantum repeater

    SciTech Connect

    Bernardes, Nadja K.; Loock, Peter van

    2011-01-15

    We present a detailed rate analysis for a hybrid quantum repeater assuming perfect memories and using optimal probabilistic entanglement generation and deterministic swapping routines. The hybrid quantum repeater protocol is based on atomic qubit-entanglement distribution through optical coherent-state communication. An exact, analytical formula for the rates of entanglement generation in quantum repeaters is derived, including a study on the impacts of entanglement purification and multiplexing strategies. More specifically, we consider scenarios with as little purification as possible and we show that for sufficiently low local losses, such purifications are still more powerful than multiplexing. In a possible experimental scenario, our hybrid system can create near-maximally entangled (F=0.98) pairs over a distance of 1280 km at rates of the order of 100 Hz.

  17. Hematuria home screening: repeat testing results.

    PubMed

    Messing, E M; Young, T B; Hunt, V B; Newton, M A; Bram, L L; Vaillancourt, A; Hisgen, W J; Greenberg, E B; Kuglitsch, M E; Wegenke, J D

    1995-07-01

    To determine at what interval screening should be repeated to detect bladder cancer before it becomes muscle invasive 856 men who had 14 negative daily home tests for hematuria with a chemical reagent strip 9 months previously performed repeat tests. Of these men 50 (5.8%) had at least 1 positive test during the second 14-day screening period and 38 were evaluated, 15 of whom (39.5%) had significant urological pathological conditions, including 8 with malignancies. Bladder cancer was noted in 7 men, with no tumor invading the muscularis propria. The finding of 7 bladder cancers in 856 men (0.82%) who had a negative test 9 months previously indicates that bladder cancer has a brief preclinical duration and that testing must be repeated at least annually for screening to detect bladder cancer consistently before invasion occurs.

  18. Scale-invariance in soft gamma repeaters

    NASA Astrophysics Data System (ADS)

    Chang, Zhe; Lin, Hai-Nan; Sang, Yu; Wang, Ping

    2017-06-01

    The statistical properties of the soft gamma repeater SGR J1550-5418 are investigated carefully. We find that the cumulative distributions of fluence, peak flux and duration can be well fitted by a bent power law, while the cumulative distribution of waiting time follows a simple power law. In particular, the probability density functions of fluctuations of fluence, peak flux, and duration have a sharp peak and fat tails, which can be well fitted by a q-Gaussian function. The q values keep approximately steady for different scale intervals, indicating a scale-invariant structure of soft gamma repeaters. Those results support that the origin of soft gamma repeaters is crustquakes of neutron stars with extremely strong magnetic fields. Supported by National Natural Science Foundation of China (11375203, 11675182, 11690022, 11603005), and Fundamental Research Funds for Central Universities (106112016CDJCR301206)

  19. Do gamma-ray burst sources repeat?

    NASA Technical Reports Server (NTRS)

    Meegan, Charles A.; Hartmann, Dieter H.; Brainerd, J. J.; Briggs, Michael S.; Paciesas, William S.; Pendleton, Geoffrey; Kouveliotou, Chryssa; Fishman, Gerald; Blumenthal, George; Brock, Martin

    1995-01-01

    The demonstration of repeated gamma-ray bursts from an individual source would severely constrain burst source models. Recent reports (Quashnock and Lamb, 1993; Wang and Lingenfelter, 1993) of evidence for repetition in the first BATSE burst catalog have generated renewed interest in this issue. Here, we analyze the angular distribution of 585 bursts of the second BATSE catalog (Meegan et al., 1994). We search for evidence of burst recurrence using the nearest and farthest neighbor statistic and the two-point angular correlation function. We find the data to be consistent with the hypothesis that burst sources do not repeat; however, a repeater fraction of up to about 20% of the observed bursts cannot be excluded.

  20. Safety of Repeated Yttrium-90 Radioembolization

    SciTech Connect

    Lam, Marnix G. E. H.; Louie, John D.; Iagaru, Andrei H.; Goris, Michael L.; Sze, Daniel Y.

    2013-10-15

    Purpose: Repeated radioembolization (RE) treatments carry theoretically higher risk of radiation-induced hepatic injury because of the liver's cumulative memory of previous exposure. We performed a retrospective safety analysis on patients who underwent repeated RE. Methods: From 2004 to 2011, a total of 247 patients were treated by RE. Eight patients (5 men, 3 women, age range 51-71 years) underwent repeated treatment of a targeted territory, all with resin microspheres (SIR-Spheres; Sirtex, Lane Cove, Australia). Adverse events were graded during a standardized follow-up. In addition, the correlation between the occurrence of RE-induced liver disease (REILD) and multiple variables was investigated in univariate and multivariate analyses in all 247 patients who received RE. Results: Two patients died shortly after the second treatment (at 84 and 107 days) with signs and symptoms of REILD. Both patients underwent whole liver treatment twice (cumulative doses 3.08 and 2.66 GBq). The other 6 patients demonstrated only minor toxicities after receiving cumulative doses ranging from 2.41 to 3.88 GBq. All patients experienced objective tumor responses. In the whole population, multifactorial analysis identified three risk factors associated with REILD: repeated RE (p = 0.036), baseline serum total bilirubin (p = 0.048), and baseline serum aspartate aminotransferase (p = 0.043). Repeated RE proved to be the only independent risk factor for REILD in multivariate analysis (odds ratio 9.6; p = 0.002). Additionally, the administered activity per target volume (in GBq/L) was found to be an independent risk factor for REILD, but only in whole liver treatments (p = 0.033). Conclusion: The risk of REILD appears to be elevated for repeated RE. Objective tumor responses were observed, but establishment of safety limits will require improvement in dosimetric measurement and prediction.

  1. The puzzle of the triple repeats

    SciTech Connect

    Morell, V.

    1993-06-04

    Two years ago, when researchers discovered the gene that causes a hereditary form of mental retardation known as fragile-X syndrome, they also turned up a mutation so unexpected geneticists are still scratching their heads over it. The defect, which makes genes balloon in size by adding extra copies of a three base-pair repeated sequence of DNA, was the first of its kind. Despite decades of study, nothing like it had ever been seen in any of the species that laid the foundations for modern genetics: bacteria, the fruit fly Drosophila melanogaster, and the mouse. The mutations caused by these expanding trinucleotide repeats turned out be common causes of human disease. In the past 2 years, they have been fingered as the culprits in three hereditary disorders besides fragile-X syndrome: myotronic dystrophy, spinobullar muscular atrophy (also known as Kennedy's disease), and just this March-Huntington's disease. The FMR-1 gene, which is the one at fault in fragile-X syndrome, shows just how much the trinucleotide repeats can expand. The normal gene carries at most 50 copies of the CGG trinucleotide. But in children who inherit the gene from these carriers and actually develop mental retardation and the other fragile-X symptoms, the FMR-1 gene may have hundreds to thousands of CGG repeats. Huge expansions of another trinucleotide repeat (CTG) can also occur from one generation to the next in the gene that causes myotonic dystrophy (DM), while smaller, although no less devastating, expansions in the CAG trinucleotide repeat lead to Huntington's and Kennedy's diseases.

  2. Repeat Gamma Knife Radiosurgery for Trigeminal Neuralgia

    SciTech Connect

    Aubuchon, Adam C.; Chan, Michael D.; Lovato, James F.; Balamucki, Christopher J.; Ellis, Thomas L.; Tatter, Stephen B.; McMullen, Kevin P.; Munley, Michael T.; Deguzman, Allan F.; Ekstrand, Kenneth E.; Bourland, J. Daniel; Shaw, Edward G.

    2011-11-15

    Purpose: Repeat gamma knife stereotactic radiosurgery (GKRS) for recurrent or persistent trigeminal neuralgia induces an additional response but at the expense of an increased incidence of facial numbness. The present series summarized the results of a repeat treatment series at Wake Forest University Baptist Medical Center, including a multivariate analysis of the data to identify the prognostic factors for treatment success and toxicity. Methods and Materials: Between January 1999 and December 2007, 37 patients underwent a second GKRS application because of treatment failure after a first GKRS treatment. The mean initial dose in the series was 87.3 Gy (range, 80-90). The mean retreatment dose was 84.4 Gy (range, 60-90). The dosimetric variables recorded included the dorsal root entry zone dose, pons surface dose, and dose to the distal nerve. Results: Of the 37 patients, 81% achieved a >50% pain relief response to repeat GKRS, and 57% experienced some form of trigeminal dysfunction after repeat GKRS. Two patients (5%) experienced clinically significant toxicity: one with bothersome numbness and one with corneal dryness requiring tarsorraphy. A dorsal root entry zone dose at repeat treatment of >26.6 Gy predicted for treatment success (61% vs. 32%, p = .0716). A cumulative dorsal root entry zone dose of >84.3 Gy (72% vs. 44%, p = .091) and a cumulative pons surface dose of >108.5 Gy (78% vs. 44%, p = .018) predicted for post-GKRS numbness. The presence of any post-GKRS numbness predicted for a >50% decrease in pain intensity (100% vs. 60%, p = .0015). Conclusion: Repeat GKRS is a viable treatment option for recurrent trigeminal neuralgia, although the patient assumes a greater risk of nerve dysfunction to achieve maximal pain relief.

  3. Formation of the Arabidopsis pentatricopeptide repeat family.

    PubMed

    Rivals, Eric; Bruyère, Clémence; Toffano-Nioche, Claire; Lecharny, Alain

    2006-07-01

    In Arabidopsis (Arabidopsis thaliana) the 466 pentatricopeptide repeat (PPR) proteins are putative RNA-binding proteins with essential roles in organelles. Roughly half of the PPR proteins form the plant combinatorial and modular protein (PCMP) subfamily, which is land-plant specific. PCMPs exhibit a large and variable tandem repeat of a standard pattern of three PPR variant motifs. The association or not of this repeat with three non-PPR motifs at their C terminus defines four distinct classes of PCMPs. The highly structured arrangement of these motifs and the similar repartition of these arrangements in the four classes suggest precise relationships between motif organization and substrate specificity. This study is an attempt to reconstruct an evolutionary scenario of the PCMP family. We developed an innovative approach based on comparisons of the proteins at two levels: namely the succession of motifs along the protein and the amino acid sequence of the motifs. It enabled us to infer evolutionary relationships between proteins as well as between the inter- and intraprotein repeats. First, we observed a polarized elongation of the repeat from the C terminus toward the N-terminal region, suggesting local recombinations of motifs. Second, the most N-terminal PPR triple motif proved to evolve under different constraints than the remaining repeat. Altogether, the evidence indicates different evolution for the PPR region and the C-terminal one in PCMPs, which points to distinct functions for these regions. Moreover, local sequence homogeneity observed across PCMP classes may be due to interclass shuffling of motifs, or to deletions/insertions of non-PPR motifs at the C terminus.

  4. Repeatability of peripheral aberrations in young emmetropes.

    PubMed

    Baskaran, Karthikeyan; Theagarayan, Baskar; Carius, Staffan; Gustafsson, Jörgen

    2010-10-01

    The purpose of this study is to assess the intrasession repeatability of ocular aberration measurements in the peripheral visual field with a commercially available Shack-Hartmann aberrometer (complete ophthalmic analysis system-high definition-vision research). The higher-order off-axis aberrations data in young healthy emmetropic eyes are also reported. The aberrations of the right eye of 18 emmetropes were measured using an aberrometer with an open field of view that allows peripheral measurements. Five repeated measures of ocular aberrations were obtained and assessed in steps of 10° out to ±40° in the horizontal visual field (nasal + and temporal -) and -20° in the inferior visual field. The coefficient of repeatability, coefficient of variation, and the intraclass correlation coefficient were calculated as a measure of intrasession repeatability. In all eccentric angles, the repeatability of the third- and fourth-order aberrations was better than the fifth and sixth order aberrations. The coefficient of variation was <30% and the intraclass correlation coefficient was >0.90 for the third and fourth order but reduced gradually for higher orders. There was no statistical significant difference in variance of total higher-order root mean square between on- and off-axis measurements (p > 0.05). The aberration data in this group of young emmetropes showed that the horizontal coma (C(3)(1)) was most positive at 40° in the temporal field, decreasing linearly toward negative values with increasing off-axis angle into the nasal field, whereas all other higher-order aberrations showed little or no change. The complete ophthalmic analysis system-high definition-vision research provides fast, repeatable, and valid peripheral aberration measurements and can be used efficiently to measure off-axis aberrations in the peripheral visual field.

  5. Therapeutics development for triplet repeat expansion diseases.

    PubMed

    Di Prospero, Nicholas A; Fischbeck, Kenneth H

    2005-10-01

    The underlying genetic mutations for many inherited neurodegenerative disorders have been identified in recent years. One frequent type of mutation is trinucleotide repeat expansion. Depending on the location of the repeat expansion, the mutation might result in a loss of function of the disease gene, a toxic gain of function or both. Disease gene identification has led to the development of model systems for investigating disease mechanisms and evaluating treatments. Examination of experimental findings reveals similarities in disease mechanisms as well as possibilities for treatment.

  6. [VESTIBULAR FUNCTION AFTER REPEATED SPACE FLIGHTS].

    PubMed

    Naumov, I A; Kornilova, L N; Glukhikh, D O; Pavlova, A S; Khabarova, E V; Ekimovsky, G A; Vasin, A V

    2015-01-01

    Results of the vestibular function testing of 32 cosmonauts on return from repeated 125- to 215-day space flights (SF) on the International space station are presented. The cosmonauts were tested twice before flight (baseline data collection) and on days 1-2, 4-5 and 8-9 after landing. Electro- and video-oculography were used to register simultaneously eye and head movements. It was found that deadaptation following a repeated stay in long-duration SF takes statistically much shorter time. Most often, atypical vestibular disorders and changed patterns of the otolith-semicircular canal interaction are observed in cosmonauts who have made their maiden flights to microgravity.

  7. Effect of Repeated Evaluation and Repeated Exposure on Acceptability Ratings of Sentences

    ERIC Educational Resources Information Center

    Zervakis, Jennifer; Mazuka, Reiko

    2013-01-01

    This study investigated the effect of repeated evaluation and repeated exposure on grammatical acceptability ratings for both acceptable and unacceptable sentence types. In Experiment 1, subjects in the Experimental group rated multiple examples of two ungrammatical sentence types (ungrammatical binding and double object with dative-only verb),…

  8. Structures of designed armadillo-repeat proteins show propagation of inter-repeat interface effects

    PubMed Central

    Reichen, Christian; Madhurantakam, Chaithanya; Hansen, Simon; Grütter, Markus G.; Plückthun, Andreas; Mittl, Peer R. E.

    2016-01-01

    The armadillo repeat serves as a scaffold for the development of modular peptide-recognition modules. In order to develop such a system, three crystal structures of designed armadillo-repeat proteins with third-generation N-caps (YIII-type), four or five internal repeats (M-type) and second-generation C-caps (AII-type) were determined at 1.8 Å (His-YIIIM4AII), 2.0 Å (His-YIIIM5AII) and 1.95 Å (YIIIM5AII) resolution and compared with those of variants with third-generation C-caps. All constructs are full consensus designs in which the internal repeats have exactly the same sequence, and hence identical conformations of the internal repeats are expected. The N-cap and internal repeats M1 to M3 are indeed extremely similar, but the comparison reveals structural differences in internal repeats M4 and M5 and the C-cap. These differences are caused by long-range effects of the C-cap, contacting molecules in the crystal, and the intrinsic design of the repeat. Unfortunately, the rigid-body movement of the C-terminal part impairs the regular arrangement of internal repeats that forms the putative peptide-binding site. The second-generation C-cap improves the packing of buried residues and thereby the stability of the protein. These considerations are useful for future improvements of an armadillo-repeat-based peptide-recognition system. PMID:26894544

  9. AGG interspersions within the FMR1 CGG repeat: Mechanisms and models of triplet repeat instability

    SciTech Connect

    Eichler, E.E.; Nelson, D.L.

    1994-09-01

    Fragile X syndrome CGG repeat alleles are typically classified as normal, premutation, or full mutation based on the length of the repeat in the 5{prime} UTR of the FMR1 gene. The distinction between high-end normals and low-end premutation alleles, however, is not always clear since repeats of similar size differ markedly in their intergenerational stability. This fact suggest that differences in sequence content may play a key role in determining an allele`s predisposition to instability. It has been postulated that the loss of AGG interruptions within the CGG tract may trigger this instability. To test this model, we have developed a simple indirect method to determine the presence or absence of internal AGGs within the FMR1 CGG repeat tract. Analysis of 84 human X chromosomes for the presence of interrupting AGG trinucleotides revealed that most alleles possess two interspersed AGGs at a periodicity of 9 or 10 CGGs. The longest tract of uninterrupted CGG repeats is usually found at the 3{prime} end indicating that variation in the length of the repeat is polar. Alleles containing between 34 and 55 repeats, with documented unstable transmissions, were shown to have lost one or both AGG interruptions when compared to stable alleles of similar length. These comparisons define an instability threshold between 34 and 38 uninterrupted CGG repeats. Analysis of premutation alleles in fragile X syndrome carriers reveals that 70% of these alleles contain a single AGG interruption. Population studies confirm that such highly punctuated FMR1 CGG repeats are virtually static in terms of length variation. These data suggest that the loss of an AGG is an important mutational event in the generation of unstable alleles predisposed to the fragile X syndrome. Loss of AGG trinucleotides and polarized variability support Okazaki fragment slippage as a model for CGG repeat instability and hyperexpansion.

  10. Building Fluency through the Repeated Reading Method

    ERIC Educational Resources Information Center

    Cohen, Joshua

    2011-01-01

    For the last two years the author has used Repeated Reading (RR) to teach reading fluency in English as a Foreign Language classrooms in colleges and universities in Japan. RR is a method where the student reads and rereads a text silently or aloud from two to four times to reach a predetermined level of speed, accuracy, and comprehension. RR…

  11. Y Se Repite = And It Repeats Itself

    ERIC Educational Resources Information Center

    Katzew, Adriana

    2010-01-01

    In this article, the author discusses Y Se Repite [And It Repeats Itself], a project she conceptualized due to the growing number of Latino/a Mexican migrant workers in dairy farms in the state of Vermont. In 2006, approximately 2,000 Latinos/as--most of them undocumented Mexican migrant workers--worked throughout the state's dairy farms, yet…

  12. Longer-baseline telescopes using quantum repeaters.

    PubMed

    Gottesman, Daniel; Jennewein, Thomas; Croke, Sarah

    2012-08-17

    We present an approach to building interferometric telescopes using ideas of quantum information. Current optical interferometers have limited baseline lengths, and thus limited resolution, because of noise and loss of signal due to the transmission of photons between the telescopes. The technology of quantum repeaters has the potential to eliminate this limit, allowing in principle interferometers with arbitrarily long baselines.

  13. Photometric Repeatability of Scanned Imagery: UVIS

    NASA Astrophysics Data System (ADS)

    Shanahan, Clare E.; McCullough, Peter; Baggett, Sylvia

    2017-08-01

    We provide the preliminary results of a study on the photometric repeatability of spatial scans of bright, isolated white dwarf stars with the UVIS channel of the Wide Field Camera 3 (WFC3) on the Hubble Space Telescope (HST). We analyze straight-line scans from the first pair of identical orbits of HST program 14878 to assess if sub 0.1% repeatability can be attained with WFC3/UVIS. This study is motivated by the desire to achieve better signal-to-noise in the UVIS contamination and stability monitor, in which observations of standard stars in staring mode have been taken from the installation of WFC3 in 2009 to the present to assess temporal photometric stability. Higher signal to noise in this program would greatly benefit the sensitivity to detect contamination, and to better characterize the observed small throughput drifts over time. We find excellent repeatability between identical visits of program 14878, with sub 0.1% repeatability achieved in most filters. These! results support the initiative to transition the staring mode UVIS contamination and photometric stability monitor from staring mode images to spatial scans.

  14. Triggering of repeating earthquakes in central California

    USGS Publications Warehouse

    Wu, Chunquan; Gomberg, Joan; Ben-Naim, Eli; Johnson, Paul

    2014-01-01

    Dynamic stresses carried by transient seismic waves have been found capable of triggering earthquakes instantly in various tectonic settings. Delayed triggering may be even more common, but the mechanisms are not well understood. Catalogs of repeating earthquakes, earthquakes that recur repeatedly at the same location, provide ideal data sets to test the effects of transient dynamic perturbations on the timing of earthquake occurrence. Here we employ a catalog of 165 families containing ~2500 total repeating earthquakes to test whether dynamic perturbations from local, regional, and teleseismic earthquakes change recurrence intervals. The distance to the earthquake generating the perturbing waves is a proxy for the relative potential contributions of static and dynamic deformations, because static deformations decay more rapidly with distance. Clear changes followed the nearby 2004 Mw6 Parkfield earthquake, so we study only repeaters prior to its origin time. We apply a Monte Carlo approach to compare the observed number of shortened recurrence intervals following dynamic perturbations with the distribution of this number estimated for randomized perturbation times. We examine the comparison for a series of dynamic stress peak amplitude and distance thresholds. The results suggest a weak correlation between dynamic perturbations in excess of ~20 kPa and shortened recurrence intervals, for both nearby and remote perturbations.

  15. Rectourethral fistula after repeat transrectal prostate biopsy.

    PubMed

    Loran, Oleg B; Veliev, Evgeny I; Sokolov, Egor A; Dadashev, Elmar O; Guspanov, Renat I

    2013-09-01

    Transrectal prostate biopsy is considered a relatively safe procedure, with a quite small number of complications. We report a patient with a rectourethral fistula after a repeat transrectal prostate biopsy. To our knowledge, this is the first incident in the published literature.

  16. Y Se Repite = And It Repeats Itself

    ERIC Educational Resources Information Center

    Katzew, Adriana

    2010-01-01

    In this article, the author discusses Y Se Repite [And It Repeats Itself], a project she conceptualized due to the growing number of Latino/a Mexican migrant workers in dairy farms in the state of Vermont. In 2006, approximately 2,000 Latinos/as--most of them undocumented Mexican migrant workers--worked throughout the state's dairy farms, yet…

  17. Repeated Random Sampling in Year 5

    ERIC Educational Resources Information Center

    Watson, Jane M.; English, Lyn D.

    2016-01-01

    As an extension to an activity introducing Year 5 students to the practice of statistics, the software "TinkerPlots" made it possible to collect repeated random samples from a finite population to informally explore students' capacity to begin reasoning with a distribution of sample statistics. This article provides background for the…

  18. Repeater For A Digital-Communication Bus

    NASA Technical Reports Server (NTRS)

    Torres-Guzman, Esteban; Olson, Stephen; Heaps, Tim

    1993-01-01

    Digital repeater circuit designed to extend range of communication on MIL-STD-1553 bus beyond original maximum allowable length of 300 ft. Circuit provides two-way communication, one way at time, and conforms to specifications of MIL-STD-1553. Crosstalk and instability eliminated.

  19. Is Retrieval Mediated after Repeated Testing?

    ERIC Educational Resources Information Center

    Kole, James A.; Healy, Alice F.

    2013-01-01

    In 2 main experiments, the mediated priming effect was used to determine whether retrieval continues to be mediated after repeated testing. In each experiment, participants used the keyword method to learn French vocabulary, then completed a modified lexical decision task in which they first translated a French word, and then made a lexical…

  20. Repeat abortions in New York City, 2010.

    PubMed

    Toprani, Amita; Cadwell, Betsy L; Li, Wenhui; Sackoff, Judith; Greene, Carolyn; Begier, Elizabeth

    2015-06-01

    This study aims to describe factors associated with the number of past abortions obtained by New York City (NYC) abortion patients in 2010. We calculated rates of first and repeat abortion by age, race/ethnicity, and neighborhood-level poverty and the mean number of self-reported past abortions by age, race/ethnicity, neighborhood-level poverty, number of living children, education, payment method, marital status, and nativity. We used negative binomial regression to predict number of past abortions by patient characteristics. Of the 76,614 abortions reported for NYC residents in 2010, 57% were repeat abortions. Repeat abortions comprised >50% of total abortions among the majority of sociodemographic groups we examined. Overall, mean number of past abortions was 1.3. Mean number of past abortions was higher for women aged 30-34 years (1.77), women with ≥5 children (2.50), and black non-Hispanic women (1.52). After multivariable regression, age, race/ethnicity, and number of children were the strongest predictors of number of past abortions. This analysis demonstrates that, although socioeconomic disparities exist, all abortion patients are at high risk for repeat unintended pregnancy and abortion.

  1. [Preventive maintenance of repeated ischemic insults].

    PubMed

    Gavrilenko, A V; Kuklin, A V; Kravchenko, A A; Agafonov, I N

    2008-01-01

    In the review we offer analysis of the effectiveness of carotid endarterectomy in treatment of post-functional apoplexy or stroke patients. Published results of the researches specify possible efficiency of carotid endarterectomy in preventive maintenance against repeated apoplectic attack or strokes. Yet the criteria of usage and execution of the carotid endarterectomy are still to be discussed.

  2. Chlorinated hydrocarbons in women with repeated miscarriages.

    PubMed Central

    Gerhard, I; Daniel, V; Link, S; Monga, B; Runnebaum, B

    1998-01-01

    This study was conducted to investigate a possible etiological role of chlorinated hydrocarbons in the pathogenesis of repeated miscarriages. The blood levels of chlorinated hydrocarbons [CHCs: pentachlorophenol, hexachlorocyclohexane, hexachlorobenzene, the dichlorodiphenyltrichloroethane (DDT) group, polychlorinated biphenyls] were determined in 89 women with repeated miscarriages, who were referred to the University Hospital of Obstetrics and Gynecology of Heidelberg for investigations between 1989 and 1993, and compared to a previously investigated reference population. In more than 20% of the women, at least one of the CHC levels exceeded the reference range. CHC levels did not differ significantly between women with primary or secondary and early or late miscarriages; neither did they differ between women with hormonal or immunological disorders as causes of repeated miscarriages or women with idiopathic repeated miscarriages. No significant associations were detected between CHC levels and further conceptions or the outcome of further pregnancies. As significant associations were found between increasing CHC blood concentrations and immunological and hormonal changes, CHCs may have an impact on the pregnancy course in certain cases. PMID:9755145

  3. Epigenetics and Triplet-Repeat Neurological Diseases

    PubMed Central

    Nageshwaran, Sathiji; Festenstein, Richard

    2015-01-01

    The term “junk DNA” has been reconsidered following the delineation of the functional significance of repetitive DNA regions. Typically associated with centromeres and telomeres, DNA repeats are found in nearly all organisms throughout their genomes. Repetitive regions are frequently heterochromatinized resulting in silencing of intrinsic and nearby genes. However, this is not a uniform rule, with several genes known to require such an environment to permit transcription. Repetitive regions frequently exist as dinucleotide, trinucleotide, and tetranucleotide repeats. The association between repetitive regions and disease was emphasized following the discovery of abnormal trinucleotide repeats underlying spinal and bulbar muscular atrophy (Kennedy’s disease) and fragile X syndrome of mental retardation (FRAXA) in 1991. In this review, we provide a brief overview of epigenetic mechanisms and then focus on several diseases caused by DNA triplet-repeat expansions, which exhibit diverse epigenetic effects. It is clear that the emerging field of epigenetics is already generating novel potential therapeutic avenues for this group of largely incurable diseases. PMID:26733936

  4. A Structured Group Program for Repeat Dieters.

    ERIC Educational Resources Information Center

    McNamara, Kathleen

    1989-01-01

    Describes a structured group program for women who repeatedly diet and may be at risk of developing more serious eating disorders. Discusses sessions focusing on eating behavior as well as internal factors that contribute to low body esteem and food and weight preoccupation. Evaluates effectiveness of program by self-reports of members of two…

  5. Human adaptation to repeated cold immersions.

    PubMed Central

    Golden, F S; Tipton, M J

    1988-01-01

    1. The present investigation was designed to examine human adaptation to intermittent severe cold exposure and to assess the effect of exercise on any adaptation obtained. 2. Sixteen subjects were divided into two equal groups. Each subject performed ten head-out immersions; two into thermoneutral water which was then cooled until they shivered vigorously, and eight into water at 15 degrees C for 40 min. During the majority of the 15 degrees C immersions, one group (dynamic group) exercised whilst the other (static group) rested. 3. Results showed that both groups responded to repeated cold immersions with a reduction in their initial responses to cold. The time course of these reductions varied, however, between responses. 4. Only the static group developed a reduced metabolic response to prolonged resting immersion. 5. It is concluded that repeated resting exposure to cold was the more effective way of producing an adaptation. The performance of exercise during repeated exposure to cold prevented the development of an adaptive reduction in the metabolic response to cold during a subsequent resting immersion. In addition, many of the adaptations obtained during repeated resting exposure were overridden or masked during a subsequent exercising immersion. PMID:3411500

  6. Testing Multiple Outcomes in Repeated Measures Designs

    ERIC Educational Resources Information Center

    Lix, Lisa M.; Sajobi, Tolulope

    2010-01-01

    This study investigates procedures for controlling the familywise error rate (FWR) when testing hypotheses about multiple, correlated outcome variables in repeated measures (RM) designs. A content analysis of RM research articles published in 4 psychology journals revealed that 3 quarters of studies tested hypotheses about 2 or more outcome…

  7. A Repeated Measures Design for Treatment Evaluation.

    ERIC Educational Resources Information Center

    Hser, Y.; And Others

    A repeated measures design was used to assess the effects of a methadone maintenance program in several California locations. Subjects were 720 Chicano and Anglo men and women participating in rehabilitation programs for heroin addicts. The subjects were interviewed between 1978-1981, and the average follow-up time after initial treatment was 4-6…

  8. Episodes of repeated sudden deafness following pregnancies.

    PubMed

    Pawlak-Osinska, Katarzyna; Burduk, Pawel K; Kopczynski, Andrzej

    2009-04-01

    Sex hormones influence and provoke changes in hearing levels. Sudden deafness is rarely observed in pregnant women. The effective treatment of sudden deafness in pregnant women is a challenging problem. We present a case of repeatable, completely regressed sudden deafness in a woman during her first and second pregnancies.

  9. Is Retrieval Mediated after Repeated Testing?

    ERIC Educational Resources Information Center

    Kole, James A.; Healy, Alice F.

    2013-01-01

    In 2 main experiments, the mediated priming effect was used to determine whether retrieval continues to be mediated after repeated testing. In each experiment, participants used the keyword method to learn French vocabulary, then completed a modified lexical decision task in which they first translated a French word, and then made a lexical…

  10. Testing Multiple Outcomes in Repeated Measures Designs

    ERIC Educational Resources Information Center

    Lix, Lisa M.; Sajobi, Tolulope

    2010-01-01

    This study investigates procedures for controlling the familywise error rate (FWR) when testing hypotheses about multiple, correlated outcome variables in repeated measures (RM) designs. A content analysis of RM research articles published in 4 psychology journals revealed that 3 quarters of studies tested hypotheses about 2 or more outcome…

  11. History repeats itself: genomic divergence in copepods.

    PubMed

    Renaut, Sébastien; Dion-Côté, Anne-Marie

    2016-04-01

    Press stop, erase everything from now till some arbitrary time in the past and start recording life as it evolves once again. Would you see the same tape of life playing itself over and over, or would a different story unfold every time? The late Steven Jay Gould called this experiment replaying the tape of life and argued that any replay of the tape would lead evolution down a pathway radically different from the road actually taken (Gould 1989). This thought experiment has puzzled evolutionary biologists for a long time: how repeatable are evolutionary events? And if history does indeed repeat itself, what are the factors that may help us predict the path taken? A powerful means to address these questions at a small evolutionary scale is to study closely related populations that have evolved independently, under similar environmental conditions. This is precisely what Pereira et al. (2016) set out to do using marine copepods Tigriopus californicus, and present their results in this issue of Molecular Ecology. They show that evolution can be repeatable and even partly predictable, at least at the molecular level. As expected from theory, patterns of divergence were shaped by natural selection. At the same time, strong genetic drift due to small population sizes also constrained evolution down a similar evolutionary road, and probably contributed to repeatable patterns of genomic divergence. © 2016 John Wiley & Sons Ltd.

  12. The Effect of Repeaters on Equating

    ERIC Educational Resources Information Center

    Kim, HeeKyoung; Kolen, Michael J.

    2010-01-01

    Test equating might be affected by including in the equating analyses examinees who have taken the test previously. This study evaluated the effect of including such repeaters on Medical College Admission Test (MCAT) equating using a population invariance approach. Three-parameter logistic (3-PL) item response theory (IRT) true score and…

  13. Repeated Random Sampling in Year 5

    ERIC Educational Resources Information Center

    Watson, Jane M.; English, Lyn D.

    2016-01-01

    As an extension to an activity introducing Year 5 students to the practice of statistics, the software "TinkerPlots" made it possible to collect repeated random samples from a finite population to informally explore students' capacity to begin reasoning with a distribution of sample statistics. This article provides background for the…

  14. The Effect of Repeaters on Equating

    ERIC Educational Resources Information Center

    Kim, HeeKyoung; Kolen, Michael J.

    2010-01-01

    Test equating might be affected by including in the equating analyses examinees who have taken the test previously. This study evaluated the effect of including such repeaters on Medical College Admission Test (MCAT) equating using a population invariance approach. Three-parameter logistic (3-PL) item response theory (IRT) true score and…

  15. Automated quality checks on repeat prescribing.

    PubMed Central

    Rogers, Jeremy E; Wroe, Christopher J; Roberts, Angus; Swallow, Angela; Stables, David; Cantrill, Judith A; Rector, Alan L

    2003-01-01

    BACKGROUND: Good clinical practice in primary care includes periodic review of repeat prescriptions. Markers of prescriptions that may need review have been described, but manually checking all repeat prescriptions against the markers would be impractical. AIM: To investigate the feasibility of computerising the application of repeat prescribing quality checks to electronic patient records in United Kingdom (UK) primary care. DESIGN OF STUDY: Software performance test against benchmark manual analysis of cross-sectional convenience sample of prescribing documentation. SETTING: Three general practices in Greater Manchester, in the north west of England, during a 4-month period in 2001. METHOD: A machine-readable drug information resource, based on the British National Formulary (BNF) as the 'gold standard' for valid drug indications, was installed in three practices. Software raised alerts for each repeat prescribed item where the electronic patient record contained no valid indication for the medication. Alerts raised by the software in two practices were analysed manually. Clinical reaction to the software was assessed by semi-structured interviews in three practices. RESULTS: There was no valid indication in the electronic medical records for 14.8% of repeat prescribed items. Sixty-two per cent of all alerts generated were incorrect. Forty-three per cent of all incorrect alerts were as a result of errors in the drug information resource, 44% to locally idiosyncratic clinical coding, 8% to the use of the BNF without adaptation as a gold standard, and 5% to the inability of the system to infer diagnoses that, although unrecorded, would be 'obvious' to a clinical reading the record. The interviewed clinicians supported the goals of the software. CONCLUSION: Using electronic records for secondary decision support purposes will benefit from (and may require) both more consistent electronic clinical data collection across multiple sites, and reconciling clinicians

  16. Repeated sprint training in normobaric hypoxia

    PubMed Central

    Galvin, Harvey M; Cooke, Karl; Sumners, David P; Mileva, Katya N; Bowtell, Joanna L

    2013-01-01

    Repeated sprint ability (RSA) is a critical success factor for intermittent sport performance. Repeated sprint training has been shown to improve RSA, we hypothesised that hypoxia would augment these training adaptations. Thirty male well-trained academy rugby union and rugby league players (18.4±1.5 years, 1.83±0.07 m, 88.1±8.9 kg) participated in this single-blind repeated sprint training study. Participants completed 12 sessions of repeated sprint training (10×6 s, 30 s recovery) over 4 weeks in either hypoxia (13% FiO2) or normoxia (21% FiO2). Pretraining and post-training, participants completed sports specific endurance and sprint field tests and a 10×6 s RSA test on a non-motorised treadmill while measuring speed, heart rate, capillary blood lactate, muscle and cerebral deoxygenation and respiratory measures. Yo-Yo Intermittent Recovery Level 1 test performance improved after RS training in both groups, but gains were significantly greater in the hypoxic (33±12%) than the normoxic group (14±10%, p<0.05). During the 10×6 s RS test there was a tendency for greater increases in oxygen consumption in the hypoxic group (hypoxic 6.9±9%, normoxic (−0.3±8.8%, p=0.06) and reductions in cerebral deoxygenation (% changes for both groups, p=0.09) after hypoxic than normoxic training. Twelve RS training sessions in hypoxia resulted in twofold greater improvements in capacity to perform repeated aerobic high intensity workout than an equivalent normoxic training. Performance gains are evident in the short term (4 weeks), a period similar to a preseason training block. PMID:24282212

  17. Repeated sprint training in normobaric hypoxia.

    PubMed

    Galvin, Harvey M; Cooke, Karl; Sumners, David P; Mileva, Katya N; Bowtell, Joanna L

    2013-12-01

    Repeated sprint ability (RSA) is a critical success factor for intermittent sport performance. Repeated sprint training has been shown to improve RSA, we hypothesised that hypoxia would augment these training adaptations. Thirty male well-trained academy rugby union and rugby league players (18.4 ± 1.5 years, 1.83 ± 0.07 m, 88.1 ± 8.9 kg) participated in this single-blind repeated sprint training study. Participants completed 12 sessions of repeated sprint training (10 × 6 s, 30 s recovery) over 4 weeks in either hypoxia (13% FiO₂) or normoxia (21% FiO₂). Pretraining and post-training, participants completed sports specific endurance and sprint field tests and a 10 × 6 s RSA test on a non-motorised treadmill while measuring speed, heart rate, capillary blood lactate, muscle and cerebral deoxygenation and respiratory measures. Yo-Yo Intermittent Recovery Level 1 test performance improved after RS training in both groups, but gains were significantly greater in the hypoxic (33 ± 12%) than the normoxic group (14 ± 10%, p<0.05). During the 10 × 6 s RS test there was a tendency for greater increases in oxygen consumption in the hypoxic group (hypoxic 6.9 ± 9%, normoxic (-0.3 ± 8.8%, p=0.06) and reductions in cerebral deoxygenation (% changes for both groups, p=0.09) after hypoxic than normoxic training. Twelve RS training sessions in hypoxia resulted in twofold greater improvements in capacity to perform repeated aerobic high intensity workout than an equivalent normoxic training. Performance gains are evident in the short term (4 weeks), a period similar to a preseason training block.

  18. 14CO2 in combination with root-exclusion can be used to estimate plant-induced decomposition of soil organic matter

    NASA Astrophysics Data System (ADS)

    Heinonsalo, Jussi; Kulmala, Liisa; Mäkelä, Annikki; Oinonen, Markku; Fontaine, Sebastien; Palonen, Vesa; Pumpanen, Jukka

    2017-04-01

    In ecosystem models, the decomposition of soil organic matter (SOM) is estimated using temperature and moisture as main controlling parameters. However, there is increasing evidence that the decomposition is significantly affected by easily available carbohydrates. The C assimilation by the boreal forest trees will increase in the future due to climate change. As trees allocate large part of assimilated C to roots and soil microorganisms, particularly to ectomycorrhizal fungi, the rhizosphere priming effect (RPE) is assumed to increase. The aim of the experiment was to identify and quantify RPE in the field conditions. We established a three-year long trenching experiment in a boreal Scots pine forest where the belowground C flow from standing pine forest was controlled using root-exclusion with mesh fabrics. The mesh size of 1 μm excluded both tree roots and fungal hyphae and served as priming controls with decreased C supply. The unaltered C input entered the non-trenched field plots. Soil CO2 flux and 14C concentrations were measured. We were able to quantify the RPE in field conditions and show that plant-derived C flow into the soil increases SOM decomposition. Quantification of RPE allows more detailed estimation of soil organic matter decomposition in future changing climate.

  19. Atmosphere-based estimates of non-CO2 greenhouse gas emissions for the U.S. derived from 14CO2 during 2009-2012.

    NASA Astrophysics Data System (ADS)

    Montzka, S. A.; Miller, J. B.; Lehman, S.; Miller, B.; Hu, L.; Andrews, A. E.; Sweeney, C.; Dlugokencky, E. J.; Southon, J. R.; Wolak, C.; Elkins, J. W.; Tans, P. P.; Turnbull, J. C.; LaFranchi, B. W.; Guilderson, T. P.; Fischer, M. L.

    2014-12-01

    Atmospheric measurements of trace gases with 'known' emissions provide a means to derive emission magnitudes of other simultaneously measured trace gases, provided sources are co-located and co-varying. Here we consider atmospheric mixing ratio covariations in the fossil fuel derived component of observed CO2 (Cff; derived from high-precision measurements of the radiocarbon fraction of atmospheric CO2) relative to more than 20 other anthropogenic trace gases including CO, CH4, N2O, SF6, and halo- and hydro-carbons over large industrialized land areas. Pairing Cff with boundary-layer concentration enhancements of these gases allows us to determine apparent emission ratios for each gas with respect to Cff. When combined with sample-specific model-derived spatial footprints and the relatively accurate U.S. inventory of fossil fuel emissions (i.e., estimated uncertainty of ±10%), absolute emission rates for the correlate gases are derived. Here we will present U.S. annual emission magnitudes for select gases based on year-round measurements from tall towers and aircraft profiling sites in California, Texas, the mid-west, south-east and north-east for the 2009-2012 period. Statistically significant and coherent spatial and seasonal patterns in emission ratios and absolute emissions are determined for many gases based on these measurements. For HFC-134a and HCFC-22, results derived with this approach generally agree very well with an independent Bayesian-inversion based analysis of the larger number of samples collected and analyzed in our network, but that are not paired with Cff measurements. We believe this approach provides reliable 'top down', observationally-based emission estimates for these gases, many of which influence climate, air quality and stratospheric ozone.

  20. Breathing response of the tegu lizard to 1-4% CO2 in the mouth and nose or inspired into the lungs.

    PubMed

    Ballam, G O

    1985-12-01

    This study investigated the influence on ventilation of elevated CO2 in the nasal and buccal cavities (NaBuCO2) vs the effect of elevated CO2 levels inspired into the lungs (LuCO2). Separate gas sources were used to independently alter NaBuCO2 and LuCO2. As little as 1% NaBuCO2 or LuCO2 significantly increased the pause duration between the active expiratory-inspiratory cycles. Elevated NaBuCO2 caused minor changes in tidal volume, mean inspiratory and expiratory flow, and inspiratory and expiratory durations with a significant reduction in total ventilation. Elevated LuCO2 had little effect on inspiratory or expiratory durations but unlike CO2 in the upper airways, significantly increased tidal volume and mean inspiratory and expiratory flows. This study demonstrates that the increased pause duration seen in the tegu lizard to elevated environmental CO2 is due to a receptor response in the buccal or nasal cavities and also to elevated CO2 concentrations inspired into the lungs. Sensitivity of the ventilatory responses to CO2 in the upper airways is well within a physiologically relevant range.

  1. A semi-preparative enzymic synthesis of malonyl-CoA from [14C]acetate and 14CO2: labelling in the 1, 2 or 3 position.

    PubMed

    Roughan, G

    1994-06-01

    A semi-preparative enzymic synthesis of [1-14C]malonyl-CoA from [1-14C]acetate and bicarbonate, and of [3-14C]malonyl-CoA from Na2(14)CO3 and acetate, was achieved by using chloroplasts rapidly isolated from 7-8-day-old pea shoots. Around 70% of the [1-14C]acetate was converted into malonyl-CoA in 2-3 h, and the specific radioactivity of [3-14C]malonyl-CoA synthesized in the system was 25-30 Ci/mol. Reactions were monitored and labelled products were purified by h.p.l.c.

  2. Atmospheric 14CO2 Constraints on and Modeling of Net Carbon Fluxes 06-ERD-031 An LLNL Exploratory Research in the Directorate's Final Report

    SciTech Connect

    Guilderson, T P; Cameron-Smith, P; Bergmann, D; Graven, H D; Keeling, R; Boering, K; Caldeira, K

    2009-03-18

    A critical scientific question is: 'what are the present day sources and sinks of carbon dioxide (CO{sub 2}) in the natural environment, and how will these sinks evolve under rising CO{sub 2} concentrations and expected climate change and ecosystem response'? Sources and sinks of carbon dioxide impart their signature on the distribution, concentration, and isotopic composition of CO{sub 2}. Spatial and temporal trends (variability) provide information on the net surface (atmosphere to ocean, atmosphere to terrestrial biosphere) fluxes. The need to establish more reliable estimates of sources and sinks of CO{sub 2} has lead to an expansion of CO{sub 2} measurement programs over the past decade and the development of new methodologies for tracing carbon flows. These methodologies include high-precision pCO{sub 2}, {delta}{sup 13}CO{sub 2}, and [O{sub 2}/N{sub 2}] measurements on atmospheric constituents that, when combined, have allowed estimates of the net terrestrial and oceanic fluxes at decadal timescales. Major gaps in our understanding remain however, and resulting flux estimates have large errors and are comparatively unconstrained. One potentially powerful approach to tracking carbon flows is based on observations of the {sup 14}C/{sup 12}C ratio of atmospheric CO{sub 2}. This ratio can be used to explicitly distinguish fossil-fuel CO{sub 2} from other sources of CO{sub 2} and also provide constraints on the mass and turnover times of carbon in land ecosystems and on exchange rates of CO{sub 2} between air and sea. Here we demonstrated measurement of {sup 14}C/{sup 12}C ratios at 1-2{per_thousand} on archived and currently collected air samples. In parallel we utilized the LLNL-IMPACT global atmospheric chemistry transport model and the TransCom inversion algorithm to utilize these data in inversion estimates of carbon fluxes. This project has laid the foundation for a more expanded effort in the future, involving collaborations with other air-sampling programs and modeling groups.

  3. RepeatsDB 2.0: improved annotation, classification, search and visualization of repeat protein structures.

    PubMed

    Paladin, Lisanna; Hirsh, Layla; Piovesan, Damiano; Andrade-Navarro, Miguel A; Kajava, Andrey V; Tosatto, Silvio C E

    2017-01-04

    RepeatsDB 2.0 (URL: http://repeatsdb.bio.unipd.it/) is an update of the database of annotated tandem repeat protein structures. Repeat proteins are a widespread class of non-globular proteins carrying heterogeneous functions involved in several diseases. Here we provide a new version of RepeatsDB with an improved classification schema including high quality annotations for ∼5400 protein structures. RepeatsDB 2.0 features information on start and end positions for the repeat regions and units for all entries. The extensive growth of repeat unit characterization was possible by applying the novel ReUPred annotation method over the entire Protein Data Bank, with data quality is guaranteed by an extensive manual validation for >60% of the entries. The updated web interface includes a new search engine for complex queries and a fully re-designed entry page for a better overview of structural data. It is now possible to compare unit positions, together with secondary structure, fold information and Pfam domains. Moreover, a new classification level has been introduced on top of the existing scheme as an independent layer for sequence similarity relationships at 40%, 60% and 90% identity. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  4. RepeatsDB 2.0: improved annotation, classification, search and visualization of repeat protein structures

    PubMed Central

    Paladin, Lisanna; Hirsh, Layla; Piovesan, Damiano; Andrade-Navarro, Miguel A.; Kajava, Andrey V.; Tosatto, Silvio C.E.

    2017-01-01

    RepeatsDB 2.0 (URL: http://repeatsdb.bio.unipd.it/) is an update of the database of annotated tandem repeat protein structures. Repeat proteins are a widespread class of non-globular proteins carrying heterogeneous functions involved in several diseases. Here we provide a new version of RepeatsDB with an improved classification schema including high quality annotations for ∼5400 protein structures. RepeatsDB 2.0 features information on start and end positions for the repeat regions and units for all entries. The extensive growth of repeat unit characterization was possible by applying the novel ReUPred annotation method over the entire Protein Data Bank, with data quality is guaranteed by an extensive manual validation for >60% of the entries. The updated web interface includes a new search engine for complex queries and a fully re-designed entry page for a better overview of structural data. It is now possible to compare unit positions, together with secondary structure, fold information and Pfam domains. Moreover, a new classification level has been introduced on top of the existing scheme as an independent layer for sequence similarity relationships at 40%, 60% and 90% identity. PMID:27899671

  5. Vectorette PCR isolation of microsatellite repeat sequences using anchored dinucleotide repeat primers.

    PubMed Central

    Lench, N J; Norris, A; Bailey, A; Booth, A; Markham, A F

    1996-01-01

    We have developed a vectorette PCR approach to provide an improved method for isolation of microsatellite repeats. The modified procedure relies on PCR amplification using a vectorette-specific primer in combination with one of a panel of anchored dinucleotide repeat primers. The target DNA to be screened for microsatellite sequences can be from YAC, P1, cosmid, bacteriophage or plasmid clones. We have used this technique to isolate novel, polymorphic microsatellite repeats from clones containing the amelogenin gene (AMGX) located on human chromosome Xp22.3. PMID:8668553

  6. Stability of dental waxes following repeated heatings.

    PubMed

    Kotsiomiti, E; McCabe, J F

    1995-02-01

    The flow and strength properties of dental waxes were examined following excessive and repeated heatings of the materials. For one product, the flow at 40 +/- 0.5 degrees C was reduced by 25.3% following heating above 200 degrees C. A decrease of the elastic modulus at 20 +/- 1 degree C by approximately 66% was observed in some cases after the heating temperature had been increased to 300 degrees C. Property variations were related to compositional changes, which were investigated by infrared spectoscopy and thermal analysis. Exposure of dental waxes to temperatures higher than 200 degrees C, particularly if it is repeated, may affect the composition and properties, resulting in inferior materials.

  7. Learning with repeated-game strategies.

    PubMed

    Ioannou, Christos A; Romero, Julian

    2014-01-01

    We use the self-tuning Experience Weighted Attraction model with repeated-game strategies as a computer testbed to examine the relative frequency, speed of convergence and progression of a set of repeated-game strategies in four symmetric 2 × 2 games: Prisoner's Dilemma, Battle of the Sexes, Stag-Hunt, and Chicken. In the Prisoner's Dilemma game, we find that the strategy with the most occurrences is the "Grim-Trigger." In the Battle of the Sexes game, a cooperative pair that alternates between the two pure-strategy Nash equilibria emerges as the one with the most occurrences. In the Stag-Hunt and Chicken games, the "Win-Stay, Lose-Shift" and "Grim-Trigger" strategies are the ones with the most occurrences. Overall, the pairs that converged quickly ended up at the cooperative outcomes, whereas the ones that were extremely slow to reach convergence ended up at non-cooperative outcomes.

  8. Mutagenic inverted repeat assisted genome engineering (MIRAGE).

    PubMed

    Nair, Nikhil U; Zhao, Huimin

    2009-01-01

    Here we describe a one-step method to create precise modifications in the genome of Saccharomyces cerevisiae as a tool for synthetic biology, metabolic engineering, systems biology and genetic studies. Through homologous recombination, a mutagenesis cassette containing an inverted repeat of selection marker(s) is integrated into the genome. Due to its inherent instability in genomic DNA, the inverted repeat catalyzes spontaneous self-excision, resulting in precise genome modification. Since this excision occurs at very high frequencies, selection for the integration event can be followed immediately by counterselection, without the need for growth in permissive conditions. This is the first time a truly one-step method has been described for genome modification in any organism.

  9. Mutagenic inverted repeat assisted genome engineering (MIRAGE)

    PubMed Central

    Nair, Nikhil U.; Zhao, Huimin

    2009-01-01

    Here we describe a one-step method to create precise modifications in the genome of Saccharomyces cerevisiae as a tool for synthetic biology, metabolic engineering, systems biology and genetic studies. Through homologous recombination, a mutagenesis cassette containing an inverted repeat of selection marker(s) is integrated into the genome. Due to its inherent instability in genomic DNA, the inverted repeat catalyzes spontaneous self-excision, resulting in precise genome modification. Since this excision occurs at very high frequencies, selection for the integration event can be followed immediately by counterselection, without the need for growth in permissive conditions. This is the first time a truly one-step method has been described for genome modification in any organism. PMID:19050015

  10. Overcoming fixation with repeated memory suppression.

    PubMed

    Angello, Genna; Storm, Benjamin C; Smith, Steven M

    2015-01-01

    Fixation (blocks to memories or ideas) can be alleviated not only by encouraging productive work towards a solution, but, as the present experiments show, by reducing counterproductive work. Two experiments examined relief from fixation in a word-fragment completion task. Blockers, orthographically similar negative primes (e.g., ANALOGY), blocked solutions to word fragments (e.g., A_L_ _GY) in both experiments. After priming, but before the fragment completion test, participants repeatedly suppressed half of the blockers using the Think/No-Think paradigm, which results in memory inhibition. Inhibiting blockers did not alleviate fixation in Experiment 1 when conscious recollection of negative primes was not encouraged on the fragment completion test. In Experiment 2, however, when participants were encouraged to remember negative primes at fragment completion, relief from fixation was observed. Repeated suppression may nullify fixation effects, and promote creative thinking, particularly when fixation is caused by conscious recollection of counterproductive information.

  11. Quantum repeater with continuous variable encoding

    NASA Astrophysics Data System (ADS)

    Li, Linshu; Albert, Victor V.; Michael, Marios; Muralidharan, Sreraman; Zou, Changling; Jiang, Liang

    2016-05-01

    Quantum communication enables faithful quantum state transfer between different parties and protocols for cryptographic purposes. However, quantum communication over long distances (>1000km) remains challenging due to optical channel attenuation. This calls for investigation on developing novel encoding schemes that correct photon loss errors efficiently. In this talk, we introduce the generalization of multi-component Schrödinger cat states and propose to encode quantum information in these cat states for ultrafast quantum repeaters. We detail the quantum error correction procedures at each repeater station and characterize the performance of this novel encoding scheme given practical imperfections, such as coupling loss. A comparison with other quantum error correcting codes for bosonic modes will be discussed.

  12. Accumulate-Repeat-Accumulate-Accumulate Codes

    NASA Technical Reports Server (NTRS)

    Divsalar, Dariush; Dolinar, Samuel; Thorpe, Jeremy

    2007-01-01

    Accumulate-repeat-accumulate-accumulate (ARAA) codes have been proposed, inspired by the recently proposed accumulate-repeat-accumulate (ARA) codes. These are error-correcting codes suitable for use in a variety of wireless data-communication systems that include noisy channels. ARAA codes can be regarded as serial turbolike codes or as a subclass of low-density parity-check (LDPC) codes, and, like ARA codes they have projected graph or protograph representations; these characteristics make it possible to design high-speed iterative decoders that utilize belief-propagation algorithms. The objective in proposing ARAA codes as a subclass of ARA codes was to enhance the error-floor performance of ARA codes while maintaining simple encoding structures and low maximum variable node degree.

  13. Repeated interactions in open quantum systems

    SciTech Connect

    Bruneau, Laurent; Joye, Alain; Merkli, Marco

    2014-07-15

    Analyzing the dynamics of open quantum systems has a long history in mathematics and physics. Depending on the system at hand, basic physical phenomena that one would like to explain are, for example, convergence to equilibrium, the dynamics of quantum coherences (decoherence) and quantum correlations (entanglement), or the emergence of heat and particle fluxes in non-equilibrium situations. From the mathematical physics perspective, one of the main challenges is to derive the irreversible dynamics of the open system, starting from a unitary dynamics of the system and its environment. The repeated interactions systems considered in these notes are models of non-equilibrium quantum statistical mechanics. They are relevant in quantum optics, and more generally, serve as a relatively well treatable approximation of a more difficult quantum dynamics. In particular, the repeated interaction models allow to determine the large time (stationary) asymptotics of quantum systems out of equilibrium.

  14. Repeat-PPM Super-Symbol Synchronization

    NASA Astrophysics Data System (ADS)

    Connelly, J.

    2016-11-01

    To attain a wider range of data rates in pulse position modulation (PPM) schemes with constrained pulse durations, the sender can repeat a PPM symbol multiple times, forming a super-symbol. In addition to the slot and symbol synchronization typically required for PPM, the receiver must also properly align the noisy super-symbols. We present a low-complexity approximation of the maximum-likelihood method for performing super-symbol synchronization without use of synchronization sequences. We provide simulation results demonstrating performance advantage when PPM symbols are spread by a pseudo-noise sequence, as opposed to simply repeating. Additionally, the results suggest that this super-symbol synchronization technique requires signal levels below those required for reliable communication. This validates that the PPM spreading approach proposed to CCSDS can work properly as part of the overall scheme.

  15. 2D Metals by Repeated Size Reduction.

    PubMed

    Liu, Hanwen; Tang, Hao; Fang, Minghao; Si, Wenjie; Zhang, Qinghua; Huang, Zhaohui; Gu, Lin; Pan, Wei; Yao, Jie; Nan, Cewen; Wu, Hui

    2016-10-01

    A general and convenient strategy for manufacturing freestanding metal nanolayers is developed on large scale. By the simple process of repeatedly folding and calendering stacked metal sheets followed by chemical etching, free-standing 2D metal (e.g., Ag, Au, Fe, Cu, and Ni) nanosheets are obtained with thicknesses as small as 1 nm and with sizes of the order of several micrometers.

  16. Hypoglycaemic hemiplegia: a repeat SPECT study.

    PubMed Central

    Shintani, S; Tsuruoka, S; Shiigai, T

    1993-01-01

    During a hypoglycaemic right hemiplegia induced by a deliberate overdose of oral hypoglycaemics, brain CT and angiography revealed no abnormalities. SPECTs made one day and six days later showed relative hypoperfusion in the left hemisphere. Repeat SPECT study suggested that the left hemisphere was more vulnerable than the right in the cerebral blood perfusion. This vulnerability might provoke the right hemiplegia in a critical condition, such as severe hypoglycaemia. Images PMID:8509788

  17. Automatic-repeat-request error control schemes

    NASA Technical Reports Server (NTRS)

    Lin, S.; Costello, D. J., Jr.; Miller, M. J.

    1983-01-01

    Error detection incorporated with automatic-repeat-request (ARQ) is widely used for error control in data communication systems. This method of error control is simple and provides high system reliability. If a properly chosen code is used for error detection, virtually error-free data transmission can be attained. Various types of ARQ and hybrid ARQ schemes, and error detection using linear block codes are surveyed.

  18. Nucleosome repeat lengths and columnar chromatin structure.

    PubMed

    Trifonov, Edward N

    2016-06-01

    Thorough quantitative study of nucleosome repeat length (NRL) distributions, conducted in 1992 by J. Widom, resulted in a striking observation that the linker lengths between the nucleosomes are quantized. Comparison of the NRL average values with the MNase cut distances predicted from the hypothetical columnar structure of chromatin (this work) shows a close correspondence between the two. This strongly suggests that the NRL distribution, actually, reflects the dominant role of columnar chromatin structure common for all eukaryotes.

  19. Repeatability of Response to Asthma Medications

    PubMed Central

    Wu, Ann; Tantisira, Kelan; Li, Lingling; Schuemann, Brooke; Weiss, Scott

    2010-01-01

    Background Pharmacogenetic studies of drug response in asthma assume that patients respond consistently to a treatment but that treatment response varies across patients, however, no formal studies have demonstrated this. Objective To determine the repeatability of commonly used outcomes for treatment response to asthma medications: bronchodilator response, forced expiratory volume in 1 second (FEV1), and provocative concentration of methacholine producing a 20% decline in FEV1 (PC20). Methods The Childhood Asthma Management Program (CAMP) was a multi-center clinical trial of children randomized to receiving budesonide, nedocromil, or placebo. We determined the intraclass correlation coefficient (ICC) for each outcome over repeated visits over four years in CAMP using mixed effects regression models. We adjusted for the covariates: age, race/ethnicity, height, family income, parental education, and symptom score. We incorporated each outcome for each child as repeated outcome measurements and stratified by treatment group. Results The ICC for bronchodilator response was 0.31 in the budesonide group, 0.35 in the nedocromil group, and 0.40 in the placebo group, after adjusting for covariates. The ICC for FEV1 was 0.71 in the budesonide group, 0.60 in the nedocromil group, and 0.69 in the placebo group, after adjusting for covariates. The ICC for PC20 was 0.67 in the budesonide and placebo groups and 0.73 in the nedocromil group, after adjusting for covariates. Conclusion The within treatment group repeatability of FEV1 and PC20 are high; thus these phenotypes are heritable. FEV1 and PC20 may be better phenotypes than bronchodilator response for studies of treatment response in asthma. PMID:19064281

  20. Identical repeated backbone of the human genome

    PubMed Central

    2010-01-01

    Background Identical sequences with a minimal length of about 300 base pairs (bp) have been involved in the generation of various meiotic/mitotic genomic rearrangements through non-allelic homologous recombination (NAHR) events. Genomic disorders and structural variation, together with gene remodelling processes have been associated with many of these rearrangements. Based on these observations, we identified and integrated all the 100% identical repeats of at least 300 bp in the NCBI version 36.2 human genome reference assembly into non-overlapping regions, thus defining the Identical Repeated Backbone (IRB) of the reference human genome. Results The IRB sequences are distributed all over the genome in 66,600 regions, which correspond to ~2% of the total NCBI human genome reference assembly. Important structural and functional elements such as common repeats, segmental duplications, and genes are contained in the IRB. About 80% of the IRB bp overlap with known copy-number variants (CNVs). By analyzing the genes embedded in the IRB, we were able to detect some identical genes not previously included in the Ensembl release 50 annotation of human genes. In addition, we found evidence of IRB gene copy-number polymorphisms in raw sequence reads of two diploid sequenced genomes. Conclusions In general, the IRB offers new insight into the complex organization of the identical repeated sequences of the human genome. It provides an accurate map of potential NAHR sites which could be used in targeting the study of novel CNVs, predicting DNA copy-number variation in newly sequenced genomes, and improve genome annotation. PMID:20096123

  1. Agreement and repeatability of an infrared thermometer.

    PubMed

    Kelechi, Teresa J; Good, Angela; Mueller, Martina

    2011-01-01

    Recently, manufacturers have devised thermometers for home use by patients, such as the TempTouch Infrared Thermometer (TTIR; Diabetica Solutions, San Antonio, TX), which is designed with a long handle that can be used for self-monitoring localized skin temperature of the feet and legs. This study assessed the level of agreement and repeatability of the TTIR compared to a thermistor-type thermometer (TT; PeriFlux, 5020 Temperature Unit, Perimed, Stockholm, Sweden), the reference standard. In 17 healthy subjects, localized skin temperature was measured 8 cm above the right medial malleolus at baseline (Time 1), after a 10-minute rest period (Time 2), and after 10 minutes of cold provocation (Time 3) with a cryotherapy gel wrap placed around the lower legs using the TTIR and TT for temperature measurement. Scatter plots and correlation coefficients showed strong positive relationships between the two measurement methods at all three time points (Time 1: r = 0.95; Time 2: r = 0.97; and, Time 3: r = 0.87). Results showed a reasonable level of agreement between the two methods at Times 1 and 2 but not after cold provocation. Agreement between the methods appears to be better than repeatability within each method. Results for repeatability from both the TT and TTIR were very similar suggesting that there was a systematic bias with increasing temperatures between Time 1 and Time 2.

  2. Landauer's Principle in Repeated Interaction Systems

    NASA Astrophysics Data System (ADS)

    Hanson, Eric P.; Joye, Alain; Pautrat, Yan; Raquépas, Renaud

    2017-01-01

    We study Landauer's Principle for Repeated Interaction Systems (RIS) consisting of a reference quantum system S in contact with a structured environment E made of a chain of independent quantum probes; S interacts with each probe, for a fixed duration, in sequence. We first adapt Landauer's lower bound, which relates the energy variation of the environment E to a decrease of entropy of the system S during the evolution, to the peculiar discrete time dynamics of RIS. Then we consider RIS with a structured environment E displaying small variations of order {T^{-1}} between the successive probes encountered by S, after {n ˜eq T} interactions, in keeping with adiabatic scaling. We establish a discrete time non-unitary adiabatic theorem to approximate the reduced dynamics of S in this regime, in order to tackle the adiabatic limit of Landauer's bound. We find that saturation of Landauer's bound is related to a detailed balance condition on the repeated interaction system, reflecting the non-equilibrium nature of the repeated interaction system dynamics. This is to be contrasted with the generic saturation of Landauer's bound known to hold for continuous time evolution of an open quantum system interacting with a single thermal reservoir in the adiabatic regime.

  3. Repeated-sprint ability: where are we?

    PubMed

    Dawson, Brian

    2012-09-01

    Repeated-sprint ability (RSA) is now well accepted as an important fitness component in team-sport performance. It is broadly described as the ability to perform repeated short (~3-4 s, 20-30 m) sprints with only brief (~10-30 s) recovery between bouts. Over the past 25 y a plethora of RSA tests have been trialed and reported in the literature. These range from a single set of ~6-10 short sprints, departing every 20-30 s, to team-sport game simulations involving repeating cycles of walk-jog-stride-sprint movements over 45-90 min. Such a wide range of RSA tests has not assisted the synthesis of research findings in this area, and questions remain regarding the optimal methods of training to best improve RSA. In addition, how RSA test scores relate to player "work rate," match performance, or both requires further investigation to improve the application of RSA testing and training to elite team-sport athletes.

  4. Accumulate-Repeat-Accumulate-Accumulate-Codes

    NASA Technical Reports Server (NTRS)

    Divsalar, Dariush; Dolinar, Sam; Thorpe, Jeremy

    2004-01-01

    Inspired by recently proposed Accumulate-Repeat-Accumulate (ARA) codes [15], in this paper we propose a channel coding scheme called Accumulate-Repeat-Accumulate-Accumulate (ARAA) codes. These codes can be seen as serial turbo-like codes or as a subclass of Low Density Parity Check (LDPC) codes, and they have a projected graph or protograph representation; this allows for a high-speed iterative decoder implementation using belief propagation. An ARAA code can be viewed as a precoded Repeat-and-Accumulate (RA) code with puncturing in concatenation with another accumulator, where simply an accumulator is chosen as the precoder; thus ARAA codes have a very fast encoder structure. Using density evolution on their associated protographs, we find examples of rate-lJ2 ARAA codes with maximum variable node degree 4 for which a minimum bit-SNR as low as 0.21 dB from the channel capacity limit can be achieved as the block size goes to infinity. Such a low threshold cannot be achieved by RA or Irregular RA (IRA) or unstructured irregular LDPC codes with the same constraint on the maximum variable node degree. Furthermore by puncturing the accumulators we can construct families of higher rate ARAA codes with thresholds that stay close to their respective channel capacity thresholds uniformly. Iterative decoding simulation results show comparable performance with the best-known LDPC codes but with very low error floor even at moderate block sizes.

  5. Orthologous repeats and mammalian phylogenetic inference

    PubMed Central

    Bashir, Ali; Ye, Chun; Price, Alkes L.; Bafna, Vineet

    2005-01-01

    Determining phylogenetic relationships between species is a difficult problem, and many phylogenetic relationships remain unresolved, even among eutherian mammals. Repetitive elements provide excellent markers for phylogenetic analysis, because their mode of evolution is predominantly homoplasy-free and unidirectional. Historically, phylogenetic studies using repetitive elements have relied on biological methods such as PCR analysis, and computational inference is limited to a few isolated repeats. Here, we present a novel computational method for inferring phylogenetic relationships from partial sequence data using orthologous repeats. We apply our method to reconstructing the phylogeny of 28 mammals, using more than 1000 orthologous repeats obtained from sequence data available from the NISC Comparative Sequencing Program. The resulting phylogeny has robust bootstrap numbers, and broadly matches results from previous studies which were obtained using entirely different data and methods. In addition, we shed light on some of the debatable aspects of the phylogeny. With rapid expansion of available partial sequence data, computational analysis of repetitive elements holds great promise for the future of phylogenetic inference. PMID:15998912

  6. Genomic Repeat Abundances Contain Phylogenetic Signal

    PubMed Central

    Dodsworth, Steven; Chase, Mark W.; Kelly, Laura J.; Leitch, Ilia J.; Macas, Jiří; Novák, Petr; Piednoël, Mathieu; Weiss-Schneeweiss, Hanna; Leitch, Andrew R.

    2015-01-01

    A large proportion of genomic information, particularly repetitive elements, is usually ignored when researchers are using next-generation sequencing. Here we demonstrate the usefulness of this repetitive fraction in phylogenetic analyses, utilizing comparative graph-based clustering of next-generation sequence reads, which results in abundance estimates of different classes of genomic repeats. Phylogenetic trees are then inferred based on the genome-wide abundance of different repeat types treated as continuously varying characters; such repeats are scattered across chromosomes and in angiosperms can constitute a majority of nuclear genomic DNA. In six diverse examples, five angiosperms and one insect, this method provides generally well-supported relationships at interspecific and intergeneric levels that agree with results from more standard phylogenetic analyses of commonly used markers. We propose that this methodology may prove especially useful in groups where there is little genetic differentiation in standard phylogenetic markers. At the same time as providing data for phylogenetic inference, this method additionally yields a wealth of data for comparative studies of genome evolution. PMID:25261464

  7. Repeat Stereotactic Radiosurgery for Acoustic Neuromas

    SciTech Connect

    Kano, Hideyuki; Kondziolka, Douglas; Niranjan, Ajay M.Ch.; Flannery, Thomas J.; Flickinger, John C.; Lunsford, L. Dade

    2010-02-01

    Purpose: To evaluate the outcome of repeat stereotactic radiosurgery (SRS) for acoustic neuromas, we assessed tumor control, clinical outcomes, and the risk of adverse radiation effects in patients whose tumors progressed after initial management. Methods and Materials: During a 21-year experience at our center, 1,352 patients underwent SRS as management for their acoustic neuromas. We retrospectively identified 6 patients who underwent SRS twice for the same tumor. The median patient age was 47 years (range, 35-71 years). All patients had imaging evidence of tumor progression despite initial SRS. One patient also had incomplete surgical resection after initial SRS. All patients were deaf at the time of the second SRS. The median radiosurgery target volume at the time of the initial SRS was 0.5 cc and was 2.1 cc at the time of the second SRS. The median margin dose at the time of the initial SRS was 13 Gy and was 11 Gy at the time of the second SRS. The median interval between initial SRS and repeat SRS was 63 months (range, 25-169 months). Results: At a median follow-up of 29 months after the second SRS (range, 13-71 months), tumor control or regression was achieved in all 6 patients. No patient developed symptomatic adverse radiation effects or new neurological symptoms after the second SRS. Conclusions: With this limited experience, we found that repeat SRS for a persistently enlarging acoustic neuroma can be performed safely and effectively.

  8. A Unified Model for Repeating and Non-repeating Fast Radio Bursts

    NASA Astrophysics Data System (ADS)

    Bagchi, Manjari

    2017-04-01

    The model that fast radio bursts (FRBs) are caused by plunges of asteroids onto neutron stars can explain both repeating and non-repeating bursts. If a neutron star passes through an asteroid belt around another star, there would be a series of bursts caused by a series of asteroid impacts. Moreover, the neutron star would cross the same belt repetitively if it were in a binary with the star hosting the asteroid belt, leading to a repeated series of bursts. I explore the properties of neutron star binaries that could lead to the only known repeating FRB so far (FRB121102). In this model, the next two epochs of bursts are expected around 2017 February 27 and 2017 December 18. On the other hand, if the asteroid belt is located around the neutron star itself, then a chance fall of an asteroid from that belt onto the neutron star would lead to a non-repeating burst. Even a neutron star grazing an asteroid belt can lead to a non-repeating burst caused by just one asteroid plunge during the grazing. This is possible even when the neutron star is in a binary with the asteroid-hosting star, if the belt and the neutron star orbit are non-coplanar.

  9. Oxygen uptake during repeated-sprint exercise.

    PubMed

    McGawley, Kerry; Bishop, David J

    2015-03-01

    Repeated-sprint ability appears to be influenced by oxidative metabolism, with reductions in fatigue and improved sprint times related to markers of aerobic fitness. The aim of the current study was to measure the oxygen uptake (VO₂) during the first and last sprints during two, 5 × 6-s repeated-sprint bouts. Cross-sectional study. Eight female soccer players performed two, consecutive, 5 × 6-s maximal sprint bouts (B1 and B2) on five separate occasions, in order to identify the minimum time (trec) required to recover total work done (Wtot) in B1. On a sixth occasion, expired air was collected during the first and last sprint of B1 and B2, which were separated by trec. The trec was 10.9 ± 1.1 min. The VO₂ during the first sprint was significantly less than the last sprint in each bout (p<0.001), and the estimated aerobic contribution to the final sprint (measured in kJ) was significantly related to VO₂max in both B1 (r=0.81, p=0.015) and B2 (r=0.93, p=0.001). In addition, the VO₂ attained in the final sprint was not significantly different from VO₂max in B1 (p=0.284) or B2 (p=0.448). The current study shows that the VO₂ increases from the first to the last of 5 × 6-s sprints and that VO₂max may be a limiting factor to performance in latter sprints. Increasing V˙O₂max in team-sport athletes may enable increased aerobic energy delivery, and consequently work done, during a bout of repeated sprints. Copyright © 2014 Sports Medicine Australia. Published by Elsevier Ltd. All rights reserved.

  10. Repeatability of a running heat tolerance test.

    PubMed

    Mee, Jessica A; Doust, Jo; Maxwell, Neil S

    2015-01-01

    At present there is no standardised heat tolerance test (HTT) procedure adopting a running mode of exercise. Current HTTs may misdiagnose a runner's susceptibility to a hyperthermic state due to differences in exercise intensity. The current study aimed to establish the repeatability of a practical running test to evaluate individual's ability to tolerate exercise heat stress. Sixteen (8M, 8F) participants performed the running HTT (RHTT) (30 min, 9 km h(-1), 2% elevation) on two separate occasions in a hot environment (40 °C and 40% relative humidity). There were no differences in peak rectal temperature (RHTT1: 38.82 ± 0.47 °C, RHTT2: 38.86 ± 0.49 °C, Intra-class correlation coefficient (ICC)=0.93, typical error of measure (TEM) = 0.13 °C), peak skin temperature (RHTT1: 38.12 ± 0.45, RHTT2: 38.11 ± 0.45 °C, ICC = 0.79, TEM = 0.30 °C), peak heart rate (RHTT1: 182 ± 15 beats min(-1), RHTT2: 183 ± 15 beats min(-1), ICC = 0.99, TEM = 2 beats min(-1)), nor sweat rate (1721 ± 675 g h(-1), 1716 ± 745 g h(-1), ICC = 0.95, TEM = 162 g h(-1)) between RHTT1 and RHTT2 (p>0.05). Results demonstrate good agreement, strong correlations and small differences between repeated trials, and the TEM values suggest low within-participant variability. The RHTT was effective in differentiating between individuals physiological responses; supporting a heat tolerance continuum. The findings suggest the RHTT is a repeatable measure of physiological strain in the heat and may be used to assess the effectiveness of acute and chronic heat alleviating procedures.

  11. Repeatability and Reproducibility of Virtual Subjective Refraction.

    PubMed

    Perches, Sara; Collados, M Victoria; Ares, Jorge

    2016-10-01

    To establish the repeatability and reproducibility of a virtual refraction process using simulated retinal images. With simulation software, aberrated images corresponding with each step of the refraction process were calculated following the typical protocol of conventional subjective refraction. Fifty external examiners judged simulated retinal images until the best sphero-cylindrical refraction and the best visual acuity were achieved starting from the aberrometry data of three patients. Data analyses were performed to assess repeatability and reproducibility of the virtual refraction as a function of pupil size and aberrometric profile of different patients. SD values achieved in three components of refraction (M, J0, and J45) are lower than 0.25D in repeatability analysis. Regarding reproducibility, we found SD values lower than 0.25D in the most cases. When the results of virtual refraction with different pupil diameters (4 and 6 mm) were compared, the mean of differences (MoD) obtained were not clinically significant (less than 0.25D). Only one of the aberrometry profiles with high uncorrected astigmatism shows poor results for the M component in reproducibility and pupil size dependence analysis. In all cases, vision achieved was better than 0 logMAR. A comparison between the compensation obtained with virtual and conventional subjective refraction was made as an example of this application, showing good quality retinal images in both processes. The present study shows that virtual refraction has similar levels of precision as conventional subjective refraction. Moreover, virtual refraction has also shown that when high low order astigmatism is present, the refraction result is less precise and highly dependent on pupil size.

  12. Repeated-sprint ability and aerobic fitness.

    PubMed

    Thébault, Nicolas; Léger, Luc A; Passelergue, Philippe

    2011-10-01

    The purpose of this study was to reinvestigate the relationship between aerobic fitness and fatigue indices of repeated-sprint ability (RSA), with special attention to methodological normalization. Soldiers were divided into low (n = 10) and high (n = 9) fitness groups according to a preset maximal aerobic speed (MAS) of 17 km·h(-1) (∼60 ml O2·kg(-1)·min) measured with the University of Montreal Track Test (UMTT). Subjects' assessment included the RSA test (3 sets of 5 40-m sprints with 1-minute rest between sprints and 1.5 minutes between sets), a 40-m sprint (criterion test used in the computation of fatigue indices for the RSA test), strength and power measurement of the lower limbs, and the 20-m shuttle run test (20-m SRT) and the UMTT, which are measures of maximal aerobic power. The highest correlation with the RSA fatigue indices was obtained with the 20-m SRT (r = 0.90, p = 0.0001, n = 19), a test with 180° direction changes and accelerations and decelerations. The lower correlation (r = 0.66, p < 0.01, n = 19) with the UMTT (continuous forward running) suggests that some aerobic tests better disclose the importance of aerobic fitness for RSA and that aerobic power is not the sole determinant of RSA. However, neither strength nor vertical jumping power was correlated to the RSA fatigue indices. Subjects with greater MAS were able to maintain almost constant level of speed throughout series of repeated sprints and achieved better recovery between series. A MAS of at least 17 km·h(-1) favors constant and high speed level during repeated sprints. From a practical point of view, a high aerobic fitness is a precious asset in counteracting fatigue in sports with numerous sprint repetitions.

  13. Platelet peripheral benzodiazepine receptors in repeated stress.

    PubMed

    Dar, D E; Weizman, A; Karp, L; Grinshpoon, A; Bidder, M; Kotler, M; Tyano, S; Bleich, A; Gavish, M

    1991-01-01

    [3H]PK 11195 binding to platelet membranes and plasma stress hormones were studied in soldiers at the beginning of a parachute training course, following 6 days of preparatory exercises, and after the fourth actual parachute jump. A slight reduction (15%; NS) in the number of peripheral benzodiazepine receptors (PBR) was detected at the end of the exercise period, prior to the first jump. Reduced (26%; P less than 0.05) density of PBR was observed immediately after the repeated actual jumps. Equilibrium dissociation constants were not affected by the stressful situation. Plasma cortisol and prolactin levels remained unaltered during the entire study period.

  14. Spectral Character of Repeated GPS Measurements

    NASA Astrophysics Data System (ADS)

    Turen, Yener; Ugur Sanli, D.

    2017-04-01

    We need GPS campaigns because we are not always able to monitor natural hazards using CORS. Prime examples in regard to the above statement are landslides and local subsidence. For instance, we are reluctant to install permanent GPS equipment in a landslide area because the equipment might be destroyed due to the sudden flow of the ground. Similarly, the CORS might not be covering the area in which a local subsidence happening. Obviously more examples can be given. We take repeated (campaign) GPS to such case study areas. Therefore, similar to the continuous GPS, we also need to study the properties of the repeated GPS. Upto now, the positioning accuracy and the accuracy of velocity estimation have been documented well for the repeated measurements. The spectral character is one such issue that we desire to look along with the other investigations. Thanks to the IGS and its data and analysis center SOPAC, we are able to simulate possible campaign senarios and apply variety of statistics using their products. Thanks also to NASA, JPL; using the PPP module of GIPSY/OASIS II software, we are able to study the direct absolute deformations of the earth at the mm level. These investigations should shed light into multi-GNSS experiments. We generate monthly sampled GPS campaigns from the continuous IGS data and estimate station velocities from repeated GPS measurements. Then, we test the statistical significancy of the estimated trends against SOPAC derived station velocities. The analysis procedure includes the computation of periodograms for the campaign solutions and determine significant periodicities in the data. We ceheck the obtained periodicities with those of the SOPAC time series analysis of the continuous GPS data. As might be expected, the spectral character of the campaign solutions differ from those of the daily sampled continuous GPS solutions implemented by SOPAC. For instance, the typical annual signal on the vertical componenet might disappear at some

  15. Distillation by repeated measurements: Continuous spectrum case

    SciTech Connect

    Bellomo, Bruno; Compagno, Giuseppe; Nakazato, Hiromichi; Yuasa, Kazuya

    2010-12-15

    Repeated measurements on one part of a bipartite system strongly affect the other part that is not measured, the dynamics of which is regulated by an effective contracted evolution operator. When the spectrum of this operator is discrete, the nonmeasured system is driven into a pure state, irrespective of the initial state, provided that the spectrum satisfies certain conditions. We show here that, even in the case of continuous spectrum, an effective distillation can occur under rather general conditions. We confirm it by applying our formalism to a simple model.

  16. Platelet peripheral benzodiazepine receptors in repeated stress

    SciTech Connect

    Dar, D.E.; Bidder, M.; Gavish, M. ); Weizman, A.; Karp, L.; Tyano, S. ); Grinshpoon, A.; Bleich, A.

    1991-01-01

    ({sup 3}H)PK 11195 binding to platelet membranes and plasma stress hormones were studied in soldiers at the beginning of a parachute training course, following 6 days of preparatory exercises, and after the fourth actual parachute jump. A slight reduction (15%; NS) in the number of peripheral benzodiazepine receptors (PBR) was detected at the end of the exercise period, prior to the first jump. Reduced density of PBR was observed immediately after the repeated actual jumps. Equilibrium dissociation constants were not affected by the stressful situation. Plasma cortisol and prolactin levels remained unaltered during the entire study period.

  17. Repeats identification using improved suffix trees.

    PubMed

    Huo, Hongwei; Wang, Xiaowu; Stojkovic, Vojislav

    2009-01-01

    The suffix tree data structure plays an important role in the efficient implementations of some querying algorithms. This paper presents the fast Rep(eats)Seeker algorithm for repeats identification based on the improvements of suffix tree construction. The leaf nodes and the branch nodes are numbered in different ways during the construction of a suffix tree and extra information is added to the branch nodes. The experimental results show that improvements reduce the running time of the RepSeeker algorithm without losing the accuracy. The experimental results coincide with the theoretical expectations.

  18. Are all repeats created equal? Understanding DNA repeats at an individual level.

    PubMed

    Yang, Jinpu; Li, Fei

    2017-02-01

    Repetitive DNA sequences, comprising up to 50 % of the genome in all eukaryotes, play important roles in a wide range of cellular functions, such as transcriptional regulation, genome stability, and cellular differentiation. However, due to technical difficulties in differentiating their sequences, DNA repeats remain one of the most mysterious parts of eukaryotic genomes. Key questions, such as how repetitive entities behave at individual level and how the internal architecture of these repeats is organized, are still poorly understood. Recent advances from our group reveal unexpected position-dependent variation within tandem DNA repeats in fission yeast. Despite sharing identical DNA sequences, the peri-centromeric repeats are organized into diverse epigenetic states and chromatin structures. We demonstrate that this position-dependent variation requires key heterochromatin factors and condensin. Our works further suggest that the peri-centromeric repeats are organized into distinct higher order structures that ensure a proper positioning of CENP-A, the centromere-specific histone H3 variant, to centromeres. These most recent developments offer insights into the mechanisms underlying the position effect within tandem DNA arrays, and have broad implications in the field of epigenetics and chromatin biology.

  19. Nanostructured functional films from engineered repeat proteins

    PubMed Central

    Grove, Tijana Z.; Regan, Lynne; Cortajarena, Aitziber L.

    2013-01-01

    Fundamental advances in biotechnology, medicine, environment, electronics and energy require methods for precise control of spatial organization at the nanoscale. Assemblies that rely on highly specific biomolecular interactions are an attractive approach to form materials that display novel and useful properties. Here, we report on assembly of films from the designed, rod-shaped, superhelical, consensus tetratricopeptide repeat protein (CTPR). We have designed three peptide-binding sites into the 18 repeat CTPR to allow for further specific and non-covalent functionalization of films through binding of fluorescein labelled peptides. The fluorescence signal from the peptide ligand bound to the protein in the solid film is anisotropic, demonstrating that CTPR films can impose order on otherwise isotropic moieties. Circular dichroism measurements show that the individual protein molecules retain their secondary structure in the film, and X-ray scattering, birefringence and atomic force microscopy experiments confirm macroscopic alignment of CTPR molecules within the film. This work opens the door to the generation of innovative biomaterials with tailored structure and function. PMID:23594813

  20. Airborne Radar Interferometric Repeat-Pass Processing

    NASA Technical Reports Server (NTRS)

    Hensley, Scott; Michel, Thierry R.; Jones, Cathleen E.; Muellerschoen, Ronald J.; Chapman, Bruce D.; Fore, Alexander; Simard, Marc; Zebker, Howard A.

    2011-01-01

    Earth science research often requires crustal deformation measurements at a variety of time scales, from seconds to decades. Although satellites have been used for repeat-track interferometric (RTI) synthetic-aperture-radar (SAR) mapping for close to 20 years, RTI is much more difficult to implement from an airborne platform owing to the irregular trajectory of the aircraft compared with microwave imaging radar wavelengths. Two basic requirements for robust airborne repeat-pass radar interferometry include the ability to fly the platform to a desired trajectory within a narrow tube and the ability to have the radar beam pointed in a desired direction to a fraction of a beam width. Uninhabited Aerial Vehicle Synthetic Aperture Radar (UAVSAR) is equipped with a precision auto pilot developed by NASA Dryden that allows the platform, a Gulfstream III, to nominally fly within a 5 m diameter tube and with an electronically scanned antenna to position the radar beam to a fraction of a beam width based on INU (inertial navigation unit) attitude angle measurements.

  1. Aggregating quantum repeaters for the quantum internet

    NASA Astrophysics Data System (ADS)

    Azuma, Koji; Kato, Go

    2017-09-01

    The quantum internet holds promise for accomplishing quantum teleportation and unconditionally secure communication freely between arbitrary clients all over the globe, as well as the simulation of quantum many-body systems. For such a quantum internet protocol, a general fundamental upper bound on the obtainable entanglement or secret key has been derived [K. Azuma, A. Mizutani, and H.-K. Lo, Nat. Commun. 7, 13523 (2016), 10.1038/ncomms13523]. Here we consider its converse problem. In particular, we present a universal protocol constructible from any given quantum network, which is based on running quantum repeater schemes in parallel over the network. For arbitrary lossy optical channel networks, our protocol has no scaling gap with the upper bound, even based on existing quantum repeater schemes. In an asymptotic limit, our protocol works as an optimal entanglement or secret-key distribution over any quantum network composed of practical channels such as erasure channels, dephasing channels, bosonic quantum amplifier channels, and lossy optical channels.

  2. Repeatable assessment protocol for electromagnetic trackers

    NASA Astrophysics Data System (ADS)

    Haidegger, Tamas; Sirokai, Beáta; Fenyvesi, Gábor; Kovács, Levente; Benyó, Balázs; Benyó, Zoltán

    2012-02-01

    In the past decades, many new trends appeared in interventional medicine. One of the most groundbreaking ones is Image-Guided Surgery (IGS). The main benefit of IGS procedures is the reduction of the patient's pain and collateral damage through improved accuracy and targeting. Electromagnetic Tracking (EMT) has been introduced to medical applications as an effective tool for navigation. However, magnetic fields can be severely distorted by ferromagnetic materials and electronic equipment, which is a major barrier towards their wider application. The focus of the study is to determine and compensate the inherent errors of the different types of EMTs, in order to improve their accuracy. Our aim is to develop a standardized, simple and repeatable assessment protocol; to determine tracking errors with sub-millimeter accuracy, hence increasing the measurement precision and reliability. For initial experiments, the NDI Aurora and the Ascension medSAFE systems were used in a standard laboratory environment. We aim to advance to the state-of-the art by describing and disseminating an easily reproducible calibration method, publishing the CAD files of the accuracy phantom and the source of the evaluation data. This should allow the wider spread of the technique, and eventually lead to the repeatable and comparable assessment of EMT systems.

  3. Repeated proton beam therapy for hepatocellular carcinoma

    SciTech Connect

    Hashimoto, Takayuki |. E-mail: hashimoto@pmrc.tsukuba.ac.jp; Tokuuye, Koichi |; Fukumitsu, Nobuyoshi |; Igaki, Hiroshi |; Hata, Masaharu |; Kagei, Kenji |; Sugahara, Shinji; Ohara, Kiyoshi; Matsuzaki, Yasushi; Akine, Yasuyuki |

    2006-05-01

    Purpose: To retrospectively evaluate the safety and effectiveness of repeated proton beam therapy for newly developed or recurrent hepatocellular carcinoma (HCC). Methods and Materials: From June 1989 through July 2000, 225 patients with HCC underwent their first course of proton beam therapy at University of Tsukuba. Of them, 27 with 68 lesions who had undergone two or more courses were retrospectively reviewed in this study. Median interval between the first and second course was 24.5 months (range 3.3-79.8 months). Median total dose of 72 Gy in 16 fractions and 66 Gy in 16 fractions were given for the first course and the rest of the courses, respectively. Results: The 5-year survival rate and median survival period from the beginning of the first course for the 27 patients were 55.6% and 62.2 months, respectively. Five-year local control rate for the 68 lesions was 87.8%. Of the patients, 1 with Child-Pugh class B and another with class C before the last course suffered from acute hepatic failure. Conclusions: Repeated proton beam therapy for HCC is safe when the patient has a target in the peripheral region of the liver and liver function is Child-Pugh class A.

  4. Distributed parameter modeling of repeated truss structures

    NASA Technical Reports Server (NTRS)

    Wang, Han-Ching

    1994-01-01

    A new approach to find homogeneous models for beam-like repeated flexible structures is proposed which conceptually involves two steps. The first step involves the approximation of 3-D non-homogeneous model by a 1-D periodic beam model. The structure is modeled as a 3-D non-homogeneous continuum. The displacement field is approximated by Taylor series expansion. Then, the cross sectional mass and stiffness matrices are obtained by energy equivalence using their additive properties. Due to the repeated nature of the flexible bodies, the mass, and stiffness matrices are also periodic. This procedure is systematic and requires less dynamics detail. The first step involves the homogenization from a 1-D periodic beam model to a 1-D homogeneous beam model. The periodic beam model is homogenized into an equivalent homogeneous beam model using the additive property of compliance along the generic axis. The major departure from previous approaches in literature is using compliance instead of stiffness in homogenization. An obvious justification is that the stiffness is additive at each cross section but not along the generic axis. The homogenized model preserves many properties of the original periodic model.

  5. Adverse childhood experiences and repeat induced abortion.

    PubMed

    Bleil, Maria E; Adler, Nancy E; Pasch, Lauri A; Sternfeld, Barbara; Reijo-Pera, Renee A; Cedars, Marcelle I

    2011-02-01

    The objective of the study was to characterize the backgrounds of women who have repeat abortions. In a cross-sectional study of 259 women (mean age, 35.2 ± 5.6 years), the relation between adverse experiences in childhood and risk of having 2 or more abortions vs 0 or 1 abortion was examined. Self-reported adverse events occurring between the ages of 0 and 12 years were summed. Independent of confounding factors, women who experienced more abuse, personal safety, and total adverse events in childhood were more likely to have 2 or more abortions vs 0 abortions (odds ratio [OR], 2.56; 95% confidence interval [CI], 1.15-5.71; OR, 2.74; 95% CI, 1.29-5.82; and OR, 1.59; 95% CI, 1.21-2.09, respectively) and vs 1 abortion (OR, 5.83; 95% CI, 1.71-19.89; OR, 2.23; 95% CI, 1.03-4.81; and OR, 1.37; 95% CI, 1.04-1.81, respectively). Women who experienced more family disruption events in childhood were more likely to have 2 or more abortions vs 0 abortions (OR, 1.75; 95% CI, 1.14-2.69) but not vs 1 abortion (OR, 1.16; 95% CI, 0.79-1.70). Women who have repeat abortions are more likely to have experienced childhood adversity than those having 0 or 1 abortion. Copyright © 2011 Mosby, Inc. All rights reserved.

  6. Learning with repeated-game strategies

    PubMed Central

    Ioannou, Christos A.; Romero, Julian

    2014-01-01

    We use the self-tuning Experience Weighted Attraction model with repeated-game strategies as a computer testbed to examine the relative frequency, speed of convergence and progression of a set of repeated-game strategies in four symmetric 2 × 2 games: Prisoner's Dilemma, Battle of the Sexes, Stag-Hunt, and Chicken. In the Prisoner's Dilemma game, we find that the strategy with the most occurrences is the “Grim-Trigger.” In the Battle of the Sexes game, a cooperative pair that alternates between the two pure-strategy Nash equilibria emerges as the one with the most occurrences. In the Stag-Hunt and Chicken games, the “Win-Stay, Lose-Shift” and “Grim-Trigger” strategies are the ones with the most occurrences. Overall, the pairs that converged quickly ended up at the cooperative outcomes, whereas the ones that were extremely slow to reach convergence ended up at non-cooperative outcomes. PMID:25126053

  7. Analysis of a random repeated impact process

    NASA Astrophysics Data System (ADS)

    Wood, L. A.; Byrne, K. P.

    1981-10-01

    A simple random repeated impact process similar to the classical random walk process is analyzed. The process, which consists of a ball bouncing on a randomly vibrating surface, is analogous to loss-of-contact situations which can occur in linkages and vibrating tools. It also has relevance to rolling contact where the rolling element may separate from the surface and sustain repeated impacts. A coefficient of restitution is used to describe impact, and some important assumptions limit the analysis to values of this coefficient greater than 0°8. The Markov nature of the process is demonstrated by its one-step "memory". It may be regarded as a discrete Markov process "imbedded" in continuous time. A difference equation governing the process is developed and analyzed for the case where the vibrating surface has a Gaussian distribution of velocities. With the one-step transition probability density function a linear weighting function is used to account for the weighting effect of the ball's velocity on the distribution of table velocities at impact. The resulting integral equation is solved iteratively to yield the probability density function of ball velocities after impact. This information may then be used to predict the magnitudes of the impacts and the time between them.

  8. Chromosome-specific DNA Repeat Probes

    SciTech Connect

    Baumgartner, Adolf; Weier, Jingly Fung; Weier, Heinz-Ulrich G.

    2006-03-16

    In research as well as in clinical applications, fluorescence in situ hybridization (FISH) has gained increasing popularity as a highly sensitive technique to study cytogenetic changes. Today, hundreds of commercially available DNA probes serve the basic needs of the biomedical research community. Widespread applications, however, are often limited by the lack of appropriately labeled, specific nucleic acid probes. We describe two approaches for an expeditious preparation of chromosome-specific DNAs and the subsequent probe labeling with reporter molecules of choice. The described techniques allow the preparation of highly specific DNA repeat probes suitable for enumeration of chromosomes in interphase cell nuclei or tissue sections. In addition, there is no need for chromosome enrichment by flow cytometry and sorting or molecular cloning. Our PCR-based method uses either bacterial artificial chromosomes or human genomic DNA as templates with {alpha}-satellite-specific primers. Here we demonstrate the production of fluorochrome-labeled DNA repeat probes specific for human chromosomes 17 and 18 in just a few days without the need for highly specialized equipment and without the limitation to only a few fluorochrome labels.

  9. Exhaustive whole-genome tandem repeats search.

    PubMed

    Krishnan, Arun; Tang, Francis

    2004-11-01

    Approximate tandem repeats (ATR) occur frequently in the genomes of organisms, and are a source of polymorphisms observed in individuals, and thus are of interest to those studying genetic disorders. Though extensive work has been done in order to identify ATRs, there are inherent limitations with the current approaches in terms of the number of pattern sizes that can be searched or the size of the input length. This paper describes (1) a new algorithm which exhaustively finds all variable-length ATRs in a genomic sequence and (2) a precise description of, and an algorithm to significantly reduce, redundancy in the output. Our ATR definition is parameterized by a mismatch ratio p which allows for more mismatches in longer tandem repeats (and fewer in shorter). Furthermore, our algorithm is embarrassingly parallel and thus can attain near-linear speed-up on Beowulf clusters. We present results of our algorithm applied to sequences of widely differing lengths (from genes to chromosomes). Source and binaries are available on request.

  10. Sequences flanking the repeat arrays of human minisatellites: association with tandem and dispersed repeat elements.

    PubMed Central

    Armour, J A; Wong, Z; Wilson, V; Royle, N J; Jeffreys, A J

    1989-01-01

    We present DNA sequences flanking cloned hypervariable human minisatellites. In addition to providing confirmatory evidence that minisatellites cluster with other tandem repeats, these flanking sequences contain a high frequency of interspersed repetitive elements. These elements include a retroviral LTR-like sequence, from which one of the minisatellites appears to have expanded, and a recently described short interspersed repeat. We present our own findings concerning this element, in particular that those examples studied do not show significant evolutionary conservation, despite suggestions that the element may have a cis-acting function. Images PMID:2762114

  11. Analysis of LRRK2 accessory repeat domains: prediction of repeat length, number and sites of Parkinson's disease mutations.

    PubMed

    Mills, Ryan D; Mulhern, Terrence D; Cheng, Heung-Chin; Culvenor, Janetta G

    2012-10-01

    Various investigators have identified the major domain organization of LRRK2 (leucine-rich repeat kinase 2), which includes a GTPase ROC (Ras of complex proteins) domain followed by a COR (C-terminal of ROC) domain and a protein kinase domain. In addition, there are four domains composed of structural repeat motifs likely to be involved in regulation and localization of this complex protein. In the present paper, we report our bioinformatic analyses of the human LRRK2 amino acid sequence to predict the repeat size, number and likely boundaries for the armadillo repeat, ankyrin repeat, the leucine-rich repeat and WD40 repeat regions of LRRK2. Homology modelling using known protein structures with similar domains was used to predict structures, exposed residues and location of mutations for these repeat regions. We predict that the armadillo repeats, ankyrin repeats and leucine-rich repeats together form an extended N-terminal flexible 'solenoid'-like structure composed of tandem repeat modules likely to be important in anchoring to the membrane and cytoskeletal structures as well as binding to other protein ligands. Near the C-terminus of LRRK2, the WD40 repeat region is predicted to form a closed propeller structure that is important for protein complex formation.

  12. Tandem-repeat internal mapping (TRIM) of the involucrin gene: Repeat number and repeat-pattern polymorphism within a coding region in human populations

    SciTech Connect

    Urquhart, A.; Gill, P. )

    1993-07-01

    The authors have analyzed the human involucrin gene in 41 British African-Caribbeans and 37 British white Caucasians by tandem-repeat internal mapping and DNA sequencing. A point mutation (i.e., B[sub c]) in the last B repeat unit was found in 98.6% of British white Caucasians and in 52.4% of British African-Caribbeans. The distribution of repeat patterns was also different between the two populations. Nine previously unreported repeat pattern alleles, 4 with and 5 without the B[sub c] repeat, have been found, increasing the range of variation in humans to 15 reported repeat patterns, 6 with and 9 without the Caucasian mutation. Three further sequence variations, each occurring in a single individual, were found. The evolutionary significance of variation in the human involucrin gene is discussed. 30 refs., 4 figs., 2 tabs.

  13. Erroneous Memories Arising from Repeated Attempts to Remember

    ERIC Educational Resources Information Center

    Henkel, Linda A.

    2004-01-01

    The impact of repeated and prolonged attempts at remembering on false memory rates was assessed in three experiments. Participants saw and imagined pictures and then made repeated recall attempts before taking a source memory test. Although the number of items recalled increased with repeated tests, the net gains were associated with more source…

  14. Erroneous Memories Arising from Repeated Attempts to Remember

    ERIC Educational Resources Information Center

    Henkel, Linda A.

    2004-01-01

    The impact of repeated and prolonged attempts at remembering on false memory rates was assessed in three experiments. Participants saw and imagined pictures and then made repeated recall attempts before taking a source memory test. Although the number of items recalled increased with repeated tests, the net gains were associated with more source…

  15. Repeat Testing Effects on Credentialing Exams: Are Repeaters Misinformed or Uninformed?

    ERIC Educational Resources Information Center

    Feinberg, Richard A.; Raymond, Mark R.; Haist, Steven A.

    2015-01-01

    To mitigate security concerns and unfair score gains, credentialing programs routinely administer new test material to examinees retesting after an initial failing attempt. Counterintuitively, a small but growing body of recent research suggests that repeating the identical form does not create an unfair advantage. This study builds upon and…

  16. Repeat Testing Effects on Credentialing Exams: Are Repeaters Misinformed or Uninformed?

    ERIC Educational Resources Information Center

    Feinberg, Richard A.; Raymond, Mark R.; Haist, Steven A.

    2015-01-01

    To mitigate security concerns and unfair score gains, credentialing programs routinely administer new test material to examinees retesting after an initial failing attempt. Counterintuitively, a small but growing body of recent research suggests that repeating the identical form does not create an unfair advantage. This study builds upon and…

  17. Tandemly repeated exons encode 81-base repeats in multiple, developmentally regulated Schistosoma mansoni transcripts.

    PubMed Central

    Davis, R E; Davis, A H; Carroll, S M; Rajkovic, A; Rottman, F M

    1988-01-01

    The adult Schistosoma mansoni cDNA clone 10-3 encodes an antigen that is recognized by sera from infected humans. We characterized multiple developmentally regulated transcripts homologous to the 10-3 cDNA and portions of the complex genomic loci encoding those transcripts. Transcripts of approximately 950, 870, and 780 nucleotides were expressed in adults, whereas only the 780-nucleotide transcript was observed in the larval stage. These transcripts were highly similar, containing variable numbers of identical direct tandem repeats of 81 bases. Although the sequence of the repeating elements and sequences 3' to them were identical in all the transcripts, sequences 5' of the repeating elements exhibited variations, including a 27-base insertion, alternative start sites for transcription, and alternate 5' exon usage. These transcripts appeared to be derived in part by the developmentally controlled alternative splicing of small exons and the use of alternative transcription initiation sites from the one or two complex loci of at least 40 kilobase pairs. Each 81-base repeat in the transcripts was encoded by three dispersed 27-base-pair exons. These 27-base-pair exons were contained within highly conserved, reiterated 3-kilobase-pair genomic tandem arrays. Images PMID:3211127

  18. Who Repeats Algebra, and How Does Initial Performance Relate to Improvement When the Course Is Repeated?

    ERIC Educational Resources Information Center

    Fong, Anthony; Jaquet, Karina; Finkelstein, Neal

    2016-01-01

    The information provided in this report shows how students perform when they repeat algebra I and how the level of improvement varies depending on initial course performance and the academic measure (course grades or CST scores). This information can help inform decisions and policies regarding whether and under what circumstances students should…

  19. Design principles for efficient, repeated jumpgliding.

    PubMed

    Desbiens, Alexis Lussier; Pope, Morgan T; Christensen, David L; Hawkes, Elliot W; Cutkosky, Mark R

    2014-06-01

    Combined jumping and gliding locomotion, or 'jumpgliding', can be an efficient way for small robots or animals to travel over cluttered terrain. This paper presents functional requirements and models for a simple jumpglider which formalize the benefits and limitations of using aerodynamic surfaces to augment jumping ability. Analysis of the model gives insight into design choices and control strategies for higher performance and to accommodate special conditions such as a slippery launching surface. The model informs the design of a robotic platform that can perform repeated jumps using a carbon fiber spring and a pivoting wing. Experiments with two different versions of the platform agree with predictions from the model and demonstrate a significantly greater range, and lower cost-of-transport, than a comparable ballistic jumper.

  20. Quantum repeaters using continuous-variable teleportation

    NASA Astrophysics Data System (ADS)

    Dias, Josephine; Ralph, T. C.

    2017-02-01

    Quantum optical states are fragile and can become corrupted when passed through a lossy communication channel. Unlike for classical signals, optical amplifiers cannot be used to recover quantum signals. Quantum repeaters have been proposed as a way of reducing errors and hence increasing the range of quantum communications. Current protocols target specific discrete encodings, for example quantum bits encoded on the polarization of single photons. We introduce a more general approach that can reduce the effect of loss on any quantum optical encoding, including those based on continuous variables such as the field amplitudes. We show that in principle the protocol incurs a resource cost that scales polynomially with distance. We analyze the simplest implementation and find that while its range is limited it can still achieve useful improvements in the distance over which quantum entanglement of field amplitudes can be distributed.

  1. Simple sequence repeats in bryophyte mitochondrial genomes.

    PubMed

    Zhao, Chao-Xian; Zhu, Rui-Liang; Liu, Yang

    2016-01-01

    Simple sequence repeats (SSRs) are thought to be common in plant mitochondrial (mt) genomes, but have yet to be fully described for bryophytes. We screened the mt genomes of two liverworts (Marchantia polymorpha and Pleurozia purpurea), two mosses (Physcomitrella patens and Anomodon rugelii) and two hornworts (Phaeoceros laevis and Nothoceros aenigmaticus), and detected 475 SSRs. Some SSRs are found conserved during the evolution, among which except one exists in both liverworts and mosses, all others are shared only by the two liverworts, mosses or hornworts. SSRs are known as DNA tracts having high mutation rates; however, according to our observations, they still can evolve slowly. The conservativeness of these SSRs suggests that they are under strong selection and could play critical roles in maintaining the gene functions.

  2. Repeatability of mixed-mode adhesive debonding

    NASA Technical Reports Server (NTRS)

    Everett, R. A., Jr.; Johnson, W. S.

    1984-01-01

    The repeatability of debond growth rates in adhesively bonded subjected to constant-amplitude cyclic loading was studied. Debond growth rates were compared from two sets of cracked-lap-shear specimens that were fabricated by two different manufacturers and tested in different laboratories. The fabrication method and testing procedures were identical for both sets of specimens. The specimens consisted of aluminum adherends bonded with FM-73 adhesive. Critical values of strain-energy-release rate were also determined from specimens that were monotonically loaded to failure. The test results showed that the debond growth rates for the two sets of specimens were within a scatter band which is similar to that observed in fatigue crack growth in metals. Cyclic debonding occurred at strain-energy-release rates that were more than an order of magnitude less than the critical strain-energy-release rate in static tests.

  3. Repeat Gamma Knife surgery for vestibular schwannomas

    PubMed Central

    Lonneville, Sarah; Delbrouck, Carine; Renier, Cécile; Devriendt, Daniel; Massager, Nicolas

    2015-01-01

    Background: Gamma Knife (GK) surgery is a recognized treatment option for the management of small to medium-sized vestibular schwannoma (VS) associated with high-tumor control and low morbidity. When a radiosurgical treatment fails to stop tumor growth, repeat GK surgery can be proposed in selected cases. Methods: A series of 27 GK retreatments was performed in 25 patients with VS; 2 patients underwent three procedures. The median time interval between GK treatments was 45 months. The median margin dose used for the first, second, and third GK treatments was 12 Gy, 12 Gy, and 14 Gy, respectively. Six patients (4 patients for the second irradiation and 2 patients for the third irradiation) with partial tumor regrowth were treated only on the growing part of the tumor using a median margin dose of 13 Gy. The median tumor volume was 0.9, 2.3, and 0.7 cc for the first, second, and third treatments, respectively. Stereotactic positron emission tomography (PET) guidance was used for dose planning in 6 cases. Results: Mean follow-up duration was 46 months (range 24–110). At the last follow-up, 85% of schwannomas were controlled. The tumor volume decreased, remained unchanged, or increased after retreatment in 15, 8, and 4 cases, respectively. Four patients had PET during follow-up, and all showed a significant metabolic decrease of the tumor. Hearing was not preserved after retreatment in any patients. New facial or trigeminal palsy did not occur after retreatment. Conclusions: Our results support the long-term efficacy and low morbidity of repeat GK treatment for selected patients with tumor growth after initial treatment. PMID:26500799

  4. The Effects of Repeated Writing and Repeated Revision Strategies on Composing Fluency of Learning Disabled Adolescents. Final Report.

    ERIC Educational Resources Information Center

    Harriman, Nancy E.; Gajar, Anna H.

    The study investigated the use of repeated writings as a means of increasing written language fluency with 48 learning disabled students in senior high school resource room English classes. Subjects received one of four treatments for 4 days: repeated writing with structural cues, repeated revision with structural cues, writing on a new topic with…

  5. Mutational dynamics of short tandem repeats in human genome

    NASA Astrophysics Data System (ADS)

    Borstnik, B.; Pumpernik, D.

    2004-01-01

    The evolutionary dynamics of short tandem repeats of nucleotide sequences of the human genome is studied. It is shown that a model due to which the evolutionary repeat dynamics consists of elongations and shortenings of the repeats, combined with point mutations, is degenerate in the sense that an ambiguity exists regarding the role of point mutations and slippage asymmetry. By introducing a measure of the correlations between the positions of the repeats along the DNA sequences we were able to remove the degeneracy and to show that the slippage events which are the main factor in repeat evolution exhibit more frequent shortenings than elongations.

  6. In situ detection of tandem DNA repeat length

    SciTech Connect

    Yaar, R.; Szafranski, P.; Cantor, C.R.; Smith, C.L.

    1996-11-01

    A simple method for scoring short tandem DNA repeats is presented. An oligonucleotide target, containing tandem repeats embedded in a unique sequence, was hybridized to a set of complementary probes, containing tandem repeats of known lengths. Single-stranded loop structures formed on duplexes containing a mismatched (different) number of tandem repeats. No loop structure formed on duplexes containing a matched (identical) number of tandem repeats. The matched and mismatched loop structures were enzymatically distinguished and differentially labeled by treatment with S1 nuclease and the Klenow fragment of DNA polymerase. 7 refs., 4 figs.

  7. The excess of small inverted repeats in prokaryotes.

    PubMed

    Ladoukakis, Emmanuel D; Eyre-Walker, Adam

    2008-09-01

    Recent analyses have shown that there is a large excess of perfect inverted repeats in many prokaryotic genomes but not in eukaryotic ones. This difference could be due to a genuine difference between prokaryotes and eukaryotes or to differences in the methods and types of data analyzed--full genome versus protein coding sequences. We used simulations to show that the method used previously tends to underestimate the expected number of inverted repeats. However, this bias is not large and cannot explain the excess of inverted repeats observed in real data. In contrast, our method is unbiased. When both methods are applied to bacterial protein coding sequences they both detect an excess of inverted repeats, which is much lower than previously reported in whole prokaryotic genomes. This suggests that the reported large excess of inverted repeats is due to repeats found in intergenic regions. These repeats could be due to transcription factor binding sites, or other types of repetitive DNA, on opposite strands of the DNA sequence. In contrast, the smaller, but significant, excess of inverted repeats that we report in protein coding sequences may be due to sequence-directed mutagenesis (SDM). SDM is a process where one copy of a small, imperfect, inverted repeat corrects the other copy via strand misalignment, resulting in a perfect repeat and a series of mutations. We show by simulation that even very low levels of SDM, relative to the rate of point mutation, can generate a substantial excess of inverted repeats.

  8. Genesis, effects and fates of repeats in prokaryotic genomes.

    PubMed

    Treangen, Todd J; Abraham, Anne-Laure; Touchon, Marie; Rocha, Eduardo P C

    2009-05-01

    DNA repeats are causes and consequences of genome plasticity. Repeats are created by intrachromosomal recombination or horizontal transfer. They are targeted by recombination processes leading to amplifications, deletions and rearrangements of genetic material. The identification and analysis of repeats in nearly 700 genomes of bacteria and archaea is facilitated by the existence of sequence data and adequate bioinformatic tools. These have revealed the immense diversity of repeats in genomes, from those created by selfish elements to the ones used for protection against selfish elements, from those arising from transient gene amplifications to the ones leading to stable duplications. Experimental works have shown that some repeats do not carry any adaptive value, while others allow functional diversification and increased expression. All repeats carry some potential to disorganize and destabilize genomes. Because recombination and selection for repeats vary between genomes, the number and types of repeats are also quite diverse and in line with ecological variables, such as host-dependent associations or population sizes, and with genetic variables, such as the recombination machinery. From an evolutionary point of view, repeats represent both opportunities and problems. We describe how repeats are created and how they can be found in genomes. We then focus on the functional and genomic consequences of repeats that dictate their fate.

  9. Studies of an expanded trinucleotide repeat in transgenic mice

    SciTech Connect

    Bingham, P.; Wang, S.; Merry, D.

    1994-09-01

    Spinal and bulbar muscular atrophy (SBMA) is a progressive motor neuron disease caused by expansion of a trinucleotide repeat in the androgen receptor gene (AR{sup exp}). AR{sup exp} repeats expand further or contract in approximately 25% of transmissions. Analogous {open_quotes}dynamic mutations{close_quotes} have been reported in other expanded trinucleotide repeat disorders. We have been developing a mouse model of this disease using a transgenic approach. Expression of the SBMA AR was documented in transgenic mice with an inducible promoter. No phenotypic effects of transgene expression were observed. We have extended our previous results on stability of the expanded trinucleotide repeat in transgenic mice in two lines carrying AR{sup exp}. Tail DNA was amplified by PCR using primers spanning the repeat on 60 AR{sup exp} transgenic mice from four different transgenic lines. Migration of the PCR product through an acrylamide gel showed no change of the 45 CAG repeat length in any progeny. Similarly, PCR products from 23 normal repeat transgenics showed no change from the repeat length of the original construct. Unlike the disease allele in humans, the expanded repeat AR cDNA in transgenic mice showed no change in repeat length with transmission. The relative stability of CAG repeats seen in the transgenic mice may indicate either differences in the fidelity of replicative enzymes, or differences in error identification and repair between mice and humans. Integration site or structural properties of the transgene itself might also play a role.

  10. Factors associated with HD CAG repeat instability in Huntington disease.

    PubMed

    Wheeler, V C; Persichetti, F; McNeil, S M; Mysore, J S; Mysore, S S; MacDonald, M E; Myers, R H; Gusella, J F; Wexler, N S

    2007-11-01

    The Huntington disease (HD) CAG repeat exhibits dramatic instability when transmitted to subsequent generations. The instability of the HD disease allele in male intergenerational transmissions is reflected in the variability of the CAG repeat in DNA from the sperm of male carriers of the HD gene. In this study, we used a collection of 112 sperm DNAs from male HD gene-positive members of a large Venezuelan cohort to investigate the factors associated with repeat instability. We confirm previous observations that CAG repeat length is the strongest predictor of repeat-length variability in sperm, but we did not find any correlation between CAG repeat instability and either age at the time of sperm donation or affectedness status. We also investigated transmission instability for 184 father-offspring and 311 mother-offspring pairs in this Venezuelan pedigree. Repeat-length changes were dependent upon the sex of the transmitting parent and parental CAG repeat length but not parental age or birth order. Unexpectedly, in maternal transmissions, repeat-length changes were also dependent upon the sex of the offspring, with a tendency for expansion in male offspring and contraction in female offspring. Significant sibling-sibling correlation for repeat instability suggests that genetic factors play a role in intergenerational CAG repeat instability.

  11. The effect of repeated testing vs repeated practice on skills learning in undergraduate dental education.

    PubMed

    Sennhenn-Kirchner, S; Goerlich, Y; Kirchner, B; Notbohm, M; Schiekirka, S; Simmenroth, A; Raupach, T

    2017-01-24

    Recent studies in undergraduate medical education have demonstrated the advantage of repeated testing over repeated practice with regard to knowledge and skills retention. The aim of this study was to investigate whether this "testing effect" also applies to skills retention in undergraduate dental education. In this prospective, randomised controlled trial, fourth-year dental students at Göttingen University Medical Centre participated in a training session on surgical suturing in winter term 2014/2015. Following this, they were either assigned to two sessions of additional skills training (group A) or two sessions of skills assessment with feedback (group B). These sessions were spaced over a period of 4 weeks. Skills retention was assessed in a summative objective structured clinical examination (OSCE) at the end of term, that is 6 months after the initial teaching session. A total of 32 students completed the study. With regard to suturing, OSCE performance was significantly better in group B than group A (81.9±13.1% vs 63.0±15.4%; P=0.001; Cohen's d=1.33). There was no significant OSCE performance difference in the two groups with regard to other learning objectives that were addressed in the end-of-term examination. Thus, the group difference was specific to suturing skills. This is the first study to demonstrate that in dental education, repeated testing produces more favourable skills retention than repeated practice. Test-enhanced learning might be a viable concept for skills retention in undergraduate dentistry education. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  12. Comparison of simple sequence repeats in 19 Archaea.

    PubMed

    Trivedi, S

    2006-12-05

    All organisms that have been studied until now have been found to have differential distribution of simple sequence repeats (SSRs), with more SSRs in intergenic than in coding sequences. SSR distribution was investigated in Archaea genomes where complete chromosome sequences of 19 Archaea were analyzed with the program SPUTNIK to find di- to penta-nucleotide repeats. The number of repeats was determined for the complete chromosome sequences and for the coding and non-coding sequences. Different from what has been found for other groups of organisms, there is an abundance of SSRs in coding regions of the genome of some Archaea. Dinucleotide repeats were rare and CG repeats were found in only two Archaea. In general, trinucleotide repeats are the most abundant SSR motifs; however, pentanucleotide repeats are abundant in some Archaea. Some of the tetranucleotide and pentanucleotide repeat motifs are organism specific. In general, repeats are short and CG-rich repeats are present in Archaea having a CG-rich genome. Among the 19 Archaea, SSR density was not correlated with genome size or with optimum growth temperature. Pentanucleotide density had an inverse correlation with the CG content of the genome.

  13. Evolution of subterminal satellite (StSat) repeats in hominids.

    PubMed

    Koga, Akihiko; Notohara, Morihiro; Hirai, Hirohisa

    2011-02-01

    Subterminal satellite (StSat) repeats, consisting of 32-bp-long AT-rich units (GATATTTCCATGTT(T/C)ATACAGATAGCGGTGTA), were first found in chimpanzee and gorilla (African great apes) as one of the major components of heterochromatic regions located proximal to telomeres of chromosomes. StSat repeats have not been found in orangutan (Asian great ape) or human. This patchy distribution among species suggested that the StSat repeats were present in the common ancestor of African great apes and subsequently lost in the lineage leading to human. An alternative explanation is that the StSat repeats in chimpanzee and gorilla have different origins and the repeats did not occur in human. The purpose of the present study was quantitative evaluation of the above alternative possibilities by analyzing the nucleotide variation contained in the repeats. We collected large numbers of sequences of repeat units from genome sequence databases of chimpanzee and gorilla, and also bonobo (an African great ape phylogenetically closer to chimpanzee). We then compared the base composition of the repeat units among the 3 species, and found statistically significant similarities in the base composition. These results support the view that the StSat repeats had already formed multiple arrays in the common ancestor of African great apes. It is thus suggested that humans lost StSat repeats which had once grown to multiple arrays.

  14. ATXN2 trinucleotide repeat length correlates with risk of ALS.

    PubMed

    Sproviero, William; Shatunov, Aleksey; Stahl, Daniel; Shoai, Maryam; van Rheenen, Wouter; Jones, Ashley R; Al-Sarraj, Safa; Andersen, Peter M; Bonini, Nancy M; Conforti, Francesca L; Van Damme, Philip; Daoud, Hussein; Del Mar Amador, Maria; Fogh, Isabella; Forzan, Monica; Gaastra, Ben; Gellera, Cinzia; Gitler, Aaron D; Hardy, John; Fratta, Pietro; La Bella, Vincenzo; Le Ber, Isabelle; Van Langenhove, Tim; Lattante, Serena; Lee, Yi-Chung; Malaspina, Andrea; Meininger, Vincent; Millecamps, Stéphanie; Orrell, Richard; Rademakers, Rosa; Robberecht, Wim; Rouleau, Guy; Ross, Owen A; Salachas, Francois; Sidle, Katie; Smith, Bradley N; Soong, Bing-Wen; Sorarù, Gianni; Stevanin, Giovanni; Kabashi, Edor; Troakes, Claire; van Broeckhoven, Christine; Veldink, Jan H; van den Berg, Leonard H; Shaw, Christopher E; Powell, John F; Al-Chalabi, Ammar

    2017-03-01

    We investigated a CAG trinucleotide repeat expansion in the ATXN2 gene in amyotrophic lateral sclerosis (ALS). Two new case-control studies, a British dataset of 1474 ALS cases and 567 controls, and a Dutch dataset of 1328 ALS cases and 691 controls were analyzed. In addition, to increase power, we systematically searched PubMed for case-control studies published after 1 August 2010 that investigated the association between ATXN2 intermediate repeats and ALS. We conducted a meta-analysis of the new and existing studies for the relative risks of ATXN2 intermediate repeat alleles of between 24 and 34 CAG trinucleotide repeats and ALS. There was an overall increased risk of ALS for those carrying intermediate sized trinucleotide repeat alleles (odds ratio 3.06 [95% confidence interval 2.37-3.94]; p = 6 × 10(-18)), with an exponential relationship between repeat length and ALS risk for alleles of 29-32 repeats (R(2) = 0.91, p = 0.0002). No relationship was seen for repeat length and age of onset or survival. In contrast to trinucleotide repeat diseases, intermediate ATXN2 trinucleotide repeat expansion in ALS does not predict age of onset but does predict disease risk.

  15. A theoretical model for the mechanical unfolding of repeat proteins.

    PubMed

    Makarov, Dmitrii E

    2009-03-18

    We consider the mechanical stretching of a polypeptide chain formed by multiple interacting repeats. The folding thermodynamics and the interactions among the repeats are described by the Ising model. Unfolded repeats act as soft entropic springs, whereas folded repeats respond to a force as stiffer springs. We show that the resulting force-extension curve may exhibit a pronounced force maximum corresponding to the unfolding of the first repeat. This event is followed by the unfolding of the remaining repeats, which takes place at a lower force. As the protein extension is increased, the force-extension curve of a sufficiently long repeat protein displays a plateau, where the force remains nearly constant and the protein unfolds sequentially so that the number of unfolded repeats is proportional to the extension. Such a sequential mechanical unfolding mechanism is displayed even by the repeat proteins whose thermal denaturation is highly cooperative, provided that they are long enough. By contrast, the unfolding of short repeat progressions can be cooperative.

  16. A Theoretical Model for the Mechanical Unfolding of Repeat Proteins

    PubMed Central

    Makarov, Dmitrii E.

    2009-01-01

    We consider the mechanical stretching of a polypeptide chain formed by multiple interacting repeats. The folding thermodynamics and the interactions among the repeats are described by the Ising model. Unfolded repeats act as soft entropic springs, whereas folded repeats respond to a force as stiffer springs. We show that the resulting force-extension curve may exhibit a pronounced force maximum corresponding to the unfolding of the first repeat. This event is followed by the unfolding of the remaining repeats, which takes place at a lower force. As the protein extension is increased, the force-extension curve of a sufficiently long repeat protein displays a plateau, where the force remains nearly constant and the protein unfolds sequentially so that the number of unfolded repeats is proportional to the extension. Such a sequential mechanical unfolding mechanism is displayed even by the repeat proteins whose thermal denaturation is highly cooperative, provided that they are long enough. By contrast, the unfolding of short repeat progressions can be cooperative. PMID:19289042

  17. PRIGSA: protein repeat identification by graph spectral analysis.

    PubMed

    Chakrabarty, Broto; Parekh, Nita

    2014-12-01

    Repetition of a structural motif within protein is associated with a wide range of structural and functional roles. In most cases the repeating units are well conserved at the structural level while at the sequence level, they are mostly undetectable suggesting the need for structure-based methods. Since most known methods require a training dataset, de novo approach is desirable. Here, we propose an efficient graph-based approach for detecting structural repeats in proteins. In a protein structure represented as a graph, interactions between inter- and intra-repeat units are well captured by the eigen spectra of adjacency matrix of the graph. These conserved interactions give rise to similar connections and a unique profile of the principal eigen spectra for each repeating unit. The efficacy of the approach is shown on eight repeat families annotated in UniProt, comprising of both solenoid and nonsolenoid repeats with varied secondary structure architecture and repeat lengths. The performance of the approach is also tested on other known benchmark datasets and the performance compared with two repeat identification methods. For a known repeat type, the algorithm also identifies the type of repeat present in the protein. A web tool implementing the algorithm is available at the URL http://bioinf.iiit.ac.in/PRIGSA/.

  18. Ataxin-2 repeat-length variation and neurodegeneration

    PubMed Central

    Ross, Owen A.; Rutherford, Nicola J.; Baker, Matt; Soto-Ortolaza, Alexandra I.; Carrasquillo, Minerva M.; DeJesus-Hernandez, Mariely; Adamson, Jennifer; Li, Ma; Volkening, Kathryn; Finger, Elizabeth; Seeley, William W.; Hatanpaa, Kimmo J.; Lomen-Hoerth, Catherine; Kertesz, Andrew; Bigio, Eileen H.; Lippa, Carol; Woodruff, Bryan K.; Knopman, David S.; White, Charles L.; Van Gerpen, Jay A.; Meschia, James F.; Mackenzie, Ian R.; Boylan, Kevin; Boeve, Bradley F.; Miller, Bruce L.; Strong, Michael J.; Uitti, Ryan J.; Younkin, Steven G.; Graff-Radford, Neill R.; Petersen, Ronald C.; Wszolek, Zbigniew K.; Dickson, Dennis W.; Rademakers, Rosa

    2011-01-01

    Expanded glutamine repeats of the ataxin-2 (ATXN2) protein cause spinocerebellar ataxia type 2 (SCA2), a rare neurodegenerative disorder. More recent studies have suggested that expanded ATXN2 repeats are a genetic risk factor for amyotrophic lateral sclerosis (ALS) via an RNA-dependent interaction with TDP-43. Given the phenotypic diversity observed in SCA2 patients, we set out to determine the polymorphic nature of the ATXN2 repeat length across a spectrum of neurodegenerative disorders. In this study, we genotyped the ATXN2 repeat in 3919 neurodegenerative disease patients and 4877 healthy controls and performed logistic regression analysis to determine the association of repeat length with the risk of disease. We confirmed the presence of a significantly higher number of expanded ATXN2 repeat carriers in ALS patients compared with healthy controls (OR = 5.57; P= 0.001; repeat length >30 units). Furthermore, we observed significant association of expanded ATXN2 repeats with the development of progressive supranuclear palsy (OR = 5.83; P= 0.004; repeat length >30 units). Although expanded repeat carriers were also identified in frontotemporal lobar degeneration, Alzheimer's and Parkinson's disease patients, these were not significantly more frequent than in controls. Of note, our study identified a number of healthy control individuals who harbor expanded repeat alleles (31–33 units), which suggests caution should be taken when attributing specific disease phenotypes to these repeat lengths. In conclusion, our findings confirm the role of ATXN2 as an important risk factor for ALS and support the hypothesis that expanded ATXN2 repeats may predispose to other neurodegenerative diseases, including progressive supranuclear palsy. PMID:21610160

  19. Repeated-sprint and effort ability in rugby league players.

    PubMed

    Johnston, Rich D; Gabbett, Tim J

    2011-10-01

    The aim of this study was to (a) investigate the influence of tackling on repeated-sprint performance; (b) determine whether repeated-sprint ability (RSA) and repeated-effort ability (REA) are 2 distinct qualities; and (c) assess the test-retest reliability of repeated-sprint and repeated-effort tests in rugby league. Twelve rugby league players performed a repeated-sprint (12 × 20-m sprints performed on a 20-second cycle) and a repeated-effort (12 × 20-m sprints with intermittent tackling, performed on a 20-second cycle) test 7 days apart. The test-retest reliability of these tests was also established. Heart rate and rating of perceived exertion were recorded throughout the tests. There was a significantly greater (p ≤ 0.05) and large effect size (ES) differences for total sprint time (ES = 1.19), average heart rate (ES = 1.64), peak heart rate (ES = 1.35), and perceived exertion (ES = 3.39) for the repeated-effort test compared with the repeated-sprint test. A large difference (ES = 1.02, p = 0.06) was detected for percentage decrement between the 2 tests. No significant relationship was found between the repeated-sprint and repeated-effort tests for any of the dependent variables. Both tests proved reliable, with total sprint time being the most reliable method of assessing performance. This study demonstrates that the addition of tackling significantly increases the physiological response to repeated-sprint exercise and reduces repeated-sprint performance in rugby league players. Furthermore, RSA and REA appear to be 2 distinct qualities that can be reliably assessed with total time being the most reliable measure of performance.

  20. The genomic landscape of rapid repeated evolutionary ...

    EPA Pesticide Factsheets

    Atlantic killifish populations have rapidly adapted to normally lethal levels of pollution in four urban estuaries. Through analysis of 384 whole killifish genome sequences and comparative transcriptomics in four pairs of sensitive and tolerant populations, we identify the aryl hydrocarbon receptor–based signaling pathway as a shared target of selection. This suggests evolutionary constraint on adaptive solutions to complex toxicant mixtures at each site. However, distinct molecular variants apparently contribute to adaptive pathway modification among tolerant populations. Selection also targets other toxicity-mediatinggenes and genes of connected signaling pathways; this indicates complex tolerance phenotypes and potentially compensatory adaptations. Molecular changes are consistent with selection on standing genetic variation. In killifish, high nucleotide diversityhas likely been a crucial substrate for selective sweeps to propel rapid adaptation. This manuscript describes genomic evaluations that contribute to our understanding of the ecological and evolutionary risks associated with chronic contaminant exposures to wildlife populations. Here, we assessed genetic patterns associated with long-term response to an important class of highly toxic environmental pollutants. Specifically, chemical-specific tolerance has rapidly and repeatedly evolved in an estuarine fish species resident to estuaries of the Atlantic U.S. coast. We used laboratory studies to ch

  1. Seafloor geodesy from repeated sidescan sonar surveys

    NASA Astrophysics Data System (ADS)

    DeSanto, John B.; Sandwell, David T.; Chadwell, C. David

    2016-07-01

    Accurate seafloor geodetic methods are critical to the study of marine natural hazards such as megathrust earthquakes, landslides, and volcanoes. We propose digital image correlation of repeated shipboard sidescan sonar surveys as a measurement of seafloor deformation. We test this method using multibeam surveys collected in two locales: 2500 m deep lightly sedimented seafloor on the flank of a spreading ridge and 4300 m deep heavily sedimented seafloor far from any plate boundary. Correlation of these surveys are able to recover synthetic displacements in the across-track (range) direction accurate to within 1 m and in the along-track (azimuth) direction accurate to within 1-10 m. We attribute these accuracies to the inherent resolution of sidescan data being better in the range dimension than the azimuth dimension. These measurements are primarily limited by the accuracy of the ship navigation. Dual-frequency GPS units are accurate to ˜10 cm, but single-frequency GPS units drift on the order of 1 m/h and are insufficient for geodetic application.

  2. Hydrological Modeling and Repeatability with Brokering

    NASA Astrophysics Data System (ADS)

    Easton, Z. M.; Collick, A.; Srinivasan, R.; Braeckel, A.; Nativi, S.; McAlister, C.; Wright, D. J.; Khalsa, S. J. S.; Fuka, D.

    2014-12-01

    Data brokering aims to provide those in the hydrological sciences with access to relevant data to represent physical, biological, and chemical characteristics researchers need to accelerate discovery in their domain. Environmental models are useful tools to understand the behavior of hydrological systems. Unfortunately, parameterization of these models requires many different data sources from different disciplines (e.g., atmospheric, geoscience, ecology). In hydrological modeling, the traditional procedure for model initialization starts with obtaining elevation models, land-use characterizations, soils maps, and weather data. It is often the researcher's past experience with these datasets that determines which datasets will be used in a study, and often newer, more suitable data products exist. An added complexity is that various science communities have differing data formats, storage protocols and manipulation methods, which makes use by a non domain scientist difficult and time consuming. We propose data brokering as a means to address several of these challenges. We present two test case scenarios in which researchers attempt to reproduce hydrological model results using 1) general internet based data gathering techniques, and 2) a scientific data brokering interface. We show that data brokering increases the efficiency with which data are collected, models are initialized, and results are analyzed. As an added benefit, it appears brokering significantly increases the repeatability of a study.

  3. Repeatability of sonographic measurements in clubfeet.

    PubMed

    Aurell, Y; Adlercreutz, C; Andriesse, H; Jonsson, K

    2004-10-01

    To assess the intra- and interobserver agreement of ultrasound assessment of clubfoot patho-anatomy in early childhood. Seventeen clubfeet in 12 children were sequentially scanned by 2 examiners and repeat assessments were carried out independently. Three well-defined imaging planes were chosen to evaluate navicular displacement: the medial malleolus-navicular (MM-N) distance, soft tissue thickness, talar deformity and the calcaneo-cuboid (C-C) distance. Intra- and interobserver agreement was analysed using Cohen's kappa for the discrete variables and by Bland-Altman's graphic technique for measurements. Kappa values for intra-observer agreement were 0.82 for navicular displacement, 0.93 for "talar head pointing laterally", and 0.70 for medial deviation of the talar neck. The corresponding interobserver kappa values were 0.70, 0.68, and 0.36. The mean difference between the two observers for the MM-N distance was 0.42 +/- 3.0 mm and for the soft tissue thickness 0.35 +/- 2.0 mm; the C-C distance showed a mean interobserver distance of 0.0 +/- 2.8 mm. The imaging planes used to study the talo-navicular and calcaneo-cuboid relationships are reproducible and relatively easy to learn. Intra- and interobserver assessments were acceptable for MM-N distance, soft tissue thickness, navicular displacement and "talar head pointing laterally", but questionable for the C-C distance and medial deviation of the talar neck.

  4. Power Line Integrity Monitor and Repeater

    SciTech Connect

    Svoboda, John

    2005-09-30

    The Idaho National Laboratory (INL) has developed a power system integrity monitor and repeater that provide real time status of the integrity of the physical structure of power poles and transmission towers. It may be applied to other structures, such as pipelines or cell towers, which have multiple segments that can cover hundreds of miles. Sensors and on-board processing provide indication of tampering or impending damage to the structure with information provided to the central operations center or supervisory control and data acquisition (SCADA) for mitigative actions. This software runs on a series of small, inexpensive, low power electronic sensor platforms that are mounted on each tower of an electric power transmission or distribution system for the purpose of communicating system integrity to a central location. The software allows each platform to: 1) interface with sensors that monitor tower integrity, 2) record and analyze events, 3) communicate sensor information to other sensor platforms located on adjacent towers or to a central monitoring location, and 4) derive, conserve, and store platform power from the transmission of electric power.

  5. Repeated learning makes cultural evolution unique

    PubMed Central

    Strimling, Pontus; Enquist, Magnus; Eriksson, Kimmo

    2009-01-01

    Although genetic information is acquired only once, cultural information can be both abandoned and reacquired during an individual's lifetime. Therefore, cultural evolution will be determined not only by cultural traits' ability to spread but also by how good they are at sticking with an individual; however, the evolutionary consequences of this aspect of culture have not previously been explored. Here we show that repeated learning and multiple characteristics of cultural traits make cultural evolution unique, allowing dynamical phenomena we can recognize as specifically cultural, such as traits that both spread quickly and disappear quickly. Importantly, the analysis of our model also yields a theoretical objection to the popular suggestion that biological and cultural evolution can be understood in similar terms. We find that the possibility to predict long-term cultural evolution by some success index, analogous to biological fitness, depends on whether individuals have few or many opportunities to learn. If learning opportunities are few, we find that the existence of a success index may be logically impossible, rendering notions of “cultural fitness” meaningless. On the other hand, if individuals can learn many times, we find a success index that works, regardless of whether the transmission pattern is vertical, oblique, or horizontal. PMID:19666615

  6. Autonomy facilitates repeated maximum force productions.

    PubMed

    Iwatsuki, Takehiro; Abdollahipour, Reza; Psotta, Rudolf; Lewthwaite, Rebecca; Wulf, Gabriele

    2017-08-30

    Performer autonomy (or self-control) has consistently been shown to enhance motor learning, and it can also provide immediate benefits for motor performance. Autonomy is also a key variable in the OPTIMAL theory of motor learning (Wulf & Lewthwaite, 2016). It is assumed to contribute to enhanced expectancies and goal-action coupling, affecting performance effectiveness and efficiency. The purpose of the present study was to examine whether providing autonomy support by giving performers choices would enhance their ability to maintain maximum force levels. Participants were asked to repeatedly produce maximum forces using a hand dynamometer. After 2 initial trials with the dominant and non-dominant hand, stratified randomization was used to assign participants with the same average maximum force to one of two groups, choice or yoked control groups. Choice group participants were able to choose the order of hands (dominant, non-dominant) on the remaining trials (3 per hand). For control group participants, hand order was determined by choice-group counterparts. Maximum forces decreased significantly across trials in the control group, whereas choice group participants were able to maintain the maximum forces produced on the first trial. We interpret these findings as evidence that performer autonomy promotes movement efficiency. The results are in line with the view that autonomy facilitates the coupling of goals and actions (Wulf & Lewthwaite, 2016). Copyright © 2017 Elsevier B.V. All rights reserved.

  7. Superfamily of ankyrin repeat proteins in tomato.

    PubMed

    Yuan, Xiaowei; Zhang, Shizhong; Qing, Xiaohe; Sun, Meihong; Liu, Shiyang; Su, Hongyan; Shu, Huairui; Li, Xinzheng

    2013-07-10

    The ankyrin repeat (ANK) protein family plays a crucial role in plant growth and development and in response to biotic and abiotic stresses. However, no detailed information concerning this family is available for tomato (Solanum lycopersicum) due to the limited information on whole genome sequences. In this study, we identified a total of 130 ANK genes in tomato genome (SlANK), and these genes were distributed across all 12 chromosomes at various densities. And chromosomal localizations of SlANK genes indicated 25 SlANK genes were involved in tandem duplications. Based on their domain composition, all of the SlANK proteins were grouped into 13 subgroups. A combined phylogenetic tree was constructed with the aligned SlANK protein sequences. This tree revealed that the SlANK proteins comprise five major groups. An analysis of the expression profiles of SlANK genes in tomato in different tissues and in response to stresses showed that the SlANK proteins play roles in plant growth, development and stress responses. To our knowledge, this is the first report of a genome-wide analysis of the tomato ANK gene family. This study provides valuable information regarding the classification and putative functions of SlANK genes in tomato.

  8. Repeat mitral valve replacement: 30-years' experience.

    PubMed

    Expósito, Víctor; García-Camarero, Tamara; Bernal, José M; Arnáiz, Elena; Sarralde, Aurelio; García, Iván; Berrazueta, José R; Revuelta, José M

    2009-08-01

    Prosthetic heart valve dysfunction is an acquired condition that carries a significant risk of emergency surgery. However, the long-term natural history of the condition is not well understood. Between 1974 and 2006, 1535 isolated mitral valve replacements were performed at our hospital (in-hospital mortality 5%). In total, 369 patients needed a second operation (in-hospital mortality 8.1%), while 80 (age 59.8+/-11.4 years) needed a third. The reasons for the third intervention were structural deterioration (67.5%), paravalvular leak (20%) and endocarditis (6.3%). Some 15 patients died in hospital (18.8%). After a mean follow-up period of 17.8 years, 21 patients needed another intervention (i.e., a fourth intervention). The actuarial reoperation-free rate at 20 years was 40.1+/-13.8%. The late mortality rate was 58.5% (18-year survival rate 15.4+/-5.4%). Indications for repeat mitral valve replacement must be judged on an individual basis given the high risk associated with surgery.

  9. Regeneration of Human Liver After Hepatic Lobectomy Studied by Repeated Liver Scanning and Repeated Needle Biopsy

    PubMed Central

    Lin, Tien-Yu; Lee, Chue-Shue; Chen, Chiou-Chiang; Liau, Kuong-Yi; Lin, Wen-Shih-Jen

    1979-01-01

    Regeneration of the residual lobe of the liver after hepatic lobectomy in humans was studied by repeated liver scanning in seven noncirrhotic and three cirrhotic patients. Each patient was studied for several months during the study which lasted from 1-12 years. Regeneration was apparent in noncirrhotic liver remnants following hepatic lobectomy. In the case of a long standing, space occupying lesions such as benign giant cysts, the liver remnant would complete its regeneration process rather early, usually within a few months of hepatic lobectomy. In hepatoma cases, however, regeneration of the residual lobe after hepatic resection usually took five or six months for completion. On the contrary, no definite increase in the size of the liver remnant was seen on repeated liver scanning in cirrhotic patients. Histologic study of the residual lobe was repeated on needle biopsy specimens in two noncirrhotic and four cirrhotic patients. Regenerative hyperplasia of liver cells with large hyperchromatic, or double nuclei never seen in the preresection liver appeared in the liver remnant five, 11, and 27 days after hepatic lobectomy in noncirrhotic patients. In cirrhotics, however, there were no histologic changes between the preresection liver and the postresection remnant studied three, five, 15, 40 days or even two years and 8 months after hepatic lobectomy. ImagesFig. 1.Fig. 2.Fig. 3.Fig. 4.Fig. 5.Fig. 6. PMID:464678

  10. Genomic DNA repeat from Leishmania (Viannia) braziliensis (Venezuelan strain) containing simple repeats and microsatellites.

    PubMed

    Rodriguez, N; De Lima, H; Rodriguez, A; Brewster, S; Barker, D C

    1997-10-01

    In this paper the Leishmania (Viannia) braziliensis complex is defined as containing all species of the actual subgenus Viannia. Organisms of the L. (V) braziliensis complex are the causative agents of localized human cutaneous and mucocutaneous leishmaniasis in South America, much of Central America and some ares of North America. In our search for better species and subspecies diagnostic probes we focused our research on repetitive DNA, since it provides a greater number of target sites for hybridization. In this work we report the isolation and sequencing of a 1.8 kb DNA region, LbJ38, which is probably tandemly repeated or dispersed at least 4 times along one chromosome and is naturally present in L. (V) braziliensis genomic DNA. This region contains microsatellites and simple repeat DNA sequences and was isolated by screening a genomic DNA cosmid library with complex- and species-specific probes. No homology was found with other Leishmania microsatellite or repetitive DNA. The utility of this repetitive sequence and primers derived from it in the identification of L. (V) braziliensis is demonstrated. As far as we are aware, this is the first report of sequence characterized repetitive microsatellite and GC rich simple repeat DNA from the nuclear genome of New World Leishmania.

  11. Hypoxic Repeat Sprint Training Improves Rugby Player's Repeated Sprint but Not Endurance Performance

    PubMed Central

    Hamlin, Michael J.; Olsen, Peter D.; Marshall, Helen C.; Lizamore, Catherine A.; Elliot, Catherine A.

    2017-01-01

    This study aims to investigate the performance changes in 19 well-trained male rugby players after repeat-sprint training (six sessions of four sets of 5 × 5 s sprints with 25 s and 5 min of active recovery between reps and sets, respectively) in either normobaric hypoxia (HYP; n = 9; FIO2 = 14.5%) or normobaric normoxia (NORM; n = 10; FIO2 = 20.9%). Three weeks after the intervention, 2 additional repeat-sprint training sessions in hypoxia (FIO2 = 14.5%) was investigated in both groups to gauge the efficacy of using “top-up” sessions for previously hypoxic-trained subjects and whether a small hypoxic dose would be beneficial for the previously normoxic-trained group. Repeated sprint (8 × 20 m) and Yo-Yo Intermittent Recovery Level 1 (YYIR1) performances were tested twice at baseline (Pre 1 and Pre 2) and weekly after (Post 1–3) the initial intervention (intervention 1) and again weekly after the second “top-up” intervention (Post 4–5). After each training set, heart rate, oxygen saturation, and rate of perceived exertion were recorded. Compared to baseline (mean of Pre 1 and Pre 2), both the hypoxic and normoxic groups similarly lowered fatigue over the 8 sprints 1 week after the intervention (Post 1: −1.8 ± 1.6%, −1.5 ± 1.4%, mean change ± 90% CI in HYP and NORM groups, respectively). However, from Post 2 onwards, only the hypoxic group maintained the performance improvement compared to baseline (Post 2: −2.1 ± 1.8%, Post 3: −2.3 ± 1.7%, Post 4: −1.9 ± 1.8%, and Post 5: −1.2 ± 1.7%). Compared to the normoxic group, the hypoxic group was likely to have substantially less fatigue at Post 3–5 (−2.0 ± 2.4%, −2.2 ± 2.4%, −1.6 ± 2.4% Post 3, Post 4, Post 5, respectively). YYIR1 performances improved throughout the recovery period in both groups (13–37% compared to baseline) with unclear differences found between groups. The addition of two sessions of “top-up” training after intervention 1, had little effect on either

  12. Improving repeated sprint ability in young elite soccer players: repeated shuttle sprints vs. explosive strength training.

    PubMed

    Buchheit, Martin; Mendez-Villanueva, Alberto; Delhomel, Gregory; Brughelli, Matt; Ahmaidi, Said

    2010-10-01

    To compare the effects of explosive strength (ExpS) vs. repeated shuttle sprint (RS) training on repeated sprint ability (RSA) in young elite soccer players, 15 elite male adolescents (14.5 ± 0.5 years) performed, in addition to their soccer training program, RS (n = 7) or ExpS (n = 8) training once a week for a total of 10 weeks. RS training consisted of 2-3 sets of 5-6 × 15- to 20-m repeated shuttle sprints interspersed with 14 seconds of passive or 23 seconds of active recovery (≈2 m·s⁻¹); ExpS training consisted of 4-6 series of 4-6 exercises (e.g., maximal unilateral countermovement jumps (CMJs), calf and squat plyometric jumps, and short sprints). Before and after training, performance was assessed by 10 and 30 m (10 and 30 m) sprint times, best (RSAbest) and mean (RSAmean) times on a repeated shuttle sprint ability test, a CMJ, and a hopping (Hop) test. After training, except for 10 m (p = 0.22), all performances were significantly improved in both groups (all p's < 0.05). Relative changes in 30 m (-2.1 ± 2.0%) were similar for both groups (p = 0.45). RS training induced greater improvement in RSAbest (-2.90 ± 2.1 vs. -0.08 ± 3.3%, p = 0.04) and tended to enhance RSAmean more (-2.61 ± 2.8 vs. -0.75 ± 2.5%, p = 0.10, effect size [ES] = 0.70) than ExpS. In contrast, ExpS tended to induce greater improvements in CMJ (14.8 ± 7.7 vs. 6.8 ± 3.7%, p = 0.02) and Hop height (27.5 ± 19.2 vs. 13.5 ± 13.2%, p = 0.08, ES = 0.9) compared with RS. Improvements in the repeated shuttle sprint test were only observed after RS training, whereas CMJ height was only increased after ExpS. Because RS and ExpS were equally efficient at enhancing maximal sprinting speed, RS training-induced improvements in RSA were likely more related to progresses in the ability to change direction.

  13. Hypoxic Repeat Sprint Training Improves Rugby Player's Repeated Sprint but Not Endurance Performance.

    PubMed

    Hamlin, Michael J; Olsen, Peter D; Marshall, Helen C; Lizamore, Catherine A; Elliot, Catherine A

    2017-01-01

    This study aims to investigate the performance changes in 19 well-trained male rugby players after repeat-sprint training (six sessions of four sets of 5 × 5 s sprints with 25 s and 5 min of active recovery between reps and sets, respectively) in either normobaric hypoxia (HYP; n = 9; FIO2 = 14.5%) or normobaric normoxia (NORM; n = 10; FIO2 = 20.9%). Three weeks after the intervention, 2 additional repeat-sprint training sessions in hypoxia (FIO2 = 14.5%) was investigated in both groups to gauge the efficacy of using "top-up" sessions for previously hypoxic-trained subjects and whether a small hypoxic dose would be beneficial for the previously normoxic-trained group. Repeated sprint (8 × 20 m) and Yo-Yo Intermittent Recovery Level 1 (YYIR1) performances were tested twice at baseline (Pre 1 and Pre 2) and weekly after (Post 1-3) the initial intervention (intervention 1) and again weekly after the second "top-up" intervention (Post 4-5). After each training set, heart rate, oxygen saturation, and rate of perceived exertion were recorded. Compared to baseline (mean of Pre 1 and Pre 2), both the hypoxic and normoxic groups similarly lowered fatigue over the 8 sprints 1 week after the intervention (Post 1: -1.8 ± 1.6%, -1.5 ± 1.4%, mean change ± 90% CI in HYP and NORM groups, respectively). However, from Post 2 onwards, only the hypoxic group maintained the performance improvement compared to baseline (Post 2: -2.1 ± 1.8%, Post 3: -2.3 ± 1.7%, Post 4: -1.9 ± 1.8%, and Post 5: -1.2 ± 1.7%). Compared to the normoxic group, the hypoxic group was likely to have substantially less fatigue at Post 3-5 (-2.0 ± 2.4%, -2.2 ± 2.4%, -1.6 ± 2.4% Post 3, Post 4, Post 5, respectively). YYIR1 performances improved throughout the recovery period in both groups (13-37% compared to baseline) with unclear differences found between groups. The addition of two sessions of "top-up" training after intervention 1, had little effect on either group. Repeat-sprint training in

  14. Repeating microearthquake sequences interact predominantly through postseismic slip.

    PubMed

    Lui, Semechah K Y; Lapusta, Nadia

    2016-10-05

    Studying small repeating earthquakes enables better understanding of fault physics and characterization of fault friction properties. Some of the nearby repeating sequences appear to interact, such as the 'San Francisco' and 'Los Angeles' repeaters on the creeping section of the San Andreas Fault. It is typically assumed that such interactions are induced by static stress changes due to coseismic slip. Here we present a study of the interaction of repeating earthquakes in the framework of rate-and-state fault models using state-of-the-art simulation methods that reproduce both realistic seismic events and long-term earthquake sequences. Our simulations enable comparison among several types of stress transfer that occur between the repeating events. Our major finding is that postseismic creep dominates the interaction, with earthquake triggering occurring at distances much larger than typically assumed. Our results open a possibility of using interaction of repeating sequences to constrain friction properties of creeping segments.

  15. Survey of simple sequence repeats in woodland strawberry (Fragaria vesca).

    PubMed

    Guan, L; Huang, J F; Feng, G Q; Wang, X W; Wang, Y; Chen, B Y; Qiao, Y S

    2013-07-30

    The use of simple sequence repeats (SSRs), or microsatellites, as genetic markers has become popular due to their abundance and variation in length among individuals. In this study, we investigated linkage groups (LGs) in the woodland strawberry (Fragaria vesca) and demonstrated variation in the abundances, densities, and relative densities of mononucleotide, dinucleotide, and trinucleotide repeats. Mononucleotide, dinucleotide, and trinucleotide repeats were more common than longer repeats in all LGs examined. Perfect SSRs were the predominant SSR type found and their abundance was extremely stable among LGs and chloroplasts. Abundances of mononucleotide, dinucleotide, and trinucleotide repeats were positively correlated with LG size, whereas those of tetranucleotide and hexanucleotide SSRs were not. Generally, in each LG, the abundance, relative abundance, relative density, and the proportion of each unique SSR all declined rapidly as the repeated unit increased. Furthermore, the lengths and frequencies of SSRs varied among different LGs.

  16. An Expanded CAG Repeat in Huntingtin Causes +1 Frameshifting.

    PubMed

    Saffert, Paul; Adamla, Frauke; Schieweck, Rico; Atkins, John F; Ignatova, Zoya

    2016-08-26

    Maintenance of triplet decoding is crucial for the expression of functional protein because deviations either into the -1 or +1 reading frames are often non-functional. We report here that expression of huntingtin (Htt) exon 1 with expanded CAG repeats, implicated in Huntington pathology, undergoes a sporadic +1 frameshift to generate from the CAG repeat a trans-frame AGC repeat-encoded product. This +1 recoding is exclusively detected in pathological Htt variants, i.e. those with expanded repeats with more than 35 consecutive CAG codons. An atypical +1 shift site, UUC C at the 5' end of CAG repeats, which has some resemblance to the influenza A virus shift site, triggers the +1 frameshifting and is enhanced by the increased propensity of the expanded CAG repeats to form a stem-loop structure. The +1 trans-frame-encoded product can directly influence the aggregation of the parental Htt exon 1.

  17. Repeats in transforming acidic coiled-coil (TACC) genes.

    PubMed

    Trivedi, Seema

    2013-06-01

    Transforming acidic coiled-coil proteins (TACC1, 2, and 3) are essential proteins associated with the assembly of spindle microtubules and maintenance of bipolarity. Dysregulation of TACCs is associated with tumorigenesis, but studies of microsatellite instability in TACC genes have not been extensive. Microsatellite or simple sequence repeat instability is known to cause many types of cancer. The present in silico analysis of SSRs in human TACC gene sequences shows the presence of mono- to hexa-nucleotide repeats, with the highest densities found for mono- and di-nucleotide repeats. Density of repeats is higher in introns than in exons. Some of the repeats are present in regulatory regions and retained introns. Human TACC genes show conservation of many repeat classes. Microsatellites in TACC genes could be valuable markers for monitoring numerical chromosomal aberrations and or cancer.

  18. Modal sensitivity for structural systems with repeated frequencies

    NASA Technical Reports Server (NTRS)

    Ojalvo, I. U.

    1987-01-01

    Repeated or closely packed modal frequencies are common physical occurrences for vibrating structures which are complex or possess multi-planes of symmetry. The computation of the sensitivity to structural modifications for these frequencies and mode shapes is made difficult by the fact that the mode shapes are not unique, since any linear combination of eigenvectors corresponding to a repeated eigenvalue is also an eigenvector. The work of Chen and Pan is extended, who used modal expansion techniques for accommodating the sensitivity analysis of structures with repeated eigenvalues. Starting with a discussion of the physical significance of sensitivity analysis for repeated frequency modes, a derivation is presented of the governing equations for the derivatives of a repeated eigenvalue. This is followed with a small example to illustrate the results. An efficient computation procedure, based upon an expansion of Nelson's ideas for large banded systems, is then proposed for systems with repeated or closely spaced eigenvalues.

  19. Repeating microearthquake sequences interact predominantly through postseismic slip

    PubMed Central

    Lui, Semechah K. Y.; Lapusta, Nadia

    2016-01-01

    Studying small repeating earthquakes enables better understanding of fault physics and characterization of fault friction properties. Some of the nearby repeating sequences appear to interact, such as the ‘San Francisco' and ‘Los Angeles' repeaters on the creeping section of the San Andreas Fault. It is typically assumed that such interactions are induced by static stress changes due to coseismic slip. Here we present a study of the interaction of repeating earthquakes in the framework of rate-and-state fault models using state-of-the-art simulation methods that reproduce both realistic seismic events and long-term earthquake sequences. Our simulations enable comparison among several types of stress transfer that occur between the repeating events. Our major finding is that postseismic creep dominates the interaction, with earthquake triggering occurring at distances much larger than typically assumed. Our results open a possibility of using interaction of repeating sequences to constrain friction properties of creeping segments. PMID:27703151

  20. Repeating microearthquake sequences interact predominantly through postseismic slip

    NASA Astrophysics Data System (ADS)

    Lui, Semechah K. Y.; Lapusta, Nadia

    2016-10-01

    Studying small repeating earthquakes enables better understanding of fault physics and characterization of fault friction properties. Some of the nearby repeating sequences appear to interact, such as the `San Francisco' and `Los Angeles' repeaters on the creeping section of the San Andreas Fault. It is typically assumed that such interactions are induced by static stress changes due to coseismic slip. Here we present a study of the interaction of repeating earthquakes in the framework of rate-and-state fault models using state-of-the-art simulation methods that reproduce both realistic seismic events and long-term earthquake sequences. Our simulations enable comparison among several types of stress transfer that occur between the repeating events. Our major finding is that postseismic creep dominates the interaction, with earthquake triggering occurring at distances much larger than typically assumed. Our results open a possibility of using interaction of repeating sequences to constrain friction properties of creeping segments.

  1. Tandem repeats discovery service (TReaDS) applied to finding novel cis-acting factors in repeat expansion diseases

    PubMed Central

    2012-01-01

    Background Tandem repeats are multiple duplications of substrings in the DNA that occur contiguously, or at a short distance, and may involve some mutations (such as substitutions, insertions, and deletions). Tandem repeats have been extensively studied also for their association with the class of repeat expansion diseases (mostly affecting the nervous system). Comparative studies on the output of different tools for finding tandem repeats highlighted significant differences among the sets of detected tandem repeats, while many authors pointed up how critical it is the right choice of parameters. Results In this paper we present TReaDS - Tandem Repeats Discovery Service, a tandem repeat meta search engine. TReaDS forwards user requests to several state of the art tools for finding tandem repeats and merges their outcome into a single report, providing a global, synthetic, and comparative view of the results. In particular, TReaDS allows the user to (i) simultaneously run different algorithms on the same data set, (ii) choose for each algorithm a different setting of parameters, and (iii) obtain a report that can be downloaded for further, off-line, investigations. We used TReaDS to investigate sequences associated with repeat expansion diseases. Conclusions By using the tool TReaDS we discover that, for 27 repeat expansion diseases out of a currently known set of 29, long fuzzy tandem repeats are covering the expansion loci. Tests with control sets confirm the specificity of this association. This finding suggests that long fuzzy tandem repeats can be a new class of cis-acting elements involved in the mechanisms leading to the expansion instability. We strongly believe that biologists can be interested in a tool that, not only gives them the possibility of using multiple search algorithm at the same time, with the same effort exerted in using just one of the systems, but also simplifies the burden of comparing and merging the results, thus expanding our

  2. Swelfe: a detector of internal repeats in sequences and structures.

    PubMed

    Abraham, Anne-Laure; Rocha, Eduardo P C; Pothier, Joël

    2008-07-01

    Intragenic duplications of genetic material have important biological roles because of their protein sequence and structural consequences. We developed Swelfe to find internal repeats at three levels. Swelfe quickly identifies statistically significant internal repeats in DNA and amino acid sequences and in 3D structures using dynamic programming. The associated web server also shows the relationships between repeats at each level and facilitates visualization of the results. http://bioserv.rpbs.jussieu.fr/swelfe. Supplementary data are available at Bioinformatics online.

  3. Diverse functions of WD40 repeat proteins in histone recognition

    PubMed Central

    Suganuma, Tamaki; Pattenden, Samantha G.; Workman, Jerry L.

    2008-01-01

    WD40 repeat proteins have been shown to bind the histone H3 tail at the center of their β-propeller structure. In contrast, in this issue of Genes & Development, Song and colleagues (pp. 1313–1318) demonstrate that the WD40 repeat protein p55 binds a structured region of H4 through a novel binding pocket on the side of β-propeller, illustrating a diversity of histone recognition by WD40 repeat proteins. PMID:18483215

  4. Repeated fecal microbiota transplantation in a child with ulcerative colitis.

    PubMed

    Shimizu, Hirotaka; Arai, Katsuhiro; Abe, Jun; Nakabayashi, Kazuhiko; Yoshioka, Takako; Hosoi, Kenji; Kuroda, Makoto

    2016-08-01

    We report the case of an 11-year-old girl with ulcerative colitis refractory to conventional therapy, who was subsequently treated successfully with repeated fecal microbiota transplantation (FMT). The patient was steroid dependent despite several infliximab treatments, and colectomy was proposed to improve quality of life. After repeated FMT, she was able to maintain remission with on minimal dose of steroid. Although her fecal microbiota was dysbiotic before FMT, it was restored to a similar pattern as the donor after repeated FMT.

  5. Comparative Genomics and Molecular Dynamics of DNA Repeats in Eukaryotes

    PubMed Central

    Richard, Guy-Franck; Kerrest, Alix; Dujon, Bernard

    2008-01-01

    Summary: Repeated elements can be widely abundant in eukaryotic genomes, composing more than 50% of the human genome, for example. It is possible to classify repeated sequences into two large families, “tandem repeats” and “dispersed repeats.” Each of these two families can be itself divided into subfamilies. Dispersed repeats contain transposons, tRNA genes, and gene paralogues, whereas tandem repeats contain gene tandems, ribosomal DNA repeat arrays, and satellite DNA, itself subdivided into satellites, minisatellites, and microsatellites. Remarkably, the molecular mechanisms that create and propagate dispersed and tandem repeats are specific to each class and usually do not overlap. In the present review, we have chosen in the first section to describe the nature and distribution of dispersed and tandem repeats in eukaryotic genomes in the light of complete (or nearly complete) available genome sequences. In the second part, we focus on the molecular mechanisms responsible for the fast evolution of two specific classes of tandem repeats: minisatellites and microsatellites. Given that a growing number of human neurological disorders involve the expansion of a particular class of microsatellites, called trinucleotide repeats, a large part of the recent experimental work on microsatellites has focused on these particular repeats, and thus we also review the current knowledge in this area. Finally, we propose a unified definition for mini- and microsatellites that takes into account their biological properties and try to point out new directions that should be explored in a near future on our road to understanding the genetics of repeated sequences. PMID:19052325

  6. Assembly of Repeat Content Using Next Generation Sequencing Data

    SciTech Connect

    labutti, Kurt; Kuo, Alan; Grigoriev, Igor; Copeland, Alex

    2014-03-17

    Repetitive organisms pose a challenge for short read assembly, and typically only unique regions and repeat regions shorter than the read length, can be accurately assembled. Recently, we have been investigating the use of Pacific Biosciences reads for de novo fungal assembly. We will present an assessment of the quality and degree of repeat reconstruction possible in a fungal genome using long read technology. We will also compare differences in assembly of repeat content using short read and long read technology.

  7. Artificial leucine rich repeats as new scaffolds for protein design.

    PubMed

    Baabur-Cohen, Hemda; Dayalan, Subashini; Shumacher, Inbal; Cohen-Luria, Rivka; Ashkenasy, Gonen

    2011-04-15

    The leucine rich repeat (LRR) motif that participates in many biomolecular recognition events in cells was suggested as a general scaffold for producing artificial receptors. We describe here the design and first total chemical synthesis of small LRR proteins, and their structural analysis. When evaluating the tertiary structure as a function of different number of repeating units (1-3), we were able to find that the 3-repeats sequence, containing 90 amino acids, folds into the expected structure.

  8. Polyglutamine expansion diseases: More than simple repeats.

    PubMed

    Silva, Alexandra; de Almeida, Ana Viana; Macedo-Ribeiro, Sandra

    2017-09-18

    Polyglutamine (polyQ) repeat-containing proteins are widespread in the human proteome but only nine of them are associated with highly incapacitating neurodegenerative disorders. The genetic expansion of the polyQ tract in disease-related proteins triggers a series of events resulting in neurodegeneration. The polyQ tract plays the leading role in the aggregation mechanism, but other elements modulate the aggregation propensity in the context of the full-length proteins, as implied by variations in the length of the polyQ tract required to trigger the onset of a given polyQ disease. Intrinsic features such as the presence of aggregation-prone regions (APRs) outside the polyQ segments and polyQ-flanking sequences, which synergistically participate in the aggregation process, are emerging for several disease-related proteins. The inherent polymorphic structure of polyQ stretches places the polyQ proteins in a central position in protein-protein interaction networks, where interacting partners may additionally shield APRs or reshape the aggregation course. Expansion of the polyQ tract perturbs the cellular homeostasis and contributes to neuronal failure by modulating protein-protein interactions and enhancing toxic oligomerization. Post-translational modifications further regulate self-assembly either by directly altering the intrinsic aggregation propensity of polyQ proteins, by modulating their interaction with different macromolecules or by modifying their withdrawal by the cell quality control machinery. Here we review the recent data on the multifaceted aggregation pathways of disease-related polyQ proteins, focusing on ataxin-3, the protein mutated in Machado-Joseph disease. Further mechanistic understanding of this network of events is crucial for the development of effective therapies for polyQ diseases. Copyright © 2017 Elsevier Inc. All rights reserved.

  9. Long terminal repeat retrotransposons of Oryza sativa

    PubMed Central

    McCarthy, Eugene M; Liu, Jingdong; Lizhi, Gao; McDonald, John F

    2002-01-01

    Background Long terminal repeat (LTR) retrotransposons constitute a major fraction of the genomes of higher plants. For example, retrotransposons comprise more than 50% of the maize genome and more than 90% of the wheat genome. LTR retrotransposons are believed to have contributed significantly to the evolution of genome structure and function. The genome sequencing of selected experimental and agriculturally important species is providing an unprecedented opportunity to view the patterns of variation existing among the entire complement of retrotransposons in complete genomes. Results Using a new data-mining program, LTR_STRUC, (LTR retrotransposon structure program), we have mined the GenBank rice (Oryza sativa) database as well as the more extensive (259 Mb) Monsanto rice dataset for LTR retrotransposons. Almost two-thirds (37) of the 59 families identified consist of copia-like elements, but gypsy-like elements outnumber copia-like elements by a ratio of approximately 2:1. At least 17% of the rice genome consists of LTR retrotransposons. In addition to the ubiquitous gypsy- and copia-like classes of LTR retrotransposons, the rice genome contains at least two novel families of unusually small, non-coding (non-autonomous) LTR retrotransposons. Conclusions Each of the major clades of rice LTR retrotransposons is more closely related to elements present in other species than to the other clades of rice elements, suggesting that horizontal transfer may have occurred over the evolutionary history of rice LTR retrotransposons. Like LTR retrotransposons in other species with relatively small genomes, many rice LTR retrotransposons are relatively young, indicating a high rate of turnover. PMID:12372141

  10. [Repeated head injury during judo practice].

    PubMed

    Fujiwara, Kazue

    2014-01-01

    Mild traumatic brain injuries, if repeated, can cause permanent brain damage, or even death. I examined five published documents(three judicial decisions, one official injury report, and one book)to analyze incidents in which high school students who, while practicing judo, experienced acute subdural hematoma(ASDH)with grave outcomes, despite the fact that they had been examined by neurosurgeons. The five students, first-grade boy and girl of junior high school and two first-grade boys and one second-grade girl of senior high school, were hit on the head during extracurricular judo practice and were taken to the neurosurgery department of different hospitals. They were all novices or unskilled players. The initial diagnoses were ASDH in three cases, concussion in one, and headache in one. Although the surgeons, except in one case, prohibited the students from returning to play, the juveniles resumed judo practice soon. Some of them complained of continued headaches, but they kept practicing. Between 17 and 82 days after the first injury, they received the fateful hits to their heads, and they were brought to the emergency rooms. MRI and CT revealed ASDH in all;two of them died, and the other three remain in persistent vegetative state. Neurosurgeons should take the initiative to prevent severe brain injury of young athletes through collaborations with the athletes themselves, fellow athletes, family members, coaches, teachers, athletic directors, and other physicians. They should pay close attention to headaches and other signs and symptoms of concussion and prohibit the athletes from returning to play until they are confirmed to be symptom free for recommended periods, insisting that safety comes first.

  11. Simple sequence repeats in prokaryotic genomes

    PubMed Central

    Mrázek, Jan; Guo, Xiangxue; Shah, Apurva

    2007-01-01

    Simple sequence repeats (SSRs) in DNA sequences are composed of tandem iterations of short oligonucleotides and may have functional and/or structural properties that distinguish them from general DNA sequences. They are variable in length because of slip-strand mutations and may also affect local structure of the DNA molecule or the encoded proteins. Long SSRs (LSSRs) are common in eukaryotes but rare in most prokaryotes. In pathogens, SSRs can enhance antigenic variance of the pathogen population in a strategy that counteracts the host immune response. We analyze representations of SSRs in >300 prokaryotic genomes and report significant differences among different prokaryotes as well as among different types of SSRs. LSSRs composed of short oligonucleotides (1–4 bp length, designated LSSR1–4) are often found in host-adapted pathogens with reduced genomes that are not known to readily survive in a natural environment outside the host. In contrast, LSSRs composed of longer oligonucleotides (5–11 bp length, designated LSSR5–11) are found mostly in nonpathogens and opportunistic pathogens with large genomes. Comparisons among SSRs of different lengths suggest that LSSR1–4 are likely maintained by selection. This is consistent with the established role of some LSSR1–4 in enhancing antigenic variance. By contrast, abundance of LSSR5–11 in some genomes may reflect the SSRs' general tendency to expand rather than their specific role in the organisms' physiology. Differences among genomes in terms of SSR representations and their possible interpretations are discussed. PMID:17485665

  12. Rhythm Facilitates the Detection of Repeating Sound Patterns

    PubMed Central

    Rajendran, Vani G.; Harper, Nicol S.; Abdel-Latif, Khaled H. A.; Schnupp, Jan W. H.

    2016-01-01

    This study investigates the influence of temporal regularity on human listeners' ability to detect a repeating noise pattern embedded in statistically identical non-repeating noise. Human listeners were presented with white noise stimuli that either contained a frozen segment of noise that repeated in a temporally regular or irregular manner, or did not contain any repetition at all. Subjects were instructed to respond as soon as they detected any repetition in the stimulus. Pattern detection performance was best when repeated targets occurred in a temporally regular manner, suggesting that temporal regularity plays a facilitative role in pattern detection. A modulation filterbank model could account for these results. PMID:26858589

  13. Variable Glutamine-Rich Repeats Modulate Transcription Factor Activity

    PubMed Central

    Gemayel, Rita; Chavali, Sreenivas; Pougach, Ksenia; Legendre, Matthieu; Zhu, Bo; Boeynaems, Steven; van der Zande, Elisa; Gevaert, Kris; Rousseau, Frederic; Schymkowitz, Joost; Babu, M. Madan; Verstrepen, Kevin J.

    2015-01-01

    Summary Excessive expansions of glutamine (Q)-rich repeats in various human proteins are known to result in severe neurodegenerative disorders such as Huntington’s disease and several ataxias. However, the physiological role of these repeats and the consequences of more moderate repeat variation remain unknown. Here, we demonstrate that Q-rich domains are highly enriched in eukaryotic transcription factors where they act as functional modulators. Incremental changes in the number of repeats in the yeast transcriptional regulator Ssn6 (Cyc8) result in systematic, repeat-length-dependent variation in expression of target genes that result in direct phenotypic changes. The function of Ssn6 increases with its repeat number until a certain threshold where further expansion leads to aggregation. Quantitative proteomic analysis reveals that the Ssn6 repeats affect its solubility and interactions with Tup1 and other regulators. Thus, Q-rich repeats are dynamic functional domains that modulate a regulator’s innate function, with the inherent risk of pathogenic repeat expansions. PMID:26257283

  14. Coexistence of 3G repeaters with LTE base stations.

    PubMed

    Yeo, Woon-Young; Lee, Sang-Min; Hwang, Gyung-Ho; Kim, Jae-Hoon

    2013-01-01

    Repeaters have been an attractive solution for mobile operators to upgrade their wireless networks at low cost and to extend network coverage effectively. Since the first LTE commercial deployment in 2009, many mobile operators have launched LTE networks by upgrading their 3G and legacy networks. Because all 3G frequency bands are shared with the frequency bands for LTE deployment and 3G mobile operators have an enormous number of repeaters, reusing 3G repeaters in LTE networks is definitely a practical and cost-efficient solution. However, 3G repeaters usually do not support spatial multiplexing with multiple antennas, and thus it is difficult to reuse them directly in LTE networks. In order to support spatial multiplexing of LTE, the role of 3G repeaters should be replaced with small LTE base stations or MIMO-capable repeaters. In this paper, a repeater network is proposed to reuse 3G repeaters in LTE deployment while still supporting multilayer transmission of LTE. Interestingly, the proposed network has a higher cluster throughput than an LTE network with MIMO-capable repeaters.

  15. Bidirectional transcription of trinucleotide repeats: roles for excision repair

    PubMed Central

    Budworth, Helen; McMurray, Cynthia T.

    2013-01-01

    SUMMARY Genomic instability at repetitive DNA regions in cells of the nervous system leads to a number of neurodegenerative and neuromuscular diseases, including those with an expanded trinucleotide repeat (TNR) tract at or nearby an expressed gene. Expansion causes disease when a particular base sequence is repeated beyond the normal range, interfering with the expression or properties of a gene product. Disease severity and onset depend on the number of repeats. As the length of the repeat tract grows, so does the size of the successive expansions and the likelihood of another unstable event. In fragile X syndrome, for example, CGG repeat instability and pathogenesis are not typically observed below tracts of roughly 50 repeats, but occur frequently at or above 55 repeats, and are virtually certain above 100–300 repeats. Recent evidence points to bidirectional transcription as a new aspect of TNR instability and pathophysiology. Bidirectional transcription of TNR genes produces novel proteins and/or regulatory RNAs that influence both toxicity and epigenetic changes in TNR promoters. Bidirectional transcription of the TNR tract appears to influence aspects of its stability, gene processing, splicing, gene silencing, and chemical modification of DNAs. Paradoxically, however, some of the same effects are observed on both the expanded TNR gene and on its normal gene counterpart. In this review, we discuss the possible normal and abnormal effects of bidirectional transcription on trinucleotide repeat instability, the role of DNA repair in causing, preventing, or maintaining methylation, and chromatin environment of TNR genes. PMID:23669397

  16. Coexistence of 3G Repeaters with LTE Base Stations

    PubMed Central

    Yeo, Woon-Young

    2013-01-01

    Repeaters have been an attractive solution for mobile operators to upgrade their wireless networks at low cost and to extend network coverage effectively. Since the first LTE commercial deployment in 2009, many mobile operators have launched LTE networks by upgrading their 3G and legacy networks. Because all 3G frequency bands are shared with the frequency bands for LTE deployment and 3G mobile operators have an enormous number of repeaters, reusing 3G repeaters in LTE networks is definitely a practical and cost-efficient solution. However, 3G repeaters usually do not support spatial multiplexing with multiple antennas, and thus it is difficult to reuse them directly in LTE networks. In order to support spatial multiplexing of LTE, the role of 3G repeaters should be replaced with small LTE base stations or MIMO-capable repeaters. In this paper, a repeater network is proposed to reuse 3G repeaters in LTE deployment while still supporting multilayer transmission of LTE. Interestingly, the proposed network has a higher cluster throughput than an LTE network with MIMO-capable repeaters. PMID:24459420

  17. A Comparison of First Time and Repeat Rural DUI Offenders.

    PubMed

    Dickson, Megan F; Wasarhaley, Nesa E; Webster, J Matthew

    The purpose of the current study was to examine whether the differences found between first time and repeat rural DUI offenders were the same as those found previously in urban samples. A total of 118 rural DUI offenders were interviewed, approximately half (51.7%) of which were repeat offenders. Although demographic and mental health characteristics were similar across the two groups, repeat offenders reported more extensive substance use and criminal histories. Results suggest that the pattern of differences between rural first time and repeat DUI offenders may be different from the pattern found in prior urban-based studies. Treatment implications are discussed.

  18. A Comparison of First Time and Repeat Rural DUI Offenders

    PubMed Central

    Dickson, Megan F.; Wasarhaley, Nesa E.; Webster, J. Matthew

    2015-01-01

    The purpose of the current study was to examine whether the differences found between first time and repeat rural DUI offenders were the same as those found previously in urban samples. A total of 118 rural DUI offenders were interviewed, approximately half (51.7%) of which were repeat offenders. Although demographic and mental health characteristics were similar across the two groups, repeat offenders reported more extensive substance use and criminal histories. Results suggest that the pattern of differences between rural first time and repeat DUI offenders may be different from the pattern found in prior urban-based studies. Treatment implications are discussed. PMID:26225118

  19. Impact of small repeat sequences on bacterial genome evolution.

    PubMed

    Delihas, Nicholas

    2011-01-01

    Intergenic regions of prokaryotic genomes carry multiple copies of terminal inverted repeat (TIR) sequences, the nonautonomous miniature inverted-repeat transposable element (MITE). In addition, there are the repetitive extragenic palindromic (REP) sequences that fold into a small stem loop rich in G-C bonding. And the clustered regularly interspaced short palindromic repeats (CRISPRs) display similar small stem loops but are an integral part of a complex genetic element. Other classes of repeats such as the REP2 element do not have TIRs but show other signatures. With the current availability of a large number of whole-genome sequences, many new repeat elements have been discovered. These sequences display diverse properties. Some show an intimate linkage to integrons, and at least one encodes a small RNA. Many repeats are found fused with chromosomal open reading frames, and some are located within protein coding sequences. Small repeat units appear to work hand in hand with the transcriptional and/or post-transcriptional apparatus of the cell. Functionally, they are multifaceted, and this can range from the control of gene expression, the facilitation of host/pathogen interactions, or stimulation of the mammalian immune system. The CRISPR complex displays dramatic functions such as an acquired immune system that defends against invading viruses and plasmids. Evolutionarily, mobile repeat elements may have influenced a cycle of active versus inactive genes in ancestral organisms, and some repeats are concentrated in regions of the chromosome where there is significant genomic plasticity. Changes in the abundance of genomic repeats during the evolution of an organism may have resulted in a benefit to the cell or posed a disadvantage, and some present day species may reflect a purification process. The diverse structure, eclectic functions, and evolutionary aspects of repeat elements are described.

  20. Repeatability study of replicate crash tests: A signal analysis approach.

    PubMed

    Seppi, Jeremy; Toczyski, Jacek; Crandall, Jeff R; Kerrigan, Jason

    2017-10-03

    To provide an objective basis on which to evaluate the repeatability of vehicle crash test methods, a recently developed signal analysis method was used to evaluate correlation of sensor time history data between replicate vehicle crash tests. The goal of this study was to evaluate the repeatability of rollover crash tests performed with the Dynamic Rollover Test System (DRoTS) relative to other vehicle crash test methods. Test data from DRoTS tests, deceleration rollover sled (DRS) tests, frontal crash tests, frontal offset crash tests, small overlap crash tests, small overlap impact (SOI) crash tests, and oblique crash tests were obtained from the literature and publicly available databases (the NHTSA vehicle database and the Insurance Institute for Highway Safety TechData) to examine crash test repeatability. Signal analysis of the DRoTS tests showed that force and deformation time histories had good to excellent repeatability, whereas vehicle kinematics showed only fair repeatability due to the vehicle mounting method for one pair of tests and slightly dissimilar mass properties (2.2%) in a second pair of tests. Relative to the DRS, the DRoTS tests showed very similar or higher levels of repeatability in nearly all vehicle kinematic data signals with the exception of global X' (road direction of travel) velocity and displacement due to the functionality of the DRoTS fixture. Based on the average overall scoring metric of the dominant acceleration, DRoTS was found to be as repeatable as all other crash tests analyzed. Vertical force measures showed good repeatability and were on par with frontal crash barrier forces. Dynamic deformation measures showed good to excellent repeatability as opposed to poor repeatability seen in SOI and oblique deformation measures. Using the signal analysis method as outlined in this article, the DRoTS was shown to have the same or better repeatability of crash test methods used in government regulatory and consumer evaluation test

  1. Cardiorespiratory Coordination in Repeated Maximal Exercise.

    PubMed

    Garcia-Retortillo, Sergi; Javierre, Casimiro; Hristovski, Robert; Ventura, Josep L; Balagué, Natàlia

    2017-01-01

    Increases in cardiorespiratory coordination (CRC) after training with no differences in performance and physiological variables have recently been reported using a principal component analysis approach. However, no research has yet evaluated the short-term effects of exercise on CRC. The aim of this study was to delineate the behavior of CRC under different physiological initial conditions produced by repeated maximal exercises. Fifteen participants performed 2 consecutive graded and maximal cycling tests. Test 1 was performed without any previous exercise, and Test 2 6 min after Test 1. Both tests started at 0 W and the workload was increased by 25 W/min in males and 20 W/min in females, until they were not able to maintain the prescribed cycling frequency of 70 rpm for more than 5 consecutive seconds. A principal component (PC) analysis of selected cardiovascular and cardiorespiratory variables (expired fraction of O2, expired fraction of CO2, ventilation, systolic blood pressure, diastolic blood pressure, and heart rate) was performed to evaluate the CRC defined by the number of PCs in both tests. In order to quantify the degree of coordination, the information entropy was calculated and the eigenvalues of the first PC (PC1) were compared between tests. Although no significant differences were found between the tests with respect to the performed maximal workload (Wmax), maximal oxygen consumption (VO2 max), or ventilatory threshold (VT), an increase in the number of PCs and/or a decrease of eigenvalues of PC1 (t = 2.95; p = 0.01; d = 1.08) was found in Test 2 compared to Test 1. Moreover, entropy was significantly higher (Z = 2.33; p = 0.02; d = 1.43) in the last test. In conclusion, despite the fact that no significant differences were observed in the conventionally explored maximal performance and physiological variables (Wmax, VO2 max, and VT) between tests, a reduction of CRC was observed in Test 2. These results emphasize the interest of CRC evaluation in

  2. The Bangla clubfoot tool: a repeatability study.

    PubMed

    Evans, Angela Margaret; Perveen, Roksana; Ford-Powell, Vikki A; Barker, Simon

    2014-01-01

    'Walk for Life' (WFL) is the sustainable clubfoot program in Bangladesh, where there are many challenges in implementing the Ponseti technique in a poor and highly populated country. The relapsing tendency of congenital clubfoot deformity means that initial results may well differ from those of the medium and longer term. Over 10000 children with16668 clubfeet have been treated by WFL since its inception in 2009. Such a large project provides both the need to evaluate each individual child's case, and also the opportunity to evaluate the wider WFL program results. Such systematic review requires a measure that is sufficiently robust, yet contextually practical, hence the aim of this work was to develop a tool for this purpose, and to report the examiner reliability. The Bangla clubfoot tool was largely developed from components of existing validated clubfoot assessment measures, and adapted for local use. Three areas of examination are included: parent satisfaction, gait, clinical examination of the clubfoot. A same-subject repeated measures study design was used to assess the intra-rater reliability of a local WFL physiotherapist, and a visiting WFL volunteer. The inter-rater reliability was also assessed, which is relevant for other examiners and other clubfoot projects undertaking evaluation of medium and longer term results. The reliability study was conducted in 37 children who had commenced treatment for congenital clubfoot deformity using Ponseti method within the previous two years. The mean age of the children was 2.6 years, with gender 28 male: 9 female. The intra-rater reliability results [ICCs (95% CI)] were: 0.87 (0.76 - 0.93) for the local WFL examiner, and 0.82 (0.64 - 0.91) for the visiting examiner. Inter-rater reliability results [ICCs (95% CI)] were: 0.92 (0.88 - 0.96). Hence the tool showed very good intra-rater and inter-rater reliability, rendering it suitable for use. The Bangla clubfoot tool has been developed to suit the context of the

  3. The Bangla clubfoot tool: a repeatability study

    PubMed Central

    2014-01-01

    Background ‘Walk for Life’ (WFL) is the sustainable clubfoot program in Bangladesh, where there are many challenges in implementing the Ponseti technique in a poor and highly populated country. The relapsing tendency of congenital clubfoot deformity means that initial results may well differ from those of the medium and longer term. Over 10000 children with16668 clubfeet have been treated by WFL since its inception in 2009. Such a large project provides both the need to evaluate each individual child’s case, and also the opportunity to evaluate the wider WFL program results. Such systematic review requires a measure that is sufficiently robust, yet contextually practical, hence the aim of this work was to develop a tool for this purpose, and to report the examiner reliability. Methods The Bangla clubfoot tool was largely developed from components of existing validated clubfoot assessment measures, and adapted for local use. Three areas of examination are included: parent satisfaction, gait, clinical examination of the clubfoot. A same-subject repeated measures study design was used to assess the intra-rater reliability of a local WFL physiotherapist, and a visiting WFL volunteer. The inter-rater reliability was also assessed, which is relevant for other examiners and other clubfoot projects undertaking evaluation of medium and longer term results. Results The reliability study was conducted in 37 children who had commenced treatment for congenital clubfoot deformity using Ponseti method within the previous two years. The mean age of the children was 2.6 years, with gender 28 male: 9 female. The intra-rater reliability results [ICCs (95% CI)] were: 0.87 (0.76 – 0.93) for the local WFL examiner, and 0.82 (0.64 – 0.91) for the visiting examiner. Inter-rater reliability results [ICCs (95% CI)] were: 0.92 (0.88 – 0.96). Hence the tool showed very good intra-rater and inter-rater reliability, rendering it suitable for use. Conclusions The Bangla clubfoot tool

  4. Cardiorespiratory Coordination in Repeated Maximal Exercise

    PubMed Central

    Garcia-Retortillo, Sergi; Javierre, Casimiro; Hristovski, Robert; Ventura, Josep L.; Balagué, Natàlia

    2017-01-01

    Increases in cardiorespiratory coordination (CRC) after training with no differences in performance and physiological variables have recently been reported using a principal component analysis approach. However, no research has yet evaluated the short-term effects of exercise on CRC. The aim of this study was to delineate the behavior of CRC under different physiological initial conditions produced by repeated maximal exercises. Fifteen participants performed 2 consecutive graded and maximal cycling tests. Test 1 was performed without any previous exercise, and Test 2 6 min after Test 1. Both tests started at 0 W and the workload was increased by 25 W/min in males and 20 W/min in females, until they were not able to maintain the prescribed cycling frequency of 70 rpm for more than 5 consecutive seconds. A principal component (PC) analysis of selected cardiovascular and cardiorespiratory variables (expired fraction of O2, expired fraction of CO2, ventilation, systolic blood pressure, diastolic blood pressure, and heart rate) was performed to evaluate the CRC defined by the number of PCs in both tests. In order to quantify the degree of coordination, the information entropy was calculated and the eigenvalues of the first PC (PC1) were compared between tests. Although no significant differences were found between the tests with respect to the performed maximal workload (Wmax), maximal oxygen consumption (VO2 max), or ventilatory threshold (VT), an increase in the number of PCs and/or a decrease of eigenvalues of PC1 (t = 2.95; p = 0.01; d = 1.08) was found in Test 2 compared to Test 1. Moreover, entropy was significantly higher (Z = 2.33; p = 0.02; d = 1.43) in the last test. In conclusion, despite the fact that no significant differences were observed in the conventionally explored maximal performance and physiological variables (Wmax, VO2 max, and VT) between tests, a reduction of CRC was observed in Test 2. These results emphasize the interest of CRC evaluation in

  5. Repeated Reading, Turn Taking, and Augmentative and Alternative Communication (AAC)

    ERIC Educational Resources Information Center

    Edmister, Evette; Wegner, Jane

    2015-01-01

    This single participant multiple baseline research design measured the effects of repeatedly reading narrative books to children who used voice output augmentative communication devices to communicate. The study sought to determine if there was a difference observed in the number of turns taken when reading stories repeatedly. Three girls ranging…

  6. Training repeated effort ability in national team male volleyball players.

    PubMed

    Sheppard, Jeremy M; Gabbett, Tim; Borgeaud, Russell

    2008-09-01

    This case study evaluated the effect of repeated lateral movement and jumping training on repeated effort ability in a group of national team male volleyball players. Twelve volleyball players were assessed on their volleyball-specific repeated movement and jumping abilities using a volleyball-specific repeated effort test (RET) before and after 12 weeks of training. The athletes performed between 8 and 9 volleyball training sessions per week, with 5 to 6 of these sessions including specific training aimed at improving repeated effort ability. Typically these training sessions involved 8 to 12 repetitions of 2 to 3 block jumps over a 9-m lateral distance (ie, the athletes had to perform jumps and lateral movements, typical of front court play in volleyball). Population-specific repeatability data were used to determine whether any changes that may have occurred in this study were beyond the minimal clinically important difference (MCID) for this testing procedure. Improvements in all variables of the RET were observed for each athlete involved in the study, with a small-to-moderate magnitude observed for the mean changes in each variable (Cohen's d, 0.21 to 0.59). All of the improvements in the results exceeded the MCID. These findings demonstrate that the RET is sensitive to training-induced changes. Lateral movement speed and repeated lateral movement speed, as well as jumping and repeated jumping ability are trainable qualities in high-performance volleyball players.

  7. Generation of Repeater F Waves in Healthy Subjects.

    PubMed

    Chroni, Elisabeth; Veltsista, Dimitra; Papapaulou, Chris; Trachani, Eftychia

    2017-05-01

    F waves identical in latency, size, and shape, known as repeater F waves, have been observed occasionally in normal motor conduction recordings. The purpose of this study was to examine the occurrence and characteristics of repeater F waves in healthy subjects under different testing conditions, aiming to selectively excite lower and higher threshold motor fibers. Sessions of 40 traces were recorded from the ulnar nerve in 12 volunteers, applying/using supramaximal, submaximal stimuli (intensity able to elicit 30% and 60% of the maximum compound muscle action potential amplitude), and a collision technique. Repeater F waves were identified and their numbers and relative frequency were estimated. For this purpose, a custom-designed software program was developed, to avoid misjudgments of simple visual inspection. Repeater occurrence was significantly higher using 30% submaximal intensity compared with the standard supramaximal stimulation. There was an inverse significant association between repeater index and overall F wave quantity. Repeaters' latency, amplitude, and duration measurements were within the ranges of the nonrepeaters. We herein showed that in healthy subjects the presence of repeater F waves might increase, when stimulation conditions other than standard single, supramaximal impulses were used. The frequency of repeaters was dependent on the overall F wave persistence, but there was no evidence to support a relationship with the type of motoneurons that was preferentially stimulated.

  8. Contagion and Repeat Offending among Urban Juvenile Delinquents

    ERIC Educational Resources Information Center

    Mennis, Jeremy; Harris, Philip

    2011-01-01

    This research investigates the role of repeat offending and spatial contagion in juvenile delinquency recidivism using a database of 7166 male juvenile offenders sent to community-based programs by the Family Court of Philadelphia. Results indicate evidence of repeat offending among juvenile delinquents, particularly for drug offenders. The…

  9. Repeated Reading: Testing Alternative Models for Efficient Implementation

    ERIC Educational Resources Information Center

    Lewis, Greg

    2012-01-01

    An investigation was conducted to determine the best criterion for advancement to a new reading passage during the commonly used classroom strategy of repeated reading. Knowing when to move students to a new passage during the repeated reading process was considered of value to teachers in efficiently using student learning time. The study also…

  10. Repeat Pregnancy among Urban Adolescents: Sociodemographic, Family, and Health Factors.

    ERIC Educational Resources Information Center

    Coard, Stephanie Irby; Nitz, Katherine; Felice, Marianne E.

    2000-01-01

    Examines sociodemographic, family, and health factors associated with repeat pregnancy in a clinical sample of urban, first-time mothers. Results indicate that postpartum contraceptive method was associated with repeat pregnancy at year one; contraceptive use, maternal age, history of miscarriages, and postpartum contraceptive method were…

  11. Secret key rates for an encoded quantum repeater

    NASA Astrophysics Data System (ADS)

    Bratzik, Sylvia; Kampermann, Hermann; Bruß, Dagmar

    2014-03-01

    We investigate secret key rates for the quantum repeater using encoding [L. Jiang et al., Phys. Rev. A 79, 032325 (2009), 10.1103/PhysRevA.79.032325] and compare them to the standard repeater scheme by Briegel, Dür, Cirac, and Zoller. The former scheme has the advantage of a minimal consumption of classical communication. We analyze the trade-off in the secret key rate between the communication time and the required resources. For this purpose we introduce an error model for the repeater using encoding which allows for input Bell states with a fidelity smaller than one, in contrast to the model given by L. Jiang et al. [Phys. Rev. A 79, 032325 (2009), 10.1103/PhysRevA.79.032325]. We show that one can correct additional errors in the encoded connection procedure of this repeater and develop a suitable decoding algorithm. Furthermore, we derive the rate of producing entangled pairs for the quantum repeater using encoding and give the minimal parameter values (gate quality and initial fidelity) for establishing a nonzero secret key. We find that the generic quantum repeater is optimal regarding the secret key rate per memory per second and show that the encoded quantum repeater using the simple three-qubit repetition code can even have an advantage with respect to the resources compared to other recent quantum repeater schemes with encoding.

  12. 40 CFR 1610.2 - Repeated attorney misconduct, sanctions, hearings.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 32 2010-07-01 2010-07-01 false Repeated attorney misconduct, sanctions, hearings. 1610.2 Section 1610.2 Protection of Environment CHEMICAL SAFETY AND HAZARD INVESTIGATION BOARD ADMINISTRATIVE INVESTIGATIONS § 1610.2 Repeated attorney misconduct, sanctions, hearings....

  13. Large Polyglutamine Repeats Cause Muscle Degeneration in SCA17 Mice

    PubMed Central

    Huang, Shanshan; Yang, Su; Guo, Jifeng; Yan, Sen; Gaertig, Marta A.; Li, Shihua; Li, Xiao-Jiang

    2015-01-01

    SUMMARY In polyglutamine (polyQ) diseases, large polyQ repeats cause juvenile cases with different symptoms than adult-onset patients, who carry smaller expanded polyQ repeats. The mechanisms behind the differential pathology mediated by different polyQ repeat lengths remain unknown. By studying knock-in mouse models of spinal cerebellar ataxia-17 (SCA17), we found that a large polyQ (105 glutamines) in the TATA box-binding protein (TBP) preferentially causes muscle degeneration and reduces the expression of muscle-specific genes. Direct expression of TBP with different polyQ repeats in mouse muscle revealed that muscle degeneration is mediated only by the large polyQ repeats. Different polyQ repeats differentially alter TBP’s interaction with neuronal and muscle-specific transcription factors. As a result, the large polyQ repeat decreases the association of MyoD with TBP and DNA promoters. Our findings suggest that specific alterations in protein interactions by large polyQ repeats may account for the unique pathology in juvenile polyQ diseases. PMID:26387956

  14. Intrinsic unsharpness and approximate repeatability of quantum measurements

    NASA Astrophysics Data System (ADS)

    Carmeli, Claudio; Heinonen, Teiko; Toigo, Alessandro

    2007-02-01

    The intrinsic unsharpness of a quantum observable is studied by introducing the notion of resolution width. This quantification of accuracy is shown to be closely connected with the possibility of making approximately repeatable measurements. As a case study, the intrinsic unsharpness and approximate repeatability of position and momentum measurements are examined in detail.

  15. Effect of Repeated Simulations by Standardized Patients on Intercase Reliability.

    ERIC Educational Resources Information Center

    Colliver, Jerry A.; And Others

    1991-01-01

    A study using five Southern Illinois University senior medical school classes (n=350 students) investigated whether having a standardized patient simulate a case repeatedly in postclerkship medical student evaluation affects the measure's reliability. Results suggest that repeated simulation had little or no effect on intercase reliability of…

  16. Preschool Children's Memory for Repeated Changes in the Lunch Routine.

    ERIC Educational Resources Information Center

    Krackow, Elisa

    An experiment examined the possibilities that: (1) repeated deviations in a routine event become fused into the general event representation (GER) for that event; and (2) when deviations go unreported, it is because they have been forgotten. Preschool children were interviewed to get their script reports before and after repeated deviations in the…

  17. Factors associated with HD CAG repeat instability in Huntington disease

    PubMed Central

    Wheeler, V C; Persichetti, F; McNeil, S M; Mysore, J S; Mysore, S S; MacDonald, M E; Myers, R H; Gusella, J F; Wexler, N S

    2007-01-01

    Background The Huntington disease (HD) CAG repeat exhibits dramatic instability when transmitted to subsequent generations. The instability of the HD disease allele in male intergenerational transmissions is reflected in the variability of the CAG repeat in DNA from the sperm of male carriers of the HD gene. Results In this study, we used a collection of 112 sperm DNAs from male HD gene‐positive members of a large Venezuelan cohort to investigate the factors associated with repeat instability. We confirm previous observations that CAG repeat length is the strongest predictor of repeat‐length variability in sperm, but we did not find any correlation between CAG repeat instability and either age at the time of sperm donation or affectedness status. We also investigated transmission instability for 184 father–offspring and 311 mother–offspring pairs in this Venezuelan pedigree. Repeat‐length changes were dependent upon the sex of the transmitting parent and parental CAG repeat length but not parental age or birth order. Unexpectedly, in maternal transmissions, repeat‐length changes were also dependent upon the sex of the offspring, with a tendency for expansion in male offspring and contraction in female offspring. Conclusion Significant sibling–sibling correlation for repeat instability suggests that genetic factors play a role in intergenerational CAG repeat instability. PMID:17660463

  18. Impact of Inclusion or Exclusion of Repeaters on Test Equating

    ERIC Educational Resources Information Center

    Puhan, Gautam

    2011-01-01

    This study examined the effect of including or excluding repeaters on the equating process and results. New forms of two tests were equated to their respective old forms using either all examinees or only the first timer examinees in the new form sample. Results showed that for both tests used in this study, including or excluding repeaters in the…

  19. PCR-free digital minisatellite tandem repeat genotyping.

    PubMed

    Chen, Yuchao; Seo, Tae Seok

    2011-06-01

    We demonstrated a proof-of-concept for novel minisatellite tandem repeat typing, called PCR-free digital VNTR (variable number tandem repeat) typing, which is composed of three steps: a ligation reaction instead of PCR thermal cycling, magnetic bead-based solid-phase capture for purification, and an elongated sample stacking microcapillary electrophoresis (μCE) for sensitive digital coding of repeat number. We designed a 16-bp fluorescently labeled ligation probe which is complementary to a repeat unit of a biotinylated synthetic template mimicking the human D1S80 VNTR locus and is randomly hybridized with the minisatellite tandem repeats. A quick isothermal ligation reaction was followed to link the adjacent ligation probes on the DNA templates, and then the ligated products were purified by streptavidin-coated magnetic beads. After a denaturing step, a large amount of ligated products whose size difference was equivalent to the repeat unit were released and recovered. Through the elongated sample stacking μCE separation on a microdevice, the fluorescence signal of the ligated products was generated in the electropherogram and the peak number was directly counted which was exactly matched with the repeat number of VNTR locus. We could successfully identify the minisatellite tandem repeat number with only 5 fmol of DNA template in 30 min.

  20. Absence of bacterial resistance following repeat exposure to photodynamic therapy

    NASA Astrophysics Data System (ADS)

    Pedigo, Lisa A.; Gibbs, Aaron J.; Scott, Robert J.; Street, Cale N.

    2009-06-01

    The prevalence of antibiotic resistant bacteria necessitates exploration of alternative approaches to treat hospital and community acquired infections. The aim of this study was to determine whether bacterial pathogens develop resistance to antimicrobial photodynamic therapy (aPDT) during repeated sub-lethal challenge. Antibiotic sensitive and resistant strains of S. aureus and antibiotic sensitive E. coli were subjected to repeat PDT treatments using a methylene blue photosensitizer formulation and 670 nm illumination from a non-thermal diode laser. Parameters were adjusted such that kills were <100% so that surviving colonies could be passaged for subsequent exposures. With each repeat, kills were compared to those using non-exposed cultures of the same strain. Oxacillin resistance was induced in S. aureus using a disc diffusion method. For each experiment, "virgin" and "repeat" cultures were exposed to methylene blue at 0.01% w/v and illuminated with an energy dose of 20.6 J/cm2. No significant difference in killing of E. coli (repeat vs. virgin culture) was observed through 11 repeat exposures. Similar results were seen using MSSA and MRSA, wherein kill rate did not significantly differ from control over 25 repeat exposures. In contrast, complete oxacillin resistance could be generated in S. aureus over a limited number of exposures. PDT is effective in the eradication of pathogens including antibiotic resistance strains. Furthermore, repeated sub-lethal exposure does not induce resistance to subsequent PDT treatments. The absence of resistance formation represents a significant advantage of PDT over traditional antibiotics.

  1. Contagion and Repeat Offending among Urban Juvenile Delinquents

    ERIC Educational Resources Information Center

    Mennis, Jeremy; Harris, Philip

    2011-01-01

    This research investigates the role of repeat offending and spatial contagion in juvenile delinquency recidivism using a database of 7166 male juvenile offenders sent to community-based programs by the Family Court of Philadelphia. Results indicate evidence of repeat offending among juvenile delinquents, particularly for drug offenders. The…

  2. 47 CFR 90.247 - Mobile repeater stations.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... of the mobile unit and an automatic time-delay device that de-activates the transmitter after any... 47 Telecommunication 5 2014-10-01 2014-10-01 false Mobile repeater stations. 90.247 Section 90.247... MOBILE RADIO SERVICES Non-Voice and Other Specialized Operations § 90.247 Mobile repeater stations. A...

  3. 47 CFR 90.247 - Mobile repeater stations.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... of the mobile unit and an automatic time-delay device that de-activates the transmitter after any... 47 Telecommunication 5 2012-10-01 2012-10-01 false Mobile repeater stations. 90.247 Section 90.247... MOBILE RADIO SERVICES Non-Voice and Other Specialized Operations § 90.247 Mobile repeater stations. A...

  4. Repeated Reading: Testing Alternative Models for Efficient Implementation

    ERIC Educational Resources Information Center

    Lewis, Greg

    2012-01-01

    An investigation was conducted to determine the best criterion for advancement to a new reading passage during the commonly used classroom strategy of repeated reading. Knowing when to move students to a new passage during the repeated reading process was considered of value to teachers in efficiently using student learning time. The study also…

  5. Witness recall across repeated interviews in a case of repeated abuse.

    PubMed

    Brubacher, Sonja P; La Rooy, David

    2014-02-01

    In this illustrative case study we examine the three forensic interviews of a girl who experienced repeated sexual abuse from ages 7 to 11. She disclosed the abuse after watching a serialized television show that contained a storyline similar to her own experience. This triggered an investigation that ended in successful prosecution of the offender. Because this case involved abuse that was repeated on a weekly basis for 4 years we thus investigated the degree to which the child's narrative reflected specific episodes or generic accounts, and both the interviewer's and child's attempts to elicit and provide, respectively, specific details across the 3 interviews collected in a 1 month period. Across the 3 interviews, the child's account was largely generic, yet on a number of occasions she provided details specific to individual incidents (episodic leads) that could have been probed further. As predicted: earlier interviews were characterized more by episodic than generic prompts and the reverse was true for the third interview; the child often responded using the same style of language (episodic or generic) as the interviewer; and open questions yielded narrative information. We discuss the importance of adopting children's words to specify occurrences, and the potential benefits of permitting generic recall in investigative interviews on children's ability to provide episodic leads. Despite the fact that the testimony was characterized by generic information about what usually happened, rather than specific episodic details about individual occurrences, this case resulted in successful prosecution.

  6. Polymorphic GGC repeat differentially regulates human reelin gene expression levels.

    PubMed

    Persico, A M; Levitt, P; Pimenta, A F

    2006-10-01

    The human gene encoding Reelin (RELN), a pivotal protein in neurodevelopment, includes a polymorphic GGC repeat in its 5' untranslated region (UTR). CHO cells transfected with constructs encompassing the RELN 5'UTR with 4-to-13 GGC repeats upstream of the luciferase reporter gene show declining luciferase activity with increasing GGC repeat number (P < 0.005), as predicted by computer-based simulations. Conversely, RELN 5'UTR sequences boost reporter gene expression above control levels in neuronal SN56 and N2A cell lines, but 12- and 13-repeat alleles still yield 50-60% less luciferase activity compared to the more common 8- and 10-repeat alleles (P < 0.0001). RELN "long" GGC alleles significantly blunt gene expression and may, through this effect, confer vulnerability to human disorders, such as schizophrenia and autism.

  7. Study of repeater technology for advanced multifunctional communications satellites

    NASA Technical Reports Server (NTRS)

    1972-01-01

    Investigations are presented concerning design concepts and implementation approaches for the satellite communication repeater subsystems of advanced multifunctional satellites. In such systems the important concepts are the use of multiple antenna beams, repeater switching (routing), and efficient spectrum utilization through frequency reuse. An information base on these techniques was developed and tradeoff analyses were made of repeater design concepts, with the work design taken in a broad sense to include modulation beam coverage patterns. There were five major areas of study: requirements analysis and processing; study of interbeam interference in multibeam systems; characterization of multiple-beam switching repeaters; estimation of repeater weight and power for a number of alternatives; and tradeoff analyses based on these weight and power data.

  8. Biochemical analysis of oligomerization of expanded polyalanine repeat proteins.

    PubMed

    Nojima, Jun; Oma, Yoko; Futai, Eugene; Sasagawa, Noboru; Kuroda, Reiko; Turk, Boris; Ishiura, Shoichi

    2009-08-01

    Many human proteins contain amino acid repeats that can form homopolymeric amino acid (HPAA) tracts. HPAA tract proteins that contain polyalanine sequences promote diseases, including oculopharyngeal muscular dystrophy. The pathological properties of these proteins develop when the repeats match or exceed approximately 20 residues. We analyzed the oligomerization of yellow fluorescent protein (YFP) and GST fusion proteins containing >20 alanine repeats by using sucrose density gradient centrifugation. YFP and GST fusion proteins having 23 polyalanine residues sedimented readily in sucrose density gradients, suggesting instability and oligomerization of proteins with an excess of 20 alanine repeats. Moreover, GST fusion proteins were resistant to trypsin digestion after oligomerization. Oligomerized artificial proteins with long polyalanine repeats may be suitable models for studying polyalanine-related diseases.

  9. Effects of 3-repeat tau on taxol mobility through microtubules

    NASA Astrophysics Data System (ADS)

    Park, Hyunjoo; Fygenson, Deborah; Kim, Mahn Won

    2005-03-01

    Both the anti-cancer drug taxol and the microtubule-associated protein tau suppress dynamics of microtubules (MT). We have observed taxol mobility with full-length 3-repeat tau, one of six tau isoforms, using fluorescence recovery after photobleaching (FRAP) on MTs and compare with earlier results on recombinant full-length adult 4-repeat tau. Taxol mobility becomes highly sensitive to taxol concentration in the presence of 3-repeat tau (up to 1:1 molar ratio) as it does in the presence of 4-repeat tau, but is 2 to 3 times faster at low taxol concentrations. Fitting to a mean-field binding reaction model [J.L. Ross et.al, PNAS 101:12910-5 (2004)] suggests that the presence of 3-repeat tau enhances taxol movement through pores in the MT walls.

  10. mreps: efficient and flexible detection of tandem repeats in DNA

    PubMed Central

    Kolpakov, Roman; Bana, Ghizlane; Kucherov, Gregory

    2003-01-01

    The presence of repeated sequences is a fundamental feature of genomes. Tandemly repeated DNA appears in both eukaryotic and prokaryotic genomes, it is associated with various regulatory mechanisms and plays an important role in genomic fingerprinting. In this paper, we describe mreps, a powerful software tool for a fast identification of tandemly repeated structures in DNA sequences. mreps is able to identify all types of tandem repeats within a single run on a whole genomic sequence. It has a resolution parameter that allows the program to identify ‘fuzzy’ repeats. We introduce main algorithmic solutions behind mreps, describe its usage, give some execution time benchmarks and present several case studies to illustrate its capabilities. The mreps web interface is accessible through http://www.loria.fr/mreps/. PMID:12824391

  11. Repeat proteins challenge the concept of structural domains.

    PubMed

    Espada, Rocío; Parra, R Gonzalo; Sippl, Manfred J; Mora, Thierry; Walczak, Aleksandra M; Ferreiro, Diego U

    2015-10-01

    Structural domains are believed to be modules within proteins that can fold and function independently. Some proteins show tandem repetitions of apparent modular structure that do not fold independently, but rather co-operate in stabilizing structural forms that comprise several repeat-units. For many natural repeat-proteins, it has been shown that weak energetic links between repeats lead to the breakdown of co-operativity and the appearance of folding sub-domains within an apparently regular repeat array. The quasi-1D architecture of repeat-proteins is crucial in detailing how the local energetic balances can modulate the folding dynamics of these proteins, which can be related to the physiological behaviour of these ubiquitous biological systems.

  12. Disease-associated repeat instability and mismatch repair.

    PubMed

    Schmidt, Monika H M; Pearson, Christopher E

    2016-02-01

    Expanded tandem repeat sequences in DNA are associated with at least 40 human genetic neurological, neurodegenerative, and neuromuscular diseases. Repeat expansion can occur during parent-to-offspring transmission, and arise at variable rates in specific tissues throughout the life of an affected individual. Since the ongoing somatic repeat expansions can affect disease age-of-onset, severity, and progression, targeting somatic expansion holds potential as a therapeutic target. Thus, understanding the factors that regulate this mutation is crucial. DNA repair, in particular mismatch repair (MMR), is the major driving force of disease-associated repeat expansions. In contrast to its anti-mutagenic roles, mammalian MMR curiously drives the expansion mutations of disease-associated (CAG)·(CTG) repeats. Recent advances have broadened our knowledge of both the MMR proteins involved in disease repeat expansions, including: MSH2, MSH3, MSH6, MLH1, PMS2, and MLH3, as well as the types of repeats affected by MMR, now including: (CAG)·(CTG), (CGG)·(CCG), and (GAA)·(TTC) repeats. Mutagenic slipped-DNA structures have been detected in patient tissues, and the size of the slip-out and their junction conformation can determine the involvement of MMR. Furthermore, the formation of other unusual DNA and R-loop structures is proposed to play a key role in MMR-mediated instability. A complex correlation is emerging between tissues showing varying amounts of repeat instability and MMR expression levels. Notably, naturally occurring polymorphic variants of DNA repair genes can have dramatic effects upon the levels of repeat instability, which may explain the variation in disease age-of-onset, progression and severity. An increasing grasp of these factors holds prognostic and therapeutic potential.

  13. Repeatability Evaluation of Finger Tapping Device with Magnetic Sensors

    NASA Astrophysics Data System (ADS)

    Sano, Yuko; Kandori, Akihiko; Shima, Keisuke; Tamura, Yasuhiro; Takagi, Hiroshi; Tsuji, Toshio; Noda, Masafumi; Higashikawa, Fumiko; Yokoe, Masaru; Sakoda, Saburo

    We tested the repeatability of a finger tapping device with magnetic sensors to determine its reliability. This device, which was developed to assist in the diagnosis of movement disorders such as Parkinson's disease (PD) and strokes, measures the distance between the first and index fingers during finger tapping movements (opening and closing the fingers repeatedly). We evaluated three types of repeatability based on ICC (interclass correlation coefficient) and Welch's test (test for equal means in a oneway layout): repeatability when measured at different times, when using different devices, and when using different measurers. We calculated these three types for three finger tapping tasks on both hands for 21 characteristics calculated from finger tapping waveforms. Results demonstrated that the repeatability when using different devices is high regardless of the task or hand. The repeatability when measuring at different times and when using different measurers is high at some tasks, but not all. One of the finger tapping tasks (finger tapping movement with the largest amplitude and highest velocity), which is used in a conventional PD diagnosis method (UPDRS), does not have enough repeatability, while other tasks show high repeatability. Results also showed that five characteristics have the highest repeatability (ICC ≥ 0.5 or significance probability of Welch's test ≥ 5% in all tasks): “total moving distance,” “average of local minimum acceleration in opening motion,” “average of local minimum acceleration in closing motion,” “average of local maximum distance” and “average of local minimum velocity”. These results clearly demonstrate the strong repeatability of this device and lead to more precise diagnosis of movement disorders.

  14. Repeating and not so Repeating Large Earthquakes in the Mexican Subduction Zone

    NASA Astrophysics Data System (ADS)

    Hjorleifsdottir, V.; Singh, S.; Iglesias, A.; Perez-Campos, X.

    2013-12-01

    The rupture area and recurrence interval of large earthquakes in the mexican subduction zone are relatively small and almost the entire length of the zone has experienced a large (Mw≥7.0) earthquake in the last 100 years (Singh et al., 1981). Several segments have experienced multiple large earthquakes in this time period. However, as the rupture areas of events prior to 1973 are only approximately known, the recurrence periods are uncertain. Large earthquakes occurred in the Ometepec, Guerrero, segment in 1937, 1950, 1982 and 2012 (Singh et al., 1981). In 1982, two earthquakes (Ms 6.9 and Ms 7.0) occurred about 4 hours apart, one apparently downdip from the other (Astiz & Kanamori, 1984; Beroza et al. 1984). The 2012 earthquake on the other hand had a magnitude of Mw 7.5 (globalcmt.org), breaking approximately the same area as the 1982 doublet, but with a total scalar moment about three times larger than the 1982 doublet combined. It therefore seems that 'repeat earthquakes' in the Ometepec segment are not necessarily very similar one to another. The Central Oaxaca segment broke in large earthquakes in 1928 (Mw7.7) and 1978 (Mw7.7) . Seismograms for the two events, recorded at the Wiechert seismograph in Uppsala, show remarkable similarity, suggesting that in this area, large earthquakes can repeat. The extent to which the near-trench part of the fault plane participates in the ruptures is not well understood. In the Ometepec segment, the updip portion of the plate interface broke during the 25 Feb 1996 earthquake (Mw7.1), which was a slow earthquake and produced anomalously low PGAs (Iglesias et al., 2003). Historical records indicate that a great tsunamigenic earthquake, M~8.6, occurred in the Oaxaca region in 1787, breaking the Central Oaxaca segment together with several adjacent segments (Suarez & Albini 2009). Whether the updip portion of the fault broke in this event remains speculative, although plausible based on the large tsunami. Evidence from the

  15. Exploring the repeat protein universe through computational protein design

    SciTech Connect

    Brunette, TJ; Parmeggiani, Fabio; Huang, Po-Ssu; Bhabha, Gira; Ekiert, Damian C.; Tsutakawa, Susan E.; Hura, Greg L.; Tainer, John A.; Baker, David

    2015-12-16

    A central question in protein evolution is the extent to which naturally occurring proteins sample the space of folded structures accessible to the polypeptide chain. Repeat proteins composed of multiple tandem copies of a modular structure unit are widespread in nature and have critical roles in molecular recognition, signalling, and other essential biological processes. Naturally occurring repeat proteins have been re-engineered for molecular recognition and modular scaffolding applications. In this paper, we use computational protein design to investigate the space of folded structures that can be generated by tandem repeating a simple helix–loop–helix–loop structural motif. Eighty-three designs with sequences unrelated to known repeat proteins were experimentally characterized. Of these, 53 are monomeric and stable at 95 °C, and 43 have solution X-ray scattering spectra consistent with the design models. Crystal structures of 15 designs spanning a broad range of curvatures are in close agreement with the design models with root mean square deviations ranging from 0.7 to 2.5 Å. Finally, our results show that existing repeat proteins occupy only a small fraction of the possible repeat protein sequence and structure space and that it is possible to design novel repeat proteins with precisely specified geometries, opening up a wide array of new possibilities for biomolecular engineering.

  16. Exploring the repeat protein universe through computational protein design

    DOE PAGES

    Brunette, TJ; Parmeggiani, Fabio; Huang, Po-Ssu; ...

    2015-12-16

    A central question in protein evolution is the extent to which naturally occurring proteins sample the space of folded structures accessible to the polypeptide chain. Repeat proteins composed of multiple tandem copies of a modular structure unit are widespread in nature and have critical roles in molecular recognition, signalling, and other essential biological processes. Naturally occurring repeat proteins have been re-engineered for molecular recognition and modular scaffolding applications. In this paper, we use computational protein design to investigate the space of folded structures that can be generated by tandem repeating a simple helix–loop–helix–loop structural motif. Eighty-three designs with sequences unrelatedmore » to known repeat proteins were experimentally characterized. Of these, 53 are monomeric and stable at 95 °C, and 43 have solution X-ray scattering spectra consistent with the design models. Crystal structures of 15 designs spanning a broad range of curvatures are in close agreement with the design models with root mean square deviations ranging from 0.7 to 2.5 Å. Finally, our results show that existing repeat proteins occupy only a small fraction of the possible repeat protein sequence and structure space and that it is possible to design novel repeat proteins with precisely specified geometries, opening up a wide array of new possibilities for biomolecular engineering.« less

  17. Genomic repeats, genome plasticity and the dynamics of Mycoplasma evolution

    PubMed Central

    Rocha, Eduardo P. C.; Blanchard, Alain

    2002-01-01

    Mycoplasmas evolved by a drastic reduction in genome size, but their genomes contain numerous repeated sequences with important roles in their evolution. We have established a bioinformatic strategy to detect the major recombination hot-spots in the genomes of Mycoplasma pneumoniae, Mycoplasma genitalium, Ureaplasma urealyticum and Mycoplasma pulmonis. This allowed the identification of large numbers of potentially variable regions, as well as a comparison of the relative recombination potentials of different genomic regions. Different trends are perceptible among mycoplasmas, probably due to different functional and structural constraints. The largest potential for illegitimate recombination in M.pulmonis is found at the vsa locus and its comparison in two different strains reveals numerous changes since divergence. On the other hand, the main M.pneumoniae and M.genitalium adhesins rely on large distant repeats and, hence, homologous recombination for variation. However, the relation between the existence of repeats and antigenic variation is not necessarily straightforward, since repeats of P1 adhesin were found to be anti-correlated with epitopes recognized by patient antibodies. These different strategies have important consequences for the structures of genomes, since large distant repeats correlate well with the major chromosomal rearrangements. Probably to avoid such events, mycoplasmas strongly avoid inverse repeats, in comparison to co-oriented repeats. PMID:11972343

  18. Environmental stress induces trinucleotide repeat mutagenesis in human cells.

    PubMed

    Chatterjee, Nimrat; Lin, Yunfu; Santillan, Beatriz A; Yotnda, Patricia; Wilson, John H

    2015-03-24

    The dynamic mutability of microsatellite repeats is implicated in the modification of gene function and disease phenotype. Studies of the enhanced instability of long trinucleotide repeats (TNRs)-the cause of multiple human diseases-have revealed a remarkable complexity of mutagenic mechanisms. Here, we show that cold, heat, hypoxic, and oxidative stresses induce mutagenesis of a long CAG repeat tract in human cells. We show that stress-response factors mediate the stress-induced mutagenesis (SIM) of CAG repeats. We show further that SIM of CAG repeats does not involve mismatch repair, nucleotide excision repair, or transcription, processes that are known to promote TNR mutagenesis in other pathways of instability. Instead, we find that these stresses stimulate DNA rereplication, increasing the proportion of cells with >4 C-value (C) DNA content. Knockdown of the replication origin-licensing factor CDT1 eliminates both stress-induced rereplication and CAG repeat mutagenesis. In addition, direct induction of rereplication in the absence of stress also increases the proportion of cells with >4C DNA content and promotes repeat mutagenesis. Thus, environmental stress triggers a unique pathway for TNR mutagenesis that likely is mediated by DNA rereplication. This pathway may impact normal cells as they encounter stresses in their environment or during development or abnormal cells as they evolve metastatic potential.

  19. Environmental stress induces trinucleotide repeat mutagenesis in human cells

    PubMed Central

    Chatterjee, Nimrat; Lin, Yunfu; Santillan, Beatriz A.; Yotnda, Patricia; Wilson, John H.

    2015-01-01

    The dynamic mutability of microsatellite repeats is implicated in the modification of gene function and disease phenotype. Studies of the enhanced instability of long trinucleotide repeats (TNRs)—the cause of multiple human diseases—have revealed a remarkable complexity of mutagenic mechanisms. Here, we show that cold, heat, hypoxic, and oxidative stresses induce mutagenesis of a long CAG repeat tract in human cells. We show that stress-response factors mediate the stress-induced mutagenesis (SIM) of CAG repeats. We show further that SIM of CAG repeats does not involve mismatch repair, nucleotide excision repair, or transcription, processes that are known to promote TNR mutagenesis in other pathways of instability. Instead, we find that these stresses stimulate DNA rereplication, increasing the proportion of cells with >4 C-value (C) DNA content. Knockdown of the replication origin-licensing factor CDT1 eliminates both stress-induced rereplication and CAG repeat mutagenesis. In addition, direct induction of rereplication in the absence of stress also increases the proportion of cells with >4C DNA content and promotes repeat mutagenesis. Thus, environmental stress triggers a unique pathway for TNR mutagenesis that likely is mediated by DNA rereplication. This pathway may impact normal cells as they encounter stresses in their environment or during development or abnormal cells as they evolve metastatic potential. PMID:25775519

  20. Expanded C9ORF72 Hexanucleotide Repeat in Depressive Pseudodementia

    PubMed Central

    Bieniek, Kevin F.; van Blitterswijk, Marka; Baker, Matthew C.; Petrucelli, Leonard; Rademakers, Rosa; Dickson, Dennis W.

    2014-01-01

    Importance Expanded hexanucleotide repeats in C9ORF72 are a common genetic cause of frontotemporal dementia and amyotrophic lateral sclerosis. Repeat expansions have also been detected infrequently in other disorders, including Alzheimer’s disease, dementia with Lewy bodies and Parkinsonian disorders. Objective To assess the incidence of the expanded C9ORF72 repeat in cases of depressive pseudodementia. Design An immunohistochemical screen of autopsied brains collected between 1998 and 2013. Setting Brain bank at Mayo Clinic Florida, a large tertiary care research institution. Participants Thirty one neuropathologically normal individuals (no atrophy, neuronal loss, or gliosis beyond what would be expected for age) with an antemortem clinical history or diagnosis of depression and/or dementia. Main Outcome Measures Presence of the hexanucleotide repeat was established using immunohistochemistry with a highly disease-specific antibody (C9RANT), and was further validated in carriers using repeat-primed polymerase chain reaction and Southern blotting. Results Of the 31 cases studied, 2 (6.45%) individuals harbored the C9ORF72 repeat expansion. Both patients were men with refractory depression. One patient experienced drug-induced Parkinsonism and sudden-onset dementia, while the other patient had a more insidious disease course suspected to be Alzheimer’s disease. Clinical and neuropathologic features are described. Conclusions and Relevance This report expands the range of clinicopathologic presentations of C9ORF72 expanded hexanucleotide repeat to include psychiatric disorders such as depressive pseudodementia. PMID:24756204

  1. Signal Hill solar-powered repeater report and recommendations

    NASA Astrophysics Data System (ADS)

    Smith, G. R.

    1984-08-01

    The parially active repeater (PAR) discussed is the GTE Lenkurt 700C1 repeater. The 700C1 repeater is the first radio of its kind to operate in the 7/8 GHz frequency band. The 700C1's low power consumption makes it ideal to be powered by solar voltaic cells. A new PAR site costs substantially less to develop than a fully active repeater since less support equipment is needed, no a-c power has to be brought to the site, and the building can be as small as 6' x 6'. A prototype 700C1 solar powered repeater was installed to eventually replace the existing poor microwave path between Big Eddy Substation and Wasco Radio Station. The repeater's RF performance is better than BPA's original specifications. The solar panels did not generate power during the winter months, so additional solar panels were added in May 1982. The new microwave path between Wasco and Big Eddy, via Signal Hill, is a large improvement over the previous path, which was via a double passive repeater; noise levels were reduced and signal strength improved.

  2. Exploring the repeat protein universe through computational protein design.

    PubMed

    Brunette, T J; Parmeggiani, Fabio; Huang, Po-Ssu; Bhabha, Gira; Ekiert, Damian C; Tsutakawa, Susan E; Hura, Greg L; Tainer, John A; Baker, David

    2015-12-24

    A central question in protein evolution is the extent to which naturally occurring proteins sample the space of folded structures accessible to the polypeptide chain. Repeat proteins composed of multiple tandem copies of a modular structure unit are widespread in nature and have critical roles in molecular recognition, signalling, and other essential biological processes. Naturally occurring repeat proteins have been re-engineered for molecular recognition and modular scaffolding applications. Here we use computational protein design to investigate the space of folded structures that can be generated by tandem repeating a simple helix-loop-helix-loop structural motif. Eighty-three designs with sequences unrelated to known repeat proteins were experimentally characterized. Of these, 53 are monomeric and stable at 95 °C, and 43 have solution X-ray scattering spectra consistent with the design models. Crystal structures of 15 designs spanning a broad range of curvatures are in close agreement with the design models with root mean square deviations ranging from 0.7 to 2.5 Å. Our results show that existing repeat proteins occupy only a small fraction of the possible repeat protein sequence and structure space and that it is possible to design novel repeat proteins with precisely specified geometries, opening up a wide array of new possibilities for biomolecular engineering.

  3. Triplet-repeat microsatellites shared among hard and soft pines.

    PubMed

    Kutil, B L; Williams, C G

    2001-01-01

    Vascular plant species have shown a low level of microsatellite conservation compared to many animal species. Finding trans-specific microsatellites for plants may be improved by using a priori knowledge of genome organization. Fifteen triplet-repeat microsatellites from hard pine (Pinus taeda L.) were tested for trans-specific amplification across seven hard pines (P. palustris Mill., P. echinata Mill., P. radiata D. Don., P. patula Schiede et Deppe, P. halepensis Mill., P. kesiya Royle), a soft pine (P. strobus L.), and Picea rubens Sargent. Seven of 15 microsatellites had trans-specific amplification in both hard and soft pine subgenera. Two P. taeda microsatellites had conserved flanking regions and repeat motifs in all seven hard pines, soft pine P. strobus, and P. rubens. Perfect triplet-repeat P. taeda microsatellites appear to be better candidates for trans-specific polymorphism than compound microsatellites. Not all perfect triplet-repeat microsatellites were conserved, but all conserved microsatellites had perfect repeat motifs. Persistent microsatellites PtTX2123 and PtTX3020 had highly conserved flanking regions and a conserved repeat motif composition with variable repeat unit numbers. Using trinucleotide microsatellites improved trans-specific microsatellite recovery among hard and soft pine species.

  4. Oxidative Stress Adaptation with Acute, Chronic and Repeated Stress

    PubMed Central

    Pickering, Andrew M.; Vojtovich, Lesya; Tower, John; Davies, Kelvin J. A.

    2013-01-01

    Oxidative stress adaptation or hormesis is an important mechanism by which cells and organisms respond to, and cope with, environmental and physiological shifts in the level of oxidative stress. Most studies of oxidative stress adaption have been limited to adaptation induced by acute stress. In contrast, many if not most environmental and physiological stresses are either repeated or chronic. In this study we find that both cultured mammalian cells, and the fruit fly Drosophila melanogaster, are capable of adapting to chronic or repeated stress by up-regulating protective systems, such as their proteasomal proteolytic capacity to remove oxidized proteins. Repeated stress adaptation resulted in significant extension of adaptive responses. Repeated stresses must occur at sufficiently long intervals, however (12 hours or more for MEF cells and 7 days or more for flies), for adaptation to be successful, and the level of both repeated and chronic stress must be lower than is optimal for adaptation to acute stress. Regrettably, regimens of adaptation to both repeated and chronic stress that were successful for short-term survival in Drosophila, nevertheless also caused significant reductions in lifespan for the flies. Thus, although both repeated and chronic stress can be tolerated, they may result in a shorter life. PMID:23142766

  5. Methods for analysing cardiovascular studies with repeated measures.

    PubMed

    Cleophas, T J; Zwinderman, A H; van Ouwerkerk, B M

    2009-11-01

    Background. Repeated measurements in a single subject are generally more similar than unrepeated measurements in different subjects. Unrepeated analyses of repeated data cause underestimation of the treatment effects.Objective. To review methods adequate for the analysis of cardiovascular studies with repeated measures.Results. (1) For between-subjects comparisons, summary measures and random-effects mixedlinear models are possible. Examples of summary measures include the area under the curve of drug time-concentration and time-efficacy curves, maximal values, mean values, and changes from baseline. A problem is that precision is lost because averages, rather than individual data, are applied. Random-effects mixed-linear models, available in SPSS statistical software and other software programmes, provide better precision for that purpose. (2) For within-subjects comparisons, repeated-measures ANOVAs are available in SPSS and other software programmes. Subgroup factors such as gender differences and age class can be included.Discussion. For non-Gaussian data, Wilcoxon's and Friedman's tests are available, for binary data McNemar's tests can be used in case of two repeated observations. No standard methods are available for repeated binary measures with more than two observations. The purpose of this review was not to present a complete report but, rather, to underline that ample efforts should be made to account for the special nature of repeated measures. (Neth Heart J 2009;17:429-33.).

  6. Repeatability of agronomic traits in Panicum maximum (Jacq.) hybrids.

    PubMed

    Braz, T G S; Fonseca, D M; Jank, L; Cruz, C D; Martuscello, J A

    2015-12-29

    When evaluating plants, in particular perennial species, it is common to obtain repeated measures of a given trait from the same individual to evaluate the traits' repeatability in successive harvests. The degree of correlation among these measures defines the coefficient of repeatability, which has been widely utilized in the study of forage traits of interest for breeding. The objective of the present study was to evaluate the repeatability of agronomic traits in Panicum maximum hybrids. Hybrids from three progenies totaling 320 hybrids were evaluated in an incomplete-block design, with consideration of production and morpho-agronomic traits. Of the production traits, total dry matter and leaf dry matter showed the highest repeatability and varied from 0.540 to 0.769, whereas stem dry matter had lower coefficients (0.265-0.632). Among the morpho-agronomic traits, plant height and incidence of Bipolaris maydis had higher coefficients (0.118-0.460). The repeatability values of the agronomic traits were low-to-moderate, and six evaluations were sufficient to provide accuracy in the selection of hybrids regarding total dry matter, leaf dry matter, plant height, and incidence of B. maydis, whereas the other traits require more repeated measures to increase reliability in the prediction of their response.

  7. Identification, variation and transcription of pneumococcal repeat sequences

    PubMed Central

    2011-01-01

    Background Small interspersed repeats are commonly found in many bacterial chromosomes. Two families of repeats (BOX and RUP) have previously been identified in the genome of Streptococcus pneumoniae, a nasopharyngeal commensal and respiratory pathogen of humans. However, little is known about the role they play in pneumococcal genetics. Results Analysis of the genome of S. pneumoniae ATCC 700669 revealed the presence of a third repeat family, which we have named SPRITE. All three repeats are present at a reduced density in the genome of the closely related species S. mitis. However, they are almost entirely absent from all other streptococci, although a set of elements related to the pneumococcal BOX repeat was identified in the zoonotic pathogen S. suis. In conjunction with information regarding their distribution within the pneumococcal chromosome, this suggests that it is unlikely that these repeats are specialised sequences performing a particular role for the host, but rather that they constitute parasitic elements. However, comparing insertion sites between pneumococcal sequences indicates that they appear to transpose at a much lower rate than IS elements. Some large BOX elements in S. pneumoniae were found to encode open reading frames on both strands of the genome, whilst another was found to form a composite RNA structure with two T box riboswitches. In multiple cases, such BOX elements were demonstrated as being expressed using directional RNA-seq and RT-PCR. Conclusions BOX, RUP and SPRITE repeats appear to have proliferated extensively throughout the pneumococcal chromosome during the species' past, but novel insertions are currently occurring at a relatively slow rate. Through their extensive secondary structures, they seem likely to affect the expression of genes with which they are co-transcribed. Software for annotation of these repeats is freely available from ftp://ftp.sanger.ac.uk/pub/pathogens/strep_repeats/. PMID:21333003

  8. Tandem-repeat protein domains across the tree of life

    PubMed Central

    Jernigan, Kristin K.

    2015-01-01

    Tandem-repeat protein domains, composed of repeated units of conserved stretches of 20–40 amino acids, are required for a wide array of biological functions. Despite their diverse and fundamental functions, there has been no comprehensive assessment of their taxonomic distribution, incidence, and associations with organismal lifestyle and phylogeny. In this study, we assess for the first time the abundance of armadillo (ARM) and tetratricopeptide (TPR) repeat domains across all three domains in the tree of life and compare the results to our previous analysis on ankyrin (ANK) repeat domains in this journal. All eukaryotes and a majority of the bacterial and archaeal genomes analyzed have a minimum of one TPR and ARM repeat. In eukaryotes, the fraction of ARM-containing proteins is approximately double that of TPR and ANK-containing proteins, whereas bacteria and archaea are enriched in TPR-containing proteins relative to ARM- and ANK-containing proteins. We show in bacteria that phylogenetic history, rather than lifestyle or pathogenicity, is a predictor of TPR repeat domain abundance, while neither phylogenetic history nor lifestyle predicts ARM repeat domain abundance. Surprisingly, pathogenic bacteria were not enriched in TPR-containing proteins, which have been associated within virulence factors in certain species. Taken together, this comparative analysis provides a newly appreciated view of the prevalence and diversity of multiple types of tandem-repeat protein domains across the tree of life. A central finding of this analysis is that tandem repeat domain-containing proteins are prevalent not just in eukaryotes, but also in bacterial and archaeal species. PMID:25653910

  9. Coding Tandem Repeats Generate Diversity in Aspergillus fumigatus Genes▿ †

    PubMed Central

    Levdansky, Emma; Romano, Jacob; Shadkchan, Yona; Sharon, Haim; Verstrepen, Kevin J.; Fink, Gerald R.; Osherov, Nir

    2007-01-01

    Genes containing multiple coding mini- and microsatellite repeats are highly dynamic components of genomes. Frequent recombination events within these tandem repeats lead to changes in repeat numbers, which in turn alters the amino acid sequence of the corresponding protein. In bacteria and yeasts, the expansion of such coding repeats in cell wall proteins is associated with alterations in immunogenicity, adhesion, and pathogenesis. We hypothesized that identification of repeat-containing putative cell wall proteins in the human pathogen Aspergillus fumigatus may reveal novel pathogenesis-related elements. Here, we report that the genome of A. fumigatus contains as many as 292 genes with internal repeats. Fourteen of 30 selected genes showed size variation of their repeat-containing regions among 11 clinical A. fumigatus isolates. Four of these genes, Afu3g08990, Afu2g05150 (MP-2), Afu4g09600, and Afu6g14090, encode putative cell wall proteins containing a leader sequence and a glycosylphosphatidylinositol anchor motif. All four genes are expressed and produce variable-size mRNA encoding a discrete number of repeat amino acid units. Their expression was altered during development and in response to cell wall-disrupting agents. Deletion of one of these genes, Afu3g08990, resulted in a phenotype characterized by rapid conidial germination and reduced adherence to extracellular matrix suggestive of an alteration in cell wall characteristics. The Afu3g08990 protein was localized to the cell walls of dormant and germinating conidia. Our findings suggest that a subset of the A. fumigatus cell surface proteins may be hypervariable due to recombination events in their internal tandem repeats. This variation may provide the functional diversity in cell surface antigens which allows rapid adaptation to the environment and/or elusion of the host immune system. PMID:17557878

  10. ACCA phosphopeptide recognition by the BRCT repeats of BRCA1.

    PubMed

    Ray, Hind; Moreau, Karen; Dizin, Eva; Callebaut, Isabelle; Venezia, Nicole Dalla

    2006-06-16

    The tumour suppressor gene BRCA1 encodes a 220 kDa protein that participates in multiple cellular processes. The BRCA1 protein contains a tandem of two BRCT repeats at its carboxy-terminal region. The majority of disease-associated BRCA1 mutations affect this region and provide to the BRCT repeats a central role in the BRCA1 tumour suppressor function. The BRCT repeats have been shown to mediate phospho-dependant protein-protein interactions. They recognize phosphorylated peptides using a recognition groove that spans both BRCT repeats. We previously identified an interaction between the tandem of BRCA1 BRCT repeats and ACCA, which was disrupted by germ line BRCA1 mutations that affect the BRCT repeats. We recently showed that BRCA1 modulates ACCA activity through its phospho-dependent binding to ACCA. To delineate the region of ACCA that is crucial for the regulation of its activity by BRCA1, we searched for potential phosphorylation sites in the ACCA sequence that might be recognized by the BRCA1 BRCT repeats. Using sequence analysis and structure modelling, we proposed the Ser1263 residue as the most favourable candidate among six residues, for recognition by the BRCA1 BRCT repeats. Using experimental approaches, such as GST pull-down assay with Bosc cells, we clearly showed that phosphorylation of only Ser1263 was essential for the interaction of ACCA with the BRCT repeats. We finally demonstrated by immunoprecipitation of ACCA in cells, that the whole BRCA1 protein interacts with ACCA when phosphorylated on Ser1263.

  11. Secure quantum network coding for controlled repeater networks

    NASA Astrophysics Data System (ADS)

    Shang, Tao; Li, Jiao; Liu, Jian-wei

    2016-07-01

    To realize efficient quantum communication based on quantum repeater, we propose a secure quantum network coding scheme for controlled repeater networks, which adds a controller as a trusted party and is able to control the process of EPR-pair distribution. As the key operations of quantum repeater, local operations and quantum communication are designed to adopt quantum one-time pad to enhance the function of identity authentication instead of local operations and classical communication. Scheme analysis shows that the proposed scheme can defend against active attacks for quantum communication and realize long-distance quantum communication with minimal resource consumption.

  12. Swelfe: a detector of internal repeats in sequences and structures

    PubMed Central

    Abraham, Anne-Laure; Rocha, Eduardo P. C.; Pothier, Joël

    2008-01-01

    Summary: Intragenic duplications of genetic material have important biological roles because of their protein sequence and structural consequences. We developed Swelfe to find internal repeats at three levels. Swelfe quickly identifies statistically significant internal repeats in DNA and amino acid sequences and in 3D structures using dynamic programming. The associated web server also shows the relationships between repeats at each level and facilitates visualization of the results. Availability: http://bioserv.rpbs.jussieu.fr/swelfe Contact: annela@abi.snv.jussieu.fr Supplementary information: Supplementary data are available at Bioinformatics online. PMID:18487242

  13. A selective-repeat ARQ scheme with finite receiver buffer

    NASA Astrophysics Data System (ADS)

    Lin, S.; Wang, Y.-M.

    A group automatic repeat request (ARQ) error detection scheme for data communications systems are analyzed theoretically. Three types of ARQ error detection schemes are considered: a stop-and-wait ARQ, a go-back-N ARQ and a selective repeat ARQ. The throughput performance of each scheme was determined mathematically. It is found that the selective repeat ARQ offers much better throughput performance than the other two schemes, particularly when applied to error control in high bit rate channels with considerable round trip delay between the transmission of a data block and acknowledgement.

  14. The Unstable Repeats - Three Evolving Faces of Neurological Disease

    PubMed Central

    Nelson, David L.; Orr, Harry T.; Warren, Stephen T.

    2013-01-01

    Disorders characterized by expansion of an unstable nucleotide repeat account for a number of inherited neurological diseases. Here, we review examples of unstable repeat disorders that nicely illustrate the three of the major pathogenic mechanisms associated with these diseases: loss-of-function typically by disrupting transcription of the mutated gene, RNA toxic gain-of-function, and protein toxic gain-of-function. In addition to providing insight into the mechanisms underlying these devastating neurological disorders, the study of these unstable microsatellite repeat disorders has provided insight into very basic aspects of neuroscience. PMID:23473314

  15. Measurement of Force Balance Repeatability and Reproducibility in the NTF

    NASA Technical Reports Server (NTRS)

    Hemsch, M. J.; Tuttle, D. G.; Houlden, H. P.; Graham, A. B.

    2004-01-01

    A recently published statistical approach for measuring and evaluating wind tunnel force balance repeatability and reproducibility is applied to three check standard tests in the National Transonic Facility at NASA Langley Research Center. Two different airframe models and force balances were used. The short-term repeatability and within-test reproducibility are separately estimated and correlations with tunnel parameters are carried out. Conjectures are presented for the development of scaling laws for predicting the repeatability and reproducibility of other force balance tests in the tunnel.

  16. Large Tandem, Higher Order Repeats and Regularly Dispersed Repeat Units Contribute Substantially to Divergence Between Human and Chimpanzee Y Chromosomes

    NASA Astrophysics Data System (ADS)

    Paar, Vladimir; Glunčić, Matko; Basar, Ivan; Rosandić, Marija; Paar, Petar; Cvitković, Mislav

    2011-01-01

    Comparison of human and chimpanzee genomes has received much attention, because of paramount role for understanding evolutionary step distinguishing us from our closest living relative. In order to contribute to insight into Y chromosome evolutionary history, we study and compare tandems, higher order repeats (HORs), and regularly dispersed repeats in human and chimpanzee Y chromosome contigs, using robust Global Repeat Map algorithm. We find a new type of long-range acceleration, human-accelerated HOR regions. In peripheral domains of 35mer human alphoid HORs, we find riddled features with ten additional repeat monomers. In chimpanzee, we identify 30mer alphoid HOR. We construct alphoid HOR schemes showing significant human-chimpanzee difference, revealing rapid evolution after human-chimpanzee separation. We identify and analyze over 20 large repeat units, most of them reported here for the first time as: chimpanzee and human ~1.6 kb 3mer secondary repeat unit (SRU) and ~23.5 kb tertiary repeat unit (~0.55 kb primary repeat unit, PRU); human 10848, 15775, 20309, 60910, and 72140 bp PRUs; human 3mer SRU (~2.4 kb PRU); 715mer and 1123mer SRUs (5mer PRU); chimpanzee 5096, 10762, 10853, 60523 bp PRUs; and chimpanzee 64624 bp SRU (10853 bp PRU). We show that substantial human-chimpanzee differences are concentrated in large repeat structures, at the level of as much as ~70% divergence, sizably exceeding previous numerical estimates for some selected noncoding sequences. Smeared over the whole sequenced assembly (25 Mb) this gives ~14% human--chimpanzee divergence. This is significantly higher estimate of divergence between human and chimpanzee than previous estimates.

  17. Large tandem, higher order repeats and regularly dispersed repeat units contribute substantially to divergence between human and chimpanzee Y chromosomes.

    PubMed

    Paar, Vladimir; Glunčić, Matko; Basar, Ivan; Rosandić, Marija; Paar, Petar; Cvitković, Mislav

    2011-01-01

    Comparison of human and chimpanzee genomes has received much attention, because of paramount role for understanding evolutionary step distinguishing us from our closest living relative. In order to contribute to insight into Y chromosome evolutionary history, we study and compare tandems, higher order repeats (HORs), and regularly dispersed repeats in human and chimpanzee Y chromosome contigs, using robust Global Repeat Map algorithm. We find a new type of long-range acceleration, human-accelerated HOR regions. In peripheral domains of 35mer human alphoid HORs, we find riddled features with ten additional repeat monomers. In chimpanzee, we identify 30mer alphoid HOR. We construct alphoid HOR schemes showing significant human-chimpanzee difference, revealing rapid evolution after human-chimpanzee separation. We identify and analyze over 20 large repeat units, most of them reported here for the first time as: chimpanzee and human ~1.6 kb 3mer secondary repeat unit (SRU) and ~23.5 kb tertiary repeat unit (~0.55 kb primary repeat unit, PRU); human 10848, 15775, 20309, 60910, and 72140 bp PRUs; human 3mer SRU (~2.4 kb PRU); 715mer and 1123mer SRUs (5mer PRU); chimpanzee 5096, 10762, 10853, 60523 bp PRUs; and chimpanzee 64624 bp SRU (10853 bp PRU). We show that substantial human-chimpanzee differences are concentrated in large repeat structures, at the level of as much as ~70% divergence, sizably exceeding previous numerical estimates for some selected noncoding sequences. Smeared over the whole sequenced assembly (25 Mb) this gives ~14% human-chimpanzee divergence. This is significantly higher estimate of divergence between human and chimpanzee than previous estimates.

  18. Repeatable measurements in quantum theory: Their role and feasibility

    SciTech Connect

    Busch, P.; Grabowski, M.; Lahti, P.J.

    1995-09-01

    Recent advantages in experimental quantum physics call for a careful reconsideration of the measurements process in quantum mechanics. In this paper we describe the structure of the ideal measurements and their status among the repeatable measurements. Then we provide an exhaustive account of the interrelations between repeatability and the apparently weaker notions of value reproducible or first-kind measurements. We demonstrate the close link between repeatable measurements and discrete observables and show how the ensuing measurement limitations for continuous observables can be lifted in a way that is in full accordance with actual experimental practice. We present examples of almost repeatable measurements of continuous observables and some realistic models of weakly disturbing measurements.

  19. Optimum periodicity of repeated contractile actions applied in mass transport

    PubMed Central

    Ahn, Sungsook; Lee, Sang Joon

    2015-01-01

    Dynamically repeated periodic patterns are abundant in natural and artificial systems, such as tides, heart beats, stock prices, and the like. The characteristic repeatability and periodicity are expected to be optimized in effective system-specific functions. In this study, such optimum periodicity is experimentally evaluated in terms of effective mass transport using one-valve and multi-valve systems working in contractile fluid flows. A set of nanoscale gating functions is utilized, operating in nanocomposite networks through which permeates selectively pass under characteristic contractile actions. Optimized contractile periodicity exists for effective energy impartment to flow in a one-valve system. In the sequential contractile actions for a multi-valve system, synchronization with the fluid flow is critical for effective mass transport. This study provides fundamental understanding on the various repeated periodic patterns and dynamic repeatability occurring in nature and mechanical systems, which are useful for broad applications. PMID:25622949

  20. Repeat laparotomy in a developing world tertiary level surgical service.

    PubMed

    Scriba, Matthias F; Laing, Grant L; Bruce, John L; Clarke, Damian L

    2015-10-01

    Repeat laparotomy is associated with significant morbidity and mortality; however, developing world data are scarce. This study reviews the spectrum and outcomes of relaparotomy in a developing world setting. Prospectively collected data from adult patients needing repeat laparotomy over an 18-month period were analyzed. Relaparotomy rate was 24% and average age was 38 years with a male predominance (70%). Appendicitis and trauma were the most common diagnoses. Planned relaparotomy rate was high (41%); however, negative relaparotomy rate was only 9%. Need for intensive care unit admission (51%) and morbidity rate (64%) were both high, but overall mortality rate was 14%. Patients requiring multiple relaparotomies had further worsened outcomes. The need for repeat laparotomy in the developing world is high and it is associated with significant morbidity and need for intensive care unit admission. However, mortality rates and negative repeat laparotomy rates were low. Copyright © 2015 Elsevier Inc. All rights reserved.

  1. Correct use of repeated measures analysis of variance.

    PubMed

    Park, Eunsik; Cho, Meehye; Ki, Chang-Seok

    2009-02-01

    In biomedical research, researchers frequently use statistical procedures such as the t-test, standard analysis of variance (ANOVA), or the repeated measures ANOVA to compare means between the groups of interest. There are frequently some misuses in applying these procedures since the conditions of the experiments or statistical assumptions necessary to apply these procedures are not fully taken into consideration. In this paper, we demonstrate the correct use of repeated measures ANOVA to prevent or minimize ethical or scientific problems due to its misuse. We also describe the appropriate use of multiple comparison tests for follow-up analysis in repeated measures ANOVA. Finally, we demonstrate the use of repeated measures ANOVA by using real data and the statistical software package SPSS (SPSS Inc., USA).

  2. Semiparametric bayesian inference for multilevel repeated measurement data.

    PubMed

    Müller, Peter; Quintana, Fernando A; Rosner, Gary L

    2007-03-01

    We discuss inference for data with repeated measurements at multiple levels. The motivating example is data with blood counts from cancer patients undergoing multiple cycles of chemotherapy, with days nested within cycles. Some inference questions relate to repeated measurements over days within cycle, while other questions are concerned with the dependence across cycles. When the desired inference relates to both levels of repetition, it becomes important to reflect the data structure in the model. We develop a semiparametric Bayesian modeling approach, restricting attention to two levels of repeated measurements. For the top-level longitudinal sampling model we use random effects to introduce the desired dependence across repeated measurements. We use a nonparametric prior for the random effects distribution. Inference about dependence across second-level repetition is implemented by the clustering implied in the nonparametric random effects model. Practical use of the model requires that the posterior distribution on the latent random effects be reasonably precise.

  3. An unusual case of repeated intracranial hemorrhage in vestibular schwannoma

    PubMed Central

    Banaama, Saeed; van Overbeeke, Jacobus; Temel, Yasin

    2016-01-01

    Background: Symptomatic intratumoral hemorrhage (ITH) in vestibular schwannoma (VS) is rare. A repeated hemorrhage is, therefore, even more exceptional. Repeated ITH has been reported in four cases thus far in English literature. Here, we describe a patient with a Koos grade D VS who presented to our Skull Base team with repeated ITH and an unexpected disease course. Case Description: A 76-year-old woman presented with hearing loss due to polycystic VS on the left side. Five years later, the patient was presented with facial palsy caused by hemorrhage in the VS. The patient had an eventful medical history that necessitated the use of anti-coagulants. The patient suffered from three subsequent hemorrhages preoperatively and one hemorrhage 36 h postoperatively. Conclusion: We have experienced multiple repeated hemorrhages in a patient with a polycystic VS, and despite surgical intervention, the outcome was unfavorable. PMID:27999710

  4. Optimum periodicity of repeated contractile actions applied in mass transport

    NASA Astrophysics Data System (ADS)

    Ahn, Sungsook; Lee, Sang Joon

    2015-01-01

    Dynamically repeated periodic patterns are abundant in natural and artificial systems, such as tides, heart beats, stock prices, and the like. The characteristic repeatability and periodicity are expected to be optimized in effective system-specific functions. In this study, such optimum periodicity is experimentally evaluated in terms of effective mass transport using one-valve and multi-valve systems working in contractile fluid flows. A set of nanoscale gating functions is utilized, operating in nanocomposite networks through which permeates selectively pass under characteristic contractile actions. Optimized contractile periodicity exists for effective energy impartment to flow in a one-valve system. In the sequential contractile actions for a multi-valve system, synchronization with the fluid flow is critical for effective mass transport. This study provides fundamental understanding on the various repeated periodic patterns and dynamic repeatability occurring in nature and mechanical systems, which are useful for broad applications.

  5. An optimal property of the repeated significance test

    PubMed Central

    Lerche, Hans Rudolf

    1986-01-01

    It is shown that the repeated significance test is a Bayes test for testing sequentially the sign of the drift of a Brownian motion. Its relation to Wald's sequential probability ratio test is studied. PMID:16593662

  6. A General Computational Approach for Repeat Protein Design

    PubMed Central

    Parmeggiani, Fabio; Huang, Po-Ssu; Vorobiev, Sergey; Xiao, Rong; Park, Keunwan; Caprari, Silvia; Su, Min; Jayaraman, Seetharaman; Mao, Lei; Janjua, Haleema; Montelione, Gaetano T.; Hunt, John; Baker, David

    2014-01-01

    Repeat proteins have considerable potential for use as modular binding reagents or biomaterials in biomedical and nanotechnology applications. Here we describe a general computational method for building idealized repeats that integrates available family sequences and structural information with Rosetta de novo protein design calculations. Idealized designs from six different repeat families were generated and experimentally characterized; 80% of the proteins were expressed and soluble and more than 40% were folded and monomeric with high thermal stability. Crystal structures determined for members of three families are within 1 Å root-mean-square deviation to the design models. The method provides a general approach for fast and reliable generation of stable modular repeat protein scaffolds. PMID:25451037

  7. Evolution of vulnerability of communities facing repeated hazards

    PubMed Central

    Guikema, Seth D.; Zhu, Laiyin; Igusa, Takeru

    2017-01-01

    The decisions that individuals make when recovering from and adapting to repeated hazards affect a region’s vulnerability in future hazards. As such, community vulnerability is not a static property but rather a dynamic property dependent on behavioral responses to repeated hazards and damage. This paper is the first of its kind to build a framework that addresses the complex interactions between repeated hazards, regional damage, mitigation decisions, and community vulnerability. The framework enables researchers and regional planners to visualize and quantify how a community could evolve over time in response to repeated hazards under various behavioral scenarios. An illustrative example using parcel-level data from Anne Arundel County, Maryland—a county that experiences fairly frequent hurricanes—is presented to illustrate the methodology and to demonstrate how the interplay between individual choices and regional vulnerability is affected by the region’s hurricane experience. PMID:28953893

  8. Highly Informative Simple Sequence Repeat (SSR) Markers for Fingerprinting Hazelnut

    USDA-ARS?s Scientific Manuscript database

    Simple sequence repeat (SSR) or microsatellite markers have many applications in breeding and genetic studies of plants, including fingerprinting of cultivars and investigations of genetic diversity, and therefore provide information for better management of germplasm collections. They are repeatab...

  9. Markerless modification of trinucleotide repeat loci in BACs.

    PubMed

    Benzow, Kellie A; Koob, Michael D

    2013-01-01

    Transcription and splicing of human genes are regulated by nucleotide sequences encoded across large segments of our genome, and trinucleotide repeat expansion mutations can have both profound and subtle effects on these processes. In the course of our work to understand the impact of the Spinocerebellar Ataxia type 8 (SCA8) CTG repeat expansion on the transcription and splicing of the RNAs encoded near the SCA8 locus, we have developed a set of reagents and protocols for modifying large genomic BAC clones of this region. We describe the two-step procedure that allows us to precisely replace unexpanded trinucleotide repeats with expanded variants of these repeat sequences without leaving any exogenous sequences in the final constructs, and we discuss how this approach can be adapted to make other desired sequence changes to these genomic clones.

  10. Relationship between quantum repeating devices and quantum seals

    SciTech Connect

    He Guangping

    2009-07-15

    It is revealed that quantum repeating devices and quantum seals have a very close relationship, thus the theory in one field can be applied to the other. Consequently, it is shown that the fidelity bounds and optimality of quantum repeating devices for decoding quantum information can be violated when they are used for decoding classical information from quantum states and the security bounds for protocols sealing quantum data exist.

  11. Repeated nondiagnostic result of thyroid fine-needle aspiration biopsy

    PubMed Central

    Kopczyński, Janusz; Kowalska, Aldona

    2017-01-01

    Aim of the study Fine-needle aspiration biopsy (FNAB) is the most accurate and cost-effective method to evaluate the risk of malignancy of thyroid nodules, but approximately 1–24% of FNABs generate a nondiagnostic result (ND-FNAB). The aim of this study was to determine the predictive factors of a repeated nondiagnostic result of FNAB. Material and methods A total of 4018 FNABs performed in a territorial referral centre were analysed, of which 288 (7.17%) were nondiagnostic. Medical records were available for 245 biopsies performed in 228 patients. The retrospective analysis of factors that may influence a repeat ND-FNAB, including demographic, clinical and ultrasound characteristics, was performed. Results A repeat FNAB was performed in 159 nodules giving a diagnostic result in 79.2% of cases. The time between the biopsies ranged from 1 to 611 days (mean 154.4, median 119). The timing of a repeat FNAB did not significantly alter the diagnostic output (p = 0.29). In the univariate analysis, significant predictors of a repeat ND-FNAB were older patient age (p = 0.02), L-thyroxine supplementation (p = 0.05), and a history of 131I therapy (p < 0.0001). In the multivariate analysis, only a history of 131I therapy was a statistically significant risk factor for a repeat ND-FNAB (p = 0.002). Conclusions Patients with a history of 131I therapy and ND-FNAB should undergo periodic ultrasonographic assessment rather than a repeat biopsy. The interval between repeated FNABs recommended by guidelines does not affect the diagnostic output. PMID:28239289

  12. Repeatability and Reproducibility of Decisions by Latent Fingerprint Examiners

    PubMed Central

    Ulery, Bradford T.; Hicklin, R. Austin; Buscaglia, JoAnn; Roberts, Maria Antonia

    2012-01-01

    The interpretation of forensic fingerprint evidence relies on the expertise of latent print examiners. We tested latent print examiners on the extent to which they reached consistent decisions. This study assessed intra-examiner repeatability by retesting 72 examiners on comparisons of latent and exemplar fingerprints, after an interval of approximately seven months; each examiner was reassigned 25 image pairs for comparison, out of total pool of 744 image pairs. We compare these repeatability results with reproducibility (inter-examiner) results derived from our previous study. Examiners repeated 89.1% of their individualization decisions, and 90.1% of their exclusion decisions; most of the changed decisions resulted in inconclusive decisions. Repeatability of comparison decisions (individualization, exclusion, inconclusive) was 90.0% for mated pairs, and 85.9% for nonmated pairs. Repeatability and reproducibility were notably lower for comparisons assessed by the examiners as “difficult” than for “easy” or “moderate” comparisons, indicating that examiners' assessments of difficulty may be useful for quality assurance. No false positive errors were repeated (n = 4); 30% of false negative errors were repeated. One percent of latent value decisions were completely reversed (no value even for exclusion vs. of value for individualization). Most of the inter- and intra-examiner variability concerned whether the examiners considered the information available to be sufficient to reach a conclusion; this variability was concentrated on specific image pairs such that repeatability and reproducibility were very high on some comparisons and very low on others. Much of the variability appears to be due to making categorical decisions in borderline cases. PMID:22427888

  13. The evolution of filamin-a protein domain repeat perspective.

    PubMed

    Light, Sara; Sagit, Rauan; Ithychanda, Sujay S; Qin, Jun; Elofsson, Arne

    2012-09-01

    Particularly in higher eukaryotes, some protein domains are found in tandem repeats, performing broad functions often related to cellular organization. For instance, the eukaryotic protein filamin interacts with many proteins and is crucial for the cytoskeleton. The functional properties of long repeat domains are governed by the specific properties of each individual domain as well as by the repeat copy number. To provide better understanding of the evolutionary and functional history of repeating domains, we investigated the mode of evolution of the filamin domain in some detail. Among the domains that are common in long repeat proteins, sushi and spectrin domains evolve primarily through cassette tandem duplications while scavenger and immunoglobulin repeats appear to evolve through clustered tandem duplications. Additionally, immunoglobulin and filamin repeats exhibit a unique pattern where every other domain shows high sequence similarity. This pattern may be the result of tandem duplications, serve to avert aggregation between adjacent domains or it is the result of functional constraints. In filamin, our studies confirm the presence of interspersed integrin binding domains in vertebrates, while invertebrates exhibit more varied patterns, including more clustered integrin binding domains. The most notable case is leech filamin, which contains a 20 repeat expansion and exhibits unique dimerization topology. Clearly, invertebrate filamins are varied and contain examples of similar adjacent integrin-binding domains. Given that invertebrate integrin shows more similarity to the weaker filamin binder, integrin β3, it is possible that the distance between integrin-binding domains is not as crucial for invertebrate filamins as for vertebrates. Copyright © 2012 Elsevier Inc. All rights reserved.

  14. The evolution of filamin – A protein domain repeat perspective

    PubMed Central

    Light, Sara; Sagit, Rauan; Ithychanda, Sujay S.; Qin, Jun; Elofsson, Arne

    2013-01-01

    Particularly in higher eukaryotes, some protein domains are found in tandem repeats, performing broad functions often related to cellular organization. For instance, the eukaryotic protein filamin interacts with many proteins and is crucial for the cytoskeleton. The functional properties of long repeat domains are governed by the specific properties of each individual domain as well as by the repeat copy number. To provide better understanding of the evolutionary and functional history of repeating domains, we investigated the mode of evolution of the filamin domain in some detail. Among the domains that are common in long repeat proteins, sushi and spectrin domains evolve primarily through cassette tandem duplications while scavenger and immunoglobulin repeats appear to evolve through clustered tandem duplications. Additionally, immunoglobulin and filamin repeats exhibit a unique pattern where every other domain shows high sequence similarity. This pattern may be the result of tandem duplications, serve to avert aggregation between adjacent domains or it is the result of functional constraints. In filamin, our studies confirm the presence of interspersed integrin binding domains in vertebrates, while invertebrates exhibit more varied patterns, including more clustered integrin binding domains. The most notable case is leech filamin, which contains a 20 repeat expansion and exhibits unique dimerization topology. Clearly, invertebrate filamins are varied and contain examples of similar adjacent integrin-binding domains. Given that invertebrate integrin shows more similarity to the weaker filamin binder, integrin β3, it is possible that the distance between integrin-binding domains is not as crucial for invertebrate filamins as for vertebrates. PMID:22414427

  15. Repeated nondiagnostic result of thyroid fine-needle aspiration biopsy.

    PubMed

    Ziemiańska, Klaudia; Kopczyński, Janusz; Kowalska, Aldona

    2016-01-01

    Fine-needle aspiration biopsy (FNAB) is the most accurate and cost-effective method to evaluate the risk of malignancy of thyroid nodules, but approximately 1-24% of FNABs generate a nondiagnostic result (ND-FNAB). The aim of this study was to determine the predictive factors of a repeated nondiagnostic result of FNAB. A total of 4018 FNABs performed in a territorial referral centre were analysed, of which 288 (7.17%) were nondiagnostic. Medical records were available for 245 biopsies performed in 228 patients. The retrospective analysis of factors that may influence a repeat ND-FNAB, including demographic, clinical and ultrasound characteristics, was performed. A repeat FNAB was performed in 159 nodules giving a diagnostic result in 79.2% of cases. The time between the biopsies ranged from 1 to 611 days (mean 154.4, median 119). The timing of a repeat FNAB did not significantly alter the diagnostic output (p = 0.29). In the univariate analysis, significant predictors of a repeat ND-FNAB were older patient age (p = 0.02), L-thyroxine supplementation (p = 0.05), and a history of (131)I therapy (p < 0.0001). In the multivariate analysis, only a history of (131)I therapy was a statistically significant risk factor for a repeat ND-FNAB (p = 0.002). Patients with a history of (131)I therapy and ND-FNAB should undergo periodic ultrasonographic assessment rather than a repeat biopsy. The interval between repeated FNABs recommended by guidelines does not affect the diagnostic output.

  16. Cumulative effects from repeated exposures to ultraviolet radiation

    SciTech Connect

    Kaidbey, K.H.; Kligman, A.M.

    1981-05-01

    Repeated exposures to subliminal doses of UVR, given at 24-hr intervals, resulted in a lowering of the erythema threshold dose. At erythemogenically equivalent doses, UV-A was the most effective and UV-C the least. A similar and more pronounced effect was observed following repeated exposures to subthreshold doses of UV-A and topically applied 8-methoxypsoralen. These findings provide quantitative evidence for the cumulative nature of acute UVR damage in human skin.

  17. Optimal entanglement generation for efficient hybrid quantum repeaters

    SciTech Connect

    Azuma, Koji; Sota, Naoya; Yamamoto, Takashi; Koashi, Masato; Imoto, Nobuyuki; Namiki, Ryo; Oezdemir, Sahin Kaya

    2009-12-15

    We propose a realistic protocol to generate entanglement between quantum memories at neighboring nodes in hybrid quantum repeaters. Generated entanglement includes only one type of error, which enables efficient entanglement distillation. In contrast to the known protocols with such a property, our protocol with ideal detectors achieves the theoretical limit of the success probability and the fidelity to a Bell state, promising higher efficiencies in the repeaters. We also show that the advantage of our protocol remains even with realistic threshold detectors.

  18. Repeated swim stress alters brain benzodiazepine receptors measured in vivo

    SciTech Connect

    Weizman, R.; Weizman, A.; Kook, K.A.; Vocci, F.; Deutsch, S.I.; Paul, S.M.

    1989-06-01

    The effects of repeated swim stress on brain benzodiazepine receptors were examined in the mouse using both an in vivo and in vitro binding method. Specific in vivo binding of (/sup 3/H)Ro15-1788 to benzodiazepine receptors was decreased in the hippocampus, cerebral cortex, hypothalamus, midbrain and striatum after repeated swim stress (7 consecutive days of daily swim stress) when compared to nonstressed mice. In vivo benzodiazepine receptor binding was unaltered after repeated swim stress in the cerebellum and pons medulla. The stress-induced reduction in in vivo benzodiazepine receptor binding did not appear to be due to altered cerebral blood flow or to an alteration in benzodiazepine metabolism or biodistribution because there was no difference in (14C)iodoantipyrine distribution or whole brain concentrations of clonazepam after repeated swim stress. Saturation binding experiments revealed a change in both apparent maximal binding capacity and affinity after repeated swim stress. Moreover, a reduction in clonazepam's anticonvulsant potency was also observed after repeated swim stress (an increase in the ED50 dose for protection against pentylenetetrazol-induced seizures), although there was no difference in pentylenetetrazol-induced seizure threshold between the two groups. In contrast to the results obtained in vivo, no change in benzodiazepine receptor binding kinetics was observed using the in vitro binding method. These data suggest that environmental stress can alter the binding parameters of the benzodiazepine receptor and that the in vivo and in vitro binding methods can yield substantially different results.

  19. Evolutionary dynamics of satellite DNA repeats from Phaseolus beans.

    PubMed

    Ribeiro, Tiago; Dos Santos, Karla G B; Richard, Manon M S; Sévignac, Mireille; Thareau, Vincent; Geffroy, Valérie; Pedrosa-Harand, Andrea

    2017-03-01

    Common bean (Phaseolus vulgaris) subtelomeres are highly enriched for khipu, the main satellite DNA identified so far in this genome. Here, we comparatively investigate khipu genomic organization in Phaseolus species from different clades. Additionally, we identified and characterized another satellite repeat, named jumper, associated to khipu. A mixture of P. vulgaris khipu clones hybridized in situ confirmed the presence of khipu-like sequences on subterminal chromosome regions in all Phaseolus species, with differences in the number and intensity of signals between species and when species-specific clones were used. Khipu is present as multimers of ∼500 bp and sequence analyses of cloned fragments revealed close relationship among khipu repeats. The new repeat, named jumper, is a 170-bp satellite sequence present in all Phaseolus species and inserted into the nontranscribed spacer (NTS) of the 5S rDNA in the P. vulgaris genome. Nevertheless, jumper was found as a high-copy repeat at subtelomeres and/or pericentromeres in the Phaseolus microcarpus lineage only. Our data argue for khipu as an important subtelomeric satellite DNA in the genus and for a complex satellite repeat composition of P. microcarpus subtelomeres, which also contain jumper. Furthermore, the differential amplification of these repeats in subtelomeres or pericentromeres reinforces the presence of a dynamic satellite DNA library in Phaseolus.

  20. Impact of Repeated Exposures on Information Spreading in Social Networks.

    PubMed

    Zhou, Cangqi; Zhao, Qianchuan; Lu, Wenbo

    2015-01-01

    Clustered structure of social networks provides the chances of repeated exposures to carriers with similar information. It is commonly believed that the impact of repeated exposures on the spreading of information is nontrivial. Does this effect increase the probability that an individual forwards a message in social networks? If so, to what extent does this effect influence people's decisions on whether or not to spread information? Based on a large-scale microblogging data set, which logs the message spreading processes and users' forwarding activities, we conduct a data-driven analysis to explore the answer to the above questions. The results show that an overwhelming majority of message samples are more probable to be forwarded under repeated exposures, compared to those under only a single exposure. For those message samples that cover various topics, we observe a relatively fixed, topic-independent multiplier of the willingness of spreading when repeated exposures occur, regardless of the differences in network structure. We believe that this finding reflects average people's intrinsic psychological gain under repeated stimuli. Hence, it makes sense that the gain is associated with personal response behavior, rather than network structure. Moreover, we find that the gain is robust against the change of message popularity. This finding supports that there exists a relatively fixed gain brought by repeated exposures. Based on the above findings, we propose a parsimonious model to predict the saturated numbers of forwarding activities of messages. Our work could contribute to better understandings of behavioral psychology and social media analytics.

  1. Quantum repeater based on cavity QED evolutions and coherent light

    NASA Astrophysics Data System (ADS)

    Gonţa, Denis; van Loock, Peter

    2016-05-01

    In the framework of cavity QED, we propose a quantum repeater scheme that uses coherent light and chains of atoms coupled to optical cavities. In contrast to conventional repeater schemes, in our scheme there is no need for an explicit use of two-qubit quantum logical gates by exploiting solely the cavity QED evolution. In our previous work (Gonta and van Loock in Phys Rev A 88:052308, 2013), we already proposed a quantum repeater in which the entanglement between two neighboring repeater nodes was distributed using controlled displacements of input coherent light, while the produced low-fidelity entangled pairs were purified using ancillary (four-partite) entangled states. In the present work, the entanglement distribution is realized using a sequence of controlled phase shifts and displacements of input coherent light. Compared to previous coherent-state-based distribution schemes for two-qubit entanglement, our scheme here relies only upon a simple discrimination of two coherent states with opposite signs, which can be performed in a quantum mechanically optimal fashion via a beam splitter and two on-off detectors. For the entanglement purification, we employ a method that avoids the use of extra entangled ancilla states. Our repeater scheme exhibits reasonable fidelities and repeater rates providing an attractive platform for long-distance quantum communication.

  2. The meaning of sampling density in multiple repeat prostate biopsies

    PubMed Central

    Čapoun, Otakar; Minárik, Ivo; Kýr, Michal; Hanuš, Tomáš; Babjuk, Marek; Sobotka, Roman

    2016-01-01

    Introduction Extended transrectal ultrasound-guided prostate biopsy is a state-of-the-art tool for prostate cancer detection. Nevertheless, approximately 1/3 of cancers are missed when using this method and repeat biopsy sessions are often required. The aim of this study was to investigate how sampling density (a compound variable reflecting the number of biopsy cores and prostate volume) impacts on detection rate in multiple repeat TRUS-biopsies. Material and methods A total of 1007 consecutive patients undergoing their 1st, 2nd, 3rd and any further repeat prostate biopsies were included. The relationship between sampling density and other clinical variables (age, prostate-specific antigen level, free/total PSA ratio, digital rectal examination, number of previous biopsies) and cancer detection rate were assessed by interaction analysis. Results There were 562 primary re-biopsies, 267 second re-biopsies and 178 third and further re-biopsies included in the study. Detection rate was 25.4%, 25.8% and 25.3%, respectively. Interaction of sampling density with age was demonstrated in patients undergoing their first repeat biopsy (but not further re-biopsies). No interaction was observed with other variables investigated. Conclusions A more extensive prostate sampling leads to a higher cancer detection rate on repeat prostate biopsies, as shown previously. However, this effect seems to be particularly pronounced in men younger than 65 years undergoing their first repeat prostate biopsy. PMID:28127449

  3. Ising Model Reprogramming of a Repeat Protein's Equilibrium Unfolding Pathway.

    PubMed

    Millership, C; Phillips, J J; Main, E R G

    2016-05-08

    Repeat proteins are formed from units of 20-40 aa that stack together into quasi one-dimensional non-globular structures. This modular repetitive construction means that, unlike globular proteins, a repeat protein's equilibrium folding and thus thermodynamic stability can be analysed using linear Ising models. Typically, homozipper Ising models have been used. These treat the repeat protein as a series of identical interacting subunits (the repeated motifs) that couple together to form the folded protein. However, they cannot describe subunits of differing stabilities. Here we show that a more sophisticated heteropolymer Ising model can be constructed and fitted to two new helix deletion series of consensus tetratricopeptide repeat proteins (CTPRs). This analysis, showing an asymmetric spread of stability between helices within CTPR ensembles, coupled with the Ising model's predictive qualities was then used to guide reprogramming of the unfolding pathway of a variant CTPR protein. The designed behaviour was engineered by introducing destabilising mutations that increased the thermodynamic asymmetry within a CTPR ensemble. The asymmetry caused the terminal α-helix to thermodynamically uncouple from the rest of the protein and preferentially unfold. This produced a specific, highly populated stable intermediate with a putative dimerisation interface. As such it is the first step in designing repeat proteins with function regulated by a conformational switch.

  4. Repeated measurement sampling in genetic association analysis with genotyping errors.

    PubMed

    Lai, Renzhen; Zhang, Hong; Yang, Yaning

    2007-02-01

    Genotype misclassification occurs frequently in human genetic association studies. When cases and controls are subject to the same misclassification model, Pearson's chi-square test has the correct type I error but may lose power. Most current methods adjusting for genotyping errors assume that the misclassification model is known a priori or can be assessed by a gold standard instrument. But in practical applications, the misclassification probabilities may not be completely known or the gold standard method can be too costly to be available. The repeated measurement design provides an alternative approach for identifying misclassification probabilities. With this design, a proportion of the subjects are measured repeatedly (five or more repeats) for the genotypes when the error model is completely unknown. We investigate the applications of the repeated measurement method in genetic association analysis. Cost-effectiveness study shows that if the phenotyping-to-genotyping cost ratio or the misclassification rates are relatively large, the repeat sampling can gain power over the regular case-control design. We also show that the power gain is not sensitive to the genetic model, genetic relative risk and the population high-risk allele frequency, all of which are typically important ingredients in association studies. An important implication of this result is that whatever the genetic factors are, the repeated measurement method can be applied if the genotyping errors must be accounted for or the phenotyping cost is high.

  5. DNA methylation and triplet repeat stability: New proposals addressing actual questions on the CGG repeat of fragile X syndrome

    SciTech Connect

    Woehrle, D.; Schwemmle, S.; Steinbach, P.

    1996-08-09

    Methylation of expanded CGG repeats in the FMR1 gene may well have different consequences. One is that methylation, extending into upstream regulatory elements, could lead to gene inactivation. Another effect of methylation, which we have obtained evidence for, could be stabilization of the repeat sequence and even prevention of premutations from expansion to full mutation. The full mutation of the fragile X syndrome probably occurs in an early transitional stage of embryonic development. The substrate is a maternally inherited premutation. The product usually is a mosaic pattern of full mutations detectable in early fetal life. These full mutation patterns are mitotically stable as, for instance, different somatic tissues of full mutation fetuses show identical mutation patterns. This raised the following questions: What triggers repeat expansion in that particular stage of development and what causes subsequent mitotic stability of expanded repeats? 21 refs., 1 fig.

  6. Filamin repeat segments required for photosensory signalling in Dictyostelium discoideum

    PubMed Central

    Annesley, Sarah J; Bandala-Sanchez, Esther; Ahmed, Afsar U; Fisher, Paul R

    2007-01-01

    Background Filamin is an actin binding protein which is ubiquitous in eukaryotes and its basic structure is well conserved – an N-terminal actin binding domain followed by a series of repeated segments which vary in number in different organisms. D. discoideum is a well established model organism for the study of signalling pathways and the actin cytoskeleton and as such makes an excellent organism in which to study filamin. Ddfilamin plays a putative role as a scaffolding protein in a photosensory signalling pathway and this role is thought to be mediated by the unusual repeat segments in the rod domain. Results To study the role of filamin in phototaxis, a filamin null mutant, HG1264, was transformed with constructs each of which expressed wild type filamin or a mutant filamin with a deletion of one of the repeat segments. Transformants expressing the full length filamin to wild type levels completely rescued the phototaxis defect in HG1264, however if filamin was expressed at lower than wild type levels the phototaxis defect was not restored. The transformants lacking any one of the repeat segments 2–6 retained defective phototaxis and thermotaxis phenotypes, whereas transformants expressing filaminΔ1 exhibited a range of partial complementation of the phototaxis phenotype which was related to expression levels. Immunofluorescence microscopy showed that filamin lacking any of the repeat segments still localised to the same actin rich areas as wild type filamin. Ddfilamin interacts with RasD and IP experiments demonstrated that this interaction did not rely upon any single repeat segment or the actin binding domain. Conclusion This paper demonstrates that wild type levels of filamin expression are essential for the formation of functional photosensory signalling complexes and that each of the repeat segments 2–6 are essential for filamins role in phototaxis. By contrast, repeat segment 1 is not essential provided the mutated filamin lacking repeat segment

  7. Fracture prediction from repeat BMD measurements in clinical practice.

    PubMed

    Leslie, W D; Brennan-Olsen, S L; Morin, S N; Lix, L M

    2016-01-01

    We investigated whether repeat BMD measurements in clinical populations are useful for fracture risk assessment. We report that repeat BMD measurements are a robust predictor of fracture in clinical populations; this is not affected by preceding BMD change or recent osteoporosis therapy. In clinical practice, many patients selectively undergo repeat bone mineral density (BMD) measurements. We investigated whether repeat BMD measurements in clinical populations are useful for fracture risk assessment and whether this is affected by preceding change in BMD or recent osteoporosis therapy. We identified women and men aged ≥ 50 years who had a BMD measurement during 1990-2009 from a large clinical BMD database for Manitoba, Canada (n = 50,215). Patient subgroups aged ≥ 50 years at baseline with repeat BMD measures were identified. Data were linked to an administrative data repository, from which osteoporosis therapy, fracture outcomes, and covariates were extracted. Using Cox proportional hazards models, we assessed covariate-adjusted risk for major osteoporotic fracture (MOF) and hip fracture according to BMD (total hip, lumbar spine, femoral neck) at different time points. Prevalence of osteoporosis therapy increased from 18 % at baseline to 55 % by the fourth measurement. Total hip BMD was predictive of MOF at each time point. In the patient subgroup with two repeat BMD measurements (n = 13,481), MOF prediction with the first and second measurements was similar: adjusted-hazard ratio (HR) per SD 1.45 (95 % CI 1.34-1.56) vs. 1.64 (95 % CI 1.48-1.81), respectively. No differences were seen when the second measurement results were stratified by preceding change in BMD or osteoporosis therapy (both p-interactions >0.2). Similar results were seen for hip fracture prediction and when spine and femoral neck BMD were analyzed. Repeat BMD measurements are a robust predictor of fracture in clinical populations; this is not affected by preceding BMD change or recent

  8. Tandem repeats of Allium fistulosum associated with major chromosomal landmarks.

    PubMed

    Kirov, Ilya V; Kiseleva, Anna V; Van Laere, Katrijn; Van Roy, Nadine; Khrustaleva, Ludmila I

    2017-04-01

    Tandem repeats are often associated with important chromosomal landmarks, such as centromeres, telomeres, subtelomeric, and other heterochromatic regions, and can be good candidates for molecular cytogenetic markers. Tandem repeats present in many plant species demonstrate dramatic differences in unit length, proportion in the genome, and chromosomal organization. Members of genus Allium with their large genomes represent a challenging task for current genetics. Using the next generation sequencing data, molecular, and cytogenetic methods, we discovered two tandemly organized repeats in the Allium fistulosum genome (2n = 2C = 16), HAT58 and CAT36. Together, these repeats comprise 0.25% of the bunching onion genome with 160,000 copies/1 C of HAT58 and 93,000 copies/1 C of CAT36. Fluorescent in situ hybridization (FISH) and C-banding showed that HAT58 and CAT36 associated with the interstitial and pericentromeric heterochromatin of the A. fistulosum chromosomes 5, 6, 7, and 8. FISH with HAT58 and CAT36 performed on A. cepa (2n = 2C = 16) and A. wakegi (2n = 2C = 16), a natural allodiploid hybrid between A. fistulosum and A. cepa, revealed that these repeats are species specific and produced specific hybridization patterns only on A. fistulosum chromosomes. Thus, the markers can be used in interspecific breeding programs for monitoring of alien genetic material. We applied Non-denaturing FISH that allowed detection of the repeat bearing chromosomes within 3 h. A polymorphism of the HAT58 chromosome location was observed. This finding suggests that the rapid evolution of the HAT58 repeat is still ongoing.

  9. Repeated high-intensity exercise in professional rugby union.

    PubMed

    Austin, Damien; Gabbett, Tim; Jenkins, David

    2011-07-01

    The aim of the present study was to describe the frequency, duration, and nature of repeated high-intensity exercise in Super 14 rugby union. Time-motion analysis was used during seven competition matches over the 2008 and 2009 Super 14 seasons; five players from each of four positional groups (front row forwards, back row forwards, inside backs, and outside backs) were assessed (20 players in total). A repeated high-intensity exercise bout was considered to involve three or more sprints, and/or tackles and/or scrum/ruck/maul activities within 21 s during the same passage of play. The range of repeated high-intensity exercise bouts for each group in a match was as follows: 11-18 for front row forwards, 11-21 for back row forwards, 13-18 for inside backs, and 2-11 for outside backs. The durations of the most intense repeated high-intensity exercise bouts for each position ranged from 53 s to 165 s and the minimum recovery periods between repeated high-intensity exercise bouts ranged from 25 s for the back row forwards to 64 s for the front row forwards. The present results show that repeated high-intensity exercise bouts vary in duration and activities relative to position but all players in a game will average at least 10 changes in activity in the most demanding bouts and complete at least one tackle and two sprints. The most intense periods of activity are likely to last as long as 120 s and as little as 25 s recovery may separate consecutive repeated high-intensity exercise bouts. The present findings can be used by coaches to prepare their players for the most demanding passages of play likely to be experienced in elite rugby union.

  10. Intra-examiner repeatability and agreement in accommodative response measurements.

    PubMed

    Antona, B; Sanchez, I; Barrio, A; Barra, F; Gonzalez, E

    2009-11-01

    Clinical measurement of the accommodative response (AR) identifies the focusing plane of a subject with respect to the accommodative target. To establish whether a significant change in AR has occurred, it is important to determine the repeatability of this measurement. This study had two aims: First, to determine the intraexaminer repeatability of AR measurements using four clinical methods: Nott retinoscopy, monocular estimate method (MEM) retinoscopy, binocular crossed cylinder test (BCC) and near autorefractometry. Second, to study the level of agreement between AR measurements obtained with the different methods. The AR of the right eye at one accommodative demand of 2.50 D (40 cm) was measured on two separate occasions in 61 visually normal subjects of mean age 19.7 years (range 18-32 years). The intraexaminer repeatability of the tests, and agreement between them, were estimated by the Bland-Altman method. We determined mean differences (MD) and the 95% limits of agreement [coefficient of repeatability (COR) and coefficient of agreement (COA)]. Nott retinoscopy and BCC offered the best repeatability, showing the lowest MD and narrowest 95% interval of agreement (Nott: -0.10 +/- 0.66 D, BCC: -0.05 +/- 0.75 D). The 95% limits of agreement for the four techniques were similar (COA = +/- 0.92 to +/-1.00 D) yet clinically significant, according to the expected values of the AR. The two dynamic retinoscopy techniques (Nott and MEM) had a better agreement (COA = +/-0.64 D) although this COA must be interpreted in the context of the low MEM repeatability (COR = +/-0.98 D). The best method of assessing AR was Nott retinoscopy. The BCC technique was also repeatable, and both are recommended as suitable methods for clinical use. Despite better agreement between MEM and Nott, agreement among the remaining methods was poor such that their interchangeable use in clinical practice is not recommended.

  11. Effect of repeated Kangaroo Mother Care on repeated procedural pain in preterm infants: A randomized controlled trial.

    PubMed

    Gao, Haixia; Xu, Guihua; Gao, Honglian; Dong, Rongzhi; Fu, Hongjie; Wang, Danwen; Zhang, Heng; Zhang, Hua

    2015-07-01

    Preterm infants' repeated exposure to painful procedures may lead to negative consequences. Thus, non-pharmacological pain management is essential due to medication side effects. Kangaroo Mother Care, which aims at offering human care to neonates, has been established for the treatment of a single painful procedure, but the effectiveness of Kangaroo Mother Care across repeated painful procedures is unknown. To test the effectiveness of repeated Kangaroo Mother Care on repeated heel-stick pain in preterm neonates. Randomized controlled trial. Level III Neonatal Intensive Care Unit at a large teaching hospital in northeast China. Preterm infants (gestational age less than 37 weeks) (n=80) were recruited and randomly assigned using a random table format to either an incubator group (n=40) or Kangaroo Mother Care group (n=40). Pain assessments were carried out during four routine heel stick procedures. For the first heel stick, preterm infants in each group received no intervention (routinely stayed in incubator). During the next three heel sticks, the infants in Kangaroo Mother Care group received heel sticks during Kangaroo Mother Care, while infants in the incubator group received heel sticks in incubator. The procedure of each heel stick included 3 phases: baseline, blood collection and recovery. Crying, grimacing and heart rate in response to pain were evaluated at each phase across four heel sticks by three trained independent observers who were blinded to the purpose of the study. Data were analyzed by analysis of variance (ANOVA), with repeated measures at different evaluation phases of heel stick. 75 preterm infants completed the protocol. Between-group comparison revealed that preterm infants' heart rate was significantly lower, and the duration of crying and facial grimacing were both significantly shorter in the Kangaroo Mother Care group (n=38) than the incubator group (n=37) from the blood collection phase to recovery phase during repeated heel sticks. No

  12. Elective repeat cesarean sections: how many could be vaginal births?

    PubMed Central

    Norman, P; Kostovcik, S; Lanning, A

    1993-01-01

    OBJECTIVE: To determine (a) the proportion of women undergoing elective repeat cesarean section without a trial of labour who were eligible for such a trial by the 1986 guidelines of the panel of the National Consensus Conference on Aspects of Cesarean Birth, (b) whether vaginal birth after cesarean section (VBAC) was discussed with these women and (c) the reasons cited for not having a trial of labour. DESIGN: Chart audit. SETTING: Level 2 perinatal care centre in a general teaching hospital. PATIENTS: All 313 women with a history of previous cesarean section who gave birth at the centre during 1989. RESULTS: Only 93 (30%) of the 313 women underwent a trial of labour. According to the 1986 guidelines 71% were eligible. A further 13% would have been eligible according to the revised 1991 guidelines. Of the 220 women who underwent elective repeat cesarean section, only 24 (11%) had a discussion of VBAC noted in their hospital charts. However, of all 117 patients whose charts indicated discussion of VBAC 93 (79%) chose to try it. Most of the women had either questionable indications or no indication noted for undergoing repeat cesarean section. CONCLUSION: Most of the women who underwent repeat cesarean section were eligible for a trial of labour. However, few charts noted a discussion of VBAC. Further physician and patient education is necessary to promote the appropriate use of VBAC and repeat cesarean section. PMID:8348425

  13. Maternal views and experiences regarding repeat Caesarean section.

    PubMed

    Olofinbiyi, B A; Olofinbiyi, R O; Aduloju, O P; Atiba, B P; Olaogun, O D; Ogundare, O R

    2015-01-01

    The aim was to determine maternal views and experiences regarding repeat caesarean section. A pretested and validated semi-structured questionnaire was administered to women with prior cesarean section by trained research assistants and resident doctors; anonymity and confidentiality were strictly observed. The questionnaire comprised information reflecting patients' sociodemographic structure, level of education, number of previous cesarean section, maternal complications following previous cesarean and opinions about acceptance and refusal of cesarean section. Two hundred and twenty-seven women participated in the study out of which 157 (69.2%) would accept a repeat cesarean section and 70 (30.8%) would not accept. Significant proportion of respondents above 35 years of age would refuse a repeat cesarean section (58.6%). Religious belief (39.7%) and pain (26.5%) were the most common reasons for refusal of cesarean section. Appreciable proportion of women with previous caesarean section will decline a repeat cesarean section. Re-orientation, reappraisal and appropriate corrective action in the areas of religious belief and postoperative pain management will positively influence our women's acceptance of a repeat cesarean section.

  14. Diagnosis of repeated failures in discrete event systems.

    SciTech Connect

    Garcia, H. E.; Jiang, S.; Kumar, R.; Univ. of Kentucky; Iowa State Univ.

    2002-01-01

    We introduce the notion of repeated failure diagnosability for diagnosing the occurrence of a repeated number of failures in discrete event systems. This generalizes the earlier notion of diagnosability that was used to diagnose the occurrence of a failure, but from which the information regarding the multiplicity of the occurrence of the failure could not be obtained. It is possible that in some systems the same type of failure repeats a multiple number of times. It is desirable to have a diagnoser which not only diagnoses that such a failure has occurred but also determines the number of times the failure has occurred. To aide such analysis we introduce the notions of K-diagnosability (K failures diagnosability), [1, K]-diagnosability (1 through K failures diagnosability), and [1, /spl infin/]-diagnosability (1 through /spl infin/ failures diagnosability). Here the first notion is the weakest of all three, and the earlier notion of diagnosability is the same as that of K-diagnosability or that of [1, K]-diagnosability with K=1. We give polynomial algorithms for checking these various notions of repeated failure diagnosability, and also present a procedure of polynomial complexity for the online diagnosis of repeated failures.

  15. Diagnosis of repeated/intermittent failures in discrete event systems.

    SciTech Connect

    Garcia, H. E.; Jiang, S.; Kumar, R.

    2003-04-01

    We introduce the notion of repeated failure diagnosability for diagnosing the occurrence of a repeated number of failures in discrete event systems. This generalizes the earlier notion of diagnosability that was used to diagnose the occurrence of a failure, but from which the information regarding the multiplicity of the occurrence of the failure could not be obtained. It is possible that in some systems the same type of failure repeats a multiple number of times. It is desirable to have a diagnoser which not only diagnoses that such a failure has occurred but also determines the number of times the failure has occurred. To aide such analysis we introduce the notions of K-diagnosability (K failures diagnosability), [1,K]-diagnosability (1 through K failures diagnosability), and [1,1]-diagnosability (1 through 1 failures diagnosability). Here the rst (resp., last) notion is the weakest (resp., strongest) of all three, and the earlier notion of diagnosability is the same as that of K-diagnosability or that of [1,K]- diagnosability with K = 1. We give polynomial algorithms for checking these various notions of repeated failure diagnosability, and also present a procedure of polynomial complexity for the on-line diagnosis of repeated failures.

  16. Implementation of bipartite or remote unitary gates with repeater nodes

    NASA Astrophysics Data System (ADS)

    Yu, Li; Nemoto, Kae

    2016-08-01

    We propose some protocols to implement various classes of bipartite unitary operations on two remote parties with the help of repeater nodes in-between. We also present a protocol to implement a single-qubit unitary with parameters determined by a remote party with the help of up to three repeater nodes. It is assumed that the neighboring nodes are connected by noisy photonic channels, and the local gates can be performed quite accurately, while the decoherence of memories is significant. A unitary is often a part of a larger computation or communication task in a quantum network, and to reduce the amount of decoherence in other systems of the network, we focus on the goal of saving the total time for implementing a unitary including the time for entanglement preparation. We review some previously studied protocols that implement bipartite unitaries using local operations and classical communication and prior shared entanglement, and apply them to the situation with repeater nodes without prior entanglement. We find that the protocols using piecewise entanglement between neighboring nodes often require less total time compared to preparing entanglement between the two end nodes first and then performing the previously known protocols. For a generic bipartite unitary, as the number of repeater nodes increases, the total time could approach the time cost for direct signal transfer from one end node to the other. We also prove some lower bounds of the total time when there are a small number of repeater nodes. The application to position-based cryptography is discussed.

  17. Repeat instability during DNA repair: Insights from model systems

    PubMed Central

    Usdin, Karen; House, Nealia C. M.; Freudenreich, Catherine H.

    2015-01-01

    The expansion of repeated sequences is the cause of over 30 inherited genetic diseases, including Huntington disease, myotonic dystrophy (types 1 and 2), fragile X syndrome, many spinocerebellar ataxias, and some cases of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Repeat expansions are dynamic, and disease inheritance and progression are influenced by the size and the rate of expansion. Thus, an understanding of the various cellular mechanisms that cooperate to control or promote repeat expansions is of interest to human health. In addition, the study of repeat expansion and contraction mechanisms has provided insight into how repair pathways operate in the context of structure-forming DNA, as well as insights into non-canonical roles for repair proteins. Here we review the mechanisms of repeat instability, with a special emphasis on the knowledge gained from the various model systems that have been developed to study this topic. We cover the repair pathways and proteins that operate to maintain genome stability, or in some cases cause instability, and the cross-talk and interactions between them. PMID:25608779

  18. Polymorphism of CAG repeats in androgen receptor of carnivores.

    PubMed

    Wang, Qin; Zhang, Xiuyue; Wang, Xiaofang; Zeng, Bo; Jia, Xiaodong; Hou, Rong; Yue, Bisong

    2012-03-01

    Androgen effect is mediated by the androgen receptor (AR). The polymorphism of CAG triplet repeat (polyCAG), in the N-terminal transactivation domain of the AR protein, has been involved either in endocrine or neurological disorders in human. We obtained partial sequence of AR exon 1 in 10 carnivore species. In most carnivore species, polyglutamine length polymorphism presented in all three CAG repeat regions of AR, in contrast, only CAG-I site polymorphism presented in primate species, and CAG-I and CAG-III sites polymorphism presented in Canidae. Therefore, studies focusing on disease-associated polymorphism of poly(CAG) in carnivore species AR should investigate all three CAG repeats sites, and should not only consider CAG-I sites as the human disease studies. The trinucleotide repeat length in carnivore AR exon 1 had undergone from expansions to contractions during carnivores evolution, unlike a linear increase in primate species. Furthermore, the polymorphisms of the triplet-repeats in the same tissue (somatic mosaicism) were demonstrated in Moutain weasel, Eurasian lynx, Clouded leopard, Chinese tiger, Black leopard and Leopard AR. And, the abnormal stop codon was found in the exon 1 of three carnivore species AR (Moutain weasel, Eurasian lynx and Black leopard). It seemed to have a high frequency presence of tissue-specific somatic in carnivores AR genes. Thus the in vivo mechanism leading to such highly variable phenotypes of the described mutations, and their impact on these animals, are worthwhile to be further elucidated.

  19. Electromyographic analysis of repeated bouts of eccentric exercise.

    PubMed

    McHugh, M P; Connolly, D A; Eston, R G; Gartman, E J; Gleim, G W

    2001-03-01

    The repeated bout effect refers to the protective effect provided by a single bout of eccentric exercise against muscle damage from a similar subsequent bout. The aim of this study was to determine if the repeated bout was associated with an increase in motor unit activation relative to force production, an increased recruitment of slow-twitch motor units or increased motor unit synchronization. Surface electromyographic (EMG) signals were recorded from the hamstring muscles during two bouts of submaximal isokinetic (2.6 rad x s(-1)) eccentric (11 men, 9 women) or concentric (6 men, 4 women) contractions separated by 2 weeks. The EMG per unit torque and median frequency were analysed. The initial bout of eccentric exercise resulted in strength loss, pain and muscle tenderness, while the repeated eccentric bout resulted in a slight increase in strength, no pain and no muscle tenderness (bout x time effects, P < 0.05). Strength, pain and tenderness were unaffected by either bout of concentric exercise. The EMG per unit torque and median frequency were not different between the initial and repeated bouts of eccentric exercise. The EMG per unit torque and median frequency increased during both bouts of eccentric exercise (P < 0.01) but did not change during either concentric bout. In conclusion, there was no evidence that the repeated bout effect was due to a neural adaptation.

  20. Computer Simulation Studies of CTG Triplet Repeat Sequences

    NASA Astrophysics Data System (ADS)

    Rasaiah, Jayendran. C.; Lynch, Joshua

    1998-03-01

    Long segments of CTG trinucleotide repeats in human DNA are correlated with a class of neurological diseases (myotonic dystrophy, fragile-X syndrome, and Kenndy's disease). These diseases are characterized by genetic anticipation and are thought to arise from replication errors caused by unusual conformations of CTG repeat segments. We have studied the properties of a single short segment of double starnded DNA with CTG repeats in 0.5 M sodium chloride solution with molecular dynamics simulations. The simulations are carried out in the micro canonical ensemble using an all-atom force field with CHARMM parameters. The TIPS3 water model is used to simulate a molecular solvent. Electrostatic interactions are calculated by Ewald summation and the equations of motion integrated using a Verlet algorithm in conjunction with SHAKE constrained dynamics to maintain bond lengths. The simulation of CTG repeat sequence is compared with a control system containing CAG triplet repeats to determine possible differencesin the conformation and elasticity of the two sequences.

  1. Design and analysis of communication protocols for quantum repeater networks

    NASA Astrophysics Data System (ADS)

    Jones, Cody; Kim, Danny; Rakher, Matthew T.; Kwiat, Paul G.; Ladd, Thaddeus D.

    2016-08-01

    We analyze how the performance of a quantum-repeater network depends on the protocol employed to distribute entanglement, and we find that the choice of repeater-to-repeater link protocol has a profound impact on entanglement-distribution rate as a function of hardware parameters. We develop numerical simulations of quantum networks using different protocols, where the repeater hardware is modeled in terms of key performance parameters, such as photon generation rate and collection efficiency. These parameters are motivated by recent experimental demonstrations in quantum dots, trapped ions, and nitrogen-vacancy centers in diamond. We find that a quantum-dot repeater with the newest protocol (‘MidpointSource’) delivers the highest entanglement-distribution rate for typical cases where there is low probability of establishing entanglement per transmission, and in some cases the rate is orders of magnitude higher than other schemes. Our simulation tools can be used to evaluate communication protocols as part of designing a large-scale quantum network.

  2. Discrepancy variation of dinucleotide microsatellite repeats in eukaryotic genomes.

    PubMed

    Gao, Huan; Cai, Shengli; Yan, Binlun; Chen, Baiyao; Yu, Fei

    2009-01-01

    To address whether there are differences of variation among repeat motif types and among taxonomic groups, we present here an analysis of variation and correlation of dinucleotide microsatellite repeats in eukaryotic genomes. Ten taxonomic groups were compared, those being primates, mammalia (excluding primates and rodentia), rodentia, birds, fish, amphibians and reptiles, insects, molluscs, plants and fungi, respectively. The data used in the analysis is from the literature published in the Journal of Molecular Ecology Notes. Analysis of variation reveals that there are no significant differences between AC and AG repeat motif types. Moreover, the number of alleles correlates positively with the copy number in both AG and AC repeats. Similar conclusions can be obtained from each taxonomic group. These results strongly suggest that the increase of SSR variation is almost linear with the increase of the copy number of each repeat motif. As well, the results suggest that the variability of SSR in the genomes of low-ranking species seem to be more than that of high-ranking species, excluding primates and fungi.

  3. Repeat expansion and autosomal dominant neurodegenerative disorders: consensus and controversy.

    PubMed

    Rudnicki, Dobrila D; Margolis, Russell L

    2003-08-22

    Repeat-expansion mutations cause 13 autosomal dominant neurodegenerative disorders falling into three groups. Huntington's disease (HD), dentatorubral pallidoluysian atrophy (DRPLA), spinal and bulbar muscular atrophy (SBMA), and spinocerebellar ataxias (SCAs) types 1, 2, 3, 7 and 17 are each caused by a CAG repeat expansion that encodes polyglutamine. Convergent lines of evidence demonstrate that neurodegeneration in these diseases is a consequence of the neurotoxic effects of abnormally long stretches of glutamines. How polyglutamine induces neurodegeneration, and why neurodegeneration occurs in only select neuronal populations, remains a matter of intense investigation. SCA6 is caused by a CAG repeat expansion in CACNA1A, a gene that encodes a subunit of the P/Q-type calcium channel. The threshold length at which the repeat causes disease is much shorter than in the other polyglutamine diseases, and neurodegeneration may arise from expansion-induced change of function in the calcium channel. Huntington's disease-like 2 (HDL2) and SCAs 8, 10 and 12 are rare disorders in which the repeats (CAG, CTG or ATTCT) are not in protein-coding regions. Investigation into these diseases is still at an early stage, but it is now reasonable to hypothesise that the net effect of each expansion is to alter gene expression. The different pathogenic mechanisms in these three groups of diseases have important implications for the development of rational therapeutics.

  4. Alanine repeats influence protein localization in splicing speckles and paraspeckles.

    PubMed

    Chang, Shuo-Hsiu; Chang, Wei-Lun; Lu, Chia-Chen; Tarn, Woan-Yuh

    2014-12-16

    Mammalian splicing regulatory protein RNA-binding motif protein 4 (RBM4) has an alanine repeat-containing C-terminal domain (CAD) that confers both nuclear- and splicing speckle-targeting activities. Alanine-repeat expansion has pathological potential. Here we show that the alanine-repeat tracts influence the subnuclear targeting properties of the RBM4 CAD in cultured human cells. Notably, truncation of the alanine tracts redistributed a portion of RBM4 to paraspeckles. The alanine-deficient CAD was sufficient for paraspeckle targeting. On the other hand, alanine-repeat expansion reduced the mobility of RBM4 and impaired its splicing activity. We further took advantage of the putative coactivator activator (CoAA)-RBM4 conjoined splicing factor, CoAZ, to investigate the function of the CAD in subnuclear targeting. Transiently expressed CoAZ formed discrete nuclear foci that emerged and subsequently separated-fully or partially-from paraspeckles. Alanine-repeat expansion appeared to prevent CoAZ separation from paraspeckles, resulting in their complete colocalization. CoAZ foci were dynamic but, unlike paraspeckles, were resistant to RNase treatment. Our results indicate that the alanine-rich CAD, in conjunction with its conjoined RNA-binding domain(s), differentially influences the subnuclear localization and biogenesis of RBM4 and CoAZ.

  5. The second STEP: the feasibility of repeat serial transverse enteroplasty.

    PubMed

    Piper, Hannah; Modi, Biren P; Kim, Heung Bae; Fauza, Dario; Glickman, John; Jaksic, Tom

    2006-12-01

    Serial transverse enteroplasty (STEP) lengthens and tapers dilated bowel. Redilation of the STEP segment occurs in some patients with intestinal failure. The feasibility of a repeat STEP procedure in a pig model is evaluated. Six pigs underwent reversal of an intestinal segment distal to the ligament of Treitz. At 6-week intervals after reversal, each animal had 2 STEP procedures on the bowel proximal to the reversed segment. Necropsy was performed up to 6 weeks after repeat STEP. Bowel length increased by 11.3 +/- 3.9 cm and bowel diameter decreased from a mean of 5.3 +/- 0.8 to 1.8 +/- 0.4 cm (P < .0001) after the first STEP. After repeat STEP, bowel length increased by 16.7 +/- 13.3 cm (P < .01), and the bowel was tapered from a mean of 5.4 +/- 0.9 to 2.2 +/- 0.4 cm (P < .01). Five pigs did well after repeat STEP, and 1 pig had early necropsy for bowel obstruction. None had histologic evidence of bowel ischemia in the repeat STEP segment. A second STEP operation is feasible in a pig model and may be considered to optimize bowel length and function in select patients with intestinal failure.

  6. Transcription-induced DNA toxicity at trinucleotide repeats

    PubMed Central

    Wilson, John H

    2011-01-01

    Trinucleotide repeats (TNRs) are a blessing and a curse. In coding regions, where they are enriched, short repeats offer the potential for continuous, rapid length variation with linked incremental changes in the activity of the encoded protein, a valuable source of variation for evolution. But at the upper end of these benign and beneficial lengths, trinucleotide repeats become very unstable, with a dangerous bias toward continual expansion, which can lead to neurological diseases in humans. The mechanisms of expansion are varied and the links to disease are complex. Where they have been delineated, however, they have often revealed unexpected, fundamental aspects of the underlying cell biology. Nowhere is this more apparent than in recent studies, which indicate that expanded CAG repeats can form toxic sites in the genome, which can, upon interaction with normal components of DNA metabolism, trigger cell death. Here we discuss the phenomenon of TNR-induced DNA toxicity, with special emphasis on the role of transcription. Transcription-induced DNA toxicity may have profound biological consequences, with particular relevance to repeat-associated neurodegenerative diseases. PMID:21293182

  7. Analysing two dinucleotide repeats of FVIII gene in Iranian population.

    PubMed

    Rabbani, B; Rezaeian, A; Khanahmad, H; Bagheri, R; Kamali, E; Zeinali, S

    2007-11-01

    Using dinucleotide repeats for carrier detection and prenatal diagnosis of haemophilia A patients, led us to find different alleles and their frequencies in Iranian population. Polymerase chain reaction (PCR) amplification of two short tandem repeat (STR) loci of factor VIII (FVIII) gene was performed, and the PCR products were resolved on 10% native polyacrylamide gel, and samples were analysed with sequenced DNA markers made of PCR cloning of the dinucleotide FVIII gene fragments. Seven different alleles were observed for intron 13 STR, having 18-24 (CA) repeating units and five alleles for intron 22 STR having 24-28 repeating units of (CACT). Bands produced during dinucleotide study were defined in detail so this could improve the genotyping of heterozygotes and homozygotes. Conformational band produced were characterized to specify the dinucleotide pattern. Our results confirm the Hardy-Weinberg proportions of the heterozygosity rate of the 85 analysed individuals. The observed heterozygosity rate for intron 13 and 22 was 52% and 59% respectively. Our data also indicate that our population is closer to caucasians than to any other populations. Finding different dinucleotide repeat alleles and their frequencies has made it possible to identify carriers and provide prenatal diagnosis with more confidence. This allows antenatal diagnosis to be performed in the vast majority of carriers.

  8. Time course of the attenuation effect of repeated antipsychotic treatment on prepulse inhibition disruption induced by repeated phencyclidine treatment

    PubMed Central

    Li, Ming; He, Erik; Volf, Nick

    2011-01-01

    Antagonism of prepulse inhibition (PPI) deficits produced by psychotomimetic drugs has been widely used as an effective tool for the study of the mechanisms of antipsychotic action and identifying potential antipsychotic drugs. Many studies have relied on the acute effect of a single administration of antipsychotics, whereas patients with schizophrenia are treated chronically with antipsychotic drugs. The clinical relevance of acute antipsychotic effect in this model is still an open question. In this study, we investigated the time course of repeated antipsychotic treatment on persistent PPI deficit induced by repeated phencyclidine (PCP) treatment. After a baseline test with saline, male Sprague-Dawley rats were repeatedly injected with either vehicle, haloperidol (0.05 mg/kg), clozapine (5.0 or 10.0 mg/kg), olanzapine (2.0 mg/kg), risperidone (1.0 mg/kg) or quetiapine (10 mg/kg), followed by PCP (1.5 mg/kg, sc) and tested for PPI once daily for 6 consecutive days. A single injection of PCP disrupted PPI and this effect was maintained with repeated PCP injections throughout the testing period. Acute clozapine, but not other antipsychotic drugs, attenuated acute PCP-induced PPI disruption at both tested doses. With repeated treatment, clozapine and quetiapine maintained their attenuation, while risperidone enhanced its effect with a significant reduction of PCP-induced disruption toward the end of treatment period. In contrast, repeated haloperidol and olanzapine treatments were ineffective. The PPI effects of these drugs were more conspicuous at a higher prepulse level (e.g. 82 dB) and were dissociable from their effects on startle response and general activity. Overall, the repeated PCP-PPI model appears to be a useful model for the study of the time-dependent antipsychotic effect, and may help identify potential treatments that have a quicker onset of action than current antipsychotics. PMID:21402097

  9. A PLL Synthesizer with Learning Repeatable Fluctuation of Input Signal

    NASA Astrophysics Data System (ADS)

    Ono, Hiroyuki

    This paper describes a high frequency PLL (Phase Locked Loop) synthesizer with a function of learning then eliminating repeatable fluctuation of timing intervals on series input pulses. Typical spindle encoder generates digital pulses according to the revolution speed. The intervals of each pulse have repeatable fluctuation every revolution by eccentricity or warpage of the encoder scale disk. This method provides a programmable counter for the loop counter of PLL circuit and an interval counter with memory in order to learn the repeatable fluctuation. After the learning process, the PLL generates very pure tone clock signal based on the real flutter components of the spindle revolution speed without influenced by encoder errors. This method has been applied to a hard disk test system in order to generate 3GHz read/write clock.

  10. Repeat expansion disease: Progress and puzzles in disease pathogenesis

    PubMed Central

    La Spada, Albert R.; Taylor, J. Paul

    2015-01-01

    Repeat expansion mutations cause at least 22 inherited neurological diseases. The complexity of repeat disease genetics and pathobiology has revealed unexpected shared themes and mechanistic pathways among the diseases, for example, RNA toxicity. Also, investigation of the polyglutamine diseases has identified post-translational modification as a key step in the pathogenic cascade, and has shown that the autophagy pathway plays an important role in the degradation of misfolded proteins – two themes likely to be relevant to the entire neurodegeneration field. Insights from repeat disease research are catalyzing new lines of study that should not only elucidate molecular mechanisms of disease, but also highlight opportunities for therapeutic intervention for these currently untreatable disorders. PMID:20177426

  11. Assessing agreement with repeated measures for random observers.

    PubMed

    Chen, Chia-Cheng; Barnhart, Huiman X

    2011-12-30

    Agreement studies are often concerned with assessing whether different observers for measuring responses on the same subject or sample can produce similar results. The concordance correlation coefficient (CCC) is a popular index for assessing the closeness among observers for quantitative measurements. Usually, the CCC is used for data without and with replications based on subject and observer effects only. However, we cannot use this methodology if repeated measurements rather than replications are collected. Although there exist some CCC-type indices for assessing agreement with repeated measurements, there is no CCC for random observers and random time points. In this paper, we propose a new CCC for repeated measures where both observers and time points are treated as random effects. A simulation study demonstrates our proposed methodology, and we use vertebral body data and image data for illustrations. Copyright © 2011 John Wiley & Sons, Ltd.

  12. REPPER—repeats and their periodicities in fibrous proteins

    PubMed Central

    Gruber, Markus; Söding, Johannes; Lupas, Andrei N.

    2005-01-01

    REPPER (REPeats and their PERiodicities) is an integrated server that detects and analyzes regions with short gapless repeats in protein sequences or alignments. It finds periodicities by Fourier Transform (FTwin) and internal similarity analysis (REPwin). FTwin assigns numerical values to amino acids that reflect certain properties, for instance hydrophobicity, and gives information on corresponding periodicities. REPwin uses self-alignments and displays repeats that reveal significant internal similarities. Both programs use a sliding window to ensure that different periodic regions within the same protein are detected independently. FTwin and REPwin are complemented by secondary structure prediction (PSIPRED) and coiled coil prediction (COILS), making the server a versatile analysis tool for sequences of fibrous proteins. REPPER is available at . PMID:15980460

  13. Nonlinear analysis of correlations in Alu repeat sequences in DNA

    NASA Astrophysics Data System (ADS)

    Xiao, Yi; Huang, Yanzhao; Li, Mingfeng; Xu, Ruizhen; Xiao, Saifeng

    2003-12-01

    We report on a nonlinear analysis of deterministic structures in Alu repeats, one of the richest repetitive DNA sequences in the human genome. Alu repeats contain the recognition sites for the restriction endonuclease AluI, which is what gives them their name. Using the nonlinear prediction method developed in chaos theory, we find that all Alu repeats have novel deterministic structures and show strong nonlinear correlations that are absent from exon and intron sequences. Furthermore, the deterministic structures of Alus of younger subfamilies show panlike shapes. As young Alus can be seen as mutation free copies from the “master genes,” it may be suggested that the deterministic structures of the older subfamilies are results of an evolution from a “panlike” structure to a more diffuse correlation pattern due to mutation.

  14. Effects of repeated production on vowel distinctiveness within nonwords.

    PubMed

    Sasisekaran, Jayanthi; Munson, Benjamin

    2012-04-01

    In the present study acoustic distinctiveness of vowels within nonwords with repeated production was investigated. Participants were 9 males and 15 females divided into two groups. Participants repeated 6 nonwords varying in phonemic composition. The mean Euclidean distance (MED) of the vowels from each production of a nonword from the center of the F1/F2 space was calculated. The changes in MED with repeated production were analyzed using linear mixed effects regression. Results revealed an increase in MED, indicating greater vowel dispersion, for the three-syllable nonwords and a significant decrease, i.e., greater reduction, in vowel dispersion for the six-syllable nonwords. Findings support the dynamic influence of sublexical processes on phonetic realization in speech production.

  15. Tandem repeat distribution of gene transcripts in three plant families

    PubMed Central

    2009-01-01

    Tandem repeats (microsatellites or SSRs) are molecular markers with great potential for plant genetic studies. Modern strategies include the transfer of these markers among widely studied and orphan species. In silico analyses allow for studying distribution patterns of microsatellites and predicting which motifs would be more amenable to interspecies transfer. Transcribed sequences (Unigene) from ten species of three plant families were surveyed for the occurrence of micro and minisatellites. Transcripts from different species displayed different rates of tandem repeat occurrence, ranging from 1.47% to 11.28%. Both similar and different patterns were found within and among plant families. The results also indicate a lack of association between genome size and tandem repeat fractions in expressed regions. The conservation of motifs among species and its implication on genome evolution and dynamics are discussed. PMID:21637460

  16. Behavior changes during repeated eight-day extinctions1

    PubMed Central

    Anger, Douglas; Anger, Kathleen

    1976-01-01

    Pigeons were given repeated two-day conditionings alternating with eight-day extinctions using a trial procedure. One group had different key colors during each of the first five conditioning-extinction pairs; another group had the same key color throughout. Total extinction responses of both groups were quite constant over successive extinctions. This finding differs from the rapid declines found in most previous studies with bar-press and key-peck responses. The difference probably was due to our longer extinctions, because responses early in each extinction did decrease. However, that decrease was neutralized by increases in responses late in each extinction. The two opposite changes indicate the influence of two different factors during repeated extinctions, with neither factor having much stimulus specificity. The reduction of early responses may result from feeding changes confounded with extinction. The increase in later extinction responses may result from a decrease in the effect of unreinforced responses after their repeated occurrence. PMID:16811939

  17. Archery performance level and repeatability of event-related EMG.

    PubMed

    Soylu, A R; Ertan, H; Korkusuz, F

    2006-12-01

    The purpose of the current study was to compare the repeatability of electromyographic linear envelopes (LE) of archery groups. Surface electromyography (EMG) signals of musculus flexor digitorum superficialis (MFDS) and extensor digitorum (MED) of 23 participants (seven skilled, six beginner archers and ten non-archers) were recorded during archery shooting. Two-second periods (clicker falls at first second) of 12 shots' EMG data were recorded, full-wave rectified and filtered (60 ms moving-average filter) for each participant's drawing arm. Repeatability was investigated by using a statistical criterion, variance ratio (VR). Archers' performances were evaluated in terms of FITA scores. The results showed that FITA scores were significantly correlated to the VRs of MFDS and MED. EMG LEs were more repeatable among archers than non-archers. Therefore, we inferred that VRs of MFDS and MED might be important variables for (a) assessing shooting techniques, (b) evaluation of archers' progress, and (c) selection of talented archers.

  18. Structural analysis of a multifunctional, tandemly repeated inositol polyphosphatase.

    PubMed

    Gruninger, Robert J; Selinger, L Brent; Mosimann, Steven C

    2009-09-11

    Mitsuokella multacida expresses a unique inositol polyphosphatase (PhyAmm) that is composed of tandem repeats (TRs). Each repeat possesses a protein tyrosine phosphatase (PTP) active-site signature sequence and fold. Using a combination of structural, mutational, and kinetic studies, we show that the N-terminal (D1) and C-terminal (D2) active sites of the TR have diverged and possess significantly different specificities for inositol polyphosphate. Structural analysis and molecular docking calculations identify steric and electrostatic differences within the substrate binding pocket of each TR that may be involved in the altered substrate specificity. The implications of our results for the biological function of related PTP-like phytases are discussed. Finally, the structures and activities of PhyAmm and tandemly repeated receptor PTPs are compared and discussed. To our knowledge, this is the first example of an inositol phosphatase with tandem PTP domains possessing substrate specificity for different inositol phosphates.

  19. Recognition of hypermethylated triplet repeats in vitro by cationic nanoparticles

    NASA Astrophysics Data System (ADS)

    Gearheart, Latha A.; Caswell, Kimberlyn; Murphy, Catherine J.

    2001-04-01

    Genomic DNA contains many higher-order structural deviations from the Watson-Crick global average. The massive expansion and hypermethylation of the duplex triplet repeat (CCG)n(CGG)n has characteristic higher-order structures that are associated with the fragile X syndrome. We have used luminescent mineral nanoparticles of protein-sized cadmium sulfide in optical assays to detect anomalous DNA structures. The photoluminescence of these particles is sensitive to the presence and nature of adsorbates. We previously found that our nanoparticles bind the fragile X repeat well but do not bind to normal double-helical DNA. In this study, we have determined that these particles are also able to detect the hypermethylated forms of these triplet repeats. Therefore, these nanoparticles may form the basis for future optical assays of higher-order DNA structures, especially those associated with human disease.

  20. Precise estimation of repeating earthquake moment: Example from parkfield, california

    USGS Publications Warehouse

    Rubinstein, J.L.; Ellsworth, W.L.

    2010-01-01

    We offer a new method for estimating the relative size of repeating earthquakes using the singular value decomposition (SVD). This method takes advantage of the highly coherent waveforms of repeating earthquakes and arrives at far more precise and accurate descriptions of earthquake size than standard catalog techniques allow. We demonstrate that uncertainty in relative moment estimates is reduced from ??75% for standard coda-duration techniques employed by the network to an uncertainty of ??6.6% when the SVD method is used. This implies that a single-station estimate of moment using the SVD method has far less uncertainty than the whole-network estimates of moment based on coda duration. The SVD method offers a significant improvement in our ability to describe the size of repeating earthquakes and thus an opportunity to better understand how they accommodate slip as a function of time.

  1. Identification of repeats in DNA sequences using nucleotide distribution uniformity.

    PubMed

    Yin, Changchuan

    2017-01-07

    Repetitive elements are important in genomic structures, functions and regulations, yet effective methods in precisely identifying repetitive elements in DNA sequences are not fully accessible, and the relationship between repetitive elements and periodicities of genomes is not clearly understood. We present an ab initio method to quantitatively detect repetitive elements and infer the consensus repeat pattern in repetitive elements. The method uses the measure of the distribution uniformity of nucleotides at periodic positions in DNA sequences or genomes. It can identify periodicities, consensus repeat patterns, copy numbers and perfect levels of repetitive elements. The results of using the method on different DNA sequences and genomes demonstrate efficacy and accuracy in identifying repeat patterns and periodicities. The complexity of the method is linear with respect to the lengths of the analyzed sequences. The Python programs in this study are freely available to the public upon request or at https://github.com/cyinbox/DNADU. Copyright © 2016 Elsevier Ltd. All rights reserved.

  2. DNA Inversions between Short Inverted Repeats in Escherichia Coli

    PubMed Central

    Schofield, M. A.; Agbunag, R.; Miller, J. H.

    1992-01-01

    Using site-specific mutagenesis in vitro, we have constructed Escherichia coli strains that allow the detection of the inversion of an 800-bp segment in the lac region. The invertible segment is bounded by inverted repeats of either 12 or 23 bp. Inversions occurring at these inverted repeats will restore the Lac(+) phenotype. Inversions can be detected at both short homologies at frequencies ranging from 0.5 X 10(-8) to 1 X 10(-7). These events, which have been verified by DNA sequence analysis, are reduced up to 1000-fold in strains deficient for either RecA, RecB or RecC. They are not reduced in strains deficient in the RecF,J pathway. These results show that the RecB,C,D system can mediate rearrangements at short sequence repeats, and probably plays a major role in cellular rearrangements. PMID:1427029

  3. Predictors of repeat pregnancy in a program for pregnant teens.

    PubMed

    Pfitzner, Mark A; Hoff, Charles; McElligott, Kathleen

    2003-04-01

    To describe repeat pregnancy among adolescents and to compare those who experienced a repeat pregnancy to those who did not. Retrospective case control of all adolescents who entered and exited the Teen Mother & Child Program, a multidisciplinary clinic for pregnant and parenting teens and their children, between 1985 and 2000. Repeat pregnancy. Over the 16-yr study period, 1838 teens entered and exited the program with the mean time in the program of 1.9 yrs. 194 (10.6%) teens went on to have a second pregnancy, and 4 of those had a third pregnancy. Ninety-two percent (n=175) of these pregnancies resulted in a live birth. The mean interval between delivery of the initial child and delivery of the second child was 21.8 months (range 5.4-53.2). Teens repeating (R) were compared to those who did not repeat (NR). R were younger at entry and older at exit from the program (both P<0.0001). R were more likely to be Hispanic (P=0.009) or have a partner who was Hispanic (P=0.02). R were more likely to have experienced a poor initial pregnancy outcome (miscarriage, stillbirth) (P=0.03). R were more likely than NR to be in a stable relationships with the father of the baby (i.e., married or engaged) (P=0.03). Self-report of physical and sexual abuse, depression, and substance abuse were common, but did not differ between R and NR. However, R were more likely than NR to self-report suicide gestures/attempts and to have a significant psychiatric history (P=0.01, P=0.004). Only 24% of R and 26% of NR had completed high school by the time of exit from the program. Ten percent of adolescents served by comprehensive multidisciplinary teen pregnancy program experienced a repeat pregnancy while in the program. Compared to nonrepeaters, adolescents who experienced a repeat pregnancy were younger, were more frequently Hispanic, and were more likely to be in a stable relationship with the baby's father. Many of the program's clients have psychosocial factors reported in the literature

  4. Chronic adhesive arachnoiditis after repeat epidural blood patch.

    PubMed

    Carlswärd, C; Darvish, B; Tunelli, J; Irestedt, L

    2015-08-01

    Epidural blood patching is an effective treatment for postdural puncture headache but has potential risks. Arachnoiditis is a very rare disabling condition and few cases have been described following an epidural blood patch. We present a case of chronic adhesive arachnoiditis in a parturient treated with a repeat epidural blood patch. A healthy 29-year-old woman had an accidental dural puncture following epidural insertion during labour. Initial treatment of postdural puncture headache with an epidural blood patch was ineffective and was therefore repeated. She gradually developed severe neurological symptoms consistent with arachnoiditis confirmed with magnetic resonance imaging. Despite intensive multimodal treatment with analgesics and physiotherapy, her neurological condition remains unresolved two years later. This serious but rare complication should encourage caution when treating parturients with postdural puncture headache with a repeat epidural blood patch.

  5. Gene conversion homogenizes the CMT1A paralogous repeats.

    PubMed

    Hurles, M E

    2001-01-01

    Non-allelic homologous recombination between paralogous repeats is increasingly being recognized as a major mechanism causing both pathogenic microdeletions and duplications, and structural polymorphism in the human genome. It has recently been shown empirically that gene conversion can homogenize such repeats, resulting in longer stretches of absolute identity that may increase the rate of non-allelic homologous recombination. Here, a statistical test to detect gene conversion between pairs of non-coding sequences is presented. It is shown that the 24 kb Charcot-Marie-Tooth type 1A paralogous repeats (CMT1A-REPs) exhibit the imprint of gene conversion processes whilst control orthologous sequences do not. In addition, Monte Carlo simulations of the evolutionary divergence of the CMT1A-REPs, incorporating two alternative models for gene conversion, generate repeats that are statistically indistinguishable from the observed repeats. Bounds are placed on the rate of these conversion processes, with central values of 1.3 x 10(-4) and 5.1 x 10(-5) per generation for the alternative models. This evidence presented here suggests that gene conversion may have played an important role in the evolution of the CMT1A-REP paralogous repeats. The rates of these processes are such that it is probable that homogenized CMT1A-REPs are polymorphic within modern populations. Gene conversion processes are similarly likely to play an important role in the evolution of other segmental duplications and may influence the rate of non-allelic homologous recombination between them.

  6. Gene conversion homogenizes the CMT1A paralogous repeats

    PubMed Central

    Hurles, Matthew E

    2001-01-01

    Background Non-allelic homologous recombination between paralogous repeats is increasingly being recognized as a major mechanism causing both pathogenic microdeletions and duplications, and structural polymorphism in the human genome. It has recently been shown empirically that gene conversion can homogenize such repeats, resulting in longer stretches of absolute identity that may increase the rate of non-allelic homologous recombination. Results Here, a statistical test to detect gene conversion between pairs of non-coding sequences is presented. It is shown that the 24 kb Charcot-Marie-Tooth type 1A paralogous repeats (CMT1A-REPs) exhibit the imprint of gene conversion processes whilst control orthologous sequences do not. In addition, Monte Carlo simulations of the evolutionary divergence of the CMT1A-REPs, incorporating two alternative models for gene conversion, generate repeats that are statistically indistinguishable from the observed repeats. Bounds are placed on the rate of these conversion processes, with central values of 1.3 × 10-4 and 5.1 × 10-5 per generation for the alternative models. Conclusions This evidence presented here suggests that gene conversion may have played an important role in the evolution of the CMT1A-REP paralogous repeats. The rates of these processes are such that it is probable that homogenized CMT1A-REPs are polymorphic within modern populations. Gene conversion processes are similarly likely to play an important role in the evolution of other segmental duplications and may influence the rate of non-allelic homologous recombination between them. PMID:11801183

  7. Repeatability of locomotor performance and morphology-locomotor performance relationships.

    PubMed

    Conradsen, Cara; Walker, Jeffrey A; Perna, Catherine; McGuigan, Katrina

    2016-09-15

    There is good evidence that natural selection drives the evolution of locomotor performance, but the processes that generate the among-individual variation for selection to act on are relatively poorly understood. We measured prolonged swimming performance, Ucrit, and morphology in a large cohort (n=461) of wild-type zebrafish (Danio rerio) at ∼6 months and again at ∼9 months. Using mixed-model analyses to estimate repeatability as the intraclass correlation coefficient, we determined that Ucrit was significantly repeatable (r=0.55; 95% CI: 0.45-0.64). Performance differences between the sexes (males 12% faster than females) and changes with age (decreasing 0.07% per day) both contributed to variation in Ucrit and, therefore, the repeatability estimate. Accounting for mean differences between sexes within the model decreased the estimate of Ucrit repeatability to 21% below the naïve estimate, while fitting age in the models increased the estimate to 14% above the naïve estimate. Greater consideration of factors such as age and sex is therefore necessary for the interpretation of performance repeatability in wild populations. Body shape significantly predicted Ucrit in both sexes in both assays, with the morphology-performance relationship significantly repeatable at the population level. However, morphology was more strongly predicative of performance in older fish, suggesting a change in the contribution of morphology relative to other factors such as physiology and behaviour. The morphology-performance relationship changed with age to a greater extent in males than females.

  8. Impact of Repeated Exposures on Information Spreading in Social Networks

    PubMed Central

    Zhou, Cangqi; Zhao, Qianchuan; Lu, Wenbo

    2015-01-01

    Clustered structure of social networks provides the chances of repeated exposures to carriers with similar information. It is commonly believed that the impact of repeated exposures on the spreading of information is nontrivial. Does this effect increase the probability that an individual forwards a message in social networks? If so, to what extent does this effect influence people’s decisions on whether or not to spread information? Based on a large-scale microblogging data set, which logs the message spreading processes and users’ forwarding activities, we conduct a data-driven analysis to explore the answer to the above questions. The results show that an overwhelming majority of message samples are more probable to be forwarded under repeated exposures, compared to those under only a single exposure. For those message samples that cover various topics, we observe a relatively fixed, topic-independent multiplier of the willingness of spreading when repeated exposures occur, regardless of the differences in network structure. We believe that this finding reflects average people’s intrinsic psychological gain under repeated stimuli. Hence, it makes sense that the gain is associated with personal response behavior, rather than network structure. Moreover, we find that the gain is robust against the change of message popularity. This finding supports that there exists a relatively fixed gain brought by repeated exposures. Based on the above findings, we propose a parsimonious model to predict the saturated numbers of forwarding activities of messages. Our work could contribute to better understandings of behavioral psychology and social media analytics. PMID:26465749

  9. Repeatability of Electromyographic Waveforms During the Naeryo Chagi in Taekwondo

    PubMed Central

    Aggeloussis, Nickos; Gourgoulis, Vassilis; Sertsou, Maria; Giannakou, Erasmia; Mavromatis, George

    2007-01-01

    The purpose of the research was to study the repeatability of electromyographic (EMG) waveforms of major lower limb muscles during the naeryo chagi (axe kick) in taekwondo. Six male and female athletes, aged between 20 and 24 years served as volunteers. All participants were black belt holders and performed the naeryo chagi with their right leg. The electromyographic activity of rectus femoris, biceps femoris, gastrocnemius lateralis and tibialis anterior was recorded during the kick through four preamplified surface electrodes. The participants preformed 10 successive kicks to a fixed target with 1 min inter-trial interval. The electromyograms were recorded during each kick at a sampling frequency of 1000Hz. After the processing of the raw EMG data, myoelectrical activity was normalized on the time and amplitude domain. The coefficient of variation (CV), intra-class correlation coefficient (ICC) and coefficient of multiple correlation (CMC) were computed to test the repeatability of the electromyographic waveforms in each participant. The electromyographic activity during the naeryo chagi demonstrated poor repeatability. More specifically, all CVs were greater than 80%, all CMCs were lower than 0.75 and the majority of the average measure ICCs as well as all single measure ICCs were lower than 0.55. It seemed that only ensemble averages of EMG waveforms obtained from more than ten kicks may be considered as representatives of the muscle function in naeryo chagi and conclusions that have been drawn from a single trial should be reconsidered. Key points The paper is the only known paper focused on the EMG repeatability of a taekwondo kick (naeryo chagi). The paper is among the few papers of repeatability dealing with the whole EMG waveforms and not with discrete EMG parameters. Repeatability was tested using all the available statistical indices. The results suggested that conclusions drawn from a single trial in EMG studies of taekwondo kicks and probably in other

  10. Repeating earthquakes analysis in the Taiwan-Ryukyu subduction zone

    NASA Astrophysics Data System (ADS)

    Chang, Y. E.; Chen, K. H.; Chen, S.

    2012-12-01

    The understanding of interplate slip has been limited in the Taiwan-Ryukyu subduction zone due to sparse sampling of seismic and geodetic stations. Repeating earthquakes study has been proposed to improve the understanding of deep fault behavior. However, in this particular regions where spatial coverage of seismic station is sparse and one sided with high noise level or where starting catalog origin times are inaccurate; establishing waveform cross-correlation method (wcc) for rapid detection of repeating earthquakes is problematic. When the wcc method is applied over a large area of 100 Km x 300 km for M>2 earthquakes at a depth range of 0-50 km (12932 events in total), a large number of false detections occurred due to low-amplitude signal templates. This leads additional time-consumingefforts on manual re-identification. In this study we propose an efficient repeating sequence identification scheme in the regions where the station coverage is sparse with low signal to noise ratio. Using this identification method, we found 9 (M2.5~4.5) interplate repeating sequences in the Taiwan-Ryukyu subduction zone at 35-45 km depth. The interplate repeating earthquakes tend to be short-lived in the form of doublet or multiplet, which the association between doublet/multiplet generation and subduction zone processes requires further study. Other crustal repeating earthquakes occurred at shallow depth above 20 km; these sequences have occurrence rate strongly associated with the nearby M6 earthquakes. This identification scheme will be applied to deeper events (> 50 km depth) for a more complete image of spatial and temporal distribution of interpolate aseismic slip in the Taiwan-Ryukyu subduction zone .

  11. Repeat workers' compensation claims: risk factors, costs and work disability

    PubMed Central

    2011-01-01

    Background The objective of our study was to describe factors associated with repeat workers' compensation claims and to compare the work disability arising in workers with single and multiple compensation claims. Methods All initial injury claims lodged by persons of working age during a five year period (1996 to 2000) and any repeat claims were extracted from workers' compensation administrative data in the state of Victoria, Australia. Groups of workers with single and multiple claims were identified. Descriptive analysis of claims by affliction, bodily location, industry segment, occupation, employer and workplace was undertaken. Survival analysis determined the impact of these variables on the time between the claims. The economic impact and duration of work incapacity associated with initial and repeat claims was compared between groups. Results 37% of persons with an initial claim lodged a second claim. This group contained a significantly greater proportion of males, were younger and more likely to be employed in manual occupations and high-risk industries than those with single claims. 78% of repeat claims were for a second injury. Duration between the claims was shortest when the working conditions had not changed. The initial claims of repeat claimants resulted in significantly (p < 0.001) lower costs and work disability than the repeat claims. Conclusions A substantial proportion of injured workers experience a second occupational injury or disease. These workers pose a greater economic burden than those with single claims, and also experience a substantially greater cumulative period of work disability. There is potential to reduce the social, health and economic burden of workplace injury by enacting prevention programs targeted at these workers. PMID:21696637

  12. Repeated adaptive divergence of microhabitat specialization in avian feather lice

    PubMed Central

    2012-01-01

    Background Repeated adaptive radiations are evident when phenotypic divergence occurs within lineages, but this divergence into different forms is convergent when compared across lineages. Classic examples of such repeated adaptive divergence occur in island (for example, Caribbean Anolis lizards) and lake systems (for example, African cichlids). Host-parasite systems in many respects are analogous to island systems, where host species represent isolated islands for parasites whose life cycle is highly tied to that of their hosts. Thus, host-parasite systems might exhibit interesting cases of repeated adaptive divergence as seen in island and lake systems. The feather lice of birds spend their entire life cycle on the body of the host and occupy distinct microhabitats on the host: head, wing, body and generalist. These microhabitat specialists show pronounced morphological differences corresponding to how they escape from host preening. We tested whether these different microhabitat specialists were a case of repeated adaptive divergence by constructing both morphological and molecular phylogenies for a diversity of avian feather lice, including many examples of head, wing, body and generalist forms. Results Morphological and molecular based phylogenies were highly incongruent, which could be explained by rampant convergence in morphology related to microhabitat specialization on the host. In many cases lice from different microhabitat specializations, but from the same group of birds, were sister taxa. Conclusions This pattern indicates a process of repeated adaptive divergence of these parasites within host group, but convergence when comparing parasites across host groups. These results suggest that host-parasite systems might be another case in which repeated adaptive radiations could be relatively common, but potentially overlooked, because morphological convergence can obscure evolutionary relationships. PMID:22717002

  13. Rate-loss analysis of an efficient quantum repeater architecture

    NASA Astrophysics Data System (ADS)

    Guha, Saikat; Krovi, Hari; Fuchs, Christopher A.; Dutton, Zachary; Slater, Joshua A.; Simon, Christoph; Tittel, Wolfgang

    2015-08-01

    We analyze an entanglement-based quantum key distribution (QKD) architecture that uses a linear chain of quantum repeaters employing photon-pair sources, spectral-multiplexing, linear-optic Bell-state measurements, multimode quantum memories, and classical-only error correction. Assuming perfect sources, we find an exact expression for the secret-key rate, and an analytical description of how errors propagate through the repeater chain, as a function of various loss-and-noise parameters of the devices. We show via an explicit analytical calculation, which separately addresses the effects of the principle nonidealities, that this scheme achieves a secret-key rate that surpasses the Takeoka-Guha-Wilde bound—a recently found fundamental limit to the rate-vs-loss scaling achievable by any QKD protocol over a direct optical link—thereby providing one of the first rigorous proofs of the efficacy of a repeater protocol. We explicitly calculate the end-to-end shared noisy quantum state generated by the repeater chain, which could be useful for analyzing the performance of other non-QKD quantum protocols that require establishing long-distance entanglement. We evaluate that shared state's fidelity and the achievable entanglement-distillation rate, as a function of the number of repeater nodes, total range, and various loss-and-noise parameters of the system. We extend our theoretical analysis to encompass sources with nonzero two-pair-emission probability, using an efficient exact numerical evaluation of the quantum state propagation and measurements. We expect our results to spur formal rate-loss analysis of other repeater protocols and also to provide useful abstractions to seed analyses of quantum networks of complex topologies.

  14. A selective-repeat ARQ scheme and its throughput analysis

    NASA Astrophysics Data System (ADS)

    Chitre, D. M.

    A selective-repeat ARQ (automatic repeat request) scheme that uses a finite receiver buffer is investigated. A Markov process is identified which describes the proposed ARQ scheme with a receiver buffer of size N. It leads to an irreducible, aperiodic, finite, and stationary Markov chain. The resulting stationary probability distribution is then used to compute exactly the throughput efficiency. Analytical results show that the proposed protocol significantly outperforms the go-back-N ARQ protocol and its variations over a wide range of channel capacities and bit error rates.

  15. Repeated recall and PKMζ maintain fear memories in juvenile rats.

    PubMed

    Oliver, Chicora F; Kabitzke, Patricia; Serrano, Peter; Egan, Laura J; Barr, Gordon A; Shair, Harry N; Wiedenmayer, Christoph

    2016-12-01

    We examined the neural substrates of fear memory formation and maintenance when repeated recall was used to prevent forgetting in young animals. In contrast to adult rats, juveniles failed to show contextual fear responses at 4 d post-fear conditioning. Reconsolidation sessions 3 and 6 d after conditioning restored contextual fear responses in juveniles 7 d after initial training. In juveniles that received reconsolidation sessions, protein kinase M zeta (PKMζ) increased in the amygdala, but not in the hippocampus. These data suggest that repeated reminders and increased PKMζ maintain fear responses in juvenile animals that otherwise would not exhibit this behavior.

  16. The Repeat Expansion Diseases: the dark side of DNA repair?

    PubMed Central

    Zhao, Xiao-Nan; Usdin, Karen

    2015-01-01

    DNA repair normally protects the genome against mutations that threaten genome integrity and thus cell viability. However, growing evidence suggests that in the case of the Repeat Expansion Diseases, disorders that result from an increase in the size of a disease-specific microsatellite, the disease-causing mutation is actually the result of aberrant DNA repair. A variety of proteins from different DNA repair pathways have thus far been implicated in this process. This review will summarize recent findings from patients and from mouse models of these diseases that shed light on how these pathways may interact to cause repeat expansion. PMID:26002199

  17. Practical repeaters for ultralong-distance quantum communication

    NASA Astrophysics Data System (ADS)

    Vinay, Scott E.; Kok, Pieter

    2017-05-01

    Quantum repeaters enable long-range quantum communication in the presence of attenuation. Here we propose a method to construct a robust quantum repeater network using only existing technology. We combine the ideas of brokered graph-state construction with double-heralded entanglement generation to form a system that is able to perform all parts of the procedure in a way that is highly tolerant to photon loss and imperfections in detectors. We show that when used in quantum key distribution this leads to secure kilohertz bit rates over intercontinental distances.

  18. Two random repeat recall methods to assess alcohol use.

    PubMed Central

    Midanik, L T

    1993-01-01

    Two random repeat recall methods were compared with a summary measure to assess alcohol use. Subjects (n = 142) were randomly assigned to one of two groups; they were called either on 14 random days during three 30-day waves and asked about drinking yesterday, or on 2 random days during each wave and asked about drinking in the past week. Follow-up telephone interviews obtained summary measures for each wave. Random repeat methods generally obtained higher estimates. However, the high dropout rate makes questionable the feasibility of using this approach with general population samples. PMID:8498631

  19. GTAG- and CGTC-tagged palindromic DNA repeats in prokaryotes

    PubMed Central

    2013-01-01

    Background REPs (Repetitive Extragenic Palindromes) are small (20–40 bp) palindromic repeats found in high copies in some prokaryotic genomes, hypothesized to play a role in DNA supercoiling, transcription termination, mRNA stabilization. Results We have monitored a large number of REP elements in prokaryotic genomes, and found that most can be sorted into two large DNA super-families, as they feature at one end unpaired motifs fitting either the GTAG or the CGTC consensus. Tagged REPs have been identified in >80 species in 8 different phyla. GTAG and CGTC repeats reside predominantly in microorganisms of the gamma and alpha division of Proteobacteria, respectively. However, the identification of members of both super- families in deeper branching phyla such Cyanobacteria and Planctomycetes supports the notion that REPs are old components of the bacterial chromosome. On the basis of sequence content and overall structure, GTAG and CGTC repeats have been assigned to 24 and 4 families, respectively. Of these, some are species-specific, others reside in multiple species, and several organisms contain different REP types. In many families, most units are close to each other in opposite orientation, and may potentially fold into larger secondary structures. In different REP-rich genomes the repeats are predominantly located between unidirectionally and convergently transcribed ORFs. REPs are predominantly located downstream from coding regions, and many are plausibly transcribed and function as RNA elements. REPs located inside genes have been identified in several species. Many lie within replication and global genome repair genes. It has been hypothesized that GTAG REPs are miniature transposons mobilized by specific transposases known as RAYTs (REP associated tyrosine transposases). RAYT genes are flanked either by GTAG repeats or by long terminal inverted repeats (TIRs) unrelated to GTAG repeats. Moderately abundant families of TIRs have been identified in

  20. Cumulative effects of repeated subthreshold doses of ultraviolet radiation

    SciTech Connect

    Parrish, J.A.; Zaynoun, S.; Anderson, R.R.

    1981-05-01

    For fair Caucasian skin, the minimal delayed erythema dose (MED) 24 hr after exposure to broadband UVA is about 1200 times greater than the MED of broadband UVB, for both single and multiple daily exposures. Repeated daily exposure to doses less than MED results in cumulative effects manifest by gradual lowering of the daily dose threshold for delayed erythema and pigmentation induced by UVA or UVB. At threshold doses, UVB is more erythemogenic than melanogenic; the opposite is true for UVA. Repeated daily UVA exposure greatly enhances melanogenesis such that markedly suberythemogenic exposure doses of UVA result in true melanogenesis.

  1. Deletion of internal structured repeats increases the stability of a leucine-rich repeat protein, YopM

    PubMed Central

    Barrick, Doug

    2011-01-01

    Mapping the stability distributions of proteins in their native folded states provides a critical link between structure, thermodynamics, and function. Linear repeat proteins have proven more amenable to this kind of mapping than globular proteins. C-terminal deletion studies of YopM, a large, linear leucine-rich repeat (LRR) protein, show that stability is distributed quite heterogeneously, yet a high level of cooperativity is maintained [1]. Key components of this distribution are three interfaces that strongly stabilize adjacent sequences, thereby maintaining structural integrity and promoting cooperativity. To better understand the distribution of interaction energy around these critical interfaces, we studied internal (rather than terminal) deletions of three LRRs in this region, including one of these stabilizing interfaces. Contrary to our expectation that deletion of structured repeats should be destabilizing, we find that internal deletion of folded repeats can actually stabilize the native state, suggesting that these repeats are destabilizing, although paradoxically, they are folded in the native state. We identified two residues within this destabilizing segment that deviate from the consensus sequence at a position that normally forms a stacked leucine ladder in the hydrophobic core. Replacement of these nonconsensus residues with leucine is stabilizing. This stability enhancement can be reproduced in the context of nonnative interfaces, but it requires an extended hydrophobic core. Our results demonstrate that different LRRs vary widely in their contribution to stability, and that this variation is context-dependent. These two factors are likely to determine the types of rearrangements that lead to folded, functional proteins, and in turn, are likely to restrict the pathways available for the evolution of linear repeat proteins. PMID:21764506

  2. Isolation and characterization of recombinant DNAs containing repeated elements of barley genome: identification of individual actively transcribed families of repeats

    SciTech Connect

    Prosnyak, M.I.; Kartel', N.A.; Ryskov, A.P.

    1986-05-01

    A bank of Escherichia coli clones containing fragments of barley nuclear DNA was obtained using plasmid pBR 322. Clones carrying repeated sequences of the plant genome were selected by means of colony and blot hybridization. Clones with actively transcribed sequences were selected by hybridization to complementary DNA synthesized by means of reverse transcription on a template of total barley poly(A)-containing RNA. Individual families of repeats, two of which contained transcriptionally active sequences of the barley genome, were identified by blot hybridization of recombinant plasmids containing labeled DNA fragments of the inserts of three different clones.

  3. The Analysis of Repeated Measures Designs Involving Multiple Dependent Variables.

    ERIC Educational Resources Information Center

    Schutz, Robert W.; Gessaroli, Marc E.

    1987-01-01

    The article discusses the concepts and interpretations for four methods of testing differences among means in a mixed model repeated measures design. The four methods discussed are: traditional ANOVA and the MANOVA methods for the single dependent variable case, and a Multivariate Mixed Model analysis and a Doubly Multivariate analysis for the…

  4. 47 CFR 90.247 - Mobile repeater stations.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... repeater to extend the communications range of hand-carried units subject to the following: (a) Mobile... same frequency is also used by the same station for direct communication with vehicular mobile units or... of the mobile unit and an automatic time-delay device that de-activates the transmitter after...

  5. Results of 1993 Repeat-Pass SAR Interferometry Experiments

    NASA Technical Reports Server (NTRS)

    Klein, J. D.; Hensley, S.; Madsen, S. N.; Webb, F. H.

    1994-01-01

    In this talk we present results of a repeat-pass SAR interferometry experiment performed in June 1993 near Portage, Maine. Differential GPS data accurate to +/-10cm were acquired to aid in motion compensation and geolocation of targets in the imagery. The experiment and data analysis will be discussed, and results will be shown during the presentation.

  6. A Deluge of Complex Repeats: The Solanum Genome

    PubMed Central

    Mehra, Mrigaya; Gangwar, Indu; Shankar, Ravi

    2015-01-01

    Repetitive elements have lately emerged as key components of genome, performing varieties of roles. It has now become necessary to have an account of repeats for every genome to understand its dynamics and state. Recently, genomes of two major Solanaceae species, Solanum tuberosum and Solanum lycopersicum, were sequenced. These species are important crops having high commercial significance as well as value as model species. However, there is a reasonable gap in information about repetitive elements and their possible roles in genome regulation for these species. The present study was aimed at detailed identification and characterization of complex repetitive elements in these genomes, along with study of their possible functional associations as well as to assess possible transcriptionally active repetitive elements. In this study, it was found that ~50–60% of genomes of S. tuberosum and S. lycopersicum were composed of repetitive elements. It was also found that complex repetitive elements were associated with >95% of genes in both species. These two genomes are mostly composed of LTR retrotransposons. Two novel repeat families very similar to LTR/ERV1 and LINE/RTE-BovB have been reported for the first time. Active existence of complex repeats was estimated by measuring their transcriptional abundance using Next Generation Sequencing read data and Microarray platforms. A reasonable amount of regulatory components like transcription factor binding sites and miRNAs appear to be under the influence of these complex repetitive elements in these species, while several genes appeared to possess exonized repeats. PMID:26241045

  7. Mourning and Guilt among Greek Women Having Repeated Abortions.

    ERIC Educational Resources Information Center

    Naziri, D.; Tzavaras, A.

    1993-01-01

    Conducted clinical study concerning bereavement process of Greek women after abortion. Found strong identificatory tendencies on both mother and father images. Argues that, in cases of repeated abortion, mourning and guilt do not only refer to murdered and lost "person-fetus" but principally to death and loss of object of ambiguous…

  8. Validity of repeated initial rise thermoluminescence kinetic parameter determinations

    SciTech Connect

    Kierstead, J.A.; Levy, P.W.

    1990-01-01

    The validity of thermoluminescence (TL) analysis by repeated initial rise measurements has been studied by computer simulation. Thermoluminescence described by 1st Order, 2nd Order, General One Trap and Interactive TL Kinetics was investigated. In the simulation each of the repeated temperature increase and decrease cycles contains a linear temperature increase followed by a decrease appropriate for radiative cooling, i.e. the latter is approximated by a decreasing exponential. The activation energies computed from the simulated emission are readily compared with those used to compute the TL emission. In all cases studied, the repeated initial rise technique provides reliable results only for single peak glow curves or for glow curves containing peaks that do not overlap and, if sufficiently separated, the lowest temperature peak in multipeak curves. Also the temperatures, or temperature cycles corresponding to correct activation energies occur on the low temperature side of the normal glow curve, often well below the peak temperature. A variety of misleading and/or incorrect results an be obtained when the repeated initial rise technique is applied to TL systems that produce overlapping peaks in the usual glow curve. 6 refs., 10 figs.

  9. 35. ALTERNATE DESIGN USING THROUGH ARCH SPANS, WITH ARCH REPEATED ...

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

    35. ALTERNATE DESIGN USING THROUGH ARCH SPANS, WITH ARCH REPEATED BETWEEN TOWER LEGS, AND ASHLAR MASONRY WALLS AND PYLONS Pen-and-ink drawing by project architect Alfred Eichler, 1934. - Sacramento River Bridge, Spanning Sacramento River at California State Highway 275, Sacramento, Sacramento County, CA

  10. On Partial Fraction Decompositions by Repeated Polynomial Divisions

    ERIC Educational Resources Information Center

    Man, Yiu-Kwong

    2017-01-01

    We present a method for finding partial fraction decompositions of rational functions with linear or quadratic factors in the denominators by means of repeated polynomial divisions. This method does not involve differentiation or solving linear equations for obtaining the unknown partial fraction coefficients, which is very suitable for either…

  11. Simple sequence repeat markers that identify Claviceps species and strains

    USDA-ARS?s Scientific Manuscript database

    Claviceps purpurea is a pathogen that infects most members of the Pooideae subfamily and causes ergot, a floral disease in which the ovary is replaced with a sclerotium. This study was initiated to develop Simple Sequence Repeat (SSRs) markers for rapid identification of C. purpurea. SSRs were desi...

  12. [Analysis of unknown cause subarachnoid hemorrhage with repeated negative angiogram].

    PubMed

    Fujii, Mutsumi; Takasato, Yoshio; Masaoka, Hiroyuki; Ohta, Yoshihisa; Hayakawa, Takanori; Honma, Masato

    2006-06-01

    Seven hundred and fifty five cases of acute non-traumatic subarachnoid hemorrhage were admitted to the department of neurosurgery of our hospital from July, 1995 to March, 2004. In 555 patients cerebral angiography was conducted but initial angiography was negative in 30 patients. Except 10 general condition poor patients, in 20 initial angiogram-negative patients were undergone repeated angiography. The cause of SAH could not be demonstrated in 13 cases. The SAH in perimesencephalic and non-perimesencephalic cisturns was seen in 7 and 6 cases, respectively. Occipital and/or neck pain on admission was statistically more common among patients with perimesencephalic SAH than those with non-perimesencephalic SAH (p = 0.029), and the prognosis of perimesencephalic SAH was good. We conclude that repeat angiography should not be recommended in patients with perimesencephalic SAH. Patients with non-perimesencephalic SAH had a higher rate of complication. In the non-perimesencephalic group, 3 patients developed hydrocephalus and 3 patients had vasospasm, which were found by repeated angiography. Therefore, repeated angiography is recommended for better clinical outcome by early detection and management of serious complications in this group of patients.

  13. Statistical Analyses of Repeated Measures Designs: Problems and Some Solutions.

    ERIC Educational Resources Information Center

    Rosmann, Michael R.

    When repeated measures are obtained on the same subjects, interobservation dependencies frequently are generated. The major ways in which these dependencies can arise are illustrated and it is shown how these dependencies may invalidate the use of analysis of variance (ANOVA) and its extension, trend analysis, as methods of evaluating the data of…

  14. Repeatedly Reactivated Memories Become More Resistant to Hippocampal Damage

    ERIC Educational Resources Information Center

    Lehmann, Hugo; McNamara, Kathryn C.

    2011-01-01

    We examined whether repeated reactivations of a context memory would prevent the typical amnesic effects of post-training damage to the hippocampus (HPC). Rats were given a single contextual fear-conditioning session followed by 10 reactivations, involving a brief return to the conditioning context (no shock). Subsequently, the rats received sham…

  15. On Entropy Production of Repeated Quantum Measurements I. General Theory

    NASA Astrophysics Data System (ADS)

    Benoist, T.; Jakšić, V.; Pautrat, Y.; Pillet, C.-A.

    2017-07-01

    We study entropy production (EP) in processes involving repeated quantum measurements of finite quantum systems. Adopting a dynamical system approach, we develop a thermodynamic formalism for the EP and study fine aspects of irreversibility related to the hypothesis testing of the arrow of time. Under a suitable chaoticity assumption, we establish a Large Deviation Principle and a Fluctuation Theorem for the EP.

  16. Experimentally Induced Repeated Anhydrobiosis in the Eutardigrade Richtersius coronifer

    PubMed Central

    2016-01-01

    Tardigrades represent one of the main animal groups with anhydrobiotic capacity at any stage of their life cycle. The ability of tardigrades to survive repeated cycles of anhydrobiosis has rarely been studied but is of interest to understand the factors constraining anhydrobiotic survival. The main objective of this study was to investigate the patterns of survival of the eutardigrade Richtersius coronifer under repeated cycles of desiccation, and the potential effect of repeated desiccation on size, shape and number of storage cells. We also analyzed potential change in body size, gut content and frequency of mitotic storage cells. Specimens were kept under non-cultured conditions and desiccated under controlled relative humidity. After each desiccation cycle 10 specimens were selected for analysis of morphometric characteristics and mitosis. The study demonstrates that tardigrades may survive up to 6 repeated desiccations, with declining survival rates with increased number of desiccations. We found a significantly higher proportion of animals that were unable to contract properly into a tun stage during the desiccation process at the 5th and 6th desiccations. Also total number of storage cells declined at the 5th and 6th desiccations, while no effect on storage cell size was observed. The frequency of mitotic storage cells tended to decline with higher number of desiccation cycles. Our study shows that the number of consecutive cycles of anhydrobiosis that R. coronifer may undergo is limited, with increased inability for tun formation and energetic constraints as possible causal factors. PMID:27828978

  17. Genome Wide Characterization of Simple Sequence Repeats in Cucumber

    USDA-ARS?s Scientific Manuscript database

    The whole genome sequence of the cucumber cultivar Gy14 was recently sequenced at 15× coverage with the Roche 454 Titanium technology. The microsatellite DNA sequences (simple sequence repeats, SSRs) in the assembled scaffolds were computationally explored and characterized. A total of 112,073 SSRs ...

  18. Comparative Analysis of Alu Repeats in Primate Genomes

    USDA-ARS?s Scientific Manuscript database

    Background: Alu repeats are SINEs (Short intersperse repetitive elements) which enjoy a successful application in genome evolution, population biology, phylogenetics and forensics. Human Alu consensus sequences were widely used as surrogates in nonhuman primate studies with an assumption that all p...

  19. Effects of repeated precommercial thinnings in central hardwood sapling stands

    Treesearch

    Donald E. Hilt; Martin E. Dale

    1982-01-01

    Precommercial thinnings were repeated four times in a central hardwood sapling stand beginning at age 8 and ending at age 22. Treated plots were thinned on an area-wide basis to specified density levels of 30-, 50-, and 70-percent stocking. The species composition of all stems in the stand was altered somewhat by thinning, but similar trends occurred on control plots....

  20. Repeated Reading Intervention Effects in Kindergartners with Partial Letter Knowledge

    ERIC Educational Resources Information Center

    van Gorp, Karly; Segers, Eliane; Verhoeven, Ludo

    2014-01-01

    The direct, transfer and retention effects of a repeated reading intervention study of single CVC (consonant in the onset and a vowel and consonant in the rime) words in kindergartners with partial letter knowledge were examined. A total of 26 second-year kindergartners participated in this study. Participants were divided over two feedback…

  1. Response of two prairie forbs to repeated vole herbivory.

    PubMed

    Sullivan, Amy T; Howe, Henry F

    2011-04-01

    Vertebrate herbivores as diverse as ungulates, geese, and rabbits preferentially feed on plants that have previously experienced herbivory. Here, we ask whether smaller grassland "cryptic consumers" such as voles (Microtus ochrogaster and M. pennsylvanicus) preferentially clip (cut stems for access to leaves or seeds) or avoid previously clipped individuals of two tallgrass prairie species (Desmanthus illinoensis and Echinacea purpurea) within a growing season. Further, we ask how these plants respond to repeated clipping within a growing season, and whether the effects of this herbivory last into the subsequent growing season. Voles preferentially clipped stems of D. illinoensis and E. purpurea plants that had been previously clipped. The exception was indiscriminant clipping of stems of E. purpurea late in the growing season when its achenes, a favorite vole food, ripened. For D. illinoensis, repeated clipping resulted in a 59% reduction in biomass, 42% lower ratio of reproductive to vegetative biomass, and 57% fewer seeds produced per plant compared with unclipped plants. These effects lasted into the following growing season in which plants were protected from voles. In contrast, the only effect of repeated clipping for E. purpurea was that the number of achenes per plant was substantially reduced by three episodes of clipping. This effect did not carry over to the next growing season. Such differences in D. illinoensis and E. purpurea response to repeated stem clipping by voles offer insights into how these small rodents can effect major changes in composition and dominance in grassland communities.

  2. Physiological responses to repeated transportation of gestating Brahman cows

    USDA-ARS?s Scientific Manuscript database

    The transportation process acts as a stressor with adverse effects on animal health and performance. The purpose of this study was to examine physiological responses to repeated transportation of gestating Brahman cows, previously classified as mature cows, into temperament groups of calm, moderate,...

  3. Beyond Repeat after Me: Teaching Pronunciation to English Learners

    ERIC Educational Resources Information Center

    Yoshida, Marla Tritch

    2016-01-01

    This engaging text clearly presents essential concepts that teachers need to guide their students toward clearly intelligible pronunciation and more effective communication skills. Based on a sound theoretical background, the book presents practical, imaginative ways to teach and practice pronunciation that go beyond simple "Repeat after…

  4. The development of ingroup favoritism in repeated social dilemmas

    PubMed Central

    Dorrough, Angela R.; Glöckner, Andreas; Hellmann, Dshamilja M.; Ebert, Irena

    2015-01-01

    In two comprehensive and fully incentivized studies, we investigate the development of ingroup favoritism as one of two aspects of parochial altruism in repeated social dilemmas. Specifically, we test whether ingroup favoritism is a fixed phenomenon that can be observed from the very beginning and remains stable over time, or whether it develops (increases vs. decreases) during repeated contact. Ingroup favoritism is assessed through cooperation behavior in a repeated continuous prisoner's dilemma where participants sequentially interact with 10 members of the ingroup (own city and university) and subsequently with 10 members of the outgroup (other city and university), or vice versa. In none of the experiments do we observe initial differences in cooperation behavior for interaction partners from the ingroup, as compared to outgroup, and we only observe small differences in expectations regarding the interaction partners' cooperation behavior. After repeated interaction, however, including a change of groups, clear ingroup favoritism can be observed. Instead of being due to gradual and potentially biased updating of expectations, we found that these emerging differences were mainly driven by the change of interaction partners' group membership that occurred after round 10. This indicates that in social dilemma settings ingroup favoritism is to some degree dynamic in that it is enhanced and sometimes only observable if group membership is activated by thinking about both the interaction with the ingroup and the outgroup. PMID:25972821

  5. Insertion device and method for accurate and repeatable target insertion

    DOEpatents

    Gubeli, III, Joseph F.; Shinn, Michelle D.; Bevins, Michael E.; Dillon-Townes, Lawrence; Neil, George R.

    2017-07-04

    The present invention discloses a device and a method for inserting and positioning a target within a free electron laser, particle accelerator, or other such device that generates or utilizes a beam of energy or particles. The system includes a three-point registration mechanism that insures angular and translational accuracy and repeatability of positioning upon multiple insertions within the same structure.

  6. Beyond Repeat after Me: Teaching Pronunciation to English Learners

    ERIC Educational Resources Information Center

    Yoshida, Marla Tritch

    2016-01-01

    This engaging text clearly presents essential concepts that teachers need to guide their students toward clearly intelligible pronunciation and more effective communication skills. Based on a sound theoretical background, the book presents practical, imaginative ways to teach and practice pronunciation that go beyond simple "Repeat after…

  7. Protein binding to expanded telomere repeats in Tetrahymena thermophila.

    PubMed

    McGuire, Jennifer M; Gana, Joyce Ache; Petcherskaia, Marina; Kirk, Karen E

    2003-01-01

    The ends of eukaryotic chromosomes are protected by DNA-protein structures called telomeres. Telomeric DNA is highly conserved, usually consisting of long tracts of a repeating G-rich sequence. Tetrahymena thermophila telomeric DNA consists of alternating blocks of GGGG and TT sequences (i.e. a G4T2 repeat sequence). We examined the relative importance of the guanine and thymine elements of the repeat sequence in promoting in vitro binding by T. thermophila proteins. We identified single- and, for the first time, double-stranded telomere binding activities from a crude T. thermophila protein extract and tested the binding of these activities to altered telomere repeat sequences. All deletions or substitutions made to the guanine element virtually abolished binding, indicating that four G's are essential for recognition by the binding activity. However, G's alone are not sufficient for efficient binding, as elimination of the thymine element dramatically reduced binding. By contrast, substantial expansion of the thymine element was well tolerated, even though one such change, G4T4, is lethal in vivo. We tested up to a four-fold expansion of the thymine element and found that highly efficient binding was still achieved. These results suggest a minimal recognition sequence for T. thermophila proteins, with the T element providing an important spacer between essential G elements.

  8. Analysis of Repeated Measures Designs with Nested Incomplete Samples.

    ERIC Educational Resources Information Center

    Halperin, Si

    A statistical method has been developed for nested incomplete samples in a longitudinal study in which part of the sample has dropped out in such a way that the data have a nested pattern. A procedure which performed well in a Monte Carlo experiment was extended to a two-factor incomplete design with repeated measures on one factor. Methods…

  9. Properties of Forested Loess Soils After Repeated Prescribed Burns

    Treesearch

    D.M. Moehring; C.X. Grano; J.R. Bassett

    1966-01-01

    Nine annual burns have had little effect on the nutrient content and structure of the surface 4 inches of loess soils on flat terrain.Because prescribed burns must often be repeated to obtain desired results, many foresters are apprehensive about the possible deleterious effects on soils. In 1954 the Timber Management Laboratory at Crossett, Arkansas, in co-...

  10. Problem Solving with Guided Repeated Oral Reading Instruction

    ERIC Educational Resources Information Center

    Conderman, Greg; Strobel, Debra

    2006-01-01

    Many students with disabilities require specialized instructional interventions and frequent progress monitoring in reading. The guided repeated oral reading technique promotes oral reading fluency while providing a reliable data-based monitoring system. This article emphasizes the importance of problem-solving when using this reading approach.

  11. Repeatability of a new method for measuring tear evaporation rates.

    PubMed

    Petznick, Andrea; Tan, Jen Hong; Boo, Shiao Khee; Lee, Sze Yee; Acharya, U Rajendra; Tong, Louis

    2013-04-01

    The purpose of this study was to evaluate the repeatability of tear evaporimetry based on infrared thermography in a clinical room setting and to test the effect of changing environmental humidity on ocular surface temperature (OST) and tear evaporation rates (TERs) in a controlled adverse environmental (CAE) chamber. Twenty-six healthy participants were enrolled, of whom 16 underwent repeatability measurements in a clinical room and 10 were exposed to a constant temperature of 30°C with a humidity of 45 and 65% in a CAE. Participants were acclimatized to each condition for at least 20 minutes before OSTs were taken. Tear film breakup time was assessed in the CAE only. Number of blinks and OSTs were continuously measured for 20 seconds for the cornea, conjunctiva, and overall ocular surface with an infrared camera; corresponding TERs were calculated. The OSTs and TERs showed acceptable strength of agreement between the first and second measurements. The coefficients of repeatability were 0.4°C for OST and 6.0 W m for TER. An increase in chamber humidity (from 45 to 65%) increased OST (p < 0.05). The TER was not changed significantly (p > 0.05). The tear film breakup time and number of blinks were not significantly affected by different humidity conditions. This technique has acceptable repeatability and has potential to document individual tear evaporation changes with time where humidity may differ by less than 20%.

  12. Central effects following repeated treatment with antidepressant drugs.

    PubMed

    Maj, J

    1984-01-01

    The review sums up the results of experiments in which there were studied central effects following repeated administration of various antidepressant drugs (AD) in rats and mice. A number of typical and atypical AD, except for selective inhibitors of 5-hydroxytryptamine (5-HT) uptake, potentiate the clonidine aggressiveness in mice (medicated by alpha 1-adrenoceptors). These results indicate that the repeated AD administration enhances responsiveness of central postsynaptic alpha 1-adrenoceptors. This assumption is in accordance with electrophysiological literature data. A few AD (including citalopram, a selective inhibitor of the 5-HT uptake), administered repeatedly, potentiate the locomotor hyperactivity induced by D-amphetamine or apomorphine, without affecting the stereotypy evoked by both dopaminomimetics. It may be supposed that AD enhance the responsiveness of a dopamine (DA) system, probably the mesolimbic one (but not the striatal one). A repeated administration of various AD also counteracts the locomotor hypoactivity induced by salbutamol (mediated by a beta-adrenoceptor). The importance of the effects stated above (alpha 1 up-regulation, DA up-regulation, beta down-regulation) for the mechanism of antidepressant action has been discussed.

  13. Effects of Repeated Performance Objectives Upon Student Achievement and Attitude.

    ERIC Educational Resources Information Center

    Ferre, Alvin Victor

    The purpose of this study was to assess the effectiveness of repeating performance objectives upon student academic learning and attitude. A program was studied by three groups of subjects: (1) 20 students who were given no performance objectives; (2) 39 students who were given the performance objectives once at the beginning of each unit; and (3)…

  14. Repeated Interviews with Children Who Have Intellectual Disabilities

    ERIC Educational Resources Information Center

    Cederborg, A.-C.; La Rooy, D.; Lamb, M. E.

    2008-01-01

    Background: We predicted that repeated interviewing would improve the informativeness of children with intellectual disabilities who were questioned in criminal investigations. Materials: The chronological ages of the 19 children, involved in 20 cases, ranged between 4.7 and 18 years (M = 10.3 years) at the time of the first alleged abuse. Method:…

  15. Experimentally Induced Repeated Anhydrobiosis in the Eutardigrade Richtersius coronifer.

    PubMed

    Czernekova, Michaela; Jönsson, K Ingemar

    2016-01-01

    Tardigrades represent one of the main animal groups with anhydrobiotic capacity at any stage of their life cycle. The ability of tardigrades to survive repeated cycles of anhydrobiosis has rarely been studied but is of interest to understand the factors constraining anhydrobiotic survival. The main objective of this study was to investigate the patterns of survival of the eutardigrade Richtersius coronifer under repeated cycles of desiccation, and the potential effect of repeated desiccation on size, shape and number of storage cells. We also analyzed potential change in body size, gut content and frequency of mitotic storage cells. Specimens were kept under non-cultured conditions and desiccated under controlled relative humidity. After each desiccation cycle 10 specimens were selected for analysis of morphometric characteristics and mitosis. The study demonstrates that tardigrades may survive up to 6 repeated desiccations, with declining survival rates with increased number of desiccations. We found a significantly higher proportion of animals that were unable to contract properly into a tun stage during the desiccation process at the 5th and 6th desiccations. Also total number of storage cells declined at the 5th and 6th desiccations, while no effect on storage cell size was observed. The frequency of mitotic storage cells tended to decline with higher number of desiccation cycles. Our study shows that the number of consecutive cycles of anhydrobiosis that R. coronifer may undergo is limited, with increased inability for tun formation and energetic constraints as possible causal factors.

  16. Teaching the Repeated Prisoner's Dilemma with a Computerized Tournament

    ERIC Educational Resources Information Center

    Lange, Carsten; Baylor, Amy L.

    2007-01-01

    The authors present a constructivist approach for teaching game theory, on the basis, in part, of Axelrod's research approach. Using the Axelrod tournament multi-user system (ATMUS) software, students create strategies for a repeated prisoner's dilemma (RPD). Later, these strategies are matched with those of their classmates' in a classroom…

  17. 47 CFR 90.247 - Mobile repeater stations.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... repeaters and/or associated hand-carried transmitters may be assigned separate base/mobile frequencies for... with one or more base stations. (f) When automatically retransmitting messages originated by or... access signal can be achieved by use of digital or analog methods....

  18. 47 CFR 90.247 - Mobile repeater stations.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... repeaters and/or associated hand-carried transmitters may be assigned separate base/mobile frequencies for... with one or more base stations. (f) When automatically retransmitting messages originated by or... access signal can be achieved by use of digital or analog methods....

  19. Repeated Instant Self-healing Shape Memory Composites

    NASA Astrophysics Data System (ADS)

    Wang, C. C.; Ding, Z.; Purnawali, H.; Huang, W. M.; Fan, H.; Sun, L.

    2012-12-01

    We present a shape memory composite which is made of two types of shape memory materials, namely shape memory alloy (SMA) and shape memory hybrid. This composite has repeated instant self-healing function by means of not only shape recovery but also strength recovery (over 80%). The activation of the self-healing function is triggered by joule heating the embedded SMA.

  20. Monitoring selective logging in western Amazonia with repeat lidar flights

    Treesearch

    H.E. Andersen; S.E. Reutebuch; R.J. McGaughey; M.V.N. d' Oliveira; M. Keller

    2014-01-01

    The objective of this study was to test the use of repeat flight, airborne laser scanning data (lidar) for estimating changes associated with low-impact selective logging (approx. 10-15 m3 ha−1 = 5-7% of total standing volume harvested) in natural tropical forests in the Western Brazilian Amazon. Specifically, we investigated change in area...